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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