Monday 9 26 05

9/26/05
• There are four different types of bonds:
1. covalent bonds- strong interactions
2. electrostatic bonds- cations and anions in aqueous solution.
3. hydrogen bond – form between hydrogen donors and hydrogen acceptors
4. van der Waals bonds – weak, non-polar interactions, not good in aqueous solution.
• Water must be excluded in major catabolic pathways so it does not compete for bonds. Very important for the formation of complex proteins.
Amino Acids and Proteins
• In all cases but one all proteins are optical active. Glycine is the exception because it has hydrogen for its R group.
• Alanine is the simplest, optical active, protein because it has CH3 for its R group.
• Figure 3-3 L form is standard, this means the carboxyl group is north and the amine group is east. The L form is what is commonly found in nature. D form is rare, and when found it is usually changed to the L form with enzymes.
• Figure 3-5 The 20 amino acids are subdivided into 4 groups based on the R chain. (He wants you to know all 20 and what makes them chemically different, he said names are not so important.)
• Non-polar, aliphatic (hydrophobic) R group – glycine, alanine, praline, valine, leucine, isooleucine, methionine.
• Aromatic R group – Phenylalanine, tyrosine, tryptophan. All can absorb UV light. Tryptophan absorbs more than tyrosine and phenylalanine absorbs the least amount. Figure 3-6 shows the absorption levels of tryptophan and tyrosine.
• Polar, uncharged R groups – serine, threonine, cystine, asparagines, and glutamine.
• Positively charge R groups- lysine, arginine, histidine. These are basic R groups.
• Negatively charged R group – aspartate, glutamate. Acidic R groups, second carboxyl group attached.
• Cysteine has a self hydrogenating group with SH
• Figure 3-7 2 cystEINE can form a disulfide bond to make cystINE. Similar words, very different compounds, be careful.
• Figure 3-8 The uncommon amino acids: 4-hydroxyproline, 5-hydroxyproline, 6-N-methyllysine, y-carboxyglutamte, desmosine, selenocysteine.
• Figure 3-9 Nonionic and zwitterionic forms. Zwitterionic is common in neutral pH. They differ because the H is pulled off the OH, given O a negative charge that balances with the positive N.
• Isoelectric point – where the pH at which there is no electrical charge on the molecule. To find it, you take the to pKa from the titration and average them. What happens when there are three? (He did not answer his own question, he left it up to us.)
• Figure 3-10 The titration graph shows the two pKa’s where there is a buffering going on and the pI (isoelectric point) is in the middle of the sharp incline.
• Figure 3-11 This chart shows the power of proteins. If you look at the acetic acid, it has a pH of 4.8. But the alpha-Amino acid, with the acetic acid on it, has a higher pH 2.34 because the N from the amine is pushing the H off. Looking at the Methylamine, it is very basic with a pH of 10.6. The alpha-Amino acid has a lower pH at 9.6 because of the carboxyl group pulling the H towards it.
• Histidine is the only protein that acts as a buffer in biological neutrality, making it very important to catabolic pathways. Its pKa is close to 6.