Lectures 1-> 6 Minimum Competency Objectives

STRUCTURE OF BACTERIA
1. Describe the major structural components of bacterial cells. Which are analogous to
those of eukaryotic cells and how do they differ?
Nuclear Structure and Prokaryotes Eukaryotes
Function

Nuclear Membrane Nearly always absent Present

DNA Present; mostly single, Present; linear, > 1;

circular structure mitochondria--multiple
circles

Division Binary fission--membrane- Mitosis

bound, septal ring structure

Sexual Reproduction Absent; horizontal gene Meiosis

transfer

Cytoplasmic Prokaryotes Eukaryotes

Structure/Organization

Ribosomes 70S (50S + 30S) 80S (60S + 40S) EXCEPT

70S mitochondria

Endomembrane System W/ NA--absent (mito, W/ NA--Present; W/out

(EMS)--with or w/out chloro); w/out NA--absent NA--present
Nucleic Acids (NA) mostly (golgi bodies and
ER)

Microcompartments Present Absent

Cytoskeleton Present Present

Endospores Present (resists heat, Absent

drying, chemicals)

Cell Membrane Present but usually lacks Present--contains sterols

sterols
 Cytoplasmic Prokaryotes Eukaryotes
Structure/Organization

Ribosomes 70S (50S + 30S) 80S (60S + 40S) EXCEPT

70S mitochondria

Endomembrane System W/ NA--absent (mito, W/ NA--Present; W/out

(EMS)--with or w/out chloro); w/out NA--absent NA--present
Nucleic Acids (NA) mostly (golgi bodies and
ER)

Microcompartments Present Absent

Respiratory System Present in PM Present in mitochondria

(ETC/ATP synthesis)

Cellular Size Prokaryotes Eukaryotes

Cellular Size Usually < 2 um Usually 2 -> 100 um

Cell Walls Prokaryotes Eukaryotes

Cell Walls Present--most posses ONLY plants and fungi--

peptidoglycan polysaccharide cell wall

Motility Prokaryotes Eukaryotes

Flagella (motility in liquid) Present--submicroscopic Present--microscopic 9 + 2

single repeating peptide MT arrangement

Surface Translocation Present Present

(gliding)
2. Describe the common shapes and arrangements of bacteria.
A. Cell shape is determined by both Murrain sacculus and cytoskeleton
B. Cocci--round
i. Arrangement (IMPORTANT):
A. Diplococcus (pairs)
B. Chains
C. Clusters
C. Bacillus--bacilli/rod (arrangement does NOT matter)
A. Very short rod--coccobacilli
B. Short, thin rods
C. Short, thin needle-shaped rods
D. Long, thick rods
 E. Long, thin rods
F. Clubbed shaped rods
A. Thin branching filamentous rods w/ clubbed endings
D. Helicoidal
A. Shape:
A. Curved/comma-shaped rod
B. Spirochetes
C. Spirillum
E. Pleomorphic
A. Varies in size and shape

3. Describe the Gram stain procedure and its clinical significance; list the Gram-positive
genera.
A. Gram Stain Procedure
i. Crystal Violet--primary stain; positive stain
ii. Iodine--mordant/fixative; forms a complex w/ crystal violet in both +
and - bacteria
iii. Alcohol--decolorizer/destain; differentiates b/w + and -
i. Insufficient application--everything is purple
ii.Excess application--everything is pink
iv. Safranin--counter stain; positive stain
B. Differential, positive staining procedure
i. Gram positive cell wall’s extensive peptidoglycan layer RETAINS crystal
violet-iodine complex
ii. Gram negative’s thin peptidoglycan layer does NOT RETAIN crystal
violet-iodine post alcohol exposure
i. Destained cells can be stained w/ any stain but Safranin is
normally used
iii. Excluding acid-fast and Gram-positive bacteria, ALL OTHER
medically significant prokaryotic genera stain Gram-negative!!
C. Clinical significance--bacteria cannot be identified based on size, shape, cell
arrangement, or Gram Stain reaction alone. However, the results of a gram-stained
clinical specimen:
I. Often determines/influences initial antimicrobial therapy
II. Aids in identification of the etiologic agent

D. Gram-Positive Genera
*Actinomyces
*Bacillus
*Bifidobacterium
*Clostridium
*Corynebecaterium, Propionibacterium, and other diphtheria's
 *Enterococcus
*Gardnerella
*Lactobacillus
*Listeria
*Mobiluncus
*Peptostreptococcus
*Staphylococcus
*Streptococcus

4. Discuss the composition, function(s), and clinical significance of capsule and

biofilms, flagella, and fimbriae/pili.
 Flagella Pili (Fimbriae) Capsules

Composition *Repeating *Repeating Polymers that may

polypeptide units polypeptide units consist of either:
*Different primary *Different than A. Repeating units
AA sequence than flagella of a simple sugar
pili polypeptide molecules
units B. Repeating units
of complex
polysaccharides
C. Repeating units
of D-glutamic acid
D. In some Gram-
negative bacteria,
the O-antigen of
LPS is the capsule
and then NO K
antigen is
expressed
E. NOTE: a, b, and
c are K antigens--d
is not

Types/Structure *Plain (extend out *Normal pili extend Mucoid like coat
from cell surface out from cell around the cell
into environment) surface into which are: cell
*Endoflagella of environment--types surface associated;
spirochetes I-IV slime layer; both-
(internal structure) *Sex pilus extends cell surface
out from cell associated and a
surface into slime layer
environment
 Flagella Pili (Fimbriae) Capsules

Function *Motility (primarily *Normal pili--1. Aid *Protective structure

liquid/some surface in adherence to in which
translocation) host cells (virulence microcolonies are
*Controlled by factor) 2. Are enmeshed in a
sensory system to antiphagocytic (v. mucoid
move cell two or Factor) 3. Motility-- exoposylaccharide
away from surface film that adheres to
substances-- translocation (v. wet surfaces (inert
chemotaxis Factor for many or living)
human pathogens) *Bacteria in the
4. Form biofilm PERSIST
nanowires--very even in the
conductive--e- flow presence of
b/w bacteria in antimicrobial agents
them to which they are
*Sex pilus-- normally
conjugation--spread susceptible--
of antibiotic Multidrug resistant
resistance among (MDR) usually to
bacteria very high
concentrations of
antibiotics

Clinical *Flagella/H- *Avid adherence to

Significance antigen--aids in host tissues and
identification surfaces--enable
*Virulence factor-- bacteria to
motility grow/thrive in a
moving solution
*Protection against
phagocytosis/WVC,
serum factors,
antibodies
*Protection against
antibiotics
*Protection against
desiccation (drying
out)
*Antigen used to
identify some
human pathogens
5. List the main components commonly found in the cell membrane and cell walls of
Gram negative and Gram positive bacteria and discuss their function and medical
significance, if any:
a. Function/significant of the cell walls of both positive/negative bacteria
i. Determines/maintains cell shape due to presence of peptidoglycan layer
ii. Differential staining occurs here
iii. Shield against environmental changes
1. Molecular sieve--screens large molecules
2. Prevents cell bursting--osmotic forces
3. Mechanical strength--peptidoglycan layer
iv. Interaction of bacteria w/ environment
1. Contains virulence and toxicity factors
2. Major antigenic components located here
3. Macromolecules are receptors
4. Anchors external structures made my bacteria
v. Some pathogenic bacteria lack peptidoglycan
1. Mycoplasma
2. Rickettsia
3. Ehrlichia
4. Anaplasma
5. Chlamydia
b. Structure of gram-negative cell wall
i. Periplasm--functions in osmotic protection (peptidoglycan located here)
ii. Outer wall layer--Outer Membrane (OM)
1. Composition
a. LPS
b. Phospholipid
c. Proteins--Outer membrane proteins (OMP)
2. Structure
a. Lipid bilayer
i. LPS--outer leaflet
1. Lipid A + Core + O-antigenic chain
a. Lipid A--disaccharide, phosphate groups, ,and FA
i. Toxicity of LPS primarily associated
2. Core oligosaccharide
a. Ketodeoxyoctulonate (KDO)
3. Terminal polysaccharide (AKA O-Ag)
a. Structure--unit repeated N number of times
b. Highly specific
c. Highly variable
4. Chromosomal encoded
 5. Broad specificity
a. Pyrogenicity
b. Can active alternative C’ path
c. Activator of Hageman factor (factor XII)
d. Induction and release of endogenous mediators
i. IL-1, IL-6, TNF alpha
6. Heat stable
a. Strong oxidizing agent or burning/incineration will destroy it
7. Does not form toxoids
ii. Phospholipid--inner leaflet
b. Porins--OMP form aqueous channels which allow hydrophilic
substances to pass
c. Lipooligosaccharide (LOS)--Lipid A + extended core
i. Lacks O -Ag chain
ii. Synthesized in place of LPS
Gram-Positive Gram-Negative

Peptidoglycan layer MUCH THICKER Thinner--in the periplasm

Polysaccharides covalently Yes--to peptidoglycan layer NO

bind

Lipoteichoic acid polymers Yes NO

extend through the
peptidoglycan layer

Outer membrane w/ LPS NO Yes

A. Describe and then list the clinical significance of spores
A. Spores are a complete, BUT INACTIVE cell in a protective shell
A. When environmental conditions are again favorable, SPORE
GERMINATES
B. Helps survival during adverse conditions
B. MOST BACTERIA DO NOT FORM SPORES
A. 2 medically important spore-forming bacteria: (genera)
A. Bacillus
B. Clostridium
C. VS vegetative cells spores have INCREASED:
A. Longevity
B. Resistance to:
A. Heat/temp
B. Desiccation
C. Chemical agents
 D. Any medical equipment/surfaces that may be contaminated
require SPECIAL DISINFECTANTS/STERILIZATION via an
autoclave
B. Describe and then list the clinical significance of small cell (colony) variants
A. Growth-deficient variants
B. Form colonies 1/10 of normal size due to deficiencies in energy
metabolism
C. Possess ENHANCED resistance to antibiotics
D. Formed by BOTH Gram-positive and negative bacteria
E. Associated w/ chronic recurrent infections of:
A. Bones
B. Heart
C. Lungs
D. Urinary tract

6. Discuss the structure, characteristics, properties, and medical significance of

lipopolysaccharide:
A. What component is associated with the toxicity of LPS?
A. Lipid A
B. Explain how this component is toxic to humans.
A. It is a potent immunomodulatory substance --> Systemic
Inflammatory Response Syndrome (SIRS) --> distributive shock
(DS)
B. Physiological processes that make up Septic Shock:
A. SYSTEMIC INFLAMMATION/HYPERINFLAMMATORY STATE
B. ACTIVATION OF COAGULATION
C. INHIBITION OF FIBRINOLYSIS
A. B and C result from LPS activation of Hageman Factor -->
activation of clotting system and fibrinolysis
A. Fibrinolysis subsequently INHIBITED by
plasminogen-activator iNHIBITOR
B. RESULT: accumulation of undissolved thrombin
in microcirculation (DIC) which may -->
MULTIORGAN FAILURE and/or Purpuric skin
lesions
A. DIC--disseminated intravascular
coaulation
C. If patients survive hyperinflammatory phase then immunoparalysis
occurs:
A. Loss of delayed type hypersensitivity response
B. Failure to clear primary infection
C. Development of NEW secondary infections
 D. Otherwise DORMANT VIRUSES ARE REACTIVATED--CMV and
HSV
C. Explain the pathophysiology of and describe the manifestations of:
i. Systemic Inflammatory Response Syndrome (SIRS)
i. Temp >38 or < 36
ii.Tachycardia >90 bpm
iii. Tachypnea >20 bpm
iv. Leukocytosis or leukopenia
ii. Sepsis, severe sepsis, septic shock
i. Sepsis--BOTH:
i. PROVEN infection
ii.Presence of TWO OR MORE manifestations of SIRS
ii. Severe Sepsis--BOTH:
i. Sepsis
ii.Organ failure (one or more organs)
i. Primarily heart, lungs, liver, and kidneys
iii. Septic shock--BOTH:
i. Severe sepsis
ii.Refractory hypotension
iii. Distributive shock (DS); warm shock
i. Endothelial cell dysfunction/capillary leakiness-->loss of plasma
from vascular system INTO tissue spaces-->HYPOtension
ii. Loss of vascular resistance-->HYPOtension
iii. Coagulopathy/DIC
iv. Septic Cardiomyopathy-->DECREASED CO
i. LPS; C5A; IL-1b and TNFalpha
ii.REVERSIBLE!

BACTERIAL NUTRITION, METABOLISM, AND GROWTH

1. List and describe those factors which may influence bacterial growth and their clinical
impact. Explain oxygen tolerance and intolerance in some bacteria and its clinical
significance.
a. Organic requirements
i. Order of organic molecules utilized
1. Carbs
2. Protein
3. Lipid
ii. Fastidious vs. Non-fastidious microbes
1. Fastidious--will NOT grow on blood agar--complex growth requirements
2. NON-fastidious--will grow on blood agar
b. Optimum growth temp/temp requirements
i. Optimal growth occurs closer to the MAXIMUM than the minimum temp
range
ii. Temp minimum is determined by REDUCED enzyme activity and
REDUCED membrane fluidity
iii. Temp maximum determed by protein DENATURATION
iv. Categories of bacteria in relation to temp:
1. Mesophiles--20-55* C
a. MOST PATHOGENS--35-36* BEST
2. Thermophiles-->55*
3. Psycrophiles or cryophiles--<20*
a. A few human pathogens are facultative psychrophiles
4. Refrigeration is NOT an acceptable method of maintaining/obtaining sterile
conditions
c. Optimum Oxygen/Oxygen requirements--broad range
i. Obligate aerobic organisms
1. ONLY grow in the presence of O2
ii. Microaerophilic organisms
1. Grow in the presence of REDUCED conc of O2
iii. Facultative anaerobic organisms
1. MANY PATHOGENS
2. Use aerobic respiration for growth when O2 is present and
fermentation when O2 is absent
a. Respiration is MUCH MORE EFFICIENT
b. Early in infection when number of bacteria are low, O2 is plentiful--
respiration/replication
i. As the infection progresses and NUMBERS OF BACTERIA
INCREASE, O2 levels drop --> use of fermentation for continued
growth
iv.Aerotolerant anaerobic organisms
1. Can grow in the presence of O2 BUT GROW BEST in the absence of O2
2. Utilizes ONLY fermentation
v. Obligate anaerobic organisms
1. Can ONLY grow in the absence of O2
2. ONLY utilizes fermentation
vi. O2’s effect on ANAEROBES:
1. All bacteria generate toxic agents in the presence of O2--O2- and H202
a. Can inhibit growth or cause death
2. Oxygen tolerant bacteria (aerobes) produce enzymes that detoxify these
toxic agents
a. If a bacteria is oxygen INTOLERANT (anaerobic) they lack the enzymes
to get rid of the toxic agents --> death of the cell
 vii. Special requirements are needed to collect and culture anaerobes
from specimens b/c of death
1. Certain antibiotics are used for anaerobes
d. Inorganic requirements
i. Special ionic requiremens
1. NON-halophiles vs halophiles
ii. HIGH or LOW levels of an ion that is required for a bacteria can TRIGGER
changes in the bacterial phenotypes
1. Low iron --> diphtheria to produce diphtheria toxin
2. Low calcium --> plague --> endotoxins
3. Low magnesium --> s. Aureus --> TSST-1
e. Ph Optimum
i. Phyisiological
2. Define and explain heterotrophic and autotrophic metabolism, aerobic and anaerobic
respiration, and fermentation w/ regard to bacterial metabolism and growth.
a. Heterotrophic metabolism--catabolic paths that utilize organic carbon as sources
of E and carbon
i. All bacteria which cause disease in humans are heterotrophs
ii. Catabolism--enzyme mediated-oxidation of reduced carbon molecules
(glucose) to simpler oxidized carbon compounds and which MAY result in E
production
1. Glycolysis
2. May result in additional E if their end-products become substrates for:
a. TCA cycle--generates reducing power-->ATP and recycling NADH2
i. Completes oxidation of organic carbon into CO2
b. Fermentation path--may generate ATP via substrate level
phosphorylation
i. Sole E source for fermentation
iii. Forms:
1. Respiration
2. Fermentation
b. Autotrophic metabolism--fix CO2; source of building blocks used in synthesis of
cell constituents is CO2
i. Cellular E is obtained from EITHER:
1. Oxidation/reduction of inorganic ions (chemoautotroph)
2. Harvesting light energy (photoautotroph)
c. Respiration--UNIQUE enzymatic process b/c most of the process MUST
occur in a membrane vesicle or sack (enzyme-membrane complex_
i. Function: GENERATE E = ION CURRENT = PMF FOR ATP SYNTHESIS
1. Occurs during the conversion (recycling) of NADH2 to NAD+ (reduced to
oxidized forms)
ii. 2 parts:
 1. ETC transfers e- and H+ from NADH2 to the terminal electron acceptor
(TEA) generating BOTH PMF AND REDUCED TEA
a. Oxidase test--determines the presence of an ETC component
(cytochrome C) in SOME bacteria
i. Enterobacteria are oxidase negative
ii. Other gram negative rods are oxidase POSITIVE
2. ATP syntheses used PMF to synthesize ATP from ADP and Pi
iii. Two forms of bacterial respiration; differ in compounds that serve as
TEA for the ETC
1. Aerobic respiration--oxidative phosphorylation
a. O2 serves as TEA which is REDUCED TO H2O
2. Anaerobic respiration
a. Inorganic compounds (nitrate, sulfate, etc) serve as TEA
i. MEDICAL SIGNIFICANCE:
1. MetHB occurs when elevated levels of NO3 occur in drinking
water
a. GI tract normal flora convert NO3 (TEA) to NO2 to MetHb
b. Especially a risk for unborn children
d. Fermentation--catabolic paths in which organic compounds serve as the
electron donors and electron acceptors.
i. Simpler than respiration
ii. Results in INCOMPLETE OXIDATION of carbon substrate
1. End products:
a. 1-, 2-, 3-, or 4-C compounds and some CO2
b. Excreted/released from the cell
iii. Uses substrates LESS efficiently but is efficient enough for fermentative
bacteria to GROW AND THRIVE
iv.Paths occur in the cytosol NOT a membrane vesicle
v. DOES NOT DIRECTLY PRODUCE a PMF/ion gradient
vi. MEDICAL SIGNIFICANCE OF MICROBIAL END PRODUCTS
1. Dental caries--lactic acid
2. Acidic pH of vagina/skin
a. Lactobacillus--lactic acid
b. P. Acnes--propionic acid, acetic acid, CO2
3. Abscesses; acidic and anaerobic
a. Many antibiotics are NOT EFFECTIVE AT LOW PH
1. Low pH kills surrounding viable human cells --> release of
compounds that bacteria REQUIRE FOR GROWTH
a. Sulfa drugs are not effective
4. ID bacteria based on the fermentative acidic end products they produce
5. Certain bacteria can ONLY grow fermentatively
a. Lack cytochrome/ETC systems OR cannot use it for E production
 b. Do NOT use NAD+ or NADP+; FERREDOXIN IS USED
i. Must still be recycled from reduced to oxidized form
c. Infections by organisms, such as Clostridium perfringens (obligate
anaerobe), which can cause GAS GANGRENE; H2 is generated in
HUGE AMOUNTS
i. H2 gas is INSOLUBLE in tissue
ii. H2 gas tracks along fascial planes
1. Separates mm tissue
2. Collapses b.v --> impede perfusion --> creating anaerobic
conditions
e. Describe enzymes/products of bacterial fermentation/growth and their clinical
significance.
i. Aerotolerant anaerobes streptococcus and lactobacillus:
1. Produce lactic acid and H202
a. H202 from recycling of FERREDOXIN which is used as NAD+/NADP+
are
b. H202 is detoxified by human host produced peroxidase
i. W/out it they CANNOT grow in the presence of air
f. List the bacterial process associated w/ alkaline end-products, describe the
enzymes involved, the products produced and their clinical significance.
i. Proteus spa (bacterium) are responsible for some UTIs which promote the
formation of kidney stones
1. Release the extracellular enzyme urease
a. Hydrolyzes urea in urine --> NH4+ (ammonia) and CO2
b. Ammonia RAISES PH OF URINE which allows proteus to grow
2. Calcium and Ammonia ions form salts which may precipitate at ALKALINE
PH forming renal calcium composed of triphosphate
ii. H. Pylori--causes type b and duodenal ulcers
1. Produces urease-->increased microenvironment pH of stomach
mucous lining so H. Pylori can grow
3. List the steps in DNA replication, transcription, and translation noting the similarities
and differences b/w these processes in prokaryotes and eukaryotes.
a. DNA synthesis/Replication
i. Synthesis
1. REQUIRES DNA dependent DNA polymerase
2. DNA is the template
3. Base pairing b/w dATP/GTP/CTP/TTP is crucial
4. REQUIRES DNA helices--separated d.s. DNA into single strands
a. Generates TREMENDOUS TORSIONAL STRESS
5. REQUIRES PRIMASE--synthesizes shorts ssRNA primers
6. REQUIRES DNA GYRASE (topoisomerase II)--negatively supercoils -->
DECREASED torsional stress
 7. REQUIRES TOPOISOMERASE IV--required for decaffeination
ii. Replication
1. Semi-conservative
2. Requires an ORI
3. Must be primed by DNA or RNA for both EUK/PRO
4. 5’-->3’ for both strands and EUK/PRO
5. Semi-discontinuous
a. Lagging strand only
b. Okazaki fragments
6. Bi-directional for both EUK/PRO
7. Timing
a. S-phase in eukaryotes; lag and exponential phase in prokaryotes
iii. RNA SYNTHESIS (TRANSCRIPTION)
1. REQUIRES DNA DEPENDENT RNA POLYMERASE
2. REQUIRES DNA HELICES--separates d.s. DNA into single strands
3. DNA is the template
4. Products:
a. mRNA
i. VERY SHORT HALF LIFE vs eukaryotes (sec/min vs h/days)
ii. Antimicrobial protein synthesis inhibitors are EFFECTIVE
b. tRNA
c. rRNA
5. Sometimes requires DNA gyrase
iv.PROTEIN SYNTHESIS (TRANSLATION)
1. OCCURS IN THE CYTOPLASM
2. Ribosomes are FREE--NOT membrane bound
3. Requires 70s ribosomes + accessory components
4. Uses charged-tRNAS (ammoniacal-tRNA syntheses)
5. mRNA is the template
a. Requires accurate codon-anticodon base pairing
6. rRNA catalyzes peptide bond formation
7. Product--polypeptide
8. Protein turnover (half life) is MUCH SHORTER in prokaryotes vs
eukaryotes so antibiotics that INHIBIT PROTEIN SYNTHEIS are
EFFECTIVE
4. List the steps in peptidoglycan synthesis.
a. Synthesis of amino sugars/peptidoglycan subunits
i. Uracil Diphosphate (UDP)--cytoplasmic/cytosolic tag which allows for
DIRECTED synthesis of these subunits
ii. NAG/NAM synthesis occurs while bound to UDP
b. Assembly and translocation of peptidoglycan subunits through the CM
 i. The complete peptideglycan subunit (NAM---NAG) is ASSEMBLED,
BOUND TO BACTOPRENOL, and TRANSLOCATED ACROSS CM
1. Sequential transfer of components from UDP to bactoprenol w/
release of UMPs
c. Addition of subunit to GROWING END of peptidoglycan chain
(TRANSGLYCOSYLATION)
d. Final cross linking (TRANSPEPTIDATION) of peptide stems is done by
enzymes--transpeptidases or penicillin binding proteins (PBP)
i. 2 AA subunits are COVALENTLY BONDED
ii. Completes syntheis of fabril shell around the bacteria --> mechanical strength
and rigidity
5. Define bacterial growth, binary fission, and generation time.
a. Bacterial growth--Dependent on many factors:
i. Nutrient conditions
ii. Cultivation conditions
iii. Genotype that encodes for catabolic and anabolic paths
iv. The growth of a population of a PURE CULTURE of bacteria in a liquid
medium can be GRAPHICALLY ILLUSTRATED by plotting the log of the
number of bacteria produced vs the time required to grow them
1. Four phases:
a. LAG PHASE--cell volume and mass increase, chromosome/DNA
replication/synthesis begins, but NO CELL DIVISION TAKES PLACE
AND THERE IS NO CHANGE IN CELL NUMBERS
b. EXPONENTIAL/LOG PHASE--balanced growth occurs
i. Cell number, mass, volume, and cell component amounts
INCREASE by the same exponential factor
1. Logarithmic incrases in cell number
ii. Expressed as generation time
c. STATIONARY PHASE--NO NET INCREASE in cell numbers
d. DEATH PHASE--log DECREASES in cell number
i. Bacteria autolyse
b. Binary fission--
c. Generation time--time required for one bacterium to divide into 2 cells; time
required for a cell to replicate
d. How may the growth curve of pathogenic bacteria relate to acute and chronic
forms of disease?
i. Rapidly growing bacteria:
1. ACUTE disease
2. RAPID ONSET AND PROGRESSION (FULMINANT) DISEASE
3. HIGH Ag dose in host
4. STRONG IMMUNE RESPONSE
ii. Slow growing bacteria
 1. CHRONIC diseases
2. SLOW onset and progression
3. LOW Ag dose
4. WEAK IMMUNE RESPONSE
iii. Bacteria with a SHORT GT often produce:
1. Rapidly progressive (fulminant) disease w/ high Ag dose in host
iv. LONG GT Bacteria often produce:
1. Chronic diseases w/ low Ag disease in the host
v. Selection of antibiotics
1. INHIBITORS of protein/peptidoglycan syntheis are MORE EFFECTIVE
against fast-growing bacteria
2. Organisms in STATIONARY PHASE also less sensitive to
antimicrobials

MICROBIAL GENETICS--BACTERIAL VARIATION

1. Define terms including genome, genotype, phenotype, replicon, bacteriophage, etc

a. Genome--physical structure of an organism that consists of the chromosome or all
the chromosome PLUS any extrachromosomal elements (plasmids) deemed to be
crucial for the organism
b. Genotype--complete listing of ALL GENES present in an organism
c. Phenotype--complete listing of all PHYSICAL CHARACTERISTICS that an
organism expresses under a defined set of conditions
d. Replicon--DNA or RNA molecules that controls its own replication so is capable
of self-duplication
e. Extra chromosomal elements (ECE)--replicons in a cell, excluding host cell DNA
f. Plasmic--form of ECE present in bacterial cells
g. Bacteriophage--virus replicons (either DNA or RNA) which infect bacterial cells
h. Recombination--exchange of recipient DNA w/ donor DNA
i. Breakage and joining of replicon DNA molecules to form hybrid, recombinant
molecules
ii. Can ONLY occur IN A CELL
2. Describe the different types of plasmids w/ regard to their functions, transmissibility,
and significance for survival of a bacterium.
a. Plasmids are a form of ECE present in bacterial cells
i. Mostly d.s. Covalently closed circular DNA which reside in the bacterial
cytoplasm
ii. Replicons
1. Control their own DNA replication
2. Control copy number
3. Replicate in cytoplasm
 iii. Types of plasmids
1. Conjugative plasmids--encode for a mechanism to transfer a copy of
itseful from the cell that it currently resides in (donor cell) to a cell lacking
the particular plasmid (recipient cell)
2. Resistance (R) plasmids--possess antibiotic RESISTANCE
determinants
iv.Encode for ancillary info--info not absolutely required for cell viability
1. HOUSEKEEPING GENES ARE REQUIRED FOR VIABILITY!!
2. Can be acquired or lost from bacterial cells b/c they encode for ancillary
info and are a METABOLIC BURDEN ON THE HOST
3. Briefly explain legitimate and site specific recombination.
a. Homologous/legitimate recombination in prokaryotes
i. Donor DNA is INTEGRATED into recipient chromosome and the excised,
recipient DNA fragment is DELETED
ii. REQUIRES ENZYME--RecA
iii. FUNCTION--allows gene transfer/exchange
b. Site specific/DNA sequence specific (AKA illegitimate/non-homologous
recombination)
i. Insertion of or replication of genetic elements in DNA w/ recominbation
RESTRICTED to identical sites (DNA SEQUENCES) at two locations on one
replicon or at identical locations on two replicons
ii. RecA INDEPENDENT
iii. Types mediated by mobile genetic elements:
1. Insertion sequences
2. Transposons
iv. Genetic elements CANNOT move themselves--horizontal gene transfer must
occur (HGT)
4. List the different processes of bacterial variation and explain why bacterial variation is
significant. Briefly explain and then compare and contrast genotypic and phenotypic
conversion.
a. Phenotypic variation--event in which ALL cells in a population respond to
environmental stimuli in the same fashion --> production of a new/altered
phenotype via the expression of a gene(s)
i. NO GENETIC VARIATION INVOLVED
ii. At any one tinme the expressed phenotype of microorganisms is LESS THATN
the full potential encoded by the genotype--can occur for more traits than
currently expressed
1. Different environments require different phenotypes
2. Saves energy to only use genes that are needed for the environment that
the organism is currently in
b. Genotypic variation--event in which the genome of one or more cells in a
population is altered; bacteria acquire NEW genetic info
 i. Two mechanisms:
1. Internally by mutation
a. No foreign/donated DNA involved
b. Frequency is RARE but the number of bacteria are GREAT
c. Selection for beneficial mutation occurs
d. Medically significant mutations occur
2. Externally (HGT)--involves the transfer of genetic material from one
bacterial cell (DONOR) to another bacterial cell (RECIPIENT) via:
a. Transformation
b. Conjugation
c. Transduction
5. Explain the acquisition of drug (antibiotic) resistance (single and MDR) by bacterial
cells by the processes of transformation, conjugation, transduction (generalized and
lysogenic) and the clinical significance of each process in the acquisition of drug
resistance.
a. Describe lysogenic conversion and list some clinically important examples.
b. Compare and contrast the life cycles of lytic and temperate bacteriophages.
6. Briefly explain the principle behind, process of, and clinical usefulness of Plasmid
analysis, DNA probes, RNA probes Ribotyping, Restriction Fragment Length
Polymorphism (RFLP), and Polymerase Chain Reaction (PCR) techniques.
a. Plasmid analysis
b. DNA probes
c. RNA probes
d. Ribotyping
e. RFLP
f. PCR

BASIC VIROLOGY

1. Compare and contrast a virus w/ cellular life:

a. Describe the basic virus unit, the virion.
b. Describe and explain in detail, the general properties/characteristics of viruses
and how they are classified.
c. Explain what a viral clade is and why clades are important.
2. Describe each event of the virus replication cycle, and briefly explain how DNA and
RNA viruses replicate:
a. Recognize that host and tissue tropism relates to virus specificity and disease
manifestations.
3. List and briefly discuss potential consequences of virus infection of a host:
a. Explain the multiple factors related to viral infection of a host, i.e. Primary and
secondary infection, viral spread, etc.
b. Describe the mechanisms by which a virus may damage the host cell:
i. Define and describe each type of productive and persistent viral infection.
ii. Explain viral oncogenesis.
iii.