Enzymes Biochemistry Notes PDF 2024

2nd year Fund Module Enzymes By Dr. Noha M. Abd El-Fadeal Associate Professor of Biochemistry ISNC- 2024  Objective By the end of this Lecture, students should be able to: ◼ Illustrat...

2nd year Fund Module Enzymes By Dr. Noha M. Abd El-Fadeal Associate Professor of Biochemistry ISNC- 2024  Objective By the end of this Lecture, students should be able to: ◼ Illustrate the function of enzymes. ◼ Illustrate different mechanisms of enzyme activation with examples of enzyme activators. ◼ Illustrate different mechanisms of enzyme inhibition with examples of enzyme inhibitors.  What are enzymes? - Enzymes are biological catalyst. - Play a crucial role in the regulation of metabolic pathways - Accelerate the speed of a chemical reaction. - They are not changed or consumed by the reaction A→ B - Enzymes are complex proteins  Properties of Enzymes o Synthesized in the cell but can act either intra or extracellular. o Made of protein. o Are specific. o Speed up reactions. o Not used up during the reaction. o Require optimum conditions at which they work best. o At high temperature they become denatured. Substrate: ( the reactant ) a molecule upon which an enzyme acts. Active site: the region of an enzyme surface to which a substrate binds. The allosteric site: is a site that allows another molecule to either activate or inhibit enzyme activity.  Mechanism of enzyme action The enzyme molecule (E) first combines with a substrate molecule (S) to form an enzyme substrate (ES) complex which further dissociates to form product (P) and enzyme (E) back. Mechanism of action involve 2 models: 1- Lock and Key Model 2- Induced Fit Model  Lock-and-Key model (Enzyme and substrate fit together like a key in a lock) Mechanism: The enzyme’s active site is a specific shape that perfectly matches the substrate. Key Points: - Specificity: Enzyme only binds with a specific substrate. - No Change: The enzyme’s active site does not change shape.  Induced Fit model (Enzyme and substrate interaction induces a change in the enzyme’s shape) Mechanism: The enzyme’s active site adjusts to fit the substrate more precisely upon binding. Key Points: - Flexibility: Enzyme undergoes conformational changes upon substrate binding. - Enhanced Binding: This adjustment improves the fit and catalysis. Listen the video  Cofactors Cofactors: are (Nonprotein molecules) that help some enzymes to perform their function). Two types of cofactors: 1- Metal ions: Mg, Mn, Zn, Fe called cofactors 2- Organic molecules: thermostable, low molecular weight called Coenzymes. Many Coenzymes are derived from vitamins Coenzyme Vitamin precursor Coenzyme A Pantothenic acid (vitamin B5) Pyridoxal B6 phosphate Tetrahydrofolate Folic acid NAD, NADP Niacin (B1) FAD, FMN Riboflavin (B2) ◼ Most coenzymes are linked to enzymes by noncovalent forces. ◼ Those that form covalent bonds with the enzyme and thus do not dissociate from it are called the prosthetic group. ◼ Holoenzyme: refers to the enzyme with its coenzyme. (Enzyme + Coenzyme) ◼ Apoenzyme: refers to the protein portion of the holoenzyme. (only the Enzyme) Listen the video  Enzyme Nomenclature ◼ Name is based on: what with or how -ase it reacts ending Examples To react with lactose. lactase To remove hydrogen from pyruvate. pyruvate dehydrogenase  Classification of enzymes based on the international union of biochemists (IUB) 1-Oxidoreductase -----Catalyzes a redox reaction 2-Transferase-----------Transfer a group 3-Hydrolase-------------Catalyzes hydrolysis reactions 4-Lyase------------------Make or break the double bonds 5-Isomerases------------Rearrange atoms 6-Ligase------------------Join two molecules  Enzyme activity Definition: Enzyme activity is expressed as the number of μmoles of substrate converted to product per minute under specified assay conditions. There are many factors that affect the enzyme activity  Enzyme inhibitors - They are chemicals that reduce the rate of enzymic reactions. - Many drugs and poisons are inhibitors of enzymes. types of inhibition 1- Irreversible inhibition: the inhibitors permanently turn off the enzyme. bind to an enzyme by covalent bond, Example: heavy metals (Hg ++), cyanides. 2- Reversible inhibition: bind to an enzyme by noncovalent bonds so can be removed. (competitive and non competitive).  Two types of reversible inhibition Competitive inhibitors: are chemicals that resemble an enzyme’s normal substrate and compete with it for the active site. Noncompetitive inhibitors: that do not enter the active site, but bind to the allosteric site of the enzyme causing the enzyme to change its shape, which in turn alters the active site independent Site (Allosteric site)  Regulation of enzyme activity The action of enzyme should be allowed only where needed and when needed. Metabolic pathways are usually controlled by regulating the activity of one enzyme, called the rate-limiting or key enzyme, which usually catalyzes an irreversible reaction in the pathway. These enzymes respond to: 1- Feed back regulation. 2- Rates of enzyme synthesis (induction or repression). 3- Allosteric effectors (most common). 4- Covalent modification 1- Feed back regulation: A mechanism where the end product of a metabolic pathway influences the activity of an enzyme involved earlier in the pathway.  2- Rates of enzyme synthesis (induction or repression). - The quantity of an enzyme in the cell is determined by the rates of synthesis and degradation. - Enzyme synthesis is controlled by regulating gene transcription and translation. - Stimulation of enzyme synthesis by this mechanism is called enzyme induction, while inhibition is called enzyme repression. - Since this mechanism depends on protein synthesis, it takes hours or days to show full effect.  3- Allosteric effectors (most common). Allosteric modifiers: Small organic molecules that bind to an enzyme at a site other than the active site (the allosteric site), causing a change in the enzyme’s shape and affecting its activity. If the catalytic site becomes more suitable to the substrate, the substance causing this change is called “positive effector” or allosteric activator. On the other hand, if the catalytic site becomes less suitable to the substrate, the substance causing this change is called “negative effector” or allosteric inhibitor.  Negative effector Positive effector or allosteric inhibitor or allosteric activator 4- Covalent modification Addition or removal of phosphate groups to the enzyme  Enzymes in clinical diagnosis Enzymes may be measured in cells, such as red blood cells, white blood cells, and other tissue cells to detect enzyme deficiency in certain diseases e.g. deficiency of red cell glucose 6-phosphate dehydrogenase in favism.  Plasma enzymes The presence of increased levels of enzymes in plasma may reflects damage to the corresponding tissue. Example: Alanine transaminase (ALT) and Aspartate transaminase (AST) are abundant in the liver. So, the appearance of elevated levels in plasma signals possible damage to hepatic tissue.  Isoenzymes Isoenzymes: are enzymes that catalyze the same reaction but differ in their structure (amino acid sequence), properties (and enzymatic activities. Examples of isoenzymes present in humans are lactate dehydrogenase, creatine kinase and alkaline phosphatase. Many isozymes contain different subunits in various combinations. Example: CK occurs in 3 isoenzymes. Each is a dimer composed of 2 subunits (B & M): CK1 = BB (Brain) CK2 = MB (Cardiac muscle) CK3 = MM (Skeletal muscle)  References Harpers Illustrated Biochemistry, 29th edition, Robert k. Murray, David A. Bender, Kathleen M. Bothman, Victor W. Rodwell. Lange Medical Books/McGraw-Hill Chapter 8, P:78, 82. Biochemistry, 8th Edition, Jeremy M. Berg, John L. Tymoczko, Lubert Stryer. W.H. Freeman & Company, Chapter 7, P:239-273. Lehninger Principles of Biochemistry, 8th Edition, David L. Nelson, Michael M. Cox. W.H. Freeman & Company, Chapter 6, P:175-210.