1. What is the difference between the major and minor grooves of double-stranded DNA?
The deep, wide groove made by the truns in double-stranded DNA constitutes the major groove. The shallow, narrow groove between the anti-parallel single strand of DNA makes up the minor groove.
2. A new virus is discovered, the genome of which is found to be 28% A, 23% T, 24% C, and 25% G. What does this tell you about the genome of the virus?
The virus must have as its genome a single-stranded DNA molecule (at least one), because [A]+[G] is not equal to [T]+[C]
3. In a double-stranded DNA molecule, what is the relationship between [A]+[G] and [C]+[T], and between [A]+[T] and [G]+[C]?
In a double-stranded molecule, [A]+[G] = [T]+[C]. The relationship between [A]+[T] and [G]+[C] varies from molecule to molecule.
4. In what circumstances does a double-stranded DNA molecule form an A helix? a B helix? a Z helix?
The B helix is considered to be the common form of DNA, but DNA forms an A helix under conditions of dehydration. AZ helix is favored by segments with alternating Gs and Cs
5. Could a supercoiled DNA molecule be formed by:
(a) joining the ends of a linear DNA molecule and twisting the resulting circle?
(b) twisting the ends of a linear DNA molecule and then linking the ends together?
(c) linking together the ends of a linear DNA molecule?
(a) No-There would be nothing to prevent the circle from untwisting.
(b) Yes-this would form a supercoil
(c) G; No-this would merely form a relaxed circle.
6. What noncovalent interactions are involved in maintaining the double-helical conformation of DNA?
Hydrophobic and hydrophilic properties of the bases and phosphate groups, respectively, and hydrogen bonding between the base of a base pair.
7. Why are salt concentration and temperature important to the renaturation of DNA?
The salt concentration must be high enough to neutralize the mutually repulsive negative charges of the phosphate groups, and the temperature
8. What would happen if double-stranded DNA were placed in distilled water?
With no cations to complex with the phosphate groups, the repulsion among them would be great enough to denature the DNA.
9. Suppose that a nonsupercoiled DNA molecule is composed of 4,800 base pairs. How many helical turns are present? How long is the linear, double-helical form of this molecule?
480 turns of the helix are present (4,800 bases at 10 bases per turn). The molecule would be 1.632 um long (480 turnsX34A/turn)
10. Could an exonuclease remove nucleotides from a circular DNA molecule?
No, there would be no free ends to the molecule.
1. The DNA molecules below are denatured and then allowed to reanneal. Which of the two is least likely to re-form the original structure? What would prevent that molecule from doing so?
(a) would be least likely to re-form the original structure, as it could have extensive intrastrand base pairing.
2. Which of the two molecules shown above would have the highest Tm? Why? Which would require a higher temperature for renaturation?
(a) would require a higher temperature fro reannealing (relative to its Tm)
(b) Would have the highest Tm, as it has the highest G+C content.
3. The following gel pattern was obtained in an attempt to sequence a DNA molecule using the Sanger method. What is the sequence of the DNA molecule in question?
4. Suppose, by mistake, too much dideoxy T was used in the “T reaction mixture” for the gel described in the previous question. How would the bands in the T lane appear?
With too much ddT, chain termination would occur abruptly, and, thus, the fragments would be shorter and found toward the bottom of the gel.
5. Which of the following types of RNA would likely be more stable (i.e., resistant to nuclease digestion) in the living cell: ribosomal, mRNA, or tRNA?
Ribosomal RNA. It is complexed with several dozen proteins to form a compact structure that is not easily attacked by RNase.
6. The melting curve below was obtained from a solution of DNA. What does this curve tell you about the composition of the solution?
The solution contained a mixture of copies of two different DNA molecules. One type had a considerably higher G+C content than the other.
1. What features of the DNA double helix facilitate its replication? What features might make its replication complicated?
2. In what ways does RNA represent the ideal molecule for converting the information encoded in a nucleotide sequence into the structural and catalytic macromolecules of a cell?
3. With modern DNA sequencing techniques it is now feasible to sequence all the DNA in a human cell. Social, moral, and ethical considerations can, however, be raised. Should such a major sequencing endeavor nevertheless be encouraged?