Proteins PDF

Proteins Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structur...

Proteins Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Functions of Protein Synthesis of enzymes, certain hormones and some blood components For maintenance and repair of existing tissues For synthesis of new tissues Sometimes for energy  Proteins account for about 15% of Characteristic of Proteins cell’s overall mass All proteins contains the elements carbon, hydrogen, oxygen and nitrogen, most also sulfur. Other elements, such as phosphorus and iron are essential constituents of certain specialized proteins Casein – the main protein of milk contains phosphorus, an element very important in the diet of infants and children. Hemoglobin – the oxygen transporting protein of blood, contains iron What is a protein? Protein - A naturally occurring, unbranched polymer in which the monomer units are amino acids Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Amino Acids Is an organic compound that contains both an amino (-NH2) group and a carboxy group (-COOH) The amino acids found in proteins are always α- amino acids α-amino acids – is an amino acid in which the amino group and the carboxyl group are attached to the α carbon α-amino acid α-amino acids – is an amino α acid in which the amino group and the carboxyl group are attached to the α carbon α carbon - is the central point in the R Side Chain backbone of every amino acid. - The nature of the side chain distinguishes α-amino acid from each other - Connects the amino group - Side chains can vary in size, shape, acidity, to the acid carboxyl group functional group present, hydrogen bonding ability and chemical reactivity  Nonpolar Amino Acid - Is an amino acid that contains one amino group, one carboxyl group, and a nonpolar side chain Polar Neutral Amino Acid - Is an amino acid that contains one amino group, one carboxyl group, and a side chain that is polar but neutral Standard Amino Acid - one of the 20 α-amino acid normally found in proteins Polar Acidic Amino Acid - Is an amino acid that contains one amino group and two carboxyl group, the second carboxyl group being part of the side chain Polar Basic Amino Acid - Is an amino acid that contains two amino group and one carboxyl group, the second amino group being part of the side chain Nonpolar Amino Acid - Is an amino acid that contains one amino group, one carboxyl group, and a nonpolar side chain Polar Neutral Amino Acid - Is an amino acid that contains one amino group, one carboxyl group, and a side chain that is polar but neutral Polar Acidic Amino Acid - Is an amino acid that contains one amino group and two carboxyl group, the second carboxyl group being part of the side chain Polar Basic Amino Acid - Is an amino acid that contains two amino group and one carboxyl group, the second amino group being part of the side chain Amino acid α-amino acids – is an amino acid in which the amino group and the carboxyl group are attached to the α carbon Nonpolar Amino Acid Polar Neutral Amino Acid Standard Amino Acid Polar Acidic Amino Acid Polar Basic Amino Acid Standard Amino Acids More than 700 different amino acids are known Only 20 of them are called “standard amino acid” and are normally present in proteins All 20 standard amino acids are necessary constituents of human proteins 11 out of 20 standard amino acids can be synthesized from carbohydrates and lipids in the body if a source of nitrogen is also available 9 out of 20 standard amino acids cannot be produce and adequate amount by human body - these 9 standard amino acids are called essential amino acids - Essential amino acids must be obtained from dietary protein Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Essential Amino Acids  Essential Amino Acids Is a standard amino acid needed for protein synthesis that must be obtained from dietary sources because the human body cannot synthesize it in adequate amounts from other substances Complete Incomplete Complementary Dietary Protein Dietary Protein Dietary Protein -is a protein that contains -is a protein that does not contain an adequate -are two or more incomplete all of the essential amino amounts, relative to the body’s needs, of one or dietary proteins that, when acids in the same relative more of the essential amino acids. combined, provide an adequate amount in which the body amount of all essential amino needs them. Limiting amino acids – an essential amino acids relative to the body’s need. acid that is missing, or present in adequate amounts, in an incomplete dietary protein. Acid – Base Properties of Amino Acids Acid – Base Properties of Amino Acids Acid – Base Properties of Amino Acids Zwitter Ion – is a molecule that has a positive charge on one atom and a negative charge on another atom, but which has no net charge Isoelectronic Point – is the pH at which an amino acid exists primarily in its zwitterion form Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Peptides Is an unbranched chain of amino acids Classification of peptides according to the number of amino acid 1. Dipeptide – compound containing two amino acids 2. Tripeptide - compound containing three amino acids 3. Oligopeptide – referred to peptides with 10 to 20 amino acids 4. Polypeptide – a long unbranched chain of amino acids Peptide Bond – is a covalently bond between the carboxyl group of one amino acid and the amino group of another amino acid Amino acid residue – is the portion of an amino acid structure that remains, after the release if H2O, when amino acid participates in peptide bond formation as it becomes part of a peptide chain Peptides Is an unbranched chain of amino acids Peptide Nomenclature Glu – Ser – Ala glutamylserylalanine Glutamate becomes glutamyl Serine becomes seryl Alanine becomes alanine Biochemically Important Small Peptides 1. Small Peptide Hormones 2. Small Peptide Neurotransmitters 3. Small Peptide Antioxidants Small Peptide Hormones 1. Oxytocin – regulates 2. Vasopressin uterine and lactation regulates the excretion of water by the kidneys Another name is ADH (antidiuretic hormone - This name relates of vasopressin’s function in the kidneys, which is to decrease water elimination from the body - Such action is necessary when the body becomes dehydrated Small Peptide Neurotransmitters 1. Enkephalins - are pentapeptide neurotransmitters produced by the brain itself that bind at the receptor sites in the brain to reduce pain - Best known enkephalins are Met-enkephalin and Leu- enkephalin Small Peptide Antioxidants 1. Glutathione – is present in significant concentrations in most cells and is of considerable physiological importance as a regulator of oxidation-reduction reactions Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation -Is an organic compound that - Is an unbranched - Is a peptide in which atleast 40 contains both an amino (-NH2) chain of amino acids amino acid residues are present group and a carboxy group (-COOH) Protein Is a relatively long polypeptide with this, “polypeptide” and protein are often used interchangeably Protein is reserved for peptides with large number of amino acids More than 10,000 amino acids resides in several proteins 400-500 amino acid residues are common in proteins Small proteins contain 40-100 amino acid residues Protein A. Classification of Proteins based on peptide chain present 1. Monomeric protein – is a protein in which only one peptide chain is present 2. Multimeric protein – is a protein in which more than one peptide chain is present. Protein subunits – are peptide chain present in multimeric proteins Protein B. Classification of Proteins based of chemical composition 1. Simple protein – is a protein in which only amino acid residues are present 2. Conjugated protein – is a protein that has one or more non amino acid entities present in its structure in addition to one or more peptide chains. Prosthetic Group - Is a non-amino acid group present in a conjugated protein - These non-amino acid components that are present in a conjugated protein can be organic or inorganic Examples: Lipoproteins, glycoproteins and metalloproteins Protein Protein C. Classification of Proteins based on Structure 1. Primary Protein Structure – is the order in which amino acids are linked together in a protein 2. Secondary Protein Structure – is the arrangement in space adopted by the backbone portion of a protein 3. Tertiary Protein Structure – is the overall three-dimensional shape of a protein that results from the interactions between amino acid chains (R group) that are widely separated from each other within a peptide chain 4. Quaternary Protein Structure – is the organization among the various peptide subunits in a multimeric protein Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Primary protein structure – is the order in which amino acids are linked together in a protein Every protein has its own unique amino acid sequence Involves the order of attachment of the amino acids to each other through peptide bonds Insulin - First protein which primary structure was determined - The hormone that regulates blood-glucose level has 51 amino acids  Insulin - The hormone that regulates blood- Primary protein structure glucose level has 51 amino acids Secondary protein structure – is the arrangement in space adopted by the backbone portion of a protein – the type of interaction responsible for common types of secondary structure is hydrogen bonding between a carbonyl oxygen atom of a peptide linkage and the hydrogen atom of an amino group of another peptide linkage farther along the protein backbone Secondary protein structure 2 Common Types of Secondary Structure 1. The Alpha Helix – is a protein structure in which single protein chain adopts a shape that resembles a coiled spring (helix), with the coil configuration maintained by hydrogen bonds The twist of helix forms a right-handed, or clockwise, spiral The hydrogen bonds between carbonyl and amino groups entities are oriented parallel to the axis of the helix All amino acid R group extends outward from spiral Secondary protein structure 2 Common Types of Secondary Structure 2. The Beta Pleated Sheet – is a protein secondary structure in which two fully extended protein chain segments in the same or different molecules are held together by hydrogen bonds Hydrogen bonds form between oxygen and hydrogen peptide linkage atoms that are either in different parts of a single chain that folds back on itself (intrachain bonds) or between atoms in different peptide chains in those proteins that contain more than once chain (interchain bonds) Secondary protein structure 2 Common Types of Secondary Structure 2. The Beta Pleated Sheet – In molecules where β pleated sheet involves a single molecule, several U- turns in the protein chain arrangements are needed in order to form the structure – The “U-turn structure” is the most frequently encountered type of β pleated sheet structure – The figure shows a representation of the β pleated sheet structure that occurs when portions of 2 different peptide chains are aligned parallel to each other (interchain bond) – The term “pleated sheet” arises from the repeated zigzag pattern in the structure Secondary protein structure Unstructured Protein Segment Is a protein secondary structure that is neither an α helix nor a β pleated sheet “unstructure” is essential to the functioning of many proteins It confers flexibility to proteins,, thereby allowing them to interact with several different substances, an important mechanism for rapid response to changing cellular conditions Secondary protein structure Analogy of Protein Structures Tertiary protein structure – is the overall three-dimensional shape of a protein that results from the interactions between amino acids (R group) that are widely separated from each other within a peptide chain Myoglobin Tertiary structure of the single- chain protein Found mainly in muscle tissue where it serves as an intracellular storage site for oxygen Tertiary protein structure 4 types of stabilizing interactions contribute to the tertiary structure of a protein 1. Covalent disulfide bonds 2. Electrostatic attractions (salt bridges) 3. Hydrogen bonds 4. Hydrophobic attractions ** Tertiary – structure interactions involve the R groups of amino acid while secondary – structure interactions involve the peptide linkages between amino acid residues Tertiary protein structure 4 types of stabilizing interactions contribute to the tertiary structure of a protein 1. Covalent disulfide bonds – the strongest of the tertiary – structure interactions, result from the –SH groups of two cysteine residues reacting with ach other to form covalent disulfide bond 2. Electrostatic attractions (salt bridges) – also called as salt bridges, always involve the interaction between an acidic side chain (R group) and a basic side chain (R group) – electrostatic interaction occurs between the two types of side chains is positive – negative ion – ion attraction Tertiary protein structure 4 types of stabilizing interactions contribute to the tertiary structure of a protein 3. Hydrogen bonds – occur between amino acids with polar R groups – are relatively weak and are easily disrupted by changes in pH and temperature 4. Hydrophobic interactions – result when two non polar side chain are close to each other – the cumulative effect of hydrophobic interaction in tertiary protein can be greater than the effects of a hydrogen bonding Tertiary protein structure 4 types of stabilizing interactions contribute to the tertiary structure of a protein 1. Covalent disulfide bonds 2. Electrostatic attractions (salt bridges) 3. Hydrogen bonds 4. Hydrophobic attractions  Myoglobin Tertiary protein structure Tertiary structure of the single-chain protein Found mainly in muscle tissue where it serves as an intracellular storage site for oxygen Tertiary protein structure Myoglobin Tertiary structure of the single-chain protein Found mainly in muscle tissue where it serves as an intracellular storage site for oxygen The tertiary structure of myoglobin 8 alpha helices, designated A through H, that are connected by short non- helical regions It cab be present in 2 forms; oxymyoglobin (oxygen bound) and deoxymyoglobin (oxygen free) Protein C. Classification of Proteins based on Structure Quaternary protein structure – is the highest level of protein organization – is the organization among the various peptide subunits in a multimeric protein Quaternary protein structure – is the highest level of protein organization – is the organization among the various peptide subunits in a multimeric protein – most multimeric proteins contain an even number of subunits 2 subunits = dimer 4 subunits = tetramer – the subunits are held together by the same types of noncovalent interactions that contribute to tertiary structure (electrostatic interactions, hydrogen bonds and hydrophobic interactions) – Noncovalent interactions that contribute to quaternary structure are weaker and thus more easily disrupted Primary Structure – the sequence amino acids present in a protein’s peptide chain or chains Secondary Structure – the regularly Alpha Helix – hydrogen repeating ordered spatial bonds between every fourth arrangements of amino acid near each amino acids other in protein chain, which result Beta Pleated Sheet – from hydrogen bonds between hydrogen bonds between two carboxyl oxygen atoms and amino side by side chains, or a single hydrogen atoms chain that is folded back on itself Tertiary Structure – the overall three-dimensional shape that results Disulfide bonds from the attractive forces between Electrostatic interactions amino acid side chains (R groups) that Hydrogen bonds are not near each other in the protein Hydrophobic interactions chain Quaternary Structure – the overall three-dimensional shape of a protein Electrostatic interactions consisting of two or more independent Hydrogen bonds peptide subunits, which results from Hydrophobic interactions noncovalent interactions between R groups Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Protein Denaturation – is the partial or complete disorganization of a protein’s characteristic three-dimensional shape as a result of disruption of its secondary, tertiary and quaternary structural interactions Protein Denaturation – the result of denaturation is loss of biochemical activity – some proteins lose all of their three-dimensional structural characteristics upon denaturation, most proteins maintain some three dimensional structures Renaturation – for limited denaturation, it is possible to find conditions under which the effects of denaturation can be reversed – the restoration process in which the proteins are “refolded” *** for extensive denaturation changes, the process is usually irreversible Protein Denaturation Factors that leads to protein denaturation Physical Agent Factor 1. Heat 2. Violent shaking or agitation 3. Hydrostatic pressure 4. UV Radiation Chemical Agent Factor 1. Acid and alkali 2. Organic solvents 3. Salts and heavy metals 4. Altered pH Protein Denaturation Factors that leads to protein denaturation Physical and Chemical Denaturing Protein Denaturation Examples Most dramatic example of protein denaturation occurs when egg white (a concentrated solution of the protein albumin) is poured onto a hot surface The clear albumin solution immediately changes into a white solid with a jellylike consistency Egg white = protein albumin Protein Denaturation Examples A similar process occurs when hamburger juices encounter a hot surface A brown jellylike sold forms When protein-containing foods are cooked, protein denaturation occurs “Cooked” protein is more easily digested because it is easier for digestive enzymes to “work on” Hamburger patty juices encounter a hot denatured protein surface. A brown jellylike solid forms Cooking food also kills microorganism through protein denaturation Protein Denaturation Examples Heat induced denaturation is also used in sterilizing surgical instruments and in canning foods Bacteria are destroyed when the heat denatures their protein Cauterization - Process involves denaturation where heat is used to seal small blood vessels in a surgery Protein Denaturation Examples Yogurt is prepared by growing lactic acid producing bacteria in skim milk The coagulated denatured protein gives yogurt its semi-solid consistency The more protein in milk, the thicker the yogurt The casein (protein) cluster in milk thicken yogurt by unraveling and forming a three-dimensional mesh when exposed to the lactic acid created by culturing Heating milk before culturing denatures the protein and effectively increase the Protein casein in milk amount of protein in the milk that will be available to thicken the yogurt Proteins 1. Characteristics of Proteins 2. Amino Acids 3. Essential Amino Acids 4. Peptides 5. Biochemically Important Small Peptides 6. General Structural Characteristics of Proteins 7. Primary Structure of Proteins 8. Secondary Structure of Proteins 9. Tertiary Structure of Proteins 10. Quaternary Structure of Proteins 11. Protein Denaturation Protein Three dimensional conformation, unique sequence, order, amino acid and structures of protein is significant as it dictates the three dimensional conformation of the folded protein The conformation will determine the function of protein Proteins which: catalyze biochemical reactions are called enzyme are responsible for transportation of metabolites or gases (like oxygen and carbon dioxide) are called transport proteins control metabolic pathways are called regulatory proteins like insulin, hormone receptors are responsible to protect from infection and other toxic substances are called antibodies or defense protein are required to give strength to cells and tissues are called structural proteins are required to carry out mechanical work are called muscle proteins Problem Set #1 1. What is protein? 2. Define peptide and the classification of peptides according to the number of amino acid. 3. Give 5 examples of essential amino acid and its function. 4. What are the 3 biochemically important small peptide and give examples of it. **Write your answers on yellow paper