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Amino Acids

Amino Acids

Aliphatic Amino Acids
Aliphatic R groups are nonpolar and hydrophobic. Hydrophobicity increases with increasing number of C atoms in the hydrocarbon chain. The six aliphatic amino acids are Glycine, Alanine, Valine, Leucine, Isoleucine and Proline.
Glycine (Gly or G) is an organic compound with the formula NH2CH2COOH. Having a hydrogen substituent as its side-chain, glycine is the smallest of the 20 amino acids commonly found in proteins, and indeed is the smallest possible. Glycine is a colourless, sweet-tasting crystalline solid. It is unique among the proteinogenic amino acids in that it is achiral. It can fit into hydrophilic or hydrophobic environments, due to its minimal side chain of only one hydrogen atom.
Alanine (Ala or A) is an α-amino acid with the chemical formula CH3CH(NH2)COOH. The α-carbon atom of alanine is bound with a methyl group (-CH3), making it one of the simplest α-amino acids with respect to molecular structure and also resulting in alanine’s being classified as an aliphatic amino acid. The methyl group of alanine is non-reactive. The L-isomer is one of the 20 amino acids encoded by the genetic code.
Leucine (Leu or L) is a branched-chain α-amino acid with the chemical formula HO2CCH(NH2)CH2CH(CH3)2. Leucine is a branched-chain amino acid (BCAA) since it possesses an aliphatic side-chain that is non-linear. Leucine is classified as a hydrophobic amino acid due to its aliphatic isobutyl side chain.
Isoleucine (Ile or I) is an α-amino acid with the chemical formula HO2CCH(NH2)CH(CH3)CH2CH3. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested. With a hydrocarbon side chain, isoleucine is classified as a hydrophobic amino acid. Isoleucine is one of two common amino acids that have a chiral side chain.
Proline (Pro or P) is an α-amino acid, one of the twenty DNA-encoded amino acids. It is not an essential amino acid, which means that the human body can synthesize it. It is unique among the 20 protein-forming amino acids in that the amine nitrogen is bound to not one but two alkyl groups, thus making it a secondary amine. The more common L form has S configuration.

Aromatic amino acids (AAA) are amino acids that include an aromatic ring. They must be planar (usually sp2 hybridized) with the hybridized p orbital overlapping to form a continuous ring of planar orbitals. The ring must follow Huckel’s rule, having 4n+2 electrons in its system of conjugated p-orbital clouds. The Aromatic amino acids are Phenylalanine (F), Tyrosine (Y) and Tryptophan (W).
PhenylalaninePhe or F) is an α-amino acid with the formula C6H5CH2CH(NH2)COOH. This essential amino acid is classified as nonpolar because of the hydrophobic nature of the benzyl side chain.
Tyrosine (Tyr or Y) or 4-hydroxyphenylalanine, is one of the 22 amino acids that are used by cells to synthesize proteins. Its codons are UAC and UAU. It is a non-essential amino acid with a polar side group.
Tryptophan (Trp or W) is one of the 22 standard amino acids and an essential amino acid in the human diet. It is encoded in the standard genetic code as the codon UGG. Only the L-stereoisomer of tryptophan is used in structural or enzyme proteins, but the R-stereoisomer is occasionally found in naturally produced peptides (for example, the marine venom peptide contryphan). The distinguishing structural characteristic of tryptophan is that it contains an indole functional group.

Alcohol Amino Acids
Serine 
(Ser or S) is an amino acid with the formula HO2CCH(NH2)CH2OH. It is one of the proteinogenic amino acids. Serine differs from alanine in that one of the methylenic hydrogens is replaced by a hydroxyl group. Serine is one of two hydroxyl amino acids. Both are commonly considered to by hydrophilic due to the hydrogen bonding capacity of the hydroxyl group.
Threonine
(Thr or T) is an α-amino acid with the chemical formula HO2CCH(NH2)CH(OH)CH3. This essential amino acid is classified as polar. Threonine is an other hydroxyl-containing amino acid.

Basic Amino Acids
Basic amino acids are polar and positively charged at pH values below their pKa‘s, and are very hydrophilic. Even though the basic amino acids are almost always in contact with the solvent, the side chain of lysine has a marked hydrocarbon character, so it is often found NEAR the surface, with the amino group of the side chain in contact with solvent. There are three amino acids that have basic side chains at neutral pH are histidine (His), lysine (Lys) and arginine (Arg).
Histidine, an essential amino acid, has as a positively charged imidazole functional group. The imidazole makes it a common participant in enzyme catalyzed reactions. The unprotonated imidazole is nucleophilic and can serve as a general base, while the protonated form can serve as a general acid. The residue can also serve a role in stabilizing the folded structures of proteins.
Lysine (Lys or K)  is an α-amino acid with the chemical formula HO2CCH(NH2)(CH2)4NH2. It is an essential amino acid for humans. Lysine has a positively charged ε-amino group (a primary amine). Lysine is basically alanine with a propylamine substituent on the β-carbon. The ε-amino group has a significantly higher pKa (about 10.5 in polypeptides) than does the α-amino group.
Arginine (Arg or R) is an α-amino acid. The L-form is one of the 20 most common natural amino acids. Arginine was first isolated from a lupin seedling extract.

Sulphur containing Amino Acids
Sulfur containing amino acids contribute substantially to the maintenance and integrity of cellular systems by influencing cellular redox state and cellular capacity to detoxify toxic compounds, free radicals and reactive oxygen species. The sulfur-containing amino acids are generally considered to be nonpolar and hydrophobic. Methionine and cysteine are the two primary sulfur-containing amino acids in mammals.
Methionine (Met or M) is an α-amino acid with the chemical formula HO2CCH(NH2)CH2CH2SCH3. This amino acid is classified as nonpolar as it has a straight side chain that possess a S-methylthioether (i.e. C–S–C bonding) at the γ-carbon. It is an essential amino acid in all metazoa.
Cysteine (Cys or C) is an α-amino acid with the chemical formula HO2CCH(NH2)CH2SH. It is a semi-essential amino acid, which means that it can be biosynthesized in humans. The thiol side chain in cysteine often participates in enzymatic reactions, serving as a nucleophile. The thiol is susceptible to oxidization to give the disulfide derivative cystine, which serves an important structural role in many proteins.

Acid Amino Acids
Two amino acids have acidic side chains at neutral pH. These are aspartic acid or aspartate (Asp) and glutamic acid or glutamate (Glu). Their side chains have carboxylic acid groups whose pKa’s are low enough to lose protons, becoming negatively charged in the process.
Aspartic acid (Asp or D) is an α-amino acid with the chemical formula HOOCCH(NH2)CH2COOH. The carboxylate anion and salts of aspartic acid are known as aspartate. The L-isomer of aspartate is one of the 23 proteinogenic amino acids, i.e., the building blocks of proteins. Aspartic acid is, together with glutamic acid, classified as an acidic amino acid with a pKa of 3.9, however in a peptide the pKa is highly dependent on the local environment. A pKa as high as 14 is not at all uncommon. Aspartate is pervasive in biosynthesis. As with all amino acids, the presence of acid protons depends on the residue’s local chemical environment and the pH of the solution.
Glutamic acid (Glu or E) is one of the 20-23 proteinogenic amino acids. 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 excitatory neurotransmitter that plays the principal role in neural activation.

Amide Amino Acids
Asparagine is the amide of aspartic acid. The amide group does not carry a formal charge under any biologically relevant pH conditions. The amide is rather easily hydrolyzed, converting asparagine to aspartic acid. This process is thought to be one of the factors related to the molecular basis of aging. Asparagine has a high propensity to hydrogen bond, since the amide group can accept two and donate two hydrogen bonds. It is found on the surface as well as buried within proteins. Asparagine is a common site for attachment of carbohydrates in glycoproteins.
Glutamine (Gln or Q) is one of the 20 amino acids encoded by the standard genetic code. It is considered a conditionally essential amino acid. Its side-chain is an amide formed by replacing the side-chain hydroxyl of glutamic acid with an amine functional group, making it the amide of glutamic acid.

Properties

1. Acids and Base are CHARGED AMINO ACIDS.
2. All Aliphatic Amino Acid + Methionine + phenylalanine /Tryptophan are NON POLAR AMINO ACIDS
3. All Alcohols and Amides + Cysteine + Tyrosine are POLAR AMINO ACIDS.

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