Chapter five
Microbial metabolism
section A Heterotrophic pathways
section B Electron transport and
oxidative phosphorylation
section C Autotrophic metabolism
Section D Biosynthetic pathways
Metabolism is divided into those pathways
that are degradative (catabolic) and those that
are involved in synthesis,Catabolic pathways
often produce energy,Microbes that utilize
organic molecules as a source of energy are
called heterotrophs,Phototrophs obtain energy
from light,and lithotrophs(无机营养菌 ) obtain
energy from inorganic compounds.
Key notes (1)
Nutritional types
Metabolism in all cells is divided into catabolic (those
pathways involved in breakdown of organic molecules for
energy and the production of small compounds that may be
used for synthesis) and anabolic (pathways involved in
synthesis) processes.
In all organisms these pathways are balanced as the
energy required for anabolic processes is produced by
catabolic pathways,
In mammalian cells,energy production has been
maximized by the use of oxygen and thus the cell is usually
well supplied with energy; however,in microbes this is not
always the case,
catabolic and anabolic metabolism
Microbes can be divided into metabolic classes which
relate to the sources of energy they use,The three
groups are:
1,heterotrophs which utilize organic molecules as a
source of energy (these are also called chemo-
organotrophs化能有机营养型 );
2,phototrophs which obtain energy from light
3,lithotrophs which obtain energy from inorganic
compounds,
Carbon(碳素 ) for cell synthesis is obtained from organic
molecules; however,some microbes,including the
phototrophs,fix CO2.
Microbial metabolic types
Catabolism
Metabolism
anabolism
①complex molecule simple molecules +ATP+[H]*
（ Organic material ） ②
*[H] stands for reducing power (还原力 )
① catabolism enzyme complex（分解代谢酶系）
② anabolism enzyme complex （合成代谢酶系）
organic material
Primary energy sources (最初能源 ) ray irradiation(light)
Chemoheterotrophs reduced inorganic material
Phototrophs
chemoautotrophs
universal energy source (通用能源 )—— ATP
Energy metabolism
Section A
Heterotrophic pathways
Biological oxidation is referred to as all the
energy-producing oxidative reactions in the living
organism.
Definition:A series of energy-producing oxidative reactions
occurs in the living cells are called biological oxidation.
The process of biological oxidation (生物氧化的过程 )
1.Remove of hydrogen (脱氢 )
2.Transfer of hydrogen (递氢 )
3.Receive of hydrogen (受氢 )
Biological oxidation
(生物氧化）
Function of biological oxidation(生物氧化的功能 )
1,Produce energy (产能 )
2,Produce reducing power [H] (产还原力 )
3,Small intermediate metabolites (产小分子中间代谢物 )
Types of biological oxidation:
1,Aerobic respiration (好氧呼吸 )
2,Anaerobic respiration(厌氧呼吸 )
3,Fermentation (发酵 )
Pathways of removing of hydrogen,(in the case of Glucose )
1,EMP (glycosis)
2,HMP (pentose phosphate pathway or WD)
3,ED (KDPG)
4,TCA cycle (citric acid cycle)
Removin
g
remove transfer receive
（ or organic or inorganic oxide）
（ organic or inorganic deoxide）
Four pathways of [H]
removing from substrate
Most microbes utilize the glycolytic（糖酵解）
pathway for the catabolism of carbohydrates such as
glucose and fructose,The products of this pathway
are pyruvate,which can be further metabolized via the
citric acid cycle,forming adenosine 5’-triphosphate
(ATP) and the reduced form of nicotinamide adenine
dinucleotide (烟酰胺腺嘌呤核苷酸 NADH + H+,） This
pathway is located in the cytoplasm of microbes and
can function in the presence or absence of oxygen.
Key notes(2)
Glycolysis(EMP pathway)
The bacterial genera Pseudomonas,Rhizobium
（根瘤菌） and Agrobacter （农杆菌） substitute
the Entner-Doudoroff pathway for the glycolytic
pathway,This pathway is not as efficient in
producing energy,with 1 mole of ATP being
formed for each mole of glucose metabolized.
Key notes (3)
The ED pathway
The pentose phosphate pathway or hexose
monophosphate pathway may operate at the same
time as glycolysis or the Entner-Doudoroff pathway,
This pathway can also operate either in the presence
or absence of oxygen,The pentose phosphate
pathway is an important source of energy in many
microorganisms; however,its major role would seem
to be for biosynthesis,The basic outline of this
pathway is shown in the Fig,The pathway produces
NADPH,
Key notes (4)
pentose phosphate pathway (HMP)
The pentose phosphate pathway（戊糖磷酸途径）
produces NADPH +H+ and sugars (4 C,5 C),These
are required for many synthetic reactions,When
organisms are growing on a pentose (5 C) sugar,the
pathway can be used to produce carbohydrates for
cell-wall synthesis,Glyceraldehyde-3-phosphate (三磷酸甘油醛 )formed by the pathway can be used to
generate energy by glycolysis or by the Entner-
Doudoroff pathway.
Key notes (4)
pentose phosphate pathway
The metabolism of pyruvate (formed by glycolysis)
to CO2 by the citric acid cycle is the major mechanism
of ATP generation in the cell and is also an important
source of carbon skeletons for biosynthesis,The fully
（完整的柠檬酸循环途径的功能） functioning pathway
requires oxygen; however,some organisms possess
an incomplete cycle that can function in the presence
or absence of oxygen but generates little or no energy.
Key notes (5)
Citric acid cycle
Many microbes use EMP pathways,although energy-
producing efficiency is low,it has extremely important
physiological functions; most aerobic and facultative
anaerobic microbes use both HMP and EMP pathways,
The feature of it is that G can be thoroughly oxidized
through EMP and TCA cycle,ED pathway is a microbe
specific substitute way replaces EMP in those microbes
that lacks the full EMP pathway,
NADH + H+ produced by catabolic reactions such as
the citric acid cycle can be oxidized by the electron-
transport pathway in the presence of oxygen,
However,in the absence of oxygen,many microbes
utilize fermentation reactions to reoxidize NADH + H+,
Microbial fermentations are characterized by the end
products formed.(微生物所进行的各种发酵,常常是以他们所形成的终产物而命名 ) Clostridia(梭菌则通常通过氨基酸发酵 Stickland
反应形成 ATP) are unusual in that they form ATP from the
fermentation of ammo acids by the Stickland reaction.
Key notes (6)
fermentations
The citric acid cycle is the most efficient
mechanism for generating ATP from glucose in
the presence of oxygen,For microbes that live
in environments where oxygen is absent or only
present intermittently,ATP generation is less
efficient.(生活在厌氧或间歇供氧环境中的微生物,ATP产生的效率是低的 )
Key notes (7)
ATP yields(产率 )
The majority of microbes utilize the glycolytic pathway
(糖酵解途径 also known as the Embden-Meyerhof pathway)
for the catabolism of carbohydrates such as glucose and
fructose,This series of reactions occurs in the
cytoplasm of microbes and can operate either
anaerobically (in the absence of oxygen) or aerobically
(in the presence of oxygen),The overall equation for this
pathway is
Glucose + 2ADP + 2Pi + 2NAD+ 2 pyruvate + 2ATP +
2NADH + 2H+
Glycolysis (糖酵解 )
EMP
brief figure of EMP pathway
2 stages
3 products
10 reactions
Pyr
ATP consuming ATP producing
1,Pyruvate formed by glycolysis can be further metabolized in the
presence of oxygen to generate energy via the citric acid cycle
or can be used for synthesis of other compounds such as amino
acids,
2,Adenosine triphosphate (ATP) can be used directly to
drive uptake of substrates or can be used to drive synthetic
reactions,
3,NADH + H+ can be used to produce energy via oxidative
phosphorylation (a method of ATP formation that requires
electron transport ) or can be used as a source of H+ for
reduction reactions,
The product of EMP pathway
Some organisms such as the bacteria Clostridia
utilize inorganic pyrophosphate (无机焦磷酸盐 )
(PPi)) in place of ATP as a source of energy to
drive the formation of pyruvate from phosphoenolp
yruvat-e (磷酸烯醇式丙酮酸 )and for the conversion
of fructose-6-phosphate into fructose-1,6-bisphos-
phate.
Exception
A minority of bacteria including Pseudomonas,
Rhizobium and Agrobacter substitute the Entner-
Doudoroff pathway for the glycolytic pathway,The
pathway yields 1 mole each of ATP,NADPH + H+ and
NADH + H+ for each mole of glucose metabolized,The
products of this pathway,like those of glycolysis,can be
used for a variety of functions; however,the NADPH +
H+ formed is used for synthetic reactions.
ED pathway
ED pathway
ethanolPyr
①
②
Brief pattern of ED pathway
① In the presence of oxygen via respiratory pathway
② fermentation while avoid of oxygen
Through only 4 steps from G
Characteristics of ED pathway:
1.FeatuKDPGred by the reaction that KDPG
was catalyzed into pyruvate and
glyceraldehyde-3-phosphate.
2,Characterized by an special enzyme ——
KDPG醛缩酶
3.Two molecules of pyruvates came from
different pathways.
4,Low energy-yielding efficiency —— 1mol
ATP/1 mol G
The pentose phosphate pathway or hexose
monophosphate pathway(己糖单磷酸途径 ) may operate
at the same time as glycolysis or the Entner-Doudoroff
pathway,This pathway can also operate either in the
presence or absence of oxygen,The pentose phosphate
pathway is an important source of energy in many
microorganisms; however,its major role would seem to
be for biosynthesis,
HMP
pathway
Breif pattern of HMP pathway
After a series of reactions,hexose were synthesized again
The basic outline of this pathway is shown in Fig,
The pathway produces NADPH and sugars (4C,5C),
which are required for the synthesis of aromatic
amino acids and nucleotides,When organisms are
growing on a pentose (5 C) sugar,the pathway can
also be used to produce carbohydrates for cell-wall
synthesis,Glyceraldehyde-3-phosphate (3-磷酸甘油醛 )can be used to generate energy via the
glycolytic/ Entner-Doudoroff pathways.
Although energy is obtained from the breakdown of pyruvate
by one of the previous pathways,a significantly greater yield can
be achieved in the presence of oxygen from the further oxidation
of pyruvate to CO2 via the citric acid cycle also known as the
tricarboxylic acid cycle,Pyruvate does not enter this pathway
directly,it must first undergo conversion into acetyl coenzyme A
(acetyl CoA):
Pyruvate + NAD+ + CoA → Acetyl CoA + NADH + H+
This reaction is catalyzed by pyruvate dehydrogenase,a large
complex containing three enzymes,
Citric acid cycle
(TCA)
Acetyl CoA can also be produced by the catabolism of lipids
and amino acids as well as a wide range of carbohydrates,ATP
can be formed from NADH + H+ by oxidative phosphorylation,
This pathway is also an important source of carbon skeletons
for use in biosynthesis,Citric acid cycle enzymes are widely
distributed in most microbes and other microorganisms,
Functional and complete cycles are found in most aerobic
microbes,algae,fungi and protozoa; however,in facultative
organisms (兼性微生物 those that can grow in the presence or
absence of oxygen) the complete citric acid cycle would only be
functional in the presence of oxygen,Many anaerobic
organisms have an incomplete cycle,which is used for the
production of synthetic precursors.
TC
A c
yc
le
12ATP
2ATP
Respiratory chain
Respiratory chain
（ substrate level） ATP
Major products of
TCA cycle
carbohydrates
fat
protein
The critical status of TCA cycle in the
catabolic and anabolic metabolism
How 38 ATP is formed from 1 glucose
via EMP and TCA？
① is EMP,② is TCA,③ is repiration chain,
framed is final product
Characteristics of TCA ctycle:
1.Functioning only aerobically(in the
prescence of oxygen),although O2 isn’t
directly involved in,
2,High energy yielding efficient with 4
mole of NADH+H+,1 mole of FADH2 and 1
mole of GTP were formed from 1 mole of
pyruvate,equally 15 mole ATP.
3.Located in a critical and connecting point
between catabolic and anabolic metabilism.
substrate
level
net ATP
2（ about 6 ATP）
12（ about 36ATP）
1（ about 3ATP）
1（ about 3ATP）
2（ about 2ATP）
2+8*（ about 30ATP）
2（ about 4 ATP）
Energy-yielding efficient of glucose
via different dehydrate pathways
Section B
Electron transport and
oxidative phosphorylation
NADH + H+ and FADH2 formed by catabolic
reactions are used to produce ATP by the
action of an electron-transport chain which is
composed of a series of electron carriers,In
bacteria,electron transport occurs in the inner
cell membrane(细胞质内膜 ),In other microbes
(eukaryotes),electron transport occurs in the
inner membrane of the mitochondria,Most
bacterial electron-transport chains are
branched unlike those in mammalian
mitochondria,
Key notes,electron-transport chain
All electron-transport pathways function in a similar
manner,requiring a series of oxidation and reduction
reactions,The oxidation of a molecule involves the
loss of electrons,and reduction involves the addition
of electrons,
Since electrons are conserved in chemical reaction,
oxidations must be coupled with reduction reactions
(redox reactions),
The oxidation-reduction potential (redox
potential) of a compound is a measure of its
affinity for electrons,The difference in redox
potential between NADH + H+ / NAD and 1/2O2
/H2O drives the movement of electrons through
a series of electron carriers from NADH + H+
to 02,Energy is released as electrons move
between carriers,This can also be linked to
ATP formation.
The chemiosmotic hypothesis(化学渗透学说 ) is a widely
accepted theory that explains how ATP is produced by
electron transport,ATP production requires that H+
move across the membrane where electron transport
occurs,producing a transmembrane H+ gradient,The H+
moves back across the membrane via ATP synthase,The
movement of H+ is coupled with large releases of energy
associated with electron transport,such that when
NADH + H+ is the electron donor and oxygen is the
terminal electron acceptor,H+ movement across the
membrane occurs at three sites,In microbes with short
pathways or where NADH + H+ is not the electron donor,
less ATP is produced.
Formation of ATP
NADH + H+ and flavin adenine dinucleotide (reduced
form) (FADH2) formed by the catabolism of organic
molecules are used to produce ATP by the action of an
electron-transport chain that is composed of a series of
electron carriers which transfer electrons to a terminal
electron acceptor such as oxygen,This final reduction is
performed by a terminal oxidase,Oxygen is not the
only useful electron acceptor,
1.Electron-transport chain(1)
In bacteria,electron transport occurs in the
inner cell membrane,but in algae,fungi and
many protozoa,electron transport and
oxidative phosphorylation occur in the inner
membrane of the,mitochondria,
1.Electron-transport chain(2)
Most bacterial electron-transport chains are
different to that found in mammalian
mitochondria and many like E,coli are branched,
Some chains are short and this reduces their
capacity for ATP production,Electrons can enter
bacterial electron-transport chains at various
points and this increases the number of
substrates that can be used for ATP synthesis.
1.Electron-transport chain(3)
All electron-transport pathways function in a
similar manner,requiring a series of oxidation
and reduction reactions,The oxidation of a
molecule involves the loss of electrons,and
reduction involves the addition of electrons,
Since electrons are conserved in chemical
reactions,oxidation must be coupled with
reduction (redox reactions).
1.Electron-transport chain(4)
The oxidation-reduction potential (redox
poten tial) of a compound is a measure of its affinity
for electrons,Redox potentials are measured
relative to hydrogen; thus,a positive redox potential
indicates that the compound has a greater affinity
for electrons than has hydrogen and would accept
electrons from hydrogen,A negative redox potential
indicates a lower affinity and thus the molecule
would donate electrons to hydrogen,
1.Electron-transport chain(5)
The difference in redox potential between NADH +
H+/NAD+ (-0.32 V) and O2/H2O (+0.82 V) drives the
movement of electrons through a series of electron
carriers which are arranged to accept electrons from
a carrier with a more negative redox potential and
donate to the next carrier which has a more positive
redox potential,Energy is released as the electrons
move between carriers,If the energy release is large
this can be coupled with the movement of H+ across
the membrane,which can generate ATP,The number
of sites where this can occur depends on the
difference between the redox potential of the
substrate and the final electron acceptor.
1.Electron-transport chain(6)
The chemiosmotic hypothesis is a widely accepted
theory that explains how the movement of protons
is linked to the formation of ATP,According to this
hypothesis the electron-transport pathway is
organized such that when elec trons move through
the chain,protons are transferred from one side of
the membrane to the other via a series of pumps,
When NADH + H4^ is the elec tron donor and
oxygen is the terminal electron acceptor,proton
movement occurs at three sites,which are
associated with large free energy changes,The
sites are NADH dehydrogenase,cytochrome be,
complex and the terminal oxidase,
2.Formation of ATP
In microbes with short pathways or where electrons
enter at other sites in the chain (and have a more
positive redox potential than that of the DH+H+/NAD+
couple) less ATP is produced,The pumping of H+ across
the membrane produces a proton motive force (PMF),
which is produced as a result of the uneven distribution
of H+ across the membrane (the membrane acts as a
barrier as it is impermeable to H+),When H+ are
transported back into the cell energy is released and
this drives the synthesis of ATP,This process is
catalyzed by ATP synthase (ATPase) which allows H4^
to move through the membrane,and the energy
released is coupled with ATP synthesis,PMF can be
used directly to drive some processes such as active
transport and rotation of bacterial flagella.
2.Formatiion of ATP (2)
Transfer and receive of the hydrogen
The potential chemical energy stored in the organic molecules
such as G is released by the transferring of [H] produced through
four pathways we discussed above to the hydrogen receptor,On
the basis of the attributes of hydrogen receptor,biological
oxidation can be classified as the following three types:
1.Respiration
2.Anearobic respiration
3,fermentation
Transfer and
receive
Respiration a.k.a,Aerobic respiration is the
most universal and the most important biological
oxidation or energy-yielding way,the [H] removed
from the substrate through conventional channels
were transported via fully respiratory chain,that
is,electron transport chain(ETC),and finally were
accepted by the extraneous oxygen molecules,
simultaneously releasing energy and water,It’s a
high-efficient energy-yielding style which
transfering and reception of H in the presence of
oxygen.
1,respiration
2.Anaerobic
respiration
The terminal hydrogen receptor of anaerobic
respiration is extraneous inorganic (only a few are
organic) oxidative compounds(无机氧化物 ),,It’s a
special respiratory with rather low energy-yielding
efficiency in the absence of oxygen,The [H] is
transported by partial ETC,it can be divided into
many types on the bases of the terminal [H]
receptor.
A,Nitrate respiration
B,Sulfate respiration
C,Sulfer respiration
D,Iron respiration
E,Carbonate respiration
F,Fumarate respiration (延胡索酸呼吸 )
Types of anaerobic respiration
A,Nitrate respiration (denitrification)
(硝酸盐呼吸又称反硝化作用 )
Assimilative nitrate reduction in the presence or absence of oxygen
(同化型硝酸盐还原作用 )
Dissimilative nitrate reduction anearobically
(异化型硝酸盐还原作用 ) nitrate NO,N2O,or even N2
Many microbes live in environments devoid of oxygen,To utilize
electron-transport mechanisms for ATP synthesis,alternative
inorganic electron acceptors such as nitrate,sulfate and CO2 are
used instead of oxygen,Those organisms that are facultative(兼性微生物 ) will use oxygen for aerobic respiration when available,
Microbes that use nitrate(硝酸盐 ) as an electron acceptor reduce
nitrate to nitrite(亚硝酸盐 ) and ammonia by the action of nitrate and
nitrite reductase:
NO3- + NADPH + H+ → NO2- + NADP+ + H2O
NO2- → [NH 2OH] →NH3
3.Anaerobic respiration
This is a largely inefficient method for the production of
ATP; thus,a large amount of nitrate is required to produce
sufficient ATP for the cell,Nitrite can also be reduced to N2
by a more efficient mechanism,This process is known as
denitrification(反硝化作用 ) and is performed by
Pseudomonas and some Bacillus species:
2N03- + lOe-+ 12H+→N 2+6H2O
Other groups that use alternative electron acceptors include
methanogens(产甲烷菌 ),which are obligate anaerobes and
reduce CO2 or carbonate(碳酸盐 ) to methane (methanogenesis):
HCO3- + H+ + 4H2 → CH4 + 3H20
and those that can reduce sulfate(硫酸盐 ) to sulfide(硫化物 )
(Desulfovibrio脱硫弧菌 ):
S042- + 8e- + 8H+ → S2- + 4H2O
Anaerobic respiration is much less efficient than aerobic
respiration; however,the yield of ATP by this mechanism is much
greater than that obtained by fermentation alone.
(无氧呼吸比有氧呼吸产能效率更低 ;然而,通过无氧呼吸这个机制,ATP产率比单独发酵却大得多 )
A major product in the catabolic pathways described previously
is NADH + H+ In the presence of oxygen this can be oxidized by
the electron-transport pathway,
However,in the absence of oxygen,this must be oxidized back
to NAD+,Many microbes utilize derivatives of pyruvate as
electron and H+ acceptors and this allows NADH + H+ to be re-
oxidized to NAD+,This process may lead to an increase in ATP
synthesis,an important factor for organisms growing in the
absence of oxygen (anaerobes),Such pathways are commonly
termed fermentation reactions.
Fermentation
(definition)
fermentatio
n
3.fermentatio
n
broadly or generally speaking it is referred to
as any production of the useful metabolites,
foods or beverage by aerobic or anaerobic
microbes.
Narrowly speaking,it’s a energy-producing
biological oxidation through substrate-level
phosphoration,the [H] removed from the
substrate was directly transferred to one of
some endogenesis(内源性 ) intermediate metabilte
without the transportation by respiratory chain.
4 types of important fermentation:
A,Fermentation started from pyruvate
derived from EMP pathway
B,Fermentation through HMP pathway
C,fermentation through ED pathway
D,stickland reaction—— amino acid
fermentation
Homoalcoholic fermentation
Homolactic fermentation
丙酸发酵
Mixed acid fernentation
Butanediol fermentation
Butyric acid fermentation丁酸发酵
EMP
1,Lactic acid fermentation is a common type of
fermentation characteristic of lactic acid bacteria
and some Bacillus(芽孢杆菌 )species,Lactic acid
fermentation can be divided into homolactic
fermentation,where all the pyruvate is reduced
to lactic acid,and heterolactate fermentation
where other products may be formed,such as
ethanol and CO2,
Fermemtation
(types)
2,Formic acid fermentation is associated with the
Enterobacteriaceae.(甲酸发酵与肠杆菌科有关 )
Formic acid fermentation can also be divided into
mixed acid fermentation,which results in the
production of ethanol and a mixture of acids such as
acetic,lactic and succinic(琥珀酸 ),This is a
characteristic of E.coil and Salmonella,The second
type is butanediol fermentation (丁二醇发酵 )where
2,3-butanediol,ethanol and smaller amounts of
organic acids are formed,These are characteristic of
Serratia(沙雷氏菌属 ) and Enterobacteriaceae,These
reactions are useful for the identification of members
of the Enterobacteriaceae,
3,A different type of bacterial fermentation is
that of amino acids by Clostridia,These
reactions can produce ATP by oxidizing one
amino acid and using another as an electron
acceptor in a process called the Stickland
reaction.
HMP
Heterolactic fermentation
Classical pathway by L.mesenteroides
Bifidobacteria pathway by Bifibobacteria
ATP yields of the major catabolic pathways are
shown in Table 1,The citric acid cycle is the most
efficient mechanism for generating ATP from
glucose; however,this requires oxygen as most of
the ATP is generated by oxidative phosphorylation,
For microbes that live in environments where
oxygen is absent or only present intermittently,ATP
generation is less efficient and often the limiting
factor for growth,
ATP yields
Pathway Yield of ATP (moles) produced per mole of glucose
Glycolysis 2
Entner-Doudoroff 1
Pentose phosphate No direct production of ATP
Citric acid 30*
Fermentations 2 or 3 if acetate formed
(the use of alternative electron and H* acceptors to
reoxidize NADH + H* will increase ATP production)
*most of the ATP is formed from the re-oxidation of NADH + H* by
oxidative phosphorylation
Table 1,ATP yields of the major catabolic pathways
Section C
Autotrophic metabolism
Microbes that obtain energy by the oxidation of inorganic
compounds are termed chemolithotrophs(化能无机营养菌 ) or
chemoautotrophs,These microbes are autotrophic (they fix CO2);
however,some are capable of heterotrophic metabolism if
organic compounds are available,Carbon dioxide is fixed by the
majority of these organisms using the Calvin cycle(卡尔文循环 ),
The energy required for CO2 fixation must be obtained from the
oxidation of inorganic molecules,Many of the chemolithotrophic
bacteria have considerable ecological significance,for example
Nitrosomonas(硝化单胞菌属 ) and Nitrobacter (硝化杆菌属 ) play
major roles in the nitrogen cycle.
Key notes (1)
chemolithotrophs
Photosynthesis in microbes can be either anoxygenic (does not
form oxygen as a product of photosynthesis) or oxygeniec(forms
oxygen),Photosynthesis in algae is always oxygenic,There are
four groups of microbes that carry out anoxygenic photosynthesis,
and the Cyanobacteria perform oxygenic photosynthesis,In
Cyanobacteria,the photosynthetic apparatus is localized in
membranous systems called thylacoids(类囊体 ),The pigments
involved in the trapping of light energy by microbes are
chlorophylls,carotenoids and phycobiliproteins (藻胆蛋白,辅助色素
accessory pigments),These pigments are arranged in highly
organized systems termed photosystems.
Key notes (2)
photosynthesis
When photosystem I (光合系统 PS I) in Cyanobacteria
transfers light energy to the chlorophyll P700 the molecule
undergoes a change in reduction potential还原电位 (becomes
more negative) and donates an electron to another chlorophyll
molecule,This electron is then transferred to a ferridoxin(铁氧还蛋白 ) and then on through either cyclical and non-cyclical
routes(环式或非环式途径 ),In the cyclical route the electron
returns to P700 with the formation of one ATP,The non-cyclical
route involves the light activation of chlorophyll P680 (PS II)
and another electron transfer,This route generates 1 ATP,1
NADPH +H+ and 1/2O2.
Key notes (3) 放氧性光合磷酸化
Oxygenic photophosphorylation
Green and purple bacteria(绿色硫细菌和兰色硫细菌 )
differ from Cyanobacteria in that most are strict
anaerobes,These organisms use H2,H2S and elemental
sulfur as electron donors and possess different light-
harvesting pigments than those observed in the
Cyanobacteria,These microbes lack PS II and exhibit
cyclic electron transport,which can be used to generate
ATP,Green sulfur bacteria,however,exhibit a form of
non-cyclic photosynthetic electron flow in order to
reduce NADP.
Key notes (4)
Anoxygenic photosynthesis
When growing with CO2 as carbon source,
Cyanobacteria and the purple bacteria use the
Calvin cycle for fixation,In the green bacteria,a
reductive citric acid cycle is used to fix CO2 into
acetyl CoA.
Key notes (5)
Dark reactions
Section D
Biosynthetic pathways
Synthesis of glucose from non-carbohydrate
precursors is termed gluconeogenesis(糖原异生作用 ),The pathway involved is the reverse of
glycolysis except for three points where the
glycolytic reaction is irreversible,At these points
the glycolytic enzyme is replaced.
Key notes (1)
Carbohydrates
Bacteria and algae can assimilate nitrogen(能同化的氮素如,)
as ammonia,nitrate and nitrogen,Fungi and protozoa can
assimilate nitrogen only as ammonia or nitrate,Only ammonia
can be incorporated directly,The simplest mechanisms
involve the formation of alanine and glutamate; these amino
acids can be used to synthesize a number of new amino acids
by transamination reactions (reactions involving the transfer
of amino groups),Nitrate is more oxidized than ammonia and
must first be reduced to ammonia before it can be
incorporated by bacteria; this process is termed assimilatory
nitrate reduction(同化型硝酸盐还原 ),Nitrogen can also be
utilized if reduced to ammonia (nitrogen fixation).
key notes (2)
Synthesis of amino acids
Lipids are made up from long-chain fatty acids or their
derivatives,These fatty acids contain on average 18 carbon
atoms and may be saturated (no double bonds present in the
chain) or unsaturated (contain one or more double bonds),
Some may also be branched,The synthesis of fatty acids is
catalyzed by the action of the fatty acid synthetase complex,
Acetyl CoA and malonyl CoA are the building blocks for
synthesis,Unsaturated fatty acids are formed in aerobic
bacteria and most eukaryotes via the action of desaturase
enzymes on the saturated fatty acid,In anaerobic and
facultative organisms such as E.coli and Clostridium sp;
double bonds are formed during fatty acid synthesis.
Key notes (3)
Synthesis of lipids
Purines and pyrimidines are cyclic nitrogenous compounds,
Purines (adenine and guanine) consist of two joined nitrogen-
containing rings,and pyrimidines (uracil,cytosine and thyamine)
have only one,A pyrimidine or purine joined to a pentose sugar
(either ribose or deoxyribose) is called a nuclcoside,A nucleotide
(building blocks of DNA or RNA) is a nucleoside with one or more
phosphate groups attached to the sugar.
Key notes (4)
Synthesis of Purines,pyrimidines
and nucleiotides
Synthesis of glucose from non-carbohydrate
precursors is termed gluconeogenesis and is
performed by organisms that do not synthesize
glucose from CO2,The pathway involved is the
reverse of glycolysis except for three points where
the glycolytic reaction is irreversible,At these points
the glycolytic enzyme is replaced such that:
carbohydrates
Glucose
1,The conversion of pyruvate into phosphoenol pyruvate(磷酸烯醇式丙酮酸 )is catalyzed by two enzymes,phosphoenol
pyruvate carboxykinase and pyruvate kinase (glycolytic
enzyme pyruvate kinase).(丙酮酸激酶 → 烯醇丙酮酸羧激酶和丙酮酸激酶 ))
2,The conversion of fructose-l,6-bisphosphate is catalyzed by
fructose bisphosphatase (glycolytic enzyme
phosphofructokinase).(果糖磷酸激酶 → 果糖二磷酸酶 )
3,The conversion of glucose-6-phosphate into glucose is
catalyzed by glucose-6-phosphatase (glycolytic enzyme
hexokinase),(己糖激酶 → 葡萄糖 6-磷酸酶 )
Fructose can also be synthesized by this route.
Glucose and fructose
The synthesis of other sugars can occur by simple
rearrangement such as the production of
mannose by mannose-6-phosphate isomerase:
Fructose-6-phosphate? Mannose-6-
phosphate
The synthesis of several sugars requires that precursors are
bound to nucleoside diphosphates,
(几种糖的合成需要糖结合成核苷二磷酸前体 )
For example,undine diphosphate glucose (UDPG) is
required for the synthesis of galactose(半乳糖 ),Nucleoside
diphosphate (ADP linked) sugars are also required for the
synthesis of polysaccharides(多糖 ):
ATP + Glucose-1-phosphate→ ADP-Glucose + PPi
(Glucose)n+ ADP-glucose → (Glucose) n+1+ ADP
Glucose-1-phosphate is formed from glucose-6-phosphate by
the action of phosphoglucomutase(葡萄糖磷酸变位酶 ).
Galactose and polysaccharides
Bacteria and algae can assimilate nitrogen in a variety of forms
(e.g,ammonia,nitrate and nitrogen),Fungi and protozoa cannot fix
nitrogen and assimilate only nitrate or ammonia,Ammonia can be
incorporated directly as it is more reduced than other forms,The
simplest mechanisms found in all microorganisms involve the
formation of alanine and glutamate:
Pyruvate + NH3+ NAD(P)H + H+? L-Alanine + NAD(P)+ + H20
α-Ketoglutarate + NH3 + NAD(P)H +H+? Glutamate + NAD(P)+ +H2O
The formation of glutamate catalyzed by glutamate
dehydrogenase(谷氨酸脱氢酶 ) occurs in many bacteria and fungi,
These amino acids can then be used to synthesize a number of new
amino acids by transfer of their α-amino group via transamination
reactions,
Amino acids
Nitrate must first be reduced to ammonia before it can be incorporated,
This process is termed assimilatory nitrate reduction(同化型硝酸盐还原 ),and requires two enzymes,nitrate and nitrite reductase,The
ammonia formed by these reactions can be incorporated into amino
acids,Nitrogen can also be utilized if reduced to ammonia (nitrogen
fixation固氮作用 ).
Bacteria such as Azotobacteria(固氮菌 ),Clostridium(梭菌 ),Rhizobium
(根瘤菌 )and some Cyanobacteria can fix nitrogen,This process requires
the enzyme nitrogenase(固氮酶 ) and a mechanism of electron transport,
The overall reaction is
N2 + 6H+ + 6e+ 12ATP + 12H20 → 2NH3 + 12ADP +12Pi
Source of ammonia
Lipids are the major components of membranes,They are made
up from long-chain fatty (organic) acids,The fatty acid chains in
lipids contain,on average,18 carbon atoms and are saturated (no
double bonds present in the chain) or contain only one double bond
(unsaturated),Some may also be branched,The synthesis of fatty
acids is catalyzed by the action of the fatty acid synthetase
complex(脂肪酸合成酶多酶复合体 ),Acetyl CoA and malonyl CoA (丙二酸单酰 CoA)are the building blocks for synthesis,Unsaturated
fatty acids are formed in aerobic bacteria and most eukaryotes via
the action of desaturase(脱氢酶 ) enzymes on the saturated fatty acid,
In anerobic and facultative bacteria (e.g,E,coli and Clostridium sp.)
double bonds are formed during the initial stages of fatty acid
synthesis.
lipids
Purines and pyrimidines are cyclic nitrogenous compounds,
Purines (adenine and guanine) consist of two joined rings,and
pyrimidines (uracil,cytosine and thyamine) have only one,A
pyrimidine or purine joined to a pentose sugar (either ribose or
deoxyribose) is a nucleoside(核苷 ),Nucleotides(核苷酸 ) are the
building blocks of DNA or RNA and consist of a nucleoside with
one or more phosphate groups attached to the sugar,Purines are
synthesized from seven different compounds,The sources of
carbon and nitrogen in the purine ring are shown in Fig,3a.
Purines,pyrimidines and nucleiotide
Pyrimidine biosynthesis starts with the
condensation of aspartic acid and carbamyl
phosphate by aspartate carbamyltransferase,The
product of this reaction,carbamoylaspartate is then
converted into a common intermediate of pyrimidine
biosynthesis,orotic add,After synthesis of the
pyrimidine skeleton a nucleotide is produced by the
addition of ribose-5-phosphate.
Connection
of catabolic
and anabolic
metabolism
Amphibolic pathway
(两用代谢途径 )
EMP
HMP
TCA
Anaplerotic sequence
(代谢物回补顺序 )
Glyoxylate cycle (shunt)
(乙醛酸循环或支路 )
Microbial metabolism
section A Heterotrophic pathways
section B Electron transport and
oxidative phosphorylation
section C Autotrophic metabolism
Section D Biosynthetic pathways
Metabolism is divided into those pathways
that are degradative (catabolic) and those that
are involved in synthesis,Catabolic pathways
often produce energy,Microbes that utilize
organic molecules as a source of energy are
called heterotrophs,Phototrophs obtain energy
from light,and lithotrophs(无机营养菌 ) obtain
energy from inorganic compounds.
Key notes (1)
Nutritional types
Metabolism in all cells is divided into catabolic (those
pathways involved in breakdown of organic molecules for
energy and the production of small compounds that may be
used for synthesis) and anabolic (pathways involved in
synthesis) processes.
In all organisms these pathways are balanced as the
energy required for anabolic processes is produced by
catabolic pathways,
In mammalian cells,energy production has been
maximized by the use of oxygen and thus the cell is usually
well supplied with energy; however,in microbes this is not
always the case,
catabolic and anabolic metabolism
Microbes can be divided into metabolic classes which
relate to the sources of energy they use,The three
groups are:
1,heterotrophs which utilize organic molecules as a
source of energy (these are also called chemo-
organotrophs化能有机营养型 );
2,phototrophs which obtain energy from light
3,lithotrophs which obtain energy from inorganic
compounds,
Carbon(碳素 ) for cell synthesis is obtained from organic
molecules; however,some microbes,including the
phototrophs,fix CO2.
Microbial metabolic types
Catabolism
Metabolism
anabolism
①complex molecule simple molecules +ATP+[H]*
（ Organic material ） ②
*[H] stands for reducing power (还原力 )
① catabolism enzyme complex（分解代谢酶系）
② anabolism enzyme complex （合成代谢酶系）
organic material
Primary energy sources (最初能源 ) ray irradiation(light)
Chemoheterotrophs reduced inorganic material
Phototrophs
chemoautotrophs
universal energy source (通用能源 )—— ATP
Energy metabolism
Section A
Heterotrophic pathways
Biological oxidation is referred to as all the
energy-producing oxidative reactions in the living
organism.
Definition:A series of energy-producing oxidative reactions
occurs in the living cells are called biological oxidation.
The process of biological oxidation (生物氧化的过程 )
1.Remove of hydrogen (脱氢 )
2.Transfer of hydrogen (递氢 )
3.Receive of hydrogen (受氢 )
Biological oxidation
(生物氧化）
Function of biological oxidation(生物氧化的功能 )
1,Produce energy (产能 )
2,Produce reducing power [H] (产还原力 )
3,Small intermediate metabolites (产小分子中间代谢物 )
Types of biological oxidation:
1,Aerobic respiration (好氧呼吸 )
2,Anaerobic respiration(厌氧呼吸 )
3,Fermentation (发酵 )
Pathways of removing of hydrogen,(in the case of Glucose )
1,EMP (glycosis)
2,HMP (pentose phosphate pathway or WD)
3,ED (KDPG)
4,TCA cycle (citric acid cycle)
Removin
g
remove transfer receive
（ or organic or inorganic oxide）
（ organic or inorganic deoxide）
Four pathways of [H]
removing from substrate
Most microbes utilize the glycolytic（糖酵解）
pathway for the catabolism of carbohydrates such as
glucose and fructose,The products of this pathway
are pyruvate,which can be further metabolized via the
citric acid cycle,forming adenosine 5’-triphosphate
(ATP) and the reduced form of nicotinamide adenine
dinucleotide (烟酰胺腺嘌呤核苷酸 NADH + H+,） This
pathway is located in the cytoplasm of microbes and
can function in the presence or absence of oxygen.
Key notes(2)
Glycolysis(EMP pathway)
The bacterial genera Pseudomonas,Rhizobium
（根瘤菌） and Agrobacter （农杆菌） substitute
the Entner-Doudoroff pathway for the glycolytic
pathway,This pathway is not as efficient in
producing energy,with 1 mole of ATP being
formed for each mole of glucose metabolized.
Key notes (3)
The ED pathway
The pentose phosphate pathway or hexose
monophosphate pathway may operate at the same
time as glycolysis or the Entner-Doudoroff pathway,
This pathway can also operate either in the presence
or absence of oxygen,The pentose phosphate
pathway is an important source of energy in many
microorganisms; however,its major role would seem
to be for biosynthesis,The basic outline of this
pathway is shown in the Fig,The pathway produces
NADPH,
Key notes (4)
pentose phosphate pathway (HMP)
The pentose phosphate pathway（戊糖磷酸途径）
produces NADPH +H+ and sugars (4 C,5 C),These
are required for many synthetic reactions,When
organisms are growing on a pentose (5 C) sugar,the
pathway can be used to produce carbohydrates for
cell-wall synthesis,Glyceraldehyde-3-phosphate (三磷酸甘油醛 )formed by the pathway can be used to
generate energy by glycolysis or by the Entner-
Doudoroff pathway.
Key notes (4)
pentose phosphate pathway
The metabolism of pyruvate (formed by glycolysis)
to CO2 by the citric acid cycle is the major mechanism
of ATP generation in the cell and is also an important
source of carbon skeletons for biosynthesis,The fully
（完整的柠檬酸循环途径的功能） functioning pathway
requires oxygen; however,some organisms possess
an incomplete cycle that can function in the presence
or absence of oxygen but generates little or no energy.
Key notes (5)
Citric acid cycle
Many microbes use EMP pathways,although energy-
producing efficiency is low,it has extremely important
physiological functions; most aerobic and facultative
anaerobic microbes use both HMP and EMP pathways,
The feature of it is that G can be thoroughly oxidized
through EMP and TCA cycle,ED pathway is a microbe
specific substitute way replaces EMP in those microbes
that lacks the full EMP pathway,
NADH + H+ produced by catabolic reactions such as
the citric acid cycle can be oxidized by the electron-
transport pathway in the presence of oxygen,
However,in the absence of oxygen,many microbes
utilize fermentation reactions to reoxidize NADH + H+,
Microbial fermentations are characterized by the end
products formed.(微生物所进行的各种发酵,常常是以他们所形成的终产物而命名 ) Clostridia(梭菌则通常通过氨基酸发酵 Stickland
反应形成 ATP) are unusual in that they form ATP from the
fermentation of ammo acids by the Stickland reaction.
Key notes (6)
fermentations
The citric acid cycle is the most efficient
mechanism for generating ATP from glucose in
the presence of oxygen,For microbes that live
in environments where oxygen is absent or only
present intermittently,ATP generation is less
efficient.(生活在厌氧或间歇供氧环境中的微生物,ATP产生的效率是低的 )
Key notes (7)
ATP yields(产率 )
The majority of microbes utilize the glycolytic pathway
(糖酵解途径 also known as the Embden-Meyerhof pathway)
for the catabolism of carbohydrates such as glucose and
fructose,This series of reactions occurs in the
cytoplasm of microbes and can operate either
anaerobically (in the absence of oxygen) or aerobically
(in the presence of oxygen),The overall equation for this
pathway is
Glucose + 2ADP + 2Pi + 2NAD+ 2 pyruvate + 2ATP +
2NADH + 2H+
Glycolysis (糖酵解 )
EMP
brief figure of EMP pathway
2 stages
3 products
10 reactions
Pyr
ATP consuming ATP producing
1,Pyruvate formed by glycolysis can be further metabolized in the
presence of oxygen to generate energy via the citric acid cycle
or can be used for synthesis of other compounds such as amino
acids,
2,Adenosine triphosphate (ATP) can be used directly to
drive uptake of substrates or can be used to drive synthetic
reactions,
3,NADH + H+ can be used to produce energy via oxidative
phosphorylation (a method of ATP formation that requires
electron transport ) or can be used as a source of H+ for
reduction reactions,
The product of EMP pathway
Some organisms such as the bacteria Clostridia
utilize inorganic pyrophosphate (无机焦磷酸盐 )
(PPi)) in place of ATP as a source of energy to
drive the formation of pyruvate from phosphoenolp
yruvat-e (磷酸烯醇式丙酮酸 )and for the conversion
of fructose-6-phosphate into fructose-1,6-bisphos-
phate.
Exception
A minority of bacteria including Pseudomonas,
Rhizobium and Agrobacter substitute the Entner-
Doudoroff pathway for the glycolytic pathway,The
pathway yields 1 mole each of ATP,NADPH + H+ and
NADH + H+ for each mole of glucose metabolized,The
products of this pathway,like those of glycolysis,can be
used for a variety of functions; however,the NADPH +
H+ formed is used for synthetic reactions.
ED pathway
ED pathway
ethanolPyr
①
②
Brief pattern of ED pathway
① In the presence of oxygen via respiratory pathway
② fermentation while avoid of oxygen
Through only 4 steps from G
Characteristics of ED pathway:
1.FeatuKDPGred by the reaction that KDPG
was catalyzed into pyruvate and
glyceraldehyde-3-phosphate.
2,Characterized by an special enzyme ——
KDPG醛缩酶
3.Two molecules of pyruvates came from
different pathways.
4,Low energy-yielding efficiency —— 1mol
ATP/1 mol G
The pentose phosphate pathway or hexose
monophosphate pathway(己糖单磷酸途径 ) may operate
at the same time as glycolysis or the Entner-Doudoroff
pathway,This pathway can also operate either in the
presence or absence of oxygen,The pentose phosphate
pathway is an important source of energy in many
microorganisms; however,its major role would seem to
be for biosynthesis,
HMP
pathway
Breif pattern of HMP pathway
After a series of reactions,hexose were synthesized again
The basic outline of this pathway is shown in Fig,
The pathway produces NADPH and sugars (4C,5C),
which are required for the synthesis of aromatic
amino acids and nucleotides,When organisms are
growing on a pentose (5 C) sugar,the pathway can
also be used to produce carbohydrates for cell-wall
synthesis,Glyceraldehyde-3-phosphate (3-磷酸甘油醛 )can be used to generate energy via the
glycolytic/ Entner-Doudoroff pathways.
Although energy is obtained from the breakdown of pyruvate
by one of the previous pathways,a significantly greater yield can
be achieved in the presence of oxygen from the further oxidation
of pyruvate to CO2 via the citric acid cycle also known as the
tricarboxylic acid cycle,Pyruvate does not enter this pathway
directly,it must first undergo conversion into acetyl coenzyme A
(acetyl CoA):
Pyruvate + NAD+ + CoA → Acetyl CoA + NADH + H+
This reaction is catalyzed by pyruvate dehydrogenase,a large
complex containing three enzymes,
Citric acid cycle
(TCA)
Acetyl CoA can also be produced by the catabolism of lipids
and amino acids as well as a wide range of carbohydrates,ATP
can be formed from NADH + H+ by oxidative phosphorylation,
This pathway is also an important source of carbon skeletons
for use in biosynthesis,Citric acid cycle enzymes are widely
distributed in most microbes and other microorganisms,
Functional and complete cycles are found in most aerobic
microbes,algae,fungi and protozoa; however,in facultative
organisms (兼性微生物 those that can grow in the presence or
absence of oxygen) the complete citric acid cycle would only be
functional in the presence of oxygen,Many anaerobic
organisms have an incomplete cycle,which is used for the
production of synthetic precursors.
TC
A c
yc
le
12ATP
2ATP
Respiratory chain
Respiratory chain
（ substrate level） ATP
Major products of
TCA cycle
carbohydrates
fat
protein
The critical status of TCA cycle in the
catabolic and anabolic metabolism
How 38 ATP is formed from 1 glucose
via EMP and TCA？
① is EMP,② is TCA,③ is repiration chain,
framed is final product
Characteristics of TCA ctycle:
1.Functioning only aerobically(in the
prescence of oxygen),although O2 isn’t
directly involved in,
2,High energy yielding efficient with 4
mole of NADH+H+,1 mole of FADH2 and 1
mole of GTP were formed from 1 mole of
pyruvate,equally 15 mole ATP.
3.Located in a critical and connecting point
between catabolic and anabolic metabilism.
substrate
level
net ATP
2（ about 6 ATP）
12（ about 36ATP）
1（ about 3ATP）
1（ about 3ATP）
2（ about 2ATP）
2+8*（ about 30ATP）
2（ about 4 ATP）
Energy-yielding efficient of glucose
via different dehydrate pathways
Section B
Electron transport and
oxidative phosphorylation
NADH + H+ and FADH2 formed by catabolic
reactions are used to produce ATP by the
action of an electron-transport chain which is
composed of a series of electron carriers,In
bacteria,electron transport occurs in the inner
cell membrane(细胞质内膜 ),In other microbes
(eukaryotes),electron transport occurs in the
inner membrane of the mitochondria,Most
bacterial electron-transport chains are
branched unlike those in mammalian
mitochondria,
Key notes,electron-transport chain
All electron-transport pathways function in a similar
manner,requiring a series of oxidation and reduction
reactions,The oxidation of a molecule involves the
loss of electrons,and reduction involves the addition
of electrons,
Since electrons are conserved in chemical reaction,
oxidations must be coupled with reduction reactions
(redox reactions),
The oxidation-reduction potential (redox
potential) of a compound is a measure of its
affinity for electrons,The difference in redox
potential between NADH + H+ / NAD and 1/2O2
/H2O drives the movement of electrons through
a series of electron carriers from NADH + H+
to 02,Energy is released as electrons move
between carriers,This can also be linked to
ATP formation.
The chemiosmotic hypothesis(化学渗透学说 ) is a widely
accepted theory that explains how ATP is produced by
electron transport,ATP production requires that H+
move across the membrane where electron transport
occurs,producing a transmembrane H+ gradient,The H+
moves back across the membrane via ATP synthase,The
movement of H+ is coupled with large releases of energy
associated with electron transport,such that when
NADH + H+ is the electron donor and oxygen is the
terminal electron acceptor,H+ movement across the
membrane occurs at three sites,In microbes with short
pathways or where NADH + H+ is not the electron donor,
less ATP is produced.
Formation of ATP
NADH + H+ and flavin adenine dinucleotide (reduced
form) (FADH2) formed by the catabolism of organic
molecules are used to produce ATP by the action of an
electron-transport chain that is composed of a series of
electron carriers which transfer electrons to a terminal
electron acceptor such as oxygen,This final reduction is
performed by a terminal oxidase,Oxygen is not the
only useful electron acceptor,
1.Electron-transport chain(1)
In bacteria,electron transport occurs in the
inner cell membrane,but in algae,fungi and
many protozoa,electron transport and
oxidative phosphorylation occur in the inner
membrane of the,mitochondria,
1.Electron-transport chain(2)
Most bacterial electron-transport chains are
different to that found in mammalian
mitochondria and many like E,coli are branched,
Some chains are short and this reduces their
capacity for ATP production,Electrons can enter
bacterial electron-transport chains at various
points and this increases the number of
substrates that can be used for ATP synthesis.
1.Electron-transport chain(3)
All electron-transport pathways function in a
similar manner,requiring a series of oxidation
and reduction reactions,The oxidation of a
molecule involves the loss of electrons,and
reduction involves the addition of electrons,
Since electrons are conserved in chemical
reactions,oxidation must be coupled with
reduction (redox reactions).
1.Electron-transport chain(4)
The oxidation-reduction potential (redox
poten tial) of a compound is a measure of its affinity
for electrons,Redox potentials are measured
relative to hydrogen; thus,a positive redox potential
indicates that the compound has a greater affinity
for electrons than has hydrogen and would accept
electrons from hydrogen,A negative redox potential
indicates a lower affinity and thus the molecule
would donate electrons to hydrogen,
1.Electron-transport chain(5)
The difference in redox potential between NADH +
H+/NAD+ (-0.32 V) and O2/H2O (+0.82 V) drives the
movement of electrons through a series of electron
carriers which are arranged to accept electrons from
a carrier with a more negative redox potential and
donate to the next carrier which has a more positive
redox potential,Energy is released as the electrons
move between carriers,If the energy release is large
this can be coupled with the movement of H+ across
the membrane,which can generate ATP,The number
of sites where this can occur depends on the
difference between the redox potential of the
substrate and the final electron acceptor.
1.Electron-transport chain(6)
The chemiosmotic hypothesis is a widely accepted
theory that explains how the movement of protons
is linked to the formation of ATP,According to this
hypothesis the electron-transport pathway is
organized such that when elec trons move through
the chain,protons are transferred from one side of
the membrane to the other via a series of pumps,
When NADH + H4^ is the elec tron donor and
oxygen is the terminal electron acceptor,proton
movement occurs at three sites,which are
associated with large free energy changes,The
sites are NADH dehydrogenase,cytochrome be,
complex and the terminal oxidase,
2.Formation of ATP
In microbes with short pathways or where electrons
enter at other sites in the chain (and have a more
positive redox potential than that of the DH+H+/NAD+
couple) less ATP is produced,The pumping of H+ across
the membrane produces a proton motive force (PMF),
which is produced as a result of the uneven distribution
of H+ across the membrane (the membrane acts as a
barrier as it is impermeable to H+),When H+ are
transported back into the cell energy is released and
this drives the synthesis of ATP,This process is
catalyzed by ATP synthase (ATPase) which allows H4^
to move through the membrane,and the energy
released is coupled with ATP synthesis,PMF can be
used directly to drive some processes such as active
transport and rotation of bacterial flagella.
2.Formatiion of ATP (2)
Transfer and receive of the hydrogen
The potential chemical energy stored in the organic molecules
such as G is released by the transferring of [H] produced through
four pathways we discussed above to the hydrogen receptor,On
the basis of the attributes of hydrogen receptor,biological
oxidation can be classified as the following three types:
1.Respiration
2.Anearobic respiration
3,fermentation
Transfer and
receive
Respiration a.k.a,Aerobic respiration is the
most universal and the most important biological
oxidation or energy-yielding way,the [H] removed
from the substrate through conventional channels
were transported via fully respiratory chain,that
is,electron transport chain(ETC),and finally were
accepted by the extraneous oxygen molecules,
simultaneously releasing energy and water,It’s a
high-efficient energy-yielding style which
transfering and reception of H in the presence of
oxygen.
1,respiration
2.Anaerobic
respiration
The terminal hydrogen receptor of anaerobic
respiration is extraneous inorganic (only a few are
organic) oxidative compounds(无机氧化物 ),,It’s a
special respiratory with rather low energy-yielding
efficiency in the absence of oxygen,The [H] is
transported by partial ETC,it can be divided into
many types on the bases of the terminal [H]
receptor.
A,Nitrate respiration
B,Sulfate respiration
C,Sulfer respiration
D,Iron respiration
E,Carbonate respiration
F,Fumarate respiration (延胡索酸呼吸 )
Types of anaerobic respiration
A,Nitrate respiration (denitrification)
(硝酸盐呼吸又称反硝化作用 )
Assimilative nitrate reduction in the presence or absence of oxygen
(同化型硝酸盐还原作用 )
Dissimilative nitrate reduction anearobically
(异化型硝酸盐还原作用 ) nitrate NO,N2O,or even N2
Many microbes live in environments devoid of oxygen,To utilize
electron-transport mechanisms for ATP synthesis,alternative
inorganic electron acceptors such as nitrate,sulfate and CO2 are
used instead of oxygen,Those organisms that are facultative(兼性微生物 ) will use oxygen for aerobic respiration when available,
Microbes that use nitrate(硝酸盐 ) as an electron acceptor reduce
nitrate to nitrite(亚硝酸盐 ) and ammonia by the action of nitrate and
nitrite reductase:
NO3- + NADPH + H+ → NO2- + NADP+ + H2O
NO2- → [NH 2OH] →NH3
3.Anaerobic respiration
This is a largely inefficient method for the production of
ATP; thus,a large amount of nitrate is required to produce
sufficient ATP for the cell,Nitrite can also be reduced to N2
by a more efficient mechanism,This process is known as
denitrification(反硝化作用 ) and is performed by
Pseudomonas and some Bacillus species:
2N03- + lOe-+ 12H+→N 2+6H2O
Other groups that use alternative electron acceptors include
methanogens(产甲烷菌 ),which are obligate anaerobes and
reduce CO2 or carbonate(碳酸盐 ) to methane (methanogenesis):
HCO3- + H+ + 4H2 → CH4 + 3H20
and those that can reduce sulfate(硫酸盐 ) to sulfide(硫化物 )
(Desulfovibrio脱硫弧菌 ):
S042- + 8e- + 8H+ → S2- + 4H2O
Anaerobic respiration is much less efficient than aerobic
respiration; however,the yield of ATP by this mechanism is much
greater than that obtained by fermentation alone.
(无氧呼吸比有氧呼吸产能效率更低 ;然而,通过无氧呼吸这个机制,ATP产率比单独发酵却大得多 )
A major product in the catabolic pathways described previously
is NADH + H+ In the presence of oxygen this can be oxidized by
the electron-transport pathway,
However,in the absence of oxygen,this must be oxidized back
to NAD+,Many microbes utilize derivatives of pyruvate as
electron and H+ acceptors and this allows NADH + H+ to be re-
oxidized to NAD+,This process may lead to an increase in ATP
synthesis,an important factor for organisms growing in the
absence of oxygen (anaerobes),Such pathways are commonly
termed fermentation reactions.
Fermentation
(definition)
fermentatio
n
3.fermentatio
n
broadly or generally speaking it is referred to
as any production of the useful metabolites,
foods or beverage by aerobic or anaerobic
microbes.
Narrowly speaking,it’s a energy-producing
biological oxidation through substrate-level
phosphoration,the [H] removed from the
substrate was directly transferred to one of
some endogenesis(内源性 ) intermediate metabilte
without the transportation by respiratory chain.
4 types of important fermentation:
A,Fermentation started from pyruvate
derived from EMP pathway
B,Fermentation through HMP pathway
C,fermentation through ED pathway
D,stickland reaction—— amino acid
fermentation
Homoalcoholic fermentation
Homolactic fermentation
丙酸发酵
Mixed acid fernentation
Butanediol fermentation
Butyric acid fermentation丁酸发酵
EMP
1,Lactic acid fermentation is a common type of
fermentation characteristic of lactic acid bacteria
and some Bacillus(芽孢杆菌 )species,Lactic acid
fermentation can be divided into homolactic
fermentation,where all the pyruvate is reduced
to lactic acid,and heterolactate fermentation
where other products may be formed,such as
ethanol and CO2,
Fermemtation
(types)
2,Formic acid fermentation is associated with the
Enterobacteriaceae.(甲酸发酵与肠杆菌科有关 )
Formic acid fermentation can also be divided into
mixed acid fermentation,which results in the
production of ethanol and a mixture of acids such as
acetic,lactic and succinic(琥珀酸 ),This is a
characteristic of E.coil and Salmonella,The second
type is butanediol fermentation (丁二醇发酵 )where
2,3-butanediol,ethanol and smaller amounts of
organic acids are formed,These are characteristic of
Serratia(沙雷氏菌属 ) and Enterobacteriaceae,These
reactions are useful for the identification of members
of the Enterobacteriaceae,
3,A different type of bacterial fermentation is
that of amino acids by Clostridia,These
reactions can produce ATP by oxidizing one
amino acid and using another as an electron
acceptor in a process called the Stickland
reaction.
HMP
Heterolactic fermentation
Classical pathway by L.mesenteroides
Bifidobacteria pathway by Bifibobacteria
ATP yields of the major catabolic pathways are
shown in Table 1,The citric acid cycle is the most
efficient mechanism for generating ATP from
glucose; however,this requires oxygen as most of
the ATP is generated by oxidative phosphorylation,
For microbes that live in environments where
oxygen is absent or only present intermittently,ATP
generation is less efficient and often the limiting
factor for growth,
ATP yields
Pathway Yield of ATP (moles) produced per mole of glucose
Glycolysis 2
Entner-Doudoroff 1
Pentose phosphate No direct production of ATP
Citric acid 30*
Fermentations 2 or 3 if acetate formed
(the use of alternative electron and H* acceptors to
reoxidize NADH + H* will increase ATP production)
*most of the ATP is formed from the re-oxidation of NADH + H* by
oxidative phosphorylation
Table 1,ATP yields of the major catabolic pathways
Section C
Autotrophic metabolism
Microbes that obtain energy by the oxidation of inorganic
compounds are termed chemolithotrophs(化能无机营养菌 ) or
chemoautotrophs,These microbes are autotrophic (they fix CO2);
however,some are capable of heterotrophic metabolism if
organic compounds are available,Carbon dioxide is fixed by the
majority of these organisms using the Calvin cycle(卡尔文循环 ),
The energy required for CO2 fixation must be obtained from the
oxidation of inorganic molecules,Many of the chemolithotrophic
bacteria have considerable ecological significance,for example
Nitrosomonas(硝化单胞菌属 ) and Nitrobacter (硝化杆菌属 ) play
major roles in the nitrogen cycle.
Key notes (1)
chemolithotrophs
Photosynthesis in microbes can be either anoxygenic (does not
form oxygen as a product of photosynthesis) or oxygeniec(forms
oxygen),Photosynthesis in algae is always oxygenic,There are
four groups of microbes that carry out anoxygenic photosynthesis,
and the Cyanobacteria perform oxygenic photosynthesis,In
Cyanobacteria,the photosynthetic apparatus is localized in
membranous systems called thylacoids(类囊体 ),The pigments
involved in the trapping of light energy by microbes are
chlorophylls,carotenoids and phycobiliproteins (藻胆蛋白,辅助色素
accessory pigments),These pigments are arranged in highly
organized systems termed photosystems.
Key notes (2)
photosynthesis
When photosystem I (光合系统 PS I) in Cyanobacteria
transfers light energy to the chlorophyll P700 the molecule
undergoes a change in reduction potential还原电位 (becomes
more negative) and donates an electron to another chlorophyll
molecule,This electron is then transferred to a ferridoxin(铁氧还蛋白 ) and then on through either cyclical and non-cyclical
routes(环式或非环式途径 ),In the cyclical route the electron
returns to P700 with the formation of one ATP,The non-cyclical
route involves the light activation of chlorophyll P680 (PS II)
and another electron transfer,This route generates 1 ATP,1
NADPH +H+ and 1/2O2.
Key notes (3) 放氧性光合磷酸化
Oxygenic photophosphorylation
Green and purple bacteria(绿色硫细菌和兰色硫细菌 )
differ from Cyanobacteria in that most are strict
anaerobes,These organisms use H2,H2S and elemental
sulfur as electron donors and possess different light-
harvesting pigments than those observed in the
Cyanobacteria,These microbes lack PS II and exhibit
cyclic electron transport,which can be used to generate
ATP,Green sulfur bacteria,however,exhibit a form of
non-cyclic photosynthetic electron flow in order to
reduce NADP.
Key notes (4)
Anoxygenic photosynthesis
When growing with CO2 as carbon source,
Cyanobacteria and the purple bacteria use the
Calvin cycle for fixation,In the green bacteria,a
reductive citric acid cycle is used to fix CO2 into
acetyl CoA.
Key notes (5)
Dark reactions
Section D
Biosynthetic pathways
Synthesis of glucose from non-carbohydrate
precursors is termed gluconeogenesis(糖原异生作用 ),The pathway involved is the reverse of
glycolysis except for three points where the
glycolytic reaction is irreversible,At these points
the glycolytic enzyme is replaced.
Key notes (1)
Carbohydrates
Bacteria and algae can assimilate nitrogen(能同化的氮素如,)
as ammonia,nitrate and nitrogen,Fungi and protozoa can
assimilate nitrogen only as ammonia or nitrate,Only ammonia
can be incorporated directly,The simplest mechanisms
involve the formation of alanine and glutamate; these amino
acids can be used to synthesize a number of new amino acids
by transamination reactions (reactions involving the transfer
of amino groups),Nitrate is more oxidized than ammonia and
must first be reduced to ammonia before it can be
incorporated by bacteria; this process is termed assimilatory
nitrate reduction(同化型硝酸盐还原 ),Nitrogen can also be
utilized if reduced to ammonia (nitrogen fixation).
key notes (2)
Synthesis of amino acids
Lipids are made up from long-chain fatty acids or their
derivatives,These fatty acids contain on average 18 carbon
atoms and may be saturated (no double bonds present in the
chain) or unsaturated (contain one or more double bonds),
Some may also be branched,The synthesis of fatty acids is
catalyzed by the action of the fatty acid synthetase complex,
Acetyl CoA and malonyl CoA are the building blocks for
synthesis,Unsaturated fatty acids are formed in aerobic
bacteria and most eukaryotes via the action of desaturase
enzymes on the saturated fatty acid,In anaerobic and
facultative organisms such as E.coli and Clostridium sp;
double bonds are formed during fatty acid synthesis.
Key notes (3)
Synthesis of lipids
Purines and pyrimidines are cyclic nitrogenous compounds,
Purines (adenine and guanine) consist of two joined nitrogen-
containing rings,and pyrimidines (uracil,cytosine and thyamine)
have only one,A pyrimidine or purine joined to a pentose sugar
(either ribose or deoxyribose) is called a nuclcoside,A nucleotide
(building blocks of DNA or RNA) is a nucleoside with one or more
phosphate groups attached to the sugar.
Key notes (4)
Synthesis of Purines,pyrimidines
and nucleiotides
Synthesis of glucose from non-carbohydrate
precursors is termed gluconeogenesis and is
performed by organisms that do not synthesize
glucose from CO2,The pathway involved is the
reverse of glycolysis except for three points where
the glycolytic reaction is irreversible,At these points
the glycolytic enzyme is replaced such that:
carbohydrates
Glucose
1,The conversion of pyruvate into phosphoenol pyruvate(磷酸烯醇式丙酮酸 )is catalyzed by two enzymes,phosphoenol
pyruvate carboxykinase and pyruvate kinase (glycolytic
enzyme pyruvate kinase).(丙酮酸激酶 → 烯醇丙酮酸羧激酶和丙酮酸激酶 ))
2,The conversion of fructose-l,6-bisphosphate is catalyzed by
fructose bisphosphatase (glycolytic enzyme
phosphofructokinase).(果糖磷酸激酶 → 果糖二磷酸酶 )
3,The conversion of glucose-6-phosphate into glucose is
catalyzed by glucose-6-phosphatase (glycolytic enzyme
hexokinase),(己糖激酶 → 葡萄糖 6-磷酸酶 )
Fructose can also be synthesized by this route.
Glucose and fructose
The synthesis of other sugars can occur by simple
rearrangement such as the production of
mannose by mannose-6-phosphate isomerase:
Fructose-6-phosphate? Mannose-6-
phosphate
The synthesis of several sugars requires that precursors are
bound to nucleoside diphosphates,
(几种糖的合成需要糖结合成核苷二磷酸前体 )
For example,undine diphosphate glucose (UDPG) is
required for the synthesis of galactose(半乳糖 ),Nucleoside
diphosphate (ADP linked) sugars are also required for the
synthesis of polysaccharides(多糖 ):
ATP + Glucose-1-phosphate→ ADP-Glucose + PPi
(Glucose)n+ ADP-glucose → (Glucose) n+1+ ADP
Glucose-1-phosphate is formed from glucose-6-phosphate by
the action of phosphoglucomutase(葡萄糖磷酸变位酶 ).
Galactose and polysaccharides
Bacteria and algae can assimilate nitrogen in a variety of forms
(e.g,ammonia,nitrate and nitrogen),Fungi and protozoa cannot fix
nitrogen and assimilate only nitrate or ammonia,Ammonia can be
incorporated directly as it is more reduced than other forms,The
simplest mechanisms found in all microorganisms involve the
formation of alanine and glutamate:
Pyruvate + NH3+ NAD(P)H + H+? L-Alanine + NAD(P)+ + H20
α-Ketoglutarate + NH3 + NAD(P)H +H+? Glutamate + NAD(P)+ +H2O
The formation of glutamate catalyzed by glutamate
dehydrogenase(谷氨酸脱氢酶 ) occurs in many bacteria and fungi,
These amino acids can then be used to synthesize a number of new
amino acids by transfer of their α-amino group via transamination
reactions,
Amino acids
Nitrate must first be reduced to ammonia before it can be incorporated,
This process is termed assimilatory nitrate reduction(同化型硝酸盐还原 ),and requires two enzymes,nitrate and nitrite reductase,The
ammonia formed by these reactions can be incorporated into amino
acids,Nitrogen can also be utilized if reduced to ammonia (nitrogen
fixation固氮作用 ).
Bacteria such as Azotobacteria(固氮菌 ),Clostridium(梭菌 ),Rhizobium
(根瘤菌 )and some Cyanobacteria can fix nitrogen,This process requires
the enzyme nitrogenase(固氮酶 ) and a mechanism of electron transport,
The overall reaction is
N2 + 6H+ + 6e+ 12ATP + 12H20 → 2NH3 + 12ADP +12Pi
Source of ammonia
Lipids are the major components of membranes,They are made
up from long-chain fatty (organic) acids,The fatty acid chains in
lipids contain,on average,18 carbon atoms and are saturated (no
double bonds present in the chain) or contain only one double bond
(unsaturated),Some may also be branched,The synthesis of fatty
acids is catalyzed by the action of the fatty acid synthetase
complex(脂肪酸合成酶多酶复合体 ),Acetyl CoA and malonyl CoA (丙二酸单酰 CoA)are the building blocks for synthesis,Unsaturated
fatty acids are formed in aerobic bacteria and most eukaryotes via
the action of desaturase(脱氢酶 ) enzymes on the saturated fatty acid,
In anerobic and facultative bacteria (e.g,E,coli and Clostridium sp.)
double bonds are formed during the initial stages of fatty acid
synthesis.
lipids
Purines and pyrimidines are cyclic nitrogenous compounds,
Purines (adenine and guanine) consist of two joined rings,and
pyrimidines (uracil,cytosine and thyamine) have only one,A
pyrimidine or purine joined to a pentose sugar (either ribose or
deoxyribose) is a nucleoside(核苷 ),Nucleotides(核苷酸 ) are the
building blocks of DNA or RNA and consist of a nucleoside with
one or more phosphate groups attached to the sugar,Purines are
synthesized from seven different compounds,The sources of
carbon and nitrogen in the purine ring are shown in Fig,3a.
Purines,pyrimidines and nucleiotide
Pyrimidine biosynthesis starts with the
condensation of aspartic acid and carbamyl
phosphate by aspartate carbamyltransferase,The
product of this reaction,carbamoylaspartate is then
converted into a common intermediate of pyrimidine
biosynthesis,orotic add,After synthesis of the
pyrimidine skeleton a nucleotide is produced by the
addition of ribose-5-phosphate.
Connection
of catabolic
and anabolic
metabolism
Amphibolic pathway
(两用代谢途径 )
EMP
HMP
TCA
Anaplerotic sequence
(代谢物回补顺序 )
Glyoxylate cycle (shunt)
(乙醛酸循环或支路 )
