Microbial Genetic Diversity And Mutation Part 2 Flashcards
What is the function of a protein determined by?
It’s amino acid sequence.
What do eukaryotic microbes have the ability to do to increase their genetic diversity that prokaryotes do not?
They can increase their genetic diversity through meiosis and sexual reproduction.
Where do prokaryotes genetic diversity come primarily from? (2 things)
- Mutation
- Transfer of DNA between individuals of the same species (sometimes different) called horizontal gene transfer.
What are the 2 ways mutations can occur?
- Spontaneous mutations
- Induced mutations
What do spontaneous mutations occur from? (3 things)
- Errors in the processes of DNA replication and DNA repair.
- Natural chemical instability of DNA bases
- Damage caused by highly reactive molecules produced by cellular metabolism. (E.g reactive oxygen species (ROS) formed during aerobic metabolism.
What are induced mutations caused by? Give some examples.
The presence of intense radiation or chemicals that can damage DNA structure.
E.g X-rays or UV radiation, mutagenic/carcinogenic compounds
What are the 3 major types of mutation? Explain them
- Substitutions where one nucleotide base is replaced with another. The gene sequences stays the same length.
- Deletions: One or more nucleotides in the genetic sequence are permanently removed. Sequence gets shorter.
- Insertions: one or more nucleotides in the genetic sequence are permanently added. Sequence gets longer.
Mutations in genes have varying effects on the ___________ made from those genes. Can vary from ___________________ to ____________________ depending on the nature of the mutation.
Proteins
Invisible
Catastrophic
An mRNA contains the codon CAA. What amino acid does this code for?
Mutation: a base substitution to CAG. What amino acid does this code for?
Different mutation: a base substitution to GAA. What amino acid does acid does this code for?
Glutamine (Gln)
Gln
Glutamic acid (Glu)
What is referred to as “lesions”?
DNA damage
What are errors in DNA that are not or can’t be repaired called?
Mutations
What does the SOS response represent?
An important trade off between genomic stability and genomic plasticity
What is the alternative to the SOS response typically?
Cell death due to inability to replicate the chromosome.
Translesion DNA synthesis benefits the bacterial community by _______________________.
Increasing genetic diversity and causing mutations, some of which may confer a competitive advantage to offspring cells.
SOS response is an important mechanism in generating _______________________.
Resistance to certain classes of antibiotics.
Where does much of the genetic plasticity of bacteria and archaea come from?
The horizontal gene transfer (HGT) which is defined as the transfer of genetic material between individuals rather than from parent to offsprings
What does most of HGT depend upon?
The cell’s ability to perform homologous recombination
What happens in homologous recombination?
Transferred DNA is incorporated into the cells chromosome using matching (homologous) sequences between transferred DNA and the chromosome. The transferred DNA is first nicked and unwound into a ssDNA form.
During homologous recombination, the sDNA is “saved” from the breakdown of the cell by ______________________.
ssbinding protein (SSB)
SSB coated DNA is bound by __________ which ___________________________?
RecA
Swaps one strand of the donor DNA with one strand of the recipient DNA. (Cross strand exchange) It must occur where the donor DNA can base pair with the recipient DNA.
What happens after the cross strand exchange?
The crossed strands are cut and nicks sealed by DNA ligase.
What are the 3 major mechanisms of HGT that differ mostly by the source of transferred DNA?
- Transformation
- Transduction
- Conjugation
Explain transformation.
Fragments of bacterial DNA are absorbed from the environment and incorporated into the chromosome. Plasmid DNA is also absorbed from some sources. It occurs when a cell incorporates DNA absorbed from the environment.
Transduction
Fragments of bacterial DNA are transferred by a virus and incorporated into the chromosome.
Explain conjugation
Plasmid or chromosomal DNA is directly transferred from one cell to another.
What is a cell called that can be transformed by DNA environments?
Competent
________________________ is only found in some bacteria and requires cellular systems that can absorb environmental DNA.
Natural competence
_________________________ can be produced in a lab and is done using laboratory treatments that make the cell membrane permeable to DNA.
Artificial competence
What is artificial competence used in laboratories for?
To transform plasmid DNA into bacterial cells for genetic experimentation.
Naturally competent bacteria have ____________________ that can bind and absorb DNA fragments from the environment.
Cell membrane proteins
Where do the DNA fragments usually come from?
The chromosomal DNA released during the death of nearby microbial cells
Absorbed DNA has one of its strands destroyed by a ____________________. Which creates a ___________________ that can be recombined into the chromosome using _________________________ performed by RecA.
Nuclease enzyme
Single stranded DNA
Homologous recombination
Natural competence is highly _________________ by the cell. For many species, competence is induced by the ___________________.
Regulated
SOS response
What is quorum sensing?
A process that adjusts gene expression based on how many bacterial cells are nearby.
During growth, B. Subtilis releases a short peptide signal called _____________. The amount of __________ in the environment is proportional to the number of nearby cells. Once these level reach a critical level, they activate a receptor (_______) that sends a signal to transcribe genes that permit natural competence.
ComX
ComX
ComP
Transduction is the transfer of DNA via _______________.
________________________ are known as bacteriophages or “phages.”
Viruses
Bacterial viruses
Wha are virulent phages?
Phages that will rapidly replicate in bacterial cells and destroy them.
What are temperate phages?
They will insert their genome into the bacterial cell’s chromosome.
Virulent phages have a replication cycle that ends with ___________________. During this process, the bacterial cell’s DNA _____________________________________.
Cystolysis
Break apart into fragments.
What may occasionally happen using the assembly of the virus in Virulent phages replication process? What does this create?
Package random chunks of bacterial DNA into the capsid rather than viral DNA. This creates a defective virus (one that cannot replicate) called a Transducing particle
What happens when the transducing particle attempts to infect another cell? How can the DNA be incorporated into the bacterial chromosome?
It releases bacterial DNA into the cell it’s trying to infect.
homologous recombination.
Define generalized transduction.
When DNA fragments come from anywhere in the the bacterial chromosome
Temperate phages incorporate their DNA into the bacterial chromosome as a ____________________. Explain the process.
Prophage
When a virus is ready to replicate, the prophage forms a loop and removes itself from the chromosome. Rarely this loop will form incorrectly and include some nearby genes from the bacterial DNA. These are defective transducing particles.
What do transducing particles do? When do the genes become a part of the chromosome? What kind of transduction is this?
Carry genes into the next bacterial cell during the next infection cycle.
When a new prophage is formed.
Specialized transduction because this process can only transfer genes near the prophage.
What is conjugation? What does it require?
A form of transfer that occurs between bacterial cells.
A donor cell that carries a conjugate plasmid.
What does the conjugate plasmid contain?
The genes for the proteins needed to transfer that plasmid from the donor to the recipient.
Also often have genes for antibiotic resistance and metabolic enzymes.
How is conjugation typically accomplished?
By the formation of a conjugation bridge. Which is a physical connection between 2 cell that allows transfer of the plasmid.
What is a well known conjugative plasmid?
the E. Coli F plasmid which codes for genes that form the F pilus
What is the F pilus?
the conjugative bridge and is a hollow tube that plasmid DNA is transferred through.
What happens once the F plasmid is connected?
The F plasmid DNA is replicated and transferred through the pilus as ssDNA. Transferred F plasmid ssDNA is replicated by the recipient to form a complete transferred F-plasmid.
What happens in some strains of E. Coli involving the F-plasmid? What are they called?
What do they do when conjugation begins?
the F-plasmid is integrated into the chromosome.
Hfr strains.
Hfr strains will replicate and transfer the chromosomal DNA which can be incorporated into the recipient cell chromosome by homologous recombination.
What are the effects of substitution mutations?
Silent mutations
Missense mutations
Nonsense mutations
What are silent mutations?
Occur when a substitution does not result in a change in a proteins sequence.
What are missense mutations? What is an example?
These occur when a substitution changes one amino acid to another in the proteins sequence.
Covid spike protein
What are nonsense mutations? Give an example.
These occur when a substitution changes one amino acid to a stop codon.
Ochre mutation
Insertions and deletions often result in a different effect called ________________. They shift the genetic sequence within its ____________________.
Frameshift
Reading frame
Occasionally the wrong nucleotide may pair at the active site of ______________________. If this incorrect nucleotide is added to the growing DNA strand, it becomes a _____________________.
DNA polymerase 3
DNA mismatch error
In addition to DNA synthesis, DNA polymerase 3 can perform a type of error correction called?
DNA proofreading
What happens if a mismatched base is added?
It will not be able to properly base pair with parental DNA strand which will cause distortion of the shape of the DNA backbone.
What do distortions in the DNA molecule cause?
The replisome to stop elongating (stalling)
What is the second enzyme activity of DNA polymerase called?
An Exonuclease which removes the incorrect nucleotide.
What happens once the incorrect base pair is removed?
DNA polymerase 3 can add the correct nucleotide using its DNA synthesis enzyme.
What happens if DNA polymerase does not properly proofread?
The cells have a back up system called the Methyl-directed mismatch repair.
What does methyl-directed mean?
After replication, enzymes add methyl (-CH3) groups to A and C bases. DNA methylation has a variety of functions but during replication it identifies the parental DNA strands.
For a short time after replication, the newly replicated DNA strand has _____________________ because they haven’t been added yet.
No methyl groups
How do the lack of methyl groups help proteins in methyl directed mismatch repair?
They can identify newly replicated DNA strands by their lack of methyl groups.
Explain how Methyl-directed mismatch repair works.
Mut proteins work together to forma large complex that scans the DNA in search of the backbone distortions. Once identified, Mut proteins unwind the DNA and cut the back bone of a large region of the unmenthylated DNA strand. Then DNA polymerase 1 will bind to the gap and synthesize new DNA to replace the mismatch.
the cut region during methyl directed mismatch repair is removed when the base pairing in the region is broken by the ______________________________ called __________. This creates a ________________________________.
DNA helicase enzyme
UvrD
Single stranded binding protein (SSB)
What polymerase is known as the gap-filling polymerase. What enzymes is used to seal the nicks on each side of the gap?
DNA polymerase 1
DNA ligase
What happens when a DNA strand is too extensively damaged to be repaired normally?
Cells activate recombination repair system.
What is recombination repair lead by? Explain what it does.
A protein called RecA.
RecA binds in the replication fork to both the leading and lagging strand. Once bound, RecA cuts the DNA backbones and swaps the gapped DNA with the DNA from the other strand. This allows DNA polymerase 1 to fill the gap using undamaged DNA on the opposite side.
How is DNA damage that occurs outside of replication repaired? (2 systems)
- Nucleotide excision repair
- base excision repair
Explained Nucleotide excision repair briefly.
Done by proteins of the uvr operon and is similar to mismatch repair.
Only works in the regions of the damaged DNA with a distorted backbone.
How does nucleotide excision repair work? (6 steps)
- UrvA binds to and then moves along DNA, scanning for distortions.
- When a distortion is identified, UrvA stalls and causes UvrB to bind.
- UrvB acts as a marker that identifies damaged regions of DNA to UvrC.
- UvrC binds to the DNA and cuts the backbone on both sides of the damage.
- The UvrD helicase enzyme removes the damaged section by breaking base pairing.
- The DNA gap created by this is filled by DNA polymerase 1 and sealed by DNA ligase.
Explained Base excision repair and how it works.
Base excision is needed because some types of DNA damage do not distort the DNA backbone.
It works by an enzyme called DNA glycosylase which can recognize damaged bases and cuts out only the base. Then an enzyme called AP endonuclease can recognize AP sites (sites in DNA with a backbone and no base) and cut the DNA backbone to create a DNA gap.
The DNA gap is filled by DNA polymerase 1 and sealed by DNA ligase.
