FHMS 116_Proteins_Classification of Amino Acids_2023.pdf

Amino Acids Properties and Classification E. Agyarko Learning Objectives At the end of the topic, students should be able to Describe the general properties of amino acids Classify amino acids according to chemical properties of the side chains Relate the properties of...

Amino Acids Properties and Classification E. Agyarko Learning Objectives At the end of the topic, students should be able to Describe the general properties of amino acids Classify amino acids according to chemical properties of the side chains Relate the properties of amino acids to their relative position in a protein. Explain how amino acids are joined to form proteins that have unique three-dimensional structures, making them capable of performing specific biological functions Demonstrate how a protein’s structure affects its specificity in function Overview of Proteins Proteins are the most abundant cellular components and they account for more than 50% of the dry mass of most cells. A human has tens of thousands of different proteins, each with a specific structure and function. Proteins are the most structurally sophisticated molecules known and they have diverse functions as well. Proteins are all polymers constructed from the same set of 20 amino acids. Polymers of amino acids are called polypeptides. A protein consists of one or more polypeptides, each folded and coiled into a specific three-dimensional structure.  Functions of Proteins Type of Protein Function Examples Enzymatic proteins Selective acceleration of Digestive enzymes catalyze the hydrolysis of the polymers in food. chemical reations Structural proteins Support Collagen and elastin provide a fibrous framework in animal connective tissues. Keratin is the protein of hair, horns, feathers, and other skin appendages. Storage proteins Storage of amino acids and Ovalbumin is the protein of egg white, used as an amino acid source other small molecules and ions for the developing embryo. Casein, the protein of milk, is the major source of amino acids for baby mammals. Transport proteins Transport of other substances Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Hormonal proteins Coordination of an organism’s Insulin, a hormone secreted by the pancreas, helps regulate the activities concentration of sugar in the blood of vertebrates. Receptor proteins Response of cell to chemical Receptors built into the membrane of a nerve cell detect chemical and other stimuli signals released by other nerve cells Contractile and Movement Actin and myosin are responsible for the contraction of muscles. motor proteins Defensive proteins Protection against disease Antibodies combat bacteria and viruses. Amino Acids Amino acids are the monomeric units of proteins. There are 20 amino acids that cells use to build the thousands of proteins. These are referred to as the standard amino acids and they are encoded by DNA. There are other amino acids that may be produced from chemical modification of standard amino acids (eg. Hydroxyproline). In addition to their function in building proteins, amino acids and their derivatives are useful for physiological processes eg. nerve impulse transmission eg. glutamate biosynthesis of important molecules eg. Glutamine in purine and pyrimidine synthesis. NB: Selenocysteine and pyrrolysine have recently been introduced as the 21st and 22nd amino acids.  Overview of Amino Acid Structure Each amino acid has a carboxyl group, an amino group, a hydrogen atom and a distinctive side chain (R group) bonded to the α-carbon atom. At physiological pH (~7.4), the carboxyl group is dissociated, forming the negatively charged carboxylate ion (−COO−), and the amino group is protonated (−NH3+). It is the nature of the side chains that ultimately dictates the role an amino acid plays in a protein. Amino acids are therefore classified according to the properties of their side chains. Classification of Amino Acids Amino acids are classified based on properties of their R groups: amino acids with non-polar (hydrophobic) side chains amino acids with polar, uncharged side chains amino acids with polar, charged side chains  Amino acids with non-polar (hydrophobic) side chains Unable to bind or give off protons They do not participate in hydrogen bonding They do not engage in ionic bonding They participate in hydrophobic interactions because the side chains are lipophilic. When present in proteins found in aqueous environments amino acids with these side chains cluster together in the interior of the protein For proteins that are located in a hydrophobic environment, such as a membrane, the nonpolar amino acids are found on the outside surface of the protein, interacting with the lipid environment. Location of Amino Acids with Nonpolar Side Chains in Proteins Amino Acids with Non-polar Side Chains Side chain of proline and α-amino nitrogen form a rigid, five-membered ring structure. ie. it has a secondary amino group. It interrupts the α-helices found in globular proteins but is useful for the fibrous structure of collagen Amino Acids with Polar, Uncharged Side Chains At physiological pH, they are uncharged (ie. they have zero net charge) Their side chains contain functional groups that can participate in hydrogen bonds with water. This makes them polar or hydrophilic. Because of their hydrophilicity, these amino acids are frequently found on the surface of water-soluble globular proteins. Amino Acids with Polar, Uncharged Side Chains Amino Acids with Polar, Charged Side Chains These are amino acids with side chains that are charged (positive or negative) at physiological pH. There are two forms based on the charge they carry: Acidic (they carry a negative charge) Basic (their side chains carry a positive charge)  Amino Acids with Acidic Side Chains These amino acids are proton donors. At physiologic pH, the side chains of these amino acids are fully ionized. They contain a negatively charged carboxylate group (−COO-) at physiological pH.  Amino Acids with Basic Side Chains The side chains of the basic amino acids accept protons. At physiologic pH, the R groups of lysine and arginine are fully ionized and positively charged. Histidine on the other hand is weakly basic and largely uncharged at physiologic pH.  Amino Acid Isomers With the exception of glycine, the α- carbon of amino acids is an asymmetric/chiral carbon atom (ie. it has four different substituents). Amino acids with a chiral α-carbon exist in two different isomeric forms, designated D and L, which are enantiomers, or mirror images. All amino acids found in mammalian proteins are of the L configuration. Acid-Base Properties of Amino Acids In aqueous solution, the carboxyl group and amino group are weakly acidic and basic respectively. This is because they can give off protons or accept protons depending on the pH of the solution. Thus, amino acids can act as buffers. Net charge on an amino acid depends on pH The charged state of the amine and carboxylic acid functional groups on amino acids depends on the pH of the solution, which in turn is related to the functional groups' pKa When the pH of the solution is above the pKa, the group will be in its deprotonated state. Conversely, when the pH of the solution is below the pKa, the group will be in its protonated state. Acid-Base Properties of Amino Acids At low pH, the amino acid is protonated at both the amine and carboxyl functional groups. At this pH it carries a net positive charge and can be treated as a diprotic acid, an acid with two pKa's. At high pH, both the carboxyl and amine groups are deprotonated. At these pH values, the amino acid carries a net negative charge, and is dibasic. At some intermediate pH, the amino acid is a zwitterion, and carries no net charge. This is called the isoelectric point of the amino acids, and is designated pHI. Acid-Base Properties of Amino Acids The quantitative relationship between the pH of the solution and concentration of a weak acid (HA) and its conjugate base (A−) is described by the Henderson-Hasselbalch equation. The equation can be used to calculate how the pH of a physiologic solution responds to changes in the concentration of a weak acid and/or its corresponding salt form. Peptide Bonds and Protein Structure Amino Acid Polymers (Formation of Peptide Bonds) When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction. The resulting covalent bond is called a peptide bond. Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds. Polypeptides range in length from a few monomers to a thousand or more. Each specific polypeptide has a unique linear sequence of amino acids determined by inherited genetic information (specific DNA sequence). Peptide Bonds Peptide Bonds Peptide bonds are rigid and are unable to rotate (around C-N axis) because they have a partial double bond character (no rotation). Bonds adjacent the peptide bonds however rotate freely. Protein Structure Proteins have a three-dimensional (3-D) structure, and their specific activities depend on this intricate 3-D structure. The basic level of this organization is the sequence of amino acids which make up the protein structure. And it is the amino acid sequence of each polypeptide that determines what three-dimensional structure the protein will have. All proteins share three levels of structure, known as primary, secondary, and tertiary structure. A fourth level, quaternary structure, arises when a protein consists of two or more polypeptide chains. Primary Structure of Proteins This is simply the unique sequence of amino acids that a protein is made of. For instance, if a protein is made up of 100 amino acids, then its primary structure is the way in which those hundred amino acids are arranged in a sequence. In that case each of the 100 positions in the protein is occupied by one of the 20 amino acids. The precise primary structure of a protein is determined by inherited genetic information and not by a random linking of amino acids. Primary Structure of Proteins Example of a sequence of amino acids in the primary structure of a protein Secondary Structure of Proteins The secondary structure describes the repeated coils and folds that exist in certain segments of a polypeptide chain as result of hydrogen bonds. Hydrogen bonding between the peptide bond carbonyl oxygens and amide hydrogens (~ 4 residues ahead) stabilize the secondary structures. There are two basic types of secondary structure, both determined by hydrogen bonding between the amino acids that make up the primary structure: the α helix and the β pleated sheet. Many proteins contain regions of both α helix and β pleated sheet in the same polypeptide chain. Secondary Structure of Proteins Tertiary Structure of Proteins Tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids. The tertiary structure is stabilized by several forces: hydrogen bonding hydrophobic interactions (leading to van der Waals interactions) ionic bonding covalent disulphide bonds. Tertiary Structure of Proteins Bonds that Stabilize the Tertiary Structure 1. Electrostatic/ionic 2. Hydrogen bonding 3. Hydrophobic interaction 4. Disulfide bond Quaternary Structure This structure results from the aggregation of several polypeptide chains to form a compact 3D structure. Not all proteins have the quaternary structure. It is those proteins which contain more than one polypeptide chain which show the quaternary structure. The quaternary structure is stabilized by several forces, including hydrogen bonding hydrophobic interactions ionic bonding disulphide bonds The weak nature of these bonds allow for conformational changes in the native structure. Quaternary Structure Factors that determine the structure of a protein Amino acid sequence A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a three-dimensional shape determined and maintained by the interactions responsible for secondary and tertiary structure. Protein structure also depends on the physical and chemical conditions of the protein's environment. If the pH, salt concentration, temperature, or other aspects of its environment are altered, the protein may unravel and lose its native shape, a change called denaturation. Protein Denaturation This is the process through which the weak forces that maintain the secondary, tertiary or quaternary structures are disrupted, so that the ordered 3-D conformation of the protein is broken down for random coils to be formed. Because it is misshapen, the denatured protein is biologically inactive. Proteins can be denatured by nonenzymatic modification of amino acids in the protein or by some physical factors Protein Denaturation Nonenzymatic modification of amino acids Amino acids on proteins can undergo a number of chemical modifications (such as glycosylation or oxidation) that are not catalyzed by enzymes. Such modifications usually lead to a loss of function of the protein and sometimes to a form that cannot be degraded in the cell. An example is the glycosylation of haemoglobin, leading to the formation of HbA1c Non-enzymatic glycation increases hemoglobin-oxygen affinity and reduces oxygen delivery to tissues by altering the structure and function of hemoglobin.  Factors that Cause Denaturation Temperature: temperature increases the vibrational energies of the atoms pH: At a low pH, ionic bonds and hydrogen bonds formed by carboxylate groups would be disrupted; at a very alkaline pH, hydrogen and ionic bonds formed by the basic amino acids would be disrupted High concentrations of polar and non polar substances: Classification of Proteins Proteins may be classified as Globular Fibrous depending on their overall 3-D structure.  Globular Proteins Globular proteins are proteins whose tertiary and/or quaternary structure are spherical in shape. Usually, they are compact and water soluble Hydrophobic interior, hydrophilic surface Examples Enzymes myoglobin and haemolobin - Transport proteins Hormones – regulatory proteins  Fibrous Proteins Fibrous proteins exhibit special properties that provide mechanical support Often assembled into large cables or threads Examples α-Keratins: major components of hair and nails Collagen: major component of tendons, skin, bones