Genome Structure Flashcards
3 basic shapes of bacteria
- bacilli
- cocci
- spirilla
Types of bacterial pathogens
- conditional pathogens
- opportunistic pathogens
- obligate intracellular
- facultative pathogens
How do prokaryotes reproduce?
- asexually by binary fission
Explain the process of initiation of DNA replication
- DnaA binds to series of DnaA boxes of oriC (becomes negatively supercoiled)
- upstream region of oriC becomes melted
- DnaA recruits hexameric helicase to opposite ends of melted DNA (replication fork)
- ss binding proteins prevent ssDNA forming secondary structures and prevent re-annealing
Describe the process of elongation of DNA replication
- DnaG (primase) binds
- DnaB unwinds DnaA proteins and synthesizes an RNA primer
- DNA gyrase relieves stress by introducing negative supercoils
- DNA polymerase binds DNA and replication occurs in 5’-3’ direction
- 3’-5’ strand synthesised by Okazaki fragments and filled in by ligase
Types of DNA polymerases
- Pol I (joining Okazaki fragments)
- Pol II (DNA repair)
- Pol III (DNA replication)
What is a transition?
- pyrimidine to pyrimidine
What is a transversion?
- pyrimidine to purine
DNA repair mechanisms
- direct reversal of base damage
- excision repair
Describe direct reversal of base damage
- spontaneous addition of methyl group to Cs, followed by deamination to T
- glycosylases remove mismatched T, restoring correct C (no breakage of DNA backbone)
Types of excision repair
- Base excision repair (BER)
- nucleotide excision repair (NER)
- Mismatch repair (MMR)
What are transposons?
- small, modile DNA elements that encode the genes required for their own transposition
- often include antibiotic resistance markers on gene cassettes
Define polycistronic
- 1 promoter directs synthesis of 1 mRNA that can be translated to more than one polypeptide
Define monocistronic
- 1 promoter directs synthesis of 1 mRNA that usually translates to only 1 protein
Role of a sigma factor
- promoter recognition
- initiation of transcription
Role of core RNAP
transcription, elongation and termination
Components of bacterial promoter
- -35
-10
startpoint
Process of prokaryotic transcription: initiation
- binding of RNA polymerase to template
- dissociation of sigma from -35 and recognition of -10 sequence
- establishment of open-promoter complex
Process of prokaryotic transcription: elongation
- initiator nucleotide binds and first phosphodiester bond made
- release of sigma (recycles)
- RNA pol unzips dsDNA and allows incoming nucleotide to base pair with template
- RNA transcript forms secondary structures through intra-strand base-pairing
Describe Rho-independent terminators
- strong GC-rich stem and loop
- 4-6 U residues in the RNA unstable
Describe Rho-dependent
- Rho has helicase activity (unwinds the newly formed RNA from the DNA template)
What is an Rho utilisation site? (Rut)
- rich in C, poor in G
- upstream of actual terminator sequence
Describe initiation of translation
- small ribosomal subunits bind initiation factors
- complex binds to the mRNA
- fMet tRNA binds, promoting binding of tRNA to the start codon
- the complex scans along the mRNA until it finds the start codon
- large ribosomal subunit joins in
- initiation factors released
Describe elongation in translation
- each tRNA is sequentially added
- peptidyl transferase catalyses the formation of peptide bond between the 2 aas
- breaks bond between fMet and its tRMA
- whole ribosome shifts over one codon
When does translation termination occur?
- when a termination codon enters the A site
Define anabolism
Synthesis of more complex compounds
Uses energy
Define catabolism
Breakdown of substrates
Captures energy
Major advances in molecular tools
- decreasing cost of whole genome sequencing
- microarray analysis
- advent of metabolomics
- microfluidics
