BIOCHEMISTRY:
MICROBIAL PHYSIOLOGY AND GENETICS
MICROBIAL PHYSIOLOGY
INTRODUCTION
 Physiology is the study of the vital life
processes of organisms, especially how
these processes normally function in living
organisms.
 Microbial physiology concerns the vital life
processes of microorganisms.
 Each tiny single-celled bacterium strives to
produce more cells like itself, and, if water
and an adequate nutrient supply are
available, it often does so at an alarming
rate
 Most of today’s genetic knowledge was and
still is being obtained by studying these
microorganisms.
MICROBIAL NUTRITIONAL
REQUIREMENTS
 Studies of bacterial nutrition and other
aspects of microbial physiology enable
scientists to understand the vital chemical
processes that occur within every living cell,
including those of the human body.
 To build necessary cellular materials, every
organism requires a source (or sources) of
energy, a source (or sources) of carbon,
and additional nutrients.
 The term nutrients refer to the various
chemical compounds that organisms—
including microorganisms— use to sustain
life.
 Nutrients also serve as sources of carbon,
nitrogen, and other elements.
CATEGORIZING MICROORGANISMS
ACCORDING TO THEIR ENERGY AND
CARBON SOURCES
 there are microbes representing each of the
four major nutritional categories
(photoautotrophs, photoheterotrophs,
chemoautotrophs, chemoheterotrophs;
terms defined later in this chapter).
TERMS RELATING TO AN ORGANISM’S
ENERGY SOURCE
 The terms phototroph and chemotroph
pertain to what an organism uses as an
energy source.
 Phototrophs use light as an energy source,
whereas chemotrophs use chemicals as a
source of energy.
 Chemotrophs use either inorganic or
organic chemicals as an energy source.
 Chemolithotrophs (or simply
lithotrophs) are organisms that use
inorganic chemicals as an energy
source.
 Chemoorganotrophs (or simply
organotrophs) are organisms that
use organic chemicals as an energy
source.
TERMS RELATING TO AN ORGANISM’S
CARBON SOURCE
 Autotrophs use carbon dioxide as their sole
source of carbon, whereas heterotrophs use
other carbon-containing compounds as their
carbon source
 Heterotrophs are organisms that use
organic compounds other than CO2 as their
carbon source.
 Photoautotrophs are organisms (such as
plants, algae, cyanobacteria, purple, and
green sulfur bacteria) that use light as an
energy source and CO2 as a carbon
source.
 Photoheterotrophs, like purple nonsulfur
and green nonsulfur bacteria, use light as
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MICROBIAL PHYSIOLOGY AND GENETICS
an energy source and organic compounds
other than CO2 as a carbon source.
 Chemoautotrophs (such as nitrifying,
hydrogen, iron, and sulfur bacteria) use
chemicals as an energy source and CO2 as
a carbon source.
 Chemoheterotrophs use chemicals as an
energy source and organic compounds
other than CO2 as a carbon source.
 Ecology is the study of the interactions
between organisms and the world around
them.
 The term ecosystem refers to the
interactions between living organisms and
their nonliving environment.
METABOLIC ENZYMES
 Metabolism refers to all the chemical
reactions (metabolic reactions) that occur
within a living cell.
 These chemical reactions are
referred to as metabolic reactions.
 Metabolic reactions are enhanced and
regulated by enzymes, known as metabolic
enzymes.
BIOLOGIC CATALYSTS
 Enzymes are known as biologic catalysts.
 Enzymes are proteins that catalyze (speed
up or accelerate) the rate of biochemical
reactions.
 A particular enzyme can only catalyze one
chemical reaction.
 The substance upon which an enzyme acts
is known as that enzyme’s substrate.
 An enzyme does not become altered during
the chemical reaction that it catalyzes.
 Enzymes do not last indefinitely; they finally
degenerate and lose their activity.
 Enzymes produced within a cell that remain
within the cell— to catalyze reactions within
the cell—are called endoenzymes.
 Endoenzymes remain within the cell that
produced them, whereas exoenzymes leave
the cell to catalyze reactions outside of the
cell.
 Enzymes produced within a cell that are
then released from the cell—to catalyze
extracellular reactions—are called
exoenzymes.
 To catalyze a reaction, an apoenzyme must
first link up with a cofactor (either a mineral
ion or a coenzyme).
FACTORS THAT AFFECT THE
EFFICIENCY OF ENZYMES
 Certain physical or chemical changes can
diminish or completely stop enzyme activity,
because enzymes function properly only
under optimum conditions.
 An enzyme will function at peak efficiency
over a particular pH range.
 Likewise, an enzyme will function at peak
efficiency over a particular temperature
range.
 Enzyme efficiency is influenced by various
factors, including pH, temperature, and the
concentration of the substrate.
 Sometimes, a molecule that is similar in
structure to the substrate can be used as an
inhibitor to deliberately interfere with a
particular metabolic pathway.
METABOLISM
 the term metabolism refers to all the
chemical reactions occurring within a cell.
 A metabolite is any molecule that is a
nutrient, an intermediary product, or an end
product in a metabolic reaction
 Most metabolic reactions fall into two
categories: catabolism and anabolism.
 The term catabolism refers to all the
catabolic reactions that are occurring in a
cell.
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MICROBIAL PHYSIOLOGY AND GENETICS
 Catabolic reactions involve the breaking of
chemical bonds and the release of energy
 Any time that chemical bonds are broken,
energy is released. Catabolic reactions are
a cell’s major source of energy.
 Anabolism refers to all the anabolic
reactions that are occurring in a cell.
 Anabolic reactions involve the formation of
bonds, which requires energy.
 Energy is required for bond formation. Once
formed, the bonds represent stored energy.
 ATP molecules are the major energy-storing
or energy-carrying molecules within a cell.
 The energy that is released during catabolic
reactions is used to drive anabolic
reactions.
 In addition to the energy required for
metabolic pathways, energy is also required
by the organism for growth, reproduction,
sporulation, movement, and the active
transport of substances across membranes.
Some organisms (e.g., certain planktonic
dinoflagellates) even use energy for
bioluminescence
 Chemical reactions are essentially energy
transformation processes during which the
energy that is stored in chemical bonds is
transferred to produce new chemical bonds.
 The cellular mechanisms that release small
amounts of energy as the cell needs it
usually involve a sequence of catabolic and
anabolic reactions
CATABOLISM
 The key thing about catabolic reactions is
that they release energy.
 Catabolic reactions release energy because
chemical bonds are broken.
 The energy produced by catabolic reactions
can be used to wiggle flagella and actively
transport substances through membranes,
but most of the energy produced by
catabolic reactions is used to drive anabolic
reactions
 Catabolic reactions are often referred to as
degradative reactions; they degrade larger
molecules down into smaller molecules.
BIOCHEMICAL PATHWAYS
 A biochemical pathway is a series of linked
biochemical reactions that occur in a
stepwise manner, leading from a starting
material to a product.
 Glucose is the favorite “food” or nutrient of
cells, including microorganisms.
 Nutrients should be thought of as energy
sources, and chemical bonds should be
thought of as stored energy.
 Two common processes are the
biochemical pathways known as aerobic
respiration and fermentation reactions.
AEROBIC RESPIRATION OF GLUCOSE
 Aerobic respiration involves (a) glycolysis,
(b) the Kreb’s cycle, and (c) the electron
transport chain.
 The complete catabolism of glucose by the
process known as aerobic respiration (or
cellular respiration) occurs in three phases,
each of which is a biochemical pathway: (a)
glycolysis, (b) the Krebs cycle, and (c) the
electron-transport chain.
 Although the first phase—glycolysis—is an
anaerobic process, the other two phases
require aerobic conditions; hence the name,
aerobic respiration.
 Glycolysis, also known as the glycolytic
pathway, the Embden-Meyerhof pathway,
and the EmbdenMeyerhof-Parnas pathway,
is a nine-step biochemical pathway,
involving nine separate biochemical
reactions, each of which requires a specific
enzyme
 In glycolysis, a six-carbon molecule
of glucose is ultimately broken down
into two three-carbon molecules of
pyruvic acid (also called pyruvate).
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MICROBIAL PHYSIOLOGY AND GENETICS
 Krebs Cycle. The pyruvic acid molecules  The next step in fermentation reactions is
produced during glycolysis are converted the conversion of pyruvic acid into a
into acetyl-coenzyme A (acetyl-CoA) product.
molecules, which then enter the Krebs cycle  Fermentation reactions produce very little
 The Krebs cycle is a biochemical energy (approximately two ATP molecules);
pathway consisting of eight separate therefore, they are very inefficient ways to
reactions, each of which is controlled catabolize glucose
by a different enzyme.
 Electron Transport Chain. As previously
mentioned, certain of the products produced
OXIDATION-REDUCTION (REDOX)
during the Krebs cycle enter the electron
transport chain (also called the electron REACTIONS
transport system or respiratory chain).
 Oxidation-reductionon reactions are paired
 Many different enzymes are involved reactions in which electrons are transferred
in the electron transport chain, from one compound to another
including cytochrome oxidase (also
 Oxidation reactions involve the loss of an
called cytochrome c, or merely
electron, whereas reduction reactions
oxidase), the enzyme responsible for
involve the gain of an electron.
transferring electrons to oxygen, the
 The resulting gain of one or more electrons
final electron acceptor.
by a molecule is called reduction, and the
 During the electron transport chain,
molecule is said to be reduced.
many ATP molecules (32 in
procaryotic cells and 34 in
eucaryotic cells) are produced by a
process known as oxidative
phosphorylation; oxidation referring
to a loss of electrons and
phosphorylation referring to the ANABOLISM
conversion of ADP molecules to
ATP molecules.  Anabolism refers to all the anabolic
 The catabolism of glucose by aerobic reactions that are occurring in a cell.
respiration is just one of many ways in  Anabolic reactions require energy because
which cells can catabolize glucose chemical bonds are being formed.
molecules.  Most of the energy required for anabolic
reactions is provided by the catabolic
reactions that are occurring simultaneously
FERMENTATION OF GLUCOSE in the cell.
 Anabolic reactions are often referred to as
 The first thing to note about fermentation biosynthetic reactions.
reactions is that they do not involve oxygen;
therefore, fermentations usually take place
in anaerobic environments.
BIOSYNTHESIS OF ORGANIC
 The first step in the fermentation of glucose
is glycolysis, which occurs exactly as COMPOUNDS
previously described.  The biosynthesis of organic compounds
requires energy and may occur either
through photosynthesis (biosynthesis using
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MICROBIAL PHYSIOLOGY AND GENETICS
light energy) or chemosynthesis
(biosynthesis using chemical energy).
PHOTOSYNTHESIS
 In photosynthesis, light energy is converted
to chemical energy in the form of chemical
bonds
 The goal of photosynthetic processes is to
trap the radiant energy of light and convert it
into chemical bond energy in ATP
molecules and carbohydrates, particularly
glucose, which can then be converted into
more ATP molecules later through aerobic
respiration.
 Bacteria that produce oxygen by
photosynthesis are called oxygenic
photosynthetic bacteria, and the process is
known as oxygenic photosynthesis
 Photosynthetic reactions do not always
produce oxygen. Purple sulfur bacteria and
green sulfur bacteria (which are obligately
anaerobic photoautotrophs) are referred to
as anoxygenic photosynthetic bacteria
because their photosynthetic processes do
not produce oxygen (anoxygenic
photosynthesis).
CHEMOSYNTHESIS
MUTATIONS
 The chemosynthetic process involves a
chemical source of energy and raw
materials for synthesis of the metabolites
and macromolecules required for growth
and function of the organisms.
 Chemotrophs that use organic molecules
other than CO2 as their carbon source are
called chemoheterotrophs.
BACTERIAL GENETICS
 Genetics—the study of heredity.
 An organism’s genotype (or genome) is its
complete collection of genes, whereas an
organism’s phenotype is all the physical
traits, attributes, or characteristics of an
organism.
 Phenotype is the manifestation of genotype.
 Most bacteria possess one chromosome,
which usually consists of a long, continuous
(circular), double-stranded DNA molecule,
with no protein on the outside (as is found in
eucaryotic chromosomes).
 Genes are the fundamental units of heredity
that carry the information needed for the
special characteristics of each different
species of bacteria.
 Genes direct all functions of the cell,
providing it with its own traits and
individuality.
 Constitutive genes are always expressed,
whereas inducible genes are expressed
only when needed.
 Genes that are expressed always are called
constitutive genes
 Those that are expressed only when
the gene products are needed are
called inducible genes.
 Because there is only one chromosome that
replicates just before cell division, identical
traits of a species are passed from the
parent bacterium to the daughter cells after
binary fission has occurred.
 A change in the characteristics of a cell
caused by a change in the DNA molecule
(genetic alteration) that is transmissible to
the offspring is called a mutation.
 Beneficial mutations, as the name implies,
are of benefit to the organism
 the mutation enables the organism to be
resistant to a particular antibiotic.
 Beneficial mutations are of benefit to an
organism, whereas harmful mutations result
in the production of nonfunctional enzymes.
Some harmful mutations are lethal to the
organism.
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MICROBIAL PHYSIOLOGY AND GENETICS
 most mutations are silent mutations (or
neutral mutations), meaning that they have
no effect on the cell.
 spontaneous mutations (random mutations
that occur naturally) occur more or less
constantly throughout a bacterial genome.
 The mutation rate can be increased by
exposing cells to physical or chemical
agents that affect the chromosome. Such
agents are called mutagens
 The organism containing the mutation is
called a mutant.
 The types of mutagenic changes frequently
observed in bacteria involve cell shape,
biochemical activities, nutritional needs,
antigenic sites, colony characteristics,
virulence, and drug resistance.
 In a test procedure called the Ames test
(developed by Bruce Ames in the 1960s), a
mutant strain of Salmonella is used to learn
whether a particular chemical (e.g., a food
additive or a chemical used in some type of
cosmetic product) is a mutagen.
WAYS IN WHICH BACTERIA ACQUIRE
NEW GENETIC INFORMATION
 There are at least four additional ways that
the genetic composition of bacteria can be
changed:
 Lysogenic conversion (involves
bacteriophages and the acquisition
of new viral genes)
 Transduction (involves
bacteriophages and the acquisition
of new bacterial genes)
 Transformation (involves the uptake
of “naked” DNA)
 Conjugation (involves the transfer of
genetic information from one cell to
another through a hollow sex pilus)
LYSOGENIC CONVERSION
 Two categories of bacteriophages
 Virulent phages (which were
described in Chapter 4) always
cause the lytic cycle to occur, ending
with the destruction (lysis) of the
bacterial cell
 After temperate phages (also known
as lysogenic phages) inject their
DNA into the bacterial cell, the
phage DNA integrates into
(becomes part of) the bacterial
chromosome but does not cause the
lytic cycle to occur.
 This situation—in which the phage genome
is present in the cell but is not causing the
lytic cycle to occur—is known as lysogeny.
 During lysogeny, all that remains of the
phage is its DNA; in this form, the phage is
referred to as a prophage
 The bacterial cell containing the prophage is
referred to as a lysogenic cell or lysogenic
bacterium.
 A lysogenic bacterium is capable of
producing one or more new gene products
as a result of infection by a temperate
bacteriophage.
TRANSDUCTION
 Transduction means “to carry across.”
 Only small segments of DNA are transferred
from cell to cell by transduction compared
with the amount that can be transferred by
transformation and conjugation
 This phenomenon may occur after infection
of a bacterial cell by a temperate
bacteriophage.
TRANSFORMATION
 In transformation, a bacterial cell becomes
genetically transformed following uptake of
DNA fragments (“naked DNA”) from the
environment.
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MICROBIAL PHYSIOLOGY AND GENETICS
 Transformation experiments, performed by
Oswald Avery and his colleagues, proved
that DNA is indeed the genetic material
 Transformation is probably not widespread
in nature.
 Transformation was first demonstrated in
1928 by the British physician Frederick
Griffith and his colleagues, performing
experiments with S. pneumoniae and mice
 Some competent bacterial cells have
incorporated DNA fragments from certain
animal viruses.
CONJUGATION
 On conjugation, genetic material, usually in
the form of a plasmid, is transferred through
a hollow sex pilus from a donor cell to a
recipient cell.
 The transfer of genetic material by the
process known as conjugation was
discovered by Joshua Lederberg and
Edward Tatum in 1946, while experimenting
with E. coli.
 If a plasmid contains multiple genes for
antibiotic resistance, the plasmid is referred
to as a resistance factor or R-factor.
 Transduction, transformation, and
conjugation are excellent tools for mapping
bacterial chromosomes and for studying
bacterial and viral genetics.
GENETIC ENGINEERING
 An array of techniques has been developed
to transfer eucaryotic genes, particularly
human genes, into other easily cultured
cells to facilitate the large-scale production
of important gene products (proteins, in
most cases). This process is known as
genetic engineering or recombinant DNA
technology.
 Genetically engineered microorganisms can
also be used to clean up the environment
 Many industrial and medical benefits may
be derived from genetic engineering
research.
 Recombinant DNA (rDNA) technology can
be thought of as the process by which rDNA
is produced.
 Genetic engineering can be thought of as
the process by which rDNA is used to
modify an organism’s genome—often to
enable that organism to produce a particular
gene product that it previously was unable
to produce or to accomplish a task that it
previously was unable to accomplish.
 In medicine, there is potential for making
engineered antibodies, antibiotics, and
drugs; for synthesizing important enzymes
and hormones for treatment of inherited
diseases; and for making vaccines.
GENE THERAPY
 Gene therapy of human diseases
involves the insertion of a normal gene
into cells to correct a specific genetic or
acquired disorder that is being caused
by a defective gene.
 The first gene therapy trials were
conducted in the United States in 1990.
 Viral delivery is currently the most
common method for inserting genes into
cells, in which specific viruses are
selected to target the DNA of specific
cells.