Learning Strategies in Biochemistry:
Metabolism I

Essential Review:

More than any aspect of biochemistry you have studied so far, metabolism will tax your knowledge of organic structure and reaction mechanisms. If you can see familiar reaction types in somewhat complex metabolic reactions, you can make sense of what at first appear to be unfamiliar processes. Each metabolic pathway usually includes several reactions closely related to those you have studied in organic chemistry. The Essential Review sections of these Learning Strategies will provide lists of specific reaction types you should review as an aid to understanding metabolic reactions.

Essential Memory Work:

As you begin each of the chapters on metabolic pathways, look for the first chart or figure that shows the structures of all intermediates in the chapter's central pathway. As soon as you encounter this chart, MEMORIZE IT. Specifically, for each major pathway, memorize the following:

• Structures and names of all intermediates, including their stereochemistry if they are chiral.
• Names of all enzymes.
• Points of use or production of ATP, ADP, Pi, and all cofactors (NAD, FAD, TPP, and so forth).

In learning the structures of intermediates, don't memorize all the structures as if they were unrelated. Instead, memorize how to transform each intermediate into the next. Each reaction is relatively simple. Only a small part of a molecule changes in each step. So memorize the series of operations that transforms each intermediate into the next.

When you complete your memory work, you should be able to write out a chart of the pathway, with all the information described above, in no more than 10 minutes.

What's The Benefit?

You may be thinking that this task is too onerous to comtemplate. But in the end, it's a time and labor saver. If you will take the time to carry out this memory task when you first encounter each major pathway, you will have a much easier time reading the rest of the chapter with understanding. You will find that as you read about the details of specific reactions, you have a sense of where you are, and where the current subject fits into the larger scheme of the pathway. The biggest problem in learning metabolism is developing a view that encompasses both the forest and the trees. Memorizing the major pathways will help you connect a global view of the whole pathway (the forest) with the individual reactions (the trees).

Quizzes for USM Students

Each time we enter a new topic in metabolism, I will specify the pathway or pathways you should memorize. At the first class on the new topic, I will give you 10 minutes to write out the pathway, with all the details listed above. Each of these quizzes counts 1/10 of one exam.

Pathway Information Provided on USM Exams

Memorizing pathways is primarily an aid to learning more about them. Questions on exams are usually at a higher level than mere memory work. On exams that cover topics in metabolism, I will provide complete charts of any pathways you need for answering exam questions. So there is no need to come to exams prepared to regurgitate pathways. Instead, come prepared to use your experience with pathways -- gained by memory work, reading, and problem solving -- to answer questions, interpret data, and solve problems about them.

Beyond Basics: What To Look For In Pathways

As you study, pay particular attention to these five elements of all pathways. If you have a good grasp of each element, then you are on your way to a good understanding of the pathway.

1. Flow of carbon -- the intermediates of the pathway and the reactions that interconvert them.
2. Flow of phosphate groups -- one key to energy transfer in the pathway. Catabolic pathways increase the cell's supply of ATP and other compounds with high phosphate-transfer potential. Anabolic pathways consume these compounds. Look closely at the reactions that produce and consume these substances. They are keys to understanding how the cell extracts energy from its nutrients and uses it to run its household.
3. Flow of electrons -- another key to energy transfer. Catabolic pathways are generally oxidative, and they increase the cell's supply of reduced nicotinamides (NADH and NADPH) and flavins (FADH₂ and FMNH₂). Anabolic pathways are generally reductive, consuming reduced nucleotides, especially NADPH.
4. Regulation -- the pacemaker enzymes of the pathway and the chemical signals, including allosteric effectors and hormones, that control their rates. Here you see the real logic of the pathway, including how its rate changes in response to changing cellular conditions.
5. Connections to other pathways -- inputs and outputs of the pathway. Often, regulation makes more sense in the light of where the pathway's reactants come from and where its products go.

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