2. Transposition etc

Question 1

What is a transposable genetic element?

Answer 1

Specific DNA sequences that can transfer copies of themselves to other parts of the same DNA molecule, other DNA molecules or alter their orientation within a DNA molecule

Question 2

What are the 7 general classes of transposable elements?

Answer 2

Insertion sequences and composite transposons
The Tn3 family 
transposon Tn7 and relatives
Gram positive transposons
Transposable phages
Inversion sequences

Question 3

which 3 proteins does Tn3 encode and what do they do?

Answer 3

TnpA and TnpR - involved in transposition

Bla - a beta lactamase - ampicillin resistance

Question 4

Tn3 transposes via a mechanism known as replicative transposition, what does this involve?

Answer 4

1. Formation of a cointegrate, catalysed by transposase

2. Recombination between the two res site, catalysed by resolvase

Question 5

4 examples of Single base changes

Answer 5

Replication errors due to keto-enol tautomerization
Deamination of cytosine to uracil
Incorporation of U rather than T during replication
Chemical modification of bases

Question 6

4 examples of Structural distortions

Answer 6

Single strand breaks
Covalent modification of bases e.g. alkylation
Removal of a base
Interstrand and intrastrand covalent bonds

Question 7

What are the 5 types of DNA repair?

Answer 7

Direct repair
Mismatch repair
Excision repair
Tolerance systems
Retrieval systems

Question 8

What is an example of direct repair?

Answer 8

Photoreactivation by deoxyribopyrimidine photolyase - 2 chromophores absorb light energy and splits the cyclobutane structure formed

Question 9

what is an enzyme involved in mismatch repair and what does it do?

Answer 9

Uracil DNA glycosidase - removes U base and makes AP site

Question 10

Which genes is repair endonuclease in excision repair encoded by?

Answer 10

uvr A, B, C

Question 11

What are the polymerases in tolerance systems known as ?

Answer 11

TSPs

Question 12

Which type of damage is human polymeras eta efficient at bypassing and what is it defective in?

Answer 12

UV photoproduct dimer

xeroderma pigmentosum

Question 13

What normally represses expression of SOS operons in e coli?

Answer 13

Lex A binding to Lex A boxes

Question 14

What 2 things does RecA do upon DNA damage?

Answer 14

Becomes activated to RecA*, then…

1. Inhibition of the 3’-5’ editing in DNA Pol III, allowing error-prone DNA replication
2. Interacts with LexA, which autocleaves becomes inactive leading to the SOS response

Question 15

What are the subunits of the RNA pol holoenzyme?

Answer 15

α2ββ’ωσ

Question 16

What dissociates to yield the core enzyme?

Answer 16

σ factor

Question 17

On the promotor, what is the sequence of the -10 6bp sequence?

Answer 17

TATAAT

Question 18

On the promotor, what is the sequence of the -35 6bp sequence?

Answer 18

TTGACA

Question 19

What do promotor up and down mutations do?

Answer 19

UP - make promotor more similar

DOWN - make promotor less similar

Question 20

Which promotors does σ factor 32 cause to be recognised?

Answer 20

heat shock genes

Question 21

Which promotors does σ factor 28 cause to be recognised?

Answer 21

genes for motility

Question 22

Which promotors does σ factor 38/s cause to be recognised?

Answer 22

stationary phase

Question 23

Which promotors does σ factor 54 cause to be recognised?

Answer 23

nitrogen metabolism