Exam 3: Proteins

A polyubiquitin chain has been attached to a protein. The ubiquitin molecules are linked together via isopeptide bonds between Lys48 of one molecule and the carboxyl end of the next one. This protein is expected to …

Consider the proteins Ras, Src, kinesin, and the ATP synthase pump. All of them …

The number of ways in which protein domains fold in nature is limited. Which of the following is a better estimate of this number?

Which of the following can be a function for intrinsically disordered protein sequences?

In terms of molecular function, what do Ras and myosin have in common?

You have purified a multisubunit extracellular protein that has several interchain disulfide bonds. Which of the following chemicals would you add to your purified protein mixture if you wanted to eliminate the disulfide bonds?

We can try to map the surface of a globular protein in two dimensions just like we depict the surface of the Earth in a world map. On such a map, the binding site of a molecule for other molecules of the same protein (for assembly into a multisubunit complex) can be marked. In the following "maps," two molecules of the protein can bind if the points a, b, and c on the surface of one molecule can align to points a′, b′, and c′ in the other molecule, respectively. Which map corresponds to a protein whose assembly gives rise to a helix? Hint: the other maps correspond to a dimer, a ring, and a linear filament.

Which of the following is NOT true regarding the members of a protein family in general?

The turnover number for an enzyme is equivalent to the number of substrate molecules processed per second per enzyme molecule. To a test tube containing a 100 mM concentration of its substrate, you have added an enzyme at a final concentration of 10 µM, and have measured the rate of the reaction to be approximately 500 µM/sec. If the Km for the binding of the enzyme to this substrate is about 100 mM, what is the turnover number?

Two ligands, A and B, bind to two different conformations of the enzyme X. The ligand A is the enzyme's substrate, whereas ligand B binds to a remote allosteric site. Which of the following is a consequence of this arrangement?

At physiological pH, what is the approximate net charge of a hexapeptide with the following amino acid sequence? Asp-Val-Ile-Glu-Arg-Ser

The phosphofructokinase (PFK) enzyme is one of the key players in the glycolytic pathway in which glucose eventually breaks down into pyruvate, some ATP is generated, and some NAD⁺ is reduced. PFK catalyzes the committed step in the pathway and is under extensive regulation. Which of the following compounds would you expect to activate PFK?

In interactions between proteins, each hydrogen bond contributes to the free energy of binding by about -4 kJ/mole. If two proteins bind to each other through nine hydrogen bonds, six of which are eliminated when one of these proteins is mutated, how much would you expect the equilibrium constant for their binding to change as a result of the mutation? (ΔG° = -5.9 × log Kₑq)

In an ? helix, each amino acid residue is rotated by about +100° and raised by about 0.15 nm relative to the previous residue. This means that each full turn of the helix rises by … nm parallel to the helix's axis.

The observation that proteins often renature into their original conformations after they have been unfolded by denaturing solvents implies that …

A protein is drawn in the following simplified diagram undergoing a set of covalent modifications including the addition of a chain of ubiquitin protein monomers (U) to one of its lysine side chains, a phosphate moiety (P) to its tyrosine side chain, and a lipid farnesyl (F) to its cysteine side chain. Indicate the order of these modifications (1 to 3) in the diagram. Your answer would be a three-letter string composed of letters F, U, and P only, e.g. PFU. Answers

Imagine a cellular protein composed of 3000 amino acid residues in one continuous polypeptide chain. This protein is almost certainly …

The SCF ubiquitin ligase can recognize and mark various target proteins at different stages of the cell cycle. In this complex, …

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.

An enzyme acts on a tyrosine residue in a target protein to create a binding site for the SH2 domain. This enzyme is most specifically …