Exam 3: Proteins

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?

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, …

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

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.

The marking of a protein by polyubiquitylation to signify degradation …

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?

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?

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?

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.

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.

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?

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?

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?

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?

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?

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.

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.

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?

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

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