Basic of microbiology

Biophysics and the cell Doctrine

• Understanding of living system started in 1838 , when
Schleiden and Schwann first proposed the cell theory.
• All living things are made up of cells.
• Cells are the smallest working units of all living things.
• All cells come from preexisting cells through cell division.
 Scientist with cell theory
1. Schleiden (circa 1838) 2. Schwann

Onion skin cells Human red blood cells

All animals are made of cells!
All plants are made of cells!

3. Virchow

All cells come from pre-existing cells!

 The Structure of Cells
Definition : A cell is the smallest unit that is capable of performing life functions

Observation with the electron microscope have revealed two markedly different
kinds of cell
• Procaryotic Cells
• Eucaryotic Cells
 Procaryotic Cells
• Procaryotic cells or procaryotes, do not contain a membrane enclosed
nucleus.
• Relatively small and simple cell
• They usually exist alone ,not associated with other cells
• One-celled organisms, Bacteria (Example)
• The typical dimension of these cells, which may be spherical, rodlike
or spiral is from 0.5 to 3 µm.
• Typically, procaryotes are biochemically versatile; i.e. they often can
accept a wide variety of nutrients and further are capable of selecting
the best nutrient from among several available in their environment.
Basic features of Procaryotic cell
• The cell is surrounded by a rigid wall, approximately 200 oA
thick.
• This wall lends structural strength to the cell to preserve its
integrity in a wide variety of external surrounding.
• Inside this wall is the cell membrane, which typically have
thickness of about 70 oA.
• These membrane play critical role in determining which
chemical species can be transferred between the cell and its
environment as well as net rate of such transfer.
• With in cell is a large, ill-defined region called nuclear zone,
which is the dominant control center for cell operation.
• The granny dark spots in the cell interior are the ribosomes,
the sites important for biochemical reaction
 Eucaryotic Cells
• Eucaryotes may be defined most consiely as cells which possess a
membrane enclosed nucleus.
• As a rule these cells are 1000 to 10,000 times larger than procaryotes.
• All cells of higher organisms belong to this family.
• Example: animals and plants cell.
 Structure of eukaryotic cell
● A complex, convoluted membrane system, called the endoplasmic reticulum, leads from cell membrane into the cell
● The nucleus here is surrounded by a porous membrane.
● Ribosome, biochemical reaction sites seen before in procaryotes are embedded in the surface of much of the endoplasmic
reticulum.
● Mitochondria are organells with an extremely specialized and organized internal structure.
● Golgi complex, lysosomes and vacuoles are the remaining organells
Classification of Microorganism
 Diversity of Microbes

• Bacteria-single celled prokaryotes

• Protozoa-eukaryotic, single celled, colonial,
many ways of nutrition
• Fungi- absorb nutrients, single celled
filamentous
• Viruses-acellular entities
• Others- worms, insects
 Bacteria
• Bacteria are typically unicellular, but they may exist in three basic morphological forms.
• Belong to Prokaryotes and cell wall composed of Peptidoglycan layer
• For energy, use organic chemicals, inorganic chemicals, or photosynthesis
• Most cannot utilize light energy, are capable of motion (motile) and reproduce by division into two
daughter cells (binary fission)
• Gram reaction separate bacteria to gram positive or gram negative.
• Cells first stained with the dye crystal violet , then treated with an iodine solution and washed in
alcohol. Bacteria retaining blue crystal-violet color are called gram positive and loss of color indicate
gram negative.
 Bacteria :Uses
• Bacteria have a variety of important uses:
• Help make interesting food (buttermilk, yogurt, cheese, sauerkraut,
pickles, and olives, etc…)
• Decompose organic matter (recycle nutrients from dead organisms;
break down sewage into simpler compounds)
• Nitrogen fixation (chemically changes nitrogen gas, N2, into ammonia,
NH3, so plants can make amino acids)
• Human health (bacteria on skin help prevent infection & bacteria in
gut helps digest food & make vitamins)
• Biotechnology (used to make antibiotics, insulin, human growth
hormone, vitamins, and other drugs)
 Disease caused by bacteria
• A minority (less than 1%) of bacteria cause disease in humans, animals,
and plants.
• Bacteria can cause a variety of diseases:
• Food Poisoning – Scarlet Fever
• Tuberculosis – Whooping Cough
• Cholera – Bacterial Meningitis
• Syphilis – Pneumonia
• Ulcers – Leprosy
• Strep Throat – Tetanus
 Archaea
The Domain Archaea wasn't recognized as a major domain of life until quite recently. Until the 20th
century, most biologists considered all living things to be classifiable as either a plant or an animal. But
in the 1950s and 1960s, most biologists came to the realization that this system failed to accomodate
the fungi, protists, and bacteria. By the 1970s, a system of five kingdoms had come to be accepted as
the model by which all living things could be classified. At a more fundamental level, a distinction was
made between the prokaryotic bacteria and the four eukaryotic kingdoms (plants, animals, fungi, &
protists).
Common features
-Archaea are single- celled organisms that lack a
membrane-bound nucleus. - Prokaryote

-Archaea can be found in environments that are too

hostile for other life forms.
- Include:
Methanogens
Extreme halophiles
Extreme thermophiles
 Protozoa
Introduction:
The Phylum Protozoa is classified into four
subdivisions according to the methods of locomotion.
-The amoebae (Sarcodina) move by means of pseudopodia.
-The flagellates (Mastigophora) typically move by long,
whiplike flagellae.
-The ciliates (Ciliata) are propelled by rows of cilia that beat
with a synchronized wavelike motion.
-The sporozoans (Sporozoa) lack specialized organelles of
motility
Some features
• Eukaryotes
• Absorb or ingest organic chemicals
• May be motile via pseudopods, cilia, or flagella
• Most free some parasites
 Fungi
Characterstics features
● Eukaryotes
● Chitin cell walls
● Nonphotosynthetic ( heterotrophic)
● Use organic chemicals for energy
Septated
● Molds and mushrooms are multicellular consisting of masses
of mycelia, which are composed of filaments called hyphae
● Yeasts are unicellular
Structure
●Filaments of fungi are called hyphae.
Unseptated -
●The cell walls contain chitin. coenocytic
● The MYCELIUM is a mat of hyphae visible to the
unaided eye ( bread mold)
● Some hyphae may divided by cross sections called
septa
 Algae
The term "algae" covers many different organisms capable of producing oxygen through
photosynthesis. These organisms are not necessarily closely related. However, certain
features unite them, while distinguishing them from the other major group of
photosynthetic organisms: the plants.

Some features
• Eukaryotes
• Cellulose cell walls
• Use photosynthesis for energy (primary producers)
• Produce molecular oxygen and organic compounds
• Metabolically diverse
 Viruses
Sub microscopic entity consisting of a single nucleic acid surrounded by a
protein coat and capable of replication only within the living cells of
bacteria, animals or plants.

Features
• Acellular
• Consist of DNA or RNA core
• Core is surrounded by a protein coat
• Coat may be enclosed in a lipid
envelope
• Viruses are replicated only when they
are in a living host cell
 How do viruses works

 In order to replicate and make copies of itself, viruses need a host cell. Any
living cell can become a host cell (human, animal, plant, and even bacterial
cells!)
 Without a host cell, viruses cannot function (i.e.-are harmless!)
 Although any cell can theoretically become a host cell, specific viruses will
only infect specific cells
(EX: HIV will only infect human T cells, a part of your immune system)
 Disease caused by virus

• Viruses can cause disease in humans, animals, plants, and even bacteria!
• Viruses can cause a variety of diseases:
• Common cold – Polio
• Hepatitis A, B & C – Influenza
• Herpes – Mumps
• Mononucleosis – Measles
• Warts – Viral Meningitis
• Chickenpox – AIDS
Characteristics features
 Summary
Prokaryotic Cells
small cells (< 5 mm)
always unicellular
no nucleus or any membrane-
bound organelles
DNA is circular, without proteins
ribosomes are small (70S)
no cytoskeleton
cell division is by binary fission
reproduction is always asexual
Eukaryotic cells
larger cells (> 10 mm)
often multicellular
always have nucleus and other
membrane-bound organelles
DNA is linear and associated with
proteins to form chromatin
ribosomes are large (80S)
always has a cytoskeleton
cell division is by mitosis or
meiosis
reproduction is asexual or sexual
 Microbial nutrition and growth
Introduction
• A cell’s composition differ greatly from its environment. A cell must
selectively remove desirable compounds from its extracellular environment
and retain other compounds within itself.
• All organisms except viruses contain large amount of water ( about 80%).
• About 50 % of dry weight of cell is protein
• The nucleic acid content ( which contains the genetic code and machinery to
make protein) of cell varies from 10% to 20% of dry weigth
• The lipid content of most cells varies between 5% to 15% of dry weight.
• Intracellular composition of cells varies depending on the type and age of the
cells and the composition of the nutrient media.
 Elemental composition of bacteria
Element % dry weight Source
Carbon 50 organic compounds or CO2

Oxygen 20 H2O, organic compounds, CO2, and O2

Nitrogen 14 NH3, NO3, organic compounds, N2

Hydrogen 8 H2O, organic compounds, H2

Phosphorus 3 inorganic phosphates (PO4)

Sulfur 1 SO4, H2S, So, organic sulfur compounds

Potassium 1 Potassium salts

Magnesium 0.5 Magnesium salts
Calcium 0.5 Calcium salts
Iron 0.2 Iron salts
 Cell Nutrients
• Most of the products formed by organisms are produced as a result of their
response to environmental conditions, such as nutrient, growth hormones, and
ions.
• The qualitative and quantitative nutritional requirements of cells need to be
determined to optimize growth and product formation.
• Nutrients required by cells can be classified in two categories
Macronutrients: Carbon, nitrogen, oxygen, hydrogen, sulfur , phosphorus,
Mg2+ and K+ are major macronutrients
Micronutrients: Trace elements such as Mo2+, Zn2+ , Cu2+, Mn2+, Ca2+, Na+,
vitamins, growth harnomes and metabolic precursors are micronutrients.
 Macronutrients : Carbon sources
• Carbon compounds are major sources of cellular carbon and energy in most
bacteria.
• Microorganisms are classified in two categories on the basis of their carbon
sources
Heterotrophs: use organic compounds such as carbohydrates, lipids, and
hydrocarbons as a carbon and energy sources
Autotrophs: use carbon dioxide as a carbon source
• Most common carbon sources in industrial fermentations are molasses
(sucrose), starch ( glucose, dextrin), corn syrup.
• In laboratory fermentations, glucose, sucrose and fructose are the most
common carbon sources
 Growth requirements

Physical
Psychrophiles (cold loving)
•Temperature
• True psychrophiles
•pH
(optimum growth at 15 ºC)
•Osmotic pressure • Psychrotophs
•Moisture & desiccation (optimum growth at 20-30 ºC)
Mesophiles (moderate temperature loving)
Chemical
Thermophiles (heat loving)
•Carbon source
Hyperthermophiles (tolerate extreme
•Nitrogen, sulfur phosphorus temperatures)
•Oxygen
 pH
• Most medically important bacteria grow at neutral or slightly alkaline pH
(7.2 to 7.6)
• Very few bacteria grow below pH 4
• Lactobacilli grow in acidic pH; cholera vibrio grow in alkaline pH
• Growth media includes chemical buffers to prevent acid production
• Foods are preserved by acids produced by bacterial fermentation
Temperature dependence of bacterial growth
 Baceria are grown (cultured)

Growth media: Envinronmental conditions:

• Liquid (for large numbers of bcteria) optimal temperature, oxygen
• Solid (for isolation of individual concentration, pH,
bacteria)
• Semisolid ( for demonstration of
motility)
 Microbial growth

• Bacteria and other microbes have particular requirements for growth

• When they reside in and on our bodies or in the environment, they
harvest their food from us or from the environment
• When we grow bacteria in lab, we are essentially creating a captive
environment for bacteria – like a bacteria zoo.
• So we must provide the bacteria we grow in lab with all of the
materials that they need to grow
 Culture medium
Chemically defined media : is one in which the exact chemical composition is
known (energy source , carbon , nitrogen , sulfur , phosphorus , growth factors)
Complex media : in which the exact chemical composition varies slightly from
batch to batch (protein added)
Differential media : used to distinguish among different kinds of bacteria
Selective media : allow the growth of only one kind of bacteria & prevent the
growth of other by the addition f certain salts & dyes
 Types of medium
Solid media – contains 2% agar
• Colony morphology, pigmentation, hemolysis can be appreciated.
• Eg: Nutrient agar, Blood agar

Liquid media – no agar.

• For inoculum preparation, Blood culture, for the isolation of pathogens from a
mixture.
• Eg: Nutrient broth

Semi solid medium – 0.5% agar.

• Eg: Motility medium
MacConkey Agar

left: no lactose fermentation

right: lactose fermentation
 Microbes culture: Streak culture

• Used for the isolation of bacteria in pure culture from clinical specimens.
• Platinum wire or Nichrome wire is used.
• One loopful of the specimen is transferred onto the surface of a well dried plate.
• Spread over a small area at the periphery.
• The inoculum is then distributed thinly over the plate by streaking it with a loop
in a series of parallel lines in different segments of the plate.
• On incubation, separated colonies are obtained over the last series of streaks.
Streak plate method for microbes isolation