Lecture Oct 21, 2024 (Start L7)

Question 1

What is phosphorolation?

Question 2

What are the 3 main parts of a eukaryotic gene?

Answer 2

The enhancer
The class 2 promoter elements
Protein coding sequence

Question 3

snRNA meaning

Answer 3

The splicesome is madeup of a protein and a small Nuclear RNA

Question 4

snRNP

Answer 4

Small nuclear ribonuclear proteins. The name for a splicesosome

Question 5

How many different spliceosomes are there

Answer 5

5 different (for introns)

Question 6

What is a splicesosome?

Answer 6

Identifies Exon / Intron Junctions & Excises Introns- Splices Exons

Question 7

Mature mRNA vs pre-mature mRNA

Answer 7

pre-mature= BEFORE introns are removed
Mature= without introns
(only for EUKARYOTIC cells)

Question 8

Which steps are done to make mature mRNA?

Answer 8

post transcription modifications (things done after transcription is complete)
5’ capping
* splicing
* 3’ poly-adenylation

Question 9

Why is the process more complicated in Eukaryotes?

Answer 9

• We have 3 types of RNA polymerase (while others hvae 1)
• longer genes

Question 10

What is promoter in eukaryotic transcription?

Answer 10

Found in the initiator (+1)

Question 11

All parts of core promoter

Answer 11

BREU, TATA box, BRED, MTE, DPE

Question 12

TATA box location

Answer 12

-25

Question 13

Core promoter ranges from

Answer 13

Core promoter -34 to 27

Question 14

MTE location

Answer 14

17

Question 15

DPE location

Answer 15

27

Question 16

Upstream elements locations

Answer 16

-80 to -100

Question 17

Out of exons and introns, which gets transcribed?

Answer 17

Both. But, introns dont get translated

Question 18

What are the general parts of a eukaryotic gene?

Answer 18

1. Enhancers
2. Promoters
3. Protein coding sequence (Introns+exons)
4. Untranslated regions (found in 3’ and 5’ areas)

Question 19

When does the class 2 promoter occur? What are the 2 parts of it ?

Answer 19

after the enhancers.
- Made up of the core promoter
- Upstream element

Question 20

What is the purpose of the class 2 promoter?

Answer 20

Points RNA Polymerase in correct direction of transcription

Question 21

What are the main elements of the core promoter?

Answer 21

BREU, TATA, BRED, Inr, MTE, DPE

Question 22

Where do you find TTGACA on the eukaryotic?

Answer 22

Does not exist on eukaryotic gene

Question 23

When does the TATA box number?

Answer 23

-25

Question 24

What is a general transcription factor (GTFs)?

Answer 24

A protein that helps RNA polymerase 2 start transcribing on the core promoter elements

Question 25

What is a distal enhancer element?

Question 26

What do the 3 different RNA polymerases transcribe?

Answer 26

RNA Poly 1: rRNA and 5.8S, 18S, 28S (all ends with 8)
RNA Poly 2: protein
RNA Poly 3: tRNA, 5S RNA

Question 27

What does RNA Polymerase do? At what stage?

Answer 27

Creates the mRNA strand (elongation)

Question 28

What is an S-value for the RNA Polymerases?

Answer 28

Rate of sedimentation. (bigger rate of sedimentation=bigger rRNA)

Question 29

What is an rRNA where is it used?

Answer 29

ribsomal RNA, makes mRNA

Question 30

What does Polymerase 1 transcribe?

Answer 30

rRNA genes

Question 31

What does Polymerase 2 transcribe?

Answer 31

proteins mRNA, miRNA, snRNA, and snoRNA genes

Question 32

What does Polymerase 3 transcribe?

Answer 32

RNA polymerase III
transcribes tRNA and 5S rRNA
genes + other functional RNA

Question 33

How long is the enhancer element?

Answer 33

thousands of base pairs long

Question 34

What does the mediator protein do?

Answer 34

Connects to activator protein

Question 35

What is activator protein connected to?

Answer 35

The enhancer element(so it can create pre iniitation complex

Question 36

What is the D complex

Answer 36

In the first step When the TFIID is bounded to the MTE, DPE, Inr

Question 37

What is the first step of transcription initiation in eukaryote cells?

Answer 37

The TFIID bindes to the DPE, MTE, Inr

Question 38

What are the first 4 steps of transcription initaion

Answer 38

1. TFIID binds MTE, DPE, and Inr, forming D complex
2. TFIIA replaces TAF1 (subunit of TFIID)
3. TFIIA + TFIID (with its TBP subunit) bind to TATA forming DA complex
4. TFIID undergoes major conformational change, bending DNA by about 90°
5. TFIIB binds BREU and BRED

Question 39

What are the next 5 steps of RNA transcription initiation?

Answer 39

6. TFIIF is already bound to RNA
   polymerase II
7. TFIIB uses the B-ribbon to ‘hook’
   TFIIF-RNApolII into place
8. TFIIF binds DNA & stabilizes
   complex (DAB-Pol-F complex)
   * TFIIF helps RNA pol bind to a
   region from -34 to +17
   B-ribbon
   B-ribbon
9. TFIIE clamps the DNA onto the complex and locks it
   tightly (DAB-Pol-FE)
10. TFIIE recruits TFIIH to join the complex (DAB-Pol-FEH)
    * TFIIH has enzymatic activity: helicase and kinase
11. The Mediator binds to the complete, DAB-Pol-FEH
    complex to form the Pre-Initiation Complex (PIC

Question 40

Location of +1 site in Eukaryotes

Answer 40

in the Initiator (core promoter element)

Question 41

What is helicase part of?

Answer 41

The TFIIH, which also include kinase

Question 42

What keeps the DNA strands seperate for the rest of transcription

Answer 42

RNA polymerase II

Question 43

Whats kinase role?

Answer 43

Enzyme which can add
phosphates to other molecules

Question 44

What is unique about RNA Polymerase 2

Answer 44

has a unique,
7-amino acid sequence, YSPTSPS
which is repeated about 50 times

Question 45

What protein determines the start of transcription elongation?

Answer 45

TFIIH to phosphorylate (break phosphate group) the 5th serine in the RNA polymerase II CTD

Question 46

Amino acid sequence on CTD of polymerase chain

Answer 46

YSPTSPS (You should practice to see progress soon)