Chapter 2: Biomolecules in Water

Chapter 2: Biomolecules in Water 水做為溶劑之特殊性非共價作用力解離常數與pH 緩衝溶液

水為生物的首選溶劑 • Biological solvent: a medium for metabolic reactions • aquaporins: membrane channels for water transport • Essential buffer to regulate temperature and pH: high specific heat capacity and pH-regulating substances dissolved in it • Participant in many biochemical reactions: photosynthesis and hydrolysis of ATP

水是威力強大的小分子

* Weak Chemical Bonds Non-covalent interactions: • Hydrogen bonds氫鍵 • Ionic interactions離子交互作用(靜電吸引力) • Hydrophobic interactions (厭水性交互作用) • van der Waals interactions (凡得瓦爾力) 這些弱的維繫力重要性何在?

“The more complex the system, the weaker are the forces that govern its behavior”- J. R. Platt 較強較弱 Forces:核間力原子力共價鍵非共價鍵重力 _________________________________________ Structure:原子核原子簡單化合物生物巨分子宇宙簡單複雜

* The Four Weak Interactions • 共通特質： • 非共價 • 可逆 • 專一

The Polar Nature of Water • Given the difference in electronegativity between oxygen and hydrogen (3.5 - 2.1 = 1.4) and its shape, water is a polar molecule with a dipole moment of 1.85D • the net charge on oxygen is -0.66 and that on each hydrogen is +0.33

1. Hydrogen Bonds • < 5% of the bond strength of a O-H (20 vs. 460 kJ/mole) • Much longer bond distance: 0.18 vs. 0.096 nm • Highly directional • Based on the dipole moment of water • Account for the unusual properties of water as both substance and solvent

* Common Hydrogen Bonds X-H:::A X= Hydrogen bond donor N, O, S A= Hydrogen bond acceptor O, N Peptides

Hydrogen bonding in ice Ice crystal: static Water: dynamic breaking and forming 冰為何浮在水上？

重要生物分子間氫鍵

Hydrogen Bond Strength is Highly Directional Fig. 2-5

2. Ionic Interactions • They are about 5-10% the strength of a carbon-carbon bond (20-40 vs. 350 kJ/mole) • Ionically stabilized compounds (like NaCl) are readily dissolved in solvents with a high dielectric constant (like water) Why? F= Q1Q2 / er2 e: dielectric constant r: distance between the charge groups

Solvent Properties of H2O • Ionic compounds (e.g.,KCl) and low-molecular- weight polar covalent compounds (e.g., C2H5OH and CH3COCH3) tend to dissolve in water • The underlying principle is electrostatic attraction of unlike charges; the positive dipole of water for the negative dipole of another molecule, etc. • ion-dipole interaction: e.g., KCl dissolved in H2O • dipole-dipole interactions: e.g., ethanol or acetone dissolved in H2O • dipole induced-dipole interactions: weak and generally do not lead to solubility in water

Dipole-Dipole Ion-Dipole

Salts Dissolve in Aqueous “Cages of Hydration” 還有什麼因素讓鹽很容易溶於水？ Fig. 2-6

氧既是非極性，又如何支持生命？

3. Hydrophobic Interactions • They are about 2% the strength of a carbon-carbon bond (8 vs. 350 kJ/mole) • Water becomes highly ordered around hydrophobic groups • Greasy chains stay together to minimize entropy loss by water

水的退出有利酵素與受質作用

4. van der Waals Interactions • They are about 1% the strength of a carbon-carbon bond (4 vs. 350 kJ/mole) • Attraction between atoms by transiently-induced dipoles • Repulsion when the electron clouds bump together

Chapter 2: Biomolecules in Water