Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Genes to Genomes > Eukaryotic Transcription > Flashcards

Eukaryotic Transcription Flashcards

1
Q

Define a gene

A

A region of the genome transcribed into an RNA giving rise to a selectable phenotype.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Do yeast genes have introns?

A

No

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the gene density in yeast?

A

1 gene/2kbp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the gene density in humans?

A

1 gene/140kbp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How do we measure where RNA molecules arise from a genome and the quantity of RNA that is produced?

A

RNA-seq?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What does RNA-seq tell us?

A

Where RNA molecules arise from a genome and the quantity of RNA that is produced.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the 3 mains steps to RNA-seq?

A
  1. Entire RNA population is purified from a cell or cell sample, fragmented and reverse transcribed into corresponding cDNA.
  2. cDNAs are sequenced using NGS.
  3. Sequence read data is aligned back to the reference genome sequence relating to the cell type in step 1.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the two options for handling RNA-seq data?

A
  1. Plot distribution of sequence read frequency across the genome.
  2. Calculate a sum of overall RNA level for the whole transcription unit.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Why is basic RNA-seq not accurate enough to define the exact transcriptional start site of a gene?

A

Because eukaryotic RNA moelcules are processed, especially at the 5’ end.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Which technology is used to map transcriptional start sites?

A

NET-seq

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is NET-seq?

A

A modification of RNA-seq allowing you to catch RNA pol in the act of transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What isn’t accurately measured by RNA-seq?

A

RNA-seq isnt’ spatially exactly accurate, it cannot denote the point at which RNAP actually attaches to DNA and starts transcribing so the transcriptional start point is accurately mapped by RNA-seq.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How does NET-seq map the TSS?

A

An antibody is raised against the RNAP of interest and used as a molecular grab handle to purify RNA polymerase.
This allows you to grab hold of RNAP in the act of transcribing before any modifications are made to the RNA molecule.
Then the RNA is purified away from RNA polymerase and standard RNA-seq is performed.
All these sequence reads begin exactly where the gene begins giving an accurate map of the transcriptional start site.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What are the steps of NET-seq?

A

Make an antibody and use as molecular grab handle to purify RNA polymerase.
Purify nascent RNA molecules.
RNA moelcules are subjected to RNA-seq to reveal the 5’ end sequences of transcripts.
These can be mapped back to the genome to reveal locations of TSSs and surrounding regions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the complexities associated with eukaryotic transcription?

A
  1. Eukaryotes produce multiple types of transcripts not just from the nuclear genome but mitochondria (in animals and plants) and chloroplasts (in plants) have their own genoems which produce transcripts.
  2. There are 4 phases to transcription.
  3. In eukaryotes the different RNA pols negotiate the phases of transcription via recognition of specific sequence features in DNA using additional factors/enzymes.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the 3 main polymerases that transcribe within the nuclear genome?

A

RNA pol I, II, III.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the character of mitochondria and chloroplast RNA pols?

A

Bacteria-like

Phage-like

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How many DNA-dependent RNA pols are involved in nuclear transcription?

A

3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Give some examples of transcripts produced by RNA pol II?

A

mRNA, snRNA, snoRNA, miRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Give some examples of transcripts produced by RNA pol I?

A

45s rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Give some examples of transcripts produced by RNA pol III?

A

tRNA, 5s rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What % of cellular RNA is transcribed by each of the template-dependent RNA polymerases?

A

RNA pol I transcribes 80% of cellular RNA.
RNA pol II transcribes 5% of cellular RNA.
RNA pol III transcribes 15% of cellular RNA.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

By which polymerase is mRNA transcribed?

A

RNA pol II

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

By which polymerase is tRNA transcribed?

A

RNA pol III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

By which polymerase is snRNA transcribed?

A

RNA pol II

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Is mitochondrial RNA polymerase a multi-protein complex or a single polypeptide?

A

Single polypeptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What are the 4 phases of transcription?

A
  1. Binding
  2. Initiation
  3. Elongation
  4. Termination
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is the function of the RNA pol II CTD?

A

The CTD serves as an assembly platforms for proteins to attach to RNA polymerase.
The serines and tyrosines in the heptapeptide repeat are phosphorylated in a way that implies a code.
The phosphate groups are being patterned in a particular way in relation to the 4 phases of transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Which subunit of RNA pol II has an extended CTD?

A

Rpb1.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the RNA pol II CTD?

A

It contains mulitple repeats of the heptapeptide sequence YSPTSPS.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

How is the RNA pol II CTD altered by organism complexity?

A

The RNA pol II CTD increases in length with organism complexity.
Heptapeptide repeat number = 26 in yeast, 32 in C. elegans, 45 in Drosophila, 52 in humans.

32
Q

What is the heptapeptide repeat number of the RNA pol II CTD in humans?

A

52

33
Q

What does a promoter do?

A

Defines the start point of transcription.

34
Q

What do NET-seq experiments reveal about the frequency of TATA boxes?

A

NET-seq experiments uncover that a simple model of a promoter being comprised of just a TATA box and initiator is too simple.
Whereas TATA boxes were previously thought to be ubiquitous, only 5% of human promoters actually have one.

35
Q

Give some examples of RNA II pol promoter elements?

A

DPE, MTE, Ohler 1, Ohler6, Oherl7, DRE, TCT, BRE.

36
Q

What is a CpG island?

A

A tract of DNA sequence rich in sequences like CGCGCGCGC.

37
Q

How many additional proteins are required by RNA pol II in order to recognise a promoter?

A

44

38
Q

What is the name given to the 44 additional proteins required by RNA pol II to recognise a promoter?

A

General transcription factor complex.

39
Q

Give some examples of proteins that make up the general transcription factor complex?

A

TFIID, TFIIE, TFIIB, TFIIC.

40
Q

Where does the general transcription factor complex form?

A

On the unphosphorylated RNA pol II CTD during PIC formation.

41
Q

What is the name given to the ‘ready to initiate’ promoter-bound RNA pol II and GTFs?

A

The pre-initiation complex.

42
Q

Describe the structure of TFIID?

A

TFIID consists of TATA-binding protein (TBP) and up to 14 TBP-associated factors (TAFIIs).

43
Q

What is the function of TFIID?

A

TFIID recognises and binds to promoters, TBP binds directly to the TATA box when present via the DNA minor groove, however, it also binds to non-TATA promoters less specifically.

44
Q

What is the function of TFIIB?

A

TFIIB provides a physical bridge between TBP and RNA pol II and helps position DNA precisely into the pol II active site.

45
Q

What is the function of TFIIF?

A

Promotes CTD-dephosphorylation and brings RNA pol II to the promoter as a pol II:TFIIF complex.
It also stabilises the melted region of DNA at the TSS after TFIIE/H action.

46
Q

What is the function of TFIIE/TFIIH?

A

Uses energy from ATP hydrolysis (TFIIH) to melt the base-pairs within the TSS to create the transcription bubble ready for initiation.

47
Q

What is responsible for the phosphorylation of the CTD?

A

CTD kinase enzymes.

48
Q

What is the structure and function of TFIIH?

A

TFIIH contains the CDK7/cyclin H kinase which phosphorylates serines in the 5 and 7 positions of the CTD.

49
Q

What is the function of CTD phosphorylation?

A

CTD phosphorylation disengages the general transcription factors and allowing binding of elongation factors to form the transcription elongation complex.
This converts RNA pol II from an initiating form of the enzyme into an elongating form mediated by a change in phosphorylation.
Phosphorylation of the RNA pol II CTD is associated with termination of transcription.

50
Q

What is the function of the elongation factors?

A

Elongation factors are enzymes that allow RNA polymerase to zoom down the chromosome and allow it to push the chromatin proteins off DNA, help it negotiate damaged DNA and allow RNA pol II to become a processive enzyme.
Elongation factors also initiate RNA-processing reactions such as capping and splicing.

51
Q

What serine of the heptapeptide repeat is phosphorylated during elongation?

A

Serine 2

52
Q

What sequence promotes transcription termination?

A

Polyadenylation site.

53
Q

What is the structure of the rRNA encoding gene?

A

rRNA encoding genes have a promoter, a transcriptional start site and a coding region however, because of the huge quantity of rRNA needed rRNA has some unique features because lots of transcription is required from these rDNA genes.
Eukaryotic rDNA is an operon meaning more than one ultimate gene product is encoded in a polycistronic transcript - there are actually 3 separate products processed from a single transcript of the rDNA gene.

54
Q

How many gene products are processed from the rDNA transcript?

A

3

55
Q

How are rDNA genes found in eukaryotic genomes?

A

In tandem repeats to be able to generate sufficient quantities of rRNA.

56
Q

How many rDNA repeats are found in human genomes?

A

350

57
Q

How many rDNA repeats are found in E. coli?

A

7

58
Q

How many rDNA repeats are found in yeast genomes?

A

150

59
Q

How many sequence elements are found in the rDNA core promoter?

A

3

60
Q

Where in the human genome are rDNA repeats found?

A

rDNA repeats make up most of the short arms of the 5 acrocentric chromosomes (13, 14, 15, 21 and 22).

61
Q

Are rDNA promoters conserved between species?

A

The spatial organisation of rDNA promoters (a core promoter consisting of 3 mains sequences) is conserved between eukaryotic sepcies but the precise sequences are not conserved.

62
Q

Describe the factors that associate with RNA pol I for the transcription of rDNA genes?

A

RNA pol I has its own initiation factors, however, like RNA pol II, TBP is required for the formation of PIC at rDNA promoters.
RNA pol I uses the same elongation factors as RNA pol II (e.g. FACT and TFIIS) because the elongation phase is functionally the same whatever the underlying sequence.
RNA pol I has its own termination systems, compromised of a series of repeating T-rich elements which bind a particular termination factor called TTF1 which causes the transcript to be cleaved by Rnt1 endonuclease.

63
Q

Approximately how many tRNA genes are found in the human genome?

A

600

64
Q

What is interesting about tRNA encoding genes?

A

They’re really short, only 76 nucleotides long.
They have a promoter (2 conserved elements called the A box and the B box) but this exists within the coding region and makes up the T loop and the D loop.

65
Q

Describe the factors that associate with RNA pol III for the transcription of tRNA encoding genes?

A

RNA pol III has its own completley unique initiation complex called TFIIIC which sticks to DNA all the time, it is constant throughout the cell cycle etc. it is permanently attached to the A and B box (conserved promoter elements).
However, like with RNA pol I and RNA pol II, TBP plays a role in the initiation of transcription at tRNA encoding genes.
During elongation, RNA pol III is self-sufficient and able to elongate without any elongation factors (different to the other two nuclear polymerases), although RNA-binding protein Nab2 is asscoiated with RNA pol III interacting with the emerging transcript.
Like elongation, RNA pol III termination is handled by the core enzyme itself, no accessory proteins are required for termination of RNA pol III.

66
Q

What are the 2 accessory factors required by RNA pol III to form the pre-initiation complex at the promoter of tRNA-encoding genes?

A

TFIIIC and TFIIIB.

67
Q

What is the purpose of unique accessory factors for each nuclear polymerase?

A

These factors give specificity to each of the nuclear polymerases facilitating the transcription of different genes to produce different classes of RNA transcript.
E.g. these factors allow RNA pol I to recognise RNA pol I promoters (in rDNA genes) and not RNA pol II promoters.

68
Q

Which accessory factor is present in the initiation complex of all 3 nuclear polymerases?

A

TBP.

69
Q

Which nuclear polymerase is able to elongate alone (without accessory factors)?

A

RNA pol III.

70
Q

Which nuclear polymerase is able to terminate without accessory factors?

A

RNA pol III.

71
Q

What motifs are bound by TBP?

A

TBP binds AT-rich motifs in all promoters (not just TATA-box containing promoters).

72
Q

What is the function of TBP?

A

TBP binds the minor groove of DNA at AT-rich motifs in promoters and bends the helix by 80 degrees.

73
Q

How many genes are held o on the mitochondrial genome?

A

37

74
Q

How is human mitochondrial DNA transcribed?

A

As 3 operons each encoding a mixture of mRNA, tRNA and rRNA sequences which are subsequently separated by RNA processing steps.

75
Q

From what system is transcription of the mitochondrial genome based off?

A

Phage infection.

76
Q

What is the name of the single elongation factor required for the elongation phase of transcription of human mtDNA?

A

TEFM (transcription elongation factor in mitochondria).

Genes to Genomes (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions