Chapter 6 Microbial Metabolism
?Energy Metabolism
? Special Metabolism in Microbes
? The Relationship between Catabolism
and Anabolism
? Regulation of Metabolism and
Ferment Industry
An Overview metabolism
metabolism,
the sum total of all chemical reactions occurring in the cell
metabolism
catabolism
anabolism
Complex molecules
catabolism
anabolism
Simple molecules ATP [H]
Section 1 Energy Metabolism in Microbes
Primary
Energy
Organic Compounds
Sunlight
Inorganic Compounds
in Reduced State
A
T
P
ATP
Chemoheterotroph
Photoautotroph
Photoheterotroph
Chemoautotroph
summarize
The breakdown of glucose to pyruvate
fermentation
respiration （ aerobic or anaerobic respiration ）
Chemoheterotroph biological oxidation and energy
Release
Process—— Dehydrogenation,Giving Hydrogen and Accepting
Hydrogen (Electron)
Function—— Releasing Energy (ATP),Engendering Reducing
Power [H] and Producing Intermediate Metabolites
biological
oxidation
Glocose—— representative substrate of biological oxidation
Embden-Meyerhof-Parnas Pathway (Glycolysis)
Hexose Monophosphate Pathway
Entner-Doudoroff Pathway (KDPG Pathway)
PK (phosphoketolase) pathway
1 The breakdown of glucose to pyruvate
1） Embden-Meyerhof-Parnas Pathway (EMP)
(Glycolysis,Hexose Diphosphate Pathway)
glucose pyruvate
with O2, connecte EMP pathway with TCA pathway；
without O2,reduce some metabolism product,only energy-
yielding process,
generates ATP by substrate-level phosphorylation,
（ 1） glyceraldehyde 1,3-phosphate ? 3-phoshoglyceric acid +
ATP；
（ 2） PEP ? pyruvate + ATP
Ten steps
C6H12O6＋ 2NAD+＋ 2ADP＋ 2Pi→
2CH3COCOOH＋ 2NADH＋ 2H+＋ 2ATP＋ 2H2O
Uses pentoses
and NADPH
Operates with
glycolysis
2)Hexose Monophosphate Pathway (HMP)
(Pentose Phosphate Pathway,
Phosphogluconate Pathway,
Warburg-Dickens Pathway)
fructose 6-phosphates,
be converted to glucose 6-phosphates, be returned to Pentose
Phosphate Pathway
glyceraldehyde 3-phosphate,
a,through EMP pthway,be converted to pyruvate,into TCA
pthway
b,converted to Hexose Phosphate,be returned to Pentose
Phosphate Pathway
The overall reaction,
6 glucose 6-phosphates +12NADP++3H2O → 5 glucose 6-
phosphates + 6CO2+12NADPH+12H++Pi
3) Entner-Doudoroff Pathway (KDPG Pathway)
1952,Entner-Doudoroff, Pseudomonas saccharophila
process,（ 4 septs）
1 Glucose glucose 6-phosphates 6-phosphogluconate
KDPG
6-phosphogluconate dehydratase
glyceraldehyde 3-phosphate + pyruvate
2-oxo-3-deoxy-6-phosphogluconate aldolase
Produces NADPH and 1 ATP
Does not involve glycolysis
Pseudomonas,Rhizobium,Agrobacterium
4) phosphoketolase pathway (PK)
a.Pentose phosphoketolas Pathway
G xylulose 5-phosphate
acetyl phosphate + glyceraldehyde 3-phosphate
phosphoketolase
ethanol pyruvate
Lactic acid
1 G ??? Lactic acid + ethanol + 1 ATP + NADPH + H+
G fructose 6-phosphates
b.Hexose phosphoketolas Pathway (HK)
（ Bifidobacterium bifidum ）
Erythrose - 4-P + acetyl-phosphates
phosphoketolase
glyceraldehyde 3-phosphate + acetyl-phosphates
xylulose -5-P ribulose-5-P
Acetic acid phosphoketolase
fructose 6-phosphates
Lactic acid Acetic acid
1 G ??? Lactic acid + 1.5 Acetic acid + 2.5 ATP
acetokinase
1,definitions
broader, use microorganism to produce useful metabolic product
narrower,under anaerobic conditions,be defined as an energy-
yielding process using itself metabolic intermediates as the final
hydrogen (electron) accepter
organic molecules serve as both electron donors and acceptors,
trait,
1） generates ATP by substrate-level phosphorylation；
2） the glucose is partially oxidized, mostly energy in fermention
products ；
3） lower energy；
4） generates many kinds of fermention products
2 fermentantion
2,fermentation sorts
1） alcohol fermentation
a,yeasts
1 G 2 pyruvate ? 2 aldehyde + CO2
? 2 ethanol + 2 ATP
condiction,pH 3.5~4.5,without O2
Strain,Saccharomyces cerevisiae,few bacteria(Erwinia amylovora,
Sarcine vintriculi)
I,Add NaHSO4
NaHSO4 + aldehyde ? sulfonic hydroxy aldehyde
ii.weak basic（ pH ? 7.5）
2 aldehyde ? 1 acetate + 1 ethanol
glycerol fermentation,
dihydroxyacetone as hydrogen accepter,hydrolyzed to glycerol
（ EMP）
b,bacteria (Zymomonasmobili,Pseudomonas saccharophila )
homoalcohol fermentation
1 G 2 pyruvate
（ ED）
ethanol + 1ATP
heteroalcohol fermentation (Thermoanaerobacter
ethanolicu)
1 G 2 pyruvate
（ Pyruvate formate lyase ）
aldehyde ? ethanol
formic acids + acetyl-CoA
Without Pyruvatedecarboxylate
With aldehyde dehydrogenase
2） Lactic acid fermentation
Homolactate fermentation
For example,Lactobacillus delbruckii,Streptococcus faecalis
—— EMP pathway（ pyruvate lactate ）
Heterolactate fermentation （ PK pathway）
Leuconostoc mesenteroides （ PK）
generates energy,1ATP
Bifidobacterium bifidum （ PK,HK）
generates energy,2G ? 5 ATP,1G ? 2.5ATP
3) mixed acid,butanediol fermentation
a.mixed acid fermentation,
——E.coli,Salmonella,Shiella
1 G pyruvate
lactate lactate dehydrogenase
acetyl-CoA +formyl Pyruvate formate lyase
oxaloacetate Propionic acid Methylmalonyl CoA carboxyltransferase
phosphotransacetylase aldehyde dehydrogenase
acetokinase Alcohol dehydrogenase
acetate ethanol
CO2 + H2
b.butanediol fermentation
—— Enterobacter,Serratia
pyruvate acetolactate 3-hydroxy butanone
diacetyl Red substance
(acetolactate dehydrogenase)
（ OH-,O2）
neutral
butanediol
Two important reaction,
1,V,P,test 2,methylene red (M.R) test
Enterobacter aerogenes,methylene red （ -）
E.coli,V.P,（ -）,methylene red （ +）
V.P,test,
4) acetone-butanol fermentation
（ mixed,acetone:butanol, ethanol = 3,6,1）
——Clostridium acetobutyricum
2 pyruvate 2 acetyl-CoA
acetoacetyl-CoA
acetone +CO2
（ acetate CoA transferase）
butanol
acetyl-CoA acetyltransferase
（ acetoacetate decarboxylase）
5） stickland reaction
Main point,amino acid oxidation couples with other
amino acids reduction,generates 1ATP
hydrogen donors (oxidation ) amino acid,
Ala,Leu,Ile,Val,His,Ser,Phe,Tyr,Try
hydrogen acceptors (reduction) amino acid,
Gly,Pro,Arg,Met,Leo,and so on,
The Stickland reaction is used to oxidize
several amino acids,alanine,leucine,
isoleucine,valine,phenylalanine,
tryptophan,and histidine,Bacteria also
ferment amino acids (e.g.,alanine,glycine,
glutamate,threonine,and arginine) by
other mechanisms,
Oxidized glycine pyruvate -NH3
NAD+ NADH
acetyl-CoA
NAD+ NADH
acetate + ATP
alanine acetate alanine -NH
3
Reduced
one amino acid is oxidized and a second amino
acid acts as the electron acceptor,
3 Respiration
aerobic respiration
anaerobic respiration
1,Aerobic Respiration,
The final electron acceptor in the electron transport chain is
molecular oxygen (O2),
Respiration
Give the substrate and
products of the
tricarboxylic acid cycle,
To provide carbon
skeletons for use in
biosynthesis
What chemical
intermediate links
glycolysis to the TCA
cycle?
The complete cycle
appears to be
functional in many
aerobic bacteria,free-
living protozoa,and
most algae and fungi,
（ 1） Tricarboxylic Acid Cycle (Krebs Cycle)
（ 2） The Electron Transport Chain
Some important electron transport chain carriers of
the respiration chain in microbes
Nicotianamide adenine dinucleotide (NAD) and nicotianamide
adenine dinucleotide phosophate (NADP)
Flavin adenine dinucleotide (FAD) and flavin mononucleotide
(FMN)
Iron-sulphur protein
Ubiquinone (Coenzyme Q)
Cytochrome system
The Mitochondrial
Electron Transport Chain,
Many of the more
important carriers are
arranged at
approximately the correct
reduction potential and
sequence,In the
eucaryotic mitochondrial
are organized into four
complexes that are linked
by coenzyme Q (I and
cytochrome c (Cyt c),
Electrons flow from
NADH and succinl down
the reduction potential
gradient to oxygen,
The electron transport chain in Prokaryote
Main outline,
electron accepter multiplicity,O2,NO3-,NO2-,NO-,SO42-,S2-,CO32- et al；
Electron donors,H2,S,Fe2+,NH4+,NO2-,G,other orgnisim et al；
various cytochrome,
a,a1,a2,a4,b,b1,c,c1,c4,c5,d,o；
Terminal oxidase,
cyt a1,a2,a3,d,o,catalase,peroxid enzyme； Respiration Chain component
variable,being branched respiration chain,
Bacterial chains also may be shorter and have lower P／ O ratios than
mitochondrial transport chains,from the several position of electron transport
chain into and off by Terminal oxidase in several position,
E.coli （ absent O2） CoQ ? cyt.b556 ? cyt.o
cyt.b558 ? cyt.d
The cytochromes 0 branch has moderately high affinity for oxygen,is a proton
pump,and operates at higher oxygen concentrations;The cytochromes d branch has
very high affinity for oxygen and functions at low oxygen levels。
electron transport multiplicity,
（ 3） Oxidative phosphorylqtion
Chemiosmotic hypothesis
Chemiosmotic hypothesis-first formulated in 1961 by the British
biochemist Peter,Mitchell,
According to the Chemiosmotic hypothesis,the electron transport
chain is organized so that protons move outward from the
mitochondrial matrix and electrons are transported inward,Protons
movement may result either from carrier loops,as shown in figure
9.14,or from the action of special proton pumps that derive their
energy from electron transport,The result is proton motive
force(PMF),composed of a gradient of protons and a membrane
porential due to the unequal distribution of charges.When protons
return to the mitochondrial matrix driven by the proton motive
force,ATP is synthesized in a reversal of the ATP hydrolysis reaction,
The final electron acceptor in the
electron transport chain is not O2,Yields less energy than
aerobic respiration because only part of the Krebs cycles
operations under anaerobic conditions,
Nitrate Respiration（ Denitrification）
Nitrate reduction
outline,
a,have completely Respiration system；
b,in the absence of O2 only,nitrate reductase A and nitrous acid
reductase needing for Denitrification are induced,
c,facultative anaerobic
bacteria,Bacillus licheniformis,Paracoccus denitrificans,
Pseudomonas aeruginosa and so on,
2,Anaerobic Respiration
Nitrate Respiration
Homotype,
NO3- ? NH3 - N ? R - NH2
Hetertype,
in the absence of O2, use NO3-as the final hydrongen accepter
NO3- ? NO2 ? NO ? ? N2O ? N2
denitrification,
1) make N（ NO3-） in soil reduced into N2,and disappear,
reduce edaphic fertility；
2) Denitrification has the importance action in nitrogen cycle,
?
NiR N2OR NOR NaR
? ? ?
Facultative anaerobe (viz denitrify bacteriua)
Sulfate Respiration(sulfate reduction）
—— in the absent of O2,SO42-,SO32-,S2O32- as the final
electron accepter
outline,
a,obligate anaerobic bacteria ；
b,mostly ancient bacteria
c,mostil obligate chemoheterotroph,few mixed；
d,end product,H2S；
SO42- ? SO32- ? SO2 ? S ? H2S
e,use organic nutrients （ organic acid,fatty acid,醇类） as
hydrogen donors or electron donors ；
f,environment,contain SO42-,anaerobic environment（ soil,
seawater）
For example,Desulfovibrio desulfuricans,D, Gigas,Desulfotomaculum
nigrificans and so on,
Sulfur Respiration （ Sulfur reduction）
—— use element Sulfur as the final electron accepter only,
electron donors,aceticm acid,small peptide,glucose,
carbohydrate polymers;
For example,Desulfuromonas acetoxidans
Carbonate Respiration（ Carbonate reduction ）
—— use CO2,HCO3- as the final electron accepter
methane-producing bacteria,
—— use H2 as electron donors （ energy resources),CO2 as
accepter,produce CH4;
Producing acetic acid bacteria
— H2 / CO2 carry out Anaerobic Respiration, product acetic
acid
other anaerobic respiration
—— use Fe3+,Mn2+,many organic oxide as the final
electron accepter
fumaric acid ? succinate + 1 ATP
For example,Escherichia,Proteus,Salmonella,Klebsiella in
some facultative anaerobic bacteria,Bacteroides,
Propionibacterium,Vibrio succinogenes in some anaerobic
bacteria,
Use Desulfotomaculum
auripigmentum reduces AsO43-
into As2S3
Section 2 special metabolism in microbes
1 Bacterial Photosynthesis
1,Cyclic photophosphorylation
2,Noncyclic photophosphorylation
3,Photosynthesis of purple membrane in halophilic
bacteria
purple sulfur bacteria,
Chromatium
purple nonsulfur bacteria,
Rhodospirillum,
Rhodopseudomonas
green sulfur bacteria,
Chlorobium
green nonsulfur bacteria,
Chloroflexus
The photosynthetic
electron transport system
in the purple nonsulfur
bacterium,Rhodobacter
sphaeroides,
This scheme is incomplete
and tentative,
Ubiquinone (Q) is very
similar to coenzyme Q,
BPh stands
bacteriopheophytin,NAD+
and the electron source
succinate are in color,
Purple Nonsulfur Bacterial Photosynthesis,
Cyclic photophosphorylation
Light energy is used to make
ATP by cyclic
photophosphorylation
move electrons from sulfur
donors (green and blue) to
NAD+ (red),
The electron transport chain
has a quinone called
menaquinone (MK),
Green Sulfur Bacterial Photosynthesis,
The photosynthetic electron transport system in the
green sulfur bacterium,Chlorobium limicola,
2） noncyelic photophosphorylation
Electrons also can travel in a noncyclic pathway involving both
photosystems,P700 is excited and donates electrons to ferredoxin as
before,In the noncyclic route,however,reduced ferredoxin reduces
NADP+ to NADPH,
Because the electrons contributed to NADP+ cannot be used to
reduce oxidized P700,photosystem II participation is required,It
donates electrons to oxidized P700 and generates ATP in the process,
The photosystem II antenna absorbs light energy and excites P680,
which then reduces pheophytin a,Pheophytin a is chlorophyll a in
which two hydrogen atoms have replaced the central magnesium,
Electrons subsequently travel to Q (probably a plastoquinone) and
down the electron transport chain to P700,Oxidized P680 then
obtains an electron from the oxidation of water to O2,
noncyelic photophosphorylation
electrons flow from water all the way to
NADP with the aid of energy from two
photosystems,
ATP is synthesized by noncyelic
photophosphorylation,
one ATP and one NADPH are formed when
two electrons travel through noncyclic
pathway,
Outline,
3) Photosynthesis of purple membrane in
halophilic bacteria
Halobacterium uses bacteriorhodopsin,not chlorophyll,to
generate electrons for a chemiosmotic proton pump,
2 Chemolithotroph
Biological Oxidation,Energy Release and CO2
Fixation in Chemoautotroph
aerobic
Oxidation of inorganic electron donors
generates ATP by Oxidative Phosphorylation
electron donors,H,reducing nitride,reducing sulphide and Fe2＋,
Use CO2 Fixation of Calvin cycle as carbon resources
CO2 reduced to [CH2O] —— consume much energy and
reducing power
1,Energy metabolism of nitribacteria
Oxidation
Nitrobacter,NH3 NO2-
Oxidation
Nitrosomonas,NO2- NO3-
When two genera such Nitrobacter and
Nitrosomonas together in a niche,ammonia is grow
converted to nitrate,a process called nitrification
2,Hydrogen oxidizing bacteria
Main strains,
Alcaligenes,Flavobacterium Aquaspirillum
Mycobacterium Nocardia and so on,
generates energy,2H2 + O2 — ? 2 H2O
synthesize reaction,
2H2 + CO2 — ? [ CH2O ] + H2O。
3.Sulfur Bacteria
Energy Metabolism of Sulfur Bacteria
Thiobacillus
Energy source,Thiosulfate freely soluble in water
and in the neutral condition,
The respiratory chain of Thiobacilli,NADH2
dehydrogenase,Fumaric reductase,flacoprotein
（ FP）,ubliquinone（ CoQ）,cyt b,
Cytochrome oxidase aa3
energy-yielding process,
First sept,H2S,S0,S2O32－,oxidatived to SO32－
Second sept,SO32－ oxidatived to SO42－ and generates energy
(1) iron bacteria (iron oxidizing bacteria)
oxidative Fe2＋ into Fe3 ＋ and generates
energy,
For example,
Ferrobacillus,
Gallionella,Leptothrix,Crenothrix and
Sphaerotilus;
Thiobacillus frrooxidans,oxidative,S0
and reducing sulphide,and Fe2＋
oxidatived to Fe3＋, so both Sulfur
Bacteria and iron bacteria,
mostly obligate Chemoautotrophic,few
facultative Chemoautotrophic bacteria,
acidophilic bacteria,
4 iron bacteria and bacterial leaching
Iron oxidizing bacteria,energy-yielding process by
Oxidative Phosphorylation
(2) bacterial leaching
Principle,
a,
2S + 3O2 + 2H2O —? 2H2SO4
4FeSO4 + 2H2SO4 + O2 —? 2Fe2（ SO4） 3
+ 2 H2O
b,
CuS + 2 Fe2（ SO4） 3 + 2H2O + O2 —?
CuSO4 + 4FeSO4 +2H2SO4
c,
CuSO4 + Fe —? FeSO4 + Cu
3 Biologic Fixation of Nitrogen
1,Kinds of nitrogen fixing microorganism
Free-living nitrogen fixing bacteria
Symbiosis nitrogen fixing bacteria
Association nitrogen fixing bacteria
Supplying ATP
Reducing Force [H]
and its Carrier
Nitrogenase
(molebdoferredoxin,
azoferredoxin)
N2
Mg2+
Strict Anoxy
microenvironment
2,The necessary condition of Nitrogen fixation
1966,
M,J,Dilworth
and R,Scholhorn
Nitrogenase,
N2→NH 3
① N2O→N 2+H2O
② N3-→N 2+NH3
③ C2H2→C 2H4
④ HCN→CH 4+NH3+[CH3NH2]
⑤ CH3NC→CH 4+CH3NH2
+[C2H4,C2H6]
3.Determination of Nitrogenase Activity
4.The Biochemistry Pathway of Nitrogen Fixation
N2+6e+6H++12ATP→ 2NH3+12ADP+12Pi
5.Hydrogen Reaction of Nitrogenase
N2→NH 3,2H+→H 2
N2+8H++8e+16Mg-ATP→ 2NH3+H2+16Mg-ADP+16Pi
A,The Protection Mechanism in Aerobic Free-
living Nitrogen Fixting Bacteria
a,Breathing Protection
b,Conformation Protection
B,The Protection Mechanism in Cyanobacteria
a,Special Reducing Heterocysts Differentiated
b,The Protection of Nitrogenase in Cyanobacteria
that don’t form heterocysts
C,The Antioxygen Protection of Nitrogenase in
Root Nodule Bacteria
a,Symbiosis Rhizobia in Leguminous Plant
b,Symbiosis Rhizobia in nonleguminous Plant
6,The antioxygen mechamism of Nitrogenase
in Aerobic Nitrogen Fixing Bacteria
4 The Synthesis of Peptidoglycan
A The Synthesis in Bacterial Cytoplasm
a G —? G-UDP,M--UDP
G —?—? 6-P-fructose—? 6-P- glucosamine—
? —? N-acetoglucosamine -1- P
—? N-acetylglucosamine-UDP —?
N-acetylmuramic acid -UDP
b M —?,Park” nucleotide （ UDP-M-pentapeptide）
UDP as carrier sugar
D-Val-D-Val are repressed by cycloserine；
N-acetylmuramic acid,Park”nucleotide
“Park” nucleotide
hydrophilicity
—?
peptidoglycan unit synthesis
Carrier,bactoprenol（ carrier lipoid）
——C55-isoprenol（ contain 11 isoprenoid units）
combinate to G during transmembrane, link into
interpeptide bridge;
carrier lipoid,concerned with the synthesize of
polysaccharide and lipoidglycan in outer cell
( cellulose,polymannan,and so on）
vancomycin,bacitracin inhibite some reactins
B,The Synthesis in Bacterial Cytomembrane
“Park”nucleotide peptidoglycan unit
in Bacterial
Cytoplasm
in Bacterial
Cytomembrane
in outside of Bacterial
Cytomembrane
C.The Synthesis in outside of Bacterial Cytomembrane
a,glycan chain extension（ transverse link）,
peptidoglycan monomer+primer — ? glycan chain transverse
extense one disaccharide unit
b,Adjacent glycan chain connect（ vertical link）,
2 D-Val —? M-tetrapeptide + D-Val
—? cross-links occur between the distalamino group of the
diamino acid in the positon 3 of one stem peptide and D-alanine in
the positon 4 of another stem peptide,
Transpeptidation,
repressed by penicillins,
penicillins, D-Val-D-Val analog,competitive transpeptidase,
Transglycosyl（ form ?-1,4 glucosidic bond）
?
Transglycosylation and Transpeptidation
Section 3 microbial secondary metabolism
and its product
There are many kinds of secondary metabolite
which primary metabolic products serve as
substrate,some of these products have a
considerable importance in fermentation industry,
Metabolic adjustment of secondary metabolite is
similar to primary metabolism,influenced by
many factors,
Microbial secondary metabolism and its product
Regulation of secondary metabolism
1 primary metabolism
2 nitric compound
3 induction and feedback inhibition
Section 4 Regulation of metabolism and
ferment product practise,
Metabolic regulation kinds are various,
microorganism produce metabolic product to
offer service for fermentation industry and to
benefit for mankind with their relevant
knowledge of adjusting control,
Using microbial metabolic product
Metabolic product type,
1 primary metabolic products,
amino acid,enzyme or coenzyme；
2 submetabolic products,
antibiotic,hormone,alkaloid,toxin,vitamin,and so on,
Fermentation type,
1 Natural fermentation,ethanol,lacate and so on,
2 Metabolic control fermentation,
terminal products,lysine,guanylic acid,adenylic acid and so on ；
metabolic intermediates,citrate,α-ketoglutaric acid,succinate,inosinic
acid,xanthine nucleotide and so on；
Control of ferment condiction
1） cultrue condition,temperature,pH and so on;
2） nutrition component,glucose concentration,C/N,
growth factor,and so on;
3） dissolved oxygen,aeration numbr,agitation and so
on.。
Control of Metabolic regulation
（ 1） auxotrophic regulatory mutant
Lysine fermentation——(homoserine auxotrophic mutant)
Microbial metabolism and Metabolic engneering
Metabolic Engineering introduce xylose Metabolic pathway
Xylose
xylitol
Xylulose
Xlulokinase
Xylulose-5-P
Glucose
Pyruvate
Ethanol
Xylose isomerase
Xylose reductase
xylitol dehydrogenase
Pentose
phosphoketolas
Pathway
Pichia stipitis
bacteria
Glycolysis
Entner-
Doudoroff
Pathway
Using active metabolism in microbes
1 biotransformation,
2 microbial straw xylan-degrading,
3 microbiohydrometallurgy and oil extraction,
4 biodegradation
References,
Prescott LM,Harley JP,and Klein DA,Microbiology (5th ed.),Higher education press
and McGraw-Hill Companies,Inc.2002
Michael TM,John MM,Jack P,Brock biology of micoorganisms,International edition,
Pearson Education,Inc.2003
Talaro K,P,Foundations in microbiology (Fifth Edition),Higher education press and
McGraw-Hill Companies,Inc.2005
?Energy Metabolism
? Special Metabolism in Microbes
? The Relationship between Catabolism
and Anabolism
? Regulation of Metabolism and
Ferment Industry
An Overview metabolism
metabolism,
the sum total of all chemical reactions occurring in the cell
metabolism
catabolism
anabolism
Complex molecules
catabolism
anabolism
Simple molecules ATP [H]
Section 1 Energy Metabolism in Microbes
Primary
Energy
Organic Compounds
Sunlight
Inorganic Compounds
in Reduced State
A
T
P
ATP
Chemoheterotroph
Photoautotroph
Photoheterotroph
Chemoautotroph
summarize
The breakdown of glucose to pyruvate
fermentation
respiration （ aerobic or anaerobic respiration ）
Chemoheterotroph biological oxidation and energy
Release
Process—— Dehydrogenation,Giving Hydrogen and Accepting
Hydrogen (Electron)
Function—— Releasing Energy (ATP),Engendering Reducing
Power [H] and Producing Intermediate Metabolites
biological
oxidation
Glocose—— representative substrate of biological oxidation
Embden-Meyerhof-Parnas Pathway (Glycolysis)
Hexose Monophosphate Pathway
Entner-Doudoroff Pathway (KDPG Pathway)
PK (phosphoketolase) pathway
1 The breakdown of glucose to pyruvate
1） Embden-Meyerhof-Parnas Pathway (EMP)
(Glycolysis,Hexose Diphosphate Pathway)
glucose pyruvate
with O2, connecte EMP pathway with TCA pathway；
without O2,reduce some metabolism product,only energy-
yielding process,
generates ATP by substrate-level phosphorylation,
（ 1） glyceraldehyde 1,3-phosphate ? 3-phoshoglyceric acid +
ATP；
（ 2） PEP ? pyruvate + ATP
Ten steps
C6H12O6＋ 2NAD+＋ 2ADP＋ 2Pi→
2CH3COCOOH＋ 2NADH＋ 2H+＋ 2ATP＋ 2H2O
Uses pentoses
and NADPH
Operates with
glycolysis
2)Hexose Monophosphate Pathway (HMP)
(Pentose Phosphate Pathway,
Phosphogluconate Pathway,
Warburg-Dickens Pathway)
fructose 6-phosphates,
be converted to glucose 6-phosphates, be returned to Pentose
Phosphate Pathway
glyceraldehyde 3-phosphate,
a,through EMP pthway,be converted to pyruvate,into TCA
pthway
b,converted to Hexose Phosphate,be returned to Pentose
Phosphate Pathway
The overall reaction,
6 glucose 6-phosphates +12NADP++3H2O → 5 glucose 6-
phosphates + 6CO2+12NADPH+12H++Pi
3) Entner-Doudoroff Pathway (KDPG Pathway)
1952,Entner-Doudoroff, Pseudomonas saccharophila
process,（ 4 septs）
1 Glucose glucose 6-phosphates 6-phosphogluconate
KDPG
6-phosphogluconate dehydratase
glyceraldehyde 3-phosphate + pyruvate
2-oxo-3-deoxy-6-phosphogluconate aldolase
Produces NADPH and 1 ATP
Does not involve glycolysis
Pseudomonas,Rhizobium,Agrobacterium
4) phosphoketolase pathway (PK)
a.Pentose phosphoketolas Pathway
G xylulose 5-phosphate
acetyl phosphate + glyceraldehyde 3-phosphate
phosphoketolase
ethanol pyruvate
Lactic acid
1 G ??? Lactic acid + ethanol + 1 ATP + NADPH + H+
G fructose 6-phosphates
b.Hexose phosphoketolas Pathway (HK)
（ Bifidobacterium bifidum ）
Erythrose - 4-P + acetyl-phosphates
phosphoketolase
glyceraldehyde 3-phosphate + acetyl-phosphates
xylulose -5-P ribulose-5-P
Acetic acid phosphoketolase
fructose 6-phosphates
Lactic acid Acetic acid
1 G ??? Lactic acid + 1.5 Acetic acid + 2.5 ATP
acetokinase
1,definitions
broader, use microorganism to produce useful metabolic product
narrower,under anaerobic conditions,be defined as an energy-
yielding process using itself metabolic intermediates as the final
hydrogen (electron) accepter
organic molecules serve as both electron donors and acceptors,
trait,
1） generates ATP by substrate-level phosphorylation；
2） the glucose is partially oxidized, mostly energy in fermention
products ；
3） lower energy；
4） generates many kinds of fermention products
2 fermentantion
2,fermentation sorts
1） alcohol fermentation
a,yeasts
1 G 2 pyruvate ? 2 aldehyde + CO2
? 2 ethanol + 2 ATP
condiction,pH 3.5~4.5,without O2
Strain,Saccharomyces cerevisiae,few bacteria(Erwinia amylovora,
Sarcine vintriculi)
I,Add NaHSO4
NaHSO4 + aldehyde ? sulfonic hydroxy aldehyde
ii.weak basic（ pH ? 7.5）
2 aldehyde ? 1 acetate + 1 ethanol
glycerol fermentation,
dihydroxyacetone as hydrogen accepter,hydrolyzed to glycerol
（ EMP）
b,bacteria (Zymomonasmobili,Pseudomonas saccharophila )
homoalcohol fermentation
1 G 2 pyruvate
（ ED）
ethanol + 1ATP
heteroalcohol fermentation (Thermoanaerobacter
ethanolicu)
1 G 2 pyruvate
（ Pyruvate formate lyase ）
aldehyde ? ethanol
formic acids + acetyl-CoA
Without Pyruvatedecarboxylate
With aldehyde dehydrogenase
2） Lactic acid fermentation
Homolactate fermentation
For example,Lactobacillus delbruckii,Streptococcus faecalis
—— EMP pathway（ pyruvate lactate ）
Heterolactate fermentation （ PK pathway）
Leuconostoc mesenteroides （ PK）
generates energy,1ATP
Bifidobacterium bifidum （ PK,HK）
generates energy,2G ? 5 ATP,1G ? 2.5ATP
3) mixed acid,butanediol fermentation
a.mixed acid fermentation,
——E.coli,Salmonella,Shiella
1 G pyruvate
lactate lactate dehydrogenase
acetyl-CoA +formyl Pyruvate formate lyase
oxaloacetate Propionic acid Methylmalonyl CoA carboxyltransferase
phosphotransacetylase aldehyde dehydrogenase
acetokinase Alcohol dehydrogenase
acetate ethanol
CO2 + H2
b.butanediol fermentation
—— Enterobacter,Serratia
pyruvate acetolactate 3-hydroxy butanone
diacetyl Red substance
(acetolactate dehydrogenase)
（ OH-,O2）
neutral
butanediol
Two important reaction,
1,V,P,test 2,methylene red (M.R) test
Enterobacter aerogenes,methylene red （ -）
E.coli,V.P,（ -）,methylene red （ +）
V.P,test,
4) acetone-butanol fermentation
（ mixed,acetone:butanol, ethanol = 3,6,1）
——Clostridium acetobutyricum
2 pyruvate 2 acetyl-CoA
acetoacetyl-CoA
acetone +CO2
（ acetate CoA transferase）
butanol
acetyl-CoA acetyltransferase
（ acetoacetate decarboxylase）
5） stickland reaction
Main point,amino acid oxidation couples with other
amino acids reduction,generates 1ATP
hydrogen donors (oxidation ) amino acid,
Ala,Leu,Ile,Val,His,Ser,Phe,Tyr,Try
hydrogen acceptors (reduction) amino acid,
Gly,Pro,Arg,Met,Leo,and so on,
The Stickland reaction is used to oxidize
several amino acids,alanine,leucine,
isoleucine,valine,phenylalanine,
tryptophan,and histidine,Bacteria also
ferment amino acids (e.g.,alanine,glycine,
glutamate,threonine,and arginine) by
other mechanisms,
Oxidized glycine pyruvate -NH3
NAD+ NADH
acetyl-CoA
NAD+ NADH
acetate + ATP
alanine acetate alanine -NH
3
Reduced
one amino acid is oxidized and a second amino
acid acts as the electron acceptor,
3 Respiration
aerobic respiration
anaerobic respiration
1,Aerobic Respiration,
The final electron acceptor in the electron transport chain is
molecular oxygen (O2),
Respiration
Give the substrate and
products of the
tricarboxylic acid cycle,
To provide carbon
skeletons for use in
biosynthesis
What chemical
intermediate links
glycolysis to the TCA
cycle?
The complete cycle
appears to be
functional in many
aerobic bacteria,free-
living protozoa,and
most algae and fungi,
（ 1） Tricarboxylic Acid Cycle (Krebs Cycle)
（ 2） The Electron Transport Chain
Some important electron transport chain carriers of
the respiration chain in microbes
Nicotianamide adenine dinucleotide (NAD) and nicotianamide
adenine dinucleotide phosophate (NADP)
Flavin adenine dinucleotide (FAD) and flavin mononucleotide
(FMN)
Iron-sulphur protein
Ubiquinone (Coenzyme Q)
Cytochrome system
The Mitochondrial
Electron Transport Chain,
Many of the more
important carriers are
arranged at
approximately the correct
reduction potential and
sequence,In the
eucaryotic mitochondrial
are organized into four
complexes that are linked
by coenzyme Q (I and
cytochrome c (Cyt c),
Electrons flow from
NADH and succinl down
the reduction potential
gradient to oxygen,
The electron transport chain in Prokaryote
Main outline,
electron accepter multiplicity,O2,NO3-,NO2-,NO-,SO42-,S2-,CO32- et al；
Electron donors,H2,S,Fe2+,NH4+,NO2-,G,other orgnisim et al；
various cytochrome,
a,a1,a2,a4,b,b1,c,c1,c4,c5,d,o；
Terminal oxidase,
cyt a1,a2,a3,d,o,catalase,peroxid enzyme； Respiration Chain component
variable,being branched respiration chain,
Bacterial chains also may be shorter and have lower P／ O ratios than
mitochondrial transport chains,from the several position of electron transport
chain into and off by Terminal oxidase in several position,
E.coli （ absent O2） CoQ ? cyt.b556 ? cyt.o
cyt.b558 ? cyt.d
The cytochromes 0 branch has moderately high affinity for oxygen,is a proton
pump,and operates at higher oxygen concentrations;The cytochromes d branch has
very high affinity for oxygen and functions at low oxygen levels。
electron transport multiplicity,
（ 3） Oxidative phosphorylqtion
Chemiosmotic hypothesis
Chemiosmotic hypothesis-first formulated in 1961 by the British
biochemist Peter,Mitchell,
According to the Chemiosmotic hypothesis,the electron transport
chain is organized so that protons move outward from the
mitochondrial matrix and electrons are transported inward,Protons
movement may result either from carrier loops,as shown in figure
9.14,or from the action of special proton pumps that derive their
energy from electron transport,The result is proton motive
force(PMF),composed of a gradient of protons and a membrane
porential due to the unequal distribution of charges.When protons
return to the mitochondrial matrix driven by the proton motive
force,ATP is synthesized in a reversal of the ATP hydrolysis reaction,
The final electron acceptor in the
electron transport chain is not O2,Yields less energy than
aerobic respiration because only part of the Krebs cycles
operations under anaerobic conditions,
Nitrate Respiration（ Denitrification）
Nitrate reduction
outline,
a,have completely Respiration system；
b,in the absence of O2 only,nitrate reductase A and nitrous acid
reductase needing for Denitrification are induced,
c,facultative anaerobic
bacteria,Bacillus licheniformis,Paracoccus denitrificans,
Pseudomonas aeruginosa and so on,
2,Anaerobic Respiration
Nitrate Respiration
Homotype,
NO3- ? NH3 - N ? R - NH2
Hetertype,
in the absence of O2, use NO3-as the final hydrongen accepter
NO3- ? NO2 ? NO ? ? N2O ? N2
denitrification,
1) make N（ NO3-） in soil reduced into N2,and disappear,
reduce edaphic fertility；
2) Denitrification has the importance action in nitrogen cycle,
?
NiR N2OR NOR NaR
? ? ?
Facultative anaerobe (viz denitrify bacteriua)
Sulfate Respiration(sulfate reduction）
—— in the absent of O2,SO42-,SO32-,S2O32- as the final
electron accepter
outline,
a,obligate anaerobic bacteria ；
b,mostly ancient bacteria
c,mostil obligate chemoheterotroph,few mixed；
d,end product,H2S；
SO42- ? SO32- ? SO2 ? S ? H2S
e,use organic nutrients （ organic acid,fatty acid,醇类） as
hydrogen donors or electron donors ；
f,environment,contain SO42-,anaerobic environment（ soil,
seawater）
For example,Desulfovibrio desulfuricans,D, Gigas,Desulfotomaculum
nigrificans and so on,
Sulfur Respiration （ Sulfur reduction）
—— use element Sulfur as the final electron accepter only,
electron donors,aceticm acid,small peptide,glucose,
carbohydrate polymers;
For example,Desulfuromonas acetoxidans
Carbonate Respiration（ Carbonate reduction ）
—— use CO2,HCO3- as the final electron accepter
methane-producing bacteria,
—— use H2 as electron donors （ energy resources),CO2 as
accepter,produce CH4;
Producing acetic acid bacteria
— H2 / CO2 carry out Anaerobic Respiration, product acetic
acid
other anaerobic respiration
—— use Fe3+,Mn2+,many organic oxide as the final
electron accepter
fumaric acid ? succinate + 1 ATP
For example,Escherichia,Proteus,Salmonella,Klebsiella in
some facultative anaerobic bacteria,Bacteroides,
Propionibacterium,Vibrio succinogenes in some anaerobic
bacteria,
Use Desulfotomaculum
auripigmentum reduces AsO43-
into As2S3
Section 2 special metabolism in microbes
1 Bacterial Photosynthesis
1,Cyclic photophosphorylation
2,Noncyclic photophosphorylation
3,Photosynthesis of purple membrane in halophilic
bacteria
purple sulfur bacteria,
Chromatium
purple nonsulfur bacteria,
Rhodospirillum,
Rhodopseudomonas
green sulfur bacteria,
Chlorobium
green nonsulfur bacteria,
Chloroflexus
The photosynthetic
electron transport system
in the purple nonsulfur
bacterium,Rhodobacter
sphaeroides,
This scheme is incomplete
and tentative,
Ubiquinone (Q) is very
similar to coenzyme Q,
BPh stands
bacteriopheophytin,NAD+
and the electron source
succinate are in color,
Purple Nonsulfur Bacterial Photosynthesis,
Cyclic photophosphorylation
Light energy is used to make
ATP by cyclic
photophosphorylation
move electrons from sulfur
donors (green and blue) to
NAD+ (red),
The electron transport chain
has a quinone called
menaquinone (MK),
Green Sulfur Bacterial Photosynthesis,
The photosynthetic electron transport system in the
green sulfur bacterium,Chlorobium limicola,
2） noncyelic photophosphorylation
Electrons also can travel in a noncyclic pathway involving both
photosystems,P700 is excited and donates electrons to ferredoxin as
before,In the noncyclic route,however,reduced ferredoxin reduces
NADP+ to NADPH,
Because the electrons contributed to NADP+ cannot be used to
reduce oxidized P700,photosystem II participation is required,It
donates electrons to oxidized P700 and generates ATP in the process,
The photosystem II antenna absorbs light energy and excites P680,
which then reduces pheophytin a,Pheophytin a is chlorophyll a in
which two hydrogen atoms have replaced the central magnesium,
Electrons subsequently travel to Q (probably a plastoquinone) and
down the electron transport chain to P700,Oxidized P680 then
obtains an electron from the oxidation of water to O2,
noncyelic photophosphorylation
electrons flow from water all the way to
NADP with the aid of energy from two
photosystems,
ATP is synthesized by noncyelic
photophosphorylation,
one ATP and one NADPH are formed when
two electrons travel through noncyclic
pathway,
Outline,
3) Photosynthesis of purple membrane in
halophilic bacteria
Halobacterium uses bacteriorhodopsin,not chlorophyll,to
generate electrons for a chemiosmotic proton pump,
2 Chemolithotroph
Biological Oxidation,Energy Release and CO2
Fixation in Chemoautotroph
aerobic
Oxidation of inorganic electron donors
generates ATP by Oxidative Phosphorylation
electron donors,H,reducing nitride,reducing sulphide and Fe2＋,
Use CO2 Fixation of Calvin cycle as carbon resources
CO2 reduced to [CH2O] —— consume much energy and
reducing power
1,Energy metabolism of nitribacteria
Oxidation
Nitrobacter,NH3 NO2-
Oxidation
Nitrosomonas,NO2- NO3-
When two genera such Nitrobacter and
Nitrosomonas together in a niche,ammonia is grow
converted to nitrate,a process called nitrification
2,Hydrogen oxidizing bacteria
Main strains,
Alcaligenes,Flavobacterium Aquaspirillum
Mycobacterium Nocardia and so on,
generates energy,2H2 + O2 — ? 2 H2O
synthesize reaction,
2H2 + CO2 — ? [ CH2O ] + H2O。
3.Sulfur Bacteria
Energy Metabolism of Sulfur Bacteria
Thiobacillus
Energy source,Thiosulfate freely soluble in water
and in the neutral condition,
The respiratory chain of Thiobacilli,NADH2
dehydrogenase,Fumaric reductase,flacoprotein
（ FP）,ubliquinone（ CoQ）,cyt b,
Cytochrome oxidase aa3
energy-yielding process,
First sept,H2S,S0,S2O32－,oxidatived to SO32－
Second sept,SO32－ oxidatived to SO42－ and generates energy
(1) iron bacteria (iron oxidizing bacteria)
oxidative Fe2＋ into Fe3 ＋ and generates
energy,
For example,
Ferrobacillus,
Gallionella,Leptothrix,Crenothrix and
Sphaerotilus;
Thiobacillus frrooxidans,oxidative,S0
and reducing sulphide,and Fe2＋
oxidatived to Fe3＋, so both Sulfur
Bacteria and iron bacteria,
mostly obligate Chemoautotrophic,few
facultative Chemoautotrophic bacteria,
acidophilic bacteria,
4 iron bacteria and bacterial leaching
Iron oxidizing bacteria,energy-yielding process by
Oxidative Phosphorylation
(2) bacterial leaching
Principle,
a,
2S + 3O2 + 2H2O —? 2H2SO4
4FeSO4 + 2H2SO4 + O2 —? 2Fe2（ SO4） 3
+ 2 H2O
b,
CuS + 2 Fe2（ SO4） 3 + 2H2O + O2 —?
CuSO4 + 4FeSO4 +2H2SO4
c,
CuSO4 + Fe —? FeSO4 + Cu
3 Biologic Fixation of Nitrogen
1,Kinds of nitrogen fixing microorganism
Free-living nitrogen fixing bacteria
Symbiosis nitrogen fixing bacteria
Association nitrogen fixing bacteria
Supplying ATP
Reducing Force [H]
and its Carrier
Nitrogenase
(molebdoferredoxin,
azoferredoxin)
N2
Mg2+
Strict Anoxy
microenvironment
2,The necessary condition of Nitrogen fixation
1966,
M,J,Dilworth
and R,Scholhorn
Nitrogenase,
N2→NH 3
① N2O→N 2+H2O
② N3-→N 2+NH3
③ C2H2→C 2H4
④ HCN→CH 4+NH3+[CH3NH2]
⑤ CH3NC→CH 4+CH3NH2
+[C2H4,C2H6]
3.Determination of Nitrogenase Activity
4.The Biochemistry Pathway of Nitrogen Fixation
N2+6e+6H++12ATP→ 2NH3+12ADP+12Pi
5.Hydrogen Reaction of Nitrogenase
N2→NH 3,2H+→H 2
N2+8H++8e+16Mg-ATP→ 2NH3+H2+16Mg-ADP+16Pi
A,The Protection Mechanism in Aerobic Free-
living Nitrogen Fixting Bacteria
a,Breathing Protection
b,Conformation Protection
B,The Protection Mechanism in Cyanobacteria
a,Special Reducing Heterocysts Differentiated
b,The Protection of Nitrogenase in Cyanobacteria
that don’t form heterocysts
C,The Antioxygen Protection of Nitrogenase in
Root Nodule Bacteria
a,Symbiosis Rhizobia in Leguminous Plant
b,Symbiosis Rhizobia in nonleguminous Plant
6,The antioxygen mechamism of Nitrogenase
in Aerobic Nitrogen Fixing Bacteria
4 The Synthesis of Peptidoglycan
A The Synthesis in Bacterial Cytoplasm
a G —? G-UDP,M--UDP
G —?—? 6-P-fructose—? 6-P- glucosamine—
? —? N-acetoglucosamine -1- P
—? N-acetylglucosamine-UDP —?
N-acetylmuramic acid -UDP
b M —?,Park” nucleotide （ UDP-M-pentapeptide）
UDP as carrier sugar
D-Val-D-Val are repressed by cycloserine；
N-acetylmuramic acid,Park”nucleotide
“Park” nucleotide
hydrophilicity
—?
peptidoglycan unit synthesis
Carrier,bactoprenol（ carrier lipoid）
——C55-isoprenol（ contain 11 isoprenoid units）
combinate to G during transmembrane, link into
interpeptide bridge;
carrier lipoid,concerned with the synthesize of
polysaccharide and lipoidglycan in outer cell
( cellulose,polymannan,and so on）
vancomycin,bacitracin inhibite some reactins
B,The Synthesis in Bacterial Cytomembrane
“Park”nucleotide peptidoglycan unit
in Bacterial
Cytoplasm
in Bacterial
Cytomembrane
in outside of Bacterial
Cytomembrane
C.The Synthesis in outside of Bacterial Cytomembrane
a,glycan chain extension（ transverse link）,
peptidoglycan monomer+primer — ? glycan chain transverse
extense one disaccharide unit
b,Adjacent glycan chain connect（ vertical link）,
2 D-Val —? M-tetrapeptide + D-Val
—? cross-links occur between the distalamino group of the
diamino acid in the positon 3 of one stem peptide and D-alanine in
the positon 4 of another stem peptide,
Transpeptidation,
repressed by penicillins,
penicillins, D-Val-D-Val analog,competitive transpeptidase,
Transglycosyl（ form ?-1,4 glucosidic bond）
?
Transglycosylation and Transpeptidation
Section 3 microbial secondary metabolism
and its product
There are many kinds of secondary metabolite
which primary metabolic products serve as
substrate,some of these products have a
considerable importance in fermentation industry,
Metabolic adjustment of secondary metabolite is
similar to primary metabolism,influenced by
many factors,
Microbial secondary metabolism and its product
Regulation of secondary metabolism
1 primary metabolism
2 nitric compound
3 induction and feedback inhibition
Section 4 Regulation of metabolism and
ferment product practise,
Metabolic regulation kinds are various,
microorganism produce metabolic product to
offer service for fermentation industry and to
benefit for mankind with their relevant
knowledge of adjusting control,
Using microbial metabolic product
Metabolic product type,
1 primary metabolic products,
amino acid,enzyme or coenzyme；
2 submetabolic products,
antibiotic,hormone,alkaloid,toxin,vitamin,and so on,
Fermentation type,
1 Natural fermentation,ethanol,lacate and so on,
2 Metabolic control fermentation,
terminal products,lysine,guanylic acid,adenylic acid and so on ；
metabolic intermediates,citrate,α-ketoglutaric acid,succinate,inosinic
acid,xanthine nucleotide and so on；
Control of ferment condiction
1） cultrue condition,temperature,pH and so on;
2） nutrition component,glucose concentration,C/N,
growth factor,and so on;
3） dissolved oxygen,aeration numbr,agitation and so
on.。
Control of Metabolic regulation
（ 1） auxotrophic regulatory mutant
Lysine fermentation——(homoserine auxotrophic mutant)
Microbial metabolism and Metabolic engneering
Metabolic Engineering introduce xylose Metabolic pathway
Xylose
xylitol
Xylulose
Xlulokinase
Xylulose-5-P
Glucose
Pyruvate
Ethanol
Xylose isomerase
Xylose reductase
xylitol dehydrogenase
Pentose
phosphoketolas
Pathway
Pichia stipitis
bacteria
Glycolysis
Entner-
Doudoroff
Pathway
Using active metabolism in microbes
1 biotransformation,
2 microbial straw xylan-degrading,
3 microbiohydrometallurgy and oil extraction,
4 biodegradation
References,
Prescott LM,Harley JP,and Klein DA,Microbiology (5th ed.),Higher education press
and McGraw-Hill Companies,Inc.2002
Michael TM,John MM,Jack P,Brock biology of micoorganisms,International edition,
Pearson Education,Inc.2003
Talaro K,P,Foundations in microbiology (Fifth Edition),Higher education press and
McGraw-Hill Companies,Inc.2005
