Proteins 2

Table of Contents
Biomolecules Gateway Page
Jmol Tutorial

In this module:

Secondary Structure
α Helices
ß Sheets
Tertiary Structure
Disulfide Bonds, Domains
Cofactors, Quaternary Structure
Protein Folding
Alzheimer's and "Mad-Cow" Diseases

Tertiary Structure: Water-Soluble Proteins

Although the dividing line between them is somewhat vague, tertiary structure is distinguished from secondary structure by the fact that it describes the relationship between atoms far removed in the amino acid sequence. The tertiary structure is how α helices, ß sheets, other secondary structure elements, and motifs come together to form the overall structure of the protein.

Two general kinds of proteins are found in cells, water soluble and water insoluble proteins. Water soluble proteins, which include enzymes and transport proteins, are found free in cellular compartments such as the cytoplasm, nucleus, or endoplasmic reticulum. How do secondary structure elements come together to form the tertiary structure of water-soluble proteins?

Hydrophobic groups (blue) must be kept away from water, while polar groups (yellow) must be exposed to it as much as possible. Thus the interior of the protein is almost entirely hydrophobic while the exterior is more polar.*

The polar main-chain carbonyl and amine groups present in both polar and hydrophobic amino acids are kept happy by secondary structure elements such as alpha helices or beta sheets.

There is almost no free space in the interior of the protein. The various sizes and shapes of the hydrophobic amino acids ensure that every space is filled. Click on the amino acid structure icon at right to see the structures of all the amino acids.*


* These structures use the slab mode to explore the interior of the protein.

Tertiary Structure: Water-Insoluble Proteins

The other class of proteins is not water-soluble. This include proteins that cross lipid bilayers once or more (integral membrane proteins). (See the Lipids module for a discussion of lipid bilayers.) Integral membrane proteins include membrane channels, pumps, and receptors. The portions that cross the bilayer are often α helices or ß sheets. Click on the buttons below to see why.

Like in the interiors of water-soluble proteins, the polar hydrogen-bonding main-chain carbonyl and amine groups have to be kept satisfied, either by the formation of alpha helices (shown here) or beta sheets.

In membrane-spanning proteins, side chains facing the lipids are usually hydrophobic (blue); side chains facing other membrane spans or the aqueous space on either side of the membrane can be polar (yellow).


In membrane-spanning ß sheets, every other side chain faces the lipids and is usually hydrophobic.

Tertiary Structure