micro 470 exam 2

what are the examples of rNTPS

ATP, CTP, GTP, UTP

ATP is what

energy currency and an RNA building block.

is ran synthesized 5’ to 3’ or 3’ to 5’

5’ to 3’

how is RNA different than DNA in terms of structure

RNA is single stranded so it can overall and base pair with itself to form a secondary structure like a hairpin loop or a pseudo knot.

what is mRNA

a main type of RNA that encodes protiens

what is tRNA

main typeof RNA that brings amino acids to the ribosome during translation.

what is rRNA

largest part of RNA that make up ribosome along with ribosomal protein.s

what two types of RNA make up most of the RNA in the cell

tRNA and rRNA

DNA primase is a type of what

RNA polymerase

Bacteria use ____ RNA polymerase for transcription

one that is encoded by pro genes.

explain the important parts of RNA polymerase

it is a 5’ to 3’ polymerase, has rNTP substrates, uses ssDNA template, makes its own primer, processive, looks like a crab claw, and has a multisubunity enzyme found in two major forms- the core and the holoenzyme.

what are the RNAP subunits that make up the core

2 alpha, two beta, and one w

what RNAP subunit make up the holoenzyme?

all of the core plus a sigma factor. all bacteria have a major sigma ex: sigma 70 or sigma A. sigma factor number varies.

explain gene structure

there is a promoter element of DNA, transcribed region gets to RNA, and coding sequence to get to protein. the RNA sequence does not involve promoter.

where does transcription start and end?

starts at +1, it is always an A or a G, and ends at a termination Not stop or start codons.

How does RNA P(polymerase) know where to start?

it binds promoters and the sigma factor recognizes the -35 and -10 sites that are promoters, numbers relative to +1.

what is the -35 region and -10 region

-35= TTGACA

n17 spacer

-10+ TATAAT

spacer

+1 region

do the promoters have to match the consensus

No they do not exactly have to match. How strong it matches is a stronger transcription but they have be off by a few.

true or false, different sigma recognize different consensus sequences

true

what DNA strand is transcribed?

coding strand of DNA (top) is what the ribosome will read and template (bottom) strand is what RNAP uses to synthesize coding strand 5’→ 3’. SO RNA goes off the template strand of DNA

what is an operon

genes that are co transcribed on the same RNA strand

polycistronic mRNA does what

encodes multiple proteins

monocistronic mRNA does what

encodes one protein

how many promoter and terminator are per operon

one of each

explain the first step of the transcription cycle

RNAP holoenzyme
: sigma binds to core to make holoenzyme and to start initiation you need holoenzyme

explain the second step of transcription cycle

promoter recognition: holoenzyme sigma factor recognizes promoter -35 and -10 regions to start transcription, it binds to them and forms the RPc. RPc is closed complex bc DNA is closed.

explain the third step of transcription cycle

isomerization: beta prime closes around DNA forms active site channel around the template strand. sigma 2 separates dsDNA at -10 and bind coding strand. -10 is AT rich bc 2 bonds so easier to melt. sigma 2 separates DNA and forms RPo, the open complex where DNA is open.

explain the fourth step of transcription cycle

RNA is synthesized 5’ to 3’ and then step 4 is abortive initiation and promoter escape: if RNA too short and sigma 3.2 blocks exit channel then trasncrtption terminates. If sigma 3.2 is dislodges the RNA enters the exit channel and this makes the RPi, initiation complex.

explain the fifth step of transcription cycle

transcription elongation: has exit channel, active site channel with bubble around 17 bp long and secondary channel and RNA synthesis is 30-100 nt/sec in the RPe, elongation complex.

What is RNA polymerase backtracking

RNAP can pause and backtrack, often when an RNA secondary structure forms in exit channel and then the new RNA is pushed into the secondary channel and then GreA/ GreB cleave RNA in secondary channel allowing transcription to continue

what is the order of the RNAP complexes

promoter recongition forms closed complex, isomerization forms open complex, initiation for initiation complex, and escape forms the elongation complex.

explain the last step of transcription cycle

Transcription termination, and there are two types: intrinsic AKA Rho-independent AKA factor-independent, and Rho dependent AKA factor dependent.

explain intrinsic termination

it relies on the sequence of DNA itself, inverted repeats of GC form hairpin loops the causes RNAP dissociation from the template DNA and releases RNA product

what is Rho termination factor

a hexametric protein that has helices activity and translocates along RNA and binds RNA, also has ATPase.

explain rho dependent termination

catch up to DNA and break anneal between DNA and RNA. the rho binds to rut and encircles until it reaches RNA poly and disrupts the hybrid which causes RNA to dissociate.