Pines City Colleges Biochemistry Enzymes Module 4 PDF

Pines City Colleges GENERAL EDUCATION DEPARTMENT First Semester, A.Y. 2024-2025 Course Number: BIOCHEM 101 Course Title: BIOCHEMISTRY Modular Learning Guide #4 Topic: ENZYMES Expec...

Pines City Colleges GENERAL EDUCATION DEPARTMENT First Semester, A.Y. 2024-2025 Course Number: BIOCHEM 101 Course Title: BIOCHEMISTRY Modular Learning Guide #4 Topic: ENZYMES Expected Time of Completion: 3 Hours A. Learning Outcomes 1. Discuss the importance of enzymes 2. List the theories involved in enzyme activity B. Learning Content Overview MLG 4 covers a discussion about a particular type of protein which is an enzyme. You will learn about the functions, properties, classifications and activity of enzymes. Recap/Review of the Past Lesson In MLG 3, you encountered amino acids, peptides, and proteins. One class of protein based on biological significance is enzymes. As a little recap, enzymes were then described as organic catalysts formed by living cells. Catalysts are substances that affect the rate of reactions. They either speed up or slow down chemical reactions. Concept ENZYMES are biochemical catalysts synthesized by the living cell. They facilitate chemical changes and make it possible for the continuous replacement and renewal processes characteristic of all living organisms. They regulate the rates at which physiologic processes take place therefore they occupy central roles in health and disease. Functions: 1. to speed up chemical reactions 2. used in the industry for various purposes: a. Bromelain – meat tenderizer b. Papain – stabilizer in “chill-proof” beer c. Alcalase – detergent additive to remove protein stains d. Pepsin – digestive aid in pre-cooked foods e. Rennin – cheese making f. Trypsin – for wound debridement g. Amyloglucosidase – production of dextrose from starch h. Cellulase – preparation of liquid coffee concentrates i. Invertase – prevention of granulation of soft-centered candies j. Lactase – prevention of formation of lactose crystals in ice cream 3. some enzymes perform a variety of functions: a. Creatine kinase – provides metabolic energy in active muscle tissue b. DNase – breaks mucus in lungs of cystic fibrosis victims c. Collagenase – removes tail from tadpoles when they become frogs d. Pepsin – begins protein digestion in stomach e. Streptokinase – dissolves blood clots CHEMICAL NATURE: 1. colloidal substances 2. protein in nature 1|Page  3. crystalline form PROPERTIES: 1. possess enormous catalytic power – the enzyme can be used again for another catalytic reaction 2. highly specific on: (a) substrate – the substance acted upon by the enzyme (b) type of reaction catalyzed Example: Urease is the specific enzyme for the hydrolysis of urea. Types of Specificity: i. Absolute specificity – this means that the enzyme catalyzes a single reaction and a single substrate ii. Group specificity – this means that the enzyme acts on a particular chemical group iii. Relative specificity – this means that the enzyme acts on a variety of similar compounds at different rates iv. Stereochemical specificity – this means the enzyme acts only on one of the optical isomers 3. have electrical charges which depend on the pH positive (+) for those with pH greater than 7 negative (-) for those with pH less than 7 Portions of an Enzyme: 1. Active Site – functional part of an enzyme 2. Binding Site – portion of the active site that attracts the substrate 3. Catalytic Site – area within the active site of an enzyme that causes catalysis COENZYMES are heat-stable, low-molecular-weight organic compounds required for the activity of enzymes. They are linked to enzymes by non-covalent bonds. There are enzymes that need other substance (called coenzyme) to cause degradation of the substrate. The coenzyme helps by acting as an acceptor for one of the fragments. Apoenzyme refers to the protein portion of the enzyme. When this apoenzyme combines with its coenzyme, a complete enzyme called holoenzyme is formed. INTERNATIONAL CLASSIFICATION OF ENZYMES: (by International Enzyme Commission) 1. Oxido-reductases – enzymes that carry out and influence oxidation-reduction reactions; transfer of hydrogen or electrons 1.1 acts on secondary alcohols 1.2 acts of ketones 1.3 acts on alkenes 1.4 acts on primary amines 1.5 acts on secondary amines 1.6 acts on NADH, NADPH 2. Transferases – enzymes that facilitate the transfer of certain functional groups; removes groups (except hydrogen) and transfer them to acceptor molecules (except water) 2.1 one-carbon groups 2.2 aldehydric or ketonic groups 2.3 acyl groups 2.4 glycosyl groups 2.7 phosphate groups 2.8 S-containing groups 3. Hydrolases – enzymes that causes hydrolysis; catalyze the splitting of a covalent bond and the subsequent addition of H+ and OH- to the 2 fragments of the substrate molecule 3.1 esters 3.2 glycosidic bonds 3.4 peptide bonds 3.5 other C-N bonds 3.6 acyl anhydrides 4. Lyases – enzymes that allow addition to double bonds 4.1 Alkene 2|Page  4.2 ketone/aldehyde 4.3 cyanide 5. Isomerases – enzymes that promote isomerization and also catalyze various intramolecular reactions, resulting in skeletal isomerization 5.1 racemases 6. Ligases/Synthetases – enzymes that aid in the formation of bonds with ATP cleavage 6.1 C-O 6.2 C-S 6.3 C-N 6.4 C-C NOMENCLATURE: 1. Use suffix –ASE preceded by the term which indicates either one of the following: a. The general nature of the substrate Example: lipase is the enzyme acting on lipids b. The actual name of the substrate Example: sucrose is the enzyme acting on sucrose c. The type of reaction catalyzed Example: oxidase is the enzyme which catalyzes oxidation reaction d. Combination of several of these designations Example: xanthine oxidase is the enzyme that catalyzes the oxidation of xanthine 2. Use suffix –LYTIC in case of the hydrolytic enzymes. Example: amylolytic is the enzyme acting on amylose 3. For enzymes which are inactive (called proenzyme or zymogen) the suffix –OGEN is used. Example: pepsinogen is the inactive form of pepsin which is activated by hydrochloric acid 4. The IUB adopted a complex but unambiguous system of enzyme nomenclature which is based on a reaction mechanism. Skeletal Outline of the IUB System: a. Reactions and the enzymes that catalyze them form six classes, each having 4-13 subclasses. b. The enzyme name has 2 parts. The first names the substrate or substrates. The second, ending in –ase, indicates the type of reaction catalyzed. c. Additional information, if needed to clarify the reaction, may follow in parentheses. d. Each enzyme has a code number (EC) that characterizes the reaction type as to class (first digit), subclass (second digit), and sub subclass (third digit). The fourth digit is for the specific enzyme. Example: EC = 2.7.1.1 Class 2 = transferase Subclass 7 = transfer of phosphate Sub subclass 1 = an alcohol is the phosphate acceptor Fourth number 1 = hexokinase The enzyme is also known as ATP: D-hexose-6-phosphotransferase (an enzyme catalyzing phosphate transfer from ATP to the hydroxyl group of carbon 6 of glucose) ENZYME ACTIVITY: 1. Fischer’s Lock and Key Theory – the shape of the active site of the enzyme complements the shape of the substrate. 2. Koshland’s Induced Fit Theory – before the substrate 3|Page  binds to the enzyme, their shapes are uncomplimentary, hence conformational changes are made or induced. The enzyme will adjust its structure to fit the substrate. 3. Adsorption Theory – the big surface area of the enzyme serves to gather in favorable proximity, the different reactants, substrates and cofactors, producing marked local increase in concentration, so collision occurs, leading to specific reactions. 4. Activation by Strain or Bond Distortion Theory – the specific attachment to the enzyme surface induces strain or deformation of the bonds which are broken. Catalytic effectiveness comes from direct enhancement of the bond-breaking or bond-making process. 5. The Functional Groups at the Catalytic Site Theory – at the active site there are amino acid residues or other groupings such as metal ions which can serve as acid or base or as nucleophilic (electron donor) or electrophilic (electron acceptor) residues and these participate in the reactions. All catalytic reactions are brought about by the temporary union of the substrate and the enzyme. The enzyme has an active site on its surface, to which the substrate can fit. The bond of the substrate is strained which causes it to break in order to release fragments, and the enzyme is free to cause another similar reaction. Factors that Affect Enzyme Activity: 1. Enzyme concentration – increased enzyme concentration, increases the enzyme activity. 2. Substrate concentration – the velocity increases as the substrate concentration is increased up to a point where the enzyme is said to be “saturated” with substrate. 3. Temperature – raising the temperature increases the rate of an enzyme-catalyzed reaction, this holds only over a strictly limited range of temperatures. Maximum activity for enzymes happens at the optimum temperature of 37°C to 40°C. When the temperature is below the optimum, enzyme activity slows down while when it is above the optimum, enzyme activity doubles or triples. However, the temperature should not reach 70°C otherwise the enzyme will be denatured and the activity stops. 4. pH – enzyme activity is measured at several pH values, optimal activity typically is observed between pH values of 5 and 9. Example: lactase works best when pH is 5.7 and trypsin at 7.8 Note: A few enzymes (example: pepsin = 1.2 to 2.2) are active at pH values outside the range. 5. Presence of cofactors – the cofactors add up to the activity for faster reaction. Cofactors are usually metals like copper, iron, zinc, manganese, and cobalt 6. Light and other physical agents Blue and red light increases the activity of salivary amylase Ultraviolet rays and radium exert inhibitory effect Violent shaking destroys the enzyme activity 7. Presence of activators – activators are needed to transform inactive enzymes into active ones. Example Hydrochloric acid (HCl) activates pepsinogen into active pepsin; enterokinase activates trypsinogen into trypsin 8. Products of reaction – accumulation of products decreases the rate of enzyme activity due to the reversibility of enzyme action. 9. Presence of inhibitors – inhibitors block the enzyme activity by forming compounds with them. a. reversible inhibition 4|Page  b. irreversible inhibition 10. Time – there cannot be an optimum hydrogen ion concentration nor an optimum temperature independent of time. Optimum temperature is effective only if time is measured in hours. C. Learning Activities This activity is equivalent to 20 points. 1. Differentiate cofactors from coenzymes. 2. Search for an enzyme code and give the corresponding class, subclass and sub subclass of this enzyme with this code. Give also the name of this enzyme. D. Resources 1. Enzyme https://www.britannica.com/science/enzyme 2. How Do Enzymes Work? https://www.livescience.com/45145-how-do-enzymes-work.html E. Assessment The assessment for this module will be announced in class. F. References Harvey, Richard and Denise Ferrier. (2017). Lippincott’s Illustrated Reviews: Biochemistry (7th edition). U.S.A.: Wolters Kluwer. Murray, Robert K. et al. (2015). Harper’s Illustrated Biochemistry (30th edition). U.S.A.: McGraw-Hill Book Company. Prepared by Cecilia L. Cabanilla Instructor 5|Page