Bacterial Genomes and Central Processes Flashcards
What does the bacterial genome consist of?
The single covalently circular duplex molecule - bacterial chromosome
Plasmids
99% is unique DNA
What are single nucleotide variants?
Single nucleotide changes that occur over generations
Can be used in the identification of pathogenic subspecies or strains
What are pathogenicity Islands?
Cluster of genes encoding proteins involved in pathogenesis (adhesions, invasions, exotoxins and secretory pathways)
Same island can be present in different species possibly because it is a transposon
GC content of island is often different than the host genomes
What is semi-conservative replication?
each daughter duplex DNA molecule is composed of one parental strand and one newly-synthesized strand
What is the origin of replication (OriC)?
Single site on chromosome where all DNA replication is initiated
Describe bacterial DNA polymerases.
Pol I, II, and III are required for DNA synthesis
All share 5’ to 3’ polymerase activity
All share 3’ to 5’ exonuclease (proofreading) activity necessary for maintaining a lower error rate
Describe bacterial supercoiling.
Bacterial chromosomes have negative superhelicity which means that it can readily convert to a molecule with unwound helical regions
Absolutely necessary for DNA replication, and is the target of some antibiotics (e.g. quinolones)
What are the three steps in bacterial chromosome replication during cell division?
Chromosome is attached to cytoplasmic membrane protein complex
Initiation of chromosome replication coincides with septum formation
As cell wall growth elongates, chromosomes are pulled into daughter cells
What are the four types of RNA molecules in a cell?
rRNA
tRNA
mRNA
microRNA
What is DNA-dependent RNA polymerase (RNAP)?
Single enzyme that transcribes all four types of RNA
What are two alternative subunits for the RNAP holoenzyme?
Sigma factor that imparts initiation specificity to the holoenzyme - recognizes -10 and -35 positions of the promoter
Rho factor that assists in termination in some genes; other genes are rho-independent
What is a consensus sequence?
Sequence found most frequently in a survey of a large number of sequences
For promoters, the more similar a sequence is tot he consensus, the stronger the promoter
What antibiotic is used to inhibit initiation of bacterial transcription?
Rifampin (rifamycin) - binds to B subunit of RNAP and inhibits the formation of the first phosphodiester bond
What antibiotic is used to inhibit the elongation step of bacterial transcription?
Streptolydigin - binds to B subunit and blocks elongation
What are the prokaryotic ribosomal subunits and their functions?
30S subunit - plays a role in translation initiation and has site for tRNA binding
50S subunit - peptide bond formation (transpeptidase)
What are the four components of the translational machinery in bacteria?
Ribosomes
Soluble protein factors: Initiation factors, elongation factors, and release factors
tRNA
tRNA synthetases - catalyze the addition of AA to tRNA
What are some features of the triplet code?
Universal for all organisms (with some minor exceptions)
Degenerate - more than one codon can code for a given AA
Three stop or nonsense codons (not recognized by any tRNA)
All translation begins at AUG which encodes methionine (N-formylmethionine)
What are the stages of translation?
Initiation
Elongation
Termination
What is the Shine-Dalgarno (S-D) sequence?
Also called the ribosome binding site
Sequence present in the 5’ nontranslated region of all prokaryotic mRNAs, has homology to the 3’ end of 16s rRNA
What are the steps for translation elongation?
1: Charged tRNA enters A site
2: transpeptidation - transfer of peptidyl residue to free amino group of charged tRNA molecule in the A site
3: Deacylated tRNA leaves P site, peptidyl tRNA moves to P site
How is translation terminated?
Soluble release factors recognize a stop codon, causing 70s to dissociate into 50S+30S and fall off mRNA
What antibiotics block translation and how do they do so?
Streptomycin - blocks assembly of 70S initiation complex
Tetracyclines - block binding of charged tRNA to A site
Chloramphenicol - blocks peptidyltransferase reaction
Erythromycin - blocks translocation step
What are three differences of transcription/translocation in prokaryotes?
Coupling can only occur in prokaryotes, eukaryotic nucleus separates the processes
Shine-Dalgarno sequence found only in prokaryotes
Many polycistronic transcripts for prokaryotes, very few in eukaryotes
