CH 600

Nucleic Acids Problem Set

November 2014

1. Give the name of the base, the ribonucleoside or deoxyribonucleoside, and the ribonucleoside
triphosphate for A, G, C, T, and U.

2. Give the sequence on the opposite strand for ACGTAT, AGATCT, and ATGGTA (all read 5' l 3').
The sequence on the opposite strand for each of the following (all read 5 -> 3) is ACGTAT TGCATA AGATCT TCTAGA
ATGGTA TACCAT.

3.

(a) Is it biologically advantageous that DNA is stable? Why or why not? (b) Is it biologically
advantageous that RNA is unstable? Why or why not?

(a) Defi nitely yes! If there is anything that you dont want falling apart, its your storehouse of genetic instructions. (Compare
the effectiveness of a computer if all the *.exe fi les were deleted.)
(b) In the case of messenger RNA, yes. The mRNA is the transmitter of information for protein synthesis, but it is needed
only as long as a particular protein is needed. If it were long-lived, the protein would continue to be synthesized even when not needed;
this would waste energy and could cause more direct detrimental effects. Thus, most mRNAs are short-lived (minutes); if more protein
is needed, more mRNA is made.

4. What is the difference between B-DNA and Z-DNA? In what naturally occurring nucleic acids would
you expect to find A-form helices, B-form helices, Z-form helices, nucleosomes, and circular DNA?
B-DNA is a right-handed helix with specifi ed dimensions (10 base pairs per turn, signifi cant differences between major and
minor groove, etc.). Z-DNA is a left-handed double helix with different dimensions (12 base pairs per turn, similar major and minor
grooves, etc.).

5. Define supercoiling, positive supercoil, topoisomerase, and negative supercoil. If circular B-DNA is
positively supercoiled, will these supercoils left- or right-handed? Briefly describe the structure of
chromatin.
Supercoiling refers to twists in DNA over and above those of the double helix. Positive supercoiling refers to an extra twist in
DNA caused by overwinding of the helix before sealing the ends to produce circular DNA. A topoisomerase is an enzyme that induces a
single-strand break in supercoiled DNA, relaxes the supercoiling, and reseals the break. Negative supercoiling refers to unwinding of
the double helix before sealing the ends to produce circular DNA. Positive supercoils in circular DNA will be left-handed. Chromatin is
the complex consisting of DNA and basic proteins found in eukaryotic nuclei (see Figure 9.16).

6. What is the complete base composition of a double- stranded eukaryotic DNA that contains 22%
guanine?
The percentage of cytosine equals that of guanine, 22%. This DNA thus has a 44% GC content, implying a 56% AT content.
The percentage of adenine equals that of thymine, so adenine and thymine are 28% each.

7. Why does DNA with a high A/T content haven a lower transition temperature, Tm, than DNA with a
high G/Ccontent?
AT base pairs have two hydrogen bonds, whereas GC base pairs have three. It takes more energy and higher temperature
to disrupt the structure of DNA rich in GC base pairs.

8. Would you expect mRNA or rRNA to be degraded more quickly in the cell? Why?
Turnover of mRNA should be rapid to ensure that the cell can respond quickly when specifi c proteins are needed. Ribosomal
subunits, including their rRNA component, can be recycled for many rounds of protein synthesis. As a result, mRNA is degraded more
rapidly than rRNA.

9. What is the purpose of small nuclear RNA? What is an snRNP?

Small nuclear RNA (snRNA) is found in the eukaryotic nucleus and is involved in splicing reactions of other RNA types. An
snRNP is a small nuclear ribonucleoprotein particle. A complex of small nuclear RNA and protein catalyzes splicing of RNA.

10. What is RNA interference?

RNA interference is the process by which small RNAs prevent the expression of genes.

11. Which type of RNA is the biggest? Which is the smallest? Which type of RNA has the least amount of
secondary structure?

Ribosomal RNA (rRNA) is the largest. Transfer RNA (tRNA) is the smallest. Messenger RNA (mRNA) has the least amount of
secondary structure (hydrogen bonding).

12. Why does the absorbance increase when a DNA sample unwinds?
The bases in a double-stranded chain are partially hidden from the light beam of a spectrophotometer by the other bases in
close proximity, as though they were in the shadow of the other bases. When the strands unwind, these bases become exposed to the
light and absorb it; therefore, the absorbance increases.

13. Would you expect tRNA or mRNA to be more extensively hydrogen bonded? Why?
More extensive hydrogen bonding occurs in tRNA than in mRNA. The folded structure of tRNA, which determines its binding to
ribosomes in the course of protein synthesis, depends on its hydrogen-bonded arrangement of atoms. The coding sequences of mRNA
must be accessible to direct the order of amino acids in proteins and should not be rendered inaccessible by hydrogen bonding.

14. Explain briefly what happens to eukaryotic mRNA before it can be translated to protein.

Eukaryotic mRNA is initially formed in the nucleus by transcription of DNA. The mRNA transcript is then spliced to remove
introns, a poly-A tail is added at the 3 end, and a 5-cap is put on. This is the fi nal mRNA, which is then transported, in most cases, out
of the nucleus for translation by the ribosomes.

15. Explain why a 50S ribosomal subunit and a 30S ribosomal subunit combine to form a 70S subunit,
instead of an 80S
The numbers 50S, 30S, etc. refer to a relative rate of sedimentation in an ultracentrifuge and cannot be added directly. Many
things besides molecular weight infl uence the sedimentation characteristics, such as shape and density.