Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2007

Lecture Notes: 7 February

© R. Paselk 2006


3-D Structure of Proteins 3

Secondary Structure, cont.

Collagen strand: This is a specialized structure occurring in only a particular family of fibrous proteins. It does not occur in globular proteins that I am aware of.

Non-repetitive secondary elements: Proteins can also have non-repetitive secondary structures which consist of a few residues in a turn or loop. Among these are:

Tertiary Structures

The Tertiary structure describes the overall folding of a single covalent structure.

As the number of known protein structures increased additional patterns became obvious within the tertiary level of structure: Motifs & Domains.

Super Secondary structures (Motifs)

Recall the two classical structures based on the beta-strand:

Let's next look at some of the other more common motifs found in globular proteins (Fig 4.19 of your text):


Large proteins (>200 aa's) usually fold up in smaller pieces of 100-200 aa's called domains. Recall that we define a Domain as an independent folding region in a protein. Often defined by clefts in 3D structure giving globular elements connected by "hinges" (single strand segments connecting the domains). Domains have the advantages of speeding up the folding process (fold domains independently, then assemble resultant folded domains - effectively processing folding of domains in parallel). Another advantage of domain structure is that nature can take bits of DNA specifying particular domains with particular functions and assemble them in new combinations to get new activities (e.g. combine an ATP binding site and a sugar binding site to give a sugar phosphorylating protein).

Example: IgG , domains, exons and evolution. [overheads: IgG/proteins; 7.23 MvH]

In a similar manner we see that many enzymes have active sites created between two domains, often one domain binds one substrate while the second binds a second substrate.

Its as if these proteins were designed by taking "off-the-shelf" components, assembling them, and then over time (and generations) tuning the combination up.

Pathway Diagrams

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Last modified 7 February 2007