single or double st randed
I. SCOPE OF MICROBIOLOGY.
Microbiology is the study of organisms from three
domains as wel l as acellular entities that are not
considered to be living in the biological sense.
A. Domains of living organisms
1. Archaea include prokaryotes wi th cell wal ls that
are biochemical ly di f ferent f rom
bacter ia and that inhabi t ext reme envi ronments of
heat , cold, pH, or salts. Archaea
are not a medical ly impor tant domain of
microorganisms.
2. Eukarya contains some microorganismsfor
example, fungi (yeasts and molds) ,
protozoa, and algaealong wi th macroscopic
organisms such as mushrooms,
plants, and animals. Dimorphic fungi are those that
can exist in ei ther the
unicel lular (yeast ) or the f i lamentous (mold) phase,
depending on the incubat ion
temperature (e.g. , Histoplasma and Blastomyces) .
a. Fungi are classif ied into phyla based on the type of
reproductive st ructures
observed or the lack of observable sexual
reproductive st ructures.
(1) Ascomycota (ascus) (e.g. , Candida and
Histoplasma)
(2) Basidiomycota (basidium) (e.g., Cryptococcus)
(3) Zygomycota (zygote) (e.g. , Rhizopus)
(4) Deuteromycota (asexual , also cal led fungi imper
fecti ) (e.g., Coccidioides).
Recent ly, some sexual reproduct ive states have
been identi fied in fungi classif ied
as belonging to Deuteromycota.
b. Protozoa, unicel lular , nonphotosynthet ic
eukaryotes character ized by mode of
moti l ity, include the following:
(1) Mastigophora (f lagellates) (e.g. , Giardia)
(2) Sarcodina (amoebae) (e.g. , Entamoeba)
(3) Ci l iophora (cil iates) (e.g., Balant idium)
(4) Sporozoa (nonmoti le) (e.g. , Plasmodium)
3. Bacter ia contain a wide var iety of prokaryotes,
including gram-posi t ive and gramnegat
ive bacteria. Sect ions II -VI I character ize bacteria in
more detai l .
B. Nonl iving, but medical ly signi f icant enti t ies
are the fol lowing
1. Vi ruses (see VI I I ) , which are classi f ied by:
a. Capsid st ructure, which is the protein coating
around the nucleic acid
b. Type and st randedness of nucleic acid, which
could be DNA or RNA, ei ther
c. Presence or absence of a l ipid envelope sur
rounding the protein capsid
d. Presence of enzymes, which may be ei ther
incorporated into the lipid envelope
or found in the capsid near the nucleic acid
2. Pr ions, infect ious proteins, are impl icated in
some spongi form
encephalopathies (e.g. , mad cow disease,
Creutzfeldt -Jakob disease, and kuru) .
II. TAXONOMY AND
NOMENCLATURE OF BACTERIA
A. Taxonomy is classif icat ion or order ing into
groups based on degree of
relatedness. Bacteria are prokaryotes that belong to
the Bacter ia domain and the
Eubacteria kingdom and are grouped and named pr
imar ily by morphology,
biochemical and metabolic di fferences, and
immunologic and genetic relationships.
DNA technology has led to the reclassi f ication of
some organisms based on DNA
sequences and homology. Bacter ia are named using
the Linnaean or binomial
system as a genus and species (e.g., Homo sapiens
is the genus and species for
humans) .
P.176
B. Morphology is the classi ficat ion of bacteria by
shape and st ructure.
1. Cul tural morphology is based on the size, shape,
and texture of colonies that
are grown in pure culture on an agar plate. Each
colony or iginates f rom a colonyforming
unit (CFU) , consist ing of a single cel l or group of
adherent cells.
2. Microscopic morphology describes bacteria on the
basis of the size, shape, and
ar rangement of the cells (see I I .C and D) .
C. Stains. Because of thei r small size and relat ive t
ransparency, bacter ia must be
stained to be visible under the light microscope.
Staining is also used as a
classi ficat ion system. The major types of staining
react ions are the following:
1. Simple stain. A single dye (e.g. , Gent ian violet ,
saf ranin) that colors the cells.
2. Gram stain. A dif ferent ial staining procedure that
divides bacter ial cells into
ei ther gram-posit ive (purple) or gram-negative (pink)
.
3. Acid- fast stain. A procedure that stains cel ls that
have an outer layer of a waxy
l ipid (acidfast ) but not cel ls that lack that layer (non-
acid- fast) .
4. Spore stain. A procedure that uses heat to help dye
enter the spore.
5. Capsule stain. Two dyes are used to stain the cel l
and the background, allowing
visual ization of the unstained capsular material.
D. Bacter ial cel l shape and ar rangement
1. Cocci are spherical and exist in chains (St
reptococcus pyogenes), pairs or
diplococci (St reptococcus pneumoniae, Neisser ia
gonor rhoeae) , clusters
(staphylococci ) , and packets of four or eight
(sarcinae) .
2. Baci l l i are cylindr ical and rod-shaped organisms
(pseudomonads, Escher ichia) .
3. Coccobacil l i are short rounded rods (Brucel la).
4. Spi rochetes and spi ri l la are hel ical, like a
corkscrew (Treponema pallidum) ;
spi ri lla are r igid hel ices, whereas spi rochetes are f
lexible hel ices.
5. Fusobacter ia have tapered ends and are slight ly
curved (i .e., fusi form;
Fusobacter ium mort i ferum) .
6. Filamentous organisms are branching organisms
and are associated wi th moldl
ike bacter ia (Actinomyces bovis) .
7. Vibrios are comma shaped rods (Vibrio cholerae) .
8. Pleomorphic organisms exist in var ied forms
(Haemophi lus, Legionel la,
Corynebacter ia) .
E. Other classi f ication parameters
1. Presence or absence of
a. Spores used for survival (Bacil lus anthracis) .
b. Capsules or slime layers used for adherence.
Capsules are also ant iphagocyt ic
(St reptococcus pneumoniae, Neisser ia meningi tidis)
. however , the capsule of Bacil lus is
2. Mot i li ty and the type of f lagella
a. Monot richous. A single flagellum
b. Lophot r ichous. A tuf t of flagella at one pole
c. Amphi t r ichous. A f lagellum at both poles
d. Per i t richous. Flagel la dist ributed evenly over the
enti re cel l
e. Axial fi laments. Per iplasmic f lagel la wrapped
around spi rochetes
f . Gl iding mot i li ty. As demonst rated by slime
molds
P.177
III. STRUCTURE OF THE
PROKARYOTIC CELL
A. Overview. Prokaryot ic cells (bacter ia) are smal l
and relat ively simple (Figure 9-
1) . They have the fol lowing character istics:
1. Contain no internal membrane bound organel les
but have complex cell wal l
st ructures
2. Lack a t rue nucleus, a nuclear membrane, and int
racytoplasmic membranous
organelles (e.g., plast ids, endoplasmic reticulum,
vacuoles)
3. Mul t iply asexual ly by binary f ission rather than
by mi tosis or meiosis
4. Protein synthesis is mediated by 70s rather than by
80s ribosomes.
5. Bacter ial genet ic information is ar ranged on a
single supercoi led ci rcular st rand
of double-st randed DNA; the nucleoid is the area of
the cel l containing the t ightly
coiled chromosome.
6. Some bacter ia contain storage granules, or
inclusion bodies, the staining of these
granules may also be useful in identi fying the
bacteria.
B. External st ructures
1. Capsule and sl ime layer
a. The capsule is an adherent , surface coat made up
of long chain repeats of
carbohydrates or peptides. The capsule dif fers in
composit ion among bacter ia of
di f ferent genus and species. Ant igenic di fferences
among capsules can be used to
ident i fy st rains wi thin a single species of bacteria
(St reptococcus pneumoniae) .
Capsules are usually polysacchar ide in nature;
polypeptide. The capsule has several funct ions:
(1) Increases the vi rulence (degree of organism
pathogenicity) of a microorganism
(2) Prevents phagocytosis of the organism by
macrophages and neut rophi ls
(3) Aids in adherence of the organism to host cells
b. I f the polysaccharide is nonadherent, it is called a
sl ime layer .
c. Transformation f rom smooth to rough colonies on
media indicates capsule loss.
Concur rent ly, there is a loss of vi rulence. This
capsular material is immunogenic,
thereby inducing the product ion of ant ibodies, which
act as opsonins to enhance
phagocytosis (opsonization) .
2. Flagel la are proteinaceous, helically coi led organs
used for movement that
extend outward f rom the cytoplasm through the cel l
wall into the environment
(Figure 9-2) . Flagel la rotate ei ther clockwise or
counterclockwise, al lowing a series
of runs and tumbles in response to chemicals in the
envi ronment . The di rection of
movement is cont rolled by a complex mechanism
involving chemoreceptors and an
int racel lular cascade of methylation and
phosphorylat ion react ions, causing bacter ia
to move toward nut r ient chemoat t ractants and
away f rom repellants.
a. St ructure
(1) Flagel la are composed of f lagel lin, a protein
called Hantigen, which is
ant igenically distinct f rom other f lagel la in
eucaryotes.
(2) Flagel la have three par ts:
(a) Basal body
( i ) At taches the flagella to the cytoplasmic
membrane and cel l wal l
( i i ) The number of r ings that make up the basal
body di f fer in gram-posi tive ( two)
and gram-negat ive (four) organisms. The L and P r
ings are absent in Gram-posit ive
organisms.
(b) Hook
(c) Filament
b. Per iplasmic f lagella, also cal led axial f i laments,
occur in spi rochetes and are
embedded into the cel l wal l 's outer membrane.
Because they cause a corkscrew
type of mot ion on cont ract ion, these organisms are
not hindered by the viscosi ty of
media.
3. Pi li ( f imbr iae) are proteinaceous, hai r - like
extensions that are shorter than
f lagella and composed of regular ly ar ranged protein
subuni ts called pi lin or
f imbr i lin. They are more common in gram-negat ive
organisms but can be found in
gram-posit ive organisms. There are two
morphological and funct ional variet ies:
a. Common (attachment) pil i
(1) Appear in greater numbers than sex pi l i
(2) Have adhesive proper t ies, which are impor tant
in the format ion of biofilms
(3) Are lectins, which are responsible for t rophism,
the abil ity of the organism to
bind to speci fic receptors on host cel ls
b. Sex (conjugat ive or F) pi li
(1) Are longer than common pil i
(2) Form in groups of < 10
(3) Are involved in the t ranspor t of DNA between
donor and recipient cel ls
C. The cel l wall , per iplasmic space, and cytoplasmic
membrane
1. The cel l wal l is r igid. Al though i t provides the
general shape of the cell, i ts
funct ion is to protect the cel l f rom osmot ic shock. I f
the cel l wal l is destroyed, the
bacter ial cel ls are suscept ible to al terations in the
tonici ty of the envi ronment . The
wal l is composed of a basic pept idoglycan layer ,
which in turn is composed of
repeat ing disacchar ide uni ts (a polymer of N-
acetylglucosamine and Nacetylmuramic acid),
wi th a four -amino-acid side chain that is covalent ly l
inked to
amino acids f rom neighbor ing disacchar ide uni ts,
forming a stable cross-l inked
st ructure. Most bacter ia are designated as ei ther
gram-posi t ive or gram-negative,
based on fundamental dif ferences in the components
of the cell wal l . Owing to the
uniqueness and the impor tance of the cel l wall to
bacter ial viabi l ity, i t is the target
of many ant ibiot ic agents.
a. Gram-posi t ive organisms have a thick cel l wal l ,
which is 90% peptidoglycan,
wi th extensive cross- l inking that is approximately 40
layers thick and forms a
layered network around the cytoplasmic membrane.
Wi thin the cel l wall , a var iety of
elements serve to stabi l ize the cel l wall , maintain i
ts association wi th the
cytoplasmic membrane, and act as receptors and
antigenic determinants. These
elements include proteins, polysacchar ides and
teichoic acid (glycerol or r ibitol
phosphodiesters) .
(1) Teichoic acids (glycerol or ribi tol phosphodiesters)
(a) Membrane-associated teichoic acids (l ipoteichoic
acid) are covalent ly l inked to
glycol ipids of the cytoplasmic membrane.
(b) Wal l -associated teichoic acids are covalent ly l
inked to the glycan chain of
peptidoglycan.
b. Gram-negat ive organisms' cell wal ls are multi
layered wi th a thin pept idoglycan
layer that has no teichoic acids. External to this is the
outer membrane, a complex
cell wal l layer , which is linked to the pept idoglycan
layer by the l ipoprotein layer .
The outer membrane acts as a hydrophobic di f fusion
bar r ier and consists of
(1) Phosphol ipid, a bi layer simi lar to the cytoplasmic
membrane wi th protein
channels, called por ins, for nut rient t ransport . The
phospholipid layer of the outer
membrane faces the cytoplasmic membrane.
(2) The lipopolysacchar ide (LPS) component projects
f rom the cel l sur face and is
both toxic and antigenic (O ant igen) . In a gram-
negative organism, the LPS blocks
di f fusion of low molecular weight substances into
the cell , so antibiotics and
chemicals that at tack the cel l wal l (e.g. , lysozyme,
penici ll in) cannot easily pass
through. LPS, also known as endotoxin, is toxic to
humans and is composed of
three par ts:
(a) Lipid A: toxic por tion that can ei ther slough of f
intact cel ls or be released into
ci rculation upon lysis of the cel l , causing nonspeci
fic inf lammation, including
diar rhea, fever , and septic shock
P.180
(b) Core polysacchar ide: simi lar wi thin genera
(c) O-speci fic side chain: species specif ic
(3) Protein
2. The per iplasmic space, an area between the cell
wal l and the cytoplasmic
membrane, contains a gel of several types of
molecules (e.g. , hydrolytic enzymes,
per iplasmic-binding proteins) that process molecules
before they enter the
cytoplasm. I t also contains proteins that act as
chemoreceptors for chemotaxis,
others that act as carr iers of nut r ients (similar to car
riers in the cytoplasmic
membrane), and ant ibiot ic- inact ivating enzymes.
3. The cytoplasmic membrane is a phosphol ipid
bilayer mat r ix of a fatty acid core
(hydrophobic) and glycerol phosphate (hydrophi lic) .
In the presence of proteins
embedded in the mat r ix, these membranes are act
ively and passively engaged in
several cel lular functions.
a. Transpor tat ion of nutr ients through
(1) Passive di f fusion
(2) Facil itated di f fusion
(3) Act ive t ranspor t (this method is the only one that
actively uses energy because
molecules are moving into the cell against a concent
rat ion gradient )
b. The si te of respi rat ion proteins used for elect ron
t ranspor t and energy
format ion
c. Enzymes involved in the assembly of the cel l wal l
components
d. Secret ion of exotoxins and other substances for
the breakdown of
macromolecules
D. Internal st ructures
1. Storage granules are inclusion bodies used for food
or energy storage (e.g.,
polyphosphate complexes, carbohydrate).
2. Ribosomes are cel lular uni ts that synthesize
protein by the t ranslat ion of
messenger RNA (mRNA) base sequences into amino
acid protein sequences. These
r ibosomes, unlike those in eukaryot ic cells, are 70s
units and are not associated
wi th membranes such as mitochondr ia or rough
endoplasmic reticulum.
3. The nuclear region of bacter ia is a condensed
area (a nucleoid) containing the
bacter ial chromosome, which lacks a nuclear
membrane and consists of a long,
double-st randed, supercoi led, circular DNA
molecule.
4. Some organisms contain plasmids, circular double-
st randed pieces of DNA that
are found outside of the bacter ial chromosome.
These st ructures are autonomous
(not cont rol led by the bacterial chromosome) ,
contain informat ion for heavy metal
and antibiotic resistance, are conjunct ive, and car ry
genet ic elements cal led
t ransposons.
IV. MICROBIAL PHYSIOLOGY
A. Nut r i t ional types
1. Autot rophs use carbon dioxide as thei r sole or
main carbon source.
a. Photoautot rophs use l ight as an energy source.
b. Chemoautot rophs oxidize organic or inorganic
compounds to produce energy.
2. Heterot rophs use organic compounds as thei r
main carbon source.
a. Photoheterot rophs use l ight as an energy source.
b. Chemoheterot rophs oxidize organic and inorganic
compounds to produce
energy.
3. Protot rophs are parent cells that have no special
nut ri t ional requi rements. They
requi re the same nut r ients as the major number of
the natural members of the
species.
4. Auxot rophs are mutated so that they cannot
synthesize the same essent ial
nut rients (usual ly amino acids) as thei r parent cel l .
5. Subsets
a. Holophyt ic. Organisms whose nut r ients must be
in a soluble, di f fusible form
b. Holozoic. Organisms that need complex nut r ients,
often sol id mater ials that are
ingested and then broken down
c. Saprophyt ic. Organisms whose nut rients are
obtained f rom dead or decaying
organic mat ter
P.181
d. Parasi t ic. Organisms whose nut r ients are
obtained f rom and at the expense of a
l iving organism (human pathogens)
B. Nut r i t ional requi rements. Bacteria use a wide
var iety of nut rients to obtain
energy and to const ruct new cellular components.
The six elements used as the
main components of carbohydrates, l ipids, proteins,
and nucleic acids are carbon,
oxygen, hydrogen, nit rogen, phosphorus, and sulfur .
Several minor and t race
elements as wel l as cat ions play var ious roles in the
microorganisms.
C. Temperature relat ions
1. Psychrophi le, an organism that grows wel l at 0C,
has optimal growth at 15C or
less, and a maximum growth temperature of 20C
2. Mesophi le: an organism wi th opt imal growth at
20 -45C, minimum growth
temperatures between 15 and 20C, and a maximum
growth temperature of
approximately 45C (human pathogens)
3. Thermophi le: an organism that can grow at 55C
or greater , wi th a minimum
growth temperature of approximately 45C.
D. Oxygen requi rements. How organisms use
oxygen can be a major factor in thei r
classi ficat ion.
1. Aerobes have the abi li ty to grow in the presence of
atmospheric oxygen.
a. Obl igate aerobes depend completely on oxygen
for growth. Oxygen serves as
terminal elect ron acceptor in aerobic respiration.
b. Facul tat ive aerobes have the abil i ty to grow wi th
or wi thout molecular oxygen.
2. Anaerobes have the abil i ty to grow wi thout
oxygen.
a. Obl igate anaerobes do not tolerate oxygen at all
and die in i ts presence. Many
st rains lack catalase and superoxide dismutase,
which protect cel ls f rom the
dest ruct ive oxidizing capabil i ties of hydrogen
peroxide and superoxide ions, which
are normally produced under aerobic condit ions.
b. Facul tat ive anaerobes do not require oxygen but
grow bet ter in i ts presence.
3. Microaerophi les requi re oxygen levels below
normal atmospher ic pressures for
growth (e.g. , Helicobacter pylor i )
4. Capnophi les requi re higher levels of carbon
dioxide than are found at normal
atmospheric pressures for growth (e.g. , Neisseria sp.
and St reptococcus
pneumoniae) .
E. Bacter ial growth curve. Bacter ial growth is def
ined as an increase in the
number of cel ls present. Because bacter ia
reproduce by binary f ission, growth can
be plotted as the log of the cell number versus t ime
to produce a curve wi th four
dist inct phases (Figure 9-3) .
1. Lag phase. A t ransi t ion per iod dur ing which the
bacter ia are replicat ing DNA and
the enzymes needed for the new envi ronment are
being induced. The cells are
increasing in size but not in number . Dur ing this
phase of growth, the cel ls are most
permeable.
2. Logar i thmic ( log) phase. Division occurs at
constant and maximal rate, and the
number of cel ls increases in a geomet r ic
progression. The generat ion time, which
var ies among species, is usually 15-20 minutes
(Escher ichia), but may be hours
(Mycobacterium) . Because the cel l wall is being
synthesized so rapidly, bacter ial
cells are most suscept ible to cel l wal l inhibi tors dur
ing this phase.
3. Stationary phase. The growth rate tapers off and
growth and death rates are
nearly equal. A fai rly constant populat ion of viable
cells results. During this phase,
cellular metabol ites are polluting the envi ronment .
4. Death phase. When the concent rat ion of viable cel
ls decreases because of the
accumulat ion of toxic wastes and autolyt ic enzymes.
V. METABOLISM AND ENERGY
PRODUCTION.
Microorganisms der ive energy f rom nut r ients by a
ser ies of chemical react ions by
which the energy stored in chemical bonds is t ransfer
red to newly formed chemical
bonds to provide energy storage in a useful form,
such as adenosine t r iphosphate
(ATP) .
A. ATP generat ion
1. Subst rate- level phosphorylat ion releases energy
through di rect t ransfer of
high-energy phosphate groups f rom an intermediate
metabol ic compound to
adenosine diphosphate (ADP) . No molecular oxygen
or other inorganic f inal elect ron
acceptor is requi red.
2. Oxidat ive phosphorylat ion removes elect rons f
rom organic compounds and
passes these elect rons through a ser ies of elect ron
acceptors along an elect ron
t ranspor t chain, wi th molecular oxygen or some
other inorganic compound as the
f inal acceptor .
B. Fermentat ion refers to energy-producing oxidat ive
sequences, in which organic
compounds serve as both elect ron donors and
acceptors. This process occurs in the
absence of external elect ron acceptors.
1. Glycolysis is the fi rst step in fermentat ion and respi
rat ion and causes the
oxidat ion of glucose to pyruvic acid wi th a yield of
two moles of ATP. There are
di f ferent pathways for pyruvic acid product ion in
microorganisms:
a. The Embden-Meyerhof (glycolyt ic) pathway is the
major pathway.
b. The Entner -Doudoroff pathway is an al ternate.
c. The hexose monophosphate shunt used wi th the
glycolyt ic pathway is an
al ternative.
2. Secondary fermentation process. Many bacter ia
use pyruvate to oxidize
reduced nicotinamide adenine dinucleotide (NADH)
, produced in glycolysis, to
manufacture a var iety of f inal products.
a. Lact ic acid fermentat ion. The simplest process,
which conver ts pyruvate to
lactate (Lactobaci l lus, Streptococcus) .
b. Alcohol fermentat ion. Pyruvate is conver ted to
ethanol and carbon dioxide
(Saccharomyces) .
c. Mixed acid fermentation. A combinat ion of lact ic,
formic, and acet ic acids is
produced wi th ethanol , hydrogen, and carbon
dioxide (Escherichia col i ).
d. Butanediol fermentation. Pyruvate is conver ted to
acetoin, which is reduced to
2,3-butanediol (Enterobacter ).
e. Butyr ic acid fermentat ion. Butanol , isopropanol ,
and acetone are produced
(Clost r idium) .
P.183
f . Propionic acid fermentat ion. Pyruvate is conver
ted to oxaloacetate wi th the
addi t ion of carbon dioxide and then to propionic acid
(Propionibacter ium).
C. Respi rat ion refers to energy-producing oxidative
sequences, in which inorganic
compounds act as the last elect ron acceptor in a ser
ies of reactions. This process
includes glycolysis, the t r icarboxyl ic acid (TCA)
cycle, and the elect ron
t ranspor t system, which yields ATP when coupled wi
th oxidat ive phosphorylation.
1. Aerobic respi rat ion. Oxygen serves as the f inal
elect ron acceptor .
a. Pyruvate is converted to acetyl coenzyme A and
carbon dioxide and water
through the TCA cycle.
b. The elect ron t ranspor t system plays a role in the
t ranspor t of elect rons along a
ser ies of car r iers found in the cytoplasmic
membrane, each wi th successively higher
oxidat ion potent ials. Major components of the elect
ron t ransport system include
(1) Cytochromes
(2) Flavoproteins
(3) Ubiquinones
VI. GENETICS
A. Def ini t ion and terms. Genet ics is the study of
what genes are, how they car ry
informat ion, and how they are replicated and passed
on.
1. Chromosomes are bodies composed of DNA that
contain genet ic information.
Bacter ia have only one chromosomea single, cont
inuous (closed) , doublest
randed, ci rcular piece of DNA.
a. Dupl icat ion occurs by semiconservative
replication, in which the two st rands of
the helix separate (or igin) and at this point ( two repl
icat ion forks) new st rands are
synthesized, bidi rectional ly, wi th the or iginals
serving as templates.
b. St ructure. The cell membrane is at tached to the
chromosome; as the cell grows,
i t separates the daughter chromosomes. Therefore,
each daughter cel l has one
or iginal and one new st rand.
2. Genes are DNA segments that are processed in
two steps to produce var ious
proteins. A normal bacter ial cel l is haploid.
B. Regulat ion and expression of genet ic informat
ion
1. DNA has many funct ions.
a. I t is dupl icated for t ransfer to progeny dur ing cel
l division.
b. I t is t ranscr ibed into RNA, which can be t
ranslated into a protein.
c. It contains cont rol signals, which ul t imately cont
rol the synthesis of protein.
d. I t can be mutated to al ter speci fic character ist
ics encoded by genes.
e. I t can be dupl icated and t ransfer red to other
bacter ial cel ls in processes other
than cel l division (e.g. , conjugat ion) .
2. DNA repl icat ion, t ranscr ipt ion, and t ranslat ion
affect cellular growth and
development.
a. Bacter ial repl icat ion involves accurate duplicat
ion of chromosomal DNA, which
enables the formation of two ident ical daughter cel ls.
b. Transcr ipt ion of information f rom DNA to RNA is
the f i rst of two steps needed to
produce necessary proteins. One gene can be t
ranscr ibed into many copies of RNA.
Simpl istical ly, RNA polymerase locates the
beginning of the gene (promotor ) , and
this area undergoes local ized unwinding to allow
RNA polymerase to t ranscr ibe
RNA (cal led mRNA) f rom the DNA template. The
RNA is not processed, as in
eukaryotes. There are no int rons and exons, no
capping of the 5 end, and no
polyadenine tai ls added to the 3 end.
c. Translat ion is the processing of genetic information
to synthesize proteins.
Before t ranscription is completed, a ribosome wi l l
attach to the 5 end of the
message. The 70s
P.184
bacter ial ribosome is composed of two subuni ts, 30s
and 50s. The r ibosome
t ranslates the message into protein by reading the t r
iplet codon ( three
nucleot ides) which code for a speci fic amino acid.
This amino acid is car ried to the
si te by t ransfer RNA ( tRNA) and pai rs wi th the
codon by an ant icodon. Aminoacids are joined, and
the r ibosome moves to the next codon. This cont
inues unti l the
complete protein is synthesized.
3. Regulation. The products of cellular growth must
be produced in cor rect
propor t ions for the cell to l ive and funct ion. The two
most common mechanisms of
metabol ic and genet ic regulat ion are as follows:
a. Feedback inhibi tion of enzyme activi ty (metabolic
regulat ion) inhibi ts the
synthesis of the cel l growth product . The product
binds wi th an al loster ic si te on the
enzyme, thereby inact ivat ing the act ive si te.
b. Repression of enzyme act ivi ty (genetic regulat ion)
inhibi ts the synthesis of the
enzyme at the transcr ipt ional level .
c. Induct ion of enzyme activi ty act ivates the
synthesis of the enzyme at the
t ranscription level .
C. Other methods of DNA t ransfer . Microorganisms
can change thei r genetic
consti tution by the transfer of genetic material f rom a
donor chromosome to a
recipient chromosome ( recombinat ion) . Recombinat
ion occurs between homologous
segments ( those that have similar nucleot ide
sequences) . There are three general
mechanisms:
1. Transformat ion involves the recipient cel l taking
up cel l -f ree, f ragmented (i .e. ,
naked) DNA and recombining genetic elements.
a. This process is primi tive and occurs natural ly wi
thin only a few genera.
b. Requi rements include competent recipient cel ls
(exhibit ing DNA receptors) or a
leaky bacter ial cel l wal l , so that DNA can be int
roduced into the cel l .
c. It is generally associated wi th recombinant DNA
technology or cloning, a
technique to ampli fy a speci f ic gene in preparation
for analysis. In this process, the
bacter ial cel l wal ls are made leaky by chemical t
reatment .
(1) Cloning involves spl icing a gene into a plasmid
DNA (vector ) . Al l vectors share
several common character ist ics:
(a) Typical ly smal l, wel l -characterized molecules of
DNA
(b) Contain at least one replicon and can be
replicated wi thin the host even when
the vectors contain foreign DNA
(c) Code for a phenotypic t rai t that can be used to
detect the presence of foreign
DNA, which can often be used to dist inguish parental
f rom recombinant vectors
(2) Selectable markers are used to find cel ls that
contain these vectors.
(3) Plasmids cannot maintain stabi li ty unless they
are benef icial to the host , so the
plasmid should contain a gene essential for cellular
survivalei ther an enzyme
requi red in a metabolic pathway or a gene that
resists cer tain antibiotics (see
I I I .D.4) .
2. Conjugat ion is an impor tant means of gene t
ransfer , part icular ly among gramnegat
ive organisms. This process involves two mating
typesthe donor (F+ ) and
recipient (F- ) cel lsand the ext rachromosomal
piece known as the sex or fer t il i ty
factor (F factor ) . The F factor (e.g. , F plasmid or
episome) is not under the cont rol
of the chromosome and can repl icate autonomously.
Plasmid-mediated exchange of
genet ic informat ion can occur only through the
expression of t ransfer genes. The
genes encoded on the plasmid result in the transfer of
a single st rand of DNA
through the sex pi lus into the recipient cel l . The F
factor has several genes that code for format ion and
aid in donor attachment of sex pi li . Dur ing this
process, a
copy is made, a single strand is t ransfer red, and the
recipient becomes F+ . R
plasmids also exist , which encode for resistance to
cer tain antibiotics or heavy
metals. When an F plasmid integrates into the cel
lular chromosome, the bacter ial
st rain is said to be a high- f requency recombinat
ion (Hf r ) st rain. During the
conjugal t ransfer involving an Hf r st rain, depending
on the amount of t ime, the
whole bacter ial chromosome may be t ransfer red.
Ant ibiot ic- resistance genes are
of ten par ts of t ransposons (see I I I.D.4) , which are
responsible for addi t ions,
delet ions, and inversions of large (4-80 ki lobases)
sequences. When di fferent
t ransposons jump into transferable plasmids,
contagious resistance to mul t iple
ant ibiot ics can occur .
3. Transduct ion is the t ransfer of genet ic mater ial
by bacter iophages (vi ruses that
infect bacter ia). Such vi ruses can be classi f ied into
two groups:
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a. Lyt ic phages enter the cel l, replicate, and package
thei r DNA; they then lyse the
cell to release mature infective vi r ions.
b. Lysogenic ( temperate) phages can al ternate
between two pathways:
(1) The lytic pathway
(2) The lysogenic pathway- integrat ing into the host
DNA and remaining dormant
(a) The vi ral DNA does not replicate but is integrated
into the host genome and is
known as prophage.
(b) The prophage suppresses the lyt ic state by
synthesizing a protein known as a
repressor , which protects the cell f rom further
infection by a virus.
(c) Some prophages can change the cel l 's
phenotype (phage or lysogenic
conversion) , which al lows the organism to elaborate
materials (exotoxins or
vi rulence factors) that are det r imental to the human
host . Lysogenic conversion
thereby increases the vi rulence or the symptoms of a
speci f ic pathogenfor
example, Corynebacterium diphtheriae (diphther ia
toxin) , Streptococcus pyogenes
(erythrogenic toxin in scar let fever) , and Clost r idium
tetani ( tetanus toxin) .
VII. EXAMPLES OF UNIQUE
BACTERIA
A. Chlamydia are obligate int racel lular parasi tes
that
1. Lack the abil i ty to generate ATP; hence they must
obtain i t f rom the host cel l
2. Have a two-phase li fe cycle
a. The infectious form, or elementary body, is a
dense, nonrepl icat ing cel l that is
resistant to drying in the envi ronment.
b. The reticulate body forms f rom engulfed
elementary body and undergoes binary
f ission. Af ter mul tiple divisions, the reticulate bodies
become the dense, elementary
bodies, which are released f rom the host cel l (e.g. ,
Chlamydia t rachomat is, which
causes bl indness and sexual ly t ransmi t ted
diseases) .
B. Ricket tsia, obl igate int racellular parasi tes t
ransmi t ted by ar thropods, appear to
have the abil i ty to generate ATP, but instead use the
host cell products, includingATP, amino acids, nicot
inamide adenine dinucleot ide (NAD) , and
coenzyme A
(e.g., Ricket tsia r icket tsii , which causes Rocky
Mountain spotted fever ).
C. Mycoplasma, the smal lest bacter ia, are unique in
that
1. They lack a cel l wal l .
2. The plasma membrane contains sterols for added
st rength (e.g. , Mycoplasma
pneumonia, which causes an atypical or walking
pneumonia) .
VIII. VIRUSES
A. Vi ral st ructure
1. The basic structure of a vi rus is the vi r ion or
nucleocapsid. This st ructure is
composed of a protein coat , which surrounds the vi
ral genome. The shape of the
nucleocapsid is one component that determines the
classi ficat ion of the vi rus. As
noted in I .B.1.b, the viral genome is composed of ei
ther RNA or DNA and may be
single or double st randed. The nucleocapsid of vi
ruses that infect humans has two
basic shapes.
a. Icosahedral . A regular geomet r ic st ructure wi th
12 or more faces; resembles a
soccer bal l
b. Helical . The proteins that make up the st ructure
wrap in a hel ical fashion. Hel ical
capsids of ten have cone or bul let shapes.
2. The vi rion may have a l ipid envelope, which is
produced when the virus buds
f rom the host cel l. The envelope is composed of the
host cell plasma membrane and
vi ral ly coded glycoproteins.
B. Vi ral repl ication. Vi ruses are nonl iving enti t ies
that must enter a host cel l to
repl icate. Once in the host cel l , the vi rus is able to
replicate i ts genome and
produce more viruses, which wi l l infect other cel ls.
The steps in the mult ipl ication of
animal vi ruses are outl ined in Table 9-1 and involve:
1. The vi rus at taches (attachment ) to the host cel l
using viral proteins or
glycoproteins, which bind to receptors on the host cell
sur face.
2. The vi rion then enters (penet rat ion) the host cel l
. Ent ry may be accompl ished by
fusion of a vi ral envelope wi th the cell membrane or
by uptake of the vi rion into an
endocyt ic vesicle. I f the vi rus enters the cell through
an endocytic vesicle, there are
several ways for i t to leave the endocytic vesicle and
enter the cytoplasm of the
host cell .
3. Once in the host cel l , the vi rus uncoats, and the
nucleic acid is released f rom
the capsid. The f ree nucleic acid then is able to begin
the process of reproduct ion.
4. Protein synthesis occurs in two stages. Ear ly
proteins are necessary for the
synthesis of a new vi ral genome and are synthesized
immediately af ter infection.
Late proteins are synthesized af ter the vi ral genome
has been copied; these are
the proteins necessary for the assembly of the capsid,
glycoproteins for the
envelope, and any enzymes included in the
nucleocapsid.
a. For vi ruses wi th a single-st randed RNA genome,
the RNA may be a plus (+)
st rand or a minus ( -) st rand. Plus-st rand RNA
genomes are mRNAs and are
t ranslated direct ly to proteins. Minus-st rand RNA
genomes have an RNA-dependent
RNA polymerase that copies the genome into a st
rand of mRNA for transcr iption.
b. Double-st randed RNA genomes use an RNA-
dependent RNA polymerase to
t ranscribe the minus st rand of RNA into a message
for t ranslation.
c. Some plus-st rand RNA vi ruses are members of
the ret rovi rus family (e.g. , human
immunodef iciency vi rus). These viruses have an
enzyme called reverse polymerase,
which t ranscribes the RNA to double-st randed DNA.
The double-st randed DNA is
integrated into the host cell chromosome (a provi rus)
and then t ranscribed to mRNA using host cell
enzymes. The viral mRNA is then t ranslated into vi
ral
proteins.
d. In vi ruses wi th a DNA genome, the DNA may be
double st randed or single
st randed. In ei ther case, the DNA is t ranscribed to
mRNA and then t ranslated into
proteins. 2. Droplet t ransmission. Infected droplets are formed
5. Af ter genome and protein synthesis, the vi rus is when an infected individual
assembled into new vir ions. coughs or sneezes. The infected droplets t ransmit
the disease to a suscept ible
6. Af ter assembly, the vir ions are released f rom the individual when they come in contact wi th the
host cell . For nonenveloped mucous membranes of the individual 's
vi ruses, the vi r ions are released when the host cel l nose, mouth, or eyes (measles) .
lyses. Enveloped vi ruses are 3. Ai rborne t ransmission. When small contaminated
released from the host cel ls by budding out of the
dust par ticles or the residue
host cel l membrane.
f rom dr ied droplets (droplet nuclei ) remain
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suspended in the ai r for long per iods of
IX. TRANSMISSION OF t ime, they can t ransmi t disease ( inf luenza,
pneumonia, tuberculosis). These smal l
INFECTIOUS AGENTS nuclei can infect both the upper and the lower respi
ratory t ract .
A. Infectious agents are found in a number of di f 4. Food and water contaminat ion. Food or water
ferent environments, called contaminated wi th bacter ia f rom
reservoi rs. human or animal feces leads to t ransmission of
disease through the fecal -oral route.\ C. Vectors are
1. Humans are reservoirs for diseases that are
animals capable of t ransmi t ting diseases. The most
obligate human pathogens, which
common vector
include almost al l viral infect ions and many bacter ial
for disease is the mosqui to (malaria) , but other
diseases. When humans are
insects ( fleas, t icks and fl ies) are
the reservoi r for the disease, they are said to be car r also vectors (Rocky Mountain spot ted fever) . In addi
iers. tion, mammals (dogs, mice and
rats) can be vectors for disease.
a. Asymptomat ic car r iers harbor an infect ion but
D. Ent ry into a host . Bacteria can enter a host
have no symptoms. Some
through ingest ion of food or water ,
asymptomatic car r iers car ry the infect ious agent as
inhalat ion of droplets or dust par t icles, injection by
part of thei r normal flora
an insect vector , or by
(St reptococcus pyogenes) .
contaminat ion of a wound.
b. Symptomat ic car r iers have obvious signs and
symptoms of disease.
2. An animal reservoi r exists when the pr imary host
is an animal . Such animals
may be wi ld (e.g., foxes, raccoons) or domesticated (l
ivestock and pets).
3. Envi ronmental reservoi rs include soi l, lakes, and
plants.
B. The t ransmission of infectious agents depends on
the source of infect ion. For
diseases wi th human reservoi rs, the mechanisms of
t ransmission include
1. Contact
a. Di rect contact requi res physical contact between
an infected individual and a
susceptible individual (sexual ly t ransmi tted
diseases) .
b. Indi rect contact involves a susceptible individual
coming in contact wi th a
contaminated sur face (many vi ruses and bacteria) .
Fomi tes are sur faces that can
be and f requent ly are contaminated wi th
microorganisms (door knobs, counters and
other sur faces, computer keyboards, toys).