DBT2117: Biochemistry (I)
Lecture 2
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Non‐covalent interactions
Hydrogen bonding
Properties of water
Hydrophobic effect
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Covalent vs. noncovalent
Covalent bonds – formal electron sharing between two atoms. σ bond
π bonds
Noncovalent Interactions – electrostatic interactions between molecules or within a molecule. Also called non‐covalent bonds or forces
Ionic interaction
Hydrogen bonding
Van der Waals forces
Intermolecular interactions
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Covalent and noncovalent in biochemistry
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The macromolecules that participate in the
structural and functional matrix of life are
immense structures held together by strong,
covalent bonds.
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The complex 3‐D architecture of the
macromolecules is determined by noncovalent
interactions.
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Noncovalent interactions are critically important
determinants of biomolecular structure, stability,
and function.
Example: proteins
• Proteins are polymers of amino acids, held together by strong covalent amide
(peptide) bonds.
• The 3‐D structure, and hence function of
proteins are determined by a large
number of noncovalent interactions.
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Importance of non‐covalent bonds
Energies of non‐covalent interactions typically are 1 – 2 orders of magnitude weaker than energies of the covalent bonds found in biochemical (C‐C, C‐H). Why are non‐covalent interactions important for biochemistry and life in general?
They are essential because they can be continuously broken and re‐formed for dynamic interactions between compounds.
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Types of noncovalent interactions
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Charge‐Charge interactions
Force between two charges in vaccum:
(Coulomb’s Law)
Force between two charges in a medium:
Where ε is the dielectric constant
Higher the dielectric constant, lower the force between the charges.
ε
ε for water is about 80, while organic liquid typically is 1 – 10.
Water “shields” the two charges
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Charge‐Charge interactions form “salt bridges” or ionic bonds
Salt bridges provide stability to structure. (remember that ‐13 to ‐17 kJ/mol..)
(so formation of this salt bridge provides this energy)
(negative energy = favorable, so stability)
http://people.uwplatt.edu/~sundin/363‐7/image/l637‐33j.gif
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Dipole moment
Because of difference in atom’s electronegativity and molecular geometry, Electron can be “distributed” differently within a molecule.
If a molecule has a difference in electron distribution among its ends, then this molecule is Polar. Examples: Water, CO, Glycine, etc. δ is symbol used for partial charge
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Dipole moment
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Induced dipole interactions
FIGURE 2.5
Induced dipoles and dispersion forces. (a) Benzene
has neither a net charge nor a permanent dipole
moment, but a nearby charge can induce a
redistribution of electrons within the benzene ring,
producing an induced dipole moment (μ). (b) Planar
molecules like benzene have a strong tendency to
stack because fluctuations in the electron clouds of
the stacked rings interact with one another,
producing a dispersion force. (c) Although the
molecules approach closely, they do not
interpenetrate.
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Van der Waals forces
FIGURE 2.6
Noncovalent interaction energy of
two approaching particles. The
interaction energy of two atoms,
molecules, or ions is graphed
versus the distance between their
centers, r. The total interaction
energy (E) at any distance is the
sum of the energy of attraction and
the energy of repulsion. As the
distance between the particles
decreases (reading right to left
along the x-axis), both the
attractive energy (60) and the
repulsive energy (70) increase, but
at different rates. At first the longerrange attraction dominates, but
then the repulsive energy
increases so rapidly that it acts as
a barrier, defining the distance of
closest approach (rv) and the van
der Waals radii (R, described by
the orange spheres). The position
of minimum energy (r0) is usually
very close to rv.
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A particularly important Dipole‐Dipole interaction: Hydrogen bonding
For example, alcohol & carbonyl
Water & itself
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Major types of H‐bonding found in biochemistry
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Properties of Water
Hydrogen‐bond donors and acceptors in water. The two nonbonded electron pairs on O act as H‐bond acceptors and the two O H bonds act as H‐bond donors.
How many H‐bonds can each water molecule form?
How the properties of water below be explain by H‐bonding?
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Properties of Water
When ice melts, liquid Water is not as rigid, however, significant bonding pattern remains. On average, 3.4 H‐bond per water
Ice (solid water) forms with regular lattice structure – 4 H‐bond per water
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Properties of Water
Water serves as the universal intracellular and extracellular medium, thanks primarily to two properties:
• ability to form hydrogen bonds
• polar character
Substances that can take advantage of these properties so as to readily dissolve in water are called hydrophilic, or “water loving.”
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Hydration shells
Water is an excellent solvent for ionic compounds.
•The interactions of the negative ends of the water dipoles with cations
and the positive ends with anions in aqueous solution cause the ions to become hydrated, that is, surrounded by shells of water molecules called hydration shells.
•The dissolution of ionic compounds like NaCl in water can be
accounted for largely by two factors. o The formation of hydration shells is energetically favorable.
o The high dielectric constant of water screens and decreases the
electrostatic force between oppositely charged ions that would
otherwise pull them back together.
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Hydration shells
Hydration of ions in solution. A salt crystal is shown dissolving in water.
As sodium and chloride ions leave the crystal, the noncovalent interaction
between these ions and the dipolar water molecules produces a hydration
shell around each ion. The energy released in this interaction helps
overcome the charge–charge interactions stabilizing the crystal.
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Example of how polar‐charge interaction is used in biochemistry
Dipole‐charge interaction is frequently used in enzyme catalysis:
Picture below shows the first step in a protease reaction
Gly193‐N‐H
Ser195‐N‐H
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Example of hydrogen bonding – spider silk
Sinan Keten, Markus J. Buehler, 2010, Nanostructure and molecular mechanics of spider dragline silk protein assemblies, J. R. Soc. Interface 2010 ‐; DOI: 10.1098/rsif.2010.0149.
H‐bonding between Glycine amino hydrogen and neighboring chain’s alanine carbonyl Oxygen
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Example of hydrogen bonding – DNA pairing
DNA pairing is achieved through H‐bonding
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Hydrophobic effect: Hydrophobic compounds aggregates in aqueous solution and exclude water out. http://photographyblogger.net/18‐interesting‐pictures‐of‐oil‐in‐water/
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Hydrophobic effect: •
Nonpolar substances like hydrocarbons, are nonionic and cannot
form hydrogen bonds, show only limited solubility in water.
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Such nonpolar molecules are called hydrophobic, or “water fearing.”
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We can also call them lipophilic, or “fat loving.”
• When hydrophobic molecules do dissolve,
they are not surrounded by hydration shells,
rather the regular water lattice forms ice‐
like clathrate structures, or “cages,” about
the nonpolar molecules.
• This ordering of water molecules extends
well beyond the cage, corresponds to a
decrease in the entropy, or randomness, of
the mixture.
• This hydrophobic effect plays a role in
protein folding.
http://photographyblogger.net/18‐interesting‐pictures‐of‐oil‐in‐water/
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