lecture 2 - dna repair and transcription regulation

what is DNA damage

any change from normal nucleotide sequence and supercoiled double helical state

cause of damage to DNA

physical and chemical agents (UV light, free radicals produced during metabolism etc.)

errors in DNA replication

2 types of DNA damage

1. single base changes

2. structural distortions

1. produces mutations but have no effect on physical process of transcription or replication

   1. replication errors due to keto-enol type tautomerization

   2. deamination of cytosine to uracil

   3. incorporation of U rather than T during replication

   4. chemical modification of bases

2. may impede transcription and/or replication

   1. single strand breaks

   2. covalent modification of bases, e.g. alkylation

   3. removal of a base

   4. interstrand or intrastrand covalent bonds

nucleotide base tautomers

structural distortion of thymine dimer caused by UV light

adjacent thymines on same strand become covalently linked in a cyclobutane structure or a (6-4) photoproduct

how are damages repaired?

direct repair - reversal/simple removal of the damage

mismatch repair - detection and repair of mismatched bases

excision repair - excision of damaged patch of DNA and its replacement by undamaged DNA

tolerance systems - allow DNA replication to proceed through the damaged regions

retrieval systems - recombinational processes to repair damaged DNA

Direct repair by photolyase

mismatch repair : uracil DNA glycosylase

the mut system

excision repair

tolerance systems: inducible error-prone systems

retrieval systems: daughter strand gap repair

SOS response

SOS response mechanism

how is RecA involved in inducing SOS response

constitutive expression

genes that are always expressed

2 general transcriptional mechanism for control of gene expression are…

1. induction = switching on genes when required

2. repression = switching off genes when not required

operon

genes transcribed to together from a single promoter in some bacteria and archaea

operons produce polycistronic mRNA - what?

more than one gene per mRNA

induction and repression occurs when regulatory protein and DNA interact.

2 types of regulatory proteins

1. repressors - prevent transcription when bound to DNA

2. activators (apoinducers) - activate transcription when bound to DNA

regulatory proteins are converted between inactive and active states by binding of small molecules called effectors

2 types of effectors

1. inducers - activate activators (apoinducers) or inactivate repressors (aka switch genes on)

2. co-repressors - activate repressors or inactivate activators (apoinducers) (aka switch genes off)