| Chem 438 |
Introductory Biochemistry |
Spring 2007 |
| Lecture Notes: 5 February |
© R. Paselk 2006 |
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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.
- In this cylinder-like structure the amino acid residues curl around in a spring/rod-like structure.
- There is a rise/residue (movement along the axis) of 0.15 nm and a pitch (rise/turn) of 0.54 nm.
- There are 3.6 residues per turn and 13 atoms/H-bonded "ring" - this makes it a 3.613 helix.
- Very importantly, the H-bonds are nearly linear and therefore of near maximum strength. The side chains of the helix stick out from the sides.
- The stability of the helix is determined in part by the side chains. Thus glycine allows too much rotational freedom to favor this structure, while very large or like charged side chains can also destabilize it.
- As you might expect a proline residue stops a helix abruptly since proline' s angles are not accommodated in the 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].
- The beta strand is in a sense an abstract structure, since, unlike the a-helix, a beta-strand does not exist alone, there is always another strand to make a sheet.
- In the older literature beta-sheets are considered secondary structures, but they are more consistently considered super secondary with the current nomenclature.
- Beta strands are nearly fully extended, thus they have very little extensibility (stretch).
- Beta strands are stabilized by hydrogen bonding to adjacent beta-strands. Thus they are stabilized by inter-strand H-bonds whereas a-helices are stabilized by intra-strand H-bonds.
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].
Last modified 5 February 2006
Pathway Diagrams
