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UCSD BIBC 100 - Homework #1

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BIBC 100 Homework #1 Jan 18, 2008 1. Plot the following 10-residue peptide as an alpha-helix on the helical wheel. Make sure to mark the details such as N-terminus, C-terminus, the distance/angle between each residue, hydrophobic region/polar region. N-Terminus –M-T-R-A-A-S-L-I-Q-S – C-Terminus 2. Name two amino acids that are often found in the turns/loops of protein structures, and explain why. 3. Fill in the blanks or circle the right answer. Cysteine residues often form _____________ bonds in an ____________ (oxidized / reduced) state; the bonds do not form in an ___________ (oxidized / reduced) state. Because the extracellular environment is a (oxidizing / reducing ) environment, many cysteines are often present to form structural linkages in proteins that act primarily (inside / outside) the cell.4. What information is contained in a Ramachandran plot? 5. For the small peptide DENSRREETSCW, what is the overall charge of the peptide at pH 7.4? 6. What would be the approximate molecular weight of a 600 a.a. protein? 7. The molecular mass of serine is 105 Da, and thus the molecular mass of three individual molecules of serine is 315 Da. However, a tripeptide composed of three serine residues has a molecular mass of 279 Da. Why does the peptide have this smaller mass? 8. Draw the titration curve of glycine. Make sure to label the x and y axes, the pK values (approximate), the pI (approximate), and the structure of the three glycine species are where they reside on the


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UCSD BIBC 100 - Homework #1

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