CELL STRUCTURE

AND TAXONOMY
RAFAEL JHON ALCONABA.,RMT
 Introduction
❖ In biology,
❖ CELL - defined as the fundamental unit of any living
organism
❖ ROBERT HOOKE (1665)
❖ English physicist, published a book
entitled Micrographia (containing
descriptions of objects he had
observed under compound light
microscope
❖ First person to use the term cells
 Introduction
❖ In biology,
❖ CELL - defined as the fundamental unit of any living
organism
❖ RUDOLF VIRCHOW (1858)
❖ German pathologist, proposed the
theory of biogenesis
❖ THEORY OF BIOGENESIS - life can
arise only from preexisting life,
therefore cells can arise only from
preexisting life
 Introduction
❖ PROKARYOTIC CELL VS EUKARYOTIC CELL
❖ Prokaryotic cell (Prokaryotes)- less complex cells
which include Bacteria and Archae
❖ Eukaryotic cell (Eukaryotes)- more complex,
containing a true nucleus and many membrane
-bound organelles. Include algae, protozoa, fungi,
plants, animal, and humans
VIRUS
EUKARYOTIC CELL
STRUCTURE
EUKARYOTIC CELL STRUCTURE
EUKARYOTES
❖ eu = true
❖ karyo = nut or nucleus
❖ have true nucleus, the DNA is
enclosed by a nuclear
membrane
EUKARYOTIC CELL STRUCTURE
❖ CELL MEMBRANE
❖ AKA plasma, cytoplasmic, or
cellular membrane
❖ Like a “skin” around the cell
❖ Regulates passage of
nutrients, waste products,
and secretions into and out
of the cell
❖ Selectively permeable - only
certain substances can leave
and enter the cell
EUKARYOTIC CELL STRUCTURE
❖ NUCLEUS
❖ pl. nuclei
❖ Controls function of the
entire cell
❖ “Command center” of the
cell
❖ Three components:
nucleoplasm, chromosomes,
and nuclear membrane
EUKARYOTIC CELL STRUCTURE
❖ CYTOPLASM
❖ semifluid, gelatinous,
nutrient matrix
❖ Within the cytoplasm, are
found insoluble granules,
and organelles including
endoplasmic reticulum,
Golgi complex,
mitochondria, centrioles, etc
EUKARYOTIC CELL STRUCTURE
❖ ENDOPLASMIC RETICULUM
❖ Highly convoluted system of
membranes, interconnected and
arranged to form a transport
network of tubules and flattened
sacs
❖ Observed using transmission
electron microscope
❖ Rough ER - ribosomes are
attached
❖ Smooth ER - no ribosomes
attached;
EUKARYOTIC CELL STRUCTURE
❖ RIBSOMES
❖ for protein synthesis
EUKARYOTIC CELL STRUCTURE
❖ GOLGI COMPLEX
❖ Stack of flattened,
membranous sacs completes
the transformation of newly
synthesized proteins into
mature functional ones
❖ Sometimes referred to as
“packaging plants”
EUKARYOTIC CELL STRUCTURE
❖ LYSOSOMES AND
PEROXISOMES
❖ Contain lysozyme and
digestive enzymes that break
down foreign material into
the cell by phagocytosis
EUKARYOTIC CELL STRUCTURE
❖ MITOCHONDRIA
❖ “Power plants”,
“Powerhouse” or “energy
factory” of the cell
❖ Where most ATP molecules
are formed
EUKARYOTIC CELL STRUCTURE
❖ PLASTIDS
❖ Membrane-bound structures containing various synthetic
pigments (site of photosynthesis)
❖ Energy producing organelle in plants

❖ CELL WALL
❖ External structures that provide rigidity and shape, and protection
❖ Present in plants, algae, fungi, and most bacteria
❖ Absent in animals, protozoa, and Mycoplasma species
PROKARYOTIC CELL
STRUCTURE
Prokaryotic cell structure

PROKARYOTES
❖ Structurally simple
compared with eukaryotic
cells
❖ Reproduction is by binary
fission - simple division of
one cell into two cells , after
DNA replication
Prokaryotic cell structure
• Cytoplasmic structures:
Bacteria do not contain a membrane bound nucleus

Genome consists of a single circular chromosome

Bacterial ribosomes (consists of RNA and protein) are

found free in the cytoplasm and attached to the
cytoplasmic membrane.

Prokaryotic cell structure

• Cell envelope structures:

Plasma membrane (Cell membrane) - phospholipid bilayer

with embedded proteins that envelop the cytoplasm.

Prokaryotic plasma membrane is made of phospholipid and

proteins but does not contain sterols (except for mycoplasma)

Plasma membrane acts as an osmotic barrier and the

location of electron transport chain

Prokaryotic cell structure

• Cell envelope structures:

Cell wall - rigid structure that maintains the shape of the cell and
prevents bursting of the cell due to high osmotic pressure inside.

Two (2) major types of cell wall

1. Gram positive cell wall

2. Gram negative cell wall

*** Mycobacteria have a modified gram positive cell wall called acid fast
cell wall

***Mycoplasma have no cell wall

Prokaryotic cell structure
• Cell envelope structures:

Cell wall

Gram positive cell wall

Composed of very thick protective peptidoglycan (murein) layer as

principal component.

Peptidoglycan layer - composed of glycan chains of N-acetyl-d-

glucosamine (NAG) and N-acetyl-d-muramic acid (NAM)

Other components: teichoic acid and lipoteichoic acid unique to the gram
positive cell wall
Prokaryotic cell structure
• Cell envelope structures:

Cell wall

Gram negative cell wall

Composed of two layers: inner peptidoglycan layer (thinner than Gram +)

and an outer membrane which contains proteins, phospholipids, and
lipopolysaccharides (LPS)

LPS -contains three regions: antigenic O-specific polysaccharide, core

polysaccharide, and inner lipid A (endotoxin)

Periplasmic space - between the outer and inner membrane absent in

Gram positive bacteria
Prokaryotic cell structure
• Cell envelope structures:

Cell wall

Acid Fast cell wall

Mycobacterium and Nocardia have a gram positive cell wall

structure but contain a waxy layer of glycolipids and fatty acids
(mycolic acid) bound to the exterior of the cell wall.
Prokaryotic cell structure
• Cell envelope structures:

Cell wall

Absence of cell wall

Mycoplasma and Ureaplasma lack a cell wall and contain sterols

in their cell membranes
Prokaryotic cell structure
• Surface polymers

Capsule: usually made of polysaccharide polymers


act as virulence factor (evade phagocytosis)

Cell appendages

Flagella: exterior protein filaments, cause bacteria to be
motile

Prokaryotic cell structure

• Surface polymers
Cell appendages

Pili: AKA conjugation pili


nonmotile, long, hollow protein
tubes that connect two bacterial
cells and mediate DNA exchange

Fimbriae: nonflagellar, sticky,

proteinaceous, hairlike appendages
that adhere some bacterial cells to
one another
 BACTERIAL
MORPHOLOGY
CLASSIFICATION/
TAXONOMY
CLASSIFICATION/TAXONOMY
• Taxonomy -Gk. taxes: arrangement; nomos: law

Orderly classification and grouping of organisms into taxa

Based on similarities and differences in genotype and

phenotype

Genotypic: Ex. Sequencing of DNA and RNA; DNA base

composition ratio

Phenotypic: Ex. Colony morphology, bacterial size,

arrangement, staining characteristics, nutritional requirements,
biochemical characteristics, susceptibility or resistance to
antibiotics
Classification

Domain

Kingdom

Division

Class

Order

Family

Genus

Species - the proper word for the name of the species is an epithet
Nomenclature
• Naming of microorganism according to established rules and
guidelines

• Family : “-aceae"

• Genus species

• Genus species

• Streptococcus pneumoniae, Streptococcus pyogenes

• Or abbreviated S. pyogenes

• sp. or spp. when species are not specified

Classification by cellular type
MICROBIAL GROWTH
AND NUTRITION
Microbial growth and nutrition
Three Major nutritional needs for growth:

1. A source of carbon (for making cellular constituents).

2. A source of nitrogen (for making proteins).

3. A source of energy (ATP)

Microbial growth and nutrition
Nutritional Requirements for Growth

Autotrophs (lithotrophs)
Carbon dioxide as the sole source of carbon.

Obtain energy either photosynthetically (phototrophs) or by oxidation of
inorganic compounds (chemolithotrophs).

Heterotrophs
Require more complex substances for growth.

Organic source of carbon, such as glucose

Obtain energy by oxidizing or fermenting organic substances
***all bacteria that inhabit the human body
Types of growth media

Minimal medium - contents are simple; not usually used in diagnostic

microbiology laboratory

Nutrient media - more complex; made up of extracts of meat or soybeans

(nutrient broth, trypticase soy broth)

Enriched media - growth medium that contains added growth factors (e.g.
blood, vitamins, yeast extracts)

Selective media - Media containing additives that inhibit the growth of some
bacteria but allow others to grow(e.g., MacConkey agar [MAC] selective for
gram-negatives while inhibiting gram positives.

Differential media - Ingredients in media that allow visualization of metabolic

differences between groups or species of bacteria. MacConkey agar
distinguishes between lactose fermenters (pink) and nonlactose fermenters
(clear).

Transport medium - when a delay between collection of the specimen and

culturing the specimen is necessary. Stuart broth and Amies and Cary-Blair
transport media.

 Microbial growth and nutrition

Environmental Factors Influencing Growth

1. pH (most pathogenic bacteria =neutral pH)

2. Temperature

Psychrophiles - cold temperatures (optimal growth at 10° to 20° C).

Mesophiles - moderate temperatures (optimal growth at 20° to 40° C).

Thermophiles - high temperatures (optimal growth at 50° to 60° C).

3. Gaseous composition of the atmosphere


Obligate aerobes require oxygen for growth.

Aerotolerant anaerobes (facultative aerobes) can survive in the presence of
oxygen but do not use oxygen in metabolism.

Obligate anaerobes cannot grow in the presence of oxygen.

Facultative anaerobes can grow either with or without oxygen.

Capnophilic organisms grow best when the atmosphere is enriched with extra
carbon dioxide (5% to 10%).

Microaerophilic - requires reduced oxygen to grow.
Microbial growth and nutrition
Bacterial Growth

The time required for one cell to divide into two cells is
called the generation time or doubling time.
Microbial growth and nutrition
Growth curve

lag phase - bacteria are preparing to

divide,

log phase - bacteria numbers

increase logarithmically

stationary phase - nutrients are

becoming limited and the numbers of
bacteria remain constant

death phase - the number of

nonviable bacterial cells exceeds the
number of viable cells

Microbial growth and nutrition

Determination of cell numbers

Direct counting under the microscope: used to estimate

the number of bacteria present in a specimen.

Direct plate count: By growing dilutions of broth cultures

on agar plates, one can determine the number of colony-
forming units per milliliter (CFU/mL).

Density measurement: The density (referred to as

cloudiness or turbidity) of a bacterial broth culture in log
phase can be correlated to CFU/mL of the culture.
BACTERIAL BIOCHEMISTRY
AND METABOLISM
BACTERIAL BIOCHEMISTRY AND METABOLISM
Biochemical Pathways from Glucose to Pyruvic

Glucose - starting carbohydrate for bacterial

fermentations or oxidations

Three major biochemical pathways bacteria use:

(1) Embden- Meyerhof-Parnas (EMP) glycolytic

pathway

(2) Pentose phosphate pathway

(3) Entner-Doudoroff pathway

BACTERIAL BIOCHEMISTRY AND METABOLISM
EMP Glycolytic Pathway

• The major pathway in conversion of glucose to pyruvate

• Generates reducing power in the form of NADH 2

• Generates energy in the form of ATP

• Anaerobic; does not require oxygen

• Used by many bacteria, including all members of

Enterobacteriaceae
BACTERIAL BIOCHEMISTRY AND METABOLISM

EMP Glycolytic Pathway

BACTERIAL BIOCHEMISTRY AND METABOLISM
Pentose Phosphate (Phosphogluconate) Pathway

• Alternative to EMP pathway

• Produces glyceraldehyde-3-phosphate, which can be

converted to pyruvate

• Generates NADPH

• May be used to generate ATP (yield is less than with the EMP
pathway)

• Used by heterolactic fermenting bacteria, such as lactobacilli

which lacks some of the enzymes required in the EMP
pathway

BACTERIAL BIOCHEMISTRY AND METABOLISM

Entner-Doudoroff Pathway

• Converts glucose-6-phosphate (rather than glucose) to

pyruvate

• Generates one NADPH per molecule of glucose but uses

one ATP

• Aerobic process
BACTERIAL BIOCHEMISTRY AND METABOLISM

Anaerobic Utilization of Pyruvic Acid (Fermentation)

Alcoholic fermentation: Major end product is ethanol. Pathway used by

yeasts when they ferment glucose to produce ethanol.

Homolactic fermentation: End product = lactic acid. All members of the

Streptococcus genus and many members of the Lactobacillus genus
ferment pyruvate using this pathway.

Heterolactic fermentation: mixed fermentation pathway, in addition to

lactic acid, the end products include carbon dioxide, alcohols, formic acid,
and acetic acid.

Propionic acid fermentation: Propionic acid is the major end product of

fermentations carried out by Propionibacterium acnes

BACTERIAL BIOCHEMISTRY AND METABOLISM

Anaerobic Utilization of Pyruvic Acid (Fermentation)

Mixed acid fermentation: Escherichia, Salmonella, and Shigella within

the Enterobacteriaceae; end products—lactic, acetic, succinic, and formic
acids. (MR)

Butanediol fermentation: Klebsiella, Enterobacter, and Serratia within the

Enterobacteriaceae; end products are acetoin (acetyl methyl carbinol) and
2,3-butanediol. (VP)

Butyric acid fermentation: Certain obligate anaerobes, including many

Clostridium species, Fusobacterium, and Eubacterium, produce butyric
acid 




BACTERIAL BIOCHEMISTRY AND METABOLISM

Aerobic Utilization of Pyruvic Acid (Oxidation)

Krebs or TCA (tricarboxylic acid) cycle

Pyruvate is oxidized

Electrons donated by pyruvate are passed through an electron

transport chain and used to generate energy in the form of ATP.
This cycle results in the production of acid and the evolution of
carbon dioxide



BACTERIAL BIOCHEMISTRY AND METABOLISM
Carbohydrate Utilization and Lactose Fermentation

Fermentation of sugar

Usually detected by acid production and a concomitant change of

color resulting from a pH indicator present in the culture medium.

***Microorganisms ability to ferment lactose

Lactose fermenters V. Lactose nonfermenters

Lactose - disaccharide; glu+gal linked by galactoside bond

***Two steps involved:

β-galactoside permease

β-galactosidase

BACTERIAL GENETICS
BACTERIAL GENETICS

DNA V. RNA
BACTERIAL GENETICS

Genetic Elements and Alterations

Bacterial genome

Bacterial chromosome

Consists of a single, closed, circular piece of double-stranded

DNA that is supercoiled in order to fit inside the cell.

BACTERIAL GENETICS

Genetic Elements and Alterations

Extrachromosomal elements

Plasmids - extra information on small circular pieces of

extrachromosomal, double-stranded DNA

Genes that code for antibiotic resistance (and sometimes toxins

or other virulence factors) are often located on plasmids.

Located in the cytoplasm of the cell and are self-replicating

May also be passed (nonsexually) from one bacterial species to

another through conjugation.

BACTERIAL GENETICS

Genetic Elements and Alterations

Mobile Genetic Elements

Jumping genes - certain pieces of DNA are mobile and may

jump from one place in the chromosome to another place.

Insertion sequence (IS) element - when an IS element inserts

itself into the middle of a gene, it disrupts and inactivates the
gene. This can result in loss of an observable characteristic.

Transposons - Often carry antibiotic-resistance genes and are

usually located in plasmids.

BACTERIAL GENETICS

Genetic Elements and Alterations

Mutations

Changes that occur in the DNA code and often results in a

change in the coded protein or in the prevention of its synthesis.

It could be:

a change in one nucleotide base (a point mutation) that leads to

a change in a single amino acid within a protein

insertions or deletions in the genome that lead to disruption of

the gene.

MECHANISM OF GENE
TRANSFER
MECHANISM OF GENE TRANSFER

Transformation

Free or “naked” DNA is taken up by

a competent bacterial cell. After
uptake, the DNA may take one of
three courses:

(1) it is integrated into existing

bacterial genetic material,

(2) it is degraded, or

(3) if it is a compatible plasmid, it

may replicate in the cytoplasm.

MECHANISM OF GENE TRANSFER

Transduction

A phage injects DNA into the

bacterial cell.

MECHANISM OF GENE TRANSFER

Conjugation

An F+ cell connects with an F– cell

via sex pili. DNA is then transferred
from one cell to the other.