# Structural Biochemistry/Evolutionary Bases

Related closely to the study of genetics, evolution observe the changes in heredity and genes of an organism from one generation to the next. This can be best exemplified in the evolution of eukaryotic organisms leading to more complex living beings such as animals and humans.
Evolution occur with the slight changes in the genes called mutations. Organisms have the innate ability to survive. Therefore, mutation occurs in order to satisfy natural selection where only favorable traits that will be beneficial for survival can be passed down to future generations. Another mechanism for evolution is called the genetic drift. This process occur independently which produces random changes in the traits of a population. This is the mechanism that is responsible for the emergence of new species.
Since biochemistry studies the mutations that occur in the genes as well as the relationship between a certain gene, cell, or biological molecule from another, the study of biochemistry work collaboratively with genetics to produce evolution trees that enable scientists to see relationships of one organism from another as well as how closely related they are.
Evolution refers to the processes that have transformed life on Earth from its earliest forms to the vast diversity that characterizes it today. Darwin addressed the diversity or organisms, their origins and relationships, their similarities and differences, their geographical distribution and their adaptation to their surround environments.
Life originated about 3.5 billion years ago, the first form of life was most likely a membrane-closed cell containing self-replication macromolecules molecule. Speculation supposes the components of the first cell may have been produced near thermals vents of the sea bottom or other areas of high temperature where atmospheric molecules such as CO$_2$ and NH$_3$ are present. One famous experiment that demonstrated biological molecules could have been formed from inorganic components is the Miller-Urey Experiment. The two scientists recreated the environment of early earth in a flask and found that the monomer basis of macromolecules were formed.

## Pre-Biotic Theories

Pre-biotic theories attempt to explain the origins of life, more specifically the creation of complex organic chemical structures from that of inorganic chemicals. The earliest chemical explanations have stemmed from Oparin’s book, The Origin of Life. Oparin’s theory was notable for setting a starting point as an experimentally provable pre-biotic theory. Most biochemical based pre-biotic theories stem from modifications or revisions of Oparin’s original theory. The Miller-Urey Experiment simulated the conditions set by Oparin's hypothesis and provided verifiable data in support of the pre-biotic theory.

### Oparin's Theory

Oparin's theory on the evolution of life from inorganic matter is called the Pre-Biotic Theory. According to Oparin, early atmosphere was very different from today's atmosphere. The atmosphere was very chemically reductive, consisting of methane, ammonia, hydrogen, and water. Through the action of unfiltered solar radiation, as the earth's atmosphere was less protective, the reductive chemicals would react. These reactions would chemically attack one-another, forming organic molecules which would gather due to various molecular interactions, forming a "primeval soup". Within the "primeval soup" organic molecules would form coacervates, assorted chemical compounds attracted throughhydrophobic forces; such coacervates would allow semi-closed systems in which basic organic metabolisms could form. Chemical reactions would increase in complexity and size, eventually forming amino acids. These reactions were hypothesized to be the origins of modern protein structures. However, there are several problems with Oparin's theory. Oparin stated that the atmosphere was strongly reductive, as oxidative attack would have destroyed more complex amino acids. However, without oxidizing gases, no ozone layer would have blocked up excess solar radiation which would eventually split the nitrous gasses into their respective components. To some extent, the containment that a coacervate would provide is sufficient, but it is not a complete explanation or solution to the pre-biotic theory.

### The Early Earth

* Atmospheric Contents
Earth's early atmosphere was quite different from the way it is today. The hypothesis is that Earth's atmosphere has evolved many times to lead the its present atmosphere. Today's atmosphere consists mainly of Carbon, Nitrogen, Oxygen, and Hydrogen. The most popular theory about the early atmosphere is that it contained very little oxygen, and was composed mainly of ammonia, methane, hydrogen, and water. With the aid of nature's forces of lighting, erupting volcanoes, and UV irradiation, the atmosphere was able to evolve.The early atmosphere was believed to contain large amounts of hydrogen which would explain how the atmosphere evolved through oxygen reduction. The Miller-Urey experiment was able to test this hypothesis. Using only the elements that were thought to be contained in the atmosphere and electric sparks to imitate lightning, the experiment proved that it was possible for Earth's atmosphere to evolved into what it is today.The Miller-Urey experiment paved the road towards the formation of living organisms throughout the atmospheric evolution. The experiment resulted in gaseous and water phases. The gaseous phase produced carbon dioxide and carbon monoxide, while the water phase contained various compounds like aldehydes, amino acids, and hydroxy acids. This showed that the hypothesis that abiotic production of biomolecules could be possible. As more detailed experiments were tested, data showed that polypeptides and RNA-like molecules could be produced with this atmosphere.There is also evidence that life could have developed only in the early times. Some chemicals reactions like those involving amino acids would require very little oxygen be present. The early atmosphere would also explain the existence of anaerobic life forms. Many experiments have led to the conclusion that the amount of oxygen in the atmosphere has increased overtime.
In 2006, an alternative source of organic compounds was proposed: outer space. Studies from the Stardust space mission brought back tiny particles of dust from the tail of a comet which contained a variety of organic compounds.
* Primordial Sea/Soup
The Primordial sea is the collection of all the oceans on Earth that were thought to be the beginning to the development of multicellular organisms. As early earth was evolving, many organic molecules existed and were unable to replicate itself. However, since multicellular organisms were thought to have not existed at that time, organic molecules were able to somehow provide the proper environment for chemical evolution. Complex polymers were able to form in such environments as well, but this formation was not a simple process. The Primordial soup refers to the Miller-Urey experiment as well, since it involved making an ocean that was thought to exist in early times.

### The Miller-Urey Experiment

In 1953, Stanley Miller and Harold Urey (at that time at the University of Chicago), constructed an experiment within Urey’s Lab to simulate the early earth conditions that were postulated to have existed by the Oparin hypothesis. The experiment consisted of a closed system with both a liquid phase and an “atmosphere” phase (See figure below). Within the “atmosphere” bulb were NH3, CH4, and H2 gases (ammonia, methane, and hydrogen respectively), thought to have been common in the earth’s early atmosphere due to extensive volcanic activity. The liquid phase contained water that was boiled to produce water vapor. This vapor would flow into the gas container and would be exposed to electrical sparks produced by electrodes. These sparks served to simulate the frequent lightning thought to have been familiar on the early earth. The gasses in this bulb were constantly cycled through the system using a condenser to simulate rain. The compounds would be removed from the “atmosphere” stage and would be collected back in the liquid phase, serving as a representation of the primordial sea. The experimental conditions were maintained for long lengths of time, sometimes extending to as long as a week or more. Samples were periodically taken from the “sea” phase for analysis.
Analysis of the samples taken from the system revealed the presence of organic compounds that had formed. The panel of compounds discovered included HCN, aldehydes, hydroxy acids, amino acids and simple nucleotides; among these were alanine and glutamic acid. The gas phase was found to contain high concentrations of both CO and CO2 as well. The presence of these compounds led Miller and Urey to conclude that the organic compounds that are necessary to early life and proto-life could form abiotically in a strongly reducing environment under the conditions hypothesized to have existed on the early earth.

### RNA World Hypothesis

Main Article: RNA World Hypothesis.

### RNA, DNA, and Proteins: The Evolution of Biochemical Diversity

RNA, not DNA, is believed to be the first genetic material. These primitive RNA, however short and simple, were able to duplicate themselves, catalyze the process, as well as splice their own introns. As RNA grows more in size and complexity, it acquires the ability to fold itself. The rate of mutations also increases as the fidelity of RNA becomes lower due to the ever-growing complication. Because of RNA's domination in the field of inheritable information, this predated era is known as 'RNA World'.
RNA shows great durability, which is crucial for genetic information is not to be degraded. However, as DNA came into existence, RNA's stability paled in comparison. The ribose ring of RNA contain two alcohol functional groups, making RNA more vulnerable to base-catalyzed hydrolysis, while DNA only has one, which in turn increases its stability. The reverse transcription of RNA into DNA is carried out using a specific enzyme much similar to that which HIV virus uses to turn its viral RNA back into DNA and integrate it into the host's genetic components.
Using knowledge of biochemistry, geneticists also discovered that DNA can specialize, with different functions taking up different portions of genes. Some contain codes for message relaying, while others may have information on reproduction, etc. Specialization not only makes a cell more efficient, but also predictable. In application of genetics such as medicine, researchers have been able to identify the genes responsible for corresponding vulnerabilities, ranging from physiologically to psychologically. A genome then can serve as a historical record, tracking a species change as it moves through time.
While DNA becomes the blueprint, proteins assume the role of cellular activity regulator and conductor. When two proteins are derived from two different genes with similar sequence, they are homologs. Homologs can be further divided into two subunits, paralogs, when those proteins occur in the same species, and orthologs, when they take place in different species. By studying these occurrence, scientists can determine the path of evolution that different species have taken, as these finding are very valuable when constructing phylogeny.

## Distinguishing Features of Living Organisms

** Complex Internal Structures, there is a high degree of chemical complexity and microscopic organization. Thousands of molecules allow cells to maintain a very intricate interal structure, which include long polymers, each with characteristic sequences of subunits, its unique 3D strucutre and specific selection of binding sites.
** Systems are able to maintain equilibrium by extracting, transforming and using energy from the environment. This enables organisms to do mechanical, chemical and osmotic work.
** Reproduction, with defined function of organism's components, organisms are interacting with one another The interplay between organism have allowed changed in components that cause coordination and compensation to necessary adaptation to environment.
** Mechanisms for sensing and responding to alterations in organism environments A constant adjusting of internal chemistry in order to adapt to change in their local enivorment for better survival.
** Ability for precise self-replication and self-assemblyConstruction of entirely complete genetic material in each and every individual cell unique to the organism.
** A capability to evolve over time This fundamental unity of the living organism is reflected at the molecular level in similarities of gene sequences and protein structures.

### Emergence of Polymers

While the Miller-Urey experiment did provide a possible origin for organic monomers like amino acids and nucleic acids, there was no evidence of complex polymers in the samples collected during the experiment.
Several scientists have postulated that the creation of some polymers (i.e. polypeptides and small proteins) may have been facilitated by hot clay or sand poking out of the primordial sea. Other theories predict that the formation of the polymers was aided by mineral or metal catalysts in this sand or clay.
Researchers have tested this hypothesis by dripping small amounts of amino acid- or nucleic acid-rich solutions onto hot clay or sand. In many cases, the monomers would spontaneously link to form polymers, in the absence of a catalyst. However, the polypeptides formed in this process were often cross-linked and tangled and did not resemble current day proteins. Nevertheless, some of these molecules had minor catalytic capabilities, and may have participated in some reactions in this early earth.

### The Protocell and Protobionts

Protobionts primitively resemble a version of a cell, sans the "life" part of the equation. Protobionts were a collection of organic molecules and other abiotic products contained in a membrane-like structure. The membrane was commonly composed of an aggregate of hydrophobic molecules that would arrange in a bilayer, similar to the phospholipid bilayer of a plasma membrane. These membranous structures likely formed in the same manner as micelles form in aqueous solution.
Protobionts have been generated in a laboratory setting as well in the form of liposomes. These liposomes are remarkable in that the hydrophobic bilayer that surrounds the inner solution is usually selectively permeable. This selective permeability allows the liposome to store an internal solutions that varies from the surrounding media. Due to this permeability, and diffusion some of these liposomes are even able to maintain a gradient across this hydrophobic bilayer. Some of these liposomes have been seen to split into smaller bodies, although perfect replication is not observed. Liposomes are considered to be a possible model for the protocell.

### First Cells Used Inorganic Chemical Fuels

The earliest cells arose in a reducing atmosphere (no oxygen) and most likely obtained energy from abundant inorganic fuels present on the early Earth.
Most likely, the primitive unicellular organisms gradually acquired ability to derive energy from compounds from the environment however, through evolutionary years organisms started to use energy to synthesized more of their own precursors molecules. Thus, organisms became less dependent upon the external sources.
For example, photosynthesis occurred through the development of pigments capable of converting light energy or "fix" CO$_2$ into organic compounds. This evolutionary change allowed plants to become more self-efficient in surviving in their environment.
Since the atmosphere of early Earth consisted on little to almost no O$_2$, the earliest cells were anaerobic, organisms that do not depend upon the presence of O$_2$. However, with the rise of O$_2$, produced by the photosynethetic bacteria, the atmosphere became progressively richer in O$_2$. O$_2$ is a powerful oxidant and deadly poisons to anaerobics. Advantages of aerobic organism over their anaerobic counterparts in the rich O$_2$ environment, led to the dominance of aerobic organisms in O$_2$ rich environments. This proposed time of O$_2$ rich environment develop suggest a support of Darwin's Theory of "survival of the fittest" for the aerobic organisms were able to prosper in the environment due to their adaptive evolution.

## Molecular Anatomy

Studying biological evolution has allowed biochemists to trace information of molecular anatomy. Molecular anatomy reveals evolutionary relationships. Molecular phylogeny is consistent with, yet more precise than classical macroscopic phylogeny. Molecular structures and mechanisms are remarkably similar from the simplest to the most complex organisms. DNA sequences are said to be homologous when two genes share sequencing similarities and the proteins they encode are called homologs. The homologous genes are said to be paralogous if they occur within the same species and the proteins they produce are called paralogs. Usually, paralogs have similar three-dimensional structure, but acquire different functions during evolution. On the other hand, two homologous genes found in different species are said to be orthologous and their protein products are othologs. Usually, orthologs are found to have the same function. Thus, functions of gene products can be guessed from the genomic sequence. The differences between homologous genes can be a rough measurement of how far two species have diverged during evolution. The larger the number of sequence differences, the earlier the divergence in evolutionary history.

## Darwin: On the Origin of Species

Charles Darwin's Evolution Theory stated "survival of the fittest" under selective pressure, led to the idea of natural selection. Darwin claimed that mutant cells and its progeny would survive and prosper in new environments whereas wild-type (unmutated cells) cells should starve and be eliminated.
1) Species were not created in their present forms, but have evolved from ancestral species, this is not dependent upon natural selection.
2) Natural Selection is a mechanism for evolution which details that a population of organisms can change over time as a result of individuals with certain heritable traits considered favorable for their environment, are able to leave more offspring than other individuals.

### Natural Selection

According to Charles Darwin, natural selection is a phenomenon by which organisms with favorable hereditary traits become successful and dominant in survival and reproducing. Organisms with traits that are unsuitable for survival are unfavored by nature and therefore die out. This process acts on the phenotype, or the appearance of the organism. The phenotypes that an organism have acquired are a result of random mutations in its genetic code, or genotype. This means that the entire course of life on earth was directed by random mutations in the genetic code of countless organisms and that these mutations are acted upon by nonrandom environmental forces that favor a particular trait. Overall, this mechanism allows the possibility of the emergence of new species of organisms that may adapt to their environments and thrive. In conclusion, the process of natural selection favors genes that have survival value for organisms in ever changing environments. Christopher Exley from Keele University praised Darwin's idea of natural selection as a force of nature. He emphasized in his paper, "Darwin, Natural Selection and the Biological Essentiality of Aluminium and Silicon," that natural selection is important in biochemical evolution as it is in speciation and that it also defined the essentiality of elements such as aluminium and silicon. Despite the fact that aluminium and silicon are both abundant in Earth, aluminium has no essential role in the biological system while silicon is considered essential biologically. Silicon participated in natural selection partially by helping aluminium to be selected out of the biological system in unreactive form through reacting with aluminium to form HAS (hydroxyaluminosilicates), which protects the biological system against toxicity of aluminium. This significantly reduced the biological availability of aluminium as well as its biological reactivity with the biooragnic compounds, leaving aluminium out of the biochemical evolution (non-participation in natural selection). Therefore, natural selection, as a force of nature, defines that silicon, which reacts with bioinorganic compounds such as metals to keep the biological system safe, is essential while aluminium has no essentiality in the biological system due to lack of biological availability.

### Mutations

In DNA replication, mistakes, known as genetic mutations, always occur, which causes changes in the DNA sequence.
Imperfections in replication leads to changes in the DNA, producing genetic mutations. Genetic mutations can be extremely harmful if they are passed down through reproductive cells because the mutations can cause certain functions in the body, such as enzymatic reactions, to not occur. However, even though mutations are unwanted, they allow cells to evolve and become stronger. Mutations allow cells to do things that they were not able to do before. Occasionally a mutation better equips an organism or cell to survive in its environment. Hence, even though it is a mutant, if it is trying to survive in a new environment and there is an abundant amount of it, it will be able to survive in that environment better than the wild type cells, which will cause the wild type to die off and become limited. The mutant cell would have a selective advantage over the other unmutated "wild type" cells. Eventually, the wild type cells would starve and be eliminated. Sometimes, genes accidentally create a second copy of itself during DNA replication due to a mutation. The second copy is not necessary, and mutations to this gene will not be damaging. Thus, this allows the gene to have a new function while keeping the old one. As this occurs numerous times, another unexpected mutation occurs to the second copy and causes sequencing and the protein formed from this sequence to be altered. For example, as a hexokinase gene went through DNA replication, it faced a mutation, which created a duplication of it. That duplicate gene encountered another error, causing it to form a copy of the original gene and a copy of a mutated duplicated gene that can have different abilities. In some cases, these mutations actually help the formation of a new gene to evolve. DNA has evolved a plenty through time because of mutations. Moderate amounts of mutations allow DNA to grow and have variation, which accounts for the diversity of organisms.

#### Types of Mutations

There are two basic categories of mutations that occur during DNA replication. They are:
* Point Mutations, in which a single nitrogen base is changed. For example, given the sequence: GATTACA. A point mutation may result in this combination: GATAACA. Usually, the point mutations only change a pyrimidine base with another pyrimidine base, or a purine with another purine. These mutations are known as transition point mutations, and are far more common than their counterpart, the transversions, which change a purine for a pyrimidine, and vice versa. The transition mutations are also grouped into nonsense, missense, and silent mutations. Nonsense mutations involve the accidental coding of a stop sequence, which can lead to a far shorter protein that originally planned. Missense mutations cause coding for a completely different protein, and silent mutations are ones in which the protein in unaffected. They can code for the same or different amino acid, but one that doesn't affect the structure and function of the molecule as a whole.
* Frameshift Mutations, in which an addition or a deletion of a nitrogen base causes a shift of frame for the protein synthesis. For example, if the ribosome is loading the molecule three nitrogen base pairs at a time, and originally it plans on separating the following as such: /GAT/TAC/A. A frame shift would either look like this, with an addition, /AGA/TTA/CA, or with a deletion, /ATT/ACA.

#### Pros of Mutations

* Mutants can acquire different specificity that may be more advantageous or better suited for their environment, and therefore lead to a higher survival rate along with propagation of that mutation in the species gene pool. Introducing a fertile mutant into a species allows for a wider range of genetic differences than increases the virility of such.

#### Cons of Mutations

* Mutations in DNA may be harmful or even lethal because defects may occur and may cause deletions or denaturazation of enzymes or other necessary specificities required for living, resulting defectives may render incapability of completing proper functions. For example, many human genetic diseases are due to mutations in the DNA. Mutations in DNA may be harmful and even lethal. In the bacteria Escherichia coli, E.coli, when a point mutation is made in specific strains of DH5-alpha cells, the bacteria become dominant lethal, which causes the growth to completely cease and terminates the cells. It is said that many errors in replication can cause diseases such as sickle cell anemia
, in which a point mutation causes the cells to be misshapen and cluster and inhibit proper blood flow, resulting in severe pain throughout the body. UV radiation or exposure to carcinogens, can cause the occasional mutations to accumulate and cause cancer. It is said the mutation accumulation in the body is also a contributor to the aging process.
* Inheritable mutations allow organisms to become more suited for survival in an ecological niche and prosper in reproduction towards preferential selected traits. The process of mutations and natural selection is based on the theory of Darwinism evolution, which states that the fundamental similarities among all living organisms deriving from the very beginning, the first single cell.

## Genomes

The sequence of the genome, the complete genetic endowment of an organism gives biochemists an enormously ri9ch and ever increasing treasury of information that can be used to analyze evolutionary relationships and refine evolutionary theory. Through evolution, structures, processes, and mechanisms are reflected in the changing genomes of evolving organisms. Therefore, comparison of whole genomes of species in each phylum class are leading to clarification and identification of genes critical to the fundamental evolutionary changes in the body plan and development.
With sequences as quantitative comparison is possible and therefore will lead to better insight into the evolutionary process where similarities are often found among living organisms and difference will shed light upon the genetic reasons for diversity among the organisms. By identifying pathways (sets of enzymes) encoded in genome, can allow biochemists and geneticists to learn more about the genetic material of organism as well as deduce from the genomic sequence alone the organism's metabolic capabilities.
The genome for 100s of bacteria, 40 archaea, and numerous eukaryotic micro-organisms are already known, and expanding.

### Genomics

When the sequence of a genome is fully determined, and each gene is assigned a function, molecular geneticists can group genes according to processes, and thus find what fraction of the genome is allocated to each of a cell's activities. In general, the more complex an organism, the greater proportion of its genome is involved in the regulation of cellular processe.
Genes in E. coli, A. thaliana and H. sapiens consists of
* 40+% unknown function
* ~10-4% transporters
* ~6-2% encode proteins and RNA
With the newly acquired knowledge of the complete genome of organism from different branches of phylogentic tree provides insights into evolution that eventually benefit human medicine. Image:Full resolution‎

## In Vitro Evolution

Also known as SELEX (Systematic Evolution of Ligands by Exponential enrichment), in vitro evolution is the study of RNA & DNA nucleotides and its natural selection on a microscopic scale. Study of RNA and DNA functions are carried out by putting together a mix of nucleotides and observing them outside of a cell (as opposed to the inside, which is referred to as in vivo evolution). The sample is put under conditions so as to promote survival competition between the nucleotides in the sample, this "competition" is usually in regard to the survival of a specific property of the nucleotide. The nucleotides that are shown to have dominant survival are subsequently amplified.
In vitro evolution has several purposes, the main one being the creation of a nucleotide or protein to perform specific functions. SELEX has also been used to predict the evolution of nucleotides with the assumption that stimulating a sample of nucleotides can procure what would be evolutionary fit. Adaptive mutations are induced and are used either to predict the evolutionary course of a sequence of nucleotides or and/or to optimize a molecule such as a protein to better perform a specific function. For example, it can be used to increase the binding affinity of an antibody, and it can also be used to predict the development of drug resistance.
The methodology of conducting in vitro evolution studies is constantly changing. Initially mutagenesis was procured via induction at the nucleotide level. However single point mutation of nucleotides through Polymerase Chain Reaction (PCR) was rather difficult because in some cases only a small fraction of an amino acid sample were accessible by this method. Mutagenesis done on the codon-level, such as the use of trinucleotide phosphoramidites, yield more practical results in that it is less cumbersome. An example of the efficacy between PCR and Codon-level mutagenesis can be drawn: in a situation where degeneracy is being introduced to a codon, 32 sequences of nucleotides are made whereas with codon-level mutagenesis only 20 are made. Amplification of the sample with the higher combination of sequence (PCR) become a burden later on when the excess nucleotides grow exponentially.
Vital to the utility of in vitro evolution is the ability to separate desirable mutations from a large mutant population. Generally, achieving mutations towards a given function requires rapid isolation of the individual proteins using techniques based on that desired function. Separation and screening are both valuable techniques used to assay libraries. Simple screening can be useful, but because significant and specific mutations require extensive mutant libraries, higher-throughput methods are required to reliably find individuals with the needed mutations. Thus, selections are often more useful because they can evaluate a larger quantity of mutants.
Intro Vitro evolution was first introduced by Sol Spiegelman in the 1960s. He extracted RNA from the Qخ² virus. Instead of using the traditional in vivo method of replication, Spielgeman used the extracted enzymes, RNA Q-b replicase (a viral RNA molecule) to synthesis RNA in the test tube. RNA begins to replicate without cellular reproduction. Through Spiegelman’s experiment, Darwin’s evolution theory of survival of the fittest proved to apply not only to organism but to molecule as well. The RNA coded to best fit into under the optimization condition will continue to multiple while the less competitive ones would die off from the limited resource of nucleotide in solution. As a result after several replication processes, the original 4,500 nucleotides bases have shrunken to a short 218 nucleotide bases, since shorter RNA stranded tends to replicate faster. The shorten RNA chain is denoted as the Spiegelman Monster.
There is much debate whether or not in vitro evolution can accurately portray the evolution which occurs in a cell (vivo evolution). However, recent studies by Miriam Barlow and Barry G. Hall at the University of Rochester have shown that in vitro evolution have strong similarities to vivo evolution. Their study took the evolution of the TEM-1 ß-lactamase gene in vitro and compared its evolutionary path to the naturally occurring evolution. The results of their study found that a large majority of the amino acid substitutions from vivo evolution were also found in the vitro evolution. The conclusion of the study is that in vitro evolutionary techniques can be used with confidence to predict the future evolution in genes.
Although in vitro research can serve as informative research on the molecular level, many proteins and cells work interdependently. Thus, in a test tube, many interactions and functions are not the same as in an organism as a whole.

## Theory of the Acquisition of Mitochondria

See main article Structural Biochemistry/The Endosymbiotic Theory
One key difference between prokaryotic cells and eukaryotic cells are the presence of organelles in eukaryotic cells. Organelles are membrane bound “bodies” found in the cytoplasm of eukaryotic cells that carry out specific functions.
One popular theory of how these organelles were obtained is the endosymbiosis theory. This theory seeks to provide an explanation for the appearance of mitochondria and chloroplasts in eukaryotic cells. The central idea behind this theory is as follows:
One prokaryotic cell ingests (or is infected by) another prokaryotic cell. Each prokaryotic cell fails to destroy or digest the other cell. As a result, the smaller of the two cells remains alive inside the larger cell. In the case of mitochondria, the smaller of the two prokaryotic cells (an aerobic prokaryote) would have provided the host cell with a means of utilizing oxygen, while simultaneously gaining nutrients that are taken in by the host cell. This presents a symbiosis, where both a host and its symbiotic partner contribute to the wellbeing of each individual within the partnership.
A “secondary endosymbiosis” seeks to explain the presence of mitochondria and chloroplasts in plant cells and some protists.
Support for this theory include the presence of a double lipid bilayer (membrane) in mitochondria, and the presence of mitochondrial DNA.
* Whereas Eukaryotic cells acquired capacities for photosynthesis and oxidative phosphorylation from endosymbiotic bacteria, multicellular organisms developed specialized cell types that differentiated functions essential to organism’s survival.

#### A basic schematic of the endosymbiont theory of eukaryotic evolution.
## References

* ↑ Oparin, Aleksandr Ivanovich (1964). The Chemical Origin of Life publisher = C.C. Thomas. {{cite book}}: Missing pipe in: |title= (help)
1. Oparin, Aleksandr Ivanovich. The Chemical Origins of Life. C.C. Thomas, 1964.
2. http://www.sciencemag.org/cgi/content/full/308/5724/962
3. http://www.ux1.eiu.edu/~cfjps/1400/atmos_origin.html
4. 'Lehninger Principles of Biochemistry Book' by Lehninger and Nelson
5. 'Reece and Campbell. Biology, 7th ed. New York, 2005. ISBN 0-8053-7171-0 '
* Breaker, Ronald. Tutorial: In Vitro Evolution. Retrieved 2008-10-18
* Campbell, Neil A., Jane B. Reece. Biology. Seventh Edition. 2005. ISBN 0-8053-7171-0
* Predicting Evolutionary Potential Retrieved 2008-10-22
* Simon Delagrave, Dennis J. Murphy. ASSAY and Drug Development Technologies. February 1, 2003, 1(supplement 2): 187-198. doi:10.1089/154065803321537917.