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ASC222 > Topic 3 - Structure of genes, their regulation & expression > Flashcards

Topic 3 - Structure of genes, their regulation & expression Flashcards

1
Q

The major control point in prokaryotes and eukaryotes is…?

A

transcription initiation (turning genes on & off)

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2
Q

Control of transcription initiation is mediated by…?

A

promoters

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3
Q

Proteins that bind to promoters & stimulate/repress transcription are called…?

A

transcription factors

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4
Q

RNA polymerase is made up of how many subunits?

A

4 (2 alpha & 2 beta)

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5
Q

A transcription factor in prokaryotes?

A

sigma subunit

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6
Q

Sigma subunit leaves promoter during which phase?

A

elongation

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7
Q

Termination of transcription (prokaryotes) can occur in which 2 ways?

A

Rho-dependent - Rho factor pulls mRNA away from RNA polymerase
Rho-independent - stem-loop structure signals release of mRNA

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8
Q

What are inducers? In which organisms are they found?

A

factors that turn genes on/off in response to environmental cues in PROKARYOTES

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9
Q

What are some environmental cues that may affect prokaryotes…?

A 
sugars
nitrogen
heat
salt
light intensity
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10
Q

T or F - operons are found in all organisms

A

false - not present in eukaryotes

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11
Q

What are operons? What structures do they contain?

A

2 or more protein coding genes transcribed into a single polycistronic mRNA -> translated into several different proteins at ribosomes
Operons contain: promoter (DNA), repressor protein, operator (DNA) & genes (DNA)

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12
Q

What are cistrons?

A

the several structural genes next to the operator

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13
Q

What are the cistrons in lac operon? What do they encode? What are their functions?

A

lacZ - beta-galactosidase (converts lactose -> glucose & galactose)
lacY - permease (transports lactose into cell)
lacA - acetylase (acetylates lactose)

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14
Q

Why is the operon mRNA said to be ‘polycistronic’?

A

Because it is translated into several proteins

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15
Q

What are the 3 different operons…? How many cistrons in each?

A 
Lactose utilisation operon (lac operon) 3 cistrons
Histidine biosynthesis (his operon) 11 cistrons
Tryptophan biosynthesis (trp operon) 5 cistrons
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16
Q

Who discovered the lac operon?

A

Jacob & Monod

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17
Q

What does the lac operon do?

A

breaks down lactose (milk) eg. rumen bacteria of calves

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18
Q

Lac operon is said to be in ‘off’ position when lactose is …?

A

absent - lac genes can not be expressed

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19
Q

What is the repressor gene? What does it do? When is it present?

A

lacI -> mRNA -> repressor protein

expressed all the time

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20
Q

In the lac repressor, what are the 2 domains?

A

DNA-binding domain (near N terminus)

Inducer-binding domain (near C terminus)

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21
Q

Where does the lactose sugar interact on the lac repressor?

A

Inducer-binding domain (near C terminus)

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22
Q

When lactose enters cell & binds to repressor, is this +ve or -ve control?

A

-ve control

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23
Q

What is +ve control in lac operon?

A

glucose absent -> ++cAMP -> cAMP binds to CAMP receptor protein (CRP or CAP) -> cAMP-CRP complex -> lac promoter -> transcription

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24
Q

End product of lactose metabolism?

A

glucose (-ve feedback inhibition) as ++glucose -> decreased cAMP

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25
Q

How does the trp operon function…?

A

When tryptophan is present -> trp binds repressor (repressor active) -> binds operator -> transcription blocked
Opposite to lac operon function

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26
Q

What is araC?

A

positive regulator for all arabinose genes -> break down sugar arabinose

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27
Q

When arabinose is not present…?

A

AraC dimer binding at araO & araI sites -> no araBAD genes transcribed

28
Q

What does RNA polymerase I transcribe?

A

rRNA genes

29
Q

What does RNA polymerase II transcribe?

A

protein coding & micro RNA genes

30
Q

What does RNA polymerase III transcribe?

A

tRNA & small RNA genes 5S

31
Q

Where does rRNA processing occur?

A

nucleolus

32
Q

Which rRNA units make up ribosomes?

A

28S rRNA & 5.8S rRNA - large ribosomal subunit

18S rRNA - small ribosomal subunit

33
Q

Eukaryotic gene expression is controlled at 8 stages. What are they?

A 
chromatin remodelling
transcription initiation
mRNA (transcript) processing
transcript export to cytoplasm
transcript stability
translation
protein processing, folding & transport
protein stability, degradation & modification
34
Q

Draw diagram of control points

A

slide 26

35
Q

Reasons for extensive control in eukaryotes…?

A

Large genomes (extensive non-coding regions)
compartmentalisation
transcript processing (intron/exon structure)
no operons
proteins can be products of several genes (multi-subunit eg. insulin, haemoglobin)
enhancers & silencers
cell type specific expression necessary

36
Q

Re. transcriptional control of pol II genes via basal factors - what are they?

A

TATA box binding protein (TBP)

TBP associated factors (TAF)

37
Q

How do basal factors control pol II genes?

A

basal factors bind to promoter, then RNA pol II binds to basal factors

38
Q

What are cis-acting sequences? Where are they found? An e.g’s?

A

regions of DNA sequences that bind proteins which interact with RNA polymerase -> regulate transcription
Found in region of promoter or far away, but on SAME CHROMOSOME
eg. enhancers, lac operon

39
Q

What are trans-acting factors? e.g?

A

proteins that bind to cis-acting sequences distant from gene from which they were transcribed
transcription factors

40
Q

Basal factors + pol II bound to DNA = ?

A

low-level transcription

41
Q

Basal factors + pol II + activator protein bound to DNA = ?

A

high-rate of transcription

42
Q

2 common motifs…?

A

helix-loop-helix

zinc finger-leucine zipper

43
Q

Which part of the leucine zipper is the DNA-binding domain?

A

the zinc finger part

44
Q

How do steroid hormones (SH) control transcription?

A

SH binds to steroid hormone receptor -> allosteric change in receptor -> SH receptor & SH -> bind enhancer -> + transcription

45
Q

Transcription factors have a … structure?

A

modular structure - ie. have DNA binding domain separate from the activator domain

46
Q

DNA is kept within the cell via …?

A

chromatin ‘beads on a string’

47
Q

Structure(s) of chromatin…? This complex is called …?

A

2 helix loops wound around 4 histone proteins -> nucleosome

48
Q

Why is chromatin the cells normal DNA storage form?

A

Because it reduces binding to basal factors & RNA pol II to very low levels

49
Q

What do chromatin remodelling proteins do?

A

unwind DNA helix loops from histone to expose promoter so that basal factors can bind -> transcription

50
Q

What are ‘silenced’ genes/heterochromatin?

A

when DNA methylation in a region causes hypercondensation in nucleosomes -> completely inactive genes

51
Q

What is alternative splicing?

A

Different cell types process same pre-mRNA differently -> 2 different proteins from same gene

52
Q

Example of alternative splicing…?

A
  • Calcitonin mRNA in thyroid 32aa for calcium balance

- Calcitonin gene related peptide (CGRP) mRNA in hypothalamus 37aa vasodilator

53
Q

What is translation controlled by?

A

protein synthesis initiation factors & inhibitors

54
Q

Re. protein mRNA stability & half lives. Tubulin, insulin receptor, pyruvate kinase (hrs)?

A 
tubulin (4-12hr)
insulin receptor (9hr)
pyruvate kinase (30hr)
55
Q

How many micro-RNAs identified & characterised?

A

2000-2005

  • 1/4 from introns protein coding transcripts
  • 3/4 from products of primary transcripts devoid of ORFs
  • may exceed number of protein coding genes (>30000)
56
Q

How do micro-RNAs work?

A

trans-acting single stranded micro-RNAs regulate eukaryotic gene expression

57
Q

Structure of miRNA’s…?

A

60-120 ribonucleotides long segments of complimentary reverse sequence- hairpin stem-loop structures

58
Q

Applications of miRNA

A

method for developing powerful new RNA-based therapies for treatment of disease

59
Q

miRNA are processed by which 3 complexes? Where are they found?

A
  1. Drosha - cropping (nucleus)
  2. Dicer - dicing (cytoplasm)
  3. RISC - miRNA degradation (cytoplasm) => miRNA
60
Q

How do miRNAs interfere with transcript stability or translation…?

A
  • mRNA cleavage (miRISC binds to mRNA in perfect complementarity) => mRNA breaks down
  • Translational repression (2 miRISC binds to mRNA for incomplete complementarity)
61
Q

What is post-translational control?

A

modifications that occur to proteins (after translation) that give them functionality

62
Q

What are some types of post-translational control?

A

Modification
- glycosylation (addition of sugar)
- phosphorylation (addition of phosphate groups)
Removal of AAs
Assembly of proteins
Import into organelles (eg. nucleus, mitochondria)
Protein degradation (ubiquitination) eg. dissolving glue protein during anaphase so sister chromatids can seperate

63
Q

Ubiquitination example in more detail…?

A

At metaphase - sister chromatids bound together by glue proteins
At anaphase - expression of anaphase promoting complex (APC) -> attracts ubiquitinating enzyme -> adds ubiquitin to glue protein -> recognised by proteosome which dissolves glue protein -> sister chromatids can separate and continue through anaphase

64
Q

Phosphorylation example…?

A

adrenaline binds to beta-adrenergic receptor -> allosteric change -> ++HR etc. -> kinase transfers phosphate -> receptor -> Adr is removed -> phosphatase removes phosphate

65
Q

Re-draw control points for eukaryotic gene expression summary diagram

A

slide 51

ASC222 (8 decks)

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