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Unformatted text preview: Problem Set 2 for BIBC 100 Spring 2008 1a) What do the pK values in the chart below tell you? Compound pK 1 pK 2 pK R pI Glycine 2.34 9.60 5.97 Glutamate 2.19 9.67 4.25 3.22 Arginine 2.17 9.04 12.48 10.76 The pK 1 is the pH at which the terminal carboxyl groups (–COOH) are half- ionized, i.e. –COO- and –COOH exist at equimolar concentrations. The pK 2 is the pH at which the terminal amino groups (–NH 3 +) are half-ionized, i.e. –NH 3 + and –NH 2 exist at equimolar concentrations. The pK R is the pH at which the side chain is half-ionized. The pI is the pH at which the net electric charge is zero. b) Will the following amino acids have an overall positive, negative or zero charge at pH 3.22, pH 5.97, pH 10.76? Fill in the chart. pH 3.22 pH 5.97 pH 10.76 Glycine + Zero - Glutamate Zero - - Arginine + + Zero Look at the pI of the amino acid relative to the pH. Review section 3.1 in your book. 2. Calculate the net charge on the following tripeptides at pH7. a) Asp-Glu-Ser -2 b) Ser- Gly-Thr c) Gly–Lys-Arg +2 3. Refer to Table 3-2 in the textbook for this question: a) How many proteins in the table exhibit quaternary structure? How can you tell? 5 proteins consist of more than one polypeptide chain, therefore they must have a quaternary structure. b) How many proteins exhibit supersecondary structures? How can you tell? Sort of a trick question. Supersecondary structure is defined as “a recognizable folding pattern involving two or more elements of secondary structure and the connection(s) between them.” This is synonymous with “fold” or “motif”. See Chapter 4.3. So, these proteins are all large enough to probably contain supersecondary structural elements. supersecondary structural elements....
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This note was uploaded on 09/11/2009 for the course BIBC STRUCTURAL taught by Professor Towb during the Spring '09 term at UCSD.
- Spring '09