Core Concepts: Pathways and Transformations of Energy and Matter

The AAAS document, Vision and Change in Undergraduate Biology Education, defines five core concepts for biological literacy. One of the core concepts is Pathways and Transformations of Energy and Matter. This is an important one for biochemistry since we are the people charged with making sure undergraduates understand the basic core concept that life obeys the laws of physics and chemistry.

Here's how the authors of Vision and Change describe the core concept.

4. PATHWAYS AND TRANSFORMATIONS OF ENERGY AND MATTER:

Biological systems grow and change by processes based upon chemical transformation pathways and are governed by the laws of thermodynamics.

The principles of thermodynamics govern the dynamic functions of living systems from the smallest to the largest scale, beginning at the molecular level and progressing to the level of the cell, the organism, and the ecosystem. An understanding of kinetics and the energy requirements of maintaining a dynamic steady state is needed to understand how living systems operate, how they maintain orderly structure and function, and how the laws of physics and chemistry underlie such processes as metabolic pathways, membrane dynamics, homeostasis, and nutrient cycling in ecosystems. Moreover, modeling processes such as regulation or signal transduction requires an understanding of mathematical principles.

For example, knowledge of chemical principles can help inform the production of microorganisms that can synthesize useful products or remediate chemical spills, as well as the bioengineering of plants that produce industrially important compounds in an ecologically benign manner. These are topics of intense current interest.

At first glance this seems like an adequate description of a core concept but the more you think about it the more you realize that it's just a bunch of motherhood statements without any real teeth. It sounds very nice to say that students need to understand kinetics and thermodynamics but the recommendation has no substance unless you explain exactly what it is that they are supposed to understand. We all know that both these concepts are poorly taught in undergraduate courses.

When I was teaching introductory biochemistry I always asked my students the following question to make sure they had grasped the concept of where cellular energy comes from.

There are species that are autotrophs. They grow and reproduce using only inorganic molecules as their only source of essential elements. Carbon usually comes from CO₂. Some of these species are capable of photosynthesis (photoautotrophs) but others are not (chemoautotrophs). Where do chemoautotrophs get the energy to grow and reproduce if they can't carry out photosynthesis and they don't require organic molecules as food sources?

Let's look at the AAAS Project 2061 Science Assessment Website to see how they treat the topic of Matter and Energy in Living Systems. This site is for high school biology but it's the only place I know where we can assess what AAAS thinks is important in basic concepts. Students are expected to know that...

All organisms need food as a source of molecules that provide chemical energy and building materials.

1. Food consists of carbon-containing molecules in which carbon atoms are linked to other carbon atoms.
2. Carbon-containing molecules serve as the building materials that all organisms (including plants and animals) use for growth, repair, and replacement of body parts (such as leaves, stems, roots, bones, skin, muscles, and the cells that make up these structures) and provide the chemical energy needed to carry out life functions.
3. If substances do not provide both chemical energy and building material, then they are not food for an organism.
4. Chemical energy from carbon-containing molecules is the only form of energy that organisms can use for carrying out life functions.
5. Carbohydrates (including simple sugars and starch), fats, and proteins are molecules that are food.
6. Light is not food because it is not made of atoms and therefore cannot provide building material, and even though substances such as water, carbon dioxide, oxygen, and various minerals provide atoms for building materials for some types of organisms, they are not food because they do not contain carbon atoms that are linked to other carbon atoms and cannot be used as a source of chemical energy.

Oh dear. If this is an example of core concepts then we need to add one more item; namely "7. According to item #3, chemoautotrophs are not organisms."

I'm sure most of you recognize the problem. The focus is on plants and animals, ignoring protozoa and bacteria. This is not how to teach basic concepts in biology and it certainly isn't how to teach if evolution is supposed to be an important core concept. Complex plants and animals did not just poof into existence with specialized metabolic pathways.

But not to worry. Although the six statements above seem wrong, they are soon clarified in the next section ...

Plants make their own food in the form of sugar molecules from carbon dioxide molecules and water molecules. In the process of making sugar molecules, oxygen molecules are produced as well.

1. Unlike animals, plants do not take in food from their environment.
2. Plants make their own food in the form of sugar molecules by means of a chemical reaction between carbon dioxide molecules and water molecules. Oxygen molecules are also a product of this reaction.
3. The process of making sugar molecules involves linking together carbon atoms that come from molecules of carbon dioxide.
4. The chemical reactions by which sugars are made takes place inside the plants. In most familiar land plants, the carbon dioxide molecules that are used come from the air that enters the plant primarily through its leaves, and that the water molecules that are used in the reaction enter the plant through its roots.

Here's the core concept as I teach it. I'd appreciate feedback on which way is better.

Photosynthetic organisms, such as bacteria, algae, and plants, can use light as a source of energy. They convert this energy into chemical energy in the form of ATP and other cofactors. These "high energy" molecules are used to provide energy in biosynthesis reactions that make all of the important molecules in the cell including amino acids, proteins, nucleotides, nucleic acids, fatty acids, lipids & membranes, carbohydrates, and polysaccharides.

Note that point #2 above is absolutely wrong. Oxygen is NOT produced as a result of a reaction between CO₂ and H₂O. That is a major misconception. The oxygen given off by some photosynthetic species is derived directly from water as part of the photosynthetic electron transfer reactions. Some photosynthetic species don't produce oxygen yet they are perfectly capable of synthesizing nucleic acids, proteins, lipids, and carbohydrates. How do they do it? You need to understand the answer to that question if you are going to understand how eukaryotic photosynthesis evolved.

My main criticism of undergraduate biology education is that the core concepts are not being taught and, when an attempt is made, they are often taught incorrectly. The Vision and Change document doesn't make a contribution toward fixing this problem. The "core concepts" it describes are not specific enough to be helpful and when they are specific they turn out to be wrong or misleading.

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