Amino Acids PDF

Amino Acids Amino acids are molecules that combine to form proteins. The elements present in every amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N); in addition sulfur (S). As many as 300 amino acids occur in nature. Of these, only 20-known as standard amin...

Amino Acids Amino acids are molecules that combine to form proteins. The elements present in every amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N); in addition sulfur (S). As many as 300 amino acids occur in nature. Of these, only 20-known as standard amino acids are repeatedly found in the structure of proteins, isolated from different forms of life- animal, plant and microbial.  Amino Acids Share Many Features, Differing Only at the R Substituent FIGURE 3-2 General structure of an amino acid. This structure is common to all but one of the α-amino acids. (Proline, a cyclic amino acid, is the exception.) The R group, or side-chain (red), attached to the α carbon (blue) is different in each amino acid. Amino Acids Have Three Common Functional Groups Attached to the α Carbon The α carbon always has four substituents and is tetrahedral. All (except proline) have: – an acidic carboxyl group connected to the α carbon – a basic amino group connected to the α carbon – an α hydrogen connected to the α carbon The fourth substituent (R) is unique in glycine, the simplest amino acid. The fourth substituent is also hydrogen. All Amino Acids Are Chiral (Except Glycine) Proteins only contain L amino acids FIGURE 3-3 Stereoisomerism in α-amino acids. CRN Rules cLock  Amino Acids: Classification Common amino acids can be placed in five basic groups depending on their R substituents: nonpolar, aliphatic (7) aromatic (3) polar, uncharged (5) positively charged (3) negatively charged (2) These amino acid side chains absorb UV light at 270–280 nm These amino acids side chains can form hydrogen bonds. Cysteine can form disulfide bonds.  Four Levels of Protein Structure The term protein is generally used for a polypeptide containing more than 50 amino acids. The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain. The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis.  Amino Acids Polymerize to Form Peptides Peptides are small condensation products of amino acids. They are “small” compared with proteins (Mw < 10 kDa). FIGURE 3-13 Formation of a peptide bond by condensation. The α-amino group of one amino acid (with R2 group) acts as a nucleophile to displace the hydroxyl group of another amino acid (with R 1 group), forming a peptide bond (shaded in yellow). Amino groups are good nucleophiles, but the hydroxyl group is a poor leaving group and is not readily displaced.  Secondary Structure: α Helix Secondary structure refers to short-range, periodic folding elements that are common in proteins. These include the α helix, the β sheet, and turns. ❖ In the α-helix, the backbone adopts a cylindrical spiral structure in which there are 3.6 AAs per turn. ❖ The R-groups point out from the helix, and mediate contacts to other structure elements in the folded protein. ❖ The α helix is stabilized by H-bonds between backbone carbonyl oxygen and amide nitrogen atoms that are  Secondary Structure: β Sheets In β sheets, each β-strand adopts an extended conformation. β strands tend to occur in pairs or multiple copies in β sheets that interact with one another via H-bonds directed perpendicular to the axis of each strand. Carbonyl oxygens and amide nitrogens in the strands form the H-bonds. Strands can orient antiparallel or parallel to one another in β sheets. R-groups of every other amino acid point up or down relative to the sheet. Most β strands in proteins are 5 to 8 AAs long.  Tertiary Structure The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces – basically, the whole gamut of non-covalent bonds. For example, R groups with like charges repel one another, while those with opposite charges can form an ionic bond. Similarly, polar R groups can form hydrogen bonds and other dipole-dipole interactions. Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules. Finally, there’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. Covalent cross-linkages stabilise these proteins by connecting specific amino acids within a polypeptide or between polypeptide chains in multisubunit proteins. Typically such a linkage will be a covalent sulfur–sulfur bond which Figure: An example of how the forms between the –SH formation of a disulfide bond between groups of two cysteine cysteine side chains stabilize existing structures in a polypeptide. These residues that are in close bonds can form between two proximity in the folded polypeptide strands or between protein. residues in the same polypeptide. Cysteine becomes cystine through disulfide bonding with another cysteine molecule to form cystine.  Quarternary Structure Many proteins are made up of a single polypeptide chain and have only three levels of structure. However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure. The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure. The subunits are held together by hydrogen bonds and van der Waals forces between nonpolar side chains.  Denaturation & Renaturation Denaturation is the process of modifying the conformation of the protein structures without rupturing the native peptide linkages. ❖This inactivates the functionality of the protein molecules, decreases its solubility, decreases/destroys its biological activity, improves digestibility and alters the water binding ability of the molecule. ❖Denaturation of proteins is achieved by disrupting the hydrogen bonding in the peptide linkage by applying external stress. ❖It can be carried out by applying heat, treatment with alcohols, heavy metals, or acids/bases. Renaturation of a protein is the conversion of a denatured protein back into its native 3D structure. Therefore, it involves the reconstruction of a protein molecule after losing its original structure. Renaturation is the inverse process of denaturation. Renaturation is sometimes reversible. However, renaturation is not common and easy as denaturation.  Zwitter Ion A zwitter ion is a molecule with functional groups, of which at least one has a positive and one has a negative electrical charge. The net charge of the entire molecule is zero. Amino acids are the best-known examples of zwitter ions. They contain an amine group (basic) and a carboxylic group (acidic). The -NH2 group is the stronger base, and so it picks up H+ from the -COOH group to Alanine act as leave a zwitter ion (i.e. the zwitterion at pH 7.3. amine group de-protonates the carboxylic acid). Classification of Protein based on Biological Functions 1. Catalytic protein: They catalyze biochemical reaction in cells. Eg. Enzymes and co-enzymes 1. Structural protein: They make various structural component of living beings. Eg. Collagen make bone, Elastin make ligaments and keratin make hair and nails 1. Nutrient protein: They have nutritional value and provide nutrition when consumed. Eg. Casein in milk 1. Regulatory protein: They regulate metabolic and cellular activities in cell and tissue. Eg. Hormones 5. Defense protein: They provide defensive mechanism against pathogens. Eg. Antibodies, complement proteins 6. Transport protein: They transport nutrients and other molecules from one organ to other. Eg. Haemoglobin 7. Storage protein: They stores various molecules and ions in cells. Eg. Ferritin store Iron 8. Contractile or mobile protein: They help in movement and locomotion of various body parts. Eg. Actin, myosin, tubulin etc 9. Toxic protein: They are toxic and can damage tissues. Eg. Snake venom, bacterial exotoxins etc Classification of Protein based on Chemical Composition  Simple Proteins 1. Fibrous Protein Collagen 2. Globular Protein Albumin Fibrous Vs Globular Protein  Conjugated Proteins ❑ Nucleoprotein, a conjugated protein consisting of a protein linked to a nucleic acid, either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid). ❑ Glycoprotein is a compound containing carbohydrate covalently linked to protein. A mucoprotein is a glycoprotein composed primarily of mucopolysaccharides. ❑ Lipoprotein, any member of a group of substances containing both lipid (fat) and protein. ❑ Phosphoprotein is a protein that is post-translationally modified by the attachment of either a single phosphate group, or a complex molecule such as 5'-phospho-DNA, through a phosphate group. ❑ Chromoprotein is a conjugated protein that contains a pigmented prosthetic group. A common example is haemoglobin, which contains a heme cofactor, which is the iron-containing molecule that makes oxygenated blood appear red. ❑ Metalloproteins are a large group of enzyme proteins which contain metallic elements such as iron, copper, cobalt, manganese, and others. A prosthetic group is the non-amino acid component that is part of the structure of the heteroproteins or conjugated proteins.  Derived protein These protein are the derivatives of either simple or complex protein resulting from the action of heat, enzymes and chemicals. Some artificially produced protein are included in this group. Example: Albumose (derived from albumins)  Non-Standard Amino Acids Besides the 20 amino acids present in the protein structure, there are several other amino acids that are biologically important. ✔Collagen-the most abundant protein in mammals-contains 4-hydroxyproline and 5-hydroxylysine. ✔Histones-the proteins found in association with DNA, contain many methylated, phosphorylated or acetylated amino acids. ✔γ-Carboxyglutamic acid is found in certain plasma proteins involved in blood clotting. ✔D-Penicillamine (D-dimethylglycine), a metabolite of penicillin, is employed in the chelation therapy of Wilson’s disease. This is possible since D-penicillamine can effectively chelate copper.