Archaea

Archaea Katie Shikora

 Introduction: **Archaea** comes from the greek word, //archaio//, meaning ancient (billions of years, and if you don't call that old, then I don't know what is). In order to fully understand the origins of Archaea, we must look at evolutionary history. From what we understand, all living forms have descended from a Universal ancestor, which appeared through **spontaneous generation**. The term "spontaneous generation" is generally used to explain what Europeans before 1668 believed to be the cause of life, indicating that every day, living organisms were created by non living things (such as mud). This should not be confused with the modern theory of the origin of life, that abiotic amino acids were generated in the primordial soup and spontaneously joined together to form LUCA. At some point, this ancestor diverged into two prokaryotic domains: Bacteria and Archaea. This divergence was made evident through microbiologist Carl Woese's comparisons of nucleic acid sequences. Each group of organisms has its very own **signature sequences**. Until recently, the relationship between domain Bacteria and domain Archaea was thought to be a lot closer than it actually is. Besides differences in structure, archaea and bacteria also have many difference in their lifestyles, habitats, and structure.

Although most known prokaryotes are bacteria, there is most certainly a notable amount of prokaryotic organisms that belong to the domain Archaea. It is the domain most similiar to Eukarya, and evidence suggests that eukaryotes evolved from archaea. Archaea are very unique structurally, biochemically, and physiologically.   Diagnostic Characteristics of the Group:
 * membrane lipids have some branched **hydrocarbon** (specific to Archaea)
 * can grow at temperatures greater than 100˚C (specific to some species of Archaea)
 * chromosomes are circular (similar to Bacteria)
 * lack nuclear envelopes (similar to Bacteria)
 * lack membrane-enclosed organelles (similar to Bacteria)
 * **Methionine** is the initiator amino acid for protein synthesis (similar to Eukarya)
 * lack peptidoglycan in the cell wall (similar to Eukarya)
 * growth not inhibited when responding to antibiotics streptomycin and chloramphenicol (similar to Eukarya)
 * histones are associated with DNA (similar to Eukarya)
 * <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">contains several kinds of RNA polymerase (similar to Eukarya)

<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif; font-size: 140%;">Habitats: <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;"> In general, archaea are known for "livin' on the edge" like they did back in the day when the Earth was young. Unlike other organisms, archaea enjoy bathing in salt ponds and wading in hot springs. Archaea can also survive in extremely acid or alkaline environments. They can thrive in extreme climates, granting them the name **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">extremophiles **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">(lovers of extremes). Until recently, scientists believed that they were limited to living as such. Recent discoveries have been made, however, where archaea have been found inhabiting marine environments. Like they always say, "if you haven't lived like an archaean, then you haven't lived at all."

<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif; font-size: 140%;">Major Types: <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">Although prokaryotic **phylogeny** (the study of evolutionary relatadness among groups of organisms) is tentative, there are two major taxa of archaea, **Euryarchaeota** and **Crenarchaeota**. Let's break these two bad boys down: the root "eury" means broad and the root "cren" means spring.

Euryarchaeota, like its name suggests, includes archaea that have broad habitat ranges. This includes all **methanogens**, kinds of anaerobic (does not use oxygen), methane gas-producing prokaryotes, and **extreme halophiles,** kinds of salt-loving prokaryotes that form a scum pigmented purple-red by bacteriorhodopsin. In addition, Euryarchaeota includes some **thermophiles,** or heat-loving prokaryotes, but most thermophiles belong to Crenarchaeota. The species of archaea that can withstand the highest temperature of any living organism on earth is //Pyrolobus fumarii// which thrives at 113 degrees Celsius.


 * <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif; font-weight: normal;">Crenarchaeota includes archaea that inhabit deep-sea <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">hydrothermal vents <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif; font-weight: normal;">. These extreme thermophiles may very well have been the earliest prokaryotes to evolve. Two types include Sulfablus and Acidianus which both survive aerobically, although Acidianus can live anaerobically. They both are chemolithotrophs (organisms that obtain energy by the oxidation of inorganic compounds) but also have the potential to be chemoautotrophs if needed. **

<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif; font-size: 140%;">Basic Anatomy: <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">All prokaryotic organisms have basically the same structure. <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">In addition to the sharing of certain qualities with other prokaryotes, archaea also have some significant structural differences.
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Most are **unicellular**, although some cells tend to congregate together and may even live mutualistically (advantageous for each interacting organism).
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">A prokaryote may be one of three cell shapes:
 * 1) <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Spherical (cocci)
 * 2) <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Rod-shaped (bacilli)
 * 3) <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Helical
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Archea may also come in shapes such as rods, dots, triangles, discs, plates, and cup shapes.
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Prokaryotes, which are usually about 1-5 [[image:http://www.bio.miami.edu/%7Ecmallery/150/proceuc/c8.27x3.bact.shapes.jpg width="315" height="251" align="right" caption="Prokaryote cell shapes."]]<span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;"> micrometers (µm) in diameter, are noticeably smaller than eukaryotes, which are about 10-100 micrometers (µm) in diameter.
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Almost all prokaryotes have cell walls to maintain the cell shape and avoid the problem of the cell becoming **hypotonic (of higher concentration than the extracellular space). **
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Some prokaryotes adhere to one another or other substances using surface appendages called **pili,** which are hair like appendages found on bacteria.
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Many prokaryotic organisms are capable of directional movement by means of **<span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">flagella, slender, thread-like structures located in one or more places along the cell surface. **
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">All have small, simple genomes with .001X as much DNA as a Eukaryotic cell.
 * Like bacteria, archaeans have no internal membranes and their DNA exists as a single loop called a **plasmid**. However, their tRNAs have a number of features that differ from all other living things. The **tRNA** molecules (short for "transfer RNA") are important in decoding the message of DNA and in building proteins. <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Unlike bacteria, archaea lack **peptidoglycan, monomers of modified sugars cross-linked by polypeptides, in their cell walls. This makes for the cell to be completely enclosed and protected by a single molecular network. **
 * <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;">Unlike bacteria, archaea have **histones** associated with DNA.

<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif; font-size: 18px; line-height: 27px;">Transport of Materials: <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">Since archaea are prokaryotic organisms, they do not use active transport. Instead, they must passive transport in order for materials to pass in and out of the cell. **Passive transport** does not require work (from ATP) and substances move from a higher concentration to a lower concentration across the cellular membrane.

<span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; font-size: 140%; text-align: left;">Reproduction <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">Archaea reproduce as any other prokaryote would: **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">asexually **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">. And they do it fast. They must undergo a process called **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">binary fission **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">, where a single cell divides and produces identical offspring. Neither meiosis nor mitosis occur in prokaryotes, unlike all eukaryotes. **Mutation** is a huge contributor to the genetic variability in prokaryotes. The genome of the archaea is mostly held in a single circular DNA molecule. The DNA is not associated with histone proteins, but does have unique DNA binding proteins. The genomic chromosome is attached to the cell membrane at a point. Prokaryotes have three mechanisms to transport genes between individuals:
 * 1) **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">Transformation **<span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">: prokaryotic cells take up genes from their outside environment, allowing for gene trasport.
 * 2) <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">**Conjugation**: genes are directly transferred from one prokaryote to another.
 * 3) <span style="color: #008000; font-family: Tahoma,Geneva,sans-serif;">**Transduction**: viruses transfer genes between prokaryotes.

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<span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; font-size: 140%; text-align: left;">Environmental Adaptations <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; text-align: left;"> Movement is important for an archaean, specifically **taxis** **movement**, where it moves toward or away from a certain stimulus or stimuli. This can keep an archaeon away from toxins and near food or oxygen. As previously mentioned in the Basic Anatomy section, Archaea contain two very important structures that aid them in adapting to their extreme lifestyles through means of movement. First, many archaea have a flagellum or flagella, which assists them in directional movement. In addition to the use of this, archaea may also secrete filamentous chains and jets of <span style="font-family: Tahoma,Geneva,sans-serif;">slime to help them glide along surfaces. They also have a protective layer called a **capsule** so that they can adhere to these surfaces and be resistant to pathogenic prokaryotes.

Because most archaea are **photosynthetic, meaning that they use the sunlight for nutrients, they have receptor molecules to keep them as directly under the sunlight as possible. Some archaea do not require oxygen nor sunlight to perform photosynthesis, instead they take in CO2, N2, or H2S and produce methane as a waste product. Also, some archaea contain a row of magnetic particles to detect Earth's magnetic field. This allows them to differentiate between up and down, a characteristic that helps them to find the nutrient-rich sediments in the bottom of ponds or seas. ** <span style="color: #008000; display: block; font-family: Tahoma,Geneva,sans-serif; font-weight: normal; text-align: left;"> Archaea cohere in large groups, or colonies, through use of capsules. This ensures that binary fission is easy, and all three mechanisms for genetic transportation can be carried out. Additionally, they use **pili, as defined previously, for colony adherence.

Review Questions: 1. Explain the three methods of reproduction among archaeans. 2) What characteristics does the Archaea domain share with the Bacteria domain? What characteristics does it share with Eukarya? 3) What two important structures allow archaea to move around and survive in an extreme environment? 2) What is the main ability that Archaea possess which seperates them from other phyla? Give examples. 5) Explain binary fission, and explain how mutations in Archean organisms affect their genetics. 6) As extremophiles, how do Archea's environmental adaptations allow it to live in extreme conditions? 7) What method of transport do Archean organisms use? Why is this method ideal for these organisms? ** References: [] (Sara Waugh) [](Rabya Saraf) http://www.bio.miami.edu/~cmallery/150/proceuc/c8.27x3.bact.shapes.jpg (Sarah Fleming) [](Jesse Landy) [](Leo Schwartz) [] (Liz Daley) http://www.earthlife.net/prokaryotes/archaea.html (Jeremy Fransman) Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends in Genetics 14:442-444. via [] (Alysse) [][Rabya S]

[] (Jake Schwartz) [](APS) [] (Donna McDermott) http://www.ucmp.berkeley.edu/archaea/archaealh.html (Alyssa Zisk)