CHAPTER 7
Microbial Physiology and Genetics
MICROBIAL PHYSIOLOGY
 Physiology
o study of the vital life processes (nutrition,
transportation, metabolism, respiration,
reproduction) of organisms, especially how
these processes normally function in living
organisms
 Microbial Physiology
o Study vital life processes of microorganisms
 Bacteria
o ideally suited for use in studies of the basic
metabolic reactions that occur within cells
o inexpensive to maintain in the laboratory,
take up little space, and reproduce quickly
o morphology, nutritional needs, and
metabolic reactions are easily observable
o species of bacteria can be found that
represent each of the nutritional types of
organisms on Earth
o by studying the nutritional needs of
bacteria; their metabolic pathways; and why
they live, grow, multiply, or die under
certain conditions – scientists have learned
a great deal about the composition and
inner workings of cells, including human
cells
o strives to produce more cells like itself, and,
as long as water and an adequate nutrient
supply are available, it often does so at an
alarming rate
o in 24 hours, the offspring (progeny) of a
single Escherichia coli cell would
outnumber the entire human population on
Earth
Microbial Nutritional Requirements
 All living protoplasm contains six major
chemical elements: carbon, hydrogen, oxygen,
nitrogen, phosphorus, and sulfur
 required in lesser amounts, include sodium,
potassium, chlorine, magnesium, calcium, iron,
iodine, and some trace elements
 Combinations of all these elements make up the
vital macromolecules of life, including
carbohydrates, lipids, proteins, and nucleic
acids
 To build necessary cellular materials, every
organism requires a source of energy, a source
of carbon, and additional nutrients
 Nutrients
o Various chemical compounds that
organisms—including microorganisms—use
to sustain life
o Many nutrients are energy sources;
organisms will obtain energy from these
chemicals by breaking chemical bonds
o Whenever a chemical bond is broken,
energy is released
o As nutrients are broken down by enzymatic
action, smaller molecules are produced,
which are then used by cells as building
blocks.
o also serve as sources of carbon, nitrogen,
and other elements
 Essential Nutrients
o materials that organisms are unable to
synthesize, but are required for the building
of macromolecules and sustaining life
o (e.g., essential amino acids and essential
fatty acids) must be continually supplied to
an organism for it to survive.
o vary from species to species
Categorizing Microorganisms According to
Their Energy and Carbon Sources
 microbes representing each of the four major
nutritional categories – photoautotrophs,
photoheterotrophs, chemoautotrophs, and
chemoheterotrophs
 categorized to indicate an organism’s energy
source and carbon source
Terms Relating to Organism’s Energy
Source
 phototroph and chemotroph pertain to what an
organism uses as an energy source
 Phototrophs
o Use light as an energy source
o Photosynthesis: process where organisms
convert light energy into chemical energy
o producers of food and oxygen for
chemoheterotrophs (such as animals)
 Chemotrophs
o use either inorganic or organic chemicals as
an energy source
o Chemolithotrophs (or simply
lithotrophs) are organisms that use
inorganic chemicals as an energy source
o Chemoorganotrophs (or simply
organotrophs) are organisms that use
organic chemicals as an energy source
Terms Relating to Organism’s Carbon
Source
 autotroph and heterotroph pertain to what an
organism uses as a carbon source
 Autotrophs
 o use carbon dioxide (CO2) as their sole
source of carbon
o ex: photosynthetic organisms such as
plants, algae, and cyanobacteria
 Heterotrophs
o use organic compounds other than CO2 as
their carbon source
o ex: Humans, animals, fungi, and protozoa
o ex: saprophytic fungi, which live on dead
and decaying organic matter, and parasitic
fungi
 terms relating to energy source can be
combined with the terms relating to carbon
source, yielding terms that indicate both an
organism’s energy source and carbon
source
 Photoautotrophs
o use light as an energy source and CO2 as a
carbon source
o plants, algae, cyanobacteria, and purple and
green sulfur bacteria
o contribute energy to the ecosystem by
trapping energy from the sun and using it to
build organic compounds (carbohydrates,
lipids, proteins, and nucleic acids) from
inorganic materials in the soil, water, and
air
 Photoheterotrophs
o use light as an energy source and organic
compounds other than CO2 as a carbon
source
o purple nonsulfur & green nonsulfur bacteria
 Chemoautotrophs
o use chemicals as an energy source and CO2
as a carbon source
o nitrifying, hydrogen, iron, and sulfur
bacteria
 Chemoheterotrophs
o use chemicals as an energy source and
organic compounds other than CO2 as a
carbon source
o all protozoa, all fungi, and most bacteria
o All medically important bacteria
 Ecology: study of the interactions between
organisms and the world around them
 Ecosystem: interactions between living
organisms and their nonliving environment
METABOLIC ENZYMES
 Metabolism: all the chemical reactions
(metabolic reactions) that occur within any cell
 metabolic processes that occur in microbes are
similar to those that occur in cells of the human
body
 Metabolic reactions are enhanced and regulated
by enzymes, known as metabolic enzymes
 cell can only perform a certain metabolic
reaction if it possesses the appropriate
metabolic enzyme, and it can only possess that
enzyme if the genome of the cell contains the
gene that codes for production of that enzyme.
Biologic Catalysts – Enzymes
 known as biologic catalysts (a protein that
either causes a particular chemical reaction to
occur or accelerates it)
 proteins that catalyze (speed up or accelerate)
the rate of biochemical reactions, sometimes
reaction will not occur at all in the absence of
the enzyme
 very specific: particular enzyme can catalyze
only one particular chemical reaction
 sometimes, particular enzyme can exert its
effect or act on only one particular substance—
known as the substrate for that enzyme
 Its unique three-dimensional shape enables it to
fit the combining site of the substrate, much like
a key fits into a lock
 does not become altered during the chemical
reaction that it catalyzes. At the end of the
reaction, the enzyme is unchanged and is
available to drive that reaction over and over
 moves from substrate molecule to substrate
molecule at a rate of several hundred each
second, producing a supply of the end product
for as long as this particular end product is
needed by the cell
 do not last indefinitely; they finally degenerate
and lose their activity. Therefore, the cell must
synthesize and replace these important proteins
 there are thousands of metabolic reactions
continually occurring in the cell, so thousands
of enzymes must be available to control and
direct the essential metabolic pathways.
 At any particular time, all the required enzymes
need not be present; this situation is controlled
by genes on the chromosomes and the needs of
the cell, which are determined by the internal
and external environments. For example, if no
lactose is present in the organism’s external
environment, the organism does not need the
enzyme required to break down lactose
 Endoenzymes
o Enzymes produced to catalyze reactions
within a cell that remain within the cell
 o Ex: digestive enzymes within phagocyte
used to digest materials that the phagocytes
have ingested
 Exoenzymes
o Enzymes produced within a cell that are
then released from the cell—to catalyze
extracellular reactions
o Ex: cellulase and pectinase, which are
secreted by saprophytic fungi to digest
cellulose and pectin in the external
environment
 Hydrolases and polymerases are additional
examples of metabolic enzymes
 Hydrolases
o break down macromolecules by the addition
of water, in a process called hydrolysis or a
hydrolysis reaction
o hydrolysis: enable saprophytes to break
apart such complex materials as leather,
wax, cork, wood, rubber, hair, and some
plastics
 Polymerases
o enzymes involved in the formation of large
polymers such as DNA and RNA
o active each time the DNA of a cell is
replicated, and RNA polymerase is required
for the synthesis of messenger RNA
(mRNA) molecules
 Apoenzymes
o Proteins that cannot, on their own, catalyze
a chemical reaction
o must link up with a cofactor to catalyze a
chemical reaction
o Cofactors: either mineral ions
(magnesium, calcium, iron cations) or
coenzymes
 Coenzymes
o small organic, vitamin-type molecules such
as flavin adenine dinucleotide (FAD) and
nicotinamide adenine dinucleotide (NAD)
o participate in the Krebs cycle
o do not have to be present in large amounts
because they are not altered during the
chemical reaction that they catalyze
o lack of certain vitamins from which the
coenzymes are synthesized will stop all
reactions involving that particular 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
 Optimum conditions includes:
o relatively limited range of pH and
temperature
o appropriate concentration of enzyme and
substrate
 Temperature
o Extreme heat and acidity can denature
(or alter) enzymes by breaking the bonds
responsible for their three-dimensional
shape, resulting in the loss of enzymatic
activity
o If the temperature is too high or too low, the
enzyme will not function at peak efficiency,
and the reaction that the enzyme catalyzes
will not proceed at its maximum rate
 pH level
o If the pH is too high or too low, the enzyme
will not function at peak efficiency, and the
reaction that the enzyme catalyzes will not
proceed at its maximum rate
o This explains why a particular bacterium
grows best at a certain temperature and pH
 Substrate Concentration
o If the substrate concentration is too high or
too low, the enzyme will not function at
peak efficiency, and the reaction that the
enzyme catalyzes will not proceed at
maximum rate
METABOLISM
 all the chemical reactions occurring within a cell
 chemical reactions called metabolic reaction
 Metabolite: any molecule that is a nutrient, an
intermediary product, or an end product in a
metabolic reaction
 In cell, many metabolic reactions happen
simultaneously, breaking down some
compounds and synthesizing (building) others
 2 categ: catabolism and anabolism
Catabolism
 all catabolic reactions that are occurring in a
cell
 Catabolic Reactions
o involve the breaking down of larger
molecules into smaller molecules, requiring
the breaking of bonds
o Any time that chemical bonds are broken,
energy is released.
o cell’s major source of energy
o Catabolic reactions in bacteria are quite
diverse, because energy sources range from
inorganic compounds (sulfide, ferrous ion,
 hydrogen) to organic compounds (e.g.,
carbohydrates, lipids, amino acids).
o energy that is released during catabolic
reactions is used to drive anabolic reaction
o can be used to wiggle flagella and actively
transport substances through membranes
o often referred to as degradative reaction:
they degrade larger molecules down into
smaller molecules
o example, breaking down a disaccharide into
its two original monosaccharides— a
hydrolysis reaction—is an example of a
catabolic reaction
Biochemical Pathways
 series of linked biochemical reactions that occur
by step, leading from a starting material to an
end product
 Glucose: the favorite “food” or nutrient of cells
 Nutrients should be thought of as energy
sources, and chemical bonds should be thought
of as stored energy.
 Whenever the chemical bonds within the
nutrients are broken, energy is released.
 chemical processes by which glucose is
catabolized within cells:
o aerobic respiration
o fermentation reaction
o Entner–Doudoroff pathway
o pentose phosphate pathway
o anaerobic respiration
Aerobic Respiration of Glucose
 complete catabolism of glucose
 aka cellular respiration
 occurs in three phases, each of which is a
biochemical pathway:
o glycolysis (anaerobic process)
o the Krebs cycle (require aerobic conditions)
o electron transport chain (aerobic
conditions)
Glycolysis
 aka glycolytic pathway, the Embden–Meyerhof
pathway, or the Embden– Meyerhof–Parnas
pathway
 nine-step biochemical pathway, involving nine
separate biochemical reactions, each of which
requires a specific enzyme
 a six-carbon molecule of glucose is ultimately
broken down into two three-carbon molecules
of pyruvic acid (also called pyruvate)
 can take place in either the presence or the
absence of oxygen; oxygen does not participate
in this phase of aerobic respiration
 produces very little energy—a net yield of only
two molecules of ATP
 takes place in the cytoplasm of both prokaryotic
and eukaryotic cells
Kreb’s Cycle
 pyruvic acid molecules produced during
glycolysis are converted into acetyl-coenzyme A
(acetyl-CoA) molecules, which then enter the
Krebs cycle
 a biochemical pathway consisting of eight
separate reactions, each of which is controlled
by a different enzyme
 in first step, acetyl-CoA combines with
oxaloacetate to produce citric acid (a
tricarboxylic acid [TCA])
 is referred to as a cycle because at the end of the
eight reactions, the biochemical pathway ends
up back at its starting point—oxaloacetate
 Only two ATP molecules are produced during
the Krebs cycle, but several products (e.g.,
NADH, FADH2, and hydrogen ions) that are
formed during the Krebs cycle enter the
electron transport chain
 In eukaryotic cells, the Krebs cycle and the
electron transport chain are located within
mitochondria
 In prokaryotic cells, both the Krebs cycle and
the electron transport chain occur at the inner
surface of the cell membrane
Electron Transport Chain
 aka electron transport system / respiratory
chain
 products produced during the Krebs cycle enter
the electron transport chain
 consists of a series of oxidation–reduction
reactions , where energy released as electrons is
transferred from one compound to another
 compounds include flavopro-teins, quinones,
nonheme iron proteins, and cytochromes
 At the end of chain, there is oxygen referred to
as final or terminal electron acceptor
 Here, a large number of ATP molecules are
produced through phosphorylation—oxidation
referring to a loss of electrons and
phosphorylation referring to the conversion of
ADP molecules to ATP molecules
 breakdown of glucose by aerobic respiration
produces 38 ATP molecules in prokaryotic cells
and 36 to 38 ATP molecules in eukaryotic cells

 Genetic Code
 most genes code for proteins (meaning that
Anabolism
 The Central Dogma
 anabolic reactions that are occurring in a cell
 Anabolic Reactions
o involves the assembly of smaller molecules
into larger molecules, requiring the
formation of bonds
o Energy is required for bond formation. Once
formed, the bonds represent stored energy
o tend to be quite similar for all types of cells;
the pathways for the biosynthesis of
macromolecules do not differ much among
organisms
 gene expression
BACTERIAL GENETICS
Gene Expression
 Gene
o particular segment of a DNA molecule or
chromosome
o contains the instructions (the “recipe” or
“blueprint”) that will enable a cell to make
what is known as a gene product
o Contains four “letters”
o letters that stand for the four nitrogenous
bases found in DNA
o sequence of these four bases that spell out
the instructions for a particular gene
product
each gene contains the instructions for the
production of a particular protein), some code
for rRNA and tRNA molecules
o Proposed by Francis Crick in 1957
o a.k.a. one gene–one protein hypothesis
o explain the flow of genetic information
within a cell
o DNA – mRNA – protein
o States that:
 The genetic information contained in one
gene of a DNA molecule is used to make one
molecule of mRNA by a process known as
transcription.
 The genetic information in that mRNA
molecule is then used to make one protein
by a process known as translation
o When the information in a gene has been
used by the cell to make a gene product, the
gene that codes for that particular gene
product is said to have been expressed
o All genes on the chromosome are not being
expressed at any one time
o constitutive genes: genes that are
expressed at all times
o inducible genes: expressed only when the
gene products are needed