Learning Outcomes

At the end of this section of 'Why Proteins?' you should be able to:

• Understand why proteins are important in cells
• List some of the principal functional and structural roles of proteins
• Appreciate the range and diversity of both the function and structure of proteins

Prior Knowledge

To get the best out of this tutorial you are assumed to have the following prior knowledge:

• Amino acid types, structure, and physiochemical properties
• Basic protein structure
• Basic chemistry (e.g. covalent bonding, non-covalent bonding, atomic orbitals, molecular orbitals, electron configurations, lone pair electrons)
• Competence with RasMol computer molecular visualisation software

The introduction to this tutorial will briefly visit some of the basics. However, if you find that you are deficient in any of the assumed prior knowledge, then you will be best served to revise that knowledge. There are many resources available to you for revision here are just a few:

• Basic biochemistry, protein structure, amino acid structure (and properties), can be revised from textbooks such as Nelson and Cox (2002)
• Amino acid structure can also be revised by using the interactive amino acid tutorial on the Biochemistry web page found at: http://wbiomed.curtin.edu.au/teach/biochem/tutorials/tutorials.html
• Basic protein structure and using RasMol molecular visualisation software can be revised by taking the The carboxypeptidase A interactive tutorial found on the Biochemistry web page above.
• Basic chemistry can be revised from chemistry textbooks. A good online chemistry course can also be found at: http://www.cem.msu.edu/~reusch/VirtualText/intro1.htm#contnt
  

Why Proteins?

There are four principal biological 'polymer' macromolecules used by living cells¹ : carbohydrates, nucleic acids, lipids, and proteins. Each of these, except lipids, are composed of individual units (monomers) that are covalently bound in a linear sequence. Carbohydrates can also be comprised of covalent branched structures from the component monomers. Lipids are more precisely non-covalent assemblies of the component fatty acids, but are still considered macromolecules. Each of these macromolecules play important and vital roles in a living cell. Why all the interest in proteins? What is so special about proteins that affords them some special attention?

Well, it seems that proteins are where the action is!² Whenever something needs to be done, or changed, within a cell a protein is involved³. This is not to say that the other macromolecules don't participate in living processes - of course they do. It's just that proteins seem to be involved in almost all steps in any change, transformation, and action that occurs in the living cell. For example, proteins mediate, transform, transduce, amplify, transport, structurally support, communicate and regulate. Proteins also comprise most of the dry mass of the cell (essentially this is saying that because so much of the cell is protein then proteins must be important!). Consequently, we can say that proteins, like bricks for a house, are the 'building blocks' of the cell. Table 1 shows some of the main functional, and structural, roles of proteins. We won't review these roles here, but you can find abundant information in most biochemistry texts (some of the more common texts are given in the bibliography).

Concept

Proteins are vital to a cell. Affect a protein and the cell is also affected in some way. The cell may not always immediately show the effect of a change either because there are compensating mechanisms (essentially other proteins that try to minimise the change), or the protein's function is not immediately apparent in how the cell looks or behaves (that is the protein doesn't affect the cell's phenotype).

The diversity of protein function makes them ideal 'targets' for discovery including: what a protein does within a cell, how the protein itself works (usually at a molecular level), the structure of the protein, and how the protein influences the cell (through its interactions with other proteins or biomolecules). This knowledge can then be used in understanding how cells 'work', designing drugs, designing diagnostic and analytical tests, using the proteins themselves as therapeutics, and using the proteins for industry. Proteins may be acted upon by another protein or biomolecule (usually smaller molecules). That is, the protein is the object or target of a biomolecule. Alternatively, proteins may act upon other proteins or biomolecules. That is the biomolecule (which may also be a protein) is the object or 'target' of a protein. Table 2 shows some of the many biotechnology applications of proteins. 

Questions to review Learning Outcomes

• Proteins often seem to be the better target for drug design and discovery. Why is this?
• Which (if any) of the monomer components of the four principal macromolecules cannot usually be described by a single structural formula and why?
• Compare and contrast the roles of proteins with the roles of the other principal biological macromolecules
• Why are there so many biotechnological applications of proteins?

Notes

1 In this tutorial we will be using the cell as our basic unit of life. However, at least two other terms may be used interchangeably with 'cell' and these are 'organism' (as some organisms are single cells) or 'system' (as cells can also be viewed as an organised collective or system).

2 Lesk A.M. (2003) Introduction to Protein Architecture. Oxford University Press. p.15

3 If you are a fan of English grammar, then you could say that a protein is the verb of cellular grammar!

4 See Walsh (2002) Proteins. Biochemistry and Biotechnology. Wiley. for a more comprehensive, and excellent, discussion of the biotechnology applications of proteins.