1. Bacterial genomes

Question 1

What are 3 flexibilities of B form DNA?

Answer 1

Number of base pairs per turn of the helix can be altered
Helix in the cell is not straight, coiled in 3D space
Certain sequence features where bends occur

Question 2

How is torsional stress by supercoiling accommodated?

Answer 2

1. formation of superhelices

2. altering the number of base pairs per helix turn

Question 3

Define linking number (L)

Answer 3

the total number of times the two strands of a double helix of a closed molecule cross each other when constrained to lie on a plane

Question 4

How do type I topoisomerases alter L and name one example

Answer 4

break one strand, pass the other strand through the gap and seal the break. Change L by +- 1
Topoisomerase I of E. coli

Question 5

How do type II topoisomerases alter L and name one example

Answer 5

break both strands, pass another part of the helix through the gap. Change L by + - 2
DNA gyrase of E.coli

Question 6

What does the protein component of the E.coli nucleoid contain?

Answer 6

DNA gyrase and DNA topoisomerase I

A set of at least 4 proteins, HU is most abundant

Question 7

Name 4 toxins, the prophage they are encoded by, their host, and the disease caused

Answer 7

1. Diptheria toxin, beta, C. diptheriae, diptheria.
2. Shiga toxin, H-19B, E.coli, food poisoning/HUS
3. Neurotoxin, C1, C.botulinum, botulism
4. Cholera toxin, CTX, V. cholerae, cholera.

Question 8

What are two basic features that link the cell cycle and replication?

Answer 8

1. Initiation of replication commits the cell to a subsequent division
2. Cell division cannot occur until the round of replication associated with a particular initiation has been completed.

Question 9

What controls whether or not a round of replication is initiated in E. coli?

Answer 9

Dam methylase - methylates adenine residues in GATC sequences
At iniation, the 14 GATC copies in OriC are methylated

Question 10

Which subgroup of Ters in E.coli can arrest the clockwise moving fork?

Answer 10

TerB C F G J

Question 11

Which subgroup of Ters in E.coli can arrest the anticlockwise moving fork?

Answer 11

Ter A D E I H

Question 12

How is a fork arrested from only one direction?

Answer 12

Ter sites bind a Tus protein, which halts a replication fork headed in ONE direction only

Question 13

What is the difference between homologous and non homologous recombination?

Answer 13

Homologous - the two recombining sequences have extensive sequence similarity
Non-homologous - lack similarity

Question 14

What are the two types of non-homologous recombination?

Answer 14

1. transposition

2. te-specific recombination

Question 15

What are the 6 key steps of homologous recombination?

Answer 15

1. alignment
2. cleavage
3. invasion
4. branch migration
5. isomerisation
6. resolution

Question 16

What is cleavage catalysed by in E.coli?

Answer 16

RecBCD endonuclease

Question 17

What is branch migration catalysed by in E.coli?

Answer 17

RuvAB proteins

Question 18

What is resolution catalysed by?

Answer 18

RuvC

Question 19

What happens when RecBCD encounters a CHI(X) site?

Answer 19

3-5 exonuclease activity is inhibited and 5-3 exonuclease activity is stimulated