Bioenergetics and Energy Metabolism
Biological order and energy
First and second laws of thermodynamics.
"Spontaneity" is ambiguous. We will avoid it by calling such reactions thermodynamically favorable. We divide the 'universe' into systems and surroundings.
Criterion for "spontaneity": DSuniverse > 0. This is true for all favorable reactions, that is, for all reactions that actually happen. Many that don't happen are also favorable, that is, satisfy this criterion. Why don't they happen? Because they are too slow. In other words, a system might not appear to change either because of kinetic or thermodynamic stability. 'Stability' is a relative term, not absolute.
The measurement of universal quantities is not feasible. To find a system quantity that could be used as a criterion for "spontaneity", people started with the idea that for a reversible reaction (where DSuniverse = 0), at constant T,DS = DH/T where system quantities are used. This rearranges to
0 = DH - T DS which is true for any system at equilibrium (a reversible change). Now it was also known that for an irreversible reaction (all real changes),
DS > q/T where q is the heat crossing the boundary between the system and the surroundings. For most purposes, q is DH, so, rearranging:
0 > DH - T DS,
again for all real changes. Gibbs defined a new thermodynamic quantity, free energy (which we call G for Gibbs), G = H + T S. Changes in this quantity, DG's, can, in theory, be measured for a system. If the change is negative (as above), the reaction giving rise to that change is favorable.
It is important to notice the difference between DG and DG°. The first is the actual change in G associated with a reaction under the given conditions. The second is the change in G associated with a reaction under what are called standard conditions. These standard conditions may be chosen arbitrarily, and are generally chosen for convenience. Relationship between DG and DG°:DG = DG° + RT ln [products]/[reactants]
The biological standard is DG°', where the usual standard conditions are altered to include pH = 7. Since the actual conditions inside the cell are not often known, we sometimes use DG°' as an estimate for the actual DG.
One important take home lesson from these two laws of TD is the relationship between heat and entropy. We know that living things, overall, introduce order into the materials they retain for their own use (DScell < 0). A negative DS requires a negative DH to overcome its effect, that is, to make the overall DG negative. A large negative DH for the cell means that for the cell to produce order, it must release a large amount of heat to the environment. This is what results in a balancing positive DS for the surroundings, so that the overall DS for the universe is positive (as it must be). This analysis leads to a question of fundamental importance for every cell: where does this energy come from?
There is more than one answer to this question, depending on the cell we are talking about. Some plant cells obtain this energy from light. Most of that light energy is eventually released by the plant (as heat) to the environment. That release of heat can be used to "drive" the ordering of the plant cell (the unfavorable DS). Many plant cells, and animal cells generally, obtain the energy from reduced organic compounds that they find in their environments. Since our atmosphere is highly oxidizing, energy can be released by the combination of reduced compounds with atmospheric O2 (or with other highly oxidized species). This process is called respiration (it results in the production of CO2 from the reduced carbon). Again, most of this energy is absorbed by the surroundings of the cell as heat, allowing the cell itself to become more ordered. Other cells use other types of reduced compounds (inorganic ones). We won't discuss those.
How are these reduced organic compounds combined with oxygen? We know from our own experience that a match is all it takes for this reaction to proceed (gasoline, paper, forest fires). It is a favorable reaction. However, it does not proceed without the match. The match does not change the DG of the reaction. It was favorable without the match; it is favorable with the match. These reactions are kinetically slow (or challenged?). The activation energy barrier is too high - only a miniscule proportion of molecules at normal T's have sufficient energy to react - so the rate is slow enough to be undetectable to us. How can the activation energy be lowered? The match does not do this - rather, it increases the energy of sufficient molecules that the energy released by their reaction drives other molecules over the barrier. Activation energy is lowered by catalysts; biological systems use protein catalysts called enzymes (in the vast majority of cases).
How do these enzymes function to couple the release of heat with the increase in order in the cell? Combination of reduced organics (sugars, proteins and fats, mostly) with O2 is a complicated reaction with many steps, even when a match is used. Enzymes in a cell provide a reaction pathway, an ordered process for this reaction. This series of steps is called a metabolic pathway (or just a pathway). In fact, each step is catalyzed by an enzyme that is specific to that particular step (for instance, glycolysis is a series of 10 steps, catalyzed by 10 enzymes, with the product of one step becoming the reactant for the next step). As the organic molecule is oxidized, much of the energy taken from it is stored in some way in other structures in the cell. This is another reason that these energy yielding reactions are broken up into several steps - each step then involves a "reasonable" amount of energy, a packet or quantity that can reasonably be stored or used in some way by molecules that may be involved in that particular step. We will spend some time on some examples as we discuss glycolysis. In particular, enzymes provide the mechanism that allows some of this energy to be stored in ATP. ATP can then participate in other reactions where it is hydrolyzed to ADP and Pi, contributing a large, favorable DG.
Cells are examples of systems at steady-state. That is, the system itself does not change over time. Of course, there are some changes, and the term steady-state needs more precise definition, but many components of the cell do not change much in concentration over rather long periods of time (as long as the cell is alive).
It is important to distinguish steady-state from equilibrium. A system at equilibrium also does not change. So what distinguishes steady-state? In a system at steady state, many non-equilibrium processes are occurring. What prevents the system from reaching equilibrium is the flow of material and energy into the system and the flow of waste and heat out. The two "reservoirs" (that is, the sources of energy and food, and the sinks of heat and waste) are not at equilibrium (and probably not at steady-state).
Food and the derivation of cellular energy
As stated earlier, most eukaryotic cells (and many prokaryotic cells) get the energy they need from reduced organic molecules, which we can call food molecules. The main types are protein, carbohydrate, fat and nucleic acids. These larger food molecules are broken down and oxidized in three stages: monomerization, which almost always takes place outside the cell by the action of enzymes called hydrolases (nucleases, proteases, lipases, glycosidases); oxidation and/or rearrangement to a small set of intermediate organic molecules (usually acids) - this would include glycolysis for carbohydrates, b-oxidation for fatty acids; the third stage for all these food molecules is the Krebs cycle. Although energy is released from the food molecules at each stage, coupling, or energy conservation, is primarily a function of stage III (Krebs), with a small amount in stage II and none in stage I. This type of metabolism - the breaking down and oxidation of food molecules - is called catabolism. At this point we will concentrate on stage II for carbohydrates - glycolysis, and say only a little about other aspects of catabolism.
Stage I - extracellular hydrolysis. It is unlikely that the cell conserves any energy from reactions that are catalyzed extracellularly. In the case of each of these four kinds of food molecules, the individual units are held together by anhydrous bonds (bonds formed by the loss of water) and so are unstable thermodynamically in an aqueous environment. Glycosidic bonds in carbohydrates and nucleic acids, phosphodiester bonds in nucleic acids, peptide bonds in protein, ester bonds in fats, all have a negative DG for simple hydrolysis. That free energy is released as heat, not used to produce some kind of order (or to do useful work, chemically). Cells in general have the means to transport the smaller products of these hydrolysis reactions inside.
Stage II. As there are many diverse molecules produced by the hydrolysis reactions of stage I, there must be many diverse pathways for their oxidation. By and large, these pathways are designed to produce just a handful of metabolic intermediates that occur in the central pathways of the cell: glycolysis and Krebs. We will focus on glycolysis.
We will start with the big picture and eventually narrow our focus to individual reactions involving individual parts of molecules (functional groups). To facilitate the discussion, we will use the word "transformation" to describe the change in structure of the organic molecule or metabolite being processed by the pathway. Changes in coenzymes, including ATP, will not be considered part of the "transformation." The transformation of the food molecule that occurs in glycolysis is:
glucose —> 2 pyruvate
This is an oxidation. How can we tell? What is oxidation?
Oxidation is the loss of electrons (frequently accompanied by protons - making hydrogen atoms). If a molecule loses electrons, where do the electrons go? Not out into the world to seek their fortune! Except for metals and some unusual solvents, electrons don't go off on their own. They are always attached to something. So, if glucose loses electrons to become pyruvate, some other molecule must gain electrons. This gainer is said to be reduced. The terminology can become confusing, as glucose is called the reductant, and the thing gaining electrons is called the oxidant (because it oxidized glucose). You should try to think of oxidants and reductants in much the same way you do acids and bases (by the way, it is probably less confusing to call them electron acceptors and donors). An acid is a proton donor; a base is a proton acceptor. Likewise, a reductant is an electron donor; an oxidant is an electron acceptor. Like acids and bases, we can organize them in terms of their reducing strength (or, more commonly, oxidizing strength). Thus, we may have strong donors or strong acceptors (like strong acids and bases). Each donor has a conjugate acceptor; the conjugate acceptor of a strong donor is a weak acceptor, and vice versa. Reduced carbon is one of the strongest donors; O2 is one of the strongest acceptors. Combination of a strong donor and a strong acceptor is very favorable thermodynamically (although it may be kinetically slow); since there are no kinetic barriers to most proton transfers, combination of a strong acid and a strong base always results in complete and rapid reaction and the evolution of a lot of heat.
So, back to our question: where do the electrons go? They go to an acceptor. In 80-90% of the cases in the cell, this acceptor is NAD+, and so it is in glycolysis. It is not O2, even though there is plenty of O2 around, and it is a much better acceptor than NAD+. Why is this? It is, again, for kinetic reasons. The enzymes provide a pathway for electrons to go from glucose (or something derived from it) to NAD+, lowering that particular activation energy. There is no catalyst increasing the rate for passing electrons to O2 from these substrates. The pathway of glycolysis provides a means of transferring some high energy electrons from carbohydrate (glucose) to NAD+ (where they are still relatively high in energy). Thus, the energy available in the glucose molecule has not been lost, given off as heat, or used to produce order (except in a very abstract sense). It has simply been moved.
Now our view of the overall reaction in glycolysis looks like this:
glucose + 2 NAD+ —> 2 pyruvate + 2 NADH
We have two NAD+'s because there are two pyruvates; each was produced by the oxidation of a molecule derived from glucose. Is this complete? It could be, but the DG for this reaction is pretty negative; there is a lot of energy released here, some of which could be captured. Also, many prokaryotic organisms are unable to use some electron acceptor from the environment (like O2) to help in extracting the energy still stored in the NADH. They have to regenerate NAD+ for continued glycolysis, and must do so by passing the electrons back to pyruvate (or something derived from pyruvate) in a process called fermentation. In this case, no useful energy would have been extracted in the catabolism of glucose. To avoid this, most organisms use some of the excess free energy in this transformation to also make ATP. The overall reaction catalyzed by the enzymes of glycolysis, thus, is:
glucose + 2 NAD+ + 2 ADP + 2 Pi —> 2 pyruvate + 2 NADH + 2 ATP
with some waters and protons to balance the equation. This makes the overall DG for the reaction more reasonable (still negative, and large enough to make the reaction go to completion, but not so wasteful). In fact, DG ~ -20 kcal/mol. In the case of fermentation, then, the energy recovered for use by the cell is 2 ATP / glucose. It is important to bear in mind that the main product of interest to the cell here is ATP, either directly during glycolysis, or by further reactions in the mitochondrion.
Now let us look more closely at the pathway itself. This pathway of 10 steps can be divided conceptually into three parts:
1) Preparation - this includes the phosphorylation of glucose and its isomerization. ATP is expended in this phase. The phosphorylated sugars in the cell are nearly at equilibrium with one another. This means that the ratio of these sugars remains fairly constant under all conditions.
2) Energy extraction - these are the steps where the carbohydrate is oxidized, and the energy from that oxidation is transferred to our two high energy intermediates: NADH and ATP. Substrate level phosphorylation is involved.
3) Recovery - after the first two phases, the net yield of ATP is still 0. In order to actually get a net gain in ATP, it is necessary to recover the 2 ATP that were used in phase I and early in the second phase. This involves isomerization, and phosphate transfer to ADP.
It is easier to discuss the energetics of glycolysis if we introduce yet another donor-acceptor concept. This time, we consider phosphate transfer. Conceptually, this can be dealt with in exactly the same way as proton or electron transfer. Species that contain one or more phosphate groups have some potential for transferring that group to an acceptor - since P is electrophilic, these acceptors are generally nucleophiles (the O of phosphate is nucleophilic - transfer can occur this way but it is rare). Again, we can organize donors and acceptors according to strength, and each donor has a conjugate acceptor. It is also helpful to know the names of the functional groups that phosphate participates in. Phosphate is the conjugate base of phosphoric acid - it participates in typical acid derivatives. Esters are derived from an acid and an alcohol; sugar phosphates are esters. Since phosphoric acid is triprotic, it can form di- and tri-esters. The mono-esters are rather weak donors; di- and tri-esters are pretty good donors. Acids can also form anhydrides, either between similar acids, or between different ones. Anhydrides of all kinds are rather unstable in water, and these make good donors. ATP and ADP are anhydrides. So are the acyl-phosphates, like 1,3-bisphosphoglycerate. In general, the acyl-phosphates are better donors than the polyphosphates. There are other specialized functional groups, such as the enol ester in PEP (which is a very good donor). A good donor has a large negative DG°' of hydrolysis; a weak donor has a small, negative DG°'. Interestingly, DG°' for ATP hydrolysis lies right in the middle. This makes sense, as ATP must mediate between strong and weak donors: it must be able to accept phosphate from some donors, otherwise substrate level phosphorylation would be impossible. Likewise, it has to be able to donate to a lot of acceptors, in order to couple the free energy of hydrolysis to endergonic reactions.
After glycolysis, the reduced carbon moves on to the Krebs cycle. In eukaryotes, these reactions are confined to the mitochondrion. In prokaryotes, of course, they are in the cytoplasm (as is everything). Prior to the Krebs cycle, pyruvate is converted to acetyl-SCoA, by an enzyme complex called pyruvate dehydrogenase. This could actually be considered a mini-pathway, where all the enzymes involved are tightly associated into a large molecular machine. The transformation catalyzed is,HSCoA + pyruvate —> acetyl-SCoA + CO2
Now this transformation is obviously an oxidation, so far as the pyruvate is concerned. One of its carbons is converted to CO2 - as oxidized as carbon gets. Where do the electrons go? To NAD+, of course. So the overall redox reaction is,
HSCoA + pyruvate + NAD+ —> acetyl-SCoA + CO2 + NADH
with appropriate balancing. Again, the energy associated with the reduced carbon is not released, but transferred to a) NADH and b) the acetyl-S bond. Thioesters have a large negative DG°' of hydrolysis. It is, in fact, the hydrolysis of this bond at the beginning of the Krebs cycle that allows the formation of citric acid.
Now let us consider the Krebs cycle, starting with citric acid. In this pathway, citric acid is converted to oxaloacetate and two molecules of CO2. Again, this is clearly an oxidation, at least for the two carbons that are converted to CO2. Where do the electrons go? To NAD+, of course. Actually, in this case, another electron acceptor gets a part of the action - FAD. The reason for this is that NAD+ is not a good enough electron acceptor to act in one particular oxidation: the production of an alkene from alkyl carbon. FAD, a better acceptor, is used instead. Besides these energy storing molecules, one ATP (or GTP) is made during the cycle by substrate level phosphorylation, by way of an acyl-phosphate intermediate again. So the overall reaction, starting with citric acid, is,
citrate + 3 NAD+ + FAD + ADP + Pi —> oxaloacetate + 3 NADH + FADH2 + ATP + 2 CO2
so we see once again oxidation of the food molecule coupled to reduction of NAD+ (and FAD), with a small amount of energy conserved in ATP. Now in reality this is the Krebs cycle, so it starts and ends with oxaloacetate. The step which closes the cycle is the condensation of acetyl-SCoA with oxaloacetate to make citrate. As mentioned, the not very favorable condensation is driven by the hydrolysis of the thioester bond.
The Krebs cycle is known as an amphibolic pathway because it can be used both catabolically and anabolically (for biosynthesis). Several Krebs intermediates are starting points for the synthesis of important cellular components. When used in this way, the effect is to reduce the concentration of oxaloacetate (since all the intermediates eventually are converted to oxaloacetate). This has the effect of slowing the condensation between acetyl-SCoA and OAA. Remember that the Krebs cycle is catalytic in the oxidation of food molecules - reducing the amount of the catalyst reduces the rate of the reaction. It therefore becomes necessary to replenish OAA in some way (it can be replenished by adding any one of the intermediates). Such reactions are called anaplerotic. The most important of these is the conversion of pyruvate to OAA at the cost of 1 ATP. This carboxylation of pyruvate requires biotin.
At this point (i.e., through the Krebs cycle), all the carbon of glucose (or fatty acids or other food molecules) has been converted to CO2 (that is, all the electrons have been removed from C and given to O). Most of the energy associated with this change has been transferred to NADH, FADH2 or ATP. No O2 has been involved yet. Only 4 ATP have been made per glucose molecule, which is a rather small yield.
The final phase of energy extraction is called oxidative phosphorylation, to distinguish it from substrate level phosphorylation. Rather than generating a powerful phosphate donor directly from the substrate, ADP is directly phosphorylated from Pi. This phosphorylation is tightly coupled to the oxidation of NADH by O2.
Thus, we are now ready to move the electrons to the powerful electron acceptor, O2. Although this can be (and sometimes is) done directly, in a single step, the energy change associated with this transfer is too large to be captured in any useful way. Once again, in order to release the energy in usable chunks, the process is divided into smaller steps, with electron acceptors of intermediate affinity positioned between NADH and O2. These acceptors together are referred to as the electron transport chain; they are all found in the inner mitochondrial membrane. This membrane is referred to as an energy transducing membrane. Electrons pass through this chain, moving to lower and lower energy; the energy they release is captured by the pumping of protons out of the matrix, into the cytoplasm. Thus the energy that started out in the food molecule is now stored in the proton gradient. The inner membrane is extremely impermeable to protons; they can only return to the matrix by way of a protein complex called the ATP synthase, or coupling factor. As they return to the matrix, they are moving to a lower energy. The energy released is used to drive the direct synthesis of ATP. In effect, we have three forms of energy storage tightly coupled to one another in this system: NADH, the proton gradient, and ATP, and to some degree, they are all interconvertible. For instance, ATP hydrolysis can be used to pump protons out of the mitochondrion, establishing a proton gradient.
Biosynthesis and the creation of order
Many, if not most transformations in biosynthesis are endergonic and so will not occur without coupling to some exergonic reaction. Of course, this exergonic reaction is frequently ATP hydrolysis, as in the incorporation of NH3 into glutamine, or the carboxylation of pyruvate.
Sometimes both anhydride bonds of ATP are hydrolysed, to release twice as much energy, either for reactions that are difficult chemically, or for highly ordered reactions, as in protein or nucleic acid synthesis. Another example would be tRNA charging.
Another exergonic reaction that is used more directly is NADPH oxidation. Like NAD+, NADP+ is not a very good electron acceptor; thus, NADH and NADPH are very good donors, and can be used to transfer electrons to a number of groups, including, for instance, the reduction of carbonyls to hydroxyls. In general, the cell uses NADPH for biosynthetic reactions; NAD+ is reserved as an electron acceptor in catabolism.
ATP, NADH, NADPH, FADH2, CoA are all examples of what are or have been called coenzymes. These are relatively small molecules that serve to couple reactions and pathways that do not take place on the same enzyme or complex. Thus, NADPH can receive electrons from glucose in an oxidative pathway called the pentose phosphate pathway, and then donate those electrons in a pathway involved in amino acid or nucleotide synthesis. ATP, of course, stores energy from food oxidation and then releases that energy where needed in biosynthesis. All the above coenzymes (and others) contain AMP as part of their structures. Other coenzymes include a number of vitamin derivatives.
Coordination of catabolism and anabolism
Metabolism consists of many intersecting and branching pathways. Flow of material through these pathways must serve the needs of the cell, not be determined solely by thermodynamics. We will illustrate with a specific example: gluconeogenesis and glycolysis.
Gluconeogenesis, as the name implies, is the synthesis of glucose from non-carbohydrate precursors (most generally, organic acids of some type). A number of acids are glucogenic, meaning they can be used to make glucose. We will look only at pyruvate (which is easily made from lactate, for instance). Thus, the transformation that takes place in gluconeogenesis from pyruvate is:
2 pyruvate —> glucose
just the reverse of the transformation that takes place in glycolysis. Clearly, in terms of coordination, the cell cannot allow both pathways to proceed simultaneously. Nothing would be accomplished.
But it's worse than that. In order to make glucose from pyruvate, it is insufficient to just run glycolysis in reverse. The overall reaction in glycolysis is
glucose + 2 ADP + 2 Pi + 2 NAD+ —> 2 pyruvate + 2 ATP + 2 NADH
which has a DG of about -20 kcal/mol. If we tried to reverse this reaction, the DG would be +20 kcal/mol. Of course, such a reaction cannot proceed, thermodynamically. Even if we let it go as long as possible, the ratio of glucose to pyruvate would be extremely small. The pyruvate to glucose transformation of gluconeogenesis must have a relatively large and negative DG. In other words, we have an endergonic transformation that requires coupling to some exergonic reaction in order to proceed. What is the exergonic reaction likely to be? It is the hydrolysis of ATP. Given the concentrations of ATP, ADP and Pi in the cell, ATP hydrolysis is worth about 12 kcal/mol, so we would need at least 3 more ATP in the reverse reaction to get to a DG comparable to that for glycolysis. Because we start with two pyruvates, it turns out we need an even number of ATPs, 4. Thus, the overall reaction of gluconeogenesis is
2 pyruvate + 6 ATP + 2 NADH —> glucose + 2 NAD+ + 6 ADP + 6 Pi
which now has a large negative DG.
The next question is, how? What mechanism makes it possible to couple these extra ATP hydrolyses to glucose synthesis? The answer will almost always be: enzymes. Do we need a whole new set of enzymes for gluconeogenesis? Can we use some of the glycolytic enzymes, or none?
The best way to answer that question is to consider an energetic analysis of each step of glycolysis. If we plot free energy change for each step, we see three steps with large changes in free energy. The first is phosphorylation of glucose by ATP. ATP is a good phosphate donor, glucose-P is not. The reaction cannot be readily reversed. So how do we go from glucose-P to glucose? Hopefully the answer is obvious - direct hydrolysis of glucose-P to glucose and phosphate.
The next is phosphorylation of fructose-P by ATP. Again, reversal is not possible, but direct hydrolysis is.
The third is the final step in glycolysis: phosphate transfer from PEP to ADP. PEP is a great phosphate donor, ATP is a good one. Again, it cannot be reversed, and in this case, we are adding a phosphate (pyruvate to PEP) not taking one off. So, how do we reverse this exergonic reaction? The straightforward answer is to devise a mechanism to invest more energy in the reversal by coupling enough ATP hydrolysis to it. And in fact, that is what happens. Since a single ATP is insufficient to transform pyruvate into PEP (energetically), we will use two. The first is used to convert pyruvate into OAA (as in anaplerosis). This is a carboxylation reaction: we have put a CO2 onto pyruvate. In animals, these reactions always require biotin, and ATP is used to activate CO2 so that it can be attached to biotin. Now decarboxylation of OAA is coupled to phosphate transfer from ATP: the electrons left behind by the departing carboxyl group are used to make a better phosphate acceptor. The net result is
pyruvate + 2 ATP —> PEP + 2 ADP + Pi
and we have used two ATPs to accomplish it: one to generate a better phosphate acceptor (OAA) and one to donate a phosphate group to that acceptor. Now we have a pathway that allows us to convert pyruvate into glucose, bypassing all the significantly exergonic steps of glycolysis. Clearly, we are able to utilize most of the glycolytic enzymes, replacing three of them with four that are specific to gluconeogenesis.
The next question is, how does the cell control these two pathways so that we never have both operating at the same time?
Remember that biological reactions are generally thermodynamically favorable (or unstable) but kinetically stable. They require catalysis. Enzymes are the catalysts. Protein structure is the basis of the catalysis, but also makes it possible to control the catalysis. The catalytic properties of proteins are sensitive to relatively minor changes in protein shape - thus protein catalysts can be inactivated (or activated) relatively easily, even by the non-covalent binding of a small ligand. This leads to several phenomena; the most important one for us now is the control - regulation - of metabolic pathways by feedback. Feedback refers to information coming back to the beginning of the pathway from the end. What is the 'end' or goal of glycolysis? Not pyruvate - by itself, pyruvate is a waste product. Glycolysis is intended to extract energy from carbohydrates. The form this energy takes is ATP. Thus, the goal of glycolysis is the production of ATP. Under what conditions, then, should glycolysis be turned on/off? If ATP levels are high, there is no point in doing glycolysis; if low, we want glycolysis to proceed. We expect gluconeogenesis to be regulated in a complementary manner, plus some regulation based on glucose or carbohydrate availability in the environment. Cells make glucose for long-term energy storage; if there is an excess supply of protein as a fuel, for example, some glucose will be made for incorporation into starch or glycogen. Cells only become interested in long-term storage when immediate needs are well met; that is, when there is plentiful ATP.
Given these general principles, how is metabolic control accomplished, specifically? Most pathways have a control point - what is called a committed step. This is an exergonic (irreversible) step early in the pathway. Material before this point can go in more than one direction or pathway. After this point come intermediates that have no other purpose in the cell than to arrive at the endpoint of the pathway. This control step in glycolysis is the phosphorylation of fructose-P. The enzyme that catalyzes this step is PFK (phosphofructokinase). PFK's catalytic activity is controlled or regulated by the ratio of ATP to AMP in the cell. When ATP levels are high, PFK is inactivated. When AMP levels are elevated, PFK is active. There are other controls as well, that we won't get into. PFK thus acts as a spigot or valve to control flow through glycolysis. ATP closes the valve; AMP opens it. This is accomplished by a change in the shape of the enzyme triggered by the binding of either ATP or AMP in a non-covalent fashion to an enzyme site distinct from the catalytic or active site. Similar controls operate on gluconeogenesis.
Some enzymes are controlled by covalent modification, instead (or besides). The most common type is phosphorylation. The principle is the same; the binding of a small group causes a relatively small change in shape that activates or inactivates the catalysis.
Metabolism is also regulated by various means of separation or compartmentalization. Organelles specialize in different metabolic pathways. Coenzymes specialize in certain pathways also. Thus regulation of coenzyme levels or of material flow into or out of organelles can slow or speed up particular pathways.