Kinetics III and nutrients Flashcards
Nutrition in the Bacteria and the Archaea
What do we consider as key nutrients?
- macronutrients: C, H, O, N (same proprtion of these in mass)
- micronutrients: S, P, K, Cl, Na, Zn, Mg, Fe, Co, Cu…
[micronutrients vary with the organism and how it is grown]
e.g. if you grow a methanotroph on methane it will require a lot of Cu, but grown on methanol it will need much less.
- biomass has a formula: C12H24O6N3 which is about 306.34 Da. 1 mol of biomass is 306.34 g dry material.
- sometimes this is shorthanded to [CH2O]n, meaning “carbohydrate of n repeating units” really but it’s shorthand for biomass – sometimes the formula for a hexose is
used instead. These methods ignore N which is not correct. - dead biomass is necromass and sometimes has to be considered.
- C12H24O6N3 is 47 % w/w C so we always consider C as 47 % of the dry biomass.
Percentage of = Mass of C / Total Dry Biomass Mass
×100= 47% - only time you see variation in these numbers is;
1) if the biomass isn’t properly dried
2) there is e.g. glycogen granules present, which will raise the C, H and O but not the N.
where do they get their nutrients?
in complex and in defined media
(-below = defined media)
Nutrient In complex media In defined media
C amino acids, sugars, protein
H water, sugars
-defined= water
O water, sugars, molecular oxygen
-molecular oxygen
N amino acids, proteins, peptides, maybe amines
-ammonium, nitrate, nitrite, cyanate, thiocyanate, amino acids
S methionine, cysteine, cystine
-sulfate, thiosulfate, cysteine, methionine
P nucleotides, DNA, RNA
-inorganic P
Fe heme, hemin
-Fe(II), Fe(III)/Fe EDTAate
Cl dissolved inorganics
-Cl-
Mg dissolved inorganics
-Mg(II)
Mn dissolved inorganics
-Mn(II)/Mn EDTAate
Metabolic modes
where are these from?
energy
H
Carbon
what metabolic mode are viridiplantae normally?
what are Homo sapiens?
What are Thiobacillus thioparus?
What is E.coli?
- primary metabolic modes are in the form “energy, H, carbon”
- ENERGY: photo- (electromagnetic radiation) OR chemo- (from chemical reactions)
- CARBON: auto- (CO2/DIC) OR hetero- (any C compound that is not CO2/DIC)
- e.g. most Viridiplantae are photolithoautotrophs – energy is conserved from visible light, H is from an inorganic electron donor (water) and carbon is from CO2.
- e.g. Homo sapiens subsp. sapiens L is a chemoorganoheterotroph – energy is conserved from chemical redox reactions, H is from an organic electron donor (ultimately D-(+)-glucose) and carbon is from (mostly) D-glucose.
- Thiobacillus thioparus is a chemolithoautotroph – energy is conserved from oxidation of thiosulfate to sulfate, H is from thiosulfate, carbon is from CO2.
- Escherichia coli is a chemoorganoheterotroph - energy is conserved from chemical redox reactions, H is from an organic electron donor (such as sugars or amino acids) and carbon is from sugars or amino acids.
often we will abbreviate and say “autotrophs” and “heterotrophs” in general terms.
What are the key things needed for growth?
1) an energy source – this could be electromagnetic radiation or a chemical electron donor/energy source (duel function).
2) an electron donor (if not the same as the above).
3) a terminal electron acceptor (in respiratory organisms only) e.g. O2 in aerobes, sulfate in some anaerobes
4) a nitrogen source (usually NH4+, NO3- or amino acids – sometimes N2 gas in diazotrophs (L12, Metabolism VII).
vitamins and other minor growth factors
What do we do in a media even if the organism produces a vitamin e.g B12?
What can help increase growth in a media?
What may some anaerobes need in a media?
- many organisms can make their own B-complex vitamins – we say they are “prototrophic for B12”
- if they cannot, we say they are “auxotrophic for B12”
- we often provide B-complex vitamins in media even for prototrophs just because it generally speeds up growth or ensures at least that the production of those vitamins doesn’t become limiting to growth.
- we often supply lipoate (cofactor for many enzymes) in vitamin solutions added to media and this does aid growth but we don’t know if it IS being taken up or if it just stabilises the true vitamins as it is an antioxidant.
- some organisms need non-vitamin micronutrients like cholesterol, hemin, menaquinone – often these are strictly anaerobic organisms, for some reason.
- some more vague ones like boiled soil extract.
terminology re: oxygen
Can we say anaerobic conditions?
What relations with O2 may some organisms have?
- IF an organism uses molecular oxygen (O2) as the terminal electron acceptor for respiration, it is an aerobe/aerobic.
- IF an organism uses anything BUT molecular oxygen as the terminal electron acceptor for respiration, it is an anaerobe/anaerobic. (even if it uses O2 for benzene oxidation in catabolism but NO3- as terminal electron acceptor, it is still an anaerobe)
- an environment (inc. flask/reactor in the laboratory) is oxic (it it has oxygen) or anoxic (if it has no oxygen). NO SUCH THING as “grown under anaerobic conditions” or “an anaerobic sediment” – they are anoxic!
- organisms that use oxygen (regardless of what for) can have different relations with it:
- if they need high/ambient pO2, aerophiles.
- if they need a zero pO2, strict anaerobes (as they are always anaerobic respirers!)
- if they need O2 but only grow at low pO2, microaerophiles (in microxic environments)
assimilation and dissimilation
Name what gets assimilated and why
( we can also refer to these as catabolism (dissimilation) and anabolism (assimilation) although they are slightly different really.)
- in heterotrophs, C compounds are partially assimilated and partially dissimilated but not usually directly e.g. glucose is dissimilated partially to 3-phosphoglycerate (3PGA), some of which is then dissimilated to CO2 to generate energy and some is assimilated into biomass. Refer to Krebs’ cycle
and you will see where CO2 leaves and where assimilation (from intermediates) can occur. - in autotrophs, electron donors e.g. thiosulfate are dissimilated by oxidation to e.g. sulfate (in this case), yielding electrons for growth. Electron donors in autotrophs don’t get assimilated.
- other things like N compounds, S compounds etc do get assimilated as sources for biomass production e.g. NH4+ gets assimilated into amino acids, SO42- gets
assimilated into methionine and L-cysteine.
Theoretical yields of biomass
If we know an organism grows on benzene (C6H6) using molecular oxygen for respiration and we know all other growth factors are in excess, can we predict how much biomass can be growth (as a theoretical typical amount) in a 5L culture on 30 mM benzene?
equation needed for this calculation include;
conc X vol=mol
Mass=Mr x mole
Theoretical Dry Biomass= Mass of Carbon Available for Assimilation / percentage of Carbon in Biomass
Amount of Benzene:
You have a 5L culture with 30 mM benzene.
5×30=150 mmol of benzene.
Carbon Content from Benzene: Given that 1 mol of benzene (C6H6) contains 6 moles of carbon (6×C), you have
150×6=900 mmol of carbon.
Converting to moles, this is 0.9 mol of carbon.
Mass of Carbon: (mass=Mr x mole)
The atomic weight (Ar) of carbon (C) is12.011Da.
The mass of carbon in your culture is
0.9×12.011g/mol, which is approximately
10.81 g.
Dissimilation of Carbon:
Typically, 50% of the carbon is dissimilated to CO2 for energy, leaving 50% for assimilation into biomass.
Therefore,
0.5×10.81=5.40 g of carbon is available for assimilation into biomass.
Biomass Calculation:
Theoretical Dry Biomass= Mass of Carbon Available for Assimilation / percentage of Carbon in Biomass
×100
Biomass is composed of 47% w/w carbon.
5.40 / 0.47 (×100)= gives you the theoretical dry biomass of
11.50 g
In reality, the amount dissimilated can vary between 30-80%.
However, a good estimate is 50% dissimilation.
- What is the primary metabolic mode and respiratory type of an organism that uses CO2 as
its carbon source, elementary sulfur as its energy source and electron donor and ferric iron as
its terminal electron acceptor?
anaerobic chemolithoautotroph
- What is the primary metabolic mode of an organism that uses fumarate as its source of
carbon and electron donor but only under bright illumination at 700 nm?
photoorganoheterotroph
- Which of the following is an N-source used in defined media at about 7-10 mM?
tryptone, proteose, ammonium chloride, calcium bisglycinate, molecular nitrogen
- What is the proper term for a culture flask that contains no molecular oxygen?
Anoxic
