Wednesday 9 28 05

{Section notes 9/28/05
Office hours and email are posted on website.
Show as much work possible on homework for credit.
Homework tips:
Problem 1: Histidine has a lone pair of electrons on the N that is not boded to H in the book. This lone pair can pick of a H and take on a charge. This will help with parts B and C.
Problem 2: You need to use both pKa’s and the pI (which you need to find). Then use the Henderson-Hasselbalch equation (page 67.) }

9/28/05
• Different types of protein – catalytic protein in plants, transport proteins in hemoglobin, and structural proteins in skin. Figure 3-1
• For two amino acids to bond together, H2O is removed. It has an amino- terminal end and a carboxyl terminal end (you read the protein from amino to carboxyl.) The bond form is extremely stable and it retains in polarity, meaning the NH3 stays positive and the COO stays negative on the ends. The R group is not involved in the bonding.
• Polypeptide is linear structure of protein. A three letter code is used for proteins as a short hand for writing them. Table 3-3 Random distributions in proteins, not equal amounts.
• Number of bonds = amino acids -1
• Table 3-2 Molecular Data on Some Proteins. Shows their weight, how many residues and the number of polypeptide chains.
• Table 3-4 Conjugated proteins. Proteins and prosthetic groups come together to make different functioning proteins.
• Fred Sanger in the 1950’s used insulin to map the amino acids. He knew the molecular weight and started at the amino end and pulled one amino acid off at a time to chemically purify the two chains of insulin so that he could sequence.
• Primary structure- amino acid residues
• Secondary structure- alpha-helix
• Tertiary structure – polypeptide chains
• Quaternary structure – assembled subunits (All shown in Figure 3-16)
• In the 1940’s, X-ray diffraction studies shows that the proteins were 3-D.
• Water soluble proteins could also be crystallized and still be functional, showing that they proteins where is some 3-D form.
• Protein folding is very important, determines function. Will fold by non-covalent bonds in high-order folding. Primary folding is from covalent bonds.
• When folding, it is important that water is excluded because it can denature the protein. Water excludes itself because it forms stronger H bonds with other water molecules, so it finds other water to bond with, making sure it does not get in the way of the other bonds.
• Folding of Proteins
• The carbonyl oxygen has a partial negative charge and the amide nitrogen has a partial positive charge, setting up a small electric dipole. Virtually all peptide bonds in proteins occur in this Tran configuration,
• Figure 4-2 Because of this dipole and double bonds in the peptide, there are two rotation angles on the alpha carbon, creating 2 different plate alignments. (This eliminates any rings forming because of angle strain.)
• Figure 4-3 This ramachandran plot shows the different combinations of the angles that are favored thermodynamically.
• Figure 4-4 folding in an alpha helix was just a guess at first and had to be proven, it was right.
• Because of the acceptor and donor still present in the backbone of the helix, higher structures were possible because of more H bonding.
• Box 4-1 Right handed helix, thumb is pointing to the amino terminal end and fingers turn counter clock wise up the amino acids. Right handed helixes are more favored than left.
• R groups are all facing out. The sequence depends on stability of the R group. R groups can attract or repel each other. Just another factor in folding.
• Alpha helixes have dipole movement toward amino terminus, which effects which way the R group is pointing depending on it charge.
• Antiparallel- beta structure in a sheet form. Figure 4-7 (He stopped talking because time was out. He will continue here on Friday 9/30.)