1microbiology PRELIM-merged PDF

Pharmaceutical Microbiology and Parasitology
KEY TERMS:
Microbiology
o the study of microscopic organisms, such as bacteria, viruses, archaea, fungi and protozoa.
o Foundation of modern technology
o Study of microorganisms.
o Micros + bio + logos = Microbiology
(small) (life) (study of) = the study of organisms that are usually too small to
be seen by the unaided eye.
Microorganism
o a microscopic organism, especially a bacterium, virus, or fungus.
o are very small living organism which cannot be seen by naked eyes.
o they are ubiquitous.
o they are also known as “microbes” or “germs”.
Microbiome - the entire collection of genes found in all of the microbes associated with a particular host.
Microbiota - refers to all of the microorganisms that live in a particular environment.
The microbiome of the human body - especially in the intestinal tract - aid in the digestion of many
foods, the regulation of multiple host metabolic pathways, and the regulation the body's immune
defenses.
Why is it important to study microorganisms?

o Abundance
o Positive impact on humans:
- Biodegration (toxic wastes)
- Food Production
- Food Source
- Element Recycling
- Production of Industrial and Medical Products
Genetically engineered Microorganisms
o Negative impact on humans:

- Disease
- Food Spoilage
- Biodegration
Branches of Microbiology
Science Area of Study
Bacteriology Bacteria
Mycology Fungi
Parasitology Protozoa
Phycology Simple algae
Virology Viruses
Microbial morphology Detailed structure
Microbial physiology Antibiotics & toxins, chemical & physical agents on microbial growth
Microbial genetics Genetic Information
Microbial ecology Microorganisms & their habitat
Microbial Taxonomy Classifications: Naming and Identification of microorganism
Immunology Immunity
Medical microbiology Disease of humans and animals
Public health microbiology Control of the spread of communicable disease
Industrial microbiology Microorganisms used to make industrial products
Food and dairy microbiology Microbial spoilage of food & transmission of food-borne disease
Agricultural microbiology Impact of microorganism on agriculture
Molecular biology How genetic information of microorganisms regulate the development & function of
cells & organisms
Classification of Microorganisms
o Bacteria - cell walls contain a protein–carbohydrate complex called peptidoglycan.
o Archaea - cell walls, if present, lack peptidoglycan.
o Eukarya - which includes the following:
- Protists (slime molds, protozoa, and algae)
- Fungi (unicellular yeasts, multicellular molds, and mushrooms)
- Plants (mosses, ferns, conifers, and flowering plants)
- Animals (sponges, worms, insects, and vertebrates)
Kinds of Microbes
o Bacteria - are typically unicellular, microscopic, prokaryotic organisms that reproduce by binary
fission.
o Fungi - (yeasts and molds) are typically unicellular, microscopic, eukaryotic fungi that reproduce
asexually by budding.
- Molds are typically filamentous, eukaryotic fungi that reproduce by producing asexual
reproductive spores.
o Viruses - are typically submicroscopic, acellular infectious particles that can only replicate inside a
living host cell. Most viruses possess either DNA or RNA, but not both.
o Protozoa - are typically unicellular, microscopic, eukaryotic organisms that lack a cell wall
o Algae - are typically eukaryotic microorganisms that carry out photosynthesis.
Nature of Microorganisms
o 4.5 billion years ago, Earth was formed.
o 3.5 billion years ago in Northwestern Australia found in ancient rock formation fossils of primitive
microorganism wherein prokaryotes dominated and considered first life existed, Archaean’s and
Cyanobacteria.
o 1.5 billion years ago nucleated cells arise.
o 0.5 billion years ago multicellular arise.
o 900 and 650 million years ago animal made their first appearance on earth.
o Past 100,000 years ago humans have existed.
Pioneers in Microbiology
o Robert Hooke (1635 –1703)
- Father of Cell Theory.
- Discovered & described as “little boxes” on a thin slice of cork.
- Introduced agar, inoculating loop to transfer bacteria and prepare pure cultures.
- Came to be known as cells, the world’s smallest structural unit.
Cell Theory
- All living organisms are composed of cells (unicellular or multicellular).
- Cell as a basic unit of life.
- Cells arise from pre-existing cells.
o Anton von Leeuwenhoek (1632-1723)

- Father of Microbiology, Bacteriology, Protozoology.
- First to observe tiny living creature using the single lens microscope.
- “Spontaneous Generation” Abiogenesis – life can arise from non-living material.
o Louis Pasteur (1822-1895)

- French chemist discovered alcohol fermentation (yeast convert glucose in grapes to ethyl
alcohol by fermentation).
- Acetobacter convert glucose to acetic acid by fermentation
- Introduced the terms “aerobes” and “anaerobes”
- Developed Pasteurization (can kill pathogens in many types of liquids)
- Heating liquids to 63-65°C for 30 mins or 73-75°C for 15 seconds

- Discovered the infectious agent causing silkworm disease
- Developed vaccine to prevent chicken pox, cholera, anthrax, and swine erysipelas and most
especially Rabies vaccine to treat human rabies.
Louis Pasteur on Spontaneous Generation
Spontaneous Generation
- Ability of microorganisms to arise spontaneously from non-living matter.
- Belief until 2nd half of 19th proven inaccurate in 1861.
- He demonstrated the presence of microorganisms in air and their ability to contaminate sterile
solutions.
- Proved that “spontaneous” is a result of the presence of microorganisms in the air or the fluids
themselves.
o Robert Koch (1843-1910)

- Discovered the Bacillus anthracis - produces spores.
- Developed methods of fixing, staining, and photographing bacteria.
- Developed methods of cultivating bacteria in solid media.
- Germ Theory of Disease.
- Developed the germ theory of disease while studying the cattle disease anthrax.
- Established that Bacillus anthracis was the causative agent “germ” of anthrax in 1876.
- Proved that bacteria caused disease.
Koch’s Postulate
- The bacteria must be present in every case of the disease.
- The bacteria must be isolated from the host with the disease and grown in pure culture.
- The specific disease must be reproduced when a pure culture of the bacteria is inoculated into a
healthy susceptible host.
- The bacteria must be recoverable from the experimentally infected host.
o Ignaz Semmelweis
- Advocated handwashing to prevent transmission of childbirth fever.
o Joseph Lister
- Father of Antiseptic Surgery.
- Introduced Aseptic technique.
- Use of phenol (carbolic acid) as disinfectant.
o Edward Jenner
- Father of Immunology.
- Developed the first vaccine in 1798 for smallpox.
o Paul Ehrlich (1854 –1915)

- Made the first synthetic chemotherapeutic drug arsphenamine (Salvarsan), the first
effective medicinal treatment for syphilis.
- Coined the term “chemotherapy”.
o Sir Alexander Fleming (1881–1955)

- Accidentally discovered that mold (Penicillium) inhibited the growth of bacterial cultures in
his lab in 1928.
- Usefulness of penicillin was not apparent until the 1940’s.
- Clinically tested and as a result of the test, it was mass produced.
- World War II spurred on the production of penicillin as it was initially used for the war
effort.
Golden Age of Microbiology

- Rapid advances in the science of microbiology.
- Fermentation and pasteurization.
- Germ theory of disease.
I. Fermentation and Pasteurization
o Fermentation and Pasteurization - solidified the connection between microorganisms and disease.
o Pasteurization - Use of heat to kill bacteria to diminish spoilage.
o Fermentation - Discovery that yeast ferments sugar to alcohol in the absence of air.
- Souring and spoiling caused by bacteria in the presence of air.
- Sugar to beer: good
- Beer to vinegar: bad
II. Vaccination
Edward Jenner - developed the first vaccine in 1798 for smallpox.

In 1880, Pasteur discovered the use of a virulent bacteria for a vaccine against fowl
cholera and coined the term “vaccine”.
III. Birth of Modern Chemotherapy

o Chemotherapy
- Chemical treatment of a disease, including antibiotics and chemicals used to treat
cancer.
- Both synthetic drugs and antibiotics inhibit the growth or kill other microorganisms.
- First use of a chemotherapeutic agent in 1910.
- Used an arsenic containing compound to treat syphilis.
- Repeated his experiments with minor changes 605 times before he found a
concentration that worked.
o Chemotherapeutic Agents:
- Synthetic drugs - chemically prepared in the lab.
- Antibiotics - substances produced naturally by bacteria and fungus.
Modern Microbiology
New and different directions that the study of microbiology is going towards:
i. Drug resistance
ii. New branches of microbiology
iii. Develop new vaccines
iv. Recombinant DNA technology
o Drug Resistance
- Result of genetic changes in microbes.
- Production of microbial enzymes that inactivate antibiotics.
- Surface changes in microbes disallowing antibiotics from attaching to it.
- Preventing antibiotics from entering the microbe.
o New Vaccines
- As new diseases emerge, microbiologists strive to find cures.
- New vaccines appear to be the best hope as microorganisms continue to develop drug
resistance.
DISEASES CAUSED BY BACTERIA

Diphtheria Gonorrhea
Meningitis Tetanus
Pneumonia Leptospirosis
Tuberculosis Plague
Dental caries Acne
Cholera Leprosy
Staphylococcal food poisoning Gangrene
Typhoid fever Anthrax
DISEASES CAUSED BY FUNGI

Aflatoxin poisoning Dandruff
Ergot poisoning Meningitis
Ringworm of the feet (athlete’s Candidiasis
foot)
DISEASES CAUSED BY PROTOZOANS

Malaria African sleeping sickness
Amoebiasis Chagas’ disease
Giardiasis
DISEASES CAUSED BY HELMINTHS

Schistosomiasis Tapeworm infestations
Ascariasis Pinworms
Trichinosis Hookworms
DISEASES CAUSED BY VIRUSES

AIDS (Acquired Encephalitis
Immunodeficiency Syndrome)
Warts Yellow fever
Smallpox Dengue
Chickenpox Influenza
Measles Mumps
Poliomyelitis Hepatitis
Rabies
SOME OF THE MICROORGANISMS THAT CHANGED THE WORLD

Cyanobacteria – The Emergence of Multicellular Organism Yersinia pestis – Bubonic Plague
Phytophthora infestans and the Irish Potato Famine Smallpox
1918 Influenza Pandemic Treponema pallidum – Syphilis
Bacterial Pneumonia During the 1918 Flu Pandemic Novel Corona Virus – COVID-19
Penicillium and the Discovery of Penicillin
Summary:
- Bacteria, fungi, viruses, protozoa, and algae are the major groups of microorganisms.
- Most microorganisms are not harmful but rather beneficial.
VIDEO (LECTURE)
Microbes - microorganism living or non-living, especially a bacterium causing disease or fermentation
Microscope – optical instrument used to observe small objects
Pathogen – disease causing microorganism
Non-Pathogen – vast majority of known microorganism which don’t cause disease
WHY STUDY MICROBIOLOGY?
1. Indigenous Microflora
• indigenous microbiota
• Microorganisms living in our body
• Inhibit the growth of pathogen
o Food supply
o Waste (secrete toxins and antibiotics which prevent pathogens)
2. Opportunistic Pathogen
• Organisms that colonize (inhabit) our body
• Escherichia coli (E. coli) – infect
o Intestinal tract won’t harm but can harm in urinary bladder
Oxygen
- trees – 28% of global oxygen
- Oceans – 70% - produced by phytoplankton*
- Absorbs 10B tons of Carbon dioxide per year
- *tiny plants/algae; population decreased by 40% since 1950 due to global warming
3. Microbial Ecology
• Study of the relationship between microbes and the environment
4. Phytoplankton
• Marine plants and algae
• Contributes 50-85% of oxygen in Earth
5. Zooplankton
• Marine Animals
6. Decomposers/ Saprophytes
• Microorganisms involved in decomposition of dead organisms and waste products of
living organisms
7. Bioremediation
• the use of either naturally occurring or deliberately introduced microorganisms or other
forms of life to consume and break down environmental pollutants, in order to clean up a
polluted site
• Microorganisms which consume or break down environment pollutants
PRODUCTS REQUIRING MICROBIAL PARTICIPATION IN MANUFACTURING PROCESS

I. Food – bread, butter, chocolate, coffee, fish sauce, meat products, pickles, soy sauce, cheese
II. Alcoholic beverages – beer, brandy, sake (rice wine), rum, sherry, vodka, whiskey, wine
III. Chemicals – Acetic acid, butanol, acetone, ethanol, formic acid, glycerol, lactic acid
IV. Antibiotics – Amphotericin B, bacitracin, Cephalosporins
Antibiotics – substance produced by microorganisms that is effective in killing or inhibiting growth of

microorganisms
Microorganisms can cause diseases caused by pathogens:
• Infectious disease – a pathogen colonizes a body
• Microbial intoxication – a pathogen produces a toxin in vitro; a person ingests toxin
MICROSCOPY
• The technical field of using microscopes to view objects and areas that cannot be seen with the
naked eye
History of Microscope
I. Simple microscope
• Simple magnifiers
• Uses a lens to enlarge an object through angular magnification alone, giving the viewer an erect
enlarged virtual image
• The use of single convex lens or groups of lenses is found in a simple magnification devices such
as the magnifying glass, loupes, and eyepieces for telescopes and microscopes
• It is actually a convex lens of a small focal length, which is used for seeing the magnified images
of small objects
II. 1665 (17th Century)
• Robert Hooke first observed microorganisms in a “cork” using compound microscope
• Published the book Micrographia documenting his observations
III. 1674
• Anton Van Leehuenhoek used his knowledge to achieve a microscope with greater
magnification. He was also the first to make observations of bacteria on water
IV. 19th Century
• Bausch and Lomb used brass to produce a more complex type of microscope
o 1900 - They produced 30,000 microscopes
o 1906 - Doubled the sales
Microorganisms – tiny organisms

MICROSCOPES
Simple Microscopes
• Microscope containing only one magnifying lens
• 3-20x larger than the actual object size
Compound Microscope
• Microscope that contains more than one magnifying lens
• 1000x magnification
• Photomicrographs- photographs taken from compound light microscope
• Compound microscopes are also referred to as compound light microscopes
Electron Microscope
• Use an electron beam source of illumination and magnet to focus the beam
• Wavelength of electrons is 100x shorter then wavelength of the visible light
• Greater resolving power than compound microscope
CHARACTERISTICS OF VARIOUS TYPES OF MICROSCOPES

• Brightfield
o 0.2000 µm resolving power
o x1,000 useful magnification
o Used to observe morphology of microorganisms such as bacteria, protozoa, fungi, and
algae in living (unstained) and non-living (stained) state
o Objects are observed against a bright background
o Cannot observe microbes less than 0.2 µm in diameter or thickness, such as spirochetes
and viruses
• Darkfield
o 0.2000 µm resovling power
o x1,000 useful magnification
o Unstained organisms are observed against a dark background
o Useful for examining thin spirochetes
o Slightly more difficult to operate than birghtfield
• Phase-Contrast
o 0.2000 µm
o x1,000
o Can be used to observe unstained living microorganisms
• Fluorescence
o 0.2000 µm
o x1,000
o Fluorescent dye attached to organism
o Primarily an immunodiagnostic technique (immunofluorescence)
o Used to detect microbes in cells, tissues, and clinical specimens
• TEM (Transmission Electron Microscope)
o 0.0002 mm (0.2 nm)
o x200,000
o Specimen is viewed on a screen
o Excellent resolution
o Allows examination of cellular and viral ultrastructure
• SEM (Scanning Electron Microscope)
o 0.0200 mm (20 nm)
o x10,000
o Specimen is viewed on a screen
o Gives the illusion of depth (three dimensions0
o Useful for examining surface features of cells and viruses
o Specimen is nonliving
o Resolution is less than that of TEM
PARTS OF MICROSCOPE
Components of Compound Light Microscope
• Eye Piece (Ocular) – x10 magnifying lens
• Body Tube – Connects the eyepiece to the objective lenses
• Arm – The arm connects the body tube to the base of the microscope
• Revolving Nose Piece – Holds the objective piece
• Objectives ( high power, low power lenses, oil immersion) – Used to magnify objects placed
on the stage
• Stage – The flat platform where the slide is placed
• Stage Clips – Metal clips that hold the slide in place
• Condenser – Gathers and focuses light from the illuminator onto the specimen being viewed
• Iris Diaphragm – Used to adjust the amount of light passing through the condenser
• Coarse Adjustment Knob – Moves the stage up and down to focus the specimen
• Fine Adjustment Knob – Focuses the lens to have a sharper image
• Mirror – Reflect light from an external light source
• Base – Contains the light source
• Substage Adjustment Knob – condenser
o Flat – Sharper image
o Curve – brighter image
LENSES AND BENDING OF LIGHT

Refractive index
• measures the speed of light in material
• a structure slows down the velocity of light
Focal Point
• Light rays focused in a specific place
Focal Length
• Distance between the centre of the lens and the focal point
• Shorter focal point = greater magnification
• Focal point is inversely proportional to magnification
Parfocal
• Microscope remains in focus when objectives are changed
Total Magnification
• Product of the magnifications of the ocular lens and objective lens
Microscope Resolution (Resolving Power)

• Ability of a lens to separate or distinguish small objects that are close together
• Wavelength of light used is major factor of resolution
• Shorter wavelength = greater resolution
• Wavelength is inversely proportional to the resolution
• Maximum resolving power of light microscope is 0.2 µm
Working Distance
• Distance between the front surface of lens and surface of glass with specimen
MICROTECHNIQUES
A. FIXATION
• Process in which the structure of the specimen is preserved in a stare to withstand
subsequent treatments with various reagents with minimum loss of architecture
• Use 10-20x of fixative compared to the size of the specimen
• Types of Fixation
o Heat Fixation
▪ Uses heat to preserve the specimen morphologically
▪ Direct Flame
▪ Steam Fixation
o Chemical Fixation
▪ Uses chemical reagents to preserve specimen structure
▪ Alcohol
• Purpose of Fixation
o Kills bacteria so that it won’t make people sick
o Fixes the bacteria in the slide
o Increases apparent diameter of cells
✓ Cessation of normal life function in the tissue of the microorganism – killing it
✓ Stabilization of the structure of tissue for preservation
✓ Should be done after removal of tissue to prevent autolysis*
*destruction of cells or tissues by their own enzymes
B. DEHYDRATION
• The removal of water from the tissue sample by using strength of alcohol.
• 50% → 70% → 90% → 100%
C. CLEARING
• Uses an agent to make the tissue sample clearer
• E.g. Xylene, Chloroform, CCl4
D. IMPREGNATION
• Impregnates tissue with paraffin wax t 54-60°C
E. EMBEDDING/ BLCOKING
• Impregnated tissues are placed in a mold to create a tissue block ready for cutting
F. SECTIONING/ CUTTING
• Uses microtome
• 7 micron sections for light microscopy
• 70 million sections for electron microscopy
G. MOUNTING
• The use of adhesive substances to plate the cut tissue section to slide for examination
H. REHYDRATION
• Allows water into the tissue using decreasing concentration of alcohol
I. STAINING
• Process in which the tissue section is given colour for visualization of structures
• Dye (stains) – organic compound carrying chromophoric ions
• Types of Stains:
o Basic or Positively charged dye
o Acidic or Negatively charged dye
• Staining Procedures
o SIMPLE STAINING – only one dye
▪ Positive/direct – cells same color as dye
✓ Methylene blue
✓ Crystal violet
▪ Negative/indirect – cells colorless or luminous
✓ India ink
✓ Nigrosin
o DIFFERENTIAL STAINING – 2 or more dyes and/or reagents
▪ Gram Staining
✓ Gram positive (blue/violet)
✓ Gram Negative (red/pink)
▪ Acid fast Staining – diagnosis of tuberculosis
o STRUCTURAL STAINING – 2 or more dyes and/or reagents
▪ Endospore; Flagella; Capsule; Storage granules
LABORATORY INSTRUMENTS
o Autoclave
- For sterilization of glassware and Culture media.
- Equipped with accurate pressure and temperature gauges.
Autoclave Guidelines (LATER):
- In any routine monitoring of autoclave performance, biological indicators or thermocouples
should be places at the center of each load. Bacillus stearothermophilus
- Sterilizers used for waste treatment shall not be used for sterilization of equipment, food, or other
related items.
- Each bag must be exposed to a minimum of:
– 250 degrees Fahrenheit (121 C)
– 15 lbs/cm2 of pressure
– At least 20 to 30 minutes time
o Incubator & Water bath

- Capable of maintaining temperature to within + 0.5°C of 35 & 37°C and to within 44 &
44.5°C.
o Hot Air Sterilizing Oven
- For sterilization of glass wares.
o pH meter
- Should be standardized with a minimum of 2 standard buffers (pH 4.0, pH 7.0, or pH
10.0 before use.
o Colony Counter
- For enumeration of colonies.
o Thermometers
- For checking calibration of incubator and water baths.
o Laminar Flow Hood/ Sterile Bench/Biosafety Cabinet
- Containment Equipment/Facility
During SAMPLE ANALYSIS (DILUTION); BACTERIAL CULTURE
o Ventilation Devices
- Fume Hood
▪ Protect workers from chemical vapors.
▪ Handle hazardous chemicals in fume hoods whenever possible.
- Laminar Flow Hoods
▪ These hoods are only appropriate for very few purposes and they are often
misused.
▪ Don’t work with any hazardous in a laminar flow hood.
▪ They protect the working surface only, NOT the worker!
- Biological Safety Cabinet
▪ BSCs work to protect workers and material from microbes and the environment.
▪ Avoid working with volatile chemicals in a BSC.
Biosafety Cabinet:
- Level 1. Protect people working from environment.
- Level 2. Protect people working and environment and product.
- Level 3. Protect people, environment, and product also.
o Anaerobic jar
- Used for incubating anaerobic organisms.
o Stomacher
- Used to homogenized samples.
o Vortex Mixer
- Used to mix solutions.
o Blender
- Used to homogenate solid samples.
o Microwave Oven
- Used for melting agar.
o Bunsen burner & Loop Incinerator
- Used to sterilize inoculating loop/needle.
o Dessicator cabinet
- For storing highly hygroscopic media/reagents.
o Ultra Low Freezer
- Used for storing long term bacterial culture.
o Microscope
- For morphological characterization of organisms.
o Magnetic Stirrer
- To mix media/reagents.
o Pipettor
- To dispense exact amount of liquid (media, reagent, buffer or sample).
o Meter stick
- Meter sticks measure length in cm.
- 100 cm = 1 meter
- Don’t bend.
- Not a weapon.
o Triple Beam Balance
- A tool that is used to measure mass (the amount of matter) usually in grams.
- This is a close up of the numbers on the balance.
o Inoculating Loop & Inoculating Needle
- Used to transfer organism.
o Petri Dishes & Test/ Reaction/Durham Tubes
- Used to contain solid/liquid media.
o Culture Media Bottle & Staining Jars
o Test Tube Rack, Spatula, Forceps
Safety Symbol
- Know safety symbols.
- They appear in your laboratory activities.
- They will alert you possible dangers.
- They will remind you to work carefully.
Lab Safety Rules
o Use Your Head
- Exercise Caution and Good Judgment.
- Follow all instructions given by the teacher.
- Notify the teacher immediately regarding any accident or unsafe areas.
- Read lab instructions ahead of time.
- Always follow lab procedures exactly.
- Never do an unauthorized experiment.
o Eye Safety
- Wear safety goggles when working with chemicals, flames, or heating devices.
- or if possibility of flying debris.
- If you wear contact lenses let your teacher know.
- In case of emergency in which a chemical goes into one’s eye, use the eyewash station.
- Flush in water for 15 mins. and notify the teacher.
o Proper Attire
- Keep all long hair tied back.
- Do not wear loose clothing that could catch on fire.
- Footwear that completely covers the foot is required.
o Sharp Objects
- Always cut away from fingers and body.
- Always carry sharp objects with points and tips facing down and away.
- Never try to catch falling sharp instruments.
- Grasp sharp instruments only by the handles.
- Notify teacher if you get cut.
- Broken glass and sharp objects do not go in trash cans.
- Teacher will clean up broken glass.
Safety and Rules of The Lab

o Electrical Safety
- Only electrical plugs are to be placed into an electrical outlet.
- Unplug electrical equipment after use.
- Keep all electrical cords, wires, and appliances away from water.
o Physical Safety
- Handle all equipment carefully.
- Do not place a cord where someone can trip over it.
- Push all stools in out of the way.
- Keep books picked up out of walking isles.
o Heating Safety
- Tie back hair and loose clothes when working with open flames.
- Never look into a container as you are heating it.
- Never point the end of a test tube being heated at yourself or others.
- Never heat in a closed container.
- Never leave a heat source unattended.
- Heated metal and glass look cool, use tongs or gloves before handling.
- Do not place hot glassware directly on lab desk or in cold water.
o Chemical Safety
- Read all labels twice before removing a chemical from the container.
- Only use the type and amount of chemical instructed to use.
- Never touch, taste, or smell a chemical unless instructed by the teacher.
- Never mix chemicals unless instructed to do so.
- Transfer chemicals carefully!
- Keep lids on chemical containers when not in use.
- When diluting an acid, pour the acid into water.
- Consider all chemicals dangerous.
o Treatment of Specimen
- Respect the life of all laboratory specimen.
- They gave their life for your education.
o You Should Never…
- Eat or drink in the lab.
- Use lab glassware to eat or drink out of.
- Engage in…. practical jokes, horse play, and rough house.
o In case of an emergency…
- Know the locations of: fire extinguisher, fire blanket, body shower, eyewash station, first
aid kit.
- If you spill a harmful chemical on yourself or in your eyes, start rinsing immediately and
send your partner to get teacher’ s help.
o Hand Safety
- If a chemical spills on your skin, notify the teacher and rinse with water for 15 minutes.
- Wash hands after every lab.
- Handle glassware, sharp tools and heated containers carefully.
o Remember to…
- Stay at your work station.
- Maintain a clean work area.
- Read and follow all directions.
- Report any spills, accidents, or injury to the teacher immediately.
- Clean and put away all equipment at the end of the lab period.
- Dispose of waste products according to instruction.
The Importance of Hand Washing
Bacteria are easily transferred by a simple handshake! Ash your hands to fight germs.
Cell Structure and Function

Two Basic Types of Cells: Prokaryotic Cell and Eukaryotic Cell
o Prokaryotic Cell
- Simple, single-celled, yet remarkably successful organisms.
- Much simpler than the more evolutionarily advanced eukaryotic cell.
- Single-celled prokaryotes are microbes that include bacteria and their bacteria-like
cousins Archaea.
- Reproduce by binary fission (another copy by dividing).
- No cell nucleus or any other membrane-bound organelles.
- DNA travels openly around the cell.
o Eukaryotic Cell
- Animals, plants, fungi, protists, algae, and water & slime molds are
- Organisms that are composed of one or more nucleated cells.
- Most organisms that we can see, such as trees, grass, worms, flies, mice, humans,
mushrooms and yeast are eukaryotes.
- Can either be single-celled or multi-celled.
- Can reproduce in one of several ways (Ex. meiosis, mitosis).
- Have cell nucleus within containing its DNA.
- Eu =“true”, karyon=“nucleus”
- Membrane bound organelles.
- Evolved from prokaryotic cells.
PROKARYOTE GENETICS
o Nucleoid
- Region of cytoplasm where prokaryote’s genome (DNA) is located.
- Usually a singular, circular chromosome (typical in bacteria and archaea)
o Plasmid
- Small extra piece of chromosome/genetic material.
- 5 - 100 genes.
- Not critical to everyday functions.
- Can provide genetic information to promote:

▪ Antibiotic resistance
▪ Virulence factors (molecules produced by pathogen that specifically influence
host's function to allow the pathogen to thrive/the ability to cause disease)
▪ Promote conjugation (transfer of genetic material between bacteria through cellto-
cell contact) ( a bacterium’s ability to share its plasmids with other bacteria)
o Cytoplasm (both in Prokaryotic and Eukaryotic Cell)

- Also known as proto-plasm.
- Nicknames: The Matrix, Molecular Chowder
- Fills the space between the plasma membrane and the nuclear membrane.
- Gel-like matrix of water, enzymes, nutrients, wastes, and gases and contains cell structures.
- Location of growth, metabolism, and replication.
- Liquid with all of the cellular organelles suspended within.
- Consists of cytosol and cellular organelles except for the cell nucleus.
Cytosol
- is made up of water, salts, organic molecules and many enzymes that catalyze reactions.
- The part of the cytoplasm not taken up by organelles.
Cilia & Flagella
- External appendages from cell membrane.
- Aid in locomotion of the cell or movement of materials near cell.
- Motility > coordinated sliding movements of microtubules.
- Both Prokaryotes & Eukaryotes can have external appendages, but are constructed differently.
- Eukaryotes may have flagella or cilia (components of cytoskeleton covered with plasma
membrane).
- Prokaryotes may have flagella, endoflagella, fimbiae or pili (composed of protenaceous
molecules and not covered with plasma membrane).
Cilia - Microscopic hair-like projections that can move in waves. They help traffic ailed particles in the
air, and expel them when you cough.
o Granules
- Bacteria’s way of storing nutrients.
- Staining of some granules aids in identification.
o Cytoskeleton
- Cellular "scaffolding" or "skeleton" within the cytoplasm.
- Nicknames: Scaffolding, Highways
- Major advance in prokaryotic cell biology in the last decade has been discovery of the
prokaryotic cytoskeleton.
- Up until recently, thought to be a feature only of eukaryotic cells.
- Maintains cell shape and Protects the cell.
- Enables some cell movement (using structures such as flagella and cilia).
- Plays important roles in intra-cellular transport (the movement of vesicles and
organelles).
- Plays important role in cell division.
o Ribosomes
- Found within cytoplasm or attached to plasma membrane.
- Made of protein & rRNA.
- Composed of two subunits.
- Cell may contain thousand.
- Q: What do ribosomes do? Synthesize or make proteins.
- Q: What’s the relationship between the job that the ribosomes do and the genetic
instructions (nucleic acids) of the cell?
- Can be found alone in the cytoplasm, in groups called polyribosomes, or attached to the
endoplasmic reticulum.
o Plasma membrane
- Separates the cell from its environment.
- It is essentially the “bag” that holds all of the intracellular material and regulates the
movement of materials into and out of the cell.
- Phospholipid molecules oriented so that hydrophilic water-loving heads directed
outward and hydrophobic water-hating tails directed inward.
- Proteins embedded in two layers of lipids (lipid bilayer).
- Membrane is semi-permeable. Q: What does that mean? Allows the cell to control its
own biochemistry by only letting certain substances through it.
Plasma Membrane as A Barrier:
o Osmosis
- Is the diffusion of water across a semi-permeable membrane.
- Environment surrounding cells may contain amounts of dissolved substances (solutes)
that are…
▪ equal to
▪ less than
▪ greater than
…those found within the cell.
o Tonicity and Osmosis
- Isotonic: equal concentration of a solute inside and outside of cell.
- hypertonic: a higher concentration of solute.
- hypotonic: a lower concentration of solute.
- Water will always move toward a hypertonic environment!!
Osmotic Pressure (Cells & Water)

o H2O important reactant in many metabolic reactions.
o Most cells die in absence of water.
o Cell walls of bacteria and plants prevent them from exploding in a hypotonic environment, but
most bacteria are vulnerable in hypertonic environments.
o Many bacteria can be plasmolyzed by high concentrations of solutes.
o Your salty perspiration protects you from bacteria that cannot handle the high sodium chloride
concentration.
o The water moves out of the bacterium and it dies of ‘hyper-osmotic shock’ (desiccation).
Active Transport
o How most molecules move across the plasma membrane.
o Analogous to a pump moving water uphill.
o Types of active transport are classified by type of energy used to drive molecules across
membranes.
o ATP Driven Active Transport Energy from adenosine triphosphate (ATP) - drives substances
across the plasma membrane with the aid of carrier molecules.
o Cell Wall
- The rigid structure of the bacterial cell wall is due to securely linked peptidoglycan
molecules that surround the cytoplasmic membrane, giving the prokaryotic bacterial cell
shape and protection.
- Most cell walls contain a combination of the major organic molecules— proteins,
carbohydrates and lipids.
- Prevents prokaryotes from bursting in a hypotonic environment (an aqueous environment
with a lower concentration of solutes than are found within the cell).
- Most bacteria have one of two types of cell walls.
- Going further out, the bacterial world divides into two major classes (plus a couple of
odd types):
- Gram-positive Cell Wall
▪ From the peptidoglycan inwards all bacterial cells are very similar.
▪ Peptidoglycan makes up as much as 90% of the thick cell wall (more than 20 layers
stacked together).
▪ Peptidoglycan: These layers are the outermost cell wall structure of Gram+ cells.
- Gram-negative Cell Wall
▪ The cell walls of Gram- bacteria are more chemically complex, thinner and less
compact, with peptidoglycan comprising only 5 – 20% of the structure.
▪ Covered by an external lipopolysaccharide (LPS) membrane - a harmful substance
classified as an endotoxin.
Gram Stain Protocol

o Christian Gram, a Danish bacteriologist, developed a technique for staining bacteria.
o Involves the application of a series of dyes that leaves some bacteria purple (Gram+) and others
pink (Gram-).
o After the Gram stain procedure, Gram+ cells appear purple. At the end of the Gram staining
procedure, Gram-negative cells retain the secondary stain, safanin, and appear pink.
Peptidoglycan
- is a huge polymer of interlocking chains of alternating monomers.
- Provides rigid support while freely permeable to solutes.
- Archaean cell walls do not have this molecule.
Backbone of peptidoglycan molecule composed of two amino sugar derivatives of
glucose. The “glycan” part of peptidoglycan: N-acetylglucosamine (NAG) and N-
acetlymuramic acid (NAM)
- NAG / NAM strands are connected by interlocking peptide bridges. The “peptid” part of
peptidoglycan.
o Glycocalyx
- Some bacteria have an additional layer outside of the cell wall called the glycocalyx.
- This additional layer can come in one of two forms:
1. Slime Layer
▪ Glycoproteins loosely associated with the cell wall.
▪ Slime layer causes bacteria to adhere to solid surfaces and helps prevent the cell from
drying out.
▪ Streptococcus - The slime layer of Gram+ Streptococcus mutans - allows it to
accumulate on tooth enamel (yuck mouth and one of the causes of cavities). Other
bacteria in the mouth become trapped in the slime and form a biofilm & eventually a
buildup of plaque.
2. Capsule
▪ Polysaccharides firmly attached to the cell wall.
▪ Capsules adhere to solid surfaces and to nutrients in the environment also, helping
encapsulated bacteria hide from the host's immune system.
▪ Adhesive power of capsules is a major factor in the initiation of some bacterial diseases.
▪ Capsule also protect bacteria from being phagocytized by cells of the hosts immune
system.
o Endospores
- Dormant, tough, non-reproductive structure produced by small number of bacteria.
- Resistant to radiation, desiccation, lysozyme, temperature, starvation, and chemical
disinfectants.
- Endospores are commonly found in soil and water, where they may survive for very long
periods of time.
Two endospore producing bacterial genera: genus Bacillus (an obligate aerobe often living in the soil)
and the genera Clostridium (obligate anaerobes often living in the gastrointestinal tract of animals)
produce endospores.
o Surface Appendages
- Some prokaryotes have distinct appendages that allow them to move about or adhere to
solid surfaces.
- Consist of delicate stands of proteins.
- flagella: Long, thin extensions that allow some bacteria to move about freely in aqueous
environments. (singular: flagellum)
- Axial filament (endoflagella): flagella that are wrapped around corkscrew-shaped bacteria,
Wind around bacteria, causing movement in waves.
- Fimbriae: Most Gram-negative bacteria have these short, fine appendages surrounding the
cell. Gram+ bacteria don’t have. No role in motility. Help bacteria adhere to solid surfaces
and to cells they can infect. Major factor in virulence. (singular: fimbria)
- Pili: Tubes that are longer than fimbriae, usually shorter than flagella. Use for movement,
like grappling hooks, and also use conjugation pili to transfer plasmids. (singular = pilus)
Neisseria and its Fimbriae
o Gram- diplococci, resemble coffee beans when viewed microscopically.
o Neisseria gonorrhoeae causes sexually transmitted disease gonorrhoeae.
o Antibiotics applied to the eyes of neonates as a preventive measure against gonorrhoea.
o One of the most communicable disease in the U.S.
o 125 cases per 100,000. Teens 15-19 yo 634 cases per 100,000. Young adults 20-25 460 per
100,000.
o N. meningitidis most common causes of bacterial meningitis in young adults.
o Q: What makes Neisseria so tough?
- Lipopolysaccharide (LPS) of the cell wall of Neisseria acts as an endotoxin.
- Polysaccharide capsule prevents host phagocytosis and aids in evasion of the host immune
response.
- Use fimbriae to attach onto host cells; avirulent without.
- Fimbriae have adhesion proteins (adhesins) on their tips that match, lock and key, with
proteins on host epithelial cell surface.
Prokaryotes – Cell Shapes
1. bacillus (pl. bacilli) = rod-shaped
2. coccus (pl. cocci … sounds like cox-eye) = spherical
3. spiral shaped
▪ spirillum (pl. spirilla) = spiral with rigid cell wall, flagella.
▪ spirochete (pl. spirochetes) = spiral with flexible cell wall, axial filament.
There are many more shapes beyond these basic ones. A few examples:
– Coccobacilli = elongated coccal form.
– Filamentous = bacilli that occur in long threads.
– Vibrios = short, slightly curved rods.
– Fusiform = bacilli with tapered ends.
Prokaryotes – Arrangements of Cells
o bacilli divide along a single axis, seen in pairs or chains.
o cocci divide on one or more planes, producing cells in:
- pairs (diplococci)
- chains (streptococci)
- packets (sarcinae)
- lusters (staphylococci).
o Size, shape and arrangement of cells often first clues in identification of a bacterium.
o Many “look-alikes”, so shape and arrangement not enough for id of genus and species.
EUKARYOTIC GENOMES
o Like prokaryotes, and all living things, their genome is made of DNA.
o May include several to many linear chromosomes within a membrane-bound nucleus.
o Q: How many chromosomes do humans have?
o Replication (duplication of DNA prior to cell division) occurs in all living things.
o Two locations of eukaryotic DNA: Nuclear DNA and Extranuclear DNA.
o Membrane-bound Organelles
- Eukaryotic cells have many organelles.
- Prokaryotes only have ribosomes, which are not bound by a membrane.
- Membrane-bound eukaryotic organelles organize functions within the cell.
- System of internal membranes within eukaryotic cells that divide the cell into
compartments, or organelles.
- Transport system, for moving molecules, into, out of, and through interior of cell, as well
as interactive surfaces for lipid and protein synthesis.
- Membranes of the endomembrane system are made of a lipid bilayer, with proteins.
- The Endomembrane System consists of: nucleus, endoplasmic reticulum, Golgi apparatus,
vesicles, lysosomes.
Organelles: Energy-Related
o Mitochondria & Chloroplast
- Both organelles house energy in the form of ATP.
- Both ancestrally were independent cells that formed a symbiotic relationship with other
cells.
- Chloroplast - An organelle inside a plant cell where photosynthesis happens.

- Mitochondria - Specialized to perform aerobic or cellular respiration turning glucose into
atp – provides energy for all the cell’s activity.
Classification is how biologists sort out different species into taxa, or biological categories, based on
their evolutionary ancestry. Through this system, different species are hierarchically classified into
increasingly specific groupings, species being the most specific.
Biological classification includes taxonomy, the naming and grouping of living things.
Seven basic taxonomic categories are: Kingdom, Phylum, Class, Order, Family, Genus and Species;
kingdom being the broadest category, and species being the most specific. The image to the right also
includes the category of Domains (which consists of three groups Archaea, Eubacteria, Eukaryota), and
all Life.
Biological Classification:
LIFE
DOMAIN
KINGDOM
PHYLUM
CLASS
ORDER
FAMILY
GENUS
SPECIES
CLASSIFYING LIVING THINGS

o Biological classification
- Provides meaningful groupings of organisms based on evolutionary relationships.
- To learn which organisms are most closely related, evidence is gathered from:
▪ Fossil record.
▪ Comparative homologies Similarity of anatomy / physiology due to shared
ancestry.
▪ Comparative sequencing of genetic material (DNA & RNA) among organisms.
Binomial nomenclature
- In the 1700s, Carl Linnaeus, a Swedish biologist, introduced a two part naming system.
- Every species discovered is assigned a genus and species name. The scientific name for modern
humans is Homo sapiens, with Homo being our generic name, or genus, and sapiens being the
specific, or species name.
- Genus names are always capitalized

- Species names are lower case.
- Genus and species names are always italicized or underlined when written.
Three Domains
o Eubacteria
- True bacteria
- Prokaryotes
- Streptococcus pneumoniae Escherichia coli
o Archaea
- Were thought to be same as Bacteria until recently.
- Prokaryotes
- Extremophiles
o Eukaryota
- All eukayotic organisms.
- Fall into 4 Kingdoms:
▪ Protista – Ex. algae
▪ Fungi – Ex. mushroom
▪ Plantae – Ex. Maple tree
▪ Animalia – Ex. You
o Domain: Archaea
- Prokaryotic
- Lack peptidoglycan
- Binary fission
- Many live in extreme environments.
- Not known to cause disease in humans or animals.
- Had been considered bacteria until examination of their unique rRNA sequences.
- Include: Methanogens, Extreme halophiles, Extreme thermophiles.
o Domain: Eubacteria
- Prokaryotes
- Unicellular microorganisms found in every habitat on Earth.
- Peptidoglycan cell walls
- Binary fission
- There are all varieties… pathogen, opportunist, harmless & beneficial.
o Domain: Eukaryota
- Five major groups that interest microbiologists:
▪ Protozoans (some can cause infectious disease)

▪ Fungi (some can cause infectious disease)
▪ Helminths (parasitic worms that can cause infectious disease)
▪ Algae (DO NOT cause infectious disease in humans)
▪ Slime & Water Molds (DO NOT cause infectious disease in humans)
▪ Includes both human pathogens and organisms vital for human life.
Cell Structure and Function
Arvin Joseph A. Abao, RPh

Learning Outcomes
1. Differentiate Prokaryote and Eukaryote
2. Identify the parts and functions of Prokaryote and Eukaryote
3. Describe the Five Kingdom and Three-Domain system of
Classification
Two Basic Types of Cells
Prokaryotic Cell Eukaryotic Cell

Prokaryotes
Binary Fission
Prokaryote Genetics
Nucleoid
• Region of cytoplasm where prokaryote’s genome (DNA) is
located.
• Usually a singular, circular chromosome.
Plasmid
• Small extra piece of chromosome/genetic material.
• 5 - 100 genes
• Not critical to everyday functions.
• Can provide genetic information to promote:
- Antibiotic resistance
- Virulence factors
(molecules produced by pathogen that specifically influence
host's function to allow the pathogen to thrive)
- Promote conjugation
(transfer of genetic material between bacteria through cell-
to-cell contact)
Prokaryotes
Cytoplasm
• Also known as proto-plasm.
• Gel-like matrix of water, enzymes,
nutrients, wastes, and gases and
contains cell structures.
• Location of growth, metabolism, and

replication.
Granules
• Bacteria’s way of storing nutrients.
• Staining of some granules aids in

identification.
Prokaryotes
Cytoskeleton
➢ Cellular "scaffolding" or
"skeleton" within the
cytoplasm.
➢ Major advance in prokaryotic

cell biology in the last decade
has been discovery of the
prokaryotic cytoskeleton.
➢ Up until recently, thought to be

a feature only of eukaryotic
cells.
Prokaryotes
Ribosomes
➢ Found within cytoplasm or attached to
plasma membrane.
➢ Made of protein & rRNA.
➢ Composed of two subunits.
➢ Cell may contain thousands .
➢ Q: What do ribosomes do?
➢ Q: What’s the relationship between the

job that the ribosomes do and the
genetic instructions (nucleic acids) of
the cell?
Prokaryotes
Plasma Membrane
➢ Separates the cell from its
environment.
➢ Phospholipid molecules oriented so

that hydrophilic water-loving
heads directed outward and
hydrophobic water-hating tails
directed inward.
➢ Proteins embedded in two layers of

lipids (lipid bilayer).
➢ Membrane is semi-permeable. Q:
What does that mean?
Prokaryotes – Plasma Membrane as a Barrier
Osmosis
➢ Is the diffusion of water across a

semi-permeable membrane.
➢ Environment surrounding cells

may contain amounts of
dissolved substances (solutes)
that are…
- equal to
Plasma
- less than membrane
- greater than
CELL
…those found within the cell. Liquid
Liquid
environment
environment
inside the cell.
outside the cell.
Prokaryotes – Plasma Membrane as a Barrier
Tonicity and Osmosis
➢ isotonic: equal concentration of a solute

inside and outside of cell.
➢ hypertonic: a higher concentration of

solute.
➢ hypotonic: a lower concentration of

solute.
Water will always move

toward a hypertonic
environment!!
Cells & Water:
Osmotic Pressure
• H2O important reactant in many metabolic
reactions.
• Most cells die in absence of water.
• Cell walls of bacteria and plants prevent them
from exploding in a hypotonic environment, but
most bacteria are vulnerable in hypertonic
environments.
• Many bacteria can be plasmolyzed by high

concentrations of solutes.
• You salty perspiration protects you from
bacteria that cannot handle the high sodium
chloride concentration.
• The water moves out of the bacterium and it
dies of ‘hyperosmostic shock’ (desiccation).
Plasma Membrane as a Barrier
ACTIVE TRANSPORT
• How most molecules move across the plasma membrane.
• Analogous to a pump moving water uphill.
• Types of active transport are classified by type of energy used to drive molecules across
membranes.
• ATP Driven Active Transport

Energy from adenosine triphosphate (ATP) drives substances across the plasma membrane with the aid of carrier
molecules.
Prokaryotes - Cell Wall
From the peptidoglycan inwards all bacteria are very similar. Going further out, the
bacterial world divides into two major classes (plus a couple of odd types). These are:
Gram-positive Gram-negative
Bacterial Cell Wall
➢ Peptidoglycan is a huge polymer of interlocking chains of alternating
monomers.
➢ Provides rigid support while freely permeable to solutes.
➢ Backbone of peptidoglycan molecule composed of two amino sugar

derivatives of glucose. The “glycan” part of peptidoglycan:
- N-acetylglucosamine (NAG)
- N-acetlymuramic acid (NAM)
➢ NAG / NAM strands are

connected by interlocking
peptide bridges.
The “peptid” part
of peptidoglycan.
Prokaryotes - Cell Wall
Gram-Positive & Gram-Negative
Images: Sources Unknown

Q: Why are these differences in bacterial cell wall structure
so important?
Prokaryotes - Glycocalyx
Some bacteria have an additional layer outside of
the cell wall called the glycocalyx.
This additional layer can come in
one of two forms:
1. Slime Layer
- Glycoproteins loosely associated with the cell wall.
- Slime layer causes bacteria to adhere to solid

surfaces and helps prevent the cell from drying out.
- Streptococcus
The slime layer of Gram+ Streptococcus mutans allows it to
accumulate on tooth enamel (yuck mouth and one of the
causes of cavities).
Other bacteria in the mouth become trapped in the slime

and form a biofilm & eventually a buildup of plaque.
Mannitol
Salt
Prokaryotes - Glycocalyx
2. Capsule
• Polysaccharides firmly attached to the cell

wall.
• Capsules adhere to solid surfaces and to
nutrients in the environment.
• Adhesive power of capsules is a major
factor in the initiation of some bacterial
diseases.
• Capsule also protect bacteria from being

phagocytized by cells of the hosts immune
system.
Prokaryotes - Endospores
➢ Dormant, tough, non-reproductive structure
produced by small number of bacteria.
➢ Resistant to radiation, desiccation, lysozyme,

temperature, starvation, and chemical disinfectants.
➢ Endospores are commonly found in soil and water,

where they may survive for very long periods of
time. An endospore stained bacterial smear of Bacillus
subtilis showing endospores as green and
vegetative cells as red.
➢ Q: How and why do endospores form? Watch the
animated lesson “Bacterial Spore Formation” to
find out. Link also provides quiz questions to test your
understanding of the material.
➢ Q: What are the two endospore producing

bacterial genera that were introduced in our
History of Microbiology lecture?
Bacterial Genus: __________
GRAM-POSITIVE This is our lab
Obligate or facultative anaerobes, friend Bacillus
endospore producers subtilis.
bacillus-shaped
Q: Which two groups of bacteria produce

endospores?
Gram Stain
Common in soil. Only a few species cause disease

in humans.
Extremely diverse group of bacteria, includes:

- causative agent of anthrax (Bacillus
anthracis)
- species that synthesize important
antibiotics, and enzymes for detergents.
Due to extreme tolerance to both heat and Endospore

Stain
disinfectants, used to test heat sterilization
techniques and chemical disinfectants.
Prokaryotes – Surface Appendages
➢ Some prokaryotes have distinct

appendages that allow them to move
about or adhere to solid surfaces.
➢ Consist of delicate stands of proteins.
➢ flagella: Long, thin extensions that allow

some bacteria to move about freely in
aqueous environments. (singular: flagellum)
➢ axial filament (endoflagella): Wind

around bacteria, causing movement in
waves.
Prokaryotes – Surface Appendages
➢ fimbriae: Most Gram-negative

bacteria have these short, fine
appendages surrounding the cell. Gram+
bacteria don’t have.
No role in motility. Help bacteria
adhere to solid surfaces. Major
factor in virulence.
(singular: fimbria)
➢ pili:Tubes that are longer than fimbriae,

usually shorter than flagella.
Use for movement, like grappling

hooks, and also use conjugation pili
to transfer plasmids. (singular = pilus)
Meet the Microbe! Neisseria and its Fimbiriae
• Gram- diplococci, resemble coffee beans when viewed microscopically.
• Neisseria gonorrhoeae causes sexually transmitted disease gonorrhoeae.
• Antibiotics applied to the eyes of neonates as a preventive measure
against gonorrhoea.
• One of the most communicable disease in the U.S.
• 125 cases per 100,000. Teens 15-19 yo 634 cases per 100,000. Young
adults 20-25 460 per 100,000.
• N. meningitidis most common causes of bacterial meningitis in young
adults.
Q: What makes Neisseria so tough?

• Lipopolysaccharide (LPS) of the cell wall of Neisseria acts as an
endotoxin.
• Polysaccharide capsule prevents host phagocytosis and aids in evasion

of the host immune response.
• Use fimbriae to attach onto host cells; avirulent without. Fimbriae have
adhesion proteins (adhesins) on their tips that match, lock and key, with
proteins on host epithelial cell surface.
Prokaryotes – Cell Shapes
Most bacteria are classifies according to shape:
1. bacillus (pl. bacilli) = rod-shaped
2. coccus (pl. cocci … sounds like cox-eye) = spherical
3. spiral shaped
a. spirillum (pl. spirilla) = spiral with rigid cell wall,
flagella
b. spirochete (pl. spirochetes) = spiral with

flexible cell wall, axial filament
There are many more shapes beyond these basic ones. A few
examples:
– Coccobacilli = elongated coccal form
– Filamentous = bacilli that occur in long threads
– Vibrios = short, slightly curved rods
– Fusiform = bacilli with tapered ends

Prokaryotes – Arrangements of Cells
• Bacteria sometimes occur in groups, rather

than singly.
• bacilli divide along a single axis, seen in

pairs or chains.
• cocci divide on one or more planes,

producing cells in:
- pairs (diplococci)
- chains (streptococci)
- packets (sarcinae)
- clusters (staphylococci).
• Size, shape and arrangement of cells often

first clues in identification of a bacterium.
• Many “look-alikes”, so shape and

arrangement not enough for id of genus
and species.
Eukaryotic Cell
Structure &
Function
Two Basic Types of Cells
Prokaryotes
• Single-celled.
• Reproduce by binary fission (another copy by dividing).
• No cell nucleus or any other membrane-bound organelles.
DNA travels openly around the cell.
• All bacteria are prokaryotes.
Eukaryotes
• Most organisms that we can see, such as trees, grass, worms,
flies, mice, humans, mushrooms and yeast are eukaryotes.
• Can either be single-celled or multi-celled.
• Can reproduce in one of several ways (Ex. meiosis, mitosis).
• Have cell nucleus within containing its DNA.
• Nucleus most evident distinction between these cell types.
Eukaryotic Cells
➢ Eu =“true”, karyon=“nucleus”
➢ Genetic material contained in a

nuclear membrane.
➢ Membrane bound organelles.
➢ Include animal, plant, fungi, algae

cells as well as other microscopic
eukaryotes.
➢ Evolved from prokaryotic cells.

Eukaryotic Genomes
➢ Like prokaryotes, and all living things, their
genome is made of DNA.
➢ May include several to many linear

chromosomes within a membrane-bound
nucleus.
➢ Q: How many chromosomes do humans

have?
➢ Replication (duplication of DNA prior to cell

division) occurs in all living things.
➢ Two locations of eukaryotic DNA

– Nuclear DNA
– Extranuclear DNA
Cytoplasm
Nicknames: The Matrix,
Molecular Chowder
➢ Fills the space between the plasma

membrane and the nuclear membrane
➢ A water-like substance that fills cells.
➢ Consists of cytosol and cellular

organelles except for the cell nucleus.
➢ cytosol is made up of water, salts, organic

molecules and many enzymes that catalyze
reactions.
Q: Eukaryotes? Prokaryotes? Both?

Cytoskeleton
Nicknames: Scaffolding,
Highways
• Maintains cell shape.

• Protects the cell.
• Enables some cell movement (using
structures such as flagella and cilia).
• Plays important roles in intra-cellular

transport (the movement of vesicles and
organelles).
• Plays important role in cell division.
Q: Eukaryotes? Prokaryotes? Both?

Cilia & Flagella • External appendages from cell
membrane.
• Aid in locomotion of the cell

or movement of materials
near cell.
• Motility > coordinated sliding

movements of
microtubules.
• Both Prokaryotes &

Eukaryotes can have
external appendages, but
are constructed differently.
• Eukaryotes may have flagella

or cilia (components of
cytoskeleton covered with
plasma membrane).
• Prokaryotes may have

flagella, endoflagella,
fimbiae or pili (composed
of protenaceous molecules
and not covered with
plasma membrane).
Ribosomes
➢ Q: What do ribosomes do?
➢ Q: What are they made of?
➢ Can be found alone in the

cytoplasm, in groups called
polyribosomes, or attached to the
endoplasmic reticulum.
➢ Q: Eukaryotes? Prokaryotes? Both?

Membrane-bound Organelles
➢ Eukaryotic cells have

many organelles.
➢ Prokaryotes only have

ribosomes, which are not
bound by a membrane.
➢ Membrane-bound
eukaryotic organelles
organize functions within
the cell.
System of internal membranes within eukaryotic cells that divide the cell into compartments, or
organelles.
Transport system, for moving molecules, into, out of, and through interior of cell, as well as
interactive surfaces for lipid and protein synthesis.
Membranes of the endomembrane system are made of a lipid bilayer, with proteins.
The Endomembrane System

consists of:
1. nucleus
2. endoplasmic reticulum
3. Golgi apparatus
4. vesicles
5. lysosomes
6… Q: What other membranous part of
the cell should also be included in this
list?
Organelles: Energy-Related
Mitochondria
Found in
& nearly all
eukaryotes
Chloroplast
• Both organelles house energy
in the form of ATP.
• Both ancestrally were

independent cells that formed
a symbiotic relationship with Found in
other cells. plants &
algae &
• Q: Eukaryotes? Prokaryotes? some
Both? microbes
Biological
Classification
Classifying Living Things
Biological classification provides meaningful
groupings of organisms based on
evolutionary relationships.
To learn which organisms are most closely Eubacteria Archaea Eukaryota

related, evidence is gathered from:
– Fossil record
– Comparative homologies
Similarity of anatomy / physiology due to shared ancestry
– Comparative sequencing of genetic

material (DNA & RNA) among organisms
Q: Which of these three methods do you think is most

reliable in helping us understand the “relatedness” of
living things?
Three Domains
Prokaryotes Eukaryotes
Eubacteria
- True bacteria
- Prokaryotes Eubacteria Archaea Eukaryota
Exs. Streptococcus pneumoniae
Escherichia coli
Archaea
- Were thought to be same as
Bacteria until recently.
- Prokaryotes
Ex. Extremophiles
Eukaryota
- All eukayotic organisms.
Fall into 4 Kingdoms:

Protista – Ex. algae
Fungi – Ex. mushroom
Plantae – Ex. Maple tree
Animalia – Ex. you
The hierarchy of biological classification has

eight major taxonomic ranks which
encompass all known life.
How about a trick to help us remember them?
And a little “Classification Rap” to help as well?
Word to your
Mat’!
Domain: Archaea
• Prokaryotic
• Lack peptidoglycan
• Binary fission
• Many live in extreme environments.
• Not known to cause disease in

humans or animals.
• Had been considered bacteria until

examination of their unique rRNA
sequences.
• Include:
– Methanogens
– Extreme halophiles
– Extreme thermophiles
Domain: Eubacteria
• Prokaryotes
• Unicellular microorganisms
found in every habitat on
Earth.
• Peptidoglycan cell walls
• Binary fission
• There are all varieties…
pathogen, opportunist,
harmless & beneficial.
• In this class, we will be
meeting just g a few
representative prokaryotes.
Domain: Eukaryota
• Five major groups that interest microbiologists:
• Protozoans
(some can cause infectious disease)
• Fungi
(some can cause infectious disease)
• Helminths
(parasitic worms that can cause infectious disease)
• Algae
(DO NOT cause infectious disease in humans)
• Slime & Water Molds

(DO NOT cause infectious disease in humans)
• Includes both human pathogens and organisms vital for

human life.
Q: What was that clue to help us
remember the hierarchy of biological
classification?
Classification of Organisms by Kingdom
Eukaryotes
Prokaryotes
Monera
Classifying Living Things: A Little Name Calling
Binomial nomenclature: A system of naming organisms first proposed in the 1700s by Swedish scientist
Carolus Linnaeus.
In binomial nomenclature, each organism is given two Latinized names:

- Generic name (genus, pl. genera)
- Specific name (species)
Genus names are always capitalized; species names are lower case.
Genus and species names are always italicized or underlined when written.
Q: Why does everything need to have a name? And why a universally understood name?
Acer pseudoplatanus Canis lupus Vibrio cholerae Homo sapiens

Dichotomous Key
Simple Stain
Cocci
Bacilli
Gram Stain
Gram Stain
Gram Gram positive bacilli
Gram Gram negative
negative cocci positive bacilli Acid Fast stain
cocci
MacConkey’s
Acid Fast Not
Mannitol Salt
acid
No fast
Pink Mycobacterium
color
change colonies tuberculosis
Endospore stain
yellow pink
Salmonella
pullorum E. coli Forms
Intense pink
Staphylococcus Staphylococcus endospores
Enterobacter
aureus epidermis aerogenes
Light, uneven pink
Bacillus subtilus
References
1. Tortora GJ, BR Funke & CL Case. (2019). Microbiology: An Introduction. Bridge Parkway, CA: The Benjamin
Cummings Publishing Company, Inc.
2. Riedel S., Morse A., Mietzner T & Miller S., (2019) .Jawetz, Melnick, & Adelberg’s Medical Microbiology 28th
edition, Mc Graw Hill
3. Denyer S., Hodges N., Gorman S., Gilmore B., (2011). Hugo and Russell’s Pharmaceutical Microbiology 8th
edition. Blackwell Publishing Ltd
AUTOCLAVE
= FOR STERILIZATION OF GLASSWARE AND

CULTURE MEDIA
= EQUIPPED WITH ACCURATE PRESSURE
AND TEMPERATURE GAUGES
INCUBATOR WATER BATH
= CAPABLE OF MAINTAINING TEMPERATURE to

within + 0.5oC of 35 & 37oC and to within 44 & 44.5oC
HOT AIR STERILIZING OVEN
= FOR STERILIZATION OF GLASSWARES

Autoclave Guidelines (LATER)
• In any routine monitoring of autoclave
performance, biological indicators or
thermocouples should be places at the center
of each load. Bacillus stearothermophilus
• Sterilizers used for waste treatment shall not
be used for sterilization of equipment, food,
or other related items.
• Each bag must be exposed to a minimum of:
– 250 degrees Fahrenheit (121 C)
– 15 lbs/cm2 of pressure
– At least 20 to 30 minutes time
PH METER
= should be standardized with a minimum of 2 standard

buffers (pH 4.0, pH 7.0, or pH 10.0 before use
COLONY COUNTER
= FOR ENUMERATION OF COLONIES

THERMOMETERS
= FOR CHECKING CALIBRATION OF INCUBATOR

AND WATER BATHS
LAMINAR FLOW HOOD/ STERILE BENCH/
BIOSAFETY CABINET
= Containment Equipment/Facility
During SAMPLE ANALYSIS (DILUTION);
BACTERIAL CULTURE
Ventilation Devices
• Fume Hood
• Laminar Flow Hoods
• Biological Safety Cabinet
Fume Hoods
• Fume hoods protect

workers from
chemical vapors.
• Handle hazardous
chemicals in fume
hoods whenever
possible.
Laminar Flow Hoods
• These hoods are only

appropriate for very
few purposes and
they are often
misused.
• Don’t work with any
hazardous in a
laminar flow hood.
• They protect the
working surface only,
NOT the worker!
Biological Safety Cabinets (BSC)
• BSCs work to protect

workers and material
from microbes and
the environment
• Avoid working with
volatile chemicals in a
BSC.
BIOSAFETY CABINET
• LEVEL 1. PROTECT PEOPLE WORKING FROM

ENVIRONMENT.
• LEVEL 2. PROTECT PEOPLE WORKING AND

ENVIRONMENT AND PRODUCT.
• LEVEL 3. PROTECT PEOPLE,ENVIRONMENT

AND PRODUCT ALSO.
ANAEROBIC JAR
= USED FOR INCUBATING ANAEROBIC ORGANISMS

STOMACHER
= USED TO HOMOGENIZED SAMPLES

VORTEX MIXER
= USED TO MIX SOLUTIONS

BLENDER
= USED TO HOMOGENATE SOLID SAMPLES

MICROWAVE OVEN
= USED FOR MELTING AGAR

BUNSEN BURNER LOOP INCINERATOR
= USED TO STERILIZE INOCULATING LOOP/NEEDLE

DESSICATOR CABINET
= FOR STORING HIGHLY HYGROSCOPIC

MEDIA/REAGENTS
ULTRA LOW FREEZER
= USED FOR STORING LONG TERM

BACTERIAL CULTURE
MICROSCOPE
= FOR MORPHOLOGICAL CHARACTERIZATION

OF ORGANISMS
MAGNETIC STIRRER
= To mix media/reagents
PIPETTOR
= To dispense exact amount of liquid

(media, reagent, buffer or sample)
Meter stick
• Meter sticks measure

length in cm
• 100 cm = 1 meter
• Don’t bend
• Not a weapon
Triple Beam Balance
• A tool that is used to measure mass (the
amount of matter) usually in grams.
• This is a close up of the numbers on the
balance.
INOCULATING INOCULATING
LOOP NEEDLE
= used to transfer organism

PETRI DISHES TEST/ REACTION/
DURHAM TUBES
= used to contain solid/liquid media

CULTURE
STAINING JARS
MEDIA BOTTLE
TEST TUBE RACK
FORCEPS
SPATULA
Lab Safety Rules
Safety Symbols
• Know safety symbols

• They appear in your
laboratory activities
• They will alert you
to possible dangers
• They will remind you
to work carefully
Use Your Head
• Exercise Caution and
Good Judgment
• Follow all instructions
given by the teacher
• Notify the teacher
immediately regarding
any accident or unsafe
areas
Use Your Head
• Read lab instructions ahead of time
• Always follow lab procedures exactly
• Never do an unauthorized experiment
Protect Yourself
Eye Safety
• Wear safety goggles when
working with chemicals, flames,
or heating devices
• or if possibility of flying debris
• If you wear contact

lenses let your
teacher know
Protect Yourself
Eye Safety
• In case of emergency
in which a chemical
goes into one’s eye,
use the eyewash
station
• Flush in water for

15 mins. and
notify the teacher
Protect Yourself
Proper Attire
• Keep all long hair
tied back
• Do not wear loose
clothing that could
catch on fire
• Foot wear that

completely covers the
foot is required
t
h
e
r
s
h
Sharp Objects
a
r
p
o • Always cut away from fingers
b
j and body
e
c
t
• Always carry sharp objects
s
a
with points and tips facing
l
w
down and away
a
y • Never try to catch falling
s
w sharp instruments
a
l
k
• Grasp sharp instruments
w
i
only by the handles
t
h
t
h
t
h
e
r
s
h
Sharp Objects
a
r
p
o • Notify teacher if you get cut
b
j
e
• Broken glass and sharp objects
c
t
do not go in trash cans
s
a • Teacher will clean up
l
w broken glass
a
y
s
w
a
l
k
w
i
t
h
t
h
Safety and
Rules of
the Lab
Electrical Safety
• Only electrical plugs
are to be placed into
an electrical outlet
• Unplug electrical
equipment after use
• Keep all electrical
cords, wires, and
appliances
away from
water
Physical Safety
• Handle all equipment carefully
• Do not place a cord where
someone can trip over it
• Push all stools in out of the
way
• Keep books picked up out
of walking isles
Heating Safety
• Tie back hair and loose
clothes when working
with open flames
• Never look into a
container as you
are heating it
• Never point the end of
a test tube being heated
at yourself or others
• Never heat in a closed container
Heating Safety
• Never leave a heat source unattended
• Heated metal and glass looks
cool, use tongs or gloves
before handling
• Do not place hot glassware
directly on lab desk or in
cold water
Chemical Safety
• Read all labels twice before removing
a chemical from the container
• Only use the type and
amount of chemical
instructed to use
• Never touch, taste, or
smell a chemical unless
instructed by the teacher
• Never mix chemicals
unless instructed to do so
Chemical Safety
• Transfer chemicals carefully!
• Keep lids on chemical
containers when not in use
• When diluting an acid, pour the
acid into water
• Consider all chemicals
dangerous
Treatment of Specimen
• Respect the life of all
laboratory specimen
• They gave their life for

your education
You Should Never…
• Eat or drink in the lab
• Use lab glass-ware to
eat or drink out of
You Should Never…
• Engage in….
– practical jokes
– horse play
– rough house
In case of an emergency…
• Know the locations of:
– fire extinguisher
– fire blanket
– body shower
– eyewash
station
– first aid kit
• If you spill a harmful

chemical on yourself or in
your eyes, start rinsing
immediately and send your
partner to get teacher’s
help
Protect Yourself
Hand Safety
• If a chemical spills on your skin, notify the

teacher and rinse with water for 15 minutes
• Wash hands after every lab
• Handle
glassware,
sharp tools
and heated
containers
carefully
Protect Yourself
Hand Safety
Remember to…
• Stay at your work station
• Maintain a clean work area
• Read and follow all directions
• Report any spills, accidents,
or injury to the teacher
immediately
• Clean and put away all equipment
at the end of the
lab period
• Dispose of waste products
according to instruction
The Importance of Hand
Washing
Bacteria are easily transferred by a simple
handshake!

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Pharmaceutical Microbiology and Parasitology

Microbiota - refers to all of the microorganisms that live in a particular environment.

Why is it important to study microorganisms?

o Negative impact on humans:

o Algae - are typically eukaryotic microorganisms that carry out photosynthesis.

o Anton von Leeuwenhoek (1632-1723)

o Louis Pasteur (1822-1895)

- Heating liquids to 63-65°C for 30 mins or 73-75°C for 15 seconds

o Robert Koch (1843-1910)

o Paul Ehrlich (1854 –1915)

o Sir Alexander Fleming (1881–1955)

Golden Age of Microbiology

I. Fermentation and Pasteurization

Edward Jenner - developed the first vaccine in 1798 for smallpox.

III. Birth of Modern Chemotherapy

DISEASES CAUSED BY BACTERIA

DISEASES CAUSED BY FUNGI

DISEASES CAUSED BY PROTOZOANS

DISEASES CAUSED BY HELMINTHS

DISEASES CAUSED BY VIRUSES

SOME OF THE MICROORGANISMS THAT CHANGED THE WORLD

PRODUCTS REQUIRING MICROBIAL PARTICIPATION IN MANUFACTURING PROCESS

Antibiotics – substance produced by microorganisms that is effective in killing or inhibiting growth of

Microorganisms – tiny organisms

CHARACTERISTICS OF VARIOUS TYPES OF MICROSCOPES

LENSES AND BENDING OF LIGHT

Microscope Resolution (Resolving Power)

o Incubator & Water bath

Safety and Rules of The Lab

Cell Structure and Function

- Can provide genetic information to promote:

o Cytoplasm (both in Prokaryotic and Eukaryotic Cell)

Osmotic Pressure (Cells & Water)

Gram Stain Protocol

- Chloroplast - An organelle inside a plant cell where photosynthesis happens.

CLASSIFYING LIVING THINGS

- Genus names are always capitalized

▪ Protozoans (some can cause infectious disease)

Arvin Joseph A. Abao, RPh

Prokaryotic Cell Eukaryotic Cell

• Location of growth, metabolism, and

• Staining of some granules aids in

➢ Major advance in prokaryotic

➢ Up until recently, thought to be

➢ Made of protein & rRNA.

➢ Composed of two subunits.

➢ Cell may contain thousands .

➢ Q: What do ribosomes do?

➢ Q: What’s the relationship between the

➢ Phospholipid molecules oriented so

➢ Proteins embedded in two layers of

➢ Is the diffusion of water across a

➢ Environment surrounding cells

Tonicity and Osmosis

➢ isotonic: equal concentration of a solute

➢ hypertonic: a higher concentration of

➢ hypotonic: a lower concentration of

Water will always move

• Many bacteria can be plasmolyzed by high

• How most molecules move across the plasma membrane.

• Analogous to a pump moving water uphill.

• ATP Driven Active Transport