Pharmaceutical Biochemistry, 341C NAME

Exam #3,
Dr. Dalby, ___________
100pts; 30 Single answer questions, (Print legibly)
December 5th, 2002.

INSTRUCTIONS
There is one single answer for each question.
Use the scantron to mark your results.
Hand in BOTH this exam sheet and your scantron with your name
on both.

ONE SINGLE
ANSWER

1 Which of the following statements about mitochondria is/are

false?
a. They contain proteins that participate in glycolysis. A. a and b are false
b. The region enclosed by the inner membrane is termed the B. only b is false
matrix. C. only a is false
c. The inner membrane is permeable to most small D. b and c are false
molecules. E. a and c are false
d. They generate NADH as part of the Krebs cycle.

A is false because all glycolytic enzymes are found in the

cytoplasm. The pyruvate dehydrogenase complex is not part of
the glycolytic pathway. C is false because the inner mitochondrial
membrane is impermeable to most small molecules.

2 Which of the following statements is/are false?

A. a and b are false
a. In the cytoplasm pyruvate is converted to acetyl CoA B. b and c are false
b. Aerobic glycolysis produces NADH in the mitochondria C. only b is false
c. A transport system takes the pyruvate from the cytoplasm D. a and d are false
to the inner mitochondrial membrane. E. c and d are false
d. NADH cannot enter the mitochondrial matrix from the
cytosol.

Pyruvate is converted to acetyl CoA in the mitochondria by the

pyruvate dehydrogenase complex. PDH is a large cluster of
three enzymes (E1, E2, E3) in the mitochondrial matrix of
eukaryotic cells. Aerobic glycolysis produces NADH in the
cytoplasm. The electrons in NADH are transported into the
mitochondria by the glycerol phosphate shuttle or the malate-
aspartate shuttle, which is found in the kidney, liver and heart.

3 Identify the fused ring lipid

a. Phosphatidylinositol. A. a
b. Ceramide. B. b
c. A bile acid. C. c
d. AMP. D. d
 e. RNA. E. e

a and b are membrane lipids, with long chains. AMP (adenosine monophosphate) and RNA are not lipids.

4 Which of the following statements (a-d) is/are true?

A. a and c are true
a. Acetyl CoA is a biosynthetic precursor of fatty acids. B. a and b are true
b. Triacylglycerols contain two carboxylic ester bonds. C. only c is true
c. The metabolically active form of a fatty acid (for D. only d is true
oxidation) is a thioester. E. a and d are true
d. pyrophosphate hydrolysis is thermodynamically
unfavorable.

B is false because TAGS contain 3 carboxylic ester bonds not 2. D is false because the hydrolysis of
pyrophosphate is thermodynamically favorable, because pyruvate contains a high energy phosphoanyhdride
linkage

5 Which of the following statements is false?

a. The oxidative degradation of fatty acids to give acetyl A. a and b are false
CoA generates NADH, but not FADH2. B. only b is false
b. Nearly all fatty acids found in plants have an odd number C. only a is false
of carbons. D. only c is false
c. The oxidation of fatty acids occurs in the mitochondria of E. None are false
a cell.

A is false because FADH2 is formed by acyl-CoA dehydrogenase

(reaction 1) of beta-oxidation. B is wrong because most are even.

6 The final species to be reduced in the electron transport chain is

a. O2 A. a
b. Water B. b
c. cytochrome c C. c
d. coenzyme Q D. d
e. none of the above E. e

Oxygen is reduced by the addition of electrons in the final step to

produce water.

7 The β-oxidation of fatty acids is not characterized by

A. a
a. initiation at the methyl end of the fatty acid B. b
b. its role as primary route to degradation of fatty acids C. c
c. taking place in the mitochondrial matrix D. d
d. two-carbon units being eliminated at each step

A is false because the fatty acids are activated at the carboy end by
reacting with ATP to give RCOO-AMP which the reacts with
CoASH to give the acyl-CoA

8 Which of the following are major physiologic functions of FREE

 fatty acids? A. a and b
B. a and c
a. They stabilize the structure of membranes C. b and c
b. They serve as fuel molecules D. only a
c. They are precursors of triaclylglycerols E. all

A is false because free fatty acids do not associate with membranes.

The key to this question is to see that we are talking about FREE fatty acids not fatty acids that form part of a
phosphodiacyl glycerol
9 Advantages of fatty acids as primary energy storage molecules
include all these points except
A. a
a. they are more reduced than carbohydrates B. b
b. they are hydrophobic in nature and can pack more C. c
efficiently in fat storage cells D. d
c. they are more readily available for immediate metabolic
needs
d. they contain more energy per gram than carbohydrates

C is false because glycogen (the storage form of glucose) is more readily accessible

10 The degree of membrane fluidity depends on A. only a

B. only b
a. the percentage of lipids that contain choline C. only c
b. the percentage of glycolipids D. c and d
c. the length of the fatty acid chains E. b and c
d. the percentage of unsaturated fatty acids

The length of a fatty acid chain and the degree of unsaturation both contribute to the degree of membrane
fluidity so c and d are correct. Choline is a head group and is unlikely to contribute to the fluidity as is the case
for the sugar moiety of a glycolipid

11 The order of reactions (to the fatty acid) in beta-oxidation of

saturated fatty acids is
A. a
a. oxidation, dehydration, oxidation, cleavage B. b
C. c
b. oxidation, hydration, oxidation, cleavage
D. d
c. dehydration, oxidation, oxidation, cleavage E. e
d. cleavage, hydration, oxidation, cleavage
e. dehydration, reduction, oxidation, cleavage

Read notes

12 The unsaturated fatty acids that are intermediates in the β-oxidation

cycle have what orientation around the double bond?
A. a
a. the cis orientation B. b
b. the trans orientation C. c
c. can have either orientation D. d
d. the orientation is not known

Trans not cis which is what we find in unsaturated fatty acids that
are not interemediates

13 Which atom is X?

A. N
B. S
 O O O CH3 C. O
D. P
CH 3C-XCH 2CH2NHCCH2CH 2NHCCHCCH 2O-ADP E. C

HO CH3
Acetyl coenzyme A
(Acetyl-CoA)

It is a thioester

14 The statement about respiration that is true is:

a. Acetyl CoA is not oxidized in the TCA cycle.
b. NADH is not oxidized sequentially through the electron
transport chain.
c. All of the redox reactions in the electron transport chain A. a is true
are coupled to the transport of H + ion from the inside of B. b is true
the mitochondrion (inner mitochondrial membrane) to C. c is true
the outside. D. d is true
d. The pH gradient resulting from the transport of H+ ion E. e is true
constitutes a high energy state.
e. The net effect of all these steps is that the reduction of
acetyl CoA by oxygen is coupled to the synthesis of ATP.

Acetyl-CoA is oxidized in the TCA cycle as the electrons are

stripped from it to be stored in the form of NADH and FADH2.
NADH is then oxidized by the electron transport chain through a
series of sequential steps. The electrons from NADH can be
though of as ending up reacting with oxygen to give water. Not
all reactions are coupled to proton transport. Some of the
reactions shown in the animation (link is in the handout) are not
coupled to proton transfer across the membrane. Furthermore, the
reactions in complex II do not provide enough energy to transport
protons. Acetyl CoA oxidation not reduction is coupled to ATP
synthesis.

15 Fatty acids are transported across the inner mitochondrial

membrane esterified to

a. acyl carrier protein A. a

B. b
b. carnitine
C. c
c. cytosine nucleotide D. d
d. coenzyme A E. e
e. adenine nucleotide translocase

See notes

16
The statement about fatty acids that is true is:
a. TAGS are not components of membranes.
b. TAGS are esters of glycerol with two fatty acids A. a is true
c. The three most abundant fatty acids in phosphatidic acid B. b is true
 have more than 18 carbons C. c is true
d. A saturated fatty acid with 16 carbons has a lower D. d is true
melting point than an unsaturated fatty acid with 16 E. e is true
carbons.
e. Fatty acids are not amphipathic compounds.

TAGS have three fatty acids attached as esters. Fatty acids with
12 to 20 carbons are common. Melting points are lower the easier
it is to melt something. Unsaturation makes a fatty acid easier to
melt (melting point will be lower) than the corresponding
saturated fatty acid.

17 Membrane lipids in a lipid bilayer are held together by

A. a
a. hydrophobic interactions B. b
b. hydrogen bonds C. c
c. electrostatic forces D. d
d. covalent bonds

See notes
18
In the sodium-potassium pump

a. sodium is transported out of the cell and potassium into

the cell, both against concentration gradients A. a
b. sodium is transported into the cell and potassium out of B. b
the cell, both against concentration gradients C. c
c. sodium is transported out of the cell and potassium into D. d
the cell, both in the same direction as concentration
gradients
d. sodium and potassium are both transported out of the cell
against concentration gradients

Pumps pump against a concentration gradient. Sodium is pumped

out of the cell and potassium into the cell.

19 The following two properties are both properties of integral

membrane proteins A. a is true, b is true
B. a is true, b is false
a. They are bound by electrostatic interactions C. a is false, b is true
b. They can be removed by raising the ionic strength D. a is false, b is false

They are held by hydrophobic interactions and one needs

detergents to remove them from the membrane not just an increase
in salt.

20 Membrane proteins can be located

A. a
a. entirely within the membrane B. b
b. on the surface of the membrane C. c
c. in either position D. d
d. the position cannot be determined E. all are true
 See notes.

21
Which statement is not correct?
a. A biological membrane consists of a lipid and protein. A. a
b. Membrane proteins can be peripheral. B. b
c. The fluid mosaic model describes the interaction of lipids C. c
and proteins in biological membranes. D. d
d. Extensive formation of lipid-protein complexes take
place in this model.

The fluid mosaic model states that lipid-protein complexes do not form extensively

22 Which lipids are derived from arachidonic acid? A. a, b and c

a. Leukotrienes B. a, c and d
b. Bile acids C. a, b and d
c. Prostaglandins D. b, c, and d
d. Thromboxanes E. c, d and e
e. Sphingolipids

See notes; Leukotrienes, Thromboxanes and Prostaglandins are all eicosanoids

23
Which regions associated with a mitochondria undergoing
oxidative phosphorylation have the same pH? A. a
a. the matrix (A) and the intermembrane space (B) B. b
b. the intermembrane space (B) and the cytosol (C) C. c
c. the matrix (A) and the cytosol (C) D. d
d. The pH is different in all three regions

matrix
inner mitochondrial
membrane

intermembrane A B C
space

outer mitochondrial
membrane

The outer membrane is permeable to protons and therefore protons

can equilibrate across the outer membrane. i.e the pH is the same
on either side.

24 The difference between active transport and passive transport is

that A. a
a. concentration gradients are involved in one and not in the B. b
other C. c
b. glycolipids play a role in one and not in the other D. d
c. one requires expenditure of energy and the other does not
d. ions are transported into and out of the cell by one
process and not by the other

Pumps create a concentration gradient as part of active transport.

Ions pass doen concentration gradients to pass through channels.
 Glycolipids are not necessarily involved in either process. Passive
and active transport can occur into or out of a cell.

25 Which statement is correct? A. Only a is true

B. Only b is true
The processing of one molecule of palmitic acid (16 carbons) by C. both are true
β- oxidation D. both are false
a. requires 8 cycles of β-oxidation and produces 9 E. all are false
molecules of acetyl-CoA
b. requires 8 cycles of β-oxidation and produces 8
molecules of acetyl-CoA
c. requires 9 cycles of β-oxidation and produces 8
molecules of acetyl-CoA
d. requires 9 cycles of β-oxidation and produces 9
molecules of acetyl-CoA
e. none of the above are correct

requires 7 cycles of β-oxidation and produces 8 molecules of acetyl-CoA

26 The arrow is pointing to
a. the inner mitochondrial membrane
b. the outer mitochondrial membrane

A. a
B. b

This membrane is highly folded to provide a large surface area.

27 Cells normally maintain their [NAD+]/[NADH] ratio near 1000, A. true

while keeping their [NADPH]/[NADP+] ratio near 100. B. false

NAD+ is needed to oxidize glucose and participate in the citric

acid cycle.
NADPH is required for synthesis

28 Are any of the following statements concerning the process of

oxidative phosphorylation not true?

a. A complex protein oligomer called ATP synthase links A. a is false

oxidation and phosphorylation and spans the inner B. b is false
mitochondrial membrane and projects into the matrix. C. c is false
b. Fo spans the membrane and is a channel for protons. D. d is false
c. F1 projects into the matrix and catalyzes ATP synthesis. E. all are true
d. Protons flow back into the matrix through F0 which drive
the formation and release of ATP at F1

See notes
29
Which of these molecules, A, B, C, D or E is the product of the
reaction below
A.
O B.
H C-SCoA Enoyl-CoA C.
hydrase D.
C C + H2 O
E.
R H
A trans-enoyl-CoA

OH
O
C C
O R CH-C-SCoA
O H
H
A C
R CH-C-OH
H
H O
OH
D R
C
CH-C-SCoA
OH H
O H
B C
R CH-C-OH
H
H H
O
E C
R C-C-SCoA
H
H OH

The hydrase puts water across the double bond

30 Which arrow, A, B or C points to the cell membrane? A.

B.
C.

B points to
"I have neither participated in nor witnessed any acts of academic dishonesty
pertaining to this examination or assignment."

(signature)
 Pharmaceutical Biochemistry, 341C NAME
Exam #3,
Dr. Dalby, ___________
100pts; 30 Single answer questions, (Print legibly)
December 4th, 2003.

INSTRUCTIONS
There is one single answer for each question.
Use the scantron to mark your results.
Hand in BOTH this exam sheet and your scantron with your name on
both.

ONE SINGLE
ANSWER

1 Which of the following statements about mitochondria is/are false?

a. They contain NAD +, NADH, FAD, FADH2, and citrate.
b. When the cell is undergoing oxidative phosphorylation the A. a and b are false
matrix has a lower pH than the cytosol. B. only b is false
c. The outer membrane is permeable to most small molecules. C. only a is false
d. They contain citrate. D. only c is false
E. a and d are false

Protons are pumped out of the matrix. The pH is lower where the
protons are more concentrated, i.e outside the matrix.

2 Which of the following statements is/are false?

a. In the cytosol pyruvate is converted to acetyl CoA A. a and c are false
b. Aerobic glycolysis produces NADH B. b and c are false
c. A transport system takes NADH from the cytoplasm to the C. only c is false
inner mitochondrial membrane. D. a and d are false
d. There are 3 sites for substrate on ATP synthase. E. c and d are false

Pyruvate is converted to acetyl CoA in the matrix. There is no

transport system that actually takes NADH from the cytoplasm
to the inner mitochondrial membrane. This might be mistaken
for a shuttle that takes the electrons in NADH from the
cytoplasm to the matrix. Look in your notes for descriptions of
these shuttles.

3 Identify which complex in the electron transport chain carries out the
following two reactions. A. a
- B. b
CO2 -
H CO2 C. c
CH2 C D. d
+ E-FAD + E-FADH2
CH2 C E. e
-
CO2
- O2 C H
Succinate Fumarate

E-FADH2 + CoQ E-FAD + CoQH2

a. Complex I.
b. Complex II.
c. Complex III.
d. Complex IV.
e. None of the above.
4 Which of the following statements (a-d) is/are false?
A. a and c are false
a. Triacylglycerols are biosynthetic precursors of fatty B. a and b are false
acids. C. only a is false
b. Degradation of triacylglycerols can eventually produce D. only d is false
acetyl CoA. E. a and d are false
c. The metabolically active form of a fatty acid (for
oxidation) is a thioester.
d. Pyrophosphate contains a high energy bond.

Triacylglycerols are hydrolyzed to free up fatty acids, but it is not correct to describe them as biosynthetic
precursors. They are just the storage form of fatty acids, which are initially synthesized from free fatty acids.

5 Which of the following statements is false?

a. The oxidative degradation of fatty acids to give acetyl A. a and b are false
CoA generates NADH, FADH2 and CO2 B. a and c are false
b. Nearly all naturally occurring fatty acids are unsaturated. C. only b is false
c. The oxidation of fatty acids occurs in the mitochondria of D. only c is false
a cell. E. only a is false

The oxidative degradation of fatty acids to give acetyl CoA

generates NADH, and FADH2 but not CO2

6 In the electron transport chain electrons from NADH are

ultimately transferred to which molecule? A. a
a. O2 B. b
b. H2O C. c
c. NAD+ D. d
d. N2 E. e
e. None of the above

The electrons are ultimately transferred to oxygen to give water

7 The β-oxidation of fatty acids is not characterized by

A. a and b
a. a dehydration step B. a and c
b. the use of NADP C. b and c
c. the formation of butyrl-CoA D. d
d. two-carbon units being eliminated at each step

See notes

8 Which of the following are true of FREE fatty acids?

A. a and b
a. They are a major storage form of energy B. a and c
b. They serve as fuel molecules C. b and c
 c. A key step in their degradation by β−oxidation requires D. only a
an input of energy in the form of ATP E. all are correct

TAGS are the major storage form

9 The standard free energy change for each mole of NADH that
enters the electron transport chain is
A. a
a. (∆G°’) is –110 kJ B. b
b. (∆G°’) is –35 kJ C. c
c. (∆G°’) is +110 kJ D. d
d. (∆G°’) is +35 kJ

See notes

10 The degree of membrane fluidity depends predominantly on A. c and d

B. b and c
a. the percentage of proteins C. b and d
b. the percentage of cholesterol D. only d
c. the length of the fatty acid chains E. b, c and d
d. the percentage of unsaturated fatty acids

Cholesterol, the length of the fatty acid chains on the phosphodiacyl glycerols and the
degree of their saturation all contribute to the degree of membrane fluidity.

11 The order of reactions (to the fatty acid) in beta-oxidation of saturated fatty acids
is
A. a
a. oxidation, dehydration, oxidation, cleavage B. b
C. c
b. oxidation, hydration, oxidation, cleavage
D. d
c. dehydration, oxidation, oxidation, cleavage E. e
d. oxidation, hydration, hydration, cleavage
e. dehydration, reduction, oxidation, cleavage

12 What molecule is missing?

acetyl-CoA A. AMP
O B. ATP
synthetase
RCO- + ATP + CoA-SH C. ADP
D. Pi
O D. CO2
RC-SCoA + + PPi Pi + Pi

Activation of a fatty acid for oxidation

13 What is the most closely related biosynthetic precursor for this molecule?

A. acetyl CoA
B. arachadonic acid
C. mevalonate
D. vitamin B
E. prostaglandin
 HO H PGE2
CO2H

H S
-
CH2CH2CHCO2
NH2

It’s a prostaglandin made from arachadonic acid

15 Fatty acids are transported across the inner mitochondrial

membrane esterified to

a. acyl carrier protein A. a

B. b
b. acetyl CoA
C. c
c. citrate D. d
d. glycerol E. None

Fatty acids are transported from the cytosol into the matrix for
oxidation attached to carnitine

16
The statement about fatty acids that is true is:
a. TAGS are not components of membranes.
b. TAGS are esters of glycerol with two fatty acids A. a and c is true
c. The three most abundant fatty acids in phosphatidic acid B. b is true
have more than 12 carbons C. c is true
d. A saturated fatty acid with 16 carbons has a lower D. d is true
melting point than an unsaturated fatty acid with 16 E. e is true
carbons.
e. Fatty acids are not amphipathic compounds.

17 Part of this molecule becomes incorporated into fatty acids. True

or false? A. true
B. false
O O
C
-
O N NH
H H
NH-enzyme
S C
O

The molecule is carboxybiotin. None of the molecule becomes incorporated into fatty acids. The CO2 adds to acetyl-
CoA to make Malonyl-CoA in the early statges of synthesis. Subsequently, however it is lost as CO2 (ACP-
malonyltransferase reaction) and so does not end up in the fatty acid.
18
Which statement(s) concerning the sodium/potassium pump are
false
a. Under normal circumstances the concentration of K+ is
higher inside a cell than in extracellular fluids, but the A. a
concentration of Na+ is lower inside the cell than out B. b
b. The energy required to move sodium and potassium ions C. c
against their gradients comes from the hydrolysis of ATP D. None
to ADP + Pi
c. There is no transport of ions without hydrolysis of ATP

19 Consider fatty acid synthesis. The carbon atoms depicted by the

open circles are derived from carbon 1, 2 or 3? A. 1
B. 2
O C. 3
D. none
O
O
3
COO
CoA-S 1
2

20 In fatty acid synthesis. What is the next step?

A. Acyl transfer to the
O OH H2 synthase
C
C CH CH3 B. A dehydration step
SH C C
S
H2 H2 C. Oxidation of a
hydroxy
D. Reduction of a
carbonyl
Synthase ACP
21
Which statement is not correct?
a. A biological membrane contains both lipids and proteins. A. a
b. Membrane proteins can be peripheral. B. b
c. The fluid mosaic model describes the interaction of lipids C. c
and proteins in biological membranes where extensive D. None
formation of lipid-protein complexes take place.

22 Which statements concerning transporter proteins are false? A. a, b and c

B. b
a. A molecule or ion may be carried across a membrane by C. a, b and d
a specific transporter protein D. b, c, and d
b. Like channels transporters cannot be saturated by what E. c, d and e
they carry
c. Transporters often use a concentration gradient on one
molecule to drive the transport of a second molecule

Transporters can be saturated by ligands because they bind them, whereas channels simply provide a gateway for ions
(they don’t bind them) allowing ions to pass through essentially at the diffusion controlled limit.
23
True or false?
The chemiosmotic coupling mechanism is based entirely on A. true
the difference in pH between the inner membrane space and B. false
the matrix of an actively respiring mitochondrion

24 AB
C NH2
A.
B.
A and B
A only
D N
C. B only
N D. C and D
O O O
-
O-P-O-P-O-P-O-CH2 N N
O
- - -
O O O H H
H H
HO OH
Which arrows point to high energy linkages?

The anhydride bonds are high energy

26 Which region of a membrane A or B stabilizes membrane structures
A
A. a
B B. b
C. both have
an equal
effect

27 Which process A or B (that depict movement of lipids within cell membranes) is generally A. A
thought to be disfavored? B. B
B

28 Which assignment, A–E, concerning fatty acid degradation or synthesis, in the table below is
incorrect?

A. a is
Degradation Synthesis false
B. b is
A No malonyl-CoA Malonyl-CoA false
No biotin C. c is
Carboxylated biotin false
B
Oxidative process Reductive process D. d is
false
C requires NAD+, FAD E. all are
requires NADPH and ATP
and produces ATP true
D
Begins at carboxyl end Begins at CH3CH2 end
E
In mitochondria In cytosol
a.
29
Which of these proteins, A, B, C, or D is likely to be the easiest
protein to purify and crystallize?
A.
B.
C. C
D.
E.

30 Proteins A and B are both integral membrane proteins containing A. A

helical regions that pass through the membrane. Which protein’s B. B
helices are likely to have a greater percentage of hydrophobic C. Neither
residues?

B is correct because its likely that protein A forms a hydrophilic pore between the helicies, whereas all the helix of B
interacts with the fatty acids of the membrane.

"I have neither participated in nor witnessed any acts of academic dishonesty
pertaining to this examination or assignment."
(signature)