Proteins and Amino Acids PDF

PROTEINS AND AMINO ACIDS Dr. Shaista Zafar ❑ Proteins are of primary importance to the continuing functioning of life on Earth. ❑ Proteins catalyze the vast majority of chemical reactions that occur in the cell. ❑ They provide many of the structural elements of a cell, a...

PROTEINS AND AMINO ACIDS Dr. Shaista Zafar ❑ Proteins are of primary importance to the continuing functioning of life on Earth. ❑ Proteins catalyze the vast majority of chemical reactions that occur in the cell. ❑ They provide many of the structural elements of a cell, and they help to bind cells together into tissues ❑ Proteins of similar function have similar amino acid composition and sequence. ❑ Plants can synthesize all of the amino acids; animals cannot, even though all of them are essential for life. ❑ Proteins are highly complex substance that is present in all living organisms. ❑ Proteins are of great nutritional value and are directly involved in the chemical processes essential for life ❑ Proteins are made up of building blocks called amino acids. ❑ There are about 20 different amino acids that link together in different combinations. ❑ Your body uses them to make new proteins, such as muscle and bone, and other compounds such as enzymes and hormones. ❑ The protein content of animal organs is usually much higher than that of the blood plasma. ❑ Muscles, for example, contain about 30 percent protein, the liver 20 to 30 percent, and red blood cells 30 percent. ❑ The human body contains about 5 to 6 kilograms (11 to 13 pounds) of muscle protein ❑ Higher percentages of protein are found in hair, bones, and other organs and tissues with a low water content. ❑ The quantity of free amino acids and peptides in animals is much smaller than the amount of protein; ❑ Protein molecules are produced in cells by the stepwise alignment of amino acids and are released into the body fluids only after synthesis is complete ❑ Some of the most important proteins, such as enzymes and hormones, occur in extremely small amounts. ❑ The importance of proteins is related principally to their function. ❑ All enzymes identified thus far are proteins. ❑ Functional proteins have shapes that enable them to participate in chemical processes of the body. ❑ Functional proteins include some of hormones, growth factors, cell membrane receptors, and enzymes.  Sources of Proteins Meat Beef Poultry Eggs Fish Beans Nuts Milk  AMINO ACIDS We all know that proteins are one of the main building blocks of life. But do you know what are the building blocks of proteins? The basic building blocks of proteins what we call Amino acids. These are absolutely essential for humans. There are some 20 amino acids in the proteins that we consume. These amino acids bond together to form a larger protein molecule. Amino acid being organic compound molecules can form various different links with each other due to the versatile nature of carbon. ❑ Amino acids are the building blocks of proteins. ❑ Among the thousands of amino acids available in nature, proteins contain only 20 different kinds of amino acids, all of them are L-alpha- amino acids. ❑ The same 20 standard amino acids make proteins in all the living cells, may it either be a virus, bacteria, yeast, plant or human cell. ❑ These 20 amino acids combine in different sequences and numbers to form various kinds of proteins. In protein molecules the α-amino acids are linked to each other by peptide bonds between the amino group of one amino acid and the carboxyl group of its neighbor. The chemical bond between the carbon and nitrogen atoms of each amide group is called a peptide bond. The joining of three amino acids yields the tripeptide. Chemically, An amino acid is a carboxylic acid-containing an aliphatic primary amino group in the α position to the carboxyl group and with a characteristic stereochemistry. Proteins are biosynthesized from 20 amino acids in a system involving strict genetic control. Thus, amino acids are the basic unit of proteins. Structure of amino acid  General structure and properties of proteins/Amino acid The common property of all proteins is that they consist of long chains of α-amino (alpha amino) acids. The α-amino acids are so called because the α-carbon atom in the molecule carries an amino group (―NH 2) the α-carbon atom also carries a carboxyl group (―COOH). The general formulae for an amino acid can be written as ‘R-CH-NH2—COOH’ Depending upon the ‘R’ group present in the amino acid it is named accordingly. The 20 amino acids found in the proteins are known as primary or standard amino acids..  The amino acids present in proteins differ from each other in the structure of their side (R) chains. The simplest amino acid is glycine, in which R is a hydrogen atom. In a number of amino acids, R represents straight or branched carbon chains. Two amino acids, each containing three carbon atoms, are derived from alanine; they are serine and cysteine. Serine contains an alcohol group (―CH2OH) instead of the methyl group of alanine, and cysteine contains a mercapto group (―CH2SH). Animals can synthesize serine but not cysteine ❑ Proteins are macromolecular polypeptides—(i.e., very large molecules (macromolecules) composed of many peptide-bonded amino acids). ❑ Most of the common ones contain more than 100 amino acids linked to each other in a long peptide chain. ❑ The average molecular weight (based on the weight of a hydrogen atom as 1) of each amino acid is approximately 100 to 125; thus, the molecular weights of proteins are usually in the range of 10,000 to 100,000 Daltons (one Dalton is the weight of one hydrogen atom).  Classification of amino acids on the basis of R-group Nonpolar, Aliphatic amino acids: The R groups in this class of amino acids are nonpolar and hydrophobic. Glycine, Alanine, Valine, leucine, Isoleucine, Methionine, Proline. Aromatic amino acids: Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are relatively nonpolar (hydrophobic). All can participate in hydrophobic interactions. Polar, Uncharged amino acids: The R groups of these amino acids are more soluble in water, or more hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that form hydrogen bonds with water. This class of amino acids includes serine, threonine, cysteine, asparagine, and glutamine. Acidic amino acids: Amino acids in which R-group is acidic or negatively charged. Glutamic acid and Aspartic acid Basic amino acids: Amino acids in which R-group is basic or positively charged. Lysine, Arginine, Histidine  Classification of amino acids on the basis of nutrition Essential amino acids (9) Nine amino acids cannot be synthesized in the body and, therefore, must be present in the diet in order for protein synthesis to occur. These essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Non-essential amino acids (11) These amino acids can be synthesized in the body itself and hence do not necessarily need to be acquired through diet. These non-essential amino acids are Arginine, glutamine, tyrosine, cysteine, glycine, proline, serine, ornithine, alanine, asparagine, and aspartate.  Classification of amino acids on the basis of the metabolic fate Glucogenic amino acids: These amino acids serve as precursors of gluconeogenesis for glucose formation. Examples glutamine, proline, valine, methionine, cysteine, histidine, and arginine. Glycine, alanine, serine, aspartic acid, asparagine, Ketogenic amino acids: These amino acids break down to form ketone bodies. Examples: Leucine and Lysine. Both glucogenic and ketogenic amino acids: These amino acids break down to form precursors for both ketone bodies and glucose. Examples Isoleucine, Phenylalanine, Tryptophan, and tyrosine.  Levels of structural organization in proteins Protein molecules are large, complex molecules formed by one or more twisted and folded strands of amino acids. Each amino acid is connected to the next amino acid by covalent bonds. Primary Protein (first level) – Protein structure is a sequence of amino acids in a straight chain. Secondary Protein (secondary level) – Protein structure is formed by folding and twisting of the amino acid chain. Tertiary protein (third level) – Protein structure is formed when the twists and folds of the secondary structure fold again to form a larger three dimensional structure. E.g. fibrous and globular protein Quaternary (fourth level) – consisting of more than one folded amino acid chain. The three-dimensional arrangement of protein subunits in proteins containing two or more identical or different polypeptide chains, or subunits is the quaternary structure. They have specific spatial arrangement and interactions. Proteins can bond with other organic compounds and form “mixed” molecules. Examples Glycoproteins embedded in cell membranes are proteins with sugars attached. Lipoproteins are lipid-protein combinations. Primary, secondary, tertiary, and quaternary are the four structures of proteins found in nature. The primary structure comprises the amino acid sequence. Hydrogen bonds formed between amino acids are responsible for the formation of the secondary structure of a protein while disulfide and salt bridges form the tertiary structure. Primary structure of a protein is composed of peptide bonds formed between amino acids, secondary structure of a protein encompasses hydrogen bonds while the tertiary structure of a protein encompasses disulfide bridges, salt bridges, and hydrogen bonds. This is a main difference between primary secondary and tertiary structure of protein. Primary structure of protein is the amino acid sequence, which is linear. It is formed during translation. Secondary structure of protein is either an α-helix or β-sheet formed due to the formation of hydrogen bonds. Secondary structure of protein is formed from its primary structure, which in turns form the tertiary structure. It plays a major role in the formation of structures such as collagen, elastin, actin, myosin, and keratin fibers. The tertiary structure of proteins includes enzymes, hormones, albumin, globulin, and hemoglobin. Tertiary structure of protein is globular and it is formed due to the formation of disulfide and salt bridges. It plays a vital role in metabolism. The difference between primary secondary and tertiary structure of protein is their structure, bonds, and the role in the cell. Optical activity Proteins also are optically active. The amino acids, with the exception of glycine, exhibit optical activity (rotation of the plane of polarized light) They are usually levorotatory (i.e., they rotate the plane of polarization to the left  Chemical reactivity of proteins Protein Denaturation Protein denaturation is the process of destruction of the quaternary, tertiary, and secondary structure of proteins by the application of external force or strong chemicals like acid and base. When a protein Solution is boiled, the protein frequently becomes insoluble—i.e., it is denatured—and remains insoluble even when the solution is cooled. The denaturation of the proteins of egg white by heat—as when boiling an egg—is an example of irreversible denaturation Denaturation can be brought about in various ways. Proteins are denatured by treatment with alkaline or acid, oxidizing or reducing agents, and certain organic solvents Association of protein subunits Many proteins with molecular weights of more than 50,000 occur in aqueous solutions as complexes: dimers, tetramers, and higher polymers—i.e., as chains of two, four, or more repeating basic structural units. The linear sequence of amino acid residues in a polypeptide chain determines the three-dimensional configuration of a protein, and the structure of a protein determines its function.  Classification of protein on the basis of Structure and composition This Classification of protein is based on shape or structure and composition. 1. Fibrous protein: They are elongated or fiber like protein and static. They have less biological functions They are mostly present in animals Examples; Fibrous proteins are further classified as- simple and conjugated a) Simple fibrous protein: Examples; Scleroprotein (Keratine, elastin, collagen, fibroin etc) Scleroprotein or Albuminoids: they make animal skeleton and they are water insoluble. b) Conjugated fibrous proteins: Examples; pigments present in chicken feather. 2. Globular protein: They are spherical or globular in shape and dynamic. They have variety of biological functions Examples; enzymes, hormones etc Globular protein is further classified on the basis of composition or solubility a) Simple or homo globular protein: They are composed of amino acids only. examples are; Protamine, histone, Albumin, globulin, prolamine b) Complex or conjugate or hetero globular protein: These proteins are always linked by non-protein moiety to become functional. So, they are composed of both protein and non- protein components. The non-protein component is known as prosthetic group. On the basis of prosthetic group, they are classified as follows; Metalloprotein: They have metal prosthetic group. Some metals such as Hg, Ag, CU, Zn etc, strongly binds with proteins such as collagen, albumin, casein by –SH group of side chain of amino acids. Chromoprotein: They have colored prosthetic group. Some examples are; Haemoprotein: Haemoglobin, myoglobin, chlorophyll, cytochrome, peroxidase, haemocyanin, The chromoprotein melanin, a pigment found in dark skin, dark hair Glycoprotein/Mucoprotein: (Protein linked with carbohydrate) They have carbohydrate as prosthetic group E.g. Antibody, complement proteins, Heparin, Hyaluronic acid Phosphoprotein: They have phosphate group as prosthetic group. E.g. Casein (milk protein binds with calcium ion to form calcium salt of caseinat Lipoprotein: They have lipid as prosthetic group. e.g. cholesterol, cephalin, lecithin 3. Derived protein These protein are the derivatives of either simple or complex protein resulting from the action of heat, enzymes and chemicals. Some artificially produced protein are included in this group. They are classified as primary derived protein and secondary derived protein. a) Primary derived protein: The derived protein in which the size of protein molecules are not altered materially but only the arrangement is changed. Some examples are; Coagulated proteins are produced by the action of heat or alcohol on protein. They are insoluble in water. Eg. Coagulated egg b) Secondary derived protein : The derived protein in which size of original protein are altered. Hydrolysis has occurred due to which size of protein molecule are smaller than original one. Examples; Proteoses:  Classification of protein on the basis of biological functions: Catalytic protein: They catalyze biochemical reaction in cells. E.g. Enzymes and co-enzymes 2. Structural protein; They make various structural component of living beings. E.g. Collagen make bone, Elastin make ligamnets and keratin make hair and nails 3. Nutrient protein: They have nutritional value and provide nutrition when consumed. Eg. Casein in milk 4. Regulatory protein: They regulate metabolic and cellular activities in cell and tissue. Eg. Hormones 5. Defense protein: They provide defensive mechanism against pathogens. Eg. Antibodies, complement proteins 6. Transport protein: They transport nutrients and other molecules from one organ to other. Eg. Haemoglobin 7. Storage protein: They stores various molecules and ions in cells. Eg. Ferritin store Iron 8. Contractile or mobile protein: They help in movement and locomotion of various body parts. Eg. Actin, myosin, tubulin etc. 9. Toxic protein: They are toxic and can damage tissues. Eg. Snake venom, bacterial exotoxins etc.  Biological importance of proteins /Amino acids In particular, 20 very important amino acids are crucial for life as they contain peptides and proteins and are known to be the building blocks for all living things. Amino acids are required for the synthesis of body protein and other important nitrogen-containing compounds, such as creatine, peptide hormones, and some neurotransmitters. Amino acids are imperative for sustaining the health of the human body. They largely promote the: Production of hormones Structure of muscles Human nervous system’s healthy functioning The health of vital organs Normal cellular structure The amino acids are used by various tissues to synthesize proteins and to produce nitrogen-containing compounds (e.g., purines, heme, creatinine, epinephrine), or they are oxidized to produce energy. The breakdown of both dietary and tissue proteins yields nitrogen- containing substrates and carbon skeletons. The nitrogen-containing substrates are used in the biosynthesis of purines, pyrimidines, neurotransmitters, hormones, porphyrins, and nonessential amino acids. The carbon skeletons are used as a fuel source in the citric acid cycle, used for gluconeogenesis, or used in fatty acid synthesis Proteins are essential biomolecules that are critical to life and to perform various activities. Many proteins act as catalysts that enhance the rate of chemical reactions in various metabolic pathways. The fibrous proteins are a component of various tissues holding the skeletal elements together like collagen, which is a structural unit of connective tissues. The nucleoproteins serve as carriers of genetic characters and hence govern the inheritance of traits. Proteins also perform transport functions that regulate the transport of many compounds in and out of the cells and accumulate inside at much higher concentrations than expected from diffusion alone. Various protein hormones regulate the growth of plants and animals, besides controlling many other physiological functions.  Blood plasma has multiple soluble proteins that can be used for the treatment of shock produced by severe injuries and operations. e.g. Interferons are regulatory glycoproteins produced by many eukaryotic cells in response to virus infection, endotoxins, antigenic stimuli, and many parasitic organisms. Peptides from humans defensing are antibiotic in nature. They can also used as an energy source. Protein used to prepare Antibodies, enzymes, vaccines, Harmons (insulin), serum albumin Proteins are antioxidant, defends body against free radical damage  References ▪ Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2000). Lehninger principles of biochemistry. New York: Worth Publishers ▪ Rodwell, V. W., Botham, K. M., Kennelly, P. J., Weil, P. A., & Bender, D. A. (2015). Harper’s illustrated biochemistry (30th ed.). New York, N.Y.: McGraw-Hill Education LLC.