Amino Acids and Proteins (BCH201) PDF

Amino acids and Proteins BCH201  Amino acids Amino acids are organic compounds that contain a carboxylic acid group, hydrogen, an amino group and a distinctive side group. About 300 amino acids are known in nature, only twenty of them are commonly found as components of prote...

Amino acids and Proteins BCH201  Amino acids Amino acids are organic compounds that contain a carboxylic acid group, hydrogen, an amino group and a distinctive side group. About 300 amino acids are known in nature, only twenty of them are commonly found as components of proteins and coded for by the DNA. These are referred to as proteinogenic amino acids. The proteinogenic amino acids are classified based on their nutritional availability to vertebrates into two classes: Essential and Nonessential Amino acids. Nonessential amino acids are amino acids that can be synthesized by the vertebrates while Essential amino acids are amino acids that cannot be synthesized by vertebrates, they are sourced for by the consumption plants and lower animals.  The proteinogenic amino acids can also be classified using the polarity of their R-groups as the criterion of classification into four: 1. Uncharged non polar amino acids 2. Uncharged polar amino acids 3. Positively charged amino acids 4. Negatively charged amino acids Uncharged nonpolar Amino acids Uncharged polar Amino acids  Common Features of Amino acids 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. Because of the tetrahedral arrangement of the bonding orbitals around the α-carbon atom, the four different groups can occupy two unique spatial arrangements, and thus amino acids have at least two possible stereoisomers (exist in two forms, designated D and L, that are mirror images of each other). The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers. The enantiomers are asymmetric and are non superimposable mirror images of each other All amino acids found in proteins are of the L-configuration. However, D-amino acids are found in some antibiotics and in bacterial cell walls.  Peptide bond formation Polypeptides are linear polymers composed of amino acids linked together by peptide bonds. Peptide bonds are amide linkages between the alpha carboxyl group of one amino acid and the alpha amino group of another. The reaction by which peptide bonds are formed is a dehydration/condensation reaction in which an equivalence of water molecule is lost. Amino acids are joined to form dipeptides, tripeptides, tetrapeptides, pentapeptides, oligopeptides and polypeptides. Each component amino acid in a polypeptide is called a “residue” because it is the portion of the amino acid remaining after the loss of water molecule.  Proteins Proteins are polymers, or macromolecules of amino acids containing from just few to several thousand amino acid groups joined by peptide linkages (peptide bonds). They are the most functionally diverse molecules in living system. They function as enzymes, hormones, antibodies, receptors and play several structural roles of physiologic importance. Proteins are the most abundant biological macromolecules, occurring in all cells. They are also the most versatile organic molecule of the living systems and occurs in great variety; thousands of different kinds, ranging in size from relatively small peptides to large polymers.  Smaller proteins containing only about 10 to about 40 amino acids per molecule, are called polypeptides. The formation of peptide linkages is a condensation process involving the loss of water. A portion of the amino acid left after the elimination of H2O during polymerization is called a residue. For example, consider the condensation of alanine, leucine, and tyrosine When these three amino acids join together, two water molecules are eliminated. The product is a tri peptide since there are three amino acids involved.  Proteins can be denatured by agents such as heat and urea that cause the unfolding of polypeptide chains without causing hydrolysis of peptide bonds. The denaturing agents destroy secondary and tertiary structures, without affecting the primary structure. If a denatured protein returns to its native state after the denaturing agent is removed, the process is called renaturation.  Functions of Proteins Proteins are vital for growth and repair, and their functions are endless. They also have an enormous diversity of biological functions and are the most important final products of the information pathways. Proteins, which are composed of amino acids, serve in many roles in the body (e.g., as enzymes, structural components, hormones, and antibodies). They act as structural components such as keratin of hair and nail, collagen of bone, etc. Proteins are the molecular instruments through which genetic information is expressed. They execute their activities in the transport of oxygen and carbon dioxide by hemoglobin and special enzymes in the red cells. They function in the homeostatic control of the volume of the circulating blood and that of the interstitial fluids through the plasma proteins.  They are involved in blood clotting through thrombin, fibrinogen, and other protein factors. They act as the defense against infections by means of protein antibodies. They perform hereditary transmission by nucleoproteins of the cell nucleus. Ovalbumin, glutelin, etc. are storage proteins. Actin, myosin act as a contractile protein important for muscle contraction.  Classification of Proteins Based on the chemical nature, structure, shape, and solubility, proteins are classified as: 1. Simple proteins: They are composed of only amino acid residue. On hydrolysis, these proteins yield only constituent amino acids. It is further divided into: 1. Fibrous protein: Keratin, Elastin, Collagen 2. Globular protein: Albumin, Globulin, Glutelin, Histones 2.Conjugated proteins: They are combined with non-protein moiety. Eg. Nucleoprotein, Phosphoprotein, Lipoprotein, Metalloprotein, etc. 3.Derived proteins: They are derivatives or degraded products of simple and conjugated proteins. They may be : 1. Primary derived protein: Proteans, Metaproteins, Coagulated proteins 2. Secondary derived proteins: Proteosesn or albunoses, peptones, peptides.  Some General Features of Proteins Physical agents: Heat, radiation, pH Chemical agents: Urea solution which forms new hydrogen bonds in the protein, organic solvents, detergents. Coagulation When proteins are denatured by heat, they form insoluble aggregates known as coagulum. All the proteins are not heat coagulable, only a few like the albumins, globulins are heat coagulable. Isoelectric point The isoelectric point (pI) is the pH at which the number of positive charges equals the number of negative charges, and the overall charge on the amino acid is zero. At this point, when subjected to an electric field the proteins do not move either towards anode or cathode, hence this property is used to isolate proteins.  The structure of proteins can be divided into four levels of organization: 1. Primary Structure The primary structure of a protein consists of the amino acid sequence along the polypeptide chain. Amino acids are joined by peptide bonds. Because there are no dissociable protons in peptide bonds, the charges on a polypeptide chain are due only to the N-terminal amino group, the C-terminal carboxyl group, and the side chains on amino acid residues. The primary structure determines the further levels of organization of protein molecules. 2. Secondary Structure The secondary structure includes various types of local conformations in which the atoms of the side chains are not involved. Secondary structures are formed by a regularly repeating pattern of hydrogen bond formation between backbone atoms. The secondary structure involves α-helices, β-sheets, and other types of folding patterns that occur due to a regularly repeating pattern of hydrogen bond formation. 3. Tertiary Structure The tertiary structure of a protein refers to its overall three-dimensional conformation. The types of interactions between amino acid residues that produce the three-dimensional shape of a protein include hydrophobic interactions, electrostatic interactions, and hydrogen bonds, all of which are non-covalent. Covalent disulfide bonds also occur. It is produced by interactions between amino acid residues that may be located at a considerable distance from each other in the primary sequence of the polypeptide chain. Hydrophobic amino acid residues tend to collect in the interior of globular proteins, where they exclude water, whereas hydrophilic residues are usually found on the surface, where they interact with water. 4. Quaternary Structure Quaternary structure refers to the interaction of one or more subunits to form a functional protein, using the same forces that stabilize the tertiary structure. It is the spatial arrangement of subunits in a protein that consists of more than one polypeptide chain.  Protein Synthesis The synthesis of proteins in cells involves amino acid synthesis, transcription, translation, and post- translational events. In amino acid synthesis, there is a set of biochemical processes that produce amino acids from carbon sources like glucose and related metabolites. Not all amino acids are produced by the body; other amino acids are obtained from diet. Transcription is the process by which the mRNA template is transcribed from DNA. The template is used for the succeeding step, translation. During transcription, a section of DNA encoding a protein, known as a gene, is converted into a template molecule called messenger RNA (mRNA). This conversion is carried out by enzymes, known as RNA polymerases, in the nucleus of the cell.  The mature mRNA is exported from the cell nucleus via nuclear pores to the cytoplasm of the cell for translation to occur. During translation, the mRNA is read by ribosomes which use the nucleotide sequence of the mRNA to determine the sequence of amino acids. The ribosomes catalyze the formation of covalent peptide bonds between the encoded amino acids to form a polypeptide chain. In translation, the amino acids are linked together in a particular order based on the genetic code. After translation, the newly formed protein undergoes further processing, such as proteolysis, post-translational modification, and protein folding. the polypeptide chain must fold to form a functional protein; for example, to function as an enzyme the polypeptide chain must fold correctly to produce a functional active site.