1.  A “t” instead of an “s”? Differentiate between a nucleoside and a nucleotide. ✓ 1

2.  A lovely pair. What is a Watson–Crick base pair? ✓ 1

3.  Almost like base pairs. Match each term with its description.

4.  Chargaff rules! Biochemist Erwin Chargaff was the first to note that, in DNA, [A] = [T] and [G] = [C], equalities now called Chargaff’s rule. With the use of this rule, determine the percentages of all the bases in DNA that is 20% thymine. ✓ 1

5.  But not always. A single strand of RNA is 20% U. What can you predict about the percentages of the remaining bases?

6.  Size matters. Why are GC and AT the only base pairs permissible in the double helix? ✓ 1

7.  Complements. Write the complementary sequence (in the standard 5′ → 3′ notation) for (a) GATCAA, (b) TCGAAC, (c) ACGCGT, and (d) TACCAT.

8.  Compositional constraint. The composition (in mole-fraction units) of one of the strands of a double-helical DNA molecule is [A] = 0.30 and [G] = 0.24. (a) What can you say about [T] and [C] for the same strand? (b) What can you say about [A], [G], [T], and [C] of the complementary strand? ✓ 1

9.  Inside out. Single-stranded DNA absorbs more ultraviolet light than does double-stranded DNA. Suggest why this might be the case.

10.  Axial ratio. What is the axial ratio (length:diameter) of a DNA molecule 20 μm long?

11.  Strong, but not strong enough. Why does heat denature, or melt, DNA in solution?

12.  Coming and going. What does it mean to say that the DNA strands in a double helix have opposite directionality?

13.  Lost DNA. The DNA of a deletion mutant of λ bacteriophage has a length of 15 μm instead of 17 μm. How many base pairs are missing from this mutant?

14.  An unseen pattern. What result would Meselson and Stahl have obtained if the replication of DNA were conservative (i.e., the parental double helix stayed together)? Give the expected distribution of DNA molecules after 1.0 and 2.0 generations for conservative replication.

15.  Overcharged. DNA in the form of a double helix must be associated with cations, usually Mg²⁺. Why is this requirement the case? ✓ 2

16.  Packing it in. Does packing DNA into nucleosomes account for the compaction found in a metaphase chromosome (the most condensed form of a chromosome)? ✓ 2

17.  Resistance is futile. Chromatin viewed with the electron microscope has the appearance of beads on a string. Partial digestion of chromatin with DNAse yields the isolated beads, containing fragments of DNA approximately 200 bp in length bound to the eight histones. More extensive digestion yields a reduced DNA fragment of 145 bp bound to the histone octamer. Why is more extensive digestion required to yield the 145-bp fragment? ✓ 2

18.  Charge neutralization. Given the histone amino acid sequences illustrated here, estimate the charge of a histone octamer at pH 7. Assume that histidine residues are uncharged at this pH value. How does this charge compare with the charge on 150 base pairs of DNA? ✓ 2

19.  Around we go. Assuming that 145 base pairs of DNA wrap around the histone octamer 1¾ times, estimate the radius of the histone octamer. Assume 3.4 Å per base pair, and simplify the calculation by assuming that the wrapping is in two rather than three dimensions and neglecting the thickness of the DNA. ✓ 2

20.  3 is greater than 2. The illustration below graphs the relation between the percentage of GC base pairs in DNA and the melting temperature. Suggest a possible explanation for these results.

21.  Blast from the past. The illustration below is a graph called a C₀t curve (pronounced “cot”). The y axis shows the percentage of DNA that is double stranded. The x axis is the product of the concentration of DNA and the time required for the double-stranded molecules to form. Explain why the mixture of poly A and poly U and the three DNAs shown vary in the C₀t value (the point at which half the molecules are double stranded). MS-2 and T4 are bacterial viruses (bacteriophages) with genome sizes of 3569 and 168,903 bp, respectively. The E. coli genome is 4.6 × 10⁶ bp.

22.  Salt to taste. The graph below shows the effect of salt concentration on the melting temperature of bacterial DNA. How does salt concentration affect the melting temperature of DNA? Account for this effect.

23.  Uniqueness. The human genome contains 3 billion base pairs arranged in a vast array of sequences. What is the minimum length of a DNA sequence that will, in all probability, appear only once in the human genome? You need consider only one strand and may assume that all four nucleotides have the same probability of appearance.

24.  Information content. (a) How many different 8-mer sequences of DNA are there? (Hint: There are 16 possible dinucleotides and 64 possible trinucleotides.) We can quantify the information-carrying capacity of nucleic acids in the following way. Each position can be one of four bases, corresponding to two bits of information (2² = 4). Thus, a strand of 5100 nucleotides corresponds to 2 × 5100 = 10,200 bits, or 1275 bytes (1 byte = 8 bits). (b) How many bits of information are stored in an 8-mer DNA sequence? In the E. coli genome? In the human genome? (c) Compare each of these values with the amount of information that can be stored on a 700 megabytes CD.

25.  A tougher strand. RNA is readily hydrolyzed by alkali, whereas DNA is not. Why?

26.  A picture is worth a thousand words. Write a reaction sequence showing why RNA is more susceptible to nucleophilic attack than DNA.