Chapter 4

Fill in the blanks to identify each substance as \(\begin{array}{ll}\text { _______a) A nucleobase } & \text { _______(d) A deoxyribonucleoside }\end{array}\) _______(b) A ribonucleoside \(\quad\)_______(e) A deoxyribonucleotide _______(c) A ribonucleotide _______(f) A dinucleotide Adenosine Cytidine \(5^{\prime}\)-monophos Guanine Thymine Deoxyguanosine

Base analysis of DNA from maize (corn) shows it to have 23 mole percent cytosine (moles per 100 moles total nucleotide). What are the percentages of the other three bases?

For some DNAs, it is possible to separate the two strands, after denaturation, in a CsCl gradient. (a) What property of any DNA determines where it will band in a \(\mathrm{CsCl}\) gradient? (b) What kind of DNA might have two strands that differ sufficiently in this property that they could be separated after denaturation?

Predict the structure of a cruciform that could be formed from this oligonucleotide. 5' GCAATCGTACGATTAGGGC 3' CGTTAGCATGCTAATCCCG

DNA from a newly discovered virus was purified, and UV light absorption was followed as the molecule was slowly heated. The absorbance increase at the melting temperature was only \(10 \%\). What does this result tell you about the structure of the viral DNA?

A circular double-stranded DNA molecule contains 4200 base pairs. In solution, the molecule is in a B-form helix, with about \(10.5\) base pairs per turn. The DNA circle has 12 superhelical turns. What is its superhelix density \(\boldsymbol{\sigma}\) ?

DNA polymerase requires both a template, to be copied, and a primer, which provides a 3 ' hydroxyl from which polymerase can extend. Yet, this molecule supports DNA polymerase activity. Explain. pTGACACAGGTTTAGCCCATCGATGGG-OH

(a) What two enthalpic factors stabilize DNA in double-helical form at low temperature? (b) What entropic factor destabilizes helical DNA at high temperature? (c) Why is the double-helical structure of DNA stabilized at moderate to high ionic strength?

(a) The plasmid pBR322 (4362 base pairs) was isolated and the circular DNA was found to be underwound, with a superhelix density \((\sigma)\) of \(-0.05\). How many superhelical turns does this molecule have? (b) Suppose that the molecule was overwound, also with a superhelix density of \(0.05\). How many superhelical turns would this molecule have?

In studying the mechanism of a particular enzyme, for which the cloned gene is available, you wish to change a putative active site histidine residue to a proline by site-directed mutagenesis. The His codon to be changed is \(5^{\prime}\)-CAC. You wish to change it to \(5^{\prime}-\mathrm{CCC}\), one of four Pro codons. The nucleotide sequence surrounding the His codon is \(5^{\prime}\)-CTGGAATCTCACTTTATCTGG-3'. Write the nucleotide sequence of an oligonucleotide (a 21-mer) that could force the conversion of the CAC codon to \(\mathrm{CCC}\) in a site-directed mutagenesis operation.