Organism

From Wikipedia, the free encyclopedia

In biology, an organism (from Greek: , organismos) is any

individual entity that exhibits the properties of life. It is a synonym for
"life form".

Organisms are classified by taxonomy into specified groups such as the

multicellular animals, plants, and fungi; or unicellular microorganisms
such as a protists, bacteria, and archaea.[1] All types of organisms are
capable of reproduction, growth and development, maintenance, and
some degree of response to stimuli. Humans are multicellular animals
composed of many trillions of cells which differentiate during
development into specialized tissues and organs.
Escherichia coli is a microscopic single-
An organism may be either a prokaryote or a eukaryote. Prokaryotes are celled organism, a prokaryote.
represented by two separate domainsbacteria and archaea. Eukaryotic
organisms are characterized by the presence of a membrane-bound cell
nucleus and contain additional membrane-bound compartments called
organelles (such as mitochondria in animals and plants and plastids in plants
and algae, all generally considered to be derived from endosymbiotic
bacteria).[2] Fungi, animals and plants are examples of kingdoms of organisms
within the eukaryotes.

Estimates on the number of Earth's current species range from 10 million to 14

million,[3] of which only about 1.2 million have been documented.[4] More
than 99% of all species, amounting to over five billion species,[5] that ever
lived are estimated to be extinct.[6][7] In 2016, a set of 355 genes from the last
universal common ancestor (LUCA) of all living organisms living was
identified.[8][9]
Polypore fungi and angiosperm
trees are large many-celled
Contents organisms, eukaryotes.

1 Etymology
2 Definitions
2.1 Non-cellular life
3 Chemistry
3.1 Macromolecules
4 Structure
4.1 Cell
5 Evolution
5.1 Last universal common ancestor
6 Location of the root
6.1 Reproduction
6.2 Horizontal gene transfer
6.3 Future of life (cloning and synthetic organisms)
7 See also
8 References
9 External links

Etymology
The term "organism" (from Greek , organismos, from , organon, i.e. "instrument,
implement, tool, organ of sense or apprehension"[10][11]) first appeared in the English language in 1703 and
took on its current definition by 1834 (Oxford English Dictionary). It is directly related to the term
"organization". There is a long tradition of defining organisms as self-organizing beings, going back at least to
Immanuel Kant's 1790 Critique of Judgment.[12]

Definitions
An organism may be defined as an assembly of molecules functioning as a more or less stable whole that
exhibits the properties of life. Dictionary definitions can be broad, using phrases such as "any living structure,
such as a plant, animal, fungus or bacterium, capable of growth and reproduction".[13] Many definitions
exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the biochemical
machinery of a host cell for reproduction.[14] A superorganism is an organism consisting of many individuals
working together as a single functional or social unit.[15]

There has been controversy about the best way to define the organism[16][17][18][19][20][21][22][23][24] and indeed
about whether or not such a definition is necessary.[25][26] Several contributions[27] are responses to the
suggestion that the category of "organism" may well not be adequate in biology.[28]

Non-cellular life

Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction,
growth or metabolism. This controversy is problematic because some cellular organisms are also incapable of
independent survival (but are capable of independent metabolism and procreation) and live as obligatory
intracellular parasites. Although viruses have a few enzymes and molecules characteristic of living organisms,
they have no metabolism of their own; they cannot synthesize and organize the organic compounds from which
they are formed. Naturally, this rules out autonomous reproduction: they can only be passively replicated by the
machinery of the host cell. In this sense, they are similar to inanimate matter. While viruses sustain no
independent metabolism, and thus are usually not classified as organisms, they do have their own genes, and
they do evolve by mechanisms similar to the evolutionary mechanisms of organisms.

The most common argument in support of viruses as living organisms is their ability to undergo evolution and
replicate through self-assembly. Some scientists argue that viruses neither evolve, nor self- reproduce. In fact,
viruses are evolved by their host cells, meaning that there was co-evolution of viruses and host cells. If host
cells did not exist, viral evolution would be impossible. This is not true for cells. If viruses did not exist, the
direction of cellular evolution could be different, but cells would nevertheless be able to evolve. As for the
reproduction, viruses totally rely on hosts' machinery to replicate.[29] The discovery of viral megagenomes with
genes coding for energy metabolism and protein synthesis fueled the debate about whether viruses belong in the
tree of life. The presence of these genes suggested that viruses were once able to metabolize. However, it was
found later that the genes coding for energy and protein metabolism have a cellular origin. Most likely, these
genes were acquired through horizontal gene transfer from viral hosts.[29]

Chemistry
Organisms are complex chemical systems, organized in ways that promote reproduction and some measure of
sustainability or survival. The same laws that govern non-living chemistry govern the chemical processes of
life. It is generally the phenomena of entire organisms that determine their fitness to an environment and
therefore the survivability of their DNA-based genes.

Organisms clearly owe their origin, metabolism, and many other internal functions to chemical phenomena,
especially the chemistry of large organic molecules. Organisms are complex systems of chemical compounds
that, through interaction and environment, play a wide variety of roles.
Organisms are semi-closed chemical systems. Although they are individual units of life (as the definition
requires), they are not closed to the environment around them. To operate they constantly take in and release
energy. Autotrophs produce usable energy (in the form of organic compounds) using light from the sun or
inorganic compounds while heterotrophs take in organic compounds from the environment.

The primary chemical element in these compounds is carbon. The chemical properties of this element such as
its great affinity for bonding with other small atoms, including other carbon atoms, and its small size making it
capable of forming multiple bonds, make it ideal as the basis of organic life. It is able to form small three-atom
compounds (such as carbon dioxide), as well as large chains of many thousands of atoms that can store data
(nucleic acids), hold cells together, and transmit information (protein).

Macromolecules

Compounds that make up organisms may be divided into macromolecules and other, smaller molecules. The
four groups of macromolecule are nucleic acids, proteins, carbohydrates and lipids. Nucleic acids (specifically
deoxyribonucleic acid, or DNA) store genetic data as a sequence of nucleotides. The particular sequence of the
four different types of nucleotides (adenine, cytosine, guanine, and thymine) dictate many characteristics that
constitute the organism. The sequence is divided up into codons, each of which is a particular sequence of three
nucleotides and corresponds to a particular amino acid. Thus a sequence of DNA codes for a particular protein
that, due to the chemical properties of the amino acids it is made from, folds in a particular manner and so
performs a particular function.

These protein functions have been recognized:

1. Enzymes, which catalyze all of the reactions of metabolism

2. Structural proteins, such as tubulin, or collagen
3. Regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle
4. Signaling molecules or their receptors such as some hormones and their receptors
5. Defensive proteins, which can include everything from antibodies of the immune system, to toxins (e.g.,
dendrotoxins of snakes), to proteins that include unusual amino acids like canavanine

A bilayer of phospholipids makes up the membrane of cells that constitutes a barrier, containing everything
within the cell and preventing compounds from freely passing into, and out of, the cell. Due to the selective
permeability of the phospholipid membrane only specific compounds can pass through it. In some multicellular
organisms they serve as a storage of energy and mediate communication between cells. Carbohydrates are more
easily broken down than lipids and yield more energy to compare to lipids and proteins. In fact, carbohydrates
are the number one source of energy for all living organisms.

Structure
All organisms consist of structural units called cells; some contain a single cell (unicellular) and others contain
many units (multicellular). Multicellular organisms are able to specialize cells to perform specific functions. A
group of such cells is a tissue, and in animals these occur as four basic types, namely epithelium, nervous
tissue, muscle tissue, and connective tissue. Several types of tissue work together in the form of an organ to
produce a particular function (such as the pumping of the blood by the heart, or as a barrier to the environment
as the skin). This pattern continues to a higher level with several organs functioning as an organ system such as
the reproductive system, and digestive system. Many multicellular organisms consist of several organ systems,
which coordinate to allow for life.

Cell

The cell theory, first developed in 1839 by Schleiden and Schwann, states that all organisms are composed of
one or more cells; all cells come from preexisting cells; and cells contain the hereditary information necessary
for regulating cell functions and for transmitting information to the next generation of cells.
There are two types of cells, eukaryotic and prokaryotic. Prokaryotic cells are usually singletons, while
eukaryotic cells are usually found in multicellular organisms. Prokaryotic cells lack a nuclear membrane so
DNA is unbound within the cell; eukaryotic cells have nuclear membranes.

All cells, whether prokaryotic or eukaryotic, have a membrane, which envelops the cell, separates its interior
from its environment, regulates what moves in and out, and maintains the electric potential of the cell. Inside
the membrane, a salty cytoplasm takes up most of the cell volume. All cells possess DNA, the hereditary
material of genes, and RNA, containing the information necessary to build various proteins such as enzymes,
the cell's primary machinery. There are also other kinds of biomolecules in cells.

All cells share several similar characteristics of:[30]

Reproduction by cell division (binary fission, mitosis or meiosis).

Use of enzymes and other proteins coded by DNA genes and made via messenger RNA intermediates
and ribosomes.
Metabolism, including taking in raw materials, building cell components, converting energy, molecules
and releasing by-products. The functioning of a cell depends upon its ability to extract and use chemical
energy stored in organic molecules. This energy is derived from metabolic pathways.
Response to external and internal stimuli such as changes in temperature, pH or nutrient levels.
Cell contents are contained within a cell surface membrane that contains proteins and a lipid bilayer.

Evolution
Last universal common ancestor

The last universal common ancestor (LUCA) is the most recent

organism from which all organisms now living on Earth descend.[31]
Thus it is the most recent common ancestor of all current life on Earth.
The LUCA is estimated to have lived some 3.5 to 3.8 billion years ago
(sometime in the Paleoarchean era).[32][33] The earliest evidence for life
on Earth is graphite found to be biogenic in 3.7 billion-year-old
metasedimentary rocks discovered in Western Greenland[34] and
microbial mat fossils found in 3.48 billion-year-old sandstone
discovered in Western Australia.[35][36] Although more than 99 percent Precambrian stromatolites in the Siyeh
of all species that ever lived on the planet are estimated to be Formation, Glacier National Park. In
extinct,[6][7] there are currently 1014 million species of life on Earth.[3] 2002, a paper in the scientific journal
Nature suggested that these 3.5Gya
Information about the early development of life includes input from (billion years old) geological formations
many different fields, including geology and planetary science. These contain fossilized cyanobacteria
sciences provide information about the history of the Earth and the microbes. This suggests they are
changes produced by life. However, a great deal of information about evidence of one of the earliest known life
the early Earth has been destroyed by geological processes over the forms on Earth.
course of time.

All organisms are descended from a common ancestor or ancestral gene pool. Evidence for common descent
may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was
based solely on visible observation of morphologic similarities, such as the fact that all birds have wings, even
those that do not fly.

There is strong evidence from genetics that all organisms have a common ancestor. For example, every living
cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building
blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations)
to translate nucleic acid sequences into proteins. The universality of these traits strongly suggests common
ancestry, because the selection of many of these traits seems arbitrary. Horizontal gene transfer makes it more
difficult to study the last universal ancestor.[37] However, the universal use of the same genetic code, same
nucleotides, and same amino acids makes the existence of such an ancestor overwhelmingly likely.[38]

Location of the root

The most commonly accepted location of the root of the
tree of life is between a monophyletic domain Bacteria and
a clade formed by Archaea and Eukaryota of what is
referred to as the "traditional tree of life" based on several
molecular studies.[39][40][41][42][43][44] A very small
minority of studies have concluded differently, namely that
the root is in the domain Bacteria, either in the phylum
Firmicutes[45] or that the phylum Chloroflexi is basal to a
clade with Archaea and Eukaryotes and the rest of Bacteria
as proposed by Thomas Cavalier-Smith.[46]

Research published in 2016, by William F. Martin, by

genetically analyzing 6.1 million protein coding genes
from sequenced prokaryotic genomes of various
phylogenetic trees, identified 355 protein clusters from The LUCA used the WoodLjungdahl or reductive
amongst 286,514 protein clusters that were probably acetylCoA pathway to fix carbon.
common to the LUCA. The results "depict LUCA as
anaerobic, CO2-xing, H2-dependent with a Wood
Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N2-xing and thermophilic. LUCA's
biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence
upon transition metals, avins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and
selenium. Its genetic code required nucleoside modications and S-adenosylmethionine-dependent
methylations." The results depict methanogenic clostria as a basal clade in the 355 lineages examined, and
suggest that the LUCA inhabited an anaerobic hydrothermal vent setting in a geochemically active environment
rich in H2, CO2, and iron.[47] However, the identification of these genes as being present in LUCA was
criticized, suggesting that many of the proteins assumed to be present in LUCA represent later horizontal gene
transfers between archaea and bacteria.[48]

Reproduction

Sexual reproduction is widespread among current eukaryotes, and was likely present in the last common
ancestor.[49] This is suggested by the finding of a core set of genes for meiosis in the descendants of lineages
that diverged early form the eukaryotic evolutionary tree.[50] and Malik et al.[51] It is further supported by
evidence that eukaryotes previously regarded as "ancient asexuals", such as Amoeba, were likely sexual in the
past, and that most present day asexual amoeboid lineages likely arose recently and independently.[52]

In prokaryotes, natural bacterial transformation involves the transfer of DNA from one bacterium to another
and integration of the donor DNA into the recipient chromosome by recombination. Natural bacterial
transformation is considered to be a primitive sexual process and occurs in both bacteria and archaea, although
it has been studied mainly in bacteria. Transformation is clearly a bacterial adaptation and not an accidental
occurrence, because it depends on numerous gene products that specifically interact with each other to enter a
state of natural competence to perform this complex process.[53] Transformation is a common mode of DNA
transfer among prokaryotes.[54]

Horizontal gene transfer

The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly
supplemented with phylogeneticsthe reconstruction of phylogenies by the comparison of genetic (DNA)
sequence.

Sequence comparisons suggest recent horizontal transfer of many genes among diverse species
including across the boundaries of phylogenetic "domains". Thus determining the phylogenetic
history of a species can not be done conclusively by determining evolutionary trees for single
genes.[55]

Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome
research", therefore "biologists (should) use the metaphor of a mosaic to describe the different histories
combined in individual genomes and use (the) metaphor of a net to visualize the rich exchange and cooperative
effects of HGT among microbes."[56]

Future of life (cloning and synth etic organisms)

Modern biotechnology is challenging traditional concepts of organism and species. Cloning is the process of
creating a new multicellular organism, genetically identical to another, with the potential of creating entirely
new species of organisms. Cloning is the subject of much ethical debate.

In 2008, the J. Craig Venter Institute assembled a synthetic bacterial genome, Mycoplasma genitalium, by using
recombination in yeast of 25 overlapping DNA fragments in a single step. The use of yeast recombination
greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments.[57] Other
companies, such as Synthetic Genomics, have already been formed to take advantage of the many commercial
uses of custom designed genomes.

See also
Earliest known life forms

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