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Chapter 7 Outline
• Microbial Physiology
• Metabolism
– Introduction
– Catabolism
– Microbial Nutritional
Requirements
– Anabolism
– Categorizing
Microorganisms
According to Their
Energy and Carbon
Sources
• Metabolic Enzymes
– Biologic Catalysts
– Factors That Affect the
Efficiency of Enzymes
• Bacterial Genetics
– Mutations
– Ways in Which Bacteria
Acquire New Genetic
Information
• Genetic Engineering
• Gene Therapy
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Microbial Physiology
Introduction
• Physiology is the
study of the vital
life processes of
organisms.
– Microbial
physiology is
very much
chemical
reactions
(metabolism)
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Microbial Physiology
Nutritional Requirements
• All living protoplasm contains 6
major chemical elements: carbon,
hydrogen, oxygen, nitrogen,
phosphorus, and sulfur.
–
Combinations of these and
other elements make up vital
macromolecules of life,
including carbohydrates,
lipids, proteins, and nucleic
acids, vitamins, etc.
• Essential Nutrients:
• materials that organisms are
unable to synthesize, but are
required for building
macromolecules and sustaining
life,
• e.g., certain essential amino
acids and essential fatty acids.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Categorizing Microorganisms by
Energy and Carbon Sources
• Terms relating to an
organism’s energy source.
–
–
Phototrophs use
light as an energy
source.
organic
Chemotrophs use
either inorganic or
organic chemicals as
an energy source.
• Chemolithotrophs
use inorganic
chemicals as an
energy source.
• Chemoorganotrop
hs use organic
chemicals as an
energy source.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Microbial Physiology
Categorizing Microorganisms According to
Their Energy and Carbon Sources, cont.
• Terms relating to an organism’s carbon source:
–
Autotrophs use carbon dioxide (CO2) as their sole source of
carbon.
–
Heterotrophs use organic compounds other than CO2 as carbon
sources.
• Terms that combine both energy and carbon source:
–
Photoautotrophs use light as a carbon source and CO2 as an
energy source.
–
Chemoautotrophs use chemicals as a carbon source and CO2 as
an energy source.
–
Chemoheterotrophs use chemicals as a carbon source and
organic compounds other than CO2 as an energy source.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Categorizing Microorganisms
According to Their Energy and
Carbon Sources, cont.
• Ecology is the study of the
interactions between living
organisms and the world
around them.
• Ecosystem refers to the
interactions between living
organisms and their nonliving
environment.
• Interrelationships among the
different nutritional types are
important in the functioning
of the ecosystem.
–
Example: Phototrophs,
such as algae and
plants, are the
producers of food and
oxygen for
chemoheterotrophs,
such as animals.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolic Enzymes
• Metabolism refers to all the
chemical reactions that
occur in a cell. The
chemical reactions are
referred to as metabolic
reactions.
– Metabolic reactions are
carried out by
enzymes.
• Biologic Catalysts
– Enzymes are biologic
catalysts; they are
proteins that cause a
particular chemical
reaction to occur or
accelerate it.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolic Enzymes
Biologic Catalysts, cont.
• Enzymes are specific, they only
catalyze one particular chemical
reaction.
• An enzyme only affects one
particular substance, known as
the substrate for that enzyme.
• The unique 3-dimensional shape
of an enzyme enables it to fit the
substrate like a key fits into a
lock.
• http://youtu.be/PILzvT3spCQ
• An enzyme does not become
altered during the chemical
reaction it catalyzes. (They don’t
last forever!) Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Factors That Affect the
Efficiency of Enzymes
– pH - extreme
acidity for example
– Temperature - heat
can denature
enzymes by
breaking bonds
– Concentration of
enzyme and/or
substrate – may be
too high or too low
– Inhibitors, for
example heavy
metals like lead,
zinc, mercury and
arsenic
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolism
• Metabolism refers to all of the
chemical reactions within a cell
• A metabolite is any molecule that
is a nutrient, an intermediary
product, or an end product in a
metabolic reaction.
• Metabolic reactions fall into 2
categories: catabolism and
anabolism.
– Catabolism refers to all
catabolic reactions in a cell.
– Anabolism refers to all
anabolic reactions in a cell.
– http://youtu.be/v0OM-Qjdj88
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolism, cont.
• Catabolic reactions involve the
breaking down of larger
molecules into smaller ones.
– Energy is released. Catabolic
reactions are a cell’s major
source of energy.
• Anabolic reactions involve the
assembly of smaller molecules
into larger molecules, requiring
the formation of bonds. The
bonds are stored energy.
• Much of the energy released
during catabolic reactions is used
to build molecules in anabolic
reactions.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolism, cont.
• Energy is
temporarily stored
in bonds in
adenosine
triphosphate (ATP).
• When ATP is used
as an energy
source, it is
hydrolyzed (split)
to adenosine
diphosphate (ADP).
• ADP can be used as
an energy source
by hydrolysis to
adenosine
monophosphate
(AMP).
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Interrelationships among ATP, ADP,
and AMP molecules.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolism, cont.
a
Marine dinoflagellates use energy for bioluminescence.
Energy is required for metabolic pathways, growth, reproduction, sporulation, and
movement of the organism, and active transport of substances across
membranes.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolism
Catabolism
• Catabolic reactions release energy (by
breaking bonds) and are a cell’s major
source of energy.
–
Some energy is lost as heat in
catabolic reactions.
• Biochemical pathways are a series of
linked biochemical reactions, with a
starting chemical and an end product
(chemical).
• Think of nutrients as energy sources for
organisms and think of chemical bonds as
stored energy.
• Glucose, for example, can be catabolized
by either aerobic respiration or
fermentation.
• Glycolysis is shared by both:
http://youtu.be/pnKih-4SRAE
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
A biochemical pathway with 4 steps. Compound A is
ultimately converted to compound E. Four enzymes are
required in this biochemical pathway. Compound A is the
substrate for Enzyme 1, Compound B for Enzyme 2, etc.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Metabolism
Catabolism, cont.
• Catabolism of glucose by aerobic
respiration occurs in 3 phases
(each is a biochemical pathway):
– Glycolysis
http://youtu.be/6JGXayUyNV
w
– The Krebs cycle
– The electron transport chain
• The 1st phase (glycolysis) is
anaerobic, but the other 2 phases
are aerobic. So, the whole
process is considered aerobic.
• Glycolysis is a 9-step biochemical
pathway. Each step requires a
specific enzyme.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Aerobic Respiration of
Glucose:
First Step = Glycolysis.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Catabolism
Aerobic Respiration of Glucose,
cont.
• The Krebs Cycle, aka citric acid
cycle and TCA cycle:
– A biochemical pathway
consisting of 8 separate
reactions, each controlled by a
different enzyme.
– Only 2 ATP molecules are
produced, but NADH, H+,
FADH2 are formed, which enter
the electron transport chain.
• In eucaryotes, the Krebs/TCA cycle
and the electron transport chain
occur in mitochondria.
• In procaryotes, both occur at the
inner surface of the cell membrane.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Catabolism
Aerobic Respiration of Glucose, cont.
• The electron transport chain:
–
A series of oxidation-reduction
reactions, where energy is
released as electrons which are
transferred from one
compound to another.
–
Many enzymes are involved in
the electron transport chain,
including cytochrome oxidase,
which transfers electrons to
oxygen (the electron final
acceptor).
–
A large number of ATP
molecules are produced by
oxidative phosphorylation in
the electron transport chain.
http://youtu.be/DNReloT3QYU
• Aerobic respiration is very
efficient!
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Catabolism
Fermentation of Glucose
• Fermentation reactions do not
involve oxygen. They take place in
anaerobic (no oxygen)
environments.
– First step is glycolysis
(anaerobic).
– The next step is conversion of
pyruvic acid into an end
product.
– The end product varies from
one organism to another.
Example: yeasts are used to
make wine and beer; the
end product is ethanol.
– Fermentation reactions produce
very little energy, ~ 2 ATP
molecules. Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Catabolism
Oxidation-Reducton (Redox) Reactions
• Oxidation-reduction reactions are
paired reactions in which
electrons are transferred from
one compound to another.
• Oxidation occurs whenever an
atom, ion, or molecule loses one
or more electrons in a reaction;
in which case, the molecule is
said to be oxidized.
• The gain of one or more electrons
by a molecule is called reduction
and the molecule is said to be
reduced.
• Within a cell, an oxidation
reaction is always paired with a
reduction reaction; hence the
term, oxidation-reduction
reaction.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Catabolism
Oxidation-Reduction (Redox) Reactions, cont.
• In a redox reaction, the
electron donor (compound A)
is the reducing agent, and
the electron acceptor
(compound B) is the
oxidizing agent.
• Many biologic oxidations are
referred to as
dehydrogenation reactions
because hydrogen ions, as
well as electrons, are
removed.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Anabolism
• Anabolic reactions require
energy because chemical
bonds are being formed. The
energy that is used comes
from catabolic reactions,
which are occurring
simultaneously.
• Biosynthesis of organic
compounds requires energy.
The energy may be obtained
through photosynthesis (from
light) or chemosynthesis
(from chemicals).
–
Photosynthetic reactions
trap the radiant energy
of light and convert it
into chemical bond
energy in ATP and
carbohydrates (e.g.,
glucose).
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Bacterial Genetics
• Genetics = the study of
heredity.
• An organism’s genotype is its
complete collection of genes.
• An organism’s phenotype refers
to its physical traits (e.g.,
includes hair and eye color in
humans).
• An organism’s phenotype is the
manifestation of that
organism’s genotype because
genes control all functions of
the cell.
• Gene: a particular segment of
the chromosome.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Bacterial Genetics
Mutations
• A change in a DNA molecule
(genetic alteration) that is
transmissible to offspring is called a
mutation.
– 3 categories of mutations:
• Beneficial mutations
• Harmful mutations (some are
lethal mutations)
• Silent mutations
• Mutation rate (the rate at which
mutations occur) can be increased
by exposing cells to physical or
chemical agents called mutagens.
• The organism containing the
mutation is called a mutant.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Bacterial Genetics
Ways in Which Bacteria Acquire
New Genetic Information
• Ways in which bacteria acquire new genetic information
(i.e., acquire new genes):
– Lysogenic Conversion
– Transduction
– Transformation
– Conjugation
• An extrachromosomal DNA molecule is called a plasmid.
An organism that acquires a plasmid acquires new genes.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
(A) A disrupted E. coli cell, in which the DNA has
spilled out. A plasmid can be seen slightly to the left
of top center (arrow). (B) Enlargement of plasmid.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Ways in Which Bacteria Acquire
New Genetic Information, cont.
• Lysogenic Conversion
– Temperate phages (or lysogenic phages) inject
their DNA into a bacterial cell.
– The phage DNA integrates into the bacterial
chromosome, but does not cause the lytic cycle
to occur – this is known as lysogeny. This is the
opposite of a lytic cycle, that causes the lytic cycle TO occur,
resulting in the lysis (rupturing) of the host cell.
– A phage is called a prophage (early or first phage/virus)
when all that remains of it is its DNA.
– The bacterial cell containing the prophage is
referred to as a lysogenic cell.
– The bacterial cell exhibits new properties,
directed by the viral genes – this is referred to as
lysogenic conversion.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
how Bacteria Acquire New
Genetic Information, cont.
• Transduction (“to carry across”):
– Also involves bacteriophages.
– In transduction, bacterial
genetic material is “carried
across” from one bacterial cell
to another by a bacterial
virus; thus, in transduction,
bacteria acquire new bacterial
genes.
– Note how this differs from
lysogenic conversion, wherein
bacteria acquire new genetic
information in the form of viral
genes.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
How Bacteria Acquire New
Genetic Information, cont.
• Transformation
– A bacterial cell
becomes genetically
transformed following
the uptake of DNA
fragments (“naked
DNA”) from its
environment.
– The ability to absorb
naked DNA into the
cell is called
competence and
bacteria capable of
absorbing naked DNA
are said to be
competent bacteria.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
How Bacteria Acquire New
Genetic Information, cont.
• Conjugation
–
Involves a specialized type of
pilus called a sex pilus.
–
A bacterial cell with a sex
pilus (called the donor cell)
attaches by means of the sex
pilus to another bacterial cell
(called the recipient cell).
–
Some genetic material
(usually a plasmid) is
transferred through the
hollow sex pilus from the
donor cell to the recipient
cell.
–
A plasmid that contains
multiple genes for antibiotic
resistance is known as a
resistance factor or R-factor.
A bacterial cell that receives
a R-factor becomes a
“superbug.” Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Conjugation in Escherichia coli.
Sex pilus
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Genetic Engineering
• Genetic engineering or recombinant
DNA technology involves techniques
to transfer eucaryotic genes
(particularly human genes) into easily
cultured cells to manufacture
important gene products (mostly
proteins).
• Plasmids are frequently used as
vehicles for inserting genes into cells.
• There are many industrial and medical
benefits from genetic
engineering.
– Examples: synthesis of
antibodies, antibiotics, drugs and
vaccines; also, for synthesis of
important enzymes and
hormones for treatment of
diseases.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Gene Therapy
• Gene therapy of human
diseases involves the insertion
of a normal gene into cells to
correct a specific genetic
disorder caused by a defective
gene.
• Viral delivery is the most
common method for inserting
genes into cells; specific
viruses are selected to target
the DNA of specific cells.
• Genes may someday be
regularly prescribed as “drugs”
in the treatment of diseases
(e.g., autoimmune diseases,
sickle cell anemia, cancer,
cystic fibrosis, heart disease,
etc.)
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins