Bacterial genome Flashcards
Describe the typical bacterial genome:.
• Single circular chromosome – single origin of replication (ori).
• Small genome size – very little non-coding DNA.
• Genome is often augmented by extrachromosomal DNA molecules called plasmids:
o Small circular DNA molecules with their own ori.
o Plasmids don’t normally carry essential genes.
Describe bacterial Chromosomes:.
Describe bacterial Chromosomes:
What is the bacterial genome size:.
- Free living: 0.5Mb- 10Mb
* Symbionts: as small as: 160kb.
What does genome size correlate to?
- Genome size correlates well with gene number and in turn with morphology, physiology and metabolic complexity.
- Small genomes = small no. of genes = restricted growth to relatively few restricted niches – often pathogens
- Large genomes = large no. of genes = higher metabolic diversity.
How big is one gene roughly?
• 1kb = est. 1 gene. (average protein = aa 333 = average gene = 1000bp = 1kb.
How are related genes relative to eachother in the genome?:
• genes encoding enzymes in the same metabolic pathway are often organised into polycistronic operons.
What is the name used to describe a section of DNA/RNA that codes for a specific polypeptide?
• Cistron is the section of DNA/RNA that codes for a specific polypeptide in protein synthesis.
What is the name of an area that codes for more than one gene?
• Polycistronic operons code for more than one gene.
o Destroying the activity of any one of the gene products will block the pathway.
What are Plasmids? Draw one.
see doc or google.
• Non-essential DNA molecules with their own ori.
• Most are circular but some linear.
How big is a plasmid?
How big is a plasmid?
What are plasmids called when they occur in high/low levels?
• Number of copies of different plasmids vary:
o High copy number (small) plasmids = 50 copies/cell.
o Low copy number (large) plasmids = 1-2 copies/cell.
• Found in most bacterial species.
What are Conjugative plasmids? What do they do? What are the key words in this process?
Many large plasmids encode genes that enable the transfer of the plasmid between cells.
o DNA transferred through mating bridge whose formation depends on pilus that connects the two cells.
o Transfer process is called conjugation and the recipient is a transconjugant.
What does conjugation occur between?
• Conjugation occurs in and between species and between bacteria and plants.
What word is used to describe the replication in conjugation? Why is this? How does this affect how long it takes?
• Replication in conjugation is unidirectional = 1 rep fork. Therefore take twice as long as normal replication..
What are Non-conjugative plasmids?
• Most small plasmids are non-conjugative.
• Maintained in both daughter cells following cell division.
• Cannot transfer to another cell on their own.
o They can be mobilised by hitching a ride on a system provided by a conjugative plasmid.
• Have been employed in gene cloning technology as vectors for introducing and maintaining DNA bacteria.
What is Horizontal gene transfer (HGT)? What are the mechanisms in bacteria? SKETCH THEM ALL.
• Genetic exchange between organisms.
• Three mechanisms in bacteria:
o Transformation – naked DNA.
o Transduction – phage coated DNA.
o Conjugation – transfer through mating bridge.
• Almost all bacteria utilise at least one of the above mechanisms for genetic exchange.
What are plasmids called that allow spread into species where recombination may not occur?
• Broad Host Range plasmids allow spread into species where recombination may not occur.
What genes can be transferred from one bacterium to another? What are the most common? DRAWWWW.
• Any gene can be transferred from one bacterium to another but the most common examples are:
o Antibiotic resistance
o Pathogenicity.
o Ability to survive in different environments.
• New traits spreading through populations.
What is the The F-Plasmid? Why is it unusual?
• The F (fertility)- plasmid is an e.g. of a conjugative plasmid
• 100kb low & copy number – replicates once /cell cycle & segregates to both daughter cells.
• F+ cells contain the F-plasmid.
• F+ plasmids act as donors in the transfer via conjugation of the F plasmid to F- cells, which then become the wildtype.
o Transmission only takes a few minutes.
o F+ cells cannot transfer the plasmid to an already wild type cell due to surface exclusion and compatibility.
• Unusual because depressed for transfer:
o Not all plasmids have their genes switched on all the time.
o For F this is due to repressor gene being inactivated.
o Picking out this mutant may have occurred because of the selection experiment where it was first located.
Sketch how f factors work.
google.
What is transformation?:
- integration of exogenous DNA into genome by 2 crossovers.
What is Transduction?
- integration of exogenous DNA introduced by phage by 2 crossovers.
What are High frequency of recombination (Hfr) cells?
• F plasmid can integrate into the bacterial genome via recombination.
• Resulting cells are called Hfr.
• Results in larger bacterial genome (E.coli = 2%).
• Position and orientation of integration is (sort of) random.
o Once integrated, position is fixed.
o Different strains can have F plasmid integrated at different positions and orientations.
• Integration involves one crossover.
Can Hfr cells conjugate?
• It is possible.
What direction doesn Hfr go in?
- Transfer starts within the F-plasmid and goes on in one direction.
- Only a segment of the f plasmid is transferred before the bacterial chromosome starts to transfer.
Is it possible to transfer the whole chromosome?
• It is possible to transfer the whole chromosome but would take 100 minutes.
How many genes are normally transferred?
• Several hundred genes are normally transferred.
Why is this called F-?
- Because the whole f plasmid isn’t transferred still = F-.
* Partial diploid is transiently created.
What happens to the transferred DNA long term?
• The transferred DNA will eventually be lost but recombination allows exchange of alleles between transferred DNA and chromosome.
• Can lead to incorporation of DNA into recipient chromosome if two cross overs occur.
o Not all DNA that is transferred will recombine.
o The linear DNA will eventually be lost.
draw the thing with the donor plasmids and the F etc. etc.
i dont understand it.
What genes are most likely to be transferred to the recipient cell?
• Genes close to the F-plasmid & in direction transferred are more likely to be transferred to the recipient cell than more distant genes.
What rate does transfer occur? What does this allow?
• Transfer occurs at a relatively constant rate therefore can map relative positions of genes in mins by determining how long it takes for them to be transferred in a conjugation experiment.
What is the word used to describe anOrganism that does not require complex organic molecules for growth? What do they need?
- Prototrophs:
o Inorganic salts and a source of energy + C&N.
What is the term used to describe organisms unable to synthesise essential nutrients? Example?
• Auxotrophs:
o Unable to synthesise an essential nutrient.
o Cannot grow on minimal medium unless supplemented with essential nutrient.
o E.g. histidine dependant E. coli.
Describe Gene Nomenclature:.
o Each gene is assigned with 3 letter lowercase in italics.
o Abbreviation of pathway, mutant phenotype or function of the protein product.
o Different genes that affect the same function = same abbreviation and distinguishing capital letter.
o Wild types indicated with ‘+’.
o Mutants not usually indicated by a minus.
Describe protein Nomenclature:.
o Same as gene generally but not italics and first letter is capital.
Describe Phenotypic designations nomenclature:.
o Wild type = superscript +.
o Mutant = superscript -.
o Lowercase superscript may indicate other phenotypes.
