Bioc 462a Lecture Notes
8/19/02 12:28 PM
Noncovalent Bonds, Water, pH and Ionic Equilibria
Lecture Notes | 462a Home
Reading - Chapter 4 Practice problems - Chapter 4 - 2,3,5,6,8,10; Buffer and noncovalent interactions extra problems;
Key Concepts Noncovalent interactions (hydrogen bonds, ionic interactions, van der Waals interactions, and "hydrophobic interactions") are individually much weaker than covalent bonds, but are crucial to the structure and function of biomolecules. Properties of water are crucial to understanding the properties (structural and functional) of biomolecules because the biological milieu is primarily aqueous -- water is the solvent for most biomolecules. Most biomolecules have functional groups that are weak acids or bases, and the ionization properties of those groups are crucial to the structures and functions of the molecules; the pH determines the state of ionization of biomolecular weak acids and bases.. Biological systems, intracellular and extracellular, are BUFFERED.
Covalent Bond:
a pair of shared electrons counting as part of the outer shells of two atoms
Noncovalent Interactions: essential for proper functioning of biomolecules depend entirely on the properties of water much weaker (10-100 times) than covalent bonds weakness important noncovalent interactions continually being formed and broken life processes require this -- they're dynamic . (You can't get much biological activity from a rock!) involve electrical charges and partial charges; electrical interactions can be direct, as in ionic or dipole interactions, or indirect, as in induced dipole or dispersion forces, in which distortion of the electrons in nonpolar molecules is the basis for the interaction
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Bioc 462a Lecture Notes
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4 types of noncovalent interactions important in biochemistry: ionic interactions hydrogen bonds van der Waals interactions "hydrophobic interactions"
Relative strengths of interactions/bonds (actual strengths vary within categories -- this is a generalization): covalent bonds >> ionic interactions > hydrogen bonds > hydrophobic interactions = van der Waals interactions
1. Ionic Interactions (also called charge-charge interactions, or salt bridges): Coulomb’s Law: F = k [Q
1Q2
/ εr ] 2
F = strength (force) of interaction between charged particles, ε = dielectric constant of medium, r = distance file:///lapointe/Desktop%20Folder/Water/Matrix.html
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between charged groups force inversely proportional to the dielectric constant ( ε) of the solvent and to square of distance between charged groups Water: very polar, high dielectric constant (ε ~78) [reference ε = 1 for vacuum; ε for benzene, a very nonpolar solvent, = 4.6]
Question: Are ionic interactions stronger in polar or in nonpolar solvents? How do interactions with a polar solvent like water affect interactions between charged (or polar) solutes? Small ions in water can influence the interaction between biomolecules, by shielding the effective charge of the biomolecules. The strength of the effect of the small ions is given by the ionic strength (I) of the solution I = (1/2)
ΣMiZi2, where M i is the molarity and Zi is the charge of the ith ion in the solution.
2. Hydrogen Bonds hydrogen bond: an interaction between a hydrogen atom covalently bonded to an electronegative atom, the donor group (-O-H or -N-H), and a lone pair of non-bonded electrons on another electronegative atom, the acceptor group (O=C, O-H, N-H, =N-) In biological systems, only O and N have the appropriate electronegativity to serve as a hydrogen bond acceptor. This table summarizes the properties of a number of hydrogen bonds. energy of hydrogen bond small (≅ 20 kJ/mol) compared to O-H covalent bond strength (460 kJ/mol). However, because most biomolecules form many hydrogen bonds, they make a significant contribution to the stability of biomolecules. directionality of hydrogen bond important to its strength -- attraction between partial electrical charges is strongest when the 3 atoms involved (e.g. -O-H ----- :O= ) lie in a straight line. However, sometimes structural constraints in biomolecules result in "bent" geometry (weaker hydrogen bonds) Fig. 4-5: Directionality of the hydrogen bond
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3. van der Waals Interactions nonspecific, weak transient electrostatic forces between ANY 2 atoms that approach each other depend on outer electron orbital overlap between atoms -- attractive force increases as nuclei get closer together, until they get too close (outer electron orbitals begin to overlap), when the electron clouds begin to repel each other When attractive force = repulsive force, nuclei are in "van der Waals contact" individual interatomic interactions very weak, but collectively, many van der Waals interactions add up to significant stabilizing forces within and between molecules
3. "Hydrophobic Interactions" "hydro" "phobic" = water fearing hydrophobic effect involves association of nonpolar groups with each other in aqueous systems due to the un favorable interaction of nonpolar groups/molecules with water result = "preference" of hydrophobic groups and molecules to minimize their exposure to water
Properties of Water Unusual Properties Life as we know it could not exist without water. All cells, whether from terrestrial or aquatic organisms, are more than 70% water. The structures and properties of the biomolecules on which life depends, proteins, nucleic acids, lipids and complex carbohydrates, are entirely dependent on the unique properties of water -- no other solvent has properties similar to water. Water has unusual properties when compared to molecules with similar size or structure, e.g., NH3, HF or H2S: Higher boiling point Higher melting point Higher surface tension Higher heat of vaporization
Question: What do these unusual properties suggest about H2O?
Structure of Water - the hydrogen bond file:///lapointe/Desktop%20Folder/Water/Matrix.html
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Bioc 462a Lecture Notes
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Water molecule BENT (H-O-H bond angle is 104.5o) Electronegativity difference between H and O RESULT: strong ionic character to the O-H bond CONSEQUENCE: large dipole moment for water, making it a highly polar solvent.
What gives H2O the unique properties listed above? HYDROGEN BONDS: directional interactions between the H on one water molecule and a lone pair of electrons on the O of another water molecule. Question: In how many hydrogen bonds can each H2O molecule participate?
Because of its highly polar character , water also interacts favorably with ions. (molecular graphics - water).
Solvent Properties of Water Hydrophilic or polar molecules very soluble in water interact favorably with water by formation of hydrogen bonds or via ionic interactions
Fig. 4-6. Water dissolves ionic compounds by hydrating them (surrounding the charged group -- H2O interacts electrostatically with the solute via charge-dipole interactions), screening the electrostatic interactions between solute molecules.
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Hydrophobic or nonpolar molecules (no ionic or polar groups, can't form hydrogen bonds, lack favorable interactions with H2O) Presence of hydrophobic molecules in water makes water molecules organize around hydrophobic molecule to form a Clathrate Clathrate formation causes the order of the water molecules to increase, i.e. a decrease in entropy (thermodynamically unfavorable ). "Hydrophobic Effect: combination of lack of favorable hydrogen bonding between hydrophobic molecules and water plus the unfavorable effect of entropy change --> very low solubility of hydrophobic molecules in water
Amphipathic molecules -- 2 "parts": hydrophilic (polar) head group and hydrophobic nonpolar tail Many biomolecules are amphipathic. Result = identity crisis! Polar head group interacts favorably with water but the hydrophobic tail does not.
Fig. 4-7a. Long-chain fatty acids have very hydrophobic alkyl chains, each of which is surrounded by a layer of highly ordered H2O molecules.
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Resolution of amphipathic molecules' "identity crisis": formation of a monolayer, a micelle or a bilayer (all these self-assemble in water -- heads interacting with H2O, tails NOT in contact with H2O) Amphipathic molecules with single tails, e.g., detergents or fatty acid salts, usually --> micelles Molecules with two tails, e.g., phospholipids, --> bilayers Large areas of bilayers --> closed structures like vesicles Two-tailed amphipathic molecules = basis for formation of biological membranes
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Colligative Properties: properties of the solution that depend on the number of solute molecules present (e.g., freezing point depression, boiling point elevation and osmotic pressure). Osmotic pressure (particularly important in biological systems) -- develops when a semipermeable membrane, e.g. plasma membrane of cell, separates two solutions, one of which contains a solute that cannot pass through the membrane. Water can pass through the membrane and moves into compartment containing nonpermeable solute in attempt to make concentration (activity) of H2O the same on both sides of membrane. As illustrated below, this will cause a column of water to rise in the tube containing the solute. Osmotic pressure (π) is the amount of pressure that must be exerted on the tube to prevent the column of solution from rising; π = RTm, where R is the gas constant, T is the absolute temperature and m is the molality = mol of solute/kg of solvent.
For a cell, if water moves into the cell from the surrounding solution, the solution is said to be hypotonic - the concentration of dissolved material is less in the solution than in the cell. In such a solution the cell will expand and probably burst. if water moves out of the cell into the surrounding solution, the solution is said to be hypertonic - the concentration of dissolved material is more in the solution than in the cell. In such a solution the cell will contract.
Ionization Properties of Water Acids, Bases, Buffers For biological systems, one of the most important parameters of an aqueous solution is the concentration of +
+
-6
-8
protons ([H ]). Although the [H ] is quite low, typically 10 to 10 M, it must be maintained within this range for life to exist. Weak acids dissociate in water according to the following equation: file:///lapointe/Desktop%20Folder/Water/Matrix.html
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.
The actual reaction is
but because concentration of H 2O is constant, shorthand equation shown is used. Acid dissociation constant: Ka = [A -][H +]/[HA] . Ka values for weak acids of biological importance
