P8.11: Show starting compounds that would lead to the following products through nucleophilic substitution reactions. bc. C +Br d..0ucleotide biosya. Draw a likely mechanism for the following reaction (EC 6.3.4.2) from ribonucleotide biosynthesis. Hint: what is the nucleophilic group? How could the enzymeincrease it's nucleophilicity?PPOOH OHATPADPPPOb. Draw a mechanism for the following reaction, also from ribonucleotide biosynthesis (EC 6.3.3.1):OPNHATPADPNHHOOHOH OHOPNHHOOHΝG

Both reactions (a) catalyzed by [EC 6.3.4.2] and (b) catalyzed by [EC 6.3.3.1] involve transfer of…

Answered: ucleotide c a. Draw a likely mechanism…

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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Describe how the concentrations of the four deoxyribonucleotides are balanced by ribonucleotide reductase.
The biosynthetic pathway for the two amino acides E and H is shown schematically in the Figure below: A W E 2 Z H How would this pathway change if C was mutated and non-functional?
.Propose a mechanism for the conversion of 5- formamidoimidazole-4- carboxamide ribonucleotide into inosinate.
. Most bacterial mutants that require isoleucine for growth also require valine. Why? Which enzyme or reaction would be defective in a mutant requiring only isoleucine (not valine) for growth?
Discuss the role of feedback inhibition in the anabolism ofpurine-containing nucleotides.
Describe the mechanism of action of 1 cycle of the ubiquitin (Ub) ligase system. Describe how the E1, E2 and E3 ligases work to covalently link Ub to the target protein, including which uses an energy source (and how), and the operative amino acids on the enzymes, Ub and target protein
. (a) Explain the biochemical basis for the fact that one can synchro- nize cell populations þy treating them with deoxythymidine. (b) Explain the apparent paradox that dATP at low concentrations is an activator of ribonucleotide reductase, whereas at higher concen- trations it becomes inhibitory.
. The mechanism for lysozyme cleavage of its polysaccharide substrate requires Glu35 in its nonionized form, whereas the nearby Asp52 must be ionized (see the figure below). The pK values for the side-chain carboxyl groups on the two amino acids in solution are virtually identical. a) How can one carboxyl group be charged and the other uncharged in the active site of lysozyme? b) The pH optimum for lysozyme is about 5. Why do you suppose that the activity decreases above and below this optimum? Glu3s NAG Asp52 0-H Glu35 -C Asp52 tri-NAG NAG
Anabolism & Catabolism of Nitrogenous Bases. a. Differentiate the processes of purine nucleotide biosynthesis & pyrimidine nucleotide biosynthesis. What are the starting materials for each process? b. Differentiate the processes of purine nucleotide degradation &pyrimidine nucleotide degradation. What are the end products of each process? c. Explain how purine & pyrimidine biosynthesis is regulated to produce balanced levels ofall four nucleotides (ATP, GTP, UTP & CTP)?
(c) On the right is a diagram of the ac tive site of E. coli aspartate aminotrans- ferase illustrating the cofactor pyridoxal phosphate (labeled PLP) with the dicar- boxylic acid maleate (labeled MAL) bound in the active site. The structural formula of maleate is shown on the right. Am 194 MAL Arg292 Arg386 Ilx17 Lauf 'coo- H get H Coo- Maleate (c1) Draw the structure of L-aspartate and draw a border around the atoms in the amino acid that maleate simulates. (c2) Identify the active site residues that make hydrogen bonds and electrostatic interac- tions with the oxygen atoms of the carboxylate groups of maleate in the diagram above. Identify the carboxylate groups according to the numbering in the diagram of maleate above. Indicate the hydrogen donor groups of the active site residues. (C3) Compare and draw the structures of L-Arg and L-Lys. On the basis of the diagram why does replacement of an arginine for a lysine have an effect on substrate binding to AspAT? (c4) Of the mutant…
Briefly describe each of the following possible posttranslational protein modifications. Give an example of each. Cross-linkage glycosylation and phosphorylation cleavage assembly into polymeric proteins (> 1 polypeptide)
As described in 4C above, PLP-dependent enzymes can generate formaldehyde from serine. This compound would be toxic if widely distributed in the cell, so normally the formaldehyde is captured by tetrahydrofolate, generating N^5 ,N^10-methylene tetrahydrofolate a) Draw a general acid/general base mechanism that an enzyme might use for this transformation b) Explain the role of the coenzymes N^5 , N^10-methylene tetrahydrofolate, and NADPH in thymidylate synthase, which converts dUMP to dTMP (no mechanism needed; an accurate written description will do,

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