Category: Week 1

Thursday Notes



CHNOPS anyone?

C – Carbon: Found in all organic molecules

H – Hydrogen: Part of water

N – Nitrogen: Found in proteins (amino acids)

O – Oxygen: Part of water

P – Phosphorus: Nucleic acid

S – Sulfur: Proteins.

Molecule: More than one atom bonded together.

Types of Bonds Found in Living Things…

Hydrogen Bond – attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen has a polar bonding to another electronegative atom to create the bond. (weaker bond)

All the information I have found shows Hydrogen bonds can only happen between H and F, O or N.

Ionic Bond – a type of chemical bond formed through an electrostatic attraction between two oppositely charged ions. Ionic bonds are formed between a cation, which is usually a metal, and an anion, which is usually a nonmetal. Cation “gives” away an electron to the anion. (stronger bond)

Covalent Bond – sharing of electrons between two atoms. (strong bond)

Chemical Reactions (RXN = Reaction)

Decomposition RXN –

  • Breakdown  – A chemical reaction in which bonds are broken
  • Catabolic RXN – The sum total of decomposition reactions exhibited by an organism.

AB A + B.

Synthesis RXN – A chemical reaction in which new bonds are formed. Building larger molecules from smaller molecules.

ex.       A + B AB

Exchange RXN –

  • An individual reaction than involves both synthesis and decomposition. 
  • Implied in this definition is the idea that a collision between two molecules occurs which results in some degree of exchange of atoms and bonds, for example as occurs in hydrolysis.

ex.       AB + CD ↔ AD + CB

Hydrolysis means ‘water’ &  ‘break’

Water is Essential for Life!

Life as we know it depends on water.

  • Water is the most abundant molecule found in living things (by weight)
  • All living organisms are 70% + water
  • The chemical structure of water gives it life sustaining properties.
  • The H atoms of an individual water molecule are bound to the oxygen atom by polar covalent bonds.

Polar means one atom has a larger electronegativity pull than another atom. The electronegativity pull of an atom is based on its size, therefor the bigger the atom the more pull it will have on another atoms electrons. This makes the bigger atom negatively charged because it has more of the electron than the small atom making the small atom positively charged.

Life Sustaining Properties of Water

  1. Frozen water is less dense than liquid water. (Floats) As water cools below 4°C, the hydrogen bonds adjust to hold the negatively charged oxygen atoms apart (becoming rigid). This produces a crystal lattice, which is commonly known as ‘ice’. This allows life to go on beneath the surfaces of frozen bodies of water. 
  2. Water is a good solvent for polar molecules or ionic molecules.
  3. Water has adhesion & cohesion properties. Adhesion – Sticks to others: Important for moving water (ex. plants & roots)     Cohesion – sticks to itself: surface tension is the result of the tendency of water molecules to attract one another (called cohesion).
  4. Bodies of water have high surface tension.
  5. Water has relatively high specific heat compared to other liquids.

Specific heat – amount of energy it takes to change 1 gram of water by 1°C.

Acids & Bases

Acids – Substances that release hydrogen when added to water.

Bases – Substances that release hydroxide (OH¯) when added to water.

Each time you move up or down the pH scale it is an exponential power.

ex. going from 5pH to 8pH would be an increase of 1000.

7pH – is the middle of the scale.


Substances that resist pH changes.

4 Major Categories of Macromolecules Found in Living Things:

Carbohydrates – Hydrates of Carbon

  • Monosaccharides (monomers) – Contain C, H, O in a 1C:2H:1O ratio.  Ex. fructose, glucose, galactose
  • Disaccharide – 2 monosaccharides or monomers linked together form a covalent bond called a GLYCOSIDIC BOND :a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. ex. sucrose, lactose, maltose                      sucrose = glucose + fructose; lactose = glucose + galactose; maltose = glucose + glucose
  • Polysaccharides (polymers) – 3+ molecules of repeated monomer units joined together by glycosidic bonds. ex. cellulose, chiten (fungi cell walls), amylose (starch), glycogen (animal muscle)


Colony Morphology Terms

Form: Overall shape of entire colony : Punctiform; Circular; Irregular; Filamentous; Rhizoid

Margin: Edges: Entire; Undulate; Lobate; Serrate; Filamentous; Curled

Elevation: Flat; Raised; Convex; Pulvinate; Umbonate

Surface Texture: Shiny, smooth, glistening (wet appearance), dull/rough, wrinkled, dry or powdery.

Optical Character: opaque, translucent, opalescent or iridescent.

  • Translucent – Allowing light but not detailed images to pass through.
  • Opaque – Not allowing light to pass through
  • Opalescent – Exhibiting a milky iridescence like that of an opal.
  • Iridescent – Displaying a play of lustrous colors like those of the rainbow

Cell Morphology Terminology

Cocci – Spherical Shapes

Pairs – Diplococci

Chains – Streptococci

Four Cells – Tetrad

Clusters – Staphyloccocus (grape like)

Cubicle packet – Sarcinae

Single Cells – Singles

Bacilli – Rod-like/Cylindrical Shapes

Pairs – Diplobacilli

Chains – Streptobaccili

Side-by-side – Palisading

V-shape – Snapping

Short Rods – Coccobacilli

Spirilla – Spiral Shape

One-half spiral turn – Vibrio

Also loose spirals & tight spirals.

Direct vs. Indirect Staining

(Repeat of the notes she already gave us)


  • Microbiologist observe both living and dead microorganisms with microscopes
  • Dead organisms can be stained to make cell features more visible. (However, there shapes distort slightly when dead)
  • Stains are salts, w/ one ion being colored (chromophore – the part of a molecule responsible for its color.)
  • Direct stains: color the cell & leave the background colorless
  • Indirect stains: color the background, leaving the cell colorless.

Types of Stains:

  1. Basic Stains: Color is associated w/ the cation. Cations are attracted to cell membranes. (ex. methylene blue, crystal violet, safranin)
  2. Acidic Stains: Color is associated with the anion or the neutral particles. Anions and neutral particles are not attracted to cell membranes. (ex. Nigrosin, Congo Red) 

Direct Staining:

  1. Using aseptic technique put two “loop fulls” of water 
  2. Obtain a visible “blob” of cells & smear onto slide with water.
  3. Use sterile loop to mix until the smear is a consistency of skim milk.
  4. Air dry
  5. Heat fix. (3 swipes over flame – to kill the microorganisms)
  6. Liberally apply Methylene Blue to slide & allow to set for 60 sec.
  7. Rinse off & air dry

Indirect Staining:

  1. Using aseptic technique put two “loop fulls” of water 
  2. Obtain a visible “blob” of cells & smear onto slide with water.
  3. Use sterile loop to mix until the smear is a consistency of skim milk.
  4. Add 2 loop fulls of Nigrosin while still wet & smear in.
  5. Air dry
  6. GENTLY Heat fix. (1 swipe over flame – to kill the microorganisms)

Hope everyone’s projects are coming out good! I will put up the review questions on week 1 again for our Monday quiz.



Wednesday Notes


History Of Microbiology

The science of Microbiology began with the invention of the microscope.

  • Robert Hook (1665) – Coined the term “cell”, like a prison cell when he was the first to observe cork material from plants.
  • Anton von Leeuwenhoek (1674) – First to observe living microorganisms. He termed them “animalcules.” The picture to the right is his self made microscope. He never let anyone use, and did not teach anyone how to make them. When he died it took many years to replicate it and was partly the reason for a delay in progress.

Golden Age of Microbiology

(1857-1914) Period of time when many discoveries were made about microorganisms.

The 4 Main Questions:

  1. Is spontaneous generation (nonliving things generating living things) of life possible? 
  2. What causes fermentation?
  3. What causes disease?
  4. How can disease and infection be prevented?

Spontaneous Generation vs. Biogenesis

Spontaneous Generation- Nonliving things generating living things.

  • Francisco Redi (late 1600s) – First to document a controlled experiment. The picture to the right is the experiment he conducted, and documented.  Conclusion: Rejected hypothesis of spontaneous generation.
  • John Needham (mid-1700s) – Boiled beef gravy or plant infusions by placing them in sealed flasks & dicovered the liquids became cloudy with life/microorganisms. Conclusion: Accepted hypothesis of spontaneous generation.
  • Lazzaro Spalanzi (mid/late 1700s) – Boiled infusions more than 1 hour & then put them in very well sealed flasks. His infusions did not become cloudy.  Conclusion: Rejected hypothesis of spontaneous generation.
  • Louis Pasteur (1861) – created and used swan neck flasks to allow the passing of air/oxygen into the flasks but keep particles in the air from settling into the infusions. Conclusion: Rejected Spontaneous generation and was able to put the argument to rest.

Louis Pasteur’s other accomplishments:

  • Investigated the cause of fermentation by observing (budding yeasts) microbes in wine and other fermented foods.
  • Proved some organisms do not need oxygen to stay alive & ferment foods. These organisms are facultative anaerobes.
  • Experimented adding bacteria & yeasts to unfermented foods like grapefruit juice. Discovered that the foods did become fermented.
  • Germ Theory of Disease

The Germ Theory of Disease

Microorganisms can cause infectious diseases (Pasteur, 1857)

  • Robert Koch’s work – examined blood of animals infected w/ Bacillus anthracis (Anthrax), observing bacilli-shaped microbes in the blood. One of his most important contributions to microbiology was his postulates.

Koch’s Postulates

A series of steps that must be taken to prove the cause of any infectious disease.

  1. The suspected causative agent must be found in every case of the disease and be absent from healthy hosts.
  2. The agent must be isolated and grown outside the host.
  3. When the agent is introduced to a healthy, susceptible host, the host must get the disease.
  4. The same agent must be found in the diseased experimental host.

“agent” – can refer to any fungus, protozoan, bacterium, virus or other pathogen

Who Did What?

  • Ingaz Semmelweis: Handwashing (1848)
  • Joseph Lister: Used phenol to spray on surgical wounds to reduce infections.
  • John Snow : One of the first epidemiologists. In 1854 he investigated the source of a cholera outbreak in London. Epidemiology: “…is the study of the distribution and patterns of health-events, health-characteristics and their causes or influences in well-defined populations.” – Wikipedia
  • Florence Nightengale: Nurse during Crimean war. She was a clean freak who was the first to document her cleaning regimen and promote hygienic standards in the ward such as scrubbing floors and changing soiled clothes.
  • Edward Jenner (1796) – First to perform vaccination. (comes from the word vaca – cow, from his discovery regarding cowpox & small pox)
  • Paul Ehrlich – Searched for the “Magic Bullet” – a chemical or agent that will kill a disease causing microbe w/o harming the host.

Modern Biology

  • Biochemistry/Metabolism – Chemical reactions that take place within the cells of microbes. 
  • Molecular Biology – Genetics (study of genes) & DNA technology (in vitro manipulation of DNA)
  • Defending humans against disease
  • Environmental Microbiology
  • Industrial Microbiology (Food Industry & other products)


Culture of Microorganism & Media Preparation

Culture Media – Substance that contains nutrients for supporting the growth of microbes.

Solid Media

  • Agar that is solid at room temperature 
  • Comes from red algae
  • Discovered as a good growth media by Fanny Hess (wife/partner of Walter Hess)
  • Good growth media because it remains solid up to 45°C, melts at 100°C & microbes do not digest/degrade the agar.
  • Streak plates (petri dishes) – better to see microbes & colony morphology; however they dry out quickly.
  • “Deeps” (Deep Tubes) – are not as easy to contaminate; must stab sample to bottom of tube; better for longer storage. Cant study colony morphology.
  • Slant Tubes – Not as easy to contaminate; better for longer storage; cant study colony morphology

Liquid Media

  • Liquid at room temperature
  • Made from animal infusions.
  • Liquid media in broth tubes can also be used to predict the oxygen requirements for microbes.

Broth Tubes & Flasks – Organisms maintain their shape easily; can be extracted so that cell morphology can be studied. Samples do not get contaminated as easily. Good for calculating cell concentrations.


“An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It could possibly react negatively and may even die if oxygen is present. There are three types:

  • obligate anaerobes, which cannot use oxygen for growth and are even harmed by it
  • aerotolerant organisms, which cannot use oxygen for growth, but tolerate the presence of it
  • facultative anaerobes, which can grow without oxygen but can utilize oxygen if it is present

In humans beings these organisms are usually found in gastrointestinal tract.[1] ” – Wikipedia

“Aerobic and anaerobic bacteria can be identified by growing them in liquid culture:
1: Obligate aerobic (oxygen-needing) bacteria gather at the top of the test tube in order to absorb maximal amount of oxygen.
2: Obligate anaerobic bacteria gather at the bottom to avoid oxygen.
3: Facultative bacteria gather mostly at the top, since aerobic respiration is the most beneficial one; but, as lack of oxygen does not hurt them, they can be found all along the test tube.
4: Microaerophiles gather at the upper part of the test tube but not at the top. They require oxygen but at a low concentration.
5: Aerotolerant bacteria are not affected at all by oxygen, and they are evenly spread along the test tube.” – Wikipedia

Differential Media & Selective Media (Mannitol Salt Agar)

Selective Media – Media that promotes the growth of some types of microbes while inhibiting the growth of other types of organisms.

Differential Media – Changes colors based on types of organisms due to the pH indicators within the media

Defined Media vs. Defined Media

Defined Media: Known & measured amount of nutrients

Complex Media: Crude amounts or unknown amounts of nutrients (ex. beef broth)

Aseptic – w/o contamination or w/o microbes

Ex. Disinfecting work station; sterilizing tools

Monday Notes

Day one done!! Here is what I gathered:

Bacteria to learn:
Toxic Shock Syndrome

See “Bacteria Vocab” tab for scientific name/spellings.

Lecture Notes : Introduction to Microbiology

The study of living things that are too small to be seen w/ the naked eye.

Prokaryotes : Organisms that have prokaryotic cells. (Cells w/o a true nucleus or organelles)

  • Archaea: Extremophiles. Meaning they live in extreme environments such as acidic, salty or high temperatures. Generally not found to be harmful to humans.
  • Bacteria:Non-extermophiles.

Eukaryotes:Organisms that have eukaryotic cells. (Cells w/ a true nucleus and organelles.)

  • Fungi: Unicellular or multicellular; opportunisitic pathogens. They reproduce through asexual and sexual spores.
  • Protozoa: Direct translation is “first animals.” (though not animals) They are unicellular and most have motility.
  • Algae: Unicellular or colonial. Colonial meaning they group together, but are always unicellular. Antotrophs. (self-feeder through photosynthesis)
  • Multicellular parasites: example would be helminths (worms)
  • Vectors:  Animal (such as an insect) that can carry pathogens from one host to another.

Monday Lab Notes: Lab 1 & 2A

Lab Safety; Handwashing & Microscopes

  • In case of emergency, we are to leave the building together as a class to through the double doors to the left. We must meet together so Brahce can take roll.
  • If you get something in your eyes, you are to flush them in the back of the room for a full 15 minutes. It is best to let Brahce KNOW so she can help.
  • There is a fire hydrant, fire blanket and first aid kit in the front of the room.
  • To dispose of broken glass there is a SPECIFIED trash bin in the back of the room. Is your broken glass contaminated? Ask Brahce if it is OK to through away in the broken glass trash bin.
  • Microbe spill? Inform people around you and instructor. Cover with disinfectant. Wipe with paper towels, dispose properly and wash hands!

Where do we put things when we are done?

Top Shelf: Non-contaminated glassware.

Middle Shelf: CONTAMINATED items such as: Breakers, flasks, slides, test tubes. Test tubes need the tape removed and belong in the “50 tube rack.” Slides go in the container designated for slides.

Bottom Shelf: All materials that can be through away and will be going in the autoclave (a super duper medical grade “dishwasher”) These items will be Petri dishes, plastic pipettes, paper, other plastic items that will be disposed of.

Lab Materials & Supplies

Trays: Found by your belly… matches, metal tube holder, clothes pin for stained slides, 2 scrape sticks and ruler.

Drawer: Lens paper, slide holder, test tube holder.

  • Extra test tube racks can be found in back of classroom.
  • Sterile growth media is found in the 2 side refrigerators on right side of room. (Generally will be needing Nutrient Agar from here)
  • Stains and reagents are found on black shelf in front of room.
  • Microscopes: Cubbies.
  • Don’t use fridges on left.
  • We will be using grey incubator on the right in back of room. It is at 37 degrees C (98.6 degrees F) Place your samples UPSIDE DOWN.

Your samples can be found in the wood box with our class name on it the next day if no longer in incubator.


Normal microbiota vs. transient microbiota

Normal Microbiota: Microbes that are found on the outside and inside of the human body on a permanent basis. Help CROWD out the transient microbiota. Are useful to the bodies systems such as digestion and immune system.

Transient Microbiota: Temporary microbes acquired from environment.

  • We begin collecting our normal microbiota from the time of birth in the birth canal and from breast feeding

“Handwashing is the single most important procedure for preventing noscomial ( institutionally acquired) infections”

– Centers for Disease Control and Prevention (CDC)

“Ignaz Semmelweis was a physician on the obstetric ward…[in 1847 he] hypothesized that medical students carried ‘cadaver particles’ from their autopsy studies into the delivery rooms, and that these ‘particles’ resulted in puerperal fever…Semmelweis began requiring medical students to wash their hands with chlorinated lime water.”

Semmelweis ended up getting the shaft from the hospital due to his “barbaric ways” and returned to his home country Hungary, where he went a little mad, was admitted to a mental facility and then IRONICALLY died from an infection of streptococcus which causes PUERPERAL FEVER! He died from the disease he went crazy fighting against.

2A Microscope: Compound Light Microscope

Compound: 2 sets of lenses being used to magnify the specimen.

Objective Lens: Magnifies object/specimen.

Objective Lens Name                            Maginification    Total Mag.

    1. Scanning Objective Lens                   4x             40x
    2. Low Power Objective Lens               10x           100x
    3. High Power Objective Lens              45x          450x
    4. Oil Immersion Objective Lens         100x       1000x

Ocular Lens: Lenses you look through. Magnifies x10


Magnification: Makes specimen appear larger.

Resolution: Clarity, sharpness of the image.

Parfocal: When the specimen is in focus using one objective lens, it is in focus in all objective lenses.

Field of View: Circle of light you see when viewing a specimen.


  1. Store w/ cord between ocular lenses & underneath the stage control knobs.
  2. Scanning objective lens in place.
  3. Turn light/power off.
  4. No oil on oil immersion lens.
  5. No slides left on microscope.

This image different than your microscope but should give a general idea of where things are.

Light power/intensity dial: Turns light on, controls light brightness

Substage condenser: Focuses light gathered onto specimen. 

Iris Diagram: Widens or narrows the diameter of light coming in. (Helps w/ clarity)

Mechanical stage & stage clips: Supports slide & holds in place.

Mechanical stage & control knobs: Moves stage clips forward/back & left/right. 

Substage condenser control knob: Moves condenser closer or farther from stage.

Revolving Nosepiece: Moving part for changing objective lenses. 

Coarse Focus Knob:Moves objective lens either closer or farther from stage. (Controls working distance)

Fine Focus Knob: Makes minor movements similar to coarse focus knob.

Ocular lens adjustment dial: Moves ocular lenses closer or farther apart from one another.

Steps for Viewing Specimen:

  1. Put scanning object lens in place
  2. Place slide between clips on stage
  3. Use mechanical stage control knobs to move specimen directly under scanning objective lens
  4. Use coarse focus knob to bring specimen into focus
  5. Be sure specimen is in CENTER of field of view.
  6. Move low power objective lens into place.
  7. Use fine focus to bring specimen into focus.

Hope this helps! See you tomorrow

Tuesday Notes

Acellular – w/o cells. Viruses, Viroids & Prions, oh my!

Living? Kinda…

Viruses: Made of nucleic acid & a protein coat; obligate intracellular parasites. 

Viroids: Infectious RNA that cause plant diseases. 

Prions: Self-replicating, infectious proteins.

Ex. Encephalopathies – Causes holes in brain. (Mad Cow Disease)

General Characteristics of Living Things

  • All living things have structure/organization based on cells. (Cells being the smallest unit of life)
  • Reproduction – Passing DNA (sexual or asexual)
  • Ability to convert energy from one form to the other (Metabolize)
  • Respond to environmental stimuli
  • Evolutionary adaption
  • Regulate internal/intracellular conditions
  • Grow

Various Roles of Microbes (Many Beneficial)

  • Fermentation
  • Antibiotics – Chemicals produced by living things that kill other living things.
  • Role in immunity
  • Bioremediation – Ex: Bacteria can be used to clean up oil spills
  • Pathogens (root path: disease; gen: generate)
  • Nutrient Recycling (Ecological Role)

Overview of Taxonomy & Scientific Nomenclature

Taxonomy: The science of classifying & naming organisms.

Heirarchy: Most general category to the most specific

“Dumb kids playing chase on freeway go splat”

  1. Domain – Bacteria, Archaea or Eukarya
  2. Kingdom
  3. Phylum
  4. Class
  5. Order
  6. Family
  7. Genus – Usually a noun
  8. Species – Usually an adjective

Carolus Linnaeus (1758)

  • Developed binomial nomenclature system

The Scientific Process

  1. Observation
  2. Question.. What? How?
  3. Hypothesis
  4. Test or experiment including control groups
  5. Observations of experimental data
  6. Accept/Reject hypothesis
  7. Theory or Law or Modify/change hypothesis

Lab 2B: Microscopic Measurement

Goal: Determine the distance between each line on the ocular micrometer using a known metric standard (stage micrometer)

Ocular Micrometer: Disc of glass in one of the ocular lenses w/ equally spaced lines etched onto the surface.


Stage Micrometer: Glass slide w/ both metric & english rulers etched onto surface (the known standard)

Metric System Review:

  • Meter- standard unit of length measurement
  • We will be measuring in µm (microbes)