1- sigma factors and catabolite repression

what is a promoter?

defines a transcription start site and its direction

methionine is what starts transcription. what codes for this methionine?

AUG

describe the four subunits of RNA polymerase

alpha- 40kD, used for enzyme assembly, promoter recognition and activator binding. there are 2 alpha subunits

beta- 155/160 kD. there are two of these. used as catalytic centre and for termination of transcription

sigma- 20-70 kD, used for promoter recognition (like alpha), binds both to -10 gene box and -35. also used for gene switching

omega- not very important, used to maintain structure and assemble beta subunits

of the four subunits, which is the only one which makes specific contact with DNA?

sigma

how many different sigma factors are there?

5, each with different functions and DNA binding sites. the main one is sigma70, which has many general functions

when temperatures increase, how do well adapted bacteria use gene switching to cope?

they turn on several operons which encode chaperone proteins.

a sigma32 factor dissociates and begins to compete against sigma70, so that the proteins which are transcribed by the sigma70 are reduced and the cell can focus on making the chaperone proteins mostly instead

explain catabolite repression in the lac operon

PTS (phosphotransferase system) brings glucose into a cell by phosphorylating it

only when glucose levels are low, PTS instead starts activating adenylate cyclase, which is then phosphorylated by ATP to make cAMP.

high levels of glucose prevent cAMP formation (thus it is catabolite repression). glucose can control many operons i think

cAMP can then work with CRP to bind to alpha subunits of RNA polymerase on the promoter sequence

how does CRP interact with RNA polymerase?

in class I operons (like lac): contacts with a carboxy-terminal domain (CTD) of the alpha subunit.

in class II operons (like galp1): contacts with alpha CTD, alpha NTD (not so relevant) and sigma subunits. using more contact regions makes up for the fact that the CRP site overlaps with the sigma site (-35) which otherwise would have made for weak bonding

CRP provides universal control over many operons

what is it called when you have multiple CRP-polymerase contacts, like in class II?

synergism

describe the function of CRP as an architectural factor in Class III (araBAD)

there are 2 araC dimers, which interact with each other to repress araBAD

CRP binds in between these dimers, changing DNA conformation and preventing araC interaction, thus activating araBAD

active araBAD is used to make arabinose