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 correspondingDNA binding motif of the Prl protein. A diagram of the trp repressor dimer is also shown.TrpPrlTrpPrl80-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 570trp helix 4Prl helix80Prl helixAla-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 turn90Comparing the two protein sequences above, identify all amino acid pairs that differ in electrostaticcharge due to proton dissociable groups (assume pH 7). Indicate the charge of both residues for eachsuch pair.(b) Circle the pair of residues for which the electrostatic charge due to proton dissociable groupsis the same but the residues differ.70(c)Below the sequence of the helix-turn-helix section of the trp-repressor protein is listedaccording to the three-letter abbreviations of each amino acid residue. Write the corresponding se-quence according to the one-letter abbreviation below each amino acid residue.-Gly-Glu-Met-Ser-Gln-Arg-Glu-Leu-Lys-Asn-Glu-Leu-Gly-Ala-Gly-90Ile-Ala-Thr-Ile-Thr-Arg-Gly-Ser-Asn-Ser-Leu-Lys-Ala-Ala-

An atom's or molecule's electrostatic charge, which can be either positive or negative depending on…

Answered: 1. (a) By binding one L-tryptophan…

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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(c) By binding one L-tryptophan molecule/monomer, the trp repressor binds to DNA to suppress syn- thesis 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 different type of repressor protein. A diagram of the trp repressor dimer is also shown. reverse turn trp helix 4 70 Trp -Gly-Glu-Met-Ser-Gln-Arg-Glu-Leu-Lys-Asn-Glu-Leu-Gly-Ala-Gly- Ile- Prl -Ser-Glu-Glu-Ala-Lys-Glu-Glu-Leu-Ala-Lys-Lys-Cys-Gly-Ile-Thr- Val- Pri heilix trp helix 5 80 90 Trp Ala-Thr-Ile-Thr-Arg-Gly-Ser sgn-Ser-Leu-Lys-Ala-Ala- Prl Ser-Gln-Val-Ser-Asn-Trp-Phe-Gly-Asn-Lys-Arg-Ile-Arg- Prl helix
Consider the structure of Cro repressor protein from bacteriophage lambda E. It is a DNA binding protein, and like many sequence- specific DNA binding proteins, it must function as a homodimer Ex. Notice the mutual docking of a phenylalanine residue from each subunit into a hydrophobic pocket of the partner subunit. These hydrophobic interactions are required for dimerization. The noncovalent interactions highlighted in yellow are also required for dimerization. These interactions represent examples of: Osecondary structure O tertiary structure O quaternary structure O secondary AND quaternary structure Ⓒ tertiary AND quaternary structure
Consider the now dominant variant of the SARS-CoV-2 called the D614G mutation: a) The mutation changes an Aspartate (D, Asp) to a Glycine (G, Gly) at nucleotide position 614 (that’s why it’s called the D614G mutant) in the S1 subunit of the Spike protein. Using only the information above and a codon table, what are the mRNA codon sequences of the 2019-dominant and 2020-dominant Spike proteins? Note the figure above is not needed toanswer the question. Report in 5’ to 3' orientation __________________________________________ b) What type of substitution is this? In your answer, address the following: • The expected substitution in base sequence (e.g., A à C)• If the mutation is synonymous, nonsynonymous, or a frameshift• If the mutation is a transition or a transversion c) The mutation increases infectivity by reducing the stability of the Spike protein such that it can remain in the open conformation more often. The open conformation increases the chances of binding to the host ACE2…
Shown below is a schematic diagram illustrating a very short gene with 5000 bp region of an unknown Schizosaccharomyces pombe genome. (Note: Transcription starts at Transcription Start Site (TSS).) TSS 5. 3' 3 +1 (i) Name the specific regions that can be recognized by Transcription Factor IID (TF ID) and indicate the locations in the diagram above. (ii) List the mechanistic steps that can trigger the initiation of transcription by Transcription Factor IIH (TF IIH).
Below are shown two views of the backbone representation of the Myc-Max complex binding to DNA (PDB ID: 1NPK). Myc and Max are members of the basic helix-loop-helix (BHLH) class of DNA- binding proteins (see Chapter 29). Myc (red) and Max (blue) associ- ate via a coiled-coil interaction and bind DNA as a dimer. Side view of Myc-Max bound to DNA Top view of Myc-Max bound to DNA (looking down the DNA helical axis) (a) Are the helices bound to the DNA likely to be amphiphilic? Explain. (b) Where do you predict the N- and C-termini are located for Max?
The codon change (Gly-12 to Val-12) in human rasH that convertsit to oncogenic rasH has been associated with many types ofcancers. For this reason, researchers would like to develop drugs toinhibit oncogenic rasH. Based on your understanding of the Rasprotein, what types of drugs might you develop? In other words,what would be the structure of the drugs, and how would theyinhibit Ras protein? How would you test the efficacy of the drugs?What might be some side effects?
. a. How many ribosomes are required (at a minimum)for the translation of trpE and trpC from a singletranscript of the trp operon?b. How would you expect deletion of the two tryptophan codons in the RNA leader to affect theexpression of the trpE and trpC genes?
in m 5'- 3'- Shown below is a schematic diagram illustrating a very short gene with 3000 bp region of an unknown Escherichia coli genome. (Note: Transcription starts at Transcription Start Site (TSS).) TSS -3' -5' +1 (i) Name the specific regions that can be recognized by sigma factor and indicate the locations in the diagram above. (ii) How does Sigma factor trigger the initiation of transcription?
The E. coli genome contains approximately 4639 kb. (a) How many copies of the 6-bp recognition sequence for the trp repressor would be expected to occur in the E. coli chromosome? (b) Explain why it is advantageous for the trp repressor to be a dimer that recognizes two adjacent 6-bp sequences.
What would happen to the regulation of the tryptophan operon in bacterial cells that express a mutant form of the tryptophan repressor that (1) cannot bind to DNA, (2) cannot bind tryptophan, or (3) binds to DNA even in the absence of tryptophan?
In this chapter you were introduced to nonsense suppressor mutations in tRNA genes. However, suppressormutations also occur in protein-coding genes. Using thetertiary structure of the β subunit of hemoglobin shownin Figure 9-3(c), explain in structural terms how a mutation could cause the loss of globin protein function. Nowexplain how a mutation at a second site in the same protein could suppress this mutation and lead to a normalor near-normal protein.
The dlagram below represents the tryptophan operon with the trp leader MRNA transcript enlarged to represent the AUG transiation start codon, two consecutive tryptophan amino acld codons (UGGUGG), and 4 regions (1, 2, 3, and 4) that base pair to form different hairpin-loop structures in the MRNA leader region. What would happen in this MRNA leader region when cells encounter very low levels of tryptophan in Its environment? Leader region trpE trpD trpC trpB trpA DNA 5' 3' Transcription trp leader sequence mRNA UGGUGG (tryptophan codons) AUG UUUUUU 1 3 4. The translating ribosome would stall at the two tryptophan codons, causing the formation of a hairpin-loop botween regions 3 and 4 to promote transcription of the trp operon. The translating ribosome would stall at the two tryptophan codons causing formation of hairpin-loop between regions 2 and 3, which functions as an anti-lerminator of transcription The translating ribosome would stall at the two tryptophan codons causing formation…

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