7. DNA and Chromosome Structure

One of the most common spontaneous lesions that occurs in DNA under physiological conditions is the hydrolysis of the amino group of cytosine, converting the cytosine to uracil. What would be the effect on DNA structure of a uracil group replacing cytosine?

In some organisms, cytosine is methylated at carbon 5 of the pyrimidine ring after it is incorporated into DNA. If a 5-methyl cytosine molecule is then hydrolyzed, as described in Problem 28, what base will be generated?

Consider the drawing of a dinucleotide below. Suppose that the molecule was cleaved with the enzyme spleen phosphodiesterase, which breaks the covalent bond connecting the phosphate to C-5'. After cleavage, to which nucleoside is the phosphate now attached (A or T)?

Consider the drawing of a dinucleotide below. Is the arrow closest to the 5' or the 3' end?

Consider the drawing of a dinucleotide below. Is it DNA or RNA?

A primitive eukaryote was discovered that displayed a unique nucleic acid as its genetic material. Analysis provided the following information:About 75 percent of the sugars are deoxyribose, while 25 percent are ribose. Postulate a model for the structure of this molecule that is consistent with the foregoing observations.

A primitive eukaryote was discovered that displayed a unique nucleic acid as its genetic material. Analysis provided the following information:Base-composition analysis reveals four bases in the following proportions:Adenine = 8%Guanine = 37%Xanthine = 37%Hypoxanthine = 18%

Newsdate: March 1, 2030. A unique creature has been discovered during exploration of outer space. Recently, its genetic material has been isolated and analyzed. This material is similar in some ways to DNA in its chemical makeup. It contains in abundance the 4-carbon sugar erythrose and a molar equivalent of phosphate groups. In addition, it contains six nitrogenous bases: adenine (A), guanine (G), thymine (T), cytosine (C), hypoxanthine (H), and xanthine (X). These bases exist in the following relative proportions:A =T = H and C = G = XX-ray diffraction studies have established a regularity in the molecule and a constant diameter of about 30 Å. Together, these data have suggested a model for the structure of this molecule.Given the constant diameter of 30 Å, do you think that either (i) both H and X are purines or both pyrimidines, or (ii) one is a purine and one is a pyrimidine?

Newsdate: March 1, 2030. A unique creature has been discovered during exploration of outer space. Recently, its genetic material has been isolated and analyzed. This material is similar in some ways to DNA in its chemical makeup. It contains in abundance the 4-carbon sugar erythrose and a molar equivalent of phosphate groups. In addition, it contains six nitrogenous bases: adenine (A), guanine (G), thymine (T), cytosine (C), hypoxanthine (H), and xanthine (X). These bases exist in the following relative proportions:A =T = H and C = G = XX-ray diffraction studies have established a regularity in the molecule and a constant diameter of about 30 Å. Together, these data have suggested a model for the structure of this molecule.What base-pairing properties must exist for H and for X in the model?

Newsdate: March 1, 2030. A unique creature has been discovered during exploration of outer space. Recently, its genetic material has been isolated and analyzed. This material is similar in some ways to DNA in its chemical makeup. It contains in abundance the 4-carbon sugar erythrose and a molar equivalent of phosphate groups. In addition, it contains six nitrogenous bases: adenine (A), guanine (G), thymine (T), cytosine (C), hypoxanthine (H), and xanthine (X). These bases exist in the following relative proportions:A =T = H and C = G = XX-ray diffraction studies have established a regularity in the molecule and a constant diameter of about 30 Å. Together, these data have suggested a model for the structure of this molecule.Propose a general model of this molecule. Describe it briefly.

A sufficient amount of a small DNA fragment is available for dideoxy sequencing. The fragment to be sequenced contains 20 nucleotides following the site of primer binding:5'-ATCGCTCGACAGTGACTAGC-[primer site]-3'Dideoxy sequencing is carried out, and the products of the four sequencing reactions are separated by gel electrophoresis. Draw the bands you expect will appear on the gel from each of the sequencing reactions.

You are participating in a study group preparing for an upcoming genetics exam, and one member of the group proposes that each of you draw the structure of two DNA nucleotides joined in a single strand. The figures are drawn and exchanged for correction. You receive the accompanying diagram to correct:Draw this single-stranded segment correctly.

You are participating in a study group preparing for an upcoming genetics exam, and one member of the group proposes that each of you draw the structure of two DNA nucleotides joined in a single strand. The figures are drawn and exchanged for correction. You receive the accompanying diagram to correct:What is wrong with the way the nucleotides are joined?

You are participating in a study group preparing for an upcoming genetics exam, and one member of the group proposes that each of you draw the structure of two DNA nucleotides joined in a single strand. The figures are drawn and exchanged for correction. You receive the accompanying diagram to correct:Identify and correct at least five things that are wrong in the depiction of each nucleotide.

Electrophoresis is an extremely useful procedure when applied to analysis of nucleic acids as it can resolve molecules of different sizes with relative ease and accuracy. Large molecules migrate more slowly than small molecules in agarose gels. However, the fact that nucleic acids of the same length may exist in a variety of conformations can often complicate the interpretation of electrophoretic separations. For instance, when a single species of a bacterial plasmid is isolated from cells, the individual plasmids may exist in three forms (depending on the genotype of their host and conditions of isolation): superhelical/supercoiled (form I), nicked/open circle (form II), and linear (form III). Form I is compact and very tightly coiled, with both DNA strands continuous. Form II exists as a loose circle because one of the two DNA strands has been broken, thus releasing the supercoil. All three have the same mass, but each will migrate at a different rate through a gel. Based on your understanding of gel composition and DNA migration, predict the relative rates of migration of the three DNA structures mentionedabove.