Structural Biochemistry/Three Domains of Life

Introduction


In the past thirty years, scientists were able to use technological discoveries to redefine the classifications of life on earth. In 1977, American microbiologist, Carl Woese altered the previous two-domain system of Eukaryota (Eukarya) and Prokaryota. The Prokaryota domain was split into the two separate domains of Bacteria and Archaea. Woese was able to look at the similarities and differences of living organisms at the genetic sequencing level. More specifically, Woese analyzed how closely organisms were related based on the 16S ribosomal RNA or rRNA present in all organisms. With the new knowledge from the study of organisms' biochemical differences, scientists were able to classify life on earth into three distinctive groups, or domains: Eukarya, Bacteria, and Archaea. Archaea is more closely related to Eukaryotes than Eubacteria

Eukarya
Most living plants and animals are composed of eukaryotic cells. Eukaryotic cells receive their name from the Greek eu meaning true and karyon suggesting that they have a true nucleus which contains their DNA. The determining factor for this domain is the presence of a distinct membrane-bound nucleus in each cell. The nucleus in eukaryotes consist of nuclear material enclosed with a double membrane, the nuclear envelope. Another distinctive feature of Eukarya is the presence of membrane-bound organelles in many of the cells. This type of cell can divide in two processes mitosis and meiosis. It keeps its DNA in chromosomes. This domain includes all multicellular organisms: plants, animals, fungi and protists. Interestingly, human beings and yeast are both classified under this same domain. Ciliates, fungi, flagellates, and microsporidia also belong in this domain.

Eukaryotic cells can be categorized in to two types of cells, animal and plant cells.

Genes from natural communities continually reveal new species of microbial eukaryotes in previously unknown divisions. The genetic analysis shows that similar miniaturized eukaryotes branch from all the groups in the phylogenetic tree.

Microbes include members of the three domains of life. The three domains of life are bacteria, archaea and eukarya.

Prokaryota
Out of the two prokaryotic cells are considerably simpler than eukaryotic cells. Bacteria and archaea are considered prokaryotes. Prokaryotic comes from the Greek prefix pro which means before and the Greek root karyon which means kernel. They tend to be smaller in size and are not as complex as eukaryotic cells. As their names suggests, prokaryotic cells lack any organelles enclosed with a membrane. Their DNA is in an area called the nucleoid which also is not enclosed by a membrane. The nucleoid is not separated from the cytoplasm. Generally speaking, their chromosomes and plasmids are circular and naked, they have no nuclear envelope. In addition, prokaryotic cells control genes via operons. But, like eukaryotic cells, they have a plasma membrane surrounded by a cell wall. However, their cell wall contains petidoglycans which can't be found in Eukaryotic cells.

Prokaryotic cells have been split in to two distinct groups, bacteria and archaea.

Bacteria
This domain was considered prokaryote. It consists of all the unicellular prokaryotic microorganisms that do not have a cell nucleus or contain any organelles in their cells. Bacteria can be spherical, rod-like, or spiral in shape. Although bacteria contain ribosomes also found in Eukaryotes and Archaebacteria, bacterial ribosomes are much different in structure. Bacteria are characterized as having a cell wall (except for mycoplasma). Their cell walls are called peptidoglycans, which is composed of peptides and sugars. The cell wall gives the cell structure and shape. It also gives rigidity to prevent water from flowing into the cell membrane of the bacteria and causing the cell to burst. The cell wall usually lies exterior to the cell membrane as in Gram Positive cells. But in the case of Gram Negative bacterial cells, there is a second cell membrane that is exterior to the cell wall. This gives these types of bacteria unique properties to help it survive. Bacteria has straight chain fatty acids ester linked to glycerol. The membrane of bacteria is bilayer. The wall of bacteria has peptidoglycan or none. An example of bacteria can be mycoplasma. Mycoplasma has no wall.

Bacteria also have flagella that help with their motility. The bacteria rotate their flagella in a counterclockwise manner and swim towards an attractant. To move away from a repellent, the flagella rotates clockwise and tumbles to change directions. Bacteria also have pili, which are used mainly for attachment and exchange of genetic information.

The gram stain differentiates bacteria into two fundamental varieties of cells based on staining properties of the cell wall. The two common types are: 1) Bacteria that retain the initial CV stain (purple) = gram +. 2) Those that are decolorized and stain pink with safranin = gram -. Gram positive has thick walls that resists de-colorization and is composed of PG and teichoic acids. Teichoic acids anchor layers of peptidoglycan together. Lipoteichoic acid connects peptidoglycan to the membrane. Some species have capsules: Sugar (polysaccharides)coating. They can protect against phagocytosis. The capsule is slippery, so when a phagocyte tries to eat the bacteria, it can slip away. It may also contribute to virulence and help cells stick to surfaces. Some species have S-layers. S-layers consist of protein or glycoprotein. Its function is not totally clear, but its tough proteins may deter predators. It may contribute to cell shape and aid in protection against osmotic stress.

Gram negative has thin peptidoglycan layer outside the inner membrane (cytoplasmic membrane). It has lipoprotein (murein lipoprotein). Lipoprotein binds peptidoglycan to the inner leaflet of the outer membrane. The outer membrane has lipid-protein bilayer, which can be disrupted by de-colorization. The outer membrane has phospholipids, porins and LPS. The outer membrane's function is to protect permeability barrier (impermeable to large molecules and hydrophobic compounds from the environment). The porins of gram negative are channels that allow for transport of molecules across the membrane (sugars, amino acids, vitamins, etc, some antibiotic get through them as well. Porins provide permeability for entering and exiting compounds. The LPS of gram negative coats the surface of the cell. It increases the negative charge of the cell membrane-excludes large hydrophobic compounds such as bile salts and antibiotics (permeable only to low molecular weight, hydrophilic molecules). LPS may play a role as an adhesin used in colonization of the host. It helps protect cell against phagocytosis. The LPS of gram negative has three parts. The three parts are lipid A, core oligosaccharide and O polysaccharide. 1) Lipid A is important pathogenic factor (endotoxin- when released into a host's blood stream or GI tract causes toxicity of gram - infection. 2)The core oligosaccharide component that attaches directly to lipid A. One of the glucosamines of lipid A is linked to the core polysaccharide, extending out from the cell. The core oligosaccharide consists of 5 sugars. 3)O polysaccharide is the outermost domain of the LPS molecule. It is a repetitive glycan polymer attached to the core oligosaccharide. The composition of the O chain varies from strain to strain. Greater 160 different O antigen structures produced by different E. coli strains. These chains form a layer that helps bacteria resist phagocytosis by white blood cells. O-polysaccharides serves as an antigen or cell surface marker. It is exposed on the very outer surface of the bacterial cell, and, as a consequence, is a target for recognition by host antibodies. Variations in LPS structure provide for the existence of different antigenic strains of a pathogen that may be able to bypass a previous immunological response to a related strain.

Some bacteria have walls of intermediate structure and they stain in a variable manner.

Mycobacteria have a cell envelope which is not typical of Gram positives or Gram negatives. The mycobacterial cell envelope does not consists of the outer membrane characteristic of Gram negative bacteria, but has a significant peptidoglycan-arabinogalactan-mycolic acid wall structure which provides an external permeability barrier. Moreover, mycobacteria contain waxy mycolic acids. They have thickest cell walls known. They are highly resistant to antimicrobials due to thick waxy envelope. The envelope also makes it hard to take up nutrients: slow growers. Mycobacteria have no dyes permeate thus neither gram positive nor gram negative.

Mycoplasma is considered to be bacteria. The lack of a cell wall makes these species resistant to antibiotics that target cell wall synthesis. There are no cell walls to protect from osmotic pressure, so they use sterols to strengthen membrane or they live inside other cells.

Bacteria inhibit soils, surface waters, tissues of other living or decaying organisms. Thermotoga, flavobacteria, cyanobacteria, purple bacteria, gram-positive bacteria, and green nonsulfur bacteria belong in this domain.

Archaea
Archaea is considered to be prokaryote. Archaea is referred to as "archaebacteria." They have the appearance of bacteria with their unicellular rod and spiral-like structures. They are prokaryotes and lack a cell nucleus and other organelles. Archaea have the most extreme variations in phospholipid side-chain structures. Archaea have a branched hydrocarbon and ether linked to glycerol. Ether links between glycerol and fatty acids. Hydrocarbon chains are branched terpenoids (polymeric structures derived from isporene-every 4th carbon extends a methyl branch). The branches strengthen the membrane by limiting movement of the hydrocarbon chains. The membrane of archaea is bilayer or monolayer. In the wall of archaea, there are peptidoglycan and S-layer. Unlike bacteria, Archaea possess genes and pathways that evolutionarily link them closer to eukaryotes than to bacteria. Archaea contain the enzymes used for transcription and translation which reflects their closer similarity to eukaryotic organisms rather than bacteria. However, they are unlike eukaryotes in that they use a larger range of sources in order to gain energy. As a result of their differences from bacteria and eukaryotes, Archaea was placed into its own category. Archaea can live in extreme and harsh conditions not suited for other living organisms. For example, thermophiles occupy hot springs or volcanoes, while halophiles inhabit salty bodies of water such as the Dead Sea. Archaea were later discovered in a broader range of habitats. The extreme environments that many archaea live in are at high pressures, salt concentrations or temperatures. Archaea are the best extremophiles. Archaea have such variability of wall structure that the Gram stain is not a useful differentiating tool.

There are other several traits of Archaea. Archaea has membrane lipids (diethers or isoprenoid L-glycerol ethers; the membrane lipid chains stiffen by covalent cross-links or by forming pentacyclic rings. Also, Archaea has Pseudomurein sacculus that contains talosaminuronic acid whereas the peptide bridges has only the L-amino acids.

In the Archaea gene regulation, the genomes of Archaea is similar to Bacteria in size and gene density, and genes of related function are often arranged in operons. Some tRNA gene sequences are interrupted by nontranslated sequences. These nontranslational sequences are called introns. So, the transcription factors is similar to eukaryotes.

Archaea includes two phyla: Crenarchaeota and Euryarchaeota. In the phylum Crenarchaeota, it has a substantial proportion of soil, marine, and benthic microbial communities. The metabolic crenarchaeotes metabolize sulfur, and it is either by aerobic oxidation or anaerobic reduction (which means no oxygen is required). However, in the phylum Euryarchaeota, it has members in soil and water. They have more metabolism than that in Crenarchaeota. Methanogens are the divergent group of Euryarchaeota.

Thermoplasma can be considered as archaea. Thermoplasma are thermoAcidophiles that thrive at pH<2. They are tetraether lipid monolayer membrane. Extreme halophiles, methanogens, and extreme thermophiles belong in this domain.