Question 1

In the following schematic diagram of a simple signaling pathway, protein Z regulates the activity of protein X, which is an upstream protein kinase, through a negative feedback loop. Which of the following better describes protein Z?

Accepted Answer

A)  It is a protein kinase that is activated by phosphorylation. 
B)  It is a protein kinase that is inactivated by phosphorylation. 
C)  It is a protein phosphatase that is activated by phosphorylation. 
D)  It is a protein phosphatase that is inactivated by phosphorylation.

Question 2

The compound GDPNP is a GTP analog that can bind to GTPases in the same way as GTP. However, unlike GTP, it cannot undergo the hydrolysis reaction that normally releases Pᵢ. Therefore, …

Accepted Answer

A)  GDPNP and GDP bind to the same conformation of a GTPase. 
B)  a GDPNP-bound Ras is constitutively active. 
C)  a GDPNP-bound EF-Tu cannot bind to tRNA molecules. 
D)  binding of GDPNP to EF-Tu allows multiple cycles of tRNA binding and release without the use of free energy. 
E)  None of the above.

Question 3

Enzymes can catalyze cellular reactions through various mechanisms. Which of the following statements is NOT true regarding enzymes?

Accepted Answer

A)  They can provide the chemical groups necessary for simultaneous acid and base catalysis. 
B)  They have a higher affinity for the transition state of the substrate than for its stable form. 
C)  They can form covalent bonds with the substrate during catalysis. 
D)  They can strain a substrate to force it toward a specific transition state. 
E)  They accelerate a cellular reaction by destabilizing the transition state.

Question 4

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-What is the amino acid sequence of the peptide depicted below? Write down the sequence from the N- to the C-terminus, and use only the one-letter abbreviations, e.g. AGCNT.

Accepted Answer

The answer of The structural formulas for the 20 naturally...

Question 5

The marking of a protein by polyubiquitylation to signify degradation …

Accepted Answer

A)  requires the hydrolysis of one ATP molecule to ADP per polyubiquitin chain. 
B)  involves covalent attachment of the target protein to the E1 enzyme. 
C)  is carried out by the proteasome complex. 
D)  is typically done on an arginine residue in the target protein. 
E)  involves the recognition of the target protein by an E2-E3 ligase.

Question 6

Many viruses have large capsids in the form of a hollow sphere, made of hundreds of identical protein subunits. What are the advantages of having coats made of several copies of only a few subunits?

Accepted Answer

A)  Assembly can be readily regulated. 
B)  Disassembly can be readily regulated. 
C)  It requires a smaller amount of genetic information. 
D)  The effect of mistakes in protein synthesis on the overall assembly is minimized. 
E)  All of the above.

Question 7

Stable β-sheet aggregates can form from many proteins, forming intertwined cross-beta strands that have the potential to kill cells or damage tissues. Which of the following is NOT true regarding these aggregates?

Accepted Answer

A)  They form almost exclusively in the cells of the nervous system. 
B)  Different types of such aggregates can form from the same protein. 
C)  Their formation is associated with conditions such as Parkinson's disease and Kuru. 
D)  They can form spontaneously, but also can be triggered to form by an infection with the same aggregate. 
E)  Some healthy cells form these aggregates to store their secretory proteins.

Question 8

Most GTPases are present inside the cell at a much higher concentration than their upstream GAP and GEF proteins. Imagine a mutation in a certain GTPase, such as a Rab protein, resulting in an extremely tight binding between the GTPase and its GEF, and a very slow dissociation. What would you expect to happen in the cell as a result?

Accepted Answer

A)  Rab proteins will be activated, because the tightly bound GEFs will be unavailable. 
B)  Rab proteins will be inactivated, because the tightly bound GEFs will be unavailable. 
C)  Rab proteins will be activated, because the Rab-GAPs will become activated. 
D)  Rab proteins will be inactivated, because their GAPs will become activated. 
E)  Rab proteins will be activated, because there are fewer GAPs available.

Question 9

The human estrogen receptor is a symmetrical dimeric nuclear protein that can regulate gene expression by binding to a DNA sequence called an estrogen response element (ERE) near the promoter of its target genes. Each subunit of the receptor binds to about six base pairs of DNA. Which of the following sequences is a likely candidate for the ERE? The sequences are written in the 5′-to-3′ direction. The letter N represents any of the four DNA bases.

Accepted Answer

A)  AGGTCANNNTGACCT 
B)  AGGTCANNNAGGTCA 
C)  AGGTCANNNACTGGA 
D)  AGGTCANNNATATAT 
E)  AGGCCTNNNTCATGA

Question 10

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-Which amino acid residues shown above have acidic side chains? Write down the one-letter abbreviations for them, in alphabetical order, e.g. ACGNV.

Accepted Answer

The answer of The structural formulas for the 20 naturally...

Question 11

The enzyme lysozyme catalyzes the cutting of a polysaccharide chain through hydrolysis. Which of the following is NOT true regarding the catalytic cycle for this enzyme?

Accepted Answer

A)  It involves acid catalysis. 
B)  It involves base catalysis. 
C)  It involves strain catalysis. 
D)  It involves covalent catalysis. 
E)  It involves metal ion catalysis.

Question 12

Imagine a protein that can be independently phosphorylated on any of its 10 tyrosine residues and acetylated on either of its 2 lysine residues. In principle, how many different combinations of these modifications are possible for this protein?

Accepted Answer

A)  2¹⁰ 
B)  2²⁰ 
C)  10¹⁰ 
D)  12²⁰ 
E)  2¹²

Question 13

A simple protein interaction map is shown below for human cytochrome c (Cyt), a heme-containing protein that is normally found inside the mitochondria and is associated with the electron-transport chain (ETC) of the inner mitochondrial membrane. Under special emergency conditions, this protein can also moonlight as a signal transducer for the onset of a pathway leading to programmed cell death (PCD). As shown in the map, it also interacts with a group of phosphoprotein phosphatases (PPP) involved in cell signaling pathways. Assuming that the functions of the proteins labeled as X, Y, and Z are unknown, which of the following points can be reasonably argued from this interaction map?

Accepted Answer

A)  The protein labeled X probably functions in PCD as well as in the ETC, because it interacts with cytochrome c, which is known to be closely involved in PCD, and it also interacts with several proteins from the ETC group. 
B)  The protein labeled Y probably has a role in PCD, especially if its orthologs in other organisms have such a role and show a similar pattern of interactions. 
C)  If the proteins in the PCD group are known to form a large complex, then the protein labeled Z is likely to be the scaffold protein for that complex. 
D)  The protein labeled Y probably has a phosphatase function, because it interacts with the proteins of the PPP group. 
E)  The protein labeled Z is probably not an essential protein because it only interacts with one other protein in this map.

Question 14

Protein A can bind to each of the proteins B or C. The association rate constants are the same for forming the AB and the AC complexes. However, the dissociation rate constant for AB is 100 times higher than that for AC. Given that every tenfold increase in the equilibrium constant (of the association reaction) corresponds to about -5.9 kJ/mole difference in the standard free-energy change for the reaction (ΔG°), what is the value of (ΔG°AB - ΔG°AC) in kJ/mole?

Accepted Answer

A)  -11.8 
B)  -5.9 
C)  0 
D)  +5.9 
E)  +11.8

Question 15

A viral version of the Src kinase called v-Src is found in some retroviruses. Unlike the cellular Src, the v-Src kinase is constitutively active, and can drive the cell into uncontrolled growth and tumor formation. Which of the following molecular differences between the two versions of Src is more likely to be responsible for this?

Accepted Answer

A)  v-Src lacks the active-site tyrosine residue. 
B)  v-Src lacks a lobe of the kinase domain. 
C)  v-Src has multiple inhibitory tyrosine phosphorylation sites in the kinase domain. 
D)  v-Src lacks the C-terminal tail that can bind to Src's SH2 domain. 
E)  v-Src has a longer C-terminal tail.

Question 16

Imagine that 1 L of a solution containing each of the 20 naturally occurring amino acids at 50 mM concentration each (total concentration of 1 M) is allowed to polymerize in a perfectly stepwise fashion such that at each step, a random amino acid can be incorporated into a growing polypeptide. The steps are repeated, until eventually the solution is only composed of 40-mers (and virtually all of the monomers have been used). What fraction of all 40-mers can possibly be present in this solution? Round your number to four decimal places. Avogadro's number is 6 × 10²³.

Accepted Answer

The answer of Imagine that 1 L of a solution...

Question 17

For each of the following cartoon representations from left to right, indicate whether the protein structure is composed of only ? helices (1), only parallel ? sheets (2), only antiparallel ? sheets (3), ? helices plus parallel ? sheets (4), or ? helices plus antiparallel ? sheets (5) as repetitive secondary structure elements. Your answer would be a four-digit number composed of digits 1 to 5 only, e.g. 5513.
  
Images created in PyMOL, from PDB entries 1STU, 2LPC, 1SA8, and 3BOB.

Accepted Answer

The answer of For each of the following cartoon representations...

Question 18

Evolutionary tracing has identified clusters of the most invariant amino acids in the SH2 domain family. Which of the following is true regarding these sites?

Accepted Answer

A)  Mutation in these sites generally keeps the protein functional. 
B)  The invariant amino acids generally have negatively charged side chains. 
C)  These sites correspond to the binding site for peptides containing phosphorylated tyrosine. 
D)  The amino acids at these sites are generally hydrophobic. 
E)  These sites have evolved fast because they have critical functions.

Question 19

Which of the following pairs of amino acid residues would you expect to form ionic bonds?

Accepted Answer

A)  Glutamic acid and glutamine 
B)  Arginine and lysine 
C)  Lysine and glutamic acid 
D)  Tryptophan and tyrosine 
E)  Tyrosine and glutamine

Question 20

Protein secondary structure elements such as α helices and β sheets constitute the major regular folding patterns in proteins. With regard to these elements, …

Accepted Answer

A)  hydrogen-bonding between the amino acid side chains defines the type of secondary structure. 
B)  a certain short amino acid sequence always adopts the same secondary structure. 
C)  only a few specific amino acid sequences can adopt these repetitive structures. 
D)  the folding patterns result from hydrogen-bonding between the N-H and C=O groups in the polypeptide backbone. 
E)  All of the above.

Exam 3: Proteins