Lecture #34
Chapter 27   CURMUDGEON GENERAL'S WARNING. These "slides" represent highlights from lecture and are neither complete nor meant to replace lecture. It is advised not to use these as a reliable means to replace missed lecture material. Do so at risk to healthy academic performance in 09-105.
Lecture Outline Proteins and Amino acids
  • Amino acids
  • alpha amino carboxylic acids
  • zwitterions
  • side groups (polar vs nonpolar)
  • peptide bond

polypeptides and proteins

primary structure


secondary structure

disulfide links

hydrogen bonds

peptide link pi-bond character

tertiary structure

Proteins are made of amino acids. Here is an introduction to amino acid structure.
 This presents six of twenty amino acids in which the polarity of the side groups is called attention to.
 At pH around 7, an amino acid actually exists as a structural isomer called a zwitterion, shown here.
 With the exception of glycine, amino acids are chiral, having tetrahedral carbons with four different groups present.
 In building proteins from amino acids, the links between amino acids are "peptide bonds" described here.
 The sequence of amino acids in a polypeptide (protein) is referred to as the primary structure.
The number of variations of amino acids in polypeptides is enormous. For 5 different amino acids in a pentapeptide, thre are 120 possible different structures.
The sequence defines the primary structure. This coils up due to properties of the peptide bond and internal hydrogen bonding to give a secondary structure. The figure on the right shows the origin of the internal hydrogen bonding. As we progress to figures on the left, less and less detail is shown.
The coiled secondary structure can further fold into a globular, tangled geometry defining its tertiary structure. A familiar example of tertiary structure is the messy result of coiled extension lines folding up as shown here.
 In forming the three dimensional structure from the linear (primary) sequence, the S-S disulfide bond plays a crucial role cross linking sections together.
 The peptide bond, which has a Lewis structure implying looseness associate with a single bond, is actually quite restricted due to partial double bond character from a contributing (minor) resonant Lewis structure as shown.
Amino acids are oxyacids in which the -OH group is bound to a carbon. That carbon is also double-bonded to a =O and single-bonded to an "amino" (ammonia-like) -NH2 group.Amino acids are connected by peptide bonds to form polypeptides. As soon as you have a number of amino acids joined, the combinatoric possibilities become staggering.
How many different arrangements of 300 amino acids are possible?
The number of different possibilities is large...indeed! The universe isn't big enough to be packed (I mean packed) with just one of each kind.

"Heme", the complex iron ion molecule that runs the essential chemistry of oxygen transport by blood. In blood, four hemes are part of a large protein structure called "hemoglobin". Shown here is "heme" with the divalent iron ion in purple at its center and the four (blue) nitrogen donor atoms as part of the heme ring coordinating ligand.

The genetic disease sickle cell anemia arises when just one of the amino acids is coded incorrectly: Glutamic acid is replaced by valine at side group position number 6 out of 300.
Normal red blood cells are smooth and rounded. In sickled cells, the hemoglobins clump together because of enhanced intermolecular attractions when the mutually repelling negatively charged glutamic acid group on each molecule within a cell is replaced by the neutral valine.
Sickled cells flowing in a blood capillary. Cell shape influences the ease of blood flow through the narrow channels.
The chemistry of oxygen in hemoglobin starts with a look at the Fe2+ at the heme site.