Bacterial Genetics Flashcards
Point mutations
A single change to one base of the DNA
Also called a single nucleotide polymorphism (SNP)
- missense
- silent
- nonsense
Frameshift
- Insertion
- Deletion
The mistake rate for DNA polymerase in bacteria is _______ million nucleotides
1/100
1% of new bacterial cells will have a mutation
Missense
base change will change the amino acid that is coded for at that codon
Silent
Base change will not change the amino acid that is coded for at that codon
Nonsense
Base change will change codon into a stop codon
this is the most significant causing change of the three
A codon encodes ____ amino acid
one
sometimes more than one codon encodes the same amino acid
Nonsense mutation lead to __________ protein
truncated
because they stop shorter than intended, the stop codon comes faster
Frame shift
coding for different codons because of one wrong or an added base to the 3 base pairings for a codon
Frame shifts happen when 1 or 2 bases in the reading frame is either removed or inserted
Insertion vs Deletion frameshift mutation
Insertion: added base to the reading frame
Deletion: base taken away from the reading frame
Transposon
A genetic element that can jump (transpose) from one piece of DNA to another
- Within the transposon there can be many genes, and one of those genes is usually a transposase
If the transposon is inserted at a gene it will disrupt the gene
Transposase
the enzyme that helps the transposon move
cuts a target DNA sequence and then inserts the transposon
How can the transposon move?
- From a plasmid to the chromosome
- From chromosome onto a plasmid
-Around the genome
Observed mutation rate
The number of mutations that are occurring vs the efficiency of repair mechanisms
E.coli has lots of molecular mechanisms to repair mutations (2)
- error free repair
- error prone
Error-free repair
Deals with mismatched bases or chemically modified bases, complementary DNA stand is there to direct a perfect pair
Error-prone
Coping with massive DNA damage, such as numerous double strand breaks, missing bases, no complementary strand is available for DNA Pol to copy
It is done by the DNA polymerase V
But imperfect repair is better than death
If a mutation can be repaired before the cell divides, offspring _____ be mutant!
won’t
Hemimethylated DNA
Many bacteria methylate their DNA (either A or C)
- It takes time to methylate the DNA, therefore after replication the new strand will be unmethylated at first
Why methylate?
- recognize incoming foreign DNA
- Can tell new from old strand - target repair to new strand (methyl mismatch repair system)
MutHSL recognizes a mismatched base pair, clips the backbone of non-methylated strand near mismatch removes a piece of one strand, DNA Pol I repairs, ligase closes
SOS response to massive DNA damage
- Stop cell divison (and sometimes metabolism as a whole
- Enhanced excision repair
Transleasion repair
repair with no DNA template as a guide using error prone DNA polymerase
*error prone DNA polymerase (Pol V) is encoded by the umuCD genes
Recombination
different regions of similar DNA sequences that are separated by a gene can base pair with each other
This can result in swapping DNA sequences so that gene x is removed
Recombination repair
- during replication, damaged DNA that cannot be recognized by DNA pol III will be skipped over and not replicated
- SSB proteins will cover these ssDNA regions
- RecA binds to SSB proteins- bound to single strand DNA
- Finds a homologous sequences in the other copy of the chromsome and initiates strand invasion to repair the gap in a “X” manner
- Original damaged bases are subsequently repaired with other mechanisms
DNA repair mechanisms
mismatch repair
thymine dimers
SOS response
RecA
Griffith’s experiment
Established that bacteria could be “transformed” by extracellular DNA
Horizontal Gene Transfer (HGT)
the movement of DNA between cells that is not linked to reproduction
Why does HGT happen?
- DNA is good food: DNA is consumed to get energy (C,N and P)
- To diversify their genomes, microbes that are abundant in a given environment are probably well adapted to their environment and if a microb takes up their DNA it might acquire their traits
- ‘Mobile DNA’ is common in microbes
Mobile Genetic Elements
DNA that has evolved to move between cells and that can evolve independently of their cellular hosts
In microbial genomes only a fraction of genes (the ______ ______) is found in all individuals. While the _____ _______ is the set of all genes found in all stains of the species
Core Genome
Pan Genome
Why does HGT matter?
- HGT has a profound effect on microbial evolution
- Molecular genetics (relies on our ability to transfer DNA between cells)
- Genetic engineering
Homologous Recombination
occurs due to RecA mediated DNA repair
What needs to happen for HGT to occur?
- Uptake of extracellular DNA cytoplasm
- The acquired DNA must be replicated
- Recombination is often required to maintain the foreign DNA
Non-homologous Recombination
due to diverse mechanisms, does not require similar DNA sequences, often requires a target sequence, requires specific enzymes
Plasmids
Small DNA elements, that have an origin, non-essential but usually beneficial genes, and often encode for their own transfer via conjugation
many plasmids have been engineered and they are an important tool biotechnology
Viruses
Infectious nucleic acids that can ‘accidently’ transfer host DNA along with viral DNA upon infection
Transposons and Integrons
DNA elements that have an enzyme ( transposase or integrase, respectively) that catalyzes excision of the element followed by insertion into a new site. Usually contain several other genes in a cassette.
Genome Islands
a region of the genome that appears to have been inherited through a single large recombination event ( e.g. pathogenicity islands)
Three types of DNA Exchange in Bacteria
- Conjugation
- Transformation
- Transduction
Transformation
the integration of extracellular DNA into the genome
Diverse bacteria and archaea can take up extracellular DNA and are said to be naturally competent (We can also induce competence in some cells using chemicals or electrical shock)
Why are some cells naturally competent?
A.It provides access to nutrients (nucleotides as food)
B. It allows cells to acquire new traits from other species
C.It allows cells to share polymorphisms within species
D.All of the above
D. all of the above
In vibrio choelerae (gram negative bacterium) , transformation requires _____ __ ______
Type 4 pilus
Type 4 pilus
elongate and contrat on the inner membrane using ATP
DNA is pulled into the cell by the pilus
Detection of transformation in the laboratory
- The Donor DNA must encode a trait lacking in the recipient strain
_ This is called the marker gene, because it marks the presence of the donor DNA
For example, the DNA donor may be trp+ (able to synthesize its own tryptophan) while the recipient is trp- (unable to synthesize tryptophan). DNA from trp+ strain is added to trp- bacteria, and the bacteria are spread on agar medium lacking tryptophan. Only trp+ colonies can grow.
Transduction
the movement of DNA between cells facilitated by viruses
Virus infection cycle
- Attachment (adsorption of phage viron)
- Penetration of viral nucleic acid (DNA ONLY not the whole viron)
- Synthesis of viral nucleic acid and protein
- Assembly and packaging of new viruses
- cell lysis and release of new virons
Lytic cycle vs Transduction
lytic cycle: Phage attaches and then DNA gets released into the cell, THEN a phage complex forms and the cll lysis and the virus gets released in the system
transduction: Phage attaches and then DNA gets released into the cell, the DNA homolougously gets recombined with original cell DNA and nothing really “forms”
Specialized transduction
a portion of host DNA is exchanged for phage DNA
defective phage can transduce galactose genes
Conjugation
directed plasmid exchange between cells
can occur via pilus attachment which causes stabilization between the the two cells and then the plasmid transfers and splits from one cell to the other
Which of the following best explains why transduction occurs?
A.It is a strategy that viruses use to evolve greater pathogenicity
B. It allows bacteria to evolve resistance to phage
C.It provides a food source to bacteria D.It occurs as an accident of viral replication
E. It occurs because it helps bacteria evolve new traits
D.It occurs as an accident of viral replication
