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NPTEL – Biotechnology – Microbiology
Module 6 – Microbial Metabolism
Lecture 1 – Overview of microbial metabolism
Metabolism refers to the sum of all chemical reactions within a living organism.
Chemical reactions either release or require energy. Metabolism can be viewed as an
energy-balancing act.
Metabolism
Release energy (catabolism)
Require energy (anabolism)
Catabolism– enzyme-regulated chemical reactions that release energy. Complex organic
compounds are broken down into simpler ones. These reactions are called catabolic or
degradative reactions. They are generally hydrolytic reactions (reactions that use water
and in which chemical bonds are broken), and they are exergonic (produce more energy
than they consume). Ex. Cells break down sugars into CO2and H2O.
Anabolism – enzyme-regulated energy requiring reactions. The building of complex
organic molecules from simpler ones. These reactions are called anabolic or biosynthetic
and they are generally dehydration synthesis reactions (reactions that release water), and
they are endergonic (consume more energy than they produce). Ex. Formation of proteins
from amino acids, nucleic acids from nucleotides, polysaccharides from simple sugars)
These reactions generate the materials for growth. This coupling of energy requiring and
energy-releasing reactions is made possible through the molecule adenosine
triphosphate (ATP). ATP stores energy derived from catabolic reactions and releases it
later to drive anabolic reactions and perform other cellular work.
Fig. 1. ATP molecule
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ATP – an adenine, a ribose and 3 phosphate groups. When terminal phosphate group is
split from ATP, ADP is formed, and energy is released to drive anabolic reactions.
ATP
ADP + Pi + energy
Then, energy from catabolic reactions is used to combine ADP and a P to resynthesize
ATP.
ADP + Pi + energy
ATP
Anabolic reactions – coupled to ATP breakdown
Catabolic reactions – ATP synthesis.
ENZYMES:
•
Substances that can speed up a chemical reaction without being permanently
altered themselves are called catalysts.
•
In living cells, enzymes serve as biological catalysts.
•
Enzymes are specific and act on specific substances called the enzyme
substrate(s) and each catalyzes only one reaction.
Ex. Sucrose is the substrate of the enzyme sucrose, which catalyzes the hydrolysis
of sucrose to glucose and fructose.
Enzyme specificity and efficiency:
Enzymes are large globular proteins that range in MW from about 10,000 to several
million. Each enzyme has a characteristic three-dimensional shape with a specific surface
configuration as a result of its primary, secondary and tertiary structures. This enables it
to find the correct substrate from among the large number of diverse molecules in the
cell. Enzymes are extremely efficient. Under optimum conditions can catalyze reactions
at rates 108 to 1010 times higher than those of comparable reactions without enzymes.
Turnover number (maximum number of substrate molecules an enzyme molecule
converts to product each second) is between 1 and 10,000 and can be high as 500,000.
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Enzyme components:
•
Some enzymes consist entirely of proteins.
•
Most consist of both a protein portion called an apoenzyme and a nonprotein
component called a cofactor.
•
Ions of iron, zinc, magnesium or calcium are examples of cofactors. If the
cofactor is an organic molecule, it is called a coenzyme.
•
Together, the apoenzyme and cofactor form a holoenzyme, or whole active
enzyme. If the cofactor is removed, the apoenzyme will not function.
•
Coenzymes assist the enzyme by accepting atoms removed from the substrate or
by donating atoms required by the substrate. Some act as electron carriers,
removing electrons from the substrate and donating them to other molecules in
subsequent reactions.
•
Many coenzymes are derived from vitamins. Two of the most important
coenzymes in cellular metabolism are
Nicotinamide adenine dinucleotide (NAD+)
Nicotinamide adenine dicucleotide phosphate (NADP+)
These contain derivatives of B vitamin nicotinic acid (niacin)
NAD+ - involved in catabolic (energy-yielding reactions)
NADP+ - involved in anabolic (energy-requiring reactions)
•
Flavin coenzymes, such as flavin mononucleotide (FMN) and flavin adenine
dinucleotide (FAD), contains derivatives of the B vitamin riboflavin and are also
electron carriers.
•
Coenzyme A (CoA) contains derivatives of pantothenic acid, another B vitamin.
This plays an important role in the synthesis and breakdown of fats and in a series
of oxidizing reactions called the Krebs cycle.
•
Some cofactors are metal ions, including Fe, Cu, Mg, Mn, Zn, Ca and Co. They
form a bridge between the enzyme and a substrate. Ex. Mg2+ is required by many
phosphorylating enzymes (enzymes that transfer a phosphate group from ATP to
another substrate).
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Energy production:
There are two general aspects of energy production; the concept of oxidation-reduction
and the mechanism of ATP generation.
Oxidation – reduction reactions:
Oxidation – is removal of electron from an atom or molecule, a reaction that often
produces energy.
Reduction – is addition of one or more electrons to an atom or molecule.
Oxidation and reductions reactions are always coupled. The pairing of these reactions is
called oxidation-reduction or redox reactions. Most biological oxidation reactions involve
the loss of hydrogen atoms, they are also dehydrogenation. Hydrogen atom contains both
electrons and protons and in cellular oxidations, electrons and protons are removed at the
same time. An organic molecule is oxidized by the loss of two hydrogen atoms, and a
molecule of NAD+ is reduced by accepting two electrons and one proton. One proton is
left over and is released into the surrounding medium. The reduced coenzyme contains
more energy than NAD+. This energy can be used to generate ATP in later reactions.
Cells use oxidation- reduction (biological) reactions in catabolism to extract energy from
nutrient molecules. Ex. Cell oxidizes a molecule of glucose to Co2 and H2O. The energy
in the glucose molecule is removed in stepwise manner and ultimately is trapped by ATP,
which can then serve as an energy source for energy requiring reactions. Thus glucose is
a valuable nutrient for organisms.
The generation of ATP:
Much of the energy released during oxidation – reduction reactions is trapped within the
cell by the formation of ATP. A phosphate group is added to ADP with the input of
energy to form ATP. Addition of a phosphate to a chemical compound is called
phosphorylation. Organisms use three mechanisms of phosphorylation to generate ATP
from ADP.
Substrate – level phosphorylation:ATP is generated when a high energy phosphate is
directly transferred from a phosphorylated compound (a substrate) to ADP. Generally the
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phosphate has acquired its energy during an earlier reaction in which the substrate itself
was oxidized.
C-C-C~ P + ADP
C-C-C + ATP
Oxidative phosphorylation: Electrons are transferred from organic compounds to one
group of electron carriers (usually to NAD+ and FAD). Then, the electrons are passed
through a series of different electron carriers to molecules of O2 or other oxidized
inorganic and organic molecules. This process occurs in the plasma membrane of
prokaryotes and in the inner mitochondrial membrane of eukaryotes. The sequence of
electron carriers used in oxidative phosphorylation is called an electron transport chain.
The transfer of electrons from one electron carrier to the next releases energy, some of
which is used to generate ATP from ADP through a process called chemiosmosis.
Photophosphorylation:Occurs only in photosynthetic cells which contain light-trapping
pigments such as chlorophylls. In photosynthesis, organic molecules, especially sugars,
are synthesized with the energy of light from the energy-poor building blocks Co2 and
H2O. Photophosphorylation starts this process by converting light energy to the chemical
energy of ATP and NADPH, which in turn, are used to synthesize organic molecules. As
in oxidative phosphorylation, an electron transport chain is involved.
All microbial metabolisms can be arranged according to three principles:
1. How the organism obtains carbon for synthesizing cell mass?
•
autotrophic – carbon is obtained from carbon dioxide (CO2)
•
heterotrophic – carbon is obtained from organic compounds
•
mixotrophic – carbon is obtained from both organic compounds and by fixing
carbon dioxide
2. How the organism obtains reducing equivalents used either in energy conservation or
in biosynthetic reactions:
•
lithotrophic – reducing equivalents are obtained from inorganic compounds
•
organotrophic – reducing equivalents are obtained from organic compounds
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3. How the organism obtains energy for living and growing:
•
chemotrophic – energy is obtained from external chemical compounds
•
phototrophic – energy is obtained from light.
•
chemolithoautotrophs obtain energy from the oxidation of inorganic compounds
and carbon from the fixation of carbon dioxide. Examples: Nitrifying bacteria,
Sulfur-oxidizing bacteria, Iron-oxidizing bacteria, Knallgas-bacteria
•
photolithoautotrophs obtain energy from light and carbon from the fixation of
carbon dioxide, using reducing equivalents from inorganic compounds. Examples:
Cyanobacteria (water (H2O) as reducing equivalent donor), Chlorobiaceae,
Chromatiaceae (hydrogen sulfide (H2S) as reducing equivalent donor),
Chloroflexus (hydrogen (H2) as reducing equivalent donor)
•
chemolithoheterotrophs obtain energy from the oxidation of inorganic
compounds, but cannot fix carbon dioxide (CO2). Examples: some Thiobacilus,
some Beggiatoa, some Nitrobacter spp., Wolinella (with H2 as reducing
equivalent donor), some Knallgas-bacteria, some sulfate-reducing bacteria
•
chemoorganoheterotrophs obtain energy, carbon, and reducing equivalents for
biosynthetic reactions from organic compounds. Examples: most bacteria, e. g.
Escherichia coli, Bacillus spp., Actinobacteria
•
photoorganoheterotrophs obtain energy from light, carbon and reducing
equivalents for biosynthetic reactions from organic compounds. Some species are
strictly heterotrophic, many others can also fix carbon dioxide and are
mixotrophic. Examples: Rhodobacter, Rhodopseudomonas, Rhodospirillum,
Rhodomicrobium, Rhodocyclus, Heliobacterium, Chloroflexus (alternatively to
photolithoautotrophy with hydrogen).
Diversity of electron acceptors for respiration
 Organic compounds:
–
Eg. fumarate, dimethylsulfoxide (DMSO), Trimethylamine-N-oxide
(TMAO)
 Inorganic compounds:
–
Eg. NO3-, NO2-, SO42-, S0, SeO42-, AsO43-
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 Metals:
–
Eg. Fe3+, Mn4+, Cr6+
 Minerals/solids:
–
Eg. Fe(OH)3, MnO2
 Gasses:
–
Eg. NO, N2O, CO2
Most microorganisms oxidize carbohydrates as their main source of cellular
energy.Microorganisms use two general processes: Cellular respiration and fermentation.
Microorganisms also use anaerobic pathway to oxidize glucose. In case of aerobic
respiration, the ultimate e- acceptor is O2 and the reduced form is H2O.There are four
stages of aerobic respiration:
Oxygen extracts chemical energy from glucose, the glucose molecule must be split up
into two molecules of pyruvate. This process also generates two molecules of adenosine
triphosphate as an immediate energy yield and two molecules of NADH.
C6H12O6 + 2 ADP + 2 Pi + 2 NAD+ → 2 CH3COCOO− + 2 ATP + 2 NADH + 2
H2O + 2H+
•
The citric acid cycle begins with the transfer of a two-carbon acetyl group from
acetyl-CoA to the four-carbon acceptor compound (oxaloacetate) to form a sixcarbon compound (citrate).
•
The citrate then goes through a series of chemical transformations, losing two
carboxyl groups as CO2. The carbons lost as CO2 originate from what was
oxaloacetate, not directly from acetyl-CoA. The carbons donated by acetyl-CoA
become part of the oxaloacetate carbon backbone after the first turn of the citric
acid cycle. Loss of the acetyl-CoA-donated carbons as CO2 requires several turns
of the citric acid cycle. However, because of the role of the citric acid cycle in
anabolism, they may not be lost, since many TCA cycle intermediates are also
used as precursors for the biosynthesis of other molecules.
•
Most of the energy made available by the oxidative steps of the cycle is
transferred as energy-rich electrons to NAD+, forming NADH. For each acetyl
group that enters the citric acid cycle, three molecules of NADH are produced.
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•
Electrons are also transferred to the electron acceptor Q, forming QH2.
•
At the end of each cycle, the four-carbon oxaloacetate has been regenerated, and
the cycle continues.
Anaerobic respiration - Microbes are capable of using all sorts of other terminal
electron accepters besides oxygen. A few examples of anaerobic respiration;
•
Final electron acceptor is an inorganic substance other than O2.
•
Some bacteria such as Pseudomonas and Bacillus can use a nitrate ion (NO-3), in
the presence of an enzyme called nitrate reductase, as a final electron acceptor,
the nitrate ion is reduced to nitrite ion (NO2-).
•
Nitrite ion can be converted to nitrous oxide (N2O), or nitrogen gas (N2)
(denitrification process) which helps in recycling of nitrogen.
•
Other bacteria like Desulfovibrio use sulfate (SO42-) as the final electron acceptor
and forms hydrogen sulfide (H2S).
•
Still other bacteria use carbonate (CO32-) to form methane (CH4).
•
Anaerobic respiration by bacteria using nitrate and sulfate as final electron
acceptors is essential for the nitrogen and sulfur cycles that occur in nature.
•
Amount of ATP generated varies with the organisms and the pathway. Because
only a part of the Krebs cycle operates and since not all the carriers in the electron
transport chain participate, ATP yield is less and accordingly anaerobes tend to
grow more slowly than aerobes.
Microbial fermentation
Fermentation is a specific type of heterotrophic metabolism that uses organic carbon
instead of oxygen as a terminal electron acceptor. This means that these organisms do
not use an electron transport chain to oxidize NADH to NAD+ and therefore must have
an alternative method of using this reducing power and maintaining a supply of NAD+
for the proper functioning of normal metabolic pathways (e.g. glycolysis). As oxygen is
not required, fermentative organisms are anaerobic.
Many organisms can use fermentation under anaerobic conditions and aerobic
respiration when oxygen is present. These organisms are facultative anaerobes. To
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avoid the overproduction of NADH, obligately fermentative organisms usually do not
have a complete citric acid cycle. Instead of using an ATP synthase as in respiration,
ATP in fermentative organisms is produced by substrate-level phosphorylation where
a phosphate group is transferred from a high-energy organic compound to ADP to form
ATP. As a result of the need to produce high energy phosphate-containing organic
compounds (generally in the form of CoA-esters) fermentative organisms use NADH
and other cofactors to produce many different reduced metabolic by-products, often
including hydrogen gas (H2). These reduced organic compounds are generally small
organic acids and alcohols derived from pyruvate, the end product of glycolysis.
Examples include ethanol, acetate, lactate, and butyrate. Fermentative organisms are
very important industrially and are used to make many different types of food products.
The different metabolic end products produced by each specific bacterial species are
responsible for the different tastes and properties of each food.
The two main types of fermentation are alcoholic fermentation and lactic acid
fermentation (Fig.2). The two main types of fermentation are:
1) Alcoholic fermentation
2) Lactic acid fermentation
Fig. 2. Lactic acid and ethanolic fermentations
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Both types have the same reactants:
Pyruvic
acid
and
NADH,
both
of
which
are
products
of
glycolysis.
In alcoholic fermentation, the major products are alcohol and carbon dioxide. In lactic
acid
fermentation,
the
major
product
is
lactic
acid.
For both types of fermentation, there is a side product: NAD+ which is recycled back to
glycolysis so that small amounts of ATP can continue to be produced in the absence of
oxygen.
The chemical equations below summarize the fermentation of sucrose, whose chemical
formula is C12H22O11. One mole of sucrose is converted into four moles of ethanol and
four moles of carbon dioxide:
C12H22O11 +H2O + invertase →2 C6H12O6
C6H12O6 + Zymase → 2C2H5OH + 2CO2
The process of lactic acid fermentation using glucose is summarized below. In
homolactic fermentation, one molecule of glucose is converted to two molecules of lactic
acid:[3]
C6H12O6 → 2 CH3CHOHCOOH
In heterolactic fermentation, the reaction proceeds as follows, with one molecule of
glucose converted to one molecule of lactic acid, one molecule of ethanol, and one
molecule of carbon dioxide:
C6H12O6 → CH3CHOHCOOH + C2H5OH + CO2
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REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
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Module 6 – Microbial Metabolism
Lecture 2 – Carbohydrate Catabolism
Most microorganisms oxidize carbohydrates as their primary source of cellular
energy. Glucose is the most common carbohydrate energy source used by cells. To
produce energy from glucose microorganisms use two general processes: cellular
respiration and fermentation. Anaerobic respiration is another mode where the final
electron acceptor is an inorganic substance other than oxygen.
Catabolism/Oxidation of carbohydrates or Aerobic respiration of carbohydrates:
–
Most efficient way to extract energy from glucose. Occurs in three principal
stages:
1. Glycolysis
2. Kreb Cycle
3. Electron transport chain
Glycolysis – Oxidation of glucose to pyruvic acid with the production of some ATP and
energy containing NADH.
Krebs cycle – Oxidation of acetyl (a derivative of pyruvic acid) to Co2, with the
production of some ATP, energy containing NADH, and another reduced electron carrier,
FADH2.
Electron Transport chain – NADH and FADH2 are oxidized, contributing the electrons,
they have carried from the substrate to a ‘cascade’ of oxidation-reduction reactions
involving a series of additional electron carriers. Energy from these reactions is used to
generate a considerable amount of ATP. In respiration, most of the ATP is generated in
this step.
Fermentation: Initial stage is also glycolysis which produces pyruvic acid. But pyruvic
acid is converted into one or more different products, depending on the type of cell.
These products might include alcohol and lactic acid. Unlike respiration, there is no
Krebs cycle or electron transport chain. Accordingly, the ATP yield is also much lower.
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Glycolysis Or Embden-Meyerhof (EMF) pathway:
In glycolysis (from the Greek glykys, meaning “sweet,”and lysis, meaning
“splitting”), a molecule of glucose is degraded in a series of enzyme-catalyzed reactions
to yield two molecules of the three-carbon
compound pyruvate. During glycolysis
NAD+ is reduced to NADH and there is a net production of 2 ATP molecules by
substrate level phosphorylation. Glycolysis does not require oxygen and can occur
whether present or not.
Reactions in glycolytic pathway
Glycolysis involves 10 enzymatic reactions, summarized in Figure 1:
1. The phosphorylation of glucose at position 6 by hexokinase,
2. The isomerization of glucose-6-phosphate to fructose-6-phosphate
by
phosphohexose isomerase,
3. The phosphorylation of fructose-6-phosphate to fructose-1,6bisphosphate by phosphofructokinase,
4. The cleavage of fructose-1,6-bisphosphate by aldolase. This yields
two different products, dihydroxyacetone phosphate and
glyceraldehyde-3-phosphate,
5. The isomerization of dihydroxyacetone phosphate to a second molecule of
glyceraldehyde phosphate by triose phosphate isomerase,
6. The dehydrogenation and concomitant phosphorylation of glyceraldehyde-3-phosphate to 1,3-bis-phosphoglycerate by glyceraldehyde-3phosphate dehydrogenase,
7. The transfer of the 1-phosphate group from 1,3-bis-phosphoglycerate to
ADP by phosphoglycerate kinase, which yields ATP and 3phosphoglycerate,
8. The isomerization of 3-phosphoglycerate to 2-phosphoglycerate by
phosphoglycerate mutase,
9. The dehydration of 2-phosphoglycerate to phosphoenolpyruvate by
enolase.
10. The transfer of the phosphate group from phosphoenolpyruvate to ADP
by pyruvate kinase, to yield a second molecule of ATP.
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Fig. 3. Glycolysis. (Source, Lehninger, Principles of Biochemistry, Fifth Edition)
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Overall reaction of glycolysis
Glucose +2NAD+ + 2ADP + 2Pi ----2 pyruvate + 2NADH + 2H+ +2ATP + 2H2O
Because 2 moleucles of ATP were needed to get glycolysis started and four molecules of
ATP are generated by the process, there is a net gain of two molecules of ATP for each
molecule of glucose that is oxidised.
Alternatives of Glycolysis:
Many bacteria have another pathway in addition to glycolysis for the oxidation of
glucose. The most common are i) pentose phosphate pathway and ii) Entner-Doudoroff
pathway
1. Pentose Phosphate pathway (Hexose monophosphate shunt): This provides a
means for the breakdown of five-carbon sugars (pentoses) as well as glucose. A key
feature is that it produces important intermediates pentoses used in the synthesis of
nucleic acids, glucose from Co2 in photosynthesis and certain amino acids. The pathway
is an important producer of the reduced coenzyme NADPH from NADP+. This pathway
yields a net gain of only one molecule of ATP for each molecule of glucose oxidised.
Bacteria that use this pathway include Bacillus subtilis, E.coli, Leuconostoc
mesenteroides and Enterococcus faecalis.
The Entner-Doudoroff pathway: For each molecule of glucose this pathway produces 2
molecules of NADPH and one molecule of ATP for use in cellular biosynthetic reactions.
Bacteria that have the enzymes for this pathway can metabolize glucose without either
glcolysis or the pentose phosphate pathway. Found in some gram-negative bacteria,
including Rhizobium, Pseudomonas and Agrobacterium; generally not found among
gram-positive bacteria.
Cellular/Aerobic respiration
After glucose has been broken down to pyruvic acid, the pyruvic acid can be channeled
into the next step of either fermentation or cellular respiration.
Cellular respiration – is defined as an ATP generating process in which molecules are
oxidized and the final electron acceptor is an inorganic molecule. Two types of
respiration occur, depending on whether an organism is an aerobe or an anaerobe. In
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aerobic respiration – the final electron acceptor is O2 and in anaerobic respiration – it is
an inorganic molecule other than O2 or rarely an organic molecule.
The Krebs cycle /Citric Acid Cycle/ Tricarboxylic Acid Cycle
The pyruvate produced by glycolysis is oxidized completely, generating
additional ATP and NADH in the citric acid cycle and by oxidative phosphorylation.
However, this can occur only in the presence of oxygen. Oxygen is toxic to organisms
that are obligate anaerobes, and are not required by facultative anaerobic organisms. In
the absence of oxygen, one of the fermentation pathways occurs in order to regenerate
NAD+; lactic acid fermentation is one of these pathways.
In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion.
Bacteria also use the TCA cycle to generate energy, but since they lack mitochondria, the
reaction sequence is performed in the cytosol with the proton gradient for ATP
production being across the plasma membrane rather than the inner membrane of the
mitochondrion.
Fig. 4. Citric Acid cycle
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•
Pyruvic acid, the product of glycolysis, cannot enter the Krebs cycle directly. In a
preparatory step; it must lose one molecule of Co2 and become a two-carbon
compound. This process is called decarboxylation. The two carbon compound
called an acetyl group, attaches to Coenzyme a through a high-energy bond, the
resulting complex is known as Acetyl Coenzyme A. During this reaction, pyruvic
acid is also oxidized and NAD+ is reduced to NADH.
•
Oxidation of one glucose molecule produces 2 molecules of pyruvic acid, so for
each molecule of glucose, 2 molecules of Co2 are released in the preparatory step,
2 molecules of NADH are produced, and 2 molecules of Acetyl Coenzyme A are
formed.
•
As Acetyl coenzyme A enters the Krebs cycle, CoA detaches from the acetyl
group. The two carbon acetyl group combines with a four carbon compound
called oxaloacetic acid to form six carbon compound, called citric acid. This
synthesis reaction requires energy, which is provided by the cleavage of the high
energy bond between the acetyl group and CoA. The formation of citric acid is
the first step in the Krebs cycle.
•
Two decorboxylation reactions take place in the Krebs cycle while converting
Isocitric acid to α – Ketoglutaric acid and this to succinyl CoA.
•
Altogether 3 decarboxylation reactions take place and hence all three carbon
atoms in pyruvic acid are eventually released as Co2 by the Krebs cycle. This
represents the conversion to Co2 by all 6 carbon atoms contained in the original
glucose molecule.
•
Oxidation-reduction reactions also occurs, where NAD+ and FAD picks up
hydrogen atoms to be reduced to NADH and FADH2.
•
On the whole, for every two molecules of acetyl CoA that enter the cycle, 4
molecules of Co2 and 6 for pyruvic acid are liberated by decorboxylation, 6/8
moelucles of NADH and 2 moleucles of FADH2 are produced by oxidationreduction reactions, and two molecules of ATP are generated by substrate- level
phosphorylation. Many of the intermediates in the Krebs cycle also play a role in
other pathways, especially in amino acid biosynthesis.
•
Reduced coenzymes NADH and FADH2 are the important products of the Krebs
cycle because they contain most of the energy originally stored in glucose. During
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the next phase of respiration, a series of reductions indirectly transfers the energy
stored in those coenzymes to ATP. These reactions are collectively called
Electron transport chain.
The Electron Transport Chain:
•
Consists of a sequence of carrier molecules that are capable of oxidation and
reduction.
•
As electrons are passed through the chain, there is a stepwise release of energy,
used to drive the chemiosmotic generation of ATP.
•
In eukaryotic cells, it is contained in the inner membrane of mitochondria.
•
In prokaryotes, it is found in the plasma membrane.
Fig. 5. Electron Transport Chain
Three classes of carrier molecules are involved:
1. Flavoproteins – these contain flavin, a coenzyme derived from riboflavin (Vitamin
B2). One important flavin coenzyme is flavin mononucleotide (FMN).
2. Cytochromes – proteins with an iron-containing group capable of existing
alternately as a reduced form (Fe2+) and an oxidized form (Fe3+). The cytochormes
include cytochrome b, C1, a, a3.
3. Ubiquinones or Coenzyme Q – these are small non-protein carriers.
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•
Electron transport chains of bacteria are somewhat diverse, and the particular
carriers and the order in which they functions may differ from those of other
bacteria and from those of eukaryotic mitochondrial systems. Much is known
about the electron transport chain in the mitochondria of eukaryotic cells.
1. Transfer of high energy electrons from NADH to FMN, the first carrier in the
chain. This transfer involves at the passage of a hydrogen atom with 2e- to FMN,
which then pick up an additional H+ from the surrounding aqueous medium.
NADH is oxidised to NAD+ and FMN reduced to FMNH2.
2. FMNH2 passes 2H+ to the other side of the mitochondrial membrane and passes
2e- to Q. As a result FMNH2 is oxidized to FMN. Q picks up an additional 2H+
from the medium and releases it on the other side of the membrane.
3. Electrons are passed successively from Q to Cyt b, cyt c1, cyt c, cyt a and cyt
a3. Each cytochrome in the chain is reduced as it picks up e-and is oxidised as it
gives up electrons. The last cyt a3 passes it electrons to molecular O2, which
becomes negatively charged and then picks up protons from the medium to form
H2O.
•
FADH2 adds its electrons to the electron transport chain at a lower level than
NADH. Because of this, the electron transport chain produces about one-third less
energy for ATP generation when FADH2 donates electrons than when NADH is
involved.
•
FMN and Q accept and release protons as well as electrons and other carrier
cytochromes transfer only electrons.
•
Electron flow down the chain is accompanied at several points by the active
transport (Pumping) of protons from the matrix side of the inner mitochondrial
membrane to the opposite side of the membrane. The result is build up of protons
on one side of the membrane, which provides energy for the generation of ATP
by the chemiosmotic mechanism.
Chemiosmotic mechanism of ATP generation:
•
Mechanism of ATP synthesis using the electron transport chain is called
chemiosmosis.
•
Substances diffuse passively across membranes from areas of high concentration
to areas of low concentration, this diffusion yields energy. In chemiosmosis, the
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energy released when a substance moves along a gradient is used to synthesize
ATP.
1. As energetic electrons from NADH (or chlorophyll) pass down the electron
transport chain, some of the carriers in the chain pump actively transport –
protons across the membrane. Such carrier molecules are called proton pumps.
2. The phospholipid membrane is normally impermeable to protons, so this onedirectional pumping establishes a proton gradient. The excess H+ on one side of
the membrane makes that side positively charged compared with the other side.
The resulting electrochemical gradient has potential energy, called the proton
motive force.
3. The protons on one side of the membrane can diffuse across the membrane
only through special protein channels that contain an enzyme called adenosine
triphosphate (ATP synthase). When this flow occurs, energy is released and is
used by the enzyme to synthesize ATP from ADP and Pi.
•
Electron transport chain also operates in photophosphorylation and is located in
the thylakoid membrane of cyanobacteria and eukaryotic chloroplasts.
Summary of Aerobic respiration:
•
Electron transport chain regenerates NAD+ and FAD+ which can be used again in
glycolysis and Krebs cycle.
•
Various electron transfers in the electron transport chain generates about 34
molecules of ATP from each molecule of glucose oxidized, 10 NADH and 2
FADH2.
•
A total of 38 ATP molecules can be generated from one molecule of glucose in
prokaryotes.
•
A total of 36 molecules of ATP are produced in eukaryotes. Some energy is lost
when electrons are shuttled across the mitochondrial membranes that separate
glycolysis (in the cytoplasm) from the electron transport chain. No such
separation exists in prokaryotes.
C6H12O6 + 6 CO2 + 38ADP + 38 Pi
→ 6CO2 + 6H2O + 38 ATP
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Fig. 6. Generation of ATPs and NADH/FADH2 during Aerobic Respiration
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
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Module 6 – Microbial Metabolism
Lecture 3 – Anaerobic respiration and Fermentation
Anaerobic Respiration
Respiration in some prokaryotes is possible using electron acceptors other than
oxygen (O2). This type of respiration in the absence of oxygen is referred to as anaerobic
respiration. Electron acceptors used by prokaryotes for respiration or methanogenesis (an
analogous type of energy generation in archaea bacteria) are described in the table below.
Terminal eAcceptor
O2
Reduced End
Product
H2O
NO3
NO2, NH3 or N2
SO4
S or H2S
fumarate
succinate
CO2
CH4
Process
aerobic respiration
Example
Escherichia,
Streptomyces
Bacillus,
Pseudomonas
anaerobic
respiration:
denitrification
anaerobic
Desulfovibrio
respiration: sulfate
reduction
anaerobic
Escherichia
respiration: using
an organic eacceptor
Methanogenesis
Methanococcus
Biological methanogenesis is the source of methane (natural gas) on the planet. Methane
is preserved as a fossil fuel (until we use it all up) because it is produced and stored under
anaerobic conditions, and oxygen is needed to oxidize the CH4 molecule.
Methanogenesis is not really a form of anaerobic respiration, but it is a type of
energy-generating metabolism that requires an outside electron acceptor in the form of
CO2.
Sulfate reduction is not an alternative to the use of O2 as an electron acceptor. It
is an obligatory process that occurs only under anaerobic conditions. Methanogens and
sulfate reducers may share habitat, especially in the anaerobic sediments of eutrophic
lakes such as Lake Mendota, where they crank out methane and hydrogen sulfide at a
surprising rate.
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Nitrate reduction
Some microbes are capable of using nitrate as their terminal electron accepter. The ETS
used is somewhat similar to aerobic respiration, but the terminal electron transport
protein donates its electrons to nitrate instead of oxygen. Nitrate reduction in some
species (the best studied being E. coli) is a two electron transfer where nitrate is reduced
to nitrite. Electrons flow through the quinone pool and the cytochrome b/c1 complex and
then nitrate reductase resulting in the transport of protons across the membrane as
discussed earlier for aerobic respiration.
N03- + 2e- + 2H+
N02-+ H20
Fig. 7. Nitrate reduction
Steps in the dissimilative reduction of nitrate. Some organisms, for example
Escherichia coli, can carry out only the first step. All enzymes involved are derepressed
by anoxic conditions. Also, some prokaryotes are known that can reduce NO3- to NH4+ in
dissimilative metabolism.
Denitrification
Denitrification is an important process in agriculture because it removes NO3 from the
soil. NO3 is a major source of nitrogen fertilizer in agriculture. Almost one-third the cost
of some types of agriculture is in nitrate fertilizers. The use of nitrate as a respiratory
electron acceptor is usually an alternative to the use of oxygen. Therefore, soil bacteria
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such as Pseudomonas and Bacillus will use O2 as an electron acceptor if it is available,
and disregard NO3. This is the rationale in maintaining well-aerated soils by the
agricultural practices of plowing and tilling. E. coli will utilize NO3 (as well as fumarate)
as a respiratory electron acceptor and so it may be able to continue to respire in the
anaerobic intestinal habitat.
Nitrite, the product of nitrate reduction, is still a highly oxidized molecule and can accept
up to six more electrons before being fully reduced to nitrogen gas. Microbes exist
(Paracoccus species, Pseudomonas stutzeri, Pseudomonas aeruginosa, and Rhodobacter
sphaeroides are a few examples) that are able to reduce nitrate all the way to nitrogen
gas. The process is carefully regulated by the microbe since some of the products of the
reduction of nitrate to nitrogen gas are toxic to metabolism. This may explain the large
number of genes involved in the process and the limited number of bacteria that are
capable of denitrification. Below is the chemical equation for the reduction of nitrate to
N2.
N03-
N02-
NO
N2O
N2
Denitrification takes eight electrons from metabolism and adds them to nitrate to form N2
Fig. 8. Denitification by Pseudomonas stutzeri
 Four terminal reductases involved in denitrification steps;
–
Nar: Nitrate reductase (Mo-containing enzyme)
–
Nir: Nitrite reductase
–
Nor: Nitric oxide reductase
–
N2Or: Nitrous oxide reductase
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 All can function independently but they operate in unison
Fermentation:
Fermentation is the process of extracting energy from the oxidation of organic
compounds, such as carbohydrates, using an endogenous electron acceptor, which is
usually an organic compound. In contrast, respiration is where electrons are donated to an
exogenous electron acceptor, such as oxygen, via an electron transport chain.
Fermentation is important in anaerobic conditions when there is no oxidative
phosphorylation to maintain the production of ATP (adenosine triphosphate) by
glycolysis.
During fermentation, pyruvate is metabolised to various compounds. Homolactic
fermentation is the production of lactic acid from pyruvate; alcoholic fermentation is the
conversion of pyruvate into ethanol and carbon dioxide; and heterolactic fermentation is
the production of lactic acid as well as other acids and alcohols.
Fermentation does not necessarily have to be carried out in an anaerobic environment.
For example, even in the presence of abundant oxygen, yeast cells greatly prefer
fermentation to oxidative phosphorylation, as long as sugars are readily available for
consumption (a phenomenon known as the Crabtree effect).
Fig. 9. Respiration and Fermentation pathways
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Lactic acid fermentation is the simplest type of fermentation. In essence, it is a redox
reaction. In anaerobic conditions, the cell’s primary mechanism of ATP production is
glycolysis. Glycolysis reduces – transfers electrons to – NAD+, forming NADH.
However there is a limited supply of NAD+ available in any given cell.
•
For glycolysis to continue, NADH must be oxidized – have electrons taken away
– to regenerate the NAD+ that is used in glycolysis. In an aerobic environment
(Oxygen is available), reduction of NADH is usually done through an electron
transport chain in a process called oxidative phosphorylation; however, oxidative
phosphorylation cannot occur in anaerobic environments (Oxygen is not
available) due to the pathways dependence on the terminal electron acceptor of
oxygen.
•
Instead, the NADH donates its extra electrons to the pyruvate molecules formed
during glycolysis. Since the NADH has lost electrons, NAD+ regenerates and is
again available for glycolysis. Lactic acid, for which this process is named, is
formed by the reduction of pyruvate.
In heterolactic acid fermentation, one molecule of pyruvate is converted to lactate; the
other is converted to ethanol and carbon dioxide.
In homolactic acid fermentation, both molecules of pyruvate are converted to lactate.
Homolactic acid fermentation is unique because it is one of the only respiration processes
to not produce a gas as a byproduct.
•
Homolactic fermentation breaks down the pyruvate into lactate. It occurs in the
muscles of animals when they need energy faster than the blood can supply
oxygen.
•
It also occurs in some kinds of bacteria (such as lactobacilli) and some fungi. It is
this type of bacteria that converts lactose into lactic acid in yogurt, giving it its
sour taste. These lactic acid bacteria can be classed as homofermentative, where
the end-product is mostly lactate, or heterofermentative, where some lactate is
further metabolized and results in carbon dioxide, acetate, or other metabolic
products.
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C6H12O6 ------- 2 CH3CHOHCOOH.
or one molecule of lactose and one molecule of water make four molecules of lactate (as
in some yogurts and cheeses):
C12H22O11 + H2O ------ 4 CH3CHOHCOOH.
In heterolactic fermentation, the reaction proceeds as follows, with one molecule of
glucose being converted to one molecule of lactic acid, one molecule of ethanol, and one
molecule of carbon dioxide:
C6H12O6 -------- CH3CHOHCOOH + C2H5OH + CO2
Before lactic acid fermentation can occur, the molecule of glucose must be split into two
molecules of pyruvate. This process is called glycolysis.
Fig. 10. Fate of pyruvate in Fermentation
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Mixed fermentations
Butanediol Fermentation. Forms mixed acids and gases as above, but, in
addition, 2,3 butanediol from the condensation of 2 pyruvate. The use of the pathway
decreases acid formation (butanediol is neutral) and causes the formation of a distinctive
intermediate, acetoin. Water microbiologists have specific tests to detect low acid and
acetoin in order to distinguish non fecal enteric bacteria (butanediol formers, such as
Klebsiella and Enterobacter) from fecal enterics (mixed acid fermenters, such as E. coli,
Salmonella and Shigella).
Butyric acid fermentations, as well as the butanol-acetone fermentation (below),
are run by the clostridia, the masters of fermentation. In addition to butyric acid, the
clostridia form acetic acid, CO2 and H2 from the fermentation of sugars. Small amounts
of ethanol and isopropanol may also be formed.
Butanol-acetone fermentation. Butanol and acetone were discovered as the main
end products of fermentation by Clostridium acetobutylicum during the World War I.
This discovery solved a critical problem of explosives manufacture (acetone is required
in the manufacture gunpowder) and is said to have affected the outcome of the War.
Acetone was distilled from the fermentation liquor of Clostridium acetobutylicum, which
worked out pretty good if you were on our side, because organic chemists hadn't figured
out how to synthesize it chemically. You can't run a war without gunpowder, at least you
couldn't in those days.
Propionic acid fermentation. This is an unusual fermentation carried out by the
propionic acid bacteria which include corynebacteria, Propionibacterium and
Bifidobacterium. Although sugars can be fermented straight through to propionate,
propionic acid bacteria will ferment lactate (the end product of lactic acid fermentation)
to acetic acid, CO2 and propionic acid. The formation of propionate is a complex and
indirect process involving 5 or 6 reactions. Overall, 3 moles of lactate are converted to 2
moles of propionate + 1 mole of acetate + 1 mole of CO2, and 1 mole of ATP is squeezed
out in the process. The propionic acid bacteria are used in the manufacture of Swiss
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cheese, which is distinguished by the distinct flavor of propionate and acetate, and holes
caused by entrapment of CO2.
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
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Module 6 – Microbial Metabolism
Lecture 4 –Protein and Lipid Catabolism
A. Protein and Amino acid Catabolism
Some bacteria and fungi particularly pathogenic, food spoilage and soil microorganisms
can use proteins as their source of carbon and energy.
1. Proteases are enzymes that break down proteins into amino acids
2. Amino acids are deaminated, and then enter the Kreb's Cycle.
Intact proteins cannot cross bacterial plasma membrane, so bacteria must produce
extracellular enzymes called proteases and peptidases that break down the proteins into
amino acids, which can enter the cell. Many of the amino acids are used in building
bacterial proteins, but some may also be broken down for energy. If this is the way amino
acids are used, they are broken down to some form that can enter the Kreb’s cycle. These
reactions include:
1. Deamination or Transamination—the amino group is removed or transferred, or
converted to an ammonium ion, and excreted. The remaining organic acid (the part of the
amino acid molecule that is left after the amino group is removed) can enter the Kreb’s
cycle.
2. Decarboxylation—the ---COOH group is removed.
3. Dehydrogenation—a hydrogen is removed.
Fig. 11. Process of Transamination
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Fig. 12. Overview of catabolism of Organic Acids
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B. Lipid Catabolism
Microorganisms frequently use lipids as energy sources. Triglycerides or
triacylglycerols, esters of glycerol and fatty acids, are common energy sources. They can
be hydrolyzed to glycerol and fatty acids by microbial lipases. The glycerol is then
phosphorylated, oxidized to dihyroxyacetone phosphate, and catabolised in the glycolytic
pathway.
1. Lipases are enzymes that break down fats into fatty acid and glycerol components
2. Beta oxidation is the breakdown of fatty acids into two carbon segments (acetyl CoA),
Which can enter the Krebs cycle.
Functions of lipids in Microbes
 Lipids are essential to the structure and function of membranes
 Lipids also function as energy reserves, which can be mobilized as sources of
carbon
 90% of this lipid is “triacyglycerol”
Triacyglycerol-----lipase----->glycerol + 3 fatty acids
 The major fatty acid metabolism is “β-oxidation”
Lipids are broken down into their constituents of glycerol and fatty acids
Glycerol is oxidised by glycolysis and the TCA cycle.
 Bacteria are capable of growth on fatty acids and lipids. Lipids are part of the
membranes of living organisms and if available (usually because the organism
that was using them dies) can be used as a food source.
 Lipids are large molecules and cannot be transported across the membrane.
 A class of extracellular enzymes called lipases are responsible for the breakdown
of lipids. Lipases attack the bond between the glycerol molecule oxygen and the
fatty acid.
 Phospholipids are attacked by phospholipases. There are four classes of
phospholipases given different names depending upon the bond they cleave.
Phospholipases are not particular about their substrate and will attack a glycerol
ester linkage containing any length fatty acid attached to it. The result of this
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digestion is a hydrophillic head molecule, glycerol and fatty acids of various
chain lengths.
 The head can be one of several small organic molecules that are funneled into the
TCA cycle by one or two reactions that we won't cover here.
 Glycerol is converted into 3-Phosphoglycerate (depending upon the action of
phospholipase C or phospholipase D) and eventually pyruvate via glycolysis.
Fig. 13. Lipid Catabolism
The β- oxidation pathway
Characteristic features;
•
Every other carbon is converted to a C=O
•
Allows nucleophilic attack by CoA-SH on remaining chain
•
1 CoA is used for every 2 carbon segment to release acetyl-CoA
•
Each round produces
1 FADH2, 1 NADH, 1 Acetyl-CoA (2 in the last round)
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Step 1:
Dehydrogenation of Alkane to Alkene Catalyzed by isoforms of acyl-
CoA dehydrogenase (AD) on the inner mitochondrial membrane
Step 2: Hydration of Alkene Catalyzed by two isoforms of enoyl-CoA hydratase:
Soluble short-chain hydratase (crotonase)Membrane-bound long-chain hydratase,
part of trifunctional complexWater adds across the double bond yielding alcohol
Step 3:
Dehydrogenation of AlcoholCatalyzed by β-hydroxyacyl-CoA
dehydrogenase The enzyme uses NAD cofactor as the hydride acceptor Only Lisomers of hydroxyacyl CoA act as substrates Analogous to malate
dehydrogenase reaction in the CAC.
Fig. 14.The β- oxidation pathway
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Step 4: Transfer of Fatty Acid Chain Catalyzed by acyl-CoA acetyltransferase (thiolase)
via covalent mechanism, The carbonyl carbon in β-ketoacyl-CoA is electrophilic Active
site thiolate acts as nucleophile and releases acetyl-CoA ; Terminal sulfur in CoA-SH
acts as nucleophile.
The fatty acid is now two carbons shorter and an Acetyl-CoA, has been generated
which can be fed into the TCA cycle. The smaller fatty acid moves through the βoxidation pathway again, producing another Acetyl-CoA and shrinking by 2 carbons.
By performing successive rounds of beta oxidation on a fatty acid, it is possible to
convert it completely to Acetyl-CoA. Often fatty acids with odd numbers of carbons, the
final reaction will yield acetyl-CoA and Coenzyme-A hooked to a three carbon fatty acid
(propionyl-CoA). Propionyl-CoA is handled differently by different bacteria. In E. coli it
is converted into pyruvate.
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
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Module 6 – Microbial Metabolism
Lecture 5 – Photosynthesis
Photosynthesis is the use of light as a source of energy for growth, more
specifically the conversion of light energy into chemical energy in the form of ATP.
Prokaryotes that can convert light energy into chemical energy include the photosynthetic
cyanobacteria, the purple and green bacteria, and the "halobacteria" (actually archaea).
The cyanobacteria conduct plant photosynthesis, called oxygenic photosynthesis; the
purple
and
green
bacteria
conduct
bacterial
photosynthesis
or
anoxygenic
photosynthesis; the extreme halophilic archaea use a type of nonphotosynthetic
photophosphorylation mediated by a pigment, bacteriorhodopsin, to transform light
energy into ATP.
Net equation:
6CO2+12H2O+LightEnergyC6H12O6+6O2+6H20
Photosynthetic reactions divided into two stages:
–
Light reaction- light energy absorbed & converted to chemical energy (ATP,
NADPH)
–
Dark reaction-carbohydrates made from CO2 using energy stored in ATP &
NADPH
Types of bacterial photosynthesis
Five photosynthetic groups within domain Bacteria (based on 16S rRNA):
1. Oxygenic Photosynthesis
•
•
Occurs in cyanobacteria and prochlorophytes
Synthesis of carbohydrates results in release of molecular O2 and removal of
CO2 from
•
atmoshphere.
Occurs in lamellae which house thylakoids containing chlorophyll a/b and
phycobilisomes pigments which gather light energy
•
Uses two photosystems (PS):
- PS II- generates a proton-motive force for making ATP.
- PS I- generates low potential electrons for reducing power.
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2. Anoxygenic Photosynthesis
•
Uses light energy to create organic compounds, and sulfur or fumarate
compounds instead of O2.
•
Occurs in purple bacteria, green sulfur bacteria, green gliding bacteria and
heliobacteria.
•
Uses bacteriochlorophyll pigments instead of chlorophyll.
•
Uses one photosystem (PS I) to generate ATP in “cyclic” manner.
Light Reaction
The Light Reactions depend upon the presence of chlorophyll, the primary
light-harvesting pigment in the membrane of photosynthetic organisms. The functional
components of the photochemical system are light harvesting pigments, a membrane
electron transport system, and an ATPase enzyme. The photosynthetic electron
transport system of is fundamentally similar to a respiratory ETS, except that there is a
low redox electron acceptor (e.g. ferredoxin) at the top (low redox end) of the electron
transport chain, that is first reduced by the electron displaced from chlorophyll.
There are several types of pigments distributed among various phototrophic
organisms. Chlorophyll is the primary light-harvesting pigment in all photosynthetic
organisms. Chlorophyll is a tetrapyrrole which contains magnesium at the center of the
porphyrin ring. It contains a long hydrophobic side chain that associates with the
photosynthetic membrane. Cyanobacteria have chlorophyll a, the same as plants and
algae. The chlorophylls of the purple and green bacteria, called bacteriochlorophylls are
chemically different than chlorophyll a in their substituent side chains. This is reflected in
their light absorption spectra. Chlorophyll a absorbs light in two regions of the spectrum,
one around 450nm and the other between 650 -750nm; bacterial chlorophylls absorb from
800-1000nm in the far red region of the spectrum.
Carotenoids are always associated with the photosynthetic apparatus. They
function as secondary light-harvesting pigments, absorbing light in the blue-green
spectral region between 400-550 nm. Carotenoids transfer energy to chlorophyll, at near
100 percent efficiency, from wave lengths of light that are missed by chlorophyll. In
addition, carotenoids have an indispensable function to protect the photosynthetic
apparatus from photooxidative damage. Carotenoids have long hydrocarbon side chains
in a conjugated double bond system. Carotenoids "quench" the powerful oxygen radical,
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singlet oxygen, which is invariably produced in reactions between chlorophyll and O2
(molecular oxygen). Some non-photosynthetic bacterial pathogens, i.e., Staphylococcus
aureus, produce carotenoids that protect the cells from lethal oxidations by singlet
oxygen in phagocytes.
Phycobiliproteins are the major light harvesting pigments of the cyanobacteria.
They also occur in some groups of algae. They may be red or blue, absorbing light in the
middle of the spectrum between 550 and 650nm. Phycobiliproteins consist of proteins
that contain covalently-bound linear tetrapyrroles (phycobilins). They are contained in
granules called phycobilisomes that are closely associated with the photosynthetic
apparatus. Being closely linked to chlorophyll they can efficiently transfer light energy to
chlorophyll at the reaction center.
All phototrophic bacteria are capable of performing cyclic photophosphorylation
as described above and in Figure 16 and below in Figure 18. This universal mechanism of
cyclic photophosphorylation is referred to as Photosystem I. Bacterial photosynthesis
uses only Photosystem I (PSI), but the more evolved cyanobacteria, as well as algae and
plants, have an additional light-harvesting system called Photosystem II (PSII).
Photosystem II is used to reduce Photosystem I when electrons are withdrawn from PSI
for CO2 fixation. PSII transfers electrons from H2O and produces O2, as shown in Figure
20.
Fig. 15. The cyclical flow of electrons during anoxygenic photosynthesis.
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Fig. 16. Electron flow in oxygenic photosynthesis.
Dark reaction
The use of RUBP carboxylase and the Calvin cycle is the most common
mechanism for CO2 fixation among autotrophs. Indeed, RUBP carboxylase is said to be
the most abundant enzyme on the planet (nitrogenase, which fixes N2 is second most
abundant). This is the only mechanism of autotrophic CO2 fixation among eucaryotes,
and it is used, as well, by all cyanobacteria and purple bacteria. Lithoautotrophic bacteria
also use this pathway. But the green bacteria and the methanogens, as well as a few
isolated groups of procaryotes, have alternative mechanisms of autotrophic CO2 fixation
and do not possess RUBP carboxylase.
RUBP carboxylase (ribulose bisphosphate carboxylase) uses
ribulose
bisphosphate (RUBP) and CO2 as co-substrates. In a complicated reaction the CO2 is
"fixed" by addition to the RUBP, which is immediately cleaved into two molecules of 3phosphoglyceric acid (PGA). The fixed CO2 winds up in the -COO group of one of the
PGA molecules. Actually, this is the reaction which initiates the Calvin cycle (Fig. 3).
The Calvin cycle is concerned with the conversion of PGA to intermediates in
glycolysis that can be used for biosynthesis, and with the regeneration of RUBP, the
substrate that drives the cycle. After the initial fixation of CO2, 2 PGA are reduced and
combined to form hexose-phosphate by reactions which are essentially the reverse of the
oxidative Embden-Meyerhof pathway. The hexose phosphate is converted to pentosephosphate, which is phosphorylated to regenerate RUBP. An important function of the
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Calvin cycle is to provide the organic precursors for the biosynthesis of cell material.
Intermediates must be constantly withdrawn from the Calvin cycle in order to make cell
material. In this regard, the Calvin cycle is an anabolic pathway. The fixation of CO2 to
the level of glucose (C6H12O6) requires 18 ATP and 12 NADPH2.
Fig. 17. The Calvin cycle and its relationship to the synthesis of cell materials.
Most of the phototrophic procaryotes are autotrophs, which mean that they are
able to fix CO2 as a sole source of carbon for growth. Just as the oxidation of organic
material yields energy, electrons and CO2, in order to build up CO2 to the level of cell
material (CH2O), energy (ATP) and electrons (reducing power) are required. The overall
reaction for the fixation of CO2 in the Calvin cycle is CO2 + 3ATP + 2NADPH2 ---------> CH2O + 2ADP + 2Pi + 2NADP. The light reactions operate to produce ATP to
provide energy for the dark reactions of CO2 fixation. The dark reactions also need
reductant (electrons). Usually the provision of electrons is in some way connected to the
light reactions.
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Fig. 18. Comparison of electron transport pathways in oxygenic and anoxygenic photosynthesis
The differences between plant and bacterial photosynthesis are summarized in
Table 3 below. Bacterial photosynthesis is an anoxygenic process. The external electron
donor for bacterial photosynthesis is never H2O, and therefore, purple and green bacteria
never produce O2 during photosynthesis. Furthermore, bacterial photosynthesis is usually
inhibited by O2 and takes place in microaerophilic and anaerobic environments. Bacterial
chlorophylls use light at longer wave lengths not utilized in plant photosynthesis, and
therefore they do not have to compete with oxygenic phototrophs for light. Bacteria use
only cyclic photophosphorylation (Photosystem I) for ATP synthesis and lack a second
photosystem.
Table 3. Differences between plant and bacterial photosynthesis
Plant photosynthesis
Bacterial photosynthesis
Organisms
Plants, algae, cyanobacteria
Purple and green bacteria
Type of chlorophyll
Chlorophyll-a and absorbs 650-750nm
bacteriochlorophyll and
absorbs 800-1000nm
Photosystem I
present
present
(cyclic
photophosphorylation)
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present
absent
Produces O2
yes
no
Photosynthetic
H2O
H2S, other sulfur compounds or
Photosystem I
(noncyclic
photophosphorylation)
certain organic compounds
electron donor
Chemosynthesis
Chemosynthesis is the biological conversion of one or more carbon molecules
(usually carbon dioxide or methane) and nutrients into organic matter using the oxidation
of inorganic molecules (e.g. hydrogen gas, hydrogen sulfide) or methane as a source of
energy, rather than sunlight, as in photosynthesis. but groups that include conspicuous or
biogeochemically-important taxa include the sulfur-oxidizing gamma and epsilon
proteobacteria, the Aquificaeles, the Methanogenic archaea and the neutrophilic ironoxidizing bacteria.
Chemoautotrophs or lithotrophs, organisms that obtain carbon through
chemosynthesis, are phylogenetically diverse, united only by their ability to oxidize an
inorganic compound as an energy source. Chemosynthesis runs through the Bacteria and
the Archaea. Chemoautotrophs are usually organized into "physiological groups" based
on their inorganic substrate for energy production and growth (see Table 2 below).
Table 2. Physiological groups of chemoautotrophs
Physiological group
Energy
Oxidized
end Organism
source
product
Hydrogen bacteria
H2
H2O
Alcaligenes, Pseudomonas
Methanogens
H2
H2O
Methanobacterium
Carboxydobacteria
CO
CO2
Rhodospirillum,
Azotobacter
Nitrifying bacteria*
NH3
NO2
Nitrosomonas
Nitrifying bacteria*
NO2
NO3
Nitrobacter
Sulfur oxidizers
H2S or S
SO4
Thiobacillus, Sulfolobus
Iron bacteria
Fe ++
Fe+++
Gallionella, Thiobacillus
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*The overall process of nitrification, conversion of NH3 to NO3, requires a consortium
of microorganisms.
The hydrogen bacteria oxidize H2 (hydrogen gas) as an energy source. The
hydrogen bacteria are facultative lithotrophs as evidenced by the pseudomonads that
fortuitously possess a hydrogenase enzyme that will oxidize H2 and put the electrons into
their respiratory ETS. They will use H2 if they find it in their environment even though
they are typically heterotrophic. Indeed, most hydrogen bacteria are nutritionally versatile
in their ability to use a wide range of carbon and energy sources.
The methanogens used to be considered a major group of hydrogen bacteria until it was discovered that they are Archaea. The methanogens are able to oxidize H2 as
a sole source of energy while transferring the electrons from H2 to CO2 in its reduction to
methane. Metabolism of the methanogens is absolutely unique, yet methanogens
represent the most prevalent and diverse group of Archaea. Methanogens use H2 and
CO2 to produce cell material and methane. They have unique enzymes and electron
transport processes. Their type of energy generating metabolism is never seen in the
Bacteria, and their mechanism of autotrophic CO2 fixation is very rare, except in
methanogens.
The carboxydobacteria are able to oxidize CO (carbon monoxide) to CO2, using
an enzyme CODH (carbon monoxide dehydrogenase). The carboxydobacteria are not
obligate CO users, i.e., some are also hydrogen bacteria, and some are phototrophic
bacteria. Interestingly, the enzyme CODH used by the carboxydobacteria to oxidize CO
to CO2, is used by the methanogens for the reverse reaction - the reduction of CO2 to CO
- in their unique pathway of CO2 fixation.
The nitrifying bacteria are represented by two genera, Nitrosomonas and
Nitrobacter. Together these bacteria can accomplish the oxidation of NH3 to NO3, known
as the process of nitrification. No single organism can carry out the whole oxidative
process. Nitrosomonas oxidizes ammonia to NO2 and Nitrobacter oxidizes NO2 to NO3.
Most of the nitrifying bacteria are obligate lithoautotrophs, the exception being a few
strains of Nitrobacter that will utilize acetate. CO2 fixation utilizes RUBP carboxylase
and the Calvin Cycle. Nitrifying bacteria grow in environments rich in ammonia, where
extensive protein decomposition is taking place. Nitrification in soil and aquatic habitats
is an essential part of the nitrogen cycle.
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Chemoautotrophic sulfur oxidizers include both Bacteria (e.g. Thiobacillus) and
Archaea (e.g. Sulfolobus). Sulfur oxidizers oxidize H2S (sulfide) or S (elemental sulfur)
as a source of energy. Similarly, the purple and green sulfur bacteria oxidize H2S or S as
an electron donor for photosynthesis, and use the electrons for CO2 fixation (the dark
reaction of photosynthesis). Obligate autotrophy, which is nearly universal among the
nitrifiers, is variable among the sulfur oxidizers. Lithoautotrophic sulfur oxidizers are
found in environments rich in H2S, such as volcanic hot springs and fumaroles, and deepsea thermal vents. Some are found as symbionts and endosymbionts of higher organisms.
Since they can generate energy from an inorganic compound and fix CO2 as autotrophs,
they may play a fundamental role in primary production in environments that lack
sunlight. As a result of their lithotrophic oxidations, these organisms produce sulfuric
acid (SO4), and therefore tend to acidify their own environments. Some of the sulfur
oxidizers are acidophiles that will grow at a pH of 1 or less. Some are
hyperthermophiles that grow at temperatures of 115°C.
Iron bacteria oxidize Fe++ (ferrous iron) to Fe+++ (ferric iron). At least two
bacteria probably oxidize Fe++ as a source of energy and/or electrons and are capable of
chemoautotrophic growth: the stalked bacterium Gallionella, which forms flocculant
rust-colored colonies attached to objects in nature, and Thiobacillus ferrooxidans, which
is also a sulfur-oxidizing lithotroph.
Fig. 19. Chemoautotrophic or Lithotrophic oxidations. These reactions produce energy for metabolism in the nitrifying and
sulfur oxidizing bacteria.
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REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
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Module 6 – Microbial Metabolism
Lecture 6 – Biosynthesis of Amino acids and Lipids
Amino acid biosynthesis
Amino acid synthesis is the set of biochemical processes (metabolic pathways) by
which the various amino acids are produced from other compounds. A fundamental
problem for biological systems is to obtain nitrogen in an easily usable form. This
problem is solved by certain microorganisms capable of reducing the inert N≡N molecule
(nitrogen gas) to two molecules of ammonia in one of the most remarkable reactions in
biochemistry. Ammonia is the source of nitrogen for all the amino acids. The carbon
backbones come from the glycolytic pathway, the pentose phosphate pathway, or the
citric acid cycle.
In amino acid production, one encounters an important problem in biosynthesis,
namely stereochemical control. Because all amino acids except glycine are chiral,
biosynthetic pathways must generate the correct isomer with high fidelity. In each of the
19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon
atom is established by a transamination reaction that involves pyridoxal phosphate.
Almost all the transaminases that catalyze these reactions descend from a common
ancestor, illustrating once again that effective solutions to biochemical problems are
retained throughout evolution.
Amino acid synthesis
Amino acids are synthesized from α-ketoacids and later transaminated from another
aminoacid, usually Glutamate. The enzyme involved in this reaction is an
aminotransferase.
α-ketoacid + glutamate ⇄ amino acid + α-ketoglutarate
Glutamate itself is formed by amination of α-ketoglutarate:
α-ketoglutarate + NH+4 ⇄ glutamate
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Nitrogen fixation: Microorganisms use ATP and a powerful reductant to reduce
atmospheric nitrogen to ammonia.
Microorganisms use ATP and reduced ferredoxin, a powerful reductant, to reduce N2 to
NH3. An iron-molybdenum cluster in nitrogenase deftly catalyzes the fixation of N2, a
very inert molecule. Higher organisms consume the fixed nitrogen to synthesize amino
acids, nucleotides, and other nitrogen-containing biomolecules. The major points of entry
of NH4+ into metabolism are glutamine or glutamate.
 Nitrifying bacteria
N 2 + 8H+ + 8e– + 16ATP + 16 H 2O
Nitrogenase
2NH3 + H 2 + 16ADP + 16P i
 Nitrate Assimilation (Green plants, some fungi and bacteria)
 Ammonium Assimilation (1) (Carbamyl Phosphate Synthetase)
 Ammonium Assimilation (2) (Biosynthetic Glutamate Dehydrogenase) and/or
(Glutamine Synthetase)
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 Glutamate (90%) and Glutamine (10%) are the main sources of organic
Nitrogen for microbes.
Biosynthesis of some Non-essential Amino Acids (Reactions)
1. Alanine Biosynthesis
2. Aspartate and Asparagine Biosynthesis.
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3. Proline Biosynthesis

Amino acids are made from intermediates of the citric acid cycle and other
major pathways
Glutamate dehydrogenase catalyzes the reductive amination of α-ketoglutarate to
glutamate. A transamination reaction takes place in the synthesis of most amino acids. At
this step, the chirality of the amino acid is established. Alanine and aspartate are
synthesized by the transamination of pyruvate and oxaloacetate, respectively. Glutamine
is synthesized from NH4+ and glutamate, and asparagine is synthesized similarly.
Proline and arginine are derived from glutamate. Serine, formed from 3phosphoglycerate, is the precursor of glycine and cysteine. Tyrosine is synthesized by the
hydroxylation of phenylalanine, an essential amino acid. The pathways for the
biosynthesis of essential amino acids are much more complex than those for the
nonessential ones. Activated Tetrahydrofolate, a carrier of one-carbon units, plays an
important role in the metabolism of amino acids and nucleotides. This coenzyme carries
one-carbon units at three oxidation states, which are interconvertible: most reduced—
methyl; intermediate—methylene; and most oxidized—formyl, formimino, and methenyl.
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Fatty Acid/ Lipid Biosynthesis
Fatty acid biosynthesis occurs in following phases;
1. Synthesis of malonyl-CoA via Acetyl-CoA Carboxylase
2. Fatty Acid Synthase
3. Fatty acid elongation and desaturation
Site: Synthesis of fatty acids takes place in the cytoplasm and involves initiation of
synthesis by the formation of acetoacetyl-ACP and then an elongation cycle where 2
carbon units are successively added to the growing chain.
Acyl carrier protein (ACP) serves as a chaperone for the synthesis of fatty acids.
The growing fatty acid chain is covalently bound to ACP during the entire synthesis of
the fatty acid and only leaves the protein when it is attached to the glycerol backbone of
the forming lipid. ACP is one of the most abundant proteins in the bacterial cell (60,000
molecules per E. coli cell) which makes sense given the amount of lipid that must be
synthesized to make an entire cell membrane. The formation of acetoacetyl-ACP can be
catalyzed by a number of enzymes, but in all cases the starting substrate is acetyl-CoA.
Once formed, acetoacetyl-ACP enters the elongation cycle for fatty acid synthesis. This
cycle is the reverse of the β-oxidation of fatty acids discussed earlier.
The first step in the elongation cycle is condensation of malonyl-CoA with a
growing acetoacetyl-ACP chain. This adds two carbons to the chain. The next three
reactions use 2 NADPH to reduce the β-ketone and generate an acyl-ACP molecule two
carbons longer than the original substrate.
The acyl-ACP molecule continues through the cycle until the appropriate chain length is
reached. In E. coli fatty acid chains in lipids are 12-20 carbons long. The length of the
fatty acid chains and the number of double bonds (unsaturation) is dependent upon the
temperature the bacteria are growing at. The membrane must remain fluid. Using short
chain fatty acids with higher degrees of unsaturation increases the fluidity of the
membrane. As the temperature increases, longer fatty acid chains with fewer double
bonds will be more prevalent in the membrane.
 The input to fatty acid synthesis is acetyl-CoA, which is carboxylated to malonylCoA.
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The ATP-dependent carboxylation provides energy input. The CO2 is lost later during
condensation with the growing fatty acid. The spontaneous decarboxylation drives the
condensation.
 Acetyl-CoA Carboxylase catalyzes the 2-step reaction by which acetyl-CoA is
carboxylated to form malonyl-CoA. As with other carboxylation reactions (e.g.,
Pyruvate Carboxylase), the enzyme prosthetic group is biotin.
ATP-dependent carboxylation of the biotin, carried out at one active site (1), is followed
by transfer of the carboxyl group to acetyl-CoA at a second active site (2).
The overall reaction, which is is spontaneous, may be summarized as:
HCO3- + ATP + acetyl-CoA -------- ADP + Pi + malonyl-CoA
Garrett & Grisham; Biochemistry, 2/e
Fig. 20. The Acyl Carrier protein (ACP)
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Garrett & Grisham; Biochemistry, 2/e
Fig. 21. Fatty acid synthesis
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Fig. 22. Synthesis of palmitic acid
The overall synthesis of palmitic acid: The fatty acyl chain grows by two-carbon units
donated by activated malonate, with loss of CO2 at each step. The initial acetyl group is
shaded yellow, C-1 and C-2 of malonate are shaded pink, and the carbon released as CO2
is shaded green. After each two-carbon addition, reductions convert the growing chain to
a saturated fatty acid of four, then six, then eight carbons, and so on. The final product is
palmitate (16:0).
Stages of Fatty acid synthesis
•
Overall goal is to attach a two-carbon acetate unit from malonyl-CoA to a
growing chain and then reduce it.
•
Reaction involves cycles of four enzyme-catalyzed steps
–
Condensation of the growing chain with activated acetate.
–
Reduction of carbonyl to hydroxyl.
–
Dehydration of alcohol to trans-alkene.
–
Reduction of alkene to alkane.
•
The growing chain is initially attached to the enzyme via a thioester linkage
•
During condensation, the growing chain is transferred to the acyl carrier protein
•
After the second reduction step, the elongated chain is transferred back to fatty
acid synthase
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Lehninger Principles of Biochemistry, Fifth Edition
Fig. 23. Stages of fatty aid synthesis
Addition of two carbons to a growing fatty acyl chain: a four-step sequence. Each
malonyl group and acetyl (or longer acyl) group is activated by a thioester that links it
to fatty acid synthase, a multienzyme system.
1. Condensation of an activated acyl group (an acetyl group from acetyl-CoA is the
first acyl group) and two carbons derived from malonyl-CoA, with elimination of
CO2 from the malonyl group, extends the acyl chain by two carbons.
The β-keto product of this condensation is then reduced in three more steps nearly
identical to the reactions of β oxidation, but in the reverse sequence:
2. The β-keto group is reduced to an alcohol,
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Lehninger Principles of Biochemistry, Fifth Edition
Fig. 24. Stages of fatty aid synthesis
Addition of two carbons to a growing fatty acyl chain: a four-step sequence. Each
malonyl group and acetyl (or longer acyl) group is activated by a thioester that links it to
fatty acid synthase, a multienzyme system described later in the text. 1 Condensation of
an activated acyl group (an acetyl group from acetyl-CoA is the first acyl group) and two
carbons derived from malonyl-CoA, with elimination of CO2 from the malonyl group,
extends the acyl chain by two carbons. The mechanism of the first step of this reaction is
given to illustrate the role of decarboxylation in facilitating condensation. The β-keto
product of this condensation is then reduced in three more steps nearly identical to the
reactions of β oxidation, but in the reverse sequence: 2 the β-keto group is reduced to an
alcohol, 3 elimination of H2O creates a double bond, and 4 the double bond is reduced to
form the corresponding saturated fatty acyl group.
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Importance in organisms; Lipids constitute a broad group of naturally occurring
molecules that include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D,
E, and K), monoglycerides, diglycerides, triglycerides, phospholipids, and others. The
main biological functions of lipids include energy storage, as structural components of
cell membranes, and as important signaling molecules.
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
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Module 6 - Metabolism
Lecture – 7 - Biosynthesis of Pyramidines
1. INTRODUCTION
Nucleotides are essential for many cellular functions, including the storage of genetic
information, gene expression, energy metabolism, cell signaling, and biosynthesis. In a
cell, nucleotides exist primarily as 5'-triphosphates. ATP is the most prevalent nucleotide,
reaching mM concentrations in many cell types, while other nucleotides may be present
at much lower concentrations (cAMP).
Biological significance of nucleotides
1. Building blocks of nucleic acids (DNA and RNA).
2. Involved in energy storage, muscle contraction, active transport, and maintenance of
ion gradients.
3. Activated intermediates in biosynthesis (e.g. UDP-glucose, S-adenosylmethionine
(SAM).
4. Components of coenzymes (NAD+, NADP+, FAD, FMN, and CoA)
5. Metabolic regulators:
a. Second messengers (cAMP, cGMP)
b. Phosphate (PO32- ) donors for phosphorylation of kinases and phosphatases in
signal transduction (ATP)
c. Regulation of some enzymes via adenylation and uridylylation
Each nucleotide contains a purine or pyrimidine base, a ribose or deoxyribose sugar, and
a phosphate:
Nucleotide
Purine or
Pyrimidine
Base
O
5'
-O
P
O
O
O-
H
4'
3'
H
O
Phosphate
H
1'
2' H
H(OH)
Pentose sugar
Nucleoside
FIG. 25. STRCUTURE OF NUCLEOTIDE
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Sources of nucleotides in a cell:
1) Degradation of nucleic acids (salvage pathways). Free purine bases can be recycled
by coupling with the ribose phosphate moiety, 5-phospho-ribosyl-1-pyrophosphate
(PRPP), to form nucleotide monophosphates:
ad enine p hosph oribosyl
transfera se
Adenine + PRPP
Adenylate + PPi
Hypoxanthine-guanine phosphoribosyl
transferase (HGPRT)
Guanine + PRPP
Hypoxanthine + PRPP
Guanylate + PPi
Inosinate+ PPi
FIG. 26. SORUCES OF NUCLEOTIDES (BENJAMIN CUMMINGS, 2008)
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DE NOVO SYNTHESIS OF PYRIMIDINES
Metabolic precursors of nucleotides include amino acids, CO2, and ribose-5-phosphate.
Sources of carbon and nitrogen atoms in pyrimidine ring
from carbamoyl phosphate
N3
C
NH2
C
4
2
1
N
5C
from aspartate
O
6C
-O
C
CH2
O
O
CH
H2N
PO32-
COO-
O3PO
CH2
O
O
-O
-O
P
P
O
OH
5-phosphoribosyl-1-pyrophosphate (PRPP) is the
source of phosphoribose
OO
O
OH
Fig. 27. Soruces of carbon and nitrogen atoms in pyrimidine ring (Stryer’s Biochemistry 4th edition)
The pyrimidine ring is synthesized in a 6-step process that requires participation of
several enzymes. Most required enzymes are cytosolic, with the exception of orotate
dehydrogenase that is localized in mitochondria (see below). The general strategy is to
use pre-assembled components (carbamoyl phosphate and aspartate) to make a
pyrimidine ring which is then attached to the phosphoribose.
Part 1. The formation of carbamoyl phosphate is catalyzed by cytosolic carbamoyl
phosphate synthetase II (CPS).
ATP
ADP
HO
(from Gln)
NH3
O
O
HO
C
C
C
CPS
O
phosphorylation
of bicarbonate
P
O
ATP
ADP
Carbamic acid
O-O
P
C
CPS
NH2
NH2
O- ammonia displaces
the phosphate
OCarboxyphosphate
Bicarbonate
HO
O
HO
O
CPS
O
Pi
O
O
C
O
phosphorylation
Carbamic acid
NH2
Carbamoyl phosphate
Fig. 28. The formation of carbamoyl phosphate
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Regulated Step in Pyrimidine Biosynthesis
General Mechanism for replacing carbonyl oxygen with amino group:
The ammonia necessary for the formation of carbamic acid originates from glutamine:
NH2
H2N
H2
C
C
O
NH2
CH
C
H2
OH
CPS
C
O
Glutamine (Gln)
NH3
H2
C
HO
C
CH
C
H2
OH
C
O
O
glutamate
Note that a single enzyme, carbamoyl phosphate synthetase II, catalyzes all 4 reactions
required for the synthesis of carbamoyl phosphate. Reaction intermediates are channeled
internally between the active sites responsible for phosphorylation, carbamic acid
formation, and glutamine hydrolysis, without dissociating from the enzyme. This is
necessary to protect unstable intermediates from hydrolysis and to drive the reactions
forward.
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Part 2. The formation of orotate
The committed step in the biosynthesis of pyrimidines is the formation of N-carbamoylaspartate from aspartate and carbamoyl phosphate. Carbamoyl aspartate is then cyclized
and oxidized by NAD+ to orotate:
O
Aspartate
Transcarbamoylase
Asp
O-O
Pi
HN
O
O
P
C
O
NH2
+
C
OOC
Asp replaces Pi
CH
H
COO
cyclization
C
H2
Carbamoyl phosphate
H2O
NH2
Dihydroorotate
Dehydrogenase
O
Dihydroorotase
HN
OOC
N-Carbamoylaspartate
CH
CH
C
H2
NADH + H
C
HN
C
NH
C
OOC
O
C
H2
C
C
H
oxidation
O
Orotate
Dihydroorotate
Electrons are
channeled directly
to the transport
chain of
mitochondria
NH2
-OOC
+
+
NAD
NH
C
O
COO-
Aspartate
Fig. 29. Formation of Orotate (Stryer's Biochemistry 5th ed)
Note:
1. Aspartate transcarbamoylase is allosterically inhibited by CTP, the final product of
pyrimidine nucleotide biosynthesis. This ensures a tight control of CTP concentrations in
a cell.
•
N-(phosphonacetyl)-L-aspartate (PALA) is a bisubstrate analog inhibitor of
aspartate transcarbamoylase. It resembles carbamoylphosphate+ aspartate
•
Human carbamoyl phosphate synthetase and aspartate transcarbamoylase are part
of the same protein.
O
O
-
C
HN
OOC
O3PO
CH2
NH
C
O
-O
Orotate
O
O
OH
PPi
-O
P
C
C
H
O
CH
O3PO
C
O
OCH2
P
O
-
C
HN
pyrimidine phosphoribosyltransferase
N
O
COO
O
OH
5-phosphoribosyl-1-pyrophosphate (PRPP)
OH
OH
Orotidylate
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Part 3: Formation of UMP. Orotate coupling to ribose in the form of 5-phosphoribosyl1-pyrophosphate (PRPP) produces orotidylate (OMP):
PRPP is produced by phosphorylation of ribose-5-phosphate (from pentose phosphate
pathway):
2-
ATP
O3PO
CH2
AMP
2-
O3PO
CH2
O
O
OH
-O
P
PRPP synthetase
OH
O
-O
P
O
OH
OH
ribose-5-phosphate
O-
O
O
OH
5-phosphoribosyl-1-pyrophosphate (PRPP)
Decarboxylation of orotidylate yields uridylate (UMP), a major pyrimidine nucleotide.
O
C
HN
-
Phosp
O
CH
O3PO
C
O
CH2
N
O
UMP
H+
CO2
-
CH
O3PO
C
C
O
CH2
COO
horylat
ion of
C
HN
N
O
C
H
UMP
synthase
OH
OH
OH
Orotidylate
OH
Uridylate (UMP)
by
kinases gives rise to UDP and UTP:
UMP kinase
UMP + ATP
UDP + ADP
nucleotide diphosphate kinase
UTP + ADP
UDP + ATP
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Formation of cytosine nucleotides
Cytidine triphosphate is formed from uridine triphosphate by the replacement of a
carbonyl group with an amino group. This is accomplished by a mechanism similar to
carbamoyl phosphate synthesis (p. 4). The O4 of the uridine is phosphorylated, followed
by displacement with ammonia. CTP synthetase is feedback-inhibited by CTP.
Gln + H2O
NH2
O
Glu
C
HN
4-
NH3
CH
O3PO3PO3PO-H2C
CH
O3PO3PO3PO-H2C
N
O
CH2
C
N
O
C
H
H
ATP
ADP + Pi
OH
OH
C
O
C
O
CH2
4-
C
N
OH
OH
CTP
UTP
Feedback Inhibition in Bacteria Pyrimidine Biosynthesis
Nucleotide concentrations and their biosynthesis are highly regulated. This tight control
is achieved by allosteric modulation (nucleotide end products act as negative effectors).
Glutamine + HCO3- + ATP
PRPP
Carbamoyl phosphate
OMP
UMP
UDP
UTP
CTP
Fig. 30. Feedback inhibition in bacterial pyrimidine biosynthesis
Examples of feedback inhibition:
Carbamoyl phosphate synthetase is feedback – inhibited by CTP .
Aspartate transcarbamoylase (ATCase) is inhibited by CTP.
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Furthermore, the concentrations of key enzymes are transcriptionally regulated during the
cell cycle, with increased rates of nucleotide synthesis in the late G1/early S phase of the
cell cycle preceding DNA replication.
Orotic acid urea: a rare disease associated with defects in pyrimidine biosynthesis
–
Symptoms: anemia, growth retardation, orotic acid excretion in urine.
–
Causes: a defect in phosphoribosyl transferase or orotidylate decarboxylase
–
Treatment: patients are fed uridine: U → UMP → UDP → UTP
UTP inhibits CPS II (regulated step), preventing the biosynthesis of orotic acid
Pyrimidine biosynthesis: Take home message
1. Pyrimidines are synthesized using both de novo and salvage pathways.
2. The pyrimidine ring is synthesized from pre-assembled ingredients (carbamoyl
phosphate and aspartate) and then attached to ribose.
3. Pyrimidine biosynthesis is tightly regulated via feedback inhibition (CTP synthetase,
ATCase) and transcriptional regulation (ATCase).
4. Most of the necessary enzymes are located in the cytosol with the exception of
dihydroorotate (localized in the mitochondria).
5. The mammalian enzymes are multifunctional, e.g. CAD (three activities), UMP
synthetase (two activities).
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
Joint initiative of IITs and IISc – Funded by MHRD
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NPTEL – Biotechnology – Microbiology
Module 6 - Metabolism
Lecture – 8 - Biosynthesis of Purines and Peptidoglycan
DE NOVO SYNTHESIS OF PURINES
Sources of carbon and nitrogen atoms in purine ring:
Gly (2)
CO2 (5)
6
Aspartate (6)
amino
1N
C
7
5
N
8
C
C
2C
C
N
N10-THF (7)
N
4
3
(the order of incorporation)
N10-THF (3)
9
Glutamine
amide (1)
Glutamine
amide (4)
Fig. 31. Sources of carbon and nitrogen in purine ring (Stryer's Biochemistry 5th ed)
General features:
1. Unlike pyrimidines that do not acquire the ribose until the base moiety is synthesized,
purine ring is assembled on PRPP.
2. IMP is synthesized first and serves as a precursor to adenine and guanine nucleotides.
Step 1: Formation of 5-phosphoribosyl-1-amine from PRPP (committed step) by the
action of glutamine phosphoribosyl amidotransferase. PRPP provides the foundation for
purine biosynthesis. Glutamine phosphoribosyl amidotransferase has two domains: one
hydrolyzes glutamine to ammonia, and the other one is phosphoribosyl transferase
domain. Ammonia is channeled to site II without leaving the enzyme.
Glu + NH3
Gln + H2O
2-
Future N-9 of the purine ring
2-
O3PO
O3PO
CH2
CH2
O
-O
O
-O
P
O
OH
β-configuration of
the sugar
OP
O
NH2
O
PPi is replaced by NH2
O inversion of configuration
OH
5-phosphoribosyl-1-pyrophosphate (PRPP)
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PPi
OH
OH
5-Phosphoribosyl-1-amine
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This is the committed step. It is feedback inhibited by IMP. GMP, AMP
Step 2: Glycine is coupled to the amino group of phosphoribosylamine
glycinamide ribonucleotide synthetase
ATP + Gly
N7
ADP + Pi
C4 C5
NH
P-ribose
P-ribose-NH2
phorphoribosyl
amine
O
C
CH2
CH2
C
O
Gly is coupled to the
amino group
-
NH3+
glycinamide
ribonucleotide
NH3+
O
This is the only step in purine biosynthesis that contributes more than one atom to the
purineskeleton.
a) The carboxylate group of Gly is activated by phosphorylation to form acylphosphate.
b) The phosphate is then displaced by the amino group of phosphoribosylamine.
O
O
-O
P OH
-O
P O
NH3+
C
OP-ribose-NH2
O- P-ribose-NH
CH2
NH3+
C
O
CH2
O
Step 3: Transfer of a formyl group from N10-formyltetrahydrofolate to the amino group of
the glycine residue (catalyzed by glycinamide ribonucleotide transferase). N10-formyltetrahydrofolate (THF) serves as a C1 carbon donor.
O
N10-formylNH3+
P-ribose
NH
C
O
Glycinamide ribonucleotide
THF
H
THF
CH2
P-ribose
α -amino terminus
is formylated
NH
C
C4
C
C8
NH N7
H2 N
H
N
N
N
N
H
CH2 C5
OH
N9
O
Formylglycinamide ribonucleotide
CH2
5
O
C
H
CH2
O
N
C
10
O-
O
C
N
H
H2 H2 O
CH C C C OH
H
10
N -formyl -tetrahydrofolate (THF)
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Step 4: The inner amide group is converted to an amidine by the replacement with
ammonia derived from glutamine:
O
O
C
H
P-ribose
NH
ATP
H
ADP + Pi
NH
C
C
C8
NH N7
N9
CH2
NH
P-ribose
Glu + NH3
Gln + H2O
O
CH2 C5
N
H
Formylglycinamidine ribonucleotide
N3
Formylglycinamide ribonucleotide
C4
C
=NH replaces =O
Note: Steps 1-4 are catalyzed by a multienzyme complex. Many of the intermediates in
purine biosynthesis are unstable in aqueous solution and only exist in solvent protected
environment. The formation of multienzyme complexes makes it possible to internally
channel the product of one reaction to the next catalytic center without solvent exposure.
Step 5: An intramolecular coupling reaction accompanied by a loss of water forms the
five-membered imidazole ring. The carbonyl is activated by phosphorylation and the
phosphate is displaced by an amino group as shown on p. 5 (top)
O
AIR synthetase
C
H
NH
ATP
C8
ADP + Pi
HC
N7
N
CH C5
P-ribose
NH
C
CH2
N
- H2O
ring closure
H
Formylglycinamidine ribonucleotide
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P-ribose
N
N9
C C4
N3 NH2
5-aminoimidazole ribonucleotide
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Step 6: Bicarbonate adds first to the exocyclic amino group and then is transferred to the
neighboring carbon atom of the imidazole ring:Enzyme: AIR carboxylase
ATP +
O
HO
N
N
HC
O-
CH
P-ribose
HC
- H2O
NH2
8
carboxyl transfer HC
CH
O
C
N
C
N
ADP + Pi
N
7
O
5
C
9N
6
O-
C 4
HN
P-ribose
carboxylation of the
amino group
P-ribose
O-
NH2
Carboxyaminoimidazole
ribonucleotide
5-aminoimidazole ribonucleotide
Step 7: The imidazole carboxylate is phosphorylated and the phosphate is displaced by
the amino group of aspartate:
ATP
O
N
ADP + Pi
HC
C
C
O-
C
N
P-ribose
- H2O
N
P-ribose
NH2
H2N
Carboxyaminoimidazole
ribonucleotide
CH CO2-
N
H
C
CH
CO2CH2
NH2
CO2-
5-aminoimidazole-4-(N-succinylcarboxamide)
ribonucleotide
CH2
Asp
O
N
HC
CO2-
Enzyme: SAICAR synthetase
Step 8. Elimination of fumarate is catalyzed by lyase. The carbon skeleton of aspartate is
lost as fumarate (only the amino group is contributed by aspartate).
Enzyme: adenylsuccinate lyase
CO2-
CH
HC
O
N
HC
N
P-ribose
N
H
NH2
CO2-
CH
HC
CH
H
CO2-
5-amidoimidazole-4-(N-succinylcarboxxamide)
ribonucleotide
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O
N
CO2-
C
C
fumarate
N
P-ribose
C
NH2
C
NH2
5-aminoimidazole-4-carboxamide ribonu
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Step 9: The second formyl group is added from N10-formyltetrahydrofolate:
O
N
HC
10
N -formylTHF
C
HC
THF
C
NH2
C
N
O
N
P-ribose
NH2
NH2
C
N
P-ribose
NH
5-aminoimidazole-4-carboxamide
ribonucleotide (AICAR)
H
C
C2
O
5-formaminoimidazole-4-carboxamide
ribonucleotide (FAICAR)
Enzyme: AICAR transformylase
Step 10: Cyclization/dehydration produces inosinate:
7
O
N
HC
8
N
P-ribose
NH2
C
NH
9
C
4
6
C
P-ribose
H
C
N
O
5
HC
AMP cyclohydrolase
C
N
3
NH 1
N
CH
2
H 2O
O
Inosinate (IMP)
5-formaminoimidazole-4-carboxamide
ribonucleotide (FAICAR)
Formation of AMP and GMP from IMP
IMP is a common precursor to both AMP and GMP.
1. Formation of adenylate (AMP): the C-6 carbonyl group of inosinate is replaced with
the amino
group from Asp.
O-
Adenylsuccinate synthetase
O
CH
GTP
O
Asp
NH
C
N
N
- H2O
N
P-ribose
N
P-ribose
N
(IMP)
Asp =
CH C
O-
H
COONH2
N
O
ON
N
- H2O
P-ribose
N
Adenylsuccinate
Adenylate (AMP)
CH2
C
H
lyase
O
H2N
Inosinate
H
fumarate
CH
HN
N
GDP + Pi
N
-OOC
C
O
OH
Note that GTP is used as a phosphate donor
instead of ATP
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2. Formation of guanylate (GMP). Inosinate is first oxidized to xanthylate, and the C2 carbonyl is then converted to an amino group:
IMP dehydrogenase
GMP synthetase
NAD+
O
H2O
N
O
O
N
NADH + H+
ATP
AMP + PPi
NH
NH
NH
N
N
N
N
N
N
H
P-ribose
P-ribose
O
H3N
+
Glu
N
H2O + Gln P-ribose
Xanthylate
Inosinate
NH2
Guanylate (GMP)
(XMP)
(IMP)
Regulation of Purine Biosynthesis:
•
AMP, GMP and IMP are feedback inhibitors of purine biosynthesis
•
Purine biosynthesis is energetically expensive (6 moles ATP used per 1 mol IMP)
•
Nucleotide concentrations are tightly regulated in a cell. Loss of regulation may
lead to clinical disease (e.g. gout).
1. PRPP synthesis is inhibited by AMP, IMP, GMP (indicators of poor energy
status)
2. The committed step (phosphoribosylamine formation) is inhibited by all purine
mononucleotides.
3. AMP and GMP inhibit their own synthesis from IMP nucleotide
Reciprocal substrate regulation balances the relative purine levels:
AMP synthesis requires GTP as the energy source
GMP synthesis requires ATP as the energy source
Fig. 32. Regulation of purine biosynthesis
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Biosynthesis of NAD+
Nicotinamide adenine dinucleotide (NAD+) and its phosphorylated analog, NADP+, are
important coenzymes that participate in a number of biological processes involving
electron transfer. NAD+ contains an AMP moiety as part of the molecule:
NAD+ is a two electron acceptor (H-)
H
O
O
Nicotinamide
O
H
H
NH2
NH2
NH2
O
P
-O
P
N
O
N
NH2
OH N
OH
N
P
P
O
R
N
O
-O
N
O
R
NAD+
Adenine
NADH
N
O
Ribose
O
OH
OH
NAD+
NAD+ synthesis requires nicotinate (vitamin B6), which is derived from tryptophan. In
the first step, nicotinate ribonucleotide is formed from nicotinate and PRPP:
COOPRPP
PPi
COO-
N
2-
O3PO
O
N
H
Nicotinate
H
H
OH
H
OH
H
Ribose-P
Nicotinate ribonucleotide
In the following steps, an AMP moiety is transferred from ATP to nicotinate
ribonucleotide to form desamido-NAD+. Finally, the carboxyl group of desamido-NAD is
converted to amide using glutamine as an ammonia donor:
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NADP is obtained by phosphorylation of the 2'-OH of the adenine ribose by ATP in the
presence of NAD+ kinase.
Purine biosynthesis:
1. Purines are synthesized using both de novo and salvage pathways.
2. The purine ring is built on a ribose skeleton to make IMP, followed by branches to
AMP and GMP. Amino acids serve as N donors, while CO2 and C1 units of N10-formylTHF are carbon donors.
3. The general mechanism involves ATP-mediated phosphorylation of carbonyl oxygen,
followed by phosphate displacement by an amine.
4.
Purine biosynthesis is tightly regulated via feedback inhibition. Formation of
phosphoribosylamine is the committed step. The loss of regulation can lead to a clinical
disease.
5.
NAD+ is biosynthesized from nicotinate, ATP, and PRPP. Glutamine is used as an
amino donor.
PEPTIDOGLYCAN SYNTHESIS:
Bacterial cell walls contain a large, complex peptidoglycan molecule consisting of
log polysaccharide chains made of alternating N-acetykmuramic acid (NAM) and Nacetylglucosamine (NAG) residues. Pentapeptide chains are attached to the NAM groups.
The polysaccharide chains are connected through their pentapeptides or by interbridges.
Peptidoglycan synthesis is a multistep process that has been best studied in the grampositive bacterium Staphylococcus aureus. Two carriers participate: uridine diphosphate
(UDP) and bactoprenol. Bactoprenol is a 55-carbon alcohol that attaches to NAM by a
pyrophosphate group and moves peptodoglycan components through the hydrophobic
membrane. Transpeptidation is an important reaction, wherein finally peptide cross-links
between peptidoglycan chains are formed. Peptidoglycan synthesis is particularly
vulnerable to disruption by antimicrobial agents. Inhibition at any stage can weaken the
cell wall and can lead to osmotic lysis. Many antibiotics interfere with peptidoglycan
synthesis. For example, Penicillin inhibits the transpeptidation reaction and bacitracin
blocks the dephosphorylation of bactoprenol pyrophosphate.
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PATTERNS OF CELL WALL FORMATION:
To grow and divide efficiently, a bacterial cell must add new peptidoglycan to its
cell wall in a precise and well-regulated way while maintaining wall shape and integrity
in the presence of high osmotic pressure. The growing bacterium must be able to degrade
it just enough to provide accept ends for the incorporation of new peptidoglycan units. It
must also reorganize peptidoglycan structure when necessary. This limited peptidoglycan
digestion is accomplished by enzymes known as autolysins, some of which attack the
polysaccharide chains, while others hydrolyze the peptide cross-links. Autolysin
inhibitors keep the activity of these enzymes under tight control.
There seems to be two general patterns of location and distribution of cell wall
synthetic activity and varies with species. Many gram-positive cocci have only one to a
few zones of growth. The principal growth zone is usually at the site of septum
formation, and new cell wall halves are synthesized back-to-back. The second pattern of
synthesis occurs in the rod shaped bacterial and occurs at the site of septum formation
just as before, but growth sites also are scattered along the cylindrical portion of the rod.
Thus growth is distributed more diffusely in rod-shaped bacteria than in the cocci.
Synthesis must lengthen rod-shaped cells as well as divide them. Presumably this
accounts for the differences in wall formation pattern.
REFERENCES:
Text Books:
1. Jeffery C. Pommerville. Alcamo’s Fundamentals of Microbiology (Tenth Edition).
Jones and Bartlett Student edition.
2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Pearson - Microbiology: An
Introduction. Benjamin Cummings.
Reference Books:
1. Lansing M. Prescott, John P. Harley and Donald A. Klein. Microbiology. Mc Graw
Hill companies.
Joint initiative of IITs and IISc – Funded by MHRD
Page 73 of 73