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Thursday, October 24, 2013

ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation


Better Biochemistry
Tansey et al. (2013) have described the five core concepts in biochemistry and molecular biology. These are the fundamental concepts that all biochemistry instructors must teach and all biochemistry students must understand.

The five core concept categories are:
  1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
  2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
  3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
  4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
  5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]
I like the idea of teaching biochemistry from a concept-driven perspective and I like the five categories. However, I was not too pleased with the description of the core concept of evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution]. It's one thing to identify the main categories but you also have to get the concepts right if you are going to advocate teaching them!

Let's see how they do with the second core concept.
Matter and Energy Transformation

The Many Forms of Energy Involved in Biological Processes

The energetics of a biological system or process—be it an ecosystem, an organism, a cell, a biochemical reaction—conforms to and is understood in terms of the fundamental laws of thermodynamics. Biological systems capture and process energy from the environment in many forms including that emanating directly from the sun (photons through photosynthesis), heat from the environment (kinetic energy), and energy rich compounds produced by geothermal processes (e.g. sulfur compounds) or other organisms (e.g. carbohydrates). Energy from all sources is chemically converted into useful chemical and physical work in a controlled and regulated fashion. The potential
energy stored in chemical bonds can used to generate motion, light, heat, and electrochemical gradients; likewise, electrochemical gradients can be used to generate motion and new chemical bonds. The input of energy from the environment allows living systems to exist in a state of nonequilibrium with their environment. The discussion of energy and matter conversions in biological systems makes use of the physical concept of changes in Gibbs free energy, or ΔG.
I think we can all agree that a basic understanding of thermodynamics is an important core concept. However, I would have worded this paragraph somewhat differently.

First, I would have mentioned that organisms can capture energy from simple inorganic compounds such as H2 or those containing Fe2+. These are energy sources for many chemoautrophic bacteria. If you are teaching biochemistry from an evolutionary perspective, it's important that students understand how these organisms capture energy. That's the process that is most like the mechanism found in the earliest living cells.1

Second, I would have put more emphasis on using captured energy in biosynthesis pathways. The paragraph mentions that energy can be used to generate new chemical bonds but that doesn't convey the importance of the process. Think about bacterial cells growing and dividing in the ocean or plants growing from a single seed. Most of the energy goes into making proteins, nucleic acids, lipids, and carbohydrates.

Third, I would drop the reference to cells being in "a state of nonequilibrium with their environment." That conceptt is covered under "homeostasis."

Biologically relevant energy and matter interconversions do not occur rapidly enough (often by many orders of magnitude) to support life. In living systems, biological catalysts called enzymes facilitate these reactions. Enzymes are macromolecules, usually proteins or RNA molecules with a catalytic function. Enzymes do not alter reaction equilibria; instead, they lower the activation barrier of a particular reaction so that reactions proceed much more rapidly. The presence of powerful enzymatic catalysts is one of the key conditions for life itself.

Description of the rates of enzymatic reactions represents the subdiscipline enzyme kinetics. Key concepts of kinetics, including the definitions of the terms vo, Vmax, Km, and kcat, constitute a common language for biochemists and molecular biologists in discussing the properties of enzymes.

Students should be able to apply their knowledge of basic chemical thermodynamics to biologically catalyzed systems, quantitatively model how these reactions occur, and calculate kinetic parameters from experimental data.
This is pretty good. I would only add that there are some fundamental concepts of enzyme mechanisms that need to be covered. The idea of a transition state is important. I put a lot of emphasis on oxidation-reduction reactions as a core concept in biochemistry.
Coupling Exergonic and Endergonic Processes

Biochemical systems couple energetically unfavorable reactions with energetically favorable reactions to allow for a wider variety of reactions to proceed.

Students should be able to discuss the concept of Gibbs free energy, and how to apply it to chemical transformations, be able to identify which steps of metabolic pathways are exergonic and which are endergonic and relate the energetics of the reactions to each other.
I have a problem with this section. I don't think that the concepts of "exergonic" and "endergonic" processes are very important in biochemistry and I don't use them in my textbook. They're not found in many other textbooks, either. Also, the idea of "coupled" reactions is very poorly taught in biochemistry courses. It's almost never true that enzymes simply link up two independent reactions, one of which is "favorable" and the other "unfavorable." What usually happens is that a completely new reaction is catalyzed. For example, ATP is not hydrolyzed but, instead, a group transfer reaction is created. This important concept is covered in the next section but the authors do not appear to have grasped its significance.

Not only that, what does it mean to say that a reaction is "energetically unfavorable"? Usually this refers to the standard Gibbs free energy (ΔG°′) but one of the most important concepts in biochemistry is the difference between the standard Gibbs free energy change and the actual Gibbs free energy change (ΔG) inside the cell. In most cases ΔG = 0.

It's true that there are potential "endergonic" reactions occurring inside cells. Think about ATP hydrolysis, for example. The concentration of ATP is maintained at a high level relative to ADP and Pi so the Gibbs free energy change in the direction of hydrolysis is actually more negative that even the standard Gibbs free energy change. What this means is the the reverse reaction is extremely "endergonic."

However, it is simply not true that there are steps in metabolic pathways that are "endergonic" as the authors state. That statement reflects a profound misunderstanding of a fundamental concept in biochemistry. There will not be any flux in the "forward" direction of a metabolic pathway as long as even one reaction is "endergonic." All reactions have to be near-equilibrium reactions or reactions with a negative ΔG that's maintained because the enzyme activity is regulated to prevent the reaction from reaching equilibrium.

The important concept is "flux" or flow of metabolites in one direction along a metabolic pathway. There are many pathways where flux can occur in either direction as in the central part of the gluconeogenesis/glycolysis pathway or the citric acid cycle. Students need to understand what controls flux in one direction or another. They should know that, like water, metabolic flux cannot flow uphill.
The Nature of Biological Energy

In biological systems, chemical energy is stored in molecules with high group transfer potential or strongly negative free energy of hydrolysis or decomposition. These molecules, particularly ATP, provide the free energy to drive otherwise unfavorable biochemical reactions or processes in tightly coupled and highly controlled fashion. Most frequently, the free energy needed for a process or metabolic pathway is provided by group transfer rather than by hydrolysis. In this way, efficient energy transfer is optimized, while inefficient energy transfer to the environment (in the form of heat for example) is minimized.

Students should be able to show how reactions that proceed with large negative changes in free energy can be used to render other biochemical processes more favorable.
The essence of these statements is correct but it is not explained very well. The important concept is not that you "couple" a "favorable" reaction like ATP hydrolysis to an "unfavorable" reaction like synthesis of glutamine from glutamate and ammonia (ΔG°′ = +14 kJ mol-1).
The point is that the enzyme (glutamine synthetase) catalzyes a completely different reaction—a phosphoryl group transfer reaction—with a negative standard Gibbs free energy change of ΔG°′ = −18 kJ mol-1.

[see Moran et al. (2011): Introduction to Metabolism]
If there were an enzyme that catalyzed the first reaction involving only glutamate and ammonia then this reaction could easily occur inside the cell in spite of the positive ΔG°′. It would be a near-equilibrium reaction with steady-state equilibrium concentrations of glutamate that were very much higher than the concentration of glutamine.

It's likely that the concentration of glutamine would then be too low to support all the reactions that require it. That's why the reaction involving ATP is more useful. It means that the steady-state concentration of glutamine can be maintained a much higher concentration. This requires regulation of glutamine synthetase in order to prevent the reaction from reaching equilibrium.

It seems to me that the authors (Tansey et al.) have not thought about the fundamental core concepts. They are promoting widespread misconceptions about thermodynamics and metabolism and they are missing some important concepts. I've already mentioned flux. The other missing concept is oxidation-reduction reactions (electron transfer) and the importance of reduction potentials. NADH, NADPH, and QH2 are important energy currencies inside the cell—just as important as ATP.

There's something seriously wrong with biochemistry teaching if ASBMB educators can't even correctly explain foundational concepts like "evolution" and "matter and energy transformation."

1. I believe that all introductory biochemistry students should be able to explain where chemoautrophs get their energy. If they can't do it, they haven't been taught the fundamental concepts.

Tansey, J.T., Baird, T., Cox, M.M., Fox, K.M., Knight, J., Sears, D. and Bell, E. (2013) Foundational concepts and underlying theories for majors in “biochemistry and molecular biology”. Biochem. Mol. Biol. Educ., 41:289–296. [doi: 10.1002/bmb.20727]


KStRNA said...

Thermodynamically can't you think of the ATP-dependent amidation of glutamate as two separate reactions? What matters are the starting and end points. Delta G is a state function. Yes students should understand physically that one reaction is taking place not two, concentrations matter, and regulation is key to avoid equilibrium. Students though should appreciate the path independence of state functions. It is a useful intellectual tool that can come in handy when modeling a system and when evaluating model.

Electrochemistry is very important. We have redone our intro chem sequence to include more electrochem given its importance in biochemistry.

For your intro biochemistry course, what chemistry experience do students come in with?

Ours take a semester of general chemistry (intro to physical chemistry & inorganic) and two semesters of organic chemistry.

Larry Moran said...

You are correct that ΔG°′ (STANDARD Gibbs free energy change) is a state function and that's part of what should be taught in a biochemistry course.

It's true that you can calculate the standard Gibbs free energy change of a new reaction by adding together the free energy changes of two individual reactions whose sum is equivalent to the new reaction. However, I think it's important to teach students that when enzymes "couple" reactions they don't just steal energy from one reaction and give it to another to make it proceed "backwards."

For your intro biochemistry course, what chemistry experience do students come in with?

Our students take a semester of organic chemistry and a semester of physical chemistry in their first year. Introductory biochemistry is a second year course that's a prerequisite for many third year courses.

First year biology (one semester of evolution and one semester of basic cell biology) is a prerequisite. Most USA schools don't require a biology course as a prerequisite, does yours?

David said...

My apologies for dragging up ID creationists, but this discussion brings to mind one of the best examples I’ve seen of a poor understanding of biological energetics and “coupled” reactions that Stephen Meyer (inadvertently) provided in Signature in the Cell. Meyer, in discussing aminoacyl tRNA synthetases, confidently states:

“Enzymes use a reaction that liberates energy to drive forward a reaction that requires energy, coupling energetically favorable and unfavorable reactions together. Enzymes can do this because they have a complex three-dimensional geometry that enables them to hold all the molecules involved in each step of the reaction together and to coordinate their interactions. But two independent catalysts cannot accomplish what a compound catalyst (i.e., an enzyme) can.” Pgs 310-311

Later in an endnote, he adds

“By coupling and enabling energetically favorable and unfavorable reactions, synthetase enzymes catalyze the production of a molecule—a charged tRNA ready for translation—that would not form in any appreciable quantities otherwise—even with the help of two separate RNA catalysts. An RNA catalyst might drive forward the energetically favorable first reaction that activates amino acids with AMP. But even a separate RNA catalyst will not drive forward the energetically unfavorable second aminoacylation reaction (unless massive amounts of the reactants are provided to overcome the unfavorable energetics).” Pgs 536-537

How surprising to hear that the second step of the synthetase reaction is unfavorable. As far as I can tell he is confusing the two actual steps performed by the synthetase, amino acid adenylation and tRNA charging (both “favorable” reactions that could be catalyzed by two separate enzymes, in principle), with the “coupled” reactions of favorable ATP hydrolysis and unfavorable aminoacylation. I was also amused to hear that only a catalyst that couples “favorable” and “unfavorable” reactions is a true enzyme.

KStRNA said...

Stealing the energy would be wrong and would do a disservice to the reality. The way I have seen coupling presented doesn't do that. It just provides a framework for accounting and it is clear it is not the actual reality. They get that message starting in intro chemistry.

Intro biology is not required for the biochemistry course I teach as I am in a chemistry department and biochemistry is required for a chemistry major to earn an ACS certified degree and intro biology is not part of the chemistry major. However most students taking biochemistry have taken intro biology, so I operate on that assumption. Evolution is interwoven throughout the two semesters I teach. The chemistry majors are smart and can catch up (and they do). Sometimes the chemistry majors are actually better off as they aren't taught incorrectly about ATP, stability of the DNA double helix, and the Central Dogma.

It helps that I teach molecular evolution like the students are seeing it for the first time (sadly because they usually are). The intro biology doesn't cover molecular evolution at my school. They don't have the neat divide found in your year one biology and cover more areas of biology including plants, animals, and ecology. Basic genetics, microbiology, and evolution are weak spots for students coming out of the first year of biology.

The biology majors take biochemistry usually in their senior year. Most regret waiting that long as they find biochemistry explains the questions they had in their other courses. Biochemistry students now start taking biochemistry during their second year. One benefit of the new MCAT is that most students are being encouraged to take biochemistry earlier. My content isn't changing. I would hate to teach or take the one semester biochemistry course that covers the material for the new MCAT.

Georgi Gladyshev said...

Origin of life and its evolution are the result of action of laws of hierarchical thermodynamics.
Thermodynamics investigates systems which can be characterized by state functions. The separation of biological systems into individual hierarchies of structures allows us to study the processes in them independently of the processes that take place in other hierarchical structures.

Criterion of evolution
The approval about the reduction of the entropy of living systems as a result of biological evolution is incorrect. The criterion of evolution of living system is the change (during evolution) of the specific free energy (Gibbs function, G) of this living system. The evolution of living system takes place against the background of flows of energy (e.g., light, energy of physical fields) from the environment. It increases its specific free energy. At the same time, the specific free energy of this living system is decreased as a result of spontaneous processes in this system.
Thus, the total change in the specific free energy of a living system is composed of two parts: 1. The change of free energy due to the inflow of external energy (G1> 0) and 2. The change of free energy due to spontaneous transformations in the system (G2 < 0) . The evolving system constantly adapts to a changing environment. The principle of substance stability contributes to this adaptation.
Thermodynamics of evolution obeys the generalized equation of Gibbs (that is the generalized equation of the first and second laws of thermodynamics)*. Biological evolution and the processes of origin of life are well described by the hierarchical thermodynamics, established on the firm foundation of theory of JW Gibbs. Our theory created without the notion on dissipative structures of I. Prigogine and negentropy of L. Boltzmann and E. Schrodinger.
“Thermodynamics serves as a basis for optimal solutions of the tasks of physiology, which are solved by organisms in the characteristic process of life: evolution, development, homeostasis, and adaptation. It is stated that the quasi-equilibrium thermodynamics of quasi-closed complex systems serves as an impetus of evolution, functions, and activities of all levels of biological systems’ organization. This fact predetermines the use of Gibbs’ methods and leads to a hierarchical thermodynamics in all spheres of physiology. The interaction of structurally related levels and sub-levels of biological systems is determined by the thermodynamic principle of substance stability. Thus, life is accompanied by a thermodynamic optimization of physiological functions of biological systems. Living matter, while functioning and evolving, seeks the minimum of specific Gibbs free energy of structure formation at all levels. The spontaneous search of this minimum takes place with participation of not only spontaneous, but also non-spontaneous processes, initiated by the surrounding environment.”
Works of the author:

Georgi Gladyshev
Professor of Physical Chemistry

*) The generalized equation of Gibbs (See: )

P.S. Lastly, it is important to take into account, from the viewpoint of hierarchical thermodynamics, that anti-aging diets and many drugs can be used for the prophylaxis and treatment of cardiovascular diseases, cancer, and for numerous other illnesses.

Linzel said...

I'd like to brush up on this material. especially the near equilibrium concentrations of the products and reactants physiologically. Where is a fairly straightforward explanation of this? What reading would you recommend - and I'm not looking for a textbook.

Newbie said...

Wow! This is a great article Larry!!! How did I miss it?

I have a question or two that may sound a bit odd:

1. Is there any scientific evidence explaining what circumstances i.e. environmental etc. would lead to higher concentrations of coenzyme NADPH in a cell?

2. What happens/would happen, if higher concentrations of coenzyme NADPH would persist a cell?

I hope I'm making myself clear.