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ID Exam I > Bacterial Gene Expression & Organization > Flashcards

Bacterial Gene Expression & Organization Flashcards

1
Q

Basic genetic info is usually on a

A

Single circular chromosome

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2
Q

Vibrio cholerae

A

2 circular chromosomes

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3
Q

Borrelia Burgdorferi

A

Single linear chromosome and many plasmids

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4
Q

Chromosome usually encodes functions required for

A

normal growth

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5
Q

Bacteria may contain non-chromosomal DNA called

A

plasmids, which usually encode functions that are not required for “normal” growth

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6
Q

Plasmids may encode functions (antibiotic resistance or virulence genes) that

A

confer a selective advantage under specific conditions

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7
Q

Bacterial genome structure is

A

heterogeneous

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8
Q

Some parts of the chromosomal DNA seem to be foreign origin due to different

A

G+C composition

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9
Q

Horizontal Gene Transfer (HGT)/Lateral Gene Transfer (LGT) =

A

Acquiring DNA from environment

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10
Q

Genomic islands

A

Patches of unusual sequence (GC content)

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11
Q

Genomic islands are obtained by

A

Horizontal gene transfer

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12
Q

Type 3 and 4 secretion systems are usually on

A

genomic islands

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13
Q

MRSA

A

Contains several islands not present in other staphylococci: One island confers resistance to almost all beta-lactams (mecA gene -altered PBP that is less sensitive.)

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14
Q

Chromosome and plasmid replication

A
  • Replicate independently
  • Each has an origin and a replication protein that recognizes their origin
  • The other machinery is shared: polymerases, helicases, topoisomerases, etc.
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15
Q

Chromosome Replication

A
  • Chromosome has a single origin of replication (oriC)
  • oriC is recognized by the initiator protein DnaA, unwinds the origin and recruits replicaiton enzymes
  • Replication is bi-directional from origin, terminating half-way around the chromosome, where replication forks meet
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16
Q

Plasmids

A
  • Covalently closed circles of DNA
  • Linear plasmids in some bacteria
  • Many bacteria have multiple plasmids, some have none
  • Encode genes that confer an advantage to the cell depending upon the environment (selective pressure). Virulence: Iron acquisition, Antibiotic resistance
  • Some encode genes that promote plasmid DNA transfer from one cell to another (conjugative plasmids)
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17
Q

Plasmid Replication

A
  • Plasmid replication is similar to chromosomal replication
  • Plasmids contain their own origin of replication (oriV)
  • Some also have (oriT): used during transfer to another cell
  • Other replication machinery is co-opted from host cell
  • Plamids have strategies to maintain their presence
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18
Q

Gene Organization

A
  • Genes are trancribed by RNA polymerase
  • Bacteria have only a single RNA polymerase
  • Genes of related function are often clustered
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19
Q

Genes in the same metabolic pathway organized in operons

A
  • Most operons consist of several genes and encode a polycistronic (multiple genes) mRNA
  • Some operons induced when metabolic pathway needed.
  • Some operons repressed when metabolic pathway not needed.
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20
Q

Promoter Region

A

Where RNA Polymerase (RNAP) will bind and start transcription

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21
Q

Genes will be transcribed until they reach

A

Terminator Sequence

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22
Q

At terminator sequence

A

RNAP falls off and mRNA has been produced

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23
Q

Terminators often have inverted repeats so that

A

As RNA is made, it forms stem-loop structure that stops RNAP

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24
Q

Operator Region

A

Region where Repressors and Activators bind and regulate transcription

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25
Q

Once mRNA is made, there is signals that

A

Tell ribosome where to start translation (AUG)

26
Q

RNA binding site

A

Where RNA and ribosome match up

27
Q

Stop Codon

A

UAG, UAA, UGA

28
Q

Control of bacterial gene expression

A
  • Bacteria have many genes that are expressed only when the gene product would be useful to the cell
  • To ensure that un-needed genes are turned off, bacteria have evolved regulatory circuits
  • Most operons controlled at the level of transcriptional initiation (E. Coli)
  • Enzymes encoded allow bacteria to utilize lactose as a carbon source, but only if the prefered carbon source, glucose is absent
29
Q

Gene Regulation

A
  • Most control is at the initiation of transcription
  • Repressors block transcription: Prevent RNAP from binding the promoter or leaving the promoter region
  • Activators promote transcription: Help to recruit RNAP to the promoter
  • Specificity is achieved by using small molecules (concentration) that bind to regulators and alter their activity
  • Co-repressors and inducers
30
Q

Negative regulation of anabolic & catabolic operons

A

Catabolic Pathway: No need to make certain enzymes if substrate is absent (lac operon)

Anabolic Pathway: No need to make product if already present (Trp biosynthesis)

31
Q

Repressor binds to

A

Operator to prevent RNAP from binding

32
Q

Inducer binds to

A

Repressor to inactivate it and allow RNAP to transcribe.

33
Q

Anabolic Pathway Repressor is only active when

A

Small metabolite (co-factor) is bound to it

34
Q

Lac operon -negative regulation, also has positive (combine to efficiently regulate lac operon -only make Lac proteins when lactose present and glucose absent).

A
  • Lac repressor (Lacl) binds to the operator to block transcription
  • In the presence of lactose, an inducer molecule binds the repressor protein. Repressor can no longer bind to operator and transcription occurs.
35
Q

Negative Regulation of Lac Operon

A
  • lacY brings lactose into cell (transporter)
  • lacz splits glucose into two sugars (conversion to allolactose/inducer)
  • allolactose binds to repressor and knocks it off
  • Operon turned on
  • lacl: gene that codes repressor. constantly made.
  • lac repressor binds to operator and keeps it off
  • Repressor is made all the time at a low level it just binds to the operator and keeps the system off.
  • If lactose is in environment, some of it will get converted to allolactose (inducer) b/c there is a small amount of expression all the time
36
Q

Lac l encodes

A

repressor and is made constitutively

37
Q

Regulatory regions include

A

Promoter and Operator

38
Q

Coding region contains genes for 3 enzymes

A

Beta galactosidase: lacZ

Permease: lacY

Transacetylase: lacA

39
Q

Positive Regulation

A

Operates via an activating protein (cAMP binding protein, CAP) and a co-activator (cAMP)

40
Q

cAMP used as a measure of

A

[glucose] in cell

41
Q

[cAMP] is inversely proportional to

A

[glucose]

42
Q

Positive regulation by CAP/cAMP found

A

in many operons. Referred to as catabolite activation.

43
Q

In presence of glucose and lactose, bacteria prefer to use

A

Glucose

44
Q

Glucose prevents

A

Full induction of lac operon

45
Q

The binding of the CAP-cAMP complex to the CAP binding site is required for

A

Induction of the lac operon

46
Q

High glucose levels =

A

Low cAMP levels

47
Q

High glucose = low cAMP =

A

no lac operon induction

48
Q

Positive regulation of operon (inducer is present so repressor is inactive)

A
  • RNAP can bind weakly (inactive repressor)
  • Activator protein (cAMP BP) needed for full expression
  • When cAMP is present, it binds to activator protein (cAMP BP)
  • Activator binds to DNA close to promoter and recruits RNAP to get full induction
49
Q

Get rid of repressor

A

Low level of lac operon expression

50
Q

Get rid of repressor. Add Activator (cAMP BP)

A

High level of lac operon expression.

51
Q

(+) Glucose & (-) Lactose

A
  • No cAMP
  • Lac repressor active so Lac Operon repressed
52
Q

(+) Glucose & (+) Lactose

A
  • no cAMP
  • Lac repressor inactive
  • Lac operon weakly expressed (10%)
53
Q

(-) Glucose & (+) Lactose

A
  • cAMP present
  • Lac repressor inactive
  • Lac operon maximally expressed
54
Q

(-) Glucose & (-) Lactose

A
  • high cAMP
  • Lac repressor active
  • Lac operon repressed
55
Q

TRP Operon: Example of Attenuation

A
  • Tryptophan (trp) operon of E. Coli (tryptophan biosynthesis) encodes enzymes to make tryptophan. Regulation prevents expression if tryptophan is present in the environment.
  • Repressor active when tryptophan is bound
  • Attenuator system (fine-tuning) measures [charged tryptophanyl RNA] (% of tRNA with tryptophan bound)
56
Q

Trp operon -attenuation -measure level of charged trp tRNA

A

High level of Tryptophan: Translation follows RNA polymerase and terminator is formed. Transcription is terminated. Enzymes not needed.

Low level of Tryptophan: Ribosome stalls (no terminator) and transcription termination is avoided. Enzymes produced to make tryptophan.

57
Q

Two-component systems

A

Sensing environmental signals

58
Q

Quorum sensing

A

Senses the number of bacteria. Two-component systems can be involved.

59
Q

Two-component regulatory systems: sensing the environment

A
  • Sensor (histidine) kinase: autophosphorylates in response to a signal
  • Response regulator: Phosphorylated by sensor kinase. Alters activity of regulator.
  • Regulator often affects transcription of many genes.
60
Q

Quorum =

A

Minimum # of members necessary to conduct business

61
Q

Density-dependent signaling:

A

More bacteria = more signal, until a threshold is reached

Behavior is regulated by the number of bacteria

ID Exam I (3 decks)

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