4_Bacteriology IV Flashcards
1
Q
what characteristics of bacteria help it make many mutations passed along during division?
A
- Bacteria are haploid –> so any mutations are passed to daughter cells upon division
- Single copy of chromosome inherited
- Effects of genetic change are not masked
2
Q
describe how DNA replication errors occur
A
- DNA polymerase can misincorporate nucleotides
- DNA polymerase normally has proofreading activity and can repair the mismatch
- occasionally mistakes are not repaired and SNP single nucleotide polymorphisms arise
3
Q
what are the types of DNA damaging agents that cause lesions in DNA?
A
- Base analogs
- 5-bromouracil (Bu)
- 2-aminopurine
- Intercalating agents
- acriflavine
- ethidium bromide
- acrydine orange
- Ultra-violet (sunlight)
- pyrimidine dimers
- Chemicals that react with DNA
- X-rays (–> free radicals –> damage to DNA)
4
Q
what induces DNA repair mechanisms?
A
- the SOS (a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis is induced. It is an error-prone repair system that contributes significantly to DNA changes observed in a wide range of species.)
- these are similar to those in humans, adn repair the DNA damage
5
Q
what induces error-prone polymerases?
A
under conditions of starvation or extreme stress (lots of DNA damage)
6
Q
what polymerases read past lesions;
what are the results of this?
A
- Error prone polymerases such as PolV and PolIV read past the lesions and do not proofread
- This causes misincorporation of nucleotides.
- These polymerases do not have proofreading capabilities so the mutations stay.
- responsible for increased mutation rates under stress
- oxidation causes DNA damage and
- starvation causes stalls in DNA replication
7
Q
how do the Pol V and Pol IV polumerases differ?
A
- Pol V replicates past pyrimidine dimers caused by UV light
- Pol IV replicates past various other lesions in DNA
8
Q
bacteria exist as populations:
define microbiota and disease
A
- microbiota: mixed species populations
-
disease: single species populations; exist as pathogens
- error prone polymerases allow cells in the population to vary in hopes that the mutations may be beneficial
9
Q
error prone polymerases help give rise to antibiotic resistant mutants.
how can we try to prevent pathogens from becoming completely resistant to antibiotics?
A
- The use of multiple antibiotics to treat infections by pathogens that use error prone polymerases, reduces the chance that these pathogens will become completely resistant to antibiotics.
- For example if 1/10-7 bacteria become resistant to a single antibiotic the risk of resistant infection is 107.
- When antibiotics are combined the chance that a bacterium will become resistant to both antibiotics becomes 1014.
10
Q
horizontal gene transfer (HGT):
define, and what are the major mechanisms
A
- horizontal gene transfer of resistance genes is an efficient way of generating antibiotic resistant bacteria.
- major mechanisms of HGT:
- transformation
- conjucation
- transduction
11
Q
what are the major mechanisms of horizontal gene transfer,
and define each
A
- transformation: trasnfer of free DNA
- conjugation: plasmid transfer
- transduction: transfer of viral delivery
12
Q
which types of bacteria can take up DNA?
A
- Only competent bacteria can take up naked DNA.
- Transformation is DNase sensitive because the DNA is free outside the cell and can be degraded by the DNase enzyme.
- Gram-positive bacteria take up any DNA
- Gram-negative bacteria can only take up OWN DNA
13
Q
how is DNA integrated in transformation?
A
homologous recombination
14
Q
what is needed for an incoming gene to be integrated into the chromosome by homologous recombination?
A
- requires a stretch of homology between the incoming DNA and the chromosomal DNA
- RecA protein
- heteroduplex formation
- replication to resolve the heteroduplex
15
Q
how can antibiotic resistance genes be integrated into the chromosome?
A
- directly if there is enough homology or
- be introduced into the DNA if flanking on both sides by genes containing homology
16
Q
what is a mechanism that allows for development of supragenome?
define the supragenome?
A
- Competence is one mechanism that allows for the development of a pan genome (supragenome)
- Bacteria with a supragenome have:
- conserved core of genes present in all strains
- genes from a pool of distributed genes that differ between strains
17
Q
bacterial plasmids:
characteristics
A
- Covalently closed, double stranded circular DNA
- Usually not essential for bacterial growth
- Replicate separately from the chromosome
18
Q
three types of bacterial plasmids
A
- Narrow host range (present in limited number of bacterial species)
- Broad host range plasmids replicate in many species
- Conjugative plasmids can transfer
19
Q
describe the transfer of plasmids by conjucation prototype F-plasmid E.Coli
A
- The F+ cell is the donor and contains the F plasmid.
- The F- cell is the recipient cell and does not contain the plasmid.
- The F+ donor synthesizes a pilus, which is a Type IV secretion system.
- One strand of the DNA is transferred to recipient.
- The strands in both cells are replicated so both the donor and recipient now have the plasmid.
- The recipient has been converted to a donor, so the process is infectious (epidemic) and the plasmid is spread. through the bacterial population
20
Q
can an F-plasmid integrate into the chromosome?
what does it form?
A
- F-plasmid can integrate into the chromosome
- Forms an Hfr
21
Q
what are the 3 outcomes of an Hfr?
A
- F+ :The F plasmid excises precisely and nothing happens to the plasmid or chromosome.
- F’ :The F plasmid excises and carries of a small piece of chromosomal DNA with it. The F’ plasmid is now infectious and the chromosomal fragment basically becomes part of the plasmid.
- Hfr mating : The pilus and Type IV secretion system are induced and a transfer event is initiated from the integrated plasmid so a large piece of chromosome is introduced into the recipient cells. The plasmid does not recircularize and is lost (NOT infectious) but genes from the donor chromosome can enter the recipient by homologous cross over events.
22
Q
how can plasmids be detected on agarose gels?
A
- Plasmids can be visualized from a DNA preparation as distinct bands on an agarose gel.
- Plasmids can be larger or smaller than the chromosomal fragments present on the gel (the chromosome shears during DNA isolation).
23
Q
between what does gene transfer events occur?
A
can occur between bacteria of different species and genera
24
Q
bacteriophages:
define, and characteristics
A
- bacterial viruses
- can switch between lytic and lysogenic phases
25
lytic cycle of bacteriophages
* In the lytic cycle, bacterial chromosomal DNA is often degraded into small pieces.
* The viruses replicate their nucleic acid, package the DNA and lyse the bacteria
26
lysogenic cycle of bacteriophage
* In the lysogenic cycle, the phage integrate into the chromosome by non-homologous self-directed recombination.
* The viral genetic material replicates as part of the chromosome.
27
how can a bacteriophage in the **lytic cycle** mediate HGT?
* by generalized transduction:
* when the bacteriophage packages a fragment of chromosomal DNA instead of viral DNA.
* the fragment is injected into a new bacterial cell.
* the chromosomal fragment can be incorporated into the bacterial chromosome by homologous recombination.
* the phage does not contain viral DNA, so the bacterial cells is not infected by the virus
28
how can a bacteriophage in the **lysogenic cycle** mediate HGT?
* by specialized transduction
* when a lysogenic phages converts to the lytic cycle it can occasional take a piece of chromosomal DNA adjacent to the integration site with it.
* the piece of chromosomal DNA is carried with the phage DNA and is introduced into the bacterial chromosome when the phage reintegrates upon entering the lysogenic cycle
* the integration is mediate by the phage and is **non-homologous recombination**
29
transposon:
define, and how is it mediated?
* A **transposon** mobile element transposes (moves) from one piece of DNA to another.
* The movement is mediated by the action of a transposase enzyme that inserts the transposon into the DNA via binding to the inverted repeats that flank the transposon (insertion sequences; IS).
30
non-homologous recombination:
define
* Since the insertion sequence and transposase direct the insertion a transposon can insert anywhere in the chromosome and does NOT require RecA or homology
* Insertion and excision are usually precise, but excision can occasionally cause deletions.
31
why are transposons not considered replicons?
* Transposons become part of the DNA, and therefore are not replicons
* Transposons are never free like phages or plasmids
32
transposons:
functions
* Transposons can carry multiple different genes between the insertion sequences.
33
conjugative transposons:
define and functions
* Conjugative transposons are also known as **ICE (integrative and conjugative elements)**
* Fxn: encode genes encoding their conjugative transfer to other bacteria.
34
MRSA SCCmec:
define
* is a **large chromosomal cassette containing the methicillin resistance genes** and can contain many other resistance and virulence factors
* this is a novel type of transposon-like mobile element whose mechanism of movement is unknown.
* the different cassettes are variable in genetic content.
* the MRSA SCCmec are **often flanked by insertion sequences, transposons and integrated plasmids in them**
35
pathogenicity islands:
define
* large mobile genetic elements encoding virulence factors
* present in pathogenic strains and absent in commensal strains of the same species
* related to transposons sometimes, but not always, have Insertion Sequence elements and integrase
* tend to be found in tRNA genes
36
what can also result from antibiotic resistance?
* often causes a loss in fitness like slower growth rate or reduced survival in stationary phase
* In the absence of antibiotic selection, antibiotic resistant strains are often outcompeted and lost from the bacterial population
37
where is antibiotic resistance more common?
* Antibiotic resistant strains are more common in hospitals where there is more antibiotic selection and less common in the community where there is less antibiotic selection.
