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Animal kingdom > Genomics 4-6 > Flashcards

Genomics 4-6 Flashcards

1
Q

What is the central dogma who designed it ?

A

DNA>RNA>Protein

Francis crick

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2
Q

What are the 4 model bacteria ?

A

Eschericha coli -
Neisseria meningitidis -
Heliobacter pylori -
Bacillus subtilis +

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3
Q

Name the 6 strains of E.coli

A 
EPEC- Enteropathogenic e.coli
EHEC- Enterohaemorrhagic e.coli 
ETEC- Enterotoxigenic e.coli
EAEC- Enteroaggregative e.coli
EIEC- Enteroinvasive e.coli
DAEC- Diffusely adherent e.coli
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4
Q

What is a pathogencity island ?

A

a series of contiguous genes including one or more that determines virulence, acquired by horizontal gene transfer. It is transposable.

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5
Q

What type of E.coli attacks the colon and secretes Shigatoxin ?

A

EHEC- Enterohaemorrhagic e.coli

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6
Q

What type of E.coli is taken up by cytosis and forms an actin tale ?

A

EIEC- Enteroinvasive e.coli

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7
Q

What is unique about DAEC- Diffusely adherent e.coli ?

A

Uses villi for protection

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8
Q

What does EAEC- Enteroaggregative e.coli form ?

A

Biofilm

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9
Q

What E.coli secretes a temperature sensitive toxin ?

A

Enterotoxigenic e.coli- Stable and labile enterotoxins

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10
Q

What does enteropathogenic e.coli do to the villi ?

A

Changes physiological structure and secretes type 3 effective molecules into the cell that take over actin cytoskeleton.

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11
Q

What is natural competence ?

A

The ability to take up DNA from the environment

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12
Q

What model bacteria use the pseudo type IV pilus system ?

A

Bacillus subtilis

Neisseria meningitidis

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13
Q

What allows heliobacter pylori to be naturally competent ?

A

Type IV secretion system

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14
Q

What do optical tweezers measure in terms of DNA uptake ?

A

Measures the force that DNA is being pulled into the cell

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15
Q

What allows nerisseria meningitidis to take up DNA that is specific to nerisseria genus ?

A

Uses a minor pilin (ComP) combined with a major pilin (PiLE)

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16
Q

What do all of the DNA uptake systems have in common ?

A

All require ATP dependent stripping of the dsDNA to ssDNA.

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17
Q

What is the pathogenecity island in heliobacter pylori ?

A

Cag- Continually takes up DNA and alters genome.

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18
Q

What allows DNA to pass through the outer membrane of neisseria meningitidis ?

A

A secreton

19
Q

What is the pilus made up of in bacillus subtilis and what are the bonds holding the proteins together ?

A

ComGC protein and disulphide bonds

20
Q

What are the minimum standards provided by genomic consortium ?

A

A table dedicated to classification.
A table dedicated to project info.
A table dedicated to genome statistics
A table dedicated to COG database

21
Q

What is special about the genome of borrellia burgdoferi ?

A

Contains linear chromosomes and linear and circular plasmids.

22
Q

What is a replicon ?

A

A region of DNA that replicates from a single origin of replication.

23
Q

What limits 16s rRNA sequences from being a good determining factor for phylogentic relationships ?

A

There tends to be more than 1 copy of genes

16s rRNA sequences can vary alot even within the same genome

24
Q

What is a biosynthetic cluster ?

A

A physical cluster of of 2 or more genes in a genome that together encode for a pathway which produces a metabolite

25
Q

What do CRISPR molecules do ?

A

Play a role in bacteria defence against phage attack

Allows uptake of exogenous genetic material

26
Q

What are the families of bioactive secondary metabolites ?

A

PKs
NRPs
RiPPs
isoprenoids

27
Q

What is the benefit of whole genome sequencing ?

A

Allows whole genome comp

28
Q

What is the problem with identifying genomes by similarity ?

A

A third of genes have insufficient similarity

Similarity based on function is often wrong

29
Q

How can microarrays be used for the identification of gene function ?

A

By knocking out the gene being identified for function and growing the bacteria in different growth conditions and then comparing to reference strain

30
Q

What is a cryptic prophage ?

A

A phage that integrates in the genome but have lost function.

31
Q

Why are cryptic phages retained ?

A

Essential for growth under stressful conditions

32
Q

What are the limitations of random barcode transposon site sequencing ?

A

Cannot recreate natural environment
Knock out gene may not show in phenotype due to synthetic lethality (other proteins producing the knock out gene product)

33
Q

What has random barcode transposon site sequencing allowed for ?

A

Allows genes of unknown function to be given a putative function as it allows comparison of multiple genomes at once
Higher throughput than microarrays

34
Q

What has transposon directed insertion site sequencing allowed for ?

A

Allows core genes for infection and colonisation to be found as bacteria are injected into real life environments

35
Q

During random barcode transposon site sequencing what allows for the identification of the unique knockouts ?

A

PCR using primers that are specific to the adapters that have been added and the barcoded transposon.

36
Q

During random barcode transposon site sequencing what allows for multiple species to be studied at once ?

A

A second primer added into the PCR

37
Q

What sort of dye do microarrays contain ?

A

Tetrazolium

38
Q

What does random barcode transposon site sequencing do ?

A

Creates library of knock outs all over the genome with an associated barcode to each unique knock out.

39
Q

What are the limitations of phenotypic microarray analysis ?

A

Low through put as a compromise of high number of mutants or high number of environmental conditions has to be made

40
Q

In B. subtilis, what does the inactivation of comEC (large polytopic transmembrane protein) prevent ?

A

prevents not only uptake of DNA, but also the degradation of the nontransforming strand

41
Q

In Bacillus subtilis what does ComFA do and what does it contain to allow this ?

A

Helicase and translocase motifs

Allows stripping of dsDNA and movement of ssDNA

42
Q

What do the binding proteins in Bacillus subtilis allow and do ?

A

Cover the DNA allowing it to be replicated and transferred into the chromosome

43
Q

What is the only DNA sequence Neisseria meningitidis recognises ?

A

GCCGTCTGAA

Known as DNA uptake sequence

44
Q

What is the major protein on heliobacter pylori’s uptake system ?

A

ComB9

Animal kingdom (13 decks)

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