Analysis of Biological System Part I: Overview

of Microbiology
Chapter 2

Introduction,, Naming, Microbial diversity,

Procaryotes, Eucaryotes, Reproduction
Analysis of Biological System
An understanding of biological system can be simplified by
analyzing the system at several different levels:

 Cell level: microbiology, cell biology;

 Molecular level: biochemistry, molecular biology;

 Population level: microbiology, ecology;

 Production level: bioprocess.

2Chapter 2 Part I
Overview of Microbiology
 Microbiology (in Greek micron = small and
biologia = studying life) is the study of
microorganisms at the cell level.

 Microorganism refers to any organism too small to

be viewed by the unaided eye, as bacteria, fungi
and algae and protozoa.

It is often illustrated using single-celled, or unicellular

organisms
Cell:
 The cell is the basic unit of life.
 Cells are packages of living matter surrounded by
membranes or walls.
 Within the cell are various organelles, an organelle is a
specialized part within a cell that has a specific function,
and it is usually separately enclosed within its own lipid
bilayer, in controlling life processes
for the cell intake of nutrients, production of energy,
discharge of waste materials, and reproduction.
Basics of Microbiology
 Naming cells
 Primary classification of microorganism
- Procaryotes: bacteria;
- Eucaryotes: fungi (yeast and mold)
algae
- Virus

 Microbial cell characteristics under each cell category

- cell structure and reproduction

I
Naming Cells
A dual name (binary nomenclature) in Latin or Latinized is used,
including
genus (plural: genera) & species
A genus: a group of related species. The term comes from the Latin
genus meaning "descent, family, type, gender
A species: includes organisms that are substantially alike.
e.g. Escherichia coli; Bacillus subtilis; Sacchromyces cerevisiae;
Penicillium chrysogenum. (in italic type)
Escherichia is the genus, the first letter is capitalized
coli is the species in lower case.
Abbreviation: E. coli
Various strain and substrains are designated by the addition of
letters and numbers. e.g. E. coli K12.
Microbial diversity
Cell adaptation to the environment
Temperature
 Psychrophiles can grow below 20oC.

e.g. Leifsonia rubra isolated from Antarctica.

 Mesophiles grow between 20-50oC.

important uses in food preparation such as cheese, yoghurt,

beer and wine making, e.g. Saccharomyces cerevisiae.
 Thermophiles can grow at temperature higher than 50oC.

Thermus aquaticus is a species of bacterium that can tolerate high

temperatures. It thrives at 70°C, but can survive at temperatures
50°-80°C .
Regular sterilization at 121oC.
pH:
 Acidophiles are microbes that tends toward acidic
conditions pH < 3
e.g Acidithiobacillus ferrooxidans in acid mine
drainage.
 Alkaliphiles are microbes that thrive in alkaline
environments with a pH of 9.
e.g. Bacillus okhensis living in carbonate soil.

Moisture:
Some cells can grow
- where the water activity is high (e.g. algae)
- on solid surface (mold)
Oxygen:

 Some microorganism requires oxygen for growth called

aerobic.

 Other organism can be inhibited by the presence of oxygen

which is called anaerobic.

 Facultative organisms can switch the metabolic pathway to

allow them to grow under either circumstance.
e.g. Saccharomyces cerevisiae.

Almost all animals, most fungi and several bacteria are

aerobes.
Most anaerobic organism are bacteria.
Nutrient sources:

Microorganism can be classified into two categories on the

basis of their carbon sources.

 Heterotrophs use organic compounds such as

carbohydrates, lipids, and hydrocarbons as a carbon and
energy source.

 Autotrophs use carbon dioxide as a carbon source.

e.g. cyanobacteria
Extremophiles:
Organism from those extreme environments.
 Acidophile: An organism with an optimum pH level at or below
pH 3.

 Alkaliphile: An organism with optimal growth at pH levels of 9

or above.

 Halophile: An organism requiring at least 0.2M of NaCl for

growth.

 Psychrophile: An organism that can thrive at temperatures of 20

°C or lower.
 Thermophile: An organism that can thrive at temperatures
between 60-80 °C.
Shape:
 coccus (cocci, plural (pl)): A cell with a
spherical or elliptical shape.
e.g. Streptococcus is a genus of spherical
bacteria
 bacillus (bacilli, pl): a cylindrical cell
e.g. Bacillus subtilis is a bacterium
that is commonly found in soil.
 spirillum (spirilla, pl): a spiral-shaped
cell.
e.g. Rhodospirillum is a bacterium.
Some cells may change shape in response to
changes in their local environment.
Section Summary
 Organism cells are highly diverse in terms of their
adaptation to the living environment:
Temperature, pH, oxygen, moisture, nutrients

 Shapes (bacteria): Coccus, Bacillus and Spirillum

 Classification of Cellular Organism
(according to cell structure)

Cellular Organism
Have nuclear membrane
not free-living organisms
and membrane –bound organells?
Yes No
Eucaryotes Procaryotes: bacteria Virus

Protists: Fungi, Algae, Eubacteria: Archaebacteria:

protozoa
Gram-positive bacteria Methanogen
Plant Gram-negative bacteria Halogen
Non-gram bacteria: Thermoacidophiles
Animal
Actinomycetes
Cynaobacteria
Eukaryote VS Prokaryote
Procaryote
 Procaryotes have no membrane around the cell genetic
information and no membrane-bound organelles

 Bacteria: e.g. E. Coli, Rhodospirillum sp.

 Size: 0.5-3µm.

 Grow rapidly: e.g. one cell can replicate into over a million
cells in just 12 hours. In contrast, a human cell takes 24 hours
to split.
 Utilize carbon sources: carbohydrates, hydrocarbon, protein
and CO2.
Procaryote Cell Structure
 Nuclear region
There is no membrane around the nuclear region containing
genetic materials such as chromosomes and DNA
(deoxyribonucleic acid).

 Chromosomes:
A chromosome is, a very long, continuous piece of DNA, which
contains many genes, regulatory elements and other
intervening nucleotide sequences.

 The DNA which carries genetic information in biological

cells is normally packaged in the chromosomes.
 Cytoplasm
 In cytoplasm, there are some visible
structures:
- ribosomes: sites of protein synthesis,
10,000 per cell,
10 -20 nm, 63% RNA and 37%
protein.

- storage granules: source of key

metabolites, containing
polysaccharides, lipids and sulfur
granules. Sizes vary between 0.5-1
µm.

- Plasmids: Plasmid is a small DNA

molecule that is physically separate
from, and can replicate independently
of, chromosomal DNA within a cell.
- Usually occur in bacteria. e.g E.coli
Application in Genetic Engineering.
 Cytoplasmic membrane

- The cytoplasm is
surrounded by a
membrane called
cytoplasmic membrane.

- The cytoplasmic
membrane contains 50%
protein, 30% lipids and
20% carbohydrates.
 Cell wall
- Eubacteria cell walls contain
lipids & peptidoglycan which
is a complex polysaccharide
with amino acids and forms a
structure somewhat like chain-
link fence.
- Archaebacteria cell walls do not
have peptidoglycan.

 Outer membrane:
Some bacteria (gram negative
cells) have:
- to retain important cellular
compounds and
- to exclude undesirable
compounds in the
environment.
Gram negative and Gram positive

22Chapter 2 Part I
Gram Negative cell wall
 Capsule:
Extracellular products can adhere to or
become incorporated within the
surface of the cell.
Certain cells have a coating outside the
cell wall called capsule.
It contains polysaccharides or polypeptide
and forms biofilm response to
environmental challenges.

 Flagellum: is for cell motion.

 Pilus (Pili, pl.)

A pilus is a hairlike structure on the surface of a cell.
Pili enable the transfer of plasmids between the bacteria.
An exchanged plasmid can add new functions to a bacterium, e.g., an antibiotic
resistance.
Procaryotes

Procaryotes include

- Eubacteria

- Archaebacteria
Eubacteria
Cell chemistry of eubacteria is similar to eucaryotes.

Classification
Gram stain: Hans Christian Gram in 1884 developed the technique of gram stain
which has been used to classify the eubacteria.
Gram staining procedure: Fixing the cells by heating
Dye with crystal violet – stain purple
Iodine and ethanol are added
a. Gram-negative: The cells are colorless after Gram staining procedure. Gram-
negative organisms will be counterstained with safranin and appear red or pink.
Such cells have outer membrane supported by peptidoglycan e.g. E. coli.
b. Gram-positive: the cells remain purple after gram staining and counterstaining
procedures. Such cells have no outer membrane but with a rigid cell wall
and thick peptidoglycan layer, e.g. B. subtilis.

https://www.youtube.com/watch?v=G85QmwjUhZ4
Other types of eubacteria:

Non gram bacteria: some bacteria are not gram-positive or

negative.
e.g Mycoplasma is non gram bacteria lack of cell wall.
It is an important cause of pneumonia and other respiratory
disorders.

Actinomycetes: bacteria but, morphologically resembles

molds with their long and high branched hyphae.

They are important source of antibiotics.

Archaebacteria
Archaebacteria cells differ greatly from eubacteria at the molecular level.
- no peptidoglycan
- The nucleotide sequences in the ribosomal RNA are similar
within the archaebacteria but distinctly different from
eubacteria.
- The lipid composition of the cytoplasm membrane is very
different for the two groups.
This category includes:
- methanogen: methane-producing bacteria
- Halogen: living only in very strong salt solutions
- Thermoacidophile: growing at high temperatures and low pH.

28Chapter 2 Part I
Procaryote Reproduction

Reproduction: exclusively asexual through binary

fission.

The chromosome is duplicated and attaches to the

cell membrane, and then the cell divides into two
equal cells.
Fission
Eucaryotes
 Eucaryotes have a true nucleus, and a number of cellular
organelles inside the cytoplasm.
 Eucaryotes include fungi (yeast and molds), algae, protozoa,
and animal and plant cells.
 Eucaryotic cells are 5 to 10 times larger than procaryotic cells
in diameter.
 Yeast is about 5 -10 µm, animal 10 µm and plant 20 µm.
Eucaryote Cell Structure
 Nucleus
 Nucleus contains chromosomes (DNA associated with small
proteins) surrounded by a membrane
 The membrane contains a pair of concentric and porous membrane.
Cell wall and membrane structure:
 Eucaryotes contain sterol which strengthen the
wall structure and make the membrane less
flexible.
 The cell wall of eucaryotes shows variations.
e.g.
- Fungi contain chitin: (C8H13O5N)n
is a long-chain polymer of a N-
acetylglucosamine, a derivative of glucose)

- Animal cells do not have cell wall but only a cytoplasmic

- Plantsocells
membrane; thatcontain cellulose
they are shear, sensitive and fragile.
Membrane-bounded organelles with
specialized functions, suspended
in the cytoplasm of a eucaryote
cell.
- Mitichondria are the powerhouses
of a eukaryote cell, where
respiration takes place. It reduces
oxygen and store energy in ATP
(Adenosine triphosphate).
Shape: Mitochondria have cylindrical
shape with 1 µm in diameter and 2-
3 µm in length.
- Endoplasmic reticulum is a complex, convoluted membrane system
leading from the cell membrane into the cell.
The rough endoplasmic reticulum containing ribosomes is the site
for protein synthesis.
The smooth one is involved with lipid synthesis.
- Lysosomes are very small
membrane-bound particles
that contain and release
digestive enzyme,
contributing to digestion of
nutrients and invading
substances.
Enzymes in lysosomes:
e.g. Lipases digest lipids.
Carbohydrases digest
Proteases digest
proteins. are low density and responsible for food digestion,
- Vacuoles
osmotic regulation and waste product storage.
- Golgi complexes are small particles composed of membrane
aggregates.
- Responsible for the secretion of certain proteins.
- Golgi are sites where proteins are modified, important for protein
function in the body. http://www.slideshare.net/eplavoi/cells-part-2
Eucaryotes
- Fungi: yeast and mold
- Algae
Fungi
Fungi are heterotrophs which need to take nutrients from the
environment for living.
 They are larger than bacteria.

Two major groups are yeast and mold.

Yeast
Yeasts are very important economically:
- Yeasts are responsible for fermentation of beer and bread.
(Saccharomyces cerevisiae)
- Ethanol production
- Wastewater treatment:
a mixed culture of yeasts Candida lipolytic Candida tropicalis,
and Yarrowia lipolytica grown on hydrocarbons, or gas oil.
Yeasts are very important economically:
- Yeasts and Bacterium xylinum
cultures produce Kombucha,
fermented sweetened tea.
Yeasts: e.g.Brettanomyces bruxellensis, Candida
stellata, Schizosaccharomyces pombe
Yeast is single-celled.
Size: yeasts are 5 to 10 µm in diameter.
Shape: spherical, cylindrical or oval.
Reproduction: asexual and sexual.

 Asexual reproduction is by either

budding or fission.
Asexual by Budding: a small bud cell
forms on the cell, which gradually
enlarge and separate from the mother
cells.
Most of the yeasts reproduce by
budding.
Baker’s yeast, Saccharomyces
cerevisiae.
Asexual by Fission:
Similar to budding but the cells grow to certain size and divide
into two equal cells. (similar to bateria)
Only a few yeast species are reproduced by fission.
e.g.Schizosaccharomyces pombe

Sexual: meiosis (formation of azygote from two haploid cells

(gamete)

Classification of yeast is based on reproduction modes;

budding or fission
Molds
Molds are filamentous fungi and have a mycelial
structure.
• Mycelium is highly branched system of
tubes that contains mobile cytoplasm with
many nuclei.
• Hyphae is long, thin filaments on the

mycelium.
 Molds are very important
economically:
- mushroom farming is a large
industry in many countries.
Agaricus bisporus
Size:
 When grow on solid surface, the filamentous form is

5-20 µm.
 When grow in submerge culture, it can form aggregates and pellets,
50 µm-1mm.
- Cause nutrient transfer problem in the pellet

Mold Reproduction:

 Either by asexual or sexual means.

 Some molds form sexual spores which provide resistance
against heat, freezing, drying and some chemical agents.
 Both asexual or sexual spores can germinate and form new
hyphae.

https://www.youtube.com/watch?v=1OOnn5JN4EI
 Food industry
The mixed culture including Penicillium sp. for cheese
production.
Aspergillus niger for citric acid production.
 Antibiotics production.
Penicillium notatum
Eucaryote-Algae
Algae are usually unicellular or plantlike multicellular organism.
 Like plants, most algae use the energy of sunlight to make their own

food, a process called photosynthesis.

 Algae lack the roots, leaves, and other structures typical of true

plants.
 Algae contain chloroplast which is responsible for photosynthesis.

 Unicellular algae are considered in Microbiology

 E.g. Chlorophyta, Chrysophyta (brown, yellow-green algae)

 They are in the size of 10-30 µm.

 Algae can reproduce asexually or sexually.
Many of algae incorporate both sexual and
asexual modes of reproduction.
 Algae contain alginic acid and agar.

https://www.youtube.com/watch?v=RQ-SMCmWB1s
Virus
 Not free-living organisms, obligate parasite of other living
cells.
 Size: 30-200 nm.
 Can not capture or store free energy.
 Not functionally active except when inside their host cells.
 Can do harm but also be useful
biotechnology tools (e.g. vaccines).
 Bacteriophage or phage: virus infecting bacteria.
 (Virus: virus infecting eukaryotes)
 Virus reproduction:
- Virus contains genetic materials such as DNA and RNA
which is covered by a protein coat called capsid.
- They can reproduce only by invading and controlling other
cells as they lack the cellular machinery for self-
reproduction.
 Section Summary
 Organism cells are highly diverse in terms of their
adaptation to the living environment:
 Temperature, pH, oxygen, moisture, nutrients
 Shapes (bacteria): Coccus, Bacillus and Spirillum
Primary Classification
Cellular Organism
Have nuclear membrane and not free-living organisms
membrane-bound organelles?

Yes No
Eucaryotes Procaryotes Virus
 Primary Classification
Cellular Organism
Have nuclear membrane and not free-living organisms
membrane-bound organelles?

Yes No

Eucaryotes Procaryotes Virus

Organelles: Fungi: yeast and mold

Mitochondria: powerhouse
Algae:
Endoplasmic reticulum: protein and lipid
synthesis (asexual or sexual reproduction)
Lysosome: nutrient digestion enzymes
Golgi: protein secretion and modification
Vacuoles: food digestion, osmotic
regulation and waste product storage
Chloroplasts: photosynthesis
 Primary Classification
Cellular Organism
Have nuclear membrane and not free-living organisms
membrane-bound organelles?

Yes No

Eucaryotes Procaryotes Virus

Cytoplasmic granules: Eubacteria: gram-positive, gram-negative,

- Ribosome: protein synthesis non-gram, actinomycetes and
- Storage granules: source of key cyanobacteria
metabolites, including polysaccharides,
lipids and sulfur granules.
Archaebactria: methanogen
- Capsule
- Pili
Halogen
- Flagella
thermoacidophiles

Mostly asexual reproduction

 Primary Classification

Cellular Organism
Have nuclear membrane and not free-living organisms
membrane-bound organelles?

Yes No

Eucaryotes Procaryotes Virus: reproduce

Asexual reproduction in the host cell

Fungi: yeast, mold Eubacteria: Archaebateria:

Algae: Gram-positive bacteria methanogen
Reproduction: asexual or Gram-negative bacteria Halogen
sexual Non-gram bacteria Thermoacidophiles
Actinomycetes
Cynaobacteria