INTO

MICROBIOLOGY
BIO 103 Microbiology

Meek Larry B. Millevo

 BIO 103
GENERAL MICROBIOLOGY

MICROBIOLOGY

- “mikros” – small, ”bios” – life, “logos” – science

- The field of science that studies microorganisms
MICROORGANISMS - can be eukaryotic, archaeal or bacterial
PROKARYOTES – lack membrane bound nucleus

THE SCIENCE OF MICROBIOLOGY

1. BASIC MICROBIOLOGY – fundamental nature

2. APPLIED MICROBIOLOGY – employed to control and use of microorganisms

BASIC MICROBIOLOGY APPLIED MICROBIOLOGY

1. Morphological Characteristic 1. Medical

2. Physiological Characteristic 2. Immunology
3. Biochemical Characteristic 3. Agriculture
4. Genetic Characteristic - Dairy
5. Disease-causing Characteristic - Soil
6. Biological Characteristic - Food
7. Nomenclature Characteristic 4. Biological Warfare

HISTORICAL ROOTS

1. ROBERT HOOKE – coined the term “cell”

2. ANTON VAN LEEUWENHOEK – “FATHER OF MICROBIOLOGY”
- used primitive microscope [200x-300x] to observe river water, pepper
infusion, saliva and feces – termed them as ‘animalcules’
- discovered bacteria in 1676
TWO SCHOOLS OF THOUGHT

1. ABIOGENESIS – life arose from non-living matter

“SPONTANEOUS GENERATION”
- JOHN NEEDHAM (1745) – supported ABIOGENESIS
- Needham’s Jar

2. BIOGENESIS – life arose from life

- FRANCESCO REDI (1668)
- LAZZARO SPALLANZANI
- JOHN TYNDALL
- LOUIS PASTEUR (1862)
 Disproved spontaneous generation
 Established that life did not arise from non-living
 Used swan-neck flask/Pasteur flask
 Spoilage and fermentation
- FERDINAND COHN
 bacillus – discovered bacterial endospores

FERMENTATION – proper selection of microbes could ensure a consistently good

product
How?

1. Heating grape juice

2. Cool and inoculate it with some high-quality wine [starter culture =
contained desired microbe]
3. Preserve wine by heating it to 50°C - 60°C [pasteurization]
Ultra High Temperature– Above 140°C [creates long life milk]
 GERM THEORY OF DISEASE
- States that some diseases are caused by growth and reproduction of
bacteria, viruses, fungi and parasites within the body.
ROBERT KOCH – development of methods for study of bacteria in pure culture

KOCH’S POSTULATE – criteria to provide a specific microbe causes a particular

disease

1. A specific microorganism should always be associated with a given

disease.
2. A microorganism should be isolated and grown in pure culture on a
laboratory.
3. Pure culture of microorganism should produce the disease when
introduced into a susceptible host.
4. Possible to recover (reisolate) the injected microorganism from the
experimentally infected host.
PURE CULTURE – single kind of microorganism culture containing

JOSEPH LISTER (1870) – aseptic technique; spraying of carbolic acid as an

antiseptic coined him the name “FATHER OF ASEPTIC SURGEON”

1. MARTINUS BEIJERINCK
- Enrichment culture technique
- Procedure that greatly improves the possibility of isolating special
kinds of microorganism
- Concept of virus [tobacco mosaic virus]

2. SERGEI WINOGRADSKY
- Concept of chemolithotrophy – the oxidation of organic compounds
- Sulfur, iron and other compounds linked to energy conservation
“WINOGRADSKY COLUMN” – microbial ecology in a bottle

3. ANGELINA FANNIE HESSE

- Wife of WALTER HESSE, R.A. OF PETRI, Suggested addition of agar for media
culture

4. JULIUS RICHARD PETRI

- Discover of Petri dish
 METAORGANISM

- Microorganism associated with other microorganisms

- Interlinked

#1 PARADIGM SHIFT: THE WORLD OF OMICS

GENOMICS – study of the total set of DNA and complete analysis of genes of
different organisms
PROTEOMICS – study of the total sets of proteins in cells
METABOLOMICS – study of the total set of metabolites in a cell, tissue or organism
TRANSCRIPTOMICS – study of the total set of RNAs in a cell, tissue or organism

METAGENOMICS – study of the entire genetic material recovered directly from an

environmental sample

SCOPE OF MICROBIOLOGY
CELL – basic unit of life structurally and functionally

a. Robert Hooke [1665]

b. Schleiden, Schwan and Virchow—cell theories

CELLS
1. PROKARYOTIC CELL
- no nucleus; bacteria and archaea
- flagellum (protein sub-units)

PLASMID carries: tolerance, immunity (non-essential genes)

: Extra-chromosomal [not part of prokaryotic chromomsome]

2. EUKARYOTIC CELL
- With nucleus; protists [protozoans, algae]
- Fungi, plants and animals
- e.g. Amoeba, Saccharomyces cerevisiae, Chlamydomonas nivalis
- tubulin (protein subunits)
 CLASSIFICATION OF MICROORGANISMS

TAXONOMY TAXA – taxonomic group where

- science which inclues: organisms are placed that share
1. CLASSIFICATION(arrangement) common characteristics
2. NOMENCLATURE (naming) SPECIES – basic taxon
3. IDENTIFICATION STRAIN – made up of the descendant
of a single colony from a pure culture

A. CAROLUS LINNAEUS (1753)

- Two-kingdom scheme: Plantae and Animalia
B. ERNST HAECKEL (1865)
- Three-kingdom scheme: Plantae, Animalia and Protista
C. WHITTAKER (1969)
- Five-kingdom classification: Protista, Monera, Fungi, Animalia and Plantae
D. CARL WOESE (1977)
- THE DOMAINS OF LIFE
1. ARCHAEA (archaebacteria) – 16S ribosomal RNA
2. EUBACTERIA
3. EUKARYOTES - 18S (fingerprint; signature sequences) ribosomal RNA

EUKARYOTES:
Hallmarks: nuclei and membrane-bound organelles
Microbial Eukaryotes:
YEAST – DIMORPHIC
- Depending on conditions; they can be unicellular or filamentous
- Pathogenic yeast
FUNGI
PROTOZOA
DIATOMS – PHYTOPLANKTON

DID YOU KNOW?

For disease to happen, there must be:
1. VIRULENT PATHOGEN (degree of pathogenicity)
2. RIGHT ENVIRONMENT
3. SUSCEPTIBLE HOST

One missing of the three, then no disease to emerge

ARCHAEA (prokaryotes): NO NUCLEI, live in extreme environments, non-
pathogenic.

BACTERIA: most are harmless

PATHOGENIC: NON-PATHOGENIC:
Escherichia coli (E. coli) Thermius aquaticus (PCR)
Streptococcus (strep throat) Lactobacillus (dairy)
Yersinia pestis (plague) Nitrosomonas (fish aquarium)
Salmonella (food poison)

PROTOZOA: single-celled eukaryotic microorganism, e.g. PARAMECIUM

- Animal-like since they ingest particular food
- Lack rigid cell wall
- Can swim
A. beating action of cilia
B. whip-like action of flagella
- PSEUDOPODIA – responsible for the locomotion known as ameboid
movement
- Spores – SPOROZOANS – fungi-resting bodies

ALGAE:
- Plant-like because of green pigment chlorophyll
- Carry-out photosynthesis
- Have rigid cell walls
- Most are aquatic
- Used as thickeners and emulsifiers
- Used as in agar

FUNGI:
- Rigid cell walls
- e.g. yeast – “budding” – asexual reproduction; ascospores
(Saccharomyces cerevisiae) – sexual reproduction
- chitin, lack cellulose
- produce enzymes that can decompose lignin-degrading enzymes
- antibiotics – Penicillium
- absorbs dissolved nutrients
- hyphae
GEOCIN (Geotrichum candidum) – gives soil a certain kind of smell
VIRUSES
- borderline between living and non-living
- not cells
- can’t live without a host
- much smaller (20 to 30 nm in diameter)
- contain only one type of nuclei acid, either RNA or DNA

VIROLOGY
a. Tobacco mosaic virus (TMV) – RNA
b. Adenovirus (DNA)
c. Influenza virus (RNA)
d. Bacteriophage

VIRION – an entire virus particle, consisting an outer protein shell called CAPSID
and inner core of RNA/DNA

VIROIDS
- are plant pathogens that consist of a short stretch of highly complementary
…
- RNA, simple strand

PRIONS – infectious agent composed primarily of proteins

Linnaeus, Whittaker
- Major goal of taxonomy is to reflect phylogenetic hierarchy
- Linneaus; goal was classifying and naming organisms as a means of
cataloging them.

DOMAINS
- Carl Woese compared nucleotide sequences of RNA subunits (changes
occur rarely)
- Determined by ribosomal nucleotide sequences
- EUKARYA, BACTERIA AND ARCHAEA
 MICROSCOPY AND STAINING

WHY ARE CELLS SMALL?

- As surface area to the volume ration gets smaller as the cell gets large
- If the cells grow beyond a certain limit, not enough material will be able to
cross the membrane fast enough to accommodate the increased cellular
volume
- When this happens, the cell must divide into smaller cells with favourable
surface area/volume ratios or cease to function.

Microscopy
 General Principles of Microscopy
- Wavelength of radiation
- Magnification
- Resolution
- Contrast
- Differences in intensity between two objects, or between an object
and background
- Important in determining resolution
- Staining increases contrast
- Use of light that is in phase increases contrast

Limits of Resolution (LOR)

- ability of a microscope to distinguish 2 points as distinct
- measure of resolving power

 Light Microscopy
- Bright-field microscopes
- Simple
 Contain a single magnifying lens
 Similar to magnifying glass
 Leeuwenhoek used simple microscope to observe
microorganisms
- Compound
 Series of lenses for magnification
 Light passes through specimen into objective lens
 Oil immersion lens increases resolution
 Have one or two ocular lenses
  Total magnification = magnification of objective lens X
magnification of ocular lens
 Most have condenser lens (direct light through specimen)

Total magnification = magnification of objective lens x magnification of ocular

lens

RI = Refractive Index
- Bending of light of a certain medium

When wavelength decreases, resolving power increases.

OBJECTIVES
 10x – Scanning (coarse focus)
 40x – High-Dry (fine)
 100x – Oil Immersion (fine)

LIGHT MICROSCOPES
1) SIMPLE (BRIGHTFIELD)
2) COMPOUND (BRIGHTFIELD)
3) DARK-FIELD
4) PHASE
5) FLUORESCENT
6) CONFOCAL

 Light Microscopy
o Dark-field microscopes
 Best for observing pale objects
 Only light rays scattered by specimen enter objective lens
 Specimen appears light against dark background
 Increases contrast and enables observation of more details
o Phase microscopes
 Used to examine living organisms or specimens that would be
damaged/altered by attaching them to sides or staining
 Light rays in phase produce brighter image, while light rays out
of phase produce darker image
 Contrast is created because light waves are out of phase
 Two types
 Phase-contrast microscope
 Differential interference contrast microscope
 o Fluorescent microscopes
 Direct UV light source at specimen
 Specimen radiates energy back as a longer, visible
wavelength
 UV light increases resolution and contrast
 Some cells are naturally fluorescent, others must be stained
 Used in immunofluorescence to identify pathogens and to
make visible a variety of proteins
o Confocal microscopes
 Use fluorescent dyes
 Use UV lasers to illuminate fluorescent chemicals in a single
pane
 Resolution increased because emitted light passes through
pinhole aperture
 Computer constructs 3-D image from digitized images
 Electron Microscopy
o Light microscopes cannot resolve structures closer than 200 nm
o Electron microscopes have greater resolving power and
magnification
o Magnifies objects 10,000X to100,000X
o Detailed views of bacteria, viruses, internal cellular structures,
molecules, and large atoms
o Two types
 Transmission electron microscopes [TEM]
 Scanning electron microscopes [SEM]
 Probe Microscopy
o Magnifies more than 100,000,000 times
o Two types
 Scanning tunneling microscopes
 Atomic force microscopes

ELECTRON MICROSCOPY
- TEM (TRANSMISSION ELECTRON MICROSCOPY)
- Used to view thin specimens (tissue sections, molecules, etc.) through
which electrons can pass generating a projection image.
- Uses transmitted electrons (electrons which are passing through the
sample) to create an image
- SEM (SCANNING ELECTRON MICROSCOPY)
- Creates an image by detecting reflected or knocked-off electrons
-
 STAINING
1) SMEAR
- Spread of thin film of material containing microorganisms over side surface
- Allow to air dry
2) FIXING
- Process that kills microorganisms and attaches them to a microscope slide
- Preserves and minimize distortion of cells
3) STAINING
- Improves contrast
- Dye emphasis certain structures

SALTS – composed of a positive ion (cation) and negative ion (anion)

CHROMOPHORE – colored iron
IONOPHORE – part of salt which is the charged component (+,-)

TWO TYPES OF DYE B) ACIDIC DYE – negative ions;

1) BASIC cell shape, size and capsules
2) ACIDIC E.g. Eosin
A) BASIC DYE – chromophore is in Negrosin
positive ion Indian ink
E.g. Crystal Violet - Negative staining, stain the
Methylene Blue background
Safranin BACTERIA (negative charge) DO NOT
Carbolfuchsin STAIN WITH ACIDIC DYES

TYPE OF STAINS
1) SIMPLE STAINS (basic dye – [+])
- Aqueous; alcohol solution of single basic dye
- Primary purpose is to stain entire microorganism to see cell shape
- MORDANT: used to increase stain intensity
- Increases affinity of stain to the specimen
2) DIFFERENTIAL STAINS
- React differently to different types of bacteria
- Has two types:
a) GRAM STAIN
b) ACID-FAST STAIN
A. GRAM STAIN
- 1884 by Hans Gram, Danish microbiologist
- GRAM POSITIVE (+)
- GRAM NEGATIVE (-)
STEPS
1)PRIMARY STAIN = CRYSTAL VIOLET (BASIC STAIN)
- all cells, gram positive and gram negative stained with CRYSTAL VIOLET
2)MORDANT – (IODINE MORDANT)
- After smear is rinsed with water; IM is applied
- Pampalakas kapit ng stain
3) DECOLORIZING
- Slide washed with alcohol which will remove stain from Gram (-) cells
GRAM (-) – decolorized (red)
- Have thinner cell walls thus it’s easy to remove CV-I complex
- 15 seconds
GRAM (+) – remain color (purple)
4) COUNTERSTAIN
- Alcohol is rinsed off, SAFRANIN is applied, which will stain cells that were
decolorized
- Counterstain only colors gram negative cells
GRAM (+) – have very thick peptidoglycan cell walls
GRAM (-) – have very thin walls
 CV-I complex is not easily removed from gram (+) cells due to thick cell wall
while CV-I complex is readily washed out of gram negative cells with
alcohol

APPLICATION AND LIMITATION

 CHEMOTHERAPY
o Overtime general gram (+) have thick cell walls are usually
susceptible to penicillins and cephalosporins
o Gram (-) cells with thin cells are resistant to these antibiotics

B. ACID FAST STAIN (ZIEHL-NIELSEN STAIN)

- 1882 – Paul Ehrlich – father of chemotherapy
- Used to detect tuberculosis and leprosy
Genus Mycobacterium and Nocardia – have waxy cell walls
STEPS
1) PRIMARY STAIN
- Carbolfuchsin – red basic dye
2) DECOLORIZING – slide is washed with acid-alcohol
- NON-ACID FAST CELLS WILL DECOLORIZE
- ACID FAST CELLS WILL REMAIN RED
3) COUNTERSTAIN
- Methylene blue stain
 C. SPECIAL STAIN
- Used to color and isolate specific parts
- ENDOSPORES
 Malachite green (dye)
 Schaeffer-fulton endospores

- CAPSULES
 NO HEAT FIX
 POLYSACCHARIDE WILL MELT
- FLAGELLA
 MORDANT – increase the thickness of flagella

EUBACTERIAL CELL PARTS

PROKARYOTIC CELLS (Pre-nucleus)

- 0.2 – 2.0 um in diameter, 2-8 um in length
INCLUSION – aggregates, storage and magnetosomes
EPS – Extracellular Polymeric substance
- GLYCOCALYX
 Sugar coating
 Allow cells to attach
 Prevents phagocytosis
CAPSULE – neatly organized
SLIME LAYER – unorganized and loose
- FLAGELLUM – protein component – FLAGELLIN
 Motility, run in a rotary movement, proton driven
 Chemo/photo sensing ability
 Chemotaxis, phototaxis, aerotaxis, magnetotaxis – (GRADIENT)
STIMULUS

ARRANGEMENT OF BACTERIAL FLAGELLA

1. Peritrichous
2. Monotrichous and polar
3. Lophotrichous and polar
4. Amphitrichous and polar
GLYCOSIDIC BOND – sugars connected together
PEPTIDE BOND – amino acids connected together

FIMBRIAE AND PILI

- Thinner than flagellum
- FIMBRIAE – allows attachment, forming biofilms
- PILLUS – gliding motility or twitching motility
- SEX PILLUS – to attach two cells during CONJUGATION

EUBACTERIAL CELL WALL

- Major function:
prevents osmotic
lysis
- Maintans SHAPE
and POINT OF
ANCHORAGE for
basal bodies
- Made of
peptidoglycan
(eubacteria only)
- GRAM POSITIVE
and GRAM
NEGATIVE
- Semi-rigid structure that lies outside the cell membrane in almost all
bacteria
- Contributes to bacterial ability to cause disease
- Site of action of some antibiotic
- Very porous and does not regulate passage of material into the cell
- Major Functions
1) Maintains characteristic shape of cell
2) Prevents the cell from bursting when fluids flow into the cell by
osmosis

CELL WALL (PEPTIDOGLYCAN) or MUREIN

- MUREIN – polymer of sugars and amino acids
- mesh-like layer
- two-sugars link alternatively:
- NAG = N-acetylglucosamine
- NAM = N-acetylmuramic acid
NAM/N-acetylmuramic acid
- Attached to adjacent NAM by TETRAPEPTIDE BOND/SIDECHAINS
NAG – peptide chain of three to five amino acids
NAM – peptide chain of one strand cross-linked to the peptide chain of another
strand forming the 30 mesh-like layer

GRAM (+) – Wall teichoic acid – found on peptidoglycan

Lipo-teichoic acid – traverse wall down to periplasmic space
GRAM (-) – outer membrane – has the capacity to regulate peptidoglycan
PORIN PROTEIN
LIPO PROTEIN
PHOSPHOLIPID – amphipathic; has polar and non-polar tail
- Parallel tetrapeptide side chains may be directly linked together by
a polypeptide cross-bridge
- Penicillin interfaces with the final linking of peptidoglycan rows
LYSIS – when cell is greatly weakened

GRAM (+)
Teichoic acids
- Alcohol and phosphate; negative charge
- May regulate movement of cations, cell growth, preventing extensive cell
breakdown
- Polysaccharides provide antigenic variation
- Disrupted by LYSOZYME (in tears) – breaks the bond between NAM and
NAG
- Penicillin sensitive
LYSOZYME – break glycosidic bonds
PENICILLIN – break peptide bonds

GRAM (-)
Lipoproteins
- Outer membrane
- Periplasmic space: Region between outer membrane and plasma
membrane
- Contains degradative enzymes and transport proteins

OUTER MEMBRANE – primary line of defense; consist of:

1) PHOSPHOLIPID BILAYER
2) LIPOPOLYSACCHARIDE (LPS) with 2 components:
 - O-polysaccharides – antigens, uses to identify bacteria
- Lipid A – [tail] – Endotoxin, causes fever and shock
3) PORINS – membrane protein that allows the passage of nucleotides,
disaccharides, peptides, amino acids, vitamins and iron.
4) LIPOPROTEINS
FUNCTIONS
- Evade phagocytosis and complement due to strong negative charge
- Barrier to antibodies, digestive enzymes (lysozymes), detergents, heavy
metals, dyes
LPS (LIPOPOLYSACCHARIDES) Composition
1 LIPID A – lipid tail – Endotoxin, primary factor
2 CORE POLYSACCHARIDE – attached to Lipid A, provide stability
3 O-POLYSACCHARIDE – functions as an antigen, useful in identification

UNUSUAL CELL STRUCTURE

*Mycobacterium: Gram (+) with mycotic acid (waxy to resist dehydration)
60% mycolic acid (impermeable to stains)
40%
*Mycoplasma – smallest bacteria without cell wall but have sterols in membrane
(resist osmotic lysis)

Cell Surface Structure of Archaea

*Archaea – no cell wall or cell wall consists of PSEUDOMUREIN

NAM, N-actetylmuramic acid (different carbohydrates or S-layer)
NAT – N-acetyltalosaminuronic acid

A. PLASMA MEMBRANE
B. PHOSPHOLIPID BILAYER OF MEMBRANE
C. PHOSPHOLIPID MOLECULES IN BILAYER
Polar (Hydrophilic) Heads (phosphate group and glycerol)
Non-polar (Hydrophobic) Tails (fatty acids)

PLASMA MEMBRANE
- Contains enzymes for metabolic reactions
- Involves ATP
- CHROMATOPHORES – infoldings containing enzymes for photosynthesis
- Disruption of membrane structure will allow leakage of cellular contents
e.g. alcohol, detergents, antibiotic (Polymuxin)
FUNCTIONS:
1. Selective Barrier – that regulates the passage of materials
2. Nutrient breakdown and energy (ATP) production
3. Synthesis of cell wall component
4. Assist with DNA replication
5. Site of photosynthesis
6. Secretes proteins
7. Contains bases of flagella
8. Responds to chemical substances in the environment.
- Damage to the plasma membrane can cause cell lysis which results in cell
death
DESTRUCTION OF PM:
1. Alcohol
2. Quaternary ammonium compounds
3. Antibiotics
Impermeable – large proteins, ions and most polar molecules
Permeable – H2O, O2, CO2, simple sugars.

CYTOPLASM
- 80% water and primarily enzymes
- Contains nucleoid, ribosomes and inclusions
- NUCLEOID
 Cell’s genetic information; not surrounded by nuclear
envelope
 PLASMIDS – not connected to main bacterial chromosome but
have very important functions needed for survival – antibiotic
resistance, tolerance to basic metals, toxin production, can be
transferred from 1 bacteria to another via conjugation
- PROKARYOTIC RIBOSOME
 Inhibit protein synthesis – Antibiotics
 Erythromycin and chloramphenicol interfere with 50S
 Gentamycin and streptomycin attach to 30S subunit and
interfere with protein synthesis

ENDOSPORES
- Two genera: Bacillus and Clostridium – Gram (+)
- Resistant to dessication, heat and chemicals
- Resting cells: when essential nutrients are depleted
- SPORULATION: endospore formation [happens when environment is
infavorable to cell]
 - GERMINATION: return to vegetative state

The Origins and Molecular Basis of Antibiotic Resistance – Walsh 2003

a. Cell Wall Biosynthesis
b. Protein Biosynthesis
c. DNA and RNA Replication
d. Folate Metabolism
e. Cell Surface decoration

- Synergy
- Combination of two drugs causes inhibition or killing when used at a
fourfold-cover concentration than of either compound drug used
separately
- Indifference
- Combined action is the same as with either component
- Antagonism
- Reduction in the activity of one or both component in the presence
of the other

ANTIOBIOTIC RESISTANCE

ANTIBIOTIC – any substance produced by a microorganism that is antagonistic to

the growth of other microorganisms in low concentration (Selman Waksma, 1997)

- Different antibiotic attack different parts of pathogenic microbial cell

CELL WALL CYTOPLASMIC MEMBRANE
- Cycloserine STRUCTURE
- Vancomycin - Polymyxins
- Bacitracin - Daptomycin
- Cephalosporins
- Monobactams FOLIC ACID METABOLISM
- Carbapenems - Trimethoprim
- Sulfonamides

DNA GYRASE
- Uncoils double stranded DNA for replication to proceed
RIBOSOMAL PROTEINS
50S 30S
- Erythromycin - Tetracyclines
- Chloramphenicol - Spectinomycin
- Clindamycin - Streptomycin
- Gentamycin
- Kanamycin

Possible/Probably antibiotic resistance exist already in a low population

THE CONNECTED ANTIMICROBIAL ECOSYSTEM

- Adapted from Martinez 2009
1. ENVIRONMENTAL ECOSYSTEM: low resistance gene selection [“THE
RESISTOME”}
2. NON-CLINICAL ECOSYSTEM: Medium Selection Pressure
3. CLINICAL ECOSYSTEM: High Selection Pressure, indicates High Frequency of
Use
 The “natural environment”, where microbes encounter low
concentrations of antimicrobial compounds produced by other
microbes and resistance is low.
 The “non-clinical environment”, where the presence of man-made
antimicrobials raises selective pressure for AMR and
 The “clinical environment” where the relative concentration of
antimicrobials is HIGHEST and consequently antimicrobial resistant in
AMR.
MECHANISMS OF ANTIMICROBIAL RESISTANCE
1) Enzymatic degradation of the drug
2) Modification of the drug’s target
3) Reduced permeability of the drug (efflux pump) – active transport
4) Active export of the drug
Most drug resistance is the result of a genetic change in the organisms caused
either by a chromosomal mutation on the acquisition of a plasmid or
transposons.

GENETIC BASIS OF RESISTANCE

1. The development of point mutations in one of the target genes
(microevolutionary change). An example of this is the alterations in the
beta-lactamase gene extending its spectrum of activity against different
beta-lactam antibiotics.
2. 2. Macroevolutionary changes includes the rearrangement of genes as
might occur with acquisition of antibiotic resistance bearing plasmids or
transposons – JUMPING GENES
3. The final way is to acquire DNA from an exogenous source. Example,
naturally transforming species such as Neisseria can acquire DNA from the
environment. It is believed that this is the way Neisseria species acquired
Antibiotic resistant genes (e.g. penicillin-resistance)
4. Chromosomal mutations – e.g. reduced permeability
5. Plasmid cause drug resistance by encoding enzymes that degrade or
modify drugs. PLASMID-MEDIATED RESISTANCE (alter target sites) – occurs at
a higher frequency.
6. Resistant Plasmids

TRANSPOSONS – small pieces of DNA that move from one site on the bacterial
chromosome to another; termed as Jumping genes by Barbara Me Clintoc
- Resistance to penicillins and cephalosporins
1) Degradation by lactamases
2) Mutation in genes for penicillin binding proteins
3) Reduced permeability
- Aminoglycosides – 30S ribosomal protein
1) Phosphorylating
2) Adenylating
3) Acetylating enzymes
- Tetracyclines – caused by reduced permeability (active transport)
- Erythromycins – plasmid encoded enzyme that methylates the 23
Ribosomal RNA – blocking binding
 - Sulfonamides – plasmid encoded enzymes that actively exports
- Quinolones – mutations in DNA gyrose
- Rilampin – caused by mutation, altering target site
- Isoniazid – loss of bacterial peroxidase (catalase) that activates isoniazid to
the metabolite that inhibits mycolic acid synthesis
- Nongenetic reasons why bacteria may not be inhibited by antibiotic are
drugs may not reach bacteria located in the center of an abcess and then
certain drugs such as penicillins, will not affect
CROSS RESISTANCE
- Single resistant mechanism confers resistance to an entire class of
antibiotics. Eg. Aminoglycoside modifying enzymes with may confer
resistance by several numbers of aminoglycosides.
- Also occurs across different catalizing agents – as a result of either
overlapping drug target as if the case with macrolites and lincosamides or
if there is a drug efflux pump with a broad range of activity.
CO-RESISTANCE
- Refers to presence of a resistance to more than one class of antibiotics in
the same bacterial strain as might occur on a plasmid (MULTIPLE
RESISTANCE)
CO-SELECTION
- Selection of multiple antibiotic resistant genes when one of these genes is
selected. The most elegant example of this is the integrin which is a cassette
of antibiotic resistance genes are expressed in a coordinate manner,
although the most downstream gene may not be as efficiently expressed
as the gene next to the promoter.

ARCHAEA

DOMAIN ARCHAEA
- Have unusual cell walls, membrane lipid, ribosomes and RNA sequence.
General facts
- Most don’t need oxygen to survive (anaerobic)
- Can produce ATP
- Survive extreme temperature i.e. sulfur springs; under [+100°C] rocks and
ocean floor vents deep below the ocean’s surface
- Tolerate huge pressure differences
- Yellowstone National Park’s Hot Springs, USA
- Size – archaea are slightly less than
- Shape – spherical or coccus, rod-shape, long and thin
- Variations of cell have been discovered in square and triangular shapes
FLAGELLA
- locus = multiple flagenes involved in synthesis, assembly function
- Flak/plbD–the preflagellin peptidase gene which encodes an essential
signal peptidase required for flagellin processing
- Archaeal flagella are more similar to bacterial type IV pili than to bacterial
flagella
- Do not possess any homologues of genes found in bacteria that are
involved with bacterial flagellum structure or assembly
- Morphologically, archaeal flagella are rotating structures with a filament as
seen in bacterial flagella
- Flagellins have conserved amino acid sequences at their N termini, both in
the mature proteins and in their class III signal peptides, which are similar to
type IV pilus.

Role of Archaeal Flagella

- Motility and Chemotaxis
- Acts as able connecting cells, as an initial prerequisite for genetic
transfer and in adhesion to abiotic surfaces
- Acts on cell-to-cell contact for the formation of a structured bispecies
biofilm

CANNULAE
- Are hollow tubes with an outside diameter of 25nm, and they appear
empty when cross-fractured or thin-sectioned
- Connect cells with each other
PILI
- Major protein is PILIN
- Protein similar to bacterial pilin but structure of pilus different in archaea
- Plays a role in adhesion of cells
- Least/recently studied structure of archaea

Cell Membrane
- Lipid Monolayer
- Allows to thrive on extreme conditions
- Have branched isoprene chains in its structure

BINDOSOME
- Pilus-like structure close to the cell membrane or integrated with the s layer
- Oligomerized complex proposed to play a role in facilitating sugar uptake
 Classification of Archaea
FIVE PHYLA
1. Crenarchaeota
2. Euryarchaeota
3. Korarchaeota
4. Thaumarchaeota
5. Nanoarchaeota

1. Crenarchaeota
- ‘scalloped archaea’
- Often irregular in shape (pleomorphic)
- Synthesize a didtinctive tertaether lipid (crenachaeol)
- Gram-negative and are morphologically diverse

2. Euryarchaeota
- Very diverse with 7 classes—Methanococcus, Methanobacteria,
Halocateria, Thermoplasmata, Thermococci, Archaeglobi and
Methanopyri
- Basis of habitat is their division into : methanogens (produce methane as
by-products) , extreme halophiles (salt-loving), sulphate reducers (acidic
water and require sulfur or calcium carbonate and alkaline springs),
extreme thermophiles (either hot water, Thermoacidophile—heat and
acid-loving, or Hyperthermophile—extreme heat lover)
3. Korarchaeota
- also known as Xenarchaeota
- found in high temperature hydrothermal environments

4. Thaumarchaeota
- ‘thaumas’—Greek for Wonder
- Identified as chemolithoautotrophic ammonia-oxidizers and may play
importatnt roles in a biogeochemical cycles such as the nitrogen cycle and
the carbon cycle
- The presence of a form of a type I topoisomerase that was previously
thought to be unique to the eukaryotes

5. Nanoarchaeota
- Highly unsual because they grow and divide on the surface of another
archaea
- Only replicates when attatched to the surface of Ignicoccus—its symbiotic
pair archaea
IMPORTANCE OF ARCHAEABACTERIA
1. Role in Chemical Cycles
- Play important role in carbon cycle, nitrogen cycle, sulfuric cycle,
etc.
- Help in researches—their ability to tolerate extreme conditions help
researchers learn about the climatic conditions, environment and
their survival on ancient earth
- Antibiotics—archaea hosts a new class of potentially useful
antibiotics

2. Sewage Treatment
Methane Gas Production
- Methanogenic Archaea—carry out anaerobic digestion and
produce biogas
- Can decompose/grow in biogas fermentators and produces
methane as by-product
Extraction of Metals
- Acidophilic Archaea—extract gold, copper and cobalt from their
ores

3. Exthermophilic Enzymes
a. Resistant to either heat or extremes of acidity and alkalinity

FUNGI, ALGAE, PROTOZOA, and PARASITES

 Some fungi have hyphae divided into

cells by septa, with pores allowing cell-
to-cell movement of organelles
 Coenocytic fungi lack septa

Specialized Hyphae in Mycorrhizal Fungi

  Some unique fungi have specialized hyphae called haustoria that allow them to
penetrate the tissue of their host

 Mycorrhizae are mutually beneficial relationships between fungi and plant roots
 Ectomycorrhizal fungi forms sheaths of hyphae over a root and also grow into the
extracellular spaces of the root cortex
 Arbuscular mycorrhizal fungi extend hyphae through the cell walls of root cells
and into tubes formed by invagination of the root cell membrane

Concept: Fungi produce spores through sexual or asexual life cycles

 Fungi propagate themselves by producing vast numbers of spores, either sexually
or asexually
 Fungi can produce spores from different types of life cycles

Sexual Reproduction
 Fungal nuclei are normally
haploid, with the exception of
transient diploid stages
formed during the sexual life
cycles
 Sexual reproduction requires
the fusion of hyphae from
different mating types
 Fungi use sexual signalling
molecules called pheromones
to communicate their mating
type
 Plasmogamy is the union of
two parent mycelia
  In most fungi, the haploid nuclei from each parent do not fuse right away; they
coexist in the mycelium, called a heterokaryon
 In some fungi, the haploid nuclei pair off two to a cell; such a mycelium is said to
be dikaryotic
 Hours, days, or even centuries may pass before the occurrence of karyogamy,
nuclear fusion
 During karyogamy, the haploid nuclei fuse, producing diploid cells
 The diploid phase is short-lived and undergoes meiosis, producing haploid spores

 Other fungi that can reproduce

asexually are yeasts, which inhabit moist
environments
 Instead of producing spores,
yeasts reproduce asexually by simple
cell division and the pinching of “bud
cells” from a parent cell
 Many molds and yeasts have no
known sexual stage
 Mycologists have traditionally
called these deuteromycetes, or
imperfect fungi
LIFE CYCLE OF FUNGI

Filamentous fungi can reproduce asexually by fragmentation of their hyphae.

Fungal spores are formed from aerial hyphae and are used for both sexual and asexual
reproduction.

1. Asexual spores: Formed by the aerial hyphae of one organism. New organisms are
identical to parent.
Conidiospore: Unicellular or multicellular spore that is not enclosed in a sac.
Chlamydospore: Thick-walled spore formed within a hyphal segment.
Sporangiospore: Asexual spore formed within a sac (sporangium).
2. Sexual spores: Formed by the fusion of nuclei from two opposite mating strains of
the same species. New organisms are different from both parents.
The Origin of Fungi
 Fungi, animals, and their protistan relatives form the opisthokonts clade

Concept: Fungi have radiated into a diverse

set of lineages
 Molecular analyses have helped clarify
evolutionary relationships among
fungal groups, although areas of
uncertainty remain

Chytrids
 Chytrids (phylum Chytridiomycota) are
found in freshwater and terrestrial habitats
 They can be decomposers, parasites, or
mutualists
 Molecular evidence supports the
hypothesis that chytrids diverged early in
fungal evolution
 Chytrids are unique among fungi in having flagellated spores, called zoospores
 Until recently, systematists thought that fungi lost flagella only once in their
evolutionary history
 Molecular data indicate that some “chytrids” are actually more closely related to
another fungal group, the zygomycetes; chytrids are a paraphyletic group
Zygomycetes
 The zygomycetes (phylum
Zygomycota) exhibit great diversity
of life histories
 They include fast-growing molds,
parasites, and commensal symbionts
 The zygomycetes are named for their
sexually produced zygosporangia
 Zygosporangia, which are resistant to
freezing and drying, can survive
unfavorable conditions
 The life cycle of black bread mold
(Rhizopus stolonifer) is fairly typical of
the phylum
 Some zygomycetes, such as
Pilobolus, can actually “aim” their sporangia toward conditions associated with
good food sources

Glomeromycetes
 The glomeromycetes (phylum Glomeromycota) were once considered
zygomycetes
 They are now classified in a separate clade
 Glomeromycetes form arbuscular mycorrhizae

Ascomycetes
 Ascomycetes (phylum Ascomycota) live in marine, freshwater, and terrestrial
habitats
 The phylum is defined by production of sexual spores in saclike asci, usually
contained in fruiting bodies called ascocarps
 Ascomycetes are commonly called sac fungi
 Ascomycetes vary in size and
complexity from unicellular yeasts
to elaborate cup fungi and morels
 Ascomycetes include plant
pathogens, decomposers, and
symbionts
 Ascomycetes reproduce
asexually by enormous numbers of
asexual spores called conidia
 Conidia are not formed inside
sporangia; they are produced
asexually at the tips of specialized
hyphae called conidiophores
  Neurospora is a model organism with a well-studied genome

Basidiomycetes
 Basidiomycetes (phylum
Basidiomycota) include mushrooms,
puffballs, and shelf fungi, mutualists,
and plant parasites
 The phylum is defined by a
clublike structure called a basidium, a
transient diploid stage in the life cycle
 The basidiomycetes are also
called club fungi
 The life cycle of a basidiomycete
usually includes a long-lived dikaryotic
mycelium
 In response to environmental
stimuli, the mycelium reproduces
sexually by producing elaborate
fruiting bodies called basidiospores

Fungi as Mutualists
 Fungi form mutualistic relationships with plants, algae, cyanobacteria, and
animals
 All of these relationship have profound ecological effects

Fungus-Plant Mutualisms
 Mycorrhizae are enormously important in natural ecosystems and agriculture
 Plants harbor harmless symbiotic endophytes that live inside leaves or other plant
parts
 Endophytes make toxins that deter herbivores and defend against pathogens

Fungus-Animal Symbioses
 Some fungi share their digestive services with animals
 These fungi help break down plant material in the guts of cows and other grazing
mammals
 Many species of ants and termites use the digestive power of fungi by raising them
in “farms”
Lichens
 A lichen is a symbiotic association
between a photosynthetic
microorganism and a fungus in
which millions of photosynthetic
cells are held in a mass of fungal
hyphae
 The fungal component of a lichen
is most often an ascomycete
 Algae or cyanobacteria occupy
an inner layer below the lichen
surface

 The algae provide carbon

compounds, cyanobacteria provide
organic nitrogen, and fungi provide
the environment for growth
 The fungi of lichens can
reproduce sexually and asexually
 Asexual reproduction is by
fragmentation or the formation of
soredia, small clusters of hyphae with
embedded algae
 Lichens are important pioneers on new rock and soil surfaces
 Lichens are sensitive to pollution, and their death can be a warning that air quality
is deteriorating
FUNGAL DISEASES IN HUMAN

Mycosis; Any fungal disease. Tend to be chronic because fungi grow slowly.

Mycoses are classified into the following categories:

I. Systemic mycoses: Fungal infections deep within the body. Can affect a
number of tissues and organs.
Usually caused by fungi that live in the soil are inhaled. Not contagious.
Examples:
Histoplasmosis (Histoplasma capsulatum): Initial infection in lungs. Later
spreads through blood to most organs.
Coccidiomycosis (Coccidoides immites): Resembles tuberculosis.

II. Opportunistic mycoses: Caused by organisms that are generally harmless

unless individual has weakened defences:
- AIDS, cancer, transplant, and diabetic patients
- Individuals treated with broad spectrum antibiotics
- Very old or very young individuals (newborns).
 Examples:
 Aspergillosis: Inhalation of Aspergillus spores.
 Yeast Infections or Candidiasis: Caused mainly by Candida
albicans. Part of normal mouth, esophagus, and vaginal flora.

III. Subcutaneous mycoses: Fungal infections beneath the skin.

 Caused by saprophytic fungi that live in soil or on vegetation.
 Infection occurs by implantation of spores or mycelial fragments into a skin wound.
 Can spread to lymph vessels.

IV. Superficial mycoses: Infections of hair shafts and superficial epidermal cells.
Prevalent in tropical climates.

ECONOMIC IMPORTANCE OF FUNGI

 25-50% of harvested fruits and vegetables are damaged by fungi.
 Fungal infections of plants are commonly called rots, rusts, blights, wilts, and smuts.
 Beneficial fungi:
o Candida oleophila: Prevents fungal growth on harvested fruits.
o Saccharomyces cerevisiae: Used to make bread and wine.
o Genetically engineered yeast strains are used to make proteins (Hepatitis
B vaccine).
o Taxomyces: Produces anticancer drug taxol.

Algae and Protozoa—Structure and Classification

ALGAE
- Diverse group of aquatic organisms that have the ability to conduct
photosynthesis
- Chlorophyll A in chloroplasts
- Range of aquatic habitats, both freshwater and saltwater
- Reproduce Asexually, Some can reproduce Sexually

STRUCTURE
- Occurs in a variety of forms and sizes
- Single and Microscopic (Unicellular) and Macroscopic (Multicellular)
- Algal Body= Thallus: Lack true roots, stems and leaves, and a vascular system
- Vegetative Structures of multicellular algae:
o THALLUS—body. Lacks conductive tissue
o HOLDFASTS—anchor alga to rock
 o STIPES—hollow, stem-like structures. Does not support weight
o BLADES—leaf-like structures
o PNEUMATOCYST—floating, gas-filled bladder
RANGE IF THALLUS STRUCTURE IN ALGAE
1. UNICELLULAR
a. Non-motile—a single non motile cell carrying out all essential functions
of life. Flagella are absent. (ex. Chlorella)
b. Motile—a single cell with flagella for locomotion (ex. Chlamydomonas)
2. MULTICELLULAR
Colony is formed by aggregation of individual cells
a. Non-motile colony—individual cell in the colony lacks flagella (ex.
Pediastrum)
b. Motile Colony—individual cells possess flagella (ex. Volvox)
c. Amorphous Colony—numerous non-motile cells are embedded in a
common mucilaginous matrix (ex. Pediastrum)
d. Dendroid Forms—the thallus appears as tree-like under microscope (ex.
Dinobryon)
e. Filamentous—cells arranged one upon the other in a definite sequence
forming filament. Filament may be branched or unbranched. (ex.
Spirogyra,Cladophora)
f. Heterotrichous Form–Presence of more than one type of filament (ex.
Draparnaldiopsis)
g. Siphonous Form – Elongated thallus with septation. Multinucleate (ex.
Vaucheria)
h. Parenchymatous Forms – cell division and associated septation lead to
the formation of a parenchymatous body (ex. Chara)
CLASSIFICATION
Fritsch’s Classification of Algae
- ‘The Structure and Reproduction of the Algae’—book proposed a system of
classification of algae. His classification of algae is mainly based upon characters
of pigments, flagella and reserve food material.
*MYXOPHYCEAE (Blue-green Algae)—now classified as CYANOBACTERIA (Domain
Bacteria)

REPRODUCTION
- Algae are capable of reproducing through asexual or vegetative methods and
via sexual reproduction
- Asexual Reproduction involves the production of a motile spore
- Vegetative methods include a simple cell division (Mitosis) to produce identical
offspring and the fragmentation of a colony
- Sexual Reproduction involves the union of Gametes (produced individually in
each parent through meiosis)
IMPORTANCE
- Probably the most important contribution of algae to our environment is the
generation of oxygen through photosynthesis
- Algae are indispensable because they produce about half the oxygen in earth’s
atmosphere
- Green Algae, Diatoms and Cyanobacteria are just some of the microalgal
species that are considered good candidates for the production of biofuel
- Algae help to keep atmospheric carbon dioxide levels stable by storing the gas
in organic materials that include oil deposits and inorganic carbonate rocks
- A few species are considered pathogenic/toxigenic
ALGAL BLOOM
- Algae, in the form of algal blooms, get a bad reputation for creating toxic
conditions in oceans and lakes
- Algal blooms refers to the uncontrolled growth of certain microalgae, which in
turn leads to the production of toxins, disruption of the natural aquatic
ecosystems
- DOMOIC ACID INTOXICATION—diatoms that can cause neurological disease
due to presence of domoic acid in mussels
ALGAES
1. Brown Algae
- Dark brown pigment and chlorophyll A and C
- Cellulose walls
- Non-motile, multicellular
- Produce Algin
- Food storage as mannitol
2. Red Algae
- Red pigment and chlorophyll A and D
- Cellulose walls
- Non-motile, multicellular
- Produce Agar
- Food storage as starch
3. Green Algae
- Cellulose walls
- Chlorophyll A and B
- Flagellated or filamentous
- Unicellular or multicellular
- Food storage as Starch
4. Diatoms
- Light brown pigment and chlorophyll A and C
- Walls of pectin and silicon oxide (glass)
- Box and lid structure
- Unicellular
- Food storage as Oil
5. Dinoflagellates
- Cellulose walls of interlocked plates
 - Unicellular, flagellated
- Food storage as starch

PROTOZA
Common Features:
- All unicellular
- All chemoheterotrophs
- Reproduce sexually or asexually
- Most are aerobic
- Require high moisture
- Have specialized structures to take-in food
- Usually covered by a pellicle (no wall)
- Digestion occurs in vacuoles
- Excretion occurs through anal pore
- TROPHOZOITE: vegetative stage which feeds upon bacteria and
particulate nutrients
- CYST: some protozoa produce a protective capsule under adverse
conditions (toxins, scarce water, food, or oxygen)
LIFE CYCLE
- Switch between two forms:
1.) TROPHOZOITE
 Vegetative state, feeding and growing
2.) CYST
 Survival state
 Form cyst when bad or need to move from one host to next
(cyst survive stomach acid)
 Cyst convert back to trophozoite in favorable conditions
(free-living ones) or intestine (parasitic ones)
ARCHAEZOA
- Lack mitochondria
- Spindle shaped
- Flagella on front end
- Common symbionts in animal GI tract
- Ex. Giardia lamblia, Trichomonas vaginalis
APICOMPLEXA
- Non-motile in mature form
- Complex organelles at apex house enzymes
- Obligate intracellular parasites
- Usually transmitted by insects
- Usually complex life cycle with different stages in different hosts
- Ex. Plasmodium
AMOEBAZOA
- Move via pseudopods
- Engulf foods
- Ex. Entamoeba
CILIOPHORA
- Move via Cilia
- Ex. Paramecium
EUGLENOZOA
- Move via flagella (zooflagellates)
- No sexual reproduction
- Divided into two groups
1.) Euglenoids
 Have pellicle
 Had flagella and eye spot
 Has chlorophyll A
 Photoautotroph or chemoheterotroph depending on light
2.) Hemoflagellates
 Transmitted by biting insects
 Live in host blood
 Long slender cells with undulating membrane and flagellum

SLIME MOLDS

SLIME MOLDS—Fungus-like Eukaryotes

1. Have both fungal and amoeba-like qualities
2. Hunters of bacteria and fungi
3. Will produce spores in unfavorable conditions (survival, not reproduction)

LIFE CYCLE
1. Life Cycle of Cellular Slime Molds
- AMOEBA STAGE—germinate from a spore
- SLUG STAGE—many amoebas aggregate and sheath forms
- FRUITING BODY—releases spores which germinate into amoebas
2. Plasmodial (Acellular) Slime Molds
- Mass of protoplasm with many nuclei (plasmodium)
- Capable of sexual reproduction
TWO PHYLA
1. CELLULAR SLIME MOLDS
- In favorable conditions exist as unicellular ‘amoeba’
- In unfavorable conditions:
a. Many cells congregate and fuse
b. Form multicellular ‘mushroom’ to generate spores
c. Return to favorable: spores germinate into unicellular amoeba

2. PLASMODIAL SLIME MOLDS

- Favorable conditions: exist as plasmodium
a. Multi-nucleate mass of protoplasm
b. Moves as giant ‘amoeba’
- Unfavorable conditions: mold-like
a. Spreads out forming ‘mycelium’
b. Produces clumps of spores on aerial hyphae
c. When conditions are favorable, spores germinate and undergo
rapid cell division to form new plasmodium

MEDICALLY IMPORTANT PROTOZOA

1. AMOEBOFLAGELLATES (Phylum Sarcomastigophora)
- Move using pseudopods (false feet) or flagella.

A. Amoebas (Subphylum Sarcodina)

- Move by extending blunt, lobelike projections (pseudopods).
- Amoebas engulf food with pseudopods and phagocytize it.
- Several species cause amoebic dysenteries of varying degrees of
severity
o Entamoeba hystolytica: Feeds on red blood cells. Produces
dysentery and extraintestinal cysts.
o Dientamoeba fragilis: Found in 4% of humans. Usually
commensal. Can cause chronic, mild diarrhea.
- Other diseases include:
o Meningoencephalitis: Caused by Naegleria fowleri. Penetrate
nasal mucosa of swimmers in warm waters. Mortality rate almost
100%.
o Keratitis: Caused by Acanthamoeba. Can cause blindness.
Associated with use of contact lenses.

B. Flagellates (Subphylum Mastigophora)

- Move by one or more whiplike flagella. Some parasitic flagellates have
up to eight flagella.
- Most are spindle-shaped with flagella projecting from anterior end.
 - Outer membrane is a tough pellicle. Food is ingested through an oral
groove or cytosotome.
- Important pathogens:
o Trichomonas vaginalis: Causes genital and urinary infections. Has
undulating membrane. Lacks a cyst stage. Transmitted sexually
or by fomites.
o Giardia lamblia: Causes a persistent intestinal infection
(giardiasis) with diarrhea, nausea, flatulence, and cramps. In U.S.
most common cause of waterborne diarrhea. About 7% of U.S.
population are healthy carriers.
o Trypanosoma brucei gambiense: Hemoflagellate (blood
parasite). Causes African sleeping sickness.
o Trypanosoma cruzi: Hemoflagellate that causes Chaga’s
disease, a cardiovascular disease common in Texas and Latin
America.

2. APICOMPLEXANS (Phylum Apicomplexa)

- Not motile in their mature form.
- Obligate intracellular parasites.
- Have specialized organelles at tip (apex) of cells that penetrate host
tissues.
- Complex life cycles. May have more than one host.
Definitive host: Harbors sexually reproducing form.
Intermediate host: In which asexual reproduction occurs.
- Important pathogens:
o Plasmodium vivax and falciparum: Cause malaria in humans
(intermediate host).
Initially treated with quinine, drug resistance is a major problem today.
Major cause of worldwide mortality. Kills 3 million people/year and infect
500 million.
Transmitted by Anopheles mosquito (definitive host)
DDT was used extensively in 1960s in an attempt to eradicate the mosquito
vector.
Successful vaccine not available yet.

Life Cycle of Plasmodium spp. The Infectious Agent of Malaria

 o Toxoplasma gondii: Causes toxoplasmosis in humans. Causes blindness and
lymphatic infections in adults. Dangerous to pregnant women, causes
severe neurological defects in unborn children. Cats are part of life cycle,
oocysts excreted in feces. Contact with infected feces or meat are means
of transmission.
o Cryptosporidium: Causes respiratory and gallbladder infections in
immunosuppressed individuals. Found in intestines of mammals and water.
Major cause of death in AIDS patients.
o Cyclospora cayetensis: New parasite (1996) caused diarrhea associated
with raspberries.

3. CILIATES (Phylum Ciliophora)

- Move and obtain food using cilia.
- Only known human pathogen is Balantidium coli, which causes a severe
intestinal infection in pigs and humans.

4. MICROSPORANS (Phylum Mycrospora)

- Obligate intracellular parasites, lack mitochondria and microtubules.
- Discovered in 1984 to cause chronic diarrhea and conjunctivitis, mainly
in AIDS patients.
 HELMINTHS (WORMS)
Characteristics
- Eukaryotic, multicellular animals that usually have digestive, circulatory,
nervous, excretory, and reproductive systems.
- Worms with bilateral symmetry, head and tail, and tissue differentiation
(endoderm, mesoderm, and ectoderm).
- Parasitic helminths spend most or all of their lives in host and usually have
the following specializations:
o May lack a digestive system. Absorb nutrients from host’s food,
body fluids, or tissues.
o Have a reduced nervous system.
o Means of locomotion is reduced or absent.
o Complex reproductive system. Individuals produce many eggs
that can infect another host.
Two main groups (phyla)
- Platyhelminthes (Flatworms)
- Nematoda (Roundworms)

Life Cycle
- Extremely complex
- Intermediate hosts harbor larval (developmental) stage.
- Definitive host harbors adult stage.
- Sexual reproduction strategies:
o Dioecious: Male and female reproductive organs are found in
separate individuals.
o Monoecious (Hermaphroditic): One animal has both male and
female sex organs. Most hermaphrodites copulate with other
animals, a few copulate with themselves.

I. PLATYHELMINTHS (Flatworms)
- Flattened from front to back.
- Include:

1. Trematodes or Flukes
- Leaf shaped bodies
- Ventral and oral suckers for attachment and sucking fluids from host.
- Some can absorb nutrients through their cuticle.
- Named for host tissues in which adult lives.

o Blood Fluke (Schistosoma spp.): Cause schistosomiasis which

affects over 400,000 immigrants in U.S. and 200 million people
worldwide.
 Cause damage to blood vessels, liver, and many other organs. Live in
waters contaminated with feces, burrow through skin of human and
enter the circulatory system, particularly abdominal and pelvic veins.

Free-Living Flatworm Planaria (Left)

Life Cycle of Blood Fluke (Schistosoma)
o Asian Liver Fluke (Clonorchis
sinensis): Infests gallbladder, bile ducts,
pancreatic ducts, causes biliary
cirrhosis, and jaundice. Cannot be
transmitted in U.S. because
intermediate hosts are not available.
o Lung Fluke (Paragonimus
westermani): Lives in bronchioles of
humans and other animals. 12 mm
long. Infection from eating
undercooked crayfish.
2. Cestodes or Tapeworms
- Long flat bodies
- Intestinal parasites
- Lack a digestive system, absorb food through cuticle.
Body Organization:
- Head or scolex has suckers for attachment.
- Body is made up of segments called proglottids.
o Each proglottid has both male and female reproductive organs.
o Proglottids farthest from head are mature and contain many
fertilized eggs.

Cestode (Tapeworm) Body Structure: Scolex and

Proglottids
- Parasitic human tapeworms:
o Beef Tapeworm (Taenia saginata): Human is
definitive host. Can reach up to 6 meters in length,
scolex is 2 mm long with hundreds of proglottids.
Infection occurs by ingestion of contaminated,
undercooked beef (“measly beef”).
o Pork Tapeworm (Taenia solium): Human is
definitive host. Infection can occur from eating
infected undercooked pork (rare in the U.S.) or from
human to human contact.
o Echinococcus granulosus: Dogs and coyotes
are definitive hosts. Humans may become infected
by contact with dog feces or saliva.
II. NEMATODES (Roundworms)
- Cylindrical body tapered at each end.
- Have a complex digestive system: mouth, intestine, and anus.
- Body is covered by tough cuticle that resists drying and crusing.
- Most species are dioecious: separate males and females.
o Males are smaller than females and have one or two spicules on
posterior end.
- Over 90,000 known species. Most are free-living. Only about 50 are
human parasites.
- Life cycle of parasitic nematodes is simpler than that of flatworms.
- Infections can be caused by eggs or larvae.

Comparison of Body Organization of

Flatworms, Roundworms, and
Earthworms
- Infectious eggs
o Pinworm (Enterobius vermicularis):
Spends entire life in human host. Adults
live in large intestine. Female lays eggs
in perianal region which causes itching.
Up to 90% of children are infected
through contaminated clothes or
bedding. Infection usually disappears
after a few years.

o Ascaris (Ascaris lumbricoides): Large nematode, up to 30 cm.

Dioecious with sexual dimorphism. Live is small intestines of
humans, horses, and pigs. Eggs can survive in soil for long time.
- Infectious larvae
o Adult Hookworm (Necator americanus): Live in small intestine of
humans, eggs are excreted in feces. Enter host by penetrating
skin. Enters bloodstream, travels to lungs, swallowed in sputum.
Avoided by wearing shoes.
o Trichinosis (Trichinella spiralis): Reproduce sexually in small
intestine of humans. Obtained from eating undercooked pork.
Larvae enter blood vessels and form cysts throughout body.
o Anisakines (Wriggly worms): Infected fish and squid.
 VIRUSES
Overview: A Borrowed Life
 Viruses called bacteriophages can infect and set in motion a genetic takeover of
bacteria, such as Escherichia coli
 Viruses lead “a kind of borrowed life” between life-forms and chemicals
 The origins of molecular biology lie in early studies of viruses that infect bacteria

Concept: A virus consists of a nucleic

acid surrounded by a protein coat
 Viruses were detected indirectly
long before they were actually seen

The Discovery of Viruses: Scientific

Inquiry
 Tobacco mosaic disease stunts
growth of tobacco plants and gives
their leaves a mosaic coloration
 In the late 1800s, researchers
hypothesized that a particle smaller
than bacteria caused the disease
 In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious
particle, now known as tobacco mosaic virus (TMV)

Structure of Viruses
 Viruses are not cells
 Viruses are very small infectious particles
consisting of nucleic acid enclosed in a
protein coat and, in some cases, a
membranous envelope

Viral Genomes
 Viral genomes may consist of either
o Double- or single-stranded DNA,
or
o Double- or single-stranded RNA
 Depending on its type of nucleic acid, a
virus is called a DNA virus or an RNA virus

Capsids and Envelopes

 A capsid is the protein shell that encloses
the viral genome
  Capsids are built from protein subunits called capsomeres
 A capsid can have various structures

 Some viruses have membranous

envelopes that help them infect hosts
 These viral envelopes surround
the capsids of influenza viruses and
many other viruses found in animals
 Viral envelopes, which are
derived from the host cell’s membrane,
contain a combination of viral and host
cell molecules
 Bacteriophages, also called
phages, are viruses that infect bacteria
 They have the most complex
capsids found among viruses
 Phages have an elongated capsid head that encloses their DNA
 A protein tail piece attaches the phage to the host and injects the phage DNA
inside

Concept: Virus reproduce only in host cells

 Viruses are obligate intracellular parasites, which means they can reproduce only
within a host cell
 Each virus has a host range, a limited number of host cells that it can infect

General Features of Viral Reproductive Cycles

 Once a viral genome has entered a cell, the cell begins to manufacture viral
proteins
 The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and
other molecules
 Viral nucleic acid molecules and capsomeres spontaneously self-assemble into
new viruses

Reproductive Cycles of Phages

 Phages are the best understood of
all viruses
 Phages have two reproductive
mechanisms: the lytic cycle and the
lysogenic cycle

The Lytic Cycle

 The lytic cycle is a phage
reproductive cycle that culminates
in the death of the host cell
  The lytic cycle produces new phages and digests the host’s cell wall, releasing the
progeny viruses
 A phage that reproduces only by the lytic cycle is called a virulent phage
 Bacteria have defences against phages, including restriction enzymes that
recognize and cut up certain phage DNA

The Lysogenic Cycle

 The lysogenic cycle replicates
the phage genome without
destroying the host
 The viral DNA molecule is
incorporated into the host
cell’s chromosome
 This integrated viral DNA is
known as a prophage
 Every time the host divides, it
copies the phage DNA and
passes the copies to daughter
cells
 An environmental signal can
trigger the virus genome to exit the bacterial chromosome and switch to the lytic
mode
 Phages that use both the lytic and lysogenic cycles are called temperate phages

Reproductive Cycles of Animal Viruses

 There are two key variables used to classify viruses that infect animals:
o DNA or RNA?
o Single-stranded or double-stranded?
Viral Envelopes
 Many viruses that infect animals have
a membranous envelope
 Viral glycoproteins on the envelope
bind to specific receptor molecules on
the surface of a host cell
 Some viral envelopes are formed from
the host cell’s plasma membrane as
the viral capsids exit
 Other viral membranes form from the
host’s nuclear envelope and are then
replaced by an envelope made from
Golgi apparatus membrane

RNA as Viral Genetic Material

 The broadest variety of RNA genomes
is found in viruses that infect animals
 Retroviruses use reverse transcriptase
to copy their RNA genome into DNA
 HIV (human immunodeficiency virus)
is the retrovirus that causes AIDS (acquired immunodeficiency syndrome)
  The viral DNA that is integrated into the host genome is called a provirus
 Unlike a prophage, a provirus remains a permanent resident of the host cell
 The host’s RNA polymerase transcribes the proviral DNA into RNA molecules
 The RNA molecules function both as mRNA for synthesis of viral proteins and as
genomes for new virus particles released from the cell

Evolution of Viruses
 Viruses do not fit our definition of living organisms
 Since viruses can reproduce only within cells, they probably evolved as bits of
cellular nucleic acid
 Candidates for the source of viral genomes are plasmids, circular DNA in bacteria
and yeasts, and transposons, small mobile DNA segments
 Plasmids, transposons, and viruses are all mobile genetic elements
 Mimivirus, a double-stranded DNA virus, is the largest virus yet discovered
 There is controversy about whether this virus evolved before or after cells

Concept: Viruses, viroids, and prions are formidable pathogens in animals and plants
 Diseases caused by viral infections affect humans, agricultural crops, and livestock
worldwide
 Smaller, less complex entities called viroids and prions also cause disease in plants
and animals, respectively

Viral Diseases in Animals

 Viruses may damage or kill cells by causing the release of hydrolytic enzymes from
lysosomes
 Some viruses cause infected cells to produce toxins that lead to disease symptoms
  Others have envelope proteins that are toxic
 Vaccines are harmless derivatives of pathogenic microbes that stimulate the
immune system to mount defences against the actual pathogen
 Vaccines can prevent certain viral illnesses
 Viral infections cannot be treated by antibiotics
 Antiviral drugs can help to treat, though not cure, viral infections

Emerging Viruses
 Emerging viruses are those that
appear suddenly or suddenly come
to the attention of scientists
 Severe acute respiratory syndrome
(SARS) recently appeared in China
 Outbreaks of “new” viral diseases in
humans are usually caused by
existing viruses that expand their host
territory
 Flu epidemics are caused by new
strains of influenza virus to which
people have little immunity
 Viral diseases in a small isolated
population can emerge and
become global
 New viral diseases can emerge
when viruses spread from animals to
humans
 Viral strains that jump species can
exchange genetic information with
other viruses to which humans have
no immunity
 These strains can cause pandemics,
global epidemics
 The “avian flu” is a virus that recently appeared in humans and originated in wild
birds.

Viral Diseases in Plants

 More than 2,000 types of viral diseases of plants are known and cause spots on
leaves and fruits, stunted growth, and damaged flowers or roots
  Most plant viruses have an RNA
genome
 Plant viruses spread disease in two
major modes:
o Horizontal transmission, entering
through damaged cell walls
o Vertical transmission, inheriting the
virus from a parent
Viroids and Prions: The Simplest
Infectious Agents
 Viroids are circular RNA molecules
that infect plants and disrupt their
growth
 Prionds are slow-acting, virtually indestructible infectious proteins that cause brain
diseases in mammals
 Prions propagate by converting normal proteins into the prion version
 Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans are
all caused by prions