Pharmaceutical Biochemistry, 341C

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

NAME ___________

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. b. The region enclosed by the inner membrane is termed the

matrix. c. The inner membrane is permeable to most small

molecules. d. They generate NADH as part of the Krebs cycle.

A. a and b are false B. only b is false C. only a is false D. b and c are false E. a and c are false

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. In the cytoplasm pyruvate is converted to acetyl CoA b. Aerobic glycolysis produces NADH in the mitochondria c. A transport system takes the pyruvate from the cytoplasm

to the inner mitochondrial membrane. d. NADH cannot enter the mitochondrial matrix from the

cytosol.

A. a and b are false B. b and c are false C. only b is false D. a and d are false E. c and d are false

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. b. Ceramide. c. A bile acid. d. AMP.

A. a B. b C. c 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. Acetyl CoA is a biosynthetic precursor of fatty acids. b. Triacylglycerols contain two carboxylic ester bonds. c. The metabolically active form of a fatty acid (for

oxidation) is a thioester. d. pyrophosphate hydrolysis is thermodynamically

unfavorable.

A. a and c are true B. a and b are true C. only c is true D. only d is true E. a and d are true

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

CoA generates NADH, but not FADH2. b. Nearly all fatty acids found in plants have an odd number

of carbons. c. The oxidation of fatty acids occurs in the mitochondria of

a cell.

A. a and b are false B. only b is false C. only a is false D. only c is false E. None are false

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 b. Water c. cytochrome c d. coenzyme Q e. none of the above

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

A. a B. b C. c D. d

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. They stabilize the structure of membranes b. They serve as fuel molecules c. They are precursors of triaclylglycerols

A. a and b B. a and c C. b and c D. only a 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. they are more reduced than carbohydrates b. they are hydrophobic in nature and can pack more

efficiently in fat storage cells c. they are more readily available for immediate metabolic

needs d. they contain more energy per gram than carbohydrates

A. a B. b C. c D. d

C is false because glycogen (the storage form of glucose) is more readily accessible 10 The degree of membrane fluidity depends on

a. the percentage of lipids that contain choline b. the percentage of glycolipids c. the length of the fatty acid chains d. the percentage of unsaturated fatty acids

A. only a B. only b C. only c D. c and d E. b and c

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. oxidation, dehydration, oxidation, cleavage b. oxidation, hydration, oxidation, cleavage c. dehydration, oxidation, oxidation, cleavage d. cleavage, hydration, oxidation, cleavage e. dehydration, reduction, oxidation, cleavage

A. a B. b C. c D. d E. e

Read notes

12 The unsaturated fatty acids that are intermediates in the β-oxidation cycle have what orientation around the double bond?

a. the cis orientation b. the trans orientation c. can have either orientation d. the orientation is not known

A. a B. b C. c D. d

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

CH3C-XCH2CH2NHCCH2CH2NHCCHCCH2O-ADP

O O

CH3

CH3

HO

O

Acetyl coenzyme A (Acetyl-CoA)

C. O D. P E. C

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

are coupled to the transport of H+ ion from the inside of the mitochondrion (inner mitochondrial membrane) to the outside.

d. The pH gradient resulting from the transport of H+ ion 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.

A. a is true B. b is true C. c is true D. d is true E. e is true

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 b. carnitine c. cytosine nucleotide d. coenzyme A e. adenine nucleotide translocase

A. a B. b C. c D. d E. e

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 c. The three most abundant fatty acids in phosphatidic acid

A. a is true B. b is true

have more than 18 carbons d. A saturated fatty acid with 16 carbons has a lower

melting point than an unsaturated fatty acid with 16 carbons.

e. Fatty acids are not amphipathic compounds.

C. c is true D. d is true E. e is true

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. hydrophobic interactions b. hydrogen bonds c. electrostatic forces d. covalent bonds

A. a B. b C. c D. d

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

the cell, both against concentration gradients c. sodium is transported out of the cell and potassium into

the cell, both in the same direction as concentration gradients

d. sodium and potassium are both transported out of the cell against concentration gradients

A. a B. b C. c D. d

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. They are bound by electrostatic interactions b. They can be removed by raising the ionic strength

A. a is true, b is true B. a is true, b is false C. a is false, b is true 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. entirely within the membrane b. on the surface of the membrane c. in either position d. the position cannot be determined

A. a B. b C. c D. d E. all are true

See notes. 21 Which statement is not correct?

a. A biological membrane consists of a lipid and protein. b. Membrane proteins can be peripheral. c. The fluid mosaic model describes the interaction of lipids

and proteins in biological membranes. d. Extensive formation of lipid-protein complexes take

place in this model.

A. a B. b C. c D. d

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

22 Which lipids are derived from arachidonic acid?

a. Leukotrienes b. Bile acids c. Prostaglandins d. Thromboxanes e. Sphingolipids

A. a, b and c B. a, c and d C. a, b and d D. b, c, and d E. c, d and e

See notes; Leukotrienes, Thromboxanes and Prostaglandins are all eicosanoids

23 Which regions associated with a mitochondria undergoing

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

outer mitochondrialmembrane

inner mitochondrialmembrane

matrix

intermembranespace

A B C

A. a B. b C. c D. d

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. concentration gradients are involved in one and not in the other

b. glycolipids play a role in one and not in the other 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

A. a B. b C. c D. d

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? The processing of one molecule of palmitic acid (16 carbons) by β- oxidation

a. requires 8 cycles of β-oxidation and produces 9 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

A. Only a is true B. Only b is true C. both are true D. both are false E. all are false

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

A. true 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 oxidation and phosphorylation and spans the inner mitochondrial membrane and projects into the matrix.

b. Fo spans the membrane and is a channel for protons. c. F1 projects into the matrix and catalyzes ATP synthesis. d. Protons flow back into the matrix through F0 which drive

the formation and release of ATP at F1

A. a is false B. b is false C. c is false D. d is false E. all are true

See notes

29 Which of these molecules, A, B, C, D or E is the product of the

reaction below

O

H

C C

C-SCoA

R H

H2O

C

OH

CH-C-SCoARH

O

H

C

O

CH-C-SCoARH

OH

H

C

H

C-C-SCoARH

O

OHH

C

O

CH-C-OHRH

O

H

C

OH

CH-C-OHRH

O

H

A

B

C

D

+

A trans-enoyl-CoA

Enoyl-CoAhydrase

E

A. B. C. D. E.

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

Exam #3, Dr. Dalby, 100pts; 30 Single answer questions, (Print legibly) December 4th, 2003.

NAME ___________

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

matrix has a lower pH than the cytosol. c. The outer membrane is permeable to most small molecules. d. They contain citrate.

A. a and b are false B. only b is false C. only a is false 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 b. Aerobic glycolysis produces NADH c. A transport system takes NADH from the cytoplasm to the

inner mitochondrial membrane. d. There are 3 sites for substrate on ATP synthase.

A. a and c are false B. b and c are false C. only c is false D. a and d are false 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. CO2

-

CH2

CH2

CO2-

Succinate

+ E-FADC

CH

H

CO2-

-O2C

+ E-FADH2

Fumarate

E-FADH2 + CoQ E-FAD CoQH2+

A. a B. b C. c D. d E. e

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. Triacylglycerols are biosynthetic precursors of fatty acids.

b. Degradation of triacylglycerols can eventually produce acetyl CoA.

c. The metabolically active form of a fatty acid (for oxidation) is a thioester.

d. Pyrophosphate contains a high energy bond.

A. a and c are false B. a and b are false C. only a is false D. only d is false E. a and d are false

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

CoA generates NADH, FADH2 and CO2 b. Nearly all naturally occurring fatty acids are unsaturated. c. The oxidation of fatty acids occurs in the mitochondria of

a cell.

A. a and b are false B. a and c are false C. only b is false D. only c is false 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. O2 b. H2O c. NAD+ d. N2 e. None of the above

A. a B. b C. c D. d E. e

The electrons are ultimately transferred to oxygen to give water

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

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

A. a and b B. a and c C. b and c D. d

See notes

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

a. They are a major storage form of energy b. They serve as fuel molecules

A. a and b B. a and c C. b and c

c. A key step in their degradation by β−oxidation requires an input of energy in the form of ATP

D. only a 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. (∆G°’) is –110 kJ b. (∆G°’) is –35 kJ c. (∆G°’) is +110 kJ d. (∆G°’) is +35 kJ

A. a B. b C. c D. d

See notes 10 The degree of membrane fluidity depends predominantly on

a. the percentage of proteins b. the percentage of cholesterol c. the length of the fatty acid chains d. the percentage of unsaturated fatty acids

A. c and d B. b and c C. b and d D. only d E. b, c and d

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. oxidation, dehydration, oxidation, cleavage b. oxidation, hydration, oxidation, cleavage c. dehydration, oxidation, oxidation, cleavage d. oxidation, hydration, hydration, cleavage e. dehydration, reduction, oxidation, cleavage

A. a B. b C. c D. d E. e

12 What molecule is missing?

RCO-

O

+ ATP + CoA-SH

RC-SCoA

O

+ + PPi

acetyl-CoAsynthetase

Pi + Pi

A. AMP B. ATP C. ADP D. Pi D. CO2

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

NH2

H S

HO H

CO2H

CH2CH2CHCO2-

PGE2

It’s a prostaglandin made from arachadonic acid

15 Fatty acids are transported across the inner mitochondrial

membrane esterified to

a. acyl carrier protein b. acetyl CoA c. citrate d. glycerol

A. a B. b C. c D. d 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 c. The three most abundant fatty acids in phosphatidic acid

have more than 12 carbons d. A saturated fatty acid with 16 carbons has a lower

melting point than an unsaturated fatty acid with 16 carbons.

e. Fatty acids are not amphipathic compounds.

A. a and c is true B. b is true C. c is true D. d is true E. e is true

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

NHN

S

O

H H

C

O

NH-enzyme

C

O

-O

A. true B. false

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 concentration of Na+ is lower inside the cell than out

b. The energy required to move sodium and potassium ions against their gradients comes from the hydrolysis of ATP to ADP + Pi

c. There is no transport of ions without hydrolysis of ATP

A. a B. b C. c D. None

19 Consider fatty acid synthesis. The carbon atoms depicted by the open circles are derived from carbon 1, 2 or 3? O

O

O

CoA-SCOO

1

2

3

A. 1 B. 2 C. 3 D. none

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

SH S

C

O

CH2

CHCH2

OH

ACPSynthase

H2C

CH3

A. Acyl transfer to the

synthase B. A dehydration step C. Oxidation of a

hydroxy D. Reduction of a

carbonyl

21 Which statement is not correct?

a. A biological membrane contains both lipids and proteins. b. Membrane proteins can be peripheral. c. The fluid mosaic model describes the interaction of lipids

and proteins in biological membranes where extensive formation of lipid-protein complexes take place.

A. a B. b C. c D. None

22 Which statements concerning transporter proteins are false?

a. A molecule or ion may be carried across a membrane by

a specific transporter protein b. Like channels transporters cannot be saturated by what

they carry c. Transporters often use a concentration gradient on one

molecule to drive the transport of a second molecule

A. a, b and c B. b C. a, b and d D. b, c, and d E. c, d and e

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 the difference in pH between the inner membrane space and the matrix of an actively respiring mitochondrion

A. true B. false

24

HH

H

O

HO OH

N

N

N

N

NH2

-O-P-O-P-O-P-O-CH2

O

O-

O

O-

O

O-

H

A BC

D

Which arrows point to high energy linkages?

A. A and B B. A only C. B only D. C and D

The anhydride bonds are high energy

26 Which region of a membrane A or B stabilizes membrane structures

A

B

A. a B. b C. both have

an equal effect

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

A

B

A. A B. B

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

a.

Degradation Synthesis

Malonyl-CoA Carboxylated biotin

No malonyl-CoA No biotin

Oxidative process

requires NAD+, FADand produces ATP

Reductive process

requires NADPH and ATP

Begins at carboxyl end Begins at CH3CH2 end

In mitochondria In cytosol

A

B

C

D

E

A. a is false

B. b is false

C. c is false

D. d is false

E. all are true

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

helical regions that pass through the membrane. Which protein’s helices are likely to have a greater percentage of hydrophobic residues?

A. A B. B C. Neither

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)