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2B: Genetics and Evolution > 1.2 - Regulation of gene expression in prokaryotes > Flashcards

1.2 - Regulation of gene expression in prokaryotes Flashcards

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Biology 101 flashcards
1
Q

What is the central dogma of molecular biology?

A

Genetic information can be transferred from DNA to RNA then into a protein. Or from RNA to DNA, but never can be converted from protein to RNA or DNA.

Was suggested by Francis Crick in mid 1950s

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2
Q

Explain transcription in bacteria

A

Transcription and translation are coupled. Since there is no nucleus, ribosomes can the stopped from translating the mRNA as it is being transcribed.

All genes are transcribed, but not all are translated.

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3
Q

Explain the gene coordinate system

A
  • +1 is the first nucleotide in the transcript, this is upstream of the first nucleotide that is going to be translated
  • -10 is the TATA box
  • -35
    both -10 and -35 and important for RNA polymerase to know where to bind on the promoters
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4
Q

what is the start codon?

A

AUG

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5
Q

what will happen to everything left of the start codon?

A

UTR (untranslated region)

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6
Q

what are the properties of the untranslated region (UTR)?

A

has a binding site where the small subunit of the ribosome (30s) will bond. At the AUG codon the large subunit (50s) will then bind.

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7
Q

What is an operon?

A

multiple genes transcribed from the same promoter. In the operon there is a ribosome binding site (RBS) for each gene and translation stat sites and termination codons

The genes in an operon are normally linked

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8
Q

What is monocistronic mRNA?

A

The mRNA only codes for one protein
Present in eukaryotes

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9
Q

What is polycistronic mRNA?

A

The mRNA codes for more than one protein
Present in prokaryotes

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10
Q

Describe the structure of RNA polymerase when inactive and what are the roles of these subunits?

A
  • 2 smaller alpha subunits - enzyme assembly and promoter recognition
  • 1 larger beta subunit - catalytic centre
  • 1 larger beta prime subunit - catalytic centre
  • 1 small omega subunit - enzyme assembly
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11
Q

Describe the structure of RNA polymerase when active and what are the roles of these subunits?

A
  • 2 smaller alpha subunits - enzyme assembly and promoter recognition
  • 1 larger beta subunit - catalytic centre
  • 1 larger beta prime subunit - catalytic centre
  • 1 small omega subunit - enzyme assembly
  • 1 sigma factor
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12
Q

Describe the process of activation of RNA polymerase

A
  • initiation -sigma factor recognised the -35 and -10 sequences and this commits the RNA polymerase to initiating transcription
  • elongation - RNA polymerase synthesises the RNA chain in a 5’ to 3’ direction and does not require a primer to start. sigma factor leaves at the start of elongation
  • termination - at the terminator sequence there is a hair pin bend flowed by a stretch of UUU as the UA base pairing is weaker than the GC base pairing. This makes it easier for the RNA to leave the DNA template
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13
Q

What can affect the ability of RNA polymerase to bind to the promoter?

A

-35 and -10 sequences can vary along with spacer length

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14
Q

How do you compare promoter strengths?

A

1 - florescent reporter gene - GFP - stronger promoter-> more GFP mRNA-> brighter GFP signal

2 - enzyme reporter gene - beta-gelatosidase - stronger promoter->more lacZ mRNA-> more beta-gal enzyme-> more reaction product

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15
Q

Name 4 different ways to change the amount of protein produced

A
  • transcription level - more RNA transcripts - more protein
  • post transcription level - more stable RNA transcripts - more protein
  • translational level - premature translational termination - less protein
  • post translational level - protein degradation - less protein; activation or inactivation of protein by covalently attaching a phosphate, acetyl, sumo, ubiquitin and others - only in eukaryotes
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16
Q

how do prokaryotes express more genes in suboptimal conditions?

A
  • alternative sigma factors
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17
Q

Give 7 examples of sigma factors in E.coli

A
  • sigma 70 - most genes in growing bacteria
  • sigma N - nitrogen-regulated genes
  • sigma S - stationary phase genes and starvation response
  • sigma H - heat-shock response
  • sigma E - response to misfolded proteins in the periplasm
  • sigma F - flagella and chemotaxis response
  • sigma Fecl - iron metabolism
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18
Q

What do sigma factors recognise?

A

-10 and -35 sequences

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19
Q

What is a regulon?

A

genes that are triggered by the same conditions

20
Q

What do genes from the same regulon have in common?

A
  • similar sequences in their promoters which are recognised by the same transcription regulators
21
Q

Explain negative gene regulation

A
  • when a repressor binds to the operator it prevents the binding of RNA polymerase to the promoter
22
Q

What is an operator?

A

DNA sequence recognised by a repressor

23
Q

Explain positive gene regulation

A
  • RNA polymerase cannot stably associate with a weak promoter
  • activator binds to the activator binding site
  • activator anchors RNA polymerase at the promoter
24
Q

What are the genes in the lac operon and what protein do these genes make?

A
  • lacZ - beta-galactosidase - breaks down lactose
  • lacY - permease - lactose transport into the cell
  • lacA - transacetylase - role not clear
25
Q

What is the overall role of the lac operon?

A

encodes proteins needed for using lactose as an energy and carbon source

26
Q

Which molecule do bacteria prefer to consume for energy?

A

glucose

27
Q

Explain the regulation of the lac operon in bacteria

A

no lactose
- under negative regulation by Lacl, preventing the RNA polymerase binding

lactose
- lactose is converted into alloLACTOSE which binds to Lacl, changing its conformation so it no longer binds to the operator

no glucose
- without the repressor RNA polymerase still cant bind strong enough
- if glucose level is low, cyclic AMP (c-AMP) accumulates
- cAMP binds to CAP (catabolite activator protein)
- CAP then binds to activator binding site
- translation happens

DRAW OUT

28
Q

how is cAMP made?

A
  • ATP makes cAMP by the enzyme adenylyl cyclase
  • adenylyl cyclase is inhibited by glucose
  • cAMP will only be made in the absence of glucose
29
Q

Explain allosteric activation

A
  • binding of an effector activates the protein
30
Q

Explain allosteric inhibition

A
  • binding of an effector inhibits the protein
31
Q

What is allosteric regulation of a protein?

A
  • when a regularity molecule (effector) interacts with the protein and affects its active site without binding to the active site
  • conformation of the protein changes after binding of effector
32
Q

What is congenital lactose deficiency?

A
  • unable to degrade lactose since birth

caused by deletion or missense mutations in the LCT gene, which codes lactase

33
Q

Name 4 functions of the bacterial plasmid

A
  • fertility - mating between bacteria
  • resistance to chemicals - antibiotics
  • degradation of rare substances
  • virulence - contain the genes allowing bacteria to become virulent
34
Q

What is a transposon?

A

mobile elements which can move around DNA (eg from plasmid to chromosome)

35
Q

Explain transposons in plasmids

A

They may contain antibiotics resistance genes and may move between cells

36
Q

What is an effector?

A

a regulatory molecule that carries out allosteric regulation

37
Q

What is lactose made of?

A

galactose and glucose

38
Q

What happens in lactose intolerance?

A
  • lactose is not broken down in the stomach
  • bacteria in colon breaks it down
  • by-products cause symptoms
39
Q

What is lactose non-persistence?

A
  • in adulthood
  • gradually decreasing expression of LCT gene (lacZ gene)
  • LCT gene expression regulated by a regulatory element called MCM6
  • some have inherited mutations in this element meaning sustained lactase production
40
Q

Name 2 producers of lactase

A
  • yeast - kluyveromyces lactic
  • mold - aspergillus niger
41
Q

explain the 3 different levels of lactase expression

A
  • no expression - LacI is bound
  • weak expression - LacI is not bound
  • full expression - LACI is not bound and CAP is
42
Q

What do regular arrows and T arrows represent?

A

regular -> positive regulation
T -> negative regulation

43
Q

What are smaller plasmids used for?

A
  • constructing cloning vectors - engineered DNA vessels t carry DNA fragments of interest
44
Q

Describe the process of conjugation

A
  • plasmid transfer is coupled with DNA replication
  • transfer through pilus
45
Q

What is the pilus?

A

tube formed between bacteria

46
Q

explain integration and excision of plasmids

A
  • integration - plasmids can become part of the chromosome
  • excision - plasmid can go from being part of the chromosome to being its own plasmid. Sometimes neighbouring sections of chromosome DNA can then be taken into this plasmid
  • if conjugation then happens the recipient will contain this chromosomal DNA and it will be partially diploid

2B: Genetics and Evolution (25 decks)

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