Midterm

More than 80 phyla have been found, but few have been studied in the lab. More than 90% of characterized bacterial species belong to four phyla: Proteobacteria, Actinobacteria, Firmicutes, and Bacterioidetes. Three divisions based on cell wall structure: Tenericutes, Gracilicutes, and Firmicutes.

Bacteria WITHOUT cell walls. One phylum: Mycoplamatota (latin for "flexible"). One class of note is Mollicutes: very small, membranes stablized with sterols, very reduced genome, must live in close association with eukaryotic cells, plant animal pathogens living in/on host cells!

GRAM NEGATIVE bacteria, with thin peptidoglycan layer, and LPS outer membrane. Cyanobacteria form symbiosis with many plants, fixing nitrogen.

GRAM POSITIVE bacteria, with thick peptidoglycan layer and embedded teichoic acids. Genus Frankia (an actinomycete) forms actinorhizal symbiosis with plants, fixes nitrogen through root nodules.

Largest + most diverse bacterial phyla, more than 1/3rd of characterized bacterial species are in this phyla, including majority of medical/industrial/agricultural signifcant species. Also contains pathogens, species involved in decomposition, nutrient tranformations and nitrogen fixation! All species are GRAM-NEG. Six classes, named after first 6 letters of greek alphabet: Alphaproteobacteria, Beta.., Gamma.., Delta.., Epsilon.., Zetaproteobacteria.

One family of note is Rhizobiaceae, aerobic chemoheterotrophic rod-shaped bacteria that contains several genera that form symbiotic relationships with plants in the legume family by forming nodules on their roots and fixing nitrogen! Most well known genus is Rhizobium.

Broad defintion: Any intimate and prolonged association between two or more dissimilar organisms
Narrow definition: As above, but implies mutalism, i.e. that each organism depends on the other for increased survival or fitness.

Takes dinitrogen (N2, a gas) to ammonium (NH4+). It takes a lot of energy to break N2, natural occurences of this include lightning, volcanic activity and combustion (forest fires). However, this can also occur biologically (though only in prokaryotes), and is a widespread characteristic in Bacteria and Archaea. Nitrogen fixation relies on the enzyme nitrogenase, and paradoxically needs a lot of aerobic cell repiration to generate ATP but aerobic conditions inactivate nitrogenase (Lhb helps with this paradox)

Enzyme composed of two subunits, the MoFe protein, which contains all machinery to perform reaction, but requires a steady source of electrons. Reaction requires six electrons for every nitrogen molecule. The other component, the Fe protein, uses the breakage of ATP to pump these electrons into the MoFe protein.

Rhizobium species were originally classifed according to the legume species they could nodulate, but these boundaries weren't absolute, which led to the concept of a Cross Inoculation Group: "legume + Rhizobium species that result in nodulation when grown together"

- Increasing flavonoid concentration near the root surface stimulates the expression of "nod" genes by Rhizobium, and nod genes cause the production of lectins by the roots.
-Bacteria attatch to root hairs, and attachment may be aided by lectins.
-Bacteria relase signals that cuase the root hair to curl around Rhizobium cells. Part of the cell wall of the root hair is degraded, allowing bacteria to enter.
- Root hair cell produces an infection thread consisting of a modified plasma membrane. New cellulose is formed on the inside of the root hair cell membrane, and at the same time some cortical cells divide in the root, forming a nodule meristem!
- Bacteria divide within the thread, the thread extends inwards penetrating through + between cells of the cortex. In the inner cortex the bacteria are released into the cytoplasm of dividing tetraploid cells.

In some legumes, like the groundnut, Rhizobium instead enters through a crack between epidermal cells and grows inside the root cortex, between root cortex cells.

Once inside root cortex cells, bacteria differentiate into their N2 fixing state (called "bacteroid"). Bacterial cells lose their cell walls, grow several times larger, usually occur in groups of about 4. Surrounded by a peribacteroid membrane formed by the host cell, membrane also encolses the peribacteroid space. Up to 20,000 bacteroid per infected root nodule cell.

Oxygen binding protein similar to hemoglobin. Very high affinity for O2, can function in O2 environments low enough for nitrogenase. Dual function:
- Lhb keeps O2 levels low enough for nitrogenase to function AND
- delivers enough O2 to the appropriate nodule microsites for adequate cell respiration to generate ATP

Lhb is present in nodule cell cytoplasm, outer layers of the nodule cell restrict gaseous diffusion, high rates of bacterial + mitochondrial respiration within the central nodule tissues to further reduce O2 concentrations.

Symbiosis between actinorhizal plant species (such as Red Alder) and nitrogen fixing bacteria in the genus Frankia (gram +, filamentous, aerobic, chemoheterotroph). Frankia infect plants either through root hair infection (Alnus) or through direct inercellular penetration of root epidermis cells and cortex, where root hairs either not present or not infected.

Frankia species have 3 cell types:
- Vegetative hyphae, prokaryotic filaments, "normal" growth state
- Vesicles, where all N2 fixation occurs, vesicle walls also regulate O2 levels (thickness + # of wall layers changes in response to external O2 concentration)
- Reproductive spores

Nitrogen-fixing blue green bacteria that are involved with many plants, such as:
- Azolla/Anabaena, heterocyst cells formed under leaves fix N2
- Gunnera, only angiosperm with stem nodules
- Cycads, caralloid roots can be infected
- Lichens, Lobaria/Nostoc

Azolla, a small water fern, is infected by Anabaena, a genus of cyanobacteria that fixes N2 by colonizing chambers underneath it's leaves, and has historically been used to fix N2 in rice paddies (grow azolla in rice paddies before planting rice, rice slowly overtakes azolla, as azolla die their nitrogen deposited into rice paddies). The cyanobacteria Anabaena forms specialized heterocyst cells to fix nitrogens! Heterocyst cells (fix N2 -> NH3) arise from the differntiation of vegetative cells (fix CO2, photosynthesis).

1 Division/Phylum: Mendosicutes (latin for faulty skin, refers to the atypical cell wall structure). Lack peptidoglycan in their cell walls, either have no cell wall or have pseudomurein (uses NAT instead of NAM). Most archaeal cell walls also have a layer of protein subunits directly associated with the outer surface of the cell. These proteins form the S-layer, and comprise one of the most abundant cellular proteins. Not susceptible to antibacterial angents like penicillin and lysozyme, which both break the bond btwn NAG and NAM.

Have thick cell walls, comprised of a matrix of long chains of 2 alternating sugars that form layers, that are linked by short chains of amino acids. These sugars and amino acids are collectively referred to as peptidoglycan. These cell walls also contain teichoic acids.

Short polysaccharide chains made of phosphate sugars. Two kinds...
Wall Teichoic Acids (WTA): occur throughout the peptidoglycan layers, help maintain cell wall structure and strengthen it.
Lipoteichoic Acids (LTA): anchor peptidoglycan to the cell membrane

Have very thin cell walls, peptidoglycan layer with no techoic acids. But, have an outer membrance and/or lipopolysaccharide (LPS) layer outside the cell wall. The space between the cell membrance and the outer membrane is called the periplasmic space, and is made up of periplasm.

Many Divisions/Phyla: 41 formally accepted, 89 recognized. Bacteria made up of peptidoglycan.

Made of repeating units of modified carbohydrate molecules, specifcally amino sugars, which form the glycan layer. Cross linked with peptide chains. Found in cell walls.

Developed by Hans Christian Gram in the 1880s, and later Carl Weigert. Due to the differences in peptidoglycan layer thickness, we can stain to differentiate between Archaea and Bacteria. The process of gram staining is...
- Apply crystal violet, all cells take up the dye
- Apply Lugol's iondine, all cells appear blue-black
- Wash with ethanol, gram +ve cells will retain dye and appear blue-purple, gram -ve will not
- Apply safranin, gram -ve cells will take up the dye and appear red

Compound found in peptidoglycan, in both Archaea and Bacteria. In Bacteria, has an O bond with NAM, and chains of NAG/NAM form strong lattice by cross linking with pentapeptides. In Archaea, has O bond with NAT, and chains of NAG/NAT form strong lattice by cross linking with pentapeptides.

Compound found in peptidoglycan, but only in Bacteria. NAM and NAG form peptidoglycan/murein.

Compound found in Archaea, acts in place of NAM. NAT and NAG form pseudomurein.

Self-assembling molecular monolayer of proteins outside the cell wall (or plasma membrane if cell wall absent). Not covalently bonded to the wall, but attached via ionic/hydrophobic-hydrophyllic/other molecular interactions. Highly regular repeating protein subunits form different lattice arrangments.
- Function as molecular sieves, ion traps, and protective coats (from viruses)
- Provide advantage in harsh environments (e.g. keep excess protons out in acids, stabilize membrane in high temps)

- lack peptiodoglycan
- major membrane lipids are ether linked to glycerol, rather than ester linked, thought to aid in heat stability
- lipids made of L-glycerol rather than D-glycerol
- cell membrane lipids made of isoprene chains, rather than fatty acids
- lipid (bi)layers in cell membranes are different, and have lower permeability
- 16S rDNA analysis
- 30S ribosomal subunit has distincitive penguin shape
- RNA polymerase have distinct subunit structures
- Flagella structures differ from Bacteria
- includes all known extreme halophilic, thermoacidophilic and methanogenic organisms (at least 5 phyla)

Ether linkages are common in Archaea, are heat stable and difficult to break.
Ester linkages are common in Bacteria, are not heat stable and easy to break.

L-glycerol has ether linkages, and is found in Archaea
D-glycerol has ester linkages, and is found in Bacteria

Archaea cell membrane lipids are made of isoprene chains, NO fatty acids
Bacteria cell membrane lipids are made of fatty acids, NO isoprene chains

Compound with numerous CH3 side groups, making their long chains branched. Monomer of rubber molecules. For greater heat stability, some isoprene chains are anchored at both ends, forming tetraether linked lipids, rather than diether linked lipids.

For even more heat stability, carbon may form rings in the long isoprenoid chains.

Archaea can have diether bilayers (require pseudomurein) OR tetraether monolayers (lack pseudomurein)
Bacteria always have diester bilayers

Archaea membranes are less premeable than bacteria membranes. Archea monolayers are less permeable than bilayers, though archeal monolayers with carbon rings are more permeable and heat stable than those without. For bacteria, more unsaturated fatty acids means more permeable membranes.

The 30S ribosomal subunit has distinctive shapes in Eukarya, Archaea, and Bacteria. In Eukarya, distinct penguin shape with bill, backpack, and two feet. In Archaea, has bill, backpack, and less differentiated feet. In Bacteria, has bill and partial backpack.

Eukaryotes have 3 RNAPS, Pol I, II, and III. Archaea and Bacteria have one RNAP each, and they are distinct from one another. Archaea's RNAP is orthologous to the eukaryotic RNAP II.

Archaea flagella are thinner than Bacteria flagella, and are not hollow. In Archaea, growth occurs at base of filament, but in Bacteria growth occurs at the end of the tail. Fuel for Archaeal flagella is ATP, Bacterial flagella use H+ (protons) or Na+ ions.

Hot springs organisms, includes most thermoacidophiles and some extreme halophiles. Few hundred species, one genera of note is Sulfolobus, whose natural habitat is volcanic hot springs, and has an optimum temperature of 75-80 C, and a max temp of 88 C. Sulfolobus has a tetraether lipid monolayer that provides high heat stability, and an internal pH of 6.5. Sulfolobus found in Yellowstone, Mt. St. Helens, and even boiling mud!

Temp minimum of 55 C, below that cells die of freezing due to a total lack of fluidity.

Optimum pH 2-3, minimum pH 1. Membranes are highly proton impermeable, some species need protons to stabilize their cell membranes, call membranes disappear at higher pH (even 3). Have an abundance of acidic amino acids and proteins that don't react with abundant cytoplasmic protons.

Includes the methanogens, extreme halophiles, and some thermophiles, ~ 200 species.

Chemoautotrophic, strict anaerobes. Produce > 50% of the world's methane. Found in pitcher plants, sweage plants, guts of ruminants, hyperthermal ocean vents, as well as cold sediments, anoxic lakes, glacial ice cores and permafrost soils. Psychrophilic methanogens thrive at low temperatures, they do this by increasing the amt of unsaturated lipids in their membranes as temps decrease, maintain their membranes in a liquid crystalline state. This occurs in both psychrophilic Archaea and Bacteria.

Require saturated salt solutions such as salt flats, saline lakes. Most are obligate aerobes and chemoheterotrophic, some facultative anaerobes.

Comes from pre-formed compounds, includes sugars, proteins, fats and other complex molecules. Most OC molecules:
- contain C-H bonds
- usually contain at least 2 carbon atoms (bonded to eachother)

Ex: Methane, Glucose, Fatty Acids

Comes from much less complex, smaller molecules. Most IC molecules:
- Lack C-H bonds
- Lack C-C bonds

Ex: CO, CO2, CO3, cyanide

"Self-Feeding". Organisms whose principal carbon source is inorganic, usually CO2.

"Other/Outside-Feeding". Organisms whose principal carbon source is organic, such as sugars.

Get energy from sunlight (photosynthesis). Two types...
Photolithoautotroph: Inorganic carbon source (CO2), energy source is sunlight. Plants, Algae, Purple and green sulfur bacteria.
Photoorganoheterotroph: Organic carbon source, energy source is sunlight. Purple and green non-sulfur bacteria, Heliobacteria.

Get energy from chemical oxidations. Three types...
Chemolithoautotroph: Inorganic carbon source (CO2), energy source is inorganic chemicals. Bacteria in nutrient cycling, Nitrifying bacteria.
Chemolithoheterotroph: Organic carbon source, energy source is inorganic chemicals
Chemoorganoheterotroph: Organic carbon source, energy source is organic chemicals (often same as carbon source). Animals, Fungi, many prokaryotes.

A bacteria that changes it's energy and carbon sources depending on what's available. Energy source:
- if there's light: phototrophic
- if no light and organic matter: chemoorganotrophic
- if no light and no organic matter: chemolithotrophic

Carbon source:
- if there's organic matter: heterotrophic
- if no organic matter: autotrophic

Organisms that need O2 to survive, i.e. are able to use O2 as terminal electron acceptor in cellular respiration.
Obligate Aerobe: Must have O2 to survive.
Microaerophilic: Requires O2 but must be below atmospheric concentration.

Organisms that don't need O2 to survive, i.e. does not use O2 as terminal electron acceptor to generate energy.
Obligate Anaerobe: Harmed or killed by exposure to O2.
Facultative Anaerobe: Will use O2 if avaible but still grow in absence of O2.
Aerotolerant Aneaerobe: Doesn't use O2 but not harmed if O2 present.

Complete oxidation of glucose to H2O and CO2.

Incomplete oxidation of glucose to an intermediate compound of repiration, i.e. lactic acid or ethanol.

Atoms or molecules with one or more unpaired electrons. These are chemically incomplete, unstable atoms or molecules that tend to steal electrons from other molecules in order to stabilize themselves. Normal aerobic metabolism produces free radicals.

Free radicals comprised of O2, also called Toxic Oxygen Species. ROS can leak away from their area of production in any sort of aerobic organism and wreak havoc. Three types produced from normal aerobic cellular respiration, in following order:
- Superoxide (O2-)
- Hydrogen Peroxide (H2O2), produced when O2- reduced
- Hydroxyl Radical (OH*), very short lived but extremely reactive and damaging

Another type produced due to absorption of light energy or transformation by some enzymes:
- Singlet Oxygen (1O2), Molecular O2 that has been raised to a higher energy level

ROS type. Molecular O2 that is partially reduced by a single electron. Formed as an intermediate during normal aerobic respiration where O2 is ultimately reduced to H2O, hence O2- constantly being produced. So toxic it is used in our immune systems by white blood cells to kill pathogenic microorganisms.

Molecular O2 that has been raised to a higher energy level, produced by absorption of light energy or transformation by enzyme. Has no additional or unpaired electrons, but spin direction of it's native electrons' changes. The outer 2 valence electrons in a "normal" ground state O2 spin in the same direction. In singlet oxygen (1O2), valence electrons spin in opposite directions. Spin shift forms a much more reactive O2 molecule.

They initiate a destructive chain reaction in fatty acid molecules of lipids called lipid peroxidation, which is the oxidative destruction of the C=C bonds in the fatty acids that comprise lipids. This causes irreparable damage to cell membrane lipids, leading to loss of membrane fluidity and semi-permeability. i.e. cells leak uncontrollably and die. Free radicals can cause:
- Membrane destruction
- DNA oxidation, particularly mitochondrial DNA in eukaryotes and chlorplast DNA in photosynthesizers. These DNA are particularly susceptible because they are the sites of electron transport activy and hence the generation of free radicals (i.e. ROS)
- Oxidation of biomolecules (enzymes, proteins, etc.), deactivating or destroying biomolecules by causing lipid-lipid, lipid-protein and protein-protein crosslinking.

Causes the formation of oxidatively modified guanine bases.

Numerous mechanisms to neutralize ROS have evolved, including:
- Detoxifying Enzymes
- Antioxidants

- Superoxide Dismutase (SOD), catalyzes O2- + O2- => O2 + H2O, dismutation refers to the simultaneous oxidation + reduction of a molecule to produce 2 different products
- Catalase, catalyzes H2O2 + H2O2 => O2 + H2O
- Peroxidase, catalyse H2O2 + NADH + H+ => H2O + H2O + NAD+

Molecules capable of slowing or preventing the oxidation of other molecules. Usually have several C=C bonds that mimic important biomolecules that would normally be damaged by ROS (namely fatty acids).
- Carotenoids, organic pigment molecules with many C=C bonds. Ex: Beta Carotene, C=C bonds react with 1O2, absorbs high E wavelengths of light to reduce the formation of 1O2, scavanges free radicals (mimics lipid peroxidation).
- Ascorbic Acid (Vitamin C), reacts with O2- and H2O2 to form dehydroascorbate.
- Tocopherol (Vitamin E), donates H atoms to "quench" ROS.
- Gluthathione (GSH), antioxidant function facilitated by the sulfhydryl group (SH) of cysteine. In the presence of an oxidant (ROS), the SH of one GSH reacts with the SH of another GSH forming a disulphide bond (S-S), thereby "quenching" ROS.

The study of organisms that live in the soil, including their metabolic activities, and their roles in
nutrient cycling and energy flow.

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
"Dear King Phillip Came Over For Good Soup"

Plantae, Animalia, Funga, Protista, Prokaryotae. **Since replaced by 3 Domain System**

Eukaryotic, multicellular, usually photosynthetic, develop from an embryo but lacks blastula

Eukaryotic, multicellular, develop from embryo with blastula

Eukaryotic, unicellular AND their multicellular descendants, develops from spore, has flagella. **All the organisms that didn't fit in other kingdoms**

Eukaryotic, develops from spore, lacks flagella

unicellular, thick walled, resistant, without food reserves

multicellular, environment capable of nurturing the plant, i.e. has endosperm/nutritive tissue/food reserves

Whip-like tail(s) that cause locomotion

An early embryonic structure produced by cleavage of a fertilized ovum and consisting of a spherical layer of cells surrounding a fluid-filled cavity

Mutualistic symbiosis between certain fungi and most plants resulting in the formation of a modified plant root.
Plants benefit from the fungus, usually through enhanced nutrient acquisition; fungus receives photosynthate (carbon) from the host plant

All prokaryotic organisms, no membrane bound nucleus or organelles.

Organisms whose cells lack a (membrane bound) nucleus and other organelles. Mostly small, unicellular, with simple structure. Two distinct groups are the Bacteria (including Cyanobacteria) and the Archeaea/Archeabacteria.

Organisms whose cells have a membrane bound nucleus and other organelles. Unicellular (protists) or multicellular (plants, animals, fungi). Less overall organisms than the prokaryotes, but due to their size the eukaryote global biomass is much larger than that of the prokaryotes.

Organisms that thrive in extreme conditions, and may die under normal conditions. Believed to be descendants of microorganisms adapted to early earth (no O2, lots of methane, CO2, extreme temperatures, boiling acidic muds, etc.). Hence called Archeabacteria (ancient bacteria). Includes the Thermophiles, Acidophiles, and Halophiles.

Organisms (mostly archeabacteria) that require high temperatures to survive, and who's enzymes and proteins function optimally at high temps. Thrive between 45 °C and 122 °C, and diversity is mostly driven by pH. Source of important enzymes such as Taq polymerase used in PCR, which comes from Thermus aquaticus!

Organisms that thrive in acid environments, with pH less than 3.0! There are even Thermoacidophiles that thrive in pH less than 4.0 and temperatures over 55 °C.

Organisms that thrive in salty environments, with salinity up to 36%. Normal saline is 0.9% and seawater is 3.5% salinity.

The structure, shape, size, look of an organism.

How an organism functions.

Hypothesized that extremophiles should not be in the same category as pther bacteria. Chose to study 16S rRNA as a molecular genetic marker. Developed the association coefficient S that represents the genetic similarity btwn species. Established the 3 domain system.

Organelles or particles that are the sites of protein synthesis. Made of RNA and proteins.

If S = 1 then a,b identical. If S = 0 then a,b completely different. S = (# of identical nucleotides)(2)/(# of total nucleotides of a and b).

Archaea (the archaebacteria), Eukarya (all eukaryotes), and Bacteria (all other prokaryotes).

Has 3 pysiological groups: the methanogens (methane producing), extreme halophiles, and thermoacidophiles.

The variety and abundance of species, their genetic composition and the communities, ecosystems and
landscapes in which they occur. The full range of life in all its natural forms, including genes, species and ecosystems, and the processes that link them.