9. METABOLISM – C TURNOVER
Two parts of metabolism – catabolism,
anabolism
Connection – by-products, energy
Preferable source of energy for
chemoorganotrophs – sugars
9.1. Catabolism
Mainly decomposition – generation of
energy (mainly ATP)
polysaccharide (cellulose)
hydrolysis
monosaccharide
glycolysis, E-D,
hexose - P-pathway → pentose - P-pathway
pyruvate
fermentation
respiration
 Glykolysis (Embden-Meyerhof pathway)
Glucose
Fosforylation +2ATP
Fructose 1,6 bisphosphate
2 trioses forming
glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
2 pyruvate + 2NADH + 2H2O + 4ATP
fermentation
(anaerobic)
respiration
(aerobic, anaerobic)
 Fermentation – donor, acceptor H+(e-)
organic
Ethanolic – Lactic – Butyric - Propionic
 Respiration - donor H+(e-) organic
inorganic; acceptor H+(e-) inorganic,
acceptor H+(e-) inorganic
 Generation ATP
Catabolism = main source of energy for
chemotrophs
Fermentation – 2ATP
Aerobic respiration – 38ATP
(Escherichia coli synthesizes 2500000
molecules ATP per second)
The use of ATP:
ATP
ADP + Pi + E
Anabolism
Nutrient uptake
Movement
Heat energy
Luminescence (light energy)
Electrical energy (electrical potential)
9.1.1. Fermentation
Anaerobic pathway, energy usually only in
the first step (glycolysis)
 Lactic acid fermentation
(Pyruvate = acceptor of H+)
Characteristics: mesophilic, aerobic –
anaerobic, chemoorganotrophs, need
for simple sugars
Homolactic fermentation – major end
product = lactic acid
Typical pathway - EM
Streptococcus – yoghurt, mouth
Lactococcus – cheese, silage
Enterococcus – gut, silage, probiotics
Lactobacillus (some species) – cheese,
yoghurt, silage, gut, vagina, probiotics
Heterolactic fermentation – important end
product = lactic acid; additional products
(ethanol, CO2, acetic acid…)
Typical pathway – pentose phosphate
Leuconostoc – sauerkraut
Lactobacillus (some species) – sauerkraut,
gut
[Bifidobacterium (60% acetic acid, 40%
lactic acid) – gut (esp. breast fed
babies), probiotics, yoghurt]
 Ethanolic fermentation
Pyruvate after decarboxylation (-CO2) to
acetaldehyde is reduced on ethanol
glucose+2ADP+Pi
2ethanol+2CO2+2ATP
Characteristics: anaerobiosis, simple
sugars
Saccharomyces – main yeast in ethanolic f.
bakery, alcoholic beverages, vitamins
 Butyric fermentation
Main products: butyric acid, butanol,
acetone, CO2, H2
Additional products: other organic acids
Characteristics: mesophilic – thermophilic,
strictly anaerobic, different C-sources
(simple and poly-sugars), different Nsources (for some N2)
Clostridium – digestive tract, soil, sewage
 Methanogenesis
Fermentation of acetate to methane (one of
variants for methane production)
CH3COO- + H+
CH4 + CO2
Typical for some chemoorganotrophic
Archea
Important for biogas production
 Propionic fermentation
Hexose --- pyruvate --- propionate + acetate
+ CO2 + H2O
Lactate --- pyruvate --- propionate +
acetate + CO2 +
H2O
Propionibacterium
Anaerobic
Simple C-substances (mono-, disaccharides)
Organic N-substances
Aerotolerant
Gastrointestinal tract (esp. rumen)
Vitamin B12 production
Cheese production - Swiss cheese
(Emmenthal cheese), characteristic
flavour and holes
Regulation of fungi
9.1.2. Respiration
 Aerobic respiration of macromolecules
Main phases:
(1) hydrolysis –macromolecules
breakdown
(2) catabolic pathway – pyruvate
formation
(3) pyruvate decarboxylation and acetylKoA formation
(4) tricarboxylic cycle (TCA) – use of
acetyl-KoA in TCA – forming of
citric acid and its biochemical
changes;
products: H2O, NADH, CO2, FADH2,
ATP
(5) respiration chain (electron transport
chain, ETC) – oxidation of H+ and
electron transport (NADH, FADH2)
H+ + O2 + Pi + ADP
H2O + ATP
ETC is located in plasma membrane
Several carriers participate in ETC
(flavoproteins, cytochromes
Result: C6H12O6 + 6O2 + 38Pi + 38ADP
6CO2 + 6H2O + 38ATP (=energy)
The best sources of energy
C-sources: cellulose, hemicellulose,
starch, lignin; mono-, di- ….
saccharides
Organisms: several fungi and bacteria,
very common process
Main mineralisation process in Cturnover
 Aerobic respiration (non-complete)
org C-subst. + O2
org C-subst. + (CO2)
+ H2O + energy
(1) Acetic fermentation
ethanol + O2
acetic acid + H2O+ E
Energy = 6ATP
Organism: Acetobacter
Production of vinegar, spoilage of
alcoholic beverages (wine, beer…)
(2) Citric acid fermentation
Saccharides+O2 citric acid + H2O + E
(molasses)
Organism: Aspergillus niger
Citric acid production for food and
beverage industry,
pharmaceutical industry
 Anaerobic respiration
In anaerobic condition oxygen (or other
inorganic acceptor) from substances can be
used for H+/e- oxidation
Dissimilative denitrification:
NO3- + H+ + Pi + ADP
N2 + H2O + ATP
Desulphurisation
SO42- + H+ + Pi + ADP
Methane formation
CO2 + H+ + Pi + ADP
S + H2O + ATP
CH4 + H2O + ATP
Assimilative denitrification:
NO3- + H+ + Pi + ADP
NH4+ +H2O+ ATP
9.2. Anabolism = Biosynthesis
 The use of energy and nutrients to
construct cell constituents.
 Several enzymes from catabolism are
shared.
Basic schema:
Inorganic molecules
(CO2, NH4+, H2O, PO43-)
(AUTOTROPHS)
Monomers, Building blocks
(nucleotides, sugars, amino acids, fatty acids)
(HETEROTROPHS)
Macromolecules
(nucleic acids, proteins, lipids, polysaccharides)
Supramolecular systems
(membranes, enzyme complexes)
„Organelles“
(nucleoid, nuclei, ribosome, flagella)
Cell
(bacteria, fungi, protozoa)
Biosynthesis in Escherichia coli:
Cell constituent Number of molecules ATP required
DNA
1
60 000
RNA
15000
75 000
Polysaccharides
39000
65 000
Lipids
15 000 000
87 000
Proteins
1 200 000
2 120 000
 Fixation of CO2
- The high need for energy – trapping
light during photosynthesis, or derive
energy from the oxidation of reduced
inorganic electron donors.
- Autotrophic fixation of CO2 is crucial,
it provides the organic matter for
heterotrophs.
- Incorporation of CO2 – several types:
Calvin cycle, pentose phosphate cycle…
- Carboxysomes typical for thiobacilli,
cyanobacteria, nitrifying bacteria –
site for CO2 fixation.
 Synthesis of sugars
Gluconeogenesis – close to glycolytic
pathway, three steps are easily
irreversible, starts with pyruvate
synthesis. Result – glucose or fructose
from which other sugars are produced.
 Phosphorus assimilation
- Necessary in nucleic acids, ATP,
NADP, proteins, phospholipids, etc.
- Easily incorporated through formation
of ATP:
(1) photophosphorylation
(2) oxidative phosphorylation
(3) substrate phosphorylation
- Preferable forms: H2PO4-, HPO42- From organic substances released by
phosphatases
 Sulphur assimilation
Sulphur is needed for synthesis of amino
acids (methionine, cysteine) and several
cofactors (coenzyme A, biotin…).
Sources: SO42- through assimilatory
sulphate reduction, amino acids, H2S
 Ammonium assimilation
Relatively easily incorporated through
amination:
Pyruvate
alanin
α-ketoglutarate
glutamate
oxalacetate
aspartate
Other amino acids synthesis through
transamination
 Nitrate assimilation
Nitrogen in NO3- is too oxidized and it
must be reduced through assimilatory
nitrate reduction
NO3NO2NH3 (NH4+)
 Nitrogen (N2) assimilation (fixation)
Nitrogen fixation occurs in:
(1) free-living bacteria (Azotobacter,
Clostridium, Klebsiella, Methanococcus)
(2) symbiotic fixation (Rhizobium….)
(3) cyanobacteria (Nostoc, Anabaema…)
Reduction N2 with enzyme nitrogenase:
N2
NH
NH2
NH3
NH4+
N2 + 8H+ + 8e- + 16ATP
2NH3 + H2 + 16ADP + 16Pi
 Protein synthesis
- Main place = ribosome
- Activity of ribosome: the use of energy
(light, chemical), interaction of r-RNA,
m-RNA and t-RNA.
- Three steps: initiation, elongation,
termination.
8.3. Regulation
 Substrate concentration
Esp. very low concentration
Ks = Michaelis constant (substrate
concentration in which the speed of
enzyme reaction is half of maximum)
 Enzyme concentration
Speed of m-RNA transcription and
speed of enzyme synthesis in
ribosomes
 Allosteric regulation
Some molecules act as effectors,
modulators
These molecules change the enzyme
conformation (result = increasing or
decreasing enzyme activity)
 Feedback effect
End product stops the enzyme reaction
in very beginning
E1
S
E2
M1
E3
M2
E4
M3
E5
M4
P
 Oxygen effect
Some anaerobes stop their metabolism
in the O2 presence (sometimes O2 toxic)
Some facultative anaerobes – change of
metabolism: in O2 presence respiration,
in O2 absence fermentation (= Pasteur
effect)
 Environment factors
Minimum – optimum – maximum
Temperature, pH…