The term “metabolism” is, mistakenly, much too open for interpretation. It has become somewhat of a buzzword, haphazardly thrown around, resulting in further misuse and confusion of a critical topic in nutrition. Supplement companies boast of their products “speeding” metabolism up and trainers assert specific exercises can influence it. Is there any truth to this? The answer is lies within education. First, always be critical (and somewhat skeptical) of a claim, especially from anyone or anything ultimately trying to sell you something. If there’s an agenda, there’s likely some form of information manipulation going on. Let’s take a big step back and learn metabolism from the ground up. Learning how to think about metabolism will empower you far more than merely being told what to think.
In this blog series I’ll (try) to describe how to study metabolic pathways:
A daunting image, yes, but it certainly does demonstrate the point: metabolism is complex, and it’ll take a lot of effort to truly grasp. I’ve had to learn and relearn this stuff nearly a dozen times by now. But by doing so, you’ll develop a sort of critical intuition. Whether you’re reading this to study for an exam or for pleasure (masochistic, but admirable), I implore you to not memorize metabolic steps – it’s a common pitfall. Rather, try to understand the chemical logic behind them. There is, in fact, a reason for it all.
As of now, there’s around 4,500 known enzymes involved in metabolism. This is a light estimate as most of these enzymes have multiple isoforms distributed in a tissue-specific way. As such, it isn’t likely that any one person grasps the details of it all. Moreover, new enzymes are continually being discovered as are new functions of existing ones. Well known pathways are still a very active area of research. So, I’m going to pick on a few central pathways and try my best to discuss how to study this stuff. Hopefully, understanding this chemical logic behind these select few carries on into whatever your area of interest is. Everything ties into a metabolic pathway one way or another – it doesn’t matter if it’s a cell signaling pathway, disease state, diet, or performance in the gym. For example, diabetes, heart disease, and (to a large extent) cancer are all metabolic diseases. Understanding the various enzymes involved in energy transduction, the generation and consumption of metabolites, and their regulation (or dysregulation) is important in the development of therapeutics to tackle disease.
What actually happens when you eat something? What’s the fate of these nutrients and how do we extract energy from them? For that matter, what even is energy? Here’s a brief overview of what I’ll go over in this blog series:
I’ll cover the catabolism and some anabolism of the macronutrients, starting with glycolysis. But first, it’s important to build a bit of a foundation before we dive in.
The Three Tenets of Metabolism
As mentioned above, the goal here is to understand metabolism, not to memorize a series of steps. So if you’re looking for a fancy pneumonic to memorize, say, the steps in the TCA cycle, this isn’t the place. To grasp what’s happening there’s three crucial aspects of metabolism to consider:
• Thermodynamics describe the energetics of metabolic conversions and ultimately dictates the sequence of reactions. We’re particularly interested in knowing which steps require energy to proceed forward, which give off energy, and how these can be coupled to derive useful work (I’m using the thermodynamic definition here). Simply getting energy out isn’t the goal – we could just set glucose on fire if that was the case. Rather, we want to extract energy in a biologically meaningful way. This can only be accomplished through a series of stepwise set of reactions that give us work.
• How does a reactant get converted to a product? Chemistry describes this mechanism. Knowing enzyme kinetics will be useful for this part – every step in a metabolic pathway is under enzymatic control. I’ve used the term “chemical logic” a couple times already, and here is where it’ll become apparent. Pay attention to the intermediate steps and ask why a molecule was changed the way it was – why, for example, would a hydroxyl group be added where it was?
• How are metabolites controlled? Your body has many intricate control mechanisms that highly regulate metabolism. As if metabolism wasn’t complicated enough, regulation occurs at multiple levels. While I’ll only dive into the chemical level of regulation in this series, know that hormonal, genetic, and circadian regulation adds another level of complexity to it all.
Principles of Metabolism
We can define metabolism as a collection of reactions that accomplishes a goal for the organism which, for us, is to reproduce. At least in this context, DNA makes people who then serve as vessels to make more DNA. Our metabolism is designed as such to fuel this process. The set of reactions that allow us to accomplish this goal and be split into catabolic and anabolic reactions. The paths that these reactions take must be different, otherwise we’ll end up with futile cycling – a sort of “cancelling out” products. We’ve evolved in a way to where these reactions have been compartmentalized. That is, anabolic and catabolic reactions take place in different places within the cell. Compartmentalization also takes place on an organ level – certain organs specialize in certain chemistries. There’re other ways these two are differentiated that will become apparent when we go over fatty acid synthesis and beta-oxidation. Similar to this is localization – the location of where a set of reactions occurs. Localization is essential to mitigate self-inhibition of metabolic enzymes by metabolic products.
Much of metabolic reactions are shared between organisms – if you understand glycolysis in E. coli, you pretty much understand it in humans. There’s a universality to it all which is hard not to appreciate. It’s a property that has allowed us to gather the knowledge we currently have – much of what we know about our metabolism is due to the work done in bacteria.
There are certain committed steps along a pathway that commit a molecule (or more specifically, its atoms) to it. That is, once a molecule has gone through a pathway’s committed step, it’s not stopping until it comes out the other end. These committed steps tend to be points of regulation.
And so, here’s everything we’ve discussed up until this point:
Hopefully all of these points will become clear over the next several blog posts.
Equilibrium is Death
Living things are open systems whose metabolic processes are characterized by non-equilibrium thermodynamics. We’re dealing with flux through a pathway here, not equilibrium. At equilibrium, free energy is zero – there’s no work that can be accomplished. There needs to be directionality in a pathway. That is, reactants must give us some desired product. In order to do so, the overall change in free energy needs to be negative. While individual steps along a pathway may not be energetically favorable by themselves, when coupled together, the net free energy change will be. We’ll see this in glycolysis.
This is largely accomplished by keeping steady state of intermediates – once a pathway gets going, the concentration of intermediates really doesn’t change much (barring a change in an environmental circumstance). As a result, we have a constant flow of intermediates through the system. This point can be a bit confusing but try thinking about it on a bigger scale: You’ve eaten and pooped out thousands of pounds of food in your lifetime and you’ll keep on doing so for decades to come. Your weight and size, however, really hasn’t changed much with respect to the amount of food you’ve consumed. If it helps, you can view flux as a sort of “equilibrium equivalent” but know that it’s not a true equilibrium. With a flux through a system, work is continually being done. At equilibrium, no work is being done. True metabolic equilibrium would result in our death. Now, there may be some enzymes along a pathway that operate with a free energy difference close to zero, but again, these reactions do not occur in isolation – they’re coupled together for an overall negative free energy difference.
A Thermodynamically Unfavorable Reaction Can be Driven By Coupling It With A Thermodynamically Favorable One
For any given metabolic pathway, two criteria are met: 1) its individual reactions must be specific (which we’ll get to) and 2) the pathway, as a whole, must be thermodynamically favorable. This is a straightforward concept – if an intermediate of a thermodynamically unfavorable reaction (positive △G) is combined with a thermodynamically favorable reaction (negative △G) that’s greater, the total will be positive (a net negative △G).
We’ll see that this is typically accomplished through ATP hydrolysis. Its hydrolysis to ADP and phosphate is quite exergonic. Let’s look at an example:
When A is at equilibrium with B, we see that its hypothetical equilibrium constant is 1.15 x 10-3 or about 1 part in a thousand – not particular great if we need product B. But take a look at what happens if ATP is hydrolyzed along with it:
When coupled together, the overall free energy change becomes negative and the equilibrium constant increases to nearly 300. It is now much more favorable to form B. Don’t worry too much about the numbers here. The takeaway is that ATP drives reactions – a point that will become exceedingly more clear as you read through this series.
While we’re at it, it’s worthwhile to briefly discuss how phosphate is transferred. Metabolism involves lower-energy phospho-compounds, such as glucose-6-phosphate and higher-energy ones such as phosphoenolpyruvate.
The phosphoesters glycerol-3-phosphate and glucose-6-phosphate are much lower in energy (-9.2 and -13.8 kJ/mol, respectively) than other phosphocompounds we’ll be dealing with. As you can see, ATP is at the center of this diagram with 1,3-bisphosphoglycerate, creatine phosphate, and phosphoenolpyruvate all having higher free energies. As such (and the main takeaway from this diagram), these higher energy compounds can be used to generate ATP – we’ll see this happen in glycolysis. Glucose-6-phopshate and glycerol-3-phosphate, being lower-energy, could not be used to make ATP without coupling some other process to it. Relative energies do in fact, matter.
ATP is our body’s energy currency – it’s not a reserve. In fact, a molecule of ATP has a half-life of about ½ a second, so we’re cycling through a lot of ATP each day. The ATP in your muscle is enough to power contraction for about a second. Kinetically speaking, it takes a lot of time to run through glycolysis and the TCA cycle to generate more ATP. Creatine phosphate helps to regenerate ATP from ADP to provide energy for the short-term. Once creatine phosphate stores are depleted, ATP will have to be generated through metabolic pathways. And so, physically-demanding tasks like exercise rely on various means of generating ATP.
Looking at this graph, we get a visual of the kinetics associated with metabolism. As creatine phosphate levels decline, anaerobic metabolism begins to predominate. In anaerobic metabolism, ATP is generating in the absence of oxygen, producing lactate in the process (we’ll get to how the body handles this). A common misconception is the notion that anerobic and aerobic metabolism occur as a dichotomy – after anaerobic metabolism cuts off, aerobic metabolism takes over. This isn’t the case. Rather, once an anaerobic threshold has been reached, aerobic metabolism will predominate. As you can see, they are both occurring simultaneously for a time. Remember this point next time you see something about anaerobic vs. aerobic workouts.
The actual chemistry between the steps in a pathway is where most falter (and I was certainly no exception when learning this). But, there’s no escaping it – to understand metabolism, you need to understand its chemistry. As such, much of the following articles will focus on this.
There are four major types of biochemical reactions that will continually pop up:
1) Group Transfer Reactions
• As its name implies, this involves the transfer of an atom or (more commonly) a group from one molecule to another. We’ll see three types of group transfers: acyl, phosphoryl (kinases and phosphatases), and glycosyl.
2) Eliminations, Isomerizations, and Rearrangements
• Eliminations, here, will typically involve dehydrating an alcohol group to form a double bond. Doing so often sets up a carbonyl to be moved or put in a particular place, which is often followed by a bond-breaking or bond-making reaction (an example of that chemical logic to be thinking about). Isomerizations, such as changing the molecule’s stereochemistry from S to R, will occur a few times. We’ll see plenty of carbon skeleton rearranging – often as a way of extracting energy or to remove a toxic metabolite. Epimerization is another important concept that will lend to the distinction between anabolic and catabolic reactions.
3) C-C Bond Making & Breaking
• This is the big one. In glycolysis, for example, the starting 6-carbon sugar, glucose, will get broken into two, 3-carbon pieces. In amino acid synthesis, we’re taking simple 1-, 2-, and 3-carbon units and assembling them into something much more complex. And so, understanding how these carbon bonds are broken and made, as well as the carbon’s fate, is essential to understanding metabolism.
4) Oxidation and Reduction
• These redox reactions are a central theme of metabolism, so it’s recommended to review this prior to diving into metabolism. Being familiar with these types of reactions is crucial for understanding how electrons are accepted and donated – an integral part of energy extraction and biosynthesis. Let’s discuss a bit about how electrons are carried.
Electron carriers are kinetically stable molecules while in the absence of a specific catalyst. Adenosine triphosphate, ATP, is a great example of this and earlier you saw how it can be used to push a thermodynamically unfavorable reaction forward. ATP is an activated carrier of phosphoryl groups, held together by high-energy phosphoanhydride bonds – that is to say, there’s a lot of energy when these bonds are broken (hence why it’s considered our body’s energy currency). High-energy bonds are often unstable, but ATP can float around without decomposing. This exemplifies the idea of kinetic stability – it won’t breakdown unless there’s an enzyme present to catalyze the hydrolysis of its bonds. Enzymes serve to direct chemistry in a spatial-temporal fashion.
The other electron carriers we’ll see are derived from vitamins. These are nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD). These cycle through oxidized and reduced states, the latter of which is the high-energy, electron-carrying state.
Going back to oxidation and reduction reactions, the redox potential of a reaction is denoted by △E in which △E = E(acceptor) – E(donor). When the △E for a process is positive, its △G will be negative. The Nernst equation is used to calculate redox potential. Don’t worry too much about this right now – it’s not terribly difficult and will become clear when we get to oxidative phosphorylation. NAD+ and FAD are particularly relevant here.
Here’s NAD+ :
The reactive sites are where hydrides are put on and taken off. With NAD+ , the reaction is quite simple:
The reduced form is NADH. We’ll typically see NAD+ oxidize alcohols to carbonyls or the reverse, NADH being used to reduce carbonyls to alcohols.
Unlike NAD, FAD has two reactive sites:
Here, I’ve shown how flavin carries two electrons. It can also carry only one as well.
These are often used to oxidize saturated carbons to form double bonds or, although not as common, the other way around.
The word “metabolism” is thrown around rather frequently (maybe too frequently) but ask its definition and you’ll likely never get a straight or consistent answer. It’s this vagueness that perpetuates much of the misinformation floating around social media and supplement companies alike. Metabolism is a tricky topic to discuss. Even this post, in which basic metabolism was barely touched upon, is a daunting read. I’m not sure why you would read through it all, but whatever your reason, hopefully you’ll gain a better understanding of it and dispel a few myths along the way.
In the next post or two, we’ll go over glycolysis and explore how carbohydrates are broken down in the body. Then, we’ll see how those end products are utilized in the TCA cycle and what happens under aerobic conditions.
Later on, the plan is to discuss gluconeogenesis, the pentose phosphate shunt, fatty acid metabolism, and the urea cycle.