Recitation-6problems
.pdf
School
College of Charleston**We aren't endorsed by this school
Course
FREN 362
Subject
Biology
Date
Dec 19, 2024
Pages
1
Uploaded by ColonelHareMaster1045
Recitation #6 Biochemistry I, Spring 2024 1.A wild-type enzyme binds a substrate with a 10 nM affinity (10 x 10-9) at 300 K. A single site mutant to this enzyme is constructed and was found to make the binding affinity worse by a binding energy of 3 kcal/mol. (a) What is binding affinity (Kd) of the mutant? (b) Can you conclude from this data that the mutation is within the binding pocket of the enzyme? Explain your rationale. 2.Below is a table of Kdvalues for FGF ligands binding to FGF receptors (from Molecules of Life). “n.d.” means the Kdvalue is > 10-4. (a)What receptor displayed does FGF1 bind strongest to? (b)What FGF ligand/receptor pair is the most specific interaction? (Specificity means a ligand binds to one protein (or receptor) among closely related proteins). 3.Using the scoring system for the identity-based scoring system discussed in lecture, calculate the score for the following alignment of the two proteins (use +10 for matches and -25 for gaps). Estimate the sequence identity and determine whether the two proteins are homologous. (1) WYLGKITRMDAEVLLKKPTVRDGHFLVTQCESSPGEFSISVRFGDSVQ-----HFKVLRDQ (2) WYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLD 4.Consider the Blosum-62 matrix displayed in lecture 11. Replacement of which three amino acids never yields a positive score? What features of these residues might contribute to this observation? 5.A comparison of aligned amino acid sequences of two proteins each consisting of 150 amino acid residues reveals them to be only 8% identical (somewhat low). However, their three-dimensional structures are very similar. Are these two proteins related evolutionarily? Explain. 6.For question #5, would you expect a Blossum-62 score to reveal greater similarity relative to the 8% identity score analysis?
