Chemistry 160 Final Exam key
Please put your name on this exam. There is some useful information on the last
page. I hope you have gotten from this class what you needed. Keep in touch.
100 points
(5) 1. Draw a peptide of the sequence S—K—I at pH 2.
O
H3N+
H
N
O
H
N
O
OH
OH
NH3+
(5) 2. Describe the 5 levels of protein structure.
Primary = amino acid sequence
Secondary = simple folding like alpha helix, beta sheet
Supersecondary = patterns of secondary…beta barrels, etc
Tertiary = 3D structure
Quaternary = subunits
(5) 3. Describe the “induced fit” for protein ligand binding.
In the induced fit model, the ligand and protein are near fits. Both change shape a bit during the
binding process.
(5) 4. Describe an alpha helix.
Right handed helix 3.6 aa/turn with backbone H-bonding between the carboxyl oxygen and
amino hydrogen 4 aa away. R- groups are perpendicular to the helix and on the outside.
Chemistry 160 Final Exam key Pg. 2
(5) 5. When an enzyme catalyzes a reaction, it somehow supplies the activation energy for the
reaction. Where does this energy come from?
Several places: expulsion of highly ordered water of hydration from the binding site, induced fit
shape changes that force the substrate into an unstable transition state
(5) 6. Draw a phosphoacylglycerol where the fatty acids are both stearate and choline is attached.
O
H2C
CH3
+
H3C
N
CH3
HC
O
O
O
P
O
O
O
(CH2)16
(CH2)16
CH3
CH3
C
H2
O
(5) 7. Describe the fluid mosaic model of the cell membrane.
Tired of drawing diagrams:
Phospholipid bilayer with proteins and cholesterol interspersed. The cholesterol regulates
fluidity. There is 2-dimensional diffusion in the membrane. A good analogy is proteins in a
lipid ocean.
(5) 8. Give three ways particles can get across a membrane.
Diffusion, facilitated diffusion, active transport, endocytosis (with and without receptors)
(5) 9. Give three roles of cholesterol.
Regulate membrane fluidity, part of bile salts, basis of steroid hormones, part of vitamin D,
Gives Pfizer a market for Lipitor
(5) 10. What is a second messenger? Give two examples of second messengers.
A molecule released on the inside of a membrane as a response to a binding event in a receptor
on the outside of the membrane. Examples include cAMP, inositol, Ca2+
Chemistry 160 Final Exam key Pg. 3
(5) 11. Draw the following:
a. glucose-glucose in an α 1,4 linkage
CH2OH
CH2OH
O
O
OH
OH
O
OH
OH
OH
OH
b. glucose-glucose in an α 1,6 linkage
CH2OH
O
OH
HO
O
OH
CH2
O
OH
HO
OH
OH
(10) 12. How much energy do we get from 2.50g of glucose in a prokaryote (180g/mol glucose,
7.3 kcal/mol ATP). Assume aerobic respiration.
2.50 g X 1 mole glucose X 32 mole ATP X 7.3 kcal = 3.2 kcal
180 g glucose
mole glucose
mole ATP
(5) 13. Where do each of the following take place:
a. glycolysis cytosol
b. beta oxidation mitochondrial matrix
c. pyruvate dehydrogenase reaction mitochondrial matrix
d. electron transport inner membrane of mitochondrion
e. Kreb’s cycle mitochondrial matrix
Chemistry 160 Final Exam key Pg. 4
(5) 14. For each cofactor below, give its role
a. GTP energy production
b. ATP energy production
c. NAD+ electron carrier (redox)
d. FAD electron carrier (redox)
e. coenzyme A acyl group transfer (acetyl)
(5) 15. Draw a GC base pair
H
N
O -- -- -- H
N
NH -- -- --
N
N
N
N
O
N H -- -- -H
Guanine
cytosine
(5) 16. Draw a short segment of RNA with the sequence G-C-C-G.
Chemistry 160 Final Exam key Pg. 5
O
5' end
N
N
O
O
P
O
G
CH2
N
O
NH2
N
O
NH2
OH
O O
O
N
P
O
C
CH2
N
O
O
O
OH
NH2
O
N
O P
O
CH2
N
O
C
O
O
O
O
OH
N
N
O P
O
CH2
N
O
N
NH2
G
OH
OH
3 ' end
Chemistry 160 Final Exam key Pg. 6
(5) 17. When we say the vectorial nature of nucleic acids is preserved through translation, what
do we mean?
The 5’ end of the RNA corresponds to the amino terminus of the protein
(10) 18. Given the DNA sequence below, determine the RNA sequence and the amino acid
sequence.
3’ DNA T C G G T A C A T G T A A T T T C T T A G T A T T C T G C 5’
5’ RNA AGCC AUG UAC AUU AAA GAA UCA UAA GACG 3’
Amino acid
start Y -
I -
K --- E -- S
stop
Chemistry 160 Final Exam key Pg. 7
Useful Information
O
H3N+
O
pK = 8.95
pK = 2.18
O
pK = 9.15
pK = 10.53
H3N+
O
NH3+
pK = 2.21
OH
Lysine (K)
serine (S)
O
pK = 9.68
H3N+
O
pK = 2.21
O
O
(CH2)16
Isoleucine (I)
CH3
stearate
O
O
CH3
+
H3C
N
CH3
Choline
OH
N
N
OH
NH2
NH
N
Guanine
NH2
N
N
Cytosine
O
H
OH
H
OH
CH2OH
ribose
Chemistry 160 Final Exam key Pg. 8
U
F
F
L
L
S
S
S
S
Y
Y
Stop
Stop
C
C
Stop
W
U
C
A
G
L
P
H
R
U
L
P
H
R
L
P
Q
R
L
P
Q
R
A
G
A
I
I
I
M, start
T
T
T
T
N
N
K
K
S
S
R
R
U
C
A
G
G
V
V
V
V
A
A
A
A
D
D
E
E
G
G
G
G
U
C
A
G
U
First
letter
Genetic Code
second letter
C
A
G
C
C
Third
letter