Chapter 2: Biomolecules in Water

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Chapter 2 Biomolecules in Water

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• 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

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Weak Chemical Bonds

• Non-covalent interactions
• Hydrogen bonds??
• Ionic interactions??????(?????)
• Hydrophobic interactions (???????)
• van der Waals interactions (?????)
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The more complex the system, the weaker are the
forces that govern its behavior - J. R.
Platt
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Structure ?? ??? ????? ????? ??
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The Four Weak Interactions

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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

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1. Hydrogen Bonds

• lt 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

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Common Hydrogen Bonds

X-HA X Hydrogen bond donor N, O, S
A Hydrogen bond acceptor O, N
Peptides
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Hydrogen bonding in ice
Ice crystal static Water dynamic breaking and
forming
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Hydrogen Bond Strength is Highly Directional

Fig. 2-5
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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
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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

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Dipole-Dipole
Ion-Dipole
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Salts Dissolve in Aqueous Cages of Hydration
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Fig. 2-6
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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

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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

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