Microbial Genetics Flashcards
What is the diference between a mutation and a mutant?
- Mutation - HERITABLE change in DNA sequence that can lead to a change in phenotype
- Mutant - a strain of any cell of virus differing from parental strain in a genotype (nucleotide sequence of genome)
Will a mutation always results in a change in the phenotype?
- Yes. that is the definition of a mutation.
What is a selectable mutation?
- give mutants a growth advantage under certain conditions
- Usefule in genetic research
What is a nonselectable mutation?
- Usually has neither an advantage nor a disadvantage over the parent
- Doesnt effect growth
- Based on appearance - color, hair etc…
What is the difference between spontaneous mutation and induced mutation?
- Spontaneous
- Mutation that occurs without external intervention
- Inherent mistakes made by polymerases during genome replication
- Induced
- mutations made environmentally or deliberately
- could results from exposure to natural radiation, or oxygen radicals
Point Mutations:
- Change only [] base pair
- Can lead to single [] [] change in a protein, an incomplete protein, or [] change at all
- Can lead to [], [], or [] mutations (occuring within the coding region)
- 1 base pair
- amino acid change, or no change
- silent, missense, or nonsense
Would a mutation in DNA have larger effect in bacteria or eukaryotes?
- Bacteria - they are haploid and have a smaller genome with less non-coding genes
What is the difference between:
Silent Mutation, Missense Mutation, Nonsense Mutation?
Where does these 3 types of mutations occur on a gene?
- Silent - different base pair at DNA/RNA level compared to the wild type. Not change in proteins though
- Missense - Change in a base pair that results in a change of a codon that codes for a different amino acid. Final structure of protein doesnt matter.
- Nonsense - addition of stop codon prematurely
- These occur in coding regions.
What is a frameshift mutation?
- small deletion or insertion that results in a shift in the reading frame.
- Typically occur in coding region and typically single base insertion/deletion
- +1 = insertion
- -1 = deletion
- Often results in complete loss of gene function
What type of double frameshift mutation can be “ok?”
+/-, +/+, or -/-
What type of triple frameshift mutation can be “ok?”
+/+/+ or -/-/-
- +/- can sometimes be ok. If the two mutations are near by
- +/+/+ or -/-/-…could be ok because it basically adds or subtracts a single amino acid to the protein. Better if close together again.
What are Transposable Elements?
- discrete segments of DNA that move as a unit from one location to another within other DNA molecules
- Found in all 3 domains of life
- Move by process called transposition
What are the 2 main types of transposable elements in bacteria?
-
Transposons and Insertion Sequences
- both carry genes encoding transposase
- both have inverted repeats at tehir and
What is transposase?
enzyme that helps mobile DNA elements cut out and then transport to new DNA site.
Insertion Sequences Facts:
- [] transposable element
- ~[] nucleotides long
- The [] gene is sandwhiched between 2 [] []
- this is its only coded gene
- Found in [] and chromosomes of [], [] and a few viruses
- simplest
- 1,000
- transposase gene, inverted repeats
- plasmids, bacteria, archea, and a few viruses
Transposons Facts:
- Has additional [] genes between the inverted repeats
- may include [] [] genes
- Transposase recognizes [] and cuts out transposon, moves to new [] [] , and re-inserts it
- accessory
- antibiotic resistance
- IRs, target site
What is the differene between a Transition Mutation and a Transversion Mutation?
- Transition - C <–> T or A<–>G
- Purine to purine or pyrimidine to pyrimidine
- Transversion - C/T <–> A/G
- Interchange of purines and pyrimidines
What would be worse?
Mutation in catalytic Site and structural site vs non-important site?
Early Frameshift vs Late Frameshift?
- Depends on where. Not all mutations are equal.
- clearly a mutation in the catalytic site could be worse than a non important site
- An early frameshit could result in an incomplete or faulty protein, but a late frameshft may not even effect the function of a protein
RNA viruses have a large error rate in terms of spontaneuous mutations.
Why is this and how could it be advantageous?
- RNA polymerases dont have proofreading
- Viruses us this to continually adapt and evolve
What is a mutagen?
- Chemical, physical, or biological agent that increases mutation rates
What are several classes of chemical mutagens?
- Nucleotide Base Analogs - resemble nucleotides
- Chemical Mutagens that induce chemical modifications
- alkylating agents like nitrosoguanidine
- Chemical mutagens that ause frameshift mutations
- intercalating agents like acridines
What is an example of an alkylating mutagen?
What is an example of an intercalating agent mutagen?
- Nitrosoguanidine
- Acridines
- can create an insertion/deletion that leads to a frameshift
What are the 2 main categories of mutagenic electrogmagnetic radiation?
- Non-ionizing (UV radiation)
- Pyrimidine dimer can results from this
- Ionizing (X-ray, cosmic rays, gamma rays)
- ionizes water and produce free radicals
- Free radicals damage macromolecules in the cell.
Can a cell repair itself after a transposon or virus has been added to the genome?
- No
- However, repair mechanisms exist for chemically or physically derived mutations.
What are the different biological mutagens?
- Transposons
- Viruses
- can insert viral genomes into host chromosomes
- Bacteria
- produce reactive oxygen and nitrogen species that act as ionizing radiation
DNA Repair Mechanisms and Associated Enzymes for single strand break repair
- Base Excision Repair
- Mismatch Repair
- Nucleotide Excision Repair
- Base Excision Repair (Single strand break repair)
- DNA glycosylase recognizes wrong base, AP Endonuclease clips the wrong base out
- Mismatch Repair (Single strand break repair)
- Mut System - helps cut away the backbone
- Ocurs after replication infidelity
- Nucleotide Excision Repair (single stand break repair)
- Occurs because of UV light exposure
- Uvr proteins fix it.
DNA Repair Mechanisms and Associated Enzymes for Double stranded break, translesion repair
- Recombinational Repair
- Translesion Synthesis
- Recombinational Repair (double strand break repair)
- RecA helps break double stranded backbone
- Happens after X-Rays exposure
- Translesion Synthesis
- Occurs after UV light creates blocking legion
- DinB helps remove lesion.
- Error prone
What is an error free mutation repair mechanism?
- Nucleotide excision repair
- UvrB recruited by UvrA and knock off RNAP
- UvrC is then recruited (this has endonuclease activity)
- UvrD removes single strand with mutation
- DNAP Pol 1 and ligase fill in gap
What type of repair is used when large scale DNA damage occurs?
- SOS regulatory system
- error prone
- replication can proceed and cell can replicate, but errors are more likely
- Translesion synthesis
- allows DNA to be synthesized with no template
SOS Reponse facts:
- What is the repressor for the SOS?
- Which, active enzyme degrades the repressor?
- LexA
- RecA
Which polymerases attach any nucleotides during the error prone mechanism of mutation repaitr? What is this mechanism called?
- Pol IV and Pol V
- Translesion Synthesis
What are the 3 methods for genetic exchange in bacteria?
- Transformation
- Conjugation
- Transduction
Transformation info:
- 2 types
- [] and [] competency
- Natural Competent
- Requires [] [] proteins and nucleases
- Species can be [] competent
- Induced Competent
- Specifc procedure to make cells competent
- [], [] , [] are examples
- Naturally Competent and Induced Competent
- DNA binding proteins
- Naturally
- Electrical shock, heat shock, differeing salt concentrations
[] is the mechanism of genetic transfer that involves cell-to-cell contact?
Conjugation
Does a sex pilus actually transfer the genetic material from cell to cell?
- No the sex pilus is retrated, bringing cells closer together.
- Genetic material is transferred through a pore.
What is the differene between and F+ and F- cell in conjugation?
- F+ has the sex pilus capability and genetic material to transfer
- F- does not
What are the 2 modes of transduction?
- The transfer of DNA from one cell to another by bacteriophage
- Generalized Transduction (think Lytic Phage)
- Specialized Transduction (Think Lysogenic PHage)
What is the difference between generalized transduction and specialized transduction?
- Generalized - DNA from any portion of the host genome is packaged inside the virion
- Specialized - DNA from a specific region of the host chromosome is integrated directly into the virus genome.
- DNA of a temperate virus excises incorrectly for example and takes adjacent host genes along with it.
What is a transducing particle?
- Phage with small bits of host DNA in the virion (comes from generalized transduction)
Four fates of foreign DNA inside cells?
- Degraded by cellular enzymes
- RMS and CRISPR system
- Stable maintenance outside chromosome
- mainly plasmids
- Needs to have replication origins recognized by/compatbile with host
- “Random” insertion into genome
- Need to have special enzymes, not truly “random”
- Transposons and pathogenicity islands insert this way
- Site-specific recombination into genome
- need specific recognition site and recombinases
- Foreign DNA needs some similarity with host genome
- Integrates through homologous recombination
What is homologous recombination?
Process that results in genetic exchange between similar DNA from two different sources
