mibo 3500 module 1

Microbes

organisms and acellular agents too small to be seen by the unaided eye

Domain Bacteria

single-celled organisms, most with peptidoglycan cell walls
they lack a membrane-bound nucleus
they can live in extreme environments
some are diseases causing, others do not cause diseases

Domain Archaea

Distinguished from Bacteria by unique rRNA gene sequences
Lack peptidoglycan in cell walls
Have unique membrane lipids
Some have unusual metabolic characteristics
Many live in extreme environments
Do not directly cause disease in humans

Domain Eukarya

includes Kingdoms Protista, Fungi, Plantae and Animalia

Protists

single-celled, but larger than bacteria and archaea
protozoa have animal like metabolism and movement
algae are photosynthetic

Fungi

unicellular or multicellular
yeast is unicellular
molds and mushrooms are multicellular

Viruses

composed of nucleic acid and protein (some have lipids too)
no "cellular" structure
invade a host organism to reproduce themselves

Prions

misfolded proteins
interactions between them and other proteins can spread misfolding to the other proteins

Robert Hooke (1635-1703)

built the first compound microscope
used it to observe mold, fleas, cork
published book Micrographia with these observations
coined the term "cell"

Antonie van Leeuwenhoek (1632-1723)

built single-lens magnifiers
first to observe single-celled microbes
he called these microbes "small animals"

spontaneous generation

the mistaken idea that living things arise from nonliving sources and debated by many historical scientists

Francesco Redi (1626-1697)

discredited spontaneous generation
showed that maggots on decaying meat came from fly eggs

Louis Pasteur (1822-1895)

showed microbes caused fermentation and spoilage (through experiment with swan-necked flask)
disproved spontaneous generation of microorganisms
developed pasteurization
demonstrated what is now known as Germ Theory of Disease

Robert Koch (1843-1910)

established his postulates - a sequence of experimental steps that verified the germ theory
identified cause of anthrax by looking at Bacillus anthracis
developed pure culture methods

Koch's Postulates

1) Pathogen must be present in all disease cases
2) Isolate pathogen, cultivate in pure culture
3) Inoculate into susceptible host, initiate disease symptoms
4) Re-isolate pathogen from 2nd host, confirm it's the same pathogen

Sergei Winogradsky (1856-1953)

among the first to study bacteria in natural habitats
built the his column: wetland model ecosystem looking at soil bacteria
showed importance of bacteria in geochemical cycling

Resolution

the ability to distinguish small objects close together

Magnification

an enlarged image of an object

Contrast

the difference in color intensity between an object and its background

light microscopes

use light and glass lenses to magnify an image, also known as compound microscopes (image formed from 2+ images)

Bright Field Microscopy

used to examine stained and unstained specimens
produces a dark image against a bright background
has several objective lenses producing different magnification
limitations

• only resolves 0.2 micrometers
• most cells are colorless, and staining kills cells
• light refraction is problematic

Refraction

bending of light as it passes through an object that slows its speed

Dark Field Microscopy

microbes are visualized as halos of bright light against darkness
this allows the detection of very narrow cells, unresolved by bright-light microscopy
light here shines at oblique angle, so only light scattered by the sample reaches the objective

Phase Contrast Microscopy

produces image of a dark microbe against a light background
deviated and undeviated light combined in a condenser to generate an image
this is a good way to observe microbial movement and detect bacterial structures

Fluorescence Microscopy

produces an image by exciting a specimen with a wavelength of light that triggers the object to emit fluorescent light
microbe is stained by fluorochromes that absorb light and emit visible fluorescent light - with antibody tags

Antibody Tags

stains linked to antibodies can identify precise strains of bacteria or even specific molecular components of cells, with fluorophores attached they can be visualized in fluorescence microscopy

Electron Microscopy

uses electrons instead of light
the shorter wavelength of electrons gives greater resolution
allows for microbial morphology to be studied in detail

Scanning Electron Microscope (SEM)

a microscope that uses an electron beam to scan the surface of a sample to study details of its topography

Transmission Electron Microscope (TEM)

a microscope that uses an electron beam to study the internal structure of samples

Gram Stain

a staining method that distinguishes between two different kinds of bacterial cell walls, identifying gram-positive and gram-negative bacteria

Peptidoglycan

a rigid structure that lies just outside the plasma membrane in bacteria, composed of sugars and amino acids

Gram-Positive Bacteria

bacteria that have a thick peptidoglycan cell wall, and no outer membrane
they stain very darkly (purple) in gram stain

Gram-Negative Bacteria

bacteria that have a thin peptidoglycan cell wall covered by an outer plasma membrane
they stain very light red in gram stain

Gram-Staining Procedure

1) crystal violet stains all cells purple
2) iodine acts as a mordant that enhances the binding of crystal violet to cell walls
3) alcohol decolorizes the sample, Gram-positive cells stay purple, Gram-negative cells lose color
4) Safranin stains Gram-negative cells pale red

Coccus

a spherical bacterium

Diplococci

bacteria which divide and remain in pairs

Streptococci

divide on 1 plane to form chains

Tetrads

divide in 2 planes forming a square of 4 cocci

Staphylococci

divide in random planes making grape-like clusters

Sarcina

divide in 3 planes making cubic packet of 8 cocci

Bacillus

Rod shaped bacteria

Coccobacilli

short and wide rods

Diplobacilli

divide and remain in pairs

Streptobacilli

divide on 1 plane to form chains

Palisades

divide on irregular plane (hinge-like)

Surface Area to Volume Ratio

a variable that decreases as cells grow, so that it sets a limit to the size of cells
high _ increases efficiency of nutrient uptake and diffusion of molecules within a cell

Plasma Membrane

a selectively-permeable phospholipid bilayer forming the boundary of the cells

Amphipathic Lipids

one end of each molecule is hydrophilic and the other end is hydrophobic

Hydrophilic Head

polar ends of phospholipid that interact with water

Hydrophobic Tail

non-polar end of phospholipid that are insoluble in water and interact with one another to form bilayer

Hopanoids

prokaryotes use these instead of cholesterol in their plasma membranes
they form functional membrane microdomains that allow for protein complex assembly
they impact fluidity and shape of the membrane - enhance stability, decrease permeability

Peripheral Membrane Proteins

proteins associated with but not embedded within the plasma membrane
they are involved in cell signaling and communication

Integral Membrane Proteins

a protein embedded in the lipid bilayer of a cell
these are typicallly cell surface receptors, channels, or pumps involved in diffusion and transport

Nucleoid

a non-membrane-bound region in a prokaryotic cell where the DNA is concentrated
it is the location of the chromosome and associated proteins
the chromosome is usually 1 closed circular dsDNA molecule

Plasmids

small circular DNA molecules that replicate separately from the bacterial chromosome
often, they carry genes that confer a selective advantage in some situations

Episomes

plasmids that can integrate into the bacterial chromosome

Inclusion Bodies

storage sites for nutrients during periods of abundance, segregating so they don't diffuse into cytoplasm
some are enclosed by a single-layered protein or lipid shell
can be referred to as microcompartments

Ribosomes

complex protein/RNA structures where proteins are synthesized
the bacterial and archaea ones are 70S
rRNA in bacteria is 16S in small subunit
rRNA in bacteria is 23S and 5S in large subunit

Sex Pili

appendages that pull two cells together prior to DNA transfer (called conjugation) from one cell to the other
they are long and thick, and there are around 10 per cell
they are encoded on plasmids

Fimbriae

short, thin, hairlike protein appendages
there around 1000 per cell
they mediate cell attachment to surfaces and motility

Flagella

whiplike tails found in one-celled organisms to aid in movement, can also help with cell attachment and virulence factors

Monotrichous

single flagellum

Polar Flagellum

flagellum at end of cell

Amphitrichous

flagella at both poles of the cell

Lophotrichous

cluster of flagella at one or both ends

Peritrichous

flagella distributed over the entire cell

Flagella Rotation

can rotate either clockwise (stop and tumble) or counterclockwise (run)
rotate rapidly, like a propellor

Sacculus

another word for cell wall

Cell Wall

confers the shape and rigidity to the cell
protects the cell membrane

Peptidoglycan Structure

disaccharide of glycan with attached peptide of 4-6 amino acids
NAG: N-acetylglycosamine (shorter, OH-H),
NAM: N-acetylmuramic acid (longer, H/O-HC-CH3-C=O-OH).
they are linked by Peptide Interbridge
they are unique to bacteria

Penicillin

an antibiotic that targets transpeptidase, which is the enzyme that cross-links the amino acids in peptidoglycan

Teichoic Acids

a glycerol or ribitol phosphodiester chain found in Gram-positive bacterial cell walls
the multiple layers of peptidoglycan in Gram-(+) are threaded with these

Lipopolysaccharides (LPS)

an endotoxin produced by gram-negative bacteria that elicit an inflammatory response if absorbed into circulation (cytokine storm overstimulates immune cells)
it consists of 3 parts

• Lipid A
• Core Polysaccharide
• O Side Chain

Lipid A

the lipid component of lipopolysaccharide, it is buried in the outer membrane

Core Polysaccharide

10 sugar structure joined to lipid A

O Side Chain (O Antigen)

polysaccharide that extends outward from the core

Hypotonic Environments

-solute concentration outside the cell is less than inside the cell
-water moves into cell and cell swells
-cell wall protects from lysis

Hypertonic Environments

-solute concentration outside the cell is greater than inside
-water leaves the cell
-plasmolysis occurs (cell wall protects from this)

Extracellular Vesicles

-small membrane-bound particles (20 to 400 nm in size)
-develop when a membrane buds out, pinches off, and is released from the cell

Gram-Positive Extracellular Vesicles

made of the plasma membrane surrounding a small amount of cytoplasm

Gram-Negative Extracellular Vesicles

made of LPS-containing outer membrane surrounding a sample of periplasm

Capsules

well organized layers made of polysaccharides that are covalently bonded and difficult to wash away
visible in light microscope
resistant to phagocytosis and protect the cell from desiccation

Slime Layers

polysaccharide layers that are unorganized and easily washed away

Glycocalyx

polysaccharide extension that aids in attachment to solid surfaces

S-Layers

geometric pattern made of protein that aid in protecting from ion and pH fluctuations
can be found in Archaea
promote adhesion to surfaces and protects cell from host defenses

Genus Mycobacterium

• contains mycolic acids (fatty acid structure/protection for cell)
• mycolic acids linked to arabinogalactan (polysaccharide) linked to peptidoglycan
• 1 plasma membrane

Genus Mycoplasma

-no cell wall/do not retain crystal violet
-pleomorphic (come in many shapes)
-extremely small (0.3 micrometers)
-grow as fried egg appearance on agar surface
-cannot synthesize peptidoglycan, but sterols can stabilize plasma membrane

Culture Medium

solid or liquid mixture of nutrients and other compounds
it must contain all growth factors a microbe requires

Peptones

partial proteolytic digestion of protein sources

Extracts

aqueous extracts that contain amino acids, peptides, nucleotides, organic acids, vitamins, and minerals
usually beef or yeast

Agar

sulfated polymer solidifying agent
most microorganisms cannot degrade it

Macronutrients

needed in large amounts:

• Carbon
• Magnesium
• Nitrogen
• Iron
• Phosphorus
• Potassium
• Hydrogen
• Calcium
• Oxygen
• Sulfur

Micronutrients

needed in small amounts:

• Cobalt
• Copper
• Manganese
• Molybdenum
• Nickel
• Zinc

Supportive Media

support the growth of many microorganisms
trytic soy broth and agar

Enriched Media

supportive media supplemented with special nutrients (blood agar)

Selective Media

suppress growth of unwanted bacteria and encourage growth of desired microbes

Differential Media

distinguish among different groups of microbes and even permit tentative identification of microbes based on their biological characteristics

Anaerobic Microbes

• these microbes cannot tolerate O2 and must be grown without O2
• anaerobic media with reducing agents
• anaerobic chamber
• hard transparent containers sealed tightly
• candle Jar

Pure (Axenic) Culture

a population of cells that are identical because they arise from a single cell

Streak Plate

a technique for isolating pure cultures by spreading organisms on an agar plate, looking for separate colonies