Download Biol160 Chemistry The Basic Chemistry of Life In order to

Biol160
Chemistry
The Basic Chemistry of Life
In order to understand living organisms and how they function, it is important to recognize the basic properties of
the fundamental substances of which we are composed. All of the “stuff” that exists in the universe, living and nonliving, is composed of matter. Matter can be found in solid, liquid, and gaseous forms, and is composed of chemical
elements. An element is a substance that cannot be broken down into anything else by basic chemical means.
There are almost 100 elements that occur naturally on Earth. However, very few elements exist in large quantities
in pure form. Through chemical bonding, elements frequently combine with others to form compounds. A
compound may consist of just two elements, or it may contain more. A single atom is the smallest stable
subdivision of a pure element. A molecule is the smallest independently-existing unit of a compound. The number
of atoms in a molecule depends on what type of molecule it is. Small molecules may be composed of only 2 or 3
atoms, while large, complex ones may have thousands of atoms.
Please note that this lab exercise includes a pre-lab worksheet, which you should complete and turn in to your
instructor before the start of your lab session.
I. Atomic structure and chemical bonds
Atoms are made up of subatomic particles, including protons, neutrons, and electrons. The table below
summarizes their properties. The central region of an atom is called the nucleus. Do not confuse this with the
nucleus of a cell, which we’ll examine in the next lab session. The electrons orbit around the nucleus very
rapidly. If an atom were modeled to scale, the nucleus might be represented as a pea hovering in the center of a
professional sports stadium, and the electrons would be tiny specks of dust zipping around somewhere within
the confines of the stadium.
The number of protons determines the type of element. For example, if an atom has 12 protons, then it is a
magnesium (Mg) atom. If it were possible for that atom to lose one proton, so that it only had 11, then we
would be dealing with the element sodium (Na). The number of neutrons and electrons present in an atom is
often the same as the number of protons. For example, a typical helium (He) atom has 2 protons, 2 neutrons,
and 2 electrons. However, numbers of neutrons and electrons can vary.
Atoms of an element that vary in mass because they have different numbers of neutrons are called isotopes.
The element oxygen (O) has seven known isotopes. For example, there are oxygen atoms that contain 8 protons
and 8 neutrons, while others contain 8 protons and 10 neutrons.
Atoms of some elements gain or lose electrons readily. Sodium (Na) atoms frequently lose one of their 11
electrons. That leaves them with 10 electrons and 11 protons, and thus one net unit of positive charge. These
charged atoms are called ions, and are symbolized like this: Na+, Ca2+ (calcium atom that has lost two electrons),
Cl- (chlorine atom that has gained one electron).
proton
Location
Mass
Electrical charge
If the number present is changed…
center of the atom
(nucleus)
1 atomic unit
positive
it is no longer the same element
it is a different isotope of the same
element
neutron
center of the atom
(nucleus)
1 atomic unit
neutral
electron
orbiting around the nucleus
almost none
negative
it gains a net charge and is called
an ion, but is still the same
element
Biol160
Chemistry
Within an atom, electrons are located at different energy levels, called electron shells, based on how far they
are from the nucleus. The number of electrons in the outermost shell determines how an atom will interact
with others. Each electron shell can “hold” a certain number of electrons. The first shell, closest to the nucleus,
can hold two electrons. Thus, helium (He), which has only two electrons, has a full outer shell. The second
electron shell can hold up to eight. Therefore, neon (Ne), which has 10 electrons, also has a full outer shell,
since it has 2 electrons in the first shell and 8 in the second. The third and fourth shells can hold more than 8
electrons, but they generally become unstable when more are present. Because of this, a general rule of thumb
is that atoms react with one another so as to end up with eight electrons in their outermost shells. In order to
achieve this, atoms can gain, lose, or share electrons. In order to picture how this will occur, it is helpful to draw
shell models to depict different types of atoms. The examples below have a grey circle for the nucleus, and
black dots as electrons.
O
H
Na
Ionic bonds
Ionic bonds form between atoms due to the attraction of opposite charges that result from the gain or loss of
electrons. Typically, atoms with 1, 2 or 3 electrons in their outer shell lose these electrons to other atoms. Look
at the shell model of sodium (Na) above. Why will losing one electron make it more stable? Atoms with 6 or 7
electrons in their outer shells are usually the ones to receive or gain those electrons. Table salt, or sodium
chloride (NaCl), is a classic example of a compound held together by ionic bonds.
Covalent bonds
Most biological macromolecules are held together primarily by covalent bonds. These occur when atoms share
electrons. One or more pairs of electrons spend part of their time in the outer shells of both atoms involved,
thus the outer shells are effectively filled. Water (H2O) is an excellent example of a molecule held together by
the sharing of electrons. Oxygen (O) has 6 electrons in its outer shell; thus, to be satisfied, it requires 2 more.
Hydrogen (H) atoms require one more, since the capacity of their outer shell is only two electrons total. So the
oxygen shares one pair of electrons with one hydrogen atom, and another pair of electrons with a second
hydrogen atom. Each pair of shared electrons consists of one that was originally part of the oxygen atom, and
one from the hydrogen. A water molecule is comprised of three atoms held together by two single bonds.
Single bonds are represented in structural formulas as single lines: H—O—H, for example. If two atoms share
two pairs of electrons, they are held together by a double bond. Oxygen gas (O2) is a good example of this, and
it would be written as O==O. The table below illustrates the bonding capabilities of the four elements that make
up over 90% of the mass of most living organisms.
Element
Number of protons
Number of outer shell
electrons
Total number of
potential bonds
hydrogen
carbon
nitrogen
oxygen
1
6
7
8
1
4
5
6
1
4
3
2
Biol160
Chemistry
Be sure to answer all of the questions on the worksheet relating to atomic structure and chemical bonds.
Unfortunately, your textbook does not provide a periodic table of the elements, so I have listed elements with
atomic numbers 1-30 on the last page of this lab write-up.
II. pH - DEMO
Because water is such a large part of living organisms and our environment, another important chemical aspect
to consider is how compounds behave when placed in water. Acids are substances that release hydrogen ions
(H+) when dissolved in water. Hydrogen chloride (HCl) is considered a strong acid, because it dissociates almost
completely into H+ and Cl- ions. Bases, also called alkaline compounds, release hydroxyl ions (OH-) when
dissolved in water. In a sample of pure water, some of the water molecules themselves dissociate into H+ and
OH- ions, but since the amounts are precisely the same, water is not considered an acid or a base. Substances
that do not release any hydrogen or hydroxyl ions when dissolved are not considered acids or bases, either.
The pH scale is used to indicate the concentration of hydrogen ions (H+) in a solution. The values range from 0
to 14. Lower pH values indicate a higher concentration of H+ ions and are considered more acidic. Each unit
represents a 10-fold change in H+ concentration. Thus, a solution with a pH of 5 has 10 times more H+ ions than
something with a pH of 6, while something with a pH of 4 is 100 times more acidic. At a pH of 7, a solution is
considered neutral, because the concentration of H+ ions is equal to the concentration of OH- ions. Note:
Although you would expect the pH of pure water to be exactly 7, when water is exposed to air, carbon dioxide from the air
dissolves in it and forms a weak acid. Thus the pH of distilled water is usually about 5.7. Solutions with pH values
greater than 7 are called basic or alkaline.
In lab today, work in groups of 4 for ALL of the following exercises.
ACTIVITY 1: Using pH test strips, determine the pH of the 8 different solutions listed below. These are all
substances you might encounter in your daily lives. Record their pH values here, and then on your worksheet,
list them in order from the most acidic to most basic, along with the pH value obtained.
Solutions for pH testing:
Alka-Seltzer solution
Ammonia
detergent solution
cola (soda pop)
vinegar
lemon juice
milk
water that has been filtered through potting soil
The processes that occur inside living organisms are often very sensitive to pH, and therefore pH must be
maintained within narrow limits in order for things to function properly. Buffers are compounds that can release
or grab H+ ions and thereby keep the pH from changing drastically. Buffers within our blood, for example,
maintain a slightly basic pH (about 7.4). The following exercise will illustrate how a buffered solution resists
changes in pH.
ACTIVITY 2:
1. Use pH strips to determine the pH of distilled water (dH2O) from your dropper bottle, and of the pH 6 buffer
solution. Record the values on the table in your worksheet.
2. Place 40 drops of dH2O in one small labeled beaker, and 40 drops of pH 6 buffer solution in another.
3. Add 1 drop of 1% hydrogen chloride (HCl) to each, and determine the pH of each by dipping a test strip into
the solution in the beaker. Record the value on your worksheet.
4. Add 4 more drops of HCl, and test the pH. Record the value.
5. Add 5 more drops of HCl, and test the pH. Record the value.
6. Add 10 more drops of HCl, and test the pH. Record the pH value.
7. Wash and dry the beakers. Repeat the experiment, using 10% sodium hydroxide (NaOH) instead of
HCl.*Handle the HCl and NaOH carefully, and rinse your hands under water if some gets on your skin.*
Biol160
Chemistry
III. Testing for carbohydrates, lipids, and proteins
Carbohydrates, lipids, and proteins are relatively large molecules that play important roles in living organisms.
Carbon atoms and the four covalent bonds they can form provide the basic framework for ALL of these
macromolecules. In this lab, we will use a suite of chemical tests to detect the types of molecules present in
various food items.
Carbohydrates come in several basic forms. The simplest sugars are called monosaccharides, and they contain
3-7 carbon atoms, often bonded together in a ring structure. Glucose is a very common 6-carbon sugar. When
two monosaccharides bond together, they form a disaccharide, such as sucrose. Many monosaccharide subunits
bonded together form a polysaccharide, a much more complex carbohydrate. Starch, cellulose and glycogen are
common examples of polysaccharides. Our tests will allow us to easily detect starch and also reducing sugars
(most 6-carbon and some 12-carbon sugars).
There are many different types of lipids. They are all grouped together as lipids because at least some part of
the molecule does not dissolve in water. Oil and vinegar salad dressing requires vigorous shaking, because the
oil and vinegar (which is a water-based solution) do not mix well. We will use two different tests to help
determine whether or not lipids are present in our samples.
Most proteins are very large molecules with complex shapes. While monosaccharides are the subunits of
polysaccharides, amino acids are the subunits of proteins. Amino acids connect via a specific type of covalent
bond called a peptide bond. The test we will perform responds to the presence of peptide bonds, and thus
indicates the presence of proteins.
ACTIVITY: Use the methods described below to test for the presence of starch, reducing sugars, lipids, and
proteins in a variety of foods. To do this, you must first prepare a set of standards. The standards demonstrate
strongly positive and strongly negative results for each test. For example, when you perform the iodine test and
the “liquid to be tested” is a solution of dissolved starch, the liquid should turn a dark blue-black color, indicating
the presence of a lot of starch (strongly positive result). When you perform the iodine test and the “liquid to be
tested” is distilled water, which contains no starch, the clear water should turn a yellow-brown color. Despite
the color change due to the addition of the iodine solution, this is a negative result—starch is not present. SAVE
YOUR PAIRS OF POSITIVE AND NEGATIVE STANDARDS FROM EACH TEST UNTIL YOU COMPLETE THE ENTIRE LAB
EXERCISE. You’ll need to compare them to the results you obtain when testing various foods. The next table
explains the substances we’ll use for creating the standards.
Test
Positive standard
Negative standard
iodine test for starch
Benedict’s test for reducing sugars
paper spot test for lipids
Sudan IV test for lipids
biuret test for proteins
0.1 % soluble starch
0.1% glucose
vegetable oil
vegetable oil
1% albumin (protein from egg whites)
distilled water
distilled water
distilled water
distilled water
distilled water
To create your set of standards, you must perform each of the five tests twice. One test will utilize the item
listed in the Positive standard column, and one will use the item in the Negative standard column (dH2O) as the
“liquid to be tested.” Specific directions for performing each of the tests are given below.
Iodine test for starch
1. Place 25 drops (about 1 mL) of the liquid to be tested into a clean test tube.
2. Add 3 drops of iodine solution (often labeled “Lugol’s IKI”) to the liquid. Swirl gently to mix.
3. Examine the resulting color: graygrayish blueblue-black = presence of starch (low concentrationhigh
concentration)
Biol160
Chemistry
Benedict’s test for reducing sugars
1. Prepare a hot water bath using a glass beaker, water, and a hot plate: Fill a 250 mL beaker halfway with
water. Place it on the hot plate, and set the hot plate to medium-high; the water should be near boiling.
2. Place 25 drops (about 1 mL) of the liquid to be tested into a clean test tube.
3. Add 3 drops of Benedict’s solution to the liquid. Swirl gently to mix.
4. Place the test tube in the beaker of near-boiling water for 4-5 minutes.
5. Examine the resulting color: light greenyelloworangebrick red = presence of reducing sugars (low
concentrationhigh concentration)
Paper spot test for lipids
1. Place a drop of the liquid to be tested on a brown piece of paper. If the substance to be tested is a solid, it
can be rubbed into the paper. Blot or wipe away any excess material.
2. Allow the paper to dry.
3. Once dry, hold the paper up to the light. A permanent translucent spot indicates the presence of lipids.
Sudan IV test for lipids
1.
2.
3.
4.
Place 25 drops (about 1 mL) of distilled water into a clean test tube.
Add 3 drops of Sudan IV dye. Swirl gently to mix.
Add 10 drops of the liquid to be tested, and mix again. Wait for 5-6 minutes.
If lipids are present, they will stain darker red than the water, and will usually form small globules floating on
the top of the mixture.
Biuret test for proteins
1. Place 25 drops (about 1 mL) of the liquid to be tested into a clean test tube.
2. Add 25 drops (about 1 mL) of 10% NaOH. Swirl gently to mix. Recall from the pH exercise that NaOH is a
strong base, and can be caustic. If you get any on your skin, wash it off immediately with a lot of water.
3. Add 5 drops of copper sulfate (CuSO4) to the liquid, mix, and wait 3 minutes.
4. A pale purple color indicates that proteins are present.
5. CuSO4 should not be dumped down the drain. Dispose of all liquid from these test tubes into the specially
marked container under the hood for proper disposal.
Once your set of standards has been created, choose at least three of the eight food items available for testing.
Perform all five tests on each food, and in each case, compare your results to the appropriate pair of positive &
negative standards to evaluate the presence or absence of that type of molecule in the food.
Food items available for testing:
sweet onion
potato
Sprite or 7-Up
soft tofu
salad dressing
energy bar
apple
cooked rice
In some cases, the food will need to be ground up using a mortar and pestle in order to obtain liquid to use in
the tests. In those cases, use the following procedure:
1.
2.
3.
4.
5.
Clean and dry the mortar and pestle before you begin.
Cut the food into very small chunks and place a spoonful-sized amount into the mortar.
Add about 5 mL of distilled water.
Use the pestle to grind the material firmly, until soupy. Add more water if necessary.
Pour the liquid into a test tube; this is your “liquid to be tested.” Note that to perform all the tests, you will
need several milliliters (mL) of solution, so be sure you obtain enough liquid when processing the food.
Biol160
Chemistry
Atomic number
(indicates the number
of protons in an
atom)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Name of element
Abbreviation
hydrogen
helium
lithium
beryllium
boron
carbon
nitrogen
oxygen
fluorine
neon
sodium
magnesium
aluminum
silicon
phosphorus
sulfur
chlorine
argon
potassium
calcium
scandium
titanium
vanadium
chromium
manganese
iron
cobalt
nickel
copper
zinc
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Biol160
Chemistry
Name ______________________________ Section ______
Chemistry Pre-Lab Worksheet
(complete this sheet individually, and turn it in at the start of lab)
Write the term or short phrase that best completes each sentence.
Large ___ may be composed of hundreds or thousands of atoms.
______________________________
Isotopes of an element contain different numbers of…
______________________________
Covalent bonds occur when atoms share…
______________________________
A solution with a pH value of ___ is strongly basic.
______________________________
Solution from the pH testing section that you would not want to eat ______________________________
Once you complete step 6 of the pH buffer experiment, indicate how many total drops of HCl you will have
added to the beakers of…
distilled water __________
pH 6 buffer solution __________
For each of the following substances, identify whether it is a carbohydrate, lipid, or protein. If it is not one of
those, write “other.”
vegetable oil _____________________
albumin ________________________
glucose ______________________
starch
sucrose ________________________
distilled water ________________
_________________________
Each of the following statements applies to one of the five tests we will perform in Part III of this lab. Give the
name of the appropriate test.
Can be performed without using a test tube
________________________________
The solution being tested may turn pale purple
________________________________
Requires that the test solution be heated
________________________________
Tests for the same type of molecule as the paper spot test
________________________________
A very dark colored solution indicates that a lot of starch is present
________________________________
Do not dump solutions from this test down the drain
________________________________
Table sugar (sucrose) might also work as a positive standard for this test ________________________________
One of the food items we will have available for testing will be an energy bar. It is likely to be lemon-flavored,
coated with yogurt. Why would a dark chocolate energy bar be more challenging to work with in this exercise?
(And since we don’t consume food in lab, the answer is not that it would be eaten before we could use it!)
Biol160
Chemistry
Biol160
Chemistry
Name _____________________________________ Section ______
Basic Chemistry of Life Homework
(complete and turn in this sheet—front and back—as an individual)
I. Atomic structure and chemical bonds
Give at least two examples of things that fit each description. You are encouraged to use tables and figures
from your textbook to help you answer these questions.
Element whose number of protons found in its atoms is a multiple of four
___________________
Element whose outer electron shell is full without gaining, losing, or sharing electrons
___________________
Element where the atoms require exactly two more electrons to fill their outer shell
___________________
Example of a molecule made of 2 atoms
___________________
Example of a molecule made of more than 2 atoms
___________________
Example of a compound composed of 2 different elements
___________________
Example of a compound composed of more than 2 different elements
___________________
A positively charged ion
___________________
Draw shell models of an atom of carbon (C) and an atom of potassium (K).
Carbon:
Potassium:
Use shell model drawings and words to explain how the compound calcium chloride (CaCl2) is held together
(what type of bond is involved), and why there are always two Cl for every one Ca. (Hint: You may find Figure
2.7A in your text helpful.)
Biol160
Chemistry
Use shell model drawings and words to explain why the element hydrogen (H) is found in the form H2 and what
type of bond holds it together.
Using the information provided about hydrogen, carbon, nitrogen, and oxygen, draw your prediction of the
structural formula for each of these molecules.
methane (CH4)
carbon dioxide (CO2)
formaldehyde (CH2O)
Ammonia is a compound formed by the elements nitrogen and hydrogen. How many atoms of each would you
predict would be present in a single molecule? In the space below, draw a shell model diagram that shows a
molecule of ammonia.
nitrogen ______
hydrogen ______
Biol160
Chemistry
Name ______________________________ Name ______________________________ Section ______
Name ______________________________ Name ______________________________
Basic Chemistry of Life Worksheet
(complete and turn in this sheet—front and back—as a group of four)
II. pH - DEMO
Solutions tested:
(give the pH
value on the
line to the right)
most acidic
most basic
____________________________
________
____________________________
________
____________________________
________
____________________________
________
____________________________
________
____________________________
________
____________________________
________
____________________________
________
Buffer solution and addition of an acid:
total drops of 1%
HCl added
0
1
5
10
20
pH of distilled
water
Buffer solution and addition of a base:
pH of buffer
solution
total drops of 10%
NaOH added
pH of distilled
water
pH of buffer
solution
0
1
5
10
20
Did this buffer solution do a better job of maintaining stable pH with the addition of an acid or a base? Explain.
Soils vary in their acidity and in the amount of buffering compounds contained in them. Suppose that acid rain
falls in an area where the soil has a high buffering capacity. Do you expect that there will be much effect on the
soil organisms living in the area? Explain your answer.
Biol160
Chemistry
III. Testing for carbohydrates, lipids, and proteins
In this table, record the results from your preparation of the set of standards. Describe the appearance of the
liquid in each tube (or the brown paper) when the test was complete.
Test
Positive standard
Negative standard
iodine test for starch
Benedict’s test for reducing sugars
paper spot test for lipids
Sudan IV test for lipids
biuret test for proteins
Record the results from testing the various food samples. Use this notation to indicate your results:
strongly positive (i.e. looked very much like positive standard)
moderately positive
weakly positive
negative
Substance
tested
Iodine
Benedict’s
Test results
Paper spot
Sudan IV
Biuret
+++
++
+
0
Your conclusions:
Compounds present in sample
Please note that these tests are not exceptionally sensitive, so keep in mind that negative results only mean that
there were not large quantities of that type of macromolecule present. For example, all living cells contain lipids
in their cell membranes, but that amount alone is too small for either of our lipid tests to detect.
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