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20 Amino Acids and their Structural Formula

We know that all the biological activities are dependent on the biological molecules which are found in the living bodies. These Biomolecules are responsible for different activities such as reproduction, movement etc. In this article we will discuss about one of the biological molecules which are named as protein. They are composed of similar monomer units which are called amino acids. They are organic molecules which are made up of carbon, hydrogen, oxygen, nitrogen and some heteroatom like sulphur etc.

Amino acids involve in peptide linkage to form polypeptide chains. The amino acids molecules contain one –NH2 and one –COOH group on the same carbon atom. This carbon atom is called as alpha carbon atom and amino acids are called as alpha amino acids. In living bodies, only alpha amino acids involve in the formation of polypeptide chains or proteins. The amino group and carboxyl group of the molecule involve in the condensation reaction to form amide bond with other molecules.

The condensation reaction involves the elimination of water molecule in each step. The sequence of amino acids in the polypeptide chains is called as primary structure of proteins which further being complicated to form secondary structure. Two possible secondary structures are alpha helical and beta plated forms in which polypeptide chains are oriented in helical or plated form with the help of H-bonds. There are 20 amino acids in the human beings which are bonded with each other in different sequences to form polypeptide chains. These 20 amino acids can be classified in different manners such as on the basis of structure or polarity or side chains. On the basis of side chain of the amino acids; they can be classified as acidic, basic and neutral amino acids. The acidic amino acids contain some acidic functional group in the molecule such as carboxyl group. The example of acidic amino acids is glutamic acid, aspartic acid etc.

The basic amino acids contain some alkaline functional group in the side chains such as amino group, amido group etc. in glutamine, asparagine. The presence of hydrocarbon chain in the side chain of makes the molecule neutral as one amino and one carboxyl group does not impart any acidic or alkaline nature to the molecule.

The amino acid molecule is usually existed in the form of Zwitter ion in which two opposite charges are found on the same carbon atom. Since basic amino group exits as –NH3+ ion and acidic –COOH group exits as –COO- ion, therefore overall molecule becomes neutral in nature and called as Zwitter ion. The Zwitter ion can show certain movement in their solution during electrolysis which is completely depend upon the pH of the solution.

Each amino acid shows no net movement towards any electrode at specific pH value which is called as isoelectric point. On the basis of polarity; they can be classify as polar and non-polar molecules. The polar molecule contains some functional group in the molecule apart from one amino and one carboxyl group while a non-polar molecule contains only hydrocarbon side chain. One basic amino group on alpha carbon atom can easily neutralise the effect of one acidic carboxyl group in the molecule.

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From Wikipedia

Proteinogenic amino acid

Proteinogenic amino acids are those amino acids that can be found in proteins and require cellular machinery coded for in the genetic code of any organism for their isolated production. There are 22 standard amino acids, but only 21 are found in eukaryotes. Of the twenty-two, twenty are directly encoded by the universal genetic code. Humans can synthesize 11 of these 20 from each other or from other molecules of intermediary metabolism, but the other 9 essential amino acids(histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine) must be consumed in the diet. The remaining two, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Proteinogenic literally means protein building. Proteinogenic amino acids can be assembled into a polypeptide (the subunit of a protein) through a process known as translation (the second stage of protein biosynthesis, part of the overall process of gene expression).

Non-proteinogenic amino acids are either not found in proteins (like carnitine, GABA, or L-DOPA), or are not produced directly and in isolation by standard cellular machinery (like hydroxyproline and selenomethionine). The latter often results from posttranslational modification of proteins.

There are clear reasons why organisms have not evolved to incorporate certain non-proteinogenic amino acids into proteins: for example, ornithine and homoserine will cyclize against the peptide backbone and fragment the protein with relatively short half-lives, and others are toxic because they can be mistakenly incorporated into proteins, such as the arginine analog canavanine.

Non-proteinogenic amino acids are found in nonribosomal peptides, which are not produced by the ribosome during translation.

Structures

The following illustrates the structures and abbreviations of the 21 amino acids that are directly encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical zwitterion forms that exist in aqueous solutions.

IUPAC/IUBMB now also recommends standard abbreviations for the following two amino acids:

Non-specific abbreviations

Sometimes the specific identity of an amino acid cannot be determined unambiguously. Certain protein sequencing techniques do not distinguish among certain pairs. Thus, the following codes are used:

In addition, the symbol X is used to indicate an amino acid that is completely unidentified.

Chemical properties

Following is a table listing the one-letter symbols, the three-letter symbols, and the chemical properties of the side-chains of the standard amino acids. The masses listed are based on weighted averages of the elemental isotopes at their natural abundances. Note that forming a peptide bond results in elimination of a molecule of water, so the mass of an amino acid unit within a protein chain is reduced by 18.01524 Da.

General chemical properties

Side chain properties

Note: The pKa values of amino acids are typically slightly different when the amino acid is inside a protein. Protein pKa calculations are sometimes used to calculate the change in the pKa value of an amino acid in this situation.

Gene expression and biochemistry

* UAG is normally the amber stop codon, but encodes pyrrolysine if a PYLIS element is present.
** UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a SECIS element is present.
† The stop codon is not an amino acid, but is included for completeness.


From Encyclopedia

Amino Acids

Amino acids are organic compounds made of carbon, hydrogen, oxygen, nitrogen, and (in some cases) sulfur bonded in characteristic formations. Strings of amino acids make up proteins, of which there are countless varieties. Of the 20 amino acids required for manufacturing the proteins the human body needs, the body itself produces only 12, meaning that we have to meet our requirements for the other eight through nutrition. This is just one example of the importance of amino acids in the functioning of life. Another cautionary illustration of amino acids' power is the gamut of diseases (most notably, sickle cell anemia) that impair or claim the lives of those whose amino acids are out of sequence or malfunctioning. Once used in dating objects from the distant past, amino acids have existed on Earth for at least three billion years—long before the appearance of the first true organisms. Amino acids are organic compounds, meaning that they contain carbon and hydrogen bonded to each other. In addition to those two elements, they include nitrogen, oxygen, and, in a few cases, sulfur. The basic structure of an amino-acid molecule consists of a carbon atom bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a fourth group that differs from one amino acid to another and often is referred to as the-R group or the side chain. The-R group, which can vary widely, is responsible for the differences in chemical properties. This explanation sounds a bit technical and requires a background in chemistry that is beyond the scope of this essay, but let us simplify it somewhat. Imagine that the amino-acid molecule is like the face of a compass, with a carbon atom at the center. Raying out from the center, in the four directions of the compass, are lines representing chemical bonds to other atoms or groups of atoms. These directions are based on models that typically are used to represent amino-acid molecules, though north, south, east, and west, as used in the following illustration, are simply terms to make the molecule easier to visualize. To the south of the carbon atom (C) is a hydrogen atom (H), which, like all the other atoms or groups, is joined to the carbon center by a chemical bond. To the north of the carbon center is what is known as an amino group (-NH2). The hyphen at the beginning indicates that such a group does not usually stand alone but normally is attached to some other atom or group. To the east is a carboxyl group, represented as-COOH. In the amino group, two hydrogen atoms are bonded to each other and then to nitrogen, whereas the carboxyl group has two separate oxygen atoms strung between a carbon atom and a hydrogen atom. Hence, they are not represented as O2. Finally, off to the west is the R -group, which can vary widely. It is as though the other portions of the amino acid together formed a standard suffix in the English language, such as -tion. To the front of that suffix can be attached all sorts of terms drawn from root words, such as educate or satisfy or revolt —hence, education, satisfaction, and revolution. The variation in the terms attached to the front end is extremely broad, yet the tail end, -tion, is a single formation. Likewise the carbon, hydrogen, amino group, and carboxyl group in an amino acid are more or less constant. The name amino acid, in fact, comes from the amino group and the acid group, which are the most chemically reactive parts of the molecule. Each of the common amino acids has, in addition to its chemical name, a more familiar name and a three-letter abbreviation that frequently is used to identify it. In the present context, we are not concerned with these abbreviations. Amino-acid molecules, which contain an amino group and a carboxyl group, do not behave like typical molecules. Instead of melting at temperatures hotter than 392°F (200°C), they simply decompose. They are quite soluble, or capable of being dissolved, in water but are insoluble in nonpolar solvents (oil-and all oil-based products), such as benzene or ether. All of the amino acids in the human body, except glycine, are either right-hand or left-hand versions of the same molecule, meaning that in some amino acids the positions of the carboxyl group and the R -group are switched. Interestingly, nearly all of the amino acids occurring in nature are the left-hand versions of the molecules, or the L-forms. (There-fore, the model we have described is actually the left-hand model, though the distinctions between "right" and "left"—which involve the direction in which light is polarized—are too complex to discuss here.) Right-hand versions (D-forms) are not found in the proteins of higher organisms, but they are present in some lower forms of life, such as in the cell walls of bacteria. They also are found in some antibiotics, among them, streptomycin, actinomycin, bacitracin, and tetracycline. These antibiotics, several of which are well known to the public at large, can kill bacterial cells by interfering with the formation of proteins necessary for maintaining life and for reproducing. A chemical reaction that is characteristic of amino acids involves the formation of a bond, called a peptide linkage, between the carboxyl group of one amino acid and the amino group of a second amino acid. Very long chains of amino acids can bond together in this way to form proteins, which are the basic building blocks of all living things. The specific properties of each kind of protein are largely dependent on the kind and sequence of the amino acids in it. Other aspects of the chemical behavior of protein molecules are due to interactions between the amino and the carboxyl groups or between the various R -groups along the long chains of amino acids in the molecule. Amino acids function as monomers, or individual units, that join together to form large, chainlike molecules called polymers, which may contain as few as two or as many as 3,000 amino-acid units. Groups of only two amino acids are called dipeptides, whereas three amino acids bonded together are called tripeptides. If there are more than 10 in a chain, they are termed polypeptides, and if there are 50 or more, these are known as proteins. All the millions of different proteins in living things are formed by the bonding of only 20 amino acids to make up long polymer chains. Like the 26 letters of the alphabet that join together to form different words, depending on which letters are used and in which sequence, the 20 amino acids can join together in different combinations and series to form proteins. But whereas words usually have only about 10 or fewer letters, proteins typically are made from as few as 50 to as many as 3,000 amino acids. Because each amino acid can be used many times along the chain and because there are no restrictions on the length of the chain, the number of possible combinations for the formation of proteins is truly enormous. There are about two quadrillion different proteins that can exist if each of the 20 amino acids present in humans is used only once. Just as not all sequences of letters make sense, however, not all sequences of amino acids produce functioning proteins. Some other sequences can function and yet cause undesirable effects, as we shall see. DNA (deoxyribonucleic acid), a molecule in all cells that contains genetic codes for inheritance, creates encoded instructions for the synthesis of amino acids. In 1986, American medical scientist Thaddeus R. Dryja (1940-) used amino-acid sequences to identify and isolate the gene for a type of cancer known as retinoblastoma, a fact that illustrates the importance of amino acids in the body. Amino acids are also present in hormones, chemicals that are essential to life. Among these hormones is insulin, which regulates sugar levels in the blood and without which a person would die. Another is adrenaline, which controls blood pressure and gives animals a sudden jolt of energy needed in a high-stress situation—running from a predator in the grasslands or (to a use a human example) facing a mugger in an alley or a bully on a playground. Biochemical studies of amino-acid sequence


From Yahoo Answers

Question:

Answers:1. Alanine (NH3CH3COOH) 2. Arginine (C6H14N4O2) 3. Asparagine ((NH2)COCH2CH(NH2)COOH) 4. Aspartic acid (COOHCH2CH(NH2)COOH) 5. Cystein ((HS)CH2CH(NH2)COOH) 6. Glutamic Acid (COOH(CH2)2CH(NH2)COOH) 7. Glutamine ((NH2)CO(CH2)2CH(NH2)COOH) 8. Glycine (NH2CH2COOH) 9. Histidine ((C3N2H)CH2CH(NH2)COOH) 10. Isoleucine (CH3CH2CH3CH(NH2)COOH) 11. Leucine ((CH3)2CH2CH(NH2)COOH) 12. Lysine ((NH2)(CH2)4CH(NH2)COOH) 13. Methionine (CH3(SH)(CH2)2CH(NH2)COOH) 14. Phenylalanine ((C6H5)CH2CH(NH2)COOH) 15. Proline ((C5H3NH2)COOH) 16. Serine ((OH)CH2CH(NH2)COOH) 17. Threonine (CH3CH(OH)CH(NH2)COOH) 18. Tryptophan ((C6H4)NH(CH)2CH2CH(NH2)COOH) 19. Tyrosine ((OHC6H4)CH2CH(NH2)COOH) 20. Valine ((CH3)2CHCH(NH2)COOH) Those are the 20 common amino acids and their condensed structural formulas (e.g for glycine instead of the simplified formula of C2H5NO2 which could represent any one of the many isomers of that composition, it is shown as NH2CH2COOH which can only represent one or at the most 2 isomers of that composition) Hope that helps.

Question:There are 20 common amino acids, a) what is the main difference between them? b) why are they labeled as L-amino acids? (illustrate as well as explain this).

Answers:The basic structure of practically all AMINO ACIDs are an amine group (-NH2) and a carboxylic acid (-COOH) separated by a carbon (hence amino acid). The difference between the amino acids are the componants on the side chain. The L- denotes the stereochemistry of the amino acid. The opposing conformation is D-. Interestingly, all natural amino acids are L-.

Question:I'm confused by what my microbiology teacher wants me to do with the following problem: "Consider the following peptide: lysine-valine-threonine- cysteine-leucine-proline- gluamine-glutamic acid-aspartic acid-tryptophan, with lysine as the amino-terminal acid and tryptophan as the carboxy-terminal amino acid in the peptide. Draw out the complete structural formula of the peptide and determine the overall ionic charge on the peptide at pH 7.0. Charge at acid pHs? Charge at alkaline pHs?" Can someone help me figure out how to draw this structure and figure out the ionic charges?

Answers:http://web.indstate.edu/thcme/mwking/amino-acids.html From the above link, you can check the structures of all your amino acids. You will see that for all your amino acids, there is an amino terminal (this is your -NH2) and your carboxylic terminal (-COOH). In peptide bonds, the amino terminal of one amino acid (it becomes =NH3+) is bonded to the carboxylic end of your next amino acid (which becomes -COO-). When you say that lysine is your amino terminal acid, this means that the -NH2 of lysine is free and is not bonded to another amino acid. it is the carboxylic end of lysine that is bonded to the amino terminal of your next amino acid, valine. Then valine's carboxylic end is connected to the amino end of threonine...so on and so forth...That is why your tryptophan is your carboxy-terminal amino acid because its carboxylic acid side is not bonded.

Question:

Answers:"Amino acids are molecules containing both amine and carboxyl functional groups." http://en.wikipedia.org/wiki/Amino_acid

From Youtube

The 20 amino acids :This video is about 20 of the 22 protein coded amino acids. I have included pictures of ball and stick models of each amino acid, downloaded from google images. I have decided not to include a song in this one due to what happened with the Stars of the Winter Hexagon video

Memorize the 20 amino acids in 20 minutes - Part 1 :In this video we share a method of remembering the structures of the 20 commonly occurring amino acids through tricks involving their single-letter abbreviations. We do not cover any amino acid chemistry in this video (like chemical properties), just the structures. We hope you find it helpful, and if you find any errors or have any suggestions for improvement, please let us know! Video by Sean Mutchnick, with special thanks to Larry Manders, Erwin Patalinghug and Jovica Veljanovski for 'peer-reviewing'.