Title: T4 / BV6 / Modul 1 / Bakteriegenetik

Q: What can be found on the bacterial chromosome?
A: - Essential genes
- Accessory genes - for special conditions
- How many it contains depends on what type of bactera it is

Q: What can be found in the plasmids?
A: - Extra chromosomal
- Accessory genes eg.:
---> Antibiotic resistances
---> Virulence genes

Q: Hur kan kromosomer variera mellan bakterier?
A: Vissa bakterier hat flera kromosomer, medan andra har linjära och andra har cirkulära, och vissa har båda

Q: What are plasmids simplified?
A: Plasmids are pieces of DNA inside the bacteria thar aren't parts of the DNA themselves, if the bacteria would lose them they wouldn't miss them

Q: WHat does the bacterial genome consist of?
A: Genome = chromosome(s) + plasmid(s)

How is replication done in prokaryotes (bacterial)?

Q: Is there a nucleus in bacteria?
A: - There is no nucleus in the bacteria
- Bacterial RNA doesn't have to be processed to be mRNA (exons and introns dont exist in bacteria) after transkription
other: eukaryotic cells are approx 100um, while bacteria is 1-2um

Q: How can the bacterial genome be modified?
A: 1. Genom mutationer
2. Genom att tillägna sig nya gener genom horizontal gene transfer

WHich 2 types of mutations occur in the bacterial genome?

What are codons?

Q: What is a point mutation?
A: Change in one nucleotide

Q: Which types of point mutations are there?
A: - Silent
- Missense
- Nonsense

Q: What is a silent point mutation?
A: Silent - change in DNA but no change in the protein - this mutation has no effect on fenotype or the bacteria itself

Q: Vad är en "missense" punktmutation?
A: När en annan aminosyra kommer kodas för

Q: What is a nonsense point mutation?
A: Nonsense - the mutation in the DNA sequence results in a stop codon

Q: What is a frameshift mutation?
A: Insertion or deletion of nucleotides that are not a multiple of 3

Q: What will a deletion or insertion lead to in the DNA (frameshift mutation)?
A: If u remove ex. 2 nucleotides it completely changes the reading frame and the sets of 3 that are read changes, it changes all the aa sequences after the deletion

Q: WHat is vertical transfer?
A: - Transfer of genetic material during cell division
- Normal inheritence of genetic material that happens during cell division

Q: How is the bacteial chromosome replicated?
A: The origin of replication is where replications starts
- Here we have an opening of DNA and a replication bubble
- This is where replication happens
- The bubble and replications proceeds bidirectionally in 2 directions and does so until it reaches the terminus, when that happens the DNA's will be separated and u have 2 copies, where one goes into the new daugther cell

Q: What is horizontal gene transfer (HGT)?
A: Transfer of genetic material between bacterial cells independently of cell dividsion

Q: What does HGT do?
A: Modifies the bacterial genome: aquisition of new genes

Q: Mellan vad kan horizontal gene transfer ske?
A: - Mellan olika typer av bakterier
- De får då helt nya gener de ej skulle fått genom vertikal överföring

Q: What is HGT and what can it occur between?
A: - Physical translocation of DNA between 2 cells
- Can occur between different clones of the same species, different species and different genera

Q: WHich 3 HGT mechanisms exist?
A: - Natural transformation
- Transduction
- Conjugation

Q: What is natural transformation?
A: Natural - bacteria uptake free DNA floating in their environment

Q: What is transduction and conjugation mediated by?
A: Mediated by mobile genetci elements (MGEs):
- Transduction is mediated by bacteriophages
- Conjugation is mediated by pilus

Q: What else can natural transformation be called?
A: Competence

Q: Vad är natural transformation och hur många bakteriearter är naturligt kompetenta?
A: - Upptag av DNA från omgivningen (eDNA = extracellulärtDNA)
- >80 olika arter

Q: What differs between different bacteria when it comes to natural transformation?
A: - What differs between them is what triggers them to uptake DNA
- Constitutively - takes up DNA all the time

Q: What s natural transformation induced by?
A: Induced by different conditions depending on the species

Q: What is the DNA uptake pilus?
A: - Conserved among tranformable bacteria
- "Fishes" the eDNA from the environment

Q: Varierar pili mellan gram+ och gram- bakterier och hur tar dne upp DNA?
A: - Gram- och + pili liknar varandra och har samma funktion
- De polymeriserar på bakteriens yta och tar upp DNA från omgivningen. DNAt görs om till ssDNA och kan tas upp av bakterien genom olika kanaler

Q: How is DNA taken up via the pilus?
A: 1. They polymerize on the surface of the bacteria and take up DNA from the environment
2. DNA is processed to ssDNA and can them be taken up in the bacteria through dfferent channels

How is DNA uptake preformed via conjugation?

How is integration of the new DNA into the chromosome preformed?

Q: How will the new uptaken DNA be integrated?
A: The new DNA must be integrated into the chromosome by recombination otherwise it will be lost

Q: What does recombinase search for?
A: Searches for homology in the chromosome - recombinase

Q: What does recombinase do?
A: - Searches for homology in the chromosome
- Recombinase finds something similar in the chromosome and will then try to integrate the new DNA
- New genes (ex. antibiotic resistanse genes) are integrated into the new chromosome through homologous recombination

What are bacteriophages?

Q: What can bacteriophages do with DNA?
A: Phages can transfer bacterial DNA via transduction

Q: Which type of parasite are bacteriophages?
A: Phages are obligate intracellular parasites

WHat do phages require their host to do?

Q: What happens in the bacteriophage lytic cycle?
A: 1. Phages in the environment, a pghe will attach to a bacterial call, inside the head of the phage is genetic material
2. The genetic material will be injected tínto the bacteria, not the phae itself
3. The phage genom will be replicated by the bacteria
4. The phage genetic material will be transcribed and translated
5. All these new bits will be assembles to phage particles and te new replicated genetics material will be placed in the phage
6. The bacteria will explode and all the phages inside will be expelled into the environment

Q: How can phages transfer bacterial DNA during their life cycle?
A: Phages can transfer bacterial DNA during their life cycle: transduction

Q: When does transduction occur?
A: Happens when phages package DNA that belongs to the bacterium by mistake

Q: What happens to the DNA that belongs to the bacterium that phages package by mistake?
A: - This DNA is then injected into the next bacteria the phage will infect
- It can then become integrated into the bacterial chromosome by recombination

Q: How will bacteriophages carry bacterial DNA between bacteria?
A: - Happens by mistake, whne the phage takes a part of bacterial DNA and packages it into its head
- So when this phage with bacterial DNA ejects into a new bacteria bacterial DNA will enter instead of phage DNA, this DNA can then be included in the bacterial genome by recombination

Q: What is conjugation?
A: Conjugation is when plasmids move from one bacteria to another

WHat are plasmids?

Q: Vad händer med plasmider som är konjugativa?
A: - De kan överföras från en bakteriecell till en annan
- De har alla gener som är nödvändiga för deras transfer

Q: Är alla plasmider likadana?
A: Det finns många typer av plasmider, olika storlekar och några är konjugativa (inte alla)

Q: What do plasmids carry?
A: Plasmids carry the gene for the code that make the conjugation possible, it produces whats is needed for conjucation itself

What are the 3 general steps for conjugative transfer (conjugation)?

Q: How will the plasmid be transferred between the donor and recipient?
A: - The plasmid will create a channel/pore between donor and recipient cell
- The plasmid will then open up and one part of the ds-plasmid will be transferred through the T4SS, while the other ssDNA will stay in the donor and the other ssDNA will go to the recipient

Q: What is the recipient bacterium called after it has recieved the plasmid?
A: Recipient is called transconjugant when it has the new plasmid - u have a new donor now
- Both these cells can now act as donors
- This is how plasmids rapidly spread

Q: Which bacterial cells can act as donors after conjugation?
A: Both celles (donor and recipient) can act as new donors

Q: WHat are mobile genetic elements (MGEs)?
A: - Segments of DNA that can move by themselves
- Not all MGEs can move between cells (HGT), some can move within the cell

Q: What do the MGEs that cant do HGT do?
A: Some MGE can't do HGT, they can only move within a cell, ex from one genetic region to another, either on a chromosome or to a plasmid

Q: Which MGEs can do HGT?
A: - Plasmids
- Bacteriophages

Q: Which MGEs can move within a cell?
A: - Transposable elements

Q: What are transposable elements?
A: The smallest MGEs

Q: What do transposable elements consist of?
A: The simplest form is the insertion sequence:
- Transposase gene
- 2 Inverted repeats

Q: What is the transposase gene responsible for?
A: Transposase is what creates the movement of the unit

Q: What is the transposition mechanism for transposable elements?
A: 1. The transposas binds and cuts at the inverted repeats, which leads to transposon excision
2. The transposase cuts the target DNA and integrates the transposon in the new site
3. Then the transposase leaves the original site and moves to another site

Q: What are examples of more complex transposable elements?
A: - Insertion sequence (IS)
- Compositie transposons

Q: What are composite transposons formed by?
A: Composite transposons are formed by 2 IS (insertion sequence) elements flanking passenger genes (ex antibiotic resistance gene)

How can transposable elements and plasmids interact?

Q: What do the interactions between transposable elements and plasmids play a huge role in?
A: This plays a huge role in accumulation of antibiotic resistance genes on plasmids

What happens with antibotic resistances on conjugative plasmids?

What is the bacterial genome composed of and how can it be modified?

Which forms of HGT exist?

Q: Vad är och gör MGEs?
A: - Kan vara stora och komplexa eller små och simpla
- Rör sig mellan celler eller inom en cell

Q: How do different sizes of MGEs travel?
A: - The large and complex move between cells
- Small and simple move within cells, but they can be carried along between cells as well