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[ONCG2002] Cancer Cell Genetics > 2: Gene Expression & Mechanisms of Gene Regulation > Flashcards

2: Gene Expression & Mechanisms of Gene Regulation Flashcards

1
Q

What does RNA polymerase do?

A

• Transcribes DNA > RNA
•RNA polymerase binds to double stranded DNA and uses the DNA sequence information to produce RNA.

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2
Q

Does RNA polymerase need a primer?

A

No

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3
Q

What are non-coding sections of RNA transcripts called?

A

Introns

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4
Q

What are exons?

A

Coding sequences within the gene

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5
Q

What is pre-mRNA spliced to remove?

A

Introns

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6
Q

What happens during mRNA processing?

A

mRNA is capped at 5’ tail and polyadenylated at 3’ tail

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7
Q

What are the 5’ and 3’ ends of DNA/RNA

A

The 5 prime end” has a free hydroxyl (or phosphate) on a 5’ carbon and the “3 prime end” has a free hydroxyl (or phosphate) on a 3’ carbon (carbon atoms in the sugar ring are numbered from 1’ to 5’)

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8
Q

What can be done to mRNA to regulate Gene expression?

A

• mRNA splicing
• mRNA export
• mRNA translation
• mRNA stability control

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9
Q

What is alternative splicing ?

A

Splicing which can produce multiple mRNAs (and thus proteins) from one gene

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10
Q

What are basal transcription factors?

A

Help RNA polymerase bind to DNA.
Required at most promoters
They are not specific to any promoters

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11
Q

What is TFIID

A

a large complex that contains TBP - TATA binding protein

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12
Q

What is TBP

A

TATA binding protein

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13
Q

How is the DAB complex formed?

A

When In vitro TFIID binds with TFIIA and TFIIB

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14
Q

What is PIC

A

Pre-initiation complex

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15
Q

How can multiple proteins be created using a single gene?

A

Through alternative splicing and alternative promoters

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16
Q

What is a holoenzyme?

A

• a complete and catalytically active enzyme consisting of protein part (apoenzyme) together with its bound coenzyme and/or metal ions (prosthetic group).
• “complex enzyme assembly”

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17
Q

What is a MED

A

Mediator complex

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18
Q

What do MEDs do

A

help to form the PIC and allow transcription to be regulated by gene specific transcription factors (aka transcription factors or TFs).

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19
Q

What are CRFs, what do they do?

A

•chromatin remodelling factors
•CRFs help to remove or reposition nucleosomes and other proteins bound to the DNA.

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20
Q

Where do gene specific transcription factors bind?

A

At the promoter, at enhancers, or to basal transcription factors

21
Q

What are enhancers?

A

DNA sequences that act independently of distance and orientation – they can even be on different chromosomes.

They increase the transcription of genes by binding TFs

They usually bind multiple transcription factors

22
Q

How can gene specific transcription factors help RNA polymerase II?

A

They can bind to mediators/ basal transcription factors to help RNA polymerase II interact with the promoter

23
Q

What are some functions of bio molecular condensates?

A

They are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction.

24
Q

What are biomolecular condensates?

A

micron-scale compartments in eukaryotic cells that lack surrounding membranes, but concentrate biomolecules including proteins and nucleic acids.

25
Q

What is an example of a gene promoter than has multiple enhancers?

A

MYC

26
Q

What is chromatin?

A

DNA-protein complex found in cells.

• DNA wrapped around histone proteins to form nucleosomes
• Histone proteins are positively charged, and bind to negatively charged DNA to form chromatin

27
Q

Where do active (transcribed) genes versus repressed genes tend to be located on the chromosome loops?

A

• active = end of loops
• repressed = condensed regions at base of loops

28
Q

What is the area of nuclear regions with a low density of DNA called?

A

Euchromatin

29
Q

What do you call a nuclear region with a lot of DNA staining?

A

Heterochromatin

30
Q

Where are most of the untranscribed/repressed genes located in the nuclear region?

A

Heterochromatin

31
Q

Where do genes move in the nuclear region when they become activated?

A

Heterochromatin

32
Q

How does nucleosome occupancy affect transcription?

A

affects the binding of transcription factors by influencing the accessibility of genome DNA

33
Q

What are housekeeping genes?

A

Genes active in all or most cell types

34
Q

What signals cause induced displacement/nucleosome exclusion?

A

Signals that turn on transcription

35
Q

What do pioneer TFs do?

A

“Opens up” chromatin to allow other TFs and RNA polymerase to bind

36
Q

What is the difference between pioneer TFs and most other TFs?

A

• Pioneer TFs bind independently to nucleosome/chromosome, other TFs allow cooperative binding
• Pioneer TFs precedes other factors binding, other TFs simultaneously bind with other factors

37
Q

How is transcription initiated?

A

when RNA polymerase binds the promoter.

38
Q

What is the role of a transcription activator ?

A

They work by binding to enhancers and recruiting RNA polymerase and other transcriptional machinery to the site. This enhances the rate of transcription, allowing for the synthesis of RNA molecules from the gene.

39
Q

What are the 4 types of RNA polymerases in humans?

A

RNA polymerase I, II, II, and mitochondrial RNA polymerase

40
Q

How does polyadenylation of pre-mRNA effect gene regulation?

A

A polyadenyl tail of the end of mRNA gives stability which in turn can regulate expression of the gene

41
Q

Why is a 5’CAP added to pre-mRNA?

A

So it can be recognized by ribosomes

42
Q

How a it possible that the human body can create more proteins than it has genes?

A

Alternative splicing- multiple proteins can be created from a single gene

43
Q

How can PIC affect gene regulation?

A

It includes TFIIH, which has helicase activity. This unwinds DNA, making it more accessible for RNApolymerase to bind to and move along DNA.

44
Q

What is the difference between the timeline of PIC formation in cells versus in labs?

A

In labs, all components are added sequentially. Whereas in cells, they all bind almost simultaneously

45
Q

How can CRFs affect gene regulation?

A

They can help to rearrange or remove nucleosomes, which can make the DNA more accessible for RNA polymerase to bind

46
Q

Describe the structure of the bio molecular condensate involving Myc.

A

There are many BRD4 molecules which stick together. They bring 7 different exons, RNA polymerase, and the myc promoter together, forming a cluster

47
Q

How might the existence of condensates for promoters affect gene regulation?

A

It means that enhancers are closer together and close to the promoter & rna polymerase. It means if one exon is mutated, the promoter can still function

48
Q

Why is it easier to transcribe genes in euchromatin

A

They are loosely packed, less dense, so easier for binding proteins to access the genes

49
Q

Where are housekeeping genes preset?

A

In the euchromatin as they are always active

[ONCG2002] Cancer Cell Genetics (6 decks)

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