Asp residue (both of which are essential for catalysis) with pK, values of 5.9 and 4.5, respectively. Ifthe enzyme is found in the lysosome (pH = 5.2), which residue will act as the general acid and whichwill act as the general base during the initial steps of the reaction? Explain your reasoning. (

In simple terms, pH indicates whether a substance is acid or base. pKa determine how strong is an…

Answered: Asp residue (both of which are…

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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Prepare a schematic diagram and present it as though it were a Figure in a publication (scientificjournal or textbook) (20%). The Figure should illustrate the interactions made between thekey components of (a) total and (b) non-specific binding reactions. In preparing your figure,you should reflect on the role of each of the components of the reaction mixtures, and whythe subtraction of non-specific from total binding allows us to calculate specific binding.
Describe the concept of isoelectric point and calculate the PI for isoleucine?
Is a protein as good a cellular buffer at physiological pH as its constituent amino acids would be if they were present as free amino acids in proportional concentrations in the cell? Explain Based on your rationale in the previous question, describe the difference in the dissociation constants of the α-COOH of GABA and glutamate, and the differences in the dissociation constants of the amino group in each of these amino acids.
5
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?
Draw the amino acid below in its most protonated form, any intermediately protonated forms, and its least protonated form. Also draw a titration curve for this amino acid, with pH on the y-axis and equivalents on the x-axis going from acidic to basic (most protonated to least protonated) using the pka values below. Match the protonated/deprotonated forms to the appropriate regions of the titration curve. Scan your drawing, and upload as a pdf, jpeg, or tiff file. H3C O NH₂ pKas are provided below: OH
Intramitochondrial ATP concentrations are about 5 mM, and phos- phate concentration is about 10 mM. If ADP is five times more abundant than AMP, calculate the molar concentrations of ADP and AMP at an energy charge of 0.85. Calculate AG for ATP hydrolysis at 37 °C under these conditions. The energy charge is the concentra- tion of ATP plus half the concentration of ADP divided by the total adenine nucleotide concentration: [ATP] + 1/2[ADP] [ATP] + [ADP] + [AMP]
the following peptide is incubated as chymotrypsin: Gly-Val-Phe-Lys-Ala. Present the detailed chemical mechanism by which chymotrypsin hydrolyzes this peptide. Briefly explain each step. Include only the structure of the final products of the reaction.
affinity of a protein-protein or protein-ligand interaction can be described by the Dissociation Constant, Kd (written below). Consider a protein P and its inhibitor, I. I inhibits P's activity when bound to it: koff _ [A][B] Dissociation Constant: Ka = koN [AB] Question When [I] is 10-7 M, 99% of P's activity is inhibited. What is the Kd of this Protein- Inhibitor interaction?
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
Which of the following statements are descriptions of metal ion catalysis or examples of metal ion catalysis? Choose all correct answers a Zn²+ cofactor may properly orient the substrate in the active site through ionic interactions. a covalent bond forms between enzyme and substrate lowers the energy or stabilizes the transition state or intermediate catalyst retains its original form after reaction occurs catalysts may participate in oxidation-reduction reactions by changes in the oxidation state
Chymotrypsin is an enzyme that is optimized to function in the small intestine (at a pH of ~7.4). Explain, given what you know about the chymotrypsin mechanism and what we learned about acid/base chemistry, why chymotrypsin would not be able to initiate catalysis if it were secreted into the stomach (pH ~2.5).

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