Figure 1 shows the structure of adenine and thymine.(i)(ii)NHadenineC-HthymineFigure 1Illustrate the potential tautomers of adenine and thymine.Draw a chemical structure of Thyminc-Adenine (T-A) base pair and label the patternsof hydrogen bond acceptors, donors in the major groove of the TA base pair.

These are cyclic compounds that contain nitrogen. They can be: Purines: a heterocyclic organic…

Answered: Figure 1 shows the structure of adenine…

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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In pyrimidine nucleosides, the anti conformation predominates. Explain. Do the purine nucleosides have similar 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
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
Hemoglobin is considered to be a tetrameric complex with a 64 kDa (α β)2. When attempting to purify hemoglobin, we must first purify the α and β monomers (about 16 kDa each) to prepare the tetramer. This is formed from the dimer intermediate: 2 α + 2 β -> 2 αβ -> (α β)2. The graph given represents a size-exclusion chromatogram after the refolding of the hemoglobin tetramer Using the size-exclusion chromatogram given, 1. Draw an SDS-Page Gel with a reducing agent such as BME using the three peaks listed on the graph.
Consider the following peptide to answer the questions below: A M A K K E S H I F T A I D E What is the total charge of this peptide at pH = 5? What is the N terminal amino acid (full name)? C terminal amino acid? How many fragments would result if this peptide underwent proteolytic cleavage with V-8 protease and what are these fragments (list them)? Would this peptide be a candidate to form an alpha helix? Why or why not
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.
(A) Give the polypeptide translation of the RNA sequence below. 5’-AUGGAAAUCAAAGUCAACCUUGAGUUUAGA-3’ (B) Write the chemical structure of the polypeptide sequence you determined in part (a) (C) Given the chemical structure of the polypeptide sequence you have written in part (b), answer True or False for each of the 5 statements below. (1) At least one of the amino acids in the sequence can undergo phosphorylation (2) The sequence looks like it could form a β turn (3) The sequence looks like it could form a β strand with one surface facing the interior of the protein and the other surface exposed to water (4) At least one of the amino acids in the polypeptide sequence can undergo oxidation to form a disulfide bridge to another polypeptide (5) The sequence looks like it could form an α helix that would be part of a coiled coil structure within a protein
Draw the molecular formula of the covalently modifi ed histone side chain of acetyllysine. How does this modifi cation alter the chemical properties of the side chain?
A protein hypothetically consists of two polypeptide chains with the given sequences in the picture. Based on the said sequences, a. Do you think it is possible that interchain disulfide bonds is present in the protein? Explain. b. Do you think it is possible that intrachain disulfide bonds is present in the protein? Explain.
Using the quarternary structure of hemoglobin shown inFigure 9-3(d), explain in structural terms how a mutation in the β subunit protein could be suppressed by amutation in the a subunit gene.
1. Consider the following α helix from myoglobin at pH 7. Gln-Gly-Ala-Met-Asn-Lys-Ala-Leu-Glu-His-Phe-Arg-Lys-Asp-Ile-Ala-Ala-Lys-Tyr(a) Label amino acids in the polypeptide above as follows: p for polar and uncharged, np for non polar, – for negatively charged, and + for positively charged.(b) How many complete turns are there in this helix?(b) Which side chains are likely to be on the side of the helix that faces the aqueous solvent? Why?(c) Which side chains are likely to face the interior of the protein? Why?

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