Microbio Unit I

Microorganism

Generally smaller than or equal to one mm in diameter. These are acellular entities that are too small to be clearly seen by the unaided eye.

Cellular microbes include

Fungi, protists, bacteria, and archaea

Acellular microbes include

Viruses, viroids, satellites, and prions

Yeasts and molds

Types of fungi

Algae, protozoa, and slime molds

Types of protists

E.coli

Type of bacteria

Methanogens

Types of archaea

Protein and nucleic acid

What viruses are composed of

RNA

What viroids are composed of

Nucleic acid, often RNA

What satellites are composed of

Protein

What prions are composed of

Properties of some cells

Differentiation, communication, motility, and horizontal gene transfer

Properties of all cells

Structure, metabolism, growth, and evolution

Cell Structure

Cytoplasmic membrane, cytoplasm, a genome made of DNA, and ribosomes

Cell metabolism

All cells take up nutrients, transform them, conserve energy, and expel wastes

Catabolism

Transforming molecules to produce energy and building blocks

Anabolism

Synthesizing macromolecules

Differentiation

Some cells can form new cell structures such as a spore

Communication

Cells interact with each other by chemical messengers

Eukaryote size

0.8 micrometer to hundreds of micrometers

Bacteria/Archaea

0.2 micrometer to 750 micrometers

Virus size

0.01 micrometer to one micrometer

Perks of having a larger surface area

More rate of diffusion and more transporters

Perks of having a small volume

Better mixing in the cell

LUCA

Last universal common ancestor

Universal Phylogenetic Tree

Woese in 1977 compared rRNA sequences — specifically the 16s in prokaryotes — and found that by comparing the nucleotide sequences, the three-domain system became.

Eukarya microbes

protists, fungi

Microbial Species

These share many stable properties and differ significantly from other groups of strains (these are monophyletic)

Microbial Strain

Descendents of a single, pure microbial culture

Importance of microorganisms

Oldest form of life, most populous and diverse group of organisms, major fraction of biomass and key reservoir of essential nutrients, recycle essential elements, influences all other living things

Robert Hooke

First to use the microscope but only saw fungi

Leuuwenhoek

First to observe and describe bacteria accurately (looked at his plaque and giardia)

Redi

Discredited spontaneous generation for large animals

Pasteur

Disproved spontaneous generation for microbes, contributed to attenuation, and created vaccinations for chickenpox, cholera, anthrax, and rabies

Lister

Said to wash surgical instruments in between patients

Semmelweis

Said to wash hands in between autopsies and child labor

Koch

Established a relationship between bacillus anthracis and anthrax. Also, investigated mycobacterium tuberculosis and tuberculosis.

Koch’s Postulates

1. Pathogen must be present in ppl with the disease and people without the disease should not have the pathogen

2. You must be able to grow the pathogen in a pure culture

3. You must be able to take the culture and put it in a healthy organism

4. The pathogen must be reisolated and shown to be the same as the original

Refractive Index (n)

Measure of how greatly a substance slows the velocity of light

Parfocal

Stays in focus

Parcentric

Stays centered

Resolution (d)

Ability of a lens to separate or distinguish small objects that are close together

Wavelength’s importance to microscopy

The shorter the wavelength, the better resolution

Numerical Aperture

Measure of light gathering ability : higher this value is, the better resolution

Heat Fixation

Organism is killed and attached to the micro slide. This preserves the morphology and shape of the organism.

Chem Fixation

Organism is used with large and more delicate organisms like tissue. This preserves internal structures.

Basic Dyes

Binds to negatively charged structures like proteins, nucleic acids, and the surface of most bacterial cells.

Acidic Dyes

Binds to positively charged structures like cytoplasm, RBCs, and collagen

Simple Staining

Single color to see shape and arrangement on a slide.

Differential staining

One or more dye to differentiate between types of cells or structures.

Steps of gram staining

Crystal violet and rinse, iodine and rinse, decolorize and rinse, safranin and rinse, and blot dry

Acid-Fast staining

Useful for staining members of the genus like mycobacterium that has high lipid content in the cell walls.

Endospore staining

Type of structural staining that requires heat and where one thing is one color and the other vegetative cell is a different color.

Capsule staining

This is a negative stain and this is colorless against a stained background

Flagella staining

Mordant is applied to increase the thickness of this.

Cell types: differential staining

Gram staining and acid-fast staining are this type of stain.

Three domains of life

Eukarya, bacteria, and archaea

Bacteria and Archaea relatedness

These are both unicellular but one has a cell membrane composition and cell wall structure

Culture Media includes

Macronutrients, micronutrients, and growth factors

Complex Media

This media is a variety of undefined components

Defined Media

This media can offer more control over the growth conditions and is used when studying specific microorganisms

Peptones

A protein in complex media that hydrolysates by partial digestion of various protein sources.

Extracts

These are in complex medias and are aqueous beef or broth

Agar

A sulfated polysacc that is used to solidify liquid media

General Purpose Media

Supports the growth of many microorganism (e.g tryptic soy agar)

Enriched Media

A general-purpose media that is supplemented by blood or other special nutrients (e.g chocolate agar)

Minimal Media

Contains the minimal necessities for growth of the wild-type and only contains inorganic salts, a simple C source, and water

Selective Media

This favors the growth of some microorganisms and inhibits the growth of others (e.g MacConkey agar, antibiotics, bile, certain dyes, high salt concentration)

Differential Media

Distinguishes between different groups of microorganisms based on their biological characteristics

Blood agar

Hemolytic versus nonhemolytic bacteria involves this agar

MacConkey agar

Lactose fermenters versus nonnfermenters involves this agar

Spread Plate

Small volume of diluted culture is transferred to agar surface, and the culture is spread evenly over surface with a sterile hockey stick

Pour Plate

These have diluted samples that are mixed with liquid agar. A mixture of cells and agar are poured into sterile culture dishes.

Both spread and pour plates provide

Isolated colonies, opportunity to enumerate the bacteria in a sample, and a countable plate

Countable plate

30-300 colonies

Major functions of cell membrane

Permeability barrier, protein anchor, and energy conservation

Hopanoids

Bacterial sterols that stabilize the membrane

Peripheral proteins

These are loosely connected to the membrane and comprise up to 20- 30% of the membrane proteins

Integral Proteins

These are embedded within the membrane and comprise up to 70-80% of the membrane proteins. They also carry out important functions such as transportation, secretion, and energy conservation.

Gram positive cell wall

Plasma membrane, gap, and heavy peptidoglycan layer

Gram-negative cell wall

Plasma membrane, gap, extremely thin peptidoglycan, huge gap, and outer membrane

Components of mesh like polymer in peptidoglycan

N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)

E. coli

This bacteria has direct linkage

S. aureus

This bacteria has indirect linkage

90%

The peptidoglycan in gram-positive cells make up this much

Teichoic acids

These are negatively charged and are in gram positive cells

Lipoteichoic acids

These are attached to the membrane of lipids

10%

The peptidoglycan in gram-neg cells make up this much

Lipids, lipoproteins, and lipopolysaccharide

What makes up the outer membrane in gram- negative cells

Periplasmic

This space is in gram-negative cells and contains hydrolytic enzymes, transport proteins, and other proteins

Braun’s lipoproteins

These connect outer membrane to peptidoglycan in gram-neg cells

Lipid A, core polysacc, a negative charge, and O antigen

Parts of a lipopolysaccharide (LPS)

Lipid A

This helps stabilize outer membrane and can act as an endotoxin

O antigen

This can protect but also trigger host defenses

Lysozome

This breaks the bond between NAG and NAM

Penicillin

This inhibits peptidoglycan synthesis

Lysozome and penicillin

If cells are treated with either of these, they will lyse in a hypotnic solution.

Capsules

Composed of polysaccharides, well organized and not easily removed from a cell, is resistant to phagocytosis, protects from desiccations, and excludes viruses and detergents.

Slime Layers

These diffuse and are easily removed. The slime aids in motility.

Fimbriae

Short and thin, hairlike appendages. These mediate attachment to surfaces.