Answered: 38. Adenosine deaminase acting on RNA… | bartleby

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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38. Adenosine deaminase acting on RNA
(ADARS) catalyzes the conversion of
Adenosine to Inosine (at right). This is an
RNA editing enzyme. Why does A to I
editing destabilize duplex RNA? Draw out
how inosine could base pair with cytosine
(Draw hydrogen bonds as dashed lines,
and draw hydrogen atoms involved in
hydrogen bonds. Indicate the position of the ribose with an "R" (you do not need to draw
the ribose).
ADAR
NH2 Editing
N-
enzyme
N-
NH
N.
N.
N.
RNA
RNA
Adenosine
Inosine

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36.Start with two exons and an intervening intron. Include the cap and poly-A tail in your starting pre-mRNA. Show 2’-OH, 3’-OH, O-P-O phosphodiester bonds for the two transesterification reactions that splice exon 1 and exon 2. Be sure to include the branchpoint A and intron consensus sequences. You will need to show where the incoming -OH attacks the O-P-O bond to allow correct splicing in the lariat and between exons. Make your arrows precise. Show the lariat with the consensus sequences. Whenever possible, show 5’ and 3’ ends. Explain the fate of the lariat after it forms?
1. (a) By binding one L-tryptophan molecule/monomer, the trp repressor binds to DNA to sup- press synthesis of L-tryptophan in E. coli. Below is the amino acid sequence of the helix - reverse turn - helix region of the trp repressor that binds to DNA compared to the sequence of the corresponding DNA binding motif of the Prl protein. A diagram of the trp repressor dimer is also shown. Trp Prl Trp Prl 80 -Gly-Glu-Met-Ser-Gln-Arg-Glu-Leu-Lys-Asn-Glu-Leu-Gly-Ala-Gly-Ile- -Ser-Glu-Glu-Ala-Lys-Glu-Glu-Leu-Ala-Lys-Lys-Cys-Gly-Ile-Thr-Val- trp helix 5 70 trp helix 4 Prl helix 80 Prl helix Ala-Thr-Ile-Thr-Arg-Gly-Ser-Asn-Ser-Leu-Lys-Ala-Ala- Ser-Gln-Val-Ser-Asn-Trp-Phe-Gly-Asn-Lys-Arg-Ile-Arg- reverse turn 90 Comparing the two protein sequences above, identify all amino acid pairs that differ in electrostatic charge due to proton dissociable groups (assume pH 7). Indicate the charge of both residues for each such pair. (b) Circle the pair of residues for which the electrostatic charge due to…
Trypsin cleaves a polypeptide backbone at the C-terminal side of Arg or Lys residues, whereas chymotrypsin cleaves after aromatic residues. A polypeptide was treated with trypsin to generate a series of fragments of the following sequences: Gly-Gly-Ile-Arg Ser-Phe-Leu-Gly Trp-Ala-Ala-Pro-Lys Ala-Glu-Glu-Gly-Leu-Arg And the same polypeptide was treated with chymotrypsin to generate the following fragments: Leu-Gly Ala-Glu-Glu-Gly-Leu-Arg-Trp Ala-Ala-Pro-Lys-Gly-Gly-Ile-Arg-Ser-Phe Assemble the protein sequence.
Treating a solution of ribonuclease with 2-mercaptoethanol and urea denatures the enzyme. If the 2-mercaptoethanol is removed, followed by the removal of urea, the ability of the enzyme solution to hydrolyse RNA is reduced by about 99%. What is the most plausible explanation for this observation? a. All of the RNase molecules have about 1% of their usual activity, due to changes to the organisation of disulphide bonds b. Random formation of disulphide bonds mean about 1% of the RNase molecules are 100% active whereas 99% have no activity c. Deprotonation of histidine in the active site of the enzyme means that only about 1% of the enzyme molecules are active d. Deprotonation of histidine in the active site of the enzyme means that all of the enzyme molecules have 1% of their usual activity
The coding (or “sense”)strand(again noticename ANDthe directionality)of DNAthat is known to encode the C-terminal end of a long E. coliprotein has the following nucleotide sequence:5′–CCATGCAAAGTAATAGGT–3′Give the sequence of the last three amino acids of the protein (label the C-terminus).
A DNA-binding protein recognizes the following double-strandedsequence:5′–GCCCGGGC–3′3′–CGGGCCCG–5′This type of double-stranded structure could also occur withinthe stem region of an RNA stem-loop. Discuss the structural differencesbetween RNA and DNA that might prevent the DNAbindingprotein from recognizing a double-stranded RNA molecule.
Given the following diagram of how protein AWESOME1 binds to it's target DNA, describe the potential effects of each of the 5 mutations shown below. The wild-type sequence of a helix #1 is also shown in the blue box, and all the mutations are in helix #1 (see numbers for identifying particular residues). a helix #1 R(1)-V-I-L-Y-F-W-I-M-Y-F-S-H-Y-W-R(16) #1 Predict the consequence of the following mutations: 1) Arg(1) to Glu 2) Arg(1) to Ala 3) Phe(6) to lle 4) Trp(7) to Phe 5) Met(9) to Pro in
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