Prokaryotic genomics & mutations Flashcards
What does it consist of?
what are plastids?
where do the essential genes for cell function reside?
what is the a correspondence with genome size?
why does mycoplasma have such a small genome?
why does streptomyces have a much larger genome?
1 circular (or linear) chromosome & a plastid in cytoplasm
extrachromosomal DNA & replicate independently of chromosome- normally circular but can be linear too
on chromosome/nucleoid
complexity of lifestyle
relies on the host
lives in harsh environments- produces lots of antibiotics to compete
how is the bacterial DNA packaged?
how many genome copies are there per cell?
what else influences genome size?
why does a short cell replication time give strong selective advantage?
what does this mean for genes along the chromosome?
tightly folded & packed into irregular structure = nucleoid
e.coli = 1 cyanobacteria = 10
- nutrients in envrionment- expensive to synthesise DNA with energy & nutrients
- time taken to replicate genome (selective pressure to keep time small as genome is small so junk DNA is eliminated)
produce large colonies very quickly & also only contains required/necessary genes & DNA
very densely packed- with genes overlapping & on both + and - strand of DNA
what are the start codons in the open reading frames ORF?
stop codons?
what is the ORF?
so where does the ribosome bind?
ATG or GTG
TAA, TAG, TGA
translated/coding region
upstream of ATG/start codon
what are the start codons in the open reading frames ORF?
stop codons?
what is the ORF?
so where does the ribosome bind?
what are the sequences near 5’ and what do they do?
what are the sequences near 3’ & what do they do?
ATG or GTG
TAA, TAG, TGA
coding region
upstream of ATG/start codon
regulatory sequences- allow repression/activation of transcription
transcription terminator region- causes RNA polymerase stall & terminate as Rho binds to RNA
What are the 2 ways of transfer for mutations?
what are spontaneous causes of mutations? how do they arise?
what form are T & G bases in? what happens in their other form?
what about C & A?
vertically- parent to offspring in replication
horizontally- uptake DNA/genes
damage in DNA bases from external factors/chemicals or error in DNA replication - wrong insertion of bases in daughter strand, slippage or tautomerisation of bases
keto, rare enol form means form 3 H bonds with keto G & T
in amino form- rare imino can join by 2H bonds to amino C & A
what are induced causes of mutations?
how does nitrous acid cause mutations in DNA?
what does ethidium bromide do?
how does non-ionizing radiation form mutations?
ionising radiation?
artificially increasing mutation frequency
converts amino groups to keto groups by oxidative deamination (so C A G convert to U, H, X)
add/deletions bases
purine & pyrimidines absorb UV - pyrimidine dimers adjacent to C & T become covalently bound = impeding DNA polymerase/increased chance misreading by DNA polymerase
X-rays, cosmic rays, gamma rays etc effect it with free radicals (e.g OH radical)
what is a single point mutation?
how does it affect outside the coding region?
inside the coding region? (4)
what are the effects of point mutations that insert/delete a single base pair?
changes a single base pair
could have none- or could change gene expression like mutation in promotor
no effect = wild type
change amino acid without affecting structure/function protein = silent
modify structure/function protein(faulty) = missense
inactivate protein completely (produce stop codon) = nonsense
outside = none, change gene exp inside = produces frameshift = inactivation of gene
larger scale mutations——-
how would these affect the DNA:
deletion of large tract of DNA
rearrangement of region DNA
duplication of region DNA
insertion DNA elements from elsewhere in genome
null mutation- complete loss function 1+ genes
might/might not be mutagenic- depends on break points
duplication gene- opportunity evolution - change function over time
might be mutagenic
what is a transposon?
what enables them to move?
where else can it move?
what can the bacteria acquire?
DNA sequence/gene that can change position in genome - cause mutations/alter identity/genome size
transposase cuts transposon
along chromosmoe but also to plasmid
antibacterial/antimicrobial resistance
what do you need to look for to detect a mutation?
why is this hard for neutral mutations?
how can you detect a mutation then?
what is a lysine auxotroph/lys-?
how would you identify these?
how would you make a replica plate?
change in phenotype- indicates change in genotype
subtle/no change in phenotype
with a scorable phenotype- like ability/inability to grow on substrate/resistance to toxin
mutant meaning can grow only if lysine is present on medium
spread cells on plates with and without lysine
press plate onto velveteen & then press this onto a clean plate
how could you set up a experiment for finding lys- revertants? aka mutations of lys- that restore original wild type phenotype
what type of test is this?
how can you increase reversion frequency?
how can you compare mutations effect on a cell with an experiment?
plate cells from auxotrophic lys- culture on plate without lysine
Ames test- test for mutagenic chemicals with treating auxotrophic culture on minimal medium with chemical
treatment of mutagens- more mutagens, more revertants obtained
since most mutations are harmful- take culture with 2 plates & expose 1 to mutagen & compare cell numbers
what is a mutator gene?
What is Müller’s ratchet/long-term problems caused by mutations?
why has this not happened? 2 ways
genes in bacteria that increase mutation rates under stress (complex/changing environments) = selective advantage
start with perfect bacteria genome for environment- replicates & mutations occur resulting in death & slower growth. at realistic mutation rates natural selection doesn’t happen fast enough to eliminate all harmful mutations = results in gradual build up of harmful mutations & eventual extinction
- repair mechanisms
- horizontal gene transfer- eliminating harmful mutations by combining good genes & traits
