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24 Feb 2019

1. What is the purpose of phosphorylation the CTD of RNA polymerase II?
​2. In what level of the protein structure does a missense mutatio in a coding region alter the encoding amino acid from basic to acidic?
​3. How do you draw a terminal nucleotide of a tRNA molecule?

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Sixta Kovacek
Sixta KovacekLv2
27 Feb 2019

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The ∆-F508 mutation, which is the most common allele linked to cystic fibrosis, results from the loss of a single codon in the CFTR gene. How does this affect the length of the coding sequence (i.e., at the nucleotide level), and the protein sequence (i.e., at the amino acid level)?

1. A polypeptide chain has a large percentage of acidic and basic amino acids in it. The R groups of these amino acids form ionic interactions, which helps the protein to maintain it’s structure. This particular polypeptide works well under an optimum pH of 7. Ignoring effects of strong acids and bases on peptide bonds, what will happen to the tertiary structure of the protein if you move it stomach acid, which has a pH of 1-2. Why? Be specific regarding what influence the pH will have on the bonds maintaining tertiary structure in the molecule. Include the amino acid charges of the acidic and basic amino acids at the acidic pH, as well as the concept of pK in your answer. Assume that acidic amino acids have a pK of approximately 4.7 and basic amino acids have a pK of approximately 10.

2. Ignoring peptide length (or lack thereof) where would this portion of a polypeptide be most likely to be found: On the inside or on the outside surface of a protein floating around in the cytoplasm? Explain

3. A mutation occurs in the SRC kinase such that the tyrosine on the loop over the active site is changed to aspartic acid. This mutation mimics phosphorylation.
a. knowing what you know about the properties of phosphate groups and aspartic acid, why does aspartic acid mimic phosphorylation?
b. What would be the implication of this mutation on the function of the SRC kinase?

1a. which is likely to be more deleterious, a 1bp deletion from an exon in the coding sequence of a gene, or a 3 bp deletion? Explain clearly what all the potential consequences of both deletions could be on the proteins amino acid sequence.

1b. how many different 9-nucleotide mRNA sequences could you make that would produce the peptide tyrosine-leucine-arginine? Assume you are using a cell-free system that does not require a START codon.

1c. imagine you have a single nucleotide substitution (an A has mutated to a G, for example) in an exon of a gene's coding region. It reduces the activity of that gene's protein in your cells to 50% of the usual level of activity. Imagine also that you have a single nucleotide substitution in the same gene's promoter region, and this mutation also reduces the activity of that gene's protein in your cells to 50% of the usual level of activity. Do the 2 mutations reduce the proteins activity level via the same mechanism? Explain your answer.

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