Amino Acids Structure

Amino Acids & Proteins• • Amino acids Structure All 20 of the common amino acids are α-amino acids. • They have a carboxyl group and an amino group that are bonded to the same carbon atom which is named α carbon Classification of amino acids Amino Acids Can Be Classified by their R Group into five main classes (Table3-1 ): • 1-nonpolar aliphatic group • 2-Aromatic R group ( nonpolar and 3-Polar uncharged R ) • 3-Polar uncharged R • 4-Positively charged group • 5-Negatively “ “ •The polarity of the R groups varies widely, from : •1-nonpolar and hydrophobic (water-insoluble) to •2-highly polar and hydrophilic (water-soluble). Clasification of amino acids based on their structure: • Nonpolar amino acids: Ala, phe, Lue, Ilu, Val, Met, Pro, Trp, • Alchoholic Amino acids: Ser, Thr • Sulphoric Amino acids: Cys, Met • Polar Uncharged Amino acids: Tyr, Gly, Asn, Gln, Ser, Thr, Cys • 4-Positively charged group: Arg, Lys, His • 5-Negatively “ “: Aps, Glu • 6- Aromatic amino acids: Phe, Tyr, Trp, His Beta Alanin Alanin • Chemical and physical properties of Amino acids • 1-Amino Acids Can Act as Acids and Bases • 2-The amino acid residues in protein molecules are exclusively L stereoisomers. Isoelectric pH or PI • The characteristic pH, in which the net electric charge of amino acid is zero is called the isoelectric point or isoelectric pH, designated pI. • Calculation of PI for all amino acids with a single -amino group, a single -carboxyl group is calculated by this formula PI for all amino acids with a single -amino group, a two-carboxyl • group is calculated by this formula • PI for all amino acids with two amino group, a two-carboxyl group is calculated by this formula • PI=1/2 (PK2+PK3) • Peptides and Proteins • Three amino acids can be joined by two peptide bonds to form a tripeptide; similarly, amino acids can be linked to form tetrapeptides, pentapeptides. • When a few amino acids (10)are joined in this fashion, the structure is called an oligopeptide. • When many amino acids (> 10) are joined, the product is called a polypeptide. • Proteins may have thousands of amino acid residues. • Each poly peptide chain has two ends: • The amino acid residue at the left end has a free -amino group, is the amino-terminal (or N-terminal) residue • The residue at the other end (Right end) has a free carboxyl group, is the carboxyl-terminal (C-terminal) residue. Kinds of proteins based on their constituents: • 1- Simple proteins: contain only amino acid • 2- Conjugated proteins: contain amino acid + non amino acid compound ( Prosthetic group) Protein structure 1- Primary structure: is the sequence of amino acid residues thar are joined to each other by peptide bond. Secondary Structure: • Polypeptide Chains Can Fold Into Regular Structures Such as the • Alpha Helix, • the Beta Sheet, • and Turns and Loops Alpha Helix • Α helix, is a rodlike structure • The a helix is stabilized by hydrogen bonds between the NH and CO groups of different amino acids in the main chain • In particular, the CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead (far) in the sequence( between AA n and AA n+3) The bulk and shape of Asn, Ser, Thr, and Cys residues can also destabilize an helix if they are close together in the chain In particular, the CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence( between AA n and AA n+4) • 2-Beta Sheets • A β sheet is formed by linking two or more β strands by hydrogen bonds • Are Stabilized by Hydrogen Bonding Between Polypeptide Strands • Kinds of β sheet • 1-Antiparallel β sheet): Two polypeptides chains have oposit direction • 2-Parallel β sheet : Two polypeptides chains have same direction (parallel β sheet). 3-Tertiary structure describes all aspects of the three-dimensional folding of a polypeptide. Folding of polypeptide is produced by interactions ( electrostatic, covalent hydrophobic) between hydrophilic amino acids and a globular shape is produced After folding, the hydrophilic amino acids will be located on surface of protein and hydrophobic amino acids are hidden inside the protein out of reach of water . These amino acids are kept near each other by hydrophobic force • 4-quaternary structure • When a protein has two or more polypeptide subunits (oligomeric protein) , their arrangement in space is referred to as quaternary structure • polypeptide subunits might be identical or equal • Hb has two a and two B subunits Classify of proteins: A- Based on shape and structure - Globular - Fibrous B- Based on components -Simple proteins - Conjugated (Complex) proteins A Proteins are classified into two major groups based on structure and shape: • 1- fibrous proteins, having polypeptide chains arranged in long strands or sheets, • Keratin, collagen, and silk fibroin • All fibrous proteins are insoluble in water, a property conferred by a high concentration of hydrophobic amino acid residues both in the interior of the protein and on its surface. • 2- globular proteins, having polypeptide chains folded into a spherical or globular shape B -Protein Classification Based on component: - 1-Simple proteins - 2- Cojugated (Complex Proteins - 1-Simple proteins are consisted of only amino acids and no other chemical constituents; these are considered simple proteins. like albumin 2- Conjugated proteins • Some proteins contain permanently associated chemical components in addition to amino acids; these are called conjugated proteins. • The non–amino acid part of a conjugated protein is usually called its prosthetic group. • Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups Fibrous proteins including: • Keratin • Colagen • Fibroin • …. • Keratin: α -keratin and B keratin • The α-keratin is a right-handed helix • α -keratin is rich in the hydrophobic residues Ala, Val, Leu, Ile, Met, and Phe. • Found in mammals, these proteins constitute almost the entire dry weight of hair, wool, nails, claws, quills, horns, hooves, and much of the outer layer of skin Collagen • Collagen Like the α-keratins, collagen has evolved to provide strength. • It is found in connective tissue such as tendons, cartilage, the organic matrix of bone, and the cornea of the eye • It is consisted of three heft handed a helix polypeptide chain that are twisting around each other to make a right handed superhelical chain . • The amino acid sequence in collagen is generally a repeating tripeptide unit, Gly–X–Y, where X is often Pro, and Y is often 4-Hyp. • Kinds of bonds In collagen: • 1- Hydrogen bond between amino and carboxyl groups of amino acids of three a helix chains • 2- Cross link be Lys and a-lys of a helix chains • The overall structure is stabilized by extensive hydrogen bonding between all peptide linkages in the polypeptides of each a helix chain • A typical mammal has more than 30 structural variants of collagen, particular to certain tissues and each somewhat different in sequence and function. Diseases • Some human genetic defects in collagen structure illustrate the close relationship between amino acid sequence and three-dimensional structure in this protein. • Osteogenesis imperfecta is characterized by abnormal bone formation in babies; • Ehlers-Danlos syndrome is characterized by loose joints. • Both conditions can be lethal, and both result from the substitution of an amino acid residue with a larger R group (such as Cys or Ser) for a single Gly residue in each chain (a different Gly residue in each disorder) Silk Fibroin • Fibroin, the protein of silk, is produced by insects and spiders. • Its polypeptide chains are predominantly in the β conformation. • Fibroin is rich in Ala and Gly residues, permitting a close packing of β sheets • The overall structure is stabilized by extensive hydrogen bonding between all peptide linkages in the polypeptides of each β sheet and by the optimization of van der Waals interactions between sheets • Globular Proteins Have a Variety of Tertiary Structures • These proteins have different amino acid sequences and different tertiary structures, reflecting differences in function • Cytochrome c is a component of the respiratory chain of mitochondria Like myoglobin, cytochrome c is a heme protein. • It contains a single polypeptide chain of about 100 residues (Mr 12,400) and a single heme group. • In this case, the protoporphyrin of the heme group is covalently attached to the polypeptide. • Only about 40% of the polypeptide is in α -helical segments, compared with 70% of the myoglobin chain. • The rest of the cytochrome c chain contains turns and irregularly coiled and extended segments. • Many proteins, for example the enzymes ribonuclease A and chymotrypsinogen, contain only amino acid residues and no other chemical constituents; these are considered simple proteins. 2- Conjugated proteins • Some proteins contain permanently associated chemical components in addition to amino acids; these are called conjugated proteins. • The non–amino acid part of a conjugated protein is usually called its prosthetic group. • Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups Protein Denaturation and unfolding • Protein structures have evolved to function in particular cellular environments. • Conditions different from those in the cell can result in protein structural changes, large and small. • A loss of three-dimensional structure sufficient to cause loss of function is called denaturation. • Unfolding is a cooperative process (like folding): loss of structure in one part of the protein destabilizes other parts. • The experiments showing that denaturation of some proteins is reversible • Renaturation • Certain globular proteins denatured by heat, extremes of pH, or denaturing reagents will regain their native structure and their biological activity if returned to conditions in which the native conformation is stable. • This process is called renaturation. • Denaturant agents • 1- Heat : most proteins can be denatured by heat, which affects the weak interactions in a protein (primarily hydrogen bonds) and are broken • If the temperature is increased slowly, a protein’s conformation generally remains intact until an abrupt loss of structure (and function) occurs over a narrow temperature range • 2- Acids and base • 3- Detergents ( urea . guanidine hydrocholoride…)