Microbial Physiology and Genetics II Flashcards
What are examples of signals within Bacterial cells?
- CO2
- Oxygen
- Glucose
E.coli size
1 micrometre in length x 0.5 micrometre x 1 micrometre
E.coli total volume
0.5 micrometre
Does the size of the genome correlate to the size of the bacteria?
No
What influences the size and shape of a bacteria?
Genes and what they code for.
How do Fimbriae and Adhesins assist E.coli infectivity?
Allow the cell to stick to different surfaces and aggregate.
Helps biofilm formation.
What does the Sex Pilus do?
Allows transfer of DNA, also allows the cell to take up DNA.
Where does E.coli get its nitrogen from?
Ammonia or a meat source
What do cyanobacteria do?
Catalyse photosynthesis
What happens when cyanobacteria is left in uncontrolled conditions?
This leads to algal bloom
Why are algal blooms detrimental?
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.
Why does an algal bloom lead to depletion of oxygen in a small freshwater system?
Population growth of cyanobacteria and algae eventually collapses, leading to decay and consumption of oxygen.
Where are streptomyces found?
Soil, desert, volcanoes and marine environments
What do streptomyces produce?
Dusty spores
What are Mycelium?
Network of fibres, provide energy cells to divide and form colonies.
What does Streptomyces produce when the cells begin to die/ run out of resources?
Pigments, which are different antibiotics.
What are the pigments highlighting?
Where the bacteria is making secondary metabolites.
What is Symbiosis?
Multiple different interactions of organisms that are helping eachother.
Leaf cutter ants + Streptomyces case
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.
Heterotrophs
Require organic material
Auxotrophy
Dependent on a specific diet - sugar, amino acid, nitrogen source
Autotrophy
Phototrophs, Chemolithotrophs –> require inorganic molecules
LacI
DNA binding protein, tells the cell whether make RNA or not
What do TFs sense?
- Glucose
- Metal
- Micronutrients
- Nitrogen
- Ammonia
- Tryptophan
Key response mechanisms of cells
- Gene expression
- Evolution/mutations
How are protein levels in a cell modulated?
- Initiation of transcription
- Premature termination of transcription (attenuation)
- Control of transcription termination (anti-termination
- Differential mRNA stability
- Changes in the rate of translation initiation
- Changes in the rate of translation elongation
- Changes in protein stability
Are rates of transcription and translation the same?
Yes, the process of protein production wouldn’t be fast if one was lagging behind the other, mRNA would be in excess.
What are evolutionary mutations caused by?
Resistance
Sensitivity
Loss of Ability
Gain of Ability
Directed Evolution experiments
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.
How did E.coli adapt to glycerol?
Mutating to have an enhanced glycerol kinase enzyme activity.
Which bacterium has the smallest genome?
Mycoplasma Laboratorium = <0.5Mb
How many genes are needed to make a minimal genome?
400
Genes
Pieces of DNA, most genes contain the information for making a specific protein.
Protein
Molecule made of amino acids.
Hypothetical genes
Genes that have never been studied before, may be essential, may not be. Genes that have never been characterised before.
DUF
Domain Unknown Function
How much of the E.coli genome is uncharacterised?
About 50%
What are the two approaches for genetic testing?
Classic - mutates DNA randomly
Reverse - specficially deletes DNA
What are tested within classic genetics?
- Open reading frames (orfs)
- Regulatory RNA
- Regulatory elements
What is the first amino acid to initiate transcription in bacteria?
Formal methionine = Fmet
Start codons
CTG, GTG, TTG
Stop codons
TAG, UGA, TAA
Wobble hypothesis
Where the ribosomes, aminoacyl-tRNA on the first codon will accept non-base pairing codons.
Happens at a lower frequency
How does tRNA recognise an alternative start codon?
Via release factor 1-3.
What is non-coding DNA?
Elements that are not translated as protein, may make up RNA, may be promotors, ribosome binding sites, transcription terminators, riboswitches.
What does studying classical genetics do?
Identify function
What does studying reverse genetics do?
Identify/prove function
How do mutations occur?
DNA replication mistakes from DNA polymerase
Mutagens + Carcinogens
Spontaneously - mutagens/stress
Horizontal gene transfer
How do mutations occur via Horizontal gene transfer?
Plasmids, phages, transposons
What changes can occur in a mutant?
- Loss of function
- Gain of function
- Silent
Types of mutation
- Point mutations
- Deletions
- Insertions
- Duplications
What is included in Classical testing?
- Random mutagenesis
- Transposon Mutagenesis
- Phenotypic screening (colony + fluorescence)
What is included in Reverse engineering?
Genome engineering –> CRISPR/Cas9 + Homologous Recombination
What is the KEIO collection?
Paper that determines what the essential genes for life are in E.coli.
What is the KEIO collection used for?
To study function of E.coli features.
What is the KEIO collection used for?
To study the function of E.coli features.
What are the mycoplasma laboratorium clinical strains?
- M.genitalium
- M.mycoides
- M.pneumoniaea
How many genes are in a minimal cell?
450, 10% of E.coli
What does Mycoplasma need to grow?
Energy + Building blocks –> Glucose, Amino acids x20, yeast extract, tryptone, peptone, thallium.
Metal and counterion –> CaCl2, MgSo4, KCL, NaHPO4
Vitamins and cofactors
What is the size of an average E.coli protein?
30,000 daltons, 1,000bp DNA.
Why does DNA have a major and minor groove?
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.
How can operons be regulated?
Catabolite control protein and Xylose utilisation
What is the most conserved sequence in DNA?
GGAGG
What is found in every single 16s ribosomal RNA sequence?
Mirror image sequence of GGAGG
Where do activators bind to in regard to the promoter?
Upstream, -50 to -100
Where do repressors bind to in regard to the promoter?
Tend to bind within the promoter sequence, -35 to -10 box
What are the two different types of promoters?
Constitutive and Inducible
What do constitutive promoters do?
Always on.
Regulated by how tight the DNA is bound.
Sequence changes, affects the binding to sigma factor.
What is Sigma 70?
Main housekeeping sigma factor
What does Sigma 70 do?
Controls core metabolism, essential genes, how cell wall made, how cell membranes are made and how DNA is resynthesized.
What do Inducible promoters do?
Regulated by TFs.
Docks onto promoter and causes problems for RNA binding or activates it by binding upstream of the box.
Cis
Intramolecular
Trans
Intermolecular
