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Cell and Molecular Biology > Gene Structure and Bacterial Transcription > Flashcards

Gene Structure and Bacterial Transcription Flashcards

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1
Q

Define gene expression

A

information encoded in a gene that is turned into a function

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2
Q

Give examples of non-coding genes

A

promoters, enhancers, silencers, tRNA and rRNAs

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3
Q

What are non-coding genes

A

they do not code for proteins

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4
Q

True or False:
There are more coding genes than non-coding genes

A
  • False
  • More non-coding genes (80%)
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5
Q

Define gene

A

a DNA sequence that encodes information for a functional product made of RNA or protein

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6
Q

Why is RNA important in gene expression

A
  • important in protein synthesis
  • important regulator of gene expression
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7
Q

What is the first step of gene expression

A

transcription

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8
Q

Why is gene expression highly controlled

A
  • not all genes need to be expressed at the same time or degree
  • cells need to differentiate into different cell types
  • cells need to respond to external stimuli
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9
Q

What are the 3 main features of bacterial gene for transcription

A
  • promoter region
  • transcriptional start site
  • transcriptional terminator sequence
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10
Q

What is the difference between a start codon and a transcriptional start site

A
  • start codon: first bases being translated
  • transcriptional start site: site of attachment for RNA polymerase
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11
Q

Why is the promoter region (and others) highly conserved

A

because they are critical/vital to prokaryotes + eukaryotes ability to express genes (transcription + translation)

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12
Q

What is the promoter region

A

sequence of DNA where RNA polymerase binds to + contains regulatory factors

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13
Q

Where is the promoter region usually located

A

upstream (before) the gene itself

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14
Q

What is the difference between regulatory factors and transcriptional factors

A

regulatory factors: DNA sequences like silencers, enhancers, TATA box
transcriptional factors: proteins that bind to regulatory DNA sequences like activators, repressors

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15
Q

What are the 2 highly conserved consensus sequences in bacteria

A

-10 and -35

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16
Q

What are consensus sequences

A
  • they indicate where to initiate transcription
  • transcription factors recognise them and recruit RNA polymerase to bind to consensus sequences
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17
Q

True or False:
Eukaryotes have consensus sequences

A
  • True
  • prokaryote: -10 & -35
  • eukaryote: TATA box
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18
Q

What are the functions of consensus sequences

A
  • serve as a recognition site for transcription factors + RNA polymerase
  • ensures transcription starts at the right place
  • helps to bind RNA polymerase
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19
Q

What is an operator

A

DNA sequences that serve as binding sites for regulatory proteins (ex: activators, repressors)

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20
Q

True or False:
Operators exists only in prokaryotes

A

True

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21
Q

What happens if a repressor protein binds to an operator

A

it stops RNA polymerase from binding to the DNA sequence and prevents transcription

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22
Q

What happens if an activator protein binds to an operator

A

it enhances the binding of RNA polymerase and promotes transcription

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23
Q

What is a terminator sequence

A

signal that tells the RNA polymerase to stop transcribing

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24
Q

How does a terminator sequence stop transcription

A
  1. when an RNA polymerase encounters a terminator sequence, it forms an RNA hairpin structure
  2. The AT-rich regions + hairpin destabilise RNA polymerase’s interaction w/ DNA
  3. RNA polymerase dissociates from DNA
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25
Q

what are monocistronic genes

A
  • 1 gene btw promoter and termination sequence
  • 1 mRNA transcript = 1 protein
  • eukaryotes
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26
Q

What are polycistronic genes

A
  • multiple genes btw promoter and termination sequence
  • multiple mRNA transcripts = multiple proteins
  • prokaryotes
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27
Q

What are type II genes

A

genes transcribed by RNA polymerase II

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28
Q

True or False:
Prokaryotes have multiple RNA polymerases?

A

False

29
Q

What is a TATA box

A
  • binding sites for TATA-binding proteins
  • transcriptional factors
  • helps position RNA polymerase
30
Q

What is the main function of upstream control elements

A

help regulate gene expression by interacting w/ transcription factors + regulatory proteins

31
Q

What are regulatory sequences

A

specific DNA sequences to which transcription factors bind to

32
Q

Where are the upstream control elements located

A

in the promoter region

33
Q

What is the function of regulatory sequences

A

ensures that the right genes are being expressed at the right time (when needed)

34
Q

What are the different types of regulatory sequences

A
  • trans-acting: far away from promoter
  • cis-acting: next to the promoter
35
Q

How does gene location affect gene expression

A
  • lot of chromatin = few genes
  • little chromatin = lot of genes
36
Q

Why do telomeres and centromeres have few genes

A
  • they have a lot of chromatin (heterochromatin)
  • continuously unwinding for gene expression would cause chromosomes to break
37
Q

True or False:
Bacteria have introns

A

False

38
Q

What are insulators

A

they are cis-acting elements that ensure other genes don’t interfere with gene expression

39
Q

What is the function of insulators

A
  • can block enhancers
  • act as a barrier against genes being silenced by heterochromatin
40
Q

Define exons

A

coding regions

41
Q

Define introns

A

non-coding regions

42
Q

What is a sigma factor

A

a polymerase subunit that recognises + binds to promoter sequences on DNA

43
Q

What is a holoenzyme

A

enzyme activated by cofactor

44
Q

What does a sigma factor bind to

A

RNA polymerase + sigma factor = holoenzyme

45
Q

What happens when sigma factor binds to RNA polymerase

A

it allows RNA polymerase to recognise the transcriptional start site

46
Q

What happens if there is no sigma factor to bind to RNA polymerase

A

RNA polymerase can’t recognise + bind to promoter and transcription won’t occur

47
Q

What is the most common type of sigma factor + why

A
  • sigma 70
  • it is responsible for housekeeping genes
48
Q

What are housekeeping genes

A

genes critical to the cell’s survival

49
Q

What is the role/function of holoenzyme

A
  • creates a transcriptional bubble
  • melts DNA strands (separates them)
50
Q

Outline initiation (bacterial transcription)

A
  • holoenzyme creates transcriptional bubble + melts DNA strands
  • RNA polymerase adds nucleotides in 5’ to 3’ direction replacing T w/ U
  • sigma factor dissociates from RNA polymerase as RNA transcript is being made
51
Q

Outline elongation (bacterial transcription)

A
  • RNA polymerase continues to add nucleotides in a 5’ to 3’ direction, replacing T w/ U
  • until it reaches termination sequence
52
Q

Outline termination (bacterial transcription)

A
  • RNA hairpin is created and AT-rich regions cause RNA polymerase to stall + dissociate from DNA
  • stops transcription
53
Q

when is the Lac Operon turned off

A

when the prokaryote has glucose and the repressor encoded by Lac I gene

54
Q

What happens when glucose is present (Lac Operon)

A
  • no need for lactose
  • repressor binds to operator in Lac Operon
  • prevents RNA polymerase from binding (no transcription)
55
Q

When happens when glucose is absent (Lac Operon)

A
  • need for lactose
  • allolactose binds to repressor
  • RNA polymerase can bind (transcription occurs)
56
Q

What does the Lac Y gene encode for

A

lactase

57
Q

Outline the binding of CAP to Lac Operon

A
  • glucose is low
  • ATP is broken down into CAMP
  • CAMP binds to CAP and changes its shape
  • it allows CAP to bind to DNA sequence (Lac Operon)
  • when CAP bound, helps RNA polymerase to transcribe lacZYA genes more effectively
58
Q

why are the lacZYA genes important

A

they encode proteins that allow bacteria to effectively utilize lactose as a source of energy when it is available

59
Q

Outline the removal of Lac Repressor

A

-lactose is present it needs to be metabolised
- some of the lactose is converted into allolactose
- allolactose binds to lac repressor changing its conformation
- it makes it unable to bind to the DNA sequence (Lac Operon)

60
Q

When is the lac Operon turned on

A
  • glucose is low
  • lactose is present
  • cAMP levels are high
61
Q

Outline the Binding of RNA polymerase (Lac Operon)

A
  • Once lac repressor is removed
  • RNA polymerase + sigma factor bind to DNA w/ CAP’s help
  • transcription occurs
  • RNA transcripts from lac ZYA genes are made allowing lactose to be transported into cell and broken down into glucose
62
Q

When is the lac Operon turned off

A
  • glucose levels are high
  • lactose is absent
  • cAMP levels are low
63
Q

How does the lac Operon get turned off

A
  • glucose becomes main energy source
  • less cAMP so less CAP to bind to
  • less CAP binds to DNA
64
Q

How do inducers and inhibitors work

A
  • they bind to DNA-binding proteins
  • cause a conformation change that alters how it binds to the DNA
  • activates or inhibits gene expression
65
Q

What are inducible repressors

A

When inducers bind to repressors, they change the repressor’s conformation and so the repressors don’t bind to DNA and transcription continues as normal

66
Q

What are Repressible repressors

A

Inhibit transcription when bound to the effector molecule

67
Q

What are Repressible activators

A

When inhibitors bind to activators, they change the activator’s conformation and so the activators don’t bind to DNA and transcription stops

68
Q

What are Inducible activators

A

Cause transcription when bound to the effector

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