CHAPTER 5. CHEMISTRY: UNDERSTANDING THE COMPOSITION OF LIVING THINGS
Student learning outcomes
At the completion of this exercise, the student will be able to:
1. Discuss the role of chemistry in the biological sciences.
2. Define elements, atoms, atomic number, atomic mass, and isotopes.
3. Define compounds and molecules.
4. Differentiate among ionic, covalent, and hydrogen bonds.
5. Distinguish between inorganic, organic, and biochemistry.
6. Define solution, aqueous solution, solvent, and solute.
7. Define and describe the properties of an acid and a base.
8. Determine the pH of a substance.
9. Define and describe the characteristics of carbohydrates.
10. Discuss the composition and functions of monosaccharaides, disaccharides and
polysaccharides.
11. Perform the Benedict’s Test for the presence of a reducing sugar.
12. Perform the Iodine Test for the presence of starch.
13. Define and describe the characteristics of lipids.
14. Perform the Grease-Spot Test for the presence of a lipid.
15. Perform the Sudan Test for the presence of lipid.
16. Define and describe the characteristics of proteins.
17. Perform the Biuret Test for the presence of a protein.
18. Define and describe the characteristics of nucleic acids.
OVERVIEW
To develop a meaningful understanding of biology, a fundamental knowledge of
chemistry is necessary (Fig. 5.2). Chemistry is the study of the composition, structure, properties,
and interaction of matter. Matter is anything that occupies space and has mass. Matter, whether it
is this page, a meteorite or a gallstone, is composed of elements. An element is a substance that
cannot be broken down into other substances by ordinary chemical means. Although more than
112 elements have been described only 92 elements are naturally occurring; the others are
human-made.”
Of the naturally occurring elements, approximately 25 are common to living systems. A
typical human is composed of 65% oxygen (O), 18.5% carbon (C), 9.5% hydrogen (H), and
3.2% nitrogen (N). Other important elements in humans and other living systems include
phosphorus (P), sulfur (S), calcium (Ca), potassium (K), sodium (NA), chorine (Cl), magnesium
(Mg), iron (Fe), and silicon (Si).
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Elements are composed of atoms. An atom is the smallest part of an element that retains
the properties of that element. Atoms are composed of a variety of subatomic particles, the best
known of which are protons, neutrons, and electrons. Positively charged protons and uncharged
neutrons can be found in the nucleus negatively charged electrons exist in orbitals surrounding
the nucleus.
The atomic number of an element reflects the number of protons in the nucleus. For
example, copper (Cu) has an atomic number of 29. The atomic mass of an element indicates the
number of protons plus the number of neutrons in the nucleus. The atomic mass of copper is
63.546.The Atomic number mass reflects that the number of neutrons can vary in the nucleus.
Atoms that have same number of protons and a varied number of neutrons are called isotopes.
For example, the element tin (Sn) has 10 isotopes. Many isotopes are radioactive.
A molecule results from the chemical union of two or more atoms. Some molecules are
simple, such as a molecule of oxygen (O2) and a molecule of water (H2O). Others are quite large,
such as a molecule of chlorophyll (C55H72O5N4Mg). Compounds are molecules composed of
different elements. Water and chlorophyll are compounds. Other examples of compounds are
glucose (C6H12O6), hydrogen peroxide (H2O2), baking soda (NaHCO3) and ethyl alcohol
(C2H5OH).
Atoms combine with other atoms by means of chemical bonds. Ionic compounds such
as salt (NaCl) are held together by an attraction between positively and negatively charged ion.
This loss or gain of electrons forms an ionic bond. When placed in water, ionic compounds
dissociate (dissolve).
1) Covalent bonds - result from sharing of electrons. Covalent bonds are strong and are
common in living systems.
2) Nonpolar covalent bonds - involve an equal sharing of electrons. Nonpolar covalent
bonds between carbon and hydrogen from a stable framework for building larger
molecules such as octane (C8H10).
3) Polar covalent bonds - involve an unequal sharing of electrons.
The most important polar molecule to life on Earth is water (H2O). Hydrogen bonds are
weak bonds between the positively charged region of a hydrogen atom of a polar covalent
molecule and the negatively charged region of oxygen or nitrogen of another polar
covalent molecule. Hydrogen bonds give shape and three-dimensional structure to
complex molecules such as proteins. Hydrogen bonds also provide water with several
special properties.
In this chapter we divide the discussion of chemistry in inorganic chemistry and
organic chemistry. Inorganic chemistry addresses chemical principles excluding the
special properties of carbon. Organic chemistry addresses chemistry involving the special
properties of carbon. Biochemistry, the study of the chemistry of life, will be discussed in
late chapters.
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EXERCISES IN INORGANIC CHEMISTRY
Understanding acids and bases
A solution is a liquid composed of a uniform mixture of two or more substances. In a
solution, the dissolving medium is the solvent, and the dissolved substance(s) is the solute. One
of the unique properties of water is that it is an excellent solvent. An aqueous solution uses water
as the solvent. Some inorganic molecules are held together by ionic bonds. In an aqueous
solution, these substances undergo dissociation and produce positive and negative ions. For
example, sodium chloride (NaCl) dissociates into sodium ions (Na) and chloride ions (Cl).
Substances that release ions in an aqueous solution are called electrolytes. Other biologically
important electrolytes include potassium chloride (KCl), calcium chloride (CaCl2), and sodium
bicarbonate (NaHCO3).
Although many people think that acids and bases are chemicals that are best left in the
laboratory, many common substances are classified as acids or a base. These substances can be
important and, in some instances, potentially dangerous to living systems.
Both inorganic and organic acids are common in nature. An acid is a substance that yields
(donates) a hydrogen ion in solution. Acids share a number of structural characteristics and
properties.
(1) Acids contribute one or more hydrogen atoms to a solution when they dissociates
in water
(2) Acids have a sour taste. (Don’t taste unknown chemicals)
(3) Acids may be corrosive or poisonous.
(4) Acids react with certain metals to liberate hydrogen.
(5) Acids neutralize bases.
(6) Acids affect the color of certain indication.
Several common inorganic acids are:
Sulfuric acid (H2SO4)
Nitric acid (HNO3)
Phosphorous acid (H3PO4)
Hydrochloric acid (HCl)
Some common organic acids are:
Citric acid (lemon juice)
Acetic acid (vinegar)
Carbonic acid (carbonated water)
Malic acid (apple juice)
Formic acid (bee stings)
Lactic acid (sour milk)
Bases are commonly known as alkalines. These chemicals share several structural characteristics
and properties.
(1) Bases decrease the hydrogen ion concentration of their aqueous solution or
release hydroxide ions (OH-) in solution.
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(2)
(3)
(4)
(5)
(6)
Bases have a bitter taste.
Bases feel slippery.
Bases may be corrosive or poisonous.
Bases neutralize acids.
Bases affect the color of certain indicators.
Some common bases are sodium hydroxide (NaOH), calcium hydroxide (Ca(OH)2), and
magnesium hydroxide (Mg(OH)2). Examples of industrial bases are potassium hydroxide,
barium hydroxide, and strontium hydroxide.
Chemists use a variety of indicators to determine if a substance is an acid or a base.
(1) Acids turn blue litmus indicators, red, are colorless in phenolphthalein, and turn
methyl orange indicator red.
(2) Bases turn red litmus indicators blue, turn phenolphthalein pink, and turn methyl
` orange indicator yellow.
Using natural pH indicators
One of the most interesting properties of acids and bases is their ability to change the
color of some plant materials. Purple cabbage and elderberry extracts respond in an amazing
manner to an acidic or basic solution. In this activity, purple (red) cabbage is used to develop an
acid or a base scale and determine the approximate pH value of various substances.
Chemistry: Understanding the composition of living things
(Biological molecules= Molecules of life)
A living cell is composed of a collection of molecules that are characterized as “organic”,
because they contain carbon and hydrogen atoms. Scientists commonly recognize four classes of
“biological molecules”: 1) Carbohydrates, 2) lipids, 3) proteins, and 4) nucleic acids. The
presence of each of these molecules can be assessed by the application of a simple chemical test.
During this laboratory exercise the student will learn how to test for the presence of three of
these classes, leaving the nucleic acids for a later lab.
1. Carbohydrates – are composed of monosaccharaides (building blocks), which may be
characterized by the number of carbon atoms they contain. They may also be
characterized by the presence of a terminal aldehyde group, or an internal ketone group.
The presence of ether of these two functional groups may be determined by testing a
substance with Benedict’s reagent (solution), which reacts with these functional groups
double-bonded oxygen atom to form a colored precipitate. See the explanation
below:
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A disaccharide may be formed by joining two monosaccharides. If all of the reactive
aldehyde groups or ketone groups are involved in the formation of a bond between the
two monosaccharides (as in sucrose), the disaccharide will react with Benedict’s reagent
thus will generate a negative reaction (-). If at least one ketone or aldehyde group remain
free to react (for example, maltose), it will generate a positive reaction (+) with
Benedict’s reagent.
4) Sugars which possess a free aldehyde or ketone group are called reducing sugars,
because they are oxidized (lose electrons (e-)) by the Cu2- in Benedict’s reagent.
Likewise, these sugars are capable of reducing other molecules, such as Benedict’s
reagent.
5) For example, glucose, maltose, and lactose will test (+) for a simple sugar test.
Sucrose will test negative (-) with Benedict’s reagent.
Note: In solution, a number of monosaccharides, including fructose and ribose, exist in a ring
form which modifies the original ketone and aldehyde groups, leaving them un-reactive to
Benedict’s reagents. In other words, sugars generally need to be in the chain form (rather
than the ring form) to react with Benedict’s reagent. When heated; sugars in the ring form
can convert to chain form. Thus: If a reducing sugar is heated in the presence of Benedict’s
reagent, the solution will change as follows.
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For example below is the molecule structure of glucose. Does glucose appear to be a reducing
sugar? YES. Why? Because the presence of: terminal aldehyde group.
1. A positive (+) control - is the known standard of the experiment that will allow the
researcher to verify the appearance of a positive reaction.
For example, glucose, maltose, and lactose will test (+) for simple sugar test.
For example, potato will test (+) for starch with Iodine/Lugol’s Sol (I2KI)
2. A negative (-) control – is the known standard of the experiment that will allow the
researcher to verify the appearance of a negative (-) reaction. In brief, water doesn’t
possess any of the macromolecules studied (proteins, carbohydrates, and lipids).
For example sucrose will test negative (-) with Benedict’s reagents.
For example water (ddH2 O) will test negative (-) for all macromolecules test.
STUDENT ACTIVITY BENEDICT’S SOLUTION
Materials
6) Hot plate
10) Sharpie
7) 500 mL beaker
11) Metric ruler
8) Test tube rack and test tube
12) Dropper
holder
13) Benedict’s reagent
9) 10 test tube
14) Test solution: distilled water, clear diet soda, clear non-diet soda, pineapple juice,
onion juice, potato juice, milk, glucose solution, sucrose solution, corn syrup, and tap
water.
[Warning: Benedict’s reagent is corrosive. If it splashes onto your skin, wash the area
immediately with soap and water.]
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Note: Label each transfer pipette with the name of the solutions that are distributed to you.
Procedure 5.5 Benedict’s Reagent test
[Warning: Benedict reagent is the only solution you will heat up.]
1. Using a sharpie, label test tube 1-15
2. Pipette 2 mL of the correct stock solution into the test tubes, as described in Table 5.4.
3. Add 2 mL of Benedict’s solution to each test tube agitate the mixture by shaking the test
tubes from side to side or with a vortex mixer, and record the color of the mixture in
Table 5.4.
4. Heat the test tubes in boiling water for 3 minutes. Remove the test tube with a test
tube holder, and record the color of each test tube in Table 5.4.
5. Discard all the solution according to the instructor’s directions. Wash each test tube and
return them to your station.
Table 5.4 Benedict’s Reagent Test for Reducing Sugars
Test
Tube
1
Solution
Distilled water
2
Glucose solution
3
Maltose solution
4
Lactose solution
5
Sucrose solution
6
Starch solution
7
Fructose solution
8
Lemon juice
9
Orange juice
10
Non-diet soda
11
Diet soda
12
Chicken broth
13
Meal Replacement
What color is it
Before heating?
What color is it
after heating?
Conclusion
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Q. In the above test, rank the solution from non-reducing sugar to stronger reducing sugar.
1. __________________________
8. _________________________
2. _________________________
9. _________________________
3. _________________________
10. _________________________
4. _________________________
11. _________________________
5. _________________________
12. _________________________
6. _________________________
13. __________________________
7. _________________________
Q. Why was Benedict’s reagent used to test the urine of diabetics before more sophisticated
methods were developed?
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STUDENT ACTIVITY - IODINE TEST (I2Kl)
Iodine Test for Starch
The iodine test using iodine-potassium iodide (I2KI) has been developed to distinguish starch
from other carbohydrates. Because starch is a coiled glucose polymer, the I2 KI solution interacts
with the starch, producing a bluish black color. The I2KI does not react with non-coiled
carbohydrates and remains a yellowish-brown color. Some carbohydrates, such as dextrin and
glycogen, will produce an intermediate color reaction.
Materials
15) I2KI solution
16) Test tube rack
17) 3-10 test tubes
18) Sharpies
19) Metric ruler
20) Dropper
21) Test solution and material: distilled water, clear diet soda, clear non-diet soda, onion
juice, potato juice, milk, glucose solution, sucrose solution, paper, and cotton
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Procedure 5.6 Lugol’s reagent test [Warning: Do not heat up this solution!]
1. Using a sharpie, label test tube 1-11
2. For test tube 1-9, pipette 3 mL of the correct stock solution in each test tube, as described in
Table 5.5. For test tubes 10 and 11, place a small amount of paper and cotton. Record the color of
each solution in Table 5.5.
3. Add 3 to 5 drops of Lugol’s [Iodine solution or reagent (I2KI)] solution to each test tube, agitate
the mixture by shaking the test tubes from side to side or with a vortex mixer, and record the
color of the mixture in Table 5.5.
4. Discard all the solution according to the instructor’s direction. Wash each test tube and return
them to your station.
Table 5.5 Iodine test for starch
Test
Tube
1
Solution
Distilled water
2
Starch solution
3
Diet soda
4
Non-diet soda
5
Onion Juice
6
Cream
7
Glucose solution
8
Potato juice
9
Chicken broth
10
Cotton
11
Paper
12
Meal Replacement
What color is it
Before heating?
What color is it
after heating?
Conclusion
Q. Which substance contained starch?
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______________________________________________________________________________
Q. Compare and contrast the reaction of potato juice and onion juice.
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ACTIVITY - Grease Spot Test
Grease-spot test for lipids: You probably have noticed lipids are greasy, especially after
eating a bag of potato chips. The grease-spot test is a simple test tube to identify the lipid nature
of substance.
Materials
22) Brown paper bag or brown
24) Rulers
wrapping paper
25) Dropper
23) Scissors
26) Test substance: water, vegetable oil, egg white, soda, potato chip, honey, salad
dressing, butter, rubbing alcohol, beef jerky
Procedure 5.7 Grease - Spot
1. Using a sharpie, label grocery bag piece 1-12.
2. Place a drop of each test substance, as described in Table 5.6, on each labeled spot
grocery bag piece. Set aside to dry for 10 minutes.
3. After 10 minutes, describe the appearance of each spot on the paper.
4. Discard all the solution according to the instructor’s directions.
Table 5.6 Grease-spot test for a lipid
Paper
Substance
1
Distilled water
2
Vegetable oil
3
Egg albumin
4
Non-diet soda
5
Potato chips
6
Honey
7
Salad dressing
8
Butter
9
Alcohol
10
Chicken broth
11
Meal Replacement
Result
Conclusion
Q. If you rub some nose grease (oil from bridge of the nose) on the paper, what will happen?
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STUDENT ACTIVITY - Sudan Test
Sudan test for a lipid
A stain known as Sudan III combines with lipid molecules to produce a brilliant orange color.
Sudan works by forming a hydrophobic interaction with nonpolar molecules. The more vivid the
orange color, the greater the intensity of the interaction.
Materials
27) Sudan III stain
30) Pencil
28) Filter paper
31) Forceps
29) Ruler
32) Test substance: distilled water, whole milk, low-fat milk, skim milk, egg white, egg
yolk, butter, margarine, corn syrup, and pineapple juice.
Procedure 5.8 Sudan Test
1. Obtain several sheets of filter paper
2. On the perimeter of the paper, draw several circles of 2 cm diameter spaced equally apart
(you may use a nickel to draw the circle). You may need more than one sheet of filter
paper to make 12 circles.
3. Number each circle according to the substance in Table 5.7.
4. Place 1 drop of each substance in the appropriate circle. Blot off any excess liquid and
allow the paper to dry completely.
5. Obtain a bowl containing Sudan III stain.
6. Dip the filter papers in the bowl and let them sit for 5 minutes.
7. Remove the filter paper with forceps.
8. Wash the filter paper in a pan of water for 1 minute.
9. Examine the color in each circle and record the color in Table 5.7.
10. Discard all the solution according to the instructor’s direction. Wash each test tube and
return them to your station.
Q. Which substance did react the greatest with Sudan III?
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Q. Which substances did not react with Sudan III?
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Table 5.7 Sudan III test for lipid
Paper
Substance
1
Distilled water
2
Vegetable oil
3
Egg albumin
4
Non-diet soda
5
Potato chips
6
Honey
7
Salad dressing
8
Butter
9
Chicken broth
10
Meal Replacement
Result
Conclusion
STUDENT ACTIVITY - Biuret's Reagent
Biuret test for protein
The Biuret test is commonly used to detect the presence of a protein. The Biuret reagent is strong
blue-green colored solution containing 1% copper sulfate (CuSO4), and sodium hydroxide
(NaOH) or potassium hydroxide (KOH). The reagent changes color from blue-green to violet in
the presence of proteins. The change in color results from the interaction between the copper ions
and the peptide bonds of the protein. The more the peptide bonds, the darker is the resulting
color.
Materials
33) Biuret reagent is extremely corrosive HANDLE WITH CARE!!!!
34) 10 test tubes
35) Sharpie
36) Dropper
37) Test substance: distilled water, sucrose solution, whole milk, bread, ground peanuts,
chicken broth, vegetable oil, egg white, egg yolk, and albumin.
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Procedure 5.9 Biuret’s Reagent
[* Caution: Biuret reagent is extremely corrosive. Handle this chemical with great
care. If you get some on your skin, wash the area with mild soap and water and
notify your lab instructor. Carefully follow your instructor's directions regarding
the use and disposal of Biuret reagent.]
[Warning: Do not heat up this solution!]
1. Using a sharpie, labeled test tube 1-6.
2. Pipette 3 mL of the correct stock solution in each test tube, as described in Table 5.8.
3. Add 2 mL of biuret’s reagent to each test tube and agitate the mixture by shaking the
test tubes from side to side or with a vortex mixer, and record the color of the mixture in
Table 5.8.
4. Discard all the solution according to the instructor’s directions. Wash each test tube and
return them to your station.
Q. Which substances were proteinaceous?
______________________________________________________________________________
______________________________________________________________________________
Table 5.8 Biuret’s Test for a protein
Paper
Substance
1
Distilled water
2
Egg albumin
3
Sucrose solution
4
Chicken broth
5
Potato juice
6
Hamburger juice
7
Meal Replacement
Color after Biuret
Conclusion
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Procedure 5.10 test for unknown
Repeat each test with the unknown solutions and record your result in Table 5.9.
Table 5.9 Test for Unknown Solution
Unknown
A
Benedict’s
test
Lugol’s
test
Grease-spot
test
Sudan III
test
Biuret’s
test
Name of the
unknown
B
C
D
E
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___________________________________________
Last Name, First Name [lab partner N0. 1]
____________________________________________
Last Name, First Name [lab partner N0. 2]
_______________________________
_______________________________
Last Name, First Name [lab
partner N0. 3]
______________________
Section
Last Name, First Name [lab
_______________
group #
partner N0. 4]
___________________
Date
Review Questions Chapter 5: Chemistry Understanding the Composition of Living Things
1. Compare and contrast an acid and a base, and provide examples of each.
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2. Distinguish between inorganic and organic molecule.
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3. Why was water or distilled water tested in each activity?
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4. Compare and contrast ionic and covalent bonds, and give an example of each?
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5. Describe what happens when a polar covalent and a nonpolar covalent substance are
combined. Provide an example of a mixture with these components.
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6. Define monosaccharides. disaccharides, and polysaccharides, and provide two examples
of each.
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7. What is a peptide bond?
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8. What are phospholipids, and where are they found?
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9. What is an essential amino acid?
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10. What is acid rain? Describe the impact of acid rain upon the environment.
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