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Genetic Information

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Entry done as an activity of the course: A General Understanding of Information, held in Munich University of Applied Sciences

Summary:

  1. Lifeforms and their genetic information
  2. DNA – structure and functionality
  3. Process of replicating information in biology
  4. Storage capacity of DNA
  5. Semantic of protein production and functionality of the DNA
  6. Signals for DNA-Transcription and information flow
  7. Influencing Factors for information coding
  8. DNA evolution recording to Darwin and evolutionary science
  9. Evolution of biological information
  10. References

1. Life forms and their genetic information

In general, cells can be determined as the minimum unit of life, through their ability to generate, duplicate and process information. A cell contains different parts, which possess a determined function and process to make the cell a machine that can react to its environment and external influences [machine is biased with the idea of created for a purpose, therefore excludes to a certain extent the concept of self-organisation] [Whats the statement behind that comment? What changes should be made?]. The ability to receive, process and create information through duplication, as in Translation/Transcription,  makes the cell a fully independent system and therefore an independent lifeform.

Cells can be separated into two different types. The one is the simplest and most basic concept of a cell structure. It’s used by bacteria and archaea, which used to be the only lifeforms on earth until more evolved cells came along through the process of evolution. These cells are called prokaryotic cells, while the others are the eukaryotic cells, which inherit a more complex cell structure. The main difference between these two cell types is the structure and form of information storage. The prokaryotic cell information, in biological terms called DNA, is stored in form of an folded structure which floats through the cell in dense supercoiled strings. On the opposite, the eukaryotic cell has a core, called the nucleus, where the DNA is stored for further use [Here you could probably mention where the naming comes from, i.e. good (eu) kernel (karyon)] . The DNA is wrapped around proteins, called histones. The structure of the nucleus is punctuated, so certain fragments can leave the containment of the nucleus through holes in the nucleus membrane.

[Refer figures with text as: 
Figure No: short description (source: XXX)
then introduce some reference within the text, for example: "as we can see in Fig.1"]

2. DNA – structure and functionality

The DNA is a short term for desoxyribonucleic acid. DNA describes the structure of the genetic information, which is based on a polynucleotide. A polynucleotide describes a long string of nucleotides that is the same in all living cells, in eukaryotes as well as prokaryotes.  Each nucleotide is based on one of four nucleobases: Adenine, Cytosine; Thymine and Guanine. Two bases are complementary to each other, Adenine to Thymine and Guanine to Cytosine, and a certain structure can be formed by the sequences of the complementary nucleobases. The nucleotide itself consist of a phosphate molecule, sugar molecule and a nucleobase. The different nucleobases are linked by a strong hydrogen bond which give the DNA a certain flexibility while maintaining the determined sequence of the nucleobases. In the cell nucleus the DNA is available in the form of a double helix to take up less space when twirled up in a tight ball in the center of the nucleus (Lara, 2009). According to Lara, each nucleotide can establish a “head-tail association with any other nucleotide” at their 5` and 3´end. That means that every nucleotide has a defined structure with two different ends to interact and link with other nucleotides. This phenomenon defines the DNA sequence which is essential to the growth and development of life forms.

The sequence of DNA was first encrypted by the scientists James Dewey Watson and Francis Crick. With their discovery of the DNA sequence, also called “Universality of the genetic code”, the focus shifted from the chemistry behind the DNA to the coding of DNA through nucleobases and the molecular structure of information in a cell (Lyre, 2002).

[This has a bit better definition]


[Though you have taken the figure from Lara, he took it from Alberts 2002, this need to be mentioned]


The sequence of DNA is used to store information about the construction of proteins and other operating functions of the cell. Through Transcription and Translation [Enter the links here] this information can be reproduced and read to construct new proteins within the cell.

3. Process of replicating information in biology

Cells have the ability to reproduce proteins, through Translation, to support the survival of the cell in the long run. Proteins are based on amino acids and every protein is distinguished by its use and function. The cell itself is separated into two different compartments. The cytoplasm surrounds all parts of the inside of the cell and these parts can float freely through the containment of the cell walls. In contrary the nucleus is a rounded shape and contains the DNA of the cell as well as equipment that manages this stored information. Even the activation and blockage of certain nucleotide sequences can be achieved with this kind of equipment (Lara, 2009: 3). Both parts, the nucleus and the cytoplasm, are separated by the nuclear envelope, which divides the different stages of information flow inside the cell physically. According to Lyre (2003: 91) [this kind of referencing is used when you quote literally], information processing consists of two different stages, the transcription and translation. In addition, the DNA can be replicated to match the need of cell division through growth.

1. Transcription[Is n't it possible to introduce this into the other article?]

The process of transcription describes the act of copying a DNA sequence into a more mobile form of information. This form is called the mRNA, which stands for messenger ribonucleic acid. It represents half of the required part of the original nucleotide helix structure.

When the messenger RNA is fully developed it travels through holes in the nucleus wall and enters the next stage of information processing, the cytoplasm.

2. Translation:

In the cytoplasm the next step of processing cell information takes place, called the translation process. The mRNA is now floating freely in the cytoplasm and a protein called the ribosome, attaches to the mRNA and begins to add a tRNA to the first codon of the mRNA. There are different tRNA´s to match the different sequences of the nucleobases attached to the mRNA structure. In reading the sequence of nucleobases an amino acid is built up and a protein develops (bioadmin, 2013). This protein travels through the cytoplasm and is built into the cell mesh which separates the inside of the cell from the outer world. Once placed inside the mesh, the protein can start to carry out different functions.

3. Replication:

The act of replicating the DNA is needed when the cell reaches a certain size. DNA is replicated to give new cell a set of information to produce proteins and function in a proper way. First, the DNA double helix is separated, and the divided complementary nucleobases are matched again with their counterparts to sustain the same set of sequences and therefore the genetic information given through the original cell DNA. 

4. Storage capacity of DNA

An amino acid is based on a codon, which contains three nucleobases. If we take into consideration that there are four different possibilities to fill these three sockets of a codon, then we can determine the complexity of a codon. The configurations for one triplet codon are which makes 64 different Codons. If we take an DNA string consisting of 100 codons, then we have  alternatives in sequences.  The average nucleotides contained in the DNA of a simple life form, for example Escherichia coli, is N=. That means if we calculate that for the alternating of sequences, it means  (Lyre, 2002, p. 94).These capabilities of storage capacity is beyond the grasp of our very own imagination. Even for the simplest of lifeforms here on earth the information about processes and substances stored are too complex to comprehend.

5. Semantic of protein production and functionality of the DNA 

The definition for semantic is “the study of meanings in language” (Cambridge, 2014) which can be applied to cells as the language of DNA coding and information flow in cellular interaction. As stated before, the genetic information is stored in the DNA of a cell through the coding of nucleotides and codons. The importance of information for the cell is the decoding of this determined sequence of nucleotides to generate amino acids and produce proteins vital for the survival of the cell itself. These proteins have a clear determined function in the cell mesh for exchanging nutrients or sustaining the cell structure. Semantic of a cell itself is based on the functionality of decoding the nucleotide sequence. A code is only useful when the set functionality of the protein is given after the synthesis and the protein functions in the way it was designed for. Lara states in his article that there are external regulators that “meditate the activation or non-activation of specific portions, which can also be regulated by agents external to the protein” (Lara, p. 3). The problem within that thesis is the complexity in relations between the information stored in the DNA and its effect on proteins. Already existing proteins enable the DNA to translate the information needed and build the proteins later in the process. The flow of information therefore must be described as a two way and therefore not the DNA or proteins can be viewed as the transmitter of the initial signal of translating pieces of DNA (Lyre, 2002).

6. Signals for DNA-Transcription and information flow

One influencing factor for the processing and storing of biological information is the nucleoid sequence. But besides that, other structural properties of the DNA can be valued as storage coding. The electronic configuration in parts of the DNA molecules or the topological, topology stands for the “study of those properties of geometric forms that remain invariant under certain transformations, as bending or stretching” (dictionary.com, 2017), properties of the DNA in its three-dimensional structure (Lyre, 2002, p. 99). These functional properties of the DNA structure can influence the storage capacity and way of information coding in cell DNA of different lifeforms. A phenomenon called “junk-DNA” can also be a determent of these properties through its repetitiveness in the general DNA. Inside the cell itself there are factors too. Regulatory molecules, enzymes and structural proteins which influence the biological cell information in a certain way. Certain genes are expressed in one kind of way to determine the structure of cultivated proteins. In the process of transcription, the previously mentioned structural proteins can activate or deactivate certain kinds of gene expressions in order to alter the overall protein composition. The protein structure is changed by using the same part of DNA through transcription but altering the expression of genes.

As well as intracellular factors, extracellular ones determine information processing. These can be distinguished into two separate parts. On the one part there are molecules which can travel through the cell membrane, based on their small structure, and adhere to special nuclear receptors and change the process of DNA translation and the synthesis of RNA for the translation process later. On the opposite side is the influencing factor of charge added by external molecules, which can change the three-dimensional structure of the protein molecule and therefore it´s functionality for the cell (Lyre, 2002, p. 100). An isolated cell can be called a self-regulated information flow and therefore an independent processing machine for information sent by the cell itself (Lara, p. 9).

7.     Influencing Factors for information coding

Regarding to Lyres explanation, the action of process information was developed through the concept of evolution through several billion years. Else, according to Lyre, there wouldn’t be any point for cells to develop a cell structure if not through changing the information in DNA and coding information in form of their cell DNA for protein synthesis (Lyre, 2002, p. 103). The concept of evolution can be described as the main force behind the DNA system all complex living things are based on. Environment and the factors that come within this complex system of coexisting lifeforms and interactions is the driving force behind the evolution of the biological information carried in a living cell. It determines “that a new cell […] diachronically [can] reconstruct[s] the structures supporting the phenotype of the individual living being” (Díaz, 2017, p. 6). As Mr. Diaz described, the evolution of genetic information is determined by the environment a living being interacts in and therefore changes the biological information over a long-time-period to adjust the phenotype of the individual being. He describes it as the “substrate upon which new determinations in the morphogenesis process take place epigenetically” (Díaz, 2017, p. 6) . Also the neural capacity of lifeforms can be different for processing given information. For example, a human can process more and more difficult information or processes as another lifeform which could have more neuronal capacity by its biological information, but the structure of the brain and the neuronal connections can not enable the full capacity of complex thinking.

Life development is determined by the instructions which lie within the genomes and external factors based on environment. Because of that statement it is no surprise that life on earth as it is today being shaped by the continuous alteration of biological information originated in bacteria and developed to phenotypes of all different kinds of living beings over the period of billions of years.

As signal receivers of the external influencing factors, the nervous system and muscle/organs. The muscle/organs can be determined as operational units which interact with the environment and change due to adapting to the environmental challenges faced due to different climates and habitats. The nervous system on the other side secures the proper function and coordination of the operational units and can be determined as a kind of metasystem which processes information and gives responses to external signals through the operational units (Díaz, 2017, pp. 6-9).

8. DNA evolution recording to Darwin and evolutionary science

Charles Darwin stands for the original concept of evolution which applies the concept of “survival of the fittest”. It says that only the strongest and most adapted individuals of a species can survive the environment they live in and carry on their genetic pool, or biological information, into the next generation while the other individuals die due to their lack of adjustment to the environment. Today’s biology scientists determine evolution as a “total of individuals that are able to generate progeny which can reproduce themselves” (Lyre, 2002, p. 108). But in a species, there are “no two individuals” with the same genetic information due to random mutation in the gene pool and recombination in the process of reproduction.  By this kind of variation of the genetic information in individuals of one species is varied in a chaotic system and not determined by any plan or fixed pattern. Just the coincidence of random mutations in the sequence of nucleobases, and therefore codons, can be described as the driving factor behind the alteration of biological information. The fittest and most adapt individuals, due to the mutation over multiple generations, can survive better than the ones without this special trait. (Lyre, 2002, pp. 109-115)

9. Evolution of biological information

The origin of a cell structure can be described as a coincidence. Strings of amino acids and nucleotides were floating around in the primeval soup, billions of years ago. Then through some sort of coincidence these strings started to organize themselves and built networks that could process given information, for example given by the environment or other cells, and react accordingly. These networks are circle shaped to ensure the whole processing of information given from external sources. That means all biological life forms evolved from one specific set of biological information and therefore descend from one archetype which developed by coincidence. This can be also seen in the development stages of embryos by various species after egg-fertilization. The embryos are similar in the early stages but develop their special properties of their species over time till they are totally distinguished by their form and abilities.

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