Test 1 Flashcards
Elements of Life
CHNOPS and Iron
How does reduction/oxidation drive bioenergetics?
Can be derived from reductive/ oxidative chemical reactions in the cystol/ membrane gradient like +NAD + 2H –> NADH + H+
When was earth formed and when did life begin
4.5 billion years ago earth was formed
4 billion years ago life began
When were Photosynthetic prokaryotes and cyanobacteria formed?
- 5 billi Photo Pro (Non oxygenic)
2. 8 bill- Photo Cyano(Oxygenic)
When were Aerobic bacteria and unicellular eukarotes formed?
2.4 bill- Aerobic bacteria
2 bill-Unicelullar Eukaryotes
When were Multicellular Eukaryotes and plants and animals formed?
.8 bil-multicellular eukaryotes
.5 bill- plants and animals
What did Carl Woese contribute?
Phylogenetic tree
2 Pro- Archaebacteria and Eubacteria
16S/ 18S rRNA tree
Formal Definition of species
DNA to DNA reassociation btwn 2 isolates is 70% or greater.
16 S rRNA has to be greater than 97%
(Bacteria and Archaea)
Open genomes
sequence isolate, see gene never seen before
Note: New genes mean different than the norm for the species
Closed Genomes
sequence another isolate, barely see differences. No more than 1% new genes in total sequence.
(Note: New genes mean different than the norm for the species)
Core Genome
Genes on all genes of strain of patho
Usual environment for Archaea
Extreme environments, High Temp/ high salt concentration
How does Archaea’s environment support Woese’s hypothesis for 3 domains of life
Woese- archaea= extreme
What does Archaea’s environment say about early evolution on earth?
Archaea=survive
humans, animals,other organisms= dead
lack of O2 and being toxic.
How does Archaea having no established pathogens support Woese’s hypothesis
Since Archea is suited for extreme environments and has already found it’s niche in the world, it is not pathogenic for plants or animals.
Minimal Medium
Minimal amount needed for an organism to grow. Usually results in slow growth.
E.Coli on this medium will oxidize glucose and O2 to produce 50% CO2 and 50% biomass
Defined Medium
Made of Pure Chemicals
Exact contents
Requirement 4 Growth
Undefined Medium
Can contain a mixed amount of nutrients or the exact contents/ amounts are unknown.
Yeast extract- cheap undefined, fast growth bc rich
Brain-heart infusions are another example
Rich medium
Plenty Nutrients
Large Growth
Prototroph
Doesn’t require a specific nutrient to grow.
Can convert any carbon source to fulfill it’s needs.
Definition of Cell Growth
Change in Mass (weight)
Inc Cell # doesn’t = growth
Turbidity/Optical Density
Measure light scattered in spectrophotometer- # cells
Assumes all cells are equal in size and linear over a range of concentrations
Total Cell Counts
Uses a counting chamber (glass slide with defined area and depth) to count number of cells.
Electronic- cells through Electric Field, count by resistance
Cons- Cant tell apart live and dead
Cant count low dense culture
Viable Cell Counts
Cells grown,plated on a growth medium.
Each colony represents a viable cell
However, clumps of cells will be represented by a single colony and most bacteria grow in clusters. Also, some cells don’t plate very well.
Dry Weight/ Protein
Cells harvested by centrifugation, dried weighed. Not typically used in today’s lab since they can’t assess a culture’s growth at several points
Lag phase
Rich –> minimal media.
Takes about 2 hrs of regulation while the cells start to make everything before they can slowly increase in size
Exponential phase
Grow as fast as possible with nutrients available
Cells are dividing and accumulating biomass.
Enters stationary phase, the number of cells increases without a change of mass/ no growth
Stationary phase
Stop Growth bc Toxic/ 0 Nutrients
What is stationary phase sigma facter
RpoS - global regulator for synthesis of around 30 proteins.
Increases during starvation
Role of Fis and H-NS
DNA binding proteins (Fis is specific, H-NS is nonspecific)
Fis activates rRNA gene transcription and is inhibited by H-NS
H-NS increases during stationary phase so less ribosomes are synthesized while Fis is high in actively growing cells
What is (p)ppGpp?
Magic Spot” or the stringent response. Causes ribosomes to stall and slows tRNA/rRNA transcription.
Mechanism- if a ribosome cannot read hrough a codon, it’s not charged or efficiently charged.
Can trigger the arrest of the replication fork”
What is the mechanism behind Diauxic Growth?
cAMP/CRP complex
global transcription regulator.
cAMP Inc bc- Carbon starvation mediated by Adenylate cyclase enzyme- start by PTS system.
What is the role of oriC, DNA-A, and Par/MukB
DNA-A= On DNA synth by bind to oriC- opens DNA duplex
Other Rep= Complex
Par and MukB- chromosome split & seperation Form Septum, inward growth, seperate, septation, parallel
How does DNA replication occur in fast growing cells vs slow growing cells?
Many Rep Forks= DNA Rep Fast
DNA Rep begins in previous generations
What effect do the amounts of DNA, RNA and protein have on growth rates
Inc Pro= Inc Synth
Inc Pro. & RNA= Fast Growth
What is growth yield, Y?
W(Cells Made)/W(Carbon used)
E.coli- glucose, aerobic conditions. Y= 0.5
(50% biomass, 50% carbon dioxide)
Chemostat
Restricts growth Limit Addt. Nutrients Dilution rate= growth yield Study Cell in diff growth rates More Control
What is ftsZ?
Bacteria, Archae and Eucarya.
3D structure
Forms protofilaments (tubulin), Ring- hire protein
Localizes in center of cell division.
Substrate level phosphorylation
Cytosol.
Electrons donors to acceptors.
Is coupled to ATP synthesis
Oxidative level Phosphorylation/ Membrane gradients
In Membrane
Electrons from donor to accept.
coupled to ATP synthesis
What did Peter Mitchell propose?
Proton Gradiant
What were the principles of Peter Mitchell’s proposal?
- CM impermeable to H+ & OH-
- Enzymes that translocate H+ outside; form electrochemical gradient = inside the membrane + use Exergonic rxn drive proton translocation
- Form EC Gradient by action of pH gradient/ CM potential
What is the Proton motive force equation?
p = ”ﾨ 60”pH
What is the difference between ∆Ψ and ∆ pH?
∆Ψ= CM potential for + ion outside cell ∆pH= Acid & Base outside
What are the 3 types of transporters
Anti- 2; oppo
Sym- 2 same
Uni- 1
What does DiNitroPhenol do to a living cell?
Symport In= H+ Out= Nothing Collapse Proton Gradient Off-oxidative phosphorylation, Cell Unable use Coupled ATP synthesis Death
How are Valinomycin and potassium used generate a ∆Ψ in membrane vesicles?
Inc K+ efflux,
Gradient- + outside; - inside
Determine if ∆Ψ drives transport substrate through Cell Membrane
How do lipophilic dyes or lipophilic fluorophores can be used to determine delta psi experimentally?
Fluoro Dye measures change in ∆p to find ∆Ψ. Quenching- 1. F Dye seen inside cell bc low conc 2. Measure Op Density
INC Dye= Inc PMF
