AP Biology, Chapter 27
Prokaryotes and the Origins of Metabolic Diversity

Summary
Introduction

THE WORLD OF PROKARYOTES
	They're (almost) everywhere an overview of prokaryotic life
		1. Describe the many unique characteristics of prokaryotes. Explain why it might be said 
		that prokaryotes are the most successful organisms ever to live.
			a. Most ancient, small, anucleate
			b. Only major taxon found everywhere, in all environments
			c. Most numerous
		2. Describe the impact of prokaryotes on humans and biological ecosystems.
			a. A minority cause disease
			b. Most are decomposers, some recycle nutrients in biogeochemical cycles
			c. Many form beneficial symbiotic relationships
			d. Origin of mitochondria and chloroplasts
	Bacteria and archaea are the two main branches of prokaryote evolution
		3. Describe the classification of the archaea and the bacteria in the three-domain system.
			a. Archaea separated by rRNA sequence and genome structure
			b. Archaea inhabit extreme enevironments: acid, salt, hot
			c. Molecular studies suggest Archaea and Eukarya share a more recent common 
			ancestor
			d. Prokaryote is a paraphyletic construction

STRUCTURE, FUNCTION, AND REPRODUCTION OF PROKARYOTES
	Introduction
		4. Describe the general size, organization, and specialization of prokaryotic organisms.
			a. Size 1-5 micrometers
			b. Unicellular with a few colonial types
			c. Rod-shaped bacilli; spherical cocci; spiral spirilli and spirochetes
	Nearly all prokaryotes have cell walls external to their plasma membranes
		5. Describe the structure, composition, and functions of prokaryotic cell walls.
			a. Nearly all have a cell wall with peptidoglycan
			b. Functions include shaping, osmotic protection, physical protection
			c. Major differences: Gram + and gram -
		6. Distinguish between the structure and staining properties of gram-positive and gram-
		negative bacteria. Explain why disease-causing gram-negative bacterial species are 
		generally more pathogenic than disease-causing gram-positive bacteria.
			a. Gram -
				i. Light pink in gram stain
				ii. Thin peptidoglycan with second membrane and lipopolysaccharide 
				(LPS)
				iii. Generally more pathogenic
				iv. Incl. Salmonella and E. coli
			b. Gram +
				i. Deep violet in gram stain
				ii. Thick peptidoglycan with no second membrane or LPS
				iii. More susceptible to lysozyme and penicillin; both act on peptidoglycan
				iv. Incl. Bacillus sp.	
	Many prokaryotes are motile
		7. Describe three mechanisms that motile bacteria use to move. Explain how prokaryotic 
		flagella work and why they are not considered to be homologous to eukaryotic flagella.
			a. Three mechanisms
				i. Stiff protruding flagella that twirl
				ii. Flagella around which the cell is coiled; corkscrews through liquid
				iii. Gliding on secreted material
			b. Protruding flagella
				i. Not homologous: no membrane, no force generated within flagella
				ii. Stiff flagella are twirled my a motor embedded in the membrane/wall; 
				energy from proton gradient
			c. Allows movement (taxis) in response to various stimuli 
	The cellular and genomic organization of prokaryotes is fundamentally different from 
	that of eukaryotes
		8. Explain how the organization of the prokaryotic genome differs from that in eukaryotic 
		cells.
			a. No nuclei; circular chromosome wound into a wad
			b. 1/1000 the size of a eukaryotic chromosome; mostly coding
			c. Small accessory plasmids may be present
	Populations of prokaryotes grow and adapt rapidly
		9. List the mechanisms that are sources of genetic variation in prokaryotes and indicate 
		which one is the major source.
			a. Mechanisms of exchange: transformation, transduction, conjugation
			b. Major source: new mutation
		10. Describe growth as it applies to prokaryotes. Explain what is meant by geometric 
		growth.
			a. Growth is mainly in numbers, not size
			b. Geometric = exponential = 124816, etc.
		11. Describe the functions of endospores.
			a. Endospores are dormant, thick-walled cells
			b. Resistant to heat, drying, digestion, poisoning
		12. Describe the natural adaptive advantage of antibiotics.
			a. Microorganisms produce antibiotics to kill competing cells
			b. Antibiotic-producers have some mechanism of resistance 

NUTRITIONAL AND METABOLIC DIVERSITY
	Introduction
	Prokaryotes can be grouped into four categories according to how they obtain energy 
	and carbon
		13. Distinguish between photoautotrophs, chemoautotrophs, photoheterotrophs, 
		chemoheterotrophs, saprobes, and parasites. Give examples of each.
			a. Photoautotrophs
				i. Light energy; CO2 for carbon
				ii. Cyanobacteria with chlorophyll a, plants, algae, and photosynthetic 
				bacteria
			b. Chemoautotrophs
				i. Inorganic compounds for energy; CO2 for carbon
				ii. Purple sulfur bacteria
			c. Photoheterotrophs
				i. Light energy; organic compounds for carbon
				ii. Purple non-sulfur bacteria
			d. Chemoheterotrophs
				i. Organic compounds for energy and carbon
				ii. Animals, fungi, a few plants, many bacteria
			e. Saprobes
				i. Chemoheterotrophs feeding on dead organisms
				ii. Include most fungi and bacteria
			f. Parasites
				i. Chemoheterotrophs feeding on live organisms
				ii. Infectious diseases
		14. Describe the process and explain the significance of nitrogen fixation.
			a. N-fixation = conversion of N2 gas into NH3 by chemoautotrophic bacteria and 
			photoautotrophic cyanobacteria
			b. Other bacteria covert ammonia to nitrites (NO2-) and nitrates (NO3-)
			c. Nitrites and nitrates are usable by plants
			d. Denitrifying bacteria convert NO2- and NO3- back to N2
		15. Distinguish among obligate aerobes, facultative anaerobes, and obligate anaerobes.
			a. Obligate aerobes require oxygen for growth
			b. Facultative anaerobes can use oxygen but don't need it
			c. Obligate anaerobes are killed by oxygen
	The evolution of prokaryotic metabolism was both cause and effect of changing 
	environments on Earth
		16. Describe, with supporting evidence, plausible scenarios for the evolution of metabolic 		diversity, including the: a) nutrition of early prokaryotes, b) origin of electron transport 
		chains, c) origin of photosynthesis, d) origin of aerobic respiration.
			a. Early prokaryotes
				i. ATP and glycolysis appeared early since they are universal
				ii. No oxygen; therefore, anaerobes
				iii. 5th edition: little organic material; therefore, first came 
				chemoautotrophs
				iv. 6th edition: enough organic material; therefore, first came 
				chemoheterotrophs
			b. Electron transport
				i. Chemoautotrophy may have yielded H2 + energy							ii. Energy may have split H2 giving a proton gradient + free electrons
				iii. Membranes capable of manipulating H/electrons would have been 
				favored
			c. Photosynthesis
				i. Pigments may have protected from UV
				ii. Energized pigments on membranes may have linked with electron 
				transport/ATP generation
				iii. Archaea use bacteriorhodopsin to generate ATP
				iv. Cyanobacteria have both photosystems and generate O2
			d. Aerobic respiration/oxidative phosphorylation/Krebs cycle
				i. Abundant H2O is an advantageous electron donor for photosynthesis
				ii. O2 released killed many, some acquired oxygen toleration mechanisms
				iii. O2 would have been useful as an electron acceptor
				iv. Purple nonsulfur bacteria use a part photosynthesis electron transport 
				chain for aerobic respiration

PHYLOGENY OF PROKARYOTES
	Introduction
	Molecular systematics is leading to a phylogenetic classification of prokaryotes
		17. Explain how molecular systematics has been used in developing a moneran 
		classification. Explain why clinical phenotypes are a poor guide to phylogeny.
			a. Little fossil evidence and very simple morphologies; rRNA is more useful
			b. Clinical phenotypes
				i. Shape, gram stain, motility, nutrition
				ii. Good for practical ID of common pathogens
				iii. Most are polyphyletic
		18. Describe the distinguishing features and give examples of the methanogens, extreme 
		halophiles, and extreme thermophiles. Explain why these groups are collectively known 
		as extremeophiles.
			a. Archaean clades are based solely on comparison of rRNA sequences
			b. Major non-clade types
				i. Methanogens oxidize H2 using CO2 to produce CH4 in intestines and 
				rotting material
				ii. Halophiles thrive in unusually salty environments; some contain 
				bacteriorhodopsin
				iii. Thermophiles withstand high temperatures
			c. Archaeans are much more pervasive than the label "extremeophile" implies

ECOLOGICAL IMPACT OF PROKARYOTES
	Introduction
	Prokaryotes are indispensable links in the recycling of chemical elements in 
	ecosystems
		19. Describe the role of prokaryotes in recycling within ecosystems.
			a. Prokaryotic decomposers release essential nutrients from dead organisms
			b. Others convert essential nutrients into usable forms
			c. Others replenish the "starting" forms
	Many prokaryotes are symbiotic
		20. Distinguish among mutualism, commensalism, and parasitism. Describe examples of 
		prokaryotes in each of these relationships.
			a. Mutualism
				i. Close association in which both benefit
				ii. Intestinal flora completes digestion, makes vitamins
				iii. Nitrogen fixing bacteria live in legume root nodules
			b. Commensalism
				i. One benefits, the other is neutral
				ii. Most bacteria on and in humans are commensals
			c. Parasitism
				i. One benefits, one is harmed
				ii. Bacterial diseases like tuberculosis, leprosy, and anthrax
		21. List Koch's postulates, which are used to substantiate a specific pathogen as the 
		cause of a disease.
			a. Find the suspected pathogen in each individual with the disease
			b. Isolate it from a diseased individual and grow it in the laboratory
			c. Cause the disease by infecting from the culture
			d. Re-isolate the pathogen from the experimental infection
	Humans use prokaryotes in research and technology
		22. Distinguish between exotoxins and endotoxins and describe examples of each.
			a. Exotoxin
				i. Toxic substances secreted by pathogens
				ii. Ex.: Clostridium botulinum makes botulinum toxin
				iii. Ex.: Vibrio cholerae makes cholera toxin
			b. Endotoxin
				i. Toxic substances that are part of the cell wall/membrane
				ii. Ex.: lipopolysaccharide in Salmonella
		23. Describe how Streptomyces can be used commercially.
			a. Production of many useful antibiotics
		24. Describe the limitations of antibiotics in combating bacterial diseases.
			a. Bacteria microevolve resistance
			b. We're running out of easily assessed microbiodiversity 
		25. Describe how humans exploit the metabolic diversity of prokaryotes for scientific and 
		commercial purposes.
			a. "Simple" microbes like E. coli are exhaustively studied
			b. Fermentation makes food and medicines
			c. Bacteria may help break down pollutants