Draw the two amino acids serine and alanine, and a dipeptide that could be formed by combiningthese two amino acids (ala-ser). Draw these molecules at a pH=7. In peptide nomenclature theamino 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 donorschange? [ Select ]

Amino acids are the building blocks of proteins which are composed of amino group (NH3+), carboxyl…

Answered: Draw the two amino acids serine and…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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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
B) An aqueous solution (pH ~7) containing mixture of three amino acids; glycine (G), arginine (R) and glutamic acid (E), was dropped onto center of a solid matrix (e.g chromatographic paper) which is incorporated in an electrical circuit (a). After applying electrostatic potential, the aminoacids are separated as shown in b. Determine amino acids that are labeled as 1, 2 and 3. a) DC Power Supply (OFF) b) DC Power Supply (ON) Solid matrix Solid matrix Cathode Anode Cathode Anode buffer buffer buffer buffer Sample containing amino acids G, R, E
4) For various amino acid pairs (for example: F to A, E to R, D to N, V to L, S to W), ask yourself: a) Based on what you know about the chemical properties of the side chains, what effect would you expect on the stability of the protein if you mutated one residue of the pair into the other in the interior of the protein? What forces might have an impact on this change (ie: what types of interactions would you expect that amino acid to be involved in?) How would your answer change if the amino acid were located on the surface of the protein? b) c)
what is the n-terminal AA residue? use one-letter code for amino acid
3
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…
Given the polypeptide chain below: Ala-Arg-Val-His-Asp-Gln 1. What kind of polypeptide is it? 2. How many peptide bonds are there?
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.
Draw the structural formula of the oligopeptide if the amino acids are arginine, glutamine, glycine, methionine and glutamic acid considering the first amino acid is the N-terminus
1. What will happen if there is a change in the configuration of a protein molecule? Provide an example. 2. Give the IUPAC name for Ala-Gly-Leu
1. Draw the tetrapeptide Met-Ala-Thr-Thr at a ph of 7? 2. Draw the tetrapeptide Met-Ala-Thr-Thr at a ph of 12?

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