3-2: Prokaryotic Genetics Flashcards
How are genes named
First three letters describe function, fourth designated specific gene
Italicized, last letter capitalized
Example of gene name
btuC (Vitamin B12 Uptake, gene C)
How are proteins named
Same, but not italicized and first letter also capitalized (e.g. BtuC)
What is a mutation
Heritable change in the DNA sequence of a genome (substitution, insertions, deletions)
What is the wild-type strain
Strain isolated from nature or parent strain
What is a mutant?
An organism whose genome carries a mutation
What is the phenotype. Eg.
Observable characteristics of an organism
E.g. metabolic, virulence, morphology
What is a genomic locus
a specific position on a gene
How are mutations named
Add number to gene name in order the mutation was isolated
e.g. hisC1
How are modern mutations named?
WT base or AA, then muber, then mutant base/AA
eg. HisC (A77K)
How is a deletion mutation shown
Delta symbol (deltabtuC)
How are phenotypes named
Three letters with (+) or (-) symbol
His+ can make histidine
What is a point mutation
Mutation to a single base pair within a protein-coding sequence
What is truncation
The premature end to a protein sequence due to a nonsense mutation
What is a deletion vs insertion mutation
Deletion: DNA lost
Insertion: DNA added
What can deletion or insertion mutations lead to
Frameshift mutation (shifts all downstream codons, scrambles sequence) = disruptive
What is a genetic reversion
Mutant that acquires another mutation and reverts back to wild-type
What is a phenotypic reversion?
Mutant strain aquires a mutation that reverts it back to the WT phenotype. May be genetic or a new mutation
What is a suppressor mutation
Causes phenotypic reversion. Mutation that compensates for the effects of a prior mutation
Give an example of supressor mutation
Eg. antibiotic resistance due to outer membrane. Mutant has no outer membrane. Can recreate original WT resistance, not by making an outer membrane, but by breaking down the antibiotic
What are 3 ways we can isolate for mutants?
Selection (eg. mutant grows, parent doesn’t)
Abscence of growth
Indicator plates (eg. colour, fluorescence)
What is beta-galactosidase used for in indicators?
Can hydrolyze X-gal, which can turn blue
What is the natural mutation rate of prokaryotes
10^6 to 10^7 per 1000 base pairs per round of replication
What is horizontal gene transfer
Acquiring new genetic material (foreign DNA) from the environment
Three ways foreign DNA can enter prokaryotic cells
Transformation
Transduction
Conjugation
What can happen to the DNA once it is inside the cell (horizontal gene transfer)
Be degraded
Replicate as separate entity (phage, plasmid)
Be integrated into chromosome (recombination, transposition)
What can happen to the DNA once it is inside the cell (horizontal gene transfer)
Be degraded
Replicate as separate entity (phage)
Be integrated into chromosome (recombination, transposition)
What is Genetic recombination?
Physical exchange of DNA between 2 oarts of the same genome
What does homologous recombination do
DNA repair mechanism (repairs double strand breaks)
How does HR result in genetic recombination?
Foreign DNA that is homologous to the host chromosome can be inserted in place of, or in addition to, the native DNA. Leads to deletions, duplications and inversion
What is a transposable element
Mobile genetic element that contains a transposae gene and inverted repeats
What enzyme is involved in transposition. What does it do
Transposase enzyme
Recognize inverted repeats, cleaves transposable element of DNA, cleaves another DNA and inserts transposable element into it
What are the two kinds of transposable elements
Conservative (cut and paste)
Replicative (copy and paste)
What are insertion sequence elements?
Have only transposition machinery
What are transposons?
Contain transposition machinery as well as extra genes (eg. antibiotic resistance)
What are transposons used for in lab
Generate mutant strains
What is Transformation?
Process by which free DNA is incorporated into a recipient cell bringing about genetic change
Where does the DNA for transformation come from
Lysed cells within their environment
How does DNA cross the cell membrane
Cell needs to actively take it up (regulated process)
What is it called when cells can take up free DNA
The cell is competent
How is DNA captured in competent cells
Pili captures it, retracts, one stand of DNA degraded and other passed through CM via a multi protein competence system
What are virions?
Protein coats that the virus DNA is packaged into
What is the lytic pathway?
Phage DNA replicated and new particles produced. Virus lyses host cell and is released to infect a new cell
What is the lysogenic pathway?
Viral DNA is integrated into the host DNA as a prophage. Can become induced into the lytic cycle
What is a temperate phage
One that can operate via lytic or lysogenic pathway
What is transduction
Virus transfers bacterial DNA from one cell to another
What are the two kinds of transduction
Generalized transduction: during lytic cycle, host cell DNA accidentally packaged into viral particle, injected into new cell
Specialized transduction: after prophage forms, its DNA is excised from genome but some neighboring host DNA is also packaged then injected into new cell
What is conjugation
Horizontal gene transfer requiring cell-cell contact
“mating”
What mediates conjugation
Conjugative plasmids (F plasmid)
What is the F plasmid
Fertility plasmid
Strains with F plasmid = F+ = donor cell
What kinds of cells can mate
F+ (donor) and F- (recipient) only
What kind of pilus do F+ cells encode
tra (transfer genes that encode a conjugative pilus that allows F+ and F- cells to attach
How is DNA copied in conjugation?
The DNA is nicked at the oriT and a single strand is copied
What secretion system is used in conjugation
Type four
Transfers F plasmid DNA from F+ cell to F- cell
What is an Hfr (high freq recombination) cell
Occurs when the F plasmid has an insertion sequence and can integrate itself into the chromosome. Conjugation machinery is still intact, and oriT now on chromosome.
What happens when Hfr strains conjugate?
Transfer their F plasmid DNA and chromosomal DNA to a F- cell which can be integrated into its genome. It doesn’t transfer the full plasmid though, so the donor is still F-
What acquired genes will be maintained
Those that provide a selective advantage
What is one way to recognize horizontally acquired DNA?
Difference in %GC content from the rest of the genome
