. The allosterically regulated enzyme ATCase binds aspartic acid as asubstrate and acylates the a-amino group. Succinate acts as a competitiveinhibitor of ATCase because it binds the active site but can't be acylated. Thedependence of vo on [aspartic acid] for ATCase is shown in panel (a) of theaccompanying figure. Panel (b) shows the effect of increasing [succinate]on v, when [Asp] is held at a low concentration (see thick vertical arrow inpanel (a)). Note that in panel (b), vo is not zero when [succinate] =0 (seethin horizontal arrow). Explain the shape of the curve in panel (b). Whydoes v, increase initially, before decreasing at higher [succinate]?Co0-COOCH2CH,HC -NH,CH,COOCOOAspSuccinate[Asp)[Succinate][Asp] inexperiment b(a)(b)

The allosterically regulated enzyme ATCase binds aspartic acid as a substrate and acylates the…

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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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Substrate A has a Km of 45uM and a kcat of 100/s with trypsin and a Km of 540mM and a kcat of 2/s with chymotrypsin. Substrate A is a better substrate of [trypsin/chymotrypsin] and likely contains a/an/some [aromatic/acidic/basic] residues(s) in its sequence. Chymotrypsin contains a [glycine/serine/aspartate] in its specificity pocket which likely [repel/attract] the residues in substrate A.
Draw the catalytic triad of a serine protease at the first tetrahedryl intermediate stage. Your drawing should include the amino acids that make up the triad, any part of the substrate that should be present, and any other molecules that are present in the active site.
Studies at diff erent pH’s show that an enzyme has two catalytically important residues whose pKs are ∼4 and ∼10. Chemical modifi cation experiments indicate that a Glu and a Lys residue are essential for activity. Match the residues to their pKs and explain whether they are likely to act as acid or base catalysts.
In addition to the reactions mentioned in Section 23.5, PLP can catalyze b-substitution reactions. Propose a mechanism for the following PLP-catalyzedb-substitution reaction:
Globular proteins with multiple disulfide bonds must be heated longer and at higher temperature to denature them. Bovinepancreatic trypsin inhibitor (BPTI), having 58 amino acids in a single chain and 3 disulfide linkages, loses its catalytic activity whenheated at nearly 90°C for 5-10 minutes. Explain the molecular basis of this observed thermal property of BPTI relative to the nativestructure and function of the protein. please do not copy from other answers here
From the complete oxidation of glucose (glucose → 6CO2), how many total nucleotide triphosphates are yielded (be sure to deduct payback) as part of substrate level phosphorylation?
“Caspase” describes the catalytic activity of this enzyme. What amino acyl residue participates in the catalytic mechanism? What substrate motif does caspase-8 recognize?
The effect of ATP on the allosteric enzyme PFK-1 is shown below. For a given concentration of fructose 6-phosphate, the PFK-1 activity increases with increasing concentrations of ATP, but a point is reached beyond which increasing the concentration of ATP inhibits the enzyme. (a) Explain how ATP can be both a substrate and an inhibitor of PFK-1. How is the enzyme regulated by ATP? (b) In what ways is glycolysis regulated by ATP levels? (c) The inhibition of PFK-1 by ATP is diminished when the ADP concentration is high, as shown in the illustration. How can this observation be explained? *A graph is included for this question*
RuBP carboxylaseis by no means an idesl enzyme. Describe some of the problems with its active site and its substrate specificity. If we compare the amino acid sequences of this enzyme from many different species, they are almost identical. What is the significance of this uniformity?
Sketch curves for reaction velocity versus [fructose-6-phosphate] for the phosphorylated and nonphosphorylated forms of PFK-2 in liver.
Parts of the mechanism for lysozyme are shown below. The catalytic lysozyme residue side chains can be identified as being above and below the polysaccharide chain shown at point A. Complete the missing structures (points B and E) and curly arrows (points A, B, C, D and E) in the mechanism, as well as from the knowledge you have gained, label the catalytic amino acids at point A in your mechanism with their correct name and residue number. A OH R OH O-R H₂C- HO NHAC NHAC E R D OH B R C H RO H3C- ° H₂C- NHAC Y R OH NHAC R R
Only a few amino acid residues are actually involved in catalysis in enzymes, yet enzymes are constructed of at least 100 amino acids, and often many more. Suggest some functions for the noncatalytic amino acids.

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