General Biology/Classification of Living Things/Classification and Domains of Life

Fundamental classification
Classification of Living Things and Naming of Organisms.
In science, the practice of classifying organisms is called taxonomy (Taxis means arrangement and nomos mean method). The modern taxonomic system was developed by the Swedish botanist Carolus Linnaeus (1707-1778). He used simple physical characteristics of organisms to identify and differentiate between different species and is based on genetics. 
Linnaeus developed a hierarchy of groups for taxonomy. To distinguish different levels of similarity, each classifying group, called taxon (pl. taxa) is subdivided into other groups. To remember the order, it is helpful to use a mnemonic device. The taxa in hierarchical order: 
The domain is the broadest category, while species is the most specific category available. The taxon Domain was only introduced in 1990 by Carl Woese, as scientists reorganise things based on new discoveries and information. For example, the European Hare would be classified as follows: 
Eukaryote --&gt; Animalia --&gt; Chordata --&gt; Mammalia --&gt; Lagomorpha --&gt; Leporidae --&gt; Lepus --&gt; "Lepus europaeus". 
Eukaryote is just one of the classes inside of the main class Phyla
Binomial nomenclature.
Binomial nomenclature is used to name an organism, where the first word beginning with a capital is the genus of the organism and the second word beginning with lower-case letter is the species of the organism. The name must be in italics and in Latin, which was the major language of arts and sciences in the 18th century. The scientific name can be also abbreviated, where the genus is shortened to only its first letter followed by a period. In our example, "Lepus europaeus" would become "L. europaeus". 
Taxonomy and binomial nomenclature are both specific methods of classifying an organism. They help to eliminate problems, such as mistaken identity and false assumptions, caused by common names. An example of the former is the fact that a North American robin is quite different from the English robin. An example of the latter is the comparison between crayfish and catfish, where one might believe that they both are fish when in fact, they are quite different.
Nomenclature is concerned with the assignment of names to taxonomic groups in agreement with published rules. To study for a test these are the best words to know taxonomist, biologist, chemist, geologist, unicellular, multicellular, bilateral symmetry, radial symmetry, chlorophyll, photosynthesis, respiration, reproduction, vertebrates, endoskeleton, exoskeleton, consumers, decomposers, heterotroph, autotroph, vascular, non-vascular. These are all part of classifying things.
Eukaryotes and Prokaryotes.
Recall that there are two basic types of cells: eukaryotes and prokaryotes. 
Eukaryotes are more complex in structure, with nuclei and membrane-bound organelles. Some characteristics of eukaryotes are:
Prokaryotes refer to the smallest and simplest type of cells, without a true nucleus and no membrane-bound organelles. Bacteria fall under this category. Some characteristics:
Three Domains and Six Kingdoms.
The three domains are organized based on the difference between eukaryotes and prokaryotes. Today's living prokaryotes are extremely diverse and different from eukaryotes. This fact has been proven by molecular biological studies (e.g. of RNA structure) with modern technology. The three domains are as follows: 
Archaea (Archaebacteria) consists of archaebacteria, bacteria which live in extreme environments. The kingdom Archaea belongs to this domain.
Eubacteria consists of more typical bacteria found in everyday life. The kingdom Eubacteria belongs to this domain.
Eukaryote encompasses most of the world's visible living things. The kingdoms Protista, Fungi, Plantae, and Animalia fall under this category.
The Six Kingdoms.
Under the three domains are six kingdoms in taxonomy:
Animalia, contains general animals and is the largest kingdom with over 1 000 000 species.
Plantae, contains all plants on Earth.
Protista, the third kingdom, was introduced by the German biologist Ernst Haeckel in 1866 to classify micro-organisms which are neither animals nor plants. Since protists are quite irregular, this kingdom is the least understood and the genetic similarities between organisms in this kingdom are largely unknown. For example, some protists can exhibit properties of both animals and plants. 
Fungi are organisms that obtain food by absorbing materials in their bodies. Mushrooms and molds belong in this kingdom. Originally, they were part of the plant kingdom but were recategorized when they were discovered not to photosynthesize.
Eubacteria are bacteria, made up of small cells, which differ in appearance from the organisms in the above kingdoms. They lack a nucleus and cell organelles. They have cell walls made of peptidoglycan. 
Archae (or Archaebacteria) are bacteria that live in extreme environments, such as salt lakes or hot, acidic springs. These bacteria are in their own category as detailed studies have shown that they have unique properties and features (ex. unusual lipids that are not found in any other organism)which differ them from other bacteria and which allow them to live where they live. Their cell walls lack peptidoglycan.
Origins of Diversity.
The diversity in our planet is attributed to diversity within a species. As the world changed in climate and in geography as time passed, the characteristics of species diverged so much that new species were formed. This process, by which new species evolve, was first described by British naturalist Charles Darwin as natural selection. 
For an organism to change, genetic mutations must occur. At times, genetic mutations are accidental, as in the case of prokaryotes when they undergo asexual reproduction. For most eukaryotes, genetic mutations occur through sexual reproduction, where meiosis produces haploid gametes from the original parent cells. The fusion of these haploid gametes into a diploid zygote results in genetic variation in each generation. Over time, with enough arrangement of genes and traits, new species are produced. Sexual reproduction creates an immense potential of genetic variety.
One goal of taxonomy is to determine the evolutionary history of organisms. This can be achieved by comparing species living today with species in the past. The comparison in anatomy and structure is based on data from development, physical anatomy, biochemistry, DNA, behaviour, and ecological preferences. The following are examples of how such data is used:
Although a horse and a human may look different, there is evidence that their arm structures are quite similar. Their arms' sizes and proportions may be different, but the anatomical structures are quite similar. Such evidence reveals that animals in different taxa may not be that different. Biological features from a common evolutionary origin are known as homologous.
Biochemical analysis of animals similar in appearance have yielded surprising results. For example, although guinea pigs were once considered to be rodents, like mice, biochemistry led them to be in their taxon of their own.
Phylogeny, Cladistics, and Cladograms.
Modern taxonomy is based on many hypotheses' of the evolutionary history of organisms, known as phylogeny. As with the Scientific Method, scientists develop a hypothesis on the history of an animal and utilise modern science and technology to prove the phylogeny. 
Cladistics is a classification system which is based on phylogeny. Expanding on phylogeny, cladistics is based on the assumption that each group of related species has one common ancestor and would therefore retain some ancestral characteristics. Moreover, as these related species evolve and diverge from their common ancestor, they would develop unique characteristics. Such characteristics are known as derived characteristics
The principles of phylogeny and cladistics can be expressed visually as a cladogram, a branching diagram which acts as a family (phylogenetic) tree for similar species. A cladogram can also be used to test alternative hypotheses for an animal's phylogeny. In order to determine the most likely cladogram, the derived characteristics of similar species are matched and analysed.
Classification of Living Things Practice Questions.
1. If taxonomists had to select an existing kingdom to reclassify, which of the six would most likely be chosen? Why? 
2. Complete the following without consulting external sources:
a) The species "caudatum" is in the family "Paramecidae". What would be the binomial name of this organism? 
b) Give the abbreviation of the binomial name.
3. 
a) Irish moss belongs to the genus "Chondrus". The name for this species is "crispus". Give the binomial name.
b) Give the abbreviation of the binomial name. 
4. Humans and chimpanzees are alike. Which of the following data would most accurately prove this correct?
5. Which of the following is out of order?
6. A taxonomist discovers Organism A and Organism B and wishes to classify them. Which of the following choices is the most informative?
7. DNA analysis is usually done using DNA found in a cell's mitochondria, and not in a cell's nucleus. From your knowledge of mitosis, explain why this is so.
1. Archaebacteria
3.a) Chondrus crispus
b) C. cripus
4. B
5. G
6. B