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What is BIOLOGY?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Chapter 1: Exploring Life
•
Biology is the scientific study of life
•
Biologists are moving closer to understanding:
–
How a single cell develops into an organism
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How plants convert sunlight to chemical energy
–
How the human mind works
–
How living things interact in communities
–
How life’s diversity evolved from the first microbes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Outline
•
1) Biological Organization
•
2) DNA and Cells
–
•
The human genome project
3) Systems Biology and putting together information
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Feedback systems in living cells
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4) Taxonomy – naming all of the organisms
•
5) Diversity of species
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The theory of evolution
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The theory of natural selection
•
6) The scientific method
•
7) Examples of field studies employing the scientific method
•
8) Theories in science
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Biologists study the properties of life!
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Life’s basic characteristic is a high degree of order
•
Biologists explore life from the microscopic (Microbiology) to the global
scale (Ecology and Evolution)
•
The study of life extends from molecules and cells to the entire living
planet
•
Biological organization is based on a hierarchy of structural levels
•
Each level of biological organization has its own set of properties
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
A Hierarchy of Biological Organization
1. Biosphere: all environments on Earth – basically encompasses
the entire planet.
2. Ecosystem: all living and nonliving things in a particular area.
3. Community: all living organisms present in an ecosystem. Each
identical life form is known as a species.
4. Population: all individuals of a species living within a particular
area.
5. Organism: an individual living thing.
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A Hierarchy of Biological Organization (continued)
6. Organ and organ systems: specialized body parts made up of
tissues comprise an organ. Several organs come together to
form an organ system.
7. Tissue: a group of similar cells.
8. Cell: life’s fundamental unit of structure and function. Some
organisms consist of single cells (unicellular organisms), while
others contain billions of cells (multicellular organisms).
9. Organelle: a functional or structural component of a cell.
10. Molecule: a chemical structure consisting of two or more atoms.
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A Hierarchy of Biological Organization (continued)
The biosphere
Ecosystems
Organelles
1 µm
Cell
Cells
Atoms
10 µm
Communities
Molecules
Tissues
50 µm
Populations
Organs and organ systems
Organisms
A Closer Look at Ecosystems
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Each organism interacts with its environment
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Both organism and environment affect each other
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The dynamics of an ecosystem include two major processes:
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Cycling of nutrients, in which materials acquired by plants
eventually return to the soil
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The flow of energy from sunlight to producers – which are plants
and other photosynthetic organisms that convert light energy to
chemical energy.
–
This chemical energy then flows to consumers – which are
organisms that feed on producers and other consumers.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Energy Conversion
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Activities of life require the
living organism to do some
type of work
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Work depends on sources of
energy
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Energy exchange between
an organism and
environment often involves
energy transformations i.e.
from sunlight to chemical
energy
•
In transformations, some
energy is lost as heat
•
Energy flows through an
ecosystem, usually entering
as light and exiting as heat
Sunlight
Ecosystem
Cycling
of
chemical
nutrients
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Producers
(plants and other
photosynthetic
organisms)
Heat
Chemical energy
Consumers
(such as animals)
Heat
A Closer Look at Cells
•
The cell is the smallest level of biological organization that can perform
all activities of life
•
The ability of cells to divide is the basis of all reproduction, growth, and
repair of multicellular organisms
25 µm
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Cell’s Heritable Information
•
Cells contain DNA, deoxyribonucleic acid, the heritable information that
directs the cell’s activities
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DNA is what contains our genes
•
Genes are the units of inheritance that transmit genetic information
from parents to offspring
Sperm cell
Nuclei
containing
DNA
Egg cell
Fertilized egg
with DNA from
both parents
Embryo’s cells
With copies of
inherited DNA
Offspring with traits
inherited from both parents
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Two experiments showed that DNA is the genetic material
1. Griffith observed that virulent Streptococcus bacteria, when heat-inactivated
and mixed with a nonvirulent strain, could “transform” the nonvirulent strain and
make it virulent.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Which component of the dead donor cells caused transformation?
S cell
extract
minus …
Nothing
Lipids
Polysacchs
mouse
dies
Avery, McLeod, and McCarty:
-individually destroyed components,
-found that DNA is the transforming
agent
mouse
dies
Protein
DNA
RNA
mouse
dies
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
mouse
dies
mouse
dies
mouse
lives
Two experiments showed that DNA is the genetic material
2. Hershey-Chase experiment:
-radiolabeled either the DNA or the protein in a bacteriophage
-found that only labeled DNA ended up inside the cell
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
What is DNA?
•
Each DNA molecule is made up of two long chains arranged in a
double helix
•
Each link of a chain is one of four kinds of chemical building blocks
called nucleotides
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
What is DNA made of?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Chargaff’s rules: his studies of DNA of many different organisms led to the
1.
2.
3.
4.
following conclusions:
The total amount of pyrimidine nucleotides always equals the total amount
of purine nucleotides
The molar amount of T always equals that of A.
The molar amount of G always equals that of C.
The amounts of A + T does NOT equal that of G + C.
X-Ray diffraction of DNA, Rosalind Franklin and Maurice Wilkins
-DNA is long and skinny, with two similar parts that are parallel to each other
-DNA is helical
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
In 1953, Watson and Crick suggested a 3D structure for DNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Watson and Crick’s Structure
•Two parallel strands of nucleotides in the shape
of a double helix, with sugars and phosphates
alternating to form the backbone
•strands held together by hydrogen bonds between
the bases (A pairs with T, G pairs with C)
•the double helix forms two grooves, a major
groove, and a minor groove
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Watson and Crick’s Structure
•linkage in the backbone is from the
phosphate group on the 5’ carbon of the
sugar ring to the 3’ carbon of the next
nucleotidea phosphodiester bond
•therefore the strand is polarized: one end
is the 5’ end, the other is the 3’ end
•in double stranded DNA, the backbones
have opposite polarity: they are
antiparallel
•G-C pairs form three hydrogen bonds,
while A-T pairs form only two
•G-C pairs form stronger bonds (are more
stable) than A-T pairs because of the
additional hydrogen bond
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Structure of DNA
Nucleus
DNA
Nucleotide
Cell
DNA double helix
Single strand of DNA
Two Main Forms of Cells
•
•
Characteristics shared by all cells:
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Enclosed by a membrane
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Use DNA as genetic information
Two main types of cells:
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Eukaryotic: cells are divided into organelles; DNA is contained
within a nucleus
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Prokaryotic: lack organelles; DNA not separated in a nucleus
• MUCH more simple than eukaryotic cells
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EUKARYOTIC CELL
PROKARYOTIC CELL
DNA
(no nucleus)
Membrane
Membrane
Cytoplasm
Organelles
Nucleus (contains DNA)
1 µm
Biological systems are complicated!!
•
A biological system is a combination of components that form a more
complex organization
•
Cells, organisms, and ecosystems are some examples of biological
systems
•
Sooo, how can we possibly study all of the complicated things that
make up life? We try and study things in controlled environments so
we can study SPECIFIC nuances of life by a process known as
reductionism.
–
Reductionism is reducing complex systems to simpler
components that are easier to study
–
The studies of DNA structure by Watson and Crick and the
Human Genome Project are examples of reductionism
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Example - Sequencing the human genome
•In 1990 our government launched the Human Genome Project (HGP)
•it was expected to take 15 years and cost over 3 billion dollars
•goals of the project:
1. map all of the human genes
2. construct a detailed physical map of the entire human genome
3. determine the nucleotide sequences of all 24 human chromosomes
•actual sequencing progress was slow until 1998
2 things happened: -Perkin Elmer invented high-throughput sequencing
machines
-Craig Venter formed a company, Celera Genomics, and
he claimed he would sequence the human genome in 3
years.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Celera Genomics vs. HGP
•as a “practice run” for the human genome, Venter decided to team up with the
Drosophila genome project and sequence the Drosophila genome in one year
•the Drosophila genome is only 150 million bp (vs 3 billion bp in humans)
•they did it!
The race was on: HGP vs Celera
-In 2001, several years ahead of schedule, both
groups published their “first draft”
-the HGP continued to work, and in 2004
released a more complete sequence
2001 HGP: 2.69 billion bp
147,821 gaps
31,778 estimated genes
2001 Celera: 2.65 billion bp
105,264 gaps
26,588 estimated genes
2004 HGP: 2.85 billion bp
341 gaps
22,287 genes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Systems Biology
•
Systems biology seeks to create models of the dynamic behavior of whole
biological systems
•
An example is a systems map of interactions between proteins in a fruit fly cell
•
Such models may predict how a change in one part of a system will affect the
rest of the system
Outer membrane
and cell surface
Cytoplasm
CELL
Nucleus
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Systems biology uses three key research developments:
–
High-throughput technology: new methods used to generate large
data sets rapidly - microarrays
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Bioinformatics: using computers and software to process and
integrate large data sets
–
Interdisciplinary research teams – many large research
institutions have one, including Princeton University here in NJ
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Feedback Regulation in Biological Systems
•
Regulatory systems ensure a dynamic balance in living systems
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Chemical processes are catalyzed (accelerated) by enzymes
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Many biological processes are self-regulating: the product regulates
the process itself. The end product of a specific reaction works to
feed-back on the process.
•
In negative feedback, the accumulation of a product slows down the
process itself
•
In positive feedback (less common), the product speeds up its own
production
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
W
W
Enzyme 4
Enzyme 4
X
X
Enzyme 5
Enzyme 5
Y
Y
Enzyme 6
Enzyme 6
Z
Z
Positive
feedback
Z
Z
Z
Z
Z
Z
Z
Z
Z
A
Z
Z
Z
Z
Z
Z
Z
Z
A
Enzyme 1
Enzyme 1
B
B
Enzyme 2
C
C
Enzyme 3
D
D
D
D
D
D
Negative
feedback
D
D
D
D
D
movies
Biologists explore life of MANY species
•
Biologists have named about 1.8 million species
•
Estimates of total species living in the biosphere range from 10 million
to over 200 million
•
How do we organize species within the framework of biological
organization? Within the biosphere, how do we organize the naming of
the individual species?
–
Taxonomy is the branch of biology that names and classifies
species into a hierarchical order
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Kingdoms and domains are the broadest units of classification
• Levels of Taxonomic organization (ordered largest to smallest):
–
Domain, Kingdom, Phylum or Division , Class , Order, Family,
Genus, Species
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Taxonomic organization of a Black bear
Species Genus Family
Order
Class Phylum Kingdom Domain
Ursus
americanus
(American
black bear)
Ursus
Ursidae
Carnivora
Mammalia
Chordata
Humans full name is: Eukarya
anamalia chordata mammalia
Animalia
primates hominoidea homo sapiens
Eukarya
The Three Domains of Life
•
At the highest level, life is classified into three domains:
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Eubacteria – prokaryotes, true bacteria
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Archaea – prokaryotes, odd bacteria that live in extreme
environments, high salt, heat, etc
–
Eukarya – eukaryotes that have a nucleus, & organelles,
Eukaryotes include protists and the kingdoms Plantae, Fungi, and
Animalia
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Examples of species in the three domains
Eubacteria
Bacteria
Archaea
Archaea
Eukarya
4 µm
0.5 µm
Protists
Kingdom Fungi
100 µm
Kingdom Plantae
Kingdom Animalia
Nomenclature we will use, and is most commonly used in science
•
Binomial (scientific) nomenclature
•
Genus – Bacillus, always capitalized
•
species - subtilis, lowercase
•
Both italicized or underlined
–
Bacillus subtilis (B. subtilis)
–
Escherichia coli
(E. coli)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Where does diversity between species come from?
•
The theory of evolution has been proposed by biologists to explain the
diversity that arises between species
•
The history of life is a saga of a changing Earth billions of years old
•
The evolutionary view of life came into sharp focus in 1859, when
Charles Darwin published On the Origin of Species by Natural
Selection
•
“Darwinism” became almost synonymous with the concept of evolution
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Origin of Species articulated two main points:
•
Descent with modification (the view that contemporary species arose
from a succession of ancestors)
•
Natural selection (a proposed mechanism for descent with
modification)
•
Darwin inferred natural selection by connecting two observations:
•
–
Observation: Individual variation in heritable traits – inference:
unequal reproductive success
–
Observation: Overpopulation and competition - inference:
Evolutionary adaptation
Natural selection can “edit” a population’s heritable variations
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The theory of Natural Selection
•within individuals in a species there exists variation (principle of
variation)
•certain characteristics cause individuals to be more “fit”, to survive
and reproduce better than others
•more “fit” individuals will contribute more offspring to the next
generation than less fit individuals (or, in a competition for survival
among individuals, more “fit” individuals will predominate) (principle
of selection)
•offspring tend to resemble their parents; the characteristics that
cause individuals to be more “fit” are heritable (principle of heredity)
•Natural selection is often evident in adaptations of organisms to
their way of life and environment
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
What drives evolution/change?
Population
of organisms
Hereditary
variations
Overproduction
and competition
Environmental
factors
Differences in
reproductive success
of individuals
Evolution of adaptations
in the population
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The theory of Natural Selection
Population with varied inherited traits
Elimination of individuals with certain traits
Reproduction of survivors
Increasing frequency of traits that enhance
survival and reproductive success
Methods used to study life
•
Inquiry is a search for information and explanation, often focusing on
specific questions
•
The process of science blends two main processes of scientific inquiry:
–
Discovery science: describing nature – slowly finding things that
describe data that you obtain when doing experiments
–
Hypothesis-based science: explaining nature – slowly finding
out and trying to explain what you see in nature
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Discovery Science
•
Discovery science describes nature through careful observation and
data analysis
•
Examples of discovery science:
•
•
–
understanding cell structure
–
expanding databases of genomes
Two types of data, or recorded observations generated during the
course of an experiment:
–
Quantitative data: numerical measurements
–
Qualitative data: recorded descriptions
Inductive reasoning involves generating ideas to explain many specific
observations or data
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Hypothesis-Based Science
•
In science, inquiry usually involves proposing and testing hypotheses
•
Hypotheses are hypothetical explanations that you try to
experimentally test to show that the explanation describes nature
•
In science, a hypothesis is a tentative answer to a well-framed question
•
A role of a hypothesis is that it is an explanation on trial, making a
prediction that can be tested
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Step 1: Formulating hypotheses
Observations
Question
Hypothesis #1:
Dead batteries
Hypothesis #2:
Burnt-out bulb
Step 2: Testing your hypotheses
Hypothesis #1:
Dead batteries
Hypothesis #2:
Burnt-out bulb
Prediction:
Replacing batteries
will fix problem
Prediction:
Replacing bulb
will fix problem
Test prediction
Test prediction
Test falsifies hypothesis
Test does not falsify hypothesis
Deduction: The “If…then” Logic of Hypothesis-Based Science
•
In deductive reasoning, the logic flows from the general to the specific
•
If a hypothesis is correct, then we can expect a particular outcome
•
A scientific hypothesis must have two important qualities:
–
It must be testable
–
It must be falsifiable
•
Hypothesis-Based science is the traditional, basic view of how
scientific research is performed
•
The scientific method is an idealized process of inquiry
•
Very few scientific inquiries adhere rigidly to the “textbook” scientific
method
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Survival in the wild by mimicry
•
In mimicry, a harmless species resembles a harmful species
•
An example of mimicry is a stinging honeybee and a nonstinging
mimic, a flower fly
Flower fly (nonstinging)
Honeybee (stinging)
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Field study: Researching mimicry in the wild
•
This case study examines king snakes’ mimicry of poisonous coral
snakes
•
The hypothesis states that mimics benefit when predators mistake
them for harmful species
•
The mimicry hypothesis predicts that predators in non–coral snake
areas will attack king snakes more frequently than will predators that
live where coral snakes are present
Scarlet king snake
Key
Range of scarlet
king snake
Range of eastern
coral snake
Eastern coral
snake
North
Carolina
South
Carolina
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Scarlet king snake
Field Experiments with Artificial Snakes
•
To test this mimicry hypothesis, researchers made hundreds of artificial
snakes:
–
An experimental group resembling king snakes
–
A control group resembling plain brown snakes
•
Equal numbers of both types were placed at field sites, including areas
without coral snakes
•
After four weeks, the scientists retrieved the artificial snakes and
counted bite or claw marks
•
The data fit the predictions of the mimicry hypothesis
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(a) Artificial king snake
(b) Artificial brown snake that has been attacked
17%
In areas where coral snakes
were absent, most attacks
were on artificial king snakes.
83%
Key
North
Carolina
% of attacks on
artificial king snakes
% of attacks on
brown artificial snakes
Field site with
artificial snakes
South
Carolina
16%
84%
In areas where coral
snakes were present,
most attacks were on
brown artificial snakes.
Designing Controlled Experiments
•
Scientists do not control the experimental environment by keeping all
variables constant
•
Researchers usually “control” unwanted variables by using control
groups to cancel their effects
•
The limitations of science are set by its naturalism
–
Science seeks natural causes for natural phenomena
–
Science cannot support or falsify supernatural explanations, which
are outside the bounds of science
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Theories in Science
•
A scientific theory is much broader than a hypothesis
•
A scientific theory is:
–
broad in scope
–
general enough to generate new hypotheses
–
supported by a large body of evidence
•
Models are often used to explain and simplify observations. Models
are representations of ideas, structures, or processes
•
Models may range from lifelike representations to symbolic schematics
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Culture of Science and technology
•
Science is an intensely social activity
•
Individuals in science work together towards a common goal, and
MUST be able to communicate very effectively
•
Both cooperation and competition characterize scientific culture
•
The goal of science is to understand natural phenomena
•
Technology applies scientific knowledge for some specific purpose –
basic scientific research may be used to make makeup for Revlon,
healthy aluminum siding for DuPont or safe foods for Lean Cuisine.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Vocabulary: Intra- vs. Inter•
REMEMBER THIS FOR TERMS IN SCIENCE!!!!!
•
A word beginning with the prefix intra- means within something
•
A word beginning with the prefix inter- means between two or more
things
•
For example: INTRAmural athletics – sports/games played by teams
or people WITHIN the same school
•
INTERcollegiate athletics – sports/games played by teams or people
from two or more different schools
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings