BIOC 384 EXAM 2

Consider a system where a passive transport channel is available for a neutral molecule X. If RTln(C2/C1) is zero, then

no net transport will occur

Representative Protein a. Telomerase b. Protein Kinase A _ c. Actin polymer ____ d. Lactose permease ____ e. Hexokinase Major Protein Class 1. Cell signaling 2. Transport protein 3. Genomic caretaker 4. Structural protein 5. Metabolic enzyme A. 5, 3, 2, 1, 4 B. 3, 5, 4, 2, 3 C. 3, 4, 1, 5, 2 D. 3, 1, 4, 2, 5 E. 1, 3, 2, 4, 5

D. 3, 1, 4, 2, 5

Order the five steps in the actin-myosin reaction cycle;; Which STEP is the power stroke? 1. ATP hydrolysis induces the recovery conformation. 2. ADP release empties the nucleotide binding site in myosin. 3. Ca2+ binding to troponin uncovers myosin binding sites on actin. 4. ATP binding causes myosin to dissociate from actin. 5. Pi release pulls the active filament toward the center A. 3, 5, 2, 1, 4;; STEP 1 B. 1, 5, 2, 4, 3;; STEP 5 C. 3, 5, 1, 4, 2;; STEP 1 D. 3, 5, 2, 4, 1;; STEP 5 E. None of these are correct.

D. 3, 5, 2, 4, 1;; STEP 5

The cross-linked nature of the acrylamide media in SDS-PAGE can limit migration through the polymer matrix. Based on the figure to the right put the SDS-PAGE gels in the correct order of lowest to highest acrylamide concentration using A, B, and C. A. A < B < C B. C < B < A C. C < B < A D. B < C < A E. None are correct.

D. B < C < A

Which statement most accurately describes the structure and function of O transport proteins. A. Functional myoglobin and hemoglobin both contain a heme group with a coordinated Fe3+ atom. B. Hemoglobin and myoglobin are identical in every way except the diameter of the iron heme group. C. Hemoglobin is found in all tissues except red blood cells, whereas myoglobin is only in red blood cells. D. Hemoglobin is a tetramer that can bind BPG and O whereas myoglobin binds O2 but cannot bind BPG. E. None of the above statements is correct.

D. Hemoglobin is a tetramer that can bind BPG and O whereas myoglobin binds O2 but cannot bind BPG.

In one type of hemoglobin mutant the amino acid change generates a strong ionic interaction stabilizing the T state conformation but only under conditions of lower pH, e.g., at pH 7.2 compared to pH 7.6. What effect would this mutation have on the amount of O2 delivered to the tissue and why? A. Less O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in lungs. B. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the R state in tissues. C. Less O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in tissues. D. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in tissues. E. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in lungs.

D. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in tissues.

Which of the reactions are two examples of reversible modifications mediated by enzymes. A. Methylation of phosphatidylinositols in the membraneand phosphorylation of cytosines in nucleic acid. B. Stabilization of the transition state and formation of covalent enzyme-substrate complexes. C. Isomerization reactions that do not change the molecular formula and hydrolysis reactions. D. Phosphorylation of phosphatidylinositols in the membrane and methylation of cytosine on nucleic acids. E. Condensation reactions that combine substrates and phosphorylation of serine or threonine residues.

D. Phosphorylation of phosphatidylinositols in the membrane and methylation of cytosine on nucleic acids.

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

LMYKWDERMGFCE

An enzyme can increase the rate of a reaction inside a cell by ____________ the energy of the____________ .

Lowering; transition state

The five major protein classes are _____________, structural proteins, _____________, genomic caretaker proteins, and __________________.

Metabolic enzyme, structural proteins, cell signaling, genomic caretaker, transport protein,

The primary functions of myoglobin and hemoglobin are best described by

Myglobin stores oxygen whereas hemoglobin transports oxygen

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 × 102 mmol/sec and the catalyzed rate is 2.4 × 104 mmol/sec?

200

Which of the following peptides would be eluted last when separated using gel filtration chromatography?

360g/mol (weighs the least)

Which percentage of polyacrylamide would give the best separation for large proteins?

5% (smallest percentage)

Choose the most correct statement below regarding the function of the two histidine residues in globin proteins that are responsible for oxygen binding

The proximal histidine moves toward the heme group in response to oxygen binding

Secondary active symporter

The transport system shown below is a(n)

In isoelectric focusing, a protein with a pH below the pI would

cathode

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first?

+1 (positive charge)

The selectivity of aquaporin for H2O relies on which of the following? Choose the correct 3.

- A 2.8 A constriction point within the protein - hydrogen bonding to Asn - inverted alpha-helix dipoles

Identify three proteins below that are considered to be genomic caretaker proteins

- RNA polymerase, topoisomerase, DNA polymerase

The glutamate side chain in the active site of HMG-CoA reductase acts as a general base only after

A conformational change triggers the exchange of NADP+ for NADPH.

ion transport across the cell membrane by the Na+-K+ ATPase transporter protein at 37ºC under conditions in which the membrane potential is 70 mV (outside of the cell is positive relative to the inside) and the ion concentrations are as follows: [K+]outside= 5 mM, [K+]inside= 140 mM, [Na+]outside= 150 mM, [Na+]inside= 10 mM What is the energy requirement to transport 2 moles of K+ from the outside to inside? A. +3.7 kJ D. +1.8 kJ B. -26.2 kJ E. +41.2 kJ C. -41.2 kJ

A. +3.7 kJ

Choose the five correct labels for the figure to the right. "Transition State" = TS A. 1. ES 2. TS 3. EP 4. E+P 5. Substrate B. 1. E+P 2. TS 3. EP 4. ES 5. Enzyme C. 1. EP 2. TS 3. ES 4. E+P 5. Product D. 1. ES 2. EX 3. EP 4. E+P 5. TS E. 1. ET 2. ES 3. E+P 4. TS 5. Ligand

A. 1. ES 2. TS 3. EP 4. E+P 5. Substrate

The transition state theory states that the enzyme active site makes the most contacts with the high energy transition state, which occurs midway between ESEP, than it does with either S or P. What evidence described below best supports the transition state theory? A. Transition state analogs bind tightly to enzyme active sites, for example adenosine deaminase inhibitors. B. Products of a reaction dissociate only after cleavage of enzyme intermediate in the enzyme active site. C. The activation energy of a catalyzed reaction is lower than an uncatalyzed reaction. D. Multiple substrates bind in an ordered fashion, i.e., substrate A binds before B that binds before C. E. The activation energy of a reaction is not altered by the catalytic activity of enzymes .

A. Transition state analogs bind tightly to enzyme active sites, for example adenosine deaminase inhibitors.

This question has two parts. a) What provides the energy for a secondary active symporter to move molecules against a concentration gradient? b) Give an example of a secondary symporterprotein. A. a) ATP-dependent transport of solute by a primary active transporter, b) sodium-iodide symporter B. a) ATP-dependent transport of solvent by a primary active transporter, b) lactose permease C. a) Antiporter activity of a primary active transporter, b) sarcoplasmic reticulum calcium transporter D. a) Conformational changes in an ion gated channel protein, b) serotonin symporter protein E. None of the above statements provide a correct answer for both parts (a) and (b)

A. a) ATP-dependent transport of solute by a primary active transporter, b) sodium-iodide symporter

Refer to the reaction coordinate diagram at right that compares catalyzed and uncatalyzed reactions. Which of the following labels are correct? "Activation energy" = AE. A. 3 = Reactant, 6 = G, 2 = AE for the catalyzed rxn B. 6 = AE for catalyzed rxn, 5 = Product, 1 = G C. 7 = G, 1 = G‡, 4 = AE for the catalyzed rxn D. 6 = AE for uncatalyzed rxn, 3 = Substrate, 2 = G‡ E. 3 = Substrate, 2 = AE for catalyzed rxn, 7 = G‡‡

B. 6 = AE for catalyzed rxn, 5 = Product, 1 = G

Which of the experimental steps listed at the right is considered the most challenging in X-ray crystallography? A. Mounting the crystal on the X-ray B. Determining the phases of the diffracted X rays C. Dissolving the protein in the appropriate solvent D. Using the correct radio frequency for nuclear spin E. Isolating epitope-tagged proteins from bacteria.

B. Determining the phases of the diffracted X rays

Which of the following is a way that an enzyme can increase the reaction rate inside a cell? A. Binding tighter to the substrate than the product. B. Orienting substrates appropriately for the reaction to occur. C. Increasing the activation energy at the transition state. D. Provide a path that forms a covalent bond to the product. E. By lowering the standard free energy change for the reaction.

B. Orienting substrates appropriately for the reaction to occur.

Chymotrypsin is a serine protease requiring the formation of a (covalent / noncovalent) enzyme complex as a critical step in the reaction. The amino acid residue histidine has a central role in the reaction mechanism, which is described as a(n) (acid-base / metal-ion) catalysis mechanism. The reaction sequence results in the release of the (carboxyl / amino) terminal fragment first as a result of the His 57 residue (abstracting / donating) a proton to the substrate. The chymotrypsin reaction relies on water to generate a (nucleophile / electrophile) that attacks the (carbonyl carbon / amide nitrogen) at the cleavage site. Both the (Gly 193 / Asp 102) and Serine 195 residues are essential to stabilization of the oxyanion intermediate. A. covalent, covalent, amino, abstracting, nucleophile, carbonyl carbon, Asp 102 B. covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbon, Gly 193 C. noncovalent, acid-base, carboxyl, abstracting, nucleophile, amide nitrogen, Gly 193 D. covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbon, Asp 102 E. covalent, acid-base, amino, abstracting, nucleophile, amide nitrogen, Asp 102

B. covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbon, Gly 193

ion transport across the cell membrane by the Na+-K+ ATPase transporter protein at 37ºC under conditions in which the membrane potential is 70 mV (outside of the cell is positive relative to the inside) and the ion concentrations are as follows: [K+]outside= 5 mM, [K+]inside= 140 mM, [Na+]outside= 150 mM, [Na+]inside= 10 mM What is the energy requirement to transport 3 moles of Na+ from the inside to outside? A. +13.7 kJ D. +3.7 kJ B. +1.8 kJ E. -13.7 kJ C. +41.2 kJ

C. +41.2 kJ

Which are critical features or properties of nearly all protein enzymes? Choose all that apply 1. Enzymes usually display high affinity and specificity for their substrates. 2. A covalent bond forms between an enzyme and substrate following substrate binding. 3. Enzyme activity is often highly regulated to provide maximum control of catalysis. 4. Histidine is found in the enzyme active site to facilitate acid-base catalysis 5. Conformational changes, both small and large, can occur after substrate binding. 6. Enzymes alter the change in free energy without altering the rates of reactions. A. 2 and 4 B. 1,2,4,5 C. 1,3,5 D. 2,4,6 E. 5 only

C. 1,3,5

Which of the TWO following statements about myosin are true? 1. The A band and I band belong to the Z club and meet up at the T tubule to disco nightly. 2. The myosin head has a binding site foractin, titin, troponin, tropomyosin, and ATP. 3. Thick and thin filaments slide past each other during contraction to lengthen the muscle. 4. Myosin-actin reaction cycle requires hydrolysis of 1 ATP per myosin head in each cycle. 5. The myosin head functions like molecular lever during the power stroke of contraction. 6. The interaction between myosin and actin converts chemical energy to mechanical work. A. 4 and 5 B. 1 and 3 C. 4 and 6 D. 3 and 4 E. 5 and 6

C. 4 and 6

Which separation technique exploits the density differences of biomolecules and organelles? A. Dialysis using dialysis tubing in a beaker with buffer. B. Salting out by ammonium sulfate using a beaker and stir bar. C. Centrifugation using centrifuge tubes in a rotor placed in a centrifuge. D. An ionic exchange column using a charge resin at an optimal pH. E. An affinity column using a solid matrix with a specific ligand attached.

C. Centrifugation using centrifuge tubes in a rotor placed in a centrifuge.

What protein feature will cause the protein to bind to a metal in chelation affinity chromatography—specifically, a resin with immobilized Ni2+? . proteins with antigenic affinity for divalent cations. B. proteins that have a heme that can bind divalent cation metals, such as iron or nickel. C. recombinant proteins engineered to have six histidines at the N or C terminus of the protein. D. proteins with a negative charge on the amino terminus and a positive charge on the carboxyl terminus. E. proteins that bind cadmium to form a nickel-cadmium compound similar to batteries.

C. recombinant proteins engineered to have six histidines at the N or C terminus of the protein.

What are the THREE key assumptions of Michaelis-Menten kinetics. 1. Substrates and products are chemically inert until enzymes are added, catalysts = life. 2. The reaction is analyzed at a time in the reaction that negligible product is formed. 3. Catalysts alter the free energy of the reaction without altering the equilibrium constant. 4. The steady state condition is reached quickly under conditions where [S] >> [E]. 5. Enzymes have higher binding affinities for products than the transition state. 6. Product release is assumed to be a rapid step in the process. A. 1, 2, 4 B. 1, 4, 5 C. 3, 4, 6 D. 1, 3, 6 E. 2, 4, 6

E. 2, 4, 6

If SERCA is not functioning in a myoblast, which of the processes described at the right is most likely to occur? A. The myofibrils can lengthen but not shorten. B. Actin will not be able to bind to the thin filament. C. ATP cannot be hydrolyzed to drive the power stroke D. Myosin will not be able to mediate the power stroke. E. Muscle contraction occurs but not muscle relaxation.

E. Muscle contraction occurs but not muscle relaxation.

Which of the following statements about association and dissociation constants describing the binding of Ligands X and Y to Protein Z is the most correct? A. Ligand X has a Kd = 0.2 mM, while Ligand Y has aKd = 0.6 mM. Ligand X therefore has a lower affinity for Protein Z than does Ligand Y. B. The larger the Kd value is, the larger the Ka value will be for binding of Ligands X and Y to Protein Z. C. Ligand X has a Ka = 0.2 mM, while Ligand Y has aKd = 0.6 mM. Ligand X therefore has a higher affinity for Protein Z than does Ligand Y. D. The smaller the Kd value is, the smaller the Ka value will be for binding of Ligands X and Y to Protein Z. E. None of these answers are correct.

E. None of these answers are correct.

Sodium dodecylsulfate (SDS) plays an important role in SDS PAGE. Selectthe correct description of what SDS does in denatured electrophoresis. A. Because SDS is a detergent, it supports the native state by interacting with the nonpolar portions of a protein, stabilizing the three-dimensional structure of a protein so that it can migrate based on shape. B. SDS forms hydrogen bonds with the carbonyl carbon and amide nitrogen of the polypeptide backbone. C. SDS is a charged detergent that neutralizes the protein, allowing the protein to migrate through the gel. D. SDS is a bivalent cation that can interact with two negatively charged carboxyl groups at the same time. E. SDS is an amphipathic compound that binds tothe hydrophobic portion of proteins and give a negative charge derived from the polar head group such that proteins have a proportional charge to mass ratio.

E. SDS is an amphipathic compound that binds tothe hydrophobic portion of proteins and give a negative charge derived from the polar head group such that proteins have a proportional charge to mass ratio.

Cofactors with organic components are called coenzymes. Which two are coenzymes? A. Biotin/Selenium B. Zinc/FADH2 C. Thymidine/Lipoamide D.NADH/Calcium E. Tetrahydrofolate/NADP+

E. Tetrahydrofolate/NADP+

Assume that in the graph at the right, the curve represented by Y is normal adult hemoglobin at pH 7.4 with normal levels of 2,3-BPG. Which of the statements below is the most correct regarding curves X and Z? A. X represents O2 binding in cells with elevated 2,3-BPG, whereas Z represents O2 binding in cells with decreased 2,3-BPG. B. Z represents O2 binding in cells at a higher pH, whereas X represents O binding in cells with a lower pH. C. Z represents O2 binding in cells with a lower pH, whereas X represents O binding in cells with elevated 2,3-BPG. D. X represents O2 binding in cells at a higher pH, whereas Z represents O2 binding in cells completely lacking 2,3-BPG. E. Z represents O2 binding in cells with elevated 2,3-BPG, whereas X represents O2 binding in cells with decreased 2,3-BPG.

E. Z represents O2 binding in cells with elevated 2,3-BPG, whereas X represents O2 binding in cells with decreased 2,3-BPG.

Which three of the following allosteric effectors characterize the Bohr effect and contribute to shifting the equilibrium for hemoglobin from the R state conformation to the T state conformation?

H+, CO2, 2,3-bisphosphoglycerate

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin?

His57

If an enzyme carries out acid-base catalysis, which of the following amino acids could act as general acid?

Histidine

B , C

Refer to the reaction coordinate diagram below. The change in the activation energy of the reaction because of the presence of an enzyme is illustrated by the energy of ____________minus the energy of ____________ .

Passive transport of molecules down a concentration gradient

What type of transport is depicted in the figure below?

Primary active ABC transporters and P-type transporters both require

a protein conformational change to function.

Identify the three types of enzyme-mediated reactions from the list below.

coenzyme-dependent redox reactions, reversible covalent modification, and metabolite transformation reactions.

Oxygen binds to a single subunit of a multi-subunit hemoglobin protein. As a result, all subunits switch to the R state. This is an example of the ______________ model of allostery (best answer to fill in the blank).

concerted

Thick filaments________________ , but thin filaments do/are not.

contain myosin

One explanation for the prevalence of the sickle cell anemia trait in the human population in Africa is

heterozygous individuals carrying the Va;-6 mutation are less susceptible to malaria because their red blood cells are resistant to infection by the malarial parasite.

Based on how data is collected in the techniques of X-ray crystallography compared to NMR, the technique of NMR is the only choice for studying

protein unfolding

Which of the following statements applies to hemoglobin but not to myoglobin?

subunit interactions are critical for function

If SERCA (calcium transporter) is not functioning in a myoblast, which of the following may occur?

the myofibrils can shorten but not lengthen

Which of the following accounts for some of the specificity of the K+ channel?

the orientation of the backbone carbonyl oxygen atoms in the channel