Proteins (and some other things)for Exam 2

Question 1

Type 1A topoisomerases

Answer 1

useful in taking 2 DNA circles apart in bacterial replication termination
can cut ss regions, DNA pol fills in the gap (ATP required)

Question 2

SeqA

Answer 2

method of refiring regulation in bacteria
when hemi-methylated, origin is blocked by SeqA (delays methylation)
(blocks origin to delay methylation)

Question 3

TERT

Answer 3

in eukaryotes
protein component of telomerase

Question 4

Telomerase

Answer 4

maintains telomere in euks
made up of 2 components (TERT and TERC)

Question 5

DNA pol 𝛿

Answer 5

Eukaryotic lagging strand polymerase
not part of replisome

Question 6

RFC

Answer 6

eukaryotic clamp loader

Question 7

RNA pol I

Answer 7

in eukaryotes
ribosomal RNA pol

Question 8

ASF1

Answer 8

helps FACT in moving nucleosomes out of the way in eukaryotic replication

Question 9

-35 box, -10 box

Answer 9

in bacteria, promoter elements
-35 consensus sequence is TTGACA
-10 consensus sequence is TATAAT
“consensus is best”

Question 10

Tau subunit (s)

Answer 10

binds itself + DNA pol III (and clamp loader and helicase) which allows coordination of leading and lagging strands in bacterial DNA rep elongation

Question 11

DNA pol III

Answer 11

main replication enzyme in bacteria

Question 12

DnaB

Answer 12

helicase in bacteria
breaks H bonds between bases

Question 13

RNA pol II

Answer 13

in eukaryotes
main/most complicated one we focus on
all mRNAs, some regulatory RNAs

Question 14

DnaC

Answer 14

Helicase (DnaB) loader in bacteria

Question 15

RNA pol III

Answer 15

tRNA, ssRNAs, regulatory RNAs

Question 16

Fen1

Answer 16

endonuclease in eukaryotes that cuts of “flap” after pol (𝛿) peels back the DNA that includes the primer

Question 17

Type 2 topoisomerases

Answer 17

useful in taking 2 DNA circles apart in bacterial replication termination
can make double stranded cuts (requires ATP)

Question 18

Type 1B topoisomerases

Answer 18

useful in taking 2 DNA circles apart in bacterial replication termination
cuts 1 strand and lets it unwind (no ATP required)

Question 19

TFIIE, TFIIF

TFIIH also exists

Answer 19

one of the multiple proteins eukaryotes require to recognize the many different promoter elements (BRE-TATA-INR-DPE-etc)
help pol II and TFIIH bind

Question 20

DNA pol 𝝴

Answer 20

eukaryotic leading strand polymerase

Question 21

DNA pol I

Answer 21

in bacteria, helps with primer removal
binds 3’ OH and removes some of the new strand (including the primer), synthesizing where it goes

Question 22

TERC

Answer 22

in eukaryotes
RNA template component of telomerase

Question 23

Ter

Answer 23

in bacteria
DNA sequences that bind Tus proteins

Question 24

𝞼 subunit

Answer 24

in bacterial txn
binds core enzyme (𝛂2, β, β’) to make holoenzyme
part that recognizes promoter
doesnt bind DNA unless attached to core enzye
several types of 𝞼 subunits - good for cell because they can bind promoters in diff conditions (diff consensus sequences)
binds -35 and -10 box

Question 25

Cdt2 and Cdc6

Answer 25

in eukaryotes part of licensing help MCM binds are degraded after this

Question 26

DDK

Answer 26

in eukaryotes, part of firing of origins a kinase regulated by Cdk phosphorylated + thus activates

Question 27

TFIIA, TFIIB, TFIID

Answer 27

transcription factors involved in DNA binding one of the multiple proteins eukaryotes require to recognize the many different promoter elements (BRE-TATA-INR-DPE-etc) D recognizes TATA, INR B recognizes BRE A helps the 𝞼 equivalents in eukaryotes

Question 28

ORC

Answer 28

Origin recognition complex (eukaryotes) made up of 6 polypeptides

Question 29

TATA box

Answer 29

in eukaryotes TATAAAA ------25bp----+1

Question 30

DNA pol 𝛂

Answer 30

works with primase in eukaryotes to synthesize primer - adds few nucleotides for initiation

Question 31

FACT

Answer 31

histone chaperone in eukaryotes FAcilitates Chromatin Transcription binds H3:H4 dimer + moves it behind replisome with help of ASF1 interacts with CMG helicase and DNA pol 𝛂 at fork

Question 32

MCM complex

Answer 32

helicase for eukaryotes in replication unwinds origin

Question 33

DnaA

Answer 33

origin binding protein in bacteria DNA coils around it either bound to ATP (associated) or ADP (dissociates)

Question 34

DAT sites

Answer 34

in bacteria regulation of origin refiring DAT sites bind DnaA:ATP with higher affinity than origin so when more of them (after replication there are 2) titrate out DnaA:ATP

Question 35

DnaN

Answer 35

B-clamp (sliding clamp) in bacteria

Question 36

DnaG

Answer 36

primase in bacteria

Question 37

Tus

Answer 37

In bacteria termination factor - orientation of these proteins dictate direction DNA pol III can move

Question 38

PCNA

Answer 38

Sliding (Beta) clamp for eukaryotes

Question 39

TATA binding protein (TBP)

Answer 39

the one protein required for transcription initiation by all eukaryotic polymerases a subunit of TFIID