MCB100A_ps3_F2010 - Problem Set 3 Chem C130/MCB C100A UC...

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Hand in your answers to the 5 questions marked with a * on Thursday, September 16 . A. Multiple choice, TRUE/FALSE or fill in the blanks: Q1. Larger proteins are constructed by putting together smaller modules of protein structure known as “domains”. Shown below are a set of proteins involved in cell signaling. The domains are indicated by boxes, and are named SH2, SH3, Kinase, etc. to denote different functions. A) Each kind of domain has a three-dimensional fold that is conserved amongst all examples of that kind of domain. Comparing pairs of the same kind of domain between the different proteins to what extent do you expect the sequences to be identical? Choose one of the ranges below, and explain your answer. (i) 10%-20% identical in sequence (ii) 30-40% identical in sequence (iii) 10%-100% identical in sequence (iv) greater than 50% identical in sequence B) Which region of the domain would you expect to be most highly conserved in sequence? (i) The surface of the protein (ii) The active site or binding site (iii) The hydrophobic core (iv) The loop regions C) How many different kinds of folds for protein domains are there expected to be found in nature? (i) several thousand (ii) several millions (iii) essentially unlimited D) Circle the correct answer: The tertiary structure of a protein refers to: Problem Set 3. Chem C130/MCB C100A. UC Berkeley Fall 2010 Page 1 of 10
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(a) the sequence of the gene coding for the protein (b) the assembled structure of a multi-subunit protein (c) the structure of α -helices and β -strands in the protein (d) the three-dimensional structure of the protein Q2. Many different protein sequences code for the globin fold, but the pairwise sequence similarity between many members of the family is insignificant. For example, if we compare human hemoglobin and a plant globin, the sequence identity between them is only 14%. This is close to the level of sequence identity between pairs of proteins that are unrelated to each other in terms of structure or function. Nevertheless, we are fairly certain that the human and plant globins have a common ancestral protein and that variation and natural selection resulted in these two kinds of globins. State whether each of the following statements is true or false, explaining your answer clearly in each case. A) Because all the globins bind the heme group and oxygen, they must have evolved from a common ancestor. B) All the globins that the same three-dimensional fold, so they must have evolved from a common ancestor. C) Although the sequence similarity is low, the same sets of residues are always conserved in the globins, so they must have evolved from a common ancestor. D) The determination of large numbers of globin sequences from many different organisms allows evolutionary trees to be constructed that connect closely related globins to more distantly related ones. * Q3.
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This note was uploaded on 01/27/2011 for the course MCB 100A taught by Professor Kuryian during the Spring '09 term at Berkeley.

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MCB100A_ps3_F2010 - Problem Set 3 Chem C130/MCB C100A UC...

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