Lecture 4

Question 1

What is a genome

Answer 1

Entire haploid set of genetic information.

Question 2

Describe the structure of B DNA including the diameter and no of base pairs per turn

Answer 2

2 polynucleotide chains in opposite directions, regular right handed double helix, diameter of 2nm and complete turn every 3.4nm, 10.5 base pairs per every turn of the helix

Question 3

How does supercoiling occur?

Answer 3

Additional turns are introduced into the DNA double helix (+ supercoiling) or removed from the double helix (- supercoiling)

Question 4

Define L

Answer 4

linking number

number of times the 2 strands of the double helix of a closed molecule cross each other when in a plane

Question 5

What does the protein component of the E. Coli nucleoid include?

Answer 5

DNA gyrase
DNA topoisomerase I
these maintain the supercoiled state of the DNA

Question 6

How does HU work

Answer 6

forms tetramers around which the DNA is wound, in approximately units of 60bp.

Question 7

What is the 3 ways HGT occurs

Answer 7

• Genomic islands
• Encoded on a prophage
• Transposable genetic elements

Question 8

What is a replicon

Answer 8

A DNA molecule or sequence with a functional origin of replication. Basic unit of replication

Question 9

Explain the cell cycle and replication in E Coli

Answer 9

has a single origin of replication (OriC)

bidirectional replication leading to a theta structure

Question 10

Describe the structure of OriC

Answer 10

245bp long and contains:
4/5 9bp sequence in RHS
3 copies of an AT rich 13bp sequence in LHS
14 copies of GATC

Question 11

What does Dam methylase do?

Answer 11

Methylates adenine residues GATC motifs in OriC. Replication only initiates if all 14 GATC are methylated

Question 12

Where is hemi-methylated DNA put?

Answer 12

Sequestered to membrane site and isn’t available for replication

Question 13

What are the two types of non-homologous recombination?

Answer 13

Transposition

Site specific recombination

Question 14

What is the activity of RecBCD? (5)

Answer 14

ssDNA exonuclease (5' to 3' and 3' to 5')
ssDNA endonuclease
dsDNA exonuclease
DNA dependent ATPase
DNA helicase

Question 15

When RecBCD encounters a chi site what happens?

Answer 15

3’ to 5’ exonuclease activity inhibited
5’ to 3’ exonuclease activity is stimulated.
Helicase activity is unaffected
RecBCD thus produces a ssDNA tail with a 3’ end and RecA binds to the ssDNA tail