bio 207 lecture 7: molecular biology differences in bacteria, archaea, eukaryotes

prokaryotes tend to have (?)% non-coding DNA, while eukaryotes tend to have (?)%

15; 90

most bacteria and archaea have what type of chromosome?

one circular

noncoding DNA of eukarya includes

introns and pseudogenes (inactivated genes)

some archaeal genes have introns too but are rare

operon

contains one or more structural genes which are generally transcribed into a polycistronic mRNA (one mRNA that codes for more than one protein)

found in bacteria, archaea

phases of bacterial DNA replication

• begins at the origin of replication (oriC)

• replication fork separates two strands of DNA

• new synthesis occurs bidirectionally where the replication forks are moving in opposite directions around the chromosome

• replication ends at defined termination (ter) sites

differences in DNA replication between domains

• bacteria: single oriC

• archaea: one or multiple replication origins

• eukarya: many oriCs and DNA replication as a phase part of the cell cycle

key differences in DNA replication machinery

• bacteria; DNA polymerase III

• eukary: many different DNA polymerases

• archaea: unique DNA polymerase; other replication proteins are more closely related to eukarya than bacteria

plasmids

• extra chromosomal circular DNA molecules found in cells

• contain nonessential genes that can still play a critical role in certain situations (ex. antibiotic resistance)

• can be transferred between cells

• found in archaea, bacteria, and eukaryotic microbes

a gene can be transcribed independently of others (monocistronic) in which organisms?

all

(means that RNA is produced from a single gene which produces a single protein)

RNA polymerase is made up of

• four subunits: two alpha, one beta, one beta prime

• multiple binding sites for RNA/DNA substrates and RNA product

in bacteria, RNA polymerase is called (?) and is made up of

a holoenzyme; core polymerase with four subunits (2 a, 1 b, 1 b’) + a sigma factor subunit

what is the core promoter?

sequences on the sigma subunit of holoenzyme (bacterial RNA polymerase) that specify binding to specific upstream transcription start sites

where bacteria use holoenzymes and sigma factors, eukaryotes and archaea use

differnt core enzymes and no sigma factor but transcription factors instead

what is the function of a sigma factors?

helps the core enzyme detect the promoter, which will signal the beginning of the transcript

“housekeeping” sigma factors

• special type of sigma factor

• every bacterial cell has one

• sigma-70 in e coli

• helps recognize the promoter consensus sequence (common nucleotides) at 10 and 35 positions

• transcribes most genes in growing cells

in bacteria, the promoter consists of conserved sequences situated

10 and 35 bases ahead of the transcription initiation site

a single bacterial species can produce several different kinds of sigma factors coordinating gene expression in response to

environmental change (heat, sporulation, nitrogen, shock, motility)

three phases of transcription

• initiation

• elongatoin

• termination

rho dependent termination in prokaryotic transcription

protein rho binds to c-rich regions (pause site) → RNA threaded through rho protein → RNA polymerase pulled towards rho → contact → stops

rho independent transcription termination in prokaryotes

translational stop codon → sequence informs a hairpin stem loop with poly-U sequence (4 - 8 consecutive U residues)→ weaker association between DNA and RNA → termination

antibiotics that affect transcription

• rifamycin B - selectively binds bacterial RNA polymerase, polymerase may still bind to promoter but RNA cannot exit, inhibits initiation

• actinomycin D - non selectively intercalates between GC base pairs in DNA, inhibits transcription elongation

subunits of prokaryotic ribosomes

30s and 50s = 70s ribosome

initiation of translation in bacteria involves coordination of mRNA binding with

16S rRNA 3’ end of ribosome + the ribosome binding site sequence (shine-dalgarno sequence) of mRNA

antibiotics that inhibit protein synthesis in bacteria

• streptomycin

• tetracycline

• chloramphenicol

• erythromycin

two types of gene transfer include

viertical transmission and horizontal transmission

vertical transmission

passing down genes from parent to child via reproduction; mutations may lead to small genetic changes

horizontal transmission

transfer of pieces of DNA from one cell to another; can include lots of mutations and can be from anything (same species, different species, other domains of life)

very common in prokaryotes and rarely in eukaryotes

mutations in vertical gene transfer are rare but can arise because of

• rare chemical bondd shifts in DNA that alter base-pairing nproperties

• oxidative deamination of bases (increases stress)

• damage caused by reactive oxygen species, other chemical agents, and electromagnetic radiation

point mutation

change to one nucleotide

silent mutation

alters nucleotide sequence but leaves amino acid unchanged

missense mutation

different amino acid used, may or may not alter phenotype

nonsense mutation

stop codon forms prematurely → truncated gene product

spontaneous mutation rates for bacteria average

1 mutation for every 100 - 1000 DNA replications

what is the mutation rate for an e coli culture whose last duplication involves 5 × 10^9 replications?

• mutation rate = the number of mutations formed per cell doubling

5 × 10^9 × 1 mutation/100 - 1000 replications = 5 × 10^6 to 5 ×10^7 mutations

in order for a donor DNA to be maintained and expressed in a cell it must be

able to replicate autonomously or integrated into the recipient’s genonme

generalized recombination

• method of horizontal gene transfer and gene recombination

• requires enzyme RecA and homology between recombining molecules

site-specific recombination

• method of horizontal gene transfer and genome recombination

• RecA independent

• can recombine any region of the chromosome - no sequence homology required except between donor and target DNAs

three mechanisms of horizontal gene transfer

• transformation: cell takes up free naked DNA from environment

• conjugation: donor cell with pilus interacts with recipient cell leading to transfer of plasmid or part of a chromosome

• phage transduction: virus used to transfer DNA