There are many examples of polymerization reactions in biochemistry: DNA/RNA synthesis, protein synthesis, carbohydrate synthesis and fatty acid synthesis. In some cases the polymer consists of a string of identical monomers (e.g. some carbohydrates, fatty acids) while in other cases the polymer can be a mixture of several different kinds of monomers (e.g. nucleic acids, proteins).
There are two basic strategies of polymerization: head growth and tail growth. The basic concept is often presented in the textbooks when DNA synthesis or protein synthesis is described.
I posed a simple question yesterday and got some comments on the blog and in my email [Are You as Smart as a Second Year University Student? Q6]. Some people didn't have a clue what the question was about and some people declared that the question was silly. One commenter said, "Sounds like a stupid question that has something to do with memorizing someone's silliness and nothing to do with understanding biochemistry."
Let's see if you agree that this is a silly question that has nothing to do with understanding biochemistry.
In head growth the head of the growing polymer is "activated"—it carries the energy for the addition of the next monomer. This "activation" energy is depicted below as a red bond. Each of the incoming monomers is also "activated" but the energy of the activated bond will be used for the next addition once the monomer is added to the growing polymer.
The classic example of head growth is protein synthesis. Fatty acids are also made in this way.
In tail growth the head of the growing polymer is not activated. The energy for the addition of each monomer is supplied by the incoming activated monomer.
The best examples of tail growth strategy are nucleic acid synthesis, where the activated monomers are nucleoside triphosphates, and synthesis of storage polysaccharides, where the activated monomer is UDP-glucose.
Why is it important to understand the difference between head growth and tail growth? Because one type is unidirectional whereas the other type is compatible with both lengthening and shortening of the polymer.
Let's look at the process of error correction as seen in the proofreading reaction of DNA biosynthesis. Imagine that the replication complex makes a mistake and adds the wrong nucleotide to the growing DNA molecule. The incorrect nucleotide is subsequently removed by the proofreading activity of DNA polymerase. Since DNA synthesis is a tail growth mechanism, the removal of the most recently added monomer doesn't change the chemical reactivity of the growing end of the chain so the reaction can now continue in the direction of lengthening as shown by the green check mark in the figure.
If DNA synthesis utilized a head growth mechanism, then proofreading would not have evolved since removal of the last monomer also removes the activated head of the growing chain.1 That's why there's no proofreading in protein synthesis.
The synthesis of storage carbohydrates such as starch and glycogen doesn't involve proofreading but there's still a very good reason why the mechanism is tail growth. Recall that starch and glycogen are polymers of glucose and their role is to store glucose as a potential carbon source in time of need. When the need arises, the ends of the polysaccharide chains are nibbled back releasing glucose molecules (as glucose-6-phosphate). These molecules enter the glycolysis pathway.
The degradation reaction terminates when the immediate need for glucose has been met. Later on, in time of plenty, the starch and glycogen chains can be re-extended by adding more glucose residues. The reason why this is possible is because starch and glycogen synthesis is an example of tail growth just like nucleic acid synthesis. If nibbling the ends of the polysaccaride chains removed the activated head, as it would in the case of head growth, then the synthesis reaction could not occur. Thus, the fundamental reason why tail growth evolved in both nucleic acid synthesis and glycogen synthesis is the same.
One of the other reasons for discussing this concept in introductory biochemistry classes is that it gets students thinking about the big picture. Rather than focusing on the details of any one type of polymerization reaction they are encouraged to think about general strategies and they are stimulated to compare and contrast different types of reactions. Unfortunately this approach is rapidly disappearing from introductory biochemistry courses because they are often taught in sections where the lecturer in each section is a specialist in information flow, carbohydrate metabolism, or protein structure. These lecturers often don't know enough about the other subjects to make the relevant comparisons.
That wouldn't matter a great deal as long as the introductory biochemistry textbooks did the job for them. There are two reasons why that doesn't seem to work. First, many team-taught courses don't use a textbook because the individual experts in each section think they know everything they need to know and the students can just rely on the lecture notes.
Second, the comparative biochemistry concepts and principles are disappearing from the textbooks. This is partly because of the way courses are taught and the way students are examined—once the exam on carbohydrate metabolism is over, students don't have to remember anything about carbohydrates while preparing for the next test on lipids and membranes. It's also partly because some biochemistry courses don't cover all aspects of biochemistry in a single course. Many introductory biochemistry courses, for example, separate information flow (DNA replication, transcription, translation) from the rest of biochemistry.
Because of the negative feedback from the customers (Professors) my textbook does not mention head growth and tail growth. The concept is also missing in all of the other introductory biochemistry textbooks.
I'm putting it back in the next edition of my book even if it means losing some adoptions.
1. Admittedly, one could imagine evolving ways around this limitation; by re-activating the end in a separate reaction, for example.