Lecture 9 - Bacterial Genetics Flashcards
what is bacterial genetics?
how bacteria get different genes
do bacteria have a lot of genetic diversity?
yes
genetic change can add new ___?
traits
what are two types of ways that add more genetic diversity/traits?
- Mutations
- Gene transfer
what are mutations? are they good or bad?
mutations are random changes in DNA sequence. they can be neutral/good/bad.
what do mutations create?
they create mutants.
when can mutations happen?
they can happen when we are replicating DNA - there can be errors.
Or can be induced by mutagens - chemical or physical
can bacteria repair mutations?
Yes, bacteria can repair mutations using repair enzymes like DNA polymerase and mismatch repair.
what is gene transfer?
when DNA is transferred through pili: bacterial sex
what is natural selection?
it is a mutation that gives you some sort of advantage. it selects advantageous genes.
what are the two types of mutations?
- spontaneous
- induced
what is spontaneous mutation? what are the two subtypes?
Spontaneous mutation is due to errors during DNA replication.
The type subtypes:
1. Base substitution
2. Base addition/deletion (frameshift mutation)
what is base substitution? what are the 3 types?
Base substitutions are point mutations.
1. Missense mutation: when the DNA, mRNA, and product all change. The end product (the protein) changes.
2. Nonsense mutation: When the DNA, mRNA, and transcribed codon are all changed. However, the codon that results is the stop codon in this situation. So the process of translation stops here. It is usually a bad mutation since we get an incomplete and short protein.
3. Silent mutation: when the end product (the protein) is the same, but the DNA and mRNA change.
what are two types of silent mutation?
- Genotype: which is the DNA sequence. This changes.
- Phenotype: which are the observable characteristic. These stay the same. The phenotype changes in nonsense and missense, but not silent mutation.
what is a wild type?
the normal version of the translated protein
what is the base addition/deletion mutation?
the frameshift mutation, which is usually bad. It is when there is an additional base added, and so the next bases are messed up. All the downstream codons are affected.
what is ‘induced via mutagens’?
A mutagen is a substance that causes mutations. It is any chemical or physical agent.
why would we want to induce mutations?
-Mutations help to study the functions of genes.
-Mutations help industries to have the best-performing gene/cell.
-Mutations help with chemotherapy, and help with killing both cancerous cells and normal cells.
what do the chemicals that are induced via mutagens do?
-They modify bases
-Base analogs
-Intercalating agents (when DNA inserts a random base because of the random intercalating agent that is inserted)
what is the first thing that changes from a mutation?
DNA
what is an example of a chemical that modifies bases? what does it do?
alkylating agents: used in chemotherapy to kill cancerous cells
what are base analogs?
they are structurally similar to bases and they mimic the bases, but they don’t follow pairing rules. They look like bases, and DNA polymerase adds the wrong base and causes mutations since it thinks its an actual base.
what are two types of radiation that are induced via mutagens?
- UV light
- Ionizing radiation
what does the UV light do?
Exposure to UV light causes two adjacent thymines to become cross-linked, which then forms a thymine dimer. This disrupts their normal base pairing.
Cells induce error-prone SOS repair mechanisms for survival. This is where it tells DNA polymerase to hurry up and pair with the base, which causes mutations since the thymines are bonded together.
what do ionizing radiation do?
it breaks down DNA. Examples are X-rays and gamma rays.
What are two ways that damaged DNA is repaired? How do we try to repair the errors that are happening?
- DNA polymerase goes the opposite way of how it usually does to go back and proofread. It goes from 3’ to 5’ to proofread.
- Mismatch repair: This is when enzymes fix mismatched pairs by cutting out the mismatched bases and then adding the correct bases like it normally does.
mutations (changes to DNA) are:
1. Good
2. Bad
3. Neutral
4. Can be all of the above
- can be all of the above
what are the three steps to gene transfer? is gene transfer a horizontal or vertical process, and what does this mean?
- Transformation
- Transduction
- Conjugation
It is a horizontal process, meaning it gets gene info from neighbors, rather than parents.
what is genetic recombination?
The process of forming new combinations of genes in recombinants. Bacterium has some extra genes, causing a recombinant.
what two things can bacteria transfer?
- DNA segments: narrow host range - meaning bacteria can only share with neighbors that are similar to them.
- Plasmids: ex. R plasmids - narrow to broad host range - meaning the bacteria can share with ANY bacteria. This can cause a lot of different bacteria to be resistant to antibiotics.
If a transfer occurs, bacteria much have what to be passed on to the progeny (offspring)?
Origin of replication
Do linear DNA segments have an OriR?
No they do not
what do linear DNA segments have to undergo in order to do genetic recombination?
Homologous recombination
what is homologous recombination?
When the DNA segment has to undergo homologous recombination, the two bacteria have to be similar.
It is when a bacteria cuts and pastes itself into a similar neighboring host.
what happens when a linear piece of DNA enters a cell that is not similar to it?
It will be chopped up, unless it goes into a similar neighbor, then it will be recognized in that case. Then it will be cut and pasted it.
T/F: homologous replication helps all cells have a copy of the DNA, whereas when a DNA fragment tries to go in another cell without homologous replication, only one of the cells have the DNA fragment, which is useless in this case.
True
how are plasmids transferred?
they are self-replicating since they have an Origin of replication, and do not undergo homologous replication.
what is transformation? what is the buzz word?
Transformation is when naked DNA enters competent cells.
Buzz-words:
1. Naked DNA (free DNA floating in the environment of the bacterial cell, due to a cell lysing/bursting and the DNA being alone without a cell).
2. Competent cells (Any cell that is ready to take up the free DNA)
how many strands enter into the neighboring cell in transformation?
one one strand
Linear DNA doesn’t have OriR, so what does it perform?
Homologous recombination
are all cells competent?
no, not all cells are ready to take up this free DNA
what do plasmids under to enter the neighboring cell?
they are self-replicating since they have an OriR. This way they can replicate without undergoing homologous replication.
what is transduction? what is the buzz-word?
When bacteriophages (bacterial viruses) accidentally pick up bacteria DNA during replication and assembly.
Buzz-word: phages
what do bacteriophages transfer in transduction?
they transfer bacterial genes to new cells
what process do bacteriophages undergo in transduction?
homologous replication
summarize transduction from the video
- A bacteriophage (bacterial virus) carries a section of DNA from one bacterial cell to another (called the host cell).
- The phage attaches to this bacterial host cell and injects its nucleic acid (DNA) into this host cell.
- A phage enzyme is now produced. This enzyme breaks down the host’s DNA into smaller fragments.
- The phage DNA is now replicated and phage proteins are produced.
- While the phage particles mature and form, a few of these phages will engulf some of the host’s DNA, instead of the phage DNA.
- The phage particle carrying the bacterial host’s DNA, goes and infects another cell. This transfers the old bacterial host’s DNA to the new bacterial host’s DNA.
- When the old bacterial DNA is introduced into the new host cell, it can be integrated into the bacterial chromosome and multiply, while carrying new genetic material.
- This is a mutation
what is conjugation? what is the buzz-word?
It is bacterial sex, which is also the buzz-word.
what is plasmid transfer in conjugation?
when one donor cell gives a recipient cell a plasmid.
1. The plasmid in the donor cell starts unwinding at the Origin of Transfer.
2. Only one strand unwinds, the other remains how it is.
3. The F pilus extends from the donor cell and brings the recipient cell closer.
4. The plasmid enters the recipient cell, and both the old and new plasma create another strand of the DNA.
5. At the end, both the donor and the recipient now have a copy of the plasmid.
6. Also at the end, the recipient can now act as a donor.
what are transposons?
when plasmids can facilitate the transfer of chromosome segments and transposons (jumping genes)
what can transposons do?
they can just from one place in a genome to another - no homology needed
could transposons be agents of mutations as well?
yes, because the DNA sequence is changed
what type of gene transfer involves viruses?
Transduction
what is naked DNA?
free-floating DNA that is not within a cell
what will happen to a linear piece of DNA inside a cell?
it will undergo homologous recombination
what will happen to a plasmid DNA inside a cell?
it will self-replicate since it has its own OriR
what is a competent cell?
a cell that excepts naked DNA
what is a bacteriophage?
a bacterial virus
how can bacterial DNA end up in a phage?
some of the phages engulf bacterial DNA when they are trying to engulf their own DNA
once phage injects bacterial DNA into a cell, how is the DNA able to replicate inside the new cell?
the bacterial DNA integrates into the chromosome through homologous recombination. the bacteria multiply with the new genetic material, and the replaced host DNA is degraded ?*
where is transfer initiated in the plasmid?
at the origin of transfer
how many strands of plasmid are transferred?
1
at the end of conjugation, is the plasmid present in the donor, recipient, or both?
both
are all mutations spontaneous?
no
Antibiotics
1. increase the rate of spontaneous mutation.
2. provide an environment in which preexisting mutants survive.
4. destroy all mutant bacteria.
5. cause mutations to occur.
- provide an environment in which preexisting mutants survive.
Gene transfer that requires cell-to-cell contact is…
conjugation
T/F: Double-stranded DNA enters the recipient cell during transformation.
False
Base analogs:
1. Can be incorporated into DNA during replication
2. Often result in point mutations
3. Mimic bases chemically
4. a and b are correct
5. All of the above are correct
- All of the above are correct
Which of the following is not true about mismatch repair?
1. It repairs point mutations
2. It uses DNA polymerase
3. It uses DNA ligase
4. It removes not only the mismatched base, but several adjacent bases
5. It removes both DNA strands in the mismatch area
- It removes both DNA strands in the mismatch area
In conjugation:
1. The entire chromosome is transferred to a new cell
2. DNA is transferred vertically to daughter cells
3. DNA is transferred to neighbor cells
4. Naked DNA is taken up from the environment
5. Plasmids travel to a new cell and are lost to the original cell
- DNA is transferred to neighbor cells
Gene transfer that requires a bacteriophage vector is called:
1. Conjugation
2. Transposition
3. Transduction
4. Translation
5. Transformation
- Transduction
When it comes to mutation, there are two commonly held misconceptions. First, people think of mutations as a bad thing (this is probably due to the negative connotation of the word, “mutant,” and the knowledge that genetic diseases and cancers are caused by mutation). Second, people think that adaptation via mutation happens purposefully e.g. bacteria purposely mutate to develop antibiotic resistance mutations when exposed to antibiotics. Discuss the flaws in these two misconceptions.
Answer: The first misconception is flawed because mutations are not inherently bad. They happen randomly and can be good, bad or neutral for an organism. A mutation will be bad for an organism if it creates altered proteins that bring about dysfunction or death. It is good if the mutation creates some adaptive advantage for the organism in comparison to others of its kind. Finally, it can be neutral if the mutation is silent and no protein changes occur.
The second misconception is flawed because mutations are completely random; they do not happen purposefully. What is seen with scenarios like the development of antibiotic resistance is a preexisting random mutation that benefits the organism in a particular circumstance. The organism, when exposed to antibiotics, survives and outcompetes its neighbors. From here, it passes these beneficial genes onto its progeny, thereby propagating the mutation. What appears to be a purposeful adaptation is a random mutation followed by the process of natural selection (“survival of the fittest”).
If naked DNA is a linear piece of DNA, how can it replicate inside the bacterial cell?
By inserting into bacterial chromosomes through homologous recombination.
How does bacterial DNA get packaged into a phage?
Bacterial DNA gets packaged into a phage accidentally when the phage packages a piece of bacterial DNA into its protein coat.
Which bacterial structure is required for conjugation?
Sex Pilus.
Why do we need to evolve enzymes?
To make them more efficient at catalyzing the formation of products that we need like medicines, biofuels, etc.
Which macromolecule do we need to change to make a change in an enzyme?
DNA
How can we induce a change in this macromolecule (DNA)?
Using chemical or physical mutagens
Once you have the modified macromolecule, you need to introduce it into a bacterium to produce the “new” enzyme. Which method can you use to introduce this modified macromolecule into a bacterial cell?
Any gene transfer mechanism like transformation, transduction, or conjugation
