1.3 - Regulation of Gene Expression in Eukaryotes

Question 1

What is the difference between transcription and translation in prokaryotes and eukaryotes?

Answer 1

• uncoupled in eukaryotes as separated in the nuclear membrane
• coupled in prokaryotes as no membrane to separate them

Question 2

Explain mRNA processing in eukaryotes

Answer 2

• 5’ end capping
• 3’ end polyadenylation
• splicing

Question 3

What is 5’ end capping?

Answer 3

addition of altered nucleotide onto the 5’ end of the primary transcript that stops the strand being recognised by nucleases

Question 4

What is 3’ end polyadenylation?

Answer 4

• sequence at the end of gene which is recognised by specific nucleases and cleaved
• adenines are then added
• proteins bind to polyA tail and 5’ cap
• protects the ends of mRNA
• polyA tail gets shorter in translation as nucleases degrade it
• proteins will no longer bind to poly A tail
• mRNA looses protection

Question 5

Is eukaryotic DNA monocistronic or polycistronic?

Answer 5

monocistronic

Question 6

What does it mean if DNA is monocistronic?

Answer 6

every gene has its own promoter and every mRNA codes for its own protein

Question 7

How many RNA polymerases are there in prokaryotes and eukaryotes?

Answer 7

prokaryotes - 1
eukaryotes - 3

Question 8

What are the 3 RNA polymerase in prokaryotes?

Answer 8

Pol I - transcribe structural RNA
Pol II - transcribe all of the protein code in genes
Pol III - transcribe structural RNA

Question 9

What is the difference in promoters between prokaryotes and eukaryotes?

Answer 9

• in eukaryotes there is extended promoters up to 1000 bps from core promoter

Question 10

explain transcription regulation

Answer 10

• RNA Pol II binds to TATA box in both activated and inactive states
• promoter proximal elements bind proteins to the RNA Pol II
• sequences called enhancers or silencers bind either activators or repressors and then bind this to the RNA Pol II

Question 11

What is the structure of eukaryotic promoter?

Answer 11

Promoter proximal elements
- GC - rich box - -200bp
- CCAAT - -100bp
Promoter
- TATA - -30bp

Question 12

What is euchromatin?

Answer 12

open form of chromatin accessible to TFs

Question 13

What is heterochromatin?

Answer 13

highly packed chromatin poorly accessible to TFs

Question 14

Explain genes in heterochromatin and euchromatin

Answer 14

Heterochromatin
- silenced
- TFs cannot get through

Euchromatin
- active
- TFs can access

Question 15

What is spliceosome?

Answer 15

• ribonucleoprotein complex (made of RNA and proteins)
• recognised the 5’ and 3’ end of exons
• brings them together

Question 16

How does the spliceosome do alternative splicing?

Answer 16

• brings the 3’ end of one intron to the 5’ end of another

Question 17

What is the role of alternative mRNA spacing in sex determination of drosophila?

Answer 17

• pre-RNA == double sex - has everything for both sexes
• DNA binding domain is created which is the same in both sexes (exons 1, 2, 3)
• remain exons are spliced in a combination that makes 2 different repressors(f = 4, M = 5, 6)
• in females - represses male genes
• in males - represses female genes

Question 18

Why are post-translational modifications important?

Answer 18

• allows quick response to environmental signals - don’t wait for transcription and translation
• most are reversible
• energy saving

Question 19

Which enzyme phosphorylates a protein?

Answer 19

kinase

Question 20

Which enzyme dephosphorylates a protein?

Answer 20

phosphatase

Question 21

What is the role of protein kinases?

Answer 21

• transfer a phosphate group using ATP to serine, threonine or tyrosine
• as phosphate needs OH acceptor

Question 22

How does phosphorylation regulate protein-protein interactions?

Answer 22

• protein A interacts with protein B
• protein A is phosphorylates
• protein A will no longer interact with protein B - may be due to size or charge
• protein A does not interact with protein C
• protein A is phosphorylates
• protein A interacts with protein C - may be due to shape or charge

Question 23

What is needed for the increase and decrease of cyclin-CDKs?

Answer 23

increase - transcriptional activation
decrease - protein degradation

Question 24

How do cells degrade proteins that regulate the cell cycle?

Answer 24

• ubiquitin is added to protein’s lysines that are to be degraded
• more ubiquitin can be attached to the first lysine
• proteasome then recognises ubiquitin and degrades the protein

Question 25

What is ubiquitin?

Answer 25

• short 76 amino acid peptide that can be attached to lysines
• it contains lysines so they can attach to themselves

Question 26

What is a proteasome?

Answer 26

• Huge protein complex shaped like a barrel
• ubinquinated proteins are degraded by it

Question 27

Explain post translational modification in bacteria

Answer 27

they do not have it

Question 28

Explain protein degradation in bacteria

Answer 28

• signal peptide attached to substrate
• adaptor protein recognises this and binds to the signal peptide
• adaptor proteins then bring the substrate to proteases where it is degraded
• bacteria have multiple proteases

Question 29

Name 8 model organisms

Answer 29

• M. musculus
• D. rerio
• X. tropicalis
• D. melanogaster
• C. elegans
• E. coli
• S. ceravisae
• A. thaliana

Question 30

name 9 requirements of model organisms

Answer 30

• easy to grow and maintain in a lab
• short generation time
• large number of offspring
• well studied genome
• efficient manipulation of genomes
• researchers can share strains / genetic constructs
• no ethical concerns
• decreased complexity compared to humans
• well suited to study fundamental biological processes conserved in all eukaryotes

Question 31

Explain how phosphorylation cascades work

Answer 31

• kinase is activated
• phosphorylates more kinases
• these phosphorylate more kinases
• which then phosphorylate the protein