Draw the two amino acids serine and alanine, and a dipeptide that could be formed by combining these two amino acids (ala-ser). Draw these molecules at a pH=7. In peptide nomenclature the amino terminus is on the left and the carboxyl terminus is on the right. 1. How many waters were released by formation of this dipeptide from individual amino acids? [ Select ] 2. How many hydrogen bond donors does your dipeptide have? [ Select ] 3. If you were to draw this dipeptide at a pH = 1, would the number of hydrogen bond donors change? [ Select ]

Consider a protein in which a negatively charged glutamic acid side chain (pKa=4.2) makes a salt bridge (ion-ion interaction) with a positively charged histidine side chain (pKa=6.5). Part C: Justify your answer with calculations of partial charges on these amino acid side chains at pH=7.9.(Hint: Consider lessons from Coulomb's law, and the Henderson-Hasselbalch equation.)

What are the charges of the following amino acids peptides at ph 14? 1. GLAVV 2. RRKKQ

You will now build a 15 amino acid peptide using another paper or wire backbone as you did above.  You will pick 15 amino acids, matching the criteria below, and put them onto your backbone about 3 inches apart.  This will be the primary structure of your novel protein.  Select  15 amino acids that meet the following criteria 6 hydrophobic R groups 2 acidic R groups 2 basic R groups 2 cysteine R groups 3 hydrophilic R groups  Place the R groups in any order you choose on your paper or wire backbone as you did above. Start at the N-terminus and place each R group about 3 inches apart until all 15 are attached to the mini toolbar. You have just built the primary structure of your protein.     Question 1:  Record the sequence of amino acids in your protein, starting with the N-terminus.  The N-terminus is the end of the polypeptide that has a free nitrogen group.  The C-terminus, or carboxyl end, will have a free carboxyl group. You can use the three letter amino acid abbreviation to…