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BIOCHEM > final > Flashcards

final Flashcards

1
Q

In DNA the phosphate groups are on the outside of the helix. Why does this stabilize the structure?

ionic interactions with the solvent

hydrogen bonding with itself

covalent binding to the solvent

It does not stabilize the structure.

A

ionic interactions with the solvent

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2
Q

What is the final molecule made from the oxidation of H2O by solar energy?

ozone

glucose

fructose

carbon dioxide

A

glucose

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3
Q

The change in entropy of a system is a function of a change in

temperature and pressure.

volume and pressure.

enthalpy and pressure.

enthalpy and temperature.

A

enthalpy and temperature

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4
Q

Predict the complementary strand of the following DNA sequence:

5’-TCTAAGTCTA-3’

5’-TAGACTTAGA’-3’

5’-ATCTGAATCT’-3’

5’-AGATTCAGAT-3’

A

5’-AGATTCAGAT-3’

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5
Q

The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tm will

remain the same.

decrease.

`increase.

vary unpredictably.

A

increase

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6
Q

This method of analyzing RNA transcripts relies on a predetermined collection of complementary DNA sequences.

plasmid cloning

viral transduction

RNA-seq

gene-expression microarrays

A

gene-expression microarrays

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7
Q

The chirality of naturally occurring amino acids in proteins is

R.

L.

D.

the same as glyceraldehyde.

A

L.

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8
Q

The peptide bond is stronger than the ester bond. What structural feature of the peptide bond gives it additional bond strength?

Resonance structures give the peptide bond some double bond character.

The peptide bond is between carbon and nitrogen instead of carbon and oxygen atoms.

The peptide bond is more polar.

Peptide bonds can hydrogen bond.

A

Resonance structures give the peptide bond some double bond character.

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9
Q

What is the minimum number of amino acids needed to make one turn of an alpha-helix?

3

4

6

7

A

4

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10
Q

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

glutamate–aspartate.

leucine–aspartate.

glutamate–lysine.

phenylalaninelysine.

A

glutamate–lysine.

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11
Q

Which gives rise to a favorable enthalpic (delta S) driving force for protein folding?

The lining up of hydrogen bonds as the protein folds.

The limiting of possible conformations as the protein folds.

The decrease in ordered water molecules as hydrophobic amino acids pack together.

The stabilization caused by favorable electrostatic interactions of amino acid side chains.

A

The decrease in ordered water molecules as hydrophobic amino acids pack together.

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12
Q

Calculate the specific activity when 500 mg of protein has an activity of 18,000 units.

0.28 units/mg protein

36 units/mg protein

9000 units/mg protein

13,000 units/mg protein

A

9000 units/mg protein

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13
Q

Which enzyme or reagent cleaves a peptide at the carboxyl side of a methionine residue?

trypsin

chymotrypsin

V-8 protease

cyanogen bromide

A

cyanogen bromide

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14
Q

In tandem mass spectrometry, the first mass spectrometer

determines the nuclear spin of the atoms.

determines the mass of peptide subfragments.

uses bioinformatics to compare the masses of the peptides.

uses electrospray ionization to select peptide fragments.

A

uses electrospray ionization to select peptide fragments.

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15
Q

In tandem mass spectrometry, the second mass spectrometer

determines the nuclear spin of the atoms.

determines the mass of peptide subfragments.

uses bioinformatics to compare the masses of the peptides.

uses electrospray ionization to select peptide fragments.

A

uses electrospray ionization to select peptide fragments.

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16
Q

In an ELISA, the detection antibody is a __________ antibody.

monoclonal primary

polyclonal tertiary

monoclonal secondary

polyclonal secondary

A

monoclonal primary

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17
Q

Which technique can be combined with mass spectrometry to identify protein antigens in large cellular complexes?

immunofluorescence

Western blot

immunoprecipitation

ELISA

A

immunoprecipitation

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18
Q

Which of the following statements is true for hemoglobin but NOT myoglobin?

The tertiary structure is made up of a globin fold.

The surface of its tertiary structure contains many hydrophobic amino acids.

It contains a proximal histidine that coordinates the heme group.

It contains a single carboxyl-terminal amino acid.

A

The surface of its tertiary structure contains many hydrophobic amino acids.

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19
Q

Which of the following is NOT a transport protein?

maltoporin

hemoglobin

Na+ channel

DNA polymerase

A

DNA polymerase

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20
Q

Oxygen binding is monitored for a solution of hemoglobin. During the experiment, the curve changes from sigmoidal to hyperbolic. Which of the following may be the reason for the change?

A positive allosteric effector was added.

A negative allosteric effector was added.

The protein dissociated into individual subunits.

The protein denatured.

A

The protein dissociated into individual subunits.

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21
Q

Which of the following is true of sickle cell anemia?

It is a dominant genetic disease.

It is caused by a mutation in the mc120-1.jpg-globin gene.

It is caused by an amino acid substitution in the F helix.

It results in a hemoglobin that contains a hydrophobic amino acid on the surface.

A

It results in a hemoglobin that contains a hydrophobic amino acid on the surface.

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22
Q

The mutation that would lead to the most dramatic effect on Ca2+ transport is a mutation of

Ser16 in phospholamban.

Thr17 in phospholamban.

Asp351 in SERCA.

Ser17 in E2P.

A

Asp351 in SERCA.

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23
Q

An oxygen binding curve of fractional saturation versus pO2 displays a sigmoidal shape. This is the oxygen binding curve for

myoglobin.

hemoglobin that has been dissociated into individual subunits.

hemoglobin in the presence of 2,3-BPG.

myoglobin in the presence of 2,3-BPG.

A

hemoglobin in the presence of 2,3-BPG.

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24
Q

Passive transporter proteins allow molecules to move across a membrane in response to

chemical gradients.

ADP/ATP ratio.

ATP/ADP ratio.

activated signal transduction pathways.

A

chemical gradients.

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25
Q

Which of the following is NOT a passive transporter protein?

porin

Cl− channel

Ca2+-ATPase transporter protein

Ca2+ channel

A

Ca2+-ATPase transporter protein

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26
Q

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 x 10^2 mmol/sec and the catalyzed rate is 2.4 x 10^4 mmol/sec?

0.005

200

2.88 x 10^6

2

A

200

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27
Q

An enzyme that requires the coenzyme nicotinamide adenine dinucleotide belongs to which enzyme class?

transferases

isomerases

ligases

oxidoreductases

A

oxidoreductases

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28
Q

A reaction coordinate diagram comparing an uncatalyzed reaction with an enzyme-catalyzed reaction can directly illustrate that the enzyme __________, but will not directly illustrate that the enzyme __________.

orients the substrates appropriately for the reaction to occur; provides an alternative path for product formation

provides an alternative path for product formation; stabilizes the transition state

stabilizes the transition state; orients the substrates appropriately for the reaction to occur

stabilizes the transition state; provides an alternative path for product formation

A

stabilizes the transition state; orients the substrates appropriately for the reaction to occur

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29
Q

Many medicinal drugs are transition state analogs. They are good drugs because they can interact with the target enzyme active site and are

higher in energy than the transition state.

identical in structure to the transition state.

stable.

polar.

A

stable.

30
Q

Which type of reaction does not change the molecular formula of the product compared with that of the substrate?

condensation

reduction

hydrolysis

isomerization

A

isomerization

31
Q

Which of the following is NOT a function of the Mg2+ ions in the mechanism of enolase?

orientation of substrate in the active site

stabilizing the intermediate

making the proton at the C-2 position more acidic

electrophilic attack on the scissile bond

A

electrophilic attack on the scissile bond

32
Q

The role of Glu211 in the mechanism of enolase is to

facilitate the orientation of the phosphate group of the substrate.

act as a general base on the substrate.

act as a general acid on the intermediate.

make the proton at the C-2 position more acidic.

A

act as a general acid on the intermediate.

33
Q

For a reaction of Q + R mc145-1.jpg P, the rate constant

is equal to [Q][R] / [P].

has units of s−1.

is a second-order rate constant.

is equal to [P] / [Q][R].

A

is a second-order rate constant.

34
Q

The Lineweaver–Burk plot shows data obtained for an enzyme in the absence and presence of a reversible inhibitor. Which type of inhibitor was used in the experiment?

competitive

uncompetitive

mixed

noncompetitive

A

noncompetitive

35
Q

Glutamine synthetase is in the R state when Tyr397 is

deadenylated.

uridylated.

phosphorylated.

dephosphorylated.

A

deadenylated.

36
Q

First messengers, but NOT second messengers

bind to a protein.

act as a transcription factor.

are located extracellularly.

are an allosteric effector.

A

are located extracellularly

37
Q

Estradiol is secreted by the ovaries, travels through the bloodstream, and interacts with estrogen receptors on breast epithelial cells. In this scenario estradiol is acting through which type of mechanism?

synacrine

paracrine

endocrine

autocrine

A

endocrine

38
Q

If protein kinase A is activated in a liver cell in response to glucagon binding to the mc164-1.jpg2-adrenergic receptor, which of the following will result?

Glycogen synthesis will be turned on.

Glycogen degradation will be turned on.

Glucose synthesis will be turned off.

GLUT1 expression will be upregulated.

A

Glycogen degradation will be turned on.

39
Q

Below is the molecular structure of a single bovine B-arrestin subunit. Two locations are indicated. What is most likely to interact with the protein at these locations?

Beta ARK

GTP-bound G alpha

dephosphorylated GPCR

phosphorylated GPCR

A

phosphorylated GPCR

40
Q

On binding of an insulin molecule to the insulin receptor, a conformational change occurs that
Incorrect Response
increases the affinity of a second insulin binding site.

causes the dimerization of the receptor.

brings the L1 region of the alpha subunit closer to the membrane.

stimulates tyrosine autophosphorylation in the B subunits.

A

stimulates tyrosine autophosphorylation in the B subunits.

41
Q

Caspases contain

phosphorylated tyrosines when activated.

death domains.

an active site cysteine residue.

SODD.

A

an active site cysteine residue.

42
Q

Phosphorylation of which of the following is necessary for the increased expression of antiapoptotic genes?

RIP

TNF receptor

FADD

IKK

A

IKK

43
Q

Consider a mutation in procaspase 3 that changes Asp28 to an amino acid that is no longer a substrate for autocleavage. This mutant would

no longer be cleaved by caspase 8.

no longer obtain a quaternary structure.

be partially activated.

be fully activated.

A

be partially activated.

44
Q

The result of TRADD proteins binding to TNF receptors is that

TRADD is phosphorylated.

an activated adaptor complex is formed.

downstream signaling proteins are inactivated.

TNF is degraded.

A

an activated adaptor complex is formed.

45
Q

For the following reaction A→ B, if at equilibrium Delta DG > 0, what can be said about the directionality of the reaction?

strongly favored in the forward direction

strongly favored in the reverse direction

strongly favored in both directions

Not enough information is given.

A

strongly favored in the reverse direction

46
Q

Which of the following pathways are found in both plants and animals?

photosynthesis and carbon fixation

urea cycle

nitrogen fixation

citrate cycle

A

citrate cycle

47
Q

Review the figure below. Shared intermediates are used so effectively in coupled reactions because they

allow products to diffuse through membrane to increase concentration gradient.

increase the value of mc181-2.jpg.

decrease the value of Q.

limit product diffusion and allow intermediates to channel from one enzyme to the next.

A

limit product diffusion and allow intermediates to channel from one enzyme to the next.

48
Q

Which of the following is an energy conversion pathway?

urea cycle

citrate cycle

nitrogen fixation and assimilation

fatty acid degradation and synthesis

A

citrate cycle

49
Q

Which of the following is NOT a reason why glycolysis is considered one of the core metabolic pathways in nature?

Glycolytic enzymes are hugely conserved among all living organisms.

It is a primary pathway for ATP generation under anaerobic conditions.

Metabolites of glycolysis are precursors for a large number of interdependent pathways.

It is a primary pathway for nitrogen generation.

A

It is a primary pathway for nitrogen generation.

50
Q

How does phosphoglycerate kinase make glycolysis energy neutral at this step?

It uses ATP to produce 3-phosphoglycerate.

It produces 2 ATP along with 3-phosphoglycerate.

It results in a reaction at equilibrium.

It results in a reaction is endergonic.

A

It produces 2 ATP along with 3-phosphoglycerate.

51
Q

If blood glucose levels are elevated, what does glucokinase do in response?

inhibits glycolysis

stimulates the production of more hexokinase

stimulates the release of insulin

inhibits production of 2,3-BPG

A

stimulates the release of insulin

52
Q

The rate limiting step can be defined as a level of enzyme activity that can be regulated to be __________ even when substrate levels are __________.

high; high

low; high

high; low

low; low

A

low; high

53
Q

During glycolysis, the steps between glucose and formation of glyceraldehyde-3-phosphate

consume 2 ATP and 2 NADH.

consume 2 ATP.

produce 2 ADP and 2 NADH.

produce 2 ATP and 2 NADH.

A

consume 2 ATP.

54
Q

Coenzyme A is derived from which of the following vitamins?

thiamine

pantothenic acid

riboflavin

niacin

A

pantothenic acid

55
Q

Which vitamin is the precursor to the coenzyme that functions as a reductant in the pyruvate dehydrogenase complex in the final step of the reaction?

thiamine

pantothenic acid

riboflavin

niacin

A

riboflavin

56
Q

The disease beriberi is a result of which vitamin deficiency?

thiamine

pantothenic acid

riboflavin

niacin

A

thiamine

57
Q

A patient seeks medical attention for ulcerous skin lesions. The patient is diagnosed with

arsenic exposure.

a deficiency in vitamin B3.

beriberi.

cheilosis.

A

arsenic exposure.

58
Q

How would an increased level of acetyl-CoA be expected to affect the pyruvate dehydrogenase reaction?

The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an inhibition of pyruvate dehydrogenase activity.

The last step of the pyruvate dehydrogenase reaction would be blocked, resulting in a decrease in activity.

The E1 subunit would be phosphorylated by pyruvate dehydrogenase kinase, and the catalytic activity of pyruvate dehydrogenase would decrease.

The pyruvate dehydrogenase phosphatase-1 enzyme would increase, resulting in pyruvate dehydrogenase activation at an accelerated rate.

A

The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an inhibition of pyruvate dehydrogenase activity.

59
Q

The reaction catalyzed by __________ is likely to be reversible under cellular conditions according to the delta G.

malate dehydrogenase

citrate synthase

succinate dehydrogenase

alpha-ketoglutarate dehydrogenase

A

succinate dehydrogenase

60
Q

A high concentration of which molecule would inhibit citrate synthase in the citrate cycle?

AMP

ADP

NAD+

ATP

A

ATP

61
Q

Which citrate cycle metabolite is used as a precursor for heme biosynthesis?

succinyl Co-A

oxaloacetate

alpha-ketoglutarate

malate

A

succinyl Co-A

62
Q

Predict the fate of alpha-ketoglutarate when it is not used in the citrate cycle.

cholesterol synthesis

heme synthesis

gluconeogenesis

amino acid synthesis

A

amino acid synthesis

63
Q

The ultimate electron acceptor of the mitochondrial electron transport system is

O2.

NADH.

H2O.

cytochrome c.

A

O2.

64
Q

Studies of the inner mitochondrial membrane reveal its composition to be approximately 20% lipid bilayer and 80% protein. What is true of these proteins?

Abundant collagen proteins form connective tissues to strengthen the membrane against the pH gradient.

High levels of proteins are required to metabolize glucose in the glycolysis pathway for rapid energy production.

The proteins form highly folded cristae structures.

The proteins are largely electron transport complexes and ATP synthase enzymes.

A

The proteins are largely electron transport complexes and ATP synthase enzymes.

65
Q

What is the fate of NADH after it donates its electrons to the electron transport system?

NAD+ is excreted from the cell and sent to the liver for final degradation.

NADH is used for cellular biosynthesis.

NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated.

NAD+ is fed into the TCA cycle for oxidation of CO2.

A

NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated.

66
Q

Which of the following is NOT a part of oxidative phosphorylation?

NADH is oxidized to NAD+.

O2 is reduced to H2O.

Electrons from O2 are transferred to ATP.

The pumping of protons is coupled with the formation of ATP.

A

Electrons from O2 are transferred to ATP.

67
Q

The electron transport complexes found in the electron transport system

contain multiple electron transfer cofactors that facilitate electron transfer through the complexes.

are bound to the outer mitochondrial membrane.

pump protons from outside the mitochondria to the mitochondrial matrix on electron transfer.

absorb light energy that results in electron transfer.

A

contain multiple electron transfer cofactors that facilitate electron transfer through the complexes.

68
Q

What would happen to a mutated ATP synthase enzyme where the proton binding aspartate residue on the c subunits was mutated to an alanine?

The enzyme would make ATP as normal in the presence of a proton gradient.

The enzyme would not make ATP in the presence of a proton gradient.

The enzyme would make ATP without the need for a proton gradient.

The rotor would rotate in response to a proton gradient, but no ATP would be made.

A

The enzyme would not make ATP in the presence of a proton gradient.

69
Q

The main activator molecule of the ATP synthesis and the electron transport system is

ATP.

H+.

ADP.

NAD+.

A

ADP.

70
Q

What happens to patients given the proton gradient uncoupler 2,4-dinitrophenol?

They undergo rapid decrease in body temperature as a result of lack of mitochondrial electron transport.

They experience lower cellular pH as a result of rapid proton gradient dissipation.

Their mitochondrial membranes fail as a result of rapid proton gradient release.

Their body temperatures rise as a result of heat release from gradient uncoupling.

A

They undergo rapid decrease in body temperature as a result of lack of mitochondrial electron transport.

71
Q

What is the cellular location of eukaryotic thermogenin (or uncoupling protein)?

mitochondrial inner membrane

mitochondrial matrix

cytoplasm

both cytoplasm and mitochondrial matrix

A

mitochondrial inner membrane

BIOCHEM (7 decks)

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