bch final E1

Question 1

A protein that binds a ligand is found to have a hill coefficient of 1.5. Which of the following is TRUE regarding its cooperativity?

Answer 1

Binding of the first molecule of ligand increases the binding for the second molecule

Question 2

The helical wheel projection shown above represents a 14-residue alpha-helix that is part of a larger protein structure. Which of the following would apply?

Answer 2

At neutral pH, the alpha-helix is amphipathic with respect to charge.

Question 3

The basis of cooperativity in hemoglobin relies on:

Answer 3

Re-arrangement of hydrogen bonds, salt-bridge interactions, and hydrophobic contacts between the alpha1 and beta2 subunits.

Question 4

A kinetics experiment reveals that a Michaelis constant (Km) of an enzyme for its substrate is equal to 7microM. What can you safely conclude regarding the behavior of the enzyme?

Answer 4

The reaction Vmax occurs at greater than 7microM substrate concentration.

Question 5

The thermodynamics of a biochemical reaction can be driven by either favorable changes in enthalpy or favorable changes in entropy, but not by both. True or false?

Answer 5

False

Question 6

Hydrogen bonds are weak electrostatic interactions that are made possible by the presence of partial charges on H-bond donors and acceptors. T/F?

Answer 6

True

Question 7

Formation of a new peptide bond produces one molecule of water and one hydroxide ion. T/F?

Answer 7

False

Question 8

The sigmoidal oxygen-binding curve of hemoglobin is an indicator of cooperativity between the hemoglobin subunits. T/F?

Answer 8

True

Question 9

Which of the following statements are TRUE regarding X-ray crystallography

Answer 9

It involves interpretation of a diffraction pattern

Question 10

Which of the following is NOT a feature of the Bohr effect:

Answer 10

The Oxy(R state) is stabilized, thus more oxygen can readily bind

Question 11

Peptide bonds are planar due to the partial double bond character of neighboring R-groups. T/F?

Answer 11

False

Question 12

A reaction with a delta G equal to zero can best be described as:

Answer 12

A system that has reached an equilibrium.

Question 13

Fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin because:

Answer 13

It has a lower affinity for 2,3-BPG.

Question 14

The polypeptide shown below needs to be separated from other polypeptides of similar size (at pH 7.0). What purification technique is best suited to isolate this peptide? RKGYWPSDDEDHTERSAVLIDEQNT

Answer 14

Anion exchange chromatography, since the polypeptide has a net negative charge.

Question 15

Which of the following is NOT a feature of an alpha-helix?

Answer 15

Hydrogen bonding patterns occur between every n+3 residues.

Question 16

You are attempting to purify a protein that is 25 kDa in size by using a column that has been prepared with a solution of nickel sulfate. However, when you run SDS-PAGE to analyze the different steps of the protocol, your gel looks like the one shown here. Which of the following statements could best describe your results.

Answer 16

The protocol did not work and one possible reason is that the buffers had a pH of 4.5

Question 17

Small proteins elute earliest in a gel filtration column, but travel fastest on SDS-PAGE. T/F?

Answer 17

False

Question 18

In an experiment, researchers have replaced the distal histidine of myoglobin with a serine, which has a shorter side chain than histidine. This has the effect of increasing the distance from the distal residue to the iron. What would you predict will happen to the P50 value of this mutant protein?

Answer 18

The P50 value will increase because oxygen will now bind more weakly.

Question 19

A copper deficiency may result in which of the following

Answer 19

Weakening of the coiled-coil of tropocollagen

also later accepted: Loss of lysine hydroxylase activity

Question 20

Upon adding a catalyst, the delta delta G of a reaction becomes very large. What can you conclude about the rate constant of the reaction?

Answer 20

It has most likely increased

Question 21

The following primary sequence of residues folds into a structure that is mostly alpha-helical. How many separate alpha-helices are there in the protein fold? GMTRAVLSRDAPGTRSPYVWIARKCHTWSGPGVIDEEDPTA

Answer 21

3

Question 22

The classical protein folding experiment with Ribonuclease A demonstrated that:

Answer 22

The primary amino acid sequence contains the necessary information to fold a protein

Question 23

The small side chain of glycine allows it to do which of the following:

Answer 23

Fit into the small space at the center of beta-turns.

Question 24

Use the following chart to answer this question. Which of the following sets of residues would most likely be found on a protein surface:

Answer 24

glycine, arginine, histidine, glutamate

Question 25

Upon running SDS-PAGE on a protein complex that consists of 5 subunits, of which 3 subunits are the same size and two have distinct sizes (different from each other and different from the other three), how many bands should you expect to see the gel?

Answer 25

three bands

Question 26

In protein folding, the hydrophobic effect and van der Waals interactions both contribute favorably to the entropy component of the Gibbs free energy equation. T/F?

Answer 26

False

Question 27

Protein folding is made energetically favorable because of the combined contributions of the hydrophobic effect, van der Waals interactions, hydrogen-bonding, salt bridge interactions, and disulfide bonds. T/F?

Answer 27

True

Question 28

You'd like to solve the high resolution structure of a very small protein of 60 residues. Based on the strengths and weakness of different structural techniques, which ones are most suitable to try?

Answer 28

Both X-ray crystallography and NMR are suitable

Question 29

Carbonic acid has a pKa of 6.37; acetic acid has a pKa of 4.76; therefore, carbonic acid is the stronger acid. T/F?

Answer 29

False

Question 30

Under conditions where [S]>>Km, enzymatic reactions become zero order with respect to substrate because:

Answer 30

The enzyme becomes saturated with enzyme and is performing catalysis at maximum capacity.

Question 31

alpha-keratins have a pseudo-repeat motif of (abcdef)g, in which a and d are negatively charged residues. T/F?

Answer 31

False