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Chlamydia, Spirochetes, Cyanobacteria, and Gram-positive bacteria are described in this table. Note that bacterial shape is not phylum-dependent; bacteria within a phylum may be cocci, rod-shaped, or spiral. (credit “Chlamydia trachomatis”: modification of work by Dr. Lance Liotta Laboratory, NCI; credit “Treponema pallidum”: modification of work by Dr. David Cox, CDC; credit “Phormidium”: modification of work by USGS; credit “Clostridium difficile”: modification of work by Lois S. Wiggs, CDC; scale-bar data from Matt Russell)
Characteristics of the four phyla of archaea are described. Euryarchaeotes includes methanogens, which produce methane as a metabolic waste product, and halobacteria, which live in an extreme saline environment. Methanogens cause flatulence in humans and other animals. Halobacteria can grow in large blooms that appear reddish, due to the presence of bacterirhodopsin in the membrane. Bacteriorhodopsin is related to the retinal pigment rhodopsin. Micrograph shows rod-shaped Halobacterium. Members of the ubiquitous Crenarchaeotes phylum play an important role in the fixation of carbon. Many members of this group are sulfur-dependent extremophiles. Some are thermophilic or hyperthermophilic. Micrograph shows cocci-shaped Sulfolobus, a genus which grows in volcanic springs at temperatures between 75° and 80°C and at a pH between 2 and 3. The phylum Nanoarchaeotes currently contains only one species, Nanoarchaeum equitans, which has been isolated from the bottom of the Atlantic Ocean, and from the a hydrothermal vent at Yellowstone National Park. It is an obligate symbiont with Ignococcus, another species of archaebacteria. Micrograph shows two small, round N. equitans cells attached to a larger Ignococcus cell. Korarchaeotes are considered to be one of the most primitive forms of life and so far have only been found in the Obsidian Pool, a hot spring at Yellowstone National Park. Micrograph shows a variety of specimens from this group which vary in shape.
Archaea are separated into four phyla: the Korarchaeota, Euryarchaeota, Crenarchaeota, and Nanoarchaeota. (credit “Halobacterium”: modification of work by NASA; credit “Nanoarchaeotum equitans”: modification of work by Karl O. Stetter; credit “korarchaeota”: modification of work by Office of Science of the U.S. Dept. of Energy; scale-bar data from Matt Russell)

The plasma membrane

The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers ( [link] ).

This illustration compares phospholipids from Bacteria and Eukarya to those from Archaea. In Bacteria and Eukarya, fatty acids are attached to glycerol by an ester linkage, while in Archaea, isoprene chains are linked to glycerol by an ether linkage. In the ester linkage, the first carbon in the fatty acid chain has an oxygen double-bonded to it, whereas in the ether linkage, it does not. In Archaea, the isoprene chains have methyl groups branching off from them, whereas such branches are absent in Bacteria and Eukarya.  Both types of phospholipids result in similar lipid bilayers.
Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways. First, they have branched phytanyl sidechains instead of linear ones. Second, an ether bond instead of an ester bond connects the lipid to the glycerol.

The cell wall

The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.

Bacterial cell walls contain peptidoglycan    , composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. Proteins normally have only L-amino acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell wall development. There are more than 100 different forms of peptidoglycan. S-layer    (surface layer) proteins are also present on the outside of cell walls of both archaea and bacteria.

Bacteria are divided into two major groups: Gram positive    and Gram negative    , based on their reaction to Gram staining. Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla (Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms ( [link] ). Up to 90 percent of the cell wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids . Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.

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At high concentrations (>0.01 M), the relation between absorptivity coefficient and absorbance is no longer linear. This is due to the electrostatic interactions between the quantum dots in close proximity. If the concentration of the solution is high, another effect that is seen is the scattering of light from the large number of quantum dots. This assumption only works at low concentrations of the analyte. Presence of stray light.
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Source:  OpenStax, Ucd bis2a intro to biology v1.2. OpenStax CNX. Sep 22, 2015 Download for free at https://legacy.cnx.org/content/col11890/1.1
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