Microbial Genetics I & II Flashcards
What genetic diversity of bacteria is composed of what two categories of genetic information?
1) core gene pool of chromosomal DNA
2) flexible gene pool
What are some genes that the flexible gene pool may contain?
1) pathogenicity factors
2) abx resistance
What does the core gene pool contain?
Genes that are essential to the bacteria such as those for ribosomes, cell envelope, DNA replication, etc.
The DNA for bacteria has a noticeable lack of what element which is present in eukaryotic DNA?
1) non-coding DNA
2) introns
Which gene pool is larger?
Flexible gene pool is considerably larger. Has ~16k genes which are distinct
What is the approximate size of the different gene pools for an E. coli?
Core: 2k genes
Variable: 2-3.5k genes
What are phages?
bacterial viruses
What is a prophage?
A phage already integrated into a bacteria’s genome
What are some flexible genetic elements?
1) plasmids
2) phages
3) integrons
4) transposons
5) genomic islands/islets
What are genomic islands?
Long block of DNA which is from another organism and is associated with a particular function
The integration of things like a phage, or a plasmid into the DNA of a commensal E. coli might do what?
-confer toxicity or pathogenicity to the bacteria
What are the three mechanisms of horizontal gene transfer?
1) transformation
2) transduction
3) conjugation
What is transformation?
transfer of free DNA
What is transduction?
transfer by viral delivery
What is conjugation?
plasmid transfer
How do free fragments of DNA enter the cell in transformation?
through DNA binding proteins
In what form does bacteria take up DNA?
single strand
What proteins facilitate the recombination of free ssDNA?
recA, and rec proteins
How does transformed DNA add into the genome?
true recombination, so alleles are traded for one another or the same one
What is competence?
the preparation necessary to make a cell ready for taking up free DNA
When does transformation and competence usually happen in the bacterial cell cycle?
stationary phase
Which strains are constitutively competent?
Neisseria and H. influenzae
What is one phenotypic change that bacteria undergo to become competent?
includes the expression of pore proteins
How does a bacterium normally protect itself from foreign DNA?
restriction modification systems
How do restriction enzymes work?
These enzymes make cuts at certain points in the DNA thus cutting it out of the genome
How does a bacterium differentiate between its own DNA and foreign DNA?
methylation protects the bacterium’s own DNA
How do we induce E.coli to become competent in the lab?
- salt treatments
- electroporation
What is the general shape of a bacteriophage?
- filamentous
- icosahedral head
- head and tail form together in “sputnik”-like shape
What location on the bacteriophage does it recognize cell surface receptors?
at the base plate
What limits host ranges for phages?
cell surface protein specificity
What are the two types of phage?
1) virulent
2) temperate`
What are the two life cycles of the phage?
lytic and lysogenic
Describe the lytic cycle.
The lytic cycle is when a phage will enter a bacterium, and use the cell’s machinery to produce daughter phages. The cell is killed in the process.
Describe the lysogenic cycle.
The lysogenic cycle is when a phage’s DNA integrates with the bacterial genome and propagates itself in this fashion.
What is a bacterial cell with a prophage called?
A lysogenic cell
At what sites do phages combine their DNA in the lysogenic cycle?
ATT sites
What types of infections, diseases, etc. are effectively treated with bacteriophages?
- wounds
- suppurative infections
- gut infections
What is lysogenic conversion?
A new phenotypic property is conferred on a bacteria carrying that phage
What usually causes the toxigenicity of bacteria?
incorporation of phage elements and viral dna
What is transduction?
the transfer of DNA to another bacterium by viral delivery
What are the two types of transduction?
1) generalized
2) specialized
Which type of transduction is more common?
generalized
Describe generalized transduction.
Phage enters the cell and while assembling phage components a portion of bacterial DNA gets into a phage. The phage then propagates this DNA
What cycle does generalized transduction depend upon?
lytic cycle
Describe specialized transduction.
Phage DNA will integrate with the bacterial DNA and enter the lysogenic cycle. This segment can pop in and out and sometimes will take bacterial DNA with it
What is CRISPR?
Clustered regularly interspaced short palindromic repeats
What is thought to be the function of CRISPR in bacteria?
bacterial immunity
How does CRISPR work in general?
In general, there is an array of repeated sequences which allow the integration of foreign DNA in between. These sequences then get transcribed and eventually act as primers for foreign DNA.
How long are the non-repeating sections of the CRISPR array?
20-25 base pairs
What chops up foreign DNA to put it into CRISPR DNA?
cas complex
What is conjugation?
DNA transfer through plasmid DNA
What is F factor?
fertility factor
What does F factor confer to the bacterium?
Ability to transfer DNA via conjugation
What is a bacterium with F factor called? one without F factor?
with F factor: F+; without: F-
What are incompatibility groups?
groups which are defined by a set of genes that cannot coexist in bacteria to successfully reproduce, although they can exist in a bacterium at the same time
What types of genes are on the F plasmid?
- transfer genes
- insertional sequences
- incompatibility group genes
What is Hfr?
A bacterium which has had plasmid DNA inserted into its genome
Can a HFr bacterium conjugate with a F- bacterium?
Yes.
What are the two types of resistance?
1) intrinsic
2) acquired
What is intrinsic resistance?
intrinsic mechanisms of bacteria that might make them resistant to antibiotics
To what types of antibiotics is mycoplasma resistant?
those that target the cell wall, as it has none
What are the two types of acquired resistance?
1) vertical transfer
2) horizontal transfer
How is vertical transfer of antibiotic resistance conferred?
through mutations
How is horizontal transfer of abx resistance conferred?
through plasmids
Plasmids contain what kind of DNA?
circular dsDNA
What is “selfish DNA”?
DNA that copies itself numerous times in the genome and confers no advantage to its host
Why do some plasmids have selfish DNA?
if their DNA is gotten rid of it will kill the bacterium
What the three types of transfer of plasmid DNA?
1) conjugative
2) non-conjugative but mobilizable
3) non-conjugative non-mobilizable
What are the two most medically-important function of plasmids?
1) confer resistance to antibiotics
2) confer resistance to heavy metals
What are the three main ways that plasmids can specify resistance?
1) efflux pumps
2) modifying enzymes, modifying target of abx or the abx itself
3) degrading enzymes
How is antibiotic resistance to tetracycline commonly conferred?
efflux pumps, but sometimes thru modification of the elongation element it identifies
