Assume you have a long polypeptide chain of Ser-Asp dipeptides linked end to end.  Explain the likely tertiary structure of this polypeptide chain.  For example, is the chain likely to form an alpha helix, a beta sheet, or some other structure?  Is the structure likely to display lots of folding, or very little folding?  Can you make any other predictions about the tertiary structure?  Explain your reasoning in a well-developed paragraph.

Consider protein folding that results when the following components interact:   Where the solution is at a pH of 7, green (thick-dotted line) represents aspartic acid (R group contains a carboxylic acid with pKa = 4), orange (thick-solid line) represents lysine (R group contains an amine with pKa = 10), and blue (thin-solid line) represents hydrophilic groups. Rank the three complexes in order from lowest to highest dissociation constants Kd (low Kd values correspond to good binding constants and low energy, while high Kd values correspond to low binding constants and high energy) as determined by intermolecular charge-charge interactions. For those complexes with charge-charge interactions being equal, look at the possibility for the formation of hydrogen bonds via carboxylic acid dimers (only possible when the carboxylic acid is protonated) which are low energy structures.

A schematic diagram of the helical structure of cytochrome b562 is reproduced below. Thisprotein belongs to the family of -proteins that have a four-helix bundle. Number the helices 1 – 4according to their N  C direction. Indicate relative orientations of the macrodipoles of helices 1 – 4adjacent to the diagram of cytochrome b562. Remember that according to the definition of a dipolethat the arrow points towards the positive end.

You have a peptide that has the following amino acid sequence: GPMG Draw the structure of the polypeptide's most protonated form, and its charge. Then draw the structures of the increasingly deprotonated forms, along with their charges. Use the information from these structures to calculate the pl (isoelectric point) of the peptide using the pKa values provided in the table below. Write the pl as x.yz, for example, 7.62 or 3.09. Group Terminal a carboxyl group Aspartic acid Glutamic acid Histidine Terminal a-amino group Cysteine Lysine Tyrosine Arginine Acid EM 2-0" + H -N H H N-H H N-H T Base 1 1. تر H -5 H H O™ N-H Typical pK, 3.1 4.1 6.0 8.0 8.3 10.8 10.9 12.5

How does the structure of chymotrypsin enable it to cleave only peptide bonds that are adjacent to aromatic R groups? Suppose a protease could only cleave adjacent to Lysine and Arginine; how would the structure of this protein differ from that of chymotrypsin?