• the study of organisms too small to be seen with the human eye
• bacteriology, virology, mycology, parasitology, foor microbiology, environmental microbiology, forensic microbiology

• says organisms can arise from non-living matter
• theory was disproved by Leeuwenhooke with the meat in the jar test -Biogenesis theory is accepted now (organisms arise only from other living organisms)

• father of modern microbiology
• demonstrated that the air is filled with microorganisms using the swan-necked flasks and the cotton plugs

• food production (fermentation)
• bioremediation (degrade environmental waste)
• synthesis (of ethanol, pesticides, antibiotics, dietary amino acids)
• genetic engineering (produce medically important products)

1. infectious diseases
2. emerging diseases

1. 750 million cases each year in the U.S. resulting in 200,000 deaths
2. diseases that increased in incidence in the past 20 years; examples: Legionnaire's, Lyme, West Nile, SARS

• diseases thought to be "defeated" increasing in frequency
• often more serious
• reasons for resurgence: increased visitors of one region to another bringing foreign organisms, unvaccinated individuals

1. incidence
2. prevalence
3. incubation period
4. zoonotic

1. # of new cases
2. total # of cases
3. symptom-free period of a disease
4. prevalent in animals

• metabolism same as high forms of life
• genetic properties mimic other organisms
• building blocks of macromolecules same as other life forms
• "what is true for an elephant is also true of a bacteria"

• Bacteria
• Archaea
• Eucarya

• single-celled organisms
• PROKARYOTES (no membrane-bound nucleus)
• no membrane-bound organelles
• cytoplasm is surrounded by rigid cell wall 

• may be single or multicellular
• EUKARYOTES (contain membrane-bound nucleus)
• contain membrane-bound organelles

• most common type in human infection
• have specific shapes, rigid cell walls, multiply by binary fission, some are motile

• almost the same as Bacteria (same shapes, mode of multiplication and motility)
• chemical compostion of cell wall differs
• organisms of this domain are found in extreme environments (extreme temperatures, high concentrations of salts)

• algae
• fungi
• protozoa

• single and multicellular organisms
• all contain chlorophyll (energy source)
• usually found near surface waters
• rigid cell wall

• single and multicellular organisms (single = yeast; multi = molds)
• gain energy from organic materials
• found mostly on land

• microscopic, single-celled organism
• found in water and on land
• complex
• no rigid cell wall
• gains energy from organic matter
• most are motile

• non-living
• called agents, not organisms

• consist of either DNA or RNA surrounded by a protein coat
• require host to replicate (inactive otherwise)
• frequently kill host cells (some live harmoniously with host)
• can infect all forms of life

• smaller and simpler than viruses
• consist only of RNA and NO protein coat
• require host for replication
• generally cause plant diseases

• infectious proteins (no DNA or RNA)
• responsible for neurodegenerative diseases

• diplo-: paired 
• strepto-: chains 
• staphylo-: clusters 
• -coccus: round
• -bacillus: rod
• -spirillum: spiral

• most widely used procedure for staining bacteria
• bacteria separated into 2 groups: Gram positive (basic, purple), Gram negative (acidic, red)
• most bacteria have negative charge so they like the BASIC stains

1. Primary Stain: crystal violet, cells stained purple
2. Mordant: iodine, cells remain purple
3. Decolorizer: alcohol, g-positive cells remain purple, g-negative cells become colorless
4. Counterstain (secondary): safranin, g-positive cells remain purple, g-negative cells become red

• fluid structure that surrounds cytoplasm
• serves as semi-permeable barrier
• phospholipid bilayer with embeded proteins
• phosphate heads are hydrophillic
• fatty acid tails are hydrophobic
• proteins function as receptors and transport gates

• thick layer of PTG
• still permeable
• has teichoic acid

• more complex than Gram positive
• thin layer of PTG sandwiched between outer membrane and cytoplasmic membrane (periplasm)
• much like lipid bilayer but has lipopolysaccharide layer instead of phospholipid

• NO cell wall
• causes mild pneumonia

• capsules and slime layers  -  functions are protection and enables attachment to other bacteria
• most are made of polysaccharide referred to as glycocalyx (sugar shell) 

• long protein structure responsibly for motility
• use propeller-like movements to push bacteria
• senses chemicals (acts as attractant for nutrients and repellent for toxins)

• much shorter and thinner than flagella (more like hair)
• made of protein also
• function are attachment, movement, DNA transfer

1. chromosome
2. plasmid
3. ribosome

1. double stranded molecule that holds all genetic info
2. DNA molecule, independent of chromosome, enhances survival
3. protein synthesis, made of riboprotein and ribosomal RNA

1. storage granules
2. gas vesicles
3. endospores

1. accumulates polymers that are in excess
2. small protein compartments
3. dormant cell types, resists damaging conditions

1. nucleus
2. mitochondria
3. chloroplast

1. distinguishing feature of eukaryotic cells, area of DNA replication
2. site of energy production, bilayer membrane, contains DNA
3. found only in plant and algae, site of photosynthesis, 2 membranes

1. endoplasmic reticulum
2. golgi apparatus
3. lysosomes
4. peroxisomes

1. rough ER: ribosomes (protein synthesis), smooth ER: lipid synthesis and degradation
2. series of membraned sacs, modifies stuff produced by the ER
3. contain degradative enzymes
4. where oxygen is used to oxidize substances, breaking down lipids

1. Metabolism
2. Catabolism
3. Anabolism

1. sum of the total chemical reactions of biosynthesis and energy harvesting
2. produces energy from degradation of molecules
3. requires the energy from catabolic reactions to synthesize new components

1. free energy
2. exergonic reaction
3. endergonic reaction

1. amount of energy available released from bonds
2. reactants have more free energy than the products so, energy is RELEASED
3. products have more free energy than the reactants so, energy is CONSUMED

1. oxidation
2. reduction

1. loses electrons
2. gains electrons

Enzymes

• act as chemical catalysts by lowering the activation energy and accelerating the conversion of substrate to product

1. substrate binds to active site of enzyme to form enzyme/substrate complex
2. products are formed
3. enzyme is released to bind to new substrate

1. Allosteric regulation
2. Feedback inhibition

1. regulates production of product by altering enzyme's affinity to substrate
2. non-competitive: inhibitor and substrate act on different sites (reversible);  competitive: inhibitor and substrate act on same site

1. cofactors
2. coenzymes

1. inorganic compounds reacting with enzyme
2. organic compounds acting as carriers for molecules and electrons (NAD, FAD, NADP+)

1. NAD
2. NADP
3. FAD

1. nicotinamide adenine dinucleotide 
2. nicotinamide adenine dinucleotide phosphate
3. flavin adenine dinucleotide 

1. ATP
2. substrate-level phosphorylation
3. oxidative phosphorylation

1. adenosine triphosphate - negatively charged phosphate groups attached to adenosine molecule, creates unstable bond thats easily broken releasing ENERGY
2. uses energy released in an exergonic reaction to add phosphate ion to ADP
3. harvests energy of proton motive force to add phosphate ion to ADP

1. 6-carbon sugar glucose
2. splits into two 3-carbon molecules
3. works in junction with pentose phosphate
4. produces two 3-carbon pyruvate molecules
5. net gain of ATP = 2 (2 expended, 4 harvested)
6. molecules of reducing power NADH = 2
7. precursor metabolites = 6

• step needed between glycolysis and Kreb's cycle
• from the pyruvate, CO₂ is removed, reducing power is generated, and it joins an acetyl group
• becomes a 2-carbon acetyl group of acetyl-CoA

• the 2-carbon acetyl group of acetyl-CoA enters and initiates a series of oxidations that result in the release of 2 molecules of CO₂.
• 2 ATP
• 6 NADH
• 2 FADH₂
• 2 precursor metabolites

• uses the reducing power accumulated in glycolysis, transition step, and Kreb's cycle to generate ATP by oxidative phosphorylation 
• in aerobic, O₂ is the terminal electron acceptor, producing water [4 ATP from glyc & kreb's + 34 ATP = 38 ATP]
• in anaerobic, an inorganic molecule other than O₂ is the terminal electron acceptor [ATP = less than aerobic]

• can not go through Kreb's or respiration
• produces relatively little ATP [2 ATP from glycolysis + 0 = 2 ATP total]
• stops short of oxidizing pyruvate and instead uses it as a terminal electron acceptor