2: Gene Expression & Mechanisms of Gene Regulation

Question 1

What does RNA polymerase do?

Answer 1

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

Question 2

Does RNA polymerase need a primer?

Answer 2

No

Question 3

What are non-coding sections of RNA transcripts called?

Answer 3

Introns

Question 4

What are exons?

Answer 4

Coding sequences within the gene

Question 5

What is pre-mRNA spliced to remove?

Answer 5

Introns

Question 6

What happens during mRNA processing?

Answer 6

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

Question 7

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

Answer 7

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’)

Question 8

What can be done to mRNA to regulate Gene expression?

Answer 8

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

Question 9

What is alternative splicing ?

Answer 9

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

Question 10

What are basal transcription factors?

Answer 10

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

Question 11

What is TFIID

Answer 11

a large complex that contains TBP - TATA binding protein

Question 12

What is TBP

Answer 12

TATA binding protein

Question 13

How is the DAB complex formed?

Answer 13

When In vitro TFIID binds with TFIIA and TFIIB

Question 14

What is PIC

Answer 14

Pre-initiation complex

Question 15

How can multiple proteins be created using a single gene?

Answer 15

Through alternative splicing and alternative promoters

Question 16

What is a holoenzyme?

Answer 16

• 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”

Question 17

What is a MED

Answer 17

Mediator complex

Question 18

What do MEDs do

Answer 18

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

Question 19

What are CRFs, what do they do?

Answer 19

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

Question 20

Where do gene specific transcription factors bind?

Answer 20

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

Question 21

What are enhancers?

Answer 21

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

Question 22

How can gene specific transcription factors help RNA polymerase II?

Answer 22

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

Question 23

What are some functions of bio molecular condensates?

Answer 23

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

Question 24

What are biomolecular condensates?

Answer 24

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

Question 25

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

Answer 25

MYC

Question 26

What is chromatin?

Answer 26

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

Question 27

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

Answer 27

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

Question 28

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

Answer 28

Euchromatin

Question 29

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

Answer 29

Heterochromatin

Question 30

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

Answer 30

Heterochromatin

Question 31

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

Answer 31

Heterochromatin

Question 32

How does nucleosome occupancy affect transcription?

Answer 32

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

Question 33

What are housekeeping genes?

Answer 33

Genes active in all or most cell types

Question 34

What signals cause induced displacement/nucleosome exclusion?

Answer 34

Signals that turn on transcription

Question 35

What do pioneer TFs do?

Answer 35

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

Question 36

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

Answer 36

• 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

Question 37

How is transcription initiated?

Answer 37

when RNA polymerase binds the promoter.

Question 38

What is the role of a transcription activator ?

Answer 38

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.

Question 39

What are the 4 types of RNA polymerases in humans?

Answer 39

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

Question 40

How does polyadenylation of pre-mRNA effect gene regulation?

Answer 40

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

Question 41

Why is a 5’CAP added to pre-mRNA?

Answer 41

So it can be recognized by ribosomes

Question 42

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

Answer 42

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

Question 43

How can PIC affect gene regulation?

Answer 43

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

Question 44

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

Answer 44

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

Question 45

How can CRFs affect gene regulation?

Answer 45

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

Question 46

Describe the structure of the bio molecular condensate involving Myc.

Answer 46

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

Question 47

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

Answer 47

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

Question 48

Why is it easier to transcribe genes in euchromatin

Answer 48

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

Question 49

Where are housekeeping genes preset?

Answer 49

In the euchromatin as they are always active