Lecture 11: Transcription

Question 1

Difference between ribose and deoxyribose

Answer 1

Ribose has 2’ OH

Question 2

Definition of gene

Answer 2

Segment of DNA containing the information for a single polypeptide chain or functional RNA

Question 3

Signs for upstream and downstream, and site at which transcription begins

Answer 3

Upstream is (-), downstream is (+), transcription is +1

Question 4

Direction of template strand

Answer 4

3’ to 5’ (same direction that RNA polymerase reads)

Question 5

At which sites is the promoter often found in prokaryotes? Also give the specific sequences

Answer 5

-35 (TTGACA) and -10 (TATATT) (both upstream)

Question 6

Closed complex vs open complex

Answer 6

Closed complex is when DNA hasn’t denatured yet, open complex is one RNA pol has opened the DNA molecule

Question 7

Structure of Rho-independent transcription termination (intrinsic terminators)

Answer 7

G/C rich sequence followed by A-rich sequence

Question 8

What happens in a Rho-independent transcription terminator?

Answer 8

RNA-RNA Stem loop forms between Gs and Cs in stem (bind with 3 H bonds instead of 2) - transcript folds to form termination hairpin and RNA chain released

Question 9

Subunits of prokaryotic RNA polymerase

Answer 9

alpha1, alpha2, ß, ß’, omega (core enzyme)

Question 10

Functions of ß and ß’ sites

Answer 10

ß is active site, ß’ is the structure that binds to DNA

Question 11

Reaction involved in RNA polymerization

Answer 11

Nucleophilic attack by 3’ oxygen of growing RNA chain on a phosphate (alpha phosphate) of the next nucleotide to be added - energetically favorable and forms phosphodiester bond

Question 12

Components of RNA polymerase holoenzyme

Answer 12

RNA (core) polymerase and σ70 factor

Question 13

Function of sigma (σ) factor

Answer 13

Subunit of RNA polymerase that recognizes and binds to promoter

Question 14

Definition of polycistronic

Answer 14

1 promoter regulates 1 mRNA, which makes multiple polypeptides (often in prokaryotic genes)

Question 15

Definition of monocistronic

Answer 15

1 promoter regulates 1 mRNA, which makes 1 protein (usually in eukaryotic genes)

Question 16

Eukaryotic RNA polymerase (II) version of ß and ß’ subunits

Answer 16

RPB2 (ß’) and RPB1 (ß)

Question 17

Eukaryotic RNA polymerase I function

Answer 17

Transcribe precursor ribosomal RNA

Question 18

Eukaryotic RNA pol II function

Answer 18

Transcribe protein coding genes to mRNA and others

Question 19

Eukaryotic Pol III function

Answer 19

Transcribe tRNA and rRNA

Question 20

What do all promoter regions contain in eukaryotic cells?

Answer 20

TATA box sequence

Question 21

Location of TATA box in eukaryotic cells

Answer 21

-35 to -25 region upstream of transcription start site

Question 22

What binds to the TATA box in eukaryotes?

Answer 22

TATA box binding protein (TBP) of TFIID complex

Question 23

Eukaryotic transcription: General transcription factors in order of binding

Answer 23

TFIID, TFIIB, TFIIF, TFIIE, TFIIH

Question 24

Structure of TBP

Answer 24

ß sheets that line up and fit in minor groove of DNA, bending the DNA structure

Question 25

Function of TFIID (TBP subunit)

Answer 25

Recognize TATA box

Question 26

Function of TFIIB

Answer 26

Recognize BRE sequence, and recruits RNA pol-TFIIF

Question 27

Function of TFIIF

Answer 27

Stabilizes interaction of RNA pol with TBP and TFIIB, and helps attract TFIIE and TFIIH

Question 28

Function of TFIIE

Answer 28

Attracts and regulates TFIIH

Question 29

Function of TFIIH

Answer 29

Helicase that phosphorylates Ser5 of RNA polymerase CTD, and releases RNA polymerase from promoter

Question 30

What is the CTD?

Answer 30

C-terminal domain of a subunit of RNA Pol II

Question 31

How does TFIIH get the energy to unwind DNA?

Answer 31

ATP hydrolysis

Question 32

Purpose of phosphorylation of CTD of RNA Pol II

Answer 32

Trigger to release polymerase from GTFs (and start actual transcription), also allows RNA-processing protein to assemble on tail of PolII

Question 33

5th AA in CTD (carboxyl terminal domain) repeated sequence?

Answer 33

Serine, where phosphorylation mainly happens

Question 34

How many repeats of the CTD sequence (of Pol II) do yeast and humans have?

Answer 34

Yeast have 27, humans have 52