Proline is one of the amino acids in the "special" groups of sidechains. One reason for this is the dramatic impact it can have on secondary structure.  a) draw the lewis structure for a tripeptide with the sequence Ala-Pro-Ala b) Proline residues are rarely found in alpha helices - in fact, they are often referred to as helix-disrupting amino acids. Thinking about intermolecular interactions, provide an explanation for why proline might disrupt alpha-helices. c) Proline also has a similar effect on beta-sheets, and is rarely found in the middle of beta sheets. Thinking about noncovalent interactions, provide an explanation for why proline might disrupt beta-sheets.

What does this statement mean: "Upon folding of a protein many main chain amides replace their hydrogen bonds to water for those with other amide bonds"  Is this true for alpha helix in proline racemase? and is there a pattern?

How does proline stabilize cis-configuration of a peptide bond, and why is this cis-configuration required for β-turns?

Write a structural formula for a tetrapeptide composed of phenyl-alanine, glycine, aspartic acid, and histidine in which the phenylalanine is N-terminal and the histidine is C-terminal. How many different tetrapeptides could be written that fit the criteria in this question?

Identify the primary structure of a hexapeptide containing five different amino acids if the following smaller peptides are among the partial hydrolysis products: Gly-Cys, Ala-Ser, Ala-Gly, and Cys-Val-Ala

Among these amino acid combinations listed above, only the combination of Lys and Glu have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein.   Explain by drawing (a) why Lys and Glu side chain interaction stabilizes the tertiary structure of a protein (b) why the pairs of Glu and Asp & Arg and Pro cannot provide the stability to the protein structure.

b) It's said that secondary structures form because of intra- and intermolecular hydrogen bonding involving the peptide bond. Describe what is going on to further stabilize secondary structure through these interactions.

6) Proteins can be modified by phosphorylation, which adds a phosphate group to the hydroxyl group of serine, threonine, or tyrosine residues. The R-group for phosphoserine is shown at right. A) The image below is an Isoelectric focusing strip that shows the unphosphorylated protein-of-interest (in blue). To which side of the unphosphorylated protein would you expect to see the phosphorylated protein? (Draw an arrow to indicate direction). Briefly justify your answer. un-phosphorylatable: Low pH Justify: B) To study the effects of phosphorylation, researchers often mutate a Ser/Thr to appear as though it is always phosphorylated or never phosphorylated at a particular site. What amino acid substitution should you use to preserve similar dimensions as Ser (or Thr) but make the side chain appear to be: constitutively (always) phosphorylated: Justify: Ser or Thr → O O=P-O O I CH₂ Ser or Thr➜ Phosphoserine High pH

Which of the following statements are False? (i)     Parallel b-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and antiparallel B-sheets are usually arranged with all their hydrophobic residues on one side of the sheet. (ii)   Planarity of the peptide bond means that no rotation occurs about the N-Ca bond while rotation is allowed about the C(O)-N and Ca-C(O) bonds. (iii) Silk fibers consist of fibroin proteins consisting of alternating A and G or S residues. (iv) If an aspartic acid residue were present in the interior of a globular protein, it would most likely be deprotonated and thus negatively charged.

Patients suffering from sickle cell anemia have a mutation in the gene that codes for one of the hemoglobin chains, in which a single glutamate is replaced by a valine. Propose an explanation for why this substitution has such a striking effect on protein structure and function with explanation.  Suggest two other amino acids that would be less likely to cause such serious impairment of hemoglobin function if each was substituted for glutamate. Briefly explain your answer.