5. Proteins & Enzymes

What you need to know...
  • The variety of protein shapes and functions arises from the sequence of amino acids.
  • Functions of proteins to include structural, enzymes, hormones, antibodies.
  • Enzymes function as biological catalysts and are made by all living cells. 
    • They speed up cellular reactions and are unchanged in the process. 
    • The shape of the active site of enzyme molecules is complementary to a specific substrate.
    • Each enzyme works best in its optimum conditions. 
    • Enzymes and other proteins can be affected by temperature and pH, which result in changes in their shape. 
    • A change in shape will affect the rate of reaction and may result in denaturation.

Source: SQA
Notes

In the previous topic we learnt how the code contained in DNA bases results in the production of proteins. Proteins are crucial for the functions of cells and in this topic we'll discuss the variety of proteins in cells and focus in on one particularly important group: enzymes. 

Variety of Proteins

There are many different proteins in cells, each carrying out a particular function. As we'll return to later in this topic, the shape of a protein is crucial to its function. If you change a protein's shape, you change its function. As we discussed in the previous topic, this protein shape is dictated by the sequence of the chain of amino acids which makes up the protein. There are twenty different amino acids and the order they're arranged in determines the shape, and therefore the function, of the protein. So the following two chains of amino acids would result in two very different proteins.


Our cells use these twenty amino acids to produce many different proteins. These can be grouped into a number of different types depending on their function. A few of these are outlined in the following table:

Type of Protein Function
Structural, e.g. Collagen Provide structural support to cells and tissues.
Enzymes, e.g. Amylase Catalyse chemical reactions.
Hormones, e.g. Insulin Chemical messengers between cells.
Antibodies Bind to foreign bodies to help prevent infection.

You can explore the world of proteins in 3-D in this clip and there are lots of cool free apps which will let you play with protein molecules such as Atomdroid on Android or Molecules for iOS.

Enzymes

Life consists of a series of complex chemical reactions. Later in this unit you will learn more about two such complex chemical reactions: respiration and photosynthesis. In order for most of the chemical reactions which take place in living things to occur they need a catalyst. Catalysts are molecules which affect the rate of a chemical reaction, normally by speeding them up, without being changed in the process. Enzymes are the catalysts of life and are made of proteins. That's why this group of proteins has been chosen to explore in more depth in this topic. DNA controls all of the chemical reactions which take place in a cell through which enzymes are produced and when. 

You're probably getting sick of hearing this by now, but the shape of enzymes (like all proteins) is crucial to their function. A key component of the shape of an enzyme is its active site. Most enzymes can only catalyse a very small number of reactions, quite often just one, because the shape of the active site of an enzyme is complimentary to the specific substrate(s) it binds to in the reaction. 

Take the enzyme amylase for example. This is found in your saliva and catalyses the breakdown of the complex carbohydrate starch into much smaller maltose sugar molecules [try keeping a plain flavoured crisp in your mouth for a few minutes without swallowing and you might just be able to taste this sugar being produced by your salivary amylase]. The shape of the active site of an amylase enzyme molecule is specific to the shape of its substrate starch.
 

Therefore, amylase can only catalyse this reaction. This is why cells must produce many different enzyme molecules, from the DNA code, for all the different chemical reactions which are catalysed in cells. Notice by the way in the diagram that enzyme molecule remains unchanged as a result of the reaction - remember this is a key feature of a catalyst along with speeding up the reaction.

As enzymes are chemical molecules they can be affected by the conditions that they're in. Remember the importance of shape to the function of proteins? Well, if the conditions change it can change the shape of the enzyme. If the active site of the enzyme changes as a result of the change of conditions, then the enzyme will not be able to bind to its substrate which will prevent the enzyme from catalysing the reaction. It is for this reason tha each enzyme has its own optimum conditions. These are the conditions which provide the right enzyme shape to allow it to effectively catalyse its reaction.

Two particular conditions which can affect the rate of an enzyme catalysed reaction are temperature and pH. If you were to carry out a series of experiments with the enzyme amylase where you measured the rate of the breakdown of starch at different temperatures and pH, you would get a set of graphs which would look something like this:


Although these graphs look quite similar, the explanations for the graphs are a little different. The first thing to notice is that from these graphs you can deduce the optimum conditions for the amylase in your saliva. The optimum temperature (B) is just below 40°C (your body temperature is 37°C) and the optimum pH (E) is approximately 7 (the same as your saliva). 

But how do we explain the other sections of the graph? Well...

A. At region A on the temperature graph, the rate of the reaction is increasing as the temperature increases. This is less to do with the shape of the enzyme and more to do with the normal effect of temperature on chemical reactions...the rate is increasing because the molecules have more and more energy causing them to collide more often.

C. However, because enzymes are made of protein, there is a limit to how high you can heat an enzyme-catalysed reaction. Once you've passed the optimum some of the enzyme molecules begin to change shape as the high energies break the bonds which hold the molecules together. At very high temperatures all of the enzyme active sites have lost their shape and it's as if there are no enzyme molecules present, so the rate of the reaction is very low. Once an enzyme molecule has lost its shape due to high temperature, it can not return to its functional shape. This is when we would describe an enzyme as being denatured. Why do think then that biological washing powders only work at low temperatures?

D. & F. The bonds which hold a protein's shape are quite sensitive to changes in pH. At the optimum pH (E) the bonds are creating the right active site shape to allow the enzymes to catalyse the reaction. However, as the pH is further from this optimum, fewer and fewer enzyme molecules have the right active site shape which reduces the rate of reaction. For many enzymes changes in shape due to changes in pH are reversible.

The diagram below shows why a denatured enzyme molecule cannot catalyse a reaction...the shape of the active site has changed which means it can no longer bind to the substrate.
 
 
There are loads of animations of enzyme activity on YouTube, many of them made by students. Why not have a go and create one of your own?