Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

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Lecture illustrations from Moran text in [Brackets]

3-D Structure of Proteins, cont.

Last time looked at Primary structure (1°), Secondary structure (2°) and Tertiary structure (3°). Continuing:

Alpha helix

The most frequent secondary structure is the right-handed alpha-helix. [Figure 4.10 , pg 90]

Beta Strand

The next secondary structural element is the beta-strand, which is seen in the supersecondary structures called parallel [Figure 4.16a]and anti-parallel beta-sheets. [Figure 4.16b]

Aside: Fibrous proteins: alpha-keratin (hair etc., alpha-helix based), stretchy, breaking and remaking H-bonds; stretched alpha-keratin (parallel beta-pleated sheet), no longer stretchy, fully extended. "Permanent wave" breaking -S-S- bonds between adjacent alpha-helix strands with thiol-reagent reducing agent, then rearrange hair and reoxidize with peroxide to lock new conformations in place.

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)

Domains

Domains are independent folding regions within a protein. [Figure 4.21] The group/pattern of secondary structures forming a Domain's tertiary structure is called a Fold [some common folds: Figure 4.25]; example proteins with domains and folds: [Figure 4.24]. (Characteristic bond type: hydrophobic; others: hydrogen, ion-pair, van der Waals.) 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).

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Last modified 11 February 2013