Cell And Molecular Biology Past Exam Paper 2024-2025 PDF

Institute of Biological Sciences CELL AND MOLECULAR BIOLOGY Academic Year: 1st Semester 2024-2025 Course code: BIO47 Instructor: Eliazar Alumbro Peniton Jr. LPT, Ph.D. Degree: PhD in Convergence Science, major...

Institute of Biological Sciences CELL AND MOLECULAR BIOLOGY Academic Year: 1st Semester 2024-2025 Course code: BIO47 Instructor: Eliazar Alumbro Peniton Jr. LPT, Ph.D. Degree: PhD in Convergence Science, major in Life Science Email Address: [email protected] Contact number: 09152791506 Consultation hours: MWF. 14:00-16:00; TTH 08:00-10:00 UNIT 1: OVERVIEW OF CELL STRUCTURE AND FUNCTION HOW CELLS OBTAIN ENERGY FROM FOODS 04 Content: Objectives: 1. To understand the principles of energy transformation I. Bioenergetics in biological systems. 2. To explore the structure, function, and kinetics of II. Enzymes enzymes as biological catalysts. III. Metabolism 3. To examine the biochemical processes that occur within living organisms. IV. Glycolysis 4. To analyze the glycolytic pathway and its significance in cellular respiration. V. Citric Acid Cycle 5. To investigate the citric acid cycle's role in energy VI. Electron Transport Chain production and metabolic integration. 6. To describe the electron transport chain's VII. Oxidative Phosphorylation structure, function, and importance in cellular respiration 7. To elucidate the process of oxidative phosphorylation and its significance in energy production. 2 BIOENERGETICS - The study of the various types of energy transformations that occur in living organisms. - A living cell bustles with numerous activities. - To maintain such high level of activity, a cell must acquire and expend energy - Energy is defined as the capacity to do work. - The energy of the universe is constant (Free energy) 3 Laws of Thermodynamics Thermodynamics - is the study of the changes in energy that accompany events in the universe. 1. Law of conservation of energy - energy can neither be created nor destroyed. - can be converted (transduced) from one form to another. - Ex. mechanical energy to electrical energy chemical energy is converted to electrical energy 4 Laws of Thermodynamics 2. Law of Entropy - in any natural process, the total entropy of a system and its surroundings will always increase. - state of higher energy to a state of lower energy. - in any energy transformation, there is a decreasing availability of energy for doing additional work. 5 Laws of Thermodynamics 2. Law of Entropy - in any natural process, the total entropy of a system and its surroundings will always increase. - state of higher energy to a state of lower energy. - in any energy transformation, there is a decreasing availability of energy for doing additional work. 6 Laws of Thermodynamics 2. Law of Entropy - the entropy of a system approaches a constant value as the temperature approaches absolute zero. - Ex. As the temperature of the ice further reduces, the movement of the molecules in them is restricted further and the entropy of the substance goes on decreasing. 7 ENZYME - Large molecules that increase the rate of chemical reactions without themselves undergoing any change. - Are biological catalyst in cells as the chemical factories. - Compound necessary for human organisms are synthesized within the cells. - Majority are globular proteins except ribozymes – made up of ribonucleic acids. 8 ENZYME - They are extremely effective, increasing reaction rates by anywhere from 109 to 1020 times. - Most are extremely specific. - Every organism has many enzymes—more than 3000 in a single cell 9 Enzymes Specificity - The enzyme urease catalyzes only the hydrolysis of urea and not that of other amides, even closely related ones. 10 Enzymes Specificity - The enzyme trypsin catalyzes the hydrolysis of the peptide bonds of protein molecules—but not every peptide bond, only those on the carboxyl side of lysine and arginine residues 11 Enzymes Specificity - The enzyme arginase hydrolyzes the amino acid L-arginine (the naturally occurring form) to a compound called L-ornithine and urea but has no effect on its mirror image, D-arginine. 12 Enzymes Specificity - Enzymes are distributed according to the body’s need to catalyze specific reactions. Protein-splitting enzymes (proteases) are in the blood, ready to promote clotting. Digestive enzymes, which also catalyze the hydrolysis of proteins, are located in the stomach and pancreas. - Some enzymes are localized according to the need for specific reactions within the cells. Enzymes that catalyze the oxidation of compounds in the citric acid cycle are located in the mitochondria. Lysozyme in the cytoplasm to catalyzes bacterial cell walls. 13 Enzymes Activity - is a measure of how fast an enzyme is able to catalyze the reaction. - μmoles of product per time. - The molecule being acted on is called the substrate. - Enzyme activity is affected by the concentration, temperature, and pH. 14 Enzymes Activity A. Enzyme substrate and concentration - If the concentration of substrate is constant and the concentration of enzyme increases, the rate increases linearly. - If the enzyme concentration doubles, the rate doubles as well. 15 Enzymes Activity A. Enzyme substrate and concentration - if the concentration of enzyme is constant and the concentration of substrate increase, the rate does not increase continuously. - A saturation point is reach thus forming a saturation curve. 16 Enzymes Activity B. Temperature - Temperature affects enzyme activity because it changes the conformation of the enzyme. - Enzymes activity depends on optimum temperature. 17 Enzymes Activity C. pH - Within a narrow pH range, changes in enzyme activity are reversible. - However, at extreme pH values (either acidic or basic), enzymes are denatured irreversibly, and enzyme activity cannot be restored by changing back to the optimal pH. 18 METABOLISM - is the sum of all the chemical reactions involved in maintaining the dynamic state of the cell. - May affect cancer cell growth, circadian rhythms, and longevity Catabolism- is the process of breaking down molecules to supply energy. Anabolism - The process of synthesizing (building up) molecules 19 Stages of Metabolism Catabolic Pathway Catabolic purposes: 1. Fulfills energy needs 2. Provides raw materials to build new compounds. ✓ Foods (carbohydrates, fats, and proteins) must be hydrolyzed into small molecules. 21 Catabolic Pathway 22 The Reaction of Glycolysis Glycolysis is the specific pathway by which the body begins to get energy from monosaccharides. A. Glucose is converted to Pyruvate - Occur in the cytoplasm - Aerobic pathway - pyruvate enters the citric acid cycle and undergoes oxidative phosphorylation - Anaerobic pathway - pyruvate converts to lactate 23 The Reaction of Glycolysis 24 The Reaction of Glycolysis B. Entrance to the Citric Acid Cycle 25 Glycerol Catabolism Fats or complex lipids must be hydrolyzed to glycerol - A net yield of 15.5-17.5 ATP molecules from each glycerol molecule. - 5.5 ATP per carbon atom. 26 β–Oxidation of Fatty Acids - Occurs in the cytosol. - The β-carbon is oxidized. - Fatty acid is activated to fatty acyl-CoA 27 27.5 β–Oxidation of Fatty Acids - β-Oxidation cleaves off two-carbon units or every two carbons. 28 SUMMARY OF CATABOLISM 29 Biochemical pathway - A series of consecutive biochemical reactions. - Catabolic pathways - is to convert the chemical energy in foods to molecules of ATP. Citric acid cycle Electron transport chain 30 Mitochondria and Their Role in Metabolism - site for catabolic pathways. - Enzymes for CAC are in the matrix 31 The Principal Compounds of Catabolic Pathways A. Agents for storage of energy and transfer of phosphate groups. Glycosidic bond - Adenine and sugar Phosphoric ester bond - Phosphate and sugar Phosphoric anhydride bond - Phosphate to phosphate 32 The Principal Compounds of Catabolic Pathways A. Agents for storage of energy and transfer of phosphate groups. Phosphoric ester bond - 3.4 kcal/mol Phosphoric anhydride bond - 7.3 kcal/mol Human body used up to 40 kg of ATP every day. - 40-60% total calorie content of food. 33 The Principal Compounds of Catabolic Pathways B. Agent for Transfer of Electrons in Biological Oxidation– Reduction Reactions NAD+ (nicotinamide adenine dinucleotide) FAD (flavin adenine dinucleotide) 34 The Citric Acid Cycle - Catabolism begins with the two-carbon atom molecule. - The acetyl portion of acetyl coenzyme A. Step 1: Acetyl coenzyme A enters the cycle by combining with a C4 compound called oxaloacetate: 35 The Citric Acid Cycle Step 2: The citrate ion is dehydrated to cis-aconitate, after which the cis- aconitate is hydrated, but this time to isocitrate instead of citrate: 36 The Citric Acid Cycle Step 3: The isocitrate undergoes oxidation and decarboxylation at the same time: 37 The Citric Acid Cycle Steps 4 and 5: Next, a complex enzyme system removes another CO2 once again from the original oxaloacetate portion rather than from the acetyl-CoA portion: 38 The Citric Acid Cycle Step 6: In this step, succinate is oxidized by FAD, which removes two hydrogens to give fumarate. 39 The Citric Acid Cycle Step 7: The fumarate is now hydrated to give the malate ion in an addition hydration reaction: 40 The Citric Acid Cycle Step 8: In the final step of the cycle, malate is oxidized to give oxaloacetate. 41 Energy Yield From Aerobic Metabolism 42 The Energy Yield from Glucose Catabolism 43 The Energy Yield from Catabolism Stearic acid 44 45 Electron Transport Chain Reduced coenzymes NADH and FADH2 are end products of the citric acid cycle. carry hydrogen ions and electrons, therefore, have the potential to yield energy when these combine with oxygen to form water: 46 Electron Transport Chain Complex I - Oxidizes NADH and reduces the Coenzyme ubiquinone (CoQ). - Release 2H+ 47 Electron Transport Chain Complex II - FADH will be oxidize - Transfer of electron to CoQ. - No pumping of 2 protons due to insufficient energy and appropriate channel. 48 Electron Transport Chain Complex III - Delivers electron from CoQH2 to cytochrome c. - Cyt c moves laterally in the intermembrane space. 49 Electron Transport Chain Complex IV - An integral protein complex. - Movement of electron from Cyt c to Cyt a to Cyt a3. - Then transferred to the oxygen molecule. - Oxidize enzymes take up two H+ - Formation of water molecule 50 Electron Transport Chain Complex IV - Pumped of H+ - Total pumped ions in the intermembrane spaces - Six H+ ions per NADH - Four H+ ions per FADH 51 Chemiosmotic Pump and ATP Production Proton-translocating ATPase - located in the inner membrane of the mitochondria. - propels the proton back from higher to lower concentration gradient. - Catalyze ADP to ATP 52 Chemiosmotic Pump and ATP Production Proton-translocating ATPase - F0 “rotor”, proton channel. - Oxygen has two functions: - Oxidize NADH and FADH. - Produce water and convert ADP to ATP - Oxidative phosphorylation 53 PHOTOSYNTHESIS AND RESPIRATION 54 ENZYMES AND ENERGY TRANSFER photosynthesis – anabolic CO2 + H2O + radiant energy → CH2O respiration – catabolic CH2O → CO2 + H2O + energy Oxidation-reduction reactions electron (energy) transfer from one molecule to another 55 ENZYMES AND ENERGY TRANSFER Oxidation the loss of one or more electrons (e-) involves the removal of e- from a compound, a proton may follow (dehydrogenation) Reduction the gain of one or more electrons involves the addition of e-(s) to a compound, a proton is added (hydrogenation) 56 THE ESSENCE OF PHOTOSYNTHESIS energy from sunlight is converted into chemical bond energy in the form of carbohydrates 57 PRINCIPAL INGREDIENTS carbon dioxide (CO2) water light chlorophyll several types all magnesium containing molecules forms light harvesting complex (photosynthetic unit) 250-400 pigment molecules 58 PRINCIPAL INGREDIENTS CO2 atmosphere: 78% nitrogen, 21% oxygen, 1% mixture common gases 0.037% CO2 Water 1% of water absorbed by plants is used in photosynthesis sole source of the oxygen released 59 PRINCIPAL INGREDIENTS violet to blue and red-orange to red used most extensively green range reflected leaves about 80% of the visible light absorb 60 EFFECT OF LIGHT 61 CHLOROPHYLL Chl a – blue-green, C55H72MgN4O5 Chl b – yellow-green, C55H70MgN4O6 62 63 MAJOR STEPS IN PHOTOSYNTHESIS I. The Light reactions a)reactions take place in thylakoid membranes of chloroplast light required b)water split (photolysis), producing H+ and electrons, O2 gas released c) ATP created d)NADPH + H+ created 64 MAJOR STEPS IN PHOTOSYNTHESIS II. The Dark reactions (Calvin cycle) a)Reactions take place in stroma of chloroplast light not required, hence "dark" reactions b)Calvin cycle 1) CO2 from air combined with 5-carbon sugar (RuBP) 2) glucose formed thru several reaction steps 65 66 LIGHT-DEPENDENT REACTION - Non-cyclic photophosphorylation - Occur in the thailakoid - Photosystem II - Reaction center (P680) - 2 water molecule - Four H electron is removed - Two O2 atom is released. - Electron is light-energized 67 LIGHT-DEPENDENT REACTION - Plastoquinone (primary electron acceptor) - Passes the b6-f complex - Pump proton into thailakoid space - Plastocyanin (pC) carries electron to Photosystem I 68 LIGHT-DEPENDENT REACTION - Photosystem I - Reaction center (P700) - Arrived electron contain half of its light-excited energy - Absorb photon from light to boost electron energy - Iron-sulfur protein - Ferredoxin (electron acceptors) - NADP reductase catalyzed electron to form NADPH 69  photosystem – light-harvesting complex found in chloroplasts about 250 - 400 pigment molecules 70 LIGHT-INDEPENDENT REACTION - Ribulose 1,5-biphosphate (RuBP) - CO2 binds to RuBP (Carbon fixation) - Ribulose biphosphate carboxylase (rubisco) - Two three-carbon phosphoglycerate 71