bibc_116_2004_exam

bibc_116_2004_exam - PROTEIN EVOLUTION / BIBC 116 MIDTERM...

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PROTEIN EVOLUTION / BIBC 116 MIDTERM EXAM, FEBRUARY 10, 2004 1. What is meant by the term structural domain of a globular protein, and what is the range in size of the structural domains observed in nature, in amino acid residues? In molecular weight? 2. A. What is the range of free energy values observed for the net stabilization of the folded conformation of a structural domain? B. What is the major destabilizing (=endergonic) contribution to the net stability? C. Name 3 principle interactions which make exergonic contributions to the net stability. 3 . Given the accompanying mutational data matrix: A. Which three amino acids are most mutable? What is the typical location of 2 of these amino acids in the folded structure of globular proteins? Explain how this location could account for their immutability. B. Would you conclude that cysteine (C) is replaced by aspartate (D) with a greater than random (average) frequency ? Explain in terms of the probable effect of this substitution on the stability of the folded state. C. Would you conclude that glutamate (E) is replaced by aspartate (D) with a greater than average frequency ? Explain in terms of the probable effect of this substitution on the stability of the folded state.
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4. A. Arrange the following regions of a protein coding gene in terms of their likely rate of nucleotide substitution (highest to lowest): non degenerate sites in exons, introns, 4 fold degenerate sites in exons, 2 fold degenerate sites in exons. B. Provide an explanation based on protein structure for why you put the regions of a protein coding gene in this order. 5. Cytochrome C molecules have been studied from a wide variety of organisms, ranging from mammals to plants, yeast, and bacteria. Does comparison of the three dimensional structures and amino acid sequences of cytochrome C molecules from these divergent species indicate that amino acid sequence is more highly conserved than 3D structure, or that 3D structure is more highly conserved than amino acid sequence? Explain.
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This test prep was uploaded on 04/07/2008 for the course BIBC 116 taught by Professor Loomis during the Spring '04 term at UCSD.

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bibc_116_2004_exam - PROTEIN EVOLUTION / BIBC 116 MIDTERM...

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