Amino Acids and Proteins PDF

Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay Amino acids and Proteins Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells. Definition : Proteins, from the Greek proteios, meaning first, are a class of org...

Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay Amino acids and Proteins Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells. Definition : Proteins, from the Greek proteios, meaning first, are a class of organic compounds which are present in and vital to every living cell. They are linear polymers built of monomer units called amino acids, which are linked end to end by peptide bonds. Amino acids are the building blocks of proteins. All proteins, whether from the most ancient lines of bacteria or from the most complex forms of life, are constructed from the same set of 20 amino acids. Proteins are polymers of amino acids joined together by peptide bonds. WHAT ARE AMINO ACIDS. Amino acids are organic compounds that combine to form proteins. They play central roles both as building blocks of proteins and as intermediates in metabolism. Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond. Proteins can be broken down (hydrolyzed) to their constituent amino acids the free amino acids derived from them. Basic Structure of an Amino Acid: Each amino acid (except for proline, which has a secondary amino group) has a amine 1- [- NH2] 2- carboxyl [-COOH] 3 -side chain [R group] The major key elements if amino acids are carbon, hydrogen, nitrogen, oxygen. About 500 amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways Carboxyl group, a primary amino group, and a distinctive side chain (R-group) bonded to the α-carbon atom. At physiologic pH (approximately pH 7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (COO-), and the amino group is protonated (NH3+). All amino acids found in proteins have the following basic structure, which differing only in the structure of the R-group or the side chain. In fact, the simplest, and smallest, amino acid found in proteins is glycine for which the R-group is hydrogen (H) 1  Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay Amino acids can be classified in the category of either essential or non-essential: Essential Nonessential Histidine Alanine Isoleucine Arginine Leucine Aspartic acid Lysine Cysteine Methionine Glutamic acid Phenylalanine Glutamine Threonine Glycine Tryptophan Proline Valine Serine Tyrosine Asparagine Selenocysteine Pyrrolysine.1 Essential amino acids are amino acids that cannot be synthesized by the human body at the level needed for normal growth, so they must be obtained from food. The 8 amino acids that humans cannot synthesize are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine and lysine..2 Non-Essential amino acids: The rest of 20 amino acids that the human body can synthesize them from other compounds at the sufficient levels. Optical properties of amino acids: The α-carbon of each amino acid is attached to four different chemical groups and is, therefore, a chiral or optically active carbon atom. Glycine is the exception because its α-carbon has two hydrogen substituents and, therefore, is optically inactive. Amino acids that have an asymmetric center at the α-carbon can exist in two forms, designated D and L that are mirror images of each other. The two forms in each pair 2  Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay are termed stereoisomers, optical isomers, or enantiomers. All amino acids found in proteins are of the L-configuration. However, D-amino acids are found in some antibiotics and in plant and bacterial cell walls. Amino acids are classification based on : 1- R group -2- Polarity and R group 3- Distribution in protein 4 -Nutritional requirements 5 --Number of amino and carboxylic groups Peptide bonds Amino acids are connected by peptide bonds to form polypeptide chains. Polypeptides have two ends, one with a free amino group, the N-terminus, and one with a free carboxylic acid group, the C-terminus. At physiological pH, both of these termini are ionized. The amide in the peptide backbone, however, cannot be protonated in water. Peptide bonds are flat and polar, and they do not rotate freely. These properties influence the conformations that the peptide backbone can adopt, ultimately influencing how proteins fold. Furthermore, the conformations of the peptide backbone are influenced by amino acid side chains, which create steric clashes that bias the peptide backbone into specific conformations. Glycine and proline have a particularly strong influence on backbone conformation. Glycine can adopt a wide range of conformations since it lacks a side chain, and as a result, polypeptides rich in glycine tend to be more flexible. Proline, however, constrains the backbone into a narrower range of conformations. Due to the unique nature of its side chain, proline can sometimes take part in cis peptide bonds, which are generally disfavored for other amino acids. The amino acids found in proteins have a diverse range of properties that resist easy categorization. Some side chains are polar, some are nonpolar, and some are slightly polar. Several are positively or negatively charged at physiological pH. And yet others 3  Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay have ring structures that simultaneously have polar and nonpolar features. In the next chapter we will see how this diversity of amino acid properties influences the structure, folding, and myriad behaviors of proteins. The general properties of proteins 1- High molecular weight substances. 2- It constitutes more than 50% of the dry weight of the cell. 3- It presents in different shapes; fibrous and globular. 4- The globular is soluble in water and diluted salt solution with different degrees 5- The chemical and physical properties depend on the amino acids forming the protein. 6- The biological properties and 3D conformation depend also on the constituting amino acids. 7- All proteins are amphoteric compounds. 8- They precipitate by heat, in alcohols and in their isoelectric point Classification of proteins Proteins can be classified according to three different criteria: A- proteins can be classified on the basis of the chemical composition. Proteins can be classified on the basis of their chemical composition into two main classes 1 -Simple proteins: are those proteins which upon hydrolysis give only amino acids. Example: ribonuclease A, chymotrypsin. 2 -conjugated proteins: are proteins which yield upon hydrolysis amino acids and non-protein part is called the prosthetic group. i) cleoproteins ii) (contains carbohydrate part) iii) proteins (contains lipid part( iv) oproteins (contains heme( v) alloproteins (contains metal( vi) hoproteins (phosphorylated protein) Example : B- proteins can be classified on the basis of shape. 4  Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay Proteins can be classified on the basis of their chemical composition into two main classes: 1- Globular proteins: They are generally soluble in water. The polypeptide chains are tightly folded into a globular shape. Example: enzymes, hemoglobin, myoglobin 2- Fibrous proteins- They are insoluble in water Their polypeptide chains are arranged in long strands (elongated in the form of fibers( Example: Collagen, elastin, keratin C- proteins can be classified on the basis of their biological function. Proteins can be classified on the basis of their biological function into: 1- Catalytic function (enzyme) 2- Transport function (hemoglobin, albumin, transferrin) 3- Nutrient and storage proteins [e.g., casein & ferritin] 4- contractile or mobile proteins [e.g., actin, myosin] 5- Structural function [Keratin, elastin, collagen] 6- Defense proteins [e.g., immunoglobulins, fibrinogen and thrombin] 7- Regulatory function, some hormones are proteins (Growth hormone [GH, somatotropin]) 8- Some toxins are proteins 9- Defense (Antibodies and coagulating factors) THE LEVELS OF PROTEIN STRUCTURE The various levels of protein structural organization are defined as follows. 1 Primary Structure The amino acid sequence is the primary (1°) structure of a protein, 2 Secondary Structure Through hydrogen bonding interactions between adjacent amino acid residues the polypeptide chain can arrange itself into characteristic helical or pleated segments. These segments constitute structural conformities, so-called regular structures that extend along one dimension, like the coils of a spring. Such architectural features of a protein are designated secondary (2°) structures Secondary structures are just one of 5  Biochemistry lectures 6 + 7 Dr. Hussein Al. Robaay the higher levels of structure that represent the three-dimensional arrangement of the polypeptide in space. 3 Tertiary Structure When the polypeptide chains of protein molecules bend and fold in order to assume a more compact three-dimensional shape, a tertiary (3°) level of structure is generated. It is by virtue of their tertiary structure that proteins adopt a globular shape. A globular conformation gives the lowest surface to- volume ratio, minimizing interaction of the protein with the surrounding environment. 4 Quaternary Structure Many proteins consist of two or more interacting polypeptide chains of characteristic tertiary structure, each of which is commonly referred to as a subunit of the protein. Subunit organization constitutes another level in the hierarchy of protein structure, defined as the protein’s quaternary (4°) structure. Denaturation: When a protein loses its native conformation. For example, egg white contains a protein called albumin which is water-soluble. However, if heated, albumin becomes denatured and loses its ability to be water-soluble. Denaturation is caused when the folded native structures break down because of the exposure of protein to one of the denaturing agents such (Heat and ultraviolet light and Strong acids or bases) which disrupts the stabilizing structures. The structure becomes random and disorganized. In this case, the protein loses its biological activity with loss of structure. 6