Chapter 29 Flashcards by Dylan Johnson

splicing removes >

introns

How well did you know this?

Not at all

Perfectly

homology between RNAPs

have central metal atom in active sites. important c terminal domain critical for processing RNa

How well did you know this?

Not at all

Perfectly

3 steps of RNA transcription

initiation, elongation, termination

How well did you know this?

Not at all

Perfectly

post-transcriptional processing in RNA

base modification (methylation), addition of nucleotides (poly A tails), splicing

How well did you know this?

Not at all

Perfectly

RNA polymerases bing to DNA sequences called ?

promoters

How well did you know this?

Not at all

Perfectly

In the absence of ? (2), RNAP can bind to promoters but cannot continue elongation steps

Mg++, NTPs

How well did you know this?

Not at all

Perfectly

binding of ? protects DNa from enzyme digestion

RNAP

How well did you know this?

Not at all

Perfectly

stronger promoters are better matches to ?

consensus

How well did you know this?

Not at all

Perfectly

optimal promoters have ? bp between consensus sequences

How well did you know this?

Not at all

Perfectly

changes in growth conditions lead to appearance of additional ?

sigma factors

How well did you know this?

Not at all

Perfectly

housekeeping sigma factor

sigma 70

How well did you know this?

Not at all

Perfectly

RNAP error

1 in 10^4

How well did you know this?

Not at all

Perfectly

RNAP elongation reaction

PPPXOH + YTP&raquo_space; PPPXPYOH + PPi

How well did you know this?

Not at all

Perfectly

RNAP polymerization reaction is identical to DNA polymerase and also requires ? assisted phosphoryl transfer

Mg++

How well did you know this?

Not at all

Perfectly

RNAP elongates at ? nucleotides/second

How well did you know this?

Not at all

Perfectly

? polymerase needs no primer

RNA

How well did you know this?

Not at all

Perfectly

RNAP uses free energy of ? to drive conformational change

PPi release

How well did you know this?

Not at all

Perfectly

Incorporation of a ? changes the active site and pushes newly formed duplex base pair into the ? region. Release of PPi returns the active site to a ? binding region

Incorporation of a NMP changes the active site and pushes newly formed duplex base pair into the helix binding region. Release of PPi returns the active site to a NTP binding region

How well did you know this?

Not at all

Perfectly

RNA:DNA hybrid is slightly more/less stable than DNA:DNA

How well did you know this?

Not at all

Perfectly

determines when transcription stops

the RNA molecule being made

How well did you know this?

Not at all

Perfectly

Three methods of Transcription pausing or termination

1) form stem loop 2) Recruit accessory proteins (attenuators) 3) additional factors can antagonize attenuation

How well did you know this?

Not at all

Perfectly

rho independent termination

formation of step loop structure causes pause. if next residues are uridines, thranscription stops and rna is released. free energy of stem loop is greater than RNA:DNA duplex

How well did you know this?

Not at all

Perfectly

Rho

a hexameric RNA helicase. binds to C rich regions. removes rna from polymerase.

How well did you know this?

Not at all

Perfectly

rifampicin

inhibitor of many bacterial RNAPs. binds to aromatic AAs at site of formation of RNA:DNA hybrid and prevents initial elongation steps. Mutations in aromatic rings leads to rifampicin resistance.

How well did you know this?

Not at all

Perfectly

In procaryotes, ? is directly used for protein synthesis

mRNA

rRNA and tRNA undergo these types of processing

Cleavage, modification, addition of nucleotides (methylation, flipping)

In E Coli, a primary transcript is cleaved by RNase 3 and RNase P to produce rRNAs and a tRNA that undergo ?. tRNAs have the nucleotide sequence ? added to their 3' ends if needed

base modifications. CCA

eucaryotes have ? RNAPs differentiated by their sensitivity to ?

3. alpha-amanitin

RNAP that is strongly inhibited by alpha-amanitin

type 2

RNAP that is inhibited by alpha-aminitin at high concentrations

type 3

A type 4 RNAP found in plants is used to make ?

siRNAs and RNA dependent RNA polymerases involved in RNA interference

Type 1 RNAPs used to make ?

rinosomal RNA

Type 2 RNAPs used to make ?

mRNA precursors and snRNA

different RNAPs transcribe from different ?

promoters

RNAP ? and ? produces RNAs needed by all cell types and have relatively simple sequences in their promoters

1 and 3

? promoters are complex

RNAP

eucaryotic RNAP binding

general transcription factors bind to promoter elements and recruit RNAPs

? elements of promoters are recognition sites for protein factors

cis

RNAP 2 is recruited by GTFs ?

TFIIA-TFIIH

In TATA-box promoters, ?, containing the TATA-binding protein binds first and distorts the DNA helix

TFIID

TATA box binding protein binds TATA box that contains sequences related to TATAAAA and ?

bends the DNA into a horseshoe shape

TFIID provides ? to form basal transcription apparatus

docking sites for additional GTFs and RNAP2

Assembly of transcription initiation complex generates a ? complex that determines the orientation of transcription

asymmetric

TFIIH functions

helicase activity opens DNA helix to start transcription. phosphorylation of C-terminal domain of RNAPII releases RNAP from initiation factors that recruited it and binds RNA processing enzymes

basal transcription complex initiates transcription at a low/high frequency

low

many promoters are activated by ? that may be far from transcription start sites either up or down stream

enhancer sequences

Cis promoter elements are recognized by ?

protein factors

complex called ? coordinates positive activators with recruitment of RNAP 2

mediator

SrB8-II represses

RNAP 2

RNAP 1 produces ? that undergo base and ribose modification in the nucleolus by ?

rRNA. snoRNPs

RNAP III transcript processing to tRNA

5' and 3' cleavage. additon of 3' CCA sequence. base and ribose modification. spliced by endonuclease and ligase

RNAP II transcript processing to mRNA

5'-5' triphosphate cap at 5' end by GTP marks as pre-mRNA and protects from exonucleases. PolyA polymerase adds a tail to 3' end. methylation can occur at 2'-OH groups of nucleotides 1 and 2

Tissue specific RNA editing. Liver produces mRNA that translates to ? while intestines generate a deaminase for the same mRNA that modifies it to translate to ?

ApoB-100. ApoB-48

ApoB-100

transports lipids to other cells

ApoB-48

Carries fat in chylomicrons

? is most common way eucaryotes generate diversity

splicing

splicing involves ? reactions

transesterification

splicing transesterification reactions are similar to tyrosine mediated reactions by ?

topo 2

Draw splicing reaction

do it. 2' Oh of branch site attacks 3' OH of phosphodiester bond at 5' splice site to generate lariat intermediate. Newly generated 3' OH attacks 3' OH of phosphodiester bond at 3' splice site

spliceosome

snRNPs that contain RNA and a large number of proteins assemble to help guide and catalyze splicing reactions

Since transesterification reactions are freely reversible, what is the energy source that drives splicing to proceed

ATP powered helicases drive the spliceosome through the conformational changes that involve the release of U1 and U4

specificity of splicing due to ?

complementary pairing of pre-mRNA and snRNAs

phosphorylation of CTD causes

release of RNAP from initiation complex and sequentially recruits enzymes of processing

15% of all genetic diseases due to ?

mutations that affect splicing

Cis effects

mutations in the pre-mRNA

Trans effects

mutations in the spliceosome

some defects in hemoglobin production are the result of a mutation within an ? that creates a new splice site

intron

ribozymes

catalytic RNAs

group 1 introns use ? to attack 5' splice site

guanosine

group 2 introns and the spliceosome activate an ? to initiate splicing

adenine