Part 1 Principles of Microbiology
The Genetics of
Chapter 6:
Microorganisms
Structure and Function of Genetic
Material
1. Genetics is the science that studies heredity.
The Structure of DNA
1. DNA is composed of the sugar deoxyribose,
phosphate, and nucleoside base. The base
may be adenine (A), guanine (G), cytosine
(C), or thymine (T).
2. Deoxyribose and phosphate form long
strands than wrap around a central core of
bases, forming a double helix. Hydrogen
bonds that form between G-C and A-T pairs
hold two strands together.
Reactions of DNA
1. DNA enters into two kinds of reactions:
replication and gene expression.
Replication of DNA
1. Replication is making a copy of a DNA
molecule from deoxyribonucleotides.
2. Replication begins by breaking the A-T and
G-C bonds within a short stretch of DNA,
forming a bubble and exposing bases to
pair with nucleoside triphosphates.
3. Each newly polymerized strand of DNA is
complementary to and has bases that pair
with the template (original strand). Each
new double helix is composed of one new
and one conserved strand. Thus, the
process is called semiconservative
replication.
4. Replication begins at a genetically specified
point on the chromosome called the origin.
5. Replication forks travel simultaneously in
opposite directions around the
chromosome. When they meet at a point
called terminus, the two completed
chromosomes separate.
6. The replication forks contain the replication
apparatus.
7. The two strands of a DNA double helix are
antiparallel; one strand runs from a 3’
carbon to a 5’ carbon and the other runs
from a 5’ to a 3’. Because DNA polymerase
III can synthesize a continuous strand of
DNA in only one direction, there is
continuous synthesis on the leading strand
and discontinuous synthesis on the lagging
strand.
Gene Expression: Transcription
1. Gene expression consists of two steps:
transcription and translation.
2. Transcription is the polymerization of
ribonucleotide building blocks into a
molecule of RNA – either messenger RNA
(mRNA), transfer RNA (tRNA), or ribosomal
RNA (rRNA).
3. Transcription begins when ribonucleoside
triphosphates pair with the exposed bases
on an exposed strand of DNA. The
information in DNA is transcribed
(rewritten): C pairs with G and A pairs with
U (uracil).
4. Transcription begins near a site on the
genome called a promoter. Here RNA
polymerase separates the two strands,
forming a bubble in the DNA, and uses one
of them as a template. Polymerization
proceeds in the 5’ to 3’ direction. It stops at
a place called the terminator. The transcript
is released, and the DNA bubble closes.
Gene Expression: Translation
1. Translation is the polymerization of amino
acids into a protein.
2. All three products of transcription
participate in translation: mRNA carries the
information that determines the order of
amino acids in the protein; rRNA is a
component of ribosomes where translation
takes place; and tRNA does the actual
translating. Each tRNA molecule has a site
that binds to mRNA and a site that binds to
an amino acid.
3. The nucleic acid-recognizing end of the
molecule consists of an anticodon that pairs
with a codon on mRNA.
4. The specificity of codon-anticodon pairing
determines the sequence of amino acids in
a protein. The correspondence between
codon and amino acid is called the genetic
code. Any of the three nonsense codons
stops translation at the end of a gene.
5. As a ribosome moves down a molecule of
mRNA, it exposes successive codons in a
region called the A site. An amino acid-
bearing tRNA molecule attaches at each
codon, positioning the amino acid to be
polymerized onto a peptide at the
ribosome’s P site. Then the ribosome moves
one codon down and the process repeats.
Regulation of Gene Expression
1. Gene expression is usually regulated by
increasing or decreasing the rate of
transcription or translation.
Part 1 Principles of Microbiology
2. Inducible enzymes are produced only when
their substate is abundant. Repressible
enzymes are produced only when their
product is scarce. Constitutive enzymes are
always produced.
3. Transcription is often regulated by
regulatory proteins that bind to DNA and
change its interaction with RNA polymerase.
When fewer transcripts are made, less
protein is made.
4. An operon is a set of genes that is regulated
and transcribed together. The lac operon in
Escherichia coli, which encodes the ability to
use lactose as a substrate, is regulated by a
repressor.
5. Attenuation regulates transcription in
bacteria by sensing relative rates of
transcription and translation. Regulation of
the histidine operon is an example. When
the supply of histidine is adequate,
translation of the leader protein occurs
quickly. The small stretch of mRNA between
RNA polymerase and the first ribosome form
an attenuator loop which prevents
transcription of the subsequent genes in the
operon. When the supply of histidine is low,
translation of the leader protein is slow. The
larger the stretch of mRNA forms an anti-
terminator loop that prevents formation of
the attenuator loop. Transcription of
subsequent operon genes proceeds.
6. Translation of mRNA encoding ribosomal
proteins is regulated by a protein with two
functions. One is to be incorporated into a
ribosome. The second is to inhibit
translation. When the supply of ribosomal
protein is just right, all the molecules are
incorporated into ribosomes. When there is
too much free ribosomal protein, the second
function is activated.
7. Catabolite repression is global regulation of
gene expression in response to the
availability of carbon. For example,
catabolite repression inhibits the lac operon
if a better substrate than lactose is
available.
8. Many responses of bacteria to
environmental signals are mediated by two-
component regulatory systems composed of
a sensor and a response regulator.
Change in a Cell’s Genetic Information
The Genome
1. The genome is the sum total of a cell’s
genetic information (DNA).
2. The genome can change by mutation or by
genetic exchange.
3. Most of a prokaryote’s genes are in its
chromosome. Some are in small circular
structures called plasmids. Most prokaryotes
have a single circular chromosome but a
few have more than one circular
chromosome and some have linear
chromosomes. Plasmids are circular. A few
are linear. Plasmids encode nonessential
features. R factors are plasmids that encode
resistance to antibiotics.
4. Most eukaryotes do not have plasmids;
most of their genome is in chromosome
pairs.
5. The genotype is the genes that a cell
contains. The phenotype is the outward
expression of a cell’s genes.
Mutations
1. A base substitution mutation is a change in
a single pair of bases to a different pair. A
deletion mutation is total removal of a
segment of DNA. An inversion mutation is
the inversion of a segment of DNA. A
transposition mutation is the movement of a
segment of DNA to a different position on
the genome. A duplication mutation is the
addition of a new segment of DNA.
2. Every time the chromosome is replicated,
mistakes can occur and mutations result.
The mutation rate is number of mutations
per cell per generation.
3. Spontaneous mutations are relatively rare
but their impact is great. Induced mutations
are caused by chemical, physical, or
biological mutagens.
4. Chemical mutagens may change a
component of DNA or become incorporated
into the DNA. Physical mutagens may
fragment the DNA backbone or cause
mistakes in replication. Biological mutations
are sequences of DNA that themselves
cause mutations by transposing.
5. Many mutations do not change the cell’s
phenotype. A missense mutation can be
serious if the new amino acid that is
encoded is not similar to the old. A
nonsense mutation (one that changes a
codon to a nonsense codon and stops
translation) usually inactivates the gene
product.
6. Lethal mutation result in destruction of an
essential gene product. An auxotroph has a
defect in a biosynthesis pathway that
confers an additional nutritional
requirement. Conditionally expressed
mutations render a gene product
nonfunctional only in certain environments.
Part 1 Principles of Microbiology
Selecting and Identifying Mutants recipient becomes F+ and is now capable of
transferring DNA to still another recipient.
1. To isolate a mutant strain by direct
6. Transduction is mediated by
selection, conditions are created that foster
bacteriophages. When a phage particle is
the growth of only the mutant strain.
assembled that contains the bacterial DNA,
2. In indirect selection (counterselection),
it can be introduced into a new cell causing
conditions are created to prevent the
genetic exchange.
growth of the desired mutant strain. Then
7. Specialized transduction occurs during
growing cells are killed.
infection by a temperate phage. A prophage
3. In the brute-strength technique, large
leaves the cell, and carries bacterial genes
numbers of cones are examined one by one
as well as phages genes. It injects them
to find the desired mutant strain. Replica
into a new bacterium.
plating is a simplified brute-strength
technique. Genetic Exchange among Eukaryotic
4. By site-directed mutagenesis a researcher Microorganisms
can introduce a particular mutation into a
1. Genetic exchange among microorganisms is
specific gene.
similar to genetic exchange in other
Uses of Mutant Strains eukaryotes (plants and animals). A diploid
cell undergoes meiosis; haploid gametes
1. The Ames test determines whether a
develop; they fuse to form a zygote or new
particular chemical is mutagenic and,
diploid cell.
therefore, potentially carcinogenic.
2. Baker’s yeast. Saccharomyces cerevisiae, is
Genetic Exchange among Bacteria a fungus that undergoes both asexual
(budding and mitosis) and sexual (meiosis)
1. Genetic exchange among bacteria is not an reproduction.
essential part of their life cycle. When it
occurs, only a portion of the genome of the Population Dynamics
donor cell transfers to the recipient cell. A
1. Mutagenic resistance to antibiotics can
merozygote is produced.
cause nosocomial (hospital-acquired)
2. A piece of transferred DNA must be
infections.
incorporated into a replicon (the
chromosome of a plasmid) before it is a
permanent part of the recipient cell’s
genome. Incorporation occurs by
recombination, or crossing over. A plasmid
transferred intact to a recipient cell does not
require recombination to become part of the
recipient cell’s genome.
3. Some bacteria are able to undergo natural
transformation. DNA leaves the donor cell.
Later it is taken up by the recipient cell and
incorporated into its genome.
4. In artificial transformation, the bacterial
cells are treated in the laboratory to make
them able to take up DNA from their
environment. Recombinant DNA technology
(genetic engineering) depends on artificial
transformation.
5. Conjugation is genetic transfer carried out
by conjugative plasmids. The best-studied
conjugative plasmid is the F plasmid in
Escherichia coli. Conjugation begins when
an F+ cell encodes a sex pilus that attaches
to an F- cell. The F plasmid is nicked and
begins producing a single strand of plasmid
DNA that enters the recipient cell. The
Part 1 Principles of Microbiology
Chapter The Science of
1:
Microbiology
The Unseen World and Our World
1. Microorganisms are living things too small
to be seen by the unaided eye.
2. Lister developed antisepsis, a technique for
preventing infection, by building on
established scientific fact, formulating a
hypothesis, and testing it with an
experiment. This approach is the basis of
the scientific method.
3. Microbiology is the study of microorganisms.
Microbes and Disease
1. Throughout history, pathogens (disease-
causing microorganisms) have had a
tremendous negative impact on human
affairs. Epidemic disease brought social and
political chaos along with human suffering.
But only a small fraction of microorganisms
is pathogenic.
Microbes and Life Today
1. The development of microbiology as a
science has allowed us to control microbes
and use them for our benefit.
2. Medical microbiology focuses on preventing
and treating infectious diseases.
3. Environment microbiology is the study of
how microorganisms affect the earth and its
atmosphere.
4. Industrial microbiology deals with
microorganism-dependent industries, such
as those producing food-stuffs, fermented
beverages, and pharmaceuticals. Industrial
microbiologists will increasingly apply
genetic engineering to solving medical,
environmental, and agricultural problems.
5. Research in agricultural microbiology has
led to healthier livestock and more disease-
free crops.
Careers in Microbiology
1. Career opportunities in microbiology depend
on training as well as interest.
The Scope of Microbiology
1. Microorganisms are usually divided into six
subgroups: bacteria, archaea, algae, fungi,
protozoa, and viruses.
2. Microbiology is a cohesive science because
of its methodology and approach to
problems, not because of the relatedness of
the organisms it studies.
3. Bacteria and archaea are prokaryotes; they
lack internal membrane-bound structures.
4. Algae, fungi, and protozoa are eukaryotes;
their organelles are membrane-bound.
5. Viruses are acellular.
Bacteria
1. Bacteria are prokaryotes.
2. Bacteria are extremely small, even for
microorganisms.
3. Bacteria vary in shape, motility, and how
they get energy. There are species that can
withstand freezing, boiling, and extreme
acidity or alkalinity.
4. Some bacteria cause disease, but others
keep our environment in life-sustaining
balance.
Archaea
1. Archaea were discovered as a separate
group of microorganisms in the 1970s.
2. At first, they were called archaebacteria.
3. Being prokaryotes and small, they resemble
bacteria superficially, but they are as
distantly related to bacteria as they are tp
eukaryotes.
4. Many but not all archaea live in extremely
hostile environments.
Algae
1. Algae are eukaryotic organisms that carry
out photosynthesis.
2. Some algae are unicellular and microscopic.
Others consist of so many cells they are
macroscopic.
3. Algae are not important medically, but they
are critically important to global ecology.
Fungi
1. Fungi include mushrooms, yeasts, and
molds. Fungi are eukaryotic and
nonphotosynthetic. Some are microscopic;
others are macroscopic.
2. A few fungi are pathogenic to humans, and
many are pathogenic to plants, causing, for
example, corn smut, wheat rust, and potato
blight.
Protozoa
1. Protozoa are eukaryotic microorganisms
that are specifically animal-like,
nonphotosynthetic, and usually motile.
2. Examples of protozoa are the amoebae,
flagellates, ciliates.
3. The study of protozoan (and helminth-
caused) diseases is call parasitology.
Part 1 Principles of Microbiology
Viruses
1. Viruses are particles of nucleic acid (either
RNA or DNA), usually enclosed in a protein
coat and sometimes surrounded by a
membrane.
2. Viruses are obligate intracellular parasites.
3. Viruses are extremely small, even compared
to bacteria.
4. Viruses can infect animals, plants, and
microorganisms.
5. Prions are even smaller infectious agents
than viruses. They are composed entirely of
protein. Their method of reproduction is not
completely understood.
Helminths
1. Helminths are macroscopic worms, but
some go through microscopic stages in their
life cycle and cause parasitic diseases in
plants and animals, including humans.
2. The helminths important to health studies
are flatworms and roundworms.
A Brief History of Microbiology
1. Once microbiology became an experimental
science in the mid-1800s, a period of
accelerating progress began.
Leeuwenhoek’s Animalcules
1. Antony van Leeuwenhoek, whose hobby
was making microscope, was the first to see
microorganisms (in about 1674). He called
them animalcules.
Hooke and the Cell Theory
1. Robert Hooke’s observation that thin slices
of cork had a honeycomb of chambers, or
cellulae, led to the formulation of the cell
theory: the cell is the basic unit of
organization for all living things.
Spontaneous Generation
1. In 1665 Francesco Redi’s experiment with
covered and uncovered meat jars proved
that maggots do not generate
spontaneously.
2. Many scientists were convinced by John
Needham’s 1745 experiment that
spontaneous generation of microorganisms
did occur. They said that Lazzaro
Spallanzani’s experiment with sealed flasks
proved only that microorganisms needed air
for spontaneous generation.
3. In 1859 Louis Pasteur finally disproved
spontaneous generation. Using special
swan-necked flasks, he performed
experiments that allowed the free passage
of air but prevented the entry of
microorganisms.
4. Pasteur’s experiments set the stage for
rapid progress of microbiology.
The Germs Theory of Disease
1. Robert Koch showed that microorganisms
(germs) cause infectious diseases, and
specific microorganisms cause specific
diseases.
2. Koch developed four postulates that, if
fulfilled, provide absolute proof that a
particular microorganism causes a particular
disease.
3. Koch also developed a technique using an
agar-solidified nutrient medium for
obtaining pure cultures.
Immunity
1. Immunity is the body’s own ability to
combat infection. The idea of immunization
was based on the recognized fact that
people who suffered once from certain
diseases did not get them again.
2. Edward Jenner used fluid from cowpox
blisters provide protection against smallpox.
Inducing immunity for protection against
infectious diseases came to be known as
vaccination.
3. Pasteur developed vaccines for anthrax and
rabies, using attenuated forms of the
disease-causing microorganism. D. E.
Salmon and Theobald Smith demonstrated
that killed microbial cells were also effective
as vaccines.
Public Hygiene
1. Acceptance of the germ theory advanced
the idea of public hygiene, promoting
cleanliness and reducing exposure to
disease, which saved even more lives than
immunization did.
2. Concern for public hygiene led to clean
drinking water, improvements in food
preservation, and hand washing in hospitals
and for personal hygiene.
Microbiology Today
1. Advances in twentieth-century microbiology
have been striking in the areas of
chemotherapy, immunology, virology, and
genetic engineering.
Chemotherapy
1. Chemotherapy is the treatment of disease
with chemicals called drugs.
Part 1 Principles of Microbiology
2. Paul Ehrlich articulated the guiding principle
of chemotherapy, selective toxicity: to be
effective against infection, a drug must kill
or inhibit the infecting microorganism
without damaging the host.
3. The first major class of drugs to gain
widespread clinical use was the sulfa drugs,
which are synthetic chemicals.
4. Antibiotics are natural chemotherapeutic
agents produced by microorganisms.
Penicillin, the first medically useful
antibiotic, was discovered in 1929 by
Alexander Fleming.

Immunology

1. Immunology studies the immune system,

which provides us protection against
pathogens.

Virology

1. Virology, the study of viruses, began in

1892 when Dmitri Iwanowski discovered the
tobacco mosaic virus. Viruses couldn’t be
seen until the electron microscope was
developed.

Genetic Engineering

1. Genetic engineering (recombinant DNA

technology) is a group of techniques for
manipulating DNA outside the organism
from which it was obtained and introducing
it into another cell where it will exert its
effect.
2. Escherichia coli is most often used as the
new host for manipulated DNA.
3. Microorganisms lend themselves to
experimentation because (1) the
metabolism and genetics of
microorganisms, particularly bacteria, are
remarkably similar to those of plants and
animals, and (2) microorganisms are easy
to culture and multiply rapidly so that
enormous numbers can be studied in short
times.

The Future

1. Genetic engineering and bioremediation,

using microorganisms to clean up toxic
chemicals added to the environment,
promise to be areas where rapid progress
will be made.
Part 1 Principles of Microbiology
Chapter 2: Basic Chemistry
The Basic Building Blocks
1. Matter is composed of small particles called
atoms. Atoms are composed of protons,
neutrons, and electrons.
2. Protons carry a positive charge, and
electrons carry a negative charge. Neutrons
have no charge.
Atoms
1. All atoms have the same basic structure. A
cloud of electrons orbits a nucleus of
densely packed neutrons and protons.
Electrons orbit at energy levels, called
shells.
2. The atomic number of an atom is the
number of protons it contains. The atomic
weight of an atom is close to the number
protons and neutrons it contains.
3. Atoms with the same atomic number but
with different atomic weights are called
isotopes.
Elements
1. Matter composed of only one kind of atom
is called an element. The most abundant
elements in living organisms are carbon,
hydrogen, nitrogen, oxygen, phosphorus,
and sulfur.
Molecules
1. A molecule consists of two or more atoms,
of the same or different elements, joined by
chemical bonds. A compound is composed
of molecules containing more than one type
of atom.
2. A molecular formula tells which atoms and
how many of each kind form a particular
molecule.
3. Avogradro’s number (6.02 × 10 23) of any
type of molecule is called a mole of that
substance. A mole is the molecular weight
of the substance in grams.
Chemical Bonds and Reactions
1. Chemical bonds form if the resultant
molecule will be at a lower energy state and
therefore more stable than the original
configuration. Energy is released when a
chemical bond forms. Energy is required to
break a chemical bond.
2. Valence electrons determine an atom’s
capacity to form chemical bonds.
3. A covalent bond is formed when atoms
share electrons. Covalent bonds are
extremely stable.
4. Covalent bonds form nonpolar molecules
(shared electrons are equally spaced) or
polar molecules (shared electrons are not
equally spaced). Polar molecules, such as
water, have a negative and positive pole.
5. Ionic bonds are formed by the attraction
between oppositely charged ions or
molecules. Ionic bonds are not as strong as
covalent bonds.
6. Hydrogen bonds form when hydrogen
atoms are shared between two molecules or
between different parts of the same
molecule. Hydrogen bonds are weak.
7. A chemical reaction occurs when reactants
are transformed into different combinations
of the same atoms or molecules; these new
combinations are called products.
8. The rate of a chemical reaction is influenced
by the energy state of the reactants, the
concentrations of reacting molecules, and
temperature.
9. Catalysts increase the rate of reaction by
decreasing the activation energy barrier. A
catalyst is not altered by the reaction it
brings out.
10. Catalysts in living things are called enzymes.
Water
1. Water is essential for life.
Special Properties of Water
1. Water’s capacity to form hydrogen bonds
gives it a relatively high boiling point and
relatively low freezing point, stabilizes
temperature inside cells, makes water
cohesive, and makes ice less dense than
water. Together these properties make life
possible.
Water as a Solvent
1. Water’s polarity makes it an excellent
solvent. Compounds that dissolve in water
are hydrophilic and those that do not are
hydrophobic.
2. Colloids are tiny solid particles that create
turbid liquids. Come colloidal dispersions
that become concentrated or cooled form
gels.
Hydrogen and Hydroxide Ions
1. Almost every chemical reaction that occurs
in living things involves the participation of
either hydrogen or hydroxide ions.
Part 1 Principles of Microbiology
2. Water ionizes (dissociates) into an equal extremes of temperature, pH, or osmotic
number of positively charged hydrogen ions strength.
and negatively charged hydroxide ions.
Nucleic Acids
3. Solutes that increase the concentration of
hydrogen ions are acids. Solutes that 1. The two kinds of nucleic acid molecules are
increase the concentration of hydroxide ions deoxyri
are bases.
4. Salts dissociate into anions and cations but
not hydrogen or hydroxide ions.
5. The pH scale (logarithmic with base 10)
describes how acidic or basic a solution is
by assigning it a number from 0 to 14.
6. Buffers are weak acids or weak bases that
stabilize the pH of a solution.

Organic Molecules
1. Biochemistry is the study of carbon-
containing molecules made by organisms.
2. A carbon atom can form 4 covalent bonds
with other atoms. Carbon atoms bind with
other carbon atoms to form the molecular
backbone of biochemicals.
3. In an organic compound, atoms other than
carbon and hydrogen are joined in patterns
called functional groups, which give a
compound its characteristic properties and
determine which other compounds it will
react with.

Macromolecules
1. Macromolecules are large molecules formed
through polymerization, a process that
removes added chemical groups from
monomers, the building blocks of
macromolecules.
2. In the opposite process, called hydrolysis,
macromolecules are broken down into
monomers to obtain nutrients or build a
new cell structure.

Protein

1. Proteins function as enzymes, as

components of cell structures, in membrane
transport, and in cell movement.
2. The building blocks of proteins are amino
acids, which are joined by peptide bonds.
3. The primary structure of a protein is its
specific order of amino acids. The secondary
structure is determined by hydrogen bonds
that arrange amino acids into an alpha helix
or a beta sheet. The tertiary structure is
determined by interactions among R
groups. Quaternary structure is the way the
different chains fit together.
4. Denaturation is the destruction of a
protein’s three-dimensional structure by