Microbiology

Microbiology is the study of very small (single-celled) organisms such as bacteria, viruses, fungi, protozoans, and algea.

Why study this field at all?
Well we need these little critters for are environment. They are all over the place, including our bodies. With Microbial Ecology they are part of the food chain, nutrient cycling and even help with photosynthesis. Within human and animal normal flora microorganisms help keep body chemistry in balance. Scientists have even exploited m.o.'s (microorganisms) to make enzymes, food additives, hormones, drugs and other items that we use in commercial and medical settings.

How did this all start?
Well way back when (1600's) a dude named Hooke invented a very crude microscope and discovered "cells" and said that all living things are composed of cells, which is the cell theory.
A few years after Hooke, van Leeuwenhoek made some improvements on the microscope and saw what he called animalcules in rain water and teeth scrapings.

Their discoveries caused people to start talking about Spontaneous Generation. Which is some forms of life can arise spontaneously from nonliving matter. A scientists named Redi was against this theory. He filled up a couple of jars with meat. One was unsealed and the other was. The unsealed one developed maggots while the sealed one did not. He claimed this proved it. But others said "You need fresh air for spontaneous generation though, you lose"
So Redi did the same experiment but on the sealed jar he used a fine net. Still no maggots appeared. This helped dispel that theory some, but others still thought the "animalcules" could easily be from spontaneous generation.

Virchow purposed biogenesis which is living cells arise only from pre-existings living cells.

Finally in 1895 Pasteur disproved this theory. He made some special flasks filled with broth that allowed air in but kept microbes out. And some of these flasks are still on display with no signs of decay. How cool is that?
Pasteur also came up with the Germ Theory of Disease- that m.o.'s can invade other organisms causeing disease and death.

Koch proved this germ theory and showed that 1 microorganisms causes 1 specific disease. He also developed lab techniques with the use of a Petri dish and agar to grow microorganisms.

Going back a little bit, Jenner developed the 1st vaccine against smallpox in the 1790's.
And Lister developed aseptic medical techniques using the chemical phenol, which greatly reduced the death rate during surgeries.

Metchnikoff discovered immune cells (what we know as white blood cells) and saw one eating another cell. He said they were phagocytes.

Ivanowski discovered the "filterable agent" that causes plant diseases

Ehrlich developed chemotherapy which is the treatment of diseases by chemical substances. He found a "magic bullet" that would find the pathogen without harming the host. He found an agent called Salvarsan which was to treat Syphilis. His drug got shot down because in the 1910's our country was still very religious and higher ups thought that those who had syphilis deserved it. Even those who were innocent and had a cheating spouse and did not know it. Salvarsan was supposed to be a "Salvation".

Fleming discovered the 1st anitbiotic by accident. He got mad because a mold had "ruined" his microorganism sample on a Petri dish, but then realized "Wait a minute! That mold is killing the M.O.!" That's the antibiotic we've all probably taken at one point or another, Penicillin.

Waksman coined the term Antibiotic and discovered many other types.

Beijerinck and Winogradsky figured out some of the roles of bacteria in recycling elements between the soil and atmosphere.

EID's are Emerging Infectious Diseases. These can be scary because since they are emerging they are newer and therefore may not have a treatment or cure yet. Causes are the spread of known diseases to new populations by traveling and increases human exposure to new unusual infectious agents in areas that are undergoing ecological changes. New strains of pre-existing human diseases can occur because the virus or bacteria becomes immune to the treatment.

Ok time for the soapbox
TAKE ALL OF YOUR ANTIBIOTICS! I don't care if you feel better after a week or so and there's still pills in the bottle. You take all of the prescription to kill off all of the virus or bacteria. If you don't finish with the treatment, you may feel better, but that little microorganism is still there and can take in some of that drug, change around how it works and become stronger. So the next time you're sick with that type of bug, it may be stronger and more immune to the old treatments. Because you didn't finish your pills the first time. These bugs can adapt to treatments and become stronger and then we end up with super bugs that there are no cures for because these bugs have outsmarted us.
FINISH THE PRESCRIPTION!
I'm done, I'll quit getting onto you like children now :)

These EID's can be caused by viruses, bacteria, protozoa's and prions. I'll list a few and what type of m.o. causes them

SARS- Severe Acute Respiratory Syndrome- bacteria
West Nile Encephalitis- virus
Bovine Spongiform Encephalopathy- aka Mad Cow Disease-prion- an infectious protein found in the protein additive given to cows
Creutzfeldt-Jakob Disease- CJD- human disease caused by a prion.
Escherichia Coli- or E. Coli- bacteria, the strain that is harmful is not the exact same as what's in our digestive tract that helps break down foodstuffs and produce certain vitamins.
Flesh-eating Bacterias- Invasive group A Streptococcus
Ebola Hemorrhagic Fever- virus
Marburg Virus
Cryptosporidiosis- protozoan
AIDS- we should know a little about this at least. Caused by the virus HIV that destroys certain white blood cells.

Ewwww Chemistry. Sorry Chemistry majors, most medical students hate this class. But trust me, this is just very basic stuff, no math! yay!

We need to understand some basic chemistry because many microorganisms are a series of chemical reactions.

Basic Principle- all living things are composed of matter; matter is composed of very small particles that form chemical building blocks.
An atom is the smallest chemical unit of matter. You can create elements which is matter composed of one kind of atom, such as oxygen which has two oxygens put together, (O2).
A molecule is two or more atoms that combine chemicall such as h2o (water), NaCl (sodium).
A Compound is molecules made up of atoms of 2 or more different elements.

Atoms contain a nucleus that contains protons (p+) and neutrons (no). Theses weigh about the same. Surrounding the atom is an Orbital that has the Electrons (e-) and have almost no mass. These spin around on electron shells that have different energy levels. The first level can fit 2 electrons, and each level after that can fit 8 electrons on it. This is helpful in a little bit.
The Atomic Number tells you how many protons are in an atom.
The Atomic Weight is the number of protons plus number of neutrons. Take the weight minus the atomic number and that's how many neutrons are in the atom. There are generally the same number of protons and neutrons.

Bonding:
The Collision theory says that all atoms and molecules are in constant motion, they collide with each otehr and transfer energy back and forth to disrupt electronic configurations (or the arrangements in the orbitals). Heat and enzymes can facilitate collision frequency and effectiveness resutling in a faster reaction rate.

Ionic bonding- is the attraction between two or more ions of opposite charges. An ion is formed because one molecule with gain or lose and electron giving that atom a positive or negative charge.
A Cation is a positively charged atom formed by the loss of an e-.
An Anion is a negatively charged atom formed the gain of an e-.
Electrons are the key here!

Covalent bonds are the strongest bonds. They share the electrons instead of stealing them. These can result in a Polar Molecule if there is an unequal distribution of electrons.
Example is H-H, or H2

Hydrogen bonds are the weakest. This is just an attraction between two or more melcules. A hydrogen atom that is covalently bonded to one oxygen or nitrogen atom that is attracted to another oxygen or nitrogen atom. These are bridges between different molecules.

Chemical Reactions
Catabolism is the decomposition of substances by a release of energy. This is an exergonic reaction. Exo means out of.

Anabolism is the synthesis of new substances that requires energy. This is an Endergonic reaction. Endo means into.

Inorganic Chemistry- this is molecules that don't have the elements C (carbon) & H (hydrogen). For microbiology purposes, Water is the most important biological inorganic molecule. Because living cells are made up of 60-80% water and most reactions in living systems occur in an aqueous environment and are very sensitive to the changes in acidity and alkalinity.
To measure the Acidity (H+) or Alkalinity (OH-) we use the pH scale. The range is 0-14. pH of 7.0 is neutral, and anything higher is alkaline, anything less than is acidic.
Buffers are chemicals that absorb excess acid or base (alkaline) so that the pH of the solution does not change. We all have buffer to maintain homeostasis with our pH. These also help m.o. to survive in adverse conditions.

Organic Chemistry is our biggie. These are molecules that ALWAYS contain C & H and are more complex in structure.

What's the big deal about Carbon?
It only has 4 electrons in the outer shell, so it can covalently bond to many elements for chemical reactivity. Generally to make Macromolecules (BIG molecules).

1. Carbohydrates- sugars and startches. Mainly for energy sources and is composed of C, H, and O.
There are 3 major groups.
a. Monosaccharides- simple sugars with 3-7 carbons. Glucose (dextrose), Fructose, and Galactose
b. Disaccharides- 2 monosaccharides linked together.
Sucrose- glucose + fructose
Maltose- glucose + glucose
Lactose- glucose + galactose
c. Polysaccharides- many monosaccharides linked together such as starch, cellulose, glycogen.

2. Lipids- faths, phospholipids and steroids. These are mostly for structural support and are composed of C, H, O and some contain P (phosphorus).
Fatty Acids are the building blocks of lipid macromolecules.

3. Proteins- mostly structural and Enzymatic, speeds up chemical reactions. Composed of C, H, O, N and sometimes S (Sulfur). Amino acids are the building blocks of proteins (contain a Carboxyl group --COOH) and are linked together by a peptide bond. These are bonded together by a release of water molecule and occurs by a dehydration synthesis.

4. Nucleic Acids- DNA and RNA and are used for the transfer of genetic information for protein synthesis. Composed of C, H, O, N, P. Nucleotides are the building blocks.

5. Adenosine Triphosphate- or ATP (eww the math crazy part)This is mainly for the transfer and storage of energy for the cell. But we won't go into the major reactions. Composed of C, H, O, N, P. Have special nucleotide structures.

I think most of us know what that is. But in Microbiology they generally use a compound Light microscope. This uses two sets of lenses (ocular & objective) and visible light to see specimens.

Total Magnification is the product of ocular and objective magnification. The ocular lens is always 10X, objective lenses are usually 4X, 10X, 40X, and 100X. So multiply 10 by whatever objective lens you're on.

Resolution is the ability of the lenses to distinguish fine detail. To keep light from bending (refractive index) we use an immersion oil, only one 1000X magnification though. This oil keeps light from bending whichever way and creating shadows on the specimens.

Staining also helps us see m.o.'s.
Simple stains- used for almost any type of cell, only one dye to color all of the cell.
Special stain- more involved process to selectively color special parts of cells
Differential stain- uses multiple dyes that react differently with different types of cells.
Gram Stain- special staining process for Microbiology.
Some genera of m.o. will stain blue/purple, these are Gram (+), others will stain red/pink, these are Gram (-).

There are two types of cells, we will deal with Procaryotic cells mostly. They have no nucleus or membrane bound organelles. Within procaryotes are Archeabacteria- m.o. that lack peptidoglycan in cell wall, found in more atypical environments.
Eubacteria- all other m.o. that contain peptidoglycan in cell wall.

Procaryotic cells are small and come in three basic shapes, Spherical (coccus), Rodlike (bacillus), and Spiral (vibrio, spirillum). Some can be Pleomorphic and have different shapes during one life cycle.

Strepto means chains of cells
Staphylo means clusters of cells
and Diplo means paired cells

Some of these cells have Glycocalyx, which is a sticky substance that surrounds the cells. There are two types
1. Capsule- thick, smooth cage
2. Slime Layer- thin, rod like.
These make staining difficult.

Flagella can be found on many cells too. This is a long filamentous appendage that rotates and allows the cells to move around or Chemotaxis- motility via random darting and tumbling in response to a chemical "Signal".
There are monotrichous with one flagellum, amphitrichous that have flagella on both ends, lophotrichous that have a cluster of flagella on one end, and peritrichous with flagella surround the cell.

Pilus and Fimbriae are short, hairlike appendages. Fimbriae allow m.o. to attach for colonization. Pili allow m.o. to attach to each other for reproduction.

A Gram (+) cell wall composition.
There is a Peptidoglycan (disaccharide) attached to polypeptides in lattice arrangement. See pictures below.
The Disaccharide has N-Actylglucosamine (NAG) and N-Acetylmeranic Acid (NAM).

The Gram (-) cell wall composition.
See picture below

An acid fast m.o. need an Acid-Fast stain, this identifies all bacteria of the genus Mycobacterium and pathogenic species of Nocardia. There is a high concentration of a hydrophobic waxy lipid (mycolic acid) that prevents uptake of dyes. These will stain reddish.

A Lysozyme is a natural enzyme found in tears, saliva, and mucus that disrupts the peptidoglycan (PG) layer of the m.o.
Antibiotics such as Penicillin interfere with m.o. synthesis of PG resulting in leaky, fragile cells.

Fluid Mosaic plasma membrane- the dynamic arrangement of phospholipids and proteins.

Almost done! Woohoo!

There are different ways materials can move in and out of cells. We'll start with passive transports

Passive transport:
1. Simple Diffusion- moves gas molecules & ions
2. Facilitated Diffusion- some larger compounds (glucose, amino acids) need help of carrier proteins called permeases to enter cells
3. Osmosis- movement of water through a semipermeable membrane.

And here is where we deal with Iso-, Hypo-, and Hypertonic solutions. See pictures below for these.

Active transport- movement of material against the concentration gradient (from low to high concentration); requires Energy (ATP) & special carrier proteins. Cells use active transport during nutrient deprivation to hoard essential material for survival.

Intracellular structures:
Cytoplasm- internal matric that is 80% water.
Ribosomes- site of protein synthesis, composed of RNA & protein.
Chromosomes- in nuclear region, double-stranded DNA, contains genes essential for survival
Plasmid- short circular moelcules of double stranded RNA; contains nonessential DNA or "Special genes"

Inclusions- storage for reserve deposits of material.
a. metachromatic granules (volutin)- excess phsphate for ATP, phospholipid synthesis.
b. Polysaccharide granules- excess starch, glycogen for Energy sources
c. Magnetosomes- iron oxide stores to provide orientation for soil & aquatic m.o. via magnetism
d. Gas vesicles- hep maintain buoyency for aquatic m.o.

Endospores- dormant stage formed when unfavorable conditions occur, only some m.o. (Gram +) can do this. Especially Clostridium sp. & Bacillus sp.

Linnaeus developed classification system of the 2 name nomenclature or taxonomy. Based on the Latin language.
There can be a 3rd name added, this is to indicate a "strain" or a slight differences between speices members or document specific isolation information.

Taxonomy Rules
1. Genus name first, Capitalize first letter.
2. Species name second, all small letters
3. Underline or italicize both words
4. strain designation goes last, may include numbers and or letters.