week 4 - what microbes need to live Flashcards
what microbes?
energy
nutrients
what microbes
- energy
o Energy sources (catabolism)
Light: phototrophs
Chemical reactions: chemotrophs
what microbes
- nutrients
o Precursors for the synthesis of biomass (anabolism)
o Which elements do microbes need to grow?
o Some bacteria may need organic growth factors
what nutrients do microbes need to grow
elements
o C, O, H, N, S
o Composition of proteins and DNA/RNA
o Ass metal ions: K, Mg
Not required by all but a large no.: Na, Ca, Fe
o Macronutrients: the above elements
o Micronutriens: Fe and many others
what nutreints do microbes need to grow
growth factors (organic compounds)
o Requiremenys vary from non to many (some bacteria have more essential amino acids than us)
o Vitamins (coenzymes), amino acids, purines, pyrimidines, etc.
macronutrients (overview)
- Biomass composition
o Approx.. like a carbohydrate (e.g. glucose): <Ch2O>n
o Plus nitrogen
Example biomass composition: yeast ash free dry mass:</Ch2O> - C1H1.83o0.56N0.17
- In mas C48%, H7%, O36%, n9%
o Rule of thumb need to remember
C 50 %
N 10%
Simplified - Petroleum (oil spill), loads of carbon but little nitrogen, microorganism needs nitrogen –> so microorganisms cannot grow in petroleum… so if want to clean up oil spill addition of nitrogen aids this (fertilizer)
Macronutrients: Carbon (C)
- Carbon sources:
o CO2 as carbon source: autotrophic microbes (autotrophs)
Phototrophic or chemotrophic - Photo trophy and autotrophy are not coupled
o Organic compounds as carbon source (heterotrophs)
Phototrophic or chemotrophic - Organic carbon also used a energy source (as electron donor that is oxidised with oxygen, nitrate, sulphate etc. as electron acceptor)
Macronutrients: Oxygen (O)
- Oxygen in catabolism:
o Electron acceptor in aerobic respiration (must be O2)
o Not forming part of biomolecules - Ocygen sources for anabolism
o Oxygen eneters synthesi of biomolecules in the form o H2O, O2 (required to make cholesterol), other organic compounds) - Oxygen relationships (Brock p. 196-200)
o Oxygen in air saturated water only ~250uM
o Quicly gone, especially when a lot of organic matter is decomposed
o Gut, sewage treatment, lake/ocean sediments, rice paddies, subsurface
aerobe
o Only grows in the presence of oxygen and respires oxygen (Homo, Bacillus, Psedomonas)
- Facultative anerobe
Aerobe that can grow without oxygen, using anaerobic respiration or fermentation (E. coli)
- Anaerobe
o Does not grow in the presence of oxygen and does not use oxygen (Clostridium. Methanobacterium (methanogenic archaeon), some fungi and protozoa
Macronutrients: other
hydrogen
o H20, H2, organic compounds
Macronutrients: other
nitrogen
o NH3 (ammonia, can be used by all bacteria and is the reduced form of N incorporated into amino groups)
o NO3- (nitrate needs to be reduced to NH3 before it can be incorporated, not all bacteria can do that)
o N2 (dinitrogen needs to be reduced to NH3 too, only some nitrogen foxing prokaryotes can do that)
o Organic nitrogen compounds
macronutrients
sulphur
o SO4^2- (sulphate, most bacteria can reduce sulphate to sulphide)
o H2S (sulphide, reduced form that can be directly incorporated into cysteine, toxic, reacts with oxygen
macronutrients
phosphorous
- PO4^3- (phosphate, full oxidised, no need to reduce before incorporation into biomass unlike nitrate and sulphate
macronutrients: metal and anions
potassium
K required for the activity of many enzymes
K is compatible at high concs. In the cell, Na+ not, so cells pump Na+ out and K+ in
macronutrients: metal and anions
sodium
o Na: sodium, Na+ (not needed by all)
Many contain some Na but do not use it, it is less compatible than K
Some use a sodium motive force instead of a proton motive force
macronutrients: metal and anions
calcium
o Ca: Calcium, Ca+ (not needed by all)
Stabilizes cell walls, large amount in endospores
macronutrients: metal and anions
magnesium
o Mg: Magnesium, Mg+
ATP really is MgATP
Mg required for stability of nucleic acids/ribosomes, membranes
macronutrients: metal and anions
anions
- Anions to balance charge
o E.g. Cl- or organic acids (electroneutrality)
micronutrients
iron
e (iron)
- Most microbes need Fe to make cytochromes and FeS protein for electron transport chains
- By taking iron away can strop microorganisms from growing
- But not all:
o E.g. lactic acid bacteria (fermentation of sugar does not need a respiratory chain), Lactobacillus acidophilus.
micronutrients
iron solubility
- Solubility of Fe low therefore difficult to take up:
o Fe2+ is relatively soluble, but oxidises (rusts) in presence of oxygen
o Fe3+ (rust) very low solubility at neutral pH
Solubility product of Fe(OH)3 = 10^-38
o Between pH 0-3, Fe3+ is soluble
o Many bacteria produce sidephores to scavenge Fe from the environment
o These have very high affinity for Fe
Usually chelated by catechol or hydroxamate groups
micronutrients
iron defence against pathogens
- Defence against pathogens:
o Keep free Fe concentration in body very low by binding loctoferrin and transferrin (nutritional immunity)
o Making it difficult for bacteria to grow in the body
The affinity of transferrin for Fe(III) is extremely high (10^23M-1 at pH 7.4)
Lactoferrin affinity for irn is 300 x higher (protection, keeps milk from spoiling)
o Demonstrates the importance of nutrition for immunity
Bacteria fight for iron
micronutrients
other transition metals
o Mn, Co, Ni, Cu, Zn, Mo, W
Like vitamins in active sites of enzymes
Only traces required
Often enough in ‘distilled’ water and as impurities in other media components
micronutrients
other trace elements
Se
- ‘rare’ ‘earth’ elements (lanthanides)
o Used as fertilizer and recently shown to ve required for some bacterial methanol dehydrogenases (pol et al., 2014)
media for growth
- defined media
o You know exactly what molecules are in the medium and how much
o Essential for physiological studies
o An contain a long list of components
o Can contain more than necessary
media for growth
- minimal media
o A defined medium that only conatins whats essential
o Lactic acid bacteria need ~40 growth factors so a minimal media may contain many different components
media for growth
complex media
o Usually digested animal or plant matter
o Beef extract = boiled cow
o Contain lots of goodies but who knows what
media for growth
LB: lysogeny Brothe
(a.k.a Luria-Bertani medium) contains per L
- 10g typronw
- 5g yeast extract
- 10g NaCl
- Tryptone: casein (predominant milk protein) digested by the protease trypsin
- Yeast extract: autolysed (self-digest) yeast cells
o Contains everything yeast and other organisms need
- This is a DEFINED MEDIUM
minimal media for E. coli
- Amounts per L distilled water, pH 7
o K2HPO4 7g
o KH2PO4 2g
o (NH4)2SO4 1g
o CaCl2 0.02g
o Glucose 5g - Assume all required trace elements including Fe are contained in the water at sufficient concentration so they are not listed here
