Proteins and Folding

From BCCD 3.0

Contents 1 Four Levels 1.1 Primary Structure 1.2 Secondary Structure 1.3 Tertiary Structure 1.4 Quaternary Structure 2 References

Four Levels

The word "protein" can mean many things. To help clarify, a standard of four different ways or structural levels of looking at a protein have been developed.

Primary Structure

The primary structure of a protein refers to the basic amino acid sequence that makes up the protein (sometimes called an "amino acid necklace"). This is the specific order of amino acids dictated in the DNA transcript that was used to make the protein. (For more information on how this is determined, see Introduction to DNA.)

The graphic to the right is an example of level one structure. The DNA, mRNA, and amino acid sequence for this protein are shown below. Notice that the protein begins with methionine. Also keep in mind that a real protein would be much larger than this!

DNA         3' end -->  TAC - AAT - TTC - GTA - GGA - AAG - GTA - CTA - CAA - ATC  <-- 5' end
mRNA        5' end -->  AUG - UUA - AAG - CAU - CCU - UUC - CAU - GAU - GUU - UAG  <-- 3' end

protein  amino end -->  met - leu - lys - his - pro - phe - his - asp - val - stop <-- carboxyl end

Secondary Structure

After initially being created from a DNA transcript, the protein begins to fold. This happens in stages. Secondary structure refers to folding on a local scale caused by attractions between the amino acids close to each other. These forces include hydrogen bonds (the same bonds that hold two DNA strands together), electrostatic forces (positives and negatives attracting), hydrophillic and hydrophobic forces on the side chains, and van der Waals forces (temporary dipoles, or charged areas, on molecules attracting). There are generally two accepted types of folding caused by local stresses: alpha (α) helices and beta (β) plates.

Tertiary Structure

Tertiary structure is the protein structure once it has fully folded on a local and global scale.

Quaternary Structure

Not all proteins have a quaternary structure. The quaternary structure refers to a protein made up of other protein subunits.

References

• Griffiths, Anthony J. F., et al. Introduction to Genetic Analysis. 8th ed. New York: W. H. Freeman and Company, 2005.
• Wikipedia: Van der Waals' forces