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Chem 331 Biochemistry

Dr. Joseph Provost 375 (Office) / 425 (Lab) SCST

e-mail: josephprovost@sandiego.edu Telephone: 7564 / 4351 (Lab)

… and now the fun begins...

Functional Groups - One of the reasons why organic chemistry is a prerequisite for the class

Just for review – recognize each of the following.

Also know…

Imidizole Guanidino

R1-C-O-C-R2 =

O

=

O Anhydride (2 carboxylic acids)

R1-C-S-R2 =O

Thioester R1-S-S-R2 Disulfide

Structure and Function The shape and role of a biomolecule is largely determined by many weak forces

•  Shape of molecules, interaction between molecules, binding of small molecules

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

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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

•  Water and salts weaken bond. •  How?

Ionic Bonds

Ionic bonds contribute to the stability of proteins

Ionic Bonds

But these bonds are not the MAIN or

largest contributor to protein structure???

Metals can bridge opposite charges.

Phosphate backbone of nucleic acid & ion

Attractive forces between polar molecules Dipole-Dipole interactions

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.

✔

Special Dipole Interaction: the Hydrogen Bond

i.  A and D are typically electronegative atoms (ie O, N, S).

ii.  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).

Acceptor Donor 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

Hydrogen Bonds

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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

Van der Waals (dipole-dipole induced interactions)

The van der Waals interaction energy profile as a function of the distance, r, between the centers of two atoms.

Intermolecular forces

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).

( ) V(r) = 4ε σr

12 6 - ( ) σ

r

Repulsive forces

dispersion forces

•  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).

Space filling models use the van der Waal Radii to depict sizes

Van der Waals (dipole-induced interactions)

The observation that hydrophobic compounds and particles or regions of molecules associate together avoiding contact with water

Hydrophobic interactions

No interaction between hydrophobic molecules = relative high order (think number of molecules organized) low entropy

Interaction between hydrophobic molecules = relative low order High entropy

The Solvent Properties of Water Derive from Its Polar Nature

Nonpolar molecules decrease the entropy of solvent water (left). When nonpolar molecules coalesce (arrow), the entropy of the solvent increases.

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

hydrophobic portions of the molecule permits the water max degrees of freedom (a minimization of entropy increase)

Hydrophobic interactions

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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