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Enzymes Harriet, Lauren and Eliza What is an enzyme? ‘A substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction’ Enzymes continued… Enzyme – Enzymes are large molecules that speed up the chemical reactions inside cells. Each type of enzyme does one specific job. Biological catalysts Due to enzymes being a biological catalyst, they speed up the rate of reaction without being used up. The reaction Due to its interaction with the substrate, it means that the reaction where the substrate becomes the products can take place without harsh environmental conditions, therefore the cell is not damaged. Lock and Key Enzymes are also proteins that are folded into complex shapes that allows smaller molecules to fit into them. Enzymes can be used to break down food into nutrients. What is the structure of an enzyme? Enzymes are proteins that consist of chains of amino acids connected together by peptide bonds. The sequence of amino acids within is distinct in each enzyme and this is what determines the unique three dimensional shape in which the chains are folded. This 3D shape is what determines the activities of the enzyme. An enzyme is a globular protein. Many enzymes also contain an extra non-protein component called a cofactor or coenzyme, this may be an organic molecule or a metal ion. Why is an enzyme specific for one substrate? How is this achieved? An enzyme is specific for one substrate because the active site has to be the right shape for the substrate molecules to fit into. This means that enzymes have a high specificity for their substrate. This is achieved because the amino acid chains are unique so the way that they bond and fold will always be different meaning that the active site will be specific. a substance produced by a living organism which acts as a biological catalyst which interacts with substrate molecules to facilitate chemical reactions. • Enzymes are made up of amino acids which are linked together via peptide bonds in a chain. The resulting amino acid chain is called a polypeptide or protein. The specific order of amino acids in the protein is encoded by the DNA sequence of the corresponding gene • Because of the hydrogen in the amino group and the oxygen in the carboxyl group, each amino acid can hydrogen bond with each other and this means that the amino acids in the same chain can interact. Polypeptide chains are folded or pleated into different shapes, called their Secondary Structure. Two common examples of secondary structures are Alpha Helices and Beta Pleated Sheets. Secondary structure is held together by many Hydrogen bonds, overall giving the shape great stability. • As a consequence of the folding-up of the 2D linear chain in the secondary structure, the protein can fold up further and in doing so gains a threedimensional structure. This is its tertiary structure Tertiary structure is held together by four different bonds and interactions: • Disulphide Bonds • Ionic Bonds • Hydrogen Bonds • Hydrophobic and Hydrophilic Interactions • The enzyme's active site binds to the substrate. Since enzymes are proteins, this site is composed of a unique combination of amino acids. Each amino acid can be large or small; weakly acidic or basic; hydrophilic or hydrophobic; and positively-charged, negativelycharged, or neutral. The positions, sequences, structures, and properties of create a very specific chemical environment within the active site. A specific chemical substrate matches this site like a jigsaw puzzle piece and makes the enzyme specific to its substrate Metabolism What is metabolism? Types of metabolism: Metabolism is the rate of chemical reactions in cells Vmax – Maximum rate of reaction Catabolic This is the breaking down of molecules into smaller units + energy Anabolic Construct molecules from smaller units Needs energy from the hydrolysis of ATP Role of enzymes What are enzymes? Enzymes are biological catalysts What is a catalyst: A catalyst provides an alternate reaction pathway that has a lower activation energy Factors Affecting Temperature Denatured pH Breaks the hydrogen and Ionic Bonds Concentration Enzyme-Substrate complexes Inhibitors Non competitive inhibitor – An inhibitor that binds to an enzyme at an allosteric site Competitive inhibitor - An inhibitor that competes with substrate to bind to active site on an enzyme LOCK AND KEY HYPOTHESIS ACTIVE SITE AND SUBSTRATE - The active site is an area within the tertiary structure of an enzyme - It has a complementary shape to the specific substrate molecule - The active site never changes its shape to fit a substrate – there is a specific substrate shape for each active site THE PROCESS Active site + substrate = enzyme-substrate complex = enzyme + products - The substrate binds to the active site where an enzyme-substrate complex is formed - The substrate then reacts because it is held in such a way by the enzyme that the right atom groups are close enough to react. The active site contains R-groups that also interact with the substrate, forming temporary bonds. These bonds put strain on the bonds within the substrate which helps the reaction along - Due to this reaction products are formed in an enzyme-product complex - The products are released from the active site – leaving the enzyme unchanged and able to take part in other reactions What is the Induced Fit Hypothesis? By Eva & Neve Induced Fit Hypothesis: More recently, evidence from research into enzyme action suggests the active site of the enzyme actually changes shape slightly as the substrate enters. This is called the induced- fit hypothesis and is a modified version of the lock and key hypothesis. Induced Fit Hypothesis: The initial interaction between the enzyme and substrate is relatively weak, but these weak interactions rapidly induce changes in the enzymes tertiary structure that strengthen binding, putting strain on the substrate molecule. This can weaken a particular bond or bonds in the substrate, therefore lowering the activation energy for the reaction. Induced Fit Model Intracellular Enzymes By Mr Bullock & Archie Brydon OBE What is an intracellular enzyme??? • An enzyme that functions within the cell in which it was produced. • Majority of enzymes fall within this category. • Intracellular enzymes are not as effective as extracellular. (Extracellular enzymes are up to 25% more efficient in breaking down the substrate) Catalase • Catalase is a common intracellular enzyme found in nearly all living organisms exposed to oxygen (such as bacteria, plants, and animals). • Breaks Hydrogen Peroxide down into water and oxygen. About catalase: • Catalase is a natural enzyme found primarily in the liver of animals. • It is the fastest acting enzyme known. • It is an important part in the bodies antioxidant defences. The reaction. • Hydrogen peroxide is toxic to cells because it reacts with the metal ions found in proteins, causing considerable damage to the structure of the protein in the process. • This is where catalase is useful to the cell, since it decomposes hydrogen peroxide • 2H2O2→2H2O+O2 • Catalase is a tetramer of four polypeptide chains, each approximately 500 amino acids long. One molecule of catalase can decompose millions of hydrogen peroxide molecules each second. Extracellular Enzymes What are extracellular enzymes? Why are they needed? • Enzymes that work outside of the cell • The enzymes are released to break down large nutrient molecules into smaller molecules. This is because the larger molecules cannot enter the cells through the cell surface membrane. • The enzyme breaks down proteins that are too big to enter the cell, into glucose and amino acids that are small enough to be absorbed. Amylase • The enzyme involved in digestion, where starch is broken down into maltose. • It is produced in the salivary glands and pancreas and is released in saliva in the mouth to break down food. Trypsin • It is a protease- an enzyme that catalyses the digestion of proteins into smaller peptide. • It is produced in the pancreas and released in pancreatic juice into the small intestine. • These can then be broken down into amino acids by other protease that can then be absorbed by cells or into the blood stream. Cofactors and Coenzymes Jess & Poppy Some enzymes need a nonprotein ‘helper’ component in order to carry out the function as a biological catalyst. Cofactors • Inorganic ions • Can transfer atoms or groups from one reaction to another or form part of the enzymes active site • Obtained via the diet as minerals including… iron, calcium, chloride, and zinc ions. For example, the enzyme amylase which catalyses the breakdown of starch – contains a chloride ion which is necessary for the formation of a correct active site. Coenzymes Alcohol dehydrogenase • Organic molecule • Usually derived from vitamins B3 - a class of organic molecule found in the diet. • For example, vitamin B3, is used to synthesise NAD (nicontinamide adenine dinucleotide) which is a coenzyme responsible for the transfer of hydrogen atoms between molecules involved in respiration. • NADP also derived from vitamin B3. H+ Ethanol, H+, and NADH are released from the active site Prosthetic Groups What is a prosthetic group? A non-protein component of a conjugated protein. They are required by certain enzymes to carry out their catalytic functions. The prosthetic group makes them ‘active’. They are tightly bound to form a permanent feature of the protein. This is what makes them a prosthetic group, not a cofactor. In an enzyme, prosthetic groups are often involved in the active site. Vitamins are a common prosthetic group, which is why they are important in the human diet. Inorganic prosthetic groups, however, are usually transition metals. Examples: Haemoglobin has a prosthetic group of iron (Fe) ions. The iron helps to transfer oxygen and carbon dioxide. Carbonic Anhydrase has zinc (Zn2+ ) ions. This is used for the metabolism of carbon dioxide. Precursor activation This is the term used when certain enzymes are produced in an inactive form. Bry + Ella Why does this happen? • This is particularly useful for enzymes that might cause damage to a cell in its active state • It is also the case for any enzyme where their action needs to be controlled and can only be activated in certain conditions What happens • Enzymes often need to undergo a change in shape (particularly in the active site to allow a reaction to occur) to activate • This is regulated by the cofactor – a molecule that is not the substrate • Before: inactive apoenzyme • After: complete and catalytically active holoenzyme Zymogens and Proenzymes • Sometimes, the change of shape of an enzyme is brought about by the action of another enzyme • Example • Protease breaks down the bonds in a molecule Or • Change in condition – pH or temperature • Example • Inactive pepsinogen is released into the stomach to digest proteins the acid pH transforms the enzyme into pepsin - an active enzyme • This protects the body tissues against the digest action of the enzyme The importance of precursor activation • Blood clotting • Clotting factor X relies on the cofactor vitamin K for activation • Factor X cleaves certain bonds in prothrombin to transform it into thrombin • Thrombin catalyses the conversion of soluble fibrinogen into soluble fibrin fibres which with platelets form a blood clot