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 properties? 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
1-pentanol
•
_•
•
Lewis structure of 1-pentanol
q\ • q\ •
•
•
•
•
. •
•
HHH
HH
III
II
H-C-C-C-C-C-O-H
HHH
Ball-and-stick model of glucose
•
•
Lewis structure of glucose
H
\
C - OH
EV I
0
HC
H\ /
\ /H
C
C
HO/ \OH
H/OH
I
I
•
0
H
Ball-and-stick model of
unsaturated fatty acid
•
• s• ,•
•
•
3
I
4
•
•
• „,. •
•
0' •
.0
•
•
•
0 '•
•,
•
0.
•
0•
.7„,....,„.7,....„-OH
H3C
IIIII
HH
ci•
*
Line drawing of 1-pentanol
•
•
•
.......---OH
0
\
Z
OH
HO
OH
?
OH
Lewis structure of unsaturated
fatty acid
0
Line drawing of glucose
H
H
H
H
0
IHIHIHIHII
C
C HI C HI C HI C
I
I
I
I
H
H
FI, I
HHH H
H\ I I
H1-1-1--H
H HH
Line drawing of unsaturated
fatty acid
V
w
l
CH3
1. Name the three molecules that are illustrated in Model 1.
1-pentanol, glucose, and a fatty acid.
2. Name the three types of drawings that are used to illustrate the molecules in Model 1.
Ball-and-stick model, Lewis structure, and line drawing.
Biochemistry Basics
OH
3. How many bonds are typically formed by each of the following atoms:
Carbon
Hydrogen
Oxygen
4 bonds
I bond
2 bonds
4. Which types of drawings in Model 1 provide more accurate images of the shape of a molecule?
Justify your reasoning.
The ball-and-stick models and the line drawings show the shapes more accurately than Lewis structures, which do not convey any three-dimensional information.
5. Refer to Model 1.
a. Symbols or atoms of what element(s) are missing from the line drawings?
Most carbon and hydrogen atoms are not shown in the line drawings.
b. In reading a line drawing, how do you know where atoms of these elements are in the structure if they are missing from the drawing?
The carbon atoms are at the vertex of each angle. The hydrogen atoms would be attached to the
carbons so that each carbon has four bonds total.
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.
TT
I
CH3 0
H
H,C
3
W
OH
111111
H-C-C-C-C-C-OH
NH2
HHHN
H Z NH
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.
HHH
I
I
H-C-C-C-H
I I
HO H
Ball-and-stick
Lewis structure
H3C
CH3
NZ
OH
Line drawing
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.
The Lewis structure would be the easiest to use because it shows the labels of all the atoms.
9. What is the advantage to a scientist in using a line drawing rather than a ball-and-stick model or
Lewis structure?
Answers will vary. Line drawings will save the scientist time in drawing details.
2
POGILTM Activities for AP* Biology
Model 2— Properties of Biological Molecules
Nonpolar Molecules
(hydrophobic)
Polar Molecules
(hydrophilic)
0
Acidic
Acidic
0
HC
OH
H3 C
OH
OH
Fatty acid
Lactic acid
Neutral
cH3
Neutral
0
H3C
“
,
OH
..3,,
CH3
CH3
NH2
Valine (amino acid)
cH3
cH 011
/OH
H
HO
OH
.0
Cholesterol
OH
HO
OH
H
Glucose
OH
H3C
OH
OH
I
H
H
OH
H
H
CH 3
\
HH
HO
H
CH 3
CH3
0 OH
CH 3
Vitamin A
OH
Lactose
Basic
OH
HO
CH
OH
CH3
HO.
CH O.
1110
Adrenaline
HO
HO
NH2
140
Testosterone
Dopamine
NH2
NH
-N
Adenine
Biochemistry Basics
lie
10. Consider the polar molecules in Model 2.
a. In general, the presence of atoms of what element(s) makes a molecule polar?
The presence of oxygen and nitrogen atoms generally makes a molecule polar.
b. What property do atoms of these elements have that helps make the molecules they are in
polar?
Atoms of oxygen and nitrogen are highly electronegative, so they attract electrons more strongly in a
covalent bond, causing an unequal charge distribution in the bond.
c. Can nonpolar molecules also have atoms of these elements? If yes, what distinguishes a nonpolar molecule from a polar molecule?
Yes, nonpolar molecules can have oxygen and/or nitrogen atoms as well, but there are usually far
fewer compared to the number of carbon atoms in the molecule. Also, some molecules with polar
bonds are nonpolar because of the overall three-dimensional shape of the 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?
Water is polar.
b. Is oil polar or nonpolar?
Oil is nonpolar.
c. Which of the substances in Model 2 would dissolve well in water? Justify your reasoning.
Any of the polar molecules from Model 2 would dissolve well in water because their polarity is
similar to that of water.
d. Which of the substances in Model 2 are more likely to dissolve well in oil? Justify your reasoning.
Most of the nonpolar molecules from Model 2 should dissolve well in oil because their polarity is
similar to that of oil.
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.
The solvent for blood is water, so the polar molecules would be found in high concentrations in
blood.
12. Refer to Model 2.
a. What is another term for a polar molecule?
Hydrophilic.
b. What is another term for a nonpolar molecule?
Hydrophobic.
c. Give the literal translation for the terms you gave in parts a and b above.
Hydrophilic = water lover; hydrophobic = water hater.
4
POGIT2m Activities for AP* Biology
13. Functional groups are key groups of atoms in biological molecules. Describe the carboxyl functional group that both acidic molecules in Model 2 have in common.
Both acidic molecules have COOH groups.
14. Recall the definition of an acid that you learned in chemistry. Explain how the reaction below
illustrates the acidic properties of lactic acid.
0
0
H3C
0- ± H 30+
OH + H20
OH
OH
Lactate ion
Lactic acid
An acid is a hydrogen ion donor, or any compound that produces hydronium ions in water. The
hydrogen from the —COOH group of lactic acid is donated to a water molecule to make a hydronium
ion in this reaction.
15. Describe the functional group, called an amine group, that the basic molecules in Model 2 all
have in common?
They all have NH, groups.
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
NI \
HO ilo
HO
,.. .3
HO is
+H20 ---).-HO
H
+IN- CH3
+ 01-1FII
Adrenaline
A base is a hydrogen ion acceptor, or any compound that produces hydroxide ions in water. A
nitrogen atom or amine group from the adenine accepts a hydrogen ion from the water molecule
leaving hydroxide ion.
17. Predict the approximate pH (pH = 7, pH > 7 or pH <7) of fairly concentrated aqueous solutions of the following compounds from Model 2.
Lactic acid
pH < 7
Dopamine
pH > 7
Amino acid
pH = 7
Lactose
pH = 7
Biochemistry Basics
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 intermolecular bond called a hydrogen bond. Hydrogen bonds are weak attractive forces between polar
molecules containing strong polar bonds such as H-0, H-N or H-F.
H. ,.H
°.
„...0,
ti
•<
•
H
Hydrogen bond
d
I<
ti.
..
N..........„....„.----„.
1:1
H
,O. H
A
H
Covalent bond
0
•
I.-1
\
0-H
Covalent bond
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 molecules of the same type) or with water molecules if in a solution?
All of the polar molecules would form hydrogen bonds with water or other molecules of the same type.
6
POGILTM Activities for AP* Biology
Extension Questions
20. Although amino acids have "acid" in their name, some are acidic in water solutions, some are
basic, and others are neutral. Propose an explanation for this observation based on the structures
and descriptions of the amino acids below.
Neutral amino acids
0
0
H3C
HO
0H
OH
NH2
NH 2
Basic amino acid
Acidic amino acid
0
0
0
OH H2N
HO
OH
NH2
NH2
Neutral amino acids have both an amine (NH) group and a carboxylic acid (COOH) group. The
two groups together cause the molecule to be neutral. Acidic amino acids have an extra carboxylic acid
group in the molecule. Basic amino acids have an extra amine group in the molecule.
21. The structure shown below is a line drawing of noncyclic AMP, an important messenger molecule in molecular communication systems.
a. Draw the missing carbon and hydrogen atoms on the molecule.
N H2
I
0
-0 -p-o
\
NN
c)
0
-0
OH 0H
1\11
NH2
I
N--.... / c
N
// C
0
H H-C
II
I
'H
N
HO- P - O - C -H N
I
/( 0 I
H H,C,
OH
14 H
H1
C ■C
I
I
OH OH
b. Write the chemical formula for a molecule of noncyclic AMP.
C10
1-1
N 07P
14 .5 7
Biochemistry Basics
22. The phosphate functional group in the noncyclic AMP molecule of Question 21 contains "acidic
hydrogens."
a. Explain what this phrase means.
The hydrogen atoms attached to the oxygen atoms of the phosphate group will get donated to water
molecules when AMP is dissolved in water.
b. Draw the noncyclic AMP molecule after it has dissolved in water.
NH2
N
0
-
H
0 - P- 0
I
-
< I
(L)
C
N
N.
N
0
OH OH
8
POGILThi Activities for AP* Biology
Teacher Resources — Biochemistry Basics
Learning Objectives
1. Interpret ball-and-stick models, Lewis structures, and line drawings of organic molecules.
2. Identify the carboxyl functional group as one that will make an organic molecule acidic.
3. Identify the amine functional group as one that will make an organic molecule basic.
4. Predict whether an organic molecule is polar or nonpolar based on the functional groups
attached to the carbon skeleton.
5. Identify regions of an organic molecule that may be able to form hydrogen bonds with other
polar molecules.
Prerequisites
1. Students should be able to "read" Lewis structures and write a chemical formula from the
drawing.
2. Students should be able to identify covalent bonds and hydrogen bonds in a drawing of several
molecules in solution.
3. Students should be able to define an acid and a base and write reactions of acidic and basic
molecules with water. See the Acids and Bases activity in POGIL Activities for High School
Chemistry.
4. Students should be familiar with the pH scale. See the pH activity in POGIL Activities for High
School Chemistry.
5. Students should be able to predict the polarity of simple molecules and explain that polarity is
due to highly electronegative atoms in a molecule. 6. Students should know that water is a polar solvent and oil is a nonpolar solvent.
Assessment Questions
1. Predict the pH of a solution of a substance with molecules that contain a carboxyl group
(—COOH).
a. pH = 7
c. pH > 7
b. pH <7
d. There is no way to accurately predict.
2. Which of the following molecules contains an amine group?
a.
HO
OH
b.
c.
HO
0
0
NH2
HO
o
HO OH
OH OH
Biochemistry Basics
9
3. Describe the problem-solving strategy you would use to determine which of the following molecules would be found in high concentrations in fat tissue of an organism.
0
a.
C..
b.
OH
HOOC
H3c
COOH
COOH
NH
1
NHC)
HO
Assessment Target Responses
1. b.
2. b.
3. c. Fat is nonpolar, so nonpolar molecules would be found in higher concentrations in fat because "like
dissolves like." Look for nitrogen and oxygen atoms in the molecules. The molecule with the fewest of
these atoms is probably the least polar.
Teacher Tips
This activity requires students to remember several concepts from a chemistry course. Rather
than give them the background, provide students with copies of introductory chemistry texts and
ask them to look for the information if they do not remember it. This allows them to practice a
valuable process skill—using a resource text. In most cases, once the students see the diagrams in
the text and read a few passages, they will remember the pertinent information.
• Adding hydrogen atoms to a line drawing can be difficult for some students. Remind them that
carbon must have a total of four bonds, so by process of elimination they can determine the
number of hydrogen atoms needed on each carbon to complete the octet.
• Point out to students that the nitrogen atom in an amine group (–NFI 2) has a nonbonded lone
pair of electrons. That is what allows the amine to accept a hydrogen ion so easily from either
water or an acid.
Alignment with AP Biology Framework
Essential knowledge 4.A.1: The subcomponents of biological molecules and their sequence
determine the properties of that molecule.
• Essential knowledge 4.B.1: Interactions between molecules affect their structure and function.
• Science Practice 1: The student can use representations and models to communicate scientific
phenomena and solve scientific problems.
10
POGILThi Activities for AP* Biology
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Biochemistry Basics