Problem_Set_3

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Feb 20, 2024

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MCB C100A/Chem C130, Spring 2024 Problem Set 3 (Due at beginning of class Weds 2/14) Question 1. (2 pts ea) Try to answer these True/False questions without looking up the answer first: (i) Choose the amino acid substitution that results in the greatest change of hydrophobicity: (a) F -> Y (b) D -> Q (c) V -> L (d) Y -> K (e) E -> H (ii) Ion pairs buried in the hydrophobic core of a protein have much more favorable interactions than ion pairs on the protein surface. Choose the best explanation: (a) Water competes with the protein backbone for hydrogen bonds (b) The dipoles of water molecules screen ions, reducing their effective charge (c) Both (a) and (b) (d) The statement is false. Water has no effect on ion pairs. (iii) The simplest form of a Ramachandran plot that works fairly well uses a hard-sphere model instead of a van der Waals energy function. (TRUE/ FALSE) (iv) Which statement is NOT true about peptide bonds in proteins? (a) Peptide bonds are similar in chemistry to the side chains of Asn and Gln. (b) Peptides adopt only one preferred dihedral angle due to pi-conjugation. (c) Peptides can be modeled with a partial negative charge on the carbonyl O. (d) Rotation about the C-N bond in peptides is slow relative to rotation around the adjacent sp 3 -hybridized backbone bonds. (v) The probability of finding a particular 6 amino sequence in a protein, assuming all amino acids are used in equal abundance in proteins, is: (a) 1 in 20 6 (b) 1 in 6 20 (c) – 6ln(20) (d) – 20ln(6) (e) None of the above (vi) Hydropathy plots use a running average of 19 amino acids on the assumption that a transmembrane spanning peptide chain will adopt an alpha helix structure (TRUE / FALSE)
MCB C100A/Chem C130, Spring 2024 Question 2. (11 pts) Consider the BLOSUM62 matrix below. You have the amino acid sequences of 4 loop regions from a transmembrane protein of a recently discovered, but long extinct, species. You want to know where to place it on a phylogenic tree. A) (6 pts) Which one of the loop regions do you expect to be most highly conserved? Use the BLOSUM-62 matrix above and give numerical evidence to justify your choice. (i) SEQLF (ii) WHERG (iii) RLKNF (iv) SAHMT
MCB C100A/Chem C130, Spring 2024 Question 2 (cont’d) B) (5 pts) Consider a fictitious amino acid with the following BLOSUM entries. Circle and name the AA below you think is most likely to substitute for the fictitious AA. Briefly explain your reasoning.
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MCB C100A/Chem C130, Spring 2024 Question 3. (10 pts) The environments coded in the 3D-1D profiling method for soluble proteins are: buried hydrophobic, buried slightly polar, buried polar, partially buried slightly polar, partially buried polar, exposed polar, as shown below. A) (6 pts) If we want to use this method for membrane proteins, would you need to add any more environment categories? Why or why not? Briefly explain your reasoning. B) (4 pts) Briefly explain the advantage of using an AA sequence to 3D profile alignment which is not present with a sequence-to-sequence alignment.
MCB C100A/Chem C130, Spring 2024 Question 4. (14 pts) Shown is the structure of a polysaccharide monooxygenase that can oxidatively cleave cellulose chains. A) (7 pts) Approximately what are the dimensions of this protein in the plane of the page? Show all of your work. Note that the extended chain is in the beta-sheet conformation. B) (7 pts) What is the amino acid sequence of the extended chain at the top (this is the C-terminus of the protein)? Give just the 1-letter code. !
MCB C100A/Chem C130, Spring 2024 Question 5 (24 pts). Many bacteria and archaea (but not eukaryotes) have adaptive immunity systems (CRISPR elements) that use a repeat RNA sequence separated by guide RNA sequences for targeting foreign DNA molecules. The repeat sequences form RNA hairpin “handles” that are recognized by a ribonuclease for cleavage. The ribonuclease has exquisite specificity, and does not target any other RNA in the cell besides these “handle” hairpins. It uses sequence recognition, as shown below. The figure to the right is a zoom-in of the boxed region to the left, with 3 amino acids blocked out. Notes: No hydrogens are shown in the figure. All of the hydrogen bonds in the two base pairs and between the bases and the protein required for recognition are shown. A) (3 pts) Which groove of the RNA helix is the protein recognizing? Explain your answer. [Covered in class, but leaving here for completeness.] B) (3 pts) Why is this recognition a surprise for RNA? [Covered in class, but leaving here for completeness.]
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MCB C100A/Chem C130, Spring 2024 Question 5 (cont’d). C) (6 pts) For boxed amino acid 1, draw the amino acid that would most likely hydrogen bond to the purine in the base pair shown. Show how it would hydrogen bond to the base in your drawing. D) (6 pts) For boxed amino acid 2, draw the amino acid that would most likely hydrogen bond to the purine in the base pair shown. Show how it would hydrogen bond to the base in your drawing.
MCB C100A/Chem C130, Spring 2024 Question 5 (cont’d). E) (6 pts) Boxed amino acid 3 stacks under the bottom base pair. Draw two amino acids that could stack well under the base pair. Explain why each is a reasonable choice.

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