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Chemistry, Biochemistry, and Cell Physiology Part 1

Chemistry, Biochemistry, and Cell Physiology Part 1. Chemistry and Physics of Life. Physiological processes are based on cellular function Cellular functions obey the laws of physics and chemistry. Thermodynamics. Chemical reactions proceed according to the rules of thermodynamics

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Chemistry, Biochemistry, and Cell Physiology Part 1

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  1. Chemistry, Biochemistry, and Cell PhysiologyPart 1

  2. Chemistry and Physics of Life • Physiological processes are based on cellular function • Cellular functions obey the laws of physics and chemistry

  3. Thermodynamics • Chemical reactions proceed according to the rules of thermodynamics • The law of conservation of energy – energy can be converted from one form to another but the total amount of energy is constant (i.e., you cannot “make” energy) • Entropy – the universe is becoming more chaotic

  4. Energy • Energy – ability to do work • Energetics – energy transfer between systems • Types of energy • Potential – trapped energy • Kinetic – energy of movement

  5. Energy Categories used in Biology • Radiant energy • Mechanical energy • Electrical energy • Thermal energy • Chemical energy • Animals rely on all five types of energy, which are interconvertible.

  6. Food Webs are Transfers of Energy Radiant energy Light photosynthesis Chemical energy

  7. Diffusion Gradients • Gradient – a difference between two points • Diffusion – molecules disperse randomly in the available space • Diffusion governs many biological processes • Diffusion leads to random distribution of molecules • Diffusion of molecules is a source of energy

  8. Electrochemical Gradients • Gradients are a form of energy storage • Potential energy • Organisms invest energy to delay diffusion • Gradients across membranes can be chemical, electrical, or both (electrochemical) • membrane potential

  9. Thermal Energy •  Thermal energy   movement of molecules   rate of chemical reactions • Most chemical reactions involve changes in thermal energy • Exothermic reactions • Endothermic reactions

  10. Chemical Reactions and Thermal Energy • Enthalpy – average thermal energy of a collection of molecules • Activation energy – energy required for a molecule to reach a transition state • Transition state – intermediate structure between a substrate and a product • Change in enthalpy (DH) = Hproducts – Hsubstrates • Exothermic: DH is negative • Endothermic: DH is positive

  11. Temperature Influences Chemical Reactions • Increasing temperature • Allows more molecules to reach activation energy • Increases the rate of the reaction • Increases the likelihood of endothermic reactions

  12. Water

  13. Solvents and Solutes • Solvent – most abundant molecule in a liquid • Solute – the other molecules in a liquid • Solution – solvents and solutes • In biological systems the solvent is usually water (i.e., aqueous solutions)

  14. Properties of Water • Liquid water is a network of interconnected water molecules • Water molecules are attracted to each other by hydrogen bonds • Surface tension – the force due to attraction between water molecules at the water–air interface

  15. Surface Tension of Water Figure 2.7

  16. Boiling and Freezing • Temperature changes the organization of water molecules • High temperature – molecules possess enough thermal energy to break the surface tension (i.e., boil) • Low temperature – stabilize molecules as a result of additional hydrogen bonds (i.e., freeze)

  17. Density of Water is Affected by Temperature • Temperature influences the density of water • Ice is less dense than liquid water • Ice has more hydrogen bonds, but molecules are held further apart • Ice floats in liquid water • Water is most dense at 4°C • Most deep waters are 4°C • Surface waters can be colder or warmer

  18. Water is a Very Stable Liquid • High melting point • High boiling point • High heat of vaporization – amount of energy to cause liquid water to boil

  19. Many Solutes can Dissolve in Water • Solutes form hydrogen bonds with water molecules • Hydration shell – solute surrounded by water molecules

  20. Solutes Affect Properties of Water • Colligative properties • Reduce freezing point • Increase • Boiling point • Vapor pressure • Osmotic pressure • Depend on the number of solutes, not their size or charge

  21. Solutes Move Through Water by Diffusion • Direction of diffusion depends on the concentration gradient • Rate of diffusion (dQs/dt) depends on many factors • Size of concentration gradient (dC/dX) • Size of molecule and hydration shell • Diffusion coefficient (Ds) • Diffusion area (A) • Fick equation: (dQs/dt) = DsA (dC/dX)

  22. Solutes Create Osmotic Pressure • Semipermeable membrane – allows some molecules to cross while restricting others • Osmosis – the diffusion of water • Osmotic pressure – force associated with the diffusion of water • Osmolarity – ability of solution to induce water to diffuse across a membrane • Determined by the concentration of dissolved particles

  23. Osmotic Pressure Figure 2.8

  24. Osmotic Pressure • Comparing two solutions • Solution with higher osmolarity is hyperosmotic • Solution with lower osmolarity is hyposmotic • If the osmolarities are the same, they are isosmotic • Water diffuses from a hyposmotic solution to a hyperosmotic solution

  25. Osmosis Across Cell Membranes • Tonicity – the affect of a solution on cell volume • Cells shrink in hypertonic solution • Water leaves the cell by osmosis • Cells swell in hypotonic solution • Water enters the cell by osmosis • Cell neither shrinks nor swells in isotonic solution • No net osmosis

  26. Osmolarity vs. Tonicity Figure 2.9

  27. pH and the Ionization of Water • Dissociation of a water molecule into ions • H:O:H  H:O:– + H+ • pH = –log [H+] • Brackets denote molar (M) concentration • Pure water is pH 7 • [H+] = 10–7 M • –log 10–7 M = 7

  28. Neutrality • Neutrality: [H+] = [OH–] or pH = pOH • Affected by temperature • The amount of dissociation increases as temperature increases • pH at neutrality (pN) varies inversely with temperature • 5°C: pN = 7.28 • 25°C: pN = 7.00 • 45°C: pN = 6.72

  29. Acids and Bases Alter the pH of Water • Acids – release protons   pH • HA  H+ + A– (reaction goes to the right) • Bases – accept protons   pH • HA  H+ + A– (reaction goes to the left) • Mass action ratio = ([H+]  [A–]) / [HA] • Equilibrium constant (Keq) – the mass action ratio at equilibrium • pK = –log Keq • pK = pH – log ([A–] / [HA]) • pK reflects the strength of acids or bases

  30. Temperature Affects Ionization State • pK increases as temperature decreases • Each ionizable group has a characteristic sensitivity to temperature • DpK / °C

  31. pH Affects Ionization State Figure 2.10

  32. Buffers Limit Changes in pH • Buffer – solute that dampens the effect of added acid or base on the pH • Mixture of protonated and deprotonated molecules • Most buffers are weak acids • A buffer is effective only over a narrow range of pH values

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