Download lecture notes-microbiology

Analysis of Biological System
An understanding of biological system can be
simplified by analyzing the system at several
different levels:
• the cell level: microbiology, cell biology;
• the molecular level: biochemistry, molecular biology;
• the population level: microbiology, ecology;
• the production level: bioprocess.
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.
(Random House Webster’s Unabridged Dictionary)
It is often illustrated using single-celled, or
unicellular organisms
Overview of Microbiology
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
in controlling life processes
for the cell intake of nutrients, production of energy,
discharge of waste materials, and reproduction.
Basics of Microbiology
• Nomenclature
• Primary classification of microorganism
- Procaryotes: bacteria;
- Eucaryotes: fungi (yeast and moled)
algae
- Virus
• Microbial cell characteristics under each cell
category
- cell structure and reproduction
Microbial nomenclature
A dual name (binary nomenclature) in Latin or
Latinized is used, including
genus & species
A genus: a group of related species
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.
Abreviation:
E. coli
Various strain and substrains are designated by the addition of letters and
numbers.
e.g. E. coliK12.
Microbial diversity
Cell adaptation to the environment
Temperature
•
Psychrophiles can grow below 20oC.
significance to food microbiologists
•
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° Celsius(158° Fahrenheit), but can survive at
temperatures 50°-80° C (122°-176° F).
Regular sterilization at 121oC.
Microbial diversity
pH:
– Acidophile is an inorganic particle or living
organism that tends toward acidic conditions
pH< 3.
– Alkaliphiles are microbes that thrive in alkaline
environments with a pH of 9 to 11.
Microbial diversity
Moisture:
Some cells can grow
- where the water activity is high (e.g.
algae),
- on solid surface (mold)
Microbial diversity
Oxygen:
• Some microorganism requires oxygen for growth called
aerobic.
• Other organism can be inhibited by the presence of
oxygen which is called anaerobic.
• Facultative organism 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.
Microbial diversity
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
Microbial diversity
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 15 °C
or lower.
• Thermophile: An organism that can thrive at temperatures between
60-80 °C.
Microbial diversity
Shape:
• coccus (cocci, pl): A cell with a spherical or elliptical
shape.
e.g. Streptococcus is a genus of spherical, Gram-positive bacteria
Microbial diversity
• bacillus (bacilli, pl): a cylindrical cell
e.g. Bacillus subtilis is a bacterium that is commonly
found in soil.
Microbial diversity
• 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
Classification of Cellular Organism
(according to cell structure)
Cellular Organism
Have nuclear membrane
and membrane –bound organells?
not free-living organisms
Yes
Eucaryotes
Protists: Fungi, Algae,
protozoa
Plant: seed plants, ferns,
mosses
Animal: vertabrates and
invertabrates
No
Procaryotes: bacteria
Virus
Eubacteria:
Archaebacteria:
Gram-positive bacteria
Gram-negative bacteria
Non-gram bacteria
Actinomycetes
Cynaobacteria
methanogen
Halogen
Thermoacidophiles
Classification of Cellular Organism
(according to cell structure)
Cellular Organism
Have nuclear membrane
and membrane –bound organells?
not free-living organisms
Yes
Eucaryotes
Protists: Fungi, Algae,
protozoa
Plant: seed plants, ferns,
mosses
Animal: vertabrates and
invertabrates
No
Procaryotes: bacteria
Virus
Eubacteria:
Archaebateria:
Gram-positive bacteria
Gram-negative bacteria
Non-gram bacteria
Actinomycetes
Cynaobacteria
methanogen
Halogen
Thermoacidophiles
Procaryote
Procaryotes have no membrane around the cell
genetic information and no membrane-bound
organelles
• Bacteria
• Size: 0.5-3µm.
• Grow rapidly, double times: 0.5 hour and several hours.
• Utilize carbon sources: carbohydrates, hydrocarbon,
protein and CO2.
http://micro.magnet.fsu.edu/cells/procaryotes/images/procaryote.jpg
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.
http://micro.magnet.fsu.edu/cells/procaryotes/images/procaryote.jpg
Procaryote Cell Structure
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.
- intracellular spores: a resistance to adverse conditions:
high temperature, radiation and toxic chemicals; 1µm;
1 pore per cell; it could germinate under favorable
conditions.
- volutin: another granular structure made of inorganic
polymetaphosphates present in some photosynthetic
species such as Rhodospirillum.
http://micro.magnet.fsu.edu/cells/procaryotes/images/procaryote.jpg
Procaryote Cell Structure
Cytoplasmic membrane
- The cytoplasm is surrounded by a membrane
called cytoplasmic membrane.
- The cytoplasmic membrane contains 50%
protein, 30% lipids and 20% carbohydrates.
- It is separated from the outer membrane of
some organism by Periplasmic space.
http://micro.magnet.fsu.edu/cells/procaryotes/images/procaryote.jpg
Procaryote Cell Structure
Cell wall
- Cell walls contain peptidoglycan which is a complex
polysaccharide with amino acids and forms a structure
somewhat like chain-link fence.
- Cell walls of bacteria are primarily used for protection
against hostile environments.
The cell envelope is the cell membrane and cell wall plus
an outer membrane. This cell envelope serves
- To retain important cellular compounds and
- To exclude undesirable compounds in the environment.
http://micro.magnet.fsu.edu/cells/procaryotes/images/procaryote.jpg
Procaryote Cell Structure
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. Gramnegative 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.
Eubacteria
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 peumonia and other respiratory disorders.
• Actinomycetes: bacteria but, morphologically resembles molds with
their long and high branched hyphae.
They are important source of antibiotics.
• Cyanobacteria: formally called green blue algae, having chlorophyll
and fixing CO2 into sugar.
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.
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 nuclear membrane and
true nucleus, and membrane-bound
organelles.
Eucaryotes include fungi (yeast and molds), algae,
protozoa, and animal and plant cells.
Eucaryotes are five to ten times larger than procaryotes
in diameter.
Yeast is about 5 -10 µm, animal 10 µm and plant 20 µm.
Eucaryote cell structure
Eucaryote structure
Nucleus
- Nucleus contains chromsomes (DNA associated with
small proteins) surrounded by a membrane.
- The membrane contains a pair of concentric and porous
membrane.
- The nucleolus is an area in the nucleus that stains
differently and is the site of ribosome synthesis.
Eucaryote cell structure
Eucaryote structure
Cell wall and membrane structure:
- Similar to procaryotes, proteins are embedded in phospholipid matrix.
- Eucaryotes contain sterol which strengthen the wall structure and
make the membrane less flexible.
- The cell wall of eucaryotes shows variations.
- Some eucaryotes contain peptidoglycan,
- plant cells contain cellulose;
- animal cells do not have cell wall so that they are shearsensitive and fragile.
Eucaryote cell structure
Eucaryote structure
Organelles are cell structures with specialized
functions , suspended in the cytoplasm of a
eucaryote cell.
-Mitochondria 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.
-
Eucaryote cell structure
Eucaryote structure
Organelles :
-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.
Eucaryote cell structure
Eucaryote structure
Organelles:
-Lysosomes are very small membrane-bound
particles that contain and release digestive
enzyme, contributing to digestion of nutrients
and invading substances.
Eucaryote cell structure
Eucaryote structure
Organelles:
-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.
Eucaryote cell structure
Eucaryote structure
Organelles
-Vacuoles are membrane-bound organelles of low
density
- responsible for food digestion, osmotic
regulation and waste-product storage.
- may occupy large fraction of cell volume (up to
90% in plant cells).
- Chloroplasts are relatively large, chlorophyllcontaining, green organelles that are
responsible for photosynthesis in algae or plant
cells.
Eucaryotic Cell Reproduction
• Mitosis: (cell division-asexual)
- Nuclear DNA replicates;
- nuclear division (mitosis);
- cell division and separation
(cytokinesis).
Cell Division Cycle (Mitosis)
Mitosis
Mitosis results in:
- two identical daughter cells with a
roughly equal distribution of organelles
and other cellular components.
- each daughter cell is the genetic
equivalent of the parent cell.
Meiosis
Meiosis forms the basis of sexual reproduction
and can only occur in eukaryotes.
- The formation of a zygote (a diploid cell) is from fusion of
two haploid cells (gametes).
- Each haploid cell has a set of chromosome.
- The diploid cells contains twice as many chromosome as
does the gamete.
- The diploid cells divide several times (meiosis) to form new
haploid cells.
Meiosis
Gamete
(haploid)
Zygote
(diploid)
DNA replication
Daughter cells
haploid)
Meiosis I
Meiosis II
Meiosis
In Meiosis
- The diploid cell's chromosomes (DNA) is
replicated once and separated twice,
producing four sets of haploid cells each
containing half of the original cell's
chromosomes.
- These resultant haploid cells will fertilize
with other haploid cells of the opposite
gender to form a diploid cell again.
Eucaryotes
- Fungi: yeast and mold
- Algae
Eucaryotes
Fungi
• Fungi are heterotrophs which need to take
nutrients from the environment for living.
• They are larger than bacteria.
Fungi
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 and
Candida tropicalis grown on hydrocarbons, or
gas oil.
Eucaryotes-Fungi
Yeast is single-celled.
• Size: yeasts are 5-, 10- µm in diameter.
• Shape: spherical, cylindrical or oval.
• Reproduction: asexual and sexual.
Eucaryotes-Fungi
Yeasts
Reproduction: asexual and sexual.
• Asexual reproduction is by either budding
or fission.
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.
Budding
Budding
Yeast Budding
Saccharomyces cerevisiae images provided by Carsten Kettner
Yeast Asexual Reproduction
Fission: similar to budding but the cells grow to
certain size and divide into two equal cells.
Only a few yeast species are reproduced by
fission.
Eucaryotes-Fungi
Yeasts
Reproduction:
Sexual reproduction involves in meiosis.
Eucaryotes-Fungi
Molds
Molds are filamentous fungi and have a mycelial
structure.
Mycelium is highly branched system of tubes that contains
mobile cytoplasm with many nuclei.
Hypha is long, thin filaments on the mycelium.
Mold
• Molds are very important economically:
- mushroom farming is a large industry in many
countries.
Agaricus bisporus
Mold
- Food industry
The mixed culture including Penicillium sp. for
cheese production.
Aspergillus niger for citric acid production.
- Antibiotics production.
Penicillium notatum
Eucaryotes-Fungi
Molds
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
Eucaryotes-Fungi
Mold Reproduction:
• Either by asexual or sexual means.
• Asexual spores are called conidia.
• 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.
Eucaryote -Fungi
Fungus Classification:
Classification of fungi is based on their sexual
reproduction modes:
- phycomycetes are algaelike fungi, but do not have
chlorophyll and cannot photosynthesize.
Aquatic and terrestrial molds belong to this category.
- ascomycetes form sexual spore called ascospores
contained in a sac (a capsule structure).
Neurospora, Aspergillus and yeast.
Eucaryote -Fungi
Classification:
- basidiomycetes reproduced by basidiospores,
which are extended from the stalks of specialized
cells called the basidia. Mushroom.
- deuteromycetes (fungi imperfecti) cannot reproduce
by sexual means. Only asexual reproduction molds
belong to this category.
Some pathogenic fungi such as Trichophyton causing
athlete’s foot belong to this category.
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.
Eucaryote-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.
Virus
Not free-living organisms, obligate parasite of other living
cells.
• Size: 30-200nm.
• 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).
SARS Coronavirus virion
Virus
• 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
membrane-bound organelles?
Yes
Eucaryotes
not free-living organisms
No
Procaryotes
Virus
Primary Classification
Cellular Organism
Have nuclear membrane and
membrane-bound organelles?
not free-living organisms
Yes
Eucaryotes
No
Procaryotes
Organelles:
Mitochondria: powerhouse
Endoplasmic reticulum: protein and lipid
synthesis
Lysosome: nutrient digestion
Golgi: protein secretion and modification
Vacuoles: food digestion, osmotic
regulation and waste product storage
Chloroplasts: photosynthesis
Virus
Fungi: yeast and mold
Algae:
(asexual or sexual reproduction)
Plant
Animal
Primary Classification
Cellular Organism
Have nuclear membrane and
membrane-bound organelles?
not free-living organisms
Yes
Eucaryotes
No
Procaryotes
Cytoplasmic granules:
Ribosome: protein synthesis
Storage granules: source of key
metabolites, including
polysaccharides, lipids and sulfur
granules.
Spores (endospores): resistance to
adverse conditions (T, Radiation)
Volutin: protein granule serve as food
reserves
Virus
Eubacteria: gram-positive, gramnegative, non-gram, actinomycetes
and cyanobacteria
Archaebactria: methanogen
Halogen
thermoacidophiles
Mostly asexual reproduction
Primary Classification
Cellular Organism
Have nuclear membrane and
membrane-bound organelles?
not free-living organisms
Yes
Eucaryotes
No
Procaryotes
Virus: reproduce
Asexual reproduction in the host cell
Fungi: yeast, mold
Eubacteria:
Archaebateria:
Algae:
Gram-positive bacteria
Gram-negative bacteria
Non-gram bacteria
Actinomycetes
Cynaobacteria
methanogen
Halogen
Thermoacidophiles
Reproduction: asexual or
sexual