An enzyme is known to contain four Cys residues that form two disulfide bonds (and no other Cys residues).

[Note that four Cys residues could randomly form three possible disulfide bond arrangements]

A researcher performs the following sequence of treatments on a sample of this enzyme:

1. Treatment with high concentrations of mercaptoethanol and urea.
2. Removal of the mercaptoethanol while keeping the urea concentration high (and avoiding formation of any intermolecular disulfide bonds).
3. Removal of the urea (returning the sample to the original buffer).

They find that the sample obtained from the final treatment has one third of the activity of the original sample of the enzyme.

Which of the following is the best conclusion from this experiment?

Consider the following two ionisable groups positioned close to each other within a protein structure:

• The carboxy terminus (pKa = 2.3)
• An arginine side chain (pKa = 12.5)

Based on the pKa values of these functional groups and their charge states when they are ionised, select the correct statement below.

[Note that these statements are specifically referring to the attraction or repulsion of ionic interactions between these groups]

Shown below is an unfolding curve for a protein that contains two domains of approximately equal size.

Which point on the curve represents the form of this protein in which one domain is fully unfolded and the other is 50% unfolded?

The protein vMIP-II from Kaposi's sarcoma-associated herpesvirus (which subverts the host immune system by blocking the migration of white blood cells) consists of a 3-stranded β-sheet packed against an α-helix.

The side chain of residue Lys-61 is located on the exposed surface of the α-helix.

Examine the structure of vMIP-II (in the vicinity of Lys-61) in the PDB 3D View or by downloading the PDB file 1HFG into PyMOL.

Which of the following mutations is most likely to result in a new ionic interaction with the side chain of Lys-61, causing the folded structure of vMIP-II to be more stable at neutral pH (but not at pH 3 or pH 11)?

A research student is investigating the factors that stabilise the folded structure of a protein. They note that residues Phe-26 and Ile-75 contribute to a well-defined hydrophobic cluster in the core of the protein. To determine the contribution of these residues’ hydrophobic side chains to protein stability, they make mutants F26A and I75A. They then determine the stability of the wild type (WT) protein and each mutant.

What is the expected order of stability (from most stable to least stable), assuming that the main contribution of these residues to stability is through their side chain hydrophobic interactions?

A research student is investigating the factors that stabilise the folded structure of a protein. They note that residues Trp-38 and Leu-144 contribute to a well-defined hydrophobic cluster in the core of the protein. To determine the contribution of these residues’ hydrophobic side chains to protein stability, they make mutants W38A and L144A. They then determine the stability of the wild type (WT) protein and each mutant.

What is the expected order of stability (from most stable to least stable), assuming that the main contribution of these residues to stability is through their side chain hydrophobic interactions?

The protein CCL7 (which regulates migration of white blood cells in inflammation) consists of a 3-stranded β-sheet packed against an α-helix.

The side chain of residue X forms ionic interactions with the side chains of both Lys-58 and Lys-65 on the surface of the α-helix. This interaction stabilises the folded structure of CCL7 at neutral pH (but not at pH 3 or pH 11).

Examine the structure of CCL7 in the PDB 3D View or by downloading the PDB file 1BO0 into PyMOL.

What is the most likely identity of residue X?

Consider the following mRNA (5'-to-3') codon:

GCU

Assuming standard base-pairing (i.e. no 'wobble'), enter the corresponding tRNA anticodon written in the 5'-to-3' orientation.

(Your answer should only include nucleotides, e.g. UUU. Do not enter 5' or 3'.)

Using your knowledge of the genetic code and the image below, which ONE of the following amino acid replacements can be caused by a single nucleotide change?

The sequence below represents the coding DNA strand of the start of a gene, including part of the 5' untranslated region.

(5')...CCGGAAGGAGGTAACCGCAATGACCGGGCCTTTGAACC...(3')

In studying disease variants, a nucleotide mutation of T→A was detected in the second base of the fifth codon. What effect would this mutation have? 

(When considering your answer, assume standard initiation of translation is numbered as codon 1.)