ACHIEVE:INTRO TO GENETIC ANALYSIS 1TERM
12th Edition
ISBN: 9781319401399
Author: Griffiths
Publisher: MAC HIGHER
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Chapter 1, Problem 14P
Summary Introduction
To determine: The effect of the relative amount of GC for AT on the heat required for denaturation.
Introduction: Denaturation is the process in which the double helix structure of the DNA is melted to produce two single strands of DNA. The denaturation involves the breaking of hydrogen bonds formed between the bases in the duplex.
Summary Introduction
To determine: The effect of length of DNA double helix in base pairs on the amount of heat required to denature it.
Introduction: The melting temperature of
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You are supplied with the following information about a DNA molecule:
The molecular weight of a typical nucleotide is 660 Da.
The linear density of double stranded DNA is 4 x 106 Da per micrometer.
There are 10 base pairs in one complete turn of the double helix.
Answer the following questions about a DNA molecule with a length of 3.3 micrometer and a base composition which contains 20% of the base adenine (A).
(a) How many phosphor atoms are present in this DNA molecule?(b) How many full turns of the DNA helix are there in this molecule?(c) What is the percentage of guanine bases in the DNA molecule?(d) How many hydrogen bonds are there in the molecule?(e) How many phosphodiester bonds are there in the molecule?( f ) What is the length in basepairs of a DNA molecule that contains 606 full turns of the double helix?
Hydrolysis of the N-glycosyl bond between deoxyribose and a
purine base in DNA creates an apurinic (AP) site. An AP site is
more thermodynamically destabilizing to a DNA molecule
than is a mismatched base pair.
Examine the structure of an AP site.
H₂N
HN
N
O™
-O-P-O-CH₂
Guanine
H₂N
N
HN
Select the chemical consequences that could contribute to DNA instability at AP sites.
H
H
1₂0/
H
fewer hydrogen bonds between the unpaired pyrimidine base and water
disruption of the base-stacking interactions
decreased interaction between the mutated DNA strand and histones
increased ability of the deoxyribose ring to open without the attachment of the purine base
H
H
Guanosine residue
(in DNA)
O™
-O-P-O-CH₂
O
H
H H
O
Apurinic residue
H
OH
H
Each group will be provided with 20 g double-stranded DNA oligomer in STE buffer (0.1M NaCl/ Tris/ 10 mM EDTA, pH 7.4). The sequence of one strand of the oligomer is:
5’-AATGGTACGTATACTTTAT-3’
- show a table of % denaturation of DNA at different temperatures, using the equation provided in “Calculation”
- plot a graph of % denaturation of DNA vs different temperatures with clear label and title, and hence determine the experimental Tm of the DNA sample
- calculate the theoretical Tm of the sample using Marmur and Doty equation, compare the
experimental Tm with theoretical Tm of the DNA sample
Chapter 1 Solutions
ACHIEVE:INTRO TO GENETIC ANALYSIS 1TERM
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- 2) When DNA is placed in distilled water, which is pH 7.0, it denatures (i.e., the two strands separate). The pH inside a cell is generally 7.2-7.5, depending on the organism, but DNA is generally double-stranded under physiological conditions. Briefly explain, in your own words, why DNA denatures when placed in distilled water but not when it is inside a cell. [Reminder: the pKa for the phosphate groups in the sugar-phosphate backbone of a strand of DNA is 2.14]arrow_forwardHydrolysis of the N-glycosyl bond between deoxyribose and a purine base in DNA creates an apurinic (AP) site. An AP site is more thermodynamically destabilizing to a DNA molecule than is a mismatched base pair. Examine the structure of an AP site. HN H₂N N 0 Guanine -O-P-O-CH₂O. H₂N H HN H H H Hod H ofo -0- Guanosine residue (in DNA) -0-CH₂ H H H Apurinic residue H OH Harrow_forwardAssume the energy of hydrogen bonds per base pair to be 5.86 kJ•mol-1. Given two complementary strands of DNA containing 145 base pairs each, calculate the ratio of two separate strands to hydrogen-bonded double helix in solution at 319 K. ratio = .283arrow_forward
- The melting temperature Tm of DNA can be predicted by calculation without actually measuring it. Calculate the Tm of the DNA double strand shown in (1) to (3), and discuss the results. The numbers in parentheses indicate the degree of polymerization of nucleotides.(1) A(10) + T(10), (2) A(15) + T(15), (3) G(10) + C(10)arrow_forwardThe two sides of the DNA double helix are connected by pairs of bases (adenine, thymine, cytosine, and guanine). Because of the geometric shape of these molecules, adenine bonds with thymine and cytosine bonds with guanine. The figure below shows the bonding of thymine and adenine. Each charge shown is +e or - e, and the H-N distance is 0.110 nm. (a) Calculate the net force that thymine exerts on adenine. Is it attractive or repulsive? To keep the calculations fairly simple, yet reasonable, consider only the forces due to the O- H-N and the N-H-N combinations, assuming that these two combinations are parallel to each other. Remember, however, that in the O-H-N set, the O- exerts a force on both the H+ and the N-, and likewise along the N–H-N set. (b) Calculate the force on the electron in the hydrogen atom, which is 0.0529 nm from the proton. Then compare the strength of the bonding force of the electron in hydrogen with the bonding force of the adenine-thymine molecules (H (H (H)…arrow_forwardIf a DNA double helix contains 28% T nucleotides, then what is the percentage of A nucleotides?arrow_forward
- The estimated half-life for P-O bonds is 1.3 x 105 a (a = annum = year). Approximately 109 such bonds are present in a strand of DNA. How long (in terms of its half life) would a single strand of DNA survive with NO cleavage (in the absence of DNA repair enzymes)? Ans: 3067 yearsarrow_forwardCalculate the weight in grams of a double-helical DNA molecule stretching from the Earth to the Moon (320000 km). Assume that the DNA double helix weighs 1 x 10-18 g per 1000 nucleotide pairs and that each base pair extends 3.4 Å weight:arrow_forwardIf the GC content of a DNA molecule is 60%, what are the molar percentages of the four bases (G, C, T, A)?arrow_forward
- The two sides of the DNA double helix are connected by pairs of bases (adenine, thymine, cytosine, and guanine). Because of the geometric shape of these molecules, adenine bonds with thymine and cytosine bonds with guanine. The figure (Figure 1) shows the thymine-adenine bond. Each charge shown is ±e, and the H−N distance is 0.110 nm . Calculate the net force that thymine exerts on adenine. To keep the calculations fairly simple, yet reasonable, consider only the forces due to the O−H−N and the N−H−N combinations, assuming that these two combinations are parallel to each other. Remember, however, that in the O−H−N set, the O− exerts a force on both the H+ and the N−, and likewise along the N−H−N set. Express your answer in newtons. Is the net force attractive or repulsive?arrow_forwardDNA in the form of a double helix must be associated with cations, usually Mg²+ . Why is this requirement the case?arrow_forwardIf the G+C content of a sample of DNA is 46%, what are the proportions of all four nucleotides?arrow_forward
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