L01 Flashcards

Eukaryotic promoters, RNA polymerases & assembly of PIN complex

1
Q

What is ‘gene expression’?

A

The process by which information in genes (DNA) is decoded into protein

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2
Q

Name the process DNA -> RNA

A

Transcription

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3
Q

Name the process RNA -> Protein

A

Translation

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4
Q

Define ‘transcription’

A

Transfer of genetic information from ds DNA to ss RNA (mRNA)

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5
Q

What is the purpose of DNA

A

Encode proteins

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6
Q

Role of gene expression

A

Determines the function of the cell/primary specifier of cell identity

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7
Q

How do cells respond to changes in the environment?

A

Gene expression is altered

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8
Q

What is the DNA sequence for -35 promoter in prokaryotes?

A

TTGACA

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9
Q

What is the DNA sequence for the -10 promoter in prokaryotes?

A

TATAAAT

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10
Q

How far is the TATA box from the TSS?

A

-31 ~ -26 (about 30 base pairs)

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11
Q

Why is it called the TATA box?

A

First 4 bases often, TATA

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12
Q

What is the pyrimidine rich sequence?

A

Inr (initiator)

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13
Q

Where is the initiator often located

A

-2 ~ +4

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14
Q

Does DNA have all the core (basal) promoter elements?

A

No

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15
Q

In mammals what percentage of protein coding genes lack obvious TATA & Inr?

A

60-70

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16
Q

How does methylation affect transcription in CpG islands?

A

Methylation of CpG islands = silencing txn
Non-methylation of CpG islands = promoting txn

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17
Q

What is methylation?

A

Addition of a methyl group

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18
Q

What residues are methylated in mammalian CpG islands?

A

Most C residues followed by a G (5-methyl C)

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19
Q

What is the catch when it comes to CpG methylation?

A

C residues are hypomethylated

20
Q

UAS

A

Upstream Activating Sequences

21
Q

URS

A

Upstream Repressing Sequences

22
Q

What tools do we use for identifying promoter elements?

A

Sequence comparison and Reporter Analysis

23
Q

What are the type of RNA polymerases in eukaryotes?

A

RNA pol I,II, III

24
Q

What does RNA pol I do?

A

Transcribes rRNA which is used to make ribosomes

25
Q

Where is the RNA pol I located?

A

Nucleolus

26
Q

What does RNA pol II do?

A

Transcribes mRNA

27
Q

Where is the RNA pol II located?

A

Nucleus

28
Q

What does RNA pol III do?

A

Transcribes tRNA which is used to translate mRNA genetic code into a sequence of amino acids

29
Q

What are the differences between prok. and euk. RNA polymerase?

A

Overall similar structure, euk. RNA polymerase is bigger (consists of 12 subunits). Prok. have one RNAp. that carry out all the functions compared to euk (3)

30
Q

What is the role of a sigma factor in bacterial prokaryotic transcription?

A

Helps bacterial RNA polymerase recognise promoter DNA

31
Q

What is the eukaryotic equivalent of sigma factors in prokaryotic transcription?

A

Transcription factors!

32
Q

Order of TFII in eukaryotes

A

TFIID, TFIIA, TFIIB, TFIIF, TFIIE, TFIIH

33
Q

What is the function of TFIID

A

Binds to TATA

34
Q

What is the function of TBP?

A

Binds to TATA

35
Q

What is the function of TAF?

A

Helps TBP fx when no TATA & in the presence of activator proteins. When not present does not work.

36
Q

What is the function of TFIIA?

A

Further stabilises complex

37
Q

What is the function of TFIIB?

A

Further stabilises complex

38
Q

What is the function of TFIIF?

A

Recruits RNA Polymerase II

39
Q

What is the function of TFIIE?

A

Recruits TFIIH & promotes promoter melting

40
Q

What is the function of TFIIH?

A

Unwinds DNA, repairs DNA, & phosphorylates

41
Q

What are the components of TFIIH and what are they responsible for?

A

CAK (Kinase) - phosphorylation
XPB/SsL2/helicase - ATPase used in promoter melting. unwinding DNA and DNA repair

42
Q

What are the elements present in eukaryotic promoters?

A

TATA/Initiator (Inr - pyrimidine rich)

43
Q

What are the functions of the eukaryotic promoters?

A

TATA - binding site for TFIID
Inr - start site for when there’s no TATA box / enhancing txn

44
Q

How can reporter genes be used to analyse promoter sequences?

A

By measuring the activity of a promoter in a cell

45
Q

How many major RNA polymerases are there in eukaryotic cells?

A

3

45
Q

How do the General Txn Factors (GTF) assemble on the promoter to form PIC?

A

TFIID - binds to TATA/promoter
TFIIA&TFIIB - bind to TFIID to stabilise complex
TFIIF - assembles with RNA polymerase to form the Polymerase II complex
TFIIE - recruits TFIIH
TFIIH - contains helicase units that unwind DNA/cause promoter melting & contains kinase units = phosphorylation

46
Q

Describe the major events during transcription initiation.

A
  • RNA polymerase binding to the DNA promoter template.
  • unwinding of DNA = creating separate strands
    = INITIATION