Biochemistry Definition Lecture

Biochemistry Definition “A living cell is a self-assembling, self-adjusting, self-perpetuating isothermal open system. This system consists of many consecutive, linked organic reactions that are promoted by organic catalysts produced by the cell; it operates on the principle of maximum economy of parts and processes.” Biochemistry Definition Complementary macromolecules dynamic “A living cell is a self-assembling, self-adjusting, Self-replicating self-perpetuating isothermal open system. This Bio-energetics system consists of many consecutive, linked metabolism organic reactions that are promoted by organic catalysts produced by the cell; itenzymes operates on the principle of maximum economy of parts and processes.” Molecular biology evolution Biochemistry Is the Chemistry of Living Matter Living matter is characterized by: • a high degree of complexity and organization • the extraction, transformation, and systematic use of energy to create and maintain structures and to do work • the interactions of individual components being dynamic and coordinated • the ability to sense and respond to changes in surroundings • a capacity for fairly precise self-replication while allowing enough change for evolution In order to understand these processes, biochemists have tended to isolate individual components and study them: reductionists Central Themes of Biochemistry I There are THREE repetitive themes: 1. Chemical Basis: try to explain life in terms of equilibria, kinetics, reactivity, and thermodynamic quantities 2. Complementarity: Form & Function. 3. The 4 S’s: Size Shape Solubility Stability For each of the biological components of life, we will describe them in these terms. History of Biochemistry Regardless of the enormity of the field of biochemistry, it is the study of SMALL things. Sizes of Things 1Å 10 Å 100 Å Å = Angstrom (diameter of hydrogen atom) Cells are complex ORGANIZED units of life The Molecular Hierarchy of Structure Nucleic Acids Proteins Membranes phospholipids Carbohydrates Nucleic Acids: covalent polymer of nucleotides Proteins: covalent polymer of amino acids Carbohydrates: covalent polymer of monosaccharides Membranes/Lipids: non-covalent supramolecular complex of phospholipids Components of Life Data from E. coli: Component Water Protein Nucleic Acids Carbohydrate Lipids Small organics Inorganics % by weight 70 15 7 3 2 2 1 Complexity* 1 3000 1001 50 40 500 12 *number of types Before we discuss each component, lets review thermodynamics that makes these possible Energetics of Life The laws of thermodynamics (thermo, “energy”; dynamics, “change”) apply to all matter and all energy transformations in the universe. 1st & 2nd Laws of Thermodynamics: 1) Energy can never be created or destroyed, but can be interconverted. 2) The universe tends toward more disorder (randomness) [When energy is converted from one form to another, some of that energy becomes unavailable to do work.] Energetics of Life Chemistry of Life: Biochemistry Organisms Work Against the Second Law BigTime to Build the Cell Complexity and Organization Take as the system, the reactions creating the cell: Chaos ⇌ Cell DSsystem = Scell – Schaos (small) DSsystem = DSuniverse > 0 (⊕) (2nd Law) DSuniverse = DSsystem + DSsurroundings ⊕ (large) ⊝ Entropy of surroundings can increase by release of heat by the system: First Law to the rescue!!! Organisms Use the First Law Big-Time (perform energy transformations) to Stay Alive • Creating and maintaining order requires work and energy. The entropy* of the universe must increase (2nd Law) • Living organisms exist in a dynamic steady state and are never at equilibrium with their surroundings. • Energy coupling allows living organisms to transform energy. *Entropy is a measure of the disorder in a system. It takes energy to impose order on a system. Unless energy is applied to a system, it will be arranged randomly or “disordered.” A little more about “coupling”…..... Equilibrium and ΔG° Measure Favorability of a Reaction Spontaneity Equilibrium and ΔG° Measure Not all biochemical reactions are favorable in the Favorability Spontaneity direction that the cell needs.of a Reaction Not all biochemical reactions are for favorable in the direction that the cell needs. Recall from gen-chem, a given reaction: Recall from gen-chem: Organisms Use the First Law Big-Time (perform energy transformations) to Stay Alive Favorable and Unfavorable Reactions • – Their cellular concentration is far higher than their equilibrium concentration. – Metabolites, such as ATP, NADH, NADPH, can be synthesized using the energy from sunlight and fuels….. DS > 0 DG°< 0 catabolism DG°> 0 anabolism The breakdown of some metabolites releases a significant amount of energy (exergonic). • Synthesis of complex molecules and many other metabolic reactions requires energy (endergonic). – A reaction might be thermodynamically unfavorable (DG°> 0). • Creating order requires work and energy. Energy Coupling • Chemical coupling of exergonic and endergonic reactions allows otherwise unfavorable reactions. • TWO basic mechanisms: – e.g., The hydrolysis of the “high-energy” molecule (ATP), which is exergonic, is coupled with an otherwise endergonic reaction during an enzyme mechanism. – e.g., a series of otherwise endergonic reactions during a metabolic pathway are linked in the reaction series to an overwhelming exergonic reaction (all catalyzed by enzymes). Inorganic phosphate = Pi Pyrophosphate = PPi Quantifying Thermodynamics In any system: Total energy = usable energy + unusable energy enthalpy (H)* = free energy (G) + entropy (S) or H = G + TS (T = absolute temperature) G = H – TS *equal to the system's internal energy plus the product of its pressure and volume. In a closed system at constant pressure, the heat absorbed or released equals the change in enthalpy. Now consider the differences in energy states between substrates and products in a reaction: S ⇌P Change in energy can be measured in calories or joules. Change in free energy (DG) in a reaction is the difference in free energy of the products and the reactants: DG = DH – TDS S P Quantifying Thermodynamics Chemistry of Life: Biochemistry For Total Energy (Enthalpy), what is magnitude of DH? Look at each side of the reaction: S ⇌P If bonds are being broken If bonds here are to be to make P, need to add broken, its at a lower energy, H is more energy state, H is less Hproduct (more heat, less bonds) – Hreactant (less heat, more bonds) = +DH Heat energy is added or adsorbed at T > 0° C ⇌ Water Less bonds Ice More bonds If the other way around, with product having more bonds, its at a lower energy state, then –DH (energy is released): S P Quantifying Thermodynamics Chemistry of Life: Biochemistry For Entropy, what is magnitude of DS? Look at each side of the reaction: If more organized, S is less S ⇌P If more disordered, S is more. Sproduct (more) – Sreactant (less) = +DS Ice Less disorder, more organized Don’t forget that a +DS will contribute to a favorable reaction due to the –TDS term being Amino a negative value. acids ⇌ Water More disorder ⇌ Protein at T > 0° C +DS adds to favorability –DS makes less favorable S P Quantifying Thermodynamics Chemistry of Life: Biochemistry For Free Energy, DG: Magnitude of DG depends on: DG = DH – TDS § DH—total energy added (DH > 0) or released (DH < 0) § DS—change in entropy, more randomness (DS > 0) or more order (DS < 0); Positive changes in entropy make DG more negative. Negative changes in entropy make DG more positive. S P Quantifying Thermodynamics Chemistry of Life: Biochemistry The interplay of enthalpy and entropy in the simple ice/water reaction, as a function of the temperature: Ice ⇌ Water –5.4 +5.6 –6.0 +6.0 –6.6 +6.4 Properties of Water 1) Water has a high boiling point and relatively low melting point; its range in the liquid state is large 2) The heat of vaporization is high (more heat to change to vapor state than to raise temperature of the liquid state) 3) Liquid is more dense than the solid (e.g., most metals and other substances the solid is more dense) 4) High viscosity relative to its molecular weight (MW) 5) High surface tension