Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2007

Lecture Notes: 5 February

© R. Paselk 2006


Peptides and Protein Primary Structure

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. 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:

Pathway Diagrams

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Lecture Notes

Last modified 2 February 2006