24. Gene expression (2 lectures)

Question 1

What is the operon and what is the concept behind it?

Answer 1

• operon - cluster of functionally related genes - can be controlled by switching on / off
• operator - the segment of DNA in the promoter region which switches on / off the operon
• operon includes: operator, promoter, genes they control

Question 2

An example of an operon and how it is controlled

Answer 2

Control of tryptophan operon:

• if trp a not present in diet - operon switched on
• if trp present in diet - operon switched off (tryptophan binds to the repressor)
• trp am a is co-repressor (binds and activates repressor)
• repressor binds to the operator - blocks binding of RNA polymerase - represses gene transcription
• trp operon is repressible operon
• NEGATIVE CONTROL (genes are switched off by active form of repressor)

Question 3

What are the types of operons?

Answer 3

Repressible and inducable

Question 4

What are repressible operons

Answer 4

Usually in anabolic pathways (build up)

Question 5

What are inducible operons

Answer 5

Usually in catabolic pathways (breakdown)

Question 6

Explain the mechanism of repressing lac operon (prokaryotes)

Answer 6

• regulatory gene produces the repressor for the trancsription of lactose genes
• lactose absent - repressor active - binds to DNA - blocks operator by binding - blocking RNA polymerase - lactose genes not transcribed
• NEGATIVE CONTROL (genes are switched off by active form of repressor)

Question 7

Explain the mechanism of activating lac operon (prokaryotes)

Answer 7

• lactose present - repressor is inactive
• lactose blocks the activity of the repressor (allolactose inducer) - RNA polymerase can bind and transcribe the gene

Question 8

Negative vs positive control of transcription (prokaryotes)

Answer 8

Negative: operon is inactivated by active represssor (usualy gene is on - off only by repressor)

Positive: activator of transcription is involved instead of repressor (usually gene is off - on only by activator or activator boost transcription )

Question 9

Give an example of operon activator (prokaryotes)

Answer 9

CRP (protein for cyclic AMP receptor) - controls catabolism of lactose when little glucose present:

• when glucose scarce - CRP activated by binding with cyclic AMP (cAMP) protein (signalling molecule)
• activated CRP binds to promoter of lac operon - increases affinity for RNA polymerase - faster transcription
• when glucose levels increase - CRP detaches - transcription at normal rate

Question 10

Key points from 18.1 gene regulation in prokaryotes

Answer 10

Question 11

What are the possible modifications during gene expression to control it?

Answer 11

Question 12

What are the possible modifications at the pre-transcriptional regulation?

Answer 12

• chromatin structure - histone acetylation and methylation - influence nucleosome packing - gene acessibility for transcription heterochromatin (tight), euchromatin (loose)
• DNA modifications (acetylation / methylation)

Question 13

How do unacetylated and acetylated histones in nucleosomes look?

Answer 13

Acetylated histones repel each other

Question 14

Explain DNA methylation

Answer 14

Question 15

What is the structure of a typical eukaryotic gene?

Answer 15

5’UTR / 3’UTR - untranslated regions

Question 16

Explain general vs specific transcription factors

Answer 16

General - essential for transcription of all genes coding for proteins (at promoters)

Specific - high transcription levels / transcription of genes which are not expressed all the time - depend on control elements which interact with specific transcription factors (at enhancers - distal control elements - distance away from the gene)

Question 17

Explain trancription factors

Answer 17

Regulate transcription of genes - structure: has DNA binding domain and activation domain

Question 18

How do activators far away from the gene activate transcription?

Answer 18

Involves protein-mediated bending of DNA strand - bound activators in conatct with mediator proteins - interact with general transcirption factors at promoters → assembly of transcription initiation complex

Question 19

What are coordinately controlled genes in eukaryotes?

Answer 19

• co-expressed genes in eukaryotes are not in operons - can be scattered across chromosomes but have similar control elements - activators recognise the control elements and promote transcription of those genes simultaneously
• In bacteria done through operons

Question 20

What are transcription factories

Answer 20

Some chromosome regions interact - chromosome territories - loops of chromatin from different chromosomes may gather - rich in transcription factors/RNA polymerases → trancsription factories specialised for a particular common function

Question 21

What are the possible post-transcriptional modifications?

Answer 21

Through RNA processing the primary mRNA transcript is made into mature mRNA

Question 22

What is alternative splicing?

Answer 22

Explanation for relatively low gene number for the number of different proteins produced

Question 23

What is the sequence of the possible gene modifications?

Answer 23

1. Chromatin modification: histone acetylation/methylation, DNA methylation
2. Gene activation / repression (level of transcription)
3. Post-transcriptional modifications: alternative splicing / poly-A tail / capping
4. Mature mRNA transported out of the nucleus into cytoplasm
5. Degradation of mRNA: stability of mRNA is encoded in UTR regions in 3’ end
6. Translational modifications: proteins bind - block assembly of ribosomes (determined by 5’ UTR)
7. Protein processing: degradation / stability / transport regulated

Question 24

Explain mRNA degradation in post-transcriptional modification: eukaryotic vs prokaryotic, what determines the lifespan of mRNA

Answer 24

Question 25

Translational modifications

Answer 25

Proteins bind - block translation by blocking ribosome assembly - 5’ UTR determines

Question 26

Explain post-translational modifications of proteins

Answer 26

• Ex: histone acetylation / methylation (protein modification - effect on packaging of chromatin)
• Phosporylation
• Ubiquitin covalently attaches unlike other modifications - recognised by proteosomes - degraded

Question 27

Main points of eukrayotic gene regualtion

Answer 27

Question 28

What are non-coding RNAs?

Answer 28

Before thought as ‘junk’

Question 29

What are micro RNAs? What are the effect sof them?

Answer 29

A group of non-coding RNAs (ncRNAs)

Question 30

What is the mechanism of miRNAs?

Answer 30

miRNA part of a complex → miRNA binds to a target → degrades the mRNA if perfect match → prevents ribosome assembly if not perfectly complete match

Question 31

What are the groups of ncRNAs?

Answer 31

miRNAs

siRNAs

lncRNAs

Question 32

What are small interferring RNAS (siRNAs)? What are the effects of siRNA?

Answer 32

• Differs from miRNAs by their production pathway
  *

Question 33

What is RNA interference (RNAi)?

Answer 33

RNA interference (RNAi) is mechanism of post-transcriptional negative gene regulation - used in laboratories - gene knock off (supressing desired genes)

Question 34

What are long non-coding RNAs (lncRNAs)? What are their effects?

Answer 34

Question 35

Classification of RNAs

Answer 35

ncRNAs regulate gene expression at multiple steps in many ways