Chapter 33

\(A^{\prime \prime} t^{\prime \prime}\) instead of an \(^{\prime \prime \prime} s^{\prime \prime} ?\) Differentiate between a nucleoside and a nucleotide.

A lovely pair. What is a Watson-Crick base pair?

Almost like base pairs. Match each term with its description. (a) Base stacking__________ (b) B-DNA (c) A-DNA__________ (d) Z-DNA__________ (e) Topoisomers__________ (f) Supercoiling__________ (g) Histone__________ (h) Chromatin__________ (i) Nucleosome__________ (j) Nucleosome core particle__________ 1\. DNA molecules with the same sequence but differ in coiling 2\. DNA in a left-handed helix 3\. Twisting of the axis of a DNA helix into a superhelix 4\. Constitute half the mass of a chromosome 5\. Composed of 200 base pairs of DNA and 8 histones 6\. Stabilization of the double helix due to van der Waals forces 7\. Results from extensive digestion of chromatin by DNAse 8\. Most common form of DNA 9\. DNA and associated proteins 10\. Form of DNA found under dehydrating conditions

Chargaff rules! Biochemist Erwin Chargaff was the first to note that, in DNA, \([\mathrm{A}]=[\mathrm{T}]\) and \([\mathrm{G}]=[\mathrm{C}],\) 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.

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

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

Complements. Write the complementary sequence (in the standard \(5^{\prime} \rightarrow 3^{\prime}\) notation) for (a) GATCAA, (b) TCGAAC, (c) ACGCGT, and (d) TACCAT.

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

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

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

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

Lost DNA. The DNA of a deletion mutant of \(\lambda\) bacteriophage has a length of \(15 \mu \mathrm{m}\) instead of \(17 \mu \mathrm{m}\). How many base pairs are missing from this mutant?

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.

Overcharged. DNA in the form of a double helix must be associated with cations, usually \(\mathrm{Mg}^{2+} .\) Why is this requirement the case?

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

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 \(200 \mathrm{bp}\) 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?

Around we go. Assuming that 145 base pairs of DNA wrap around the histone octamer 1\(^{3 / 4}\) times, estimate the radius of the histone octamer. Assume 3.4 Ä 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.

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.

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 \(\left(2^{2}=4\right) .\) Thus, a strand of 5100 nucleotides corresponds to \(2 \times 5100=\) 10,200 bits, or 1275 bytes \((1 \text { byte }=8\) 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.

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

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