CHAPTER 1: MICROBIOLOGY

LECTURE

Means MICROBIOLOGY Means the study of

very small living organism

MICRO BIOLOGY

Study of very small living organisms called

Are ubiquitous (they
are virtually
MICROORGANISM OR MICROBES everywhere)

Two categories
ACELLULAR INFECTIONS AGENTS CELLULAR MICROORGANISMS

Has no cell and Classified Has a cell and

without life into two with life

PROKARYOTES EUKARYOTES
Algae
Archaea
Prokaryotes organisms lacking Eukaryotes organisms Fungi
Bacteria true nucleus having a true nucleus
Protozoa

Pathogens – commonly known as germs that cause disease. (3% are pathogenic, 97% are
nonpathogenic)
2 Categories of Disease Caused By Pathogens
 Infectious disease – results when a pathogen colonizes the body subsequently cause disease.
 Microbial intoxication – result when a person ingests a toxin (poisonous substance) that has been
produced by a microorganism

 Microbial allies – microorganisms that help us

 Microbial enemies – microorganisms that harm us
There are 10 times as many microorganism as the total number of cells that make up our bodies.
(Approximately 100 trillion microbes). 500 to 1000 different species of microorganisms are living on & in us
 Indigenous microflora or Indigenous microbiota – harmless and beneficial microbes living on us.
 Opportunistic pathogens (opportunists) – organisms that colonize our body.
 Decomposers or Saprophytes – they are involved in the decomposition of dead organisms and waste
products of living organisms.
o Saprophytes – aid in fertilization by returning inorganic nutrients to the soil.
 Bioremediation – microorganisms that are capable of decomposing industrial wastes.
 Microbial ecology – the study of relationships between microbes and the environment this includes
nitrogen cycle.

Plankton –microscopic organisms in the ocean. They serve as the starting point of many food chain.
Phytoplankton – tiny marine plants and algae.
Zooplankton – tiny marine animals.
 Microorganisms also aid in the digestion of food and in some instances produce substances that are
value to the host animal.
 E. Coli live in the human intestinal tract – produce Vit. K & Vit B1
 Cellulose – eating protozoa in termites’ intestinal tract digest the wood that the termites consume into
smaller molecules.

 Biotechnology – microorganisms are used in various food and beverage industries, others are used to
produce enzymes & chemicals.
 Antibiotic – it is a substance produced by a microorganism that is effective in killing or inhibiting the
growth of other microorganisms
WHY STUDY MICROBIOLOGY??
• Some microbes are known as Indigenous microflora (or indigenous microbiota) that are of benefit to us.
• Some microbes are known as opportunistic pathogens that have the potential to cause infections
• Microbes are essential for life on this planet as we know it.
• Many microbes are involved in the decomposition of dead organisms and the waste products of living
organisms.
• Some microbes are capable of decomposing industrial wastes (oil spills, for example).
• Many microbes are involved in elemental cycles, such as the carbon, nitrogen, oxygen, sulfur, and
phosphorous cycles.
• Algae and Bacteria serve as food for tiny animals.
• Some microbes live in the intestinal tracts of animals, where they aid in the digestion of food and, in
some cases, produce substances that are of value to the host animal.
• Many microbes are essential in various food and beverage industries, whereas others are used to produce
certain enzymes and chemicals
• Some bacteria and fungi produce antibiotics that are used to treat patients with infectious diseases.
• Microbes are essential in the field of genetic engineering.
• For many years, microbes have been used as “cell models”.
• Finally, we come to diseases. Microbes cause two categories of diseases: infectious diseases and
microbial intoxications

FIRST MICROORGANISMS ON EARTH

• Fossils of primitive microorganisms (11 different types) found in ancient rock formations on north-
western Australia dating back to about 3.5 billion years ago. (Earth was formed 4.5 billion years ago)
• Animals appeared on Earth between 900 and 650 million years ago
• Humans (Homo Sapiens) existed for more than 100,000 years or so.
• 1st microorganisms on earth are the: Archaean & Cyanobacteria

EARLIEST KNOWN INFECTIOUS DISEASES

 3180 BC – earliest recorded pestilence occurred in Egypt. The first recorded epidemic.
 1900 BC – Greek army was decimated with bubonic plague
 1500 BC – Epidemic fevers as recorded in Ebers papyrus was discovered in a tombin Thebes, Egypt.
 1122 BC – smallpox in China
 790, 710, 640 BC – plague in Rome
 430 BC – plague in Greece
 1493 – syphilis (Neapolitan disease, French pox, etc.) in Europe
 Earliest mummies – TB, parasitic worm infxn, syphilis.

PIONEERS IN THE SCIENCE OF MICROBIOLOGY

 Anton Van Leeuwenhoek
- “Father of Microbiology”
- “Father of Bacteriology”
- “Father of Protozoology”
- First person to see live bacteria and protozoa
- he grind tiny glass lenses (single-lens microscopes or simple microscopes)
- Described what we know today as bacteria – rod shaped , spiral shaped , etc. “animalcules”
 - He is not a trained scientist, he’s a fabric merchant, a wine assayer, a surveyor, and minor official in
Delft, Holland.

 Louis Pasteur
- French scientist
- He developed process we call Pasteurization
- He proved that fermentation was caused by a microbe – yeast
- Pasteur discovered forms of life that could exist in the absence of oxygen (Anaerobes)
- He developed vaccines for rabies, anthrax, chicken cholera and swine erysipelas
- He began the revolution in science that led to the Golden Age of Microbiology (from 1857-1914)

 Robert Koch
- German physician
- He used a primitive compound (two magnifying lenses) microscope, reported that life’s smallest
units were little boxes – Cells (Cell theory)
- Germ Theory
- Koch discovered that B. anthracis produces spores, capable of resisting adverse conditions.
- Koch developed methods of fixing, staining, and photographing bacteria.
- Koch developed methods of cultivating bacteria on solid media.
- Koch discovered the bacterium (M. tuberculosis) that causes tuberculosis and the bacterium (Vibrio
cholerae) that causes cholera.
- Koch’s work on tuberculin (a protein derived from M. tuberculosis) ultimately led to the
development of a skin test valuable in diagnosing tuberculosis.
- Koch’s and Pasteur’s work helped establish the “Germ Theory of Disease” – that
microorganism’s cause disease (in people, animals, and even plants).
 Exceptions to KOCH’S Postulates
 Certain pathogens won’t grow in vitro or in artificial media. Viruses, Rickettsias, chlamydia, M. leprae
& treponema pallidum.
 Obligate intracellular pathogens or parasites – microbes that only survive & multiply within living
host cells. They are cultivated in a living human or animals, embryonated chicken eggs, testes of rabbits
& chimpanzees.
 Fastidious pathogens – fussy microbes that requires complex & demanding nutritional requirements to
be cultured.
 Species-specific pathogens –they infect only 1 species of animal.
-Some pathogens only infect humans or animals.
 Synergistic infections – infection caused not only by 1 microorganism, but by the combined effects of 2
or more pathogens.
Examples: trench ulcerative gingivitis, bacterial vaginosis.
 Certain pathogens become less pathogenic or non-pathogenic when attempting to culture in vitro.
 -not all diseases are caused by microorganisms, others are caused by dietary deficiencies (scurvy,
anemia, diabetes, rickets, cancers).

 Edward Jenner
- It is credited with first vaccine
- In epidemics of smallpox during the late 1700’s, he observed that milk maids didn’t get the disease.
- Cattle had a similar disease – cowpox. Milk maids had cow pox lesions, but not small pox, so he
purposefully took scrapings from cowpox blister and scraped an 8 year old volunteer. With the
material – child got mild illness but not small pox.

 Alexander Fleming
- Scottish physician and bacteriologist who discovered Penicillin, an antibiotic.
1. Antibiotics are natural agents
2. Synthetic drugs are chemicals produced in labs (sulfas)
3. Problems with them - toxicity, resistance, allergic reactions
4. Fleming’s work - shelved until early WWII, sulfas were failing, needed penicillin to cure battle field
wounds
5. Now have thousands of antibiotics and synthetics (and a significant problem – resistance)

 Salk
- In 1950’s, POLIO was a scary epidemic. He developed a vaccine by treating the virus with formalin
(IPV) inactivated polio virus (Salk Polio Vaccine)
 Sabin
- In 1963, developed a live Polio virus vaccine, attenuated –altered virus, OPV-oral polio vaccine
(Sabin Polio Vaccine)

OTHER NOTABLE PERSONALITIES

 Florence Nightingale – Developed modern nursing techniques that reduce the spread of disease
 Semmelweis – The physician who demonstrated the effectiveness of handwashing in reducing infections
following childbirth
 Joseph Lister - English surgeon that applied ideas of the germ theory to surgery. He proved that
antiseptic surgical technique was effective. Also proved that microbes cause surgical infections (today’s
scourge –MRSA)
 R.J. Petri - Invented a flat glass dish (now known as a Petri dish) in which to culture bacteria on solid
media.
 Frau Hesse - The wife of another of Koch’s colleagues—who suggested the use of agar (a
polysaccharide obtained from seaweed) as a solidifying agent.
 Fracastorius – The physician who described the transmission of diseases and who named the disease
syphilis.
 Tyndall – Discovered Tyndallisation, the process of boiling and cooling repeatedly to destroy spores

VARIOUS DISCIPLINES OF STUDY WITHIN MICROBIOLOGY

 Bacteriology
 Mycology
 Parasitology
 Immunology
 Epidemiology
 Biotechnology
 Virology
 Environmental Microbiology
 Bioremediation

 Microbiologist – is a scientist who studies microorganisms. He must have a bachelor’s, masters or

doctoral degree in microbiology.
 Bacteriologists – a scientist who specializes in the structure, functions, & activities of bacteria.
 Phycology or Algology – study in various types of algae.
 Protozoologist – explore the area of protozoology – the study of protozoa & their activities.
 Mycology – specializes in the study of fungi.
 Virology – study of viruses & their effects on living cells of all types.
*Virologist & Cell Biologist may become a genetic engineer. (They transfer DNA from 1 cell type to
another)
*Virologist may study prions & viroids, acellular infectious agents that are even smaller than viruses.

 Medical microbiology
- Career field for individuals with interests in medicine & microbiology.
- They study of pathogens, the disease they cause, & the body defenses against disease.
- Concerned w/ epidemiology transmission of pathogens, disease-prevention measures, aseptic
techniques, treatment of infectious diseases, immunology, & the production of vaccines to protect
humans & animals against infectious diseases.
- Technological advances in medical microbiology includes complete eradication of diseases (Polio,
smallpox), safety of modern surgery, and successful treatment of victims of infectious diseases.

 Clinical microbiology
- A branch of medical microbiology
- Concerned with laboratory diagnosis of infectious diseases of humans.

 Applied microbiology
- How a knowledge in microbiology is applied to different aspects of society, medicine, & industry.
CHAPTER 2: MICROSCOPY
 Metric System
- Used in microbiology to express the size of microorganisms
- Meter (m) is the basic unit in the metric system and is equivalent to approximately 39.4 inches


The

relative sizes of Staphylococcus and Chlamydia bacteria and several viruses.

 Poliovirus is one of the smallest viruses that infect humans

Microscope
- An optical instrument used to observe tiny objects.

 Types of Microscope
A. Simple Microscope
- A microscope containing only one magnifying lens
- Images seen when using a magnifying glass usually appear about 3 to 20 times larger than
the object’s actual size.
- Anton van Leeuwenhoek used simple microscopes to observe many tiny objects including
bacteria and protozoa.

B. Compound Microscope
- A microscope containing more than one magnifying lens.
- Hans Jansen and his son were the ones credited for being the first to use this type of
microscope
- Compound light microscopes usually magnify objects about 1,000 times
Photomicrographs – photos taken through the lens system of a compound microscope
- Also called compound light microscope because visible light (from built-in bulb) is used as
the source of illumination
- It is the wavelength of visible light (0.45 µm) that limits the size of objects that can be seen
using a compound light microscope
- The compound light microscopes used in today’s laboratories contain two magnifying lens
systems:
a. Optical lens - found within the ocular or eyepiece; usually has a magnifying power of x10
b. Objectives - located above the object to be viewed; the four objectives used in most laboratory
compound light microscopes are x4, x10, x40, and x100 objectives:
• The x4 objective is rarely used in microbiology laboratories. Usually, specimens are first observed
using the x10 objective. Once the specimen is in focus, the high-power or “high-dry” objective is then
swung into position. This lens can be used to study algae, protozoa, and other large microorganisms.
• The oil-immersion objective (total magnification = x1,000) must be used to study bacteria, because
they are so tiny. A drop of immersion oil must first be placed between the specimen and the objective;
the immersion oil reduces the scattering of light and ensures that the light will enter the oil-immersion
lens. The oil-immersion objective cannot be used without immersion oil. Oil is not required when using
the other objectives.
• The condenser, located beneath the stage, focuses light onto the specimen, adjusts the amount of light,
and shapes the cone of light entering the objective. Generally, the higher the magnification, the more
light that is needed.
• As magnification is increased, the amount of light striking the object being examined must also be
increased
 There are three correct ways to accomplish this:
a. by opening the iris diaphragm in the condenser
b. by opening the field diaphragm
c. by increasing the intensity of light being emitted from the microscope’s light bulb, by turning
the rheostat knob clockwise.

 Power of magnification
- To calculate the power of magnification, multiply the
power of the ocular lens by the power of the objective.

 Resolving power
- Image clarity depends on the microscope’s resolving
power (or resolution), which is the ability of the lens system to distinguish between two adjacent
objects.
- The resolving power or resolution of an optical instrument is its ability to distinguish between two
adjacent objects.
- The resolving power of the unaided human eye is 0.2mm.
- The resolving power of the compound light microscope is approximately 1,000 times better than the
resolving power of the unaided human eye
- Additional magnifying lenses could be added to the compound light microscope, but this would not
increase the resolving power.
- Increasing magnification without increasing the resolving power is called empty magnification. It
does no good to increase magnification without increasing resolving power.

PARTS OF A MICROSCOPE
1. Ocular (lens) eyepiece
- the lens of the microscope that you look through and has a 10x magnifies
2. Course adjustment
- the large knob on the microscope that you turn to bring the object into focus
3. Fine adjustment
- the small knob on the microscope that brings the image into focus
4. Arm
- the part of the microscope supporting the body tube
5. Body tube
- The part that holds the eyepiece and the objective lenses.
6. Revolving Nosepiece
- the part at the bottom of the body tube that holds the objective lenses and allows them to be
turned
7. High power objective lens
- The lens that magnifies the object the greatest amount. (magnifies 40x)
8. Scanning objective lens
- the lens that magnifies the object the least amount (usually used to find the object; magnifies
only 3x or 4x)
9. Low power objective lens
- the lens that usually magnifies the object more than the scanner lens, but less than the high
power lens (magnifies 10x to 20x)
10. Stage
- the flat part below the objectives lens where the slide is placed
11. Clip
- the part that holds the slide in place so it doesn’t move
12. Diaphragm
- the part that controls the amount of light entering the field of view
13. Light source
- The lamp (or mirror) under the stage that sends light through the object being viewed.
14. Base
- the bottom part that supports the rest of the microscope
 Always carry a microscope with one hand holding the arm
and one hand under the base.

 Compound microscopes: Brightfield and Darkfield

• Because objects are observed against a bright
background (or “bright field”) when using a compound
light microscope, that microscope is sometimes
referred to as a brightfield microscope.
• If the regularly used condenser is replaced with what is
known as a darkfield condenser, illuminated objects
are seen against a dark background (or “dark field”),
and the microscope has been converted into a
darkfield microscope.
• In the clinical microbiology laboratory, darkfield microscopy is routinely used to diagnose primary
syphilis
• Treponema pallidum—cannot be seen with a brightfield microscope because it is thinner than 0.2 μm
and, therefore, is beneath the resolving power of the compound light microscope.

 Compound microscope: Phase-contrast and Fluorescence

• Phase-contrast microscopes can be used to observe unstained living microorganisms. Because the light
refracted by living cells is different from the light refracted by the surrounding medium, contrast is
increased, and the organisms are more easily seen.
• Fluorescence microscopes contain a built-in ultraviolet (UV) light source. When UV light strikes
certain dyes and pigments, these substances emit a longer wavelength light, causing them to glow
against a dark background

C. Electron Microscope
- Uses an electron beam as a source of illumination and magnets to focus the beam.
- Because the wavelength of electrons traveling in a vacuum is much shorter than the wavelength
of visible light—about 100,000 times shorter—electron microscopes have a much greater
resolving power than compound light microscopes.
- It should be noted that electron microscopes cannot be used to observe living organisms.
Organisms are killed during the specimen-processing procedures..

Transmission Electron Microscopes (TEMS)

- has a tall column, at the top of which an electron gun fires a beam of electrons downward
- An image of the specimen is produced on a phosphor-coated screen at the bottom of the
microscope’s column.
- The resolving power is approximately 0.2 nm, which is about 1 million times better than the
resolving power of the unaided human eye and 1,000 times better than the resolving power of
the compound light microscope

Scanning Electron Microscopes (SEMs)

- Has a shorter column, and instead of being placed into the electron beam, the specimen is placed
at the bottom of the column.
- Electrons that bounce off the surface of the specimen are captured by detectors, and an image of
the specimen appears on a monitor.
- Used to observe the outer surfaces of specimens (i.e., surface detail).
- Although the resolving power of SEMs (about 20 nm) is not quite as good as the resolving power
of TEMs (about 0.2 nm), it is still possible to observe extremely tiny objects using an SEM.

D. Atomic Force Microscopes (AFM)

- Atomic force microscopy (AFM) enables scientists to observe living cells at extremely high
magnification and resolution under physiological conditions.
- The AFM provides a true three-dimensional surface profile.
 - Using AFM, it is possible to observe single live cells in aqueous solutions where dynamic
physiological processes can be observed in real time
 Focusing Specimens using the objective lens
1. Always start with the scanning objective. 
- Use the Coarse Knob to focus and then the fine adjustment knob until clear.
- Do not use stage clips, try moving the slide around until you find something.
2. Once you've focused on Scanning, switch to Low Power. Use the Coarse Adjustment Knob to
refocus. Then use the Fine Adjustment Knob to make the image crystal clear. Again, if you haven't
focused on this level, you will not be able to move to the next level.
3. Now switch to High Power. (If you have a thick slide, or a slide without a cover, do NOT use the
high power objective). At this point, ONLY use the Fine Adjustment Knob to focus specimens
4. Recap
5. 1.  Scanning --> use coarse and fine knob
6. 2.  Low power --> use coarse and fine knob
7. 3.  High power --> use fine knob only
NOTE: When using the oil-immersion objective A drop of immersion oil must first be placed between the
specimen and the objective.
 Troubleshooting
Occasionally you may have trouble with working your microscope.
Here are some common problems and solutions.
1. Image is too dark!
Adjust the diaphragm, make sure your light is on.
2. There's a spot in my viewing field, even when I move the slide the spot stays in the same place!
Your lens is dirty. Use lens paper, and only lens paper to carefully clean the objective and ocular lens. The
ocular lens can be removed to clean the inside.  The spot is probably a spec of dust.
3. I can't see anything under high power!
Remember the steps, if you can't focus under scanning and then low power, you won't be able to focus anything
under high power.  Start at scanning and walk through the steps again. 
4. Only half of my viewing field is lit, it looks like there's a half-moon in there!
You probably don't have your objective fully clicked into place.

Microbiology Lab
CHAPTER 1: Laboratory Safety

 Microbiology Laboratory Safety Practices

- Were first published in 1913 in a textbook by Eyre
- Included admonitions such as:
1. Wear gloves.
2. Wash hands after working with infectious materials.
3. Disinfect all instruments immediately after use.
4. Use water to moisten specimen labels rather than the tongue.
5. Disinfect all contaminated waste before discarding.
6. Report to appropriate personnel all accidents or exposures to infectious agents.
 These guidelines are still incorporated into safety programs in the diagnostic microbiology laboratory.
 Safety programs also have been expanded to include not only the proper handling of biologic hazards
encountered in processing patient specimens and handling infectious microorganisms, but also fire
safety; electrical safety; the safe handling, storage, and disposal of chemical and radioactive substances;
and techniques for safely lifting o moving heavy objects.
 In areas of the country prone to natural disasters (e.g., earthquakes, hurricanes, snowstorms), safety
programs include disaster preparedness plans that outline the steps to take in an emergency.
 Sterilization and Disinfection
 Sterilization
- Is a process that kills all forms of microbial life, including bacterial spores.
 Disinfection
- Is a process that destroys pathogenic organisms, but not necessarily all microorganisms
or spores.
• Both sterilization and disinfection may be accomplished by physical or chemical methods.

 Methods of Sterilization
- The physical methods of sterilization include:
1) Incineration
- It is the most common method of treating infectious waste.
- Hazardous material is literally burned to ashes at tempertures of 870 to 980 degrees.
- It is the safest method to ensure that no infective materials remain in samples or
containers when disposed.
- Prions, infective proteins, are not eliminated using conventional methods. Therefore
Incineration is recommended.
- Toxic air emissions and the presence of heavy metals in ash have limited the use of
incineration in most large U.S. cities.

2) Moist Heat (Steam Under Pressure)

- Is used to sterilize biohazardous trash and heat- stable objects; an autoclave is used for
this purpose.
- An autoclaves essentially a large pressure cooker.
- Moist heat in the form of saturated steam under 1 atmosphere (15 psi <pounds per square
inch>) of pressure causes the irreversible denaturation of enzymes and structural proteins.
- The two common sterilization temperatures are 121 degrees Celsius (250 degrees
Fahrenheit) and 132 degrees Celsius (270 degrees Fahrenheit).
- Items such as media, liquids, and instruments are usually autoclaved for 15 minutes at
121 degrees Celsius.
- Infectious medical waste, on the other hand, is often sterilized at 132 degrees Celsius for
30 to 60 minutes to allow penetration of the steam throughout the waste and the
displacement of air trapped inside the autoclave bag.
- Moist heat is the fastest and simplest physical method of sterilization.

3) Dry Heat

4) Filtration

5) Ionizing (gamma) radiation

CHAPTER 3: CELL STRUCTURE AND TAXONOMY

2 Major Categories of Microbes

 Acellular microbes (also called infectious particles)
Ex. Viroids, Prions, Viruses
 Virus
- Appear to be the result of regressive or reverse evolution.
- Composed of only a few genes protected by a protein coat, and sometimes may contain one or a few
enzymes.
- Depend on the energy and metabolic machinery of a host cell to reproduce.
 2. Cellular microbes (also called microorganisms)
 Ultrastructure refers to the very detailed views of cells that are beyond the resolving power of
the compound light microscope.
 Cell is defined as the fundamental unit of any living organism
 Metabolism refers to all of the chemical reactions that occur within a cell.
 Cells can mutate as a result of accidental changes in its genetic material—the deoxyribonucleic acid
(DNA) that makes up the genes of its chromosomes—and, thus, can become better or less suited to its
environment.

2 TYPES OF CELLULAR MICROBES

1) Eukaryotic cells (Eukaryotes)
- Possess a true nucleus and many membrane-bound organelles.
- Ex. Algae, protozoa, fungi, plants, animals, and humans.
2) Prokaryotic cells (Prokaryotes)
- Less complex cells with no system membranes, organelles, and true nucleus.
- Ex. Bacteria, Cyanobacteria, and Archaea.

 Cytology – the study of the structure and function of cells.

 Robert Hooke - (1665) English physicist published a book entitled MICROGRAPHIA, the book
contains the description of molds, lice, fleas, fossilized plants, rusts, & sections of cork using a
compound light microscope.
- He was the first person to use the term cells.

 Cell theory – concluded by German botanist named Matthias Schleiden & a German zoologist named
Theodor Schwann.
- All plant and animal tissues were composed of cells.

 Rudolf Virchow – a German pathologist that proposed the theory of BIOGENESIS – that life can
arise only from preexisting life, and therefore, that cells can arise only from preexisting cells.

Eukaryotes
- Nucleoid region (center) contains the DNA
- Surrounded by cell membrane & cell wall (peptidoglycan)
- Contain ribosomes (no membrane) in their cytoplasm to make proteins
 Contain 3 basic cell structures:
 Nucleus
 Cell Membrane
 Cytoplasm with organelles
 Two Main Types of Eukaryotic Cells
 PLANT CELL
 ANIMAL CELL

 EUKARYOTIC CELL STRUCTURE

- Eukaryotes (eu = true; karyo refers to a nut or nucleus)
- They have a true nucleus, in that their DNA is enclosed by a nuclear membrane.
- Most animal and plant cells are 10 to 30 μm in diameter, about 10 times larger than most
prokaryotic cells.

A TYPICAL EUKARYOTIC ANIMAL CELL

I. Cell or Plasma Membrane
- mosaic composed of large molecules of
proteins and phospholipids
- It is like a “skin” around the cell, separating
the contents of the cell from the outside world.
- Regulates the passage of nutrients, waste
products, and secretions into and out of the
cell.
 - Has the property of Selective Permeability, only certain sub-stances may enter and leave the
cell
II. Nucleus
- Controls the functions of the entire cell and can be thought of as the “command center” of the
cell.
- 3 components of nucleus
a. Nucleoplasm (a type of protoplasm) is the gelatinous matrix or base material of the nucleus.
b. Chromosomes are embedded or suspended in the nucleoplasm.
c. Nuclear Membrane -the membrane that serves as a “skin” around the nucleus; consist of
linear DNA molecules and proteins (histones & nonhistones)
o Nuclear Pores – large molecules can enter and exit the nucleus.

 GENES- are located along the DNA molecules. The bead on a string of DNA. Each gene contains the
genetic information that enables the cell to produce on or more gene products.
 Gene products –mostly proteins others are ribonucleic acid (RNA)

 2 types of RNA:
A. Ribosomal Ribonucleic Acid (rRNA) molecules
B. Transfer Ribonucleic Acid (tRNA) molecules.

 Genotype or Genome – refers to the organism’s complete collection of genes

- Different species have different numbers and sizes of chromosomes.
- Human diploid cells, for example, have 46 chromosomes (23 pairs), each consisting of thousands
of genes.
- It has been estimated that the human genome consists of between 20,000 and 25,000 genes.
- More than 97% of human genetic material is identical to a chimpanzee’s

 Nucleolus
- a dark (electron dense) area can be seen in the nucleus using transmission electron microscope.
- it is here that rRNA molecules are manufactured.
- rRNA molecules exit the nucleus & become part of the structure of ribosomes
 Nucleolus
- Inside nucleus
- Disappears when cell divides
- Makes ribosomes that make proteins
 Nuclear Envelope
- Double membrane barrier surrounding nucleus
- Also called nuclear membrane
- Contains nuclear pores for materials to enter & leave nucleus

III. Cytoplasm
- It is a semifluid, gelatinous, nutrient matrix.
- Where most of the cell’s metabolic reactions occur.
 Cytosol -the semifluid portion of the cytoplasm, excluding the granules & organelles

IV. Endoplasmic Reticulum (ER)

- It is a highly convoluted system of membranes that are interconnected and arranged to form a
transport network of tubules and flattened sacs within the cytoplasm.
 Rough endoplasmic reticulum (RER) – granular appearance when observed by
transmission electron microscopy. This rough appearance is caused by the many
ribosomes attached to the outer surface of the membranes.
 Smooth endoplasmic reticulum (SER) - ER to which ribosomes are not attached.

V. Ribosomes
- Eukaryotic ribosomes are 18 to 22 nm in diameter.
 - Consist mainly of rRNA and protein and play an important part in the synthesis (manufacture) of
proteins.
 Polyribosomes or polysomes - Clusters of ribosomes held together by a molecule of messenger RNA
(mRNA),
 2 Subunits of eukaryotic ribosome produced by the nucleolus:
1. 60S subunit – large subunit.
2. 2. 40S subunit – small subunit.
The subunits are then transported to the cytoplasm where they remain separated until they are join together with
an mRNA molecule to initiate protein synthesis.
When united, the 40S and 60S subunits form an 80S ribosome.
Note: “S” refers to Svedberg units.
40S, 60S, 80S are sedimentation coefficients.

 Sedimentation coefficient expresses the rate at which a molecule moves in a centrifugal field.
 Most of the proteins released from the ER are not mature. They must undergo further processing in an
organelle known as Golgi complex before they are able to perform their functions within or outside of
the cell.

VI. Golgi Complex or Golgi Body or Golgi apparatus

- Connects or communicates with the ER. “Packaging Plants.”
- Stack of flattened, membranous sacs completes the transformation of newly synthesized proteins
into mature, functional ones and packages them into small, membrane-enclosed vesicles for
storage within the cell or export outside the cell (exocytosis or secretion).

VII. Lysosomes
- Are small (about 1-μm diameter) vesicles that originate at the Golgi complex. They’re found in
all eukaryotic cells.
- They contain lysozyme and other digestive enzymes that break down foreign material taken into
the cell by phagocytosis.
- Also aid in breaking down worn out parts of the cell and may destroy the entire cell by a process
called autolysis if cell is deteriorating.
 Peroxisomes are membrane-bound vesicles in which hydrogen peroxide is both generated and broken
down.
- Contain the enzyme catalase, which catalyzes (speeds up) the breakdown of hydrogen peroxide
into water and oxygen.
- Found in most eukaryotic cells, but are especially prominent in mammalian liver cells.

VIII. Mitochondria (mitochondrion)

- “Power Plant”, “energy factory”, “powerhouses” of the eukaryotic cell. (0.5-1 µm dm & 7 µm in
length)
- Where the high-energy phosphate molecules the energy necessary for cellular function is formed
via cellular respiration.
 Adenosine triphosphate (ATP) - major energy-carrying or energy-storing molecules within cells.
- Energy is released from glucose molecules and other nutrients to drive other cellular functions.

IX. Plastids
- Are membrane-bound structures containing various photosynthetic pigments; sites of
photosynthesis in plant cells.
 Chloroplasts - one type of plastid, contain a green, photosynthetic pigment called chlorophyll. Found
in plant cells & algae.
 Photosynthesis
- It is the process by which light energy is used to convert carbon dioxide & water into
carbohydrates and oxygen.
- It is the conversion of light energy into chemical energy.
 X. Cytoskeleton
- System of fibers found throughout the cytoplasm.
- Network of fiber extending throughout the cytoplasm.
 3 TYPES OF CYTOSKELETAL FIBERS:
 Microtubules –slender, hollow tubules called tubulin (proteins)
 Microfilaments
 Intermediate filaments
- These cytoskeletal fibers serve to strengthen, support, and stiffen the cell, and give the cell its
shape.

XI. Cell Wall

- External structures that provide rigidity, shape, and protection.
 Cellulose – a polysaccharide found in the cell wall of algae and all plant cells.
 Chitin – a polysaccharide found in the cell wall of fungi and not in other microorganisms.

XII. Flagella (flagellum)

- Long thin structure in some eukaryotic cells (spermatozoa, algae, protozoa).
- They are motile; swim through liquid environment
- “Whip-like” motion. Organelles of locomotion
 Flagellates – are flagellated protozoa.

XIII. Cilia (Cilium)

- Organelles of locomotion.
- Tend to be shorter; “hair-like”, thinner & more numerous than flagella.
- Found in some protozoa (Ciliates) & other cells in our bodies (respiratory tract & GIT).
- Tend to beat w/ coordinated, rhythmic movement

Prokaryotes
- Cells that lack a nucleus or membrane-bound organelles
- Includes bacteria
- Simplest type of cell
- Single, circular chromosome
- Nucleoid region (center) contains the DNA
- Surrounded by cell membrane & cell wall (peptidoglycan)
- Contain ribosomes (no membrane) in their cytoplasm to make proteins

PROKARYOTIC CELL STRUCTURE

 10 times smaller than eukaryotic cells. (bacteria & archaea)
 Very simple cells when compared with eukaryotic cells
 They do not contain any membrane-bound organelles or vesicles.
 Binary Fission - Reproduction of prokaryotic cells.
 3 bacterial cell envelope:
1. Cell membrane
2. Cell wall
3. Capsule or slime layer
 Flagella, Pili or both may be observed outside the cell envelope.

i. Cell Membrane
- Similar in structure and function to the eukaryotic cell membrane. Consists of proteins and
phospholipid.
- It is flexible and so thin that it cannot be seen with a compound light microscope.
 • Mesosomes - inward foldings of the cell membranes where cellular respiration takes place in bacteria.
Similar to mitochondria.
• Photosynthetic bacteria & Cyanobacteria - Convert light energy into chemical energy. Cell
membrane contain chlorophyll

ii. Chromosome
- Prokaryotic chromosome usually consists of a single, long, supercoiled, circular DNA molecule,
which serves as the control of the bacterial cell. (only one chromosome each bacteria)
- Contains neither nucleoplasm nor a nuclear membrane.
- It is suspended or embedded in the cytoplasm.
• Bacterial nucleoid - the DNA-occupied space w/n a bacterial cell
• Plasmid – extra chromosomal DNA. Present in the cytoplasm.
- Small, circular molecules of double-stranded DNA that are not part of the chromosome.
- May contain from fewer than 10 genes to several hundred genes.
 Bacterial cell may not contain any plasmids, or it may contain 1 plasmid, multiple copies of the same
plasmid or more than 1 type.
 A typical bacterial genome

iii. Cytoplasm
- Semiliquid part of the cell that contains water, enzymes, dissolved O2,waste products, essential
nutrients, proteins, carbohydrates, & lipids. These complex mixture is needed for cell’s
metabolic functions.

iv. Cytoplasmic Particles

- Prokaryotic ribosomes are smaller than eukaryotic ribosomes, but their function is the same—
they are the sites of protein synthesis.
- A 70S prokaryotic ribosome is composed of a 30S subunit and a 50S subunit.
- Granules may consist of starch, lipids, sulfur, iron, or other stored substances.

v. Bacterial Cell Wall

- The rigid exterior cell wall that defines the shape of bacterial cells; providing rigidity, strength,
and protection.
• Peptidoglycan (Murein) -a complex macromolecular polymer that constitutes most bacterial cell wall.
Can only be found in bacteria.
 Mycoplasma genus bacteria do not have cell walls.
 Archaea have cell wall but do not contain peptidoglycan.
 L-Form or cell wall–deficient (CWD) bacteria -bacteria that lose their ability to produce cell walls.
Over 50 species are CWD.

 Structure of peptidoglycan
- Polysaccharide chains consisting of two alternating amino sugars are attached to a short peptide
chain.
- Some of the peptide chains of one polysaccharide chain are cross-linked to peptide chains of
another polysaccharide chain.

 Differences between Gram-negative and Gram-positive cell walls

o Gram-positive bacteria -Their cell walls have a thick layer of peptidoglycan combined w/ teichoic
acid & lipoteichoic acid molecules.
o Gram-negative bacteria –have a much thinner layer of peptitidoglycan, but this layer is covered
with a complex layer of lipid macromolecules, usually referred to as the outer membrane.

vi. Glycocalyx (Slime Layers and Capsules)

- It is a slimy, gelatinous material produced by the cell membrane and secreted outside of the cell
wall.
  2 TYPES OF GLYCOCALYX.
a. Slime Layer
- Not highly organized and is not firmly attached to the cell wall. It easily detaches from the
cell wall and drifts away.
- Enable certain bacteria to glide or slide along solid surfaces, and seem to protect bacteria
from antibiotics and desiccation.
- Psudomonas species.
b. Capsule
- It is highly organized and firmly attached to the cell wall.
- Usually consist of polysaccharides, which may be combined with lipids and proteins. Serves
as antiphagocytic function.
- They are able to survive longer in the human body than nonencapsulated bacteria.
 They’re detected using capsule staining procedure (The bacterial cell and background become stained,
but the capsule remains unstained)
 Encapsulated bacteria: H. influenzae, Klebsiella pneumoniae, Neisseria meningitidis, and Streptococcus
pneumoniae.
• S-colonies –colonies produced by encapsulated bacteria on nutrient agar that are smooth, mucoid, and
glistening
• R-colonies –colonies produced by nonencapsulated bacteria, they grow as dry, rough colonies.

vii. Flagella (Flagellum)

- Thread-like, protein appendages that enable bacteria to move.
a. Peritrichous bacteria - Bacteria possessing flagella over their entire surface.
b. Lophotrichous bacteria - Bacteria with a tuft of flagella at one end.
c. Amphitrichous bacteria - Those having one or more flagella at each end.
d. Monotrichous bacteria - Bacteria possessing a single polar flagellum.
 Flagella stain
- The number of flagella that a cell possesses and their locations on the cell.
- The stain adheres to the flagella, making them thick enough to be seen under the microscope.
 Flagellin
- It is a thread of protein in bacterial flagella that is twisted like a rope.
- Bacterial flagella do not contain microtubule.
 Axial filaments
- Flagella-like fibril attached to each end of spirochetes (spiral-shape).
- Spirochetes can move in a spiral, helical, or inchworm manner.

viii. Pili (Pilus) or Fimbriae (fimbria)

- Are hair-like structures, most often observed on Gram-negative bacteria.
- Pili are much thinner than flagella, have a rigid structure, and are not associated with motility.
 2 TYPES OF PILI:
a. Sex pilus - facilitates transfer of genetic material from one bacterial cell to another following
attachment of the cells to each other.
b. Enables bacteria to adhere or attach to surfaces like body tissues.
 Piliated strains are able to cause diseases, whereas nonpiliated strains of the same organisms are unable
to cause these diseases.
 Pilin – a polymerized protein molecules that is present in both pili and fimbrae.
 Salmonella cells, showing peritrichous flagella.
 Proteus vulgaris cell, possessing numerous short, straight pili and several longer, curved flagella; the cell
is undergoing binary fission.
 Conjugation - a process of transferring of plasmid (genetic material) from donor cell (bacteria w/ sex
pilus) to the recipient cell.

ix. Spores (Endospores)

- Thick-walled formed by the bacteria when their moisture or nutrient supply is low.
 - Spores are resistant to heat, cold, drying, and most chemicals.
- Spores have been shown to survive for many years in soil or dust, and some are quite resistant to
disinfectants and boiling.
- When the dried spore lands on a moist, nutrient-rich surface, it germinates, and a new vegetative
bacterial cell emerges.
- Only one spore is produced in a bacterial cell and it germinates into only one vegetative
bacterium.
 Sporulation
- It is the process of bacteria forming their endospores.
- A copy of the chromosome and some of the surrounding cytoplasm becomes enclosed in several
thick protein coats.
• Spore stain –process of staining the spores to determine whether they are terminal or subterminal
spores.
a) Terminal spore is produced at the very end of the bacterial cell.
b) Subterminal spore is produced elsewhere in the cell

 John Tyndall
- A British physicist concluded in 1876 & 1877 while performing spontaneous generation that
bacteria exist in two forms.
- A form that is readily killed by simple boiling (i.e., a heat-labile form), and a form that is not
killed by simple boiling (i.e., a heat-stable form).
 Tyndalization – a fractional sterilization technique; involves boiling, followed by incubating, and then
reboiling; these steps are repeated several times

 Ferdinand Cohn
- A German botanist described the microscopic appearance of the two forms of the “hay bacillus”.
Bacillus subtilis.
- He referred to small refractile bodies within the bacterial cells as “spores”.
- He concluded that when they were in the spore phase the bacteria were heat resistant.
• Terminal and subterminal spores. Gram-stained Clostridium tetani bacteria, revealing terminal
spores (arrows). C. tetani causes the disease known as tetanus.
• Gram-stained Clostridium difficile bacteria, revealing subterminal spores. It causes LBM

REPRODUCTION OF ORGANISMS AND THEIR CELLS

• Reproduction -referring to the manner in which organisms reproduce.
• Cell reproduction -referring to the process by which individual cells reproduce.
PROKARYOTIC CELL REPRODUCTION:
- More simple than eukaryotic cell division.
• Binary fission
- A process by which a Prokaryotic cells reproduce.
- One cell (the parent cell) splits in half to become two daughter cells.
• DNA replication –must take place before a prokaryotic cell can divide in half; chromosome must be
duplicated so that each daughter cell will possess the same genetic information as the parent cell.
• Generation time – the time it takes for one prokaryotic cell to become two cells or for binary fission to
occur.
Factors that affect the generation time:
 Bacterial species, pH, temperature, availability of nutrients.
 E. Coli has a generation time of about 20 minutes—the number of cells will double every 20 minutes.
 Generation time range from as short as 10 min. to as long as 24 hr.

• A scanning electron micrograph showing Enterococcus bacteria, many of which are in the process of
binary fission.
 • Binary fission. Note that DNA replication must occur prior to the actual splitting (fission) of the parent
cell.

TAXONOMY
- The science of classification of living organisms.
- Consists of three separate but interrelated areas: classification, nomenclature, and identification.
A. Classification
- It is the arrangement of organisms into taxonomic groups (taxa {taxon}) on the basis of similarities
or relationships.
- Taxa include kingdoms or domains, divisions or phyla, classes, orders, families, genera, & species.
- Organisms having similar characteristics are placed into the same taxon.
B. Nomenclature is the assignment of names to the various taxa according to international rules.
C. Identification
- It is the process of determining whether an isolate belongs to one of the established, named taxa
or represents a previously unidentified species.
- They gather “clues” (characteristics, attributes, properties, and traits) about the organism until
they have sufficient clues to identify (speciate) the organism.
• Organism’s phenotype –is an organism’s complete collection of physical characteristics.
• Use this mnemonics to remember the sequence of Taxa:
“King Philip Came Over For Good Spaghetti” (KDCOFGS)
[Kingdom, Division/Phylum, Class, Order, Family, Genus, Species]

MICROBIAL CLASSIFICATION:
 Carolus Linnaeus –A Swedish scientist developed the science of taxonomy based on the binomial
system of nomenclature.
- In the binomial system, each organism is given two names.
- The 1st name is the GENUS [genera], & the 2nd name is SPECIFIC EPITHET. All together they are
referred as the SPECIES.
- “Escherichia” is the genus, & the 2nd name “coli” is the specific epithet. When used together, the 1st &
2nd names “Escherichia coli” are referred to as a species
- To express the genus, capitalize the first letter of the word & underline or italicize the word.
(Escherichia)
- To express the species, capitalize the first letter of the genus name (the specific epithet is not capitalized)
& then underline or italicize the word. (Escherichia coli)
- Frequently, the genus is designated by a single-letter abbreviation. (E. coli)
• In an essay or article about Escherichia coli, Escherichia would be spelled out the first time the organism
is mentioned; thereafter, the abbreviated form, E. coli, could be used.

The abbreviation “sp.” is used to designate a single species, whereas the abbreviation “spp.” is used to
designate more than one species.
- Staphylococci (for Staphylococcus spp.), streptococci (for Streptococcus spp.), clostridia (for
Clostridium
spp.), pseudomonads (for Pseudomonas spp.), etc.
• Nicknames:
-gonococci (for Neisseria gonorrhoeae)
-meningococci (for N. meningitidis),
-pneumococci (for S. pneumoniae),
-staph (for Staphylococcus or staphylococcal),
-strep (for Streptococcus or streptococcal).
• H. Influenzae doesn’t cause influenza, it is caused by influenza virus
• What’s in a Name?
- Alexandre Emile Jean Yersin - Yersinia pestis
-Jules Bordet - Bordetella
-Theodore Escherich - Escherichia
-Albert Ludwig Neisse – Neisseria
Daniel Elmer Salmon – Salmonella

5 Kingdom System Classification (Robert H. Whittaker, 1969):

1. Prokaryotae (Bacteria and archaea)
2. Protista (Algae and protozoa)
3. Fungi
4. Plantae (Plants)
5. Animalia (Animals)
* Viruses are not included in the Five-Kingdom System of Classification because they are not living cells;
they are acellular

 Carl R. Woese - a molecular biologist devised a Three-Domain System of Classification based on

differences in the structure of certain rRNA molecules among organisms.
1. Archaea – “Ancient” bacteria
2. Eubacteria – “True” bacteria or simply bacteria.
3. Eukarya – (Protista [algae & protozioa], Fungi, Plantae , Animalia)
Evolution and the Tree of Life:
- Prokaryotes inhabited Earth from approx. 3 – 4 billion years ago.
- Eukaryotes emerged between 1.6 & 2.7 billion years ago.

 Charles Darwin – (1809-1882) British naturalist wrote that all species of life have descended over
time from common ancestors

Determining Relatedness among Organisms:

• rRNA sequencing - technique used for gauging diversity or relatedness.
subunits of Ribosomes:
1. Small subunit rRNA or SSUrRNA- contains only one RNA molecule.
a. 16S rRNA molecule
- The SSUrRNA in prokaryotic ribosomes.
- Gene that codes for the 16S rRNA molecule contains about 1,500 DNA nucleotides or 16s
rDNA sequence.
- To determine “relatedness,” researchers compare the sequence of nucleotide base pairs in
the gene, rather than comparing the actual SSUrRNA molecules.
- If the 16S rDNA sequence of one prokaryotic organism is quite similar to the 16S rDNA
sequence of another prokaryotic organism, then the organisms are closely related.
b. 18S rRNA molecule
- The SSUrRNA in eukaryotes ribosomes
- Gene that codes for the 18S rRNA molecule contains about 2,000 nucleotides.
- The 18S rDNA sequence of a human is much more similar to the 18S rDNA sequence of a
chimpanzee than to the 18S rDNA sequence of a fungus.
2. Large subunit rNA or LSUrRNA