(i) (.:, From the diagram to the right of the trp repressor in itsapproximate binding relationship to a double-stranded DNA mole-cule, what is the relative orientation of the macrodipoles of helices 4and 5 to each other? Indicate the N-terminal ends of helices 4 andDNA55? Which residue in the sequence above is the N-terminal residueof each helix?NN(ii) :. Comparing the two protein sequences above, identify allamino acid pairs that differ in electrostatic charge due to proton dis-sociable groups (assume pH 7). Indicate the charge of both residuesfor each pair.C.

Tryptophan (trp) repressor: It's a transcription factor that regulates amino acid metabolism. The…

Answered: (i) (.. From the diagram to the right…

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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Consider the following sequence of DNA: 3'-TTA CGG-5'What dipeptide is formed from this DNA after transcription and translation? b. If a mutation converts CGG to CGT in DNA, what dipeptide is formed? c. If a mutation converts CGG to CCG in DNA, what dipeptide is formed? d. If a mutation converts CGG to AGG in DNA, what dipeptide is formed?
Given the partial transposons DNA sequence 5’-ACCGTATTCGGT-3’ upstream from the central region, assuming both terminal inverted repeats and flanking direct repeats have 6 base pairs, hypothetically write the transposon structure downstream from the central region.
which of the following sequences would most likely be able to bind a cyclic amp dna binding protein? (only one strand is shown but assume dna is double stranded) a. 5' atagtcatagtc 3' b. 5' atcggtctcgat 3' c. 5' gctctagcgagc 3' d. 5' atagtaatgata 3'
Which of the following set(s) of primers a–d couldyou use to amplify the following target DNA sequence, which is part of the last protein-coding exonof the CFTR gene?5′ GGCTAAGATCTGAATTTTCCGAG ... TTGGGCAATAATGTAGCGCCTT 3′3′ CCGATTCTAGACTTAAAAGGCTC ... AACCCGTTATTACATCGCGGAA 5′a. 5′ GGAAAATTCAGATCTTAG 3′;5′ TGGGCAATAATGTAGCGC 3′b. 5′ GCTAAGATCTGAATTTTC 3′;3′ ACCCGTTATTACATCGCG 5′c. 3′ GATTCTAGACTTAAAGGC 5′;3′ ACCCGTTATTACATCGCG 5′d. 5′ GCTAAGATCTGAATTTTC 3′;5′ TGGGCAATAATGTAGCGC 3′
Assume the following DNA template strand: 3'-ATA GCG AGG AGT ATC-5' A) What would be the protein associated with this DNA template strand? Give the sequence of amino acids encoded by this fragment. Leave traces of your steps. B) In the synthesis of this protein, what are the codon and the anticodon for? Explain in one sentence for each. C) We find, in another cell, a mutation of this DNA template strand: 3' ATA GCG TGG AGT ATC-5’ 1. What type of point mutation is it? 2. Did this mutation arise during transcription, translation or DNA replication? D) If this mutation is found in a spermatozoon, will it have an effect on the individual, its offspring or both? Briefly explain
In the human gene for the beta chain of haemoglobin (the oxygen-carrying protein in the red blood cells), the first 30 nucleotides in the amino-acid-coding region is represented by the sequence: 3'-TACCACGTGGACTGAGGACTCCTCTTCAGA-5'. What is the sequence of the partner strand? 4B. If the DNA duplex for the beta chain of haemoglobin above were transcribed from left to right, deduce the base sequence of the RNA in this coding region. 4C. In NOT more than 200 words, explain how eukaryotic RNA synthesized by RNA polymerase II is modified before leaving the nucleus?
Hydroxylamine (NH2OH) converts cytosine to the compound shown below. With which base does this modifi ed cytosine pair? Does this generate atransition or a transversion mutation?
A mixture of four a-[32P]–labeled ribonucleoside triphosphates was added to permeabilized bacterial cells undergoing DNA replication in the presence of an RNA polymerase inhibitor, and incorporation into high-molecular-weight material was followed over time, as shown in the accompanying graph. After 10 minutes of incubation, a 1000-fold excess of unlabeled ribonucleoside triphosphates was added, with the results shown in the graph. (a) Why was the excess of unlabeled rNTPs added?(b) How could you tell that radioactivity is being incorporated as ribonucleotides rather than as an alternative such as reduction to deoxyribonucleotides, followed by incorporation?(c) What does this experiment tell you about the process of DNA replication?
A mixture of four a-[32P]–labeled ribonucleoside triphosphates was added to permeabilized bacterial cells undergoing DNA replication in the presence of an RNA polymerase inhibitor, and incorporation into high-molecular-weight material was followed over time, as shown in the accompanying graph. After 10 minutes of incubation, a 1000-fold excess of unlabeled ribonucleoside triphosphates was added, with the results shown in the graph. Incorporation of radioactivity, cpm Excess (a) Why was the excess of unlabeled rNTPs added?(b) How could you tell that radioactivity is being incorporated as ribonucleotides rather than as an alternative such as reduction to deoxyribonucleotides, followed by incorporation?(c) What does this experiment tell you about the process of DNA replication?
Consider a mutant form of the lac repressor protein whose ΔGo for binding DNA differs from that of the wild-type protein by 2 kcal/mol, the approximate free energy equivalent of a single hydrogen bond. What is the difference (i.e., the ratio) of the Kd values (for DNA binding) of the wild-type versus the mutant lac repressor protein?
The following represent deoxyribonucleotidesequences in the template strand of DNA:Sequence 1: 5'@CTTTTTTGCCAT@3'Sequence 2: 5'@ACATCAATAACT@3'Sequence 3: 5'@TACAAGGGTTCT@3'(a) For each strand, determine the mRNA sequencethat would be derived from transcription.(b) determine the amino acidsequence that is encoded by these mRNAs.(c) For Sequence 1, what is the sequence of the codingDNA strand?
Why do promoter mutations cluster at positions −10and −35 as shown in Figure 11-11? Which protein-DNAinteraction is disrupted by these mutations?

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