Chem153A Winter 2015

Page 1 of 9

Final

Last Name:_____________________________

Chem 153A Practice Final Exam:

This was not an actual final from any quarter, but is a combination of questions from previous finals that were not
in the study questions this quarter.

Constants and values that may be necessary for the Exam:

Abbreviations are OK
for short answer and
explain questions
1/2
1/3
1/4
1/5
1/6
1/7
1/8
1/9
1/10
1/11
1/12
1/13
1/14
1/15
1/16
1/17
1/18
1/19

Functional Group
Carboxyl-terminus
Amino-terminus
-carboxyl (free amino acid)
-amino (free amino acid)
Aspartate R group
Glutamate R group
Histidine R group
Cysteine R group
Tyrosine R Group
Lysine R group
Arginine R group

pKa
3.5
8.5
2
9.5
4
4
6
8.2
10.0
10.5
12.5

0.5
0.333
0.25
0.2
0.167
0.143
0.125
0.111
0.1
0.091
0.083
0.077
0.071
0.067
0.0625
0.059
0.056
0.053

Go of ATP Hydrolysis = -30.5 kJ/mol

Gcell of ATP Hydrolysis = -50 kJ/mol

Chem153A Winter 2015

lrnal

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Page 2 of9
1. (16 pts) Use the following peptide for the questions on this page: M
pH z.o.
a). (4 ptsl Draw the peptia"
d
(6
pts)
b).
For each amino acid provide the full name,^rF
and 3-letter

*9u-

it

+.,.t- -L| -F. -.5

cr+L

i*,,I

- |-

L^, L a,-p

oill

code

arv'

at,4n,

!"*,,]+ qrxJ" (*'*

",,*

- L1.,-! -,t - i-t E ^ I - t - "^-

C*r_

,l+

\
,4,\ct"t. C--O
L Fr.

I
Ctlf

CHr

l1Ltl;',';'

Cnsr)

L$.
I

Cu-

,,
tr 3-

^J

aNQt^trrr- &sgor^'7-tr'- Aa*-+tt

(tuel

[As,u)

G4?

c). (5 pts)Draw the titration curve forthe peptide above on the axes provided. On the graph indicate the pl, and
the exact buffering ranges ofthe peptide. (Be slre to show all vour work)

14

t2
10

CL

K,'r:

-q,>r'

4
2

/t

..1.>

4.o
b-' \

8
5

')(

?L--

3'&A9

-2.S

0
0.5

or- eq1,ii""t.n,,

2.5

2. (8 pts) Although the majority of biological macromolecular structure formation occurs in the aqueous cytosol,

some membrane proteins fold within the cell membrane.

A). (4 pta) Based on the native conformation ofwater soluble proteins, why would you not expect them to fold
properly in a cell membrane? (consider both enthalpyand entropy)
They have polar amino acids on the surfaag whlah would then have to make weaker interadionswith the nonpolai part of the membrane, This would lead to an unfavorable change in enthalpy.
This would stilllead to an increase in entropy ot water with the hydrophobic amino acids being buried.
(Or: the hydrophobic amino adds would have to be outside (not native structure))
B). (4 pts) Based on the native conformation of membrane proteins what would allow them to fold properly
within a cell membrane? {aonsider both entropy and enthalpy)

Membrane proteins have hydrophoblc amino acids outsidethat can interacl with the non-polar sections ofthe
membrane, and the polar amino acids can stillbe making tavo.able interactions insidethe protein (so the
.hange in enthalpy would still b negligible). The protein then being inserted orfolding in the membdne would
release any ordered water moleculesto get the increase in entropy to d.ive folding.

S.l S

Chem153A winter 2015

Page 3

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Final

of9

3. (14 pts) You are studying the function of Motorcadease, which converts Gridlock into Carmageddon.

Below is the lineweaver burke plot for your kinetics data with 0.001
a)- (6 pts) Calculate KM and k,", for this enzyme. Show all your work.

[M Motorcadease.

l-r

0.5

-npN-

04

L',*f Ll r
KM =

0.3
E

:--L-!,()2 = 50 ^

l-1

vn*r=# = 9.l1lv- :
6D\FF1

o.2

o.

*..,=
-0.04 -0.03 -0.02

0.01 0 0.01 0.02 0.03 0.04

lopoof

IOP oq

v-

0.0s

1/tGridlockl {1/mMl
b). {4 pts} Draw in the plot you would expect if you doubled the amount of enzyme.
c). (4 pts) Draw in the plot you would expect for a non_competitive inhibitor of MotorcadeAsE.
4. (13 pts) Below is the Binding curve for calcium binding to calmodulin.
a). (2 pts) Fully !abel anything missing on the axes.
7
b). (2 pts) what is the KD for Ca?' binding to

calmodulin?
1x1045 M

<0e

-!J'08
o.z
'/)

c). {2 pts) What does this number represent?

0.6

4
(*

halfthe
to

The aoncentration of aalcium required for

0.5

binding sites on calmodulin to be bound

calcium.

0.4
0.3
0.2
0.1
0

7.E-O7 1.E-O5 1.E-05

1.E 04

d). (3 pts) The presence of troponin increases the

affinity of Calmodulin for Calcium 10 fold. Sketch in
a calclum binding curve in the presence of an
eff ective concenttarion of troponin.

This should be a sigmoidal curve with the 0.5 point

at 1 E -0.6
explain
the biochemical basis for the curve above
4 calcium binding sites. BrieflY

roglo ICAciu-('-l (M]

e). (4 pts) calmodulin has
(30 words maximum)

Calcium binding to one site causesthe other binding sites to switch trom low to high affinity states,leading
more calcium binding, whlch makes the curve sigmoidal.

to

Chem153A Winter 2015

Final
Page 4 of 9
5. (6 pts) Why are London Dispersion forces always attractive?

Last Name:_____________________________

They are due to neighboring electron clouds causing each other to have temporary dipoles (or asymmetric
distributions of electrons around the atoms) thus there is always a partial positive charge near a partial
negative charge, which forms an attractive force.

6. (13 pts) The pathway below is a predicted biosynthetic pathway. Both of the end products are essential. You
have strains with a mutation in each of the enzymes in the pathway, and assess each strain for its ability to grow
on the known intermediates in the pathway.

a). (6 pts) Predict the results you would expect in the table below. A + would mean that when the mutant on the
left is given the intermediate at the top of the column the strain can grow.

1
2
3
4
5
6

A
+
-

B
+
-

C
-

D
+
+

E
+
+
-

F
+

G
+
+
-

b). (4 pts) You construct the strain with a mutation that fully inactivates enzyme 6. Contrary to the predicted
pathway, you find that the strain can grow under all conditions. What does this suggest to you about the role of
enzyme 6 and the pathway?
Options:
Compound D is not essential
Enzyme 6 is not actually in this pathway
c). (3 pts) If your prediction in part b is correct, what other results in your table would be different and what
would the new results be?
If D is not essential the strain with a mutation in enzyme 2 would also be able to grow under all conditions, and
strains with mutation sin enzyme 3 or 5 could grow on B and G alone.
If enzyme 6 is not in the pathway the rest the results would remain the same.

Chem153A Winter 2015

Final
Last Name:_____________________________
Page 5 of 9
7. (10 pts) You are following the metabolism of Glucose in which Carbon 2 is radioactive
a). (1 pts) Show the labeling
pattern of the pyruvate
formed at the end of
glycolysis.

COO

COO

*C

b). (1 pt) What percentage of

the pyruvate molecules
would be labeled?
50%

c). (1 pts) Indicate

which carbon would be
labeled on lactate
under anaerobic
conditions:

CH3

HC*

OH

CH3

COO

d). (3 pts) Indicate the

labeling pattern and
distribution in oxaloacetate if
50% is produced through the
TCA cycle and 50% through
pyruvate carboxylase, using
the pyruvate in part a.

25% * COO
O

C* 50%
CH2

e). (2 pts) Indicate the

labeling pattern and
distribution in isocitrate
if the oxaloacetate in
part d is used in the TCA
cycle.

25% * COO

CH2

50% HC
*
HO

COO

* 25%

CH
-

25% * COO

f). (2 pts) How is the label in part d physically distributed on actual oxaloacetate molecules?
50% of the labeled molecules have label on the carbonyl carbon, then 25% of the labeled molecules have label
on the carboxyl carbon closest to the carbonyl and 25% of the labeled molecules have label on the carboxyl
carbon farthest from the carbonyl.
8. (12 pts) Pyruvate dehydrogenase is a key step in the central metabolic pathway.
a). (4 pts) Which enzymes in the complex are non-covalently regulated and how?
Enzyme 2 by Acetyl-CoA and enzyme 3 by NADH
b). (2 pts) What type of non-covalent regulators are they?
Competitive inhibitors
c). (4 pts) How is PDH covalently regulated? Include regulation of any additional enzymes to explain this
completely.
Enzyme 1 is phosphorylated by PDH kinase, which is activated by Acetyl-CoA and NADH and inhibited by
pyruvate and ADP. It is dephosphorylated by PDH phosphatase, which is activated by insulin signaling.

c). (2 pts) -ketoglutarate dehydrogenase has high similarity to PDH. How would you expect its covalent
regulation to be regulated differently?
The kinase would be inhibited by succinyl-CoA instead of acetyl-CoA, and activated by a-ketoglutarate instead
of pyruvate. The phosphatase regulation would not be specific to glucose.

Final

Chem153A Winter 2015

Page 6

Last Name:

of9

9. (8 pts) All Enzymes require their substrate for activity, but citrate synthase is specifically labeled as being
sensitve to substrate availability.
A). (2 pts)Which substrate is it particularly sensitive to?

oxaloacelate
B). (4 pts) Give a physiologicalexplanation for th is se nsitivity. Use a sketch of a Michaelis-Menten curve

for

citrate synthase to illustrate your answer.

The concentration ofOxaloacetate i5very low and ends up
being closetothe Km of citrate synthase for oxaloacetate.
Thus smallahanges in oxalaoacelate concentration lead to
laerchanges in citrate synthase activity.

c). (2 pts) ln the context ofyour answer in part B why is citrate synthase not as sensitive to its other substrate?
The conaentration ot acetyl-coA is usually significantly highe,than the l(m ofcsfor Acetyl-coA. Thus cs is
already functioning close to its vmaxfor acetyl-coA.

10. (10 pts) Electron transport from complex I throu8h complex lll is said to be readily reversible with the
correspondin8 production of ATP, while electron transferthrough Complex 4 alone irreversible
's
halfreaction for
a). (5 pts)Show how you would calculate the AG forthese two e,ectron transfers. lncludethe
each process. (DO NOTdothe math):

6f= 6,7es-(o'ss)
(c\/
c".''-o'sts{6
rt1'
^
''a'"'r#'o=e).JJkfr4
6'2ss'l b c' =' -i,W ;r'1"rlo'r'$
lcgc(r+\g>=
Z
lr.alo.c
^" 0

(_,+\

b). (5 pts) For the transfer of electrons from I NADH through Complexes I to lll the AG*n = -105 k-ilmol and the cell
can make up to 2 ATp from this proess. While for the transfer ofelectrons to l oxygen molecule through
complex lV alone the ac.en = -220 kJ/mol, and the cell can make up to 1 ATP from this process Justify why one
process appearc to be readily reversible while the other does not.

CL-g .
CTL

'

Lk1? r- Sotl/nl E

/>G", = -

l0s&3^

\ k1P --So

U:lr.l

h"

t6u

t-w

t'l/J

uslpgl

+"

r,*j'-kt?

-stll*.ffiffiffi

-)-><;+ So t -s1*1

n br*-l''w,A LY-L C/'L -

-l7Dks/o-l

Chem153A Winter 2015

Final
Last Name:_____________________________
Page 7 of 9
11. (10 pts) The Electron transport chain is coupled to ATP synthase by a pH gradient.
a). (4 pts) What does this mean for the function of each of these processes? (40 words maximum)
Each process requires the other to function (ATP synthase needs the ETC to make the pH gradient, and the ETC
needs ATP Synthase to slightly dissipate the pH gradient)
b). (4 pts) How do uncouplers prove that the pH gradient connects the ETC to ATP synthesis? Briefly explain why
the presence of uncouplers affects the function of ATP synthase and the ETC differently?
Uncouplers permeabilize the inner mitochondrial membrane to protons (ie protons can equilibrate across the
membrane, dissipating the pH gradient)
The consequence is that ATP synthase stops running and the ETC can run without ATP synthesis. (If dissipating
the pH gradient in another way leads to ETC no longer needing ATP synthase that suggests the role of ATP
synthase is to dissipate the pH gradient.)
ATP synthase requires the pH gradient to function while the ETC requires the pH gradient to be dissipated to
function. Thus the uncoupler dissipating the pH gradient will have opposite effects on their function.

c). (2 pts) What other evidence do we have that the pH gradient itself connects ETC and ATP synthase?
(30 words maximum)
The inner membrane can maintain a pH gradient.
The ETC produces a pH gradient (pumps protons out of the mitochondria).
Decreasing the pH outside the mitochondria stimulates ATP synthesis.

12. (6 pts) How does ATP synthase use mechanical energy to convert one form of chemical energy to another?
The dissipation of the pH gradient by ATP synthase (flow of protons from IMS to matrix), which is the utilization
of the chemical energy in the pH gradient, causes the rotation of Fo (the rotor part of ATP synthase). This in
turn triggers conformational changes in F1 (the stationary part of ATP synthase). The rotation causing
conformational changes is the mechanical energy. This leads to the production of ATP, the second form of
chemical energy.

Chem153A Winter 2015

Final
Last Name:_____________________________
Page 8 of 9
13. (25 pts) Draw a diagram of glycolysis, the TCA cycle, and Oxidative phosphorylation showing the regulation
that would affect the rates of the regulated steps when oxaloacetate is removed from the TCA cycle because the
Liver is using citrate to make fatty acids. .
Be as complete as possible, but ONLY include intermediates, enzymes, or processes that are NECESSARY to
the discussion.
Do not draw structures.
You may include explanations when needed (but words or a table will only be considered if they refer to a
diagram).
Points will be deducted for excessive unnecessary information.

Include:
Glycolysis, connected to the TCA cycle (including PDH), connected to the ETC, connected to ATP synthase
Show citrate being removed to make fatty acids (this means there are biosynthetic conditions, so ATP is higher
and ADP is lower)
Inhibition by ATP at regulated steps
Lack of ADP causes a build up of NADH, which inhibits the TCA cycle.
This causes a build up of citrate, but its being removed so no inhibition from it.
Removal causes decreases of intermediates downstream of citrate, so less inhibition by succinyl-CoA and
NADH, citrate, and acetyl-CoA also.
Uncessary:
Most unregulated steps (malate dehydrogenase makes sense)
Activation by ADP
Fructose-2,6-bisphosphate regulation
Fructose-1,6-bisphosphate regulation

Briefly explain the changes that would occur when the cells Energy levels become insufficient for biosynthesis.
Biosynthesis would be inhibited by ADP/AMP, TCA cycle would be activated by ADP/AMP. Citrate wouldnt be
removed any more. Oxphos should be running so there wouldnt be a build up of NADH for inhibition any more.

Final

Chem153A Winter 2015

last Name:
Page 9 of 9
14. (21 pts) completely identifythe following compounds bygiving its comrnon name.
also briefly indicate one of its
roles{2 pts)

[/+osrrv, .-:-.

fnrlfv'4,o1v,f,"

arjd4

l,r'.'.1

lr*rfs-- 5"

Ge,,,.6r'-Q

bisq\^reLb

d,ulw-wurttt-v;

-"fL-W

v\- 6,rc

1^-+-

)
8",1 \
[" */
H\t
vH

--0.5+Ln'+*' l-1
oH
Qrn*

oH

"@{-

(2 pts)

(3 pts)

\-o
j-o"o,"
ll
cHz

S"..,iNJu';t

N"ef"(tul --

/.

d-^"A-);J/-

&t

P"i:?

P*.*)

el!A\L- La^^JtL

4t'8-1\.

ir(3 pts)

s*rzid $.b'rfu,4rJ
(2 pts)

coo'
tl
I

ll

HC
lt
CH
I

Mxk- ak

-s.Es\.t

coo.

&^- tCtr

crlt-

(.tf.'l- sy"lt",,*)

S-',.</'6f-

1c+ cy&
\^A

b (2
???

pts)lostfor fun (allanswers w;ll

be aceptedl:

u)