Microbiology & Parasitology
BERGEY’S MANUAL OF CLASSIFICATION
Cataloging Microorganisms
A. Classification Attempts to Catalog Organisms
Taxonomy
→ the science of classifying and naming
1. Aristotle (4th B.C.)
→ described over 500 species of plants and
animals.
2. Carolus Linnaeus/Carl Von Linne (1758)
→ Binomial Nomenclature
B. Classification Uses Hierarchical System
Linnaeus’s Classification Scheme
C. The Five Kingdom System Recognizes
Prokaryotic and Eukaryotic Difference
1. Robert Whittaker (1920-1980)
→ proposed the Five Kingdom System in
1969
a) Monera (Prokaryotes)
b) Protista
c) Animalia
d) Plantae
e) Fungi
2. Lynn Margulis
→ expanded the Five Kingdom System
3. Ernst H. Haeckel
→ added the third kingdom, Protista in 1866
Linnaeus proposed only two kingdoms.
Whittaker proposed taxonomic approach based on
five kingdoms: Animalia, Plantae, Fungi, Protista,
and Prokaryotae (widely accepted)
Taxonomists compare nucleotide sequences of
rRNA subunits (changes occur rarely).
Proposal of three domains based on three basic
types of cells as determined by ribosomal
nucleotide sequences.
→ Eukarya, Bacteria, and Archaea
→ Cells in the three domains also differ with
respect to many other characteristics.
D. The Three-Domain System Places the Monera
in Separate Linneages
Carl Woese (1928)
→ proposed the Three Domain System in the
1970’s which is based on molecular biology
& biochemistry they used nucleotide
sequence of smaller ribosomal RNA or
rRNA because these are present in all cells
and changes in their sequences is very
rare.
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The Three-Domains are Archaea, Eubacteria → Biochemical Tests
and Eukarya. They differ significantly in the → Serological Tests
following: → Phage Typing
a) base sequence of RNA in their ribosomes → Analysis of Nucleic Acids
b) composition of cell wall
c) types of lipids and their membranes
d) sensitivity to certain antibiotics
E. Bacterial Taxonomy Now Includes Molecular
Criteria
Molecular Taxonomy
→ is based on the universal presence of
ribosomes in all living organisms. In
particular the rRNA-is believe to be the
ultimate “molecular chronometer”.
The most important criterion influencing taxonomy
is similarity in chromosomal DNA
3 Criteria for Genetic Relatedness
1. size of the entire chromosome
2. chemical composition of DNA
3. DNA Homology
F. David Hendricks Bergey
→ he devised the first systems of AN INTRODUCTION TO CELL STRUCTURE
classification for the bacteria in 1923 AND FUNCTION
→ he published the book, Bergey’s Manual of
Determinative Bacteriology or Bergey’s Theodor Schwann (1804 – 1881) and Matthias
Manual of Systematic Bacteriology- Schleiden (1810 – 1882)
Bergey’s Manual. → They both developed the cell theory
Bergey’s Manual which states that all living things are
→ official listing of all recognized bacteria with composed of cells.
nine editions. Characteristics of Life and Their Distribution to
Bergey’s Classification of Prokaryotes Microbes
a) 1974, it separates prokaryotes in 2 Characteristic Prokaryotes Virus
divisions: &
b) Cyanobacteria and Bacteria 1984, it Eukaryotes
separates prokaryotes in 4 divisions on the Growth: increase Occur in all Does not
nature of their cell walls: in size occur
1. Graculicutes – “thin”, Gram2. Reproduction: Occur in all Occurs only
Firmicutes – “strong”, Gram+ increase in inside a host
2. Tenericutes – “soft”, wall-less number cell
3. Mendosicutes – “faulty”, with cell Responsiveness: Occur in all Occurs in
wall but lacks peptidoglycan ability to react to some
Classification of Prokaryotes are based on the environmental viruses in a
following: stimuli reaction to
1. Gram staining host cells
2. Morphology Metabolism: Occur in all Uses host
3. Ability to produce endospore controlled cell’s
4. Mechanism of metabolism chemical metabolism
5. Motility reactions of
6. Reproduction organisms
Taxonomic and identifying Characteristics
→ Physical Characteristics
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Cellular Present in all Lack
Structure: cytoplasmic
membrane membrane
bound structure or cellular
capable of all the structure
above function

1. Prokaryotes (“before nucleus”)

→ Its distinctive structural feature is not
what they have, but what they lack:
a) Lacks internal membrane – bound
structures
b) Simpler than eukaryotes External Structure of Prokaryotic Cells
c) They are also typically smaller – 1. Glycocalyces (glycocalyx)
approximately 1.0 micrometer in → A gelatinous, sticky substance
diameter, as compared to 10 – 100 surrounding outside the cell.
micrometers for eukaryotes e.g., → “sugar cup”, composed of
bacteria and archaea. polysaccharides or polypeptides or
2. Eukaryotes (“true nucleus”) both.
a) Have membrane surrounding their a) Capsule
DNA, forming a nucleus − a glycocalyx which is
b) Have “true nucleus”: with membrane – composed of
bound compartments (organelles) repeating units of
c) Larger and more complex than organic chemicals
prokaryotes e.g., plants, animals, firmly attached to the
protozoa, algae and fungi. cell surface e.g.,
Streptococcus
pneumoniae

b) Slime layer
− A loose, water soluble
glycocalyx; often
viscous (sticky)
providing attachments
to surfaces e.g., oral
bacteria

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Microbiology & Parasitology
2. Flagella → Shorter than flagella, there may be 100
→ Long whip – like structures that extend per cell
beyond the surface of the cell and the → Serves as an important function in
glycocalyx; propels the cell. biofilms – are slimy masses of bacteria
adhering to a substrate.
Fimbriae Flagellum

4. Pilli
→ Are tubules composed of a protein
called pilin.
→ Longer than fimbriae but shorter than
flagella
→ 1 – 10/ cell
→ Used by bacteria to move across a
substrate or towards another bacterium
(attachment pili)
Flagellar Arrangement of Bacteria → Mediates the transfer of DNA from one
cell to the other (conjugation pili)
Fimbriae Conjugation pili

Prokaryotic Cell Walls

→ Provides structure and shape to the cell
and protects it from osmotic forces.
→ Assists some cells in attaching to other
cells or in eluding antimicrobial drugs.
→ Note that animal cells do not have cell
walls.

3. Fimbriae
→ Non – motile extensions
→ Sticky proteinaceous, bristle – like
projections used to adhere to one
another and to substances.

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Microbiology & Parasitology
Bacterial cell walls 2. Gram negative cell walls (pink)
→ Composed of peptidoglycan, a complex → With thin layer of peptidoglycan (1
polysaccharide which is composed of two – 2% of the dry weight of the cell):
regularly alternating sugars called N – outside this layer is a bilayer
acetylglucosamine (NAG) and N – acetyl membrane composed of
muramic acid (NAM) which are structurally phospholipids, channel proteins
similar to glucose. (called porins), and
→ NAG alternates with NAM – these are the lipopolysaccharides (LPS).
“glycan” portions of peptidoglycan. → LPS
→ Chains of NAG and NAM are attached to − A union of lipid and sugar.
other chains by cross – bridges of four The lipid portion of LPS is
amino acids (tetrapeptides) – these cross known as lipid A
bridges are the “peptide” portion of (endotoxin).
peptidoglycan. − Released from dead cells
when the cell walls
disintegrate, and it may
trigger fever, inflammation,
shock, and blood clotting
in humans.

Two Basic Types of Bacterial Cell Walls:

1. Gram positive cell walls (purple)
→ With thick layer of peptidoglycan
(20% of the dry weight of the cell)
and unique polysaccharides called → Periplasmic Space
teichoic acids which are covalently − found between the cell
linked to lipids forming lipoteichoic membrane and outer
acids that anchor the membrane, this contains
peptidoglycan to the cell the peptidoglycan and
membrane. periplasm.
→ e.g., Mycobacterium have cell → Periplasm
walls up to 60% mycolic acid – a − the gel between
waxy lipid (AFB). membrane of gram –
negative cells; contains
water, nutrients and
substances secreted by
the cell (digestive
enzymes, and proteins).

Bacteria without cell walls

→ e.g., Mycoplasma pneumoniae
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Microbiology & Parasitology
Archaeal Cell Walls Transport Processes Across Prokaryotic
→ Contains a variety of specialized Cytoplasmic Membranes
polysaccharides and proteins, but no Description Substances
peptidoglycan (separate group) Transported
→ Gram (+) archaeal walls – like gram (+) Passive Processes
bacteria, they have thick wall and stains Transport require no use
purple. Processes of energy by
→ Gram (-) archaeal walls – have a layer of the cell; the
protein covering the wall, rather than a lipid electrochemical
membrane in gram (-) bacteria, but they gradient
stain pink. provides
Prokaryotic Cytoplasmic Membranes energy.
→ Beneath the glycocalyx and cell wall. Diffusion Molecules Oxygen,
→ Also referred to as cell membrane or move down carbon
plasma membrane. their dioxide, lipid
→ Composed pf lipids and associated electrochemical – soluble
proteins. gradient chemicals.
through the
phospholipid
bilayer of the
membrane.
Facilitated Molecules Glucose,
Diffusion move down fructose,
their urea, some
electrochemical vitamins
gradient
through
→ Bacterial membranes
channels or
− Contain phospholipids: some have carrier proteins.
sterol – like molecules called
Osmosis Water Water
hopanoids.
molecules
→ Archaeal membranes move down
− Composed of lipids that lack their
phosphate groups and have concentration
branched hydrocarbons linked to gradient across
glycerol by either linkage instead of a selectively
ester linkages. permeable
membrane
Active Cells expends
Transport energy in the
Processes form ATP to
move a
substance
against its
electrochemical
gradient. Some
active
processes are
linked to a
passive
process and
use the energy

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Microbiology & Parasitology
of the passive 1. Cytosol
process to → Composed of mostly water, but
carry a also contained dissolved
substance suspended substances, including
across the ions, carbohydrates, lipids, and
membrane. wastes.
Active ATP – Na+, K+, → Also contains the cell’s DNA
Transport dependent Ca2+, H+, Cl- (single, circular chromosome)
carrier proteins which is not surrounded by a
bring membrane in a region called
substances into nucleoid.
cell.
Group The substance Glucose,
Translocation is chemically mannose,
altered during fructose
transport;
found only in
some
prokaryotes

Active Transport Processes Found Only in

Eukaryotes: Endocytosis and Exocytosis
Description Substances
Transported
Endocytosis: Substances Bacteria,
phagocytosis are viruses, aged 2. Inclusions
and surrounded by and dead → Are deposits found within the
pinocytosis pseudopodia cells; liquid cytosol; may include reserve
and brought nutrients in deposits of lipids, starch or
into the cell. extracellular compounds containing nitrogen,
Phagocytosis solutions phosphate and sulfur.
involves solid → Serve as a diagnostic tool for
substances; pathogenic bacteria
pinocytosis − e.g., aquatic cyanobacteria – gas
involves vesicles (store gases in protein
liquids. sacs)
Exocytosis Vesicles Wastes, − magnetobacteria (store
containing secretions magnetites)
substances 3. Non – membranous organelles
are fused with A. Ribosomes
cytoplasmic → Site of protein synthesis;
membrane, prokaryotic cells have
dumping their about 1000 ribosomes
contents to which gives the cytoplasm
the outside a grainy appearance.
→ The approximate size of
Cytoplasm of Prokaryotes ribosomes is express in
→ The general term used to describe the semi Svedbergs (S) which is
– liquid, gelatinous material inside a cell; it’s determined by either their
a semi – transparent fluid, elastic and Sedimentation rate
aqueous it’s composed of the following

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Microbiology & Parasitology
→ Prokaryotic ribosomes are cytosol, thus, the flagella of
70S while eukaryotic eukaryotes are inside the cell, not
ribosomes are 80S extensions outside the cell.
→ All ribosomes are → May be single or multiple and are
composed of two subunits, generally found at the end of the
each of which is composed pole of the cell
of protein and a type of → Functions: undulate rhythmically
RNA called ribosomal rather than rotating; do not move in
RNA (rRNA) runs and tumbles.
→ Many antibiotics act on
prokaryotic 70S ribosomes
B. Cytoskeleton
→ Were long thought to lack
cytoskeletons, but recent
research has revealed that
rod – shaped prokaryotes
have a simple one while
spherical prokaryotes
appear to lack
cytoskeleton.
→ Internal network of fibers
which play a role in forming
a cell’s basic shape.
External Structures of Eukaryotic Cells
1. Glycocalyces
→ Present in animal and protozoan
cells but absent in eukaryotic cells
that have cell walls.
→ Functions: cells to each other;
strengthening the cell surface;
3. Cilia
protection against dehydration;
→ Hair – like structures; shorter and
cell–to–cell recognition and
more numerous than flagella
communication.
→ Composed primarily of tubulin
2. Flagella
microtubules which are arranged
→ Differs structurally from prokaryotic
in “9+2” arrangement of triplets in
cells
their basal bodies.
→ The shaft is made up of tubulin
→ No prokaryotic cells have cilia
arrange in chain to form
→ A single cell may have 100 or
microtubules
even 1000 cilia which beats
→ Has 9 + 2 arrangement
rhythmically
→ The filaments are anchored to the
→ Helps cleanse the human RT from
cell by a basal body, but no hook
dusts and MQS.
connects the two parts as in
Eukaryotic Cell Walls and Cytoplasmic
prokaryotic cells arrangement of
Membranes
microtubules.
1. Cell walls
→ The basal body has triplets of
→ Found in fungi, algae, and plants.
microtubules instead of pairs and
→ In the present of cell walls,
there are no microtubules in the
glycocalyces are absent.
center, so it has a “9 + 0”
→ Takes on one of the functions of
arrangement of microtubules.
the glycocalyx by providing
→ Surrounded by an extension of the
protection from the environment.
cell membrane and are filled with
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Microbiology & Parasitology
→ Also provides shape and support → Made up of tubulin microtubules
against osmotic pressure. (also found in flagella, cilia, and
→ Composed of various centrioles), thinner microfilaments
polysaccharides, but not the composed of actin and
peptidoglycan seen in the walls of intermediate filaments composed
most bacteria of various proteins.
− e.g., plant cells – are 3. Centrioles and Centrosome
composed of cellulose; a → Present in certain kind of
polysaccharide (paper/ eukaryotic cells.
dietary fiber) → Animal and some fungal cells
− fungi – also have walls of contain 2 centrioles which lie at
polysaccharides, including right angles to each other near the
cellulose, chitin and nucleus, in a region of the
glucomannan cytoplasm called centrosome.
− algae – composed of → Plants, algae, fungi, and
variety of polysaccharides prokaryotes lack both centrioles
and other chemicals such and centrosomes.
as cellulose, agar, → Composed of 9 triplets of
carrageenan, silicates, microtubules arrange in a way that
algin, calcium carbonates, resembles the 9+0 arrangement
or a combination. seen at the base of eukaryotic
2. Cell membrane flagella and cilia.
→ All eukaryotes have cell membrane → Play a role in mitosis (nuclear
– plasmalemma (plants, algae). division) cytokinesis (cell division)
→ They contain steroid lipids and in the formation of flagella and
(sterols), such as cholesterol in cilia.
animal cells that help maintain Membranous organelles (are not present in
fluidity. prokaryotic cells)
→ Controls the movement of material 1. Nucleus
into and out of the cell. → Spherical to ovoid; the largest
3. Cytoplasm organelle in the cell; some have
→ More complex than that of either single nucleus while others are
bacteria or archaea. multinucleated while still others
Non – membranous organelles lose their nuclei.
1. Ribosomes → “The control center of the cell”.
→ Free or attached to endoplasmic → Its semi – liquid matrix is called
reticulum nucleoplasm.
→ Larger than prokaryotic ribosomes → Which may have one or more
(80S) instead 70S nucleoli – a specialized region
→ Composed of 60S and 40S where RNA is synthesized.
subunits → Also contains chromatin – a thread
2. Cytoskeleton like mass of DNA associated with
→ Composed of network of fibers and special proteins called histones
tubules which play a role in packaging
→ Acts to anchor organelles, nuclear DNA.
functions in cytoplasmic streaming → Surrounding the nucleus is a
and in movement organelles within double membrane called nuclear
the cytosol, enables contraction of envelope – contains nuclear pores
the cell, moves the cell membrane that function to control the import
during endocytosis and amoeboid and export of substances.
action, and provides the basic
shape of many cells.
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Microbiology & Parasitology
2. Endoplasmic Reticulum
→ Function as a transport system and
is found in 2 forms:
a) Smooth ER
− Plays a role in lipid
synthesis as well
as transport
b) Rough ER
− Studded with
ribosomes:
proteins produced
here are inserted
into the lumen
(central canal) of
rough ER and
transported
throughout the
cell.
3. Golgi Apparatus
→ The shipping department of the
cell; receives, produces and
packages large molecules for
export from the cell.
→ Packages secretions in sacs are
called secretory vesicles, which
then fuse with the cell membrane
before dumping their contents
outside the cell via exocytosis.
4. Lysosomes
→ Found in animal cells, contain
catabolic enzymes that damage
the cell if they’re released from
their packaging into the cytosol.
→ Its enzymes are used during the
self – destruction of old, damaged
and diseased cells and to digest
nutrients that have been
phagocytized.
→ e.g., WBC.
5. Peroxisomes
→ Contain oxidase and catalase that
degrade poisonous metabolic
wastes (such as free radicals and
hydrogen peroxide).
→ Found in all eukaryotic cells but are
especially prominent in the kidney
and liver cells of mammals.
6. Vesicle and Vacuole
→ General terms of sacs; large
vacuoles are found in plants and
alga cells that store starch, lipids,
and other substance in the center
of the cell (central vacuole).
7. Mitochondria
→ Spherical to elongated structures
found in most eukaryotic cell: like
nuclei, they have 2 membranes,
each composed of a phospholipid
layer.
→ The inner membrane’s surface
area is often called the
“powerhouse of the cell” because
their cristae produce most of ATP
in the cell.
→ The interior matrix of the
mitochondrion contains small
“prokaryotic” 70S ribosomes and a
circular molecule of DNA – which
contains genes for some RNA
molecules and for a few
mitochondrial polypeptides that are
manufactured by mitochondria
ribosomes, however, most
mitochondrial proteins are coded
by nuclear DNA and synthesized
by cytoplasmic ribosomes – semi –
autonomous.
8. Chloroplasts
→ Light harvesting structures found in
photosynthetic eukaryotes.
→ Like mitochondria and nucleus,
chloroplast have 2 phospholipid
bilayer membranes and DNA.
→ Can also synthesized a few
polypeptides with their own 70S
ribosomes
→ Photosynthetic prokaryotes lack
chloroplast and instead have
infoldings of their cell membrane
called photosynthetic lamellae.
→ Semi – autonomous
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Microbiology & Parasitology
Non – membranous and Membranous Organelles of Cells

Some Comparative Characteristics of Gram – Positive and Gram – Negative Bacteria

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Microbiology & Parasitology
Principal differences between Prokaryotic and Eukaryotic Cells

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