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Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS Proteins Proteins are large, complex molecules that are critical for the normal functioning of the human body. They are essential for the structure, function, and regulation of the body’s tissues and organs. Proteins are made up of hundreds of smaller units called amino acids that are attached to one another by peptide bonds, forming a long chain. You can think of a protein as a string of beads where each bead is an amino acid. Image of beads on a string Classification of Protein (with examples): A) Based on composition B) Base on structure A) Based on Composition: 1) Simple Proteins 2) Conjugated Proteins 3) Derived proteins 1 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS 1) Simple Proteins: Classified according to solubility a) Albumins b) Globulins c) Glutelins d) Histones e) Protamine f) prolamines g) Scleroproteins 2) Conjugated Proteins: Contain amino acid + prosthetic group. a) Glycoproteins b) Chromoproteins c) Lipoproteins d) Nucleoproteins e) Phosphoprotein 3) Derived Proteins: Derivatives of proteins due to action of heat, enzymes, or chemical reagents. a) Primary Derived b) Secondary Derived B) Based on Structure: 1) Fibrous 2) Globular Function of Protein: 1) Storage 2) Transport 2 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS 3) Structural Material 4) Metabolic Growth Regulator 5) Control of Physiological Functions 6) Catalytic Activity 7) Hormonal 8) Toxicity by Foreign Proteins Properties of Proteins: 1) Optical Property 2) Colloidal 3) Solubility 4) Amphoteric Nature 5) Denaturation of Proteins Amino acid structure and its classification An amino acid contains both a carboxylic group and an amino group. Amino acids that have an amino group bonded directly to the alphacarbon are referred to as alpha amino acids. The simplest representation of an alpha amino acid is shown below. amino acid structure 3 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS Every alpha amino acid has a carbon atom, called an alpha carbon, bonded to a carboxylic acid, , group; an amino, , group; a hydrogen atom; and an R group that is unique for every amino acid. If you notice in the structure above, is a chiral center, that is to say, this carbon atom is attached to four different groups. Chirality refers to a molecule that has optical activity, so amino acids are optically active molecules. The only exception is glycine, the simplest amino acid, in which R = H. Commonly, amino acids are represented as follows: amino acid structures as fischer projections 4 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS L and D amino acids; Indicated by R and L As shown above, L and D amino acids are mirror images of each other and are non-superimposable on each other, just like our left and right hands. By non-superimposable, we mean that when the mirror image of the object is placed over the original object, they do not have a perfect overlap. Pairs of amino acids like these are called enantiomers. Only L-amino acids are constituents of proteins. Our body synthesizes most of its own L-amino acids; these then get incorporated into proteins. Proteins are catalysts for most of the biochemical reactions that take place in our body. Along with DNA- DNAD and RNA- RNAR proteins constitute the genetic machinery of living organisms. Proteins are often called the building blocks of life. Classification of different amino acids Groups classified by different properties; I: Non-polar side chains (hydrophobic). II: Polar, uncharged side chains. III: Charged Side Chains . Acidic side chains . Basic side chains . 5 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS GROUP I: NON-POLAR (HYDROPHOBIC) SIDE CHAINS 1 - Side chains of Group; aa’s are mainly hydrocarbons – very unreactive amino acids. 2 –sub groups: Aliphatic hydrocarbons & Aromatic hydrocarbons (have benzene rings) - These amino acids will tend to be buried (away from water) in 3-D structure of proteins - Non-polar character. GROUP II: NEUTRAL (UNCHARGED) POLAR SIDE CHAINS Polar Residues are both buried as well as on the surface of proteins. They either form hydrogen bonds with other polar residues in the protein or with water. For example, the OH group of Serine can both donate as well as accept a hydrogen bond: GROUP III: Charged Amino Acids A. ACIDIC SIDE CHAINS a. Glutamate or glutamic acid (E, Glu) and Aspartate or aspartic acid (D, Asp) Always negatively charged at physiological pH (~7.4) --------CH2-COO- B. BASIC SIDE CHAINS All gain a proton at physiological pH (Positively charged) a. Lysine (K, Lys) b. Arginine (R, Arg) c. Histidine (H, His) . amino acid structure 6 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS There are 20 common amino acids. Based on the nature of the R group, they are classified as follows: The types of amino acids; 1- Hydrophobic amino acids have nonpolar side chains, such as alkyl groups or aromatic groups. 2- Hydrophilic—neutral—amino acids contain polar side chains, such as hydroxyl, -OH negative and sulfhydryl, -SH, negative groups. 3-Hydrophilic—acidic—amino acids have side chains that contain carboxylic acid, -COOH negative groups. . . Hydrophilic—basic— amino acids have side chains that contain amine, -NH2negative start subscript, 2, end subscript, groups. 7 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS 8 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS Peptides; Peptide bond formation is a condensation reaction leading to the polymerization of amino acids into peptides and proteins. Peptides are small consisting of few amino acids. The simplest peptide, a dipeptide, contains a single peptide bond formed by the condensation of the carboxyl group of one amino acid with the amino group of the second with the concomitant elimination of water. The process of peptide bond formation can then continue to join other amino acids and yield in an amino acid chain. A peptide chain will have an unbound amino group free at one end (called the N-terminus) and a single free carboxylate group at the other end (called the C-terminus). When there are a few amino acids in a chain (usually 10 - 20) , it is called an oligopeptide. When there are many (usually more than 20) it is called a polypeptide. Although the terms "protein" and "polypeptide" are sometimes used to describe the same thing, the term polypeptide is generally used when the molecular weight of the protein is below 10,000. 9 Dh. DALIA AL-KHATEEB LACTURE 2 PROTEINS Two a-amino acids are joined by a peptide bond in alanylglycine. It is a dipeptide. 10