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Biochemistry

Biochemistry. Background. 1.Covalent and Noncovalent bond. Covalent Bonds (300-400 kJ/mol) Non-Covalent Interactions (2-40 kJ/mol) Hydrogen Bonds Charge-charge interactions Other non-covalent interactions. Charge-Charge Interactions. Coulomb's law F = k*(q 1 q 2 )/r 2

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Biochemistry

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  1. Biochemistry Background

  2. 1.Covalent and Noncovalent bond Covalent Bonds (300-400 kJ/mol) Non-Covalent Interactions (2-40 kJ/mol) Hydrogen BondsCharge-charge interactionsOther non-covalent interactions

  3. Charge-Charge Interactions • Coulomb's law • F = k*(q1q2)/r2 • dielectric medium, • F = k*(q1q2)/  r2

  4. Hydrogen Bonds • hydrogen bond donor :to which hydrogen is covalently bonded • hydrogen bond acceptor : with the nonbonded electron pair

  5. 2. The Role of Water in Biological Processes • Hydrophilic molecules in Aqueous Solution (Figure 2.11) • Hydrophobic moleculesin Aqueous Solution Clathrate cages (Figure 2.13) • Amphipathic moleculesin Aqueous

  6. Water

  7. Hydrophilic molecules

  8. Hydrophobic molecules • Clathrate cages

  9. Amphipathic molecules

  10. 3. pH • Acids and Bases: Proton Donors and Acceptors • pH = -log[H+] • Weak Acid and Base Equilibria • Ka and pKaKa=[H+][A-]/[HA]  pKa=pH-log [A-]/[HA] • Polyprotic Acids

  11. The pH Scale and the Physiologic pH Range

  12. Henderson-Hasselbalch Equation, pI • Titration of Weak Acids: The Henderson-Hasselbalch Equation: • pH = pKa +log [A-]/[HA] • pI : Each molecule has a distinct pH (called the pI or isoelectric point) at which the net average charge of all the groups adds up to zero. If acidic groups predominate, the pI will be low. If basic groups predominate, the pI will be high.

  13. Acid dissociation of glycine • Glycine has only a single acidic group and a single basic group, the pI can be determined by averaging the pKas of the two groups (from Equation 2.18) For example, the pKa values of the carboxylate and amino groups on glycine are 2.3 and 9.6, respectively. Thus, • pI = (2.3 + 9.6)/2 = 5.95

  14. The relative concentrations of the three forms of glycine as a function of pH.

  15. 4. Interactions Between Macroions in Solution • Solubility of Macroions and pH (Figure 2.20,Figure 2.21) • Repulsive effects (nucleic acids) • Attractive effects (histones to DNA) • Minimum solubility at isoelectric point • Influence of Small Ions: Ionic Strength (Figure 2.22)

  16. Figure 2.20 • Electrostatic interactions between macroions

  17. Figure 2.21

  18. Figure 2.22

  19. Debye-Huckel Theory • Salting In - adding counterions to a point increases protein solubility • Salting Out - adding very large amounts of counterions decreases protein solubility

  20. 5. Entropy and the Second Law of Thermodynamics • Entropy (S) Tendency of Systems of Molecules to RandomizationS = klnW (k = Boltzmann constant)

  21. Second Law • "The entropy of an isolated system will tend to increase to a maximum value"

  22. 6. Free Energy: The Second Law in Open Systems • G = H - TS G = H - T S G <0 means Exergonic, favorable process G >0 means Endergonic, reverse process favored

  23. Free Energy and Chemical Reactons: Chemical Equilibrium • Free Energy Change and the Equibrium Constant • = Standard State Free Energy Change = + RTln([products]/[reactants]) = + RTlnK, where K is equilbrium constant

  24. Free Energy Calculations • A Biochemical Example : • 1. G6P <=> F6P ( = +1.7 kJ/mol means equilibrium concentration has more G6P than F6P)2. Plugging this into , one finds that (F6P)/(G6P) = 0.5043. Since G = + RTln([products]/[reactants]), displacements away from equilibrium will be moved towards equilibrium by corresponding force of free energy change brought about by the change. (Figure 3.6)

  25. How Cells Use Energy • Light from the sun is the ultimate source of energy for all life on earth • photosynthetic organisms use light energy to drive the energy-requiring synthesis of carbohydrates • non-photosynthetic organisms consume these carbohydrates and use them as energy sources

  26. 7.Common Ground for Cells • Eukaryotes are complex; how did such cells arise from simplest progenitors? • Mutualism: a symbiotic association between two organisms that gives rise to a new organism combining characteristics of both original types • the lichen, which consists of a fungus and an alga • the root nodule system formed by a leguminous plant and anaerobic nitrogen-fixing bacteria • humans and bacteria such as Escherichia colithat live in the human intestinal tract

  27. Common Ground for Cells • a similar model can be proposed for the origin of chloroplasts • the fact that mitochondria and chloroplasts have their own DNA and their own apparatus for the synthesis of RNA and proteins supports this model • These proposed connections between prokaryotes and eukaryotes are not established with complete certainty • Still they provide an interesting framework from which to consider the reactions that take place in cells

  28. The root nodule(根瘤) • root nodule system formed by a leguminous plant and anaerobic nitrogen-fixing bacteria

  29. 叶状地衣 lichen 枝状地衣 丝状地衣

  30. 附：地衣中真菌的营养方式 • 吸根从真菌中长出，穿进藻类细胞，吸取营养，再回送给真菌菌丝体。

  31. Escherichia coli(大肠杆菌) • 4.7106bp，1.7mm • 编码约4300个蛋白质基因和115个稳定RNA基因

  32. End

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