B: Gene regulation eukaryotes

Question 1

—What is the difference between the function of RNA polymerase I, II and III in eukaryotes?

Answer 1

• RNA pol I: transcribes 45rs gene
• RNA pol II: transcribes protein encoding genes and some non-coding RNAs
• RNA pol III: transcribes 5s rRNA, tRNAs and other small RNAs

Question 2

—Describe the core promoter in eukaryotes.

Answer 2

Usually found upstream of a gene, contains:
- TATA element
- BRE (recognition element) for a TF called TFIIB
- Inr (initiator element)
- DPE (downstream promoter element)

Question 3

–What is the difference between general transcription factors and specific transcription factors?

Answer 3

• GTFs bind to the core promoter and sponsor basal transcription
• STFs bind to DNA sequences upstream of the core promoter (these sequences are upstream promoter elements (UPEs))

Question 4

–What is the difference between TFIID and TBP?

Answer 4

TFIID is a GTF that contains TBP (TATA binding promoter)

Question 5

Elements of trancription at low basal level

Answer 5

• RNA polymerase II
• GTFs
• Core promoter DNA
• RNA precursors

Question 6

–What is the basal transcription complex?

Answer 6

It’s the build up of GTFs in the core promoter region

Question 7

—List all the proteins that you might find in a transcription initiation complex.

Answer 7

Proteins which recruit RNA polymerase to promoter + allow it to act
- GTFs
- STFs
- Regulated STFs
- Enhancer binding proteins (including STFs)
- Mediator

Question 8

—List and explain 5 ways that transcription factors can be regulated.

Answer 8

1. Activation or inactivation of TF by addition or subtraction of small chemical groups or ligands
2. Homodimerisation or heterodimerisation of TF to form a dimer with another TF –> activated
3. Proteolytic cleavage –> activated
4. Translocation from cytoplasm to nucleus –> activated
5. Removal of repressors –> activated

Question 9

—Explain how transcription can be regulated at multiple levels.

Answer 9

• Accessibility of chromatin (10nm = euchromatin = open = accessible / 30nm = heterochromatin = closed = innaccessible)
• Methylation of DNA (can affect chromatin conformation and binding of TFs to DNA)
  ○ Methylation = condensation to 30 nm fibre = downregulation
  ○ Demethylation = 10 nm fibre = upregulation
• Repressors (negative regulation)
• Activators (positive regulation)

Question 10

What are general transcription factors:

Answer 10

Bind directly or indirectly to core promoter. Gene and promoter overlap. Consist of:
- TFIIA 2
- TFIIB 1
- TFIID 12
- TFIIE 2
- TFIIF 3
- TFIIH 9

Question 11

Difference between DNA binding domain and transcription activation domains:

Answer 11

DNA binding domain: binds an element in promoter
Activating domain: interacts directly with proteins in basal transcription complex and activates transcription.

Question 12

How do transcription factors work?

Answer 12

Many bind directly or indirectly to basal transcription complex. Some have DNA binding domain or activation domain or both.
Others alter chromatin structure

Question 13

List the DNA elements involved in a transcription initiation complex

Answer 13

• Elements in core promoter
• Upstream promoter elements
• Enhancer elements

Question 14

What is positive regulation

Answer 14

Activation of gene transcription by activators

Question 15

What is negative regulation

Answer 15

Repression of genes by repressors

Question 16

INS

Answer 16

beta cells in pancreas produce insulin

Question 17

HBB

Answer 17

beta globin (HBB) produced in erythrocytes which arise in the bone marrow

Question 18

TNNI3

Answer 18

large amounts of cardiac specific troponin - only produced in heart tissue. Amount of cardiac specific troponin in blood reflects how much damage there is to the heart

Question 19

RPS13

Answer 19

encodes ribosomal protein 13 + GAPDH which encodes an enzyme in glycolysis

Question 20

GAPDH

Answer 20

glyceraldehyde 3-phosphate dehydrogenase for glycolysis (housekeeping protein)

Question 21

Difference between TFIID and TBP?

Answer 21

TFIID is a GTF with 12 subunits and TBP is one of its subunits that binds to the TATA box in the core promoter region to initiate transcription.
TBP is called the TATA binding protein. TBP is a central TF.

Question 22

Difference between RNA polymerase I, II and III?

Answer 22

I: transcribes 45S rRNA precursor gene
II: transcribes protein encoding genes and some non-coding RNAs
III: transcribes 5S rRNA, tRNAs & other small RNAs

Question 23

Explain how mesenchymal stem cells can be converted into insulin secreting cells using TFs

Answer 23

Genes for three transcription factors (PDX-1, NeuroD1, MafA) were put into and expressed in stem cells. After a few days, insulin was produced in cells and secreted.