Microbial Genetics Flashcards
1
Q
What is the diference between a mutation and a mutant?
A
- 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)
2
Q
Will a mutation always results in a change in the phenotype?
A
- Yes. that is the definition of a mutation.
3
Q
What is a selectable mutation?
A
- give mutants a growth advantage under certain conditions
- Usefule in genetic research
4
Q
What is a nonselectable mutation?
A
- Usually has neither an advantage nor a disadvantage over the parent
- Doesnt effect growth
- Based on appearance - color, hair etc…
5
Q
What is the difference between spontaneous mutation and induced mutation?
A
- 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
6
Q
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)
A
- 1 base pair
- amino acid change, or no change
- silent, missense, or nonsense
7
Q
Would a mutation in DNA have larger effect in bacteria or eukaryotes?
A
- Bacteria - they are haploid and have a smaller genome with less non-coding genes
8
Q
What is the difference between:
Silent Mutation, Missense Mutation, Nonsense Mutation?
Where does these 3 types of mutations occur on a gene?
A
- 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.
9
Q
What is a frameshift mutation?
A
- 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
10
Q
What type of double frameshift mutation can be “ok?”
+/-, +/+, or -/-
What type of triple frameshift mutation can be “ok?”
+/+/+ or -/-/-
A
- +/- 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.
11
Q
What are Transposable Elements?
A
- 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
12
Q
What are the 2 main types of transposable elements in bacteria?
A
-
Transposons and Insertion Sequences
- both carry genes encoding transposase
- both have inverted repeats at tehir and
13
Q
What is transposase?
A
enzyme that helps mobile DNA elements cut out and then transport to new DNA site.
14
Q
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
A
- simplest
- 1,000
- transposase gene, inverted repeats
- plasmids, bacteria, archea, and a few viruses
15
Q
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
A
- accessory
- antibiotic resistance
- IRs, target site
16
Q
What is the differene between a Transition Mutation and a Transversion Mutation?
A
- Transition - C <–> T or A<–>G
- Purine to purine or pyrimidine to pyrimidine
- Transversion - C/T <–> A/G
- Interchange of purines and pyrimidines
17
Q
What would be worse?
Mutation in catalytic Site and structural site vs non-important site?
Early Frameshift vs Late Frameshift?
A
- 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
18
Q
RNA viruses have a large error rate in terms of spontaneuous mutations.
Why is this and how could it be advantageous?
A
- RNA polymerases dont have proofreading
- Viruses us this to continually adapt and evolve
19
Q
What is a mutagen?
A
- Chemical, physical, or biological agent that increases mutation rates
20
Q
What are several classes of chemical mutagens?
A
- 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
21
Q
What is an example of an alkylating mutagen?
What is an example of an intercalating agent mutagen?
A
- Nitrosoguanidine
- Acridines
- can create an insertion/deletion that leads to a frameshift
22
Q
What are the 2 main categories of mutagenic electrogmagnetic radiation?
A
- 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.
23
Q
Can a cell repair itself after a transposon or virus has been added to the genome?
A
- No
- However, repair mechanisms exist for chemically or physically derived mutations.
24
Q
What are the different biological mutagens?
A
- Transposons
- Viruses
- can insert viral genomes into host chromosomes
- Bacteria
- produce reactive oxygen and nitrogen species that act as ionizing radiation
25
DNA Repair Mechanisms and Associated Enzymes for single strand break repair
1. Base Excision Repair
2. Mismatch Repair
3. 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.
26
DNA Repair Mechanisms and Associated Enzymes for Double stranded break, translesion repair
1. Recombinational Repair
2. Translesion Synthesis
1. Recombinational Repair (double strand break repair)
1. RecA helps break double stranded backbone
2. Happens after X-Rays exposure
2. Translesion Synthesis
1. Occurs after UV light creates blocking legion
2. DinB helps remove lesion.
3. Error prone
27
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
28
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
29
SOS Reponse facts:
* What is the repressor for the SOS?
* Which, active enzyme degrades the repressor?
1. LexA
2. RecA
30
Which polymerases attach any nucleotides during the error prone mechanism of mutation repaitr? What is this mechanism called?
1. Pol IV and Pol V
2. Translesion Synthesis
31
What are the 3 methods for genetic exchange in bacteria?
1. Transformation
2. Conjugation
3. Transduction
32
Transformation info:
1. 2 types
1. [] and [] competency
2. Natural Competent
1. Requires [] [] proteins and nucleases
2. Species can be [] competent
3. Induced Competent
1. Specifc procedure to make cells competent
2. [], [] , [] are examples
1. Naturally Competent and Induced Competent
2. DNA binding proteins
3. Naturally
4. Electrical shock, heat shock, differeing salt concentrations
33
[] is the mechanism of genetic transfer that involves cell-to-cell contact?
Conjugation
34
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.
35
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
36
What are the 2 modes of transduction?
1. The transfer of DNA from one cell to another by bacteriophage
2. Generalized Transduction (think Lytic Phage)
3. Specialized Transduction (Think Lysogenic PHage)
37
What is the difference between generalized transduction and specialized transduction?
1. Generalized - DNA from any portion of the host genome is packaged inside the virion
2. Specialized - DNA from a specific region of the host chromosome is integrated directly into the virus genome.
1. DNA of a temperate virus excises incorrectly for example and takes adjacent host genes along with it.
38
What is a transducing particle?
* Phage with small bits of host DNA in the virion (comes from generalized transduction)
39
Four fates of foreign DNA inside cells?
1. Degraded by cellular enzymes
1. RMS and CRISPR system
2. Stable maintenance outside chromosome
1. mainly plasmids
2. Needs to have replication origins recognized by/compatbile with host
3. "Random" insertion into genome
1. Need to have special enzymes, not truly "random"
2. Transposons and pathogenicity islands insert this way
4. Site-specific recombination into genome
1. need specific recognition site and recombinases
2. Foreign DNA needs some similarity with host genome
3. Integrates through homologous recombination
40
What is homologous recombination?
Process that results in genetic exchange between similar DNA from two different sources
41
