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Monday, October 24, 2011

DNA-Alphabet


These "letters", or sigils, are based on the permutations of the nucleic acids in the DNA molecule which produce the mRNA instructions for the ribosomes to produce the amino acid chain. So, when you're looking at the mRNA permutations, you'll need to switch them to their opposite. For example, UUU becomes AAA, and AAA becomes TTT (since Thymine is only found in the nucleus, and Uracil takes on its role outside the nucleus). Thus, when memorized and understood, these Letters also act as a memorization tool for the nucleic acid permutations. You'll be able to look at "UUAGCGAAG..." and recognize it as if it were an old friend. "By names and symbols are all powers awakened and reawakened."

So, here is the Alphabet. Soon, we'll be moving on to the 2-letter Words (the dipeptides).




Lysine
(abbreviated as Lys or K) As an essential amino acid, lysine is not synthesized in animals, hence it must be ingested as lysine or lysine-containing proteins. In plants and bacteria, it is synthesized from aspartic acid (aspartate). Good sources of lysine are foods rich in protein such as soy, as well as meat, cheese, certain fish, and eggs.

Also, in popular fiction (Jurassic Park), Lysine was supposed to have been the amino acid "denied" to dinosaurs, making them all female.

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Asparagine
(abbreviated as Asn or N; Asx or B represent either asparagine or aspartic acid) A reaction between sparagine and reducing sugars or reactive carbonyls produces acrylamide (acrylic amide) in food when heated to sufficient temperature. These products occur in baked goods such as French fries, potato chips, and roasted coffee. Asparagine is not an essential amino acid, which means that it can be synthesized from central metabolic pathway intermediates in humans and is not required in the diet. The nervous system requires asparagine. It also plays an important role in the synthesis of ammonia.

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Isoleucine
(abbreviated as ile or I) As an essential amino acid, isoleucine is not synthesized in animals, hence it must be ingested, usually as a component of proteins. In plants and microorganisms, it is synthesized via several steps, starting from pyruvic acid and alpha-ketoglutarate. Even though this amino acid is not produced in animals, it is stored in high quantities. Foods that have high amounts of isoleucine include eggs, soy protein, seaweed, turkey, chicken, lamb, cheese, and fish. Biotin, sometimes referred to as Vitamin B7 or Vitamin H, is an absolute requirement for the full catabolism of isoleucine (as well as leucine).

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Methionine
(abbreviated as Met or M) This amino acid is also used by plants for synthesis of ethylene. The process is known as the Yang Cycle or the methionine cycle. As an essential amino acid, methionine is not synthesized de novo in humans, hence we must ingest methionine or methionine-containing proteins. In plants and microorganisms, methionine is synthesized via a pathway that uses both aspartic acid and cysteine. High levels of methionine can be found in sesame seeds, Brazil nuts, fish, meats and some other plant seeds; methionine is also found in cereal grains. Methionine is one of only two amino acids encoded by a single codon in the standard genetic code (tryptophan is the other). The mRNA codon AUG is also the "Start" message for a ribosome that signals the initiation of protein translation. As a consequence, methionine is incorporated into the N-terminal position of all proteins in eukaryotes and archaea during translation, although it is usually removed by post-translational modification.

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Arginine
(abbreviated as Arg or R) In mammals, Arginine is classified as a semiessential or conditionally essential amino acid, depending on the developmental stage and health status of the individual. Preterm infants are unable to synthesize or create arginine internally, making the amino acid nutritionally essential for them. There are some conditions that put an increased demand on the body for the synthesis of L-arginine, including surgical or other trauma, sepsis and burns. In general, most people do not need to take arginine supplements because the body usually produces enough. Arginine plays an important role in cell division, the healing of wounds, removing ammonia from the body, immune function, and the release of hormones.

(Arginine is also taken in combination with proanthocyanidins or yohimbine has also been used as a treatment for erectile dysfunction.)

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Serine
(abbreviated as Ser or S) This compound may be naturally produced when UV light illuminates simple ices such as a combination of water, methanol, hydrogen cyanide, and ammonia, suggesting that it may be easily produced in cold regions of space. It is not essential to the human diet, since it is synthesized in the body from other metabolites, including glycine. It is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine and cysteine, and tryptophan in bacteria. It is also the precursor to numerous other metabolites, including sphingolipids and folate, which is the principal donor of one-carbon fragments in biosynthesis.

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Threonine
(abbreviated as Thr or T) Together with serine, threonine is one of two proteinogenic amino acids bearing an alcohol group. As an essential amino acid, threonine is not synthesized in humans, hence we must ingest threonine in the form of threonine-containing proteins. In plants and microorganisms, threonine is synthesized from aspartic acid via α-aspartyl-semialdehyde and homoserine. Foods high in threonine include cottage cheese, poultry, fish, meat, lentils, and sesame seeds.

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STOP
In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation. Stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain. Nonsense mutations are changes in DNA sequence that introduce a premature stop codon, causing any resulting protein to be abnormally shortened. This often causes a loss of function in the protein, as critical parts of the amino acid chain are no longer created. Because of this terminology, stop codons have also been referred to as nonsense codons.

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Tyrosine
(abbreviated as Tyr or Y) In dopaminergic cells in the brain, tyrosine is converted to levodopa by the enzyme tyrosine hydroxylase, which is the rate-limiting enzyme involved in the synthesis of the neurotransmitter dopamine. In addition, in the adrenal medulla, tyrosine is converted into the catecholamine hormones norepinephrine (noradrenaline), and epinephrine(adrenaline). The thyroid hormones triiodothyronine and thyroxine in the colloid of the thyroid also are derived from tyrosine. Tyrosine can be synthesized in the body from phenylalanine, and is is found in many high protein food products such as soy products, chicken, turkey, fish, peanuts, almonds, avocados, milk, cheese, yogurt, cottage cheese, lima beans, pumpkin seeds, and sesame seeds. A tyrosine residue also plays an important role in photosynthesis. In chloroplasts, it acts as an electron donor in the reduction of oxidized chlorophyll.

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Leucine
(abbreviated as Leu or L) As an essential amino acid, leucine is unable to be synthesised by animals. Consequently, it must be ingested, usually as a component of proteins. In plants and microorganisms, leucine is synthesised from pyruvic acid by a series of enzymes. It is a major component of the subunits in ferritin, astacin and other 'buffer' proteins. Leucine is utilized in the liver, adipose tissue, and muscle tissue. In adipose and muscle tissue, leucine is used in the formation of sterols, and the combined usage of leucine in these two tissues is seven times greater than its use in the liver.

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Phenylalanine
(abbreviated as Phe or F) Phenylalanine is an essential amino acid found in the breast milk of mammals. It is a precursor for tyrosine, the monoamine signaling molecules dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline), and the skin pigment melanin. It is used in the manufacture of food and drink products and sold as a nutritional supplement for its reputed analgesic and antidepressant effects. It is a direct precursor to the neuromodulator phenylethylamine, a commonly used dietary supplement. Phenylalanine is the starting compound used in the flavonoid biosynthesis. Lignan is derived from The genetic disorder phenylketonuria (PKU) is the inability to metabolize phenylalanine and from tyrosine. Phenylalanine is converted to cinnamic acid by the enzyme phenylalanine ammonia-lyase.

The genetic disorder phenylketonuria (PKU) is the inability to metabolize phenylalanine - and the reason for the "Warning: contains phenylalanine" on Diet Coke cans.

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Cysteine
(abbreviated as Cys or C) It is a non-essential amino acid, and is biosynthesized in humans if a sufficient quantity of methionine is available. The cysteine thiol group is nucleophilic and easily oxidized. The reactivity is enhanced when the thiol is ionized, and cysteine residues in proteins have pKa values close to neutrality, so are often in their reactive thiolate form in the cell.[9] Because of its high reactivity, the thiol group of cysteine has numerous biological functions. One of the largest applications is the production of flavors. For example, the reaction of cysteine with sugars in a Maillard reaction yields meat flavors. L-cysteine is also used as a processing aid for baking.

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Tryptophan
(abbreviation: Trp or W) Tryptophan is a routine constituent of most protein-based foods or dietary proteins. For many organisms (including humans), tryptophan is an essential amino acid. This means that it cannot be synthesized by the organism and therefore must be part of its diet. It is particularly plentiful in chocolate, oats, dried dates, milk, yogurt, cottage cheese, red meat, eggs, fish, poultry, sesame, chickpeas, sunflower seeds, pumpkin seeds, corn, spirulina, and peanuts. Tryptamine, Serotonin, Dimethyltryptamine (D.M.T.), Psilocybin (et cetera) and are all derived from Tryptophan. (what a Tryp!)

Despite popular belief that turkey has a particularly high amount of tryptophan, the amount of tryptophan in turkey is typical of most poultry.

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Glutamic Acid
(abbreviated as Glu or E) It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates. In neuroscience, glutamate is an important neurotransmitter that plays a key role in long-term potentiation and is important for learning and memory. Glutamate is a key molecule in cellular metabolism. In humans, dietary proteins are broken down by digestion into amino acids, which serve as metabolic fuel for other functional roles in the body. Glutamate is the most abundant excitatory neurotransmitter in the vertebrate nervous system. At chemical synapses, glutamate is stored in vesicles. Nerve impulses trigger release of glutamate from the pre-synaptic cell. In the opposing post-synaptic cell, glutamate receptors, such as the NMDA receptor, bind glutamate and are activated.

Monosodium Glutamate, or MSG, is derived from Glutamate. According to whoever wrote the Wikipedia entry, there is nothing wrong with MSG, it takes a whole lot of it to kill a rat, and it just got a bad rap because the people who complained about it were drunks, who also ate tons of salt. However, according to a lot of other people, MSG should be avoided since it has several unpleasant effects, like headaches.

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Aspartic Acid
(abbreviated as Asp or D) The carboxylate anion, salt, or ester of aspartic acid is known as Aspartate. Aspartic acid is, together with glutamic acid, classified as an acidic amino acid with a pKa of 4.0. Aspartate is pervasive in biosynthesis. Aspartate is non-essential in mammals, being produced from oxaloacetate by transamination. It can also be made in the Urea Cycle from Ornithine and Citrulline. In plants and microorganisms, aspartate is the precursor to several amino acids, including four that are essential for humans: methionine, threonine, isoleucine, and lysine. Aspartate (the conjugate base of aspartic acid) stimulates NMDA receptors, though not as strongly as the amino acid neurotransmitter glutamate does.

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Valine
(abbreviated as Val or V) Valine is an essential amino acid, hence it must be ingested, usually as a component of proteins. It is synthesized in plants via several steps starting from pyruvic acid. Human dietary sources include cottage cheese, fish, poultry, peanuts, sesame seeds, and lentils.

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Glycine
(abbreviated as Gly or G) Glycine is a colourless, sweet-tasting crystalline solid. It is unique among the proteinogenic amino acids in that it is not chiral. It can fit into hydrophilic or hydrophobic environments, due to its two hydrogen atom side chain. Glycine is not essential to the human diet, as it is biosynthesized in the body from the amino acid serine, which is in turn derived from 3-phosphoglycerate. The principal function of glycine is as a precursor to proteins. It is also a building block to numerous natural products. Glycine is an inhibitory neurotransmitter in the central nervous system, especially in the spinal cord, brainstem, and retina. Glycine serves as a buffering agent in antacids, analgesics, antiperspirants, cosmetics, and toiletries.

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Alanine
(abbreviated as Ala or A) Alanine is a nonessential amino acid, it can be manufactured in the body from pyruvate and branched chain amino acids such as valine, leucine, and isoleucine. Alanine plays a key role in glucose–alanine cycle between tissues and liver. In muscle and other tissues that degrade amino acids for fuel, amino groups are collected in the form of glutamate by transamination. Glutamate can then transfer its amino group through the action of alanine aminotransferase to pyruvate, a product of muscle glycolysis, forming alanine and α-ketoglutarate. The alanine formed is passed into the blood and transported to the liver. A reverse of the alanine aminotransferase reaction takes place in liver. Pyruvate regenerated forms glucose through gluconeogenesis, which returns to muscle through the circulation system. Glutamate in the liver enters mitochondria and degrades into ammonium ion through the action of glutamate dehydrogenase, which in turn participate in the urea cycle to form urea.

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Glutamine
(abbreviated as Gln or Q) It is not recognized as an essential amino acid but may become conditionally essential in certain situations, including intensive athletic training or certain gastrointestinal disorders. Glutamine is synthesized by the enzyme glutamine synthetase from glutamate and ammonia. The most relevant glutamine-producing tissue is the muscle mass, accounting for about 90% of all glutamine synthesized. Glutamine is also released, in small amounts, by the lung and the brain. Although the liver is capable of relevant glutamine synthesis, its role in glutamine metabolism is more regulatory than producing, since the liver takes up large amounts of glutamine derived from the gut. The most eager consumers of glutamine are the cells of intestines, the kidney cells for the acid base balance, activated immune cells and many cancer cells. In respect to the last point mentioned, different glutamine analogues such as DON, Azaserine or Acivicin are tested as anti-cancer drugs.

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Histidine
(abbreviated as His or H) Histidine is an essential amino acid in humans and other mammals. It was initially thought that it was only essential for infants, but longer-term studies established that it is also essential for adult humans. The imidazole sidechain of histidine is a common coordinating ligand in metalloproteins and is a part of catalytic sites in certain enzymes. In catalytic triads, the basic nitrogen of histidine is used to abstract a proton from serine, threonine, or cysteine to activate it as a neucleophile.

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Proline
(abbreviated as Pro or P) It is not an essential amino acid, which means that the human body can synthesize it. Proline and its derivatives are often used as asymmetric catalysts in organic reactions. The CBS reduction and proline catalysed aldol condensation are prominent examples. L-Proline is an osmoprotectant and therefore is used in many pharmaceutical, biotechnological applications.




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