Microbial metabolism
1
Introduction
• Microbial metabolism is the means by which a microbe obtains the
energy and nutrients it needs to live and reproduce
• Bacterial growth deals with increase in size and number
• Necessary nutrients are C, H, O, N and inorganic salts
• Metabolism is the sum of all chemical reactions in the body.
• Metabolism has two components: catabolism and anabolism
• Catabolism: The processes by which a living organism obtains its energy and
raw materials from nutrients
• Anabolism: The processes by which energy and raw materials are used to
build macromolecules and cellular structures (biosynthesis)
2
Metabolism
• Catabolism: reactions that break down
large compounds and release energy.
• Anabolism: reactions that require
energy to build large compound
• Catabolic reactions furnish the energy
needed to drive anabolic reactions.
• . Energy harvested from catabolic reactions
are stored in ATP molecules.
3
Metabolism…
• Oxidation or reduction of carbon in metabolic pathways:
• reduced forms of carbon (e.g. hydrocarbons, methane, fats, carbohydrates, alcohols) carry
great potential chemical energy
• oxidized forms of carbon (e.g. ketones, aldehydes, carboxylic acids, carbon dioxide) carry
very little potential chemical energy in their bonds
• Oxidation and reduction always occur together (reduction-oxidation reaction
(redox reaction)
• Metabolism occurs in stepwise pathways catalyzed by enzymes
• Enzymes that catalyze redox reactions typically require a coenzyme
• Coenzymes “shuttle” electrons from one part of the metabolic pathway to another
• Coenzymes for redox reactions: NAD(oxidized) + H+ + pair of electrons → NADH(reduced);
FAD(oxidized) + H+ + pair of electrons → FADH(reduced)
4
Three principles for classification of
microbial metabolism
1. How the organism obtains carbon for synthesizing cell mass
2. How the organism obtains reducing equivalents (hydrogen atoms
or electrons) used either to conserve energy or in biosynthetic
reactions
3. How the organism obtains energy for survival and growth
5
Classification of types of metabolism
1. How carbon is obtained
• Autotrophic – carbon is obtained from CO2
• Heterotrophic – carbon is obtained from organic compounds
• Mixotrophic – carbon is obtained from both organic compounds and by fixing
CO2
2. How reducing equivalents are obtained:
• Lithotrophic – reducing equivalents are obtained from inorganic compounds
• Organotrophic – reducing equivalents are obtained from organic compounds
3. How energy is obtained:
• Phototrophic – energy is obtained from light
• Chemotrophic – energy is obtained from external chemical compounds
6
Classification…
• In practice, the terms are combined:
• Chemolithoautotrophs obtain energy from the oxidation of inorganic
compounds and carbon from the fixation of CO2.
• E.g. nitrifying bacteria, sulfur-oxidizing bacteria, iron-oxidizing bacteria
• Photolithoautotrophs obtain energy from light and carbon from the fixation of
carbon dioxide, using reducing equivalents from inorganic compounds.
• E.g. Cyanobacteria use H2O as reducing equivalent = hydrogen donor), Chlorobiaceae,
Chromatiaceae use H2S as hydrogen donor)
• Chemolithoheterotrophs obtain energy from the oxidation of inorganic
compounds, but cannot fix CO2.
• E.g. some Nitrobacter spp, some sulfate-reducing bacteria
7
8
Classification…
• Chemoorganoheterotrophs obtain energy, carbon, and hydrogen for
biosynthetic reactions from organic compounds.
• E.g. most bacteria, e. g. Escherichia coli, Bacillus spp., Actinomycetota
• Photoorganoheterotrophs obtain energy from light, carbon and
reducing equivalents for biosynthetic reactions from organic
compounds.
• Some species are strictly heterotrophic, others can also fix carbon dioxide and
are mixotrophic.
• E.g. Rhodobacter, Rhodopseudomonas
9
Reading assignment
• Students to discuss autotrophs: chlorophyll and photosynthesis
• Examples of bacteria that are autotrophs
• Photoautrophy
• Oxygenic and anoxygenic photosynthesis
• Compare chlorophll a and bacteriochlorophyll a
10
Metabolism Overview:
Reduction;
e- gain from
donor
Oxidation;
e- loss to
acceptor
11
Heterotrophic microbial metabolism
• Most microbes are chemoorganoheterotrophic i.e. use organic
compounds as both carbon and energy sources.
• Heterotrophic microbes can be
• commensals or parasites: survive on nutrients they obtain from living hosts
• saprophages: feed on dead organic matter
• Microbial metabolism is responsible for the decay of all organisms
after death
• Many eukaryotic microorganisms are heterotrophic by predation or
parasitism
12
Heterotrophic metabolism
• Most pathogenic bacteria are heterotrophic parasites of humans or the other
eukaryotic species.
• Heterotrophic microbes are abundant in nature
• responsible for the breakdown of cellulose, chitin or lignin which are indigestible to larger
animals
• Some bacteria can degrade more recalcitrant compounds such as petroleum
compounds or pesticides, and are useful in bioremediation
• Bacterial biochemical metabolic pathways are more diverse than in eukaryotes
• Some are unique to prokaryotes; some key central metabolic pathways have shared similarities
• e. g. glycolysis (Embden-Meyerhoff-Parnas, EMP, pathway) for sugar metabolism and the citric
acid cycle for degradation of acetate to produce energy in the form of ATP and reducing power in
the form of NADH or quinols
• Some bacteria e.g. Pseudomonas metabolize sugars using an alternative pathway known as the
keto-deoxy-phosphogluconate pathway (ED pathway)
13
Microbial Metabolism
Metabolic Reactions
Enzymology
Catabolism
Phototrophy
Anabolism
14
Metabolic Pathways
• Pathways can be linear, branched, cyclic or even spiral.
• Pathway activity is controlled in three ways:
• Metabolites and enzymes may be localized in different parts of the cell; called
metabolic channeling. (important in eukaryotes)
• Total amount of enzymes in a pathway can vary (gene expression).
• Regulation of enzymes. “Pacemaker enzymes” are often the rate-limiting step
in the pathway.
15
Metabolic Pathway Control Strategies
Feedback Inhibition:
(“end-product inhibition”; red)
• rate limiting enzyme is first in
pathway and is allosteric.
• end-product is a negative effector
(inhibitor) of first enzyme
Feed Forward Activation:
(“earlier-substrate activation”; blue)
+
• rate limiting enzyme of a branch point is
allosteric.
• earlier-substrate is a positive effector
(activator) of a forward reaction enzyme. Arrows =
enzymes
16
Electron carrier molecules
Recall: Three electron carrier molecules that are often required in
metabolic pathways are:
i. nicotinamide adenine dinucleotide (NAD+),
ii. nicotinamide adenine dinucleotide phosphate (NADP+),
iii. and flavine adenine dinucleotide (FAD).
17
Energy-rich compounds
• Chemical energy released in redox reactions is conserved in
phosphorylated compounds.
• Hydrolysis of the phosphate in energy-rich compounds releases much
energy that is used by the cell
• Phosphate can be bonded to organic compounds by either ester or
anhydride bonds
18
19
Cellular respiration
1. Cellular respiration oxidizes glucose to reduce NAD+ to NADH
(NADH is an electron carrier)
2. Cellular respiration has three stages:
i. Glycolysis
ii. Krebs cycle
iii. Electron transport.
20
CARBOHYDRATE CATABOLISM
• Key pathway for many bacteria is glycolysis.
• Alternatives to Glycolysis: pentose phosphate pathway (PPP), Entner-
Doudoroff pathway
• Cellular Respiration involves:
1. Synthesis of Acetyl-CoA and the Krebs Cycle
2. Electron Transport
3. Fermentation
21
Glucose (aerobic)
Catabolism
• ATP can be formed during
respiration or fermentation
• Both contain the glycolysis
pathway
•In aerobic metabolism, the
pyruvate from glycolysis is
oxidatively decarboxylated to
acetyl CoA
(anaerobic)
• Oxygen is not the only possible
• Fermentation
terminal electron acceptor in some proceeds when
bacteria (e.g. NO3 or SO4 can be there is no terminal
electron acceptor
used) = anaerobic respiration for respiration.
22
(ETC)
Glycolysis:
ATP is first invested to yield energy from oxidation and substrate level phosphorylation of ATP.
23
24
The Entner-Doudoroff pathway
• A few bacteria (gram-negative Pseudomonas aeruginosa and gram-
positive Enterococcus faecalis) subsitute Entner-Doudoroff pathway
(EDP) for glycolysis.
• Uses two unique enzymes, 6-phosphogluconate dehydratase aldolase
and 2-keto-deoxy-6-phosphogluconate (KDPG) aldolase, and other
common metabolic enzymes to other metabolic pathways to
catabolize glucose to pyruvate
• Yields precursor metabolites, 1 NADH, 1 NADPH, and 1 ATP for each
molecule of glucose
25
Entner–Doudoroff
pathway
KDPG: 2-keto-3-deoxy-6-
phosphogluconate)
26
Entner- Doudoroff pathway
27
Tricarboxylic acid cycle (TCA); Kreb’s Cycle
28
TCA…
• It provides a route for complete oxidation of glucose via pyruvate
• Oxidation of pyruvate to CO2 requires the concerted activity of the
citric acid cycle (CAC) and the electron transport chain (ETC)
• Oxidative decarboxylation of pyruvate to acetyl CoA requires pyruvate
dehydrogenase complex.
• Products from pyruvate: 3 CO2, 4 NADH + H+; 1 FADH2; 1 GTP=1ATP
• 12 ATPs are produced in one TCA cycle
• From TCA and the ETC, 38 ATP are produced 38 ATP when glucose
undergoes aerobic metabolism to CO2 + H2O
29
Energy yield
30
Anabolic roles of the TCA cycle
• Several CAC intermediates are used in biosynthetic reaction:
• α-ketoglutarate and oxaloacetate are precursors of several amino
acids
• Succinyl-CoA is used in synthesis of cytochromes, chlorophyll, and
several other tetrapyrroles (porphyrins)
• Oxaloacetate is metabolized to phosphoenolpyruvate, a precursor of
glucose.
• Acetyl CoA via citrate is the precursor for fatty acid biosynthesis
31
32
Glyoxylate cycle
• Is an anabolic pathway in plants, bacteria,
protists, and fungi.
• It provides an alternative for metabolism of 2-
carbon electron donors e.g. acetate when
oxaloacetate (OAA) is not available
• Acetyl CoA is used to synthesize
carbohydrates
• Has two additional enzymes to those in the
TCA cycle:
isocitrate lyase, cleaves isocitrate to succinate
and glyoxylate
malate synthase, which converts glyoxylate and
acetyl-CoA to malate
• The cycle can be connected to the TCA cycle
when malate formed from glyoxylate and
acetyl CoA forms OAA 33
Pentose phosphate pathway
• It is an alternative route for metabolism of glucose.
• Glucose-6-P is oxidized and decarboxylated to form phosphorylated
pentoses, NADPH and CO2
• The pathway produces ribose 5-P from ribulose 5-P.
• Ribose 5-P is a precursor molecule in the biosynthesis on nucleotides for
nucleic acids
• The pathway produces non-pentose sugars which can be converted to
hexoses or for biosynthesis
34
35
PPP
36
Synthesis of polysaccharides and
gluconeogenesis
• Polysaccharides are produced by microorganism during their growth
when there is excess of carbon source in the medium
• Examples are:
• storage polysaccharides e.g. glycogen, inulin
• exopolysaccarides e.g. xanthans, dextrans
• extracellular polysaccharides: used to bind microorganisms to various
surfaces (biofilm formation).
• lipopolysaccharides: attached to outer membrane of Gram negative bacteria.
• They determine immunogenic properties.
Read about production of xanthan gum and dextran from bacteria and their applications
37
Polysaccharides…
• Polysaccharides are synthesized from activated forms of glucose: uridine
diphosphoglucose (UDPG) or adenosine diphosphoglucose (ADPG).
• UDPG is the donor of glucose residues in the synthesis of structural
polysaccharides in the cell:
• N-acetylglucosamine and N-acetylmuramic acid in peptidoglycan
• Lipopolysaccharide component of the gram-negative outer membrane
• The activated glucosyl unit donor is added to an existing polymer
• E.g. UDPG + glycogen → glycogen + glucose
• Bacteria growing on other carbohydrates produce glucose in
gluconeogenesis from precursors e.g. phosphoenol pyruvate, OAA, and
CAC intermediates
38
Amino acid synthesis
39
Fermentation
• This is heterotrophic metabolism that uses organic carbon instead of
oxygen as a terminal electron acceptor.
• Fermentative organisms are anaerobic
• Organisms which use fermentation under anaerobic conditions and
anaerobic respiration when oxygen is present are known as facultative
organisms
40
Products of Fermentation
•Without any form of respiration, glycolysis products, pyruvate and NADH,
will accumulate.
•Fermenting cells convert NADH back to NAD+ reducing pyruvate. From
this many other compounds, depending on the organism.
41
42
43
Lactic acid fermentation
44
Energy Source
Overview:
• In addition to organisms feeding on
organic carbon for energy
(chemoorganotrophs).
• There are chemolithotrophs, which
gain energy from reduced inorganic
compounds (litho = rock).
• There are phototrophs that yield
energy from sunlight and do not
depend on any chemical energy
sources.
• The terminal (final) electron acceptor
determines which respiration type or
fermentation.
45
Assignment-fermentation
• Mixed-acid fermentations
• Clostridial and propionate fermentations
• Ethanol fermentation
46
Reading assignment
• Nitrifying bacteria
• Syntrophy
• Acetogenesis
• Methanogenesis
• Methanotrophy
47
