Chemistry, Biochemistry, and Cell Physiology Part 1

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