Proteins and such for Exam 3

Question 1

H2H (homeodomains)

Answer 1

in bacteria and euks, one of the many evolutionarily conserved structures found in DNA binding domains

Question 2

Zinc Fingers

Answer 2

in euks, one of the many evolutionarily conserved structures found in DNA binding domains

Question 3

Rho

Answer 3

in bacteria in factor-dependent termination
moves 5’-3’ on RNA
catches up to RNAP + basically pulls it out of bubble (e.g. if RNAP is paused)
binds CU-rich regions in RNA so doesnt work just everywhere

Question 4

CII

Answer 4

regulator in bacterial txn
decreases lysis increases lysogeny
If sufficient CII protein accumulates, it binds DNA and stimulates transcription from the Pre promoter, producing and mRNA transcript encoding the CI regulator. eventually leads to repression of transcription of lytic genes encoded by the Pl and Pr transcripts.
The mechanism by which the choice between lysis or lysogeny is made after the bacteriophage infects a host cell hinges on the activity of CII: CII is sensitive to the host cell proteases, making it unstable in the cell. If the environmental factors are such that CII accumulates and directs expression of enough CI, a lysogenic state is established. If CII is degraded, CI is not synthesized and all other bacterophage genes are expressed, allowing autonomous viral replication, packaging, and ultimately cell lysis.

Question 5

MATa,𝛂

Answer 5

locus in haploid cells that produces either a protein called a1 (if MATa) or 2 proteins called 𝛂1 and 𝛂2 (if MAT𝛂)

euks

Question 6

Q

Answer 6

regulator in bacterial txn
binds at promoter
modifies RNAP to prevent termination by preventing pausing

Question 7

CFI, CFII

in polyadenylation

Answer 7

cleave RNA at CA

Question 8

U1

Answer 8

interacts with 5’SS

Question 9

TFIIH

Answer 9

in euks has a kinase subunit that phosphorylates serine-5 which then recruits EFs

Question 10

3’SS

Answer 10

acceptor splice site
on left of exon, right of intron

Question 11

the 2 models of recognization of introns and exons by splicing complex

Answer 11

1. Exon definition - rearrangement necessary
2. intron definition - no rearrangement necessary

Question 12

Ternary complex

Answer 12

stable
1. RNA (hybridized in bubble(1 DNA strand, 1 RNA strand))
2. DNA (bubble)
3. Enzyme (RNAP)

Question 13

a1

Answer 13

repressor
requires 𝛂2
helps 𝛂2 bind

Question 14

DBD

Answer 14

DNA Binding Domain
Many activators have both a DBD and DAD

Question 15

𝛂1

Answer 15

activator - requires MCM1
helps MCM1 bend DNA

euks

Question 16

diploid cells

yeast

Answer 16

genes turned off in diploid = haploid-specific genes

Question 17

PAP

Answer 17

polyA polymerase
protein that adds ATP to end in polyadenylation process

Question 18

a cells

yeast

Answer 18

a-specific genes (asg) only transcribed + translated in a cells

euks

Question 19

Lytic Pathway

Answer 19

in bacteria
(in phage ex where infects E.coli)
phage replicates, makes lots of little λ, lyses cell, releases phages into environment

when lots of resources

Question 20

Polyadenylation complex

Answer 20

CPSF, CStF, CFI, CFII, PAP
associates with CTD of pol III

Question 21

U2

Answer 21

interacts with branchpoint A

in yeast, U2 by itself, in other euks, U2AF + BBP binds first

Question 22

DAD

Answer 22

DNA Activation Domain
many activators have both a DBD and DAD

Question 23

CPSF, CSTF

Answer 23

recognize signals in polyadenylation process

Question 24

SnRNPs

Answer 24

U1, U2, U4, U5, U6, and some other proteins (U2AF +BBP)
made up of small RNA + some core proteins + some specific proteins (specific to each SnRNP)
1. recognizes signals and 2. brings the reacting groups close to one another

Question 25

U4, U5, U6

Answer 25

interact with other SnRNPs to promote complex formation

Question 26

Lysogenic Pathway

Answer 26

In bact
in example where phage infects E.coli
txn stops at all but few genes. λ DNA is inserted into bacterial chromosome, stays stably there until is reactivated (once reactivated can undergo lytic pathway)

when few resources

Question 27

CI

Answer 27

regulator in bacterial txn
decreases lysis, increases lysogeny
stimulates transcriptiom from the weak Prm promoter, yielding a different mRNA transcript that also includes a copy of the CI gene. As it builds up, it binds to sites in the Pl and Pr promoter regions and represses transcription of the lytic genes encoded by these transcripts. It also activates transcription of the gene that encodes integrase, which mediates lambda DNA integration into the bacterial chromosome. Thus, lysogeny is established and maintained by high levels of CI

Question 28

Types of alternative splicing

Answer 28

1. exon exclusion
2. intron inclusion
3. cassette splicing
4. use of cryptic splice sites

Question 29

N

Answer 29

regulator in bacterial txn
binds RNA ____ (modifies RNAP to prevent termination by preventing pausing)
prevent stalling and termination

Question 30

b-ZIP

Answer 30

in bacteria and euks, one of the many evolutionarily conserved structures found in DNA binding domains

Question 31

Cro

Answer 31

regulator in bacterial txn
increases lysis, decreases lysogeny
If CII does not accumulate in sufficient amounts and too little CI is synthesized, Cro will bind the Prm promoter and repress transcription of the Ci gene. By preventing CI synthesis, Cro ensures expression of the lytic genes from Pl and Pr

Question 32

𝛂2

Answer 32

repressor
requires MCM1
interacts with co-repressors SSN6/TUP1
interacts with HDAC, affects chromatin structure

euks

Question 33

MCM1

Answer 33

primarily an activator
interacts with co-activators
works as an activator at bindings sites in asg but not 𝛂sg unless 𝛂1 is also present… because MCM1 bends DNA but at the 𝛂sg, that sequence doesnt bend as well, 𝛂1 helps

euks

Question 34

5’SS

Answer 34

donor splice site
on left of intron, right of exon

Question 35

CIII

Answer 35

regulator in bacterial txn
decreases lysis, increases lysogeny

Question 36

𝛂 cells

yeast

Answer 36

𝛂-specific genes (𝛂sg) only transcribed + translated in 𝛂 cells

euks