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Chapter 2

01:694:301 Chapter Notes - Chapter 2: Electronegativity, Hydrophile, Chromatin


Department
Mol Bio & Biochem
Course Code
01:694:301
Professor
murphy
Chapter
2

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Chapter 2 – The Chemical Foundation of Life: Weak Interactions in an Aqueous Environment
2.1 – THE IMPORTANCE OF NONCOVALENT INTERACTIONS IN BIOCHEMISTRY
Noncovalent bonds are important because they’re weak
oCan break & re-form easily
oMultiple noncovalent bonds sum up in energy
Stable structures (DNA, Proteins, & Membranes)
2.2 – THE NATURE OF NONCOVALENT INTERACTIONS
Type of Interaction Model Example Dependence of
Energy on Distance
Charge-charge 1/r
Charge-dipole 1/r2
Dipole-dipole 1/r3
Charge-induced
dipole
1/r4
Dipole-induced
dipole
1/r5
Dispersion (Van der
Waals)
1/r6
Hydrogen bond Bond length fixed
Charge-Charge Interactions
Ionic bonds / salt bridges
Coulomb’s Law:
oF = kq1q2/r2
Repel (++) (--), F = (+)
Attract (+-), F = (-)
oF = kq1q2/εr2
ε increases = weaker F between charges
Use energy when considering changes in noncovalent bonding interactions
oE = kq1q2/εr
Strong over greater distances compared to other noncovalent interactions
Dipole & Induced Dipole Interactions
Polar molecules have dipole moment (µ)
oDipole moment expresses magnitude of polarity
1
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Chapter 2 – The Chemical Foundation of Life: Weak Interactions in an Aqueous Environment
Van der Waals Interactions
Repulsion when 2 nonbonding molecules get too close
Repulsive energy + attractive energies = total E of noncovalent interaction
r0 = most stable distance between the centers of the 2 interacting particles
rv = R1+R2 ; rv = closest approach
Hydrogen Bonds
Hydrogen covalently bonded to another atom
H-bond donor = the atom the H is covalently bonded to
oIt has an H attached to it
H-bond acceptor = the atom with the nonbonded electron pair
oIt has lone pairs of electrons
Dotted lines represents H-bonds
Greater Electronegativity = Greater H-bond donor
oMainly O & N
Relatively high bond energy for a noncovalent bond
H-bonding is prevalent in biomolecules & stabilizes structural elements
Organizes structures like the α-helix in proteins
2.3 – THE ROLE OF WATER IN BIOLOGICAL PROCESSES
The Structure & Properties of Water
Water strongly wants to form H-bonds with other water molecules
Oxygen in H2O is a great H-bond acceptor
o–OH groups in H2O are strong H-bond donors
Each H2O is a great H-bond donor & acceptor
Can form up to 4 H-bonds simultaneously
2 H-bond donor sites (-OH)
2 H-bond acceptor sites (O with two lone pairs)
Permanent dipole
High heat capacity
oAlmost constant temperature in big bodies of water
Acts as a temperature “buffer” in oceans and lakes
Density greater in liquid
oWhen ice lattice breaks down, molecules can move closer
High viscosity (resistance to flow)
oHas many interlocked H-bonded structures with it
High surface tension because of the many H-bonds
High dielectric constant (ε)
oBecause of its polar nature
2
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