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3 Information: genes and genomes

(d) Synthesis of the lagging strand. (e) Replacing RNA primers in Okazaki fragments. (f) Sealing ‘nicks’ in the sugar phosphate backbone to link Okazaki fragments. 5. What is the accuracy of DNA replication with and without proof reading and mismatch repair?

DNA-binding proteins involved in gene transcription can bind to specific DNA sequences by recognizing these characteristic chemi cal groupings of different base pairs. For each base pair, identify chemical groups that proteins can recognize in the major and minor groove. You should be able to identify at least one example of each of the following features: (a) Hydrogen bond acceptor. (b) Hydrogen bond donor. (c) Non-polar hydrogen atom that cannot participate in hydrogen bonds. (d) Methyl group. What impact could the degree of chromatin compaction (euchro matin versus heterochromatin) have on accessibility of these groups to proteins? 12. Meselson and Stahl carried out the following experiment that dem onstrated that DNA replication is a semiconservative process: The DNA of E. coli was ‘labelled’ by growing the bacteria in a medium in which the nitrogen source was 15 N so that both DNA strands were ‘heavy’. The bacteria were then transferred to a medium containing 14 N so that all subsequent DNA chains would be ‘light’. After three generations (i.e. three rounds of replication) the DNA was analysed by density gradient centrifugation, which separates the DNA molecules according to their weight. Which of the following density gradient patterns shown in Figure Q3.12 would be observed? Explain your answer. More information on Meselson and Stahl’s experiment can be found in Further reading.

Apply the concepts 6. Compare and contrast the structures of DNA and RNA.

7. James Watson and Francis Crick’s 1953 publication A Structure for Deoxyribose Nucleic Acid states: ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.’ Explain what this statement refers to. 8. Explain why looping of the lagging strand template is needed for DNA replication. 9. While DNA Pol I and III in prokaryotes can both catalyse the synthe sis of DNA, DNA Pol I also has both 5 ′→ 3 ′ exonuclease, and 3 ′→ 5 ′ exonuclease activity, whereas DNA Pol III has only 3 ′→ 5 ′ exonucle ase activity. Explain how the different exonuclease activities reflect the functions of the two enzymes. 10. What are the main classes of repetitive DNA sequences found in the human genome? Why are some of these sequences referred to as ‘fossils’? Beyond the concepts 11. Figure Q3.11 illustrates the edges of C:G and A:T base pairs when viewed from the major and the minor grooves of a DNA molecule.

Minor groove

Minor groove

N H H

Cytosine

Guanine

Thymine

Adenine

O

H

O

N C

C

N

N

C C 1

C

N

3

3

H

N N H

1

C

C

N

C

H

H

C

N

N

N

C C

C C

C

C C

7

N 7

C

C

N

H

H

N

O

CH 3

O

N H

H

H

H

H

Major groove

Major groove

Figure Q3.11 Characteristic chemical groups are seen when DNA base pairs are viewed from either the major or the minor groove. For example, the minor groove of the G:C base pair contains N-3 of guanine, O-2 of cytosine and the amino group (–NH 2 ) attached to C-2 of guanine. Source : D. Papachristodoulou, A. Snape, W. H. Elliott and D. C. Elliott. Biochemistry and Molecular Biology .

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