Biochemistry - Proteins PDF

UNIVERSITY OF THE VISAYAS - MAIN BIOCHEMISTRY LECTURE Prepared by: Mr. Rommeljun Solijon Datiles LEARNING OBJECTIVES At the end of the lesson, the student should be able to: 1. identify the general structural features of amino acids; 2. describe t...

UNIVERSITY OF THE VISAYAS - MAIN BIOCHEMISTRY LECTURE Prepared by: Mr. Rommeljun Solijon Datiles LEARNING OBJECTIVES At the end of the lesson, the student should be able to: 1. identify the general structural features of amino acids; 2. describe the chracteristics of primary, s e c o n d a r y, t e r t i a r y, a n d q u a t e n n a r y structure of proteins; 3. describe the main features of enzymes; and 3. value the significant role of amino acids, proteins and enzymes, and its use to diagnose and treat diseases. Proteins  Of the four major groups of biomolecules --- lipids, carbohydrates, proteins, and nucleic acids --- Proteins have the widest array of functions. Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules.  Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence. Unlike lipids and carbohydrates, which the body stores for use when needed. Protein is not stored so it must be consumed on a daily basis. The current recommended daily intake for adults is 0.8g of protein per kg of body weight. Since children need protein for both growth and maintenance, the recommended daily intake is higher.  Keratin and collagen, for example form long insoluble fibers, giving strenght and support to tissues. § Hair, horns, hooves, and finger nails are all made up of keratin. § Collagen is found in bone, connective tissue, tendons, and cartilage.  Membrane proteins transport small organic molecules and ions across cell membranes. Insulin, the hormone that regulates blood glucose level.  Hemoglobin, which transports oxygen from the lungs to tissues, are proteins. Enzymes are proteins that catalyze and regulate all aspects of cellular function. What are Proteins ? Proteins are biomolecules that contain many amide bonds, formed by joining amino acids together. Proteins are long chains or polymers composed of a specific type of amino acid known as an α-amino acid. § The word protein comes from the greek proteios meaning “of first importance.” § proteins occur widely in human body, accounting for approximately 50% of its dry weight. Proteins in the Human Body Protein Types and Functions How High Proteins Affect the Body Amino Acids  “Amino Acids are the organic compounds that combine to form proteins, hence they are referred to as the building components of proteins. These biomolecules are involved in several biological and chemical functions in the human body and are the necessary ingredients for the growth and development of human beings. There are about 300 amino acids that occur in nature.” v Amino Acids To understand protein properties and structure, we must first learn the amino acids that composed them. Ø Amino acids are the fundamental building blocks of proteins and nitrogenous backbones for compounds such as neurotransmitters and hormones. v Amino Acids Ø Amino acids contain 2 functional groups -- Amino group (NH2) and a carboxyl group (COOH). Ø The amino group is bonded to the α carbon, the carbon adjacent to the carbonyl group, maing them α- amino acids. v Amino Acids Amino acids with an additionall COOH group in the side are called acidic amino acids. those with an additional basic N atom in the side chain are called basic amino acids. All others are neutral amino acids. Stereochemistry of Amino Acids L Amino acids have the -NH3+ group on the left side in the Fischer projection, common naturally occurng amino acids are L isomers. D Amino acids have -NH3+ group on the right side in the Fischer projection. D amino acids occur infrequently in nature. Exercise: General Properties of Amino Acids They have a very high melting and boiling point. Amino acids are white crystalline solid substances. In taste, few Amino acids are sweet, tasteless, and bitter. Most of the amino acids are soluble in water and are insoluble in organic solvents. Types of Amino Acids Proteins have a variety of important roles in living organisms, yet they are made from the same 20 L-amino acids. Based on the body’s capability to synthesize, amino acids can be categorized into 2 types: Ø Essential amino acids Ø Nonessential amino acids. Ø Semiessential amino acids  Types of Amino Acids Ø Essential amino Ø Nonessential Ø Semiessential acids: amino acids: amino acids: Essential amino acids Nonessential amino Semiessential are the amino acids acids need not be amino acids are which have to be taken in through diet growth-promoting taken in through diet as they can be amino acids. as they “CAN NOT” produced by the body they’re only be produced by the essential when body body is stress/ill. Types of Amino Acids Zwitterion Since amino acid contains a base (NH2 group) and an acid COOH), proton transfer from the acid to the base forms a salt called a zwitterion, which contains both a positive and a negative charge. These salts have high melting points and are water soluble. Essential Amino Acids v Lysine Lysine is necessary for promoting the formation of antibodies, hormones, and enzymes and in the development and fixation of calcium in bones. An amino acid released in the hydrolysis of many common proteins but present in small amounts or lacking in certain plant proteins; e.g., gliadin from wheat, zein from corn (maize). v Methionine Methionine is used in the treatment of kidney stones, maintaining healthy skin and also used in controlling invade of pathogenic bacteria. Sulfur-containing amino acid obtained by the hydrolysis of most common proteins Methionine accounts for about 5 percent of the weight of egg albumin; other proteins contain much smaller amounts of methionine. It is one of several so-called essential amino acids for mammals and fowl; i.e., they cannot synthesize it. v Phenylalanine Phenylalanine helps in maintaining a healthy nervous system and in boosting memory power. Human hemoglobin (the oxygen-carrying pigment of red blood cells) is one of the richest sources of phenylalanine, yielding 9.6 percent by weight. First isolated in 1881 from lupine seedlings, phenylalanine is one of several essential amino acids for fowls and mammals; i.e., they cannot synthesize it and require dietary sources. v Threonine Threonine helps in promoting the functions of the immune system. One of the last amino acids to be isolated (1935), threonine is one of several so-called essential amino acids; i.e., animals cannot synthesize it and require dietary sources v Tryptophan Tryptophan is involved in the production of vitamin B3 and serotonin hormones. This serotonin hormone plays a vital role in maintaining our appetite, regulating sleep and boosting our moods. Tryptophan is used by the body to manufacture several important substances, including the neurotransmitter serotonin and the vitamin niacin. Diets poor in tryptophan can lead to pellagra, a disease resulting from niacin deficiency; however, this disease is now rare in developed countries. v Histidine Histidine is involved in many enzymatic processes and in the synthesizing of both red blood cells (erythrocytes) and white blood cells (leukocytes). A particularly rich source, hemoglobin (the oxygen-carrying pigment of red blood cells) yields about 8.5 percent by weight of histidine. Histamine, a compound involved in the physiological processes associated with allergic reactions, is formed in the human body by decarboxylation of histidine. v Isoleucine Isoleucine plays a vital role in the formation of haemoglobin, stimulating the pancreas to synthesize insulin, and transporting oxygen from the lungs to the various parts. First isolated in 1904 from fibrin, a protein involved in blood-clot formation, isoleucine is one of several so-called essential amino acids for chicks, rats, and other higher animals, including man; i.e., they cannot synthesize it and require dietary sources. v Leucine Leucine is involved in promoting protein synthesis and growth hormones. Among the first of the amino acids to be discovered (1819), in muscle fibre and wool, it is present in large proportions (about 15 percent) in hemoglobin (the oxygen-carrying pigment of red blood cells) and is one of several so-called essential amino acids for rats, fowl, and humans; i.e., they cannot synthesize it and require dietary sources. v Valine Valine acts as an important component in promoting muscle growth. It is one of several so-called essential amino acids for fowl and mammals; i.e., they cannot synthesize it and require dietary sources. It is synthesized in plants and microorganisms from pyruvic acid (a product of the breakdown of carbohydrates) Nonessential Amino Acids v Alanine Alanine functions by removing toxins from our body and in the production of glucose and other amino acids. An especially rich source of L-alanine is silk fibroin, from which the amino acid was first isolated in 1879. Alanine is one of several so-called nonessential amino acids for birds and mammals; i.e., they can synthesize it from pyruvic acid (formed in the breakdown of carbohydrates) and do not require dietary sources. v Asparagine Asparagine is mainly involved in the transportation of nitrogen into our body cells, formations of purines and pyrimidine for the synthesis of DNA, the development of the nervous system and improving our body stamina. First isolated in 1932 from asparagus, from which its name is derived, asparagine is widely distributed in plant proteins. It is one of several so-called nonessential amino acids in warm-blooded animals: they can synthesize it from aspartic acid. v Aspartic acid Aspartic acid plays a major role in metabolism and in promoting the synthesis of other amino acids. First isolated in 1868 from legumin in plant seeds, aspartic acid is one of several so-called nonessential amino acids for mammals; i.e., they can synthesize it from oxaloacetic acid (formed in the metabolism of carbohydrates) and do not require dietary sources. v Glutamic acid Glutamic acid acts as a neurotransmitter and is mainly involved in the development and functioning of the human brain. Certain plant proteins (e.g., gliadin) yield as much as 45 percent of their weight as glutamic acid; other proteins yield 10 to 20 percent. Much of this content may result from the presence of a related substance, glutamine, in proteins; glutamine is converted to glutamic acid when a protein is hydrolyzed. v Glycine Glycine is helpful in maintaining the proper cell growth, and its function, and it also plays a vital role in healing wounds. It acts as a neurotransmitter. Sweet-tasting, it was among the earliest amino acids to be isolated from gelatin (1820). Especially rich sources include gelatin and silk fibroin. Glycine is one of several so-called nonessential amino acids for mammals; i.e., they can synthesize it from the amino acids serine and threonine and from other sources and do not require dietary sources. v Proline Proline is mainly involved in the repairing of the tissues in the formation of collagen, preventing the thickening and hardening of the walls of the arteries (arteriosclerosis) and in the regeneration of new skin. Unlike other amino acids, proline, first isolated from casein (1901), is readily soluble in alcohol. Collagen, the principal protein of connective tissue, yields about 15 percent proline. It is one of several so-called nonessential amino acids; i.e., animals can synthesize it from glutamic acid and do not require dietary sources. v Serine Serine helps in promoting muscle growth and in the synthesis of immune system proteins. First isolated in 1865 from sericin, a silk protein, serine is one of several so-called nonessential amino acids for mammals; i.e., they can synthesize it from glucose and do not require dietary sources. Serine and some of its derivatives (e.g., ethanolamine) are also important components of a class of lipids (phospholipids) found in biological membranes. Semiessential Amino Acids v Arginine Arginine helps in promoting the synthesis of proteins and hormones, detoxification in the kidneys, healing wounds, and maintaining a healthy immune system. amino acid obtainable by hydrolysis of many common proteins but particularly abundant in protamines and histones, proteins associated with nucleic acids. First isolated from animal horn (1895), arginine plays an important role in mammals in the synthesis of urea, the principal form in which these species excrete nitrogen. v Cysteine Cysteine acts as an antioxidant and provides resistance to our body; it is important for making collagen. It affects the texture and elasticity of the skin -containing nonessential amino acid. In peptides and proteins, the sulfur atoms of two cysteine molecules are bonded to each other to make cystine, another amino acid. The bonded sulfur atoms form a disulfide bridge, a principal factor in the shape and function of skeletal and connective tissue proteins and in the great stability of structural proteins such as keratin. v Glutamine Glutamine promotes a healthy brain function and is necessary for the synthesis of nucleic acids – DNA and RNA. First isolated from gliadin, a protein present in wheat (1932), glutamine is widely distributed in plants; e.g., beets, carrots, and radishes. Important in cellular metabolism in animals, glutamine is the only amino acid capable of readily crossing the barrier between blood and brain and, with glutamic acid, is thought to account for about 80 percent of the amino nitrogen (―NH2) of brain tissue. v Tyrosine Tyrosine plays a vital role in the production of the thyroid hormones -T3 and T4, in synthesizing a class of neurotransmitters and melanin, which are natural pigments found in our eyes, hair, and skin. tyrosine is particularly abundant in insulin (a hormone) and papain (an enzyme found in fruit of the papaya), which contain 13 percent by weight. Tyrosine is one of several so-called essential amino acids for certain animals; i.e., they cannot synthesize it and require dietary sources. Polypeptides v Peptides When amino acids are joined together by amide bonds, they form larger molecules called peptides and proteins. Ø A covalent bond is produced when the carboxyl group of one amino acid is joined to the amino group of another with the removal of a molecule of water. v Peptides Ø A dipeptide has two amino acids joined together by onee amino bond. The -NH3+ group of one amino acid forms an amide bond with the caroboxylate (-COO-) of another amino acid, and the elements of H2O are removed. v Peptides Ø A tripeptide has three amino acids joined together by two amide bonds. v Peptides Ø The fundamental linkage in all protein structures is generated by the chemical bond established between amino acids. The carboxyl group (COOH) of one amino acid links with the amino group (NH2) of another to produce the sequence CONH and release water in a peptide bond (H2O). v Peptides Ø The amino acid with the free -NH3+ group on the α carbon is called the N-terminal amino acid. Ø The amino acid with the free -COO- group on the α carbon is called the C-terminal amino acid. v Peptides Nomenclature Peptides are named as derivatives of the C-terminal amino acid. Ø Name all other amino acids from left to right as substituents of the C-terminal amino acid. Ø Change the -ine or -ic acid ending of the amino acid name to the suffix -yl v Peptides Nomenclature Thus peptide A, which has serine as its C-terminal amino acid, is named as alanylserine. Peptide B, which has alanine as its C- terminal amino acid, is named serylalanine. A B Exercise: Identify the N-terminal and C-terminal amino acid in each peptide. (A) Arg-His-Asn-Tyr (B) Val-Thr-Pro-Phe (C) (D) v Peptides v Polypeptides Ø Polypeptides and Proteins both have amino acids joined together in long linear chains, but the term protein is usually reserved for polymers of more than 40 amino acids. v Polypeptides Functions Ø Proteins and peptides are key biological components that carry out important tasks in cells. Proteins, for example, give cells their form and respond to signals from the extracellular environment. Peptides play an important function in controlling the activity of other substances. Proteins and peptides are structurally similar, consisting of chains of amino acids bound together by peptide bonds (also called amide bonds). Ø Peptides, on the other hand, can be classified into oligopeptides, which have a small number of amino acids, and polypeptides, which have a large number of amino acids. One or more polypeptides are linked together to make proteins. As a result, proteins are essentially very long peptides. In reality, some researchers use the term peptide to refer to oligopeptides, or short amino acid chains, while the term polypeptide is used to refer to proteins or chains of 50 or more amino acids. v Proteins Ø To understand proteins, the large polymers of amino acids that are responsible for so much of the structure and function of all living cells, we must four levels of structure, called the primary, secondary, tertiary and quaternary structure of proteins. v Proteins v Proteins Structure v Primary Structure Ø The Primary structure of a protein is the particular sequence of amino acids that is joined together by together by peptide bonds. Ø The most important element of this primary structure is the amide bond that joins the amino acids. The peptide bond between two amino acids is depicted. The shaded quadrilateral represents planar nature of this bond. By "planar" we mean that the 2 alpha carbons, the nitrogen, and carbon and oxygen associated with the peptide bond all lie in a single plane (the peptide bond is resistant to twisting). However, each amino acid can twist relative to the next amino acid between the C alpha and C carbons. Attribution: Marc T. Facciotti v Primary Structure Ø The linear sequence of amino acids in the polypeptide chain are held together by peptide bonds and result in the N-C-C-N-C-C patterned backbone. Ø The primary structure is coded for in the DNA, a process you will learn about in the Transcription and Translation modules. The primary structure of a protein is depicted here as "beads on a string" with the N- terminus and C-terminus labeled. The order in which you would read this peptide chain would begin with the N-terminus as Glycine, Isoleucine, etc and end with methionine. v Secondary Structure Ø The three-dimensional arrangement of localized regions of a protein is called its secondary structure. These regions arise due to hydrogen bonding the N-H proton of one amide and the C=O oxygen of another. Ø Two arrangements that are particularly stable are called the α-helix and the β- pleated sheet. v Secondary Structure The α-helix and β-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Although the interactions drawn are all between the atoms of the backbone, certain sequences of amino acids have a propensity to disrupt an α-helix, while others have a propensity to disrupt a β-pleated sheet. v Tertiary Structure Ø The three-dimensional shape adopted by the entire peptide chain is called its tertiary structure. Ø A peptide generally folds into a shape that maximizes its stability. In the aqueous environment of the cell, protiens often fold in such as to place a large number of polar and charged groups on their outer surface, to maximize the dipole- dipole and hydrogen bonding interactions with water. v Tertiary Structure v Tertiary Structure v Quaternary Structure Ø The shape adopted when two or more folded polypeptide chains come together into one protein complex is called the quaternary structure. Ø In nature, some proteins are formed from multiple proteins, also known as subunits, and the interaction of these subunits forms the quaternary structure. Ø Weak interactions between the subunits help to stabilize the overall structure. v Quaternary Structure Ø For example, hemoglobin consists of two subunits, encoded by the alpha- and betaglobin genes. Ø This protein complex also carries the prosthetic group hemoglobin. Ø The multi-subunit structure of this protein complex gives it regulatory characteristics not shared by its single-subunit cousin, myoglobin. v Quaternary Structure Assignment: 1. Draw the structure of each dipeptide: (a) Gly-Phe (b) Gln-Ile (c) Leu-Cys 2. (a) Draw the structures of the two possible dipeptides that can formed by combining leucine and asparagine. (b) In each dipeptide label the N- and C-terminal amino acids. (c) Name each peptide using -three abbreviations. 3. Identify the N-terminal amino acid in the tetrapeptide alanylglycylleucylmethtionine. (b) what is the C-terminal amino acid? (c) Write the peptide using three-letter sybmols for amino acids. Enzymes v Enzymes The human body is composed of different types of cells, tissues and other complex organs. For efficient functioning, our body releases some chemicals to accelerate biological processes such as respiration, digestion, excretion and a few other metabolic activities to sustain a healthy life. Hence, enzymes are pivotal in all living entities which govern all the biological processes. v Enzymes We conclude the discussion of proteins with enzymes, proteins that serve as biological catalyst in all living organisms. Ø Enzymes are crucial to the biological reactions that occur in the body, which would otherwise often proceed too slowly to be of any use. v Enzymes Functions The enzymes perform a number of functions in our bodies. These include: Enzymes help in signal transduction. The most common enzyme used in the process includes protein kinase that catalyzes the phosphorylation of proteins. They break down large molecules into smaller substances that can be easily absorbed by the body. They help in generating energy in the body. ATP synthase is the enzyme involved in the synthesis of energy. Enzymes are responsible for the movement of ions across the plasma membrane. Enzymes perform a number of biochemical reactions, including oxidation, reduction, hydrolysis, etc. to eliminate the non- nutritive substances from the body. They function to reorganize the internal structure of the cell to regulate cellular activities. v Enzymes v Enzymes v Enzymes Classification Earlier, enzymes were assigned names based on the one who discovered them. With further research, classification became more comprehensive.