3 Providing a framework: structural proteins
3.1 Protein diversity
Of course, our bodies can't just be made up of squidgy bubbles of phospholipid, or we would collapse in a heap on the floor! Stiffer frameworks, both inside and outside the cells, also exist and help to define shape and add strength. These frameworks are formed largely from structural proteins, a class of polymeric materials that form fibres and filaments to provide mechanical support for cells and tissues. Structural proteins are made inside cells but are often then moved into the space surrounding the cells, where they interact together to form a three-dimensional polymer network, permeated by fluid.
Section 2 introduced the idea of self-assembly in a simple system, but the real masterpieces of self-assembly are the proteins. As well as providing structure, proteins play a central role in defining the function of different cells. There are many of them – around 10 000 types in a typical cell – and they fulfil a wide range of functions. Some examples are listed in Table 2.
Table 2 Examples of the functions fulfilled by proteins within cells
|Type of protein||Function||Examples|
|Structural proteins||provide mechanical support for cells and tissues||skin and tendons contain collagen|
|hair, nails, beaks and feathers are all based on keratin|
|actin forms part of the skeleton within cells|
|Enzymes||biological catalysts, which speed up essential chemical reactions||many enzymes are involved in digestion, or breaking down toxins, e.g. pepsin, alcohol dehydrogenase|
|DNA polymerase enables DNA to be made|
|ATP synthase converts ADP to ATP|
|Transport proteins||transport small molecules or ions from one place to another||haemoglobin carries oxygen around in the bloodstream|
|membrane transporters carry molecules or ions across the cell membrane|
|Signalling proteins||carry signals between or within cells||hormones: for example, insulin, which controls blood sugar levels|
|Receptor proteins||detect signals and transmit them within cells||rhodopsin detects light in the eye|
|insulin receptor binds insulin|
|Motor proteins||generate movement in cells||myosin is involved in muscle movement|
|kinesin carries cargo around cells|
Proteins are also used for storage of essential nutrients, for labelling things so that they can be recognised by other cell components, for sending instructions to DNA, and for many other specialised functions.
The action of a protein is intimately linked with the three-dimensional shape that it adopts, although it is seldom possible to guess the function of a protein from its shape alone. Some examples of protein shapes are shown in Figure 7.
Structural proteins tend to be long and thin, like the strands in a rope. The molecules they are based on may be stretched out to form fibres, like the collagen in Figure 7 (a), or built up from individual units in which the chain is coiled up rather like a ball of string: the actin in Figure 7 (b) is an example, with an individual unit shown at the top of the diagram. However, most proteins have a more globular shape. In general, the globular proteins have more specialised roles than the structural proteins.
Enzymes are proteins that act as catalysts, helping to promote certain chemical reactions. In some respects all proteins can be regarded as enzymes, since they provide the means for a particular reaction to take place; however, the term tends to be reserved for those proteins whose associated chemical reaction is the primary goal of the process and not just a step on the way towards, for instance, movement. Pepsin, Figure 7(c), is an enzyme involved in breaking down food during digestion. Alcohol dehydrogenase, Figure 7 (d), is an enzyme that many of us should be grateful to: it is the body's primary defence against alcohol, a toxic chemical that compromises the function of our nervous system. This enzyme catalyses the removal of hydrogen (hence the name dehydrogenase) from alcohol, which is the first step towards breaking it down into harmless substances. The high levels of alcohol dehydrogenase in our liver and stomach detoxify about one stiff drink each hour, slow enough for us to enjoy the effects of our folly but fast enough – we hope – to avoid permanent damage. You can read a little more about how enzymes work in Box 3 Biological catalysts.
Figure 7 also shows examples of molecular pores and channels that let certain substances cross the cell membrane. The porin protein in Figure 7 (e) has three permanently open pores, while the potassium channel in Figure 7 (f) possesses a single channel that opens and closes in response to signals and is specially designed to allow only potassium ions through. In the figure, both of these are drawn as if looking down on the membrane; a potassium ion is shown in green in the centre of Figure 7 (f). Sometimes, the process of getting ions across a membrane is helped along by mechanical pumping. The calcium pump shown in Figure 7 (g), this time as a cross section through the lipid bilayer, is essential for maintaining a difference in calcium ion concentration across a cell membrane.
The insulin in Figure 7 (h) and the G-protein in Figure 7 (i) are both signalling molecules, one simple and one more complex. The message carried by insulin is passed on when it fits into a suitably shaped notch on a receptor protein within a cell membrane, while the G-protein is one of a class of proteins that carry messages into the cell itself. The two little ‘ears’ at the top of the G-protein are in fact lipid chains, which insert themselves into the lipid membrane inside the cell and keep the protein tethered there, where it is needed.
The tiny octopus-like structure called prefoldin, shown in Figure 7 (j), helps newly synthesised proteins to fold into the right shape. The restriction enzyme, Figure 7 (k), and DNA polymerase, Figure 7 (l), are both involved in DNA processing, and are shown attached to a portion of a DNA chain (coloured in pink and green). Finally, the myosin illustrated in Figure 7 (m) is a molecular motor involved in muscle contraction..
Box 3 Biological catalysts
Enzymes are biological catalysts that work by providing a low-energy pathway for a reaction, allowing it to happen more readily than would otherwise be the case. As with most proteins, it is the three-dimensional shape adopted by the enzyme protein that makes it suitable for its specific function. Enzymes have binding sites on their surface where particular molecules (ligands) can fit. In this case, the specific binding site is usually known as the active site, and the molecule that can fit into it is called the substrate. Each enzyme is precisely tailored to catalyse a specific reaction: the process is illustrated in Figure 8.
The substrate is not just a suitable shape to fit into the cavity of the active site: it also has a charge distribution that allows weak bonds to form between the two. Interactions between the enzyme and the substrate allow a chemical reaction to happen more easily, by lowering the energy barrier that has to be overcome for the reaction to take place. In many cases this is because bonds in the substrate become slightly distorted when it binds to the enzyme. Strained bonds are easier to break, so the energy required to break the substrate down into the reaction products is lower. Finally, the reaction products are released, leaving the enzyme intact to catalyse further reactions.
Enzymes are widely used in brewing and food production; they also have other domestic uses. For instance, ‘biological’ washing powders contain enzymes to help break down stubborn stains, in much the same way as food is broken down in our stomachs. These are examples in which naturally occurring enzymes are used for pretty much the same purpose as nature designed them. Nanotechnologists are now able to create new biological catalysts by ‘tweaking’ existing enzymes – for instance, to enable them to work over a wider range of temperature or acidity, or to increase their efficiency – or even by using genetic engineering to create new enzymes.
State six major functions fulfilled by proteins in cells.
Six major functions fulfilled by proteins in cells are providing structural components, acting as catalysts, moving things around, carrying signals, receiving and passing on signals, and generating movement. You could also have mentioned storage of essential nutrients, labelling things for recognition, and sending instructions to DNA.