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Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 Note: Much of this exercise is designed to help you begin learning the amino acid structures and to have you focus in on really “reading” their structures to predict their physical and chemical properties. 1. Match the following descriptions of the various amino acid side chains with a corresponding numbered structure and give the one and three letter code(s) for the indicated amino acids. It is possible to have more than one number in each box and some of these may require you to make judgement call. Most important: Zoom in on the structural diversity. Number of the described side chain One and Three Letter Code(s) Description Small Polar R group containing a hydroxyl group Structural isomers of each other Acidic R groups (proton donor) Basic R groups (proton acceptor) Sulfur Containing R group Aromatic R groups that contain a benzene ring Saturated Hydrocarbon R groups or H Does not have chirality at the alpha carbon R groups that contain alcohols or phenols Sulfur Containing R group that can participate in a disulfide bridge R group with the highest pKa value R group with the highest Ka value

Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 2. Two amino acids have chiral carbons in their side chains or R group. Identify these amino acids and draw the structures of all of the possible stereoisomers of these amino acids. The amino acid with a hydroxyl group is found in proteins with the (2S, 3R) configuration and the other amino acid is found in proteins with the (2S, 3S) configuration. Circle the structures in your answer above that correspond to these isomers. 3. Chemical Jeopardy!!! One and three-letter code for the amino acid with no chiral  -carbon. What is _________________? The one and three letter codes for the two hydrophobic amino acids that are structural isomers of each other. What are_______________ and ___________________? The structure at pH 0 of the most “basic” of all amino acids having the three letter designation Arg. What is….? (Draw structure) The one and three letter codes of two amino acids with side chains (R groups) capable of forming H bonds. What are_______________ and _________________? Draw the structure of one these amino acids with its R group hydrogen bonded to a solvent water molecule. The structure and the one and three-letter code for the amino acid with a phenol group. What is….? The one and three-letter code for the amino acid capable of forming a disulfide bond.

Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 What is ________________ Histamine, which may mediate allergy and cold symptoms, is made from the amino acid with the designation His by the loss of the carboxyl group. What is….? (Draw structure) The neurotransmitter serotonin results from the loss of the carboxylic acid group and the addition of a hydroxyl group at the 5 position on the aromatic ring of this amino acid, which is designated by the one- letter code, W. What is….? (Draw structure) Substitution on the methyl group of this amino acid with a hydroxyl group yields the amino acid designated Ser and substitution with a phenyl group yields the amino acid designated Phe. What is….? (Draw structure in zitterionic form) The one and three letter code for the amino acid whose -amino group is bonded directly to two C atoms. What is________________? The principle ionic form of the amino acid Lysine at pH=4 (pKa of the R group = 10.5) What is….? (Draw structure) 4. Glutamic acid titration curve

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Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 Figure form: https://www.chem.fsu.edu/chemlab/bch4053l/Protein%20Characterization/AA%20Titration/index.html Label the titration curve above at the appropriate position with the question letter. a. Which point represents the pKa of the  carboxyl group? b. Which point represents a 50/50 mixture of the plus 1 and 0 charged species? c. At what point does the major molecular species have a net charge of 0? d. At what point is Glu completely deprotonated? e. Which point represents the pKa of the a-amino group? f. At which point is the R group carboxyl group half ionized? g. At what point are there as many molecules that have a net charge of +1 as have a net charge of 0? 6. Draw the principle structural form of Glutamic Acid at pH3 from the information in the graph above. If a sodium cation combines with this form of Glu, you will have the food flavoring additive MSG (mono sodium glutamate). 7. Draw the tripeptide corresponding to Cys-Met-Arg 8. Much of the protein in hair is cross-linked by disulfide bonds. When a person is gets a “perm”, a reducing agent is used to the break the disulfide bonds. If the “reduced” hair is wrapped around curlers and an oxidizing agent is applied, new disulfide bonds to form between the protein hair strands, locking in the curled structure. Draw the reaction showing the formation of a disulfide bond between two cysteine molecules. OH – equivalents

Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 6. Draw out the structure of the dipeptide, Asp-Phe. Draw the methyl ester on the free  -carboxyl group of this dipeptide. This is the structure of the artificial sweetener, aspartame or NutraSweet  . 7. Draw the structure of the tripeptide, Asp-Lys-Ser, and determine its pI value. 8. Calculate the concentrations of the two major ionic species present in the 0.1 M solution of Asp at pH 4.0 and again, at pH 9.4. 9. How many moles of H 2 PO 4 1- and HPO 4 2- would be needed to prepare 1.0 L of a 0.01M phosphate buffer with a pH of 7.15? (pKa data on p. 61 of text) 10. Below, is an abstract of a journal article describing the isolation, purification, and sequence of an antibacterial peptide from the cowpea plant. It also describes the location of each of the disulfide

Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 bridges in the peptide. Using the information in the abstract, give a brief and to the point answer to each of the questions. The following is a portion of the abstract for this article. Below is a figure from the article which gives the amino acid sequence for the isolated peptide and the black lines indicate the disulfide bonds in the structure. Questions What is the N-terminal residue (one and three letter code)? What is the C-terminal residue (one and three letter code)? How many strongly basic amino acid (i.e. R group pKa > 9) residues are present in the sequence? How many acidic amino acid (i.e. R group pKa <5) residues are present in the sequence? Would you predict that the pI for this protein would be greater or less than 7? Briefly justify your choice.

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Chem 481 Online Name _________________________ HW 1 Lessons 1.1-2 Draw the structure of residue number 10 at pH 7.4 showing the absolute L stereochemical configuration. (2 pts.) How many residues in the sequence have hydrocarbon R groups that contain only H and/or C atoms. Identify these by their one and three letter codes? (2 pts.) How many residues contain sulfur and how many disulfide bridges are present in the peptide? (2 pts.) Residues that contain S: Disulfide bridges:

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