Week 2 Discussion Worksheet

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Dec 6, 2023

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CHEM153A (Michael’s sections) Name: ____________________________ Week 2 Discussion Worksheet Amino acid structures, peptide bonds, and interacting forces 1. Write the three-letter and one-letter code for the twenty amino acids below. Group them by the chemical properties of their side chains: aliphatic, hydroxyl, phenolic, aromatic, sulfur-containing, acidic and amidic, basic, and imino acid. (Note: You should know the structures and the relevant pKas!) 2. Pick your two favorite amino acids and draw a dipeptide below. Show a possible resonance structure of the peptide bond and show which atoms are in the same plane. 3. What is the physical basis for one molecule (or part of a molecule) interacting with another? What are the interacting forces that we have discussed in lecture?

4. Identify the following interactions as either ionic, dipole/induced dipole, or hydrogen bond. 5. Draw antiparallel beta sheets that are at least four residues long. Indicate where the hydrogen bonds occur. Label the N-terminus and C-terminus of each sheet. 6. The structure below has been found to function as both a local hormone and a central neurotransmitter. It is involved in the inflammatory response and has a central role as a mediator of itching (Andersen, Elberling, and Arendt-Nielsen, 2015). Draw the structure of the amino acid from which this molecule derives. What type of enzyme performs the enzymatic step to convert the amino acid to this molecule? 7. Protein kinase A (PKA) is a cyclic AMP-dependent protein kinase with several functions in the cell, including regulation of glycogen, sugar, and lipid metabolism. Phosphorylation of Thr-197 by phosphoinositide-dependent protein kinase, PDK1, is essential for the function of PKA (Cheng et al. , 1998). Draw the phosphorylation of the Thr residue below. What would be the effect if Thr-197 was mutated to Ala?

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