BIOLOGIA MOLEKULARNA – Seminarium

LISTA 1

DNA, RNA i przepływ informacji genetycznej

FIGURE 5.1

1. Which of the preceding structures in Figure 5.1

(a) contains ribose?

(g) contains a phosphodiester?

(b) contains deoxyribose?

(h) is a nucleoside?

(c) contains a purine?

(i) is a nucleotide?

(d) contains a pyrimidine?

(j) would be found in RNA?

(e) contains guanine?

(k) would be found in DNA?

(f) contains a phosphate monoester?

2. If a region of one strand of a Watson-Crick DNA double helix has the sequence ACGTAACC, what is the sequence of the complementary region of the other strand ?

3. Which of the following are characteristics of the Watson-Crick DNA double helix?

(a) The two polynucleotide chains are coiled about one another and about a common axis.

(b) Hydrogen bonds between A and C and between G and T help hold the two chains together.

(c) The helix makes one complete turn every 34 Å because each base pair is rotated by 36° with respect to adjacent base pairs and is separated by 3.4 Å from them along the helix axis.

(d) The purines and pyrimidines are on the inside of the helix and the phosphodiester linked backbones are on the outside.

(e) Base composition analyses of DNA duplexes isolated from many organisms show that the amounts of A and T

are equal as are the amounts of G and C.

(f) The sequence in one strand of the helix varies independently of that in the other strand.

BIOLOGIA MOLEKULARNA – Lista 1 – DNA, RNA i przepływ informacji genetycznej.

1

4. Match the appropriate characteristics in the right column with the structures of double strand or single-strand DNA.

(A) double-strand DNA

(1) is a rigid rod

(B) single-strand DNA

(2) shows a greater hyperchromic effect upon heating

(3) contains equal amounts of A and T bases

(4) may contain different amounts of C and G bases

(5) contains U rather than T bases

(6) may contain stem-loop structures

5. Purified duplex DNA molecules can be:

(a) linear.

(b) circular and supercoiled.

(c) linear and supercoiled.

(d) circular and relaxed, that is, not supercoiled.

6. The DNA in a bacterium is uniformly labeled with 15N, and the organism shifted to a growth medium containing 14N-labeled DNA precursors. After two generations of growth, the DNA is isolated and is subjected to density-gradient equilibrium sedimentation. What proportion of light-density DNA to intermediate-density DNA would you expect to find?

7. The genome of bacteriophage G4 is a small, single-strand circle of DNA. Replication of the circle is initiated when an RNA polymerase, a product of the dnaG gene of E. coli, synthesizes a small segment of RNA that binds to a unique sequence on the G4 chromosome. Initiation of G4 DNA synthesis does not occur in bacterial dnaG gene mutants, which have an inactive RNA polymerase. Suggest a function for the small segment of RNA.

8. You are provided with a long, single-strand DNA molecule having a base composition of C = 24.1%, G = 18.5%, T = 24.6%, and A = 32.8%; DNA polymerase; [α-32P]dATP (dATP with the innermost phosphate labeled), dCTP, dGTP, and dTTP; a short primer that is complementary to the single-strand DNA; and a buffer solution with Mg2+.

What is the base composition of the radiolabeled product DNA after the completion of one round of synthesis?

9. You are given two solutions containing different purified DNAs. One is from the bacterium P. aeruginosa and has a G + C composition of 68%, whereas the other is from a mammal and has a G + C composition of 42.5%.

(a) You measure the absorbance of ultraviolet light of each solution as a function of increasing temperature.

Which solution will yield the higher Tm value and why?

(b) After melting the two solutions, mixing them together, and allowing them to cool, what would you expect to happen?

(c) Would appreciable amounts of bacterial DNA be found associated in a helix with mammalian DNA? Explain.

BIOLOGIA MOLEKULARNA – Lista 1 – DNA, RNA i przepływ informacji genetycznej.

2

10. DNA polymerase activity requires:

(a) a template.

(b) a primer with a free 5’-hydroxyl group.

(c) dATP, dCTP, dGTP, and dTTP.

(d) ATP.

(e) Mg2+.

11. Answer the following questions about RNA.

(a) What is the name of the bond joining the ribonucleoside components of RNA to one another?

(b) Is this bond between the 2’- or the 3’-hydroxyl group of one ribose and the 5’- hydroxyl of the next?

(c) Intramolecular base pairs form what kinds of structures in RNA molecules?

(d) What bases pair with one another in RNA?

(e) What are the three major classes of RNA in a cell and which is most abundant?

12. Translation is involved in which of the following possible steps in the flow of genetic information?

(a) DNA to RNA

(b) RNA to DNA

(c) DNA to DNA

(d) RNA to protein

(e) protein to RNA

13. If you have samples of pure RNA and duplex DNA, how can you tell whether they have any complementary nucleotide sequences?

14. Which of the following are required for the DNA-dependent RNA polymerase reaction to produce a unique RNA transcript?

(a) ATP

(g) RNA

(b) CTP

(h) Mg2+

(c) GTP

(i) promoter sequence

(d) dTTP

(j) operator sequence

(e) UTP

(k) terminator sequence

(f) DNA

15. From the following nucleic acids, select those that appear during the infection of a cell with a retrovirus, for example, the AIDS virus, and place them in the order in which genetic information flows during the process of forming a new progeny virus.

(a) double-strand DNA-RNA helix in the cell

(b) single-strand RNA in the virus

(c) single-strand RNA in the cell

(d) double-strand DNA in the cell

(e) double-strand RNA in the virus

(f) double-strand RNA in the cell

16. Which of the following are characteristics or functions of tRNA?

(a) It contains a codon.

(b) It contains an anticodon.

(c) It can become covalently attached to an amino acid.

(d) It interacts with mRNA to stimulate transcription.

(e) It can have any of a number of different sequences.

(f) It serves as an adaptor between the information in mRNA and an individual amino acid.

BIOLOGIA MOLEKULARNA – Lista 1 – DNA, RNA i przepływ informacji genetycznej.

3

17. What is the minimum number of contiguous nucleotides in mRNA that can serve as a codon? Explain.

18. Explain why mitochondria can use a genetic code that is different from the standard code used in the nucleus.

19. Explain how genetic techniques and amino acid sequence analyses could be used to show the collinear relationship of a prokaryotic gene and the protein it encodes.

20. The following is a partial list of mRNA codons and the amino acids they encode: AGU = serine AGC = serine

AAU = asparagine AAC = asparagine

AUG = methionine AUA = isoleucine

Based on this list, which of the following statements are correct?

(a) The genetic code is degenerate.

(b) The alteration of a single nucleotide in the DNA directing the synthesis of these codons could lead to the substitution of a serine for an asparagine in a polypeptide.

(c) The alteration of a single nucleotide in the DNA directing the synthesis of these codons would necessarily lead to an amino acid substitution in the encoded polypeptide.

(d) A tRNA with the anticodon ACU would be bound by a ribosome in the presence of one of these codons.

21. The codons UAA, UAG, and UGA are signals for chain termination in protein synthesis because none of these codons are read by tRNA molecules. These codons are normally found at the ends of coding sequences for proteins. However, single-base mutations in certain codons can also cause premature termination of the protein chain.

(a) Which codons can be converted to the chain-termination codon UAA by a single base change?

(b) Suppose a mutation creates a UAA codon that is three codons away from the 3’ end of the normal mRNA coding sequence. Why might you assume that the prematurely terminated protein might still be functional?

BIOLOGIA MOLEKULARNA – Lista 1 – DNA, RNA i przepływ informacji genetycznej.

4