Download Intro and Non-Covalent Interactions

8/24/16 Chem 331 Biochemistry
Dr. Joseph Provost
375 (Office) / 425 (Lab) SCST
e-mail: [email protected]
Telephone: 7564 / 4351 (Lab)
Also know…
R1-S-S-R2
O
The shape and role of a biomolecule is largely
determined by many weak forces
•  Shape of molecules, interaction between
molecules, binding of small molecules
O
=
R1-C-O-C-R2
=
Anhydride (2 carboxylic acids)
Guanidino
R1-C-S-R2
Thioester
Functional Groups - One of the reasons why
organic chemistry is a prerequisite for the class
Just for review – recognize each of the following.
Structure and Function
=
Disulfide
… and now the fun begins...
O
Imidizole
Inter-Intra molecular forces
•  Covalent bonds hold atoms together so that
molecules are formed
•  Weak forces profoundly influence the
structures and behaviors of all biological
molecules
•  Weak forces create interactions that are
constantly forming and breaking under
physiological conditions
•  Energies of weak forces range from 0.4 to 30
kJ/mol
Noncovalent interactions
Weak forces include:
o Ionic interactions
o Hydrogen bonds
o Van der Waals
interactions
o Hydrophobic
interactions
Ionic>H-bond, hydrophobic>van der
Waals
1 8/24/16 Ionic Bonds
Ionic Bonds
Ionic Bonds AKA salt bridges...
Simple magnetic attraction between: Carboxy and amino
groups, metals…
•  The force of attraction (F) depends on distance and
relative shielding - Measured by Coulomb’s Law
Ionic bonds
contribute to
the stability of
proteins
But these bonds are
not the MAIN or
largest contributor to
protein structure???
•  Water and salts weaken bond.
•  How?
Dipole-Dipole interactions
Metals can bridge opposite charges.
Attractive forces between polar molecules
✔
①  A molecular dipole arises from the unequal sharing of electrons between
atoms leading to partial negative and partial positive ends of a molecule.
②  The molecular dipole, if not cancelled by the molecular geometry, results in
a polar molecule.
③  The partially positive end of a polar molecule is attracted to the partially
negative end of another.
Phosphate backbone of nucleic acid & ion
Special Dipole Interaction: the Hydrogen Bond
Acceptor
Donor
i. 
A and D are typically electronegative
atoms (ie O, N, S).
A has a lone pair of electrons (ie
Lewis base) & interacts favorably
with acidic proton bound to
electronegative D.
iii.  H bond strength range from strong
(20-40 kcal), moderate (3-12 kcal/mol)
to weak (1-5 kcal/mol).
ii. 
Hydrogen Bonds
H Bonds result from the
interactions of strong covalent
bonds between hydrogen and a
highly electronegative atom (N
and O)
Strongest bonds are when the
arraignment is linear.
The hydrogen is “shared” by a
the covalently bonded atom
and another electronegative
atom
You must be able to identify the
donor and acceptor
2 8/24/16 Van der Waals
(dipole-dipole induced interactions)
Repulsive
forces
Next to london dispersion
forces, these are the
weakest of the nonionic bonds
but are important due to the
large number of van der Waal
interactions in a protein
These bonds originate from
very small dipole moments
generated in atoms as
electrons move around the
nucleus
Intermolecular forces
dispersion
forces
12
V(r) = 4ε
The van der Waals interaction energy profile
as a function of the distance, r, between the
centers of two atoms.
Van der Waals
(dipole-induced interactions)
6
(σr ) - (σr )
•  V is the intermolecular potential
between the two atoms or molecules.
•  ϵ is the well depth and a measure of
how strongly the two particles attract
each other.
•  σ is the distance at which the
intermolecular potential between the
two particles is zero (See Figure 1.2).
•  σ gives a measurement of how close
two nonbonding particles can get and is
thus referred to as the van der Waals
radius.
•  r is the distance of separation between
both particles (measured from the
center of one particle to the center of
the other particle).
Together, attractive dispersion & repulsive
exclusion interactions define an optimum
distance separating any two neutral atoms
at which the energy of interaction is a
minimum – defining an effective radius
known as the van der Waals radius (rvdw).
Hydrophobic interactions
The observation that hydrophobic compounds and
particles or regions of molecules associate together
avoiding contact with water
No interaction between
hydrophobic molecules = relative
high order (think number of
molecules organized) low entropy
Space filling models use the van der
Waal Radii to depict sizes
The Solvent Properties of Water Derive
from Its Polar Nature
Interaction between
hydrophobic molecules = relative
low order High entropy
Hydrophobic interactions
Water forms cage-like structure around
hydrocarbons forming shells of highly
ordered water – Clathrate Cage
–  Shell formation is due to water
forming hydrogen bonds with each
other
–  Aggregation of hydrophobic
moleculules reduces total surface
area and results in less order
(increase in entropy)
–  Minimization of the
Nonpolar molecules decrease the entropy of solvent water (left). When
nonpolar molecules coalesce (arrow), the entropy of the solvent increases.
hydrophobic portions of the molecule permits the water max degrees of
freedom (a minimization of entropy increase)
3 8/24/16 Cellular organization
If you haven’t looked at this information for a while or are not
familiar – review the structure and organization of prokaryotes
and eukaryotes.
• 
Know the function of the organells for each type of cells
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