Lecture # 6: Proteins & Enzymes (Chapter 2) Objectives: Protein of influenza virus Antibody 1- Discuss protein structure and functions. 2- Discuss protein denaturation. 3- Explain how enzymes function.

Proteins are polymers of aminoacids The word protein is derived from the Greek word proteios, meaning “of first importance” Proteins ate the most versatile molecules in the body Proteins are polymers of aminoacids

Aminoacids R Aminoacid Fatty acid Carboxylic acid group Amino group Aminoacid Fatty acid They are hydrocarbon chains (R) with an amino group and a carboxylic acid group linked by a central carbon with an hydrogen attached to it Aminoacids What makes the difference between different aminoacids is the side chain (R) attached to the central carbon

20 amino acids are used to make all the proteins and they are identical except for the radical (R) group

DEHYDRATION SYNTHESIS Dipeptide Synthesis DEHYDRATION SYNTHESIS Dipeptide H2O + Peptide bond Dehydration synthesis creates a peptide bond that joins amino acids

Dipeptide Synthesis Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H O H O + N C C N C C H OH H OH R1 R2 Amino acid 1 Amino acid 2 A dipeptide H O H H O + N C C N C C H2O H OH R1 H R2 (b) Peptide bond Dehydration synthesis creates a peptide bond that joins amino acids

Peptides named for the number of amino acids: Dipeptide Peptide: It is any molecule composed of two or more amino acids joined by peptide bonds Peptides named for the number of amino acids: Dipeptides have 2 Tripeptides have 3 Oligopeptides have fewer than 10 to 15 Polypeptides have more than 15 Proteins have more than 50 A proteins is a large folded chain of more than 50 aminoacids (usually from 50 to 10,000 aminoacids)

Protein of influenza virus Conformation: It is the unique three dimensional shape of protein crucial to function Protein of influenza virus Antibody The antibody helps disable the virus by binding with it. The antibody is able to carry out this binding because it has a shape that is complementary to that of the virus molecule Proteins have three to four levels of structural complexity: 1- Primary structure 3- Tertiary structure 2- Secondary structure 4- Quaternary structure

Protein Shape Proteins have four levels of structural complexity: Primary structure It is the protein’s sequence of aminoacids, which is encoded in the genes. Secondary structure It is the arrangement of the aminoacid chain due to hydrogen bonds between atoms at different parts of the chain. Tertiary structure It is the complex bending and folding that gives a protein its final tridimensional shape of globular or fibrous shapes. It is the association between two or more peptide chains to form a protein complex. Quaternary structure

Primary structure It is the protein’s sequence of aminoacids, which is encoded in the genes.

Secondary structure The way that aminoacid chains are arranged in the space due to hydrogen bonds between the aminoacids next or near to each other d O - d H + d O - d H + d H + O -

Tertiary structure It is the complex bending and folding that gives a protein its final tridimensional shape of globular or fibrous shapes

Fibrous proteins: They form extended sheets or strands. They are tough, durable, and generally insoluble in water. They usually play structural roles

Globular proteins: They are compact, generally rounded, and readily disperse in water forming a colloid

Quaternary structure It is the association between two or more peptide chains to form a protein complex Antibodies

Four Levels of Protein Structure

Conformation: It is the unique three dimensional shape of protein crucial to function Proteins have the ability to reversibly change their conformation: Enzyme function Muscle contraction Opening and closing of cell membrane pores Denaturation: It is the extreme conformational change that destroys function Extreme heat or pH can denature the proteins

Conjugated Proteins: They are proteins that contain a non-amino acid moiety called a prosthetic group Hemoglobin contains four complex iron containing rings called a heme moieties Heme moieties

Protein Functions 1- Structure 2- Communication 3- Membrane Transport keratin – tough structural protein gives strength to hair, nails, and skin surface collagen – durable protein contained in deeper layers of skin, bones, cartilage, and teeth 2- Communication some hormones and other cell-to-cell signals receptors to which signal molecules bind ligand – any hormone or molecule that reversibly binds to a protein 3- Membrane Transport channels in cell membranes that governs what passes through carrier proteins – transports solute particles to other side of membrane turn nerve and muscle activity on and off

5- Recognition and Protection 4- Catalysis enzymes 5- Recognition and Protection immune recognition antibodies clotting proteins 6- Movement motor proteins - molecules with the ability to change shape repeatedly 7- Cell adhesion proteins bind cells together immune cells to bind to cancer cells keeps tissues from falling apart

Enzymes and Metabolism

Net energy released by reaction REACTANTS PRODUCTS HYDROLYSIS ENERGY Exergonic reaction PRODUCTS Glucose + Fructose Sucrose REACTANTS Energy hill Net energy released by reaction ENERGY

Net energy released by reaction Most chemical reactions do not occur or occur very slowly spontaneously Sucrose REACTANTS Total released energy ENERGY Activation energy PRODUCTS Glucose + Fructose Sucrose REACTANTS Activation energy Net energy released by reaction

Activation Energy: The amount of energy required to start a chemical reaction Many reactions needs a great amount of energy for activation They have a high activation energy To provide this amount of energy, the temperature will increase to values that would damage the cells For example: To digest starch in the laboratory, you must boil it in an acid solution. We could not tolerate these conditions in our body However, the human organism digest starch with the help of enzymes.

SUBSTRATE High activation energy 1000 C Enzyme Lower activation energy SUBSTRATE 370 C A B REACTANTS SUBSTRATE PRODUCTS A + B Enzymes: They are proteins that bind to the reactants and lower their activation energy

Enzymes and Activation Energy Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Activation energy Activation energy Net energy released by reaction Net energy released by reaction Energy level Free energy content of reactants Energy level of products Time Time (a) Reaction occurring without a catalyst (b) Reaction occurring with a catalyst

Enzymatic Reaction Steps The substrate approaches the active site on enzyme molecule 1 Sucrose (substrate) 1 Enzyme and substrate O Active site: Active site It is the portion of an enzyme that binds with and transforms a substrate Sucrase (enzyme) 2 The substrate binds to the active site forming the enzyme-substrate complex 2 Enzyme–substrate complex This binding is highly specific. The substrate fit a particular enzyme like a lock and key. This selectivity is called enzyme-substrate specificity O The enzyme breaks the covalent bonds between monomers in substrate by adding H+ and OH- from water (hydrolysis) 3 Glucose Fructose 3 Enzyme and reaction products The reaction products are released: glucose and fructose The enzyme remains unchanged and is ready to repeat the process Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

One enzyme molecule can consume millions of substrate molecules per minute The fastest-working enzymes can carry out 100,000 chemical transformations per second, without themselves being changed Factors that change enzyme shape: The pH and temperature alters or destroys the ability of the enzyme to bind to substrate. The enzymes vary in optimum pH: - salivary amylase works best at pH 7.0 - pepsin works best at pH 2.0 The temperature optimum for all human enzymes is the body temperature (37 degrees C)

Cofactors and Coenzymes They are inorganic substances that are required by some enzymes They bind to enzyme and induces a change in its shape, which activates the active site, which is essential to function About 2/3rds of human enzymes require a nonprotein cofactor Some cofactors are iron, copper, zinc, magnesium and calcium ions Coenzymes: They are organic cofactors that facilitate the work of the enzymes. Many coenzymes are derived from water-soluble vitamins (niacin, riboflavin) Riboflavin Niacin They accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

Metabolic Pathway: It is a chain of reactions, with each step usually catalyzed by a different enzyme Enzyme 1 Enzyme 2 Enzyme 1 Enzyme 2 Coenzyme Coenzymes accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

A B C D Metabolic Pathway: It is a chain of reactions, with each step usually catalyzed by a different enzyme. Intermediates A B C D Initial reactant Product Enzyme 1 Enzyme 2 Enzyme 3 A is initial reactant, B+C are intermediates and D is the end product. Enzyme 1 Enzyme 2 Enzyme 3 Intermediates