Bacterial Genome and Functional genomics Flashcards

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1
Q

What are some of the shapes of bacteria?

A
  • Coccus (sphere)
  • Rod
  • Spirillum (bendy rod)
  • Spirochete (wiggly, thin rod)
  • Budding and appendaged (like a sperm cell)
  • Filamentous (long, thin rods)
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2
Q

What are operons? (in terms of the E.coli genome)

A

Genes that belong to each other - they have the same function or help each other to carry out a function.

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3
Q

What are plasmids?

A

Small, extrachromosomal circular DNA. They are ‘mobile elements’ that allow bacteria to change over time. Plasmids allow diverse phenotypes and offer accessory functions.
They are 2.5% the size of a chromosome.

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4
Q

What are three mobile elements of bacteria?

A
  • Plasmids
  • bacteriophage
  • Transposons and insertion sequences
  • Integrons (pick up useful genes like antibiotic resistance)
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5
Q

What is the pangenome?

A

This is the totality of genes across all isolates of a species.

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6
Q

What are pathogenicity islands?

A

They are clusters if genes of ‘foreign’ appearance - present in only certain strains and are correlated with virulence. They contain genes useful for pathogenesis.

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7
Q

What is the E.coli genome made up of?

A

4.6 billion bp; 3μm long, the genome is would into a 1μm nucleoid. Average distance between genes is 118bp.
The E.coli genome has 5000 genes, 2000 are core shared by all isolates. The pangenome of E.coli contains 15,000 genes.

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8
Q

What are the three generations of genome sequencing?

A

Sanger method 1977 - human genome project took 11 years.
Second generation sequencer (454GS20) in 2005.
Third generation - PacBio RS in 2011 - sequencing the human genome takes 1 day.

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9
Q

How is genome sequencing useful in epidemiology?

A

= treat or quarantine patients before hospitalisation through pre screening
= identify all virulence factors and antibiotic resistances
= sequence isolates from multiple patients to find a source and track the spread.

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10
Q

How is bacteria used in water treatment plants?

A

Sludge contains microbes that metabolise organic matter to CO2, therefore cleaning out waste organic material from the water.

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11
Q

What is bioremediation?

A

Process using organisms, plants, microbial or plant enzymes to detoxify contaminants in soil and other environments. An example is hydrocarbon degrading bacteria and they occur naturally.
An example is marine microbes, they form spherical biofilms around oil in an oil spill, tehy are oil degrading microbes.
Indonella Sakaiensis can hydrolyse PET-based plastic.

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12
Q

What is biotechnology?

A

Cellular factories - living organisms that produce medically or commercially useful biomolecules such as antibiotics, enzymes, drugs and hormones.

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13
Q

How can we genetically modify bacteria?

A

By using recombinant DNA technologies, we can express mammalian or mutant proteins by making them in large quantities by bacterial fermentation. After bacterial cells are cloned and mass produced, they are lysed and the expressed protein is purified for research, commercial or medical use.

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14
Q

What is synthetic biology and bio-engineering?

A

Synthetic biology refers to the design and construction of new biological parts, devices or systems - and the redesign of existing, natural biological systems for useful purposes. Often using the concepts of engineering.

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15
Q

How does bacteria involved in gene regulation and how is temperature affecting gene expression?

A

The lac repressor (Lacl) a type of E.coli bacteria, prevents transcription of lactose utilisation genes unless lactose is present.
Prianer et al engineered proteins to respond to temp - gene expression was turned on at 40-45 dC, and the circuits dictate colour response to E.coli. it has potential applications in triggered therapeutics.

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16
Q

What is optogenetics?

A

This is an optogenetic circuit from Voigt lab (MIT). Different wavelengths of light trigger the production of different coloured compounds by E.coli. This controls gene expression through light.

17
Q

What is protein engineering?

A

Adding new functions to proteins or improving their current function (rational design of artificial evolution). This changes functionality and behaviour of the bacteria that express them.

18
Q

what is metabolic engineering and its effects?

A

Gene circuits and engineered proteins can be combined to alter or create a new metabolic process in bacteria. It can improve efficiency of current metabolic processes or allow bacteria to synthesise new compounds.