BCM 211 Chemical Bonds & Thermodynamics PDF

# DEPARTMENT OF MEDICAL BIOCHEMISTRY ## FACULTY OF BASIC MEDICAL SCIENCES ### COLLEGE OF HEALTH SCIENCES #### UNIVERSITY OF UYO - UYO **COURSE CODE:** BCM 211 **COURSE TITLE:** CELL BIOLOGY, PH AND BUFFER **SESSION:** FIRST SEMESTER 2024/2025 ## COURSE CONTENTS: ### LESSON 1 **Review of key chemi...

# DEPARTMENT OF MEDICAL BIOCHEMISTRY ## FACULTY OF BASIC MEDICAL SCIENCES ### COLLEGE OF HEALTH SCIENCES #### UNIVERSITY OF UYO - UYO **COURSE CODE:** BCM 211 **COURSE TITLE:** CELL BIOLOGY, PH AND BUFFER **SESSION:** FIRST SEMESTER 2024/2025 ## COURSE CONTENTS: ### LESSON 1 **Review of key chemistry concepts applicable to biological systems:** - Understanding key chemistry concepts is essential for grasping the complexities of biological systems. - Here is a review of important chemistry concepts applicable to biology: 1. **Atoms and Molecules** - Atoms: The basic units of matter, composed of protons, neutrons, and electrons. The arrangement of these subatomic particles determines the chemical properties of elements. - Molecules: Formed when two or more atoms bond together, either through covalent bonds (sharing electrons) or ionic bonds (transfer of electrons). 2. **Chemical Bonds** - Covalent Bonds: Strong bonds formed by the sharing of electrons between atoms. They are fundamental in forming organic molecules like proteins, nucleic acids, carbohydrates, and lipids. - Ionic Bonds: Formed when one atom donates an electron to another, creating charged ions that attract each other. Important in the structure of salts and some biomolecules. - Hydrogen Bonds: Weak attractions between polar molecules, crucial for the structure of water and the stability of DNA and proteins. 3. **Water and pH** - Properties of Water: Water is a polar molecule, which makes it an excellent solvent for many biochemical reactions. Its unique properties, like high specific heat, cohesion, and adhesion, are vital for life. - pH and Buffers: The pH scale measures the acidity or basicity of a solution. Biological systems often require specific pH levels, and buffers help maintain these levels by neutralizing excess acids or bases. 4. **Macromolecules** - Proteins: Composed of amino acids linked by peptide bonds. Their structure (primary, secondary, tertiary, quaternary) determines their function in biological systems. - Nucleic Acids: DNA and RNA are polymers of nucleotides that store and transmit genetic information. The sequence of nucleotides encodes proteins. - Carbohydrates: Made of sugar molecules (monosaccharides, disaccharides, polysaccharides), they serve as energy sources and structural components. - Lipids: Diverse group including fats, oils, phospholipids, and steroids. They are important for energy storage, membrane structure, and signaling. 5. **Enzymes and Catalysis** - Enzymes: Biological catalysts that speed up chemical reactions without being consumed. They lower the activation energy needed for reactions to occur. - Active Site and Substrate: The specific region on an enzyme where substrates bind and undergo a chemical reaction, often exhibiting specificity and regulation. 6. **Metabolism** - Anabolism and Catabolism: Anabolic reactions build larger molecules from smaller ones (e.g., protein synthesis), while catabolic reactions break down molecules for energy (e.g., cellular respiration). - ATP (Adenosine Triphosphate): The primary energy carrier in cells, driving biochemical reactions by transferring phosphate groups. 7. **Redox Reactions** - Oxidation and Reduction: These reactions involve the transfer of electrons between molecules, playing a critical role in energy production and metabolism (e.g., cellular respiration). 8. **Chemical Equilibrium** - Dynamic Equilibrium: Many biochemical reactions reach a state of equilibrium, where the rate of the forward reaction equals the rate of the reverse reaction, crucial for maintaining homeostasis in biological systems. 9. **Functional Groups** - Chemical Groups: Specific groups of atoms (e.g., hydroxyl, carboxyl, amino, phosphate) that confer distinct chemical properties to organic molecules, influencing their reactivity and interactions in biological systems. 10. **Molecular Interactions** - Van der Waals Forces: Weak attractions between molecules that are important for the stability and interaction of biomolecules. - Hydrophobic and Hydrophilic Interactions: These interactions influence protein folding, membrane formation, and the behavior of molecules in biological systems. ### Chemical Bonds: Covalent and Ionic - Chemical bonds are crucial for the formation of molecules and compounds, and they primarily include covalent and ionic bonds. - Here's an overview of both: #### Covalent Bonds - **Definition:** Covalent bonds are formed when two atoms share one or more pairs of electrons. This sharing allows each atom to achieve a more stable electron configuration, often resembling that of noble gases. - **Characteristics:** - **Strength:** Generally strong bonds; the strength can vary based on the number of shared electron pairs (single, double, or triple bonds). - **Polarity:** Covalent bonds can be polar or nonpolar: - **Polar Covalent Bonds:** Occur when electrons are shared unequally between atoms with different electronegativities (e.g., water, where oxygen is more electronegative than hydrogen). - **Nonpolar Covalent Bonds:** Occur when electrons are shared equally between atoms with similar electronegativities (e.g., molecular oxygen, O₂). - **Molecule Formation:** Covalent bonding leads to the formation of discrete molecules (e.g., H₂O, CO₂). - **Examples:** - Water (H₂O): Each hydrogen atom shares an electron with the oxygen atom. - Carbon Dioxide (CO₂): Carbon forms double bonds with two oxygen atoms. #### Ionic Bonds - **Definition:** Ionic bonds are formed when one atom transfers one or more electrons to another atom, resulting in the formation of ions. The electrostatic attraction between the positively charged cation and the negatively charged anion holds them together. - **Characteristics:** - **Formation of Ions:** One atom (often a metal) loses electrons to become a cation (positive ion), while another atom (often a nonmetal) gains electrons to become an anion (negative ion). - **Strength:** Ionic bonds are generally strong but can be affected by the environment (e.g., solubility in water). - **Structure:** Ionic compounds typically form crystalline structures (e.g., sodium chloride, NaCl) with high melting and boiling points. - **Conductivity:** In molten or dissolved states, ionic compounds can conduct electricity due to the movement of ions. - **Examples:** - Sodium Chloride (NaCl): Sodium (Na) donates an electron to chlorine (Cl), resulting in Na⁺ and Cl^- ions. - Magnesium Oxide (MgO): Magnesium (Mg) loses two electrons to become Mg²⁺, while oxygen (O) gains two electrons to become O^2-. | Feature | Covalent Bonds | Ionic Bonds | |--------------------|----------------------------------|----------------------------------------------------| | Electron Sharing | Electrons are shared | Electrons are transferred | | Types | Typically between nonmetals | Typically between metals and nonmetals | | Elements | of nonmetals | Generally strong, varies with environment | | Bond Strength | Generally strong | Forms crystalline lattice | | Molecular Structure | Forms discrete molecules | Dissolved/melted | | Conductivity | Poor conductors in solid state | Good conductors when dissolved/melted | ### BIOMOLECULES - Biomolecules are essential organic molecules that play critical roles in biological systems. - Biomolecules are the foundation of life, participating in various biological processes and forming the structure of cells and tissues. - Understanding these molecules and their functions is crucial for fields like biochemistry, molecular biology, and medicine. - They are typically classified into four major categories: carbohydrates, proteins, lipids, and nucleic acids. - Here's an overview of each category: 1. **Carbohydrates** - **Structure:** Composed of carbon, hydrogen, and oxygen, usually with a hydrogen-to-oxygen ratio of 2:1. - **Types:** - **Monosaccharides:** Simple sugars (e.g., glucose, fructose) that serve as basic energy units. - **Disaccharides:** Formed by the combination of two monosaccharides (e.g., sucrose, lactose). - **Polysaccharides:** Long chains of monosaccharides (e.g., starch, glycogen, cellulose) used for energy storage or structural support. - **Functions:** Primary energy source, structural components (e.g., cellulose in plants), and involvement in cell signaling. 2. **Proteins** - **Structure:** Composed of amino acids linked by peptide bonds. The sequence and arrangement of amino acids determine the protein's structure and function. - **Levels of Structure:** - **Primary:** Linear sequence of amino acids. - **Secondary:** Local folding into structures like alpha-helices and beta-sheets. - **Tertiary:** Overall 3D shape of a single polypeptide chain. - **Quaternary:** Arrangement of multiple polypeptide chains (e.g., hemoglobin). - **Functions:** Catalysts (enzymes), structural support (collagen), transport (hemoglobin), immune response (antibodies), and signaling (hormones). 3. **Lipids** - **Structure:** Hydrophobic or amphipathic molecules composed primarily of carbon and hydrogen, with fewer oxygen atoms than carbohydrates. - **Types:** - **Fats and Oils:** Triglycerides formed from glycerol and fatty acids; used for energy storage. - **Phospholipids:** Composed of two fatty acids, glycerol, and a phosphate group; essential for cell membrane structure. - **Steroids:** Four-ring structures (e.g., cholesterol) that play roles in membrane fluidity and signaling. - **Functions:** Energy storage, insulation, cell membrane structure, and signaling (hormones like steroids). 4. **Nucleic Acids** - **Structure:** Polymers made up of nucleotides, which consist of a sugar, a phosphate group, and a nitrogenous base. - **Types:** - **DNA (Deoxyribonucleic Acid):** Double-stranded helical structure that carries genetic information. - **RNA (Ribonucleic Acid):** Single-stranded molecule involved in protein synthesis and gene expression (types include mRNA, tRNA, rRNA). - **Functions:** Storage and transmission of genetic information (DNA) and protein synthesis (RNA). 5. **Other Important Biomolecules** - **Vitamins:** Organic compounds required in small amounts for various biochemical functions (e.g., vitamin C, vitamin D). - **Hormones:** Chemical messengers that regulate physiological processes (e.g., insulin, adrenaline). - **Coenzymes:** Non-protein molecules that assist enzymes in catalyzing reactions (e.g., NAD+, coenzyme A). ### LESSON 3 (a) #### Elementary Thermodynamics - Elementary thermodynamics is the study of heat, energy, and the relationships between them. - It covers fundamental concepts that govern the behavior of systems in thermal equilibrium and the principles that describe how energy is transferred. - These concepts provide a foundation for understanding how energy systems work, from engines to refrigerators, and are crucial in fields like engineering, chemistry, and physics. #### Key Concepts: 1. **Thermodynamic Systems:** These can be open, closed, or isolated, depending on whether they exchange matter and/or energy with their surroundings. 2. **Laws of Thermodynamics:** - **Zeroth Law:** If two systems are each in thermal equilibrium with a third system, they are in thermal equilibrium with each other. - **First Law:** Energy cannot be created or destroyed, only transformed. It relates internal energy change to heat added and work done on the system. - **Second Law:** In any energy transfer, the total entropy of an isolated system can never decrease. This explains the direction of spontaneous processes. - **Third Law:** As temperature approaches absolute zero, the entropy of a perfect crystal approaches zero. 3. **Processes:** - **Isothermal:** Constant temperature. - **Adiabatic:** No heat exchange with surroundings. - **Isobaric:** Constant pressure. - **Isochoric:** Constant volume. 4. **State Functions:** Properties like temperature, pressure, volume, and internal energy that depend only on the state of the system, not on how it got there. 5. **Thermodynamic Cycles:** Series of processes that return a system to its initial state, often used in engines (e.g., Carnot cycle, Otto cycle). 6. **Heat Engines and Refrigerators:** Devices that convert thermal energy into work and vice versa, demonstrating practical applications of thermodynamic principles. #### REACTION EQUILIBRIA - Reaction equilibria refer to the state in a chemical reaction where the rates of the forward and reverse reactions are equal, resulting in stable concentrations of reactants and products. - Here are some key concepts: 1. **Dynamic Equilibrium:** Even at equilibrium, the reaction continues in both directions, but the overall concentrations remain constant. 2. **Equilibrium Constant (K):** The ratio of the concentration of products to the concentration of reactants, each raised to the power of their coefficients in the balanced equation. 3. **Le Chatelier's Principle:** If an external change (such as concentration, temperature, or pressure) is applied to a system at equilibrium, the system will adjust to counteract that change and restore a new equilibrium. 4. **Factors Affecting Equilibrium:** - **Concentration Changes:** Adding or removing reactants or products shifts the equilibrium position. - **Temperature Changes:** For exothermic reactions, increasing temperature shifts the equilibrium left (toward reactants), while for endothermic reactions, it shifts right (toward products). - **Pressure Changes:** For reactions involving gases, increasing pressure shifts the equilibrium toward the side with fewer moles of gas. 5. **Applications:** Understanding reaction equilibria is crucial in industrial processes, environmental science, and biochemistry, where controlling reaction conditions can optimize product yield. #### Applications of the Henderson-Hasselbalch Equation