quiz 3

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.