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Year 3 > Microbial Physiology and Genetics II > Flashcards

Microbial Physiology and Genetics II Flashcards

1
Q

What are examples of signals within Bacterial cells?

A
  • CO2
  • Oxygen
  • Glucose
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2
Q

E.coli size

A

1 micrometre in length x 0.5 micrometre x 1 micrometre

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3
Q

E.coli total volume

A

0.5 micrometre

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4
Q

Does the size of the genome correlate to the size of the bacteria?

A

No

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5
Q

What influences the size and shape of a bacteria?

A

Genes and what they code for.

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6
Q

How do Fimbriae and Adhesins assist E.coli infectivity?

A

Allow the cell to stick to different surfaces and aggregate.
Helps biofilm formation.

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7
Q

What does the Sex Pilus do?

A

Allows transfer of DNA, also allows the cell to take up DNA.

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8
Q

Where does E.coli get its nitrogen from?

A

Ammonia or a meat source

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9
Q

What do cyanobacteria do?

A

Catalyse photosynthesis

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10
Q

What happens when cyanobacteria is left in uncontrolled conditions?

A

This leads to algal bloom

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11
Q

Why are algal blooms detrimental?

A

Leads to the rapid acceleration and growth of these bacteria and algae.
Produces a lot of O2 and consumes CO2
Leads to a lapse in the growth of these bacteria.
Bacteria and Algae begin to decompose and rot down.

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12
Q

Why does an algal bloom lead to depletion of oxygen in a small freshwater system?

A

Population growth of cyanobacteria and algae eventually collapses, leading to decay and consumption of oxygen.

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13
Q

Where are streptomyces found?

A

Soil, desert, volcanoes and marine environments

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14
Q

What do streptomyces produce?

A

Dusty spores

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15
Q

What are Mycelium?

A

Network of fibres, provide energy cells to divide and form colonies.

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16
Q

What does Streptomyces produce when the cells begin to die/ run out of resources?

A

Pigments, which are different antibiotics.

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17
Q

What are the pigments highlighting?

A

Where the bacteria is making secondary metabolites.

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18
Q

What is Symbiosis?

A

Multiple different interactions of organisms that are helping eachother.

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19
Q

Leaf cutter ants + Streptomyces case

A

Streptomyces was shown to produce a special type of antifungal that doesn’t kill fungi present but killed invading fungi trying to get into the ant colony.

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20
Q

Heterotrophs

A

Require organic material

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21
Q

Auxotrophy

A

Dependent on a specific diet - sugar, amino acid, nitrogen source

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22
Q

Autotrophy

A

Phototrophs, Chemolithotrophs –> require inorganic molecules

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23
Q

LacI

A

DNA binding protein, tells the cell whether make RNA or not

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24
Q

What do TFs sense?

A
  • Glucose
  • Metal
  • Micronutrients
  • Nitrogen
  • Ammonia
  • Tryptophan
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25
Q

Key response mechanisms of cells

A
  1. Gene expression
  2. Evolution/mutations
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26
Q

How are protein levels in a cell modulated?

A
  1. Initiation of transcription
  2. Premature termination of transcription (attenuation)
  3. Control of transcription termination (anti-termination
  4. Differential mRNA stability
  5. Changes in the rate of translation initiation
  6. Changes in the rate of translation elongation
  7. Changes in protein stability
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27
Q

Are rates of transcription and translation the same?

A

Yes, the process of protein production wouldn’t be fast if one was lagging behind the other, mRNA would be in excess.

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28
Q

What are evolutionary mutations caused by?

A

Resistance
Sensitivity
Loss of Ability
Gain of Ability

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29
Q

Directed Evolution experiments

A

If E.Coli is switched from glucose to glycerol = growth slows
Within experiments, it was shown that E.coli accumulated mutations that allowed them to grow at a faster rate with glycerol.

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30
Q

How did E.coli adapt to glycerol?

A

Mutating to have an enhanced glycerol kinase enzyme activity.

31
Q

Which bacterium has the smallest genome?

A

Mycoplasma Laboratorium = <0.5Mb

32
Q

How many genes are needed to make a minimal genome?

A

400

33
Q

Genes

A

Pieces of DNA, most genes contain the information for making a specific protein.

34
Q

Protein

A

Molecule made of amino acids.

35
Q

Hypothetical genes

A

Genes that have never been studied before, may be essential, may not be. Genes that have never been characterised before.

36
Q

DUF

A

Domain Unknown Function

37
Q

How much of the E.coli genome is uncharacterised?

A

About 50%

38
Q

What are the two approaches for genetic testing?

A

Classic - mutates DNA randomly
Reverse - specficially deletes DNA

39
Q

What are tested within classic genetics?

A
  1. Open reading frames (orfs)
  2. Regulatory RNA
  3. Regulatory elements
40
Q

What is the first amino acid to initiate transcription in bacteria?

A

Formal methionine = Fmet

41
Q

Start codons

A

CTG, GTG, TTG

42
Q

Stop codons

A

TAG, UGA, TAA

43
Q

Wobble hypothesis

A

Where the ribosomes, aminoacyl-tRNA on the first codon will accept non-base pairing codons.
Happens at a lower frequency

44
Q

How does tRNA recognise an alternative start codon?

A

Via release factor 1-3.

45
Q

What is non-coding DNA?

A

Elements that are not translated as protein, may make up RNA, may be promotors, ribosome binding sites, transcription terminators, riboswitches.

46
Q

What does studying classical genetics do?

A

Identify function

47
Q

What does studying reverse genetics do?

A

Identify/prove function

48
Q

How do mutations occur?

A

DNA replication mistakes from DNA polymerase
Mutagens + Carcinogens
Spontaneously - mutagens/stress
Horizontal gene transfer

49
Q

How do mutations occur via Horizontal gene transfer?

A

Plasmids, phages, transposons

50
Q

What changes can occur in a mutant?

A
  1. Loss of function
  2. Gain of function
  3. Silent
51
Q

Types of mutation

A
  1. Point mutations
  2. Deletions
  3. Insertions
  4. Duplications
52
Q

What is included in Classical testing?

A
  • Random mutagenesis
  • Transposon Mutagenesis
  • Phenotypic screening (colony + fluorescence)
53
Q

What is included in Reverse engineering?

A

Genome engineering –> CRISPR/Cas9 + Homologous Recombination

54
Q

What is the KEIO collection?

A

Paper that determines what the essential genes for life are in E.coli.

55
Q

What is the KEIO collection used for?

A

To study function of E.coli features.

56
Q

What is the KEIO collection used for?

A

To study the function of E.coli features.

57
Q

What are the mycoplasma laboratorium clinical strains?

A
  • M.genitalium
  • M.mycoides
  • M.pneumoniaea
58
Q

How many genes are in a minimal cell?

A

450, 10% of E.coli

59
Q

What does Mycoplasma need to grow?

A

Energy + Building blocks –> Glucose, Amino acids x20, yeast extract, tryptone, peptone, thallium.

Metal and counterion –> CaCl2, MgSo4, KCL, NaHPO4

Vitamins and cofactors

60
Q

What is the size of an average E.coli protein?

A

30,000 daltons, 1,000bp DNA.

61
Q

Why does DNA have a major and minor groove?

A

Due to the asymmetry of the sugar-base backbone.
Very few molecules can bind in the minor groove; not enough space.
Coiled = can be condensed into a small structure.

62
Q

How can operons be regulated?

A

Catabolite control protein and Xylose utilisation

63
Q

What is the most conserved sequence in DNA?

A

GGAGG

64
Q

What is found in every single 16s ribosomal RNA sequence?

A

Mirror image sequence of GGAGG

65
Q

Where do activators bind to in regard to the promoter?

A

Upstream, -50 to -100

66
Q

Where do repressors bind to in regard to the promoter?

A

Tend to bind within the promoter sequence, -35 to -10 box

67
Q

What are the two different types of promoters?

A

Constitutive and Inducible

68
Q

What do constitutive promoters do?

A

Always on.
Regulated by how tight the DNA is bound.
Sequence changes, affects the binding to sigma factor.

69
Q

What is Sigma 70?

A

Main housekeeping sigma factor

70
Q

What does Sigma 70 do?

A

Controls core metabolism, essential genes, how cell wall made, how cell membranes are made and how DNA is resynthesized.

71
Q

What do Inducible promoters do?

A

Regulated by TFs.
Docks onto promoter and causes problems for RNA binding or activates it by binding upstream of the box.

72
Q

Cis

A

Intramolecular

73
Q

Trans

A

Intermolecular

Year 3 (4 decks)

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