Bacterial Genetics: Bacteria as Model Organisms Flashcards

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1
Q

Why are bacteria used as model organisms? - Medical Topics

A
  • Pathogenesis ( understand diseases better that are caused by bacteria)

Leads to:
- Antibiotic development
- Understanding antimicrobial resistance

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2
Q

Why are bacteria used as model organisms? - Biotechnology

A

Bacteria can be used to manipulate genes
E.coli + Streptomyces speces can be used to understand:

  • Screen new activities
  • Protein production
  • Antibiotic production
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3
Q

Why are bacteria used as model organisms? - Fundamental Biology

A

To understand:
-DNA replication
-Mechanism of transcription
-Transcriptional regulation
-Protein synthesis
-Protein translocation
-Cell stress responses
-Biochemical pathways/Central metab.

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4
Q

Why are bacteria used as model organisms? - Environmental Science/Geology

A

To understand:
- Nitrogen cycle
-Methane production /consumption
-Hydrocarbon consumption
-Oxygen production
-CO2 production

e.g. Geobacter, Rhizobium sp.
Methanogens/-trohps, Cyanobacteria

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5
Q

Why are bacteria used as model organisms? - Agriculture

A

To understand:
- Pesticides
- Livestock health
- Antibiotic production

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6
Q

Why not bacteria? - Subcellular compartmentalisation

A

Bacteria don’t have complex membrane-bound organelles like SER/RER - can’t study all cellular processes to extrapolate such as:

-Phagocytosis
-Nonsense mediated decay
-Subcellular trafficking

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7
Q

Why not bacteria - Epigenetics

A

Do not have histones so can’t study processes like:

  • Histone modification
  • CpG methylation
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8
Q

Why not bacteria? - Lack of complex multicellularity

A

Doesn’t have the following:
- Animal development
- Plant development
- Locomotion
- Complex reasoning

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8
Q

Practical Advantages of using E.coli

A
  • Small size (1-2 micrometers)
  • Unicellular & undifferentiated
  • Divides by binary fission (limits variation in practical result)
  • Simple genome - single circular chromosome
  • Simple nutritional requirements (a sugar + some essential salts)
  • Grows rapidly ( doubles every 25 mins)
  • Each colony on a plate is derived from 1 cell + are clonal
  • No ethical considerations
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8
Q

How bacterial genetics can be used to investigate a statistically rare event

A

In E.coli, a rare event is 10^-9 to 10^-10
- In an overnight culture, there is 1 rare cell per 1ml so would be easy to detect
- Ease increases with the more plated poured

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9
Q

The Origins of a Typical Bacterial Genome

A

Caveat - bacteria are incredibly diverse - no ‘typical bacterium)

  • Diverged from archaea over 3.5 billion years ago

Evolutionary distance between Bacillus subtilis + E.coli is greater than a plant + human

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10
Q

E.coli as a typical bacterium

A
  • Been a model organism for ~90 years
    Typical bacterium refers to E.coli
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11
Q

What is a Genome

A
  1. All of genes in an organism
    * Similar to “transcriptome” or “proteome”
  2. How those genes are physically encoded and
    inherited
  • i.e. the DNA molecule(s) that encode those
    genes
  • The chromosome encodes (part of) the genome
  • Genome does not equal a chromosome
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12
Q

The typical Bacterial genome

A
  • Most bacteria have a single circular chromosome + are haploid
  • Has a simple origin of replication
  • Very little DNA that is not a gene or genetic element
  • Vary substantially in size depending on lifestyle
  • Genome can be augmented by plasmids
  • Some have linear or multiple chromosomes
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13
Q

How Bacterial Genomes are Reductionist + Have Clustered Genes

A
  • Almost all of it encodes for proteins
  • Parts that don’t tend to regulate transcription
  • Genes in the same metabolic pathway are often organised into polycistronic operons
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14
Q

What determines bacterial genome size?

A

Physical genome size (amount of DNA) correlates well with
number of genes.

  • Number of correlates with complexity (morphological,
    physiological, metabolic).
  • Large variation in genome size (both amount of DNA and
    number of genes).
15
Q

Small Bacterial Genome means..

A

Small number of genes.
* Growth often restricted to few specialised niches.
* Often pathogens or endosymbionts

16
Q

Large Bacterial Genome means..

A

Large number of genes.
* Higher metabolic diversity.
* More complex gene regulation

17
Q

All about plasmids

A
  • DNA molecules with their own origin of replication that are
    not essential for growth and replication of host.
  • Usually circular, though can be linear
  • High variable size => small (a few kb) to megaplasmids (1000s kb)
  • Highly variable variable copy number => low (1-2 per chromosome) to high (50 per)