Chemistry 153A

Practice Final Exam KEY

First letter of your last name _____
Question #
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

Value
25

Score
___________KEY______________
Print your full name
(Last Name First)

5
10
10

______________________________
Print your TA's name
______________________________
Time and day of your discussion section

7
I have read the instructions below.
14
18
15

______________________________
Signature
INSTRUCTIONS

18

READ EACH QUESTION CAREFULLY!

20

SHOW YOUR CALCULATIONS!

20

WRITE YOUR LAST NAME IN THE SPACE

PROVIDED ON EVERY PAGE OF THE EXAM.

16
25
17
15

TOTAL
TOTAL COURSE
SCORE
FINAL COURSE
GRADE

NO CREDIT WILL BE GIVEN FOR

ANYTHING WRITTEN ON THE BACK OF A
PAGE OR IN A SPACE OTHER THAN THAT
PROVIDED FOR YOUR ANSWER.
ANSWERS MUST BE BRIEF AND TO THE
POINT. WHERE WORD LIMITS ARE GIVEN,
NO CREDIT WILL BE GIVEN FOR THE PART
OF YOUR ANSWER THAT SIGNIFICANTLY
EXCEEDS THAT LIMIT.
Numbers in parentheses represent the point values.
Gas constant: R= 8.31 x 10-3 kJ/ oK/mole
Faradays constant: 96.5 kJ V-1 mol-1

Page 2
1. (25) a.

2. (5)

The complexity of living cells is indicated by the _Number _ and average _Size
(Molecular weight)_ of different molecules of which they are composed.

or

b.

The statement that water is amphoteric means that a water molecule can be a _Proton__ donor
or acceptor and can thus form a _hydroxide_ ion or a _hydronium_ ion.

c.

The extraordinary cohesiveness of water is attributed to extensive _hydrogen_ _bonding_

between molecules.

d.

pH is a property of a _solution__ while pKa is a property of a _weak acid__.

e.

If a weak acid is dissolved in a solution at a pH that is greater than its pKa by one pH unit or
less, the addition of H+ to the solution will result in increased _protonation_ of the weak acid.
This will tend to minimize the change in the _pH___ of the solution.

f.

The inductive effect of the -carboxyl group of an -amino acid will tend to lower_ the pKa of
the -amino group, and the electrostatic effect of that same -carboxyl group will tend to _raise
the pKa of the -amino group.

g.

The peptide plate concept arises from the restriction of rotation around bonds due to steric
hindrance.
TRUE
FALSE

h.

Would you expect polar amino acids at the outer surfaces of proteins to be more likely to
hydrogen bond to water molecules or to each other. _water________ Why?
They will be in close contact with many more water molecules than with other polar amino
acid side chains.

i.

Would you expect an -helix of polyalanine to be disrupted by placing the polypeptide in an

organic solvent? _No____ Explain your answer. [ 40 words]
The hydrogen bond stabilizing the -helix will be strong in the apolar organic solvent, and
contact of alanine side chains with an organic solvent at the surface of the helix would not
be unfavorable.
Which of the following forms of alanine would you be unlikely to detect in aqueous solution at
any pH? [correct answer is indicate by a check mark]

CH3
+

H3N

C
H
Alanine

CH3
COOH

H2N

C
H
Alanine

CH3
COOH

H3N

C
H
Alanine

CH3
COO

H2N

C
H
Alanine

COO

Name: ____________________________________ page 3

3. (10) Below is a depiction of the relative radial positions of amino acid residues of an alpha helix, looking
down the axis of the helix.
8

12
5

15

16

4
11

18

13
14

6
3

10

17

Circle the polypeptide below that would be most likely to form an amphipathic -helix? [check
marked below]

10 11 12

13 14 15 16 17 18 19

ser-val-ala-asn-ala-leu-met-lys-val-ala-thr-asp-phe-asp-gln-glu-leu-his-ala
ser-trp-tyr-phe-ala-thr-met-leu-his-ala- phe-arg-trp -ile-gly-glu-leu-his-ala
arg-leu-ser-ala-lys-val-glu-ile-asp-phe-his-asp-cys-gln-met-tyr-ala-asn-ala

4.(10) a.(2) How do you calculate the number of possible stereoisomers of a monosaccharide?
n

# of stereoisomers = 2 , where n = # of chiral centers (asymmetric carbons)

b. (2) Which has more stereoisomers, an aldopentose or a ketohexose? they have the same #_
c. (6) While doing ecological research in the Masi Mara plains of Africa, a friend of yours discovers a
new sub-species of Thompson Gazelle that seems to have a selective survival advantage,
enabling its population to grow rapidly relative to the general population of Thompson Gazelles.
On closer observation your friend observes that the new sub-species is capable of faster bursts of
speed, making it more successful at fleeing from lions, leopards, and cheetahs. As a renowned
biochemist and geneticist, you join her to investigate the nature of the mutations leading to this
enhanced ability. You find that there appear to be some mutations affecting the carbohydrate
storage enzymes of this sub-species leading to a change in the structure of a particular
polysaccharide. What is the identity of this polysaccharide and the nature of the structural
change? [ 30 words]
A mutation in a gene coding for a glycogen storage enzyme has resulted in synthesis of
glycogen molecules that are more highly branched. The resulting increase in non-reducing
ends allows faster mobilization of glucose providing a potential for more rapid release of
energy for running.

Name: ____________________________________ page 4

5.

(7)

a. Which of the following lipids is not a component of biological membranes?

_____C____
A. glycerophospholipids
B. sphingophospholipids
C. triacylglycerols
D. cholesterol
b. Triacylglycerols provide highly reduced energy storage.
TRUE FALSE
c. Integral membrane proteins always have a higher percentage of hydrophobic residues
than soluble aqueous proteins do.
TRUE
FALSE
d. A membrane rich in stearic acid would be less fluid than one rich in oleic acid.
TRUE

FALSE

e. Glycerol is the parent compound for the major lipids of the myelin sheath. TRUE

FALSE

TRUE

FALSE

f. Biological membranes are rich in phosphate.

g. The bonds between fatty acids and glycerol in glycerolipids are ____ester______ linkages.
6. (14)

Evidence indicates that some of the following events occur as hemoglobin carries out its natural
function. Indicate the proposed normal sequence of these events reflecting their cause and effect
relationships by assigning each event a number indicating the order of occurrence. If two events
seem to occur simultaneously give the lower number to the event that causes the other. Use an X
to indicate any event that does not normally occur.
__1__ Red blood cells containing Hb enter the lungs where pO2 is high.
__4__ Weak interactions at polypeptide contact points become strained.
__6___ All subunits change to the R state in a concerted event.
__8___ Additional O2 molecules bind with increased affinity.
__5___ Interchain H-bonds and salt bridges of the T-state break.
__X___ The heme iron, Fe2+, becomes oxidized to Fe3+.
__9___ Red blood cells containing Hb carry oxygen to the tissues where pO2 is low.
__2___ The first O2 binds with low affinity to the heme iron of an -chain of deoxy-Hb.
__3___ The F-helix shifts toward the heme ring tending to induce a conformational change in
the entire polypeptide (subunit).
_10___ Certain Hb residues become protonated as bound O2 dissociates from Hb.
__X___The R-state is stabilized by protonation of certain Hb residues and binding of 2,3
bisphosphoglycerate
__X___ The first O2 binds with low affinity to the heme iron of an -chain of deoxy-Hb.
__X___ Additional subunits (polypeptides) change to the R-state in sequence as additional O2
binds until all binding sites are occupied.
__7___ New interchain H-bonds and salt-bridges form, stabilizing the R-state

Name: ____________________________________ page 5

7. (18)

A diagram of one stage of the reaction mechanism of the enzyme, subtilisin, is shown below.
This enzyme is mechanistically related to trypsin and chymotrypsin, but not evolutionarily
related.
Ser-221
His-64

N
C

H2 C

O
H

Asp32

C
C
H2

H
R2

C
N
H

Asn
155

H2 C
O

H2
C

CH

H2 C

R1

N
H

O
Ser-125

a. (2)

Draw a single circle encompassing all the atoms of the reaction intermediate that
originated as part of the substrate.

b. (10) Suggest a role played in the catalysis by each of the following residues. Mention general
catalytic mechanisms where appropriate, but also state specifically how the effects of
each residue help to increase the rate of the reaction. [ 25 words each]
Electrostatic stabilization of his+

Asp-32:

Electrostatic catalysis:

His-64:

Acid/Base Catalysis: Proton acceptor and donor

Ser-221: Covalent catalysis: Nucleophile - forms covalent bond to

carbonyl carbon of substrate/intermediate
Asn-155: Preferential binding of transition state (intermediate): forms
hydrogen bond to oxyanion of tetrahedral intermediate
Ser-125:
c. (6)

Stabilizes binding of substrate to enzyme via hydrogen bonding

Draw curved arrows on the diagram indicating the movement of electrons in the expected
next step of the catalytic mechanism. Explain the immediate result of this step either in
words or by drawing a diagram of the result. [ 30 words]
In the next step, the amide bond breaks as the newly forming primary amino group
accepts a proton from his-64. A new covalently enzyme bound intermediate ester
forms.

Name: ____________________________________ page 6

8.

Nearly all organisms carry out glycolysis. However, a few anaerobic bacteria, such as Pseudomonas, utilize an
alternative pathway, known as the Entner-Doudoroff pathway, for the catabolism of glucose. It is shown below.
O
O
C
CH2OH
CH2OPO3=
ATP
ADP
H C OH
O
H2O + NAD
NADH + H+
O
H
H H
HO C H
H H
H
H C OH
HO OH H OH
HO OH H OH
glucokinase
H C OH
glucose-6-phosphate
dehydrogenase
OH
H
CH2OPO3=
H
OH
6-Phosphogluconate
glucose
glucose 6-Phosphate

(15)

6-phosphogluconate
dehydratase
COOPO 3=

CH2OPO3=
1,3-bisphosphoglycerate
ADP

CHO
H+ + NADH

CHOH

Pi + NAD

CHOH

H C

H C OH
H C OH
CH2OPO3=
2-keto-3-deoxy-6phosphogluconate
(KDPG)

ATP
COO-

C O

KDPG-aldolase

1,3-bisphosphoglycerate
kinase

COO-

O
C

CH2OPO3=
3-phosphoglycerate

glyceraldehyde-3-P
dehydrogenase

H 2O

H 2O

ATP

ADP

COO-

phosphoglycerate CHOPO3=
CHOH
C OPO3=
mutase
enolase
pyruvate kinase
CH
OH
CH2OPO3=
2
CH2
3-phosphoglycerate
2-phosphoglycerate
phosphoenolpyruvate

COO-

COO-

CH3
pyruvate

CH3
pyruvate
2H+

pyruvate decarboxylase

CH2OH
CH3

a. (7)
b. (4)

2NAD

2CO2

2NADH + 2H +

alcohol dehydrogenase

CHO
CH3

Write a balanced equation summarizing the net result of this pathway.

glucose + ADP + Pi + 2H+ 2 ethanol + 2 CO2 + ATP + H2O

Would the final two reactions of this pathway be necessary to an aerobic organism utilizing the Entner-Doudoroff
pathway? Why? [ 40 Words]

No, because NAD+ can be regenerated by the electron transport chain reactions.

c. (4)

Why do you suppose early evolution (natural selection) produced so many more anaerobic organisms that utilized
glycolysis than the Entner-Doudoroff pathway? [ 35 Words]

It is more efficient at energy extraction and conservation in the form of 2 ATP per glucose
as compared to 1 ATP per glucose generated by the Entner-Doudoroff pathway.

Name: ____________________________________ page 7

9. (18)

Pyruvate is a central metabolite of the aerobic cell. Name and draw the structures of three
metabolic intermediates which can be made in a mammalian muscle cell directly from pyruvate in
a net reaction catalyzed by a single enzyme or enzyme complex. Place an asterisk next to the
carbon at which you would expect to find 14C originating from carbon # 2 of pyruvate as the result
of this reaction. Name the enzyme or complex and specify the intracellular conditions (metabolic
status) that would favor that particular reaction over the others.
Compound
Enzyme & Conditions Favoring Reaction
[name & structure]

COOO
CH2
COO-

Pyruvate carboxylase
high [AcCoA]
need for carbon compounds
low energy needs

Oxaloacetate

COOH

OH
CH2

L-Lactate

O
H3 C

SCoA

Lactate dehydrogenase
high muscle activity
need for rapid ATP synthesis
anaerobic metabolism

Pyruvate dehydrogenase
low [AcCoA], low NADH
need for energy

Acetyl-coenzyme A

10. (20)

Briefly state the metabolic role of the reaction catalyzed by each of the following enzymes and give
the class to which the enzyme belongs. [ 30 words each]
a. Isocitrate lyase: lyase: part of the glyoxylate bypass to achieve net synthesis (replenish)
oxaloacetate
b. 3-phosphoglycerol dehydrogenase: oxidoreductase: shuttles electrons from cytoplasmic
NADH into electron transport chain
c. phosphoglycerate kinase: transferase: substrate level phosphorylation of ADP to make
ATP - part of glycolysis
d. hexokinase: transferase: 1st step of glycolysis - phosphorylates glucose by transfer of
phosphate from ATP. Traps glucose in the cell.

Name: ____________________________________ page 8

11.

The following cofactors participate in the reactions catalyzed by the pyruvate dehydrogenase complex.
Write the full name of each specific structure drawn below on the line directly beneath it.
Show on the next line, the enzyme (E1,E2 or E3), if any, to which each cofactor is tightly bound.
Circle the reactive atom(s) of each.

(20)

a.
b.
c.

CH3
CH2

NH2
CH2

CH2

O
O
O P O P O-

O-

OCH2

S
- OOC

CH3

(CH2 ) 4

CH

CH2

A.

thiaminepyrophospate____

__E-1______

B. __lipoic acid _______

___ E-2____
O
CH3

N
NH

CH3OH O
O CH2

O
C CH C NH CH2 CH2 C NH

CH2

CH2 SH

CH3

CH3

ADP (3'P)

(CHOH) 3
CH2

C.

__Coenzyme A ______________
__None___

CH2

O
P O AMP
O-

D.__flavin adenine dinucleotide

__E-3_____

12.(16) a. (6) Since the oxidation of NADH in electron transport results in the synthesis of more ATP, why doesnt the aerobic
cell use NAD+ exclusively as the electron acceptor in metabolic oxidation-reductions instead of sometimes using
FAD? [ 50 words]

NADH does not have a high enough reduction potential to oxidize some metabolic
intermediates (e.g., alkane to alkene) FADs reduction potential is high enough to accept
electrons from some of these compounds.
b.(10) Describe the role played by CoQ in energy metabolism. Include its properties, possible oxidation states, location,
relationship to other components of the electron transport and the postulated role of Q cycling (details of Q cycling
not required). [ 75 words]

CoQ is a mobile electron carrier of the electron transport chain. It is very hydrophobic
and thus soluble in the interior of the lipid bilayer of the mitochondrial inner membrane.
It diffuses laterally in the membrane to contact and bind the active sites of complex I,
complex II or flavoprotein dehydrogenase (FH). It accepts electrons from the redox center
of any of these sites and carries them to complex III where the electrons are passed along.
It has three oxidation states known as ubiquinone (fully oxidized), ubi-semiquinone and
unbiquinol (fully reduced). Ubiquinone acquires two electrons at I, II or FH to become
fully reduced to ubiquinol. At complex III it apparently cycles through all three oxidation
states in a complex process that enables single electrons to be passed one at a time through
the subsequent redox centers (one-electron carriers) with concomitant translocation of 4
protons from matrix to cytosol per CoQ reoxidized. This latter process is known as Q
cycling.

Name: ____________________________________ page 9

13.(25) a. (6) Write a balanced net equation summarizing the TCA cycle beginning with acetylCoA.(no
structures)

AcCoA+ 2H2O+ 3NAD++ FAD+ GDP+ Pi 2CO2+ 3 NADH + 3H+ + FADH2 + GTP + CoA
b. (3) Write a balanced net equation summarizing the synthesis of -ketoglutarate from acetylCoA
and Oxaloacetate in an aerobic cell. (no structures)
AcCoA + oxaloacetate + H2O + NAD+ -ketoglutarate + NADH + H+ + CO2
c. (3) Assume that the -ketoglutarate generated in part (b) above is used in an amino acid synthesis
pathway. What impact could the this process ultimately have on the ability of the cell to
continue to carry out the TCA cycle and why? [ 40 Words]

It would ultimately lead to the depletion of oxaloacetate. This would result in the cells
inability to carry out the TCA cycle unless oxaloacetate is replenished.
d. (3) Write a net balanced equation illustrating a means by which aerobic plant cells compensate
for the effects discussed in your answer to (c) above. (no structures)

2 AcCoA+ 2 NAD+ + FAD + 2H2O oxaloacetate 2 NADH + 2 H+ + FADH2 + 2CoA

e. (10) Calculate (and itemize) the energetic cost of the process in (d) above per acetylCoA molecule
utilized as compared to the use of acetylCoA into the complete TCA cycle. Specify each
source of energetic cost and give your final answer in terms of ATP equivalents using the
old values for P/O ratios.
Item of energy cost

2 NADH from isocitrate dehydrogenase reaction

2 NADH from -ketoglutarate dehydrogenase rx
2 GTP from succinylCoA synthetase
1 FADH2 from succinate dehydrogenase

ATP
equivalents
6
6
2
2

16 ATP equivalents lost per 2 acetylCo utilized

16

TOTAL ATP EQUIVALENTS per acetylCoA utilized

Name: ____________________________________ page 10

14.

(17)

Refer to the table below in answering the following questions.

Go of phosphate hydrolysis
Compound
Go (kJ/mol)
-61.9
PEP
-49.4
1,3-bisphosphoglcerate
-43.1
Acetylphosphate
-43.1
Phosphocreatine
-32.2
Phosphoarginine
-33.5
PPi
-32.2
ATP AMP +PPi
-3O.5
ATP ADP +Pi
-20.9
Glucose-1-phosphate
-13.8
Fructose-6-phosphate
-13.8
Glucose-6-phosphate
-9.2
Glycerol-3-phosphate

a. (6)

The phosphorylated compounds, phosphocreatine and phosphoarginine, are sometimes

used as energy reservoirs in muscle tissue. Calculate the standard free energy change for
the generation of phosphoarginine via phosphoryl transfer from ATP.
Go
kJ/mol
ATP + H2O ADP + Pi
-30.5
arginine + Pi phosphoarginine + H2O
+32.2
ATP + arginine phosphoarginine + ADP
+1.7

b. (3)

Assuming that the necessary enzyme catalysis is always available, under what conditions
would you expect the reaction in (a) above to occur in the direction of formation of
phosphoarginine in the cell? [ 35 words]
Go = -RT ln Keq thus Go = - ln Keq
1.7 kJ/mol = -ln Keq
RT
2.5 kJ/mol
ln Keq = -0.68

Keq = 0.51 thus the reaction will proceed to the right when the ratio
([phosphoarginine] [ADP]) / ([ATP] [arginine]) < 0.51
c. (8)

Explain the large difference between Go for hydrolysis of phosphate from carbon #1 of
glucose-1-phosphate and Go for hydrolysis of phosphate from carbon # 1 of 1,3bisphosphoglycerate? Suggest a thermodynamic explanation for this observed difference
(i.e. plausible reasons for relative stability of products of hydrolysis). [ 70 words]

Glucose phosphorylated at C-1 is an acetal, while the dephosphorlyated form is a

hemiacetal in equilibrium with an aldehyde. The dephosphorylation at C-1 of 1,3bisphosphoglycerate converts an ester to a carboxylic acid. Both products are
much more stable (have lower free energy) than their respective reactants, making
both dephosphorylations highly spontaneous. However, the carboxylic acid has a
greater resonance stabilization relative to the ester than the aldehyde has relative to
the acetal. Thus it has a greater relative stability contributing to a more favorable
free energy change.

Name: ____________________________________ page 11

15.(15) a. (6) If the actual E for the net electron transport complex I reaction, NADH + H+ + CoQ NAD+
+ CoQH2, is +0.36 V, and it takes 5.5 kcal/mole to pump protons across the inner
mitochondrial membrane. Approximately how many moles of protons could possibly be
translocated by complex I per mole of NADH oxidized? [No credit unless you show all of your
calculations.]

1kcal = 4.184 kJ, thus it takes 23kJ/mol of protons pumped under these conditions.
G = - nFE
G = - nF(0.36) = (2)(96.5kJ/mol)(0.36) = -69kJ/mol
-69kJ/mol = 3 protons could be translocated per transfer of electrons from NADH to CoQ
-23kJ/mol

b. (6) Assuming the same conditions as for part a, (i.e. G = -23 kJ/mol for protons flowing into
mitochondrial matrix from cytoplasm and assuming intramitochondrial concentrations of
0.005M ATP, 0.01M Pi, and 0.0001M ADP, what minimum number of protons flowing through
the ATP synthase is required to drive the synthesis of 1 ATP?

For ATP synthesis: G = Go+ RTln [ATP]/ [ADP] [Pi]

= 30.5kJ/mol + (2.5kJ/mol)(ln5000)
= 30.5kJ/mol + (2.5kJ/mol)(8.5)

= 30.5kJ/mol + 21.3kJ/mol = 51.8 kJ/mol

51.8 kJ/mol needed per ATP
per proton

= 2.25 , but pumping of fractional 23kJ/mol provided

protons is obviously not possible

Thus it will take flux of at least 3 protons per ATP

c. (3) If the order of participation in the electron transport chain is that electrons are passed to
cytochrome b566 before they are passed to cytochrome a, which would you expect to have the
higher reduction potential?
___ cytochrome a _____