Biochemistry ATP and Heme Synthesis Quiz

Final Exam Information

• Duration: 2 hours
• Exam type: Closed-book
• Calculators: Bring non-programmable calculators according to HKMU approved list
• Topics covered: Lectures 1-11 (mainly focus on lectures 6-11)
• Weight: 50% of overall grade

Final Exam Structure

• Multiple Choice Questions (20%): 20 questions, each worth 1 mark
• Short Questions (40%): 7 questions, marks vary by question
• Long Questions (40%): 5 questions, each worth 10 marks, select 4 to answer

Example of Short Questions

• Name the metabolite or enzyme from 1 to 6 in the provided diagram of the TCA cycle (diagram on page 4)
• Name five important enzymes in oxidative phosphorylation. Give one disorder related to dysfunction of oxidative phosphorylation. (page 5)
• What are the overall products of the TCA cycle? How do these products contribute to energy production? (page 5)
• Describe the four levels of protein structure. (page 5)

Example of Long Questions

• A 45-year-old male presents to the emergency department after several days of severe fasting and significant weight loss. He has a type 2 diabetes history and reports fatigue, weakness, and confusion. Blood tests reveal elevated ketone levels and high blood urea nitrogen. Identify two metabolic processes regarding the elevated ketone levels and high blood urea nitrogen in this patient. (page 6)
• How will the activity of acyl-CoA dehydrogenase change in this patient? Why? (page 6)
• For patients with type 2 diabetes, insulin levels often become insufficient to effectively manage blood glucose utilization. What is the most likely disorder this patient will develop if his diabetic condition is not well-controlled? Why? (page 6)

Lecture 1: Water and Aqueous System

• Chemical formula: H₂O
• Water is a polar molecule
• Polarity allows hydrogen bonding between water molecules.
• Important properties: Cohesion, adhesion, high boiling point, high specific heat, and excellent solvent for polar molecules
• Water can act as an acid or a base due to its polar structure.
• Autoionization of water: H₂O + H₂O ↔ H₃O⁺ + OH^–
• Equilibrium constant (K_w) at 25°C: 1.0 x 10^-14
• In pure water: [H⁺] = [OH^–] = 1.0 x 10^-7 M
• Buffers resist changes in pH.
• A buffer is a weak acid and its conjugate base, or a pair of a weak base and its conjugate acid.
• Examples of buffers: phosphate buffers

Lecture 2: Carbohydrates, Proteins, and Lipids

• Carbohydrates: glucose, galactose, mannose, fructose, ribose, deoxyribose
• Monosaccharides: single sugar units
• Disaccharides: two sugar units linked together
• Oligosaccharides: 3-10 sugar units
• Polysaccharides: many sugar units
• Proteins: composed of amino acids, 9 non-polar and 6 polar amino acids also includes positively and negatively charged amino acids; Primary, Secondary, Tertiary, Quaternary structure
• Lipids: Glycerophospholipids, Sphingolipids, Glycolipids, Fatty Acids (saturated and unsaturated (monounsaturated, polyunsaturated));
• Polyunsaturated fatty acids (PUFAs), including omega-3 and omega-6 fatty acids

Lecture 3: Nucleic Acids

• DNA: double helix structure, made of deoxyribose sugar and phosphate groups, with bases (A, T, C, G). Adenine pairs with thymine, guanine pairs with cytosine
• RNA: Single stranded structure, made of ribose sugars and phosphate groups, with bases (A, U, C, G). Adenine pairs with uracil, and guanine pairs with cytosine
• Functions of DNA: store genetic information, transmit genetic material
• Functions RNA: instruction of protein synthesis, various roles in protein synthesis

Lecture 4: Metabolism and Energy I: TCA Cycle

• The TCA cycle is a series of chemical reactions in the mitochondrial matrix that oxidizes acetyl-CoA, producing energy (ATP)
• Acetyl-CoA is a key intermediate in linking glycolysis and the TCA cycle.
• Products of each acetyl-CoA molecule in the TCA cycle are 2 CO2, 3 NADH, 1 FADH2, 1 GTP/ATP.
• TCA cycle roles: energy production, formation of metabolic intermediates, linking metabolic pathways

Lecture 5: Metabolism and Energy II: Oxidative Phosphorylation

• ATP production process via electron transport chain
• Electron transport chain (ETC) uses energy from electrons to create a proton gradient
• Chemiosmosis: protons move back across the inner mitochondrial membrane, driving ATP synthesis
• Function of oxidative phosphorylation: ATP production, cellular respiration integration, metabolic regulation, heat generation

Lecture 6: Carbohydrate Metabolism: Part I - Glycolysis

• Glycolysis: breakdown of glucose to pyruvate in the cytoplasm
• Two phases of glycolysis: preparatory phase (steps 1-5), payoff phase (steps 6-10)
• Key steps: glucose phosphorylation, isomerization, phosphorylation, cleavage, isomerization, oxidation, transfer of phosphate, isomerization, dehydration, transfer of phosphate
• Glycolysis products: 2 pyruvate, 2 NADH, and 2 ATP
• Glycolysis regulation: influenced by substrate availability, feedback inhibition

Lecture 7: Protein and Lipid Metabolism

• Protein and lipid metabolism are critical parts of overall metabolism.
• The catabolism of various biomolecules converts them into usable energy intermediates.

Lecture 8: Hemoglobin

• Hemoglobin: a globular protein in red blood cells that transports oxygen through blood
• Basic components: globin chains (alpha and beta), heme group, iron atom
• Function: oxygen transport, carbon dioxide transport, pH regulation

Lecture 9: Enzyme I: Introduction to Enzymes

• Enzymes are biological catalysts that speed up biochemical reactions
• They act by lowering activation energy
• Enzymes have specific active sites for substrate binding.

Lecture 10: Enzyme II: Enzyme Kinetics and Inhibitors

• Enzyme kinetics: study of enzyme reaction rates and their dependence on substrate concentration
• Michaelis-Menten equation: describes the relationship between reaction velocity, substrate concentration, and enzyme properties
• Enzyme inhibitors: molecules that can bind to the enzyme and reduce its activity

Lecture 11: Enzyme III: Enzyme Diagnostics and Assay

• Liver enzymes, cardiac enzymes, and pancreatic enzymes in diagnostics