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Bacteriology Lectures > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

3 basic shapes of bacteria

A
  • bacilli
  • cocci
  • spirilla
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2
Q

Types of bacterial pathogens

A
  • conditional pathogens
  • opportunistic pathogens
  • obligate intracellular
  • facultative pathogens
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3
Q

How do prokaryotes reproduce?

A
  • asexually by binary fission
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4
Q

Explain the process of initiation of DNA replication

A
  • 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
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5
Q

Describe the process of elongation of DNA replication

A
  • 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
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6
Q

Types of DNA polymerases

A
  • Pol I (joining Okazaki fragments)
  • Pol II (DNA repair)
  • Pol III (DNA replication)
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7
Q

What is a transition?

A
  • pyrimidine to pyrimidine
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8
Q

What is a transversion?

A
  • pyrimidine to purine
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9
Q

DNA repair mechanisms

A
  • direct reversal of base damage

- excision repair

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10
Q

Describe direct reversal of base damage

A
  • spontaneous addition of methyl group to Cs, followed by deamination to T
  • glycosylases remove mismatched T, restoring correct C (no breakage of DNA backbone)
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11
Q

Types of excision repair

A
  • Base excision repair (BER)
  • nucleotide excision repair (NER)
  • Mismatch repair (MMR)
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12
Q

What are transposons?

A
  • small, modile DNA elements that encode the genes required for their own transposition
  • often include antibiotic resistance markers on gene cassettes
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13
Q

Define polycistronic

A
  • 1 promoter directs synthesis of 1 mRNA that can be translated to more than one polypeptide
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14
Q

Define monocistronic

A
  • 1 promoter directs synthesis of 1 mRNA that usually translates to only 1 protein
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15
Q

Role of a sigma factor

A
  • promoter recognition

- initiation of transcription

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16
Q

Role of core RNAP

A

transcription, elongation and termination

17
Q

Components of bacterial promoter

A
  • -35
    -10
    startpoint
18
Q

Process of prokaryotic transcription: initiation

A
  • binding of RNA polymerase to template
  • dissociation of sigma from -35 and recognition of -10 sequence
  • establishment of open-promoter complex
19
Q

Process of prokaryotic transcription: elongation

A
  • 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
20
Q

Describe Rho-independent terminators

A
  • strong GC-rich stem and loop

- 4-6 U residues in the RNA unstable

21
Q

Describe Rho-dependent

A
  • Rho has helicase activity (unwinds the newly formed RNA from the DNA template)
22
Q

What is an Rho utilisation site? (Rut)

A
  • rich in C, poor in G

- upstream of actual terminator sequence

23
Q

Describe initiation of translation

A
  • 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
24
Q

Describe elongation in translation

A
  • 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
25
Q

When does translation termination occur?

A
  • when a termination codon enters the A site
26
Q

Define anabolism

A

Synthesis of more complex compounds

Uses energy

27
Q

Define catabolism

A

Breakdown of substrates

Captures energy

28
Q

Major advances in molecular tools

A
  • decreasing cost of whole genome sequencing
  • microarray analysis
  • advent of metabolomics
  • microfluidics

Bacteriology Lectures (10 decks)

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