100501011010CotDNA renaturation curves occasionally show three distinct phases of rena-turation. In this graph, DNA renaturation is plotted against "Cf" (initialconcentration times time of renaturation-essentially a measure of relativerenaturation time). See Figure 21.4.(a) Identify each part of this plot that corresponds to reannealing of(1) unique sequences, (2) moderately repetitive sequences, and (3) highlyrepetitive sequences.(b) Suppose that you cloned a single-copy gene, such as the gene for dihy-drofolate reductase (DHFR), into a plasmid vector and subjected it torenaturation analysis. Sketch the curve you might expect.(c) Suppose that you used reverse transcriptase (Chapter 24) to copy theovalbumin mRNA and cloned this complementary DNA (CDNA) intoa plasmid vector. Would you expect this CDNA to reanneal (1) moreslowly. (2) more rapidly, or (3) at the same rate as genomic DNA? Brieflyexplain your answer.% Single stranded

The denatured DNA can reformulate hydrogen bonds between complementary single strand, making it…

Answered: 100 50 10 1 10 10 Cot DNA renaturation…

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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100 50 104 1 10 104 Cot DNA renaturation curves occasionally show three distinct phases of renaturation. In this plot, DNA renaturation is plotted against “C,t" (initial concentration times time of renaturation, essentially a meas- ure of relative renaturation time). (a) Identify each part of this plot that corresponds to reannealing of (1) unique sequences, (2) moderately repetitive sequences, and (3) highly repetitive sequences. (b) Suppose that you cloned a single-copy gene, such as the gene for dihydrofolate reductase (DHFR), and subjected this to renaturation analysis. Sketch the curve you might expect. (c) Suppose that you cloned the DHFR CDNA instead of genomic DNA. Would you expect this to reanneal (1) more slowly, (2) more rapidly, or (3) at the same rate as genomic DNA? Briefly explain your answer. % Single stranded
What part(s) of a nucleotide (namely, phosphate, sugar, and/orbase) is(are) found in the major and minor grooves of doublestrandedDNA, and what part(s) is(are) found in the DNA backbone?If a DNA-binding protein does not recognize a specificnucleotide sequence, do you expect that it binds to the majorgroove, the minor groove, or the DNA backbone? Explain.
In Polymerase Chain Reaction (PCR), the temperature is one of the most important parameters that could influence the efficiency of this technique. Each cycle of this reaction has its own specific temperature. For instance, the denaturation step possesses a temperature of 94 - 98 ℃ to ensure that the double stranded DNA is fully separated. (i) (ii) (iii) Why is the annealing temperature vital in this technique? Explain how will this temperature affects the efficiency of this reaction. Why is Hot Start PCR technique preferred by some researchers? If the primers you purchased possessed the following information. 5'-GGA AAC AGC TAT GAC CAT G-3' Calculate the melting temperature of this primer and estimate the annealing temperature of this primer.
Compute the percent identity of the following pairwise sequence alignment: -TGAGACTTAGAGT |..|... | | | | | ATAGGAGCGAGAGT
Considering DNA sequencing by the Sanger method. It is correct to say that: * A)In the traditional method, radioactively “labeled” primers are used, allowing their visualization in autoradiography. B)In the automated method, a single reaction is performed containing the four “labeled” dideoxynucleotides, each with a different fluorophore. C)In both traditional and automated methods, the fragments are resolved and interpreted according to their ionization state. D)In the automated method, di-deoxynucleotides “labeled” with the same fluorophore are used, thus allowing their interpretation based on graphs of fluorescence emission. E)Sequencing reactions can use mRNA molecules, as long as they have a polyA tail.
(a) What two enthalpic factors stabilize DNA in double-helical form at lowtemperature?(b) What entropic factor destabilizes helical DNA at high temperature?(c) Why is the double-helical structure of DNA stabilized at moderate tohigh ionic strength?
What two basepair changes can occur when G tautomerizes to the enol form? Recall that the tautomerization can occur when G is a free dNTP prior to DNA replication or when G is incorporated into dsDNA just before DNA replication. Draw both of these bp changes out. Are they transitions or transversions?
For a linear B-DNA molecule of 50,000 kb, calculate (a) the contour length and (b) the length of the DNA as packaged in nucleosomes with linker histones present.
1) What happened to the DNA at the different temperatures? How does Polymerase Chain Reaction exploit this property of DNA (Word count: 200) 2) Briefly outline the steps of DNA extraction as carried out in a lab for the purposes of sequencing, with reference to a published protocol from a company that supplies regents and kits for DNA extraction (e.g Qiagen, ThermoFischer, Invitrogen, or similar). Please Include the weblink for the published protocol you used as a reference
DNA isolated from an organism can be sheared into fragments of uniform size (∼1000 bp), heated to separate the strands, then cooled to allow complementary strands to reanneal. The renaturation process can be followed over time. Explain why the renaturation of E. coli DNA is a monophasic process, whereas the renaturation of human DNA is biphasic (an initial rapid phase followed by a slower phase).
The chain terminator method was used to sequence the following DNA fragment: ACTGGGCATAAGCGGGAACTTTGCAGAACTGGCTGGCCTCAGAGCAGGGA. 1. Predict a band pattern in a gel after sequencing this DNA fragment using a radioactively labeled primer [32P]-5’- TCTGAGGCCAGCCAGTTCTGCAAAGTTC. 2. Due to an experimental mistake, dATP was not added in all four reaction mixtures. How does the band pattern change?
Compute the PERCENT IDENTITY for the following pairwise sequence alignment. ACTGATGGGGG--AGACGTA ||||| ... I ||||||| ACTG--AAAAGCTAGACGTA

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