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Microbiology > Bacterial Genetics > Flashcards

Bacterial Genetics Flashcards

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1
Q

What is the main difference in the amount of RNA polymerases produced by eukaryotic and prokaryotic organisms?

A

Prokaryotic: produce one single RNA polymerase that is responsible for transcribing all RNAs.

Eukaryotic: have many RNA polymerases

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2
Q

Where does the prokaryotic RNA polymerase bind?

A

At the promoter, upstream of every coding sequence

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3
Q

What is the operator region?

A

A sequence that usually binds proteins involved in regulation of gene’s expression

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4
Q

Where is the operator located?

A

near the promoter

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5
Q

Where does the termination of transcription occur in relation to the coding sequences?

A

Downstream. At sites designed the dissociate RNA polymerase from the DNA:RNA complex

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6
Q

What are the two main features of prokaryotes that enables coupling of transcription and translation?

A
  1. lack of introns in prok. coding sequences
  2. lack of nucleus in proks

Translation of mRNAs begins BEFORE tx is complete due to these features

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7
Q

An operon represents a major difference btwn euk and prok gene structure. What is an operon?

A

A cluster of genes typically related in function that are transcribed on a single mRNA strand

the mRNA is polycistronic = many genes. Genes are translated INDEPENDENTLY

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8
Q

The lac operon was used as an example of the operon system. 3 genes, lacZ, lacY, and lacA were shown in the coding sequence. Each gene has its own ribosome binding site because each gene translates _____.

A

Independently

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9
Q

What are 2 benefits of the operon system regarding gene regulation?

think: proximity of genes and promoter/operator regions

A
  1. Operons help to avoid loss of function since the genes are so close together, less likely to be lost in evolutionary divergence
  2. single promoter and operator regions provide co-regulation of genes in the operon which leads to coordinated expression of functionally-related genes.
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10
Q

What are the 3 types of gene regulation in bacteria?

A
  1. Constitutive
  2. Positive regulation
  3. Negative regulation
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11
Q

What is constitutive regulation?

A

There is no regulation–genes are always expressed

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12
Q

What is positive regulation?

A

An activator protein promotes RNA polymerase binding to promoters and FACILITATES expression of the genes

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13
Q

What is negative regulation?

A

A repressor protein binds the operator sequence and prevents tx by RNA polym until repressor is removed

(we see this in the lac operon)

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14
Q

Constitutive expression is RARE. Why?

A

Because transcription and translation expend energy, most wild type genes are regulated so as not to waste cell energy

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15
Q

Regulation is often provided via inducers. What are inducers?

A

molecules that:
1. interact with activator proteins, causing them to bind operators and promote RNA polym binding at nearby promoters

OR

  1. interact with repressor proteins, preventing them from binding operators and blocking tx

Inducers induce transcription

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16
Q

Considering the lac operon, what is occurring in the ABSENCE of lactose?

A

Without lactose present, the repressor is bound to the operator to prevent translation of unnecessary proteins that digest lactose.

Repressor prevents RNA polym from binding. the lacI gene (repressor gene) is constitutively expressed.

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17
Q

Considering the lac operon, what is occurring in the PRESENCE of lactose? What inducer molecule is formed?

A

Lactose is shuttled into the cell where it is converted to allolactose. This molecule is an INDUCER of lac operon gene expression. The repressor releases from operator and allolactose BINDS repressor to prevent it from binding operator again (conformational change).

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18
Q

Operons are a very efficiency way for co-regulation of functionally related genes, but not all related genes cluster into a single operon. What is a regulon?

A

A system where independently transcribed genes, or multiple operons are controlled by the same regulatory proteins.

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19
Q

Two-component signaling is an example of how even without a nucleus, bacteria still need signaling pathways. TC signaling shows how bacteria can respond to extracellular changes without needing to transport the ligand inside the cell. How does it work?

A

A sensor is in the cytoplasmic membrane and there is a transducer inside the cell. Binding of ligand to sensor leads to phosphorylation of sensor –> leads to phosphorylation of transducer. This activates transducer and it is able to act as an activator. It binds the operator of genes that will properly respond to extracellular ligand.

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20
Q

What are some examples of changes in extracellular environment that use two-component signaling?

A

Change in temperature, osmolarity, availability of iron

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21
Q

As the cell density of a bacterial population increases, the concentration of signaling molecules released increases as well. Bacteria communicate with each other via these released molecules and measuring their local concentrations. This is referred to as:

A

Quorum Sensing

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22
Q

When a concentration threshold of the signaling molecule is released, if the cell responds by turning on a new set of genes, it is sensing the cell density and utilizing ________.

A

Quorum Sensing

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23
Q

The signaling molecules are usually not peptides, but are:

A

cyclic structures, like lactones or quinolones

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24
Q

Bacteria that coordinate expression of virulence genes needed to escape immune response or establish infection are utilizing:

A

Quorum sensing

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25
Q

Most bacteria have a single piece of DNA with very few ancillary genes. Are bacterial genomes haploid or diploid?

A

Haploid

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26
Q

What are the challenges in bacterial genomes being haploid?

A
  1. mutations lead to loss-of-function since there is no second copy available to compensate
  2. phenotypic diversity is limited since there is absence of allelic pairing
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27
Q

How do bacteria overcome the challenges associated with a haploid genome? Challenges like less phenotypic diversity, mutations leading to loss of function.

A
  1. Sheer numbers! There are so many bacteria produced, that a loss of function mutation will hardly influence outcome of infection
  2. Low frequency genetic events that lead to new gene expression in a subset of the population and selective amplification of the new phenotype under the right conditions:
    Phase Variation
    Antigenic Variation
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28
Q

What is phase variation and how does it contribute to gene regulation?

A

Phase variation results in an on/off expression of a gene or a subset of genes. The genetic switch is usually an inversion of a gene so that in the “on” position it is aligned with promoter and expressed.

The coding sequence can “flip” or invert in the “off” position so that the promoter is no longer at the start of the gene and the gene will not be expressed.

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29
Q

What does the “genetic switch” sequence in phase variation usually encode?

A

A regulatory protein

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30
Q

What is an example of phase variation? (think of Dr. Ryan’s example)

A

Uropathogenic E. Coli (most common cause of UTIs). Phase variation controls expression of a regulatory protein that regulates expression of a pilus protein needed for bladder colonization

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31
Q

What is antigenic variation and how does it contribute to phenotypic diversity?

A

occurs in the expression of a large array of surface components for some bacteria. These surface components often serve as antigens for the immune system, and expression of varying antigens enables the bacteria to escape immune response and re-establish infection

32
Q

What is an example of antigenic variation given in Dr. Ryan’s handout?

A

Neisseria gonorrheae. This species can potentially express THOUSANDS of variations of surface pili due to recombination of pil genes. The pilus is a major antigen during neisserial infection, so this exhibits antigenic variation

33
Q

What is the clinical presentation of antigenic variation?

A

Recurring infection! As new variants are amplified in the face of an immune response to the previous variant, infection is re-established

34
Q

Unlike conventional gene regulation, like we saw in lac operon or two-component signaling, only a SUBSET of bacteria alter gene expression under phase and antigen variation. What does this imply for this subset’s impact on infection?

A

While phase and antigenic variation provide diversity to the population, LARGE NUMBERS of bacteria and RAPID growth must occur for the subset to impact the infection

35
Q

Because bacteria are haploid and asexually reproduce, genetic diversity is not passed down to daughter cells. What are the four methods of genetic exchange that promote acquisition of new genes?

A
  1. Transposition
  2. Conjugation
  3. Transduction
  4. Transformation
36
Q

What are transposons?

A

Mobile genetic elements. They hop from one genome to another, sometimes leaving original copy behind and increasing the amount of transposons in the genome

37
Q

What are the four basic elements of a transposon?

A
  1. Insertion sequences
  2. Transposase
  3. Repressor
  4. Antibiotic resistance gene
38
Q

What is the benefit of insertion sequences in a transposon?

A

At each end of the transposon are inverted repeats, these allow for integration of the transposon into target DNA

39
Q

What is the benefit of a transposase in a transposon?

A

It is a recombinase that executes the integration of the insertion sequences

40
Q

What is the benefit of a repressor protein in a transposon?

A

It regulates the frequency of transposition

41
Q

What is the benefit of the antibiotic-resistance gene (or a toxin or new virulence factor) in a transposon?

A

It benefits the microbe that the transposon is “hopping” into.

42
Q

Due to the size and complexity of transposons, what is their effect on normal tx and tsl?

A

Transposons often disrupt normal tx and tsl when they insert into a gene or operon

43
Q

What are the 2 main ways transposons introduce genetic diversity?

A
  1. introduction of antibiotic-resistance genes or some other new toxin or virulence factor
  2. creation of mutants lacking non-essential wild type functions
44
Q

Transposons cannot hop from one bacterium to another, therefore transposition is an __________ process.

A

Intracellular

45
Q

The introduction of a transposon from one cell to another relies on __________.

A

Conjugation

46
Q

What is conjugation?

A

Mating process occurring btwn similar species of bacteria

47
Q

What is a plasmid?

A

An extrachromosomal circular DNA found in most bacteria

48
Q

Are plasmids single or double stranded? How big are they?

A

Double stranded 2-500 kilobase pairs

49
Q

Plasmid replication is usually tied to genome replication, but some small plasmids replicate independently to ___________ ________.

A

amplify their copy number within the cell (dont know how impt this is)

50
Q

Plasmids are generally the target for ________.

A

Transposons

51
Q

Why are the antibiotic-resistance genes conferred via transposons valuable to a plasmid?

A

bc plasmids do not possess genes essential for cell survival. Transposons help the plasmid to be maintained in the bacteria population

52
Q

Considering transposons, how can you explain resistance to increased concentrations of bacteria?

A

Amplification of a plasmid with the transposon carry antibiotic resistance on it.

53
Q

In conjugation you have a donor cell and a recipient cell. What MUST the donor bacterium have in order to transfer its genes to the recipient?

A

The F (feritility) Factor!!! The donor is said to be “F+” or “male”

54
Q

What else is important about the F factor, other than its presence in the donor bacterium? What does it encode?

A

The F factor encodes a sex pilus which is necessary for the direct contact with the recipient (which lacks F factor, F-)

55
Q

Once direct contact is established btwn 2 bacterium during conjugation, what happens to the F factor?

A

It is cleaved so that plasmid and genome DNA material can enter the sex pilus into the recipient. The recipient now contains a copy of the F factor and is now F+

56
Q

How does conjugation facilitate genetic diversity?

A

the F factor can facilitate conjugation of other, non-mobile plasmids from F+ donor to recipient AND F factor can transfer parts of the donor genome to the recipient.

This all occurs after F factor has integrated into bacterial chromosome. Newly introduced genes can be recombined into recipient genome –> leading to diversity

57
Q

Cells with the integrated F factor are called ______ cells.

A

Hfr– high frequency transfer cells.

58
Q

Pathogenicity-associated islands (PAIs) in pathogenic bacteria are large regions of chromosome that encode various virulence factors. What is the major mechanism for generating these PAIs?

A

Hfr transfer !

**Non-pathogenic strains of the same bacterium lack these PAIs

59
Q

If a plasmid acquires an antibiotic-resistance gene via transposon, what is it referred to as?

A

an R-plasmid or R-factor (R for resistance)

60
Q

Why are R-factors (R-plasmids) a major reason for spread of antibiotic resistance?

A

They can be transferred across species and across genera.

R-factors can be conjugative or dependent on F-factors for conjugation

61
Q

R-factors tend to accumulate MULTIPLE antibiotic reisstance genes. This is termed as what?

A

Multidrug resistance

62
Q

What are viruses called if they prey on bacteria?

A

Bacteriophage or “phage”

63
Q

What are the two general categories of phages (bacteriophages)?

A
  1. Lytic

2. Temperate (lysogenic)

64
Q

What is a lytic phage?

A

A phage that infects, replicates in large numbers, and then releases from cells usually via cell lysis so they can infect other cells!

65
Q

What is a temperate phage?

A

A phage that infects cells and integrates its genome at specific sites in the bacterial chromosome of some cells.

66
Q

In a temperate phage, the phage integrates its genome into another cell. This integrated phage genome is known as a what?

A

Lysogen (hence, lysogenic category of phages)

67
Q

The lysogen replicates as part of the bacterial chromosome until what happens?

A

Until stress to the cell induces the lysogen to excise from the chromosome and undergo lytic replication, the cycle continues

68
Q

Some lytic and temperate phages can inadvertently transfer bacterial genes from a host to an infected cell. This transfer of genetic material from one bacterial cell to another via phage is termed __________.

A

Transduction!

69
Q

What are the two forms of transduction?

A
  1. Generalized

2. Specialized

70
Q

What is generalized transduction?

A

It is transduction carried out by lytic phage ONLY! The lytic phage cleaves the bacterial chromosome into small fragments and these can be mistakenly inserted into phage particles instead of the phage genome during replication

The mispackaged gene particles can mimic infection and insert into the bacterial chromosome in recipient cell where it can be recombined into that new genome

71
Q

What is specialized transduction?

A

Transduction that is carried out by temperate phage ONLY! Only a few specific bacterial genes can be transduced by a temperate phage due to lysogen integrating at specific sites.

72
Q

Is specialized or generalized transduction more important for providing genetic diversity/virulence factors?

A

Specialized!

73
Q

What is transformation?

A

Uptake of naked DNA from one cell to another

74
Q

Is transformation important in genetic diversity?

A

No

75
Q

If a bacterial cell can take up DNA from its surroundings, like in transformation, it is termed as being ________.

A

Competent

Microbiology (3 decks)

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