3.1: Introduction

Protein molecules, which are each comprised of one or more polypeptides, are the workhorse of the cell,responsible for just about all aspects of life:

• They are the catalysts that make biochemical reactions possible.
• They are membrane components that selectively let substances in and out of the cell.
• They allow cell-cell communication and cell’s response to environmental change.
• They form the internal structure of cells (cytoskeleton) and nuclei (nucleoskeleton).
• They enable the motility of cells and things inside cells.
• They are in fact responsible for other cell functions too numerous to summarize here!

We owe much of what we know about biomolecular structure to the development of X-ray crystallography. In fact,an early determination of the structure of insulin (as well as penicillin and vitamin B12) using X-ray crystallography earned Dorothy Hodgkin the 1964 Nobel Prize in Chemistry. In this chapter, we look at the different levels (orders) of protein structure and at what it takes to be a functional protein. The primary structure (\(1^{\circ}\) structure) of a polypeptide is its amino acid sequence.

The primary structure (\(1^{\circ}\) structure) of a polypeptide is its amino acid sequence. Interactions between amino acids near each other in the sequence cause the polypeptide to fold into secondary (\(2^{\circ}\)) structures, including a helix and b-, or pleated sheet conformations. Tertiary (\(3^{\circ}\)) structures form when non-covalent interactions between amino acid side-chains at some distance from one another in the primary sequence cause the polypeptide further folds into more a complex 3-dimensional structure. Other proteins (called chaperones!) facilitate the accurate folding of a polypeptide into correct, bioactive, 3-dimensional conformations. Quaternary (\(4^{\circ}\)) structure refers to proteins made up of two or more polypeptides. Refer to the four levels of structure on the next page as we explore how each level affects the shape and biological/biochemical function of the protein.

Covalent bonds between specific amino acids (e.g., cysteines) that end up near each other after folding may stabilize tertiary and quaternary structures. Many proteins also bind metal ions (e.g., Mg++, Mn++) or small organic molecules (e.g., heme) before they become functionally active. Finally, we look beyond these orders of structure at their domains and motifs that have evolved to perform one or another specific protein functions.

As we try to understand molecular (especially macromolecular) function, a clear recurring theme emerges: a protein’s function depends on its shape, its conformation. In turn, protein conformation is based on the location and physical and chemical properties of critical functional groups, usually amino acid side chains. Watch for this theme as we look at enzyme catalysis, the movement of molecules in and out of cells, the response of cells to changing environments, the ability of cells to travel, the ability of organelles to move around inside of cells, the process of DNA replication, the regulation of gene transcription and protein synthesis...and just about everything a cell does! We will conclude this chapter with a look at some techniques for studying protein structure.

Learning Objectives

When you have mastered the information in this chapter, you should be able to do the followings:

1. Define and distinguish between the orders of protein structure.

2. Differentiate between beta sheet, alpha helix and random coil structure based on the atomic interactions involved on each.

3. Trace the path to the formation of a polypeptide; define its primary structure and how it is determined by ‘protein sequencing’.

4. Describe how globular proteins arise from the hydrophobic and hydrophilic interactions that drive protein folding and how changes in protein shape can cause disease.

5. Formulate an hypothesis (or look one up) to explain why the amino acid glycine is a disruptor of alpha helical polypeptide structure.

6. Compare and contrast motif and domain structure of proteins and polypeptides, and their contribution to protein function.

7. Describe different techniques for studying proteins and the physical/chemical differences between proteins that make each technique possible.