Chapter 2: Biomolecules in Water

水做為溶劑之特殊性水做為溶劑之特殊性非共價作用力非共價作用力解離常數與解離常數與 pHpH緩衝溶液緩衝溶液

水為生物的首選溶劑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水是威力強大的小分子

Weak Chemical BondsWeak Chemical Bonds

Non-covalent interactions:Non-covalent interactions:

– Hydrogen bondsHydrogen bonds 氫鍵氫鍵– Ionic interactionsIonic interactions 離子交互作用離子交互作用 (( 靜電吸引力靜電吸引力 ))– Hydrophobic interactions (Hydrophobic interactions ( 厭水性交互作用厭水性交互作用 ))– van der Waals interactions (van der Waals interactions ( 凡得瓦爾力凡得瓦爾力 ))

這些弱的維繫力重要性何在這些弱的維繫力重要性何在 ??

*

““The more complex the system, the weaker The more complex the system, the weaker are the forces that govern its behavior”are the forces that govern its behavior”

- J. R. Platt- 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 InteractionsThe Four Weak Interactions *

共通特質：

1. 非共價

2. 可逆

3. 專一

The Polar Nature of WaterThe Polar Nature of Water

Given the difference in Given the difference in electronegativity electronegativity between oxygen and between oxygen and hydrogen (3.5 - 2.1 = hydrogen (3.5 - 2.1 = 1.4) and its shape, water 1.4) and its shape, water is a polar molecule with a is a polar molecule with a dipole moment of 1.85Ddipole moment of 1.85D– the net charge on oxygen the net charge on oxygen

is -0.66 and that on each is -0.66 and that on each hydrogen is +0.33hydrogen is +0.33

1. Hydrogen Bonds1. Hydrogen Bonds < 5% of the bond strength of a O-H (20 vs. 460 < 5% of the bond strength of a O-H (20 vs. 460

kJ/mole)kJ/mole) Much longer bond distance: 0.18 vs. 0.096 nmMuch longer bond distance: 0.18 vs. 0.096 nm Highly directionalHighly directional Based on the dipole moment of waterBased on the dipole moment of water Account for the unusual properties of water as both Account for the unusual properties of water as both

substance and solventsubstance and solvent

Common Hydrogen BondsCommon Hydrogen Bonds *

PeptidesX-H:::AX= Hydrogen bond donor N, O, S A= Hydrogen bond acceptor O, N

Hydrogen bonding in iceHydrogen bonding in ice

冰為何浮在水上？

Ice crystal: staticWater: dynamic breaking and forming

重要生物分子間氫鍵重要生物分子間氫鍵

Hydrogen Bond Strength is Highly Hydrogen Bond Strength is Highly DirectionalDirectional

Fig. 2-5

2. Ionic Interactions2. Ionic Interactions

They are about 5-10% the strength of a They are about 5-10% the strength of a carbon-carbon bond (20-40 vs. 350 carbon-carbon bond (20-40 vs. 350 kJ/mole)kJ/mole)

Ionically stabilized compounds (like NaCl) Ionically stabilized compounds (like NaCl) are readily dissolved in solvents with a are readily dissolved in solvents with a high dielectric constant (like water)high dielectric constant (like water)

Why?Why?

F= Q1Q2 / r2

: dielectric constant

r: distance between the charge groups

Solvent Properties of HSolvent Properties of H22OO Ionic compounds (e.g.,KCl) and low-molecular- Ionic compounds (e.g.,KCl) and low-molecular-

weight polar covalent compounds (e.g., Cweight polar covalent compounds (e.g., C22HH55OH OH and CHand CH33COCHCOCH33) tend to dissolve in water) tend to dissolve in water

The underlying principle is electrostatic The underlying principle is electrostatic attraction of unlike charges; the positive dipole attraction of unlike charges; the positive dipole of water for the negative dipole of another of water for the negative dipole of another molecule, etc.molecule, etc.– ion-dipole interactionion-dipole interaction:: e.g., KCl dissolved in H e.g., KCl dissolved in H22OO

– dipole-dipole interactionsdipole-dipole interactions:: e.g., ethanol or acetone e.g., ethanol or acetone dissolved in Hdissolved in H22OO

– dipole induced-dipole interactionsdipole induced-dipole interactions:: weak and weak and generally do not lead to solubility in watergenerally do not lead to solubility in water

Dipole-Dipole

Ion-Dipole

Salts Dissolve in Aqueous Salts Dissolve in Aqueous “Cages of Hydration”“Cages of Hydration”

Fig. 2-6還有什麼因素讓鹽很容易溶於水？

氧既是非極性，又如何支持生命？氧既是非極性，又如何支持生命？

3. Hydrophobic Interactions3. Hydrophobic Interactions

They are about 2% the strength of a carbon-They are about 2% the strength of a carbon-carbon bond (8 vs. 350 kJ/mole)carbon bond (8 vs. 350 kJ/mole)

Water becomes highly ordered around Water becomes highly ordered around hydrophobic groupshydrophobic groups

Greasy chains stay together to minimize Greasy chains stay together to minimize entropy loss by waterentropy loss by water

水的退出有利酵素與受質作用水的退出有利酵素與受質作用

4. van der Waals Interactions4. van der Waals Interactions

They are about 1% the strength of a They are about 1% the strength of a carbon-carbon bond (4 vs. 350 kJ/mole)carbon-carbon bond (4 vs. 350 kJ/mole)

Attraction between atoms by transiently-Attraction between atoms by transiently-induced dipolesinduced dipoles

Repulsion when the electron clouds bump Repulsion when the electron clouds bump together together