A t instead of an s? Differentiate between a nucleoside and a nucleotide.

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

Chargaff rules! Biochemist Erwin Chargaff was the first to note that, in DNA, [A] = [T] and [G] = [C], equalities now called Chargaff’s rule. Using 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?

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

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?

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

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

Uniqueness. The human genome contains 3 billion nucleotides 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.

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

All for one. If the forces—hydrogen bonds and stacking forces—holding a helix together are weak, why is it difficult to disrupt a double helix?

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

Not quite from A to Z. Describe the three forms that a double helix can assume.

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?

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

Guide and starting point. Define template and primer as they relate to DNA synthesis.

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.

Which way? Explain, on the basis of nucleotide structure, why DNA synthesis proceeds in the 5′-to-3′ direction.

Tagging DNA.

Finding a template. A solution contains DNA polymerase and the Mg²⁺ salts of dATP, dGTP, dCTP, and TTP. The following DNA molecules are added to aliquots of this solution. Which of them would lead to DNA synthesis?

Retrograde. What is a retrovirus and how does information flow for a retrovirus differ from that for the infected cell?

The right start. Suppose that you want to assay reverse transcriptase activity. If polyriboadenylate is the template in the assay, what should you use as the primer? Which radioactive nucleotide should you use to follow chain elongation?

Essential degradation. Reverse transcriptase has ribonuclease activity as well as polymerase activity. What is the role of its ribonuclease activity?

Virus hunting. You have purified a virus that infects turnip leaves. Treatment of a sample with phenol removes viral proteins. Application of the residual material to scraped leaves results in the formation of progeny virus particles. You infer that the infectious substance is a nucleic acid. Propose a simple and highly sensitive means of determining whether the infectious nucleic acid is DNA or RNA.

Mutagenic consequences. Spontaneous deamination of cytosine bases in DNA takes place at low but measurable frequency. Cytosine is converted into uracil by loss of its amino group. After this conversion, which base pair occupies this position in each of the daughter strands resulting from one round of replication? Two rounds of replication?

Information content.

Key polymerases. Compare DNA polymerase and RNA polymerase from E. coli in regard to each of the following features: (a) activated precursors, (b) direction of chain elongation, (c) conservation of the template, and (d) need for a primer.

Different strands. Explain the difference between the coding strand and the template strand in DNA.

Family resemblance. Differentiate among mRNA, rRNA and tRNA.

A code you can live by. What are the key characteristics of the genetic code?

Encoded sequences.

A tougher chain. 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.

Flowing information. What is meant by the phrase gene expression?

We can all agree on that. What is a consensus sequence?

A potent blocker. Cordycepin (3′-deoxyadenosine) is an adenosine analog. When converted into cordycepin 5′-triphosphate, it inhibits RNA synthesis. How does cordycepin 5′-triphosphate block the synthesis of RNA?

Silent RNA. The code word GGG cannot be deciphered in the same way as can UUU, CCC, and AAA, because poly(G) does not act as a template. Poly(G) forms a triple-stranded helical structure. Why is it an ineffective template?

Sometimes it is not so bad. What is meant by the degeneracy of the genetic code?

In fact, it can be good. What is the biological benefit of a degenerate genetic code?

To bring together as associates. Match the components in the right-hand column with the appropriate process in the left-hand column.

A lively contest. Match the components in the left-hand column with the appropriate process in the right-hand column.

Two from one. Synthetic RNA molecules of defined sequence were instrumental in deciphering the genetic code. Their synthesis first required the synthesis of DNA molecules to serve as templates. Har Gobind Khorana synthesized, by organic-chemical methods, two complementary deoxyribonucleotides, each with nine residues: d(TAC)₃ and d(GTA)₃. Partly overlapping duplexes that formed on mixing these oligonucleotides then served as templates for the synthesis by DNA polymerase of long, repeating double-helical DNA strands. The next step was to obtain long polyribonucleotide chains with a sequence complementary to only one of the two DNA strands. How did Khorana obtain only poly(UAC)? Only poly(GUA)?

Triple entendre. The RNA transcript of a region of T4 phage DNA contains the sequence 5′-AAAUGAGGA-3′. This sequence encodes three different polypeptides. What are they?

A new translation. A transfer RNA with a UGU anticodon is enzymatically conjugated to ¹⁴C-labeled cysteine. The cysteine unit is then chemically modified to alanine (with the use of Raney nickel, which removes the sulfur atom of cysteine). The altered aminoacyl-tRNA is added to a protein-synthesizing system containing normal components except for this tRNA. The mRNA added to this mixture contains the following sequence:

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5′–UUUUGCCAUGUUUGUGCU–3′

What is the sequence of the corresponding radiolabeled peptide?

A tricky exchange. Define exon shuffling and explain why its occurrence might be an evolutionary advantage.

From one, many. Explain why alternative splicing increases the coding capacity of the genome.

The unity of life. What is the significance of the fact that human mRNA can be accurately translated in E. coli?

Back to the bench. A protein chemist told a molecular geneticist that he had found a new mutant hemoglobin in which aspartate replaced lysine. The molecular geneticist expressed surprise and sent his friend scurrying back to the laboratory. (a) Why did the molecular geneticist doubt the reported amino acid substitution? (b) Which amino acid substitutions would have been more palatable to the molecular geneticist?

Eons apart. The amino acid sequences of a yeast protein and a human protein having the same function are found to be 60% identical. However, the corresponding DNA sequences are only 45% identical. Account for this differing degree of identity.

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

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 required to completely anneal. MS2 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.

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