To do list:

• Read chapter 2, work problems– Working with molarity, pH, especially– Look at Henderson-Hasselbalch

pH = pKa + log([base]/[acid])

• Work on amino acids– Names, structures, functional groups

• Paper summary (due 2/23/07)

Paper summary

• Discuss more in detail on Monday• Find an *interesting* biochemical paper

– Suggest Medline/Pubmedhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

– Biochemistry, Journal of Biological Chemistry, Biochemical Journal, etc.

– Recent: 2004-2007• Summarize the paper (1-2 pages dbl spaced)

– What’s the hypothesis/question? Why is it important? How did they address it? Conclusions?

– Is their conclusion valid? What are some alternative explanations?

• Today: ‘weak’ interactions (intramolecular bonding)

• Next week: osmosis, pH, water as a reactant

Weak interactions in biological systems

• Strong: covalent bonds

• Hydrogen bonds

• Dipole-dipole interactions

• Ionic interactions (attractive OR repulsive)

• Hydrophobic interactions

• van der Waals interactions

Electronegativity: How strongly an atom in a covalent bondpulls the shared electrons

More electronegative: Stronger pull

H C

2.1 2.5

Hydrogen: 2.1Carbon: 2.5Oxygen: 3.5Nitrogen: 3.0

H O

2.1 3.5

•Similar electronegativities•e- shared ~ equally•Non-polar bond

•~Big diff in electronegs•e- favor oxygen atom•Polar bond

+ -

Two dipoles attract

A B

A: more electronegative than B

- +

A B

- +

Water is a polar molecule

H O

H

H-bond “Donor”: O-H or N-H (or F-H)

H-bond “Acceptor”: O or N (or F)

Hydrogen bond (H-bond): strong (partial) positive charge on hydrogen attracts lone electon pair on oxygen or nitrogen

H-bond: Strength in numbers

• H-bond is weaker than a covalent bond– H-bond ~ 20 kJ/mol

– H-O covalent bond in H2O ~460 kJ/mol

• H-bond is stronger than a typical dipole-dipole interaction– Water (H2O) boiling point = 100°C

– Hydrogen sulfide (H2S) bp = -70°C

Much stronger intermolecular forces

Straight H-bonds = strongest

A driving force for the structures of protein and nucleic acid molecules

H-bond: Strength in numbers

“Hydrophobic force” “Hydrophobic interactions”

• Formation of the lipid bilayer

• Protein folding

• Protein-protein interactions

• Enzyme-substrate interactions

Water interacts with polar/charged molecules

• “Interaction” = forms bonds with

• Forming bonds = favorable enthalpically– Negative H

Entropy can drive dissolution(G = H – TS; G < 0 for spontaneous)

Enthalpy is good (plenty of bonds)Entropy is bad (limited freedom)

~same enthalpyGreat entropy S > 0

Dissolving of polar/charged solute

• Water loses hydrogen bonds (bad enthalpy)

• But makes up for them with water-solute bonds (back to ~neutral enthalpy)

Not all potential solutes can compensate for the lost H-bonding

Hydrophobic groups: G unfavorable for dissolving

S is negative:Maximizing H-bondsleads to fewerdegrees of freedom

Hydrophobic forces cause hydrophobic groups to assemble

Hydrophobic forces cause hydrophobic groups to assemble

*Positive S!*

van der Waals vs. Hydrophobic

Two dipoles attract

A B

A: more electronegative than B

- +

A B

- +

What about a non-polar molecule?

“Polarizability” increases with electron cloud size

• Benzene rings are relatively polarizable

• Nucleic acids: “stacking” of the base rings

• Proteins: interactions with phenylalanine, tyrosine, tryptophan, histidine

Types of interactions

• Covalent (intramolecular, very strong)

• Ionic • Hydrogen• Dipole-dipole• Hydrophobic• van der Waals

‘Weak’ interactions

Not unimportant