CHAPTER 5  But without microbes, there would be little

nitrogen available for most life forms.

MICROBIAL METABOLISM  Certain bacteria (such as these Rhizobium,
above, within a soybean root nodule, shown at
 Still other bacteria can live on diets of right) in the soil convert nitrogen from the
inorganic substances such as carbon dioxide, atmosphere into forms that other life forms can
iron, sulfur, hydrogen gas, and ammonia. use.
 Microbial metabolism allows some  Beverages and food: Various bacteria and
microorganisms to grow in or on the human yeasts (such as Saccharomyces cerevisiae,
body shown at right) carry out catabolic reactions
 Metabolism is the buildup and breakdown of called fermentation. Beer, wine, and foods
nutrients within a cell. These chemical such as cheeses, yogurt, pickles, sauerkraut,
reactions provide energy and create and soy sauce tap microbial metabolism as a
substances that sustain life. crucial part of production
 Two key players in metabolism are enzymes  Sewage treatment: Contaminated water
and the molecule adenosine triphosphate undergoes a variety of biological processes in
(ATP). sewage treatment facilities like the one shown
 Enzymes catalyze reactions for specific here.
molecules called substrates. During enzymatic  Many bacteria, including some species of
reactions, substrates are transformed into new cyanobacteria (shown on the right) play a role
substances called products. in removing harmful organic matter.
 Enzymes, which are generally proteins, may  Drugs: The pharmaceutical industry uses a
need other nonprotein molecules called variety of bacteria and fungi in the production
cofactors to work. Inorganic cofactors include of antibiotics, such as penicillin, (derived from
metal ions. the Penicillium fungus, shown on the right).
 Organic cofactors, or coenzymes, include  Bacitracin, erythromycin, and other
the electron carriers FAD, NAD+ and NADP+. treatments such as vaccines, vitamins, and
 without energy, certain reactions will never enzymes are also derived from microbial
occur, even if enzymes are present. metabolism.
 Adenosine triphosphate (ATP) is a molecule  Enzymes facilitate metabolic reactions.
that cells use to manage energy needs.  ATP is used by microbes and other cells to
 If a reaction results in excess energy, some manage energy needs.
can be captured in the form of ATP’s bonds.  Catabolic reactions couple with ATP
 A cell can then break those same bonds and synthesis.
use the released energy to fuel other reactions.  Anabolic reactions couple with ATP
 Energy is released when the terminal breakdown.
phosphate is split from ATP
 The chemistry of metabolism can seem CATABOLIC AND ANABOLIC
overwhelming at first, with pathways, or sets of REACTIONS
many coordinated reactions, working together
 Because chemical reactions either release
toward common goals.
or require energy, metabolism can be viewed
 But the basic rules of metabolism are
as an energy-balancing act.
actually quite simple.
 Accordingly, metabolism can be divided into
 Pathways can be categorized into two
two classes of chemical reactions: those that
general types—catabolic and anabolic.
release energy and those that require energy.
 Catabolic pathways break down
 In living cells, the enzyme-regulated
macromolecules into simple component parts,
chemical reactions that release energy are
releasing energy in the process.
generally the ones involved in catabolism, the
 Anabolic pathways build up macromolecules
breakdown of complex organic compounds into
by combining simpler molecules, using energy
simpler ones.
in the process.
 These reactions are called catabolic, or
 In other words, catabolic and anabolic
degradative, reactions.
pathways are linked by energy.
 Catabolic reactions are generally hydrolytic
 Catabolic reactions provide the energy
reactions (reactions which use water and in
needed for anabolic reactions.
which chemical bonds are broken), and they
 Although microbial metabolism can cause are exergonic (produce more energy than they
disease and food spoilage, many pathways consume).
are beneficial rather than pathogenic.
 An example of catabolism occurs when cells
 Nitrogen cycle. Nitrogen is a key component break down sugars into carbon dioxide and
in proteins, DNA and RNA, and plant water.
chlorophyll.
 The enzyme-regulated energy-requiring  The energy transferred by the particles in
reactions are mostly involved in anabolism, the the collision can disrupt their electron
building of complex organic molecules from structures enough to break chemical bonds or
simpler ones. form new bonds.
 These reactions are called anabolic, or  Several factors determine whether a
biosynthetic, reactions. collision will cause a chemical reaction: the
 Anabolic processes often involve velocities of the colliding particles, their energy,
dehydration synthesis reactions (reactions that and their specific chemical configurations.
release water), and they are endergonic  Up to a point, the higher the particles’
(consume more energy than they produce). velocities, the more probable that their collision
 Examples of anabolic processes are the will cause a reaction.
formation of proteins from amino acids, nucleic  Also, each chemical reaction requires a
acids from nucleotides, and polysaccharides specific level of energy. But even if colliding
from simple sugars. particles possess the minimum energy needed
 These biosynthetic reactions generate the for reaction, no reaction will take place unless
materials for cell growth. the particles are properly oriented toward each
 Catabolic reactions provide building blocks other.
for anabolic reactions and furnish the energy  The collision energy required for a chemical
needed to drive anabolic reactions. reaction is its activation energy, which is the
 This coupling of energy-requiring and amount of energy needed to disrupt the stable
energy-releasing reactions is made possible electronic configuration of any specific
through the molecule adenosine triphosphate molecule so that the electrons can be
(ATP). rearranged.
 ATP stores energy derived from catabolic  The reaction rate—the frequency of
reactions and releases it later to drive anabolic collisions containing sufficient energy to bring
reactions and perform other cellular work. about a reaction—depends on the number of
 When the terminal phosphate group is split reactant molecules at or above the activation
from ATP, adenosine diphosphate (ADP) is energy level.
formed, and energy is released to drive  One way to increase the reaction rate of a
anabolic reactions. substance is to raise its temperature.
 Thus, anabolic reactions are coupled to ATP  By causing the molecules to move faster,
breakdown, and catabolic reactions are heat increases both the frequency of collisions
coupled to ATP synthesis and the number of molecules that attain
 Only part of the energy released in activation energy.
catabolism is actually available for cellular  The number of collisions also increases
functions because part of the energy is lost to when pressure is increased or when the
the environment as heat. reactants are more concentrated (because the
 Because the cell must use energy to distance between molecules is thereby
maintain life, it has a continuous need for new decreased).
external sources of energy.  In living systems, enzymes increase the
 the principal properties of a group of proteins reaction rate without raising the temperature.
involved in almost all biologically important
chemical reactions: enzymes. ENZYMES AND CHEMICAL
 A cell’s metabolic pathways (sequences of REACTIONS
chemical reactions) are determined by its  Substances that can speed up a chemical
enzymes, which are in turn determined by the reaction without being permanently altered
cell’s genetic makeup themselves are called catalysts.
 In living cells, enzymes serve as biological
ENZYMES catalysts.
COLLISION THEORY  As catalysts, each enzyme acts on a specific
substance, called the enzyme’s substrate (or
 Chemical reactions occur when chemical substrates, when there are two or more
bonds are formed or broken. reactants), and each catalyzes only one
 For reactions to take place, atoms, ions, or reaction.
molecules must collide.  As catalysts, enzymes typically accelerate
 The collision theory explains how chemical chemical reactions by lowering their activation
reactions occur and how certain factors affect energy
the rates of those reactions.  The general sequence of events in enzyme
 The basis of the collision theory is that all action is as follows
atoms, ions, and molecules are continuously
moving and colliding with one another.
  The surface of the substrate contacts a  Enzymes within each of the major classes
specific region of the surface of the are named according to the more specific types
enzyme molecule, called the active site. of reactions they assist.
 A temporary intermediate compound  For example, the class called
forms, called an enzyme–substrate oxidoreductases is involved with oxidation-
complex. The enzyme orients the reduction reactions
substrate into a position that increases  Enzymes in the oxidoreductase class that
the probability of reaction, which remove hydrogen (H) from a substrate are
enables the collisions to be more called dehydrogenases; those that add
effective. electrons to molecular oxygen (O2) are called
 The substrate molecule is transformed oxidases.
by the rearrangement of existing atoms,  dehydrogenase and oxidase enzymes have
the breakdown of the substrate even more specific names, such as lactate
molecule, or in combination with another dehydrogenase and cytochrome oxidase,
substrate molecule. depending on the specific substrates on which
 The transformed substrate molecules— they act.
the products of the reaction—are
released from the enzyme molecule ENZYME COMPONENTS
because they no longer fit in the active  Although some enzymes consist entirely of
site of the enzyme proteins, most consist of both a protein portion,
 The unchanged enzyme is now free to called an apoenzyme, and a nonprotein
react with other substrate molecules. component, called a cofactor.
 An enzyme’s ability to accelerate a reaction  Ions of iron, zinc, magnesium, or calcium are
without the need for an increase in temperature examples of cofactors.
is crucial to living systems because a  If the cofactor is an organic molecule, it is
significant temperature increase would destroy called a coenzyme.
cellular proteins.  Apoenzymes are inactive by themselves;
they must be activated by cofactors.
ENZYME SPECIFICITY AND  Together, the apoenzyme and cofactor form
EFFICIENCY a holoenzyme, or whole, active enzyme
 Enzymes have specificity for particular  Cofactors may help catalyze a reaction by
substrates. forming a bridge between an enzyme and its
 The unique configuration of each enzyme substrate.
enables it to “find” the correct substrate from  Coenzymes may assist the enzyme by
among the diverse molecules in a cell. accepting atoms removed from the substrate or
 However, the active site and substrate are by donating atoms required by the substrate.
flexible, and they change shape somewhat as  Some coenzymes act as electron carriers,
they meet to fit together more tightly. removing electrons from the substrate and
 The substrate is usually much smaller than donating them to other molecules in
the enzyme, and relatively few of the enzyme’s subsequent reactions.
amino acids make up the active site.  Many coenzymes are derived from vitamins
 A certain compound can be a substrate for  Two of the most important coenzymes in
several different enzymes that catalyze cellular metabolism are nicotinamide adenine
different reactions, so the fate of a compound dinucleotide (NAD1) and nicotinamide adenine
depends on the enzyme that acts on it dinucleotide phosphate (NADP1).
 Enzymes are extremely efficient. Under  Whereas NAD+ is primarily involved in
optimum conditions, they can catalyze catabolic (energy-yielding) reactions, NADP+ is
reactions at rates 108 to 1010 times (up to 10 primarily involved in anabolic (energy-requiring)
billion times) higher than those of comparable reactions.
reactions without enzymes  The flavin coenzymes, such as flavin
 Many enzymes exist in the cell in both active mononucleotide (FMN) and flavin adenine
and inactive forms. The rate at which enzymes dinucleotide (FAD), contain derivatives of the B
switch between these two forms is determined vitamin riboflavin and are also electron carriers.
by the cellular environment.  Another important coenzyme, coenzyme A
(CoA), contains a derivative of pantothenic
NAMING ENZYMES acid, another B vitamin.
 The names of enzymes usually end in -ase.  This coenzyme plays an important role in the
 All enzymes can be grouped into six synthesis and breakdown of fats and in a
classes, according to the type of chemical series of oxidizing reactions called the Krebs
reaction they catalyze cycle.
FACTORS INFLUENCING
ENZYMATIC ACTIVITY Substrate Concentration
 Enzymes are subject to various cellular  Under conditions of high substrate
controls. concentration, an enzyme is said to be in
 Two primary types are the control of saturation; that is, its active site is always
enzyme synthesis and the control of enzyme occupied by substrate or product molecules,
activity (how much enzyme is present versus and it’s catalyzing a specific reaction at its
how active it is). maximum rate.
 Several factors influence the activity of an  This maximum rate can be attained only
enzyme. when the concentration of substrate(s) is
extremely high.
 Among the more important are temperature,
pH, substrate concentration, and the presence  In this condition, a further increase in
or absence of inhibitors. substrate concentration will not affect the
reaction rate because all active sites are
Temperature already in use
 The rate of most chemical reactions
Inhibitors
increases as the temperature increases.
 An effective way to control the growth of
 Molecules move more slowly at lower
bacteria is to control, or inhibit, their enzymes.
temperatures than at higher temperatures and
 Certain poisons, such as cyanide, arsenic,
so may not have enough energy to cause a
and mercury, combine with enzymes and
chemical reaction.
prevent the bacteria from functioning. As a
 The optimal temperature for most disease-
result, the cells stop functioning and die.
producing bacteria in the human body is
 Enzyme inhibitors are classified as either
between 35°C and 40°C.
competitive or noncompetitive inhibitors
 The rate of reaction declines beyond the
 Competitive inhibitors fill the active site of an
optimal temperature because of the enzyme’s
enzyme and compete with the normal substrate
denaturation, the loss of its characteristic three-
for the active site.
dimensional structure
 A competitive inhibitor can do this because
 Denaturation of a protein involves the
its shape and chemical structure are similar to
breakage of hydrogen bonds and other
those of the normal substrate
noncovalent bonds; a common example is the
 However, unlike the substrate, it does not
transformation of uncooked egg white (a
undergo any reaction to form products.
protein called albumin) to a hardened state by
heat.  Some competitive inhibitors bind irreversibly
 Denaturation of an enzyme changes the to amino acids in the active site, preventing any
further interactions with the substrate.
arrangement of the amino acids in the active
site, altering its shape and causing the enzyme  Others bind reversibly, alternately occupying
to lose its catalytic ability. and leaving the active site; these slow the
 In some cases, denaturation is partially or enzyme’s interaction with the substrate.
fully reversible.  Increasing the substrate concentration can
 However, if denaturation continues until the overcome reversible competitive inhibition
enzyme has lost its solubility and coagulates,  One good example of a competitive inhibitor
the enzyme cannot regain its original is sulfanilamide (a potent antibacterial drug),
properties. which inhibits the enzyme whose normal
 Enzymes can also be denatured by substrate is para-aminobenzoic acid (PABA):
concentrated acids, bases, heavy-metal ions  Noncompetitive inhibitors do not compete
(such as lead, arsenic, or mercury), alcohol, with the substrate for the enzyme’s active site;
and ultraviolet radiation instead, they interact with another part of the
enzyme
pH  In this process, called allosteric (“other
space”) inhibition, the inhibitor binds to a site
 Typically, enzymes have an optimum pH at
on the enzyme other than the substrate’s
which they are most active
binding site, called the allosteric site.
 When the H+ concentration (pH) in the
 This binding causes the active site to
medium is changed drastically, the protein’s
change its shape, making it nonfunctional. As a
three-dimensional structure is altered.
result, the enzyme’s activity is reduced.
 Extreme changes in pH can cause
 This effect can be either reversible or
denaturation. Acids (and bases) alter a
irreversible, depending on whether the active
protein’s three-dimensional structure because
site can return to its original shape.
the H+ (and OH-) compete with hydrogen and
ionic bonds in an enzyme, resulting in the  In some cases, allosteric interactions can
enzyme’s denaturation. activate an enzyme rather than inhibit it.
 Cyanide can bind the iron in iron-containing  Actually, a better term is probably unstable
enzymes, and fluoride can bind calcium or bonds.
magnesium.  Although the amount of energy in these
 Substances such as cyanide and fluoride bonds is not exceptionally large, it can be
are sometimes called enzyme poisons because released quickly and easily.
they permanently inactivate enzymes.

FEEDBACK INHIBITION
 Noncompetitive, or allosteric, inhibitors play
a role in a type of biochemical control called
feedback inhibition, or end-product inhibition.
OXIDATION-REDUCTION REACTIONS
 This control mechanism stops the cell from  Oxidation is the removal of electrons (e−)
making more of a substance than it needs and from an atom or molecule, a reaction that
thereby wasting chemical resources. often produces energy.
 In some metabolic reactions, several steps  Oxidation and reduction reactions are
are required for the synthesis of a particular always coupled: each time one substance is
chemical compound, called the end-product. oxidized, another is simultaneously reduced.
 In many metabolic pathways, the end-  The pairing of these reactions is called
product can allosterically inhibit the activity of oxidation-reduction or a redox reaction.
one of the enzymes earlier in the pathway.  In many cellular oxidations, electrons and
 The bacterium E. coli can be used to protons (hydrogen ions, H+) are removed at
demonstrate feedback inhibition in the the same time; this is equivalent to the
synthesis of the amino acid isoleucine, which is removal of hydrogen atoms, because a
required for the cell growth. hydrogen atom is made up of one proton and
 In this metabolic pathway, the amino acid one electron
threonine is enzymatically converted to  . Because most biological oxidations involve
isoleucine in five steps. the loss of hydrogen atoms, they are also
 If isoleucine is added to the growth medium called dehydrogenation reactions.
for E. coli, it inhibits the first enzyme in the  NAD+ assists enzymes by accepting
pathway, and the bacteria stop synthesizing hydrogen atoms that have been removed
isoleucine. from the substrate, in this case the organic
 This condition is maintained until the supply molecule.
of isoleucine is depleted.  The reduced coenzyme, NADH, contains
 This type of feedback inhibition is also more energy than NAD+. This energy can be
involved in regulating the cells’ production of used to generate ATP in later reactions.
other amino acids, as well as vitamins, purines,  It’s important to remember that cells use
and pyrimidines. biological oxidation-reduction reactions in
catabolism to extract energy from nutrient
RIBOZYMES molecules.
 a unique type of RNA called a ribozyme.  Cells take nutrients, some of which serve as
 Like protein enzymes, ribozymes function energy sources, and degrade them from
as catalysts, have active sites that bind to highly reduced compounds (with many
substrates, and are not used up in a chemical hydrogen atoms) to highly oxidized
reaction. compounds.
 Ribozymes cut and splice RNA and are
involved in protein synthesis at ribosomes THE GENERATION OF ATP
 Much of the energy released during
ENERGY PRODUCTION oxidation-reduction reactions is trapped within
the cell by the formation of ATP.
 Nutrient molecules, like all molecules, have
energy associated with the electrons that form  Specifically, an inorganic phosphate group,
bonds between their atoms. P smallest size, for in text is added to ADP with
the input of energy to form ATP
 When it’s spread throughout the molecule,
this energy is difficult for the cell to use.  The addition of P to a chemical compound is
Various reactions in catabolic pathways, called phosphorylation.
however, concentrate the energy into the  Organisms use three mechanisms of
bonds of ATP, which serves as a convenient phosphorylation to generate ATP from ADP.
energy carrier. Substrate-Level Phosphorylation
 ATP is generally referred to as having “high-
energy” bonds.  In substrate-level phosphorylation, ATP is
usually generated when a high-energy P is
directly transferred from a phosphorylated CARBOHYDRATE CATABOLISM
compound (a substrate) to ADP.
 Generally, the P has acquired its energy  Most microorganisms oxidize carbohydrates
during an earlier reaction in which the substrate as their primary source of cellular energy.
itself was oxidized  Carbohydrate catabolism, the breakdown of
carbohydrate molecules to produce energy, is
Oxidative Phosphorylation therefore of great importance in cell
 In oxidative phosphorylation, electrons are metabolism.
transferred from organic compounds to one  Glucose is the most common carbohydrate
group of electron carriers (usually to NAD+ and energy source used by cells.
FAD).  Microorganisms can also catabolize various
 Then the electrons are passed through a lipids and proteins for energy production
series of different electron carriers to molecules  To produce energy from glucose,
of oxygen (O2) or other oxidized inorganic and microorganisms use two general processes:
organic molecules. cellular respiration and fermentation.
 This process occurs in the plasma  Both cellular respiration and fermentation
membrane of prokaryotes and in the inner usually start with the same first step, glycolysis,
mitochondrial membrane of eukaryotes. but follow different subsequent pathways
 The sequence of electron carriers used in  The respiration of glucose typically occurs in
oxidative phosphorylation is called an electron three principal stages: glycolysis, the Krebs
transport chain (system) cycle, and the electron transport chain
 The transfer of electrons from one electron (system).
carrier to the next releases energy, some of  Glycolysis is the oxidation of
which is used to generate ATP from ADP glucose to pyruvic acid with the
through a process called chemiosmosis production of some ATP and
energy-containing NADH.
Photophosphorylation  The Krebs cycle is the oxidation
 The third mechanism of phosphorylation, of acetyl CoA (a derivative of
photophosphorylation, occurs only in pyruvic acid) to carbon dioxide,
photosynthetic cells, which contain light- with the production of some ATP,
trapping pigments such as chlorophylls. energy-containing NADH, and
 In photosynthesis, organic molecules, another reduced electron carrier,
especially sugars, are synthesized with the FADH2 (the reduced form of
energy of light from the energy-poor building flavin adenine dinucleotide).
blocks, carbon dioxide and water.  In the electron transport chain
 Photophosphorylation starts this process by (system), NADH and FADH2 are
converting light energy to the chemical energy oxidized, contributing the
of ATP and NADPH, which, in turn, are used to electrons they have carried from
synthesize organic molecules. the substrates to a “cascade” of
 As in oxidative phosphorylation, an electron oxidation-reduction reactions
transport chain is involved. involving a series of additional
electron
METABOLIC PATHWAYS OF  In respiration, most of the ATP is generated
ENERGY PRODUCTION in the third step
 Because respiration involves a long series of
 Organisms release and store energy from
oxidation-reduction reactions, the entire
organic molecules by a series of controlled
process can be thought of as involving a flow of
reactions rather than in a single burst.
electrons from the energy-rich glucose
 If the energy were released all at once as a molecule to the relatively energy-poor CO2 and
large amount of heat, it could not be readily H2O molecules.
used to drive chemical reactions and would, in
 glycolysis and the Krebs cycle generate a
fact, damage the cell.
small amount of ATP and also supply the
 To extract energy from organic compounds electrons that generate a great deal of ATP at
and store it in chemical form, organisms pass the electron transport chain stage.
electrons from one compound to another
 Typically, the initial stage of fermentation is
through a series of oxidation-reduction
also glycolysis
reactions.
 However, once glycolysis has taken place,
 Secondary products, such as CO2 and H2O,
the pyruvic acid is converted into one or more
are sometimes called by-products or waste
different products, depending on the type of
products.
cell.
 These products might include alcohol
(ethanol) and lactic acid.
 Unlike respiration, there is no Krebs cycle or of ATP are formed by
electron transport chain in fermentation. substrate-level
 Accordingly, the ATP yield, which comes phosphorylation.
only from glycolysis, is much lower.  Because two molecules of ATP were needed
to get glycolysis started and four molecules of
GLYCOLYSIS ATP are generated by the process, there is a
 Glycolysis, the oxidation of glucose to net gain of two molecules of ATP for each
pyruvic acid, is usually the first stage in molecule of glucose that is oxidized
carbohydrate catabolism. ADDITIONAL PATHWAYS TO
 Glycolysis is also called the Embden-
GLYCOLYSIS
Meyerhof pathway.
 The word glycolysis means splitting of sugar,  Many bacteria have another pathway in
and this is exactly what happens. addition to glycolysis for the oxidation of
 The enzymes of glycolysis catalyze the glucose.
splitting of glucose, a six-carbon sugar, into two  The most common alternative is the pentose
three-carbon sugars. phosphate pathway; another alternative is the
 These sugars are then oxidized, releasing Entner Doudoroff pathway.
energy, and their atoms are rearranged to form The Pentose Phosphate Pathway
two molecules of pyruvic acid.  The pentose phosphate pathway (or hexose
 During glycolysis NAD+ is reduced to monophosphate shunt) operates
NADH, and there is a net production of two simultaneously with glycolysis and provides a
ATP molecules by substrate-level means for the breakdown of five-carbon sugars
phosphorylation. (pentoses) as well as glucose
 Glycolysis does not require oxygen; it can  A key feature of this pathway is that it
occur whether oxygen is present or not. produces important intermediate pentoses
 This pathway is a series of ten chemical used in the synthesis of (1) nucleic acids, (2)
reactions, each catalyzed by a different glucose from carbon dioxide in photosynthesis,
enzyme and (3) certain amino acids.
 To summarize the process, glycolysis  The pathway is an important producer of the
consists of two basic stages, a preparatory reduced coenzyme NADPH from NADP+.
stage and an energy-conserving stage:  The pentose phosphate pathway yields a net
o First, in the preparatory gain of only one molecule of ATP for each
stage (steps 1-4) two molecule of glucose oxidized.
molecules of ATP are used  Bacteria that use the pentose phosphate
as a six-carbon glucose pathway include Bacillus subtilis, E. coli,
molecule is Leuconostoc mesenteroides and Enterococcus
phosphorylated, faecalis
restructured, and split into
two three- carbon The Entner-Doudoroff Pathway
compounds:  From each molecule of glucose, the Entner-
glyceraldehyde 3- Doudoroff pathway produces one NADPH, one
phosphate (GP) and NADH, and one ATP for use in cellular
dihydroxyacetone biosynthetic reactions
phosphate (DHAP). In step  Bacteria that have the enzymes for the
5, DHAP is readily Entner-Doudoroff pathway can metabolize
converted to GP. The glucose without either glycolysis or the pentose
conversion of DHAP into phosphate pathway.
GP means that from this  The Entner-Doudoroff pathway is found in
point on in glycolysis, two some gram-negative bacteria, including
molecules of GP are fed Rhizobium, Pseudomonas and
into the remaining Agrobacterium , it is generally not found among
chemical reactions. gram-positive bacteria.
o In the energy-conserving  Tests for the ability to oxidize glucose by
stage (6-10), the two this pathway are sometimes used to identify
three-carbon molecules Pseudomonas in the clinical laboratory.
are oxidized in several
steps to two molecules of CELLULAR RESPIRATION
pyruvic acid. In these  After glucose has been broken down to
reactions, two molecules pyruvic acid, the pyruvic acid can be channeled
of NAD+ are reduced to into the next step of either fermentation or
NADH, and four molecules cellular respiration
 Cellular respiration, or simply respiration, is that enter the cycle, four molecules of CO2 are
defined as an ATP-generating process in which liberated by decarboxylation, six molecules of
molecules are oxidized and the final electron NADH and two molecules of FADH2 are
acceptor comes from outside the cell and is produced by oxidation-reduction reactions, and
(almost always) an inorganic molecule. two molecules of ATP are generated by
 An essential feature of respiration is the substrate-level phosphorylation.
operation of an electron transport chain.  A molecule of guanosine triphosphate
 There are two types of respiration, (GTP), formed from guanosine diphosphate
depending on whether an organism is an (GDP + P), is similar to ATP and serves as an
aerobe, which uses oxygen, or an anaerobe, intermediary at this point in the cycle.
which does not use oxygen and may even be  The CO2 produced in the Krebs cycle is
killed by it. ultimately liberated into the atmosphere as a
 In aerobic respiration, the final electron gaseous by-product of aerobic respiration.
acceptor is O2; in anaerobic respiration, the  (Humans produce CO2 from the Krebs cycle
final electron acceptor is an inorganic molecule in most cells of the body and discharge it
other than O2 or, rarely, an organic molecule. through the lungs during exhalation.)
 The reduced coenzymes NADH and FADH2
are the most important products of the Krebs
Aerobic Respiration cycle because they contain most of the energy
that was originally stored in glucose.
 The Krebs Cycle, also called the  During the next phase of respiration, a
tricarboxylic acid (TCA) cycle or citric acid series of oxidation-reduction reactions
cycle, is a series of biochemical reactions in indirectly transfer the energy stored in those
which the large amount of potential chemical coenzymes to ATP.
energy stored in acetyl CoA is released step by
 These reactions are collectively called the
step
electron transport chain.
 In this cycle, a series of oxidations and
reductions transfer that potential energy, in the The Electron Transport Chain (System)
form of electrons, to electron carrier
 An electron transport chain (electron
coenzymes, chiefly NAD+ and FADH2.
transport system) consists of a sequence of
 The pyruvic acid derivatives are oxidized; carrier molecules that are capable of oxidation
the coenzymes are reduced. and reduction.
 Pyruvic acid, the product of glycolysis,  As electrons are passed through the chain,
cannot enter the Krebs cycle directly. there occurs a stepwise release of energy,
 In a preparatory step, it must lose one which is used to drive the chemiosmotic
molecule of CO2 and become a two-carbon generation of ATP
compound.  The final oxidation is irreversible.
 This process is called decarboxylation.  In eukaryotic cells, the electron transport
 The two- carbon compound, called an acetyl chain is contained in the inner membrane of
group, attaches to coenzyme A through a high- mitochondria; in prokaryotic cells, it is found in
energy bond; the resulting complex is known the plasma membrane.
as acetyl coenzyme A (acetyl CoA).  There are three classes of carrier molecules
 During this reaction, pyruvic acid is also in electron transport chains:
oxidized, and NAD+ is reduced to NADH. o Flavoproteins contain flavin, a
 The oxidation of one glucose molecule coenzyme derived from riboflavin
produces two molecules of pyruvic acid, so for (vitamin B2), and are capable of
each molecule of glucose, two molecules of performing alternating oxidations
CO2 are released, two molecules of NADH are and reductions. One important
produced, and two molecules of acetyl CoA are flavin coenzyme is flavin
formed. mononucleotide (FMN).
 Once the pyruvic acid has undergone o Cytochromes are proteins with an
decarboxylation and its derivative (the acetyl iron-containing group (heme)
group) has attached to CoA, the resulting capable of existing alternately as
acetyl CoA is ready to enter the Krebs cycle. a reduced form (Fe2+) and an
 As acetyl CoA enters the Krebs cycle, CoA oxidized form (Fe3+). The
detaches from the acetyl group. cytochromes involved in electron
 The acetyl group combines with oxaloacetic transport chains include
acid to form citric acid. cytochrome b (cyt b), cytochrome
 The formation of citric acid is thus the first c1 (cyt c1), cyt c, cyt a, cyt a3
step in the Krebs cycle o Ubiquinones, or coenzyme Q (Q),
 If we look at the Krebs cycle as a whole, we are small nonprotein carriers.
see that for every two molecules of acetyl CoA
 However, keep in mind that all electron  Generation ATP synthesis using the electron
transport chains achieve the same basic goal: transport chain is called chemiosmosis, and it
to release energy while electrons are involves oxidative phosphorylation.
transferred from higher-energy compounds to  Substances diffuse passively across
lower-energy compounds membranes from areas of high concentration to
o High-energy electrons transfer areas of low concentration; this diffusion along
from NADH to FMN, the first a concentration gradient yields energy.
carrier in the chain A hydrogen  The movement of substances against a
atom with two electrons passes to concentration gradient requires energy that is
FMN, which picks up an usually provided by ATP.
additional H+ from the  In chemiosmosis, the energy released when
surrounding aqueous medium. As a substance moves along a gradient is used to
a result NADH is oxidized to synthesize ATP.
NAD+, and FMN is reduced to  The “substance” in this case refers to
FMNH2. protons.
o FMNH2 passes 2H+ to the other  In respiration, chemiosmosis is responsible
side of the mitochondrial for most of the ATP that is generated.
membrane and passes two  The steps of chemiosmosis are as follow
electrons to Q. FMNH2 is o As energetic electrons from
oxidized to FMN. Q also picks up NADH (or chlorophyll) pass down
an additional 2H+ from the the electron transport chain,
surrounding aqueous medium some of the carriers in the chain
and releases it on the other side pump actively transport protons
of the membrane. across the membrane. Such
o Electrons are passed carrier molecules are called
successively from Q to cyt b, cyt proton pumps
c1, cyt c, cyt a, and cyt a3. Each o one-directional pumping
cytochrome in the chain is establishes a proton gradient (a
reduced as it picks up electrons difference in the concentrations of
and is oxidized as it gives up protons on the two sides of the
electrons. The last cytochrome, membrane). In addition to a
cyt a3, passes its electrons to concentration gradient, there is
molecular oxygen (O2), which an electrical charge gradient. The
becomes negatively charged and excess H+ on one side of the
picks up protons from the membrane makes that side
surrounding medium to form positively charged compared with
H2O. the other side. The resulting
 FADH2, which is derived from the Krebs electrochemical gradient has
cycle, as another source of electrons. potential energy, called the
 However, FADH2 adds its electrons to the proton motive force.
electron transport chain at a lower level than o The protons on the side of the
NADH. membrane with the higher proton
 Because of this, the electron transport chain concentration can diffuse across
produces about one-third less energy for ATP the membrane only through
generation when FADH2 donates electrons special protein channels that
than when NADH is involved. contain an enzyme called ATP
 An important feature of the electron transport synthase. When this flow occurs,
chain is the presence of some carriers, such energy is released and is used by
as FMN and Q, that accept and release the enzyme to synthesize ATP
protons and electrons, and other carriers, from ADP and P
such as cytochromes, that transfer electrons  Both prokaryotic and eukaryotic cells use the
only. chemiosmotic mechanism to generate energy
 Pumping of protons from the matrix side of for ATP production.
the inner mitochondrial membrane to the  However, in eukaryotic cells, the inner
opposite side of the membrane. mitochondrial membrane contains the
 The result is a buildup of protons on one side electron transport carriers and ATP synthase.
of the membrane.  In most prokaryotic cells, the plasma
 this buildup of protons provides energy that membrane does so.
the chemiosmotic mechanism uses to  An electron transport chain also operates in
generate ATP. photophosphorylation and is located in the
The Chemiosmotic Mechanism of ATP thylakoid membrane of cyanobacteria and
eukaryotic chloroplasts.
 each molecule of starting material) because
A Summary of Aerobic Respiration much of the original energy in glucose
 The electron transport chain regenerates remains in the chemical bonds of the organic
NAD+ and FAD, which can be used again in end-products, such as lactic acid or ethanol.
glycolysis and the Krebs cycle.  However, the advantage of fermentation for
 The various electron transfers in the electron a cell is that it produces ATP quickly.
transport chain generate about 34 molecules  During fermentation, electrons are
of ATP from each molecule of glucose transferred (along with protons) from reduced
oxidized: approximately three from each of coenzymes (NADH, NADPH) to pyruvic acid
the ten molecules of NADH (a total of 30), or its derivatives
and approximately two from each of the two  Those final electron acceptors are reduced
molecules of FADH2 (a total of four). to the end-products.
 In aerobic respiration among prokaryotes,  An essential function of fermentation is to
each molecule of glucose generates 38 ATP ensure a steady supply of NAD+ and NADP+
molecules: 34 from chemiosmosis plus 4 so that glycolysis can continue.
generated by oxidation in glycolysis and the  In fermentation, ATP is generated only
Krebs cycle during glycolysis.
 Aerobic respiration among eukaryotes  The aforementioned lactic acid is the same
produces a total of only 36 molecules of ATP. substance associated with muscle fatigue in
There are fewer ATPs than in prokaryotes your body.
because some energy is lost when pyruvate  During strenuous exercise, the
is shuttled across the mitochondrial cardiovascular system cannot supply enough
membranes oxygen to skeletal muscles and the heart for
them to generate sufficient energy. In such
cases, muscles shift from aerobic respiration
Anaerobic Respiration to fermentation.
 In the absence of oxygen, pyruvic acid is
 In anaerobic respiration, the final electron
oxidized to lactic acid.
acceptor is an inorganic substance other than
oxygen (O2).  Microorganisms can ferment various
substrates; the end products depend on the
 Some bacteria, such as Pseudomonas and
particular microorganism, the substrate, and
Bacillus, can use a nitrate ion (NO3−) as a
the enzymes that are present and active.
final electron acceptor; the nitrate ion is
reduced to a nitrite ion (NO2−), nitrous oxide  Two of the more important processes are
(N2O), or nitrogen gas (N2). lactic acid fermentation and alcohol
fermentation
 Other bacteria, such as Desulfovibrio use
sulfate (SO42−) as the final electron acceptor
Lactic Acid Fermentation
to form hydrogen sulfide (H2S)
 During glycolysis, which is the first phase of
 Some archaea use carbon dioxide to form
lactic acid fermentation, a molecule of glucose
methane (CH4).
is oxidized to two molecules of pyruvic acid
 Anaerobic respiration by bacteria using
 This oxidation generates the energy that is
nitrate and sulfate as final acceptors is
used to form the two molecules of ATP
essential for the nitrogen and sulfur cycles
that occur in nature.  In the next step, the two molecules of
pyruvic acid are reduced by two molecules of
 The ATP yield is never as high as in aerobic
NADH to form two molecules of lactic acid
respiration.
 Because lactic acid is the end-product of the
FERMENTATION reaction, it undergoes no further oxidation
 this fermentation yields only a small amount
 After glucose has been oxidized into pyruvic of energy.
acid, the pyruvic acid can be completely
 Two important genera of lactic acid bacteria
broken down in respiration
are Streptococcus and Lactobacillus
 Fermentation is defined as a process that
 Because these microbes produce only lactic
 1. releases energy from sugars or other acid, they are referred to as homolactic (or
organic molecules; homofermentative).
 2. does not require oxygen (but can occur in  Lactic acid fermentation can result in food
its presence); spoilage.
 3. does not require the use of the Krebs  However, the process can also produce
cycle or an electron transport chain; yogurt from milk, sauerkraut from fresh
 4. uses an organic molecule synthesized in cabbage, and pickles from cucumbers.
the cell as the final electron acceptor.
 Fermentation produces only small amounts Alcohol Fermentation
of ATP (only one or two ATP molecules for
 Alcohol fermentation also begins with the  Other conversions involve decarboxylation
glycolysis of a molecule of glucose to yield two (the removal of —COOH) and desulfurization
molecules of pyruvic acid and two molecules of (removal of —SH).
ATP.  Lipid catabolism. Glycerol is converted into
 In the next reaction, the two molecules of dihydroxyacetone phosphate (DHAP) and
pyruvic acid are converted to two molecules of catabolized via glycolysis and the Krebs cycle.
acetaldehyde and two molecules of CO2 (  Fatty acids undergo beta-oxidation, in which
 The two molecules of acetaldehyde are carbon fragments are split off two at a time to
reduced by two molecules of NADH to form two form acetyl CoA, which is catabolized via the
molecules of ethanol. Krebs cycle.
 Again, alcohol fermentation is a low-energy-
yield process because most of the energy BIOCHEMICAL TESTS AND
contained in the initial glucose molecule
remains in the ethanol, the end-product.
BACTERIAL IDENTIFICATION
 Alcohol fermentation is carried out by a  Biochemical testing is frequently used to
number of bacteria and yeasts. identify bacteria and yeasts because different
species produce different enzymes.
 The ethanol and carbon dioxide produced by
the yeast Saccharomyces are waste products  Such biochemical tests are designed to
for yeast cells but are useful to humans. detect the presence of enzymes.
 Ethanol made by yeasts is the alcohol in  One type of biochemical test detects amino
alcoholic beverages, and carbon dioxide made acid catabolizing enzymes involved in
by yeasts causes bread dough to rise. decarboxylation and dehydrogenation
 Organisms that produce lactic acid as well  Another biochemical test is a fermentation
as other acids or alcohols are known as test
heterolactic (or heterofermentative) and often  The test medium contains protein, a single
use the pentose phosphate pathway. carbohydrate, a pH indicator, and an inverted
Durham tube, which is used to capture gas.
 Bacteria inoculated into the tube can use the
LIPID AND PROTEIN protein or carbohydrate as a carbon and
CATABOLISM energy source.
 If they catabolize the carbohydrate and
 However, microbes also oxidize lipids and produce acid, the pH indicator changes color.
proteins, and the oxidations of all these  Some organisms produce gas as well as
nutrients are related acid from carbohydrate catabolism.
 Microbes produce extracellular enzymes  The presence of a bubble in the Durham
called lipases that break fats down into their tube indicates gas formation.
fatty acid and glycerol components.  E. coli ferments the carbohydrate sorbitol.
 The Krebs cycle functions in the oxidation of  The pathogenic E. coli O157 strain,
glycerol and fatty acids. however, does not ferment sorbitol, a
 Many bacteria that hydrolyze fatty acids can characteristic that differentiates it from
use the same enzymes to degrade petroleum nonpathogenic, commensal E. coli.
products.  the waste products of one microorganism
 Whereas beta-oxidation (fatty acid oxidation) can be used as a carbon and energy source by
of petroleum is a nuisance when these bacteria another species.
grow in a fuel storage tank, it is beneficial when  Acetobacter bacteria oxidize ethanol made
they grow in oil spills. by yeast.
 Microbes produce extracellular proteases  Propionibacterium can use lactic acid
and peptidases, enzymes that break down produced by other bacteria.
proteins into their component amino acids,  Propioni bacteria convert lactic acid to
which can cross the membranes. pyruvic acid in preparation for the Krebs cycle.
 However, before amino acids can be  During the Krebs cycle, propionic acid and
catabolized, they must be enzymatically CO2 are made.
converted to other substances that can enter  The holes in Swiss cheese are formed by
the Krebs cycle. the accumulation of CO2 gas
 In one such conversion, called deamination,  Biochemical tests are used to identify
the amino group of an amino acid is removed bacteria that cause disease.
and converted to an ammonium ion (NH4+),  All aerobic bacteria use the electron
which can be excreted from the cell. transport chain (ETC), but their ETCs are not
 The remaining organic acid can enter the all identical.
Krebs cycle.  Some bacteria have cytochrome c, but
others do not.
 In the former, cytochrome c oxidase is the  In this mechanism, light energy is absorbed
last enzyme, which transfers electrons to by chlorophyll molecules in the photosynthetic
oxygen. cell, exciting some of the molecules’ electrons.
 The oxidase test is routinely used to quickly  The chlorophyll principally used by green
identify Neisseria gonorrhoeae. plants, algae, and cyanobacteria is chlorophyll
 Neisseria is positive for cytochrome oxidase. a.
 The oxidase test can also be used to  it is located in the membranous thylakoids of
distinguish some gram-negative rods: chloroplasts in algae and green plants and in
 Pseudomonas is oxidase-positive, and the thylakoids found in the photosynthetic
Escherichia is oxidase-negative. structures of cyanobacteria.
 Shigella causes dysentery and is  Other bacteria use bacteriochlorophylls.
differentiated from E. coli by biochemical tests.  The excited electrons jump from the
 Unlike E. coli, Shigella does not produce gas chlorophyll to the first of a series of carrier
from lactose. molecules, an electron transport chain similar
 Salmonella bacteria are readily to that used in respiration.
distinguishable from E. coli by the production of  As electrons are passed along the series of
hydrogen sulfide (H2S). carriers, protons are pumped across the
 Hydrogen sulfide is released when the membrane, and ADP is converted to ATP by
bacteria remove sulfur from amino acids chemiosmosis.
 Use of peptone iron agar to detect the  Chlorophyll and other pigments are packed
production of H2S. H2S produced in the tube into thylakoids of chloroplasts and are called
precipitates with iron in the medium as ferrous photosystems.
sulfide.  Photosystem II is so numbered because
even though it was most likely the first
photosystem to evolve, it was the second one
discovered.
 It contains chlorophyll that is sensitive to
PHOTOSYNTHESIS wavelengths of light of 680 nm.
 The chlorophyll in photosystem I is sensitive
 Other organisms synthesize complex
to wavelengths of light of 700 nm.
organic compounds from simple inorganic
 Photophosphorylation.
substances.
 (a) In cyclic photophosphorylation, electrons
 The major mechanism for such synthesis is
released from chlorophyll by light in
a process called photosynthesis, which is
photosystem I return to chlorophyll after
carried out by plants and many microbes.
passage along the electron transport chain.
 Essentially, photosynthesis is the
 The energy from electron transfer is used to
conversion of light energy from the sun into
synthesize ATP.
chemical energy.
 (b) In noncyclic photophosphorylation,
 The chemical energy is then used to convert
electrons released from chlorophyll in
CO2 from the atmosphere to more reduced
photosystem II are replaced by electrons from
carbon compounds, primarily sugars.
the hydrogen atoms in water.
 The word photosynthesis summarizes the
 This process also releases hydrogen ions.
process: photo means light, and synthesis
 Electrons from chlorophyll in photosystem I
refers to the assembly of organic compounds.
are passed along the electron transport chain
 This synthesis of sugars by using carbon
to the electron acceptor NADP+.
atoms from CO2 gas is also called carbon
 NADP+ combines with electrons and with
fixation.
hydrogen ions from water, forming NADPH
 Plants, algae, and cyanobacteria use water
as a hydrogen donor, releasing O2.
 Purple sulfur and green sulfur bacteria use THE LIGHT-INDEPENDENT
H2S as a hydrogen donor, producing sulfur REACTIONS: THE CALVIN-BENSON
granules’
CYCLE
 The light-independent reactions are so
THE LIGHT-DEPENDENT named because they don’t require light directly.
REACTIONS:  They include a complex cyclic pathway
PHOTOPHOSPHORYLATION called the Calvin-Benson cycle, in which CO2
is “fixed”—that is, it’s used to synthesize
 Photophosphorylation is one of the three
sugars
ways ATP is formed, and it occurs only in
 three molecules of CO2 are fixed and one
photosynthetic cells.
molecule of glyceraldehyde 3-phosphate is
produced and leaves the cycle.
 Two molecules of glyceraldehyde 3- METABOLIC DIVERSITY AMONG
phosphate are needed to make one molecule
of glucose.
ORGANISMS
 Therefore, the cycle must turn six times for  Some microbes can sustain themselves on
each glucose molecule produced, requiring a inorganic substances by using pathways that
total investment of 6 molecules of CO2, 18 are unavailable to either plants or animals.
molecules of ATP, and 12 molecules of  All organisms, including microbes, can be
NADPH. classified metabolically according to their
nutritional pattern— their source of energy and
A SUMMARY OF ENERGY their source of carbon.
PRODUCTION MECHANISMS  First considering the energy source, we can
generally classify organisms as phototrophs or
chemotrophs.
 Organisms obtain the energy from oxidation
 Phototrophs use light as their primary
reactions.
energy source, whereas chemotrophs depend
 To obtain energy in a usable form, a cell
on oxidation-reduction reactions of inorganic or
must have an electron (or hydrogen) donor,
organic compounds for energy.
which serves as an initial energy source within
 For their principal carbon source, autotrophs
the cell.
(self-feeders) use carbon dioxide, and
 Electron donors are diverse and can include
heterotrophs (feeders on others) require an
photosynthetic pigments, glucose or other
organic carbon source.
organic compounds, elemental sulfur,
 Autotrophs are also referred to as lithotrophs
ammonia, or hydrogen gas
(rock eating), and heterotrophs are also
 Next, electrons removed from the chemical
referred to as organotrophs.
energy sources are transferred to electron
 If we combine the energy and carbon
carriers, such as the coenzymes NAD+,
sources, we derive the following nutritional
NADP+, and FAD.
classifications for organisms: photoautotrophs,
 This transfer is an oxidation-reduction
photoheterotrophs, chemoautotrophs, and
reaction; the initial energy source is oxidized as
chemoheterotrophs
this first electron carrier is reduced.
 During this phase, some ATP is produced.
 In the third stage, electrons are transferred
from electron carriers to their final electron
acceptors in further oxidation-reduction
reactions, producing more ATP. PHOTOAUTOTROPHS
 Requirements of ATP production. The
production of ATP requires  Photoautotrophs use light as a source of
energy and carbon dioxide as their chief source
 1 an energy source (electron donor),
of carbon.
 2 the transfer of electrons to an electron
 They include photosynthetic bacteria (green
carrier during an oxidation-reduction reaction,
and purple bacteria and cyanobacteria), algae,
and
and green plants.
 3 the transfer of electrons to a final electron
 In the photosynthetic reactions of
acceptor.
cyanobacteria, algae, and green plants, the
 In aerobic respiration, oxygen (O2) serves
hydrogen atoms of water are used to reduce
as the final electron acceptor.
carbon dioxide, and oxygen gas is given off.
 In anaerobic respiration, substances from
 Because this photosynthetic process
the environment other than oxygen, such as
produces O2 it is sometimes called oxygenic.
nitrate ions (NO3−) or sulfate ions (SO42−),
 These bacteria cannot use H2O to reduce
serve as the final electron acceptors.
CO2 and cannot carry on photosynthesis when
 In fermentation, compounds in the
oxygen is present (they must have an
cytoplasm serve as the final electron
anaerobic environment).
acceptors.
 Consequently, their photosynthetic process
 In aerobic and anaerobic respiration, a
does not produce O2 and is called anoxygenic.
series of electron carriers called an electron
 The anoxygenic photoautotrophs are the
transport chain releases energy that is used by
green and purple bacteria.
the mechanism of chemiosmosis to synthesize
ATP.  The green sulfur bacteria, such as
Chlorobium, use sulfur (S), sulfur compounds
 Regardless of their energy sources, all
(such as hydrogen sulfide, H2S), or hydrogen
organisms use similar oxidation-reduction
gas (H2) to reduce carbon dioxide and form
reactions to transfer electrons and similar
organic compounds.
mechanisms to use the energy released to
produce ATP.
 Applying the energy from light and the  When we discuss photoautotrophs,
appropriate enzymes, these bacteria oxidize photoheterotrophs, and chemoautotrophs, it’s
sulfide (S2-) or sulfur (S) to sulfate (SO42-) or easy to categorize the energy and carbon
oxidize hydrogen gas to water (H2O). sources because they occur as separate
 The purple sulfur bacteria, such as entities.
Chromatium , also use sulfur, sulfur  However, in chemoheterotrophs, the
compounds, or hydrogen gas to reduce carbon distinction isn’t as clear because the energy
dioxide. and carbon sources are usually the same
 They are distinguished from the green organic compound—glucose, for example.
bacteria by their type of chlorophyll, location of  Chemoheterotrophs specifically use the
stored sulfur, and ribosomal RNA. electrons from hydrogen atoms in organic
 The chlorophylls used by these compounds as their energy source.
photosynthetic bacteria are called  Heterotrophs are further classified according
bacteriochlorophylls, and they absorb light at to their source of organic molecules.
longer wavelengths than that absorbed by  Saprophytes live on dead organic matter,
chlorophyll a. and parasites derive nutrients from a living
 Bacteriochlorophylls of green sulfur bacteria host.
are found in vesicles called chlorosomes (or  Most bacteria, and all fungi, protozoa, and
chlorobium vesicles) underlying and attached animals, are chemoheterotrophs.
to the plasma membrane.  However, these same bacteria might be
 In the purple sulfur bacteria, the beneficial if they decomposed discarded rubber
bacteriochlorophylls are located in products, such as used tires.
invaginations of the plasma membrane  Rhodococcus erythropolis is widely
(chromatophores). distributed in soil and can cause disease in
humans and other animals.
PHOTOHETEROTROPHS
 However, this species is able to replace
 Photoheterotrophs use light as a source of sulfur atoms in petroleum with atoms of
energy but cannot convert carbon dioxide to oxygen.
sugar; rather, they use organic compounds,  Removing sulfur from crude oil is an
such as alcohols, fatty acids, other organic important step in the oil-refining process.
acids, and carbohydrates, as sources of  Sulfur corrodes equipment and pipelines,
carbon. and contributes to acid precipitation and
 Photoheterotrophs are anoxygenic. pollution-related respiratory problems in
 The green nonsulfur bacteria, such as people.
Chloroflexus and purple nonsulfur bacteria,
such as Rhodopseudomonas , are METABOLIC PATHWAYS OF
photoheterotrophs ENERGY
CHEMOAUTOTROPHS  Through the oxidation of organic molecules,
organisms produce energy by aerobic
 Chemoautotrophs use the electrons from respiration, anaerobic respiration, and
reduced inorganic compounds as a source of fermentation.
energy, and they use CO2 as their principal
 Much of this energy is given off as heat.
source of carbon.
 The complete metabolic oxidation of glucose
 They fix CO2 in the Calvin-Benson Cycle (
to carbon dioxide and water is considered a
 Inorganic sources of energy for these very efficient process, but about 45% of the
organisms include hydrogen sulfide (H2S) for energy of glucose is lost as heat.
Beggiatoa, elemental sulfur (S) for
 Cells use the remaining energy, which is
Acidithiobacillus thiooxidans; ammonia (NH3)
trapped in the bonds of ATP, in a variety of
for Nitrosomonas, nitrite ions (NO2−) for
ways.
Nitrobacter; hydrogen gas (H2) for
 Microbes use ATP to provide energy for the
Cupriavidus, ferrous iron (Fe2+) for
transport of substances across plasma
Acidithiobacillus ferrooxidans; and carbon
membranes by active transport.
monoxide (CO) for Pseudomonas
 Microbes also use some of their energy for
carboxydohydrogena
flagellar motion
 The energy derived from the oxidation of
 Most of the ATP, however, is used in the
these inorganic compounds is eventually
production of new cellular components.
stored in ATP, which is produced by oxidative
phosphorylation.  Autotrophs build their organic compounds by
fixing carbon dioxide in the Calvin-Benson
cycle
CHEMOHETEROTROPHS
  Heterotrophs, by contrast, must have a  A lipid of a very different structure,
ready source of organic compounds for cholesterol, is also found in plasma
biosynthesis—the production of needed membranes of eukaryotic cells.
cellular components, usually from simpler  Waxes are lipids that are important
molecules. components of the cell wall of acid-fast
 The cells use these compounds as both the bacteria.
carbon source and the energy source.  Other lipids, such as carotenoids, provide
the red, orange, and yellow pigments of some
POLYSACCHARIDE BIOSYNTHESIS microorganisms.
 Microorganisms synthesize sugars and  Lipids also function in energy storage
polysaccharides.
 The carbon atoms required to synthesize
AMINO ACID AND PROTEIN
glucose are derived from the intermediates
produced during processes such as glycolysis BIOSYNTHESIS
and the Krebs cycle, and from lipids or amino  Amino acids are required for protein
acids. biosynthesis.
 After synthesizing glucose (or other simple  Some microbes, such as E. coli, contain the
sugars), bacteria may assemble it into more enzymes necessary to use starting materials,
complex polysaccharides, such as glycogen. such as glucose and inorganic salts, for the
 For bacteria to build glucose into glycogen, synthesis of all the amino acids they need.
glucose units must be phosphorylated and  Organisms with the necessary enzymes can
linked. synthesize all amino acids directly or indirectly
 The product of glucose phosphorylation is from intermediates of carbohydrate metabolism
glucose 6-phosphate.  Other microbes require that the environment
 Such a process involves the expenditure of provide some preformed amino acids.
energy, usually in the form of ATP.  One important source of the precursors used
 In order for bacteria to synthesize glycogen, in amino acid synthesis is the Krebs cycle.
a molecule of ATP is added to glucose 6-  Adding an amine group to pyruvic acid or to
phosphate to form adenosine an appropriate organic acid of the Krebs cycle
diphosphoglucose (ADPG) converts the acid into an amino acid.
 Once ADPG is synthesized, it is linked with  This process is called amination. If the
similar units to form glycogen. amine group comes from a preexisting amino
 Using a nucleotide called uridine acid, the process is called transamination
triphosphate (UTP) as a source of energy and  Most amino acids within cells are destined to
glucose 6-phosphate, animals synthesize be building blocks for protein synthesis.
glycogen (and many other carbohydrates)  Proteins play major roles in the cell as
from uridine diphosphoglucose, UDPG enzymes, structural components, and toxins, to
 UDP-N-acetylglucosamine (UDPNAc), is a name just a few uses.
key starting material in the biosynthesis of  The joining of amino acids to form proteins
peptidoglycan, the substance that forms involves dehydration synthesis and requires
bacterial cell walls. energy in the form of ATP.
 UDPNAc is formed from fructose 6-
phosphate, and the reaction also uses UTP.
LIPID BIOSYNTHESIS
 Cells synthesize fats by joining glycerol and
fatty acids. PURINE AND PYRIMIDINE
 The glycerol portion of the fat is derived from BIOSYNTHESIS
dihydroxyacetone phosphate, an intermediate
 The informational molecules DNA and RNA
formed during glycolysis.
consist of repeating units called nucleotides,
 Fatty acids, which are long-chain
each of which consists of a purine or
hydrocarbons (hydrogen linked to carbon), are
pyrimidine, a pentose (five-carbon sugar), and
built up when two-carbon fragments of acetyl
a phosphate group
CoA are successively added to each other
 The five-carbon sugars of nucleotides are
 As with polysaccharide synthesis, the
derived from either the pentose phosphate
building units of fats and other lipids are linked
pathway or the Entner-Doudoroff pathway.
via dehydration synthesis reactions that require
 Certain amino acids—aspartic acid, glycine,
energy, not always in the form of ATP.
and glutamine—made from intermediates
 The most important role of lipids is to serve
produced during glycolysis and in the Krebs
as structural components of biological
cycle participate in the biosyntheses of purines
membranes, and most membrane lipids are
and pyrimidines
phospholipids.
 The carbon and nitrogen atoms derived from this control helps to synchronize the rates of
these amino acids form the purine and glycolysis and the Krebs cycle.
pyrimidine rings, and the energy for synthesis  Thus, if citric acid consumption increases,
is provided by ATP. either because of a demand for more ATP or
 DNA contains all the information necessary because anabolic pathways are draining off
to determine the specific structures and intermediates of the Krebs cycle, glycolysis
functions of cells. accelerates and meets the demand.
 Both RNA and DNA are required for protein
synthesis.
 In addition, nucleotides such as ATP, NAD+,
and NADP+ assume roles in stimulating and
inhibiting the rate of cellular metabolism
 The biosynthesis of amino acids.
 (a) Pathways of amino acid biosynthesis
through amination or transamination of
intermediates of carbohydrate metabolism from
the Krebs cycle, pentose phosphate pathway,
and Entner-Doudoroff pathway.
 (b) Transamination, a process by which new
amino acids are made with the amine groups
from old amino acids.
 Glutamic acid and aspartic acid are both
amino acids; the other two compounds are
intermediates in the Krebs cycle.

THE INTEGRATION OF
METABOLISM
 microbes produce energy from light,
inorganic compounds, and organic compound
 Actually, anabolic and catabolic reactions
are joined through a group of common
intermediates
 Both anabolic and catabolic reactions also
share some metabolic pathways, such as the
Krebs cycle.
 For example, reactions in the Krebs cycle
not only participate in the oxidation of glucose
but also produce intermediates that can be
converted to amino acids.
 Metabolic pathways that function in both
anabolism and catabolism are called
amphibolic pathways, meaning that they are
dual-purpose.
 Amphibolic pathways bridge the reactions
that lead to the breakdown and synthesis of
carbohydrates, lipids, proteins, and
nucleotides.
 Such pathways enable simultaneous
reactions to occur in which the breakdown
product formed in one reaction is used in
another reaction to synthesize a different
compound, and vice versa.
 For example, NAD+ is involved in catabolic
reactions, whereas NADP+ is involved in
anabolic reactions.
 Enzymes can also coordinate anabolic and
catabolic reactions by accelerating or inhibiting
the rates of biochemical reactions.
 if ATP begins to accumulate, feedback
inhibition to an enzyme shuts down glycolysis;