Proteins.pdf

PROTEINS AA.  What Are Proteins? Large molecules Made up of chains of amino acids Are found in every cell in the body Are involved in most of the body’s functions and life processes(FUNCTIONS OF PROTEINS) The sequence of amino acids is determined by DNA (GENE EXPRESSION)...

PROTEINS AA.  What Are Proteins? Large molecules Made up of chains of amino acids Are found in every cell in the body Are involved in most of the body’s functions and life processes(FUNCTIONS OF PROTEINS) The sequence of amino acids is determined by DNA (GENE EXPRESSION)  Structure of Proteins Made up of chains of amino acids; classified by number of amino acids in a chain – Peptides: fewer than 50 amino acids Dipeptides: 2 amino acids Tripeptides: 3 amino acids Polypeptides: more than 10 amino acids – Proteins: more than 50 amino acids Typically 100 to 10,000 amino acids linked together Chains are synthesizes based on specific bodily DNA Amino acids are composed of carbon, hydrogen, oxygen, and nitrogen  Structural Differences Between Carbohydrates, Lipids, and Proteins Figure The Anatomy of an Amino Acid Figure 6.2b  AMINO ACIDS When an amino acid is dissolved in water, it exists in solution as the dipolar ion, or zwitterion. Aromatic R Groups Phenylalanine, tyrosine, and tryptophan, Nonpolar, Aliphatic R Groups The R groups in this class of amino acids are nonpolar and hydrophobic. The side chains of alanine, valine, leucine, METHIONINE, PROLINE and isoleucine. Polar, Uncharged R Groups-serine, threonine, cysteine, asparagine, and glutamine Positively Charged (Basic) R Groups-LSINE ARGININE AND HISTIDINE. Negatively Charged (Acidic) R Groups The two amino acids having R groups with a net negative charge at pH 7.0 are aspartate and glutamate, Some Amino Acids Some More Amino Acids Still More Amino Acids  Peptide Bonds Link Amino Acids Form when the acid group (COOH) of one amino acid joins with the amine group (NH2) of a second amino acid Formed through condensation Broken through hydrolysis Condensation and Hydrolytic Reactions Figure  Essential, Nonessential, and Conditional Essential – must be consumed in the diet Nonessential – can be synthesized in the body Conditionally essential – cannot be synthesized due to illness or lack of necessary precursors – Premature infants lack sufficient enzymes needed to create arginine  Structure of the Protein Four levels of structure – Primary structure – Secondary structure – Tertiary structure – Quaternary structure Any alteration in the structure or sequencing changes the shape and function of the protein  Protein levels A description of all covalent bonds (mainly peptide bonds and disulfide bonds) linking amino acid residues in a polypeptide chain is its primary structure. The most important element of primary structure is the sequence of amino acid residues. Secondary structure refers to particularly stable arrangements of amino acid residues giving rise to recurring structural patterns. The beta pleated sheets and the alpha helices. Tertiary structure describes all aspects of the three-dimensional folding of a polypeptide. When a protein has two or more polypeptide subunits, their arrangement in space is referred to as quaternary structure.  Primary Structure This is the linear sequence of amino acids in a polypeptide chain. It determines the further levels of organization of protein molecule. In primary structure, the amino acids are numbered from N-terminal (which is always written on the left end) of the polypeptide chain. All the structural levels of a protein (secondary, tertiary and quaternary) are ultimately determined by the primary structure because all the information needed for the molecule to achieve its conformation is imprinted within the primary structure. It is this polypeptide chain (and its components) that determines where the proteins bend, fold, and where they can link to another polymer chain.  Secondary Structure It is formed when a polypeptide chain assumes a three-dimensional structure by folding or coiling, and results from steric interrelationships between amino acids located near each other in the chain. The tendency of the polypeptide chain is to arrange itself in space so as to form a tightly compact structure. Three types of secondary structure are possible: α-helical, reverse turn, and ß-pleated sheet. In α-helical structure, the polypeptide chain twists into a right-handed screw to form rod-like structure. In the process it brings into close proximity the amino group of one amino acid with carboxyl group of the fourth amino acid in the chain. It is stabilized by hydrogen bonds between the amino and the carboxyl group. In the coiled polypeptide chain, non-polar hydrophobic groups (side chains) tend to occupy the interior of the helix while polar hydrophilic groups are oriented towards the periphery. In Reverse Turn structure, the polypeptide chain may fold back on itself to change or even reverse the direction of the chain. Glycine and proline which have small side chains, offer convenient spots in the polypeptide chain for folding to occur. In ß-pleated sheet structure, the polypeptide chains lie side by side in an extended state to form sheets. It is stabilized by hydrogen bonds between amino and carboxyl groups in neighbouring chains. The polypeptide chains may be parallel if they run in the same direction or anti-parallel if the same chain takes a reverse turn and folds on itself.  Tertiary structure It is formed when a polypeptide chain undergo extensive coiling to produce complex rigid structure and results from steric interaction between amino acids located far apart but brought closer by folding, looping and binding. The final shape may be ellipsoid, globular or any irregular shape which is determined by the intermolecular forces involved, thus - hydrogen bonds, hydrophilic and hydrophobic interactions, disulfide forces, ionic / electrostatic forces and van der waals forces. The conformations are biologically active and are referred to as native proteins.  Quarternary structure Some protein molecules are complexes containing more than one polypeptide chain. Each chain in the molecule has its own characteristic tertiary structure and is called subunit or monomer. Two or more of the monomers are held together by hydrophobic interactions, hydrogen bonds, and electrostatic forces. The compound structure is called oligomer. For example, hemoglobin is a tetramer.  Denaturing Alteration of the protein’s shape and thus functions through the use of – Heat – Acids – Bases – Salts – Mechanical agitation Primary structure is unchanged by denaturing  Classification of Proteins Proteins are classified into three groups, namely simple proteins, conjugated proteins and, derived proteins. Simple Proteins These are proteins which contain amino acids only and have been sub-classified as:  Albumins – are soluble in water and heat coagulable. E.g. egg albumin, serum albumin, lactalbumin, and soya bean albumin.  Globulins – are insoluble in water but soluble in dilute salt solutions and heat coagulable. They occur together with albumins in same sources.  Glutelins – are soluble in acids and alkalis but insoluble in neutral solvents. They are the major proteins of wheat, rice and other cereals.  Prolamines – are soluble in 70% alcohol and are rich in proline. They occur in cereals like corn, barley and others.  Scleroproteins – are also called albuminoids and are insoluble in most solvents. They are animal proteins present in hair, hoof, horn, nails, cartilage and bone. E.g. collagen, keratin and fibroin.  Histones – are soluble in water, dilute acids and salt solutions and are rich in basic amino acids like arginine. Examples, globin in hemoglobin and protein moiety of nucleoproteins.  Protamines – have very low molecular weight but are strongly basic and rich in arginine. They occur in nucleoproteins of the sperm.  Conjugated Proteins These are proteins which contain other chemical components apart from amino acids. The non-amino acid part is called prosthetic group. Conjugated proteins are sub-classified according to the prosthetic group they contain.  Nucleoproteins – contain nucleic acids as the prosthetic group. Example, histones and protamines.  Proteoglycans and glycoproteins – contain carbohydrate as the prosthetic group. Example, Heparin, γ-globulin.  Chromoproteins – contain coloured compound as the prosthetic group. Example, hemoglobin, flavoprotein, visual purple.  Phosphoproteins – the prosthetic group is phosphoric acid attached to OH of serine or threonine. Examples, casein.  Lipoproteins – contain mainly phospholipids as the prosthetic group. Example, ß-lipoprotein of blood.  Metalloproteins – contain metallic ions (e.g. Cu, Fe, Co, Mn, Zn, Mg) as the prosthetic group. They are usually enzymes. Example, ferritin  Derived Proteins These are sub-classified into two, namely primary and secondary derived proteins.  Primary Derived Proteins – are produced as a result of denaturation. Examples: Proteans (e.g. fibrin); metaproteins, and coagulated proteins.  Secondary Derived Proteins – are produced as a result of partial digestion of proteins. Examples: proteoses, peptones and peptides. Denaturing a Protein Figure  Protein Denaturation This is the loss of the specific three-dimensional conformation of proteins, and may be temporary or permanent. It is caused by several agents:  Heat or Radiation (e.g. IR, UV light). The kinetic energy supplied to the protein causes its atoms to vibrate violently, thus disrupting the weak hydrogen bonds and ionic bonds. The protein then coagulates.  Heavy Metals (e.g. lead and mercury). Such cations form strong bonds with carboxyl groups and often disrupt ionic bonds. They also reduce electrical polarity of proteins and thus increase their solubility, causing them to precipitate in solution.  Strong Acids and Alkalis, and Concentrated Salts. Such solutions disrupt ionic bonds and the protein coagulates.  Organic Solvents and Detergents. These substances disrupt hydrophobic interactions and form bonds with hydrophobic groups.