Biochemistry Basics

What concepts from chemistry are helpful in studying biology?

Why?
Typically chemistry is a prerequisite course for advanced biology courses. This is because everything in
your body, everything in a plant, everything in a virus, etc. is made of atoms. The structures and
properties of the molecules in an organism determine the features and properties of the organism. Which
molecules are polar, which are nonpolar? Which molecules have acidic properties, which have basic prop
erties? A quick review of these concepts at the beginning of your advanced biology course will help you
to understand the molecular basis for life.

Model 1 – Molecular Drawings

Ball-and-stick model of Lewis structure of 1-pentanol Line drawing of 1-pentanol
1-pentanol

OH
H3C

Ball-and-stick model of glucose Lewis structure of glucose Line drawing of glucose

Ball-and-stick model of Lewis structure of Line drawing of

unsaturated fatty acid unsaturated fatty acid unsaturated fatty acid

1. Name the three molecules that are illustrated in Model 1.

2. Name the three types of drawings that are used to illustrate the molecules in Model 1.

Biochemistry Basics 1
3. How many bonds are typically formed by each of the following atoms:
Carbon Hydrogen Oxygen

4. Which types of drawings in Model 1 provide more accurate images of the shape of a molecule?
Justify your reasoning.

5. Refer to Model 1.
a. Symbols or atoms of what element(s) are missing from the line drawings?

b. In reading a line drawing, how do you know where atoms of these elements are in the struc
ture if they are missing from the drawing?

6. Locate the carbon and hydrogen atoms in the line drawing of isoleucine shown below and draw
them in as if the drawing were a Lewis structure.
O
CH3
C
H3 OH

NH2
Isoleucine

7. Isopropyl alcohol is a three-carbon molecule with an –OH group attached to the middle carbon
atom. Draw this molecule using all three types of drawings.

8. If you were asked to write the chemical formula for one of the compounds in Model 1, which
type of the drawing would be the easiest to use? Justify your reasoning.
 9. What is the advantage to a scientist in using a line drawing rather than a ball-and-stick model or
Lewis structure?

2 POGIL™ Activities for AP* Biology

Model 2 – Properties of Biological Molecules
Polar Molecules Nonpolar Molecules
(hydrophilic) (hydrophobic)

Acidic O Acidic
O
C
H3 OH
OH C
H3 OH Fatty acid
Lactic acid

Neutral Neutral
O
CH3 H3C CH3
CH3
H3C OH CH3
NH2 CH3

Valine (amino acid)

OH

HH HO
O
Cholesterol
OH H H
OH
HO
H
OH

Glucose H3C CH3 CH3 CH3

OH
OH

H OH
O CH3
OH

OH H H
Vitamin A
HO
O
O
H

OH H H
H
OH OH
H CH3
H
H CH3
OH

Lactose
Basic
H
OH
O
HO
N Testosterone
CH3

HO

Adrenaline
HO
NH2

HO

Dopamine
NH2

N
N

NH
N

Adenine

Biochemistry Basics 3
10. Consider the polar molecules in Model 2.
a. In general, the presence of atoms of what element(s) makes a molecule polar?

b. What property do atoms of these elements have that helps make the molecules they are in
polar?

c. Can nonpolar molecules also have atoms of these elements? If yes, what distinguishes a non
polar molecule from a polar molecule?

11. In chemistry there is a saying “like dissolves like,” which means things will mix with or dissolve
into each other best when their polarities are similar.
a. Is water polar or nonpolar?

b. Is oil polar or nonpolar?

 c. Which of the substances in Model 2 would dissolve well in water? Justify your reasoning. d.

Which of the substances in Model 2 are more likely to dissolve well in oil? Justify your

reasoning.

e. Which class of substances in Model 2, polar or nonpolar, is more likely to be found in high
concentrations in the bloodstream of a vertebrate? Justify your reasoning.

12. Refer to Model 2.

a. What is another term for a polar molecule?

b. What is another term for a nonpolar molecule?

c. Give the literal translation for the terms you gave in parts a and b above.

4 POGIL™ Activities for AP* Biology

13. Functional groups are key groups of atoms in biological molecules. Describe the carboxyl func
tional group that both acidic molecules in Model 2 have in common.

14. Recall the definition of an acid that you learned in chemistry. Explain how the reaction below
illustrates the acidic properties of lactic acid.
O C
H3 O–
H3O+
C
H3 OH OH + H O + OH
2

Lactic acid Lactate ion

 15. Describe the functional group, called an amine group, that the basic molecules in Model 2 all
have in common?

16. Recall the definition of a base that you learned in chemistry. Explain how the reaction below
illustrates the basic properties of adrenaline.
OH
H
H
+
HO HO CH3 N
HO HO N CH3

+ H2O
H + OH –

Adrenaline

17. Predict the approximate pH (pH = 7, pH > 7 or pH < 7) of fairly concentrated aqueous solu
tions of the following compounds from Model 2.
Lactic acid ____________ Dopamine ____________ Amino acid
____________ Lactose ____________

Biochemistry Basics 5
O
H

H
18. In chemistry you learned that covalent bonds are one type of intramolecular bond. They occur
between nonmetal atoms in a molecule. You may have also learned about a type of intermo lecular
O
bond called a hydrogen bond. Hydrogen bonds are weak attractive forces between polar H
molecules containing strong polar bonds such as H-O, H-N or H-F.

HH
 OO
HH

H
H
N O
H
H
O
O

HHO
H

a. Label at least two covalent bonds in the diagram above.

b. Label at least one hydrogen bond in the diagram above.
19. Which of the molecules in Model 2 would form hydrogen bonds with itself (that is, other mol
ecules of the same type) or with water molecules if in a solution?

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Extension Questions
 O
20. Although amino acids have “acid” in their name, some are acidic in water solutions, some are
O O
O
basic, and others are neutral. Propose an explanation for this observation based on the
C
structures H3 OH
C
H3 OH
and descriptions of the amino acids below.
HO OH
HO OH
NH2
Neutral amino acids
NH2
NH2 O NH2 O
O O
C
H3 OH HO OH HO OH NH2
C
H3 OH NH2 NH2
NH2

Acidic amino acid Basic amino acid O

OO
O
OO

HO OH HO OH
N N
H2 OH H2 OH

NH2 NH2 NH2

NH2
OOOO O O
N
H2 OH NH2
HO OH HO OH NH2
NH2
NH2
N
H2 OH

21. The structure shown below is a line drawing of noncyclic AMP, an important messenger mol
ecule in molecular communication systems.
a. Draw the missing carbon and hydrogen atoms on the molecule.
NH2

NN
O
 O
O
N
➾
– OH
O
P N
–
O OH

b. Write the chemical formula for a molecule of noncyclic AMP.

Biochemistry Basics 7
22. The phosphate functional group in the noncyclic AMP molecule of Question 21 contains “acidic
hydrogens.”
a. Explain what this phrase means.

b. Draw the noncyclic AMP molecule after it has dissolved in water.

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