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Biology& 100
Laboratory Manual
For Mr. B’s sections
Green River Community College
Biology& 100 Laboratory Manual
Mr. Brumbaugh
1
Revised Summer 2016
Preface
This manual has been compiled and written for your enjoyment and learning as you work
through the Biology& 100 course. The exercises selected by your instructor are meant to
accentuate your learning of the basic concepts, ideas, and hypotheses concerning biology.
Each exercise should reinforce the learning that is taking place within the confines of the
lecture portion of the course. The exercises are designed to give you a “hands on” feel for the
material presented in lecture.
Please take to heart the following suggestions for your successful completion of Biology&
100.
 Spend time before lab reading each assigned laboratory thoroughly. This
will allow you to organize your time during lab and to foresee pitfalls and
pratfalls that could prevent you from completing the lab within the
prescribed timeframe.
 As you prepare for the lab, jot down questions about concepts or
procedures that you would want answered to facilitate your lab
experience.
 Most labs will have pre-lab questions’, answer them to the best of your
ability by reading each lab completely prior to lab to assist your
understanding.
 Come prepared to discuss or turn-in the pre-lab questions.
 If you are assigned to an activity research group, plan a meeting time each
week prior to the day of the lab to finalize the understanding of the
procedures for the lab.
 Before leaving lab ensure that you have a good understanding of the
principles so that you can finish the write-up or answer the questions
associated with that lab.
 Approach lab with an open mind for learning and attempt to see the
application of the information and the relatedness to the lecture material.
 Have fun and use the time to maximize your learning of the concepts of
biology.
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Biology& 100 Laboratory Manual
Green River Community College
Table of Contents and Appendices
Please Take Note!!
It is your responsibility to read each assigned lab prior to coming to the lab and to answer any
pre-laboratory questions associated with the individual labs.
Laboratories
 Safety and Emergency Procedures
 Laboratory 1
Principles of the Scientific Method
 Laboratory 2
Microscopic Observation of Cells
 Laboratory 3
Transporting Across Boundaries
 Laboratory 4
Pea Lab: Scientific Method Applied
 Laboratory 5
Energy Harvest – Fermentation in Yeast
 Laboratory 6
Mitosis and Online Karyotyping
 Laboratory 7
Mendelian Genetics
 Laboratory 8
Modeling DNA Structure, Replication, & Protein Synthesis
 Laboratory 9
Critical Thinking and Classification
 Laboratory 10 Paper Project
pg. 05
pg. 07 - 22
pg. 23 - 38
pg. 39 - 51
pg. 53 - 59
pg. 61 - 71
pg. 73 - 79
pg. 81 - 93
pg. 95 - 108
pg. 109 - 117
pg. 119 – 123
Appendices
 Appendix
 Appendix
 Appendix
 Appendix
 Appendix
 Appendix
 Appendix
A
B
C
D
E
F
G
Biology& 100 Laboratory Manual
Mr. Brumbaugh
Criteria for Graphing Scientific Data
Metric Conversions
General Format for Writing a Scientific Paper
Drawing: The Making of a Plate or Drawing
How to Make an Oral Presentation
How to search the Literature
Animal & Plant Kingdom Highlights
3
pg. 124 - 125
pg. 126
pg. 127 - 131
pg. 132 - 134
pg. 135 - 136
pg. 137 - 139
pg. 140 - 145
Revised Summer 2016
First blank page to be used for Biological Doodling
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Biology Laboratory: Safety Procedures and Emergencies
1. No open food or drink is permitted in laboratory rooms at any time, whether a lab is in progress
or not. No eating, drinking, chewing of gum or tobacco is permitted. Never taste anything at all
while in the laboratory rooms, unless it is a part of the lab activity (such as PTC paper).
2. Know the locations of the eye wash and shower stations, fire alarm, fire extinguisher, first aid
kit, and emergency exits.
3. If you have any allergies (including latex and bee stings), please inform your instructor so that
we can be aware of your needs during lab activities and field trips.
4. Safety instructions are given at the beginning of each lab activity. Always arrive on time so that
you know what you are supposed to do and are informed of any specific safety concerns or
safety equipment associated with the day’s lab activity.
5. Wear any required personal protective equipment and appropriate attire for lab activities and
field trips (lab coat, apron, goggles, rain gear, No open toed shoes, etc.). If safety goggles are
required for a lab that means they are required for the entire lab.
6. Stash book bags safely in the spaces provided in the front of the room so that they won’t trip
people.
7. Report all illnesses, injuries, breakages, or spills to your laboratory instructor immediately.
8. Clean broken glass (glass that is not contaminated with any chemical reagents, blood, or
bacteria) can be swept up using the dust pan and placed in the broken glass container. If the
glass is contaminated in any way, keep the area clear to prevent tripping or laceration hazards,
and consult your instructor for proper disposal guidance.
9. Notify your instructor if any of the equipment is faulty.
10. Clean up your entire work area before leaving. Put away all equipment and supplies in their
original places and dispose of reagents and infectious materials in the designated receptacles.
Disinfect your work surface if the lab activity involved any infectious materials.
11. Use the appropriate waste containers provided for any infectious or hazardous materials used in
lab.
12. Safety information reagents used in the lab activities can be found in the Safety Data Sheets
(SDS’s), which are available in a binder in the lab prep room. Know the location of the SDS
binder. We (faculty and students) should be fully aware of the properties of the reagents we
are using. Please use the SDS’s. If you cannot find the SDS for the reagent you are using in lab,
inform your instructor. They are also relatively easy to find online. A Google keyword example
is “Sodium Chloride SDS.”
13. Use caution with the lab chairs. Because they are on casters, they can roll away from you when
you are standing at your workstation. Make sure your chair is where you expect it to be before
sitting down. Do not use your chair as a means of moving from one part of the lab to the other.
14. Wash your hands before and after concluding the day’s lab activities.
15. I have read the above statements and will adhere to them while in lab.
Signature:
. Date:
Print:
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Mr. Brumbaugh
.
.
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Biological Doodle Page
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Laboratory 1: Principles of the Scientific Method
Pre-lab Assignment
Before coming to lab carefully read the following pages on the Scientific Method and Appendix A
then answer the pre-lab questions, pages 21 & 22. Be prepared to hand in your responses to the prelab questions at the start of lab.
Perspectives
Biology is a dynamic field of study whose aim is to unravel the mysteries of life itself. Throughout
history, humans have been curious about the world around them. Through the millennia people have
observed the natural world and have asked, “Why?” Those that have advanced our biological
knowledge the most, whether the great scientists of the centuries before us, such as Robert Hooke
(discovered cells in 1665) and Charles Darwin (co-developer of the theory of evolution by natural
selection in 1859), or modern molecular biologists such as James Watson and Francis Crick (discovered
the structure of DNA in 1953), have certain traits in common. They had inquiring minds, great powers
of observation, and they used a systematic approach first developed by Roger Bacon an English monk
in 1265 to answer the questions that intrigued them, the scientific method, which is similar to how
you look at the world.
In this course you will have ample opportunity to develop your scientific skills. The weekly
laboratory exercises are designed not only to stimulate your curiosity and heighten your powers of
observation, but also to introduce you to and allow you to practice the scientific method. This
laboratory activity will allow you to practice the scientific method as you study the factors that
influence your heart rate and level of physical fitness. Let’s first learn a bit about the scientific method
in more detail.
Scientific Method
The scientific method is neither complicated nor intimidating, nor is it unique to science. It is a
powerful tool of logic that can be employed any time a problem or question about the world around
us arises. In fact, we all use the principles of the scientific method daily to solve problems that pop up,
but we do it so quickly and automatically that we are not conscious of the methodology. In brief, the
scientific method consists of
 Observing natural phenomena
 Asking a question based on one’s observations
 Constructing a hypothesis to answer the question
 Testing the hypothesis with experiments or pertinent observations
 Drawing conclusions about the hypothesis based on the data resulting from the experiments or
pertinent observation
 Publishing results (hopefully in a scientific journal!)
Observations
The scientific method begins with careful observation. An investigator may make observations
from nature or from the written work of other investigators, which are published in books or research
articles in scientific journals, available in the storehouses of human knowledge, libraries.
Let’s use the following example as we progress through the steps of the scientific method.
Suppose that over the last couple of years you have been observing the beautiful fall colors of the
leaves on the vine maples that grow in your yard, on campus, and in the forests in the Cascade
Mountains. You note that their leaves turn from green to yellow to orange to red as the weather
turns progressively colder and the days get shorter and shorter. However, the leaves do not always go
through their color changes on exactly the same days each year.
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Questions
It is essential that the question asked is a scientific question. I.e. The question must be testable,
definable, measurable and controllable to produce verifiable data. For example, one would have a
tough time trying to test the following question; “Did a supernatural force such as God create all life
on earth?” Moreover, since the concept of God has many different meanings and definitions, it is
difficult to define what or who God is from a science standpoint. Since this question is not a scientific
question, and hence not testable, the courts of the United States have ruled that “creation science”
should not be taught in science classes as has been demanded by various groups in this country.
However, that’s not to say that God did not create life, it’s just not testable from a science viewpoint,
but rather, a matter of faith.
Now, back to the vine maple example...Being a curious and inquisitive person you ask, “What’s
causing or stimulating the vine maple’s leaves to change color?”
Hypotheses
The next step in the scientific method is to make a hypothesis, a tentative answer to the question
that you have asked. A hypothesis is an educated guess that is based on your previous observations.
It’s a trial solution to your question that you will test through experimentation. Hypotheses are often
stated in an “If... then...” statement.
Now back to the vine maples. You have noted that vine maples change color in the fall on
approximately the same dates each year, but this varies by a week or two each year. You hypothesize,
since air temperature is not constant each year in the fall, the progressively cooler days in fall are
responsible for stimulating the color changes. Therefore, you develop and wish to test the following
hypothesis: If progressively cooler temperatures are responsible for stimulating the color changes in
the leaves of vine maples, then vine maples placed in an artificially cooled growth-house (green
house) should go through the same color changes as would the vine maples in nature, even if the
length of day/night are held constant via artificial lighting.
Testing Hypotheses via Experiments or by Pertinent Observations
The next step of the scientific method is to design an experiment or make pertinent observations
to test the hypothesis. In any experiment there are three kinds of variables.
 Independent variable: The independent variable is the single condition (variable) that is
manipulated to see what impact it has on a dependent variable (measured factor). The
independent variable is the factor that causes the dependent variable to change. E.g. the
temperature the trees are exposed to is the independent variable in this vine maple example. The
independent variable is the factor (i.e. experimental condition) you manipulate and test in an
experiment. A great challenge when designing an experiment is to be certain that only one
independent variable is responsible for the outcome of an experiment. As we shall see, there are
often many factors (known as control variables) that can influence the outcome of an
investigation. We attempt, but not always successfully, to keep all of the controlled variables
constant and change only one factor, the independent variable or control treatment, when
conducting an experiment. Once the parameters or limits (such as the amount, intensity, volume,
or etc.) of the independent variable have been delineated then the independent variable becomes
a controlled treatment for the experiment.
 Dependent Variable: The thing measured, counted, or observed in an experiment. E.g. the color
of leaves is the dependent variable in the vine maple example.
 Control Variables: These are the variables that are kept constant during an experiment. It is
assumed that the selected independent variable is the only factor affecting the dependent
variable. This can only be true if all other variables are controlled (i.e. held constant). In the vine
maple example: species of vine maple, age and health of the trees used, length of day,
environmental conditions such as humidity, watering regime, fertilizer, etc. It is quite common for
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different researchers, or for that matter, the same researcher, to get different and conflicting
results while conducting what they think is the very same experiment. Why?
In an experiment of classical design, the individuals under study are divided into two groups: an
experimental group that is exposed to the independent variable (e.g. the group of trees that are
exposed to the varying temperatures), and a control group that is not. The control group would be
exposed to the identical conditions as the experimental group, but the control group would not be
exposed to the independent variable (e.g. the control group of vine maples would be kept at a
constant temperature, everything else would remain identical.)
Sometimes the best test of a hypothesis is not an actual experiment, but pertinent observations.
One of the most important principles of biology, Darwin’s theory of natural selection, was developed
and supported by his extensive observations of the natural world. Since Darwin’s publication of his
theory, a multitude of experiments and repeated observation of the natural world continue to support
Darwin’s theory.
An important hypothesis may become a theory after it stands up consistently to repeat testing by
other researchers. A scientific theory is a hypothesis that has yet to be falsified and has stood the test
of time. Hypotheses and theories can only be supported, but cannot be proved true by
experimentation and careful observation. It is impossible to prove a hypothesis or theory to be true
since it takes an infinite number of experiments to do this, but it only takes one experiment to
disprove a hypothesis or a theory. Scientific knowledge is dynamic, forever changing and evolving as
more and more is learned and new techniques are developed.
Conclusion
Making conclusions is the next step in the scientific method. You use the results and/or pertinent
observations to test your hypothesis. However, you can never completely accept or reject a
hypothesis. All that one can do is state the probability that one is correct or incorrect. Scientists use
the branch of mathematics called statistics to quantify this probability.
Publication in a Scientific Journal
Finally, if the fruits of your scientific labor were thought to be of interest and of value to your
peers in the scientific community, then your work would be submitted as an article for publication in a
scientific journal. The goal of the scientific community is to be both cooperative as well as
competitive. Research articles both share knowledge and provide enough information so that the
results of experiments or pertinent observations described by those articles may be repeated and
tested by others (verifiable data). It is just as important to expose the mistakes of others, as it is to
praise their knowledge.
Heart Rate and Fitness Exercise
Goals of Lab Exercise
 Learn proper graphing technique
 To learn and apply the steps of the scientific method to answer questions concerning physical
fitness
 Use a computer and heart rate monitor to measure the human heart rate
 Determine the effect of body position on heart rates
 Determine the effect of exercise on heart rates
 Correlate the fitness level of individuals with factors such as smoking, the amount of daily
exercise, or other factors identified by students.
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Introduction
The Circulatory System
The circulatory system is responsible for the internal transport of many vital substances in
humans, including oxygen, carbon dioxide, and nutrients. The components of the circulatory system
include the heart, blood vessels, and blood. Heartbeats result from electrical stimulation of the heart
by the pacemaker (sino atrial node or SA Node), located in the heart’s inner wall of the right atrium.
Although the electrical activity of the pacemaker originates from within the heart, nerves outside of
the heart influence the rhythmic sequence of impulses produced by the pacemaker. Many things
might affect the rate of the heart’s beating, including the physical fitness of the individual, the
presence of drugs such as caffeine or nicotine in the blood, or the age of the person.
The increase in heartbeat rate during exercise can be measured by monitoring the individual’s
heart rate. As a rule, the maximum heart rate of all individuals of the same age and sex is about the
same, yet the time it takes individuals to reach that maximum level while exercising varies greatly.
Since physically fit people can deliver a greater volume of blood in a single cardiac cycle than unfit
individuals, they usually can sustain a greater work level before reaching the maximum heart rate.
Physically fit people not only have less of an increase in their heart rate during exercise, but their heart
rate recovers to the resting rate more rapidly than unfit people.
In this experiment, you will evaluate your physical fitness. An arbitrary rating system will be used
to “score” fitness during a variety of situations. Tests will be made while in a resting position, in a
prone position, as well as during and after physical exercise. Let’s now take a look at the Scientific
Method.
Materials
Computer
Stepping platform, 9” high
Caution!
Go-Link Interface
Hand held Heart Rate Monitor
Heart Rate Monitor Program
Recorded Metronome
Do not attempt this exercise if physical exertion will aggravate a health problem.
Inform your instructor of any concerns that you may have and if you experience
any issues following the exercise.
Procedure
Developing a Question, Hypothesis, and Experimental Procedure
1. In teams of 4, take a few minutes to discuss several specific questions about an independent
variable related to cardiovascular fitness peculiar to your group. For example, you might ask:
“Is there a difference in cardiovascular fitness between males and females?
2. Cardiovascular fitness will be assessed by determining and comparing the heart rate while
standing, reclined, going from a reclined to a standing position, and before and after physical
activity as outlined in steps 1 - 18, under Collecting Data from Test Subjects (page 11).
3. Write your group’s best question and hypothesis on the Report Sheet (page 15) and
contribute your group’s hypothesis on the front board.
4. Determine which hypothesis that the entire class will attempt to answer. Record this
hypothesis on the Report Sheet.
5. Design an experiment that will test this hypothesis. All teams will perform the same
experiment. List the generalized steps (at least 5) of the experimental design on the Report
Sheet.
6. Each group should recruit one subject for treatment 1 and another subject for treatment 2.
One test subject will complete steps 1 – 18 under the direction of the investigators (other
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group members) and then the other subject will be tested. One investigator (one of your
partners) should record your data on the Report Sheet.
The Set Up
1. Prepare the computer for data collection by opening the Biology with Computers software as
follows: Plug the hand held heart rate sensors into the Go-Link connector then go to Start 
click on Programs  open Vernier  open Logger Pro  go to File  open Biology with
Vernier  open “Exp. 27” Heart Rate & Fitness.
2. Have your first test subject grasp the sensors while sitting, ensure that the direction of the
arrow on the sensor matches the direction of the arrow on the receiver, and they are within 3
to 4 ft. of each other. Click the COLLECT button and continue collecting until the test
subjects’ heart rate is steady and within the normal range for the individual—between 55 and
85 bpm.
3. Click on the STOP button to stop data collection when you have determined that all
equipment is functioning properly.
4. To obtain the average heart rate, maximum heart rate, etc. during the test: Select “Analyze”
on the menu bar at the top of the screen and click on “Statistics”. This will place a table onto
the graph, find the mean in the box, and record on the appropriate data table on the Report
sheet when actually collecting data.
5. Erase the data from this run and begin the experiment with your first subject.
Collecting Data from Test Subject
1.
2.
3.
Start with either subject (treatments 1 or 2) and follow steps 2 - 18. After step 18, each
group should repeat steps 2-18 with a subject representing the other treatment category.
Instruct the test subject to stand upright, click the COLLECT button, and begin taking data
with the Heart Rate Monitor program. Wait until the heart rate becomes stable, record for I
minute, and then record the subject’s heart rate in the proper column in Table 6A or 6B
(page 16 or 17, respectfully) based on your assigned group number.
Compare the subject’s standing heart rate to the values in Table 1. Assign fitness points
based on Table 1 and record the fitness points on the Report Sheet.
Beats per minute
Fitness points
Beats per minute
Fitness Points
< 60 - 70
12
101 - 110
8
71 -80
11
111 - 120
7
81 - 90
10
121 -130
6
91 -100
9
131 -140
4
Table 1 Fitness Points for Standing Heart Rate Use this table to assign fitness points based on the subject’s
standing heart rate.
4.
5.
Instruct the subject to recline on a clean table with their feet on the table and knees bent.
Wait until the heart rate becomes stable, record for 1 minute, and then record the subject’s
average heart rate on the Report Sheet. The subject remains reclined until step 6.
Compare the subject’s average reclining heart rate to the values in Table 2, assign fitness
points based on Table 2, and record the fitness points on the Report Sheet.
Beats per minute
Fitness points
Beats per minute
Fitness Points
< 50 - 60
12
81 - 90
8
61 - 70
11
91 - 100
6
71 - 80
10
101 -110
4
Table 2 Fitness Points for Reclining Heart Rate Use this table to assign fitness points based on the subject’s
reclining heart rate.
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6.
7.
8.
9.
Instruct the test subject to quickly stand up next to the lab table and remain still. Measure
the subject’s peak heart rate upon standing (This takes a few moments and the number will
appear in the heart rate box on the screen.) and then record it on the Report Sheet.
Find how much the heart rate increased after standing by subtracting the reclining rate
value in Step 4 from the peak standing value in step 6.
Assign fitness points corresponding to your reclining to standing heart rate in Table 3 and
record the fitness points on the Report Sheet. Stop data collection.
Have the test subject stand and begin collecting heart rate data. Wait until the heart rate
becomes stable (Initial standing heart rate), and then record the subject’s heart rate on the
Lab Report Sheet.
Heart Rate Increase after Standing
Ave. Reclining rate (beats/min)
0–10
11–17
18–24
25–33
34+
50–60
12
11
10
8
6
61–70
12
10
8
6
4
71–80
11
9
6
4
2
81–90
10
8
4
2
0
91–100
8
6
2
0
0
101–110
6
4
0
0
0
Table 3 Fitness Points for Reclining to Standing Use this table to assign fitness points based on the subject’s
reclining to standing heart rate changes.
10. While holding the hand held sensor devices have the test subject step up and down on a
low platform about 8 to 10 inches from the ground as follows:
 Place the right foot on the top step of the stool.
 Place the left foot completely on the top step of the stool next to the right foot.
 Place the right foot back on the floor.
 Place the left foot back on the floor.
 Repeat the above stepping cycle for 3 minutes
11. Use the recording of a metronome set at 96 beats per minute to ensure that all subjects
maintain a constant step rate. The test subject should make one-foot movement for each
beat of the metronome.
12. Record on the Report Sheet the subject’s average heart rate after 3 minutes of exercise.
When the subject has completed the step exercise, quickly move to Step 13.
13. With a stopwatch or clock, begin timing to determine the test subject’s recovery time.
During the recovery period, the test subject should remain standing and still. Monitor the
heart rate and stop timing when the rate returns to the Initial standing heart rate value
before the start of the step test (recorded in Step 6). Record the recovery time on the
Report Sheet.
14. Assign fitness points based on the information in Table 4 (page 13). Record the fitness
point value on the Report Sheet.
15. To calculate the endurance heart rate, subtract the initial standing heart rate before
exercise (Step 6) from the average heart rate during exercise (Step 12). Record this heart
rate increase in the endurance row on the Report Sheet.
16. Assign fitness points based on Table 5 (page 13) and record the value on the Report Sheet.
17. Total the fitness points for the subject and use Figure 1 (page 13) to determine an arbitrary
fitness level and record on the Report Sheet.
18. Repeat steps 2 - 17 with a new test subject for the other treatment category.
19. As a group answer the questions on the Report Sheet (pages 15 through 20) and turn in one
packet per group next week at the start of the lab.
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Recovery Time (seconds)
Fitness Points
0–30
14
31–60
12
61–90
10
91–120
8
121-150
6
> 150
4
Heart rate stabilized at a higher rate than the average standing value
6
before starting the step test
Heart rate did not fall to within 6 to 10 beats/min. of the initial rate within
4
150 seconds after the cessation exercise
Table 4 Fitness Points for Recovery Time Fitness points based on the subject’s total heart rate recovery
time.
Standing rate
(beats/min)
Heart rate increase after exercise
0–10
11–20
21–30
31–40
41+
60–70
12
12
10
8
6
71–80
12
10
8
6
4
81–90
12
10
7
4
2
91–100
10
8
6
2
0
101–110
8
6
4
1
0
111–120
8
4
2
1
0
121–130
6
2
1
0
0
131+
5
1
0
0
0
Table 5 Fitness Points for Endurance Fitness points based on the subject’s endurance rate.
Fitness Scale
Low
Fitness
20
Very
Fit
Fit
30
40
50
60
Figure 1 Fitness Scale Use this scale is to chart the arbitrary fitness level for each subject.
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Page to be used for Biological Doodling
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Report Sheet
Lab Section:
Principles of the Scientific Method Exercise
Group Names:
.
.
.
.
.
Question, Hypothesis, and Experiment:
From Developing a Question, Hypothesis, and Experimental Procedure:
Group Work:
1. Your group’s best question:
Your group’s hypothesis:
Class Work:
2. Hypothesis proposed by the class:
Summary of the experimental procedure designed by the class:
3. List below the various components of the experiment designed by the class
 Dependent variable(s):
 Independent variable(s):
 Controlled variable(s):
 Control treatment:
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Data:
Treatment 1:
Situation:
Group Number

Standing heart rate
(beats/min)
Reclining heart rate
(beats/min)
Peak heart rate upon standing
(beats/min)
Initial standing heart rate just
before step test (beats/min)
Heart Rate Average after step
test (beats/min)
Recovery time (seconds)
Endurance (beats/min)
Heart Rate
1
2
3
4
5
6
Fitness Points
1
2
3
4
5
6
Total fitness points 
Average total fitness points
for treatment 1 
Arbitrary Fitness Level
Table 6A Treatment #1 Data Table Record your heart rate and fitness points on this table captured from
Treatment #1 subject.
Miscellaneous Notes and Observations:
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Data:
Treatment 2:
Situation:
Group Number

Standing heart rate
(beats/min)
Reclining heart rate
(beats/min)
Peak heart rate upon standing
(beats/min)
Initial standing heart rate just
before step test (beats/min)
Heart Rate Average after step
test (beats/min)
Recovery time (seconds)
Endurance (beats/min)
Heart Rate
1
2
3
4
5
6
Fitness Points
1
2
3
4
5
6
Total fitness points 
Average total fitness points
for treatment 2 
Arbitrary Fitness Level
Table 6B Treatment #2 Data Table Record your heart rate and fitness points on this table captured from
Treatment #2 subject.
Miscellaneous Notes and Observations:
Record the
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Graphing the Data:
1. Read carefully “Graphing of Data” in Appendix A, obtain a piece of appropriate graphing paper,
and then construct a graph that will assist you in interpreting the results from this investigation:
 Graph total fitness points for subjects 1-6 for treatment 1.
 Graph total fitness points for subjects 1-6 for treatment 2.
 Graph average total fitness points for treatment 1.
 Graph average total fitness points for treatment 2.
 Appropriately label the graph with a figure number, title, and descriptive sentence.
2. Summarize the trends in fitness displayed on your graph by referring to the data displayed on your
graph (Refer to a data by figure number).
3. Construct an additional graph to reveal some other trend from your research. For example
compare recovery time, heart rate before and after exercise, or heart rate after exercise of each
treatment. Use the graphing information to assist your design (Appendix A).
4. Summarize the trends in fitness displayed on your graph by referring to the data displayed on your
graph. (Refer to a data by figure number).
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Conclusions:
1. Does the data support or refute the hypothesis proposed by the class? Explain using data from
the experiment (Refer to a data by figure number).
2. Using your data (Refer to a data by figure number), are there additional conclusions one could
draw from this experiment?
3. Explain why an experiment has only one independent variable, and identify the independent
variable for this experiment?
4. How could this experiment be improved to get results that would allow the formulation of more
valid conclusions? Give specific ways the experiment could be improved!
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Application Questions:
1. When subjects moved from a standing position to a reclining position, how did their heart rate
change, by how much, how do you account for this change, and was the result what you
predicted? (Refer to a data by figure number)
2. When subjects moved from a reclining position to a standing position, how did their heart rate
change, by how much, how do you account for this change, and was the result what you
predicted? (Refer to a data by figure number)
3. Why does research indicate that most heart attacks occur as people get out of bed after a
night’s sleep?
4. Why would athletes need to work longer and harder before their heart rates were at the
maximum value?
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Pre-Lab Report Sheet
Lab Section:
.
Heart Rate & Fitness Exercise
Name:
.
Before coming to lab carefully read the previous pages on the Principles of the Scientific Method
then answer these pre-lab questions. Be prepared to hand in your responses to the pre-lab questions
at the start of lab.
1. Restate the following hypothesis in an “If-Then” statement. Hypothesis: Students that study twohours outside of class for every one-hour in class usually get better grades than students that
study half that amount of time.
2. Identify the independent and dependent variables in the following experiments:
Pea plant height measured daily for 30 days.
Dependent variable:
Independent variable:
Number of leaves found on pea plants 5 days after having been treated with gibberellic acid.
Dependent variable:
Independent variable:
3. Suggest a control treatment for each of the following two experiments:
Pea plants are sprayed with 5ml. aqueous solution of gibberellic acid and their height
determined daily after the spraying.
Control treatment:
Pulse rate is determined after 3 minutes of aerobic exercise. (Hint: the control is what the heart
rate after exercise will be compared to.)
Control treatment:
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4. Should the data obtained from the following experiment be plotted as a line graph or a bar
graph? Briefly explain your reasoning: Pea plant height measured daily for 30 days. (See
Appendix A for help.)
Line graph or Bar Graph (circle one)
Explain why you came to this conclusion?
5. Write a question, a hypothesis, and identify the independent, dependent and three control
variables that you would like to investigate in this laboratory (heart rate experiment). See pages
of the Perspectives for help.
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Laboratory 2: Microscopic Observation of Cells
Pre-lab Assignment
Before coming to lab carefully read the following pages on Microscopic Observation of Cells plus
Appendices B and D, then answer the pre-lab questions, pages 37 & 38.
Perspectives
The microscope is one of the principal tools of the biologist. Without the microscope, many of
the great discoveries of biology would never have been made. The light compound microscope
(Figure 1) is the type of microscope most commonly used. Proper, comfortable use of the instrument
demands practice. The practice afforded you in this exercise depends upon familiarity with the parts
of the microscope and with their interactions.
Note each of the following features of the microscope and their individual uses allow you to take
full advantage of the use of a microscope.
 Ocular: These contain lens that magnify (usually 10x) the specimen.
 Revolving Nosepiece: Device used to change magnifying lenses (objectives).
 Objective Lens: Magnifying lenses usually ranging from 4x to 100x.
 Sub-stage Condenser: This adjustable device gathers the light rays from the light source and
focuses them onto the specimen stage.
 Iris Diaphragm: This lever adjusts to control the amount of light shown onto the specimen.
 Coarse and Fine Focus Knobs: These adjustable knobs are used to focus the specimen. The
course focus knob only needs to be used with the 4x objective.
Figure 1 Compound Light Microscope A typical compound light microscope used in many biology labs.
Magnification and Resolution
In using the microscope it is important to know how much you are magnifying an object. To
compute the total magnification of any specimen being viewed multiply the power of the eyepiece
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(ocular lens) by the power of the objective lens being used. For example, if the eyepiece magnifies
10x and the objective lens magnifies 40x, then 10 times 40 gives a total magnification of 400x.
The compound microscope has certain limitations. Although the level of magnification is almost
limitless, the resolution (or resolving power) is not. Resolution is the ability to discriminate two
objects close together as being separate (clarity). The human eye can resolve objects about 100 µm
apart (note: 1 µm = 1 micrometer = 1 millionth of a meter). Under ideal conditions the compound
microscope has a resolution of 0.2 µm, about 500 times the resolving power of the human eye.
Objects closer than 0.2 µm are seen as a single fused image.
Resolving power is determined by the amount and physical properties of the visible light that
enters the microscope. In general, the greater the amount of light delivered to the objective lens, the
greater the resolution. The size of the objective lens aperture (opening) decreases with increasing
magnification, allowing less light to enter the objective lens. Thus, it is often necessary to increase the
light intensity at the higher magnifications.
Depth Perception and the Microscope
Any microscopic object viewed has depth as well as length and width. While the lens of your eye
fully adjusts to focus on an object being viewed and provides an image that allows your brain to
develop a three dimensional interpretation, the lenses of a microscope are focused mechanically and
can only “see” in two dimensions, length and width. For example, if the specimen you are examining
has three layers of cells, you will only be able to focus on one cell layer at a time. In order to perceive
the relative depth of your specimen, use the fine adjustment knob to focus through the different
planes (i.e. the three cell layers) individually to build a three-dimensional picture or interpretation of
your specimen.
The Field of View and Estimating the Size of Specimens
When you view an object under the microscope you will observe that it lies inside a circular field of view.
Each magnification lens has a different sized field of view. If you determine the diameter of the field of view
you can estimate the size of an object seen in that field. As you increase the magnification, the field of view
(and diameter) gets proportionately smaller. As a consequence, a critter that appears small under scanning
power (4x) may appear large under high power. The actual size of the critter did not change, only the space in
which you placed it for viewing.
The Oil Immersion Lens
Although the oil immersion lens (100x) when used properly offers the ability to view objects at
high magnification, the objects viewed in this lab exercise do not warrant its use. As its name implies,
an oil immersion lens requires a drop of immersion oil to be in contact between the lens and the slide
for the lens to function effectively. Since immersion oil has the same refractive index as glass, it
prevents the scattering of light as light passes from the glass slide to the objective lens (also made of
glass). Poor resolution is the result if the oil immersion lens is used without oil since light will be bent
(and thus scattered) as it passes from the slide to air, and then through the oil immersion objective
lens because air and glass bend light differently as a result of having different refractive indexes.
Care of the Microscope: Your microscope is an expensive instrument that must be given proper
care. Always follow these general instructions when using a microscope.
1. Carry the microscope with both hands, one hand under the base, and the other on the arm. When
getting ready to put the microscope away, always return it to the low power or scanning power
objective over the stage, lower the stage to its lowest position, and wrap the cord securely around
the light source and the base of the arm.
2. When setting the microscope on a table, always keep it away from the edge.
3. It is generally best to clear your lab table of items that are not being used.
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4. The lenses of the microscope cost almost as much as all of the other parts together. Never clean
them with anything other than lens paper. Paper towels and other paper tissues will scratch the
lens.
5. Please inform the instructor or the biology lab technician of any microscope damage or irregularity
in its operation as soon as possible. Do not return a faulty microscope without first informing the
instructor or lab tech.
6. You are responsible for the microscope while you are using it. Treat it with care!
Exercise: Microscope Function and Uses
Goals of this Lab Exercise
 Identify the parts of a compound light microscope and use a microscope to competently
examine biological specimens
 Determine the diameter of the field of view for the various objective lens of a microscope
 Accurately sketch, describe, and cite the major functions of the structures and organelles of the
cells examined in this lab exercise
 Estimate the size of specimens when viewed with a microscope
 Learn to use metric units correctly when measuring specimens on the compound microscope
Introduction
1. Techniques for Setting Up & Viewing Objects with a Compound Microscope.
Be familiar with the following procedures outlining the correct usage of the microscope before
coming to lab. The steps that follow should be observed in this lab exercise and all other microscope
lab activities in this and other courses/lab experiences.
A. Place the low-power objective (4x or scanning) in position over the stage by grasping the nose
piece and NOT the objectives. In changing from one objective to another, you will hear or feel a
click when the objective is set in the proper position.
B. Make certain that the lenses are clean. Dirty lenses will cause a blurring or fogging of the
image. The high power and ocular lenses are the lenses that most often get dirty. To clean a
microscope lens: 1) Place a drop of lens cleaning fluid on a piece of lens paper; 2) Clean lens
with a gentle circular motion; 3) Finally dry the lens with a fresh piece of lens paper and 4)
Dispose of lens paper in the trash. Always and only use lens paper for cleaning a microscope
lens! Any other material (including Kim wipes or your finger) may scratch the lens.
C. Plug in the electrical cord to turn on the sub-stage light, turn power switch to on, and adjust the
light control (rheostat) to dim the light to just illuminate (pale yellow) the viewing field. While
looking through the oculars (use both eyes for ease of microscope operation) turn the light
control until the light in the field of view is an evenly lit white field.
D. Position the condenser as high as it will go by turning the sub-stage adjustment knob. As you
view a specimen you will have to lower the condenser slightly to set the condenser at the
proper level. By raising or lowering the condenser, you can change the contrasting effects of
the microscope to increase the ability for you to view the specimen with more resolution.
E. Open the iris diaphragm by means of the black lever attached to the condenser apparatus,
which is found just below the stage of the microscope.
2. Getting Started Viewing Specimens Using the Compound Microscope.
A. Selecting the objective to begin.
a. If you need to scan the slide to find the location of a specimen use the low power scanning
objective (4x) with its larger field of view.
b. If you have a pretty good idea where the specimen is located on the slide it is okay to start
with the medium power objective (10x).
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B.
C.
D.
E.
F.
c. Because of the danger of damaging these lenses with their very small field of view and
shorter focal lengths, never begin microscopic examinations with the high power (40x) or the
oil immersion (100x) objectives.
d. See the previous page for information concerning the oil immersion lens.
Place the slide on the stage for viewing.
a. Make certain that the low power scanning objective (4x) or the medium power objective
(10x) is “clicked” properly in place.
b. Lower the stage away from the objective with the coarse adjustment knob.
c. Place a properly prepared slide on the stage and secure with the stage clips or mechanical
stage depending upon which is present on your microscope.
d. Viewing from the side of the stage move the part of the slide with the object to be viewed
directly above the brightly illuminated sub-stage condenser.
Proper Focusing Technique for low scanning (4x) and medium power (10x) objectives.
a. Viewing the stage from the side, use the coarse adjustment knob to raise the stage until the
stop is reached that will prevent further movement of the stage.
b. Looking through the eyepiece (ocular, usually 10x power) lower the stage slowly by turning
the coarse adjustment knob away from you until the object is in focus. It should take less
than a quarter of a turn to bring the image into focus.
c. Use the fine adjustment to bring the object into sharp focus.
d. Adjust the amount of light with the iris diaphragm and intensity of light with the condenser
for optimum viewing. Too much or too little light adversely affects the contrast of the image
viewed!
Tips!
a. When it is difficult to find a specimen to focus on (e.g. when examining cheek cells), bring
the edge of the cover-slip into the center of the field of view, and then try focusing on the
edge, then search the slide for the desired specimen.
b. Reduce the light intensity (can increase contrast) to aid in the observation of viewing
clear/transparent objects such as amoeba or cheek cells.
c. To avoid eyestrain practice keeping both eyes open. Many biologists are capable of
observing a specimen and sketching it at the same time! Try it out in today’s lab.
Switching from Lower to a Higher Power Objective.
a. First, be sure the object that you want to view at a higher magnification is in the center of
the field of view (Why?) and sharply focused under low power.
b. Switch to a higher power objective and watch from the side to make sure that the objective
lens does not touch the slide. Since most microscopes are par focal (meaning that the focal
plane of each lens is matched to be reasonably closely related) means that little refocusing is
needed when moving from one lens to another. Only fine adjustment may be required. If
properly focused at low power, and the slide is prepared correctly (i.e. the specimen is thin
and flattened by a cover slip), you should be able to switch automatically from low to high
power without fear of having the high power objective lens scraping or touching the slide.
c. The object should be in focus, or almost in focus (use only the fine focus knob).
Re-Focus with the Fine Adjustment under High Power (40x).
a. Only use the fine adjustment focus knobs at high power! To avoid damaging the lens,
never use the coarse adjustment when the high-power (40x) or oil immersion objective
(100x) is in place.
b. The working distance is the distance between the specimen viewed and the objective lens of
the microscope. As you increase magnification the working distance becomes less and less.
The objective will be almost touching the cover slip when properly focused at high power
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G. Adjust the amount and intensity of light for optimum viewing by using the iris diaphragm or
condenser. The amount of light may need to be increased since less light passes through the
high power objective at higher magnification. Do not turn or move the chrome screws under
the stage attached to the condenser apparatus as these either hold or adjust the condenser
alignment.
H. Removing the slide from the stage.
a. Switch the objective to low power (4x). Removing a slide while under high power may
scratch the lens.
b. Carefully lower the stage using the coarse adjustment knob, open the stage slide holding
mechanism, and carefully remove the slide.
I. Disposal of Wet Mounts.
a. Discard the cover slip (plastic cover slips in the trash, glass cover slips in the broken glass
container at the front of the lab).
b. Wash the slide with soap and water and then rinse the slide with deionized (dH2O) water at
the sink in the back or place into the beaker containing slide cleaning solution and skip step
c.
c. Place the slide to dry on the paper towel labeled “Wet Clean Slides” on the drain board next
to the large stainless steel sink at the front of the room.
J. Prepared slides.
a. Return to their proper location within the plastic slide container on the lab supply cart
3. Preparing a Wet Mount.
A. Place a drop of water on a clean slide with a dropper.
B. Put the object in the water drop.
C. Lower one edge of the cover-slip to the edge of the water drop as shown in the illustration
(Figure 2). Lower the cover-slip slowly to avoid air bubbles. A gentle tapping will usually
remove any bubbles that may be present. Blot any excess water with a paper towel. More
water can be added with a dropper at the edge of the cover slip. Do not let your specimen dry
out.
Figure 2 Wet Mount Preparation The critical aspect of this technique is the amount or water that is used to
make the slide.
Materials
Common Use Items on the Center Table
Lens Paper and Lens cleaning solution
Metric Rulers
Clean microscope slides
Cover slips
Eye droppers
Bottle of deionized water (dH2O)
Forceps (tweezers)
Scissors
Safety Goggles
Procedure
As a group answer the questions on the report sheet and turn in one packet next week at the
start of the lab. Answer the questions on your Report Sheet (starting on page 33) as you follow the
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procedures outlined below. Perform procedures that can only be done in the lab before doing
procedures or answering questions that can be performed outside of the biology laboratory!
Part A: Observation of a Newsprint Letter
In this part you will learn to use the microscope to examine a familiar object, a self-prepared slide
of a newsprint letter. Refer to the previous sections to prepare your slide and observe it with the
microscope. Practice adjusting your microscope to become proficient in locating a specimen, focusing
clearly, and adjusting the light (via the iris diaphragm, the condenser, or the light rheostat) for
optimum viewing.
Materials needed for Part A
Microscope slide and cover slip
Newsprint letter
Compound light microscope
Safety Goggles
Procedure:
1. Make a wet mount (Wear Safety Goggles) of a lower case letter which has been cut from
newsprint (Don’t use the letter o. Why?). When placed on the microscope stage the letter
should be in an upright position when viewed with the naked eye (i.e. not looking through the
eyepiece of the microscope) from behind the arm of the microscope.
2. Observe this under low (4x), medium (10x), and high dry power (40x).
3. Answer questions 1-10 on the Report Sheet (pages 33 & 34) as you observe the letter with a
compound light microscope.
Part B: Defining Resolution and Determining the Total Magnification
To be able to compare data with other scientists, microscopists need to know the structure and
function of the various cellular components. Reliability of size relationships is critical. The following
exercise part is designed to give the student information about the magnification of the compound
light microscope.
Materials needed for Part B
Compound light microscope
Procedure:
1. Determine the total magnification of the low, medium, high, and oil immersion fields of view.
Record the data in the first two rows of Table 1 (page 34).
Part C: Determining the Size of the Microscopic Field of View
You will often want to know the size of the objects you are observing under the microscope.
Because these objects are usually too small to permit direct measurement, it will be convenient for
you to learn a method to indirectly measure them. Estimating the diameter of the field of view for the
different objective magnifications will enable you to determine indirectly the approximate size of
objects viewed under the microscope.
Materials needed for Part C
Compound light microscope
Plastic Metric Ruler
Procedure:
The diameter of the field of view for low power is given to you in Figure 3. To verify this
diameter, do the following:
1. Be sure the low-power objective (4x) is in position. Place the graduated edge of a plastic metric
ruler across the midline (diameter) of the field of vision (Figure 3). Bring the ruler into focus
under low power (4x).
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2. Record the diameter in millimeters onto Table 1 on your Report Sheet ( page 34) and convert
the diameter in micrometers. One millimeter equals 1000 micrometer: 1 mm = 1000 µm
(Appendix B). The most common unit of measurement in microscope work is the micrometer,
µm.
3. Once you have determined the diameter for the field of view at low power you can calculate
the diameters of the fields of view for the rest of the objective lenses (Figure 4). For example,
to calculate the diameter of the high-power field knowing the diameter of the low-power field,
first find the number on each objective that indicates the magnification. Divide the high-power
by the low-power magnification to get a factor that indicates how much smaller the high power
field is compared to the lower power lens. For example, if the low-power objective reads 15x
and the high-power 45x, dividing 45 by 15 gives a factor of 3. If the diameter of the low-power
field were 1.5 mm, then the diameter of the high-power field would be 1.5 divided by 3 or 0.5
mm. Fill in the last two rows of Table 1 (page 34) on your Report Sheet.
4. Once you know the field of view diameter, you should be able to estimate the size of any
organism found within that field.
1 mm = 1000 µm
1 µm = 0.001 mm
Field of View
App. 4.5
mm
Metric Ruler (mm)
Figure 3 Microscope Field Diameter Measurement This figure shows the hypothetical determination of the
diameter of the field of view of a scanning or low power (4x) objective using a metric ruler.
Figure 4 Magnification Conversion Table This information is used to calculate the field of view by using
conversion factors of par focal objective lenses.
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Part D Depth Perception
It is important to remember that by using the coarse and fine adjustments you bring the
microscope into focus at many different levels. At each setting you can see clearly only one plane of
the object. To see other planes clearly, you must change the focus.
Materials for Part D
Nylon panty hose (~1 cm square)
Prepared slide of crossed threads
Compound Light Microscope
Safety Goggles
Bottle of deionized water (dH2O)
Cover slip and slide
Procedure:
1. Obtain a small piece of nylon hose approximately 1-cm square. Prepare a wet mount (Wear
Safety Goggles) of this material (make the nylon piece as smooth as possible on the slide).
Examine under low and high power. Notice as you rotate the fine adjustment knob back and
forth slowly, you can see the fibers at different depths. You get a three-dimensional (i.e. length,
width and depth) interpretation of the nylon.
2. Describe your impression of microscopic depth of field by answering question #12 on page 34.
3. Obtain a prepared slide with three colored cross threads (or make a wet mount if a prepared
slide is not available.)
4. Focusing with a medium power objective (10x), locate the point where the three threads cross
each other. Using proper focusing technique as outlined in the beginning of this lab determine
which thread comes into focus first. Use this information to help answer question #13 on your
Report Sheet (page 34).
Part E: Wet Mounts and Drawings
In the circles provided in the report sheet make neat and accurately labeled drawings of the cells
listed below. Your sketches should be accurate (Use textbooks and Appendix D for assistance) enough
so that an informed individual could identify the cells or organisms from your drawings.
Mammalian wet mount: Human Cheek cells
Materials for this exercise
Flat-tipped toothpick
Dropper bottle of methylene blue
Caution!
Compound Light Microscope
Bottle of deionized water (dH2O)
Safety Goggles
Cover slip and slide
Place all used toothpicks into the autoclave bag at front counter.
Procedure:
1. Wear Safety Goggles for this part of lab! Place a tiny drop of deionized water in the center of
the slide. Using the flat end of the toothpick, gently scrape the inner lining of your cheek.
Agitate the end of the toothpick containing the cheek scrapings in the drop of dH2O.
2. Add a tiny drop of methylene blue stain to the preparation and stir again with the toothpick.
Cheek epithelial cells are nearly transparent and thus difficult to see without the stain, which
colors the nuclei of the cells and makes them look much darker than the cytoplasm.
3. Add a cover slip and observe under low and then under high power. Although the cells form a
solid sheet of cells in your mouth, the scraping of the toothpick probably caused the cells to
separate from each other. Try to find a cluster of two or three cells whose shapes have not
been totally distorted. Avoid observing clumps of cells that show little cellular detail.
4. In the appropriate space on your Report Sheet (page 35), use a sharp pencil to make an
accurate sketch of a cluster of two or three cells as viewed at high dry power (or one cell if 2 or
3 cells can’t be found together). Estimate and record the approximate size (in micrometers,
µm) of a single epithelial cell in micrometers and attach a drawing scale.
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5. Identify, neatly label, and describe the general cellular function for the following cellular
structures: Plasma Membrane, Cytoplasm, and Nucleus.
Filamentous algae wet mount: Spirogyra
Materials for this exercise
Filamentous algae (Spirogyra)
Cover slip and slide
Compound Light Microscope
Pipette or dissecting needle
Safety Goggles
Procedure:
1. Wear Safety Goggles for this part of lab! Prepare a wet mount of Spirogyra: Use a pipette or a
dissecting needle to place a sample of the freshwater algae, Spirogyra, on a clean slide, cover
with a cover slip, and observe with low and high power. Use a dissecting needle to straighten
and untangle the strands of Spirogyra on your microscope slide.
2. In the appropriate space on your Report Sheet, use a sharp pencil to make an accurate sketch of
two or three consecutive cells of Spirogyra as viewed at high dry power.
3. Estimate and record next to your drawing the approximate length and width (in micrometers,
µm) of a single cell and attach a drawing scale.
4. Identify and neatly label on your sketch the following structures. Use your textbook as a
reference if needed.
 Cell Wall: Often coated with slime in filamentous algae such as Spirogyra.
 Cytoplasm: the internal aqueous environment inside the cell.
 Nucleus: Embedded within the cytoplasm of Spirogyra; Very light in color and therefore
difficult to find if the diaphragm is opened too wide and/or the condenser is not adjusted
properly.
 Chloroplast: In Spirogyra, it appears as a long spiral band that runs the length of the cell.
 Vacuole: Clear and large membrane-bound organelle within the cell that stores the sugars
produced by photosynthesis. Being clear it is difficult to observe in Spirogyra cells unless the
diaphragm is used to decrease the light intensity and the condenser and fine adjustment are
properly adjusted.
Microscopic organism of your choice: Pond Water “Scum”.
Materials for this exercise
Pond water and other cultures of microorganisms
Cover slip and Depression slide
Compound Light Microscope
Safety Goggles
Procedure:
1. Wear Safety Goggles for this part of lab! Prepare a wet mount of pond water or of other
organisms provided by your instructor by using a depression slide and cover slip, and observe
using low- and high-power.
2. In the appropriate space on your Report Sheet draw (with the magnification and a size scale) at
least two organisms of your choice as viewed at the high power or at the highest magnification
possible that allows you to view the whole organism.
3. Neatly label all cell parts as above and describe your critters means of locomotion.
4. Use the identification keys in the lab to identify the kingdom (and phylum, if possible) that the
organism belongs to.
5. Estimate the length and width (or diameter) of this organism in µm. Record these dimensions
on your drawing and attach a drawing scale.
6. Turn in pages 33 through 35 as a group to include all drawings, magnifications, and scales.
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Biological Doodling Space
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Report Sheet
Lab Section:
.
Microscopic Observation of Cells Exercise
Group Names:
Note:
.
.
.
.
Perform procedures that can only be done in the lab before doing procedures or answering
questions that can be performed outside of the biology laboratory!
1. Using low-power (4x) compare the position and orientation of the image of the letter as seen
through the ocular with the position of the letter as seen on the slide without using the
microscope. What two orientation differences of the image are there when compared to the
image seen without a microscope?
In the circle below use a sharp pencil to make a simple sketch of the letter as viewed under lowpower.
Letter viewed at magnification
x
2. While looking through the oculars slowly move the slide away from you by using the stage
control knobs. Which way does the image move?
(Place answer here)
3. While looking through the oculars, slowly move the slide from right to left using the stage
control knobs. Which way does the image move?
(Place answer here)
4. Make a rough estimate of how much of the letter is visible when viewed under high power?
(Give a percent based on the differences in the size of the field of views)
(Place answer here)
5. Does the switch from low power (4x) to high power 40x) change the position of the image?
(Place answer here)
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6. Why is it necessary to center your object (or the position of the slide you wish to view) before
changing to high power (40x)?
(Place answer here)
7. Under high power (40x) is the illumination brighter or less bright than it is with low power?
(Place answer here)
8. Move the iris diaphragm lever in each direction while observing the field. What happens?
(Place answer here)
9. Is it more desirable to increase or decrease the light when changing to a higher magnification?
(Place answer here)
10. What is the approximate actual height in millimeters and microns (µm) of your letter?
Height =
mm
=
µm (Place answers here)
11. Fill in Table 1.
Low Power
Magnification of
Objective Lens
Total
Magnification
Field Size
(diameter)
Field Size (diameter)
Medium Power
High Power
Oil Immersion
x
x
x
x
x
x
x
x
mm
mm
mm
mm
µm
µm
µm
µm
Table 1 Part B and C Data Fill out this table to show the Magnification and Field Size dimensions for your
microscope.
12. Space to describe your impression of microscopic depth of field and why this feature of a
microscope is important to microscopists?
13. Suppose a slide were set up with Yellow, Blue, and Red threads that cross at a single point top
to bottom, which thread would come into focus first if you positioned the stage as close to the
low power objective lens as possible and then brought the slide into focus? Circle the letter of
the correct response.
A. Yellow first
B. Blue first
C. Red first.
D. All three colors at once.
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14. Drawings of Wet Mounts for Part E. See Appendix D for what is required in the drawings
below.
Cheek Cell viewed at
x
Drawing Scale
Spirogyra viewed at
x
Drawing Scale
.
.
Pond Water Organisms
Organism of choice viewed at
Drawing Scale
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Organism of choice viewed at
.
Drawing Scale
35
x
.
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Biological Doodling Space
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Pre-Lab Report Sheet
Lab Section:
.
Microscope Techniques Exercise
Name:
.
Before coming to lab carefully read the previous pages on Microscope Techniques then answer
these pre-lab questions. Be prepared to hand in your responses to the pre-lab questions at the start
of lab.
A.Why is it necessary to center your object (or the position of the slide you wish to view) before
changing to high power?
Complete the table below and use the data to answer questions B and C.
Microscope Number
1
2
3
4
Objective Lens
25x
15x
20x
40x
Ocular Lens
5x
10x
10x
5x
Total Magnification
B. Given that each slide had the same density of microbes, with which microscope would you expect
to observe the greatest number of microbes at any given instant? Why?
C. If a slide showing the same organism is examined with each of the microscopes, above, with

which
two microscopes will the microbe appear to move with the same degree of rapidity? Why?

microscope will it appear to move the slowest? Why?
D.What is meant by resolution (resolving power) of a microscope?
E. After switching from one objective to another, why is it often necessary to readjust the
diaphragm and the condenser?
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Use the data in the table below for a hypothetical microscope to answer questions F and G.
Objective Used
Low power
Medium power
High power
Oil immersion
Total Magnification
30x
150x
300x
1500x
Diameter of Field of View
6000µm
F. Calculate the diameter of the field of view at medium, high, and oil immersion. Record your
answers in the table above, and show and/or explain your work below.
G. You observe an object whose length is 1/4 the diameter of the medium power field of view of
the hypothetical microscope in the table above. What is its length in microns? ____________ in
millimeters, mm? _______________. Show and/or explain your work below.
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Laboratory 3: Transporting Across Boundaries
Pre-lab Assignment
Before coming to lab carefully read the following pages on Transporting Across Boundaries then
answer the pre-lab questions, page 51, and define the terms at the end of the perspectives section.
Be prepared to hand in your responses to the pre-lab questions and the definitions at the start of lab.
Perspectives
A good way to think about the movement of substances into or out of a cell is to envision the
system that you are studying as being different compartments separated by a membrane barrier that
is permeable (allows movement across) to certain substances and impermeable (allows no movement
across) to other substances. The substances are referred to as the solute and the dissolving solution
(usually water) is referred to as the solvent. In these experiments the barrier (either a dialysis sac or
cell membrane) acts as a semi-permeable membrane. Your task is to determine what solute
molecules are allowed to move across the membrane (permeable) or not (impermeable).
The movement of solute across a semi-permeable membrane can either be an active transport
process (requiring the use of energy in the form of ATP) or a passive process (requiring no energy).
This lab will investigate passive processes. Smaller, non-polar molecules can move across a membrane
by passing between the phospholipid molecules of the membrane (called simple diffusion). While
smaller, polar molecules, and ions (charged atoms) can move through specific protein pores
embedded into the membrane (called facilitated diffusion). Both of these routes are classified as
passive transport because they require no energy input by the cell. The mechanisms or forces that
drive this process are Brownian motion (random molecular movement) and a favorable concentration
gradient (more of one solute on one side of the membrane than that same solute on the other side).
If all other factors are constant, then eventually the solute will come to equilibrium (balance) across
the membrane.
Osmosis is a special term that describes the movement of a solvent (usually water) across a semipermeable membrane by diffusion through protein channels called aquaporin. The force that moves
water, though, is not the water concentration, but rather the solute concentration across the
membrane. The solute is termed an osmotically active substance (OAS), and can be any molecule or
matter dissolved in the solvent. The trick is to measure the total OAS and then to measure the solutes
that are able to move across the semi-permeable membrane (remember they will reach their own
equilibrium). By comparing the difference between the permeability of the OAS, you can then predict
the OAS concentration at equilibrium and be able to predict the net movement of water. Three terms
are used to describe the relationship between OAS concentration across a membrane: hypertonic,
hypotonic, and isotonic. A hypertonic condition would have more OAS outside the cell, a hypotonic
condition would have more OAS inside the cell, and an isotonic condition would have a balance of OAS
across the membrane. Because of the differences or similarities of concentration, water will move to
the area of higher OAS and could cause radical changes in the shape of the cell. Hypertonic solutions
cause the cell to lose water and shrink in size or crenate; hypotonic solutions cause the cell to gain
water and expand or potentially burst (lysis), while isotonic has no net movement of water. How
would changing a cell from solution to solution affect cell function?
The key to understanding this exercise is to figure out 3 things.
1. What concentration gradients you have created?
2. In which direction will the net flow of given molecules travel within their concentration
gradient or in which direction will the net flow of molecules within their concentration
gradient try to flow?
3. To which type of molecule is the membrane permeable?
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Define each of the following terms on a separate sheet of paper: solvent, solute, precipitate,
semi-permeable membrane, passive transport, active transport, concentration gradient, osmosis,
osmotic concentration, osmotically active substance, simple diffusion, hypertonic, hypotonic, isotonic,
and transport proteins.
Exercise: Transporting Substances across Membranes
Goals of this Lab Exercise
 To understand the mechanisms used to move substances across membranes
 Understand the factors that can influence rates of transport across membranes
 Define terms associated with moving substances across membranes
 Apply the principles of moving materials across membranes to medical or environmental issues
Introduction
Through a series of demonstrations and exercises, the principles of moving substances across
membranes will be studied. Each exercise will reveal a different yet related aspect of transportation
into and out of cells. Bear in mind that these principles are put into practice continually by cells trying
to function and maintain homeostasis in an ever changing environment. Whether that environment
includes existing as a single celled protistan, like a euglena, or a multi-celled animal, like a homo
sapien, each cell needs to practice the principles for moving molecules into or out of its cellular body
or run the risk of cellular death or at the minimum, disruption of cellular function.
Each group will gather data to complete Part A, three members will complete Part B, and one
member will complete Part C. Share the data from all parts and turn in the Report Sheet next lab as
one group.
Procedure
Part A. Demonstrations of Molecular Movements through Different Media
The following demonstrations are used to show the process of molecular movements via
Brownian motion. The first is movement through a semi-permeable membrane, the third is through a
semi-solid (agarose) medium, and finally through a living membrane. Write hypotheses for each
demonstration, gather the data of the molecular movements during lab, record on the Pre-Lab Report
Sheet page 51.
Demonstrations
Students will not set-up the following demonstrations but will be required to write hypotheses
before coming to lab on page 51, and take measurements for each demonstration.
 Thistle-tube demonstration. The dialysis tubing, which is a semi-permeable membrane, contains a
concentrated sugar solution and a blue dye. This sac was then lowered into a beaker filled with
water only. What principle does this demonstration illustrate?
 The petri dish filled with agarose gel to which two different dyes were added. This represents the
third demonstration of movement through a semi- solid media. Measure the halo distance of
movement for each dye as it moves through the media. Are there differences in the rate and total
movement of each dye and why?
 The third demonstration shows the results after potato slices were left in different solutions for
about one day. Feel the slices in each watch plate and explain what could have happened to the
potato slices
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 Answer questions 1 through 3 pertaining to the demonstrations on the Report Sheet page 45 and
turnin as a group.
Part B. Diffusion through a non living membrane
The purpose of this part is to demonstrate the action of a differentially permeable non-living
membrane. Such action can then be applied to the study of transport mechanisms in living cells.
Section 1: The Set Up
Materials
1 small funnel
laboratory balance
four moistened dialysis sacs
5% I2KI (Lugol’s) solution
1 – 10 ml. graduated cylinder
pieces of string
40% glucose solution
10% Starch solution
wax pencil and scissors
2 - 400 ml. Beakers
10% NaCl solution
Safety Goggles
Procedure:
1. Formulate a hypothesis about the movement of the various solutes across the dialysis sac.
Write them down on page 46.
2. Wear Safety Goggles when transferring reagents from container to container.
3. Obtain two 400ml glass beakers and number them 1 and 2. Fill beaker 1 half full with dH2O (the
toggle switch faucet at the back sink) and fill beaker 2 half full with Lugols’ (5% I2KI) iodine
solution.
4. Obtain 2 moistened cellulose dialysis tubing lengths (Sacs 1 and 2). To open the cellulose tubing
rubs one end between your thumb and forefinger and place a funnel into the open end. Fold
over the other end of the tube (about 1 cm.) and tie with string in the middle of the folded area
(Figure 1).
400ml beaker
dH2O or 5%I2KI
Glucose and NaCl or Starch
Closed Dialysis Tube
Figure 1 Dialysis Tubing Set-up Diagram for the investigation of the permeability of dialysis
tubing.
5. To Sac 1 using a graduated cylinder and a funnel add about 5 ml of 40% glucose solution
followed by about 5 ml of the salt solution. Close the open end of the sac by pressing out the
air, folding over the open end, and tying it securely with string to form a closed leak proof sac.
Carefully remove excess string and tubing from each end of the sac (Why?).
6. To Sac 2 using the graduated cylinder and funnel after rinsing with dH2O, add about 10ml of 10%
starch solution. Close the open end of the sac by pressing out the air, folding over the open end
(about 1 cm.), and tying it securely with string to form a closed leak proof sac. Carefully remove
excess string and tubing from each end of the sacs (Why?).
7. Rinse the sacs under running tap water to remove any solution from the outside of the sacs and
carefully blot the sacs dry (Do not squeeze sacs!) with a paper towel.
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8. Determine the mass of the sacs in grams by using a weighing boat on a laboratory balance that
can be found on the side counters. Place your sac into the plastic weigh boat and zero the
scale before weighing your sample. Record the weights in Table 1 (page 45)
9. Place Sac 1 into the beaker with the dH2O and Sac 2 into the beaker with the Lugol’s iodine
solution. Start both sacs at the same time and note the time.
10. Allow the sacs to remain undisturbed in the beakers for 1 approximately hour. After one hour
you will remove each of the sacs, gently and carefully blot them dry, weigh them, record the
data in Table 1 of the Report Sheet (page 45), and begin Section 2 the Chemical Analysis.
Section 2: The Chemical Analysis
Materials
Test tube rack with 4 test tubes
600 ml beaker with boiling chips
Small plastic beaker and scissors
test tube clamps
Benedict’s solution
Safety Goggles
hot plate
silver nitrate (AgN03)
Bottle of dH2O and Transfer pipettes
Procedure:
1. Benedict’s test for the presence of sugar in the Solutions. Wear Safety Goggles!
Caution!
Benedict’s Reagent is very caustic. It can burn holes in clothing and digest skin!! Wear
goggles for eye protection! Clean up spills immediately after first neutralizing with
vinegar. If spilled on your skin (it feels slippery and begins to burn after several minutes)
wash thoroughly with tap water. Report all accidents to the instructor.
2. Label three clean test tube: control, sac, and beaker and add five drops of Benedict’s reagent to
each test tube.
3. Use scissors to cut off one end of the sac 1 and drain into a small plastic beaker.
4. Add five drops of dH20 from the dropper bottle to the “control” test tube .
5. Use a clean disposable pipette, put 5 drops of sac 1 solution in the “sac” test tube.
6. Use a clean disposable pipette to put 5 drops of beaker 1 solution in the “beaker” test tube.
7. Heat all three test tubes in a boiling water bath for about 2-3 minutes.
8. Record the colors and intensity of the colors of the solutions in your Table 2 (page 45).
9. Add five drops of the “beaker” water to a test tube and with a clean disposable pipette then
add five drops of AgNO3 (silver nitrate). Note the results in Table 2.
10. Note the presence or absence of starch in the sac 2 and the beaker 2 by noting any color
changes in Table 2.
11. Answer questions 1 through 9 on pages 46 and 47 on the report sheet and turn in a as a group.
Part 3: The Clean up
Procedure:
1. Solutions from the beakers may be poured down the sink.
2. Place used dialysis tubing in the wastebasket or taken home as a gift from GRC.
3. When finished with the hot plate turn it off and unplug it. Leave the water and boiling chips in
the 600 ml beaker on the hot plate to cool.
4. Empty the test tubes with Benedict’s and AgNO3 solutions into the waste container near the back
sink.
5. Clean the test tubes using detergent, water, and a test tube brush. Rinse with dH2O and place the
cleaned tubes upside down in a test tube rack on a paper towel on your table to dry.
6. Rinse and clean using soap and water all other glassware used, rinse with dH2O, and place them
on a paper towel on your table to dry.
7. Return all other materials (i.e. wax pencils, scissors, etc.) to their proper locations.
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8. Wipe down the surface of your lab counter and the common table with detergent and tap water
to clean up any solutions that might have leaked or spilled.
Part C. Diffusion of a solvent through a living membrane = Osmosis
The purpose of this part is to demonstrate the action of a “living” semi-permeable membrane.
How do things pass through a cells membrane? What precautions must a cell take to ensure
homeostasis and maintain functions, while still being an active vibrant cell? Think of how the
principles demonstrated here can be applied to the normal and abnormal environments cells can find
themselves involved with and yet still can maintain their lives. Remember to formulate hypotheses
for each situation in the following part of this exercise. Solutions A, B, or C are either isotonic,
hypertonic, or hypotonic. Reread the perspectives about these conditions and formulate your
hypothesis based on this information
Materials
Compound Light Microscope
Samples of Red Blood Cells
Microscope slides
Samples of Elodea canadensis
Cover slips & Safety Goggles
Solutions A, B, and C
Procedure: Red Blood Cells and Osmosis
1. Write down a hypothesis for each of the conditions A, B, C and D on page 47.
2. Label four microscope slides A, B, C, and D.
3. Wear Safety Goggles! Place a drop of blood on slide A with a cover slip and observe the shape of
the red blood cells. Record you observations in Table 3 row A of the Report Sheet (page 47).
4. Place a drop of solution A on slide B, add a cover slip. Place the slide on the stage and add a drop
of blood to the edge of the cover slip. Capillary action should move the blood under the cover
slip. Watch blood cells at the edge of the advancing blood as they meet solution A, then record
your observations in Table 3 Row B.
5. Repeat step 4 for solutions B and C.
6. Wash the slides in soap and water and place them in the slide cleaning beaker by the back sink.
7. Answer questions 2 through 5 on pages 47 and 48 on the Report Sheet as a group.
Procedure: Plant cells and Osmosis
1. Write down a hypothesis for each of the conditions A, B, C, and D on page 48.
2. Wear Safety Goggles! Place a piece of an Elodea canadensis leaf with a drop of water from the
solution the sprigs of Elodea canadensis are being held on a microscope slide mark A and add a
cover slip.
3. Place the slide on a microscope stage and observe the shape of the cells and record your
observations in Table 4 row A of the Report Sheet (page 47).
4. Place a piece of the Elodea canadensis leaf on the slide marked A cover with a cover slip and add
solution A to the slide and record your observations in Table 4 row B of the Report Sheet (page
47).
5. Repeat step 4 for solutions B and C.
6. Dispose of the Elodea canadensis leaves on a paper towel, let them dry out (desiccate), and toss
the towel into the trash.
7. Wash the slides in soap and water and place them in the slide cleaning beaker by the back sink.
8. Answer questions 2 through 5 on pages 48 and 49 on the Report Sheet as a group.
9. Answer the additional questions on page 49 on the Report Sheet on a separate sheet of paper as
a group.
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Report Sheet
Lab Section:
.
Transporting Across Boundaries Exercise
Group Names:
.
.
.
.
Part A: Demonstrations. Record your data and answer the following questions.
1. What is the principle demonstrated by the thistle-tube demo?
2. What is the principle demonstrated by the agar plates and dyes? How can you explain the
differences (if any) in the movement of the two different dyes? Write your measurements in
the space below
3. What is the principle demonstrated by the potato slices? Why do you think the slices felt
different (if they did.)?
Part B Diffusion through a non living membrane
Treatment
Beginning Weight (grams)
Sac 1: 40 % glucose and 10% NaCl solution
soaked in a beaker of distilled water
Sac 2: 10% starch solution soaked in a
beaker of I2KI and water
Final Weight (grams)
Table 1 Weights of Dialysis Tubes Beginning Weights of dialysis sacs containing various solutions and Final
Weights of dialysis sacs after being soaked in various solutions for 1 hour.
Sac and Test Performed
Test results for sac contents
(present or absent)
Test results for beaker content
(present or absent)
Sac 1: Benedicts test for Glucose
(Note and record color change)
Sac 3: Silver nitrate test for NaCl
(Note formation of a precipitate)
Sac 4: Iodine test for Starch
(Note and record color change)
Table 2 Chemical Analysis of Dialysis Tubes Results of Benedicts, Silver nitrate, and Iodine Tests on the
various sacs and their solutions.
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Answer the following questions concerning the movement of molecules across a semi-permeable
membrane.
1. State a hypothesis for each of the sac conditions.
2. In which situations or sacs did Net Osmosis or Simple Diffusion occur? Explain your reasoning?
3. Based on your data and your knowledge of chemical structures list the relative sizes in the order
of largest to smallest of the following molecules: Glucose, Starch, NaCl, and water.
4. What part of a living cell is represented by the dialysis sac?
For the next four questions use the terms diffusion and/or osmosis, hypotonic, isotonic, and/or
hypertonic in your answer.
5. Considering the results of Sac 1, explain the results you observed.
6. Was there a net movement of glucose or salt in either direction in Sac 1? Why or why not?
7. Considering the results of Sac 2, explain the results you observed.
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8. Considering the results of Sac 2, explain why there was or was not a significant change in the
weight of the sac.
9. What single characteristic of the semi-permeable membrane (dialysis sac) used in the lab
determines which substances can pass through them?
Part C Diffusion through a living membrane
Condition
A (blood only)
Appearance and Condition of Red Blood Cells
B
C
D
Table 3 RBC Data Observations of the potential changes in cell structure of Red Blood Cells in test solutions.
1. Write a hypothesis for each of the conditions using your experiences with non-living
membranes.
2. Which of the three solutions was hypertonic to the red blood cells? Explain your answer.
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3. Which of the three solutions was hypotonic to the red blood cells? Explain your answer.
4. Which of the three solutions was isotonic to the red blood cells? Explain your answer.
5. What conditions within the human body might lead to results similar to those you experienced
here?
Condition
Appearance and Condition of Elodea canadensis Cells
A (stock H2O)
B
C
D
Table 4 Elodea canadensis Data. Observations of the potential changes in cell structure in Elodea canadensis
cells in test solutions.
1. Write a hypothesis for each of the conditions using your experiences with non-living
membranes.
2. Which of the three solutions was hypertonic to the Elodea canadensis cells? Explain your
answer.
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3. Which of the three solutions was hypotonic to the Elodea canadensis cells? Explain your
answer.
4. Which of the three solutions is isotonic to the Elodea canadensis cells? Explain your answer.
5. Would you expect pond water to be isotonic, hypotonic, or hypertonic to Elodea canadensis
cells and why?
Additional Questions:
The external membrane of fish is semi-permeable. As is true for all animals, the materials that
can pass freely without the aid of intra-membrane transport proteins are oxygen, carbon dioxide, and
water. Any charged molecule such as Na+, Cl-, and any large molecules, such as sugars, requires the
aid of transport proteins. All animals have salt (Na+, Cl-) in their blood. Answer the following
questions on a separate sheet of paper.
1. What transport action could spontaneously occur in the external membrane of freshwater fish?
2. Now consider saltwater fish. What transport action could spontaneously occur in the external
membrane of saltwater fish? Only consider the situation where the salt concentration is higher
in the surrounding water than in the fish.
3. Using your text, or some other means, define both positive and negative feedback. Our bodies
have the ability to sense potentially dangerous changes in blood pressure. When our blood
pressure drops, our pituitary gland releases a hormone which enhances the ability of our
kidneys to reabsorb water, thus making our urine more concentrated. Is this positive or
negative feedback?
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Pre-Lab Report Sheet
Lab Section:
.
Transporting Across Boundaries Exercise
Name:
.
Use the diagrams below to determine the concentration gradients and expected direction of net
flow for all the different molecules in each set-up. Determine the concentration gradient for each
molecule type. Then draw an arrow showing the “expected” net movement of each molecule in the
set-up. In each of these examples NaCl is permeable, while sucrose is impermeable to the membrane.
A
100% H2O
35% NaCl
65% H2O
B
C
100% H2O
70% H2O, 10% sucrose,
20% NaCl
40% sucrose
60% H2O
60% NaCl
35% H2O
5% sucrose
1. Describe the net movements of the molecules in Condition A above.
2. Describe the net movement of the molecules in Condition B above.
3. Describe the net movement of the molecules in Condition C above.
4. Write out a hypothesis for each demonstration performed in this exercise on pages 40. Make sure
your hypothesis is in the correct format!
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Laboratory 4: Pea Lab: Scientific Method Applied
Pre-lab Assignment
Before coming to lab carefully read the previous pages on the Principles of the Scientific Method
(Lab 1) and the following pages of Pea Lab: Scientific Method Applied then answer the pre-lab
questions, page 59. Be prepared to hand in your responses to the pre-lab questions at the start of lab.
Perspectives
This lab is an opportunity to enhance your understanding and appreciation of the scientific
method process in a semi-structured situation similar to that used by researchers in their work.
Teams of students should carry out the activities in this lab. The division of labor is the
responsibility of the team. The success of the group depends on the careful and conscientious effort
of each person. This dependence on others is also characteristic of research and many other aspects
of life (as you may already know).
The work required for this lab spans two to four weeks depending on a number of factors. Your
instructor will explain the methods of storage for your experimental set-ups and how to arrange for
the use of the rooms and greenhouse to do your work.
Exercise: Applying the Scientific Method
Goals of this Lab Exercise
 To understand the mechanisms used in the scientific method
 Design an experiment and carry out the steps of a scientific experiment
 To work cooperatively in establishing a protocol for a scientific experiment
Introduction
In its simplest form, an experiment involves a check or control group compared with an
experimental or test group. The control is held under constant conditions while the test group is
exposed to the affects of various factors, one at a time. Any changes (dependent variable) that occur
in the test group, but not in the control group, are assumed to be the result of the condition that is
changed (independent variable). Each treatment, including the control, should be replicated, and the
replicate organisms should be carefully distributed so that no individuals being treated will be favored
more than others (control variables).
In the activity that follows, you will investigate a small portion of a problem in biology that lends
itself very neatly to the experimental method. It is concerned with coordination of growth and
development in plants by chemical regulators called hormones. A disease of rice plants results in
overly rapid growth of seedlings. The seedlings become tall and weak and finally fall over. Scientists
found that a fungus caused the disease. Japanese scientists were able to produce symptoms of the
disease with cell-free extracts of the fungus. From the extracts they isolated a substance, named
gibberellin, which was shown to be the active agent causing the disease. Later research revealed that
gibberellins are produced naturally by plants and are involved with regulating stem growth and other
processes.
In this project you will study the affect of gibberellic acid on pea plants whose genetic
constitution (genotype) for the trait of height is dwarf. The expression of a genotype is termed its
phenotype. The purpose of this lab is to determine whether the dwarf phenotype can be modified by
the application of gibberellic acid to these plants.
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Materials (per group of four students)
20 Little Marvel pea seeds and 2 flower pots
Growth medium (vermiculite in greenhouse)
Atomizer containing gibberellic acid solution
Atomizer of de-ionized water & Safety Goggles
Procedure
Each team should decide on its organization, discuss the problem/hypothesis, and plan the
experiment. Gather the materials needed and begin the activity. Prepare your seeds by following
steps 1 through 6.
1. Seed Preparation - Place 20 pea seeds in a plastic cup and cover them with tap water so that
the water level is about 2 cm. above the level of the pea seeds. Label the beaker with team
identification and date. Place it in a dark cupboard in the biology lab and let the pea seeds
soak overnight (process called imbibing) (i.e. 12-24 hours). The soaked seeds should now be
planted as directed below.
2. After the seeds have soaked overnight take them to the greenhouse. Prepare two 15-cm
flowerpots by adding a growth medium (vermiculite) to each pot. The containers should be
about 3/4 full. Moisten the medium (might have to add more medium after watering) with
tap water. In each pot, place ten soaked seeds and fill with more vermiculate to the brim of
the pot, and moisten. Label each pot with team identification, date, and keep them in the
greenhouse. Keep the medium moist, but not soggy wet.
3. When the seedlings are 2-3 cm. tall measure their height in millimeters. This is done by
measuring the distance from the growth medium surface to the tip of the shoot apex.
Measure all seedlings in the pot and average their heights. These lengths are the initial
measurements or length zero. Wear Safety Goggles when spraying. Hormonal treatment of
the plants follows immediately! Do the hormonal treatment outside of the greenhouse!
4. Using a hand atomizer (found in the refrigerator at the back of the lab room) containing
gibberellic acid spray the plants of one pot as this will be your experimental group. Spray the
other potted plants with the deionized water atomizer. This is the control group. Since some
of the spray for the experimental treatment may drift, do all spraying outside of the
greenhouse. Spray the plants until the leaves and shoot apex are wet enough to form
droplets which will almost run off, but do not permit appreciable amounts to drop onto the
growing medium. The spray treatment is done ONLY one time. Label each pot as “control”
or “experimental.” Be sure that both of the pots are exposed to similar light conditions. Keep
the growth medium of both pots uniformly moist, but do not spray water over the plants
themselves. Keep both pots in the greenhouse.
5. Measure the average pea plant growth in each pot (not counting weekends) for five days and
subtract the initial average from the time you first spray with the gibberellic acid and deionized water. When you measure record the heights of the plants in each pot, take note of
the general health (leaf/stem color, leaf size, and stem diameter) and appearance of the
plants, and record the data on Table 1 (page 57). In addition, on the last day, measure an
inter-node length (Figure 1, page 56) on each plant and calculate the average internode
length, and count the number of leaves produced on each plant in both the experimental
and control groups. As the plants grow tall, it may be necessary to place stakes in the pots
and tie the plants loosely to them.
6. At the conclusion of the activity, CLEAN UP all materials and equipment. Empty the used
vermiculite into the appropriate container in the greenhouse.
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Pea Lab Report:
1. Your research team will do a formal scientific paper write-up using the criteria established in
Appendices A and C as your guide (abstract not included). Assign the different components
(Title page, Introduction, Methods & Materials, Results, Discussion/Conclusions, and Reference
Page) of the paper to various team members and turn in one report per team.
2. Answering the following questions will help your group to organize their thoughts for the
scientific paper.
The major question asked in this lab is “Can the phenotype of a genetically dwarf pea plant be
altered by the addition of a plant hormone called gibberellic acid?”
1. Write a hypothesis using the “If .... Then” format for this experiment somewhere in the
introduction.
2. On the last day of observations calculate and list the average inter-node lengths of the
experimental and control plants. Include units of measure.
Control average inter-node lengths = _________________
Experimental average inter-node lengths = ____________
3. On your last day of observation calculate the average number of leaves in the experimental
and control groups and list them below.
Control average number of leaves = ________________
Experimental average number of leaves = ____________
4. Prepare graphs of the average daily heights, number of leaves, node lengths, and any other
relevant data for both the experimental and control groups. Properly title and label your graph
(Appendix A). Place average height on the vertical axis and time on the horizontal axis. Graph
both sets of data on the same graph by using different colors and a key.
5. What correlation(s) did you observe between number of leaves, inter-node length, and plant
height?
6. Explain at least three possible sources of error that may have influenced the data you
collected.
7. Suggest one additional experiment that would provide more valid data or show other pertinent
results. Be specific!!!
8. Did you confirm your hypothesis? Explain using your data?
9. Can the phenotype of a genotypically dwarf pea plant be changed? Explain and support your
answer by using specific numerical examples from the data collected.
10. According to this investigation which component of an organism’s life is more influential on its
phenotype; its genetic make-up or the surrounding environmental influences? Explain using
your data and/or observations to support your response.
11. If you were given the opportunity to apply gibberellic acid to your vegetable garden would you
do so? Use your data and/or observations to support your response.
12. Does your data agree or disagree with previously published data (literature review Appendix
F).
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Figure 1 Plant Anatomy This drawing is to be used to guide the measurement of the inter-node length.
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Data:
Control
Date:
Experimental
Initial height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Date:
Height (mm.)
Health of plants
Inter-node Length (mm.)
# of leaves
Table 1 Pea Lab Data Table Use this table to record you raw measurement data and a description of the
health of the plants.
Miscellaneous, Observations, Information, and Notes
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Pre-Lab Report Sheet
Lab Section:
.
Pea Lab: Scientific Method Applied Exercise
Name:
.
Before coming to lab carefully read the previous pages on the Pea Lab: Scientific Method Applied
then answer these pre-lab questions. Be prepared to hand in your responses to the pre-lab questions
at the start of lab.
Note:
Answer the following six questions before coming to lab, but after having read
the previous pages of this handout!
1. What is gibberellic acid?
2. Define the following:
phenotype-
genotype-
3. Write a hypothesis using the "If .... Then" format for this experiment.
4. What is the independent variable of the pea experiment?
5. What is the dependent variable of the pea experiment?
6. Name at least three variables that you will be controlling in the pea experiment?
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Laboratory 5: Energy Harvest – Fermentation in
Yeast
Pre-lab Assignment
Before coming to lab carefully read the following pages of Energy Harvest – Fermentation in
Yeast then answer the pre-lab questions, page 71. Be prepared to hand in your responses to the prelab questions at the start of lab.
Perspectives
In this lab activity you will determine which sugars (monosaccharide versus disaccharide) are best
metabolized by yeast under anaerobic conditions and then propose hypotheses to explain why some
sugars are metabolized but not others. Cultures around the world have for millennia used yeast
fermentation to produce bread and alcoholic beverages. Yeast are able to metabolize some foods, but
not others. In order for an organism to make use of a potential source of food, it must be capable of
transporting the food into its cells and have the proper enzymes capable of breaking the food’s
chemical bonds in a useful way. Sugars are vital to all living organisms. Yeasts are capable of using
some, but not all sugars as a food source. Yeast can metabolize sugar in two ways, aerobically, with
the aid of oxygen, or anaerobically, without oxygen. When yeast respire glucose aerobically, oxygen
gas is consumed at the same rate that CO2 gas is produced—there would be no change in the gas
pressure in a test tube, but since they only produce CO2 gas during anaerobic respiration the CO2 gas
pressure can be measured as a correlation to metabolism.
The net equation for the more than two dozen steps involved in the aerobic respiration of
glucose is:
Enzymes
C6Hl2O6(aq) + 6 O2(g) 6 H2O(l) + 6 CO2(g) + energy (36-38 ATP)
glucose
oxygen
water
carbon dioxide
Although the aerobic fermentation of sugars is energetically much more efficient, in this
experiment we will set the conditions so that the yeast can only complete the reactions anaerobically.
When yeast ferment the sugars anaerobically CO2 production will cause a change in the pressure of a
closed test tube system, since no oxygen is being consumed. We can use this pressure change to
monitor the rate of respiration and metabolic activity of the organism. A gas pressure sensor will be
used to monitor the fermentation of sugar.
The alcoholic fermentation of glucose is described by the following net equation:
Enzymes
C6Hl2O6(aq)  2 CH3CH2OH(aq) + 2 CO2(g) + energy (2 ATP)
glucose
ethanol
carbon dioxide
Both anaerobic fermentation and aerobic respiration are multi-step processes that involve the
transfer of energy stored in the chemical bonds of glucose to bonds in Adenosine TriphosPhate, ATP.
The energy stored in ATP can then be used to perform cellular work: provide energy for biosynthetic
reactions (e.g. growth and repair processes), move objects across membranes, etc. All organisms (i.e.
monerans, protists, fungi, plants, and animals) utilize aerobic respiration and/or fermentation
(anaerobic respiration) to produce ATP to power their cellular processes.
Note that ethanol is a by-product of alcoholic fermentation (Figure 1). Ethanol, a 2-carbon
alcohol, is also known as ethyl alcohol and, less correctly, simply as “alcohol”. Since yeast do not have
the enzymes needed to metabolize ethanol, much of the energy stored in the molecules of glucose is
trapped in the molecules of ethanol and is unavailable for use by yeast cells. The complete
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breakdown of glucose to carbon dioxide and water in aerobic respiration yields much more energy
than alcoholic fermentation: 36-38 ATP, versus only 2 ATP molecules produced by anaerobic
respiration. Ethanol molecules produced by alcoholic fermentation diffuse from yeast cells into the
surrounding aqueous environment. Since ethanol is harmful to cellular membranes yeast cells will die
if ethanol concentrations reach a critical level, usually a concentration of about 12%.
Figure 1 Glucose Summary Reactions This is a summary of three of the many possible fates of the 6-carbon
sugar glucose under anaerobic and aerobic conditions.
When anaerobic respiration occurs in animals (Figure 1) it is known as lactic acid fermentation
since lactic acid, a 3-carbon organic acid, is the end product. Like alcoholic fermentation, lactic acid
fermentation produces only 2 ATP. Perhaps if ethanol were produced anaerobically in animals more
people would take up anaerobic sports such as sprinting or weight lifting! Since lactic acid is toxic to
cells, anaerobic respiration can only occur for short periods of time in animals. In the presence of
oxygen each lactic acid can be broken down to carbon dioxide and water.
Aerobic respiration (Figure 2) occurs in three stages: glycolysis (involves soluble enzymes in the
cytoplasm), Kreb’s cycle (uses soluble enzymes in the matrix of mitochondria), and the electron
transport chain (a chain of reduction/oxidation paired electron carrier proteins called cytochromes
found embedded into the inner membrane of the mitochondria). Alcoholic and lactic acid
fermentation involve only glycolysis. Since both the Kreb’s cycle and the electron transport chain
require oxygen to function, neither process can occur under anaerobic conditions.
Glucose
Plasma
Membrane
Glucose
+
NAD
Cytoplasm
Glycolysis
NADH
ATP
Without O2
Present
Ethanol + CO2
or
Lactic Acid
Pyruvate
Mitochondrion
O2 Present
(Not drawn to
scale!!)
O2 Present
Kreb’s
Cycle
NADH
FADH2
CO2
ATP
Carrier Proteins of the
Electron Transport Chain
ATP
O2
H2O
Figure 2 Glucose Metabolism Pathways Aerobic cellular respiration consists of glycolysis, Kreb’s cycle, and
the electron transport chain. Anaerobic respiration involves only glycolysis and regenerates NAD + by either
reducing pyruvate to produce lactic acid (animals), or by decarboxylating pyruvate to produce acetaldehyde (not
shown) and then reducing acetaldehyde to produce ethanol. Under aerobic conditions the NADH produced by
glycolysis enters the mitochondria of the cell where it becomes oxidized to regenerate NAD + by donating
electrons to the electron transport chain, which results in the production of nearly 90% of the 36-38 ATP
molecules produced per glucose molecule metabolized aerobically.
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Exercise: Anaerobic Respiration
Goals of this Lab Exercise
 Describe alcoholic fermentation and aerobic respiration, noting the reactants and products, and
the relative energy efficiency of each
 Use a biology gas pressure sensor to determine which sugars are best metabolized anaerobically
by yeast
 Propose reasonable hypotheses to explain why yeast can metabolize some sugars but not others
Introduction
Today’s exercise will afford you the opportunity to measure the rate of fermentation activity by
yeast using different sugars. The equipment we will use measures the CO2 that is produced by the
fermentation process. The production volume over time will be monitored and graphed by a
computer program ready for your interpretation and analysis. The critical steps involve your ability to
maintain a tight and consistent seal during each “run” of the exercise. Without a tight seal the CO2
produced will leak from the equipment and your data will be skewed. As with any experiment, the
collection of the data is the easy part, but a clear understanding of the principles involved pose the
greatest challenge. Make sure you understand the introductory material.
Materials
Computer and Safety Goggles
Go-Link Interface
Vernier Gas Pressure Sensor
Yeast suspension and Disposable Transfer pipettes
Basting bulb, thermometer, test tube rack
Dropper bottles of: 5.0 % of glucose and sucrose
Stopper assembly fitted with tubing
10 ml. Graduated cylinder
Water bath (set at 37oC)
1L beaker (for water bath)
2 - 18 X 150 mm. test tubes
Dropper bottles of: 5.0 % of lactose and fructose
Procedure
The Set Up
1. Prepare the computer for data collection by opening the Biology with Computers software as
follows: Plug the CO2 gas sensor into the Go-Link connector. Go to Start  click on Programs
 open Vernier  open Logger Pro 3.5  open File  open Biology with Vernier  open
“Exp. O6” Enzyme Pressure. The vertical axis has pressure scaled from ~90 to ~130kPa. The
horizontal axis has time scaled from 0 to 15 minutes.
2. Adjusting the Valves to the Pressure Sensor. Open the valve (in the vertical position) on the
rubber stopper assembly so that it is open to the atmosphere (Figure 3A). The closed position,
used when monitoring the CO2 generated by the yeast, would have the knob in a horizontal
position (Figure 3B).
Figure 3A Open to the atmosphere
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3. Prepare a water bath (Figure 4) at your table for the yeast to ensure that the yeast will remain
at a constant and controlled temperature (Why?) when collecting data under data collection
below. To prepare the water bath combine warm and cool water in a 1-liter beaker until it
reaches 38 – 39oC. Fill the beaker with water until the beaker is ¾ full, but won’t spill over when
the test tube containing the yeast and sugar is placed in it. Make sure to keep the water
temperature constant at about 37oC.
Figure 4 Experimental Set-up Experimental Set-up with reaction vessel in a water bath maintained at a
constant temperature.
4. Obtain two large test tubes and label them 1 and 2.
5. Wear Safety Goggles when transferring solutions. Use a graduated cylinder to put 2.5 ml of one
of your assigned sugars into test tube 1. You will do two “runs” for each of your groups
assigned sugars and gather data from other groups to complete Table 1 (page 67) on the Report
Sheet
6. Wear Safety Goggles when transferring solutions. Obtain the yeast suspension from the water
bath at the back of the room. Constantly and Gently swirl the yeast suspension to mix the
yeast that has settled to the bottom. Use a disposable transfer pipette to put 2.5 ml of yeast
into a graduated cylinder and then into Test Tube 1.
7. Constantly and Gently swirl the yeast suspension while incubating for 10 minutes in the water
bath set to 37oC at your table with the rubber stopper of the pressure sensor assembly firmly
into Test Tube 1 and open to the atmosphere (Figure 3A) while Constantly and Gently swirling
the yeast suspension in your water bath. Check that all connections are tight. Be sure to keep
the temperature of the water bath constant. If you need to add more hot or cold water, first
remove about as much water as you will be adding or the beaker may overflow. Use a basting
bulb to remove excess water.
Data Collection
1. After the incubation period close the system to the atmosphere (Figure 3B).
2. Begin collecting data by clicking the green COLLECT button. Important: Constantly and Gently
swirl the test tube while collecting data (this helps to liberate the carbon dioxide gas from the
solution and helps to keep the contents mixed well). Monitor the temperature of the water
bath. Be sure that it does not change by more than one degree.
3. Collect data until you are certain that there is a linear relationship between the pressure and
time. Depending on the activity of the yeast, this usually takes 1 to 3 minutes. If the pressure
exceeds 130 kPa, stop the computer by clicking the red STOP button. Open the air valve on the
pressure sensor (Figure 3A) to prevent it from popping off!
Data Analysis
1. Determination of the mean rate of fermentation.
a. Move the cursor to the point where the pressure values begin to have a linear relationship.
Hold down the mouse button, drag the cursor to the end of the linear section of the curve,
and release the mouse button.
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b. Click the “Analysis” button and then the “Statistics” button. A floating box will appear on the
screen with the mean found in the box. Record this number in Table 1 of the Report Sheet
(page 67) for the sugar and your group number.
2. Repeat using the same sugar and then perform two “runs” of your other assigned sugar.
3. Share your group’s data with the class and gather their data.
Report
1. Turn in a group Report Sheet packet next lab by answering the Report Sheet questions on pages
67 through 69 as a group.
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Report Sheet
Lab Section:
.
Energy Harvest – Fermentation in Yeast Exercise
Group Names:
.
.
.
.
Data:
Group No.
Sugar Used
Glucose
Glucose
Glucose
Glucose
Glucose
Glucose
Sucrose
Sucrose
Sucrose
Sucrose
Sucrose
Sucrose
Lactose
Lactose
Lactose
Lactose
Lactose
Lactose
Fructose
Fructose
Fructose
Fructose
Fructose
Fructose
Rate of Respiration mean
Table 1 Fermentation Exercise Data
collected from the class.
Rate of Respiration Average per sugar
This table shows the fermentation rates of various sugars by yeast
Analysis and Questions of Results:
1. Graph (your Figure 1) the class data on a separate piece of graph paper to show the average rate
of respiration vs. sugar type. Label the graph fully and give it a proper title (Appendix A). Use
the space below to interpret the trends seen on your graph by referring to the graph by its figure
number.
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2. Considering the results of this experiment, can yeast utilize all of the sugars equally well? Quote
specific numerical values by citing your figure to answer this question.
3. Hypothesize why some sugars were not metabolized while other sugars were metabolized?
4. Hypothesize why the sugars that were metabolized were metabolized at different rates?
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Refer to the perspectives of this lab to answer the following questions.
1. Write the overall balanced chemical equation for both aerobic respiration and anaerobic
respiration of glucose by yeast and explain how they differ in terms of products.
2. Explain why there are different numbers of ATP produced when yeast metabolize glucose
aerobically vs. anaerobically.
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Pre-Lab Report Sheet
Lab Section:
Energy Harvest – Fermentation in Yeast Exercise
Name:
.
.
Before coming to lab carefully read the previous pages on Energy Harvest – Fermentation in
Yeast then answer these pre-lab questions. Be prepared to hand in your responses to the pre-lab
questions at the start of lab.
1. Define the following terms: aerobic respiration and anaerobic respiration?
2. Outline the steps or processes involved in the two types of respiration you defined in question 1
(see Figure 2).
3. Using your textbook or other sources, explain how enzymes are of such critical importance to
the processes involved in respiration.
4. Speculate as to why yeast ferment pyruvic acid (make alcohol) differently from animals (make
lactic acid).
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Laboratory 6: Mitosis and Online Karyotyping
Pre-lab Assignment
Before coming to lab carefully read the pages on Mitosis and Online Karyotyping and then
answer the pre-lab questions, page 79.
Perspectives
In the late 1800’s new techniques to visualize cellular structure exploded with the discovery of
vital stains and dyes. Most plant cells were fairly easy to visualize since most contain pigment
molecules for photosynthesis, but animal cells were another matter. When viewed under a
microscope lens sub-cellular structures, called organelles, were seen as simply the grainy consistency
of the cytoplasm. When scientists would apply different pigments harvested from different plants the
graininess took on distinct forms. Organelles could now be distinguished and studied as separate
structures. Differences in cellular function could be attributed to the number and types of organelles
found in various cells. By the end on the century scientist were using not only pigments from plants to
stain cells, but were beginning to use heavy metals linked to pigments to further delineate structure.
Dyes and stains became almost as an important discovery as the light microscope.
The new technology of stains allowed a number of scientists to peer into cells like they could not
have done before their discovery. One scientist, Walter Fleming, noted in salamander ovary cells that
dark staining condensations appeared within the nucleus. These condensations were then separated
toward opposite poles of the cell (“Dance of the Bodies”) just prior to the cell splitting into two new
cells. He eloquently described the continuous stages of a process called mitosis.
Today’s technology in the field of genetics and how genes affect the phenotype of an individual
started years ago (mid-1800’s) with the work of Gregor Mendel. His work with pea plants set the
stage for how chromosomes are sorted and passed from generation to generation. In the early part of
the 1900’s another geneticist, Thomas Morgan, working with fruit flies (Drosophila melangastor)
developed a technique called karyotyping that allowed him to visualize the structure of
chromosomes. This technique harvested chromosomes from cells arrested between prophase and
metaphase or pro-metaphase of mitosis, after being treated with colchicine to disrupt cellular
membranes, the condensed chromosomes are then stained with a vital stain called giemsa,
photographed/enlarged, and matched based on staining patterns and size. Harvesting the
chromosomes at this time hopefully ensures complete condensation of the genetic material into
individual units. This technique of karyotyping is used today to show the potential for genetic
abnormalities within the genome of an individual. The specificity of the technique has been refined
through the use of more specific stains (spectral analysis) which adhere to specific sites within the
DNA molecules to further highlight the differences between chromosomes.
Although mitosis is the most important process for ensuring that each daughter cell receives the
correct amount of chromosomal material, mitosis is simply a portion of the life span of a cell.
Following a nuclear division the cytoplasm is separated by a process called cytokinesis. In this process
the animal parental cell aligns proteins called actin along the equator in animal cells and these
proteins contract to pinch the membrane together forming a cleavage furrow along the metaphase
plate to separate the daughter cells. In plant parental cells vacuoles containing cell wall material are
lined across this plate. These eventually coalesce together to form a cell plate (eventually a cell wall)
between the daughter cells (I wonder why we have always called them daughters and not sons?).
Once cytokinesis is completed the cells move into the remaining portions of what is called the cell
cycle.
The cell cycle (Figure 1) is divided into interphase and division (either mitosis or meiosis followed
by cytokinesis) or the life span of an individual cell. Interphase is further subdivided into the G1 period
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(normal cell growth and function), the S period (DNA duplication), and the G2 period (synthesis of
proteins, like actin, tubulin, and histone, involved with mitosis and cytokinesis). During interphase
the normal day-to-day activities of the cell are carried out and the cell is said to be functioning
normally.
Figure 1 Cell Cycle The cell cycle of eukaryotic cells.
http://staff.jccc.net/pdecell/celldivision/images/cellcycle.gif
Exercise: On-line Karyotyping and Mitosis
Goals of this Lab Exercise
 To understand the mechanisms of the cellular process called mitosis
 To understand the process and application of the technique called karyotyping
 To apply this knowledge to issues in today’s society in relationship to karyotyping
Introduction
In the following laboratory and on-line and activity you will draw and differentiate the phases of
mitosis in botha plant and animal cells and play the role of a cytogenetic technician and complete the
karyotype for three patients, then use these karyotypes to evaluate and diagnose each patient. Be
careful! The emotional and physical well being of each patient is in your hands……or almost in your
hands!
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Materials (per group of four students)
Compound light microscope
Slides of onion root tips (Allium)
Slides of white fish blastula
PC computer with internet access
Procedure
Part 1: Visualizing the mitotic phases
1. Set-up two light microscopes at your lab table.
2. Have one group member obtain a prepared white fish blastula slide and another member a
prepared onion root tip slide.
3. Under high power (40x), draw and label the different stages of mitosis (interphase, prophase,
metaphase, anaphase, and telophase) for a plant and animal cell. Label the cells with terms
such as centrioles, spindle tubules, sister chromatids, centromere, cell membrane, and cell
wall. Make sure you attach the magnification and a drawing scale to your drawings.
4. With the assistance of your lab mates make a table comparing animal with plant mitosis and at
the bottom of the table identify two differences in the strategies between animal and plant
mitosis and cytokinesis strategies. Turn in your drawings next week with your Report Sheet.
Part 2: On-line karyotyping
1.
2.
3.
4.
Go to the Biology Project at: http://www.biology.arizona.edu/
Scroll down and click on “Human Biology”.
Scroll down to “Activities” and then click on “Web Karyotyping”.
Read the introduction and then complete the assignment as described. Record your responses
on Table 1 page 77 of the Report Sheet.
5. Go to: http://www.scirus.com or do a search for karyotyping.
6. Search for a karyotyping website and answer the questions of page 77.
Part 3: On-line Onion Root Tips: Phases of the Cell Cycle
This activity is a digital version of a classic microscope lab. You will classify cells from the tip of an
onion root into the appropriate phases of mitosis and then count up the cells found in each phase.
You can use those numbers to predict how much time a dividing cell spends in each phase. In the
process of doing this you will become familiar with the cell cycle and the process of mitosis and its
stages, which are, oddly enough, the major goals of this activity!
1. Go back to the Biology Project at: http://www.biology.arizona.edu/
2. Scroll down and click on “Cell Biology”.
3. Scroll down to “Activities” and then click on “On-line Onion Root Tips: Phases of the Cell Cycle”.
4. Read the introductory pages (about 3 total) and then complete the assignment as described.
Record your responses in Table 2 of the Report Sheet page 77.
Part 4: New Methods in Karyotyping: The Spectral Karyotype
In this activity you will learn about a new technique for diagnosing chromosomal abnormalities,
spectral karyotyping”. This technique is exciting because of its many applications, but also full of many
controversial societal issues. On your report sheet are three questions pertaining to the old and new
methods of karyotyping. Answer these questions on the report sheet as you do the following on-line
reading assignment.
1. Go back to the Biology Project at: http://www.biology.arizona.edu/
2. Scroll down and click on “Human Biology”.
3. Scroll down to “Activities” and then click on “New Methods in Karyotyping”
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4. Read the introduction.
5. To learn about the methods involved click on “Methods” at the bottom of the “Introduction”
page.
6. To learn about some of the possible applications of this new method click on “Applications” at
the bottom of the “Methods” page.
7. Don’t forget to answer questions 1-3 located in the Report Sheet page 78 and turn in as a
group.
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Report Sheet
Lab Section:
.
Mitosis and Online Karyotyping Exercise
Group Names:
.
.
.
.
Part 2: Web Karyotyping Data
Patient
Notation
Diagnosis
A
B
C
Table 1 Web Karyotyping Data Information in this table shows the results of a web karyotyping exercise.
Internet Search
URL of Site: http://
.
Title of Site:
.
Describe an interesting idea you learned at this site:
Part 3: On-line Onion Root Tips: Phases of the Cell Cycle
Interphase
Prophase
Metaphase
Anaphase
Telophase
Total
Number of
Cells
36
Percent of
Cells
100%
Table 2 Mitotic and Cell Cycle Data Information in this table shows the results of an On-line Onion Root Tips:
Phases of the Cell Cycle.
What can be concluded about cellular tasks performed during each phase from the data collected
above as it relates to cells in the cell cycle?
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Part 4: New Methods in Karyotyping: The Spectral Karyotype
1. Explain how each of the following karyotyping methods work.
The “old” method, Giemsa Dye Karyotyping:
The “new” method, Spectral Karyotyping using fluorescent dyes:
2. List and then in your own words briefly discuss at least four possible applications of spectral
karyotyping.
3. Identify and very briefly describe at least three controversial societal issues associated with
spectral karyotyping. You will need to do some thinking here since the Biology Project website
does not discuss any of the many issues involved.
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Pre-Lab Report Sheet
Lab Section:
.
Mitosis and Online Karyotyping Exercise
Name:
.
Before coming to lab carefully read the previous pages on Mitosis and Online Karyotyping then
answer these pre-lab questions. Be prepared to hand in your responses to the pre-lab questions at
the start of lab.
1. Define the following terms: centriole, spindle tubule, sister chromatids, centromere, cell
membrane, and cell wall. Draw a cell showing the location of these structures.
2. Using your text, outline the steps or phases of mitosis by describing the major events of each
phase of the process.
3. Cite three reasons why cells would undergo mitosis and explain how mitosis fits into the cell
cycle.
4. Cite when chromosomes are harvested for karyotyping during mitosis and explain why?
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Page to be used for Biological Doodling
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Laboratory 7: Mendelian Genetics
Pre-lab Assignment
Before coming to lab carefully read the pages on Mendelian Genetics then define the words at
the end of the introduction section, page 82, on a separate sheet of paper.
Perspectives
In 1866 an Austrian monk, Gregor Mendel, presented the results of painstaking experiments on
the inheritance patterns of garden peas. Those results were heard, but probably not clearly
understood, by Mendel’s audience. Now, more than a century later, Mendel’s work seems
elementary to modern–day geneticists, but its importance cannot be over stated. The principles
generated by Mendel’s pioneering experimentation are the foundation for genetic counseling so
important today to families with health disorders having a genetic basis. It’s also the framework for
the modern research that is making inroads in treating diseases previously believed to be incurable. In
this era of genetic engineering the incorporation of foreign DNA into chromosomes of unrelated
species—it easy to lose sight of the basics of the process that makes it all possible.
Geneticists depict an individual’s genetic make–up (or genotype) in a variety of different ways
depending on the particular set of alleles they are working with. This may be unfortunate for the
casual observer or the novice, but there are some commonalties that help to diffuse potential
obfuscations. A gene would be the code for the expression of a certain trait say nose shape and for
instance at a particular locus (site) on a chromosome you have an allele (an alternative expression of
a gene received from a parent) for say a long nose and another allele on the paired chromosome of
short or button nose shape. Individuals then can be classified as being homozygous (both alleles for a
gene are the same) or heterozygous (both alleles are different for that trait).
The most common system for identifying and relating genetic make–up is the use of capital and
lower case letters. For instance at a particular locus (site) you have an allele (an alternative
expression of a gene received from a parent). The dominant allele (a characteristic seen with an
increased frequency in a defined population) would be expressed by a capital letter, say “B” and the
recessive allele (a characteristic seen with a decreased frequency in a defined population and masked
by the dominant allele) by the lower case letter “b”. Homozygous would mean that both alleles are
the same and would be denoted by the same letter, whereas heterozygous would mean the alleles
are different and be denoted by an upper and a lower case letter. Homozygous dominant individuals
would be indicated by the notation BB and homozygous recessive individuals by the notation bb.
Heterozygous individuals, those that have one dominant allele and one recessive allele, would be
indicated by the notation Bb. This is called complete dominance.
For the genetics of the ABO blood groups we use the capital letter “I” and then superscript the
letter “i” with capital A’s, or B’s, or O’s to represent the alleles presence (IA, IB, IO). A similar type of
notation occurs for other types of co-dominant genetic traits.
Sometimes the apostrophe symbol is used to denote expression of a certain trait. Consider the
following example of patterned baldness.
Genotypes
Men
Phenotypes
Women
b´b´
Bald
Bald
b´b
Bald
Non-bald
bb
Non-bald
Non-bald
The apostrophe acts as an indicator of dominance in males and an indicator of recessives in
women. What this actually denotes is the carrying of the trait for baldness on the b gene.
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Another type of notation is the use of the symbols plus (+) and minus (-). The plus sign would
indicate that the allele for the expression of a particular trait is present (usually the wild type or
normal allele) and the minus sign would indicate that it is not present or that some mutated form of
the normal gene is present. Sometimes we use the phrase wild type and symbol “wild” as a
superscript to indicate the presence of the dominant naturally occurring allele. Often times you will
see other sequences of letters that indicate the presence or absence of certain alleles. These short
sequences are acronyms for a description of what the allele causes to be seen in the phenotype.
In the case of simple dominance where a single dominant allele will mask the expression of a
single recessive allele another nuance is added to the symbolic systems discussed. For example, a
gene at a single locus controls tongue rolling. Individuals that can roll their tongues (phenotype) can
have a genetic constitution (genotype) of either RR or Rr. Non tongue rollers have a genetic
constitution of rr. If you observe a person who can roll his tongue, what is his/her genetic
constitution? Well without looking at the parents maybe for more than one generation back and/or
one or more generations of progeny the answer is either RR or Rr. This is because you receive half of
your genes from each parent. So, if one is uncertain, how do you express the genetic constitution of
these individuals? The answer is R ? . We know they can roll their tongue so we know that at least
one of their alleles is the dominant R allele.
Exercise: Mendelian Genetics
Goals of this Lab Exercise
 To understand the mechanisms of Mendelian Genetics
 To understand the process and application of the technique used by geneticists
 Be able to apply this knowledge to pedigree and karyotyping analysis
Introduction
Through a series of activities we will examine some of the principles of genetics and techniques
developed by geneticists to predict mating outcomes and understand how genetic information is
passed from generation to generation.
Before coming to lab, refer to your textbook or other references and write definitions for the
following words: chromosome, genes, locus, allele, dominant allele, recessive allele, genotype,
phenotype, gamete, haploid, diploid, monohybrid, dihybrid, homozygous, heterozygous, linked genes,
autosomal chromosomes, sex chromosomes, sex-linkage, and homologous chromosomes.
Materials
Pages 83 through 93 of your lab manual
Procedure
1. Pair up with a classmate.
2. Do each of the activities on pages and answer the questions in the space provided.
3. Turn in the completed Report Sheet (pages 83 through 93) as a pair.
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Report Sheet
Lab Section:
.
Mendelian Genetics Exercise
Group Names:
.
.
Activity A: Law of Segregation separating alleles into gametes: Tongue rolling (Able to form a Ushape when sticking out their tongue.)
1. What is the phenotype of an individual whose genotype is RR?
2. What is the phenotype of an individual whose genotype is Rr?
3. What is the phenotype of an individual whose genotype is rr?
4. What are your phenotype and genotype for tongue rolling?
The distribution of alleles during the formation of gametes was one of the principles described by
Gregor Mendel. It is called the Law of Segregation. The two alleles of a gene segregate, or separate,
from each other so that each one ends up in a different gamete.
1. If a person’s genotype is RR, what are the genotypes of the resulting gametes?
2. If the person’s genotype is rr, what are the genotypes of the resulting gametes?
3. If the person’s genotype is Rr, what are the genotypes of the resulting gametes?
4. If your phenotype was tongue roller, what would you have to find out in order to know your
genotype for sure?
Activity B: Ear Lobes
An unattached earlobe (F) is dominant to attached earlobes (f). We can only guess at the
biological significance of the kind of earlobe might make. Did your grandmother or mother use yours
a lot?
1. What is the phenotype of an individual whose genotype is FF?
2. What is the phenotype of an individual whose genotype is Ff?
3. What is the phenotype of an individual whose genotype is ff?
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4. What is your phenotype and genotype with respect to earlobe attachment?
5. If a person’s genotype is FF, what are the genotypes of the resulting gametes?
6. If the person’s genotype is ff, what are the genotypes of the resulting gametes?
7. If the person’s genotype is Ff, what are the genotypes of the resulting gametes?
8. If your phenotype was unattached earlobe, what would you have to find out in order to know
your genotype for sure?
9. Joe Buxtawhody and the members of his immediate family have attached earlobes. His
maternal grandfather has unattached earlobes. What is the genotype of his maternal
grandfather?
10. His maternal grandmother is no longer living. What could have been the genotype of his
maternal grandmother?
PTC (phenylthiocarbamide) is an anti-thyroid drug that prevents the thyroid gland from
incorporating iodine into the thyroid hormone. The ability to taste PTC is associated with the
functioning of the thyroid gland. As with many patterns of inheritance, the nature of the relationship
between “tasting” and disease is unknown. The ability to taste PTC is an autosomal (found on one of
the chromosomes other than the sex chromosomes) trait. Tasting (T) is dominant to non-tasting (t).
1. Can you taste PTC?
2. What is your genotype?
3. How do you know?
Activity C: The chromosomal basis of independent assortment: a monohybrid model.
When the genotypes of the parents are known, we may determine what gametes the parents can
make and in what proportion the gametes will occur. This information allows us to predict the
genotypes and phenotypes of the offspring. The prediction is simply a matter of listing all the possible
combinations of gametes. In this section your will be doing monohybrid (one trait) crosses.
By convention, the parental generations are called P. The first generation of offspring is called F1.
F stands for filial, which refers to a son or daughter, so F1 is the first filial generation. If members of
the F1 generation are crossed, their offspring are called the F2 generation and so on.
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Predict the results of the following cross using T and t to denote tasting and non-tasting,
respectively
P generation TT x TT
1. What genotypes will be found in the F1 generation?
2. What phenotype(s) will be found in the F1 generation?
3. Explain why you made these predictions.
Predict the results of the following cross:
P generation TT x tt
1. What genotypes will be found in the F1 generation?
2. What phenotype(s) will be found in the F1 generation?
3. Explain why you made these predictions.
The previous examples were fairly simple since the parents were only able to produce one type
of gamete. However, the complexity escalates rapidly when parents can produce more than one type
of gamete. To deal with the presence of more than one type of gamete we employ the Punnett
square. This technique was developed by the geneticist Reginald Punnett in 1910 as a means of
showing the probabilities of progeny outcomes.
Consider the cross between the F1 progeny above, Tt, to produce the F2 generation.
The F1 Cross is Tt x Tt
1. What type or kind of gametes can the first parent produce?
2. What type or kind of gametes can the second parent produce?
T
3. The Punnett square would look like this.
t
T
t
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4. Fill in the Punnett square.
5. What are the possible genotypes in the F2 generation?
6. What are the phenotypes of each genotype in the F2 generation?
7. What is the genotypic ratio of this cross?
8. What is the phenotypic ratio of this cross?
9. Joe cannot taste PTC, but both his mother and his father can taste PTC. Do a Punnett square
to calculate the expected phenotypic ratio among Joe’s siblings.
Activity D: The chromosomal basis of independent assortment: a dihybrid model.
Genes that are located on the same chromosome are linked with each other. If genes are located
on separate, non-homologous chromosomes, they are not linked, or unlinked. Unlinked genes
separate independently during meiosis (gamete formation). For example, consider the allelic pair T
and t and a second allelic pair F and f. If the T gene and the F gene are not linked, their alleles can be
found in any combination in the gametes. That is, the T allele can be in the same gamete as either the
F allele or the f allele. This is Mendel’s Law of Independent Assortment. The word assortment in this
case refers to the distribution, or sorting, of alleles into gametes.
Assume the circle below represents a cell. Finish drawing the cell adhering to the following
conditions: a diploid cell, with two homologous pairs of chromosomes, with two unlinked genes
called T and F, and the cell is heterozygous with respect to both of these genes.
1. What is the genotype of this cell?
2. The T gene is for tasting PTC and the F gene is for unattached earlobes. What is the
phenotype of the individual represented by this cell?
3. Recall that when this cell undergoes meiosis, each gamete receives one member of each
homologous pair. List the possible combinations of alleles that will be found in the gametes.
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4. In what proportion would you expect these gametes to occur?
The resulting phenotypic ratios in the F2 generation of a dihybrid cross (2 traits) can be quite
different than those observed from a monohybrid cross. But the process is essentially the same. First
you list all possible gametes each parent and subsequent parents can produce. Second, you then
assign the gamete possibilities to the Punnett square and fill it in. Finally you count the progeny and
determine the number of progeny in each phenotypic category. Remember, when determining the
types of gametes possible, each gamete must have one member of each homologous pair of
chromosomes. For example, if you are considering a T gene (ability to taste PTC) and an F gene
(unattached earlobe), each gamete must have one allele for the T gene (either T or t) and one allele
for the F gene (either F or f).
1. What type of gametes will the following genotypes produce?
Genotype: TTFF
Gametes
.
Genotype: TtFF
Gametes
.
Genotype: ttFf
Gametes
.
Genotype: TtFf
Gametes
.
Cross or mate a homozygous tasting and unattached earlobe parent with a homozygous nontasting attached earlobe parent?
2. What are the genotypes of these two parents?
3. What type of gametes can each parent produce?
4. How many different types of gametes can each parent produce? Record the genotypes of
the gametes each parent can produce.
5. Construct the Punnet square that shows the cross between the parents. This can be tricky
if you don’t understand gamete production from the parents.
6. What are the possible genotype(s) of the F1 progeny?
7. What are the phenotype(s) of the F1 progeny?
8. How many different types of gametes can the F1 parent produce? Record the genotypes
of the gametes each parent can produce.
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9. Construct the Punnet square to show the possible outcomes of a dihybrid cross between a
mating of the F1 offspring. (Hint: Look at the figure on page 94 of the lab manual.)
10. What is the expected genotypic ratio of the F2 progeny?
11. What is the expected phenotypic ratio of the F2 progeny?
12. What would the expected phenotypic ratio of the F2 progeny be if the T gene and the F
gene were linked?
13. A couple with the genotypes TtFf and TtFf have 16 children. Twelve of them can taste PTC
and have unattached earlobes; the other 4 can’t taste PTC, 2 of the 4 have attached
earlobes and 2 of the 4 have unattached earlobes. Why doesn’t this family match the
expected ratio? (Hint: If the probability of having a male child is 50% why can one family
have 7 daughters and no sons?)
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Activity F: The ABO blood groups
ABO blood groups are the most commonly known blood groups. Rh factor is another commonly
known blood group. But in all fairness humans are much more complicated than that. There are
currently over 300 different types of blood factors known to hematologists. ABO is an acronym for the
three types of alleles an individual may potentially have. Of course a diploid individual can only have 2
alleles. The genotypes and phenotypes of different combinations of the three alleles are given in
Table1.
Phenotypes
Phenotypes
A
B
AB
Genotypes
Genotypes
AA, AO or IA IA , IAi
BB, BO or IB IB,, IBi
AB or IA IB
Table 1 Blood Types These are the most common blood type phenotypes and genotypes seen in humans.
Notice that phenotypes A and B can have two possible genotypes. Notice also that blood types
AB and O only have 1 possible type of genotypes. This situation is a pattern of inheritance referred to
as co-dominance. The allele A is dominant to the allele O. The allele B is dominant to the allele O, but
the allele A is co-dominant to the allele B, hence the phenotypic blood type AB.
The Rh blood factor’s pattern of inheritance is the case of simple dominance that we have been
assuming in this lab till now. The Rh blood factor is inherited as a single pair of alleles. Rh positive
(Rh+) is dominant to Rh negative (Rh-). Answer the following questions.
1. A boy wonders if he is adopted. He compares his blood type to those of his parents.
a. If the father is blood type AB and the mother is blood type O, what blood types would
indicate that the child might have been adopted?
b. If the father is blood type A and the mother is blood type B would blood typing help
the boy determine if he was adopted?
2. If you are Rh+ can you know your genotype for sure? Why?
3. If you are Rh+ and everybody in your family is Rh+ (parents, siblings, offspring) what is/are your
probable genotype? Why? Do you know your genotype with absolute certainty? Explain.
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Activity G: Color Blindness
Color blindness is a sex–linked recessive trait (Table 2). Sex linked means that the trait would be
localized to one of the two sex chromosomes. The possible genotypes and phenotypes are given
below.
Females
Genotypes
B
X XB
Males
Genotypes
Phenotypes
normal vision
XBY
Phenotypes
normal vision
XBXb
normal vision
XbY
color blind
XbXb
color blind
Table 2 Sex Linkage These are the most common designation for color blindness in humans.
1. Are you color blind?
2. If you are (or were) color blind, what is your genotype?
3. If you are a female and are not color blind, you can judge whether you are homozygous or
heterozygous by knowing if any member of your family is color blind.
a. If your father is color blind, what is your genotype?
.
b. If your mother is color blind what is your genotype?
.
c. If you know of no one in your family who is color blind, what is your probable
genotype?
.
4. The only member of Josephine’s family who is color blind is her brother.
a. What is her brother’s genotype?
.
b. Her father’s genotype?
.
c. Her mother’s genotype?
.
d. What is Josephine’s genotype if she later has a color-blind son?
.
Activity H: Determine the genotype of the unborn
Through genetic counseling, it is sometimes possible to identify parents who are likely to produce
children with genetic disorders. And then it is sometimes possible to test fetal cells to determine if the
newborn does indeed have the disorder.
Pedigree charts can be constructed to show the inheritance of a genetic disorder within a family.
Thereafter, it may be possible to determine whether any particular individual has an allele for that
disorder. Then a Punnett square can be done to determine the chances of a couple producing an
affected child. This process is called analysis by pedigree charts.
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Some genetic disorders are discovered following amniocentesis, a procedure that allows a
physician to withdraw a portion of the amniotic fluid and thereby fetal cells by means of a long needle.
The fetal cells are cultured and then a karyotype of the chromosomes is prepared. A karyotype shows
all the chromosomes of the individual arranged by homologous pairs (analysis by karyotyping, refer to
Lab 8 for information about karyotyping). Homologous chromosomes have the same size and shape.
Karyotypes can show genetic aberrations. For instance, in humans, if you have an extra chromosome
21 you will have Down syndrome.
Geneticists can now map human chromosomes, that is, they can find the exact loci for various
genes. If the exact locus for a mutant gene causing a genetic disorder is known, geneticists can make
copies of the gene and use these copies to test the chromosomes for the disorder. This is called
analysis by genetic markers and involves the use of DNA probes (the copies of mutant genes) and
restriction enzymes that cleave the DNA into manageable sizes for analysis.
Analysis by pedigree charts
There are three types of inheritance patterns you need to be aware of to complete this portion of
the activity:
 Autosomal dominant  shows with an increased frequency in a defined population
 Autosomal recessive  shows with a decreased frequency in a defined population
 Sex–linked recessive  traits linked to the sex chromosomes
A trait that is an autosomal (trait is associated with one of the chromosomes number 1 through
22) dominant trait only needs one copy of the allele for the individual to be affected. A trait that is an
autosomal recessive trait will require two copies of the recessive trait to be present in order for the
individual to be affected. Sex–linked recessive traits primarily affect men not that women are totally
excluded but the likely–hood of a women being affected is lower (Why would this trend be true?).
Look at the following table (Table 3) to see the possible genotypes and phenotypes for some common
single gene inheritance patterns.
Inheritance Pattern
Autosomal Dominant
Autosomal Recessive
Sex–linked Recessive
Genotype
BB
Bb
bb
BB
Bb
bb
XB XB
XB Xb
XbXb
XB Y
XbY
Phenotype
Affected
Affected
Not affected
Not affected
Not affected
Affected
Normal female
Normal female
Affected female
Normal male
Affected male
Table 3 Pedigree Analysis These are the most common designations for pedigree assignment in humans.
Consider the following three pedigrees. Using Table 3, determine the pattern of
inheritance and indicate the probable genotype for each individual in each pedigree (the
analysis). See page 82 to assist with your genotypic identification of the unknown members of
the pedigree.
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Pedigree #1
I
1
Male
2
II
Female
2
Unaffected
Affected
1
2
3
III
1
Analysis: (Why did you label the genotypes of the family members the way you did?)
Pedigree #2
I
1
2
3
4
II
1
2
3
4
5
III
1
Analysis:
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Pedigree #3
I
1
2
3
4
II
1
2
3
4
5
III
1
Analysis:
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Laboratory 8: Modeling DNA Structure, Replication, &
Protein Synthesis
Pre-lab Assignment
Before coming to lab, carefully read the following pages on Modeling DNA Structure, Replication,
& Protein Synthesis and then answer the pre-lab questions, pages 107 and 108. Be prepared to
discuss and hand in your responses to the pre-lab questions at the start of lab.
Perspectives
This investigation differs from those you have completed up to this point. You will use various
kinds of models to learn how DNA controls the activities of cells. Many scientists use models to
understand biological processes. Watson and Crick used models to figure out the structure of DNA
and scientists use models today to study biological problems, from the structure of proteins to making
predictions concerning how environmental factors may influence entire ecosystems.
In this investigation, you will work collaboratively with your partners to propose a structure for
DNA, show how DNA acts as a template to make RNA, and how RNA is used as a template to make
protein. To accomplish these tasks you will use models of the building blocks of DNA, RNA, and
protein to represent DNA replication and protein synthesis.
Though it comes as no surprise that the composition of DNA between different organisms is
different, it is not immediately obvious why the muscle cells, blood cells, and brain cells of any one
particular vertebrate are so different in their structure and composition when the DNA of every one of
their cells is identical. This is the key to one of the most exciting areas of modern cell biology. In
different cell types, different sets of the total number of genes (genome) are expressed. In other
words, different regions of the DNA are "active" in the muscle cells, blood cells, and brain cells.
Central Dogma of Biology: DNA RNA  Protein (Product)  Phenotype
To understand how this difference in DNA activity can lead to differences in cell structure and
composition, it is necessary to consider what is often known as the central dogma of molecular
biology (Figure 1): "DNA copied into RNA and RNA is read into protein”. In molecular terms, a gene is
that portion of DNA that encodes for a single protein. The dictum "one gene makes one protein" has
required some modification with the discovery that some proteins are composed of several different
polypeptide chains, but the "one gene makes one polypeptide" rule does hold.
Figure 1 Central Dogma The central dogma of biology states that DNA contains a genetic code that allows it to
make copies of itself.
An essential group of proteins, called enzymes, act as biological catalysts and regulate all aspects
of cell metabolism and conspire to complete the steps of DNA replication and protein synthesis or
essentially they regulate you. Their role in DNA replication and protein synthesis are vital in
maintaining the integrity of these molecules to ensure continued functioning of the cell. In fact the
structure of the enzyme is encoded into the DNA molecule.
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The Structure of DNA: Nucleotide strands
DNA is a double helix, with about 10 nucleotide pairs per helical turn (Figures 2 and 3) in an antiparallel arrangement (5’ to 3’ and 3’ to 5’ based on the position of the carbon’s in the ring of the sugar
(Figure 5)). Each spiral strand is composed of a phosphate group (P), a sugar (deoxyribose) (S), and an
attached base (B) or P-S-B that is connected to a complementary strand by hydrogen bonding
between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C). Two hydrogen
bonds (weak non-covalent bonds) connect adenine and thymine, while guanine and cytosine are
connected by three. James Watson and Francis Crick first described this structure in 1953.
Figure 2 DNA Structure DNA is a double stranded molecule, each strand consisting of a chain of nucleotides.
Each nucleotide consists of a phosphate group, a deoxyribose sugar, and a nitrogen containing base (Guanine
Cytosine, Adenine, or Thymine). Weak hydrogen bonds between the bases of each strand hold the two strands
together.
Figure 3 DNA Structure An illustration of the double helical structure of the DNA molecule.
Nucleic acids are long, chain-like molecules formed by the linking together of smaller molecules
called nucleotides. The nucleic acid DNA or DeoxyriboNucleic Acid is the material from which genes
are made. Watson and Crick used information gathered by other researchers to make models of DNA
in 1953. Their models led them to make one of the greatest scientific discoveries of the last century,
the determination of the structure of DNA.
The sugar and the phosphate part of each DNA nucleotide are the same, but the bases differ. There
are four different types of nitrogen bases in DNA nucleotides—thus there are four different types of
DNA nucleotides. Biologists typically refer to the type of nucleotide by its first letter: A = adenine, C =
cytosine, G = guanine, and T = thymine.
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Notice the polarity of DNA and RNA. There is always a 3’ and 5’ prime end of each strand (Figure
4) due to the number sequence of the carbons in the nucleotide sugar (Figure 5). The phosphate is
always attached to the 5’C of the nucleotide sugar (either deoxyribose or ribose) and the nucleotide
base is always attached to the 1’C of the sugar. This orientation leaves the 3’C available to attach to
the next nucleotide at its phosphate end (5’C). Why is this specific orientation required in both DNA
and RNA?
Figure 4 Representation of DNA Replication The two strands of the original DNA molecule separate, and then
each serves as a template in the formation of two new DNA molecules that will have the identical base sequence
as the one original DNA molecule.
Figure 5 Sugar Carbon Ring Numbering Each carbon in a sugar ring is numbered starting with the carbon to
the right of the oxygen in the ring.
DNA Replication: Semi-conservative replication
To reproduce (Why do cells reproduce?) a cell must first copy and transmit its genetic
information (DNA) to all of its progeny. To do so, DNA is replicated (During what part of the cell
cycle?) , following the process of semi-conservative replication (Figure 4) by laying down the new
bases in a 5’ to 3’ direction by reading the original strand in a 3’ to 5’ direction. Because of this
orientation the replication process follows one strand in a straight forward direction (leading strand)
while the opposite strand is read in short sequences (called Okasaki fragments) in the opposite
direction from the leading strand but in the correct direction in terms of 5’ to 3’ (lagging strand).
Each strand of the original molecule acts as a template for the synthesis of a new complementary DNA
molecule.
In the last section of their paper, Watson and Crick added this statement: “It has not escaped our
notice that the specific base pairing we have postulated immediately suggests a possible copying
mechanism for the genetic material”. The process they were thinking of involved the separation of
the two strands of DNA by an enzyme known as DNA Helicase. Once open another enzyme called
RNA Primase lays down a short sequence using RNA bases as a primer to direct the enzyme called
DNA polymerase III to read the original strand and lay down the appropriate base in the opposite
position to build a new strand of DNA. Another enzyme, called DNA polymerase I, comes along and
reads the primers as RNA and subsequently removes this portion and adds the appropriate DNA bases
to complete the new strand and finally DNA Ligase ties all the loose ends together such that two
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single-stranded sections of DNA are formed from one double-stranded molecule or from replication.
The key is the consistence to hopefully avoid copying issues or mutations.
DNA  RNA: Transcription
RNA (RiboNucleic Acid) is produced using DNA as a pattern. During this process, called
transcription, the genetic code is transferred from DNA to RNA. During transcription the two strands
of a DNA molecule become separated by a group of enzymes known as transcriptions factors along
part of the molecule’s length. One strand, the non-coding strand, remains inactive (maybe used at
another time), but the other, the coding strand, is used as a template to synthesize RNA, a single
stranded molecule.
The enzyme responsible for transcription, RNA polymerase, like DNA polymerase (III or I), can
only build RNA in the 5’ to 3’ direction (Why?). Therefore, begin transcription at the 3’ (sugar) end of
the DNA molecule by pairing each DNA nucleotide with its RNA complement. The base pairing rules
are the same as in DNA, except Uracil pairs with Adenine since RNA does not contain Thymine.
Before the synthesis of a protein begins, the corresponding RNA molecules messenger (mRNA),
transfer (tRNA), and ribosomal (rRNA) are produced by RNA transcription (Figures 5 and 6) by reading
the DNA strand in a 3’ to 5’ direction and laying RNA bases down in 5’ to 3’ direction. One strand of
the DNA double helix is used as a template (coding strand) by the enzyme RNA polymerase (under the
direction of the transcription factors) to synthesize RNA. The RNA’s migrate from the nucleus to the
cytoplasm. During this step, RNA’s go through different steps of maturation including splicing out
non-coding sequences (called introns (these regions do not code for product as far as we now know))
from coding sequences (called exons (both sides of the DNA code for product in these regions)) and
adding a GTP cap (not shown) to the 3’ end and a poly A tail (not shown) to the 5’ end of the
molecule. The coding sequence for a particular amino acid of the mRNA can be described as units of
three nucleotides called codons.
Figure 5 DNA Transcription RNA polymerase faithfully copies DNA to produce RNA molecules.
Figure 6 DNA Transcription During transcription the two strands of a DNA molecule become separated along
part of the molecule’s length. Only one of the two strands of DNA, the coding strand (the bottom strand in this
case) acts as a template during transcription. The enzyme RNA polymerase reads the coding strand to produce a
single stranded RNA molecule by following the base pairing rules used in DNA, with one exception—since
thymine is not found in RNA, uracil pairs with adenine.
Take Note... Transcription produces three major types of RNA which all get transported from the
nucleus through a nuclear pore to the cytoplasm of the cell.
 Ribosomal RNA (rRNA): Combines with proteins in the cytoplasm to form ribosomes, the protein
making factories of the cell.
 Messenger RNA (mRNA): Brings the instructions for protein synthesis (the genetic code) from
DNA in the nucleus to the ribosomes.
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 Transfer RNA (tRNA): Combine with amino acids in the cytoplasm and transport them to the
ribosome where tRNA interacts with ribosomes and mRNA to link the amino acids together to
form proteins.
There is a different tRNA molecule for each of the 20 amino acids. Each tRNA molecule consists
of about 75 nucleotides. At one end of each tRNA molecule is a three base sequence called the
anticodon, which are complementary to one of the codons in mRNA. An activating enzyme called
aminoacyl-tRNA synthetase can attach a specific amino acid to the opposite end of the tRNA
molecule. This enzyme is specific for a particular amino acid and a particular tRNA: each tRNA can
carry only one kind of the 20 naturally occurring amino acids.
RNA  Protein: Translation
The process of translation begins with the binding of a ribosome to the mRNA at the start (or
initiation) codon, AUG. The ribosome proceeds to slide down the RNA molecule reading its message
three bases (i.e. one codon) at a time (Figure 7). During this stage, complexes, composed of an amino
acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary
base pairs with the anticodon (Figure 8) of the transfer RNA (tRNA). The ribosome (containing a short
strand of rRNA) moves from codon to codon along the mRNA as amino acids are added one by one,
translated into polypeptide sequences dictated by DNA and represented by mRNA (Figure 7). At the
end, a releasing factor binds to a stop codon, terminating translation and releasing the complete
polypeptide (protein) from the ribosome. Since one specific amino acid can correspond to more than
one codon, the genetic code is said to be redundant.
Figure 7 RNA Translation or Protein Synthesis During protein synthesis, ribosomes move along the mRNA
molecule and "read" its sequence three nucleotides at a time (codon) from the 5' end to the 3' end. Each amino
acid is specified by the mRNA's codons. Each codon pairs with a specific anticodon, a sequence of three
complementary nucleotides at one end of a tRNA molecule. Since each tRNA molecule carries a specific amino
acid at one end, the order of codons on the mRNA molecule determines the order of amino acids to be linked
together during protein synthesis.
Proteins then are long chains of amino acids constructed by varied arrangements of the 20
different amino acids. As the proteins are released from the ribosome, they fold into unique shapes
(conformation) that depend on the particular sequence of amino acids in the chain. Hence, it is the
protein’s primary structure (i.e. the order of the amino acids in the protein), which is encoded in the
gene and faithfully transcribed to produce mRNA, which in turn is translated by ribosome’s into an
amino acid chain, that determines the three-dimensional structure of a protein, and thus its particular
function. The human body possesses some 30,000 different kinds of proteins and several million
copies of many of these. Each plays a specific role. For example, hemoglobin carries oxygen in the
blood; actin and myosin interact to generate muscle movement, and acetylcholine receptor molecules
mediate chemical transmission between certain nerve and muscle cells.
The versatility of proteins, the workhorse molecules of the cell, stems from the immense variety
of molecular shapes that can be created by linking amino acids together in different sequences. The
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smaller proteins consist of only a few dozen amino acids, whereas the larger ones may contain in
excess of 200 amino acids, all linked together in a linear chain by peptide bonds. There exact
sequence dictated by DNA and represented by mRNA is constructed through the joint processes of
transcription and translation.
Translation of the mRNA molecule involves each type of RNA. The ribosome (40S and 60S
template) is attached to the mRNA by reading a start codon. The shape of the ribosome allows for
only two tRNA’s to match their individual anti-codons to respective codons within the ribosome at one
time. These matching sites are called the ribosome P and A sites, respectively. Enzymes found
outside the ribosome detach the amino acid bonded to the first amino acid and attach it the second
tRNA’s amino acid. The ribosome is then shifted to open the next codon and the steps repeat to
lengthen the building protein one amino acid at a time, until a stop codon (no tRNA matches the
codon of the three stop codons) is read at the end of the mRNA. Once the stop codon is read the
resulting protein is released (What happens to it to become functional?) from the last tRNA, the
ribosome is removed, and the message is recycled. Figure 9 and Table 1 are based on the three codon
bases of mRNA.
The Genetic Code: Three Base Sequences
The process of identifying the sequence of amino acids in a protein, then reading them back into
mRNA codons, and then to DNA base sequences began in the 1930’s by work done by Tatum and
Beadle. In 1961 Nirenberg proved that by repeatedly linking uracil (UUUUUUU) into an mRNA the
resulting protein contained only one amino acid (phenylalanine). From this beginning molecular
biologists have identified the amino acid that is associated with each of the mRNA codons. The
following figures (Figure 8 and 9 plus Table 1) show this relationship and also identifies the special
start and stop codons.
Since RNA is constructed from four types of nucleotides, there are 43 or 64 possible triplet
sequences or codons. One of these codons plays a dual role in mRNA. If AUG is read in the mRNA
sequence it signifies placing a methionine in that position, but when the AUG is placed at the
beginning of the mRNA it also indicates where the rRNA is attached to begin the process of translation
or the start codon. Three other codons (UAA, UAG, or UGA) specify the termination of the
polypeptide chain and are called the "stop codons" (What happens to each of the RNA’s when
translation is completed?). The remaining 61 codons are used to specify the other 19 different amino
acids. Therefore, most of the amino acids are represented by more than one codon and the genetic
code is said to be redundant, except for UGG (codes for tryptophan) (Why?).
Figure 8 Translation The Pairing of a Codon in mRNA with an Anticodon of the tRNA inside a ribosome with
rRNA (not shown).
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Figure 9 The Genetic Code The three bases of an mRNA codon are designated here as the first, second, and
third bases, reading in the 5' to 3' direction along the mRNA. Note that UGG is the only codon for the amino acid
tryptophan, but most amino acids are specified by two or more codons. For example, both UUU and UUC code
for the amino acid Phenylalanine. When either of these codons is read by a ribosome moving along an mRNA
molecule, Phenylalanine will be incorporated into the growing protein molecule. Think of UUU and UUC as
synonyms in the genetic code. Note that AUG codes for the amino acid methionine but also functions as a
“START” signal for ribosomes to begin translating the mRNA at that location. Three of the 64 codons function as
"STOP" signals. Any one of these termination codons marks the end of the genetic message.
Ala: Alanine
Cys: Cysteine
Arg: Arginine
Asn: Asparagine
Asp: Aspartic acid
Gln: Glutamine
Glu: Glutamic acid
Gly: Glycine
His: Histidine
Ile: Isoleucine
Leu: Leucine
Lys: Lysine
Met: Methionine
Phe: Phenylalanine
Pro: Proline
Ser: Serine
Thr: Threonine
Val: Valine
Trp: Tryptophan
Tyr: Tyrosine
Table 1 Amino Acid Abbreviations This table shows the abbreviations for each of the twenty different amino
acids that are used to build proteins coded for in the DNA
Exercise: Modeling DNA Replication and Protein Synthesis
Goals of this Lab Exercise
 Describe the components of DNA and RNA nucleotides
 Explain how DNA is replicated within a cell and use models to model the process
 Explain how DNA is transcribed to produce RNA and use models to model the process
 Explain how mRNA is translated into protein and describe the role of each of the following in the
process: mRNA, tRNA molecules, amino acids, and ribosomes
 Determine the amino acid sequence of a protein when given the base order of the coding or
non-coding strand of a gene
 Compare and contrast the possible effects each of the following point mutations have on the
amino acid sequence of a protein: a single base substitution, a single base deletion, and a single
base addition
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Introduction
This lab is actually divided into two activities (building a model and answering questions) that are
reliant on each other. For you to complete each of the activities a clear understanding of the
perspectives section is imperative. Discuss the answer to the pre-lab questions with your classmates
to ensure that you have a grip on the ideas supporting this lab before proceeding.
You will be working with a group and a puzzle kit to demonstrate the structure of DNA and the
processes of DNA replication and protein synthesis. Ask questions to clarify these concepts.
Sometimes it is relatively easy to take puzzle tiles and organize them into the resulting puzzle without
ever appreciating the under lying process or the picture.
Materials
DNA Replication and Protein Synthesis modeling kit with directions
Clear desk space to build models
Procedure
Activity A.
Modeling DNA Structure
1. Follow the instructions provided by your instructor and answer the appropriate questions on
your Report Sheet to understand DNA Structure.
2. Once all group members understand the structure of DNA, call your instructor, demonstrate
the model, and have them sign Table 2 (page 104) on the Report Sheet.
Activity B.
Modeling DNA Replication
1. Follow the instructions provided by your instructor and answer the appropriate questions on
the Report Sheet to understand DNA Replication.
2. Once all group members understand the replication process of DNA, call your instructor,
demonstrate the model, and have them sign Table 2 (page 104) on the Report Sheet.
Activity C.
Modeling Protein Synthesis = Transcription
1. Follow the instructions provided by your instructor and answer the appropriate questions on
your Report Sheet To understand DNA Transcription.
2. Once all group members understand the transcription process of DNA, call your instructor,
demonstrate the model, and have them sign Table 2 (page 104) on the Report Sheet.
Activity D.
Modeling Protein Synthesis = Translation
1. Follow the instructions provided by your instructor and answer the appropriate questions on
your Report Sheet To understand RNA Translation.
2. Once all group members understand the translation process of mRNA, call your instructor,
demonstrate the model, and have them sign Table 2 (page 104) on the Report Sheet.
Activity E:
Group Report Sheet
1. As a group complete the questions on pages 103 through 106 and turn in one Report Sheet at
the start of the next lab.
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Report Sheet
Lab Section:
.
Modeling DNA Replication & Protein Synthesis Exercise
Group Names:
.
.
.
.
The following questions should be answered as you build the model to represent DNA, replicate
DNA, and synthesize a protein.
1. To which carbon of the nucleotide sugar does the nitrogen base and the phosphate group
attach?
2. If the “backbone” of one strand runs 5’ to 3’, what is the orientation of the opposing strand?
3. How are the nucleotides arranged in the DNA molecule?
4. How does DNA replicate and why is maintaining molecular orientation critically important?
5. What is a mutation and how is it reproduced?
6. How does a deoxyribose sugar differ from a ribose sugar?
7. List two ways to tell that this is a model of DNA and not RNA.
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Noncoding Strand 
Coding Strand 
3’ - C
G
G
T
C
C
A
G
T
C
C
A - 5’
m-RNA 
Amino acid sequence of peptide 
8. In what molecule(s) do you find the code, the codon, and the anti-codon sequences within
their structure?
9. Where is the eukaryotic cellular site of transcription and translation?
10. What could happen to the protein after construction but before it becomes functional?
Instructor’s Initials
Modeling DNA Structure
Modeling DNA Replication
Modeling Transcription
Modeling Translation
Table 2 Instructor’s Initials You need to obtain your instructor’s initials in each box once your group
has shown knowledge or each portion of the lab.
Application Questions:
1. The DNA sequence in the box on the next page is part of the non-coding strand of the -globin
gene (beta globin) that codes for a small portion of hemoglobin, the protein that transports
oxygen in your blood.
 Within the box write the base sequence of the coding strand in the table below - Indicate the
5’ and 3’ ends.
 Now record the base sequence that would result if this section of the -globin gene were to
be transcribed - Indicate the 5’ and 3’ ends.
 Finally, use the table of the genetic code (Figure 9 and Table 1) to translate this mRNA into
protein. List in the table below the order of the amino acids that would be found in the
resulting peptide.
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Non-coding Strand of -globin gene 
5’ - A C C C
A G A G G T T C T T T - 3’
Coding Strand 
m-RNA
Amino acid sequence 
2. The entire -globin chain has 146 amino acids. What would be the minimum number of
nucleotides in the mRNA that would encode the -globin protein? Explain your reasoning:
3. How many tRNA molecules will be needed to translate the -globin mRNA into protein?
Explain your reasoning:
4. List the base sequence of the anticodon for each of the tRNA molecules needed to translate
the -globin mRNA into protein in the table below.
Anticodon
1st
2nd
3rd
4th
5th
Base sequence in anticodon of tRNA
Table 3 tRNA Anticodons Counter match anticodons with the codons in the example mRNA above.
5. Determine the effects of the following mutations on the -globin gene. Use the three letter
amino acid abbreviations (Table 1) to write the sequence of amino acids that would result if
there was a mutation in which an “A” has substituted for the underlined C of the non-coding
strand of the -globin gene. Note: Any changes to the non-coding strand will always affect the
coding strand!
 Base sequence of coding strand of the mutant DNA:
.
 Base sequence of the new mRNA:
.
 Amino acid sequence:
.
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6. What would be the amino acid sequence if an “A” substituted for the underlined G?
 Base sequence of coding strand of the mutant DNA:
.
 Base sequence of the new mRNA:
.
 Amino acid sequence:
.
7. What would the amino acid sequence be if you deleted the underlined C of the non-coding
strand?
 Base sequence of coding strand of the mutant DNA:
.
 Base sequence of the new mRNA:
.
 Amino acid sequence:
.
8. What can you conclude about the impact on a protein from these two types of mutations? (I.e.
How does a point mutation that involves the substitution of a single base affect a protein
compared to a point mutation involving the deletion of a single nucleotide?) Explain the
reasoning behind your response.
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Pre-Lab Report Sheet
Lab Section:
Modeling DNA Structure, Replication, & Protein Synthesis Exercise
.
Name:
.
Before coming to lab carefully read the previous pages on Modeling DNA Structure, Replication,
& Protein Synthesis then answer these pre-lab questions. Be prepared to hand in your responses to
the pre-lab questions at the start of lab.
1. Explain how it is possible for you to have so many different kinds of cells in your body (e.g.
muscle cells, skin cells, liver cells, etc.) when nearly all of the cells contain the same 46
molecules of DNA (chromosomes).
2. Explain in your own words your understanding of the central dogma of biology.
3. Answer each of the following questions.
 What is the primary structure of a protein?
 Of what importance is the primary structure of a protein?
 What ultimately determines the primary structure of a protein?
 What is a mutation? During what process are mutations most likely to occur?
 Why do mutations affect the primary structure of a protein?
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4. Describe in your own words the structure of DNA.
5. Describe in your own words how DNA makes copies of itself. (I.e. Describe DNA replication.).
6. Protein synthesis involves two processes, transcription and translation. Describe in your own
words how each process occurs.
 Transcription
 Translation
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Laboratory 9: Critical Thinking and Classification
Pre-lab Assignment
Before coming to lab carefully read the Perspective and the Introductions on Critical Thinking and
Classification (pages 109 &110, 111, 113 & 114). Hurrah, hurrah no pre-lab report.
Perspectives
Since people first began to question how nature works and how they fit into nature, problems
have arisen. Answers to questions relating to man’s relationship with other creatures on the earth
posed only more questions. Organizational problems arose when dealing with knowledge. How can
we get a common language between investigators to eliminate duplication of effort or simply to
communicate our ideas with the vast varieties of native languages? How do we solve problems and
organize data became the focal point of science. Methods and processes were needed to allow
scientists to communicate worldwide.
The process of critical thinking allows scientists and you to evaluate and understand a problem,
devise a plan to solve the problem, carry out the plan, and lastly to evaluate the outcomes of the
execution of the plan. The following outline expands this process with more detail and could or
should be applied to almost any situation with which you could face in your academic life or career.
An eighteenth–century Swedish naturalist, Carolus von Linnaeus, is largely responsible for
creating the system of scientific names that we use today (Kingdom, Phylum, Class, Order, Family,
Genus, and Species (Today we have added Domain before kingdom.)). Linnaeus undertook the
formidable task of naming and classifying all plants and animals based primarily on their physical
characteristics (Why didn’t he do all the kingdoms?), assigning each organism a two–part name called
a binomial. The first word of the binomial designates the group to which the organism belongs; this is
the genus name. All oak trees belong to the genus Quercus. Each kind of organism within a genus is
given a specific epithet or species. Thus, the scientific name in the Linnaean system for white oak is
Quercus alba L. (with the L. identifying the classifier in this case Linnaeus), while that of bur oak is
Quercus macrocarpa L.
Today we use other criteria such as chemical make-up, DNA similarities, breeding habits, and/or
behavioral habits to classify the organisms. The techniques of classification are continually adapted
and being re-evaluated as new technology makes scientists aware of different aspects of the
relatedness of specimens
Exercise A: Critical Thinking and Problem Solving
Goals of Lab Exercise
 To develop some skills in solving problems
 Learn to make representative drawings of specimens
Introduction
The following exercise is designed to give the student the opportunity to develop skills in
problem solving by following a stepwise procedure. Practicing the procedure is critical in
understanding the nuances of problem solving. By critically reading the following outline the skill of
solving problems can be developed and put into practice. The application of these skills moves well
beyond the scope of this exercise and can give the student a skill that is applicable in other aspects of
their life.
A General Approach to Problem Solving
1. Understand the Problem. First, you have to understand the problem. What is the unknown?
What are the data? What is the condition? Is it possible to satisfy the condition? Is the
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condition sufficient to determine the unknown? Or is it insufficient? Or redundant? Or
contradictory? Draw a figure. Introduce suitable notation. Separate the various parts of the
condition. Can you write them down?
2. Devise a Plan. Second, find the connection between the data and the unknown. You may be
obliged to consider auxiliary problems if an immediate connection cannot be found. You should
obtain eventually a plan of the solution. Have you seen it before? Or have you seen the same
problem in slightly different form? Do you know a related problem? Do you know a theorem
that could be useful? Look at the unknown! And try to think of a familiar problem having the
same or a similar unknown. Here is a problem related to yours and solved before. Could you
use it? Could you use its result? Could you use its method? Should you introduce some
auxiliary element in order to make its use possible? Could you restate the problem? Could you
restate it still differently? Go back to definitions. If you cannot solve the proposed problem try
to solve first some related problem. Could you imagine a more accessible related problem? A
more general problem? A more special problem? An analogous problem? Could you solve a
part of the problem? Keep only a part of the condition, drop the other part; how far is the
unknown then determined, how can it vary? Could you derive something useful from the data?
Could you think of other data appropriate to determine the unknown? Could you change the
unknown or the data, or both if necessary, so that the new unknown and the new data are
nearer to each other? Did you use all the data? Did you use the whole condition? Have you
taken into account all essential notions involved in the problem?
3. Activate the Plan. Third, carry out your plan. Carrying out your plan of the solution, check each
step. Can you see clearly that the step is correct? Can you prove that it is correct? Try to
anticipate problems with the plan, but don’t radically change the plan unless an obvious failure.
4. Evaluate the Plan. Fourth, examine the solution obtained. Can you check the result? Can you
check the argument? Can you derive the result differently? Can you see it at a glance? Can you
use the result, or the method for some other problem?
Materials for this exercise
Meter Sticks, Cardboard or File Folders and Rulers
Pickle Balls
Boxes and Scissors
String
Procedure
You will work in groups of four. Be sure to list your lab partners on your write-ups. Your writeups will contain responses to all questions posed in the following exercise to include all calculations
and work. I would suggest looking at the perspectives and introduction of this lab for direction in
determining how you and your co-investigators proceed. Keep in mind that a clear presentation on
your approach to solving the problem is more important than the “correct” answer. Remember there
is more than one way to solve any of the exercises and their inclusion in your problem solving
approach and presentation will only strengthen your arguments.
In some cases you will actually be able to follow through to test your ideas. If you feel you need
materials other than what is provided you should ask.
Determine the maximum number of pickle balls that would fit in this room. Assume that the
room is completely empty (no lab benches, no people, etc.). Do not include the space in the fume
hoods or shelves (It’s a box, O.K.). Explain your procedure (What you did?) to solve this problem.
Give all measurements and show all calculations. All measurements should be done in the metric
system. A bunch of pickle balls, various containers, string, and meter sticks will be provided.
Please put your group’s names on separate paper to explain your results to include all of your
calculations, your step wise procedure, and turn in next week at the beginning of lab.
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Exercise B: Classification I
Pre-lab Assignment
Before coming to lab, carefully read the pages on critical thinking and classification.
Goals of Lab Exercise
 To use problem solving skills to classify inanimate objects
Introduction
Putting objects into groups because they share some similar characteristic is called classification.
Nearly all branches of science use systems of classification. Systems of classification are necessary to
help the scientist handle the huge amounts of data and facts that have accumulated over the years.
When individual objects are placed into groups based on properties they have in common, the study
of a large number of objects is made much easier.
In this exercise, you will have the opportunity to attempt many ways to classify a group of
objects. Each time you classify an object according to a different aspect of it, you learn more about it.
You will learn how classification of a large number of objects into a few categories makes it easier to
study the objects, because all the objects in a specific group have something in common.
In this exercise you will have a chance to devise your own classification system. You will make
your own rules for setting up categories and subcategories. To be a successful classifier, you will have
to make use of all your powers of observation, especially your sense of sight and your ability to think.
In other experiments, you’ll make use of your other senses as well. Good luck! Be sure to read and
use the guidelines above for problem solving.
Materials for this exercise
Each group will need approximately 100 buttons.
Procedure
1. You may work as a group. You will need about 100 buttons selected at random from the button
collection. Buttons, of course, are common objects that you see every day. But have you ever
stopped to think that buttons could be put into groups because they share certain similar
characteristics? Examine the buttons and decide how you want to classify them. Some people
form groups based on the sizes, shapes, colors, and other characteristics of the buttons. When
you have decided how to group the buttons, you should then form subgroups and further
subdivide, so you have at least three levels of classification (see next page for an example). For
example, if you choose to group the buttons by size, you can have large buttons, large round
buttons, and large white round buttons.
2. After you have classified them, make a chart on a separate sheet of paper showing how your
classification scheme works. Use the following example (Figure 1) to guide your creativity, but
make it your own. Also list the number of buttons in each group and subgroup. After recording
your classification scheme, repeat the experiment using different criteria for the groups.
Compare your classification system with those of other people in the class. Return the
buttons!!
3. Next take one of your schemes and condense it into a dichotomous key (Figure 2). For instance
the accompanying dichotomous key would be appropriate for the sample classification chart
(Figure 1).
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4. Group all of your buttons into the center of the table and invite a fellow scientist from another
lab to visit your lab and ask them to use your key to identify any button of their choosing. If
they are able to correctly identify the button write their names on your dichotomous key. Do
this with 2 other lab groups (three names total).
5. Please describe your strategies of classifying in words and turn in your scheme and key next
week with your group names.
Sample Classification Chart
Classification by Size, Shape, and Color
Large Buttons
10
Round Buttons
7
Blue
3
Red
4
Medium Buttons
25
Square Buttons
3
Blue
0
Red
3
Small Buttons
15
Round Buttons
12
Square Buttons
13
Round Buttons
4
Square Buttons
11
Blue
8
Blue
1
Blue
2
Blue
8
Red
4
Red
12
Red
2
Red
3
Figure 1 Classification Scheme Simple classification scheme of buttons.
1a. Buttons all large (>3cm in across)
2a. Buttons round sometimes with many straight edges approx. a circle
3a. Buttons blue
3b. Buttons red
2b. Buttons all square or rectangular
4a. Buttons blue
4b. Buttons red
1b. Buttons other than large
5a. Buttons medium (1.5–3 cm in across)
6a. Buttons round sometimes with many straight edges approx. a circle
7a. Buttons blue
7b. Buttons red
6b. Buttons all square or rectangular
8a. Buttons blue
8b. Buttons red
5b. Buttons small (<1.5 cm in across)
9a. Buttons round sometimes with many straight edges approx. a circle
10a. Buttons blue
10b. Buttons red
9b. Buttons all square or rectangular
11a. Buttons blue
11b. Buttons red
Figure 2 Dichotomous Key Simple dichotomous key based on a scheme of buttons.
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Exercise C: Classification II
Pre-lab Assignment
Before coming to lab, carefully read the pages on critical thinking and classification.
Goals of Lab Exercise
 To use classification skills to classify specimens
 Develop skills using dichotomous keys to identify specimens
 Learn to make representative drawings of specimens
Introduction
At the beginning of any serious study, it is important not only to learn precisely which species are
present, but to be able to recognize them at different stages of development. The time is not long past
when the field biologist felt well satisfied with their work after presenting a mere list of the
dominants. It is now widely acknowledged as poor policy to learn only a few of the dominants and
neglect the remaining flora and fauna. (Remember the snail darter or how about the spotted owl?)
Subordinate and even rare species often have much value for indicating special conditions (present
and past) and they sometimes foretell the future. All species have some indicator significance
whether it is known at present or not. Maybe a certain species indicates that Douglas fir will
eventually grow at a particular site or that 350 years from now the Douglas fir will be replaced by
spruce and hemlocks.
We are all great classifiers, already. Every day, we consciously or unconsciously classify and
categorize the objects around us. We recognize an organism as a cat or a dog, or an aardvark, or an
oak tree. But there are numerous kinds of oaks, so we refine our classification, giving the trees
distinguishing names such as “red oak,” “white oak,” or “bur oak”. These are examples of common
names, names with which you are probably most familiar.
Scientists are continually exchanging information about living organisms. But not all scientists
speak the same language. The common name “white oak,” familiar to an American, would probably
be unfamiliar to a Spanish biologist, even though the tree we know as white oak may exist in Spain as
well as in our own backyard. Moreover, even within our own language, the same organism may have
several common names. For example, within North America, a “gopher” may also be called a “ground
squirrel,” a “pocket mole,” or a “groundhog”. On the other hand, the same common name may
actually describe many different organisms; there are more than 300 different trees called
“mahogany”! To circumvent the problems associated with common names, biologist use scientific
names that are unique to each kind of organism and that are used throughout the world.
Taxonomy is the science of classification (categorizing) and nomenclature (naming). For the
purposes of this class we will separate all living organisms into five kingdoms, recognizing that other
classification schemes exist and are being developed and discussed in scientific circles today. The
kingdoms are outlined below. What criteria would you have used to delineate these groupings?
 Kingdom Monerae (prokaryotic organism)
 Kingdom Protistan (euglenoids, chrysophytes, diatoms, dinoflagellates, slime molds, and
protozoans)
 Kingdom Myceteae (fungi)
 Kingdom Plantae (plants)
 Kingdom Animalae (animals)
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Let’s consider some examples of the scientific system of classification using some common
species:
Category
Kingdom
Phylum (animals)
or Division (Plants)
Subphylum
Class
Order
Family
Genus
Specific epithet
Domestic Cat
Animalae
Chordata
Common Buttercup
Plantae
Anthophyta
Spider lily
Plantae
Anthophyta
Vertebrata
Mammalia
Carnivora
Felidae
Felis
silvestris
Magnoliopsida
Ranunculales
Ranunculaceae
Ranunculus
acris
Liliopsida
Liliales
Liliaceae
Hymenocaulis
carbaea
Since the naming of things is so important for study and communicating what you are studying
you need to be able to identify each organism you meet. How do you do that? You start young. You
start excited. You start now, using a dichotomous key that allows you to identify organisms. Keys are
based on dichotomous questions, meaning they give you either one choice or another, but sometimes
they are not. You will get to work with both kinds before your biological safari ends.
Materials for this exercise
Dichotomous keys and Specimens
Procedure
Your team will divide and complete the following assignments and turn in one packet at the
beginning of the next lab along with the previous assignments.
1. Using the descriptions of various phyla in the Kingdoms Plantae and Animalae Highlights in
Appendix G, each group will go out in the wilds and find a creature and identify it to the level of
Division or Phylum. Draw the critter to scale (Appendix D). Turn both your drawing and
identification in with the report sheet at the beginning of your next lab period.
2. Option 1: Complete the "Classification Table” (Table 1). Observe the specimens at each station
and identify the kingdom, phylum, and common name for each organism to complete the
columns using the provided keys, only fill-in symmetry for Animalia specimens.
3. Option 2: Using your text or other sources answer the questions on the report sheet pages 116
and 117.
4. Complete all the pages of the report sheet and turn in next week along with strategy and
calcualtions for filling the room with pickle balls, your classification schemes and dichotomous
key for the buttons, and your critter drwawing as a group.
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Report Sheet
Lab Section:
.
Critical Thinking & Classification Exercise
Group Names:
.
.
.
.
Option 1:
Station
Kingdom
Phylum
Common Name
Symmetry
1
2
3
4
5
6
7
8
9
10
11
12
Table 1 Classification Table This table is used for student classifications based on their observations of various
organisms presented in lab.
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Option 2:
Classification Questions
Taxonomy
1. Define radial and bilateral in terms of animal symmetry.
2. Why do we have a classification system? Is this system fixed?
3. Name the seven general categories used in this system.
4. What is the conventional way of writing a specific genus and species?
Systematics
1. In a few words identify what topics the study of systematics addresses.
2. Complete this table:
Symmetry type
Invertebrate representative or example
radial
bilateral
no symmetry
3. Respond to this statement: The body cavity is also called the gut.
4. During embryonic development in humans, the first opening becomes the
5. During embryonic development in mollusks, the first opening becomes the
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Phylogeny
1. In your own words define phylogeny.
2. Complete this table:
Phylum
Two examples
Two characteristics
Arthropoda
Molluska
Echinodermata
Chordata
Your choice: Name two other animal or plant Phyla or Domain plus cite 2 characteristics of each
category that you name.
1.
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The Final Biological Doodle Page
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Laboratory 10: Paper Project
Perspectives
Each person will work in a group of about 4 people (2-4) on a project that addresses a topic
related to biology. It can be a scientific question or a question arising from the application of scientific
advances to societal problems. For this assignment, the topic must have some interesting biology
associated with it. When presenting various aspects of the issue it is important that there is a
biological basis to support the various aspects of the topic. Ethics are important, but arguments that
only deal with what is moral or ethical are not sufficient.
The group will select a topic (see page 123 of this manual for ideas) and then divide the topic into
four subcategories or topics. For example the group decides to investigate Stem cell research. They
could then divide up the overarching topic into the history of stem cell research, definition and
discussion of the process of stem cell research, the protagonist’s side of stem cell research, and the
antagonist’s side of stem cell research. Each student will find their own references, write a four page
narrative summary on their individual topic, and finally the group will organize an oral presentation to
present their research to their lab section.
The Paper Project consists of four graded assignments: Project References, Initial Draft of
Position Paper, Final Draft of Position Paper, and a Group Oral Presentation. Each of these four
assignments is described on the pages that follow. Refer to the table below for dues dates and how
each assignment contributes towards your quarter grade.
Assignment
Basis for Grade
% of Grade for Paper
Due Dates for
1. Project
One list per person
10% (10 points)
At the start of your lab during
References
(Individual grade)
week 5
2. Initial Draft of
One paper per person
30% (30 points)
At the start of your lab during
Position Paper
(Individual grade)
week 7
3. Final Draft of Position One paper per person
60% (60 points)
At start of your lab during
Paper
(Individual grade)
week 9
4. Group Oral
One plan per group
70 points
At start of your lab during
Presentation
(Group grade)
either week 9 or 10
Table 1 Paper Assignment Table This table shows the due dates for each aspect of the paper project.
This assignment is to give you the opportunity to use the knowledge you have gained or will gain
throughout this course and kind of bring the ideas to bear by presenting a body of evidence to support
your premise. Approach this project with the vigor of attempting to move your peers into a realm of
questing knowledge.
Procedure
Assignment 1:
Project References = 10 points
Each group member will individually:
1. Turn in a typed list of the references, with at least 4 being referred, they have found. The list
should be in the proper format outlined in Appendix C.
2. Each reference page should have a typed working title and the authors associated with the
paper.
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Using the Holman Library (See Appendix F)
The GRCC Library offers excellent electronic methods for finding reference materials for your
projects. Most can be accessed directly via the World Wide Web. The GRCC Library Catalog contains
all of the books at the college, but books are probably not the best source for this project. Most of
your references should be periodicals as they are usually more specific and up-to-date. There are
several searchable electronic databases available for your use. A GRCC librarian will be happy to assist
you in determining the databases most appropriate for your project. You may find that some of the
periodicals that would be of greatest help for your project are not available through the GRCC Library.
If this is the case, please talk to a librarian about how to get copies of articles that you need from
other libraries in the region. Often you can get what you need in a couple of days.
The references you pick are not all created equally! The best source is information from the
scientists who conducted the study. Try to find information of this type—much of it may be too
technical but you should be able to glean some information from it. The second best source is popular
science journals such as Scientific American, Science News, American Scientist, or Discover. Most of
your references will probably be of this type. Since these periodicals are devoted to science, they tend
to be better sources of information than general magazines such as Time or Newsweek. General
popular references such as newspapers and general magazines may sometimes be helpful but don’t
limit yourself to these. Each group should try to find at least 4 references of high quality. Remember
that part of your grade for your paper is based on the quality of your references.
The World Wide Web also provides an excellent source of materials. Web pages vary in quality
enormously, so you should take care to use sources that provide accurate information. Look carefully
for the biases of the authors. Many news magazines, newspapers and journals now publish on the
web. These will tend to be more reliable than individually published web pages. The latter may be
very useful, though, particularly if they cite references. Do not limit yourself to material that is strictly
web based.
Every scientific publication provides an “Instructions to Authors” that describes the format for
the references section and all other requirements for papers they will accept. The format for citing
references varies slightly from one scientific publication to another. By following the guidelines as
outlined in Appendix C (How to cite references.) you will insure your citations are cited correctly.
Assignments 2 & 3:
Draft and Final Position Paper = 30 and 60 points respectfully
Every member will turn in a paper on one aspect of your group’s issue or investigation using the
references you have found. This report should be about 4 pages typed and double-spaced. Your title
page (containing the title, author, course # and section, due date, and Instructors name), figures, and
references should be on additional pages. High quality papers are expected. Use a word processor
and save your electronic version of the paper until after you receive your grade. Computer crashes
are not an excuse for late papers. It’s a good idea to keep a hard-copy too.
The initial draft of your paper is due at the beginning of lab during the 7th week. You should
bring 2 copies of your paper to lab. One copy will be turned in and the second copy will be given to
another member of the class. You will read another class member’s paper, make comments on the
paper, and return it to the writer after signing the title page. The final version of your paper is due at
the start of lab during the 9th week of lab. You will receive two grades for your paper: a rough grade
and a final grade. The rough paper grade will be based on the quality of your rough draft of your
paper. The final draft of your paper will be graded more carefully. You should turn in your rough
paper (with comments) and my grade rubric with your final paper.
One of the goals of this course is for you to be able to analyze and form an informed opinion
about issues related to cellular biology and genetics. Issues are questions about which informed
people disagree. Issues involve ideas that can be controversial and there is no right or wrong solution,
but your opinion needs to be supported by evidence and must also have some interesting biology
associated with it. When presenting various sides of an issue it is important that there is a biological
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basis to support the various sides. Ethics are important, but arguments that only deal with what is
moral or ethical are not sufficient.
Your paper should have three main components: problem posing, problem solving and
persuasion. It is important that all three parts are not just present but are presented clearly and
persuasively. And remember that the clarity of your writing is important, including organization,
spelling and grammar. Use the following information to assist in the organization of your paper.
1. Problem Posing
The topic should be clearly and explicitly stated in the introduction and remain as a focus through
the entire paper. Part of your job is to convince the reader that this is an important issue and
everyone should be concerned about it.
2. Problem Solving and Persuasion
Convince the reader that your opinion is correct, even if it falls somewhere between the extreme
positions. You should support your opinion with evidence from your readings. Indicate the source of
your evidence by using “in-text citations” (Appendix C), and then put a list of references at the end of
the paper. Indicate the arguments from other sides of the issue. Give references in the format
outlined in Appendix C.
Tell us why these arguments shouldn’t convince us. In other words, you need to present all sides
of the issue but convince us to agree with you. Most issues are not black or white so you may fall
somewhere between the extreme positions. If that is the case then indicate what evidence is most
convincing and what evidence is still weakly supported. Indicate what further evidence you would like
to see to solidify your position.
What does this problem and solution have to do with me? And/or what is its general significance
to the world? This should sum up your essay and leave the reader thinking: “Wow, that is an
important conclusion and I should act on it in some way.”
You should include a reference section at the end of the paper. We will evaluate the quality and
quantity of your references. Place the references in alphabetical order by author and use proper
format.
Assignment 4:
Group Oral Presentation = 50 points
The final component of this assignment is the group oral presentation (see Appendix F). This
should be a means for your group to communicate your new found knowledge to your peers in
(hopefully) a convincing manner. Each member will be involved in the presentation by presenting a
united front of ideas to the audience.
What material to present after all, a presentation is meant for conveying information? You need
to know the topic as a whole, as well as the specific aspects of it. For example, if you were giving a
presentation on vaccines against HIV, you need to have a thorough knowledge of the HIV life cycle and
the human immune system’s response to HIV, as well as a specific knowledge about how vaccines
against HIV might work and why they so are controversial.
How to organize the material; organized information is easier to remember for you and easier to
understand for others (Use the rubric in the syllabus for assistance). Notes are fine, but don’t write a
paper—an organized outline or a list is much more useful for a presentation. IMPORTANT: Eye
contact with the audience is essential—do not read directly from your notes, PowerPoint
presentation, etc.—use them only as quick reminders as to what you want to discuss—do not use
them as a “crutch,” only as an occasional aid.
How to present the information; there are many ways to present material. The best format is the
one that allows you to convey information clearly. A controversial topic might involve a debate
format, and statistics might be presented best graphically, etc. Use visual aids to facilitate the
audience’s understanding of your presentation. You can use PowerPoint, overhead projector
transparencies, video clips, etc. I can help you use these, but only if you notify me well in advance of
your presentation.
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Your group’s presentation should be about 20 minutes long. This works out to about 4 min. per
person per group and leaving additional minutes for questions/class discussions. You may incorporate
various styles; debate, skit, lecture, poster presentation, etc., or you can stick to one style. Do not to
read a prepared paper or lengthy note cards. DO NOT give too much information, but, rather,
summarize the important points in a thoughtful manner. Go slowly, and emphasize main points. Use
visual aids to facilitate the audience’s understanding of your presentation. You can use PowerPoint,
overhead projector transparencies, video clips, etc. I can help you use these, but only if you notify me
well in advance of your presentation.
How to get started!
Search existing literature, start early because searches take time (See Appendix F). You need to
know what information is available, as well as hot or controversial topics in the fields. To gain a
comprehensive view of the field, I recommend starting with a book chapter or a review article. Use
the reference sections from those to find more detailed information. Moreover, there are many links
at the class website that may prove useful.
Come talk to me in person. You can get a lot of feedback from me at any point during the
preparation. Added benefit is that you can figure out my preliminary evaluation of your presentation,
so that you will know how much and what kind of work you have to do quality work.
Organize your work. You are working with others. Clearly organizing and designating
responsibility for each is extremely important. I recommend getting together regularly (e.g. 2-3 times
week for at least 30 min. each), so that you can give each other updates on how things are going.
Your group will be scored by the rubric found in your syllabus for the group presentation.
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Possible topics for the paper:
 Biological Basis for Human Races: Is there a biological basis for dividing people into races?
 Genetic Modification of Food Crops: Are GM foods safe to eat?
 Genetic Engineering of Organisms (e.g. plants, animals, or microbes): Do the benefits outweigh the
possible drawbacks?
 The Puzzle of Hypertension in African-Americans: Why is high blood pressure the leading cause of
health problems among black Americans while the people of western Africa have among the lowest
rates of hypertension anywhere in the world?
 Somatic Cell Gene Therapy: Should somatic cell gene therapy be used to treat genetic diseases?
 Slowing Human Aging: Is it possible to slow down the aging process?
 Genetic Basis of Aging: How important are genes in determining life expectancy?
 Alzheimer's disease: Is a cure imminent? Why are more women than men affected by it?
 Abortion Pill: Is the use of RU 486 harmful to woman's health? Should it be banned?
 Attention-Deficit Hyperactivity Disorder: Is there are genetic basis to the neurological
abnormalities involved with ADHD?
 Hormone Replacement Therapy: Should postmenopausal women use hormone replacement
therapy (HRT) to reduce/prevent osteoporosis?
 Human Cloning: Should human cloning research be allowed/funded by the federal government?
 Human Fetal Tissue Research: Should the federal government allow/fund medical research
involving human fetal tissue obtained from aborted fetuses and umbilical cords or are there
alternative sources for stem cells for medical research?
 Homosexuality: Is there a genetic basis for homosexuality?
 Thrill/Novelty Seeking: Is there a genetic basis for thrill or novelty seeking?
 Obesity: Is there a genetic basis for obesity?
 Genetic Basis of Heart Disease: Are national differences in rates of heart disease environmentally
or genetically caused? What is the role of a dietary cholesterol and fat in heart disease?
 Alcoholism/Substance abuse: Is there a genetic basis for alcoholism/substance abuse?
 Alternative Cancer Therapies: Traditional (chemotherapy and radiation) vs.
alternative/experimental therapy do cancer patients have an alternative to the devastating effects
of chemotherapy and radiation therapy?
 Safety of Food Additives: Do food preservatives/additives pose a significant health risk (e.g. cancer,
developmental problems, etc.)? Are they being regulated properly?
 Hormone use by the food industry: Is it a human health hazard to eat food products derived from
hormonally treated animals?
 Depression: What is the biological cause of depression?
 Child Abuse: Should mothers of drug-addicted babies/fetal alcohol syndrome be prosecuted for
child abuse?
 Cloning for Medicine: Hype or a possible reality?
 Genetic Basis of Athletic Performance: Can anyone become a world class athlete if they train
properly? What role(s) do genes of the athlete play?
 Organic vs. “traditional” foods: Do the potential benefits of organic foods outweigh the extra costs
involved?
 Nutritional supplements: Is it worth the expense to take nutritional supplements? (e.g. Vitamin
supplements, melatonin, anti-oxidants, etc.)
 Genetic Testing and Screening: Should widespread testing for cystic fibrosis (or other genetic
diseases) be implemented?
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Appendix A: How to graph scientific data?
Often the first step in analyzing the results of an experiment is the presentation of the
data in the form of a graph. A graph is a visual representation of the data, which assists in
bringing out and finding the possible relationship(s) between the independent and dependent
variables. Examination of a graph makes it much easier to see the effect the independent
variable has on the dependent variable(s).
Accurate and clearly constructed graphs will assist in the interpretation and
communication of your data, and when presenting a well-documented argument supporting
or falsifying your hypothesis in the final steps of a scientific investigation. All graphs should
be easy to interpret and labeled fully. The following guidelines will help you construct a
proper graph.
Graphing tips
1) Use graph paper of a high quality.
2) A ruler should be used to draw axes and to plot data neatly and accurately.
3) Always graph the independent variable on the x-axis (horizontal axis), and the dependent
variable on the y-axis (vertical axis).
4) The scales of the axes should be adjusted so that the graph fills the page as much as possible.
The axes often, but not always, start at zero. Choose your intervals and scales to maximize the
use of the graph paper. Intervals should be logically spaced and easy to interpret when
analyzing the graph (e.g. intervals of 1’s, 5’s, or 10’s are easily interpreted, but non-integer
intervals (e.g. 3.25’s, 2.33’s, etc.) are not. To avoid producing a graph with a lot of wasted
space a discontinuous scale is recommended for one or both scales if the first data point is a
large number. Simply add two tic marks between the zero and your lowest number on one or
both axes to show that the scale has changed.
5) Label both axes to indicate the variable and the units of measure. Write the specific name of
the variable. Do not label the axes as the dependent variable and independent variable.
Include a legend if different colors are used to indicate different aspects of the experiment.
6) Graphs (along with drawings and diagrams) are called figures and are numbered consecutively
throughout a lab report or scientific paper. Each figure is given a number, a title that
describes contents, and an informative sentence giving enough information for the figure to
be understandable apart from the text (e.g. Figure 1 Temperature and Leaf Color Change
The relationship between the change in vine maple leaf color and changes in ambient
temperature). Generally, this information is placed below the figure or graph.
7) Choose the type of graph that best presents your data. Line and bar graphs are the most
common. The choice of graph type depends on the nature of the variable being graphed.
Line Graphs are used to graph data that only involves continuous variables. A continuous
variable is capable of having values over a continuous range (i.e. anywhere between those that were
measured in the experiment). For example, pulse rate, temperature, time, concentration, pH, etc. are
all examples of continuous variables (Figure 1).
Making Line Graphs
1) Plot data as separate points. Make each point as fine as possible and then surround each
data point with a small circle. If more than one set of data is plotted on the same graph,
distinguish each set by using circles, boxes, triangles, etc.
2) Generally, do not connect the data points dot to dot. Draw smooth curves, or if there appears
to be a linear relationship between the two variables, draw a line of best fit.
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3) If more than one set of data is plotted on a graph, provide a key of legend to indicate identify
each set. Label the graph as a figure; give it an informative title, and a descriptive sentence.
Figure 1 pH Effects on Lactase Note that a line graph was used to graph the data because both variables, pH
and the rate of digestion, are continuous variables.
Bar Graphs are used if the data involves a discrete variable (non-continuous variable). A
discrete variable, unlike a continuous variable, cannot have intermediate values between those
measured. For example, a bar graph (Figure 2) would be used to plot the data in an experiment
involving the determination of chlorophyll concentration (chlorophyll concentration is a continuous
variable) found in the leaves of different tree species (The discrete variable is the species of tree). Bar
graphs are constructed using the same principles as for line graphs, except that the vertical bars are
drawn in a series along the horizontal axis (i.e. x-axis). In the example below, a bar graph was used to
graph the data because tree species is a discrete variable since it is impossible to have a value or
species between those used.
Figure 2 Chlorophyll Concentrations The chlorophyll concentrations were measured mg/grams of leaf in
the leaves of three tree species.
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Appendix B: How to convert to the metric system?
Larger Unit
Tips for Metric Conversion:
1. When converting from a larger
1 km = 103 m = 1000 m
unit of measure to a smaller unit
of measure (e.g. from kilometers,
1 m = 100 m
km to meters, m) move the
decimal to the right. This results
-2
1 cm = 10 m = 0.01 m
in a larger number.
2. When converting from a smaller
1 mm = 10-3 m = 0.001 m
unit of measure to a larger unit of
measure (e.g. from m to km)
1 m = 10-6 m = 0.000001 m
move the decimal to the left.
This results in a smaller number.
1 nm = 10-9 m = 0.000000001 m 3. See below to determine how
many decimal places to move.
Smaller Unit
Figure 4 Metric System Relationships This figure shows the conversion relationships of common
metric measurements.
Determination of the number of decimal places to Move
The number of decimal places moved is equal to the magnitude difference between the
exponents of the two units of measure. The exponent scale below illustrates the relationship between
exponents.
-6
m
-5
-4
-3
mm
-2 -1
cm
0
m
1
2
3
km
4
Examples
1. 9.25 km =?? mm
 km to mm is a large to small unit conversion, so the decimal must move to the right.
 The magnitude of difference between the exponents of each unit of measure is 6:
km = 103, mm = 10-3; Therefore: 3 - (-3) = 6
 So the decimal place moves to the right six places giving 9,250,000 mm (or 9.25 x 106 mm)
2. 450 µm =?? mm
 µm to mm is a small to large unit conversion, so the decimal must move to the left.
 The magnitude of difference between the exponents of each unit of measure is 3:
µm = 10-6, mm = 10-3; Therefore: -3 - (-6) = 3
 So the decimal place moves to the left three places giving 0.45 mm
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Appendix C: How to write scientific papers?
Scientific papers follow a specific format in order to separate the different aspects of any study or
experiment. This allows for lucid presentation of ideas, and facilitates critical evaluation of papers.
The format below is not set in stone; it is meant to provide a structural guideline for writing your
papers. See journals in any field of environmental science for examples of variations on this nearuniversal scientific writing template (note that Science and Nature are exceptions to this rule). You
will find that writing this way may take some getting used to, but helps you to present your work more
clearly and perhaps even to think more clearly about the work you have done.
All papers should be typed, double-spaced (except the abstract), with at least one-inch margins
on all sides. Any statements not original to you should be properly cited in the text using the scientific
citation style, and listed in the section called Literature Cited at the end of your paper in the style
below.
Title Page
The title page is the first page of the paper and should contain the following:
 An informative title
 The full names of all group members
 Course number
 Instructor’s name
 Your lab day and time
 Due date for the paper
A good title is informative, i.e. it summarizes as specifically, accurately, and concisely as possible
what the paper is about. For example, if you were investigating the effect of temperature on the
feeding preferences of a certain type of caterpillar found on tobacco plants, acceptable titles might be
“Effect of Temperature on the Feeding Preferences of the Tobacco Hornworm Larvae, Manduca
sexta”, or “Does Temperature Influence which Diet the Tobacco Hornworm Larvae, Manduca sexta,
will Select? The following titles would be uninformative and too general: “Effect of Temperature on
Caterpillars”; “How Temperature Affects the Tobacco Hornworm Larvae, Manduca sexta”; “What is
the Preferred Diet of the Tobacco Hornworm, Manduca sexta?”
Abstract (optional for this class)
Present a concise statement of the questions, general procedure, basic findings, and main
conclusions. This is a brief, all-encompassing section summarizing what you discuss in the rest of the
paper, and should be written last, after you know what you have said! This section only should be
written as one single-spaced paragraph not to exceed 200 words.
Introduction
Present a background for the work you are doing and put it into an appropriate context (e.g.
scientific principles, environmental issues, etc.). Cite any references in the text you used as sources
for your background Information. What questions are you asking in your study? What organisms or
ideas were studied and why are they interesting or relevant for your study? Identify the subject(s) and
clearly state the hypotheses of your work. Tell the reader why he/she should keep reading and why
what you are about to present is interesting. Briefly state your general approach or methods (e.g.
experimental, observational, computer simulation, a combination of these, etc.) as a lead-in to the
next section. As a general rule the introduction section should be about the length of the discussion
section. Most introductions are designed to compel the reader to read the article not bog down the
reader with to much detail.
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Materials and Methods
Describe the equipment used in your study. Explain the methods in paragraph format used to
answer your questions in sufficient detail that someone else could repeat the work. Cite alreadypublished methods (e.g. lab or computer manual or handouts) but describe any modifications,
avoiding lengthy explanations. Briefly explain the relevance of the methods to the questions you
introduced above (e.g. "to determine if light limited algal growth, I measured...."). This section may be
subdivided (with subheadings) to describe distinct parts of your study or experiment. If appropriate,
include a description of the statistical methods you used in your analysis.
Results
Present in an orderly fashion what you discovered in this study (this may be subdivided as
above). Describe the results in text and if appropriate, present them also as tables or graphs, by
referring to the table of graph by number in the text. Graphs and tables should be numbered and
titled for clear reference in your results and discussion sections. Be sure to label both axes of all
graphs (e.g. growth rate, height, number of species, water consumed, etc.) and include units (e.g.
meters, gallons, seconds, etc.). Graphs should be understandable on their own without reading the
text, and be accompanied by a brief, informative caption explaining what each graph or table shows.
In referring to your results, avoid phrases like 'Table 1 shows the rate at which students fall asleep in
class as a function of the time of day that class is taught”. Rather, write: "Students fall asleep in class
twice as frequently during evening than day classes (Table 1)”. The results section should avoid
discussion and speculation. This is the place to tell the reader what you found out, not what it means.
Discussion
Explain your results in detail, speculating on trends, possible causes, and conclusions. What
conclusion can be drawn from your results? Present major findings first, then minor ones, including
any natural history descriptions or other background information that may not be necessary, but
would help fill in the bigger picture. Compare your results with those of other workers and cite the
references you used for comparisons. Put your results in the context of the hypotheses and other
material in your Introduction. Where do your data fit in to the big picture? What problems arose in
your study and how could they be avoided in the future? If your results were not consistent with the
predictions you made (what you thought would happen before you did your study, based on a specific
hypothesis or other background information) why do you think this is the case? Explain any
exceptional aspects of your data or unexpected results. Examine your results for possible error or
bias. Refer to your results to solidify your ideas.
Where does your study lead? Here you may recommend further work that could augment the
results of the study you have presented. What are your major conclusions? These ideas are what
make a discussion interesting and thought provoking for your reader.
Acknowledgements (optional)
In this section you should thank anyone who has helped you in any aspect of this project, funding
agency, or whomever. (e.g. "I thank Claudia Mills for help with the computer program, Milo Lee for
reading my electric meter, Al Gore for counting cockroaches, and Mike Kalton for valuable discussions
of the Ideas underlying these data.).
Literature Cited
In this section you list only the sources that you have actually cited in the paper, either as general
background or specific examples. It is not an exhaustive bibliography. Use the citation style below.
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How to Cite Sources in Scientific Writing
In-Text Citations
There are typically not footnotes or endnotes in scientific writing as there are in humanities and
the social sciences. Instead, all citations occur in the text in parenthetical format, with the author(s)
and date of publication. Use the following as an example:
Parsons (1996) found that naked mole rats dig six times faster in desert soils than
dung beetles dig through dung.
Alternatively,
Naked mole rats dig six times faster in desert soils than dung beetles dig through dung.
(Parsons 1996).
Or,
Naked mole rats dig six times faster in desert soils than dung beetles dig through dung. (1)
This notation (1) refers the reader to the bibliography page which is sequentially numbered and each
citation from this author is referred to in this fashion.
It's that simple! Be sure to list any sources you cite in the text in the Literature Cited section, and
only those that you cite.
As a rule of thumb, if there is more than one author of a source, simply use the first author's last
name, followed by et al. (e.g. [Parsons et al. 1996]). This is Latin for "and others". The complete list of
authors will appear in the full citation at the end of your paper.
Literature Cited or Bibliography
Your Literature Cited should appear in alphabetical order by first author, and by year if there are
multiple sources by the same author(s). Underline journal and book titles, but not the titles of
individual articles in journals or edited (multi-authored) books. Use the following as examples for
citing various kinds of sources (with thanks to M. Weis):
Citing Journal and Magazine Articles
 Format
Author(s). Publication year. Article title. Journal title volume: pages.
 Examples
Smith, D.C. and J. Van Buskirk. 1995. Phenotypic design, plasticity and
ecological performance in two tadpole species. American Naturalist 145: 211-233.
Ahlberg, P.E. 1990. Glimpsing the hidden majority. Nature 344: 23.
Epel, D. and R. Steinhardt. 1974. Activation of sea-urchin eggs by a calcium
ionophore. Proc. Natl. Acad. Sci. (USA) 71: 1915-1919.
Citing Sites on the Internet
Often electronic sources are a challenge to cite because they often lack critical information. You
should do your best to provide as much of the following as possible. The complete web address should
be presented so that anyone else could easily visit the same website.
Attempt to include the following elements (not all elements appear on all Web pages):
1. author(s) (last name, first initial)
2. date created or updated
3. title of the page
4. title of the complete web site (if different from the page)
5. URL (full web address)
6. the date accessed.
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 Format
Author's last name, First initial. (date created or updated). Title of the page. Title
of the complete site. [Online]. Available: http://full.web.address. [Date accessed].
 Example
Hammett, P. (1997). Evaluating web resources. Ruben Salazar Library, Sonoma
State University. [Online]. Available:
http://libweb.sonoma.edu/Resources/eval.html. [March 29, 1997].
Citing Books
 Format
Author(s). Publication year. Book Title, edition if known. Publisher, Place
of publication, number of pages.
 Example
Purves, W.K., G.H. Orians and H.C. Heller. 1995. Life: The Science of
Biology, 4th edition. Sinauer Associates, Inc., Sunderland, MA, 1195 pp.
Citing Book Chapters
 Format
Author(s). Publication year. Chapter title. In: Book title (Author(s)/editors, first
name first) Place of publication, pages.
 Example
Jones, C.G. and J.S. Coleman. 1991. Plant stress and insect herbivory:
Toward an integrated perspective. In: Responses of Plants to Multiple Stresses
(H.A. Mooney,W.E. Winner & E.J. Pell, editors), Academic Press, San Diego, pp.
249-280.
Citing Newspaper Articles
 Format
Author(s). Date (Year/Month/Day). Article title. Newspaper title Section: Page:
Column.
 Example
Bishop, J. E. 1982 November 4. Do flies spread ills or is that claim merely a
bugaboo? The Wall Street Journal 1: 1: 4.
Williams, M. 1997 January 5. Teaching the net. Seattle Times C: 1: 2.
Citing Newspaper Articles with no Identifiable Author
 Format
Anonymous. Date (Year/Month/Day). Article title. Newspaper title Section: page:
column.
 Example
Anonymous. 1977 September 6. Puffin, a rare seabird, returns to where many were
killed. The New York Times 3:28:1.
Citing a Video
 Format
Title of video (videocassette). editor or director. Producer’s name, producer.
[Location of Production]: Organization responsible for production, Year.
 Example
New horizons in esthetic dentistry (videocassette). Wood, R. M., editor.
Visualeyes Productions, producer. [Chicago] : Chicago Dental Society, 1989.
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Citing a Government report
 Format
Author/Agency (if no author). Publication year. Title. Publisher, Place of
publication, number of pages.
 Example
Mitchell, R.G., N.E. Johnson and K.H. Wright. 1974. Susceptibility of 10 spruce
species and hybrids to the white pine weevil (= Sitka spruce weevil) in the Pacific
Northwest. PNW-225. U.S. Department of Agriculture Forest Service,
Washington, D.C., 8 pp.
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Appendix D: How to Draw or Make a Scientific Plate or Drawing?
Why draw?
It is not the objective of this course to “make you into an artist” or even to have you produce
drawings of professional quality, even though many of you are capable of such work. It is expected,
however, that each student will produce clear and accurate drawings of the organisms and structures
that she/he actually observes. Drawing is a tool that will help you focus on what you are really seeing
at deeper level that maybe you have seen before.
Drawing is a tool that will draw you closer to the body plans of organisms and maybe for the first
time open up to you a whole new world. Seeing things for the first time the way they really are is very
exciting. It’s amazing how many times we look at something but don’t really see it. Drawing “makes it
so.”
Drawing will make the vocabulary of science more tangible and available to you. What is bilateral
symmetry in the sagittal plane of the anterior section of pineal glands of a frog really mean? Does it
mean something special for frog growth and development or is it just an accident. The metaphase
plate formed during mitosis in root tips can actually be visualized bringing the boring humdrum words
from the text into a vibrant exciting reality, right now!
Drawing will show you how things work. The functionality of different parts will be revealed. As
you look at a filter feeding daphnia filtering it’s dinner from its aqueous environment you will discover
why it is shaped the way it is shaped and “oh yeah” what those parts are for. Those parts will become
more than just parts to you.
You will find, as the quarter progresses that it becomes easier to make good, acceptable drawings
as you develop your powers of observation and become familiar with certain basic drawing
techniques. You will also discover that the preparation of these drawings is an excellent way to study
specimens, for in order to make acceptable drawings you must observe in detail the form, structure,
and interrelation of parts of the object being drawn. Your drawing will record observations clearly and
concisely that would require several pages of descriptions to duplicate. Further, you will find your
drawings to be excellent review materials, especially since many of the living organisms studied in the
laboratory will available to you only during certain laboratory periods, and your drawings will be the
only record of personal observations that you have.
You will be permitted to use these drawings for study purpose. Make all your drawings directly
from the specimens or slides and complete each drawing in the laboratory. Do not merely copy
drawings of your neighbor or plates from the textbook. Textbook illustrations are often idealized, or
may represent different species from those you are studying in the laboratory and thus do not look
like your specimen.
Procedure
1. Before you do anything else, study the material to be drawn. From what angle are you going
to prepare the drawing? Frequently, the laboratory instructions often direct you to prepare a
drawing from a specific viewpoint, such as a cross section of the sagittal plane of the anterior
section of a pineal gland. Often times the angle that is chosen depends on specific functions
to be studied or maybe just a key feature used in identification of the species.
2. Notice the outline of the entire object to be drawn?
3. Notice what structures are present (how many, how many different kinds).
4. Notice how the structures are interconnected or interrelated?
5. Notice everything that might help you draw the critter or critter part that is in front of you,
like; folds and creases connection shapes holes, hairs, and hides et cetra, et cetra, et cetra
6. After you have observed in detail the object to be drawn, you may begin the drawing. At first
you may find the following steps helpful, so do not hesitate to refer to this section as you
prepare your drawings.
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7. Determine the size that you are going to make the drawing. The size will be determined by
the size of the drawing paper (usually 8.5x11) and the shape of the object drawn. Remember
that the completed drawing will have labels so be sure to leave enough space so that the
finished drawing will not look crowded. The amount of magnification, or reduction, of your
drawing from the actual size of the specimen is always indicated as part of the title (e.g. x1/2
or x3).
8. Determine how you are going to place the drawing on the paper. Through convention, either
the anterior end (at or toward the head) or the dorsal surface (at or toward the back) is placed
toward the top of the drawing.
9. Construct, by measuring the specimen with your millimeter scale and reducing or enlarging to
appropriate lengths, any guide lines that you may find useful. Such guide lines should be
lightly made and erased when the drawing is completed. In drawing bilaterally symmetrical
structures you may find it convenient to draw a median guide line.
10. Construct outlines marking borders of the entire specimen to be drawn. At first these should
be thin, light lines until you have worked out the proper form and proportions. The finished
lines should be definite and continuous. Where two lines meet or cross, make them
continuous, not with one or more ends showing. To show structures lying beneath other
structures, use dotted lines. All light sketch lines should be erased. Fill in the details in their
proper place in the outline.
11. The dedicated drawer will use drawing pencils of medium harness (3H or 4H). Softer leads will
smear, and harder leads tend to cut the drawing paper. Usually do not use ink or colored
pencils unless so instructed or as a final step in the preparation. Since no biological structures
in nature ever have perfectly straight borders, do not use a rule to make any lines in your
finished drawing.
12. In general, do not use shading. When necessary to do shading, use stippling only. Stippling
involves making small dots with the tip of the pencil while holding the pencil at right angles to
the paper. In stippled drawings ridges and prominences are indicated by the absence of
stippling; depressions and lower parts of curved surfaces are indicated by evenly spaced dots
of uniform size placed progressively closer together as the depression becomes deeper.
13. Sometimes an insert to show a close-up of a particular part of the specimen is included on the
plate. This is done to show greater detail of the critter to emphasize structure function
relationships or key features for identification. The same process for drawing the entire
specimen should be applied to drawing the structures that appear on the insert.
14. Label the completed drawing. The labels consist of the student identification information,
(name, section, date, et cetra), the plate number and title, and the names of the structures or
parts illustrated. The student identification information will be placed in the upper right hand
corner of the plate; the plate number and title centered at the bottom of the page; and the
names of the parts placed in vertical column, parallel to each other and to the top and bottom
of the page, to the right of the drawing. Solid straight lines should lead from the label to the
structure. All labels should be neatly printed.
15. Make a legend that would indicate the actual size of the specimen in the drawing. this is
called a scale. For example the distance between Los Angeles, CA and Seattle, WA on some
maps may be only one inch but by reading the scale of the map one inch is actually about
3,000 miles. By attaching a scale to the drawing the reader is given a perspective from which
to interpret the relative size of the specimen.
Avoid the following common mistakes in drawing;
1. Making the drawings to diagrammatic–they should be good representations of the actual
structures as seen in your specimen.
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2. Poorly proportioned–the various parts and the whole should show the same size relationship
that they have in the specimen.
3. Making the drawings too small
4. Incomplete or inaccurate labels.
5. Indefinite or “fuzzy lines.”
6. Coarse, heavy lines or uneven lines resulting from use of dull pencils or from careless work.
7. Unnecessary lines or lines without meaning.
Voila, a drawing that you can treasure for the rest of your life and aid you in the successful
completion of this class. YES! Will it be easy or totally rad at first. For some students yes, for others
not so much. But if you stick to it things will happen, you will start to understand things about the
world around you that you never noticed before. MENTAL SAFARI, WOW!! You will be doing what
you came here for, learning.
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Appendix E: How to make an Oral presentation?
Oral presentations are an important means of presenting the results of your research or
literature investigations to other scientists. We will use the same format that biologists use to present
our literature search based papers at colleges and universities (where they are also known as
“seminars") and for presentations when they attend national meetings of scientific organizations. As
such, you will gain experience with a standard oral report format that you will use throughout your
career as a biologist.
Everyone realizes it can be uncomfortable to speak in front of a group, and it is especially hard
the first time. You’ll make some mistakes—that’s part of the learning process. Please realize that any
questions that you are asked by your classmates or instructor are not meant to be taken personally.
So, don’t be afraid of questions and comments—they are intended to further our understanding of
your literature investigation. The comments and questions made by one’s peers are important tools
used by the scientific community to assist in evaluating the validity of a researcher’s experimental
design, results, and conclusions.
The best preparation for presentations is to understand what you did, especially why you chose
the topic you research. Was there some outside influence say a family history with the topic or
maybe it was some topic that peaked your interest in a news story? Whatever the reason remember
that you are the “expert” in terms of our classroom, so speak confidently and calmly about your topic.
Divide your presentation minutes into the following sections as you go about designing your talk:
1. Introduction
This portion should be brief. Use these sentences to inform the audience in an overview about
what topic or issue your paper was trying to convey. Be sure to mention why you wrote your paper
and how it related to the other papers of your group. In terms of a power point this should be at most
two or three slides of mainly pictures keep the text at a bare minimum otherwise we spend all our
time reading and not listening.
2. Body
The body should be a clear and concise display of what you found. Your information should be
distilled down to the important facts and ideas about your aspect of the group’s topic. Use slides with
supporting pictures to present the major trends ideas about your topic. Be sure to note whether each
trend was significant or not significant. Make sure slides are easy to read and interpret, especially
from a distance. These slides should be simple and straight forward . Keep each slide or group of
slides with a minimum of text (that comes from YOU!) but have interesting pictures, graphs, or
figures.
3. Closing
Return to the question you posed in the introduction and summarize what you have just covered
in your presentation. Make a transition power point slide to bridge your aspect of the topic to the
next speaker.
Things to Consider while Preparing for your Presentation
 Each person in your group must speak during the presentation.
 Due to time constraints your group’s presentation should last no more than 20 minutes. Plan to
speak for 12 - 15 minutes so we will have 3 - 5 min. for questions and discussion with the rest of the
class.
 Visual aids are critical to the success of your presentation. Use PowerPoint slides to present
important questions, results, and conclusions. Practice your presentation a few times alone and
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together to ensure that your presentation flows from beginning to end within the time frame.
Combine each individual presentation into one seamless presentation in one file.
 Check with your instructor if you need special equipment for your presentation before the day your
group will be presenting and not the day of your presentation .
 You may find it helpful to keep the following questions in mind while preparing your presentation:
 Do you clearly state the question you are trying to answer?
 Is it clear what you did to try and answer your question?
 Do you convey the information if a clear concise manner?
Delivery of the Presentation
 Speak loud and clear. Project your voice to the back of the room over the ambient noise of the
room.
 Interact with your visual aids by pointing to key features as you describe them.
 Try to maintain eye contact with the audience as much as possible. Remember your are the expert
in the classroom about your topic.
 Avoid distracting behaviors, clothes, and accessories, For example, do not chew gum, lean on the
podium, twirl your hair, or wear hats or distracting clothing
Evaluation of the Presentation
Your group’s presentation will be critiqued in two ways, by your classmates and by your instructor.
Your classmates will not grade you — these comments are to help you. Each person in class will
review every group by responding to the following two questions:
 What were the strengths of this group?
 What improvements could be made by this group?
Classmate Evaluation
When making comments about the presentation of others, keep in mind the following:
 Did each speaker cover the information contained in the Introduction, Body, and Closing.
 Was the presentation balanced among all speakers
 Did the presentation flow easily from speaker to speaker
 Were they all able to speak clearly and loud enough from the folks in the back to hear.
Instructor Evaluation
In addition to all of the categories above, your instructor will be interested in the following:
 How clearly you presented your material
 Whether you display understanding of what you did and why you did it, and if the data support your
conclusions.
 You will receive an individual score. Use the rubric in your syllabus for direction.
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Appendix F: How to search the Literature?
Not all articles are created equally! The most reliable articles are from scientific journals and from
the individual who conducted the study. There are 1000’s of scientific journals in the world that deal
with the many fields of science. Journals publish the results of original scientific research. When
scientists believe they have something of value to communicate to other scientists, they submit their
work for publication. Peers that are associated with a particular society will then review it. Societies
usually consist of scientists associated with universities and colleges around the world. If the research
is judged to be of high quality and of value, it will be published in the society’s journal. (Note: The
Audubon Society, the National Geographic Society, Wikipedia, nor the Wall Street Journal are scientific
journals, reputable but not scientific!)
Although much of the information in a scientific journal may be quite technical, you should be
able to glean some information from it. After journals, the next best source is a popular science
magazine (e.g. Scientific American, Science News, American Scientist, Discover, etc.). Since these
periodicals are devoted to science, they tend to be better sources of information than general
magazines such as Time or Newsweek. General popular references such as newspapers and general
magazines may sometimes be helpful but don’t limit yourself to these since the information may be of
unreliable quality and/or incomplete.
There at several useful databases to periodicals available for your use. Some databases require
the use of a computer in the Information Commons upstairs in the Holman Library (e.g. InfoTrac
Health Index, an excellent database for our purposes); others are accessible from any campus
computer connected to the GRCC network (e.g. ProQuest Direct). The one we will have you use is
ProQuest Direct.
How to find articles in ProQuest:
 Start Netscape Navigator or Microsoft Internet Explorer and go to Holman Library's Research
Data Base Links. You should find ProQuest Direct on the list of databases (it's the second one
from the top). Now click on Search ProQuest Direct.
 Another way to get to ProQuest: Go to the Holman Library’s home page at
http://www.greenriver.edu/library/. Under “Research Tools” click on the “Databases” link. You
should find ProQuest Direct on the list of databases (it's the second one from the top). Now
click on Search ProQuest Direct.
 You are now on the Select Database screen in ProQuest. If you want to restrict your search to
Peer Reviewed Articles (i.e. articles in scientific journals), then before you type in your search
terms, find where it says "Peer Reviewed" on the screen, and check the box next to this. This
will limit your search to Peer Reviewed articles.
 Type your search criteria in the search box and click the "Search" button.
Don't forget to cite each of your articles correctly by following the guidelines for citing references
in Appendix C.
How to find books:
 Start Netscape Navigator or Microsoft Internet Explorer and go to Holman Library's home page
at http://www.greenriver.edu/library/
 Click on the "Online Catalog" link.
 Click on the "Basic Search" link.
 Type your search in the Search For: box, select "Keyword" in the Search In: box, and then click
the "Search" button.
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Unable to find a relevant book in the Holman Library, try searching at other libraries in the area by
following one or more of the links at the library site. If you are not successful finding a book related to
your topic in the Holman Library or the other libraries in the area try using ProQuest and restrict your
search to books. Still having problems finding a book related to your topic? Try searching
amazon.com. If possible, cut and paste into your Word document a short summary, description,
abstract, etc. about a book related to your topic. When citing the book you found within your Word
document be sure to follow the guidelines in Appendix B.
Excellent Biology Web Sites—Compiled by Ken Marr, Retired from GRCC Biology Dept.
 http://www.google.com (One of the best search engines around!)
 http://www.scirus.com (One of the search engines used by scientists to seek other science works)
 http://www.sciam.com/ (Scientific American magazine: An extremely high quality science magazine
containing articles written by experts in their field of study—One of my favorites)
 http://www.newscientist.com (A high quality science magazine with a biological sciences focus—
Another one of my favorites!)
 http://www.scicentral.com/ (An excellent resource for any area of science and technology—one of
my favorites—I receive weekly notices of recent papers that are of interest to me—this service is
free.)
 http://www.sciencenews.com (A high quality science magazine with a biological sciences focus)
 http://ublib.buffalo.edu/libraries/units/sel/collections/ejournal2.html
(Links to electronic versions of over 900 journals on the Web, covering all areas of science and
technology. The content of these electronic journals varies, from full text to table of contents for the
majority of journals.)
 http://biochemlinks.com/bclinks/bclinks.cfm (A guide with links to some of the best biological
sciences and chemistry sites on the web-- including some journals and science related magazines;
Includes free science related clip art and links to free clip art)
 http://www.nejm.org/content/index.asp (New England Journal of Medicine—one of the world’s
premier medical journals)
 http://www.ncbi.nlm.nih.gov/Omim/ (Online Mendelian Inheritance in Man: OMIN is a database
that contains summaries about every human gene so far investigated. You can obtain the official
gene name, the official abbreviation, the gene map locus (where the gene is located on a certain
chromosome), and information about the gene. Moreover, you can click on buttons that will give
you articles in Medline (a database for medically related journals), a list of genes near the one you
are interested in (a gene map), DNA sequences (DNA), and other information. Another useful site is
Genbank at http://www.ncbi.nlm.nih.gov/
 http://www.nlm.nih.gov/ (Medline: A database of the National Library of Medicine, part of the
National Institutes of Health (NIH). This the largest collection of medical information in the world,
containing more than 9 million references from medical journals from all over the world.
 http://cancer.med.upenn.edu/ (Oncolink: the first of its kind on the Internet—an excellent site that
disseminates cutting edge information relevant to the field of oncology (cancer research). Aims to
educate health care personnel, patients, and other interested parties.)
 http://www.quackwatch.com/ (“A Guide to Health Fraud, Quackery, and Intelligent Decisions;” An
interesting site that helps one to distinguish between legitimate healthcare treatments and
quackery—The physician responsible for this site has written many books and scientific papers over
the years. His ideas are very mainstream—perhaps too mainstream? Some of the views expressed
may not be totally objective. At times he has quite harsh comments concerning “alternative
medicine.”)
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 http://www.audubon.org/ (Audubon is a high quality magazine that deals with environmental
issues and wildlife conservation)
 http://www.biomednet.com/hmsbeagle (This is one of my favorites—A weekly publication that
covers many of the more important advances in the biological sciences. Requires membership—
which is free as is an email subscription)  home page of the H.M.S. beagle:
http://www.biomednet.com/home
 http://genetics.nature.com/ (a journal produced by Nature…Gives you access to the contents, but
you must pay to see the text of the articles—Available for free in the libraries of most research
universities)
 http://www.nature.com/ (Nature is a very prestigious scientific journal. This site gives you access to
the contents. Although some parts of the site are free, you must pay to see the text of the articles—
but they are available for free in the libraries of most research universities)
 http://flybase.bio.indiana.edu/ (FlyBase: a comprehensive searchable database for information on
the genetics and molecular biology of Drosophila—the fruit fly)
 http://www.exploratorium.edu/exhibits/mutant_flies/mutant_flies.html (Has pictures and
descriptions of mutant fruit flies)
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Appendix G: Classification of the Animal & Plant Kingdoms
Kingdom/Phylum Highlights
Kingdom Animalia
1. General Characteristics
a. Animals show a variance in form and structure but hold some characteristics in
common such as mobility, dedicated to sexual reproduction, heterotrophic, and
multi-cellular.
2. Major Taxa
a. Phylum Porifera (Pore Bearer) - the sponges (@ 9,000 sp)
 Complexity Level: Cellular level of Organization (Intracellular digestion). No
tissues or organs. No head, mouth, gut, nervous system, sense organs. The
blob that doesn't seem to care.
 Filter feeders (choanocytes and pores). On making waves, or at least
drawing a current.
 Having only one opening makes for problems. (Osculum).
 Asymmetry and/or Radial symmetry (like the spokes of a wheel) - or on
living without a head.
 Body wall made up of spongin + spicules. (75% produce chemical toxins in
walls)
b. Phylum Cnidaria - animals with stinging cells. (@9,000 sp)
 Complexity Level: Tissue level of Organization (Extracellular digestion)
Getting organized. Tissue comprised of groups of specialized cells: Nerve
cells for coordination, Muscle cells for getting around and hauling in food,
Gut cells for working over the food, and, Nematocysts (stinging cells).
 Mesoglea sandwich - Two germ layers. Only two layers of cells - or having
only an inside and outside. (Ectoderm and Endoderm)
 Blind sac body plan - gastrovascular cavity. Having only one opening makes
for problems.
 Radial symmetry (like the spokes of a wheel) - or on living without a head.
 Polymorphism: medusa and polyp body types.
 Some different kinds: Sea anemones, Hydra, Colonial Hydrozoans, Jellyfish.
c. Phylum Ctenophora - comb jellies, sea gooseberries, or sea walnuts
 Complexity Level: Between cellular and tissue.
 Active feeders with a soft body.
 Shaped like a cup or upside down bell with eight rows of cilia beating from
the base to the cup opening.
 Bi-radial symmetry.
 Only one intake and output opening
 Hermaphroditic
d. Phylum Platyhelminthes - the flat worms. (@20,000 sp)
 Complexity Level: Organ systems
 Definite polarity and Bilateral symmetry.
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e.
f.
g.
h.
 Three germ layers - add mesoderm. More than two layers of cells makes
possible some definite organs, not mere tissues, and other big deals.
 But alas, the food gathering apparatus still has only one opening. (Tubular
pharynx).
 No body cavity around the gut - Acoelomate.
 Flat, generally thin, unsegmented.
 Some different kinds: Planaria, leafworms, flukes, and tapeworms.
Phylum Nemertea - the ribbon worms
 Complexity Level: Organ systems
 Definite polarity and Bilateral symmetry.
 Tube within a tube body plan. One way traffic - or a mouth, a gut, and an
anus forming a complete system, but no body cavity around the gut Acoelomate.
 One way traffic - or a mouth, a gut, and an anus forming a complete system.
 Closed circulatory system, most primitive group with a circulatory system.
 Special body cavity (rhynchocoel) which contains a protractible proboscis.
Phylum Nematoda - round worms (>12,000 and maybe several more)
 Complexity Level: Organ System. Groups of organs now working together in
a system - the ultimate in design.
 Tube within a tube body plan. One way traffic - or a mouth, a gut, and an
anus forming a complete system.
 Pseudocoelomate - fluid filled body cavity between the digestive tract and
the body wall - derived from blastocoel (fluid filled cavity of blastula). Not
lined with peritoneum.
 Bilateral symmetry.
Numerous modifications of the animal way of life are illustrated by a variety of
phyla at about the same level of development as the round worms.
 Phylum Nematomorpha - horsehair worms
 Phylum Acanthocephala - spiny-headed worms
 Phylum Gastrotricha - spiny bodied worms
 Phylum Rotifera - wheel worms
 Phylum Bryozoa - moss animals
 Phylum Brachiopoda - lamp shells
 Phylum Phoronida - tentacle worms
 Phylum Chaetognatha - arrow worms
 Phylum Sipunculoidea - peanut worms
Phylum Mollusca - of shells and feet, and things like that and a mantle to cover
their guts (>100,000 sp) (@ 60,000 fossil sp)
 Complexity Level: Organ System. (Protostomes).
 Body - Soft with true coelom (Eucoelomate).
 Plan - Muscular Foot, Viscera, and Mantle. (Mantle = specialized dorsal body
wall which covers the internal organs and secretes the shell)
 Open circulatory system w/hemocoel.
 Bilateral symmetry or secondarily asymmetrical.
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i.
j.
k.
l.
 Unsegmented and many with a shell.
 Some different kinds:
 Class Polyplacophora (Amphineura) - chitons. Eight plates of armor.
 Class Bivalvia - Two shells and a foot for digging.
 Class Gastropoda (meaning stomach foot). On sliding around on your
belly.
 Class Scaphopoda - tooth shells.
 Class Cephalopoda (meaning head foot). Tentacles and monsters of the
deep.
Phylum Annelida - segmented worms. Tidy little compartments. (15,000 sp)
 Complexity Level: Organ-system level of development is now clearly
established. (Protostomes)
 Beginning of segmentation, an event which allows various regions of the
body to specialize. Segmented: body is arranged in a repetitive linear
sequence of similar parts. Also called metamerism (each segment called a
metamere or somite) May be external and/or internal. Segments divided
externally by grooves or serial repetition of appendages.
 Eucoelomate.
 Setae - small external bristles (except leeches). An indication of appendages
(arms and legs).
 Bilateral symmetry.
 Some different kinds: Earthworms, Clamworms, Leeches.
Phylum Tardigrada - little water bear.
Phylum Onychophora Peripatus. The missing link?
Phylum Arthropoda - animals with jointed legs. Being most popular. (1
million sp. described > 50 million more "unknown")
 Complexity Level: Organ-system level (Protostomes)
 Segmented - Jointed appendages (specialized body regions called Tagma =
Head, thorax, abdomen)
 Eucoelomate.
 Exoskeleton (chitinous).
 Bilateral symmetry.
 Why so successful?
 Highly specialized segmentation.
 Extreme polarity, allowing for such advanced coordination as flight.
 Striated (rather than smooth) muscle, allowing for rapid movement.
 Jointed appendages showing all sorts of special structural adaptations.
 All systems now present, including a skeletal system.
 Primitive intelligence and social instincts in some.
 Tremendous rates of reproduction.
 Some different kinds:
 Class Diplopoda - millipedes. Thousand legged critters.
 Class Chilopoda - centipedes.
 Class Crustacea - five pair of walking legs (crabs, shrimp, pill bugs)
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 Class Arachnida - spiders, etc. Four pair of walking legs.
 Class Insecta - three pair of legs and sometimes wings too (insects)
m. Phylum Echinodermata - Spiny-skinned animals. (7,000 sp.) On the road to
back-boned animals.
 Complexity Level: Organ System. (Deuterostomes).
 A unique water hydraulic system - the water vascular system.
 Hydraulic Tube feet.
 Some with unique hydraulic pincers - pedicellaria.
 Endoskeleton of calcareous plates.
 Adult radial symmetry (like the spokes of a wheel) - or on living without a
head.
 Unsegmented with Oral and Aboral sides.
 Eucoelomate.
 Some different kinds:
 Class Crinoidea - Sea lily and Feather Star.
 Class Asteroidea - Sea stars.
 Class Ophiuroidea - Brittle stars.
 Class Echinoidea - sand dollar, sea urchin, and heart urchin.
 Class Holothuroidea - Sea cucumbers.
n. Phylum Urochordata - sea squirts. They lose their backbone. Our distant
relatives.
o. Phylum Chordata - back-boned animals. (50,000 sp)
 Complexity Level: Organ System (Deuterostomes).
 Eucoelomate.
 Metamerism. (Somites of backbone).
 Highly cephalized.
 Bilateral symmetry.
 Unique shared characters and different kinds
 Dorsal notochord (flexible, rod-like structure that provides skeletal support
made of cartilage. Extends to tail, point of attachment for body wall
musculature).
 Single hollow dorsal nerve cord.
 Postanal tail.
 Myotomes (muscle bundles) are segmentally arranged in a non-segmented
trunk.
 Some different kinds:
 Class Agnatha - jawless fish - lampreys and hagfish.
 Class Chondrichthyes - cartilaginous fish. Life without a bony skeleton sharks and rays.
 Class Osteichthyes - bony fish. A hard skeleton a last.
 Class Amphibia - amphibians. Life in the water and on the land.
 Class Reptilia - reptiles. Spending life on the land.
 Class Aves - Birds.
 Class Mammalia - mammals. That's our crowd, gang.
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a. Subclass Prototheria - monotremes - Duck billed platypus and
echidna.
b. Subclass Metatheria - marsupials - wallabies, wombats, kangaroos,
opossums, koalas.
c. Subclass Eutheria - placentals - walrus, whales, Fido, Felix, King
Kong, You.
Kingdom Plantae
Botany and Biology texts treat the classification of the plant kingdom in different
ways. For example, the term Division is used in botany to denote the Phylum level of
classification. Biology texts tend to use the term Phylum instead of Division when
referring to this level of classification in plants.
Most texts break the plant kingdom into two groups: vascular and non-vascular
plants. The non-vascular plants are termed Bryophytes. The Bryophytes include the
groups of plants known as mosses, liverworts, and hornworts (@23,000 sp). They have
the following general characteristics in common: seedless, spore producing, nonvascular, and haploid dominance. The vascular plants are termed Tracheophytes.
Included in this group are the very simple horsetails, the ferns, large conifers, and the
flowering plants (@350,000 sp). They have a wide range of characteristics except for
each having vascular tubing cells called xylem (to move water and minerals from the
roots) and phloem (to move sugars from the leaves).
1. Division Bryophyta - Mosses
a. Life style of alternation of generation (alternates between sporophyte (makes
spores that are diploid) and gametophyte (makes gametes that are haploid))
b. Pigments of chlorophyll (green).
c. Matting shape on rocks, tree, driveway, etc., sporophytes penetrate through
gametophyte matting.
d. No roots get moisture and minerals from the air. Like moist climates.
e. Leaflets on gametophyte
2. Division Hepatophyta - Liverworts
a. Life style of alternation of generation
b. Pigments of chlorophyll
c. Grows in shaded moist areas
d. Gametophyte looks like a clump of small leaves with the sporophyte structure
growing through with a small brown knob containing the spores
e. Rudimentary vascular like cells
3. Division Anthocerophyta - Hornworts
a. Life style of alternation of generation
b. Pigments of chlorophyll some have xanthophylls (reds)
c. Grows in shaded moist areas
d. Gametophyte looks like a clump of small leaves with the sporophyte structure
growing through in a hollow tube like structure
e. Rudimentary vascular like cells
4. Division Sphenophyta - Horsetails
a. Seedless, spore producing
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b. Vascular tubes of xylem (water and minerals) and phloem (sugars)
c. Some sporophyte stems photosynthetic, others non-photosynthetic
d. Pigments of chlorophyll
e. Grow in areas with shade and more toxic soils
5. Division Pteridophyta - Ferns (@ 12,000 sp)
a. Seedless, spore producing. Largest group of seedless vascular plants
b. Vascular
c. Pigments chlorophyll
d. Mainly tropical and temperate habitats
e. Some sporophyte stems photosynthetic, others non-photosynthetic
6. Division Coniferophyta - Conifers
a. Seed-bearing
b. Vascular
c. Pigments of chlorophyll
d. Cone bearing
e. Needle-like or scale-like leaves (microphylls)
7. Division Anthophyta - Flowering plants (@ 250,000 sp).
a. Seed-bearing. Largest, most diverse group of vascular seed-bearing plants
b. Vascular with megaphyll leaves
c. Pigments of chlorophyll, carotenoid (orange), and xanthophylls
d. Only organisms that produce flower and fruits
e. Some different kinds:
 Class Dicotyledonae - dicots: rose, maples, cacti, lettuces, beans, cotton, elms,
blackberry, most trees and shrubs other than conifers and others.
 Class Monocotyledonae - monocots: palm trees, lilies, orchids, bamboo,
wheat, corn, pineapples, grasses, sugar cane and others
Characteristics of Flowering Plants
Classes
# of seed leaves
Floral parts
Leaf Vein Array
Vascular Bundles
Root Stystem
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One
In threes
Parallel Veins
Random array Pattern
Fibrous
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Dicotyledon
Two
In fours or fives
Net Veins
Ring array Pattern
Taproot
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