Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2007

Lecture Notes: 5 February

© R. Paselk 2006


Peptide Titration-Reviewed peptide structure and titration curves.

3-D Structure of Proteins 2

Secondary Structure

Tertiary structure (3°): the steric relations of residues distant in the primary sequence; the overall folding pattern of a single covalently linked molecule. (Characteristic bond type: hydrophobic; others: hydrogen, ion-pair, van der Waals, disulfide.)
  • Super secondary structure (motifs): defined associations of secondary structural elements. (Characteristic bond type: hydrogen & hydrophobic.)
  • Domains: independent folding regions within a protein. The group/pattern of secondary structures forming a Domain's tertiary structure is called a Fold. (Characteristic bond type: hydrophobic; others: hydrogen, ion-pair, van der Waals.)


Last time looked at what is possible given the bond angles etc. between amino acid residues. Now can look at specific structures.

Alpha helix: (Figure 4.10, pg 90 of your text) [overhead 2.31 S, 5.15 P] The most frequent secondary structure is the right-handed a-helix.

Beta Strand: (Figure 4.15, pg 93 of your text) [overhead 5.19 P] The next secondary structural element is the beta-strand, which is seen in the supersecondary structures called parallel and anti-parallel beta sheets [overheads 7.16 & 17 V&V].

Aside: Fibrous proteins: alpha-keratin (hair etc., alpha-helix based) [overhead 7-11 V&V, 7-25 & 26]; stretched alpha-keratin (parallel b-pleated sheet) [overhead, Figure 7-26].

Pathway Diagrams

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Lecture Notes

Last modified 5 February 2006