Lecture - 5

1. Lecture - 5 Biological Thermodynamics

2. Outline • Proteins Continued • Amino Acid Chemistry • Tertiary & Quaternary Structure • Biological Thermodynamics • Metabolic/Anabolic/Catabolic • Energy & Thermodynamics • 1st & 2nd Laws applied to biological processes • Free Energy • ATP

3. Proteins – Tertiary Structure • Interactions amongst side (R) groups • Interactions include: • hydrogen bonds • ionic bonds • hydrophobic interactions • van der Waals interactions • Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

4. Figure 5.20f Hydrogenbond Hydrophobicinteractions Disulfidebridge Ionic bond Polypeptidebackbone

5. Proteins – Tertiary Structure • Usually form between COOH and HO on different residues • Can form between N and H on different residues Hydrogenbond Polypeptidebackbone

6. Proteins – Tertiary Structure Figure 5.20f • Disulfide bridge • Covalent bond between sulfhydryl groups on two neighboring cysteine residues Disulfidebridge Polypeptidebackbone

7. Figure 5.20f Proteins – Tertiary Structure Hydrogenbond • Hydrophobic interactions • side-chains aggregate • create pockets within proteins that effectively exclude water • ionic bond • interactions between positively and negatively charged residues • occur deep in the protein, away from water Ionic bond Polypeptidebackbone

8. Proteins – Tertiary Structure • Other factors influencing folding • pH • Location of secondary structures • The chemical make-up of the solution it’s in • Temperature

9. Proteins Quaternary Structure • Multiple polypeptide subunits • Subunits may be loosely or tightly bound together • Many enzymes

10. Proteins Structure • Shape of the protein is critical for it’s function • Location of the active site • Orientation/interaction with other molecules • Loss of the proper shape can destroy function • DNA mutations • Temperature • Denaturation

11. Proteins - Review • Made out of 20 amino acids • Form follows function • Four structural levels • Important Functions • Enzymes • Structural Support (collagen/keratin) • Storage ( • Hormones • Transport • Cellular communications • Movement • Defense against foreign substances

12. Metabolism • The totality of an organism’s chemical reactions • Metabolic Pathway begins with a specific molecule and ends with a product • Each step is catalyzed by a specific enzyme

13. Figure 8.UN01 Metabolic Pathway Enzyme 2 Enzyme 3 Enzyme 1 D A C B Reaction 2 Reaction 3 Reaction 1 Startingmolecule Product

14. Catabolic pathways • Release energy • Complex Simple • Example: Cellular respiration, the breakdown of glucose in the presence of oxygen

15. Anabolic pathways • Consume energy • Simple Complex • Example: Synthesis of a protein from amino acids

16. Energy • The capacity to cause change • Forms of Energy: • Kinetic energy:energy associated with motion • Heat (thermal energy):kinetic energy associated with random movement of atoms or molecules • Potential energy:energy that matter possesses because of its location or structure • Chemical energy:potential energy available for release in a chemical reaction • Energy can be converted from one form to another

17. Energy Potential Energy Chemical Energy Heat Energy Kinetic Energy

18. Thermodynamics • The study of energy transformations • Isolated system: closed or isolated from surroundings. • Liquid in thermos • Open system: energy and matter can be transferred between the system and its surroundings • Organisms are open systems

19. First Law of Thermodynamics • The energy of the universe is constant • Energy can be transferred and transformed, but it cannot be created or destroyed • Also called the principle of conservation of energy

20. Second Law of Thermodynamics • During every energy transfer or transformation, some energy is unusable • Unusable energy is often lost as heat • The Second law of thermodynamics • Every energy transfer or transformation increases the entropy (disorder) of the universe

21. 1st & 2nd Laws Applied Chemical Energy (food) CO2 & H2O Heat Cells unavoidably convert organized forms of energy to heat

22. Spontaneous Processes • Occur without energy input; they can happen quickly or slowly • Examples: • A drop of food coloring will spread in a glass of water. • Methane (CH4) burns in O2 gas. • Ice melts in your hand. • Ammonium chloride dissolves in a test tube with water, making the test tube colder • For a process to occur without energy input, it must increase the entropy of the universe

23. Spontanious Processes

24. Biological Order/Disorder • Cells create ordered structures from less ordered materials • Does the evolution of more complex organisms violate the second law of thermodynamics?

25. Biological Order/Disorder • Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases • Organisms also replace ordered forms of matter and energy with less ordered forms • Energy flows into an ecosystem in the form of light and exits in the form of heat

26. Free-energy • The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously. • Free-energy - The energy that can do work when temperature and pressure are uniform • The energy that cells can use to do work G

27. Change in free energy (∆G) • The change in free energy (∆G)during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T) ∆G = ∆H – T∆S • Only processes with a negative ∆G are spontaneous • Spontaneous processes can be harnessed to perform work

28. Free Energy, Stability & Equilibrium • Free energy is a measure of a system’s instability, its tendency to change to a more stable state • During a spontaneous change, free energy decreases and the stability of a system increases • Equilibrium is a state of maximum stability • A process is spontaneous and can perform work only when it is moving toward equilibrium

29. Figure 8.5a • More free energy (higher G)• Less stable• Greater work capacity In a spontaneous change• The free energy of the system decreases (G 0)• The system becomes more stable• The released free energy can be harnessed to do work • Less free energy (lower G)• More stable• Less work capacity

30. Free Energy and Metabolism • The concept of free energy can be applied to the chemistry of life’s processes

31. Exergonic reaction • Proceeds with a net release of free energy and is spontaneous (DG is less than 0)

32. Endergonic Reaction • Absorbs free energy from its surroundings and is nonspontaneous (DG is greater than 0).

33. Figure 8.6a (a) Exergonic reaction: energy released, spontaneous Reactants Amount of energyreleased(G 0) Energy Free energy Products Progress of the reaction

34. Figure 8.6b (b) Endergonic reaction: energy required, nonspontaneous Products Amount of energyrequired(G 0) Energy Free energy Reactants Progress of the reaction

35. Metabolism and Equilibrium • Reactions in a closed system eventually reach equilibrium and then do no work • Cells are not in equilibrium; they are open systems experiencing a constant flow of materials • A defining feature of life is that metabolism is never at equilibrium • A catabolic pathway in a cell releases free energy in a series of reactions

36. Figure 8.7a G 0 G 0 (a) An isolated hydroelectric system

37. Figure 8.7b (b) An open hydroelectric system G 0

38. Figure 8.7c G 0 G 0 G 0 (c) A multistep open hydroelectric system

39. Exergonic & Endergonic reactions in the cell – ATP • A cell does three main kinds of work • Chemical • Transport • Mechanical • To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one • Most energy coupling in cells is mediated by ATP

40. Figure 8.8a ATP (adenosine triphosphate) • The cell’s energy shuttle • Composed of: • ribose (a sugar) • adenine (a nitrogenous base) • three phosphate groups Adenine Phosphate groups Ribose

41. Hydrolysis of ATP = ADP + Energy • The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis • Energy is released from ATP when the terminal phosphate bond is broken • This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

42. Figure 8.8b Adenosine triphosphate (ATP) Energy Inorganicphosphate Adenosine diphosphate (ADP) The hydrolysis of ATP

43. Hydrolysis of ATP • Mechanical, transport, and chemical work are powered by the hydrolysis of ATP • The energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction • Overall, the coupled reactions are exergonic

44. ATP phosphorylated intermediates • ATP drives endergonic reactions by phosphorylation • ATP can transfer a phosphate group to some other molecule, such as a reactant • Called a phosphorylated intermediate ATP ADP PO43- H2O

45. Figure 8.9 Glutamic acidconversionto glutamine (a) Conversionreactioncoupledwith ATPhydrolysis (b) (c) Free-energychange forcoupledreaction NH3 NH2 GGlu = +3.4 kcal/mol Glu Glu Glutamine Ammonia Glutamicacid NH3 P 2 1 NH2 ADP ADP P i ATP Glu Glu Glu Phosphorylatedintermediate Glutamicacid Glutamine GGlu = +3.4 kcal/mol NH2 NH3 ADP P i ATP Glu Glu GGlu = +3.4 kcal/mol GATP = 7.3 kcal/mol + GATP = 7.3 kcal/mol Net G = 3.9 kcal/mol Chemical Work

46. Figure 8.10 Transport protein Solute ATP ADP P i P P i Solute transported (a) Transport work: ATP phosphorylates transport proteins. Cytoskeletal track Vesicle ATP ADP P i ATP Motor protein Protein andvesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed.

47. Figure 8.11 Regeneration of ATP • ATP is renewable • regenerated by adding a phosphate group to adenosine diphosphate (ADP). • The energy to phosphorylate ADP comes from catabolic reactions in the cell. ATP H2O Energy for cellularwork (endergonic,energy-consumingprocesses) Energy fromcatabolism (exergonic,energy-releasingprocesses) ADP P i

48. ENZYMES • Enzymes speed up metabolic reactions by lowering energy barriers