help with part a and b please A molybdate-binding protein is shown at below that a gut bacterium uses to importMoO4 from its environment with a single MoO4 anion in the active site.(a) Identify the following secondary structural motifs in this structure: parallel ẞ-sheet; ßaß motif; antiparallel beta sheet with ẞ-turn.(b) Determine the direction of the C=O and NH groups for each of the three closestα-helices (labeled 1, 2 and 3) to the molybdate anion and explain how the orientationof the α-helices can contributes to the binding of the anion.3151618191101111121SNADEVQVAVAANFTAPIQA TAKEFEKDTG HRLVAAYGAT GOFYTQIKNG APFQVFLSAD DST PAKLEQE GEVVPGSRFT YAIGTLALWS PKAGYVDAEG EVLKSGSFRHLSIANPKTAP YGLAATQAMD KLGLAATLGP KLVEGONISQAYQFVSSGNA ELGFVALSQI YKDGKVATGS AWIVPTELHD PIRQDAVILN KGKDNAAAKA LVDYLKGA131241KAAALIKSYGYEL2511511611711811912012112212312327

Answered: A molybdate-binding protein is shown at…

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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For each of the following sequences determine if they will most likely form an amphipathic α helix, amphipathic β sheet, turn/loop or not an amphipathic structure. A) Lys-Gln-Asn-Glu-Pro-Arg-Ala-Asn-Glu B) Lys-Ser-Thr-Asn-Glu-Gln-Asn-Ser-Arg C) Gln-Ile-Thr-Phe-Thr-Leu-Gln-Val-Ser D) Asn-Leu-Ala-Asp-Ser-Phe-Arg-Gln-Ile
c) A lysine residue in the active site of UstD is involved in forming a covalent Schiff base linkage with the PLP cofactor. In order for this linkage to form, the lysine residue must be in its deprotonated form. Draw the structure of the R group of lysine in this neutral form. What is the ratio of the concentration of this form to that of its conjugate acid form at neutral pH? ( )
what is the c-terminal AA residue? use one-letter code for amino acid
A different Fab fragment binds to lysozyme with a dissociation constant of Kd=10-6 M. A 1 nM (10-9 M) solution of lysozyme is treated with increasing concentrations of this Fab fragment. At what concentration of added Fab will half of the lysozyme be bound to this Fab?
An active site of a hypothetical serine protease with a peptide substrate bound is shown below: This serine protease has 3 specificity pockets (S1, S2, S1') as shown in the figure above. S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Based on this information you can conclude that R1 is most likely side chain of a. Asp b. Lys c. Lle d. Gly e. Phe
Shown to the right is a cartoon image of ETC Complex I from Y. lipolytica. A group of authors studied this wild type Complex I and also a version where the arginine at position 121 in the chain 3 subunit was mutated to a methionine (R121M). Part of chain 3 subunit contains the peptide sequence SMITH a. Draw the titration curve for the SMITH peptide. Mark all pKa’s and the pI on your curve. For the SMITH peptide at physiological pH, explain what types of interactions you believe the side chains are or are not able to participate in.
In each of the following cases, predict whether the pKa value of the first residue will be upshifted or downshifted relative to the typical pKa value (Table 2.1) based on the microenvironment. Briefly (in no more than 2-3 sentences) explain your reasoning. (a) A His residue adjacent to two Arg residues on the surface of a protein(b) A Cys residue adjacent to an Asp residue in the active site of an enzyme(c) A Lys residue buried in the hydrophobic core of a globular protein
A heptapeptide was found to have an amino acid composition of Asp, Leu, Lys, 2 Met, Phe and Tyr. (a) Trypsin has no effect on the heptapeptide. (b) The phenyl thiohydantoin released by Edman degradation revealed phenylalanine in the N-terminus. (c) Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lys, and Met. (d) Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and free Lys. What is the amino acid sequence of this heptapeptide? Answer Format: (Three letter abbreviation with dash ie., Ala-Gly-…) *
Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid? (i) Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. (ii) Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. (iii) Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. (iv) Protein folding is determined by its primary sequence.
A protein substrate is known to be multi-monoubiquitinated. The control lane "C" in the SDS-PAGE gel shows a properly ubiquitinated protein substrate. Please draw out what the lane would look like if all lysine residues except for one are mutated to alanine residues in the protein substrate. Use one sentence to explain your rationale. C 1 Protein Substrate ||||
Consider the peptide Asp-Lys-Phe-Glu-Asn-Tyr-Gln-Val-Cys. In a single beaker, you treat this peptide with 2 proteases. One protease cleaves at the N-terminus of aromatic R groups and the other cleaves at the C-terminus of polar, non-ionizable R groups. Following the enzymatic digestion, you want to separate your peptide fragments so that you can identify them. You choose to separate the fragments using an anion exchange column. Beginning at pH=6 you apply your peptide fragments to the column and you gradually decrease the pH of the column stopping the separation when the pH of the column equals 4. Omitting chemical structures, write the amino acid sequence of the peptide fragments that are produced from this digest. Write the order that these fragments will elute from the column (if at all). (Relevant pKa values are: 2.1, 3.8, 4.3, 8.3, 9.6, 10.1, and 10.5)
A lipase enzyme has been isolated from a bacterium with a strong red color, found in industrial waste from a fishing company. This enzyme has great potential for elaboration of degreasers for industrial use as it can work at a wide range of temperature (between 4 ° and 80 ° C). However, it is estimated that its purity for industrial purposes is only 35% since it is contaminated with a low molecular weight protein that binds the smallest red pigment peptides and salts product of the purification process 1- Propose a methodology to increase the degree of purity of this enzyme, eliminatingsmall proteins and color.2- How it is ensured that the degree of purity of the enzyme has increased.

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