Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2011

Lecture Notes:

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Lecture illustrations from Moran text in [Brackets]

Note the titration behavior of amino acids, and be able to draw the structure for an amino acid at each point in the curve. [Table 3.2; Fig. 3.6, 3.7]

Peptides and Protein Primary Structure

Peptide bond formation:

Note that a peptide bond is simply an amide bond between the alpha carboxyl and amino groups of amino acids. If we write the reacting groups in their unionized (acid and amine) forms, then we can see the reaction takes place with the loss of the elements of water, via an attack of the lone-pair electrons of the amine on the carbonyl carbon of the carboxyl group [Fig 3.9]:

attack of the amino group of one amino acid on the carboxyl group of a second to form a dipeptide
Now that we have looked at peptide bond formation, we next want to look at the structure of this bond and the sequence of amino acid residues (primary structures) of proteins. (Note that "residue" refers to the remainder of a molecule after it is incorporated into a polymer.)

3-D Structure of Proteins

Overview: Proteins are commonly large (MW > 6,000), globular molecules serving many functions.

Proteins are complex systems - difficult to understand at a fundamental structural level. Thus we search for patterns using normal perceptual tools: regularity, clustering, cleavage/separation/emptiness.

We are then able to discern alpha helices, beta sheets, beta turns, and "random" regions. 310 helical regions show up with computer searches. [Figure 4.15]None of these is necessarily more or less random than others, they are simply easier or more difficult for us to perceive as ordered. They exist through our rationalization. Often structural elements also appear to serve a functional role, thou this is through our dissection of the molecular machine.

Look at theoretical possibilities resulting from the available bond angles around the peptide bond system

Let's go back and look at overall shape and interpret it. Look for substructures that recur in various molecules. Perhaps we see a globule is made of subglobules. Look closer and we see alpha helices and beta structures. Finally we can discern aa residues.

In order to understand and categorize their organization, protein structure has been divided into four hierarchical levels and a couple of sublevels [Figure 4.1]:

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Last modified 8 February 2013