study of organisms too small to be clearly seen by unaided eye

organisms are simple and lack differentiated cells and distinct tissues 

small size, simple undifferentiated structure 

presence of plasma membrane is main distinguisher

also has nucleus

lacks true membrane bound nucleus

still considered a cell since it has a plasma membrane 

membrane bound nucleus

more complex morphology

usually larger

based on ribosomal RNA genes

1. bacteria 

2. archaea

3. eukarya 

all prokaryotic

all are single-celled

most have peptidoglycan in cell wall 

can survive broad range of environments

most are non-pathogenic

nutrient recycling 

all prokaryotic

unique ribosomal RNA sequences

lack peptidoglycan

unique fatty acids/membrane lipids

many found in extreme environments

no pathogenic species known to humans 

all eukaryotic

animals, plants, eukaryotic microorganisms

m/o's include protists, protozoa, slime molds, water molds, fungi (yeast, mold)

generally larger

bacteria/archaea 

types of microbes 

rigid cell wall, no nuclear membrane 

1-5 um

prokaryote

fungi

types of microbes

rigid cell wall, nuclear membrane 

4-25 um

eukaryote

protozoa

types of microbes

no rigid cell wall, nuclear membrane

eukaryote 

algae

types of microbes

rigid cell wall, nuclear membrane 

eukaryote

helminths 

types of microbes

parasitic flat and round worms 

don't need a microscope to see but still relatively small 

acellular

cannot multiply outside host

smallest of all microbes

cause a range of diseases

nucleic acid(genome) - ss/ds DNA or ss/ds RNA

protein coat (capsid)

some have an envelope 

attack bacteria

usually ds DNA 

first person to observe and describe microorganisms accurately 

used primitive form of microscope 300x magnification 

refuted spontaneous generation theory 

fermentation

pasteurization 

contributed to germ theory

vaccine development 

system of surgery designed to prevent m/o's from entering wounds and treating instruments and dressings

used phenol

indirect evidence m/o's were causal agents of disease 

established direct evidence that m/o's cause disease

4 postulates

1. microbe must be present in all with disease and associated with lesions of the disease

2. microbe must be isolated in pure culture 

3. isolated microbe must cause disease when administered to another healthy patient

4. microbe must be isolated in pure culture with the second infected patient

cowpox lesions to protect people against smallpox

"attenuated vaccine"

immunology field 

studied soil m/o's 

discovered numerous metabolic processes 

oxidizing bacteria (use other substances as energy source)

selective media

microbial ecology 

most are compound

image formed by action of >2 lenses

use light source

dark image on light background

several objective lenses

measure of how greatly a substance slows the velocity of light

based on angle, speed

determines direction and magnitude of bending based on refractive index differences between 2 media 

distance between center of lens and point at which light rays converge

decreasing focal length increases the magnification 

resolving power

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

shorter wavelength increases resolution

n(sin)theta

relationship between focal length and working distance 

decreasing d increases resolution 

decreasing lambda increases resolution

increasing numerical aperature increases resolution 

bright image on dark background

used on living unstained organisms

converts slight differences in refractive index and cell density into easily detected variations in light density

observes living cells, internal structures 

uses dark field stop 

stain specimens with fluorochromes

expose to UV light with short wavelength and high energy

confocal scanning laser microscopy (CLSM) 

sharp composite 3D image using lawser beam, aperture, and computer interface

laser beam can view layers and then superimpose them for 3D

electrons replace light as illuminating source

short wavelength results in higher resolution

transmitted electrons under vacuum which reduces scatter and are used to produce a clear image 

complicated staining procedure

3D image of surface features

electrons released from atoms on an object's surface (secondary electrons) 

easier preparation 

1. scanning tunneling

2. atomic force 

needlelike probe with 1 atom at tip

electrong cloud just touches surface atom to create tunnel current

may examine objects immersed in water 

cantilever moves up and down to maintain constant height above organism's surface

good for samples that don't conduct electricity well 

absolute requirement for all living organisms

encompasses cytoplasm

selectively permeable barrier

interacts with external environment through receptors, transport systems, metabolixc processes 

fluid mosaic model: lipid bilayer in which proteins float

1. peripheral (loosely connected, easily removed)

2. integral (ampipathic, not easily removed)

eukaryotic: contain sterols 

bacterial: hopanoids (sterol-like molecules)

saturation levels of membrane lipids reflect living conditions

unsaturated: lower melting point

cold environments have more unsaturated fatty acids

peptidoglycan layer

rigid structure just outside plasma membrane

G(+) or G(-) based on peptidoglycan layer 

maintains shape

protects against osmotic lysis and toxic materials

may contribute to pathogenicity

thick peptidoglycan layer

purple

aka monoderm

inner wall zone/periplasmic space between peptidoglycan and plasma membrane 

large amount of techoic acids

few proteins in periplasmic space 

some have protein layer on surface of peptidoglycan 

thin peptidoglycan, outer membrane, and plasma membrane with periplasmic space 

outer membrane composed of lipids, lipoproteins and Lipopolysaccharide (LPS)

no techoic acid

many enzymes in periplasm 

Lipopolysaccharides

3 parts

1. O side chain (O Ag)

2. core polysaccharide

3. lipid A

restricts entry of bile salts

endotoxin 

mesh-like polymer of identical subunits

2 alternating sugars (NAG and NAM)

alternating D and L amino acids strengthens structure 

helical shape

peptidoglycan chains are crosslinked by peptides for strength

interbridges may form 

variety of amino acids form bridge to cross length strand so strands can become iterconnected

Additional layers outside cell wall

1. Capsule

2. Slime Layer 

3. S Layer

usually composed of polysaccharides

well organized, not easily removed from cell 

visible in light microscope via negative stain

protective advantages (resistant to phagocytosis, protect from desiccation, protect from viruses and other predators)

similar to capsule but difuse and unorganized

still made of polysaccharide

easily removed

may aid in motility

regularly structured layers of protein or glycoprotein that sel-assemble

potential use in nanotechnology

varies between species but usually consists of complex heteropolysaccharides

lack peptidoglycan but some have pseudomurein (looks like peptidoglycan but only L amino acids and NHAc instead of NAM)

most commen cell wall is S layer

unique lipids 

monolayer instead of bilayer

composed of unique lipids

isoprene units (5 carbon, branched)

ether linkages to glycerol (not ester)

some have monolayer instead of bilayer structure

substance in which nucleoid, ribosomes, and inclusion bodies are suspended 

lacks organelles bound by unit membranes

mostly water

no true cytoskeleton but homologs of eucaryotic cytoskeletal elements 

plasma membrane infoldings

in many photosynthetic bacteria 

analogous to thyladoids of chloroplasts

rxn centers for ATP formation

aggregates of organic or inorganic material thare are stockpiled by cell for future use

free in cytoplams or enclosed by membrane

vary in compostion

granules of glycogen, PHB as carbon storage

gas vacuole/vessicle provide buoyancy for many cyanobacteria 

found in aquatic bacteria

contain magnetite particles for orientation in earth's magnetic field

bacterial cytoskeletal protein MamK helps from magnetosome chain 

sites of protein synthesis

complex structures consisting of protein and ribosomal RNA 

made up with different subunits

S = svedberg unit (fxn of weight, volume, shape)

irregularly shaped region in bacteria and archaea 

no nuclear membrane

location of chromosome and associated proteins

usually 1 per cell

closed circular, ds DNA molecule

supercoiling and nucleoid proteins (HU protein) aid in folding

extrachromosomal DNA

in bacteria, archaea, some fungi

sm, closed circular DNA molecules

exist/replicate independently of chromosome

genes on plasmids are not essential but may confer selective advantage

may exist in many copies in the cell 

extend beyond cell envelope in bacteria and archaea

protection, attachment, horizontal gene transfer, cell movement

1. pili and fimbriae

2. sex pili

3. flagella 

short, think, hairlike, proteinaceous appendages

up to 1000 per cell

mediate attachment to surfaces

type IV fibriae required for motility on solid surface

uptake DNA via transformation

longer, thicker, and less numerous

genes for transformation found on plasmids

required for conjugation

direct uptake from another cell

not really sex but transfer plasmid from donor to recepient 

threadlike, locomotor appendages extending outward from plasma membrane and cell wall

swimming and swarming behaviour, attachment, virulence factor

monotrichous: 1 flagellum

polar flagellum: at one end of cell

amphitrichoud: at each end

lophotrichous: cluster at one or both ends

peritrichous: spread over entire surface

filament: extends from cell surface to tip. hollow rigid cylinder composed of flagellin protein sometimes containing outer sheath

basal body: series of rings that drive flagellar motor

hook: links filament to basal body

complex process

similar to type III secretion system

flagellin self-assemble with help of filament cap

growth from tip 

thin

more than one type of protein

not hollow

hook and basal body difficult to distinguish

more related to type IV secretion

growth at base

axial filaments found in spirochetes

exhibit flexing and spinning movements

located in periplasmic space

multiple flagella intertwined and wind around cell

complex, dormant structure formed by some bacteria

resistant to numerous environmental conditions 

calcium complexed with dipicolinic acid

small, acid-soluble, DNA binding proteins (SASPs)

dehydrated core

spore coat and other protective layers

DNA repair enzymes

protein + nucleic acid

demonstrated that the causative agent of tobacco mosaic disease passed through bacterial filters

thought agent was a toxin

complete virus particle

consists of >1 molecule of DNA or RNA enclosed in protein coat (nucleocapsid)

may have additional layers and projecting spikes

10-400nm diameter

cannot reproduce independently outside living cells 

when a temperate phage causes a change in the phenotype of an infected bacterial cell

may project from envelope surface as spikes or peplomers

mostly glycoproteins 

involved in viral attachment

may have enzymatic or other activity

used for viral ID

M protein (nonglycosylated) on inner surface for stabilizing

some are associated with the envelope or capsid but most are within capsid

may play a role in nucleic acid replication 

shaped like hollow tubes with protein walls 

protomers self-assembe 

7-8 segmented nucleocapsid 

RNA

each coated by capsid

icosahedron = regular polyhedron with 20 equilateral faces and 12 vertices

1 of natures favorite shapes

1. attachment or adsorption to host

2. entry or penetration (uncoating)

3. uncoating of genome

4. synthesis

5. assembly 

6. release