Amino Acid And Peptide

Amino acid and peptide By: Do Huong Thao Nguyen Ngoc Quynh Huong Nguyen Manh Tri Tran Buu Thuy Cat Vy Nguyen Thi Thuy Trang Thơ Tran Hoang Viet Nguyen Phu Hoai

Overview



Alpha-amino acids are the building blocks of proteins. A protein forms via the condensation of amino acids to form a chain of amino acid "residues" linked by peptide bonds. Proteins are defined by their unique sequence of amino acid residues; this sequence is the primary structure of the protein

General structure 

In the structure shown to the right, the R represents a side chain specific to each amino acid. The central carbon atom called Cα is a chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached.

Classification



Amino acids are usually classified by the properties of the side chain into four groups. The side chain can make them behave like a weak acid, a weak base, a hydrophile if they are polar, and hydrophobe if they are nonpolar. The chemical structures of the 20 standard amino acids, along with their chemical properties, are cataloged in the list of standard amino acids.





Alanine

- The second simplest amino acid, but used the most in proteins. Chemical Properties: Aliphatic. Physical Properties: Nonpolar.The alpha-carbon in alanine is substituted with a levorotatory (l)methyl group, making it one of the simplest amino acids with respect to molecular structure. This amino acid is one of the most widely used in protein construction

Cysteine

- Thiol containing amino acid involved in active sites and protein tertiary structure determination.Chemical Properties:Sulfur-containing . Physical Properties:Polar (uncharged).Cysteine

.

differs from serine in a single atom-- the sulfur of the thiol replaces the oxygen of the alcohol The side chain is also often involved in the chemistry occurring at the active sites of many enzymes. Cysteine is also critical to the metabolism of a number of essential biochemicals including coenzyme A, heparin, biotin, lipoic acid, and glutathione.



Asparagine



Arginine

- Amide derivative of aspartic acid . Chemical Properties:Neutral. Physical Properties:Polar (uncharged). 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.This amino acid plays an important role in the biosynthesis of glycoproteins and is also essential to the synthesis of a large number of other proteins.

- Amino acid often used at the active sites of enzymes. Chemical Properties:Basic. Physical Properties:Polar (positively charged).Arginine is well designed to bind the phosphate anion, and is often found in the active centers of proteins that bind phosphorylated substrates



Aspartic Acid

- Important intermediate in the citric acid cycle. Chemical Properties :Acidic.Physical properties:Polar (charged). Aspartic acid is alanine with one of the β hydrogens replaced by a carboxylic acid group.It plays a paramount role in metabolism during construction of other amino acids and biochemicals in the citric acid cycle



Glutamic Acid

- Negatively charged amino acid found on the surface of proteins. Chemical Properties :Acidic.Physical properties:Polar (charged). Glutamic acid has one additional methylene group in its side chain than does aspartic acid.The side chain carboxyl of aspartic acid is referred to as the β carboxyl group,while that of glutamic acid is referred to as the γ carboxyl group.it is usually found on the outside of proteins and enzymes where it is free to interact with the aqueous intracellular surroundings



Glutamine



Glycine - Simplest amino acid that also acts as a neurotransmitter antagonist.Chemical

- The only amino acid with the ability to easily cross the barrier between blood and brain tissue.Chemical properties: neutral.Physical properties:polar (uncharged). Glutamine is the amide of glutamic acid, and is uncharged under all biological conditions. glutamine and glutamic acid are responsible for the vast majority of the amino nitrogen located in the brain, and are of central importance in the regulation of bodily ammonia levels

properties:Aliphatic.Physical properties:nonpolar.The isoelectric point or isoelectric pH of glycine will be centered between the pKas of the two ionizable groups,the amino group and the carboxylic acid group. Glycine is also similar to gamma-aminobutyric acid and glutamic acid in the ability to inhibit neurotransmitter signals in the central nervous system.



Histidine

- Amino acid responsible for histamine biosynthesis.Chemical properties:basic.Physical properties:polar (positively charged). This amino acid is biochemically metabolized into the neurotransmitter histamine and the set of genes that produce the enzymes responsible for histidine biosynthesis are controlled by the well-studied histidine operon



Isoleucine

- Hydrophobic amino acid used almost exclusively in protein and enzyme construction.Chemical properties:Aliphatic.Physical properties:nonpolar.Isoleucine, an essential amino acid, is one of the three amino acids having branched hydrocarbon side chains. . Another feature of this class of amino acids is that they appear to have no other significant biological role than incorporation into proteins and enzymes, where their main purpose is to help dictate the tertiary structure of the macromolecules.



Leucine



Lysine

- Another hydrophobic amino acid used almost exclusively in protein and enzyme construction.It’s an essential amino acid, is one of the three amino acid with a branched hydrocarbon side chain. It has one additional methylene group in its side chain compared with valine. its cousins isoleucine and valine, is a hydrophobic amino acid that is found as a structural element on the interior of proteins and enzymes

- An essential amino acid with a positive charge on the aliphatic side chain.Chemical properties:basic.Physical properties:polar (positively charged).the side chain has three methylene groups, so that even though the terminal amino group will be charged under physiological conditions, the side chain does have significant hydrophobic character.This polar amino acid is commonly found on the surfaces of proteins and enzymes, and sometimes appears in the active site



Methionine

- An essential amino acid that helps initiate protein synthesis.Chemical properties:Sulfurcontaining.Physical properties:nonpolar(hydrophobic). This sulfur-containing amino acid is also the source of sulfur for cysteine in animals and man



Phenylalanine

- Most common aromatic amino acid found in proteins.Chemical properties:Aromatic.Physical properties :nonpolar.Phenylalanine, an essential amino acid, is a derivative of alanine with a phenyl substituent on the β carbon. Phenylalanine plays a key role in the biosynthesis of other amino acids and some neurotransmitters



Proline - Cyclic aliphatic amino acid used in the synthesis of collagen.When proline is in a peptide bond, it does not have a hydrogen on the α amino group, so it cannot donate a hydrogen bond to stabilize an α helix or a β sheet. It is often said, inaccurately, that proline cannot exist in an α helix. When proline is found in an α helix, the helix will have a slight bend due to the lack of the hydrogen bond. Proline is synthesized from glutamic acid prior to its incorporation into pro-collagen during messenger RNA translation



Serine - Amino acid alcohol found in the active site of serine proteases.Chemical Properties:Nonaromatic hydroxyl.Physical properties:polar (uncharged). 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. Serine is also found at the active site in an important class of enzymes termed "serine proteases" that include trypsin and chymotrypsin. These enzymes catalyze the hydrolysis of peptide bonds in polypeptides and proteins, a major function in the digestive process



Threonine



Tryptophan

- Amino acid alcohol involved in porphyrin metabolism. Chemical properties: Non-aromatic hydroxyl. Physical properties: polar(uncharged). Threonine is an other hydroxyl-containing amino acid. It differs from serine by having a methyl substituent in place of one of the hydrogens on the β carbon and it differs from valine by replacement of a methyl substituent with a hydroxyl group. This amino acid plays an important role along with glycine and serine in porphyrin metabolism

- used the least frequently in proteins. Chemical properties:Aromatic. Physical properties:nonpolar. Tryptophan, an essential amino acid, is the largest of the amino acids. It is also a derivative of alanine, having an indole substituent on the β carbon. The unusual indole side chain of tryptophan is also the nucleus of the important neurotransmitter serotonin, which is biosynthesized from tryptophan



Tyrosine - Hydroxyphenyl amino acid that is used to build neurotransmitters and hormones. Chemical properties:Aromatic. Physical properties:nonpolar.Tyrosine is derived from phenylalanine by hydroxylation in the para position. This hydroxylated amino acid participates in the synthesis of many important biochemicals including the thyroid hormones, the melanin biological pigments, and the catecholamines, an important class of biological regulators



Valine

- Hydrophobic aliphatic amino acid used to hold proteins together. Chemical properties:Aliphatic. Physical properties:nonpolar.Valine differs from threonine by replacement of the hydroxyl group with a methyl substituent. Valine is often referred to as one of the amino acids with hydrocarbon side chains, or as a branched chain amino acid. They are also essential amino acids and must be obtained in the diet. Important sources of valine include soy flour, cottage cheese, fish, meats, and vegetables

Peptide bond formation 

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly, instead the amino acid is activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond. As a result of this mechanism, all proteins are synthesized starting at their N-terminus and moving towards their C-terminus.



However, not all peptide bonds are formed in this way. In a few cases peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids. In the first step gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione.



In chemistry, peptides are synthesized by a variety of reactions. One of the most used in solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support