Tutorial 1

Session 201405 Week 5

UDBB2203/UDBM2204 Molecular Biology Tutorial 1 1. If one strand of DNA has the sequence AACCGTATATA, write the sequence of the complementary strand using the standard convention.

2. DNA was extracted from cells of Staphylococcus and analyzed by based composition. It was found that 45% of the bases are cytosine. Determine the percentage of adenines in this DNA.

3. A stretch of double stranded DNA contains 8000 base pairs (bp), and its base composition is 58% (G + C). How many adenine residues are in this region of DNA?

4. RNA was extracted from tobacco mosaic virus (TMV) particles and found to contain 30% cytosine. With this information, is it possible to predict what percentage of the bases in TMV are adenines? If so, what percentage? If not, why not?

5. The nucleic acids from various viruses were extracted and examined to determine their base composition. Given the following results, what can you hypothesize about the physical nature of the nucleic acids from these viruses? (a) 40% A, 40% T, 10% G, and 10% C (b)

35% A, 15% T, 25% G, and 25% C

(c)

35% A, 30% U, 30% G, and 5% C

6. A 41.5 nm-long duplex DNA molecule in the B-conformation adopts the Aconformation upon dehydration. (a) What is the approximate number of base pairs of this duplex DNA?

(b) How long is the DNA when it adopts the A-conformation? 7. A diploid nucleus of Drosophila melanogaster contains about 3.4 x 108 nucleotide pairs. Assume (1) that the entire nuclear DNA is packaged in nucleosomes and (2) that an average internucleosome linker DNA is 60 nucleotide pairs, (a) how many nucleosomes would be present in a diploid nucleus of D. melanogaster.

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Session 201405 Week 5

(b)

8.

how many molecules of histones H2A, H2B, H3, and H4 would be required?

A duplex DNA molecule of B-form has the length of 50 µm. (a)

What is its approximate number of base pairs?

(b)

Upon dehydration this B-form DNA adopts an A-conformation. How long is it now in µm?

(c)

Assume that the entire DNA is packaged in nucleosomes and an average linker DNA is 60 nucleotide base-pairs. How many nucleosomes would be present? How many molecules of each histone H2A, H2B, H3 and H4 would be required?

9.

Explain why the melting temperature of a sample of double-helical DNA increases when the Na2+ concentration increases.

10.

What might you find in comparing the GC content of DNA from Thermus aquaticus and DNA from bacteria in a typical backyard pond? Explain your answer.

11.

A previously undiscovered single-celled organism was found living at a great depth on the ocean floor. Its nucleus contained only a single linear chromosome containing 6 x 106 base pairs of DNA coalesced with three types of histone-like proteins. (a) A short micrococcal nuclease digestion on this single linear chromosome yielded DNA fractions consisting of 500, 1000, 1500, and 2000 base pairs in length. Predict what these fractions represent. What conclusion can be drawn with regard to the nuclease digestion? (b)

The analysis of the individual nucleosome revealed that each unit contained one copy of each protein, and that the short linker DNA contained no protein bound to it. If the entire chromosome consists of nucleosomes (discounting any linker DNA), (i)

how many nucleosomes are there?

(ii)

how many proteins are needed to form them?

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