Bmb 400 Exam 3

Front 1

UP elements ______ promoter strength

Back 1

increase

Front 2

the closer the promoter is to the consensus sequence, the _______ the associate of the polymerase to the binding sites

Back 2

stronger

Front 3

After holoenzyme has bound and sigma is in position, this occurs

Back 3

isomerization

Front 4

the transition to an open complex does/does not require atp

Back 4

does not require atp

Front 5

this complex is energetically favorable for the rna polymerase

Back 5

open complex

Front 6

in the open complex how much DNA unwinds?

Back 6

from the -11 to +3 positions

Front 7

since the open complex is energetically favorable in rna polymerase, it ______ in the transcription process

Back 7

locks

Front 8

Five channels in RNA pol II

Back 8

downstream dna channel, NT channel, ntp uptake channel,T-channel, rna exit channel

Front 9

role of the downstream DNA channel

Back 9

feeds DNA into holoenzyme

Front 10

role of the NT-channel

Back 10

moves nontemplate ssDNA out of active site

Front 11

role of the NTP-uptake channel

Back 11

allows rNTPs to enter active site

Front 12

role of the T-channel

Back 12

where dsDNA reforms and exits

Front 13

role of the RNA exit channel

Back 13

feeds RNA out of the holoenzyme

Front 14

which sigma domain plays a key role in the downstream DNA channel

Back 14

sigma 1.1; is - charged, sits in + charged active site of holoenzyme prior to initiation. after isomerization, subunit moves out of active site allowing DNA to move in

Front 15

explain abortive transcription in prokaryotes

Back 15

polymerase repeatedly synthesizes small rna transcripts of less than 10 NTPs that fail to elongate, simga 3.2 binds in exit channel of RNA and blocks the RNA exit channel

Front 16

describe Rho-independent termination

Back 16

hairpin loop is made that disrupts exit channel, Poly a:u region is weak and allows separation

Front 17

two proofreading mechanisms of RNA polymerase

Back 17

pyrophosphorolytic editing and hydrolytic editing

Front 18

describe Rho-dependent termination

Back 18

The 6-subunit, ring shaped Rho factor binds to the ssRNA transcript and through the hydrolysis of ATP, physically pulls the RNA transcript away from the DNA template

Front 19

describe phosphorylitic editing

Back 19

A reversal of the reaction catalyzed to add the rNTP via PPi

Front 20

describe hydrolytic editing

Back 20

Backtracks using exonuclease like hydrolysis

Front 21

TBP binding results in

Back 21

a bending of the DNA around the TATA box allowing the Beta sheet to bind the minor groove NOT an alpha-helix

Front 22

TFIID

Back 22

binds to promooter at initiator and downstream promoter element sites; provides foundation for construction of pre-transcription initiation complex; one subunit may have HAT activity

Front 23

TFIIB

Back 23

gives the directionality of transcription (unidirectional)

Front 24

TFIIA

Back 24

binds to TBP and stabilizes the binding structure; acts as an anti-repressor by blocking transcription inhibitors

Front 25

TFIIF

Back 25

binds to RNA polymerase II, this and TFIIB associate the polymerase with pre-initiation complex

Front 26

TFIIH

Back 26

two of six subunits are ATP dependent helicases with opposite polarities; asssociated with TFIIK that serves as a serine kinase used to phosphorylate C-terminal tail of RNA pol II, phosphorylation triggers transcription

Front 27

TFIIE

Back 27

binds to TFIIH, recruits TFIIH, helps to regulate helicase/kinase activity; required for RNA poly II to move into elongation mode

Front 28

TFIIS

Back 28

pushes polymerase through hard times; proofreading

Front 29

3 steps in 5' capping

Back 29

1. RNA triphosphatase removes fish phosphatase from 5'end
2. guanylyl transferase - attack of beta phosphate on alpha phosphate of G
3. methyl transferase - adds a methyl group to the 7 position of the G

Front 30

can mRNA be poly-adenylated if the CTD is unphosphorylated?

Back 30

NO, need certain phosphorylation factors to bind to get factors recruited that lead to poly A

Front 31

transfer of polyadenylation enzymes to RNA leads to three events:

Back 31

cleavage of the message, addition of many adenines to 3' end, and termination of transcription by polymerase

Front 32

when transcript is cleaved from RNA pol II/DNA complex in euk, does this constitute termination of transcription?

Back 32

no because polymerase continues along transcript and falls off later

Front 33

How do SR right proteins help guide the proper assembly of splicing factors

Back 33

sr rich proteins bind to sequences called exonic splicing enhancers which recruit splicing machinery (U1 and U2AF) to splice site

Front 34

which self-splicing ribozyme is most like a spliceosome

Back 34

group 2 introns because both have:
2 step transesterification rxn
initiates splicing at "A" branch point
intron is in a lariat structure
doesnt need a free G like group 1

Front 35

IF-1

Back 35

assists IF-3 binding

Front 36

IF-2

Back 36

binds initiator tRNA and GTP

Front 37

IF-3

Back 37

releases mRNA and tRNA from recycled 30s subunit and aids new mRNA binding

Front 38

EF-Tu

Back 38

binds aminoacyl tRNA and GTP

Front 39

EF-Ts

Back 39

displaces GDP from EF-Tu

Front 40

EF-G

Back 40

promotes translocation through GTP binding and hydrolysis

Front 41

RF-1

Back 41

recognizes UAA and UAG stop codons

Front 42

RF-2

Back 42

Recognizes UAA and UGA stop codons

Front 43

RF-3

Back 43

stimulates RF-1/RF-2 release via GTP hydrolysis

Front 44

RRF

Back 44

together with EF-G, induces ribosomal dissociation to small and large subunits

Front 45

recruits poly a polymerase

Back 45

CPSF

Front 46

these two factors recognize the poly A signal sequence

Back 46

CPSF and CstF
cleavage and polyadenylation specificity factor
cleavage stimulation factor

Front 47

two models for eukaryotic termination

Back 47

1. transfer of CPSF and CstF from CTD tail to RNA triggers conformational change, reducing processivity
2. absence of 5' cap causes rna polymerase to dissociate

Front 48

both group II introns and introns sliced by the spliceosome contain:

Back 48

G in 5' splice site, A at branch point site, and G at 3' splice site

Front 49

spliceosome is composed of:

Back 49

150 proteins and 5 RNA molecules (snRNA), when snRNA is combined with proteints, makes snRNPs like U1-U6

Front 50

these proteins recruit U1 and U2AF

Back 50

SR

Front 51

how are introns spliced by the spliceosome

Back 51

U1 snRNP binds to 5' splice site
U2AF binds to pyrmidine tract and 3' splice site, recruits BBP
U2 snRNP replaces BBP
U2AF leaves, U4, U5, U6 snRNPs join the complex
U1 leaves, U6 replaces it at 5' splice site
U4 leaves, RNA components of U2 and U6 form the active site
branch site A attacks the 5' splice site, forming the 3 way junction
5' splice site attacks 3' splice site, freeing intron lariat and forming the mRNA product

Front 52

two important parts of type I intron tertiary structure

Back 52

G binding pocket and internal guide sequence