Glover-1 Pt. 1

Question 1

What is a nucelosome core?

Answer 1

Histones octamer + DNA wrapped in it (144-147 bp DNA)

Question 2

What is chromatin?

Answer 2

DNA + proteins

Question 3

4 types of histones in histone core

Answer 3

H2A, H2B, H3, H4

Question 4

Which histones bind DNA first?

Answer 4

H3 and H4 tetramer

Question 5

Which histones are added to the ends of the tetramer?

Answer 5

H2A and H2B

Question 6

What is the linker histone?

Answer 6

• H1
• not part of histone core
• Contacts linker DNA

Question 7

What is the acidic patch?

Answer 7

Contacts surface for nucleosome binding proteins

Question 8

What part(s) of histone contact DNA?

Answer 8

N and C terminal tails

Question 9

What stabilizes histones?

Answer 9

Histone chaperones

Question 10

Name all TFs in the PIC

Answer 10

TFIID, TFIIA, TFIIB, TFIIE, TFIIH, and TFIIF

Question 11

What are 2 complexes in TFIID?

Answer 11

TBP and TAFs

Question 12

Function of TFIID (basic)

Answer 12

initial recognition of TATA box

Question 13

Function of TBP

Answer 13

recognize TATA box (

Question 14

What is the TATA box

Answer 14

• segment in the promoter sequence of DNA
• 25-30 bps upstream of DNA
• seeing TATA box means it is the promoter

Question 15

Structure of TBP

Answer 15

• horseshoe: DNA sits in the horseshoe

- lots of +ve charges in horseshoe

Question 16

Phe and TBP

Answer 16

• Phe residues are in the “stirrups” of TBP

- inserts itself in minor groove of DNA and wedge itself between adjacent A-T bps

Question 17

Why does Phe kink DNA in TBP?

Answer 17

helps unwind DNA for ease of transcription

Question 18

Why is TBP required at promoters w/o TATA boxes?

Answer 18

They facilitate protein-protein interactions among diff. TFs

Question 19

TBP

Answer 19

TATA box Binding Protein

Question 20

TAF

Answer 20

TBP-associated Factor

Question 21

Inr

Answer 21

Initiator element

Question 22

DPE

Answer 22

Downstream promoter element

Question 23

BRE

Answer 23

TFIIB recognition element

Question 24

Function of TAFs

Answer 24

• promoter recognition
• Contact other TFs to increase transcription from the basal level
• Wrapping DNA
• Histone-acetylase
• Double bromo domain

Question 25

Function of TAFII250

Answer 25

• Histone acetyltrasnferase that can either acetylate Lys residues or bind to Lys already acetylated
• is also a kinase

Question 26

Function of histone acetyltransferases

Answer 26

Acetyl groups makes histones neutral and less attractive to DNA–> easier to separate DNA from histones

Question 27

Structure of bromodomain

Answer 27

Centre of helices has pocket with acetylated Lys and hydrophobic residues line the pocket

Question 28

Specificity of TAFII250

Answer 28

only binds to H4 with double acetylation t Lys5-Lys12

Question 29

Function of bromodomain

Answer 29

Bromodomain is on the TAFII250 which helps it bind to acetylated Lys residues on H4 –> help anchor it to DNA

Question 30

What elements define the promoter?

Answer 30

TATA, Inr, BRE, and DPE

Question 31

Role of CTD in RNAPII

Answer 31

• dephosphorylated form: bound by initiation factors

- phosphorylated form: elongation, termination and mRNA processing factors bind to