Classification of Organisms

In order to comprehend a little better the vast diversity of organisms in nature, we have looked for classifications systems. Traditionally, animals have been classified based on the morphology (shape and structure, or simply "how they look like"). This led to the creation of the 5 kingdoms. Nevertheless, a better and more accurate system of classification is used today. Now, organisms are based on their:

1. Phylogenetics;
2. Cellular complexity;
3. Energy Source;
4. Carbon Source.

Classification based on phylogenetics

Phylogenetics is just a fancy word for molecular information, specifically ribosomal RNA gene sequence. Interesting enough, each organism has a specific sequence. Therefore, by comparing the sequence of genes in different organism we can see how similar they are from each other. This led us to assume that all organisms could be grouped into three different domains: (1) eukaryota, (2) bacteria, and (3) archaea.

1. Eukaryota include organisms that are relative complex compared to their other domains. They have bigger and more complex cells and membrane bound organelles also.
2. Bacteria are found in several forms and shapes. These are single-celled organisms that have a great diversity on ways to metabolise energy. Bacteria also do not have membrane bound organelles like eukaryota organisms.
3. Archae organisms are very similar to bacteria, so similar that they were once formerly considered to be bacteria! Nevertheless, by comparing rRNA, it was concluded that they belonged to different domains. These organism have very usual shapes, and live in very extreme environments, such as high salt concentration, acidic water, or thermal hot springs.

A weird fact is that the organisms from the domain archae, in phylogenetic terms, is more similar to the organism in Eukaryota than it is to the ones in bacteria. This can only suggest that these two similar domains have been diverged from a common ancestors.

Classification based on cellular complexity:

When classifying animals, we must analyse in detail the complexity within the organism. Therefore, we will divide the organisms based on the complexity of their cells. This leads us to two types of cell: (1) Prokaryotic, and (2) Eukaryotes.

1. Prokaryotic cells are small and simple when comparing to eukaryotes, therefore, having a higher surface-to-volume ratio. The do not have membrane bound molecules, and its genetic information is all around the place within the cell. By being small though, prokaryotic cells don't need much in order to maintain themselves.
2. Eukaryotic cells are way bigger and more complex. They do have membrane bound molecules, and their genetic material are located in a membrane bounded nucleus. These membrane bound molecules are very important because they allow specific compartments to carry out specific function like energy production. This allows this big cells to maintain themselves.

There are two very important misleading ideas in this topic:

- The first one is regarding the uni-cellular organisms. These are not necessarily bacteria or archea. Some are considered to be eukaryota.
- The second one is the prokaryotic organisms are not always similar to each other, we have already seem that archea is very similar to eukaryota and not to bacteria.

Interesting enough, we can think about relationships between prokaryotes and eukaryotes. Think about your mouth, there are billions of prokaryotes organisms living there, in a symbiotic relationship.

There is a theory called endosymbiotic theory. It suggests that some organelles in eukaryotic cells such as mitcochondria and chloroplasts were originated from prokaryotes! And there is some evidence for this statement: There are many symbiotic and endosymbiotic association today, these organelles have their own DNA and divid by binary fission (just like prokaryotes), and their ribossomes are more similar to prokaryotes than to eukaryotes.

Classification based on energy and carbon source

Organisms that acquire the energy from the sun are said to me phototroph, other organisms which have their energy coming from the chemical bonds of molecules are said to be chemotroph. We also know that there are two types of chemotrophs: those who get energy from organic chemical compounds (chemoorganotrophs), and those who get energy from non-organic chemical compounds (chemolithotrophs).
Now we will learn that the source of carbon can actually influence on the classification of organisms.
Those organisms that have their carbon source from carbon dioxide are said to be autotrophs, and those who get from organic compounds are said to be heterotroph. When naming, we put both energy and carbon source names into one.
For example, plants are said to be photo-auto-trophs, because they get their energy from the sun and the carbon dioxide is their source of carbon. Us, humans we are chemo-organo-hetero-trophs. Can you say why?

Summary: Phylogenetic classification of organisms based on rRNA sequences has led to classification into theree domains in life - bacteria, archae, and eukaryota. Although archae are prokaryotic cells, they are more closely genetically  related to eukaryote than bacteria as is shown by the examples in the text.  The classification of organisms based on energy source (photo- or chemo-) and carbon source (auto- or hetero-) lead to six different classes.