Biochemistry Exam 2

What is the free-energy cost at 25oC of pumping Ca2+ out of a cell when the cytoplasmic concentration is 0.4 μM, the extracellular concentration is 1.5 mM, and the membrane potential is -60 mV?

A) +32 kJ/mol

An insect aminopeptidase was purified and its catalytic activity was investigated using an artificial peptide substrate. The Vmax was 4.0 x 10-7 M/s and the KM was 1.4 x 10-4 M. The enzyme concentration used in the assay was 1.0 x 10-7 M. What is the catallytic efficiency of the enzyme?

A) 2.8 x 104 s-1.M-1

Hydrolysis of ATP by the Na,K-ATPase moves _____ while dephosphorylation moves _____.

A) 3 Na+; 2 K+

Which is not a consequence of the cis double bonds of fatty acids?

A) A higher melting temperature

Which amino acid in the aquaporin channel hydrogen bonds with water to prevent the movement of protons?

A) Asn

Which of the following second messengers would NOT be found free floating in the cytosol

A) DAG

Activity of the Ras protein is analogous to the _____ in terms of its ability to bind GTP.

A) G protein α subunit

Small mammalian hibernators can withstand body temperatures of 0oC to 5oC without injury. However, the body fats of most mammls have melting temperatures of approximately 25oC. Predict how the composition of the body fat of hibernators might differ from that of their nonhibernating cousins.

A) Hibernators will contain a higher percentage of polyunsaturated fatty acids.

Laminaria groenlandica is a type of kelp that grows along the rocky shores of Alaska. Due to its geographic distribution, this species is subjected to cold temperatures and potential freezes. Macrocystis pyrifera is a type of kelp that grows off the coast of South America and encounters much warmer temperatures. Which of these two species would you expect to have a higher composition of unsaturated fatty acid tails incorporated into its lipid bilayer?

A) Laminaria groenlandica

Which of the following is NOT a way in which biological catalysts differ from nonbiological catalysts?

A) Only biological catalysts are not permanently altered or consumed as a result of the reaction.

What is the effect of phosphofructokinase in the presence of phosphoenolpyruvate and what type of interaction do they have?

A) Phosphoenolpyruvate allosterically inhibits phosphofructokinase; engage in feedback inhibition

What amino acid performs the nucleophilic attack during the chymotrypsin mechanism?

A) Ser

A mutated form of the α subunit of the heterotrimeric G protein has been identified; this form readily exchanges nucleotides even in the absence of an activated receptor. What would be the effect on a signaling pathway containing the mutated α subunit?

A) The signaling pathway will remain activated.

Some G protein-linked receptors are associated with a protein called RGS (regulator of G protein signaling). RGS stimulates the GTPase activity of the G protein associated with the receptor. What effect does RGS have on the signaling process?

A) This will shorten the duration of signaling.

Which of the following would represent the reaction coordinate for a two-step reaction with an initial slow step?

A) Two peaks, first one has a large activation energy

Under certain conditions, peptide bond formation is more thermodynamically favorable than peptide bond hydrolysis. Would you expect chymotrypsin to catalyze peptide bond formation?

A) Yes

What is the relationship between KM and [S] when an enzyme-catalyzed reaction proceeds at 90% of Vmax?

A) [S] = 9 KM

Acetylcholine and nicotine competitively bind to nicotinic acetylcholine receptors to cause the same second messenger activation. Nicotine is considered an _______________ of the receptors.

A) agonist

The Na,K-ATPase is a(n) _____ that moves Na+ from _____ and K+ from _____. A) antiporter; inside to out; outside to in D) symporter; outside to in; outside to in B) antiporter; outside to in; inside to out E) none of the above C) symporter; inside to out; inside to out

A) antiporter; inside to out; outside to in

G proteins:

A) consist of three subunits, Gα, Gβ, and Gγ.

Which of the following may undergo transverse diffusion within the lipid bilayer?

A) membrane lipids

Which type of secondary structure present in integral membrane proteins is readily detectable in the primary structure?

A) membrane-spanning α helix

What type of chemical species can participate in catalysis by binding substrates to orient them properly, by undergoing reversible changes in oxidation state, and by stabilizing negative charges:

A) transition metal cations

Voltage-gated channels are more likely to be composed of

A) transmembrane α helices

How many acyl chains are added to a sphingosine backbone in order to form a sphingomyelin molecule?

B) 1

Rank the melting points of the following fatty acids. 1) cis-oleate (18:1) 2) trans-oleate (18:1) 3) linoleate (18:2

B) 2 > 1 > 3

Which of the following would represent the reaction coordinate for a slow reaction?

B) B

Glucose is added to cells and the rate of glucose transport is plotted against glucose concentration. In the presence of the galactose derivative 6-O-benzyl-D-galactose the curve is shifted to the right (with no other change). What kind of agent is this galactose derivative?

B) Competitive inhibitor

A mutation in the active site of an enzyme results in a large increase in stabilization of the ES complex, while there is no change in the stabilization of the transition state complex. What effect will this have on the rate of product formation?

B) Decrease rate

How does the addition of an enzyme to a chemical reaction affect the activation energy of the reaction?

B) Decreases it

Given the plot below, which enzyme would generate product more rapidly when [S] = 10 μM?

B) Enzyme B

Prodrugs are inactive compounds that need to be cleaved in order to yield an active drug. A novel tumor therapy has recently involved the delivery of an enzyme, capable of catalyzing this cleavage reaction, to the tumor site. This is followed by administration of the prodrug, which in this instance is acting as the substrate. Suppose that there are two enzymes capable of catalyzing this reaction. Enzyme A has a KM for the prodrug of 1 μM and Enzyme B has a KM of 1 nM. Which enzyme would you use in patients?

B) Enzyme B

Activation of a G protein in response to hormone binding requires binding of _____ to the _____ subunit.

B) GTP; α

What is the major factor in determining the types of secondary structures that form in the transmembrane portions of integral membrane proteins?

B) Hydrogen bonding interactions of protein backbone groups

The enzyme that catalyzes the reaction below would be classified as a(n)

B) Lyase

Which of the following amino acids could bind to the specificity pocket of Trypsin?

B) Lys

Hexokinase undergoes a large conformational change in order to exclude water from the active site. Would chymotrypsin undergo such a change upon binding its substrate?

B) No

The enzyme γ-glutamylcysteine synthase (γ-GCS) catalyzes the first step of the biosynthesis of trypanothione, a compound that enables the protozoan T. brucei to maintain redox balance. Given the information below, does this enzyme obey Michaelis-Menten kinetics? aminobutyric acid + glutamate + ATP --> --> --> trypanothione Substrate! KM (mM) Glutamate! 5.9 Aminobutyric acid! 6.1 ATP! 1.4

B) No

A pore that simultaneously transports two different molecules in the same direction is called a(n)

B) Symporter

Which of the following is NOT a general feature of the lipid bilayer in biological membranes?

B) The bilayer is stabilized by covalent interactions between the lipids molecules and integral membrane proteins.

ADP binds to platelets in order to intiate the activation process. Two binding sites were identified on platelets, one with a Kd of 350 nM and one with a Kd of 7.9 μM. Which of these is the low-affinity binding site?

B) The binding site with a Kd of 7.9 μM is the low affinity site.

Which of the following curves shows the appropriate relationship between [S] and time?

B) b

Which of the following is true regarding the glucose transporter?

B) binding of glucose causes a conformational change so that the transporter is never open on both sides of the membrane

Chymotrypsin, a serine protease, preferentially cleaves a peptide bond adjoining a bulky non-polar side chain. This is because chymotrypsin's "specificity pocket":

B) contains small hydrophobic side chains

Which of the following open in response to an extracellular stimulus such as a neurotransmitter

B) ligand-gated channels

Cerebrosides and gangliosides are glycolipids that are built on a _____ backbone.

B) sphingosine

A patient suffers from premature zymogen activation, so that the pancreatic enzymes are activated in the pancreas rather than the small intestine -- causing damage to the pancreas. Which of the following would be the most effective in preventing these effects?

B) trypsin inhibitor

Alcohol dehydrogenase (ADH) converts ethanol into acetaldehyde in the liver. The acetaldehyde is then processed by acetaldehyde dehydrogenase (ALDH) to form acetic acid, according to the scheme below. Following ingestion of a large volume of ethanol, all all of the acetaldehyde cannot be processed and builds to concentrations that result in the physiological symptoms of intoxication. The ALDH enzyme is inhibited by the compound benzaldehyde (below). ALDH has a native KM for acetaldehyde of 160 μM and a Vmax of 1.4 μmol/min, with a KI for benzaldehyde of 0.18 μM. Calculate the initial velocity (v0) expected when the ALDH assay is conducted using 48 μM of acetaldehyde in the presence of 4.2 μM benzaldehyde.

C) 0.017 μmol/min

What is responsible for the extremely rapid propagation of action potential?

C) Axons are insulated with a myelin sheath which prevents ion movement except at the nodes between myelinated segments.

Which of the following curves shows the appropriate relationship between [ES] and time in steady state kinetics?

C) Curve that increases slightly, then remains constant before slightly decreasing

Sarin gas [(CH3)2CHO]CH3P(O)F is a fatal nerve agent that acts as an irreversible inhibitor of the enzyme acetylcholine esterase. Acetylcholine esterase hydrolyzes acetylcholine to render it inactive in the synapse. Atropine is an antagonist to acetylcholine. Latrotoxins (black widow venom) act as agonists to acetylcholine. Which of the following physiological features would you expect to find in an individual exposed to sarin gas? Would you treat this individual with atropine or latrotoxins to reverse the symptoms?

C) Increased muscle contraction; atropine

23. Which of the following statements regarding kcat is FALSE?

C) It is the total number of catalytic cycles completed by all of the enzyme molecules per unit of time.

Yeast glucose-6-phosphate dehydrogenase can be inhibited by a number of cellular agents whose KI values are listed below. Which is the most effective inhibitor? Which inhibitor is likely to be completely ineffective under normal cellular conditions? Inhibitor KI (M) Inorganic phosphate 1.0 x 10-1 Glucosamine-6-phosphate 7.2 x 10-4 NADPH 2.7 x 10-5

C) Most effective: NADPH; Ineffective: inorganic phosphate

The rate constant associated with the reaction below would be

C) Second order

A membrane consisting only of phospholipids undergoes a sharp transition from the crystalline form to the fluid form as it is heated. What would be the effect on this transition in a membrane containing 80% phospholipid and 20% cholesterol?

C) The shift from the crystalline to the fluid form would be more gradual

Phorbol esters, which are compounds isolated from plants, are structurally similar to diacylglycerol. How does the addition of phorbol esters affect the signaling pathways of cells in culture?

C) They would activate protein kinase C.

In which type of reversible inhibition does binding substrate facilitate binding of the inhibitor?

C) Uncompetitive

A molecule moves across a membrane from a lower to a higher concentration with the aid of a membrane protein. This process is known as:

C) active transport

In the reaction mechanism of the glycolytic enzyme aldolase, an active site tyrosine residue accepts a proton from the substrate. In this form the side chain of Tyr must be _________ and it is acting as a(n) __________ catalyst.

C) deprotonated; base

It is necessary to know the value of [E]t in order to determine the values of

C) kcat

Which of the following is a ligand of the β2-adrenergic receptor?

C) norepinephrine

Ligand binding to a receptor tyrosine kinase causes _____ of the receptor which then _____ the next protein in the signaling pathway.

C) phosphorylation; phosphorylates

Which of the following lipid types are not found in animal membranes?

C) triacylglycerols

If an enzyme-catalyzed reaction has a velocity of 2 mM/min and a Vmax of 10 mM/min when the substrate concentration is 0.5 mM, what is the KM?

D) 2 mM

Which of the following statements about allosteric control of enzymatic activity is false?

D) Binding of the effector to the active site changes the conformation of the enzyme molecule

Which of the following is FALSE regarding transition state stabilization?

D) Enzyme cofactors are often used to stabilize transition state molecules.

Rank the melting points of the following fatty acids. Fatty acid Laurate (12:0) Linolenate (18:3) Oleate (18:1) Stearate (18:0)

D) Linolenate < Oleate < Laurate < Stearate

Renin or chymosin is a protease similar to chymotrypsin, except that it belongs to a class of enzymes called aspartyl proteases -- in which asparatate residues are found in the active site rather than serine. Renin catalyzes the hydrolysis of a peptide bond in the protein angiotensinogen, converting it to angiotensin I, a precursor of a hormone involved in regluating blood pressure. Renin inhibitors are therefore potentially valuable in the treatment of high blood pressure. Two aspartate residues in the renin active site, Asp 32 and Asp 215, constitute a catalytic dyad, rather than the catalytic triad found in chymotrypsin. Given this information and the figure below, what type of catalysis is utilized by renin? Which of the two active site Asp residues will have the lower pK value?

D) Renin uses acid-base catalysis; Asp 32 has the lower pK value

The structure of the drug prednisone is shown below. What is the most likely means of transport of this molecule into the cell? (Some steroid derivative)

D) Simple diffusion

What is the primary storage form of fatty acids?

D) Triglycerides

The drug known as Botox is a preparation of botulinum toxin. How does this account for its use by plastic surgeons to alleviate facial wrinkles?

D) all of the above

There are few examples of inhibitors that decrease Vmax but do not affect KM, these inhibitors

D) all of the above

The GLUT transporter moves glucose through a transport protein in the same direction as its concentration gradient. The action of the glucose transporter is an example of _____________. The SGLT transporter uses the sodium concentration gradient created by the sodium potassium ATPase to move glucose against its concentration gradient. The action of the SGLT transporter is an example of _______________.

D) facilitated transport, secondary active transport

The complex formed between a lipid hormone and its receptor binds to _____ which are specific DNA sequences.

D) hormone response elements

Which of the receptors below is a tyrosine kinase?

D) insulin receptor

Which of the following is the primary building block for the synthesis of molecules like cholesterol or ubiquinone?

D) isoprene

cAMP binds to the _____ subunits of protein kinase A allowing the tetramer to dissociate into _____.

D) regulatory subunits; two active monomers and an inactive dimer

The chymotrypsin/trypsin family of proteases has which combination of amino acids in the active site

D) serine, histidine, aspartic acid

Nerve cells contain high levels of _____ which is a derivative of _____.

D) sphingomyelin; sphingosine

All known porins are _____ proteins composed of _____.

D) trimeric; β-barrels

What is the ΔG for transport of glutamate from the outside of the cell, where the concentration of 0.1 mM, to the inside of the cell, where the concentration is 10 mM? Assume the cell potential is -70 mV and the temperature is 37oC.

DD) +18.6 kJ/mol

What is the membrane potential created by a sodium gradient where [Na+]out = 145 mM and [Na+]in = 12 mM at 37°C?

E) -67 mV

A 30-mM solution of hippurylphenylalanine was monitored for amide bond hydrolysis by monitoring the formation of product, phenylalanine. At the end of 50 days, 25 μM phenylalanine was detected in solution. The amide bond in hippurylphenylalanine is hydrolyzed 4.7 x 1011 times faster in the presence of an enzyme. What is the rate of formation of phenylalanine in the presence of the enzyme (M/s)?

E) 2.7 M/s

The total concentration of receptors in a sample is 25 mM. The concentration of free ligand (L) is 10 mM and Kd is 10 mM. Calculate the percentage of receptors that are occupied by ligand.

E) 50%

The glucose transporter is an example of

E) A and D

Concerning the effect of mixed inhibitors on a reaction

E) B and C

Which of the following would be a proper representation of enzyme velocity?

E) Either B or C +- d[P]/dt

What would occur when the action potential for muscle contraction reaches its terminus, if SNARE complexes were not functioning?

E) Membrane fusion would not occur and there would be no release of acetylcholine into the synaptic cleft.

The kinetics of an enzyme is measured as a function of substrate concentration in the presence and absence of 100 μM inhibitor and the data plotted as in the graphs below. Based on these data, answer the following questions: 1) what type of inhibition is indicated; and 2) what is the true value of KM?

E) Noncompetitive inhibitor; KM = 10 μM

Which of the following statements about the insulin receptor is FALSE?

E) The receptor does not undergo a conformational change upon binding insulin because it is already in the dimer form.

Kinetic studies are carried out for a Michaelis-Menten enzyme at a specific concentration of enzyme. What would be the effect on KM and Vmax if half as much enzyme is used?

E) The value of Vmax will be half but the value of KM will remain the same.

Based on the reaction below, how would the enzyme catalyzing this reaction be classified?

E) Transferase

A pH/rate curve with an inflection point at pH~4 suggests the involvement of a(n) ________ in the catalytic step.

E) acidic amino acid

Which of the following components of the insulin response pathway do NOT possess catalytic activity?

E) adapter proteins

Which of the following will cause the opening or closing of a gated ion channel?

E) all of the above