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Lecture 08: Carbon Flow: Connecting carbon to energy in heterotrophs

Oxidation of Pyruvate and the TCA Cycle

Overview of Pyruvate Metabolism and the TCA Cycle

Under appropriate conditions, pyruvate can be further oxidized. One of the most studied oxidation reactions involving pyruvate is a two-part reaction involving NAD+ and molecule called co-enzyme A, often abbreviated simply as "CoA". This reaction oxidizes pyruvate, leads to a loss of one carbon via decarboxylation, and creates a new molecule called acetyl-CoA. The resulting acetyl-CoA can enter several pathways for the biosynthesis of larger molecules or it can be routed to another pathway of central metabolism called the Citric Acid Cycle, sometimes also called the Krebs Cycle, or Tricarboxylic Acid (TCA) Cycle. Here the remaining two carbons in the acetyl group can either be further oxidized or serve again as precursors for the construction of various other molecules. We discuss these scenarios below. 

The different fates of pyruvate and other end products of glycolysis

The glycolysis module left off with the end-products of glycolysis: 2 pyruvate molecules, 2 ATPs and 2 NADH molecules. This module and the module on fermentation will explore what the cell may now do with the pyruvate, ATP and NADH that were generated. 

The fates of ATP and NADH

In general, ATP can be used for or coupled to a variety of cellular functions including biosynthesis, transport, replication etc. We will see many such examples throughout the course.  

What to do with the NADH however, depends on the conditions under which the cell is growing. In some cases, the cell will opt to rapidly recycle NADH back into to NAD+. This occurs through a process called fermentation in which the electrons initially taken from the glucose derivatives are returned to more downstream products via another redox transfer (described in more detail in the module on fermentation). Alternatively, NADH can be recycled back into NAD+ by donating electrons to something known as an electron transport chain (this is covered in the module on respiration and electron transport). 

The fate of cellular pyruvate

  • Pyruvate can be used as a terminal electron acceptor (either directly or indirectly) in fermentation reactions, and is discussed in the fermentation module. 
  • Pyruvate could be secreted from the cell as a waste product. 
  • Pyruvate could be further oxidized to extract more free energy from this fuel.
  • Pyruvate can serve as a valuable intermediate compound linking some of the core carbon processing metabolic pathways

The further oxidation of pyruvate

In respiring bacteria and archaea, the pyruvate is further oxidized in the cytoplasm. In aerobically respiring eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are sites of cellular respiration and house oxygen consuming electron transport chains (ETC in module on respiration and electron transport). Organisms from all three domains of life share similar mechanisms to further oxidize the pyruvate to CO2. First pyruvate is decarboxylated and covalently linked to co-enzyme A via a thioester linkage to form the molecule known as acetyl-CoA. While acetyl-CoA can feed into multiple other biochemical pathways we now consider its role in feeding the circular pathway known as the Tricarboxylic Acid Cycle, also referred to as the TCA cycle, the Citric Acid Cycle or the Krebs Cycle. This process is detailed below.

Conversion of Pyruvate into Acetyl-CoA

In a multistep reaction catalyzed by the enzyme pyruvate dehydrogenase, pyruvate is oxidized by NAD+, decarboxylated, and covalently linked to a molecule of co-enzyme A via a thioester bond. Remember: there are two pyruvate molecules produced at the end of glycolysis for every molecule of glucose metabolized; thus, two of the six carbons will have been removed at the end of both steps. The release of the carbon dioxide is important here, this reaction often results in a loss of mass from the cell as the CO2 will diffuse or be transported out of the cell and become a waste product. In addition, one molecule of NAD+ is reduced to NADH during this process per molecule of pyruvate oxidized.

Suggested discussion

We have already discussed the formation of a thioester bond in another unit and lecture. Where was this specifically? What was the energetic significance of this bond? What are the similarities and differences between this example (formation of thioester with CoA) and the previous example of this chemistry?


Figure 1. Upon entering the mitochondrial matrix, a multi-enzyme complex converts pyruvate into acetyl CoA. In the process, carbon dioxide is released and one molecule of NADH is formed.

Suggested discussion

Describe the flow and transfer of energy in this reaction using good vocabulary - (e.g. reduced, oxidized, redox, endergonic, exergonic, thioester, etc. etc.). You can peer edit - someone can start a description, another person can make it better, another person can improve it more etc. . .


In the presence of a suitable terminal electron acceptor, acetyl CoA delivers (exchanges a bond) its acetyl group to a four-carbon molecule, oxaloacetate, to form citrate (designated the first compound in the cycle). This cycle is called by different names: the citric acid cycle (for the first intermediate formed—citric acid, or citrate), the TCA cycle (since citric acid or citrate and isocitrate are tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles.

The Tricarboxcylic Acid (TCA) Cycle

In bacteria and archaea reactions in the TCA cycle typically happen in the cytosol. In eukaryotes, the TCA cycle takes place in the matrix of mitochondria. Almost all (but not all) of the enzymes of the TCA cycle are water soluble (not in the membrane), with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion (in eukaryotes). Unlike glycolysis, the TCA cycle is a closed loop: the last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one ATP, and reduced forms of NADH and FADH2.

Figure 2. In the TCA cycle, the acetyl group from acetyl CoA is attached to a four-carbon oxaloacetate molecule to form a six-carbon citrate molecule. Through a series of steps, citrate is oxidized, releasing two carbon dioxide molecules for each acetyl group fed into the cycle. In the process, three NAD+ molecules are reduced to NADH, one FAD molecule is reduced to FADH2, and one ATP or GTP (depending on the cell type) is produced (by substrate-level phosphorylation). Because the final product of the TCA cycle is also the first reactant, the cycle runs continuously in the presence of sufficient reactants.

Attribution: “Yikrazuul”/Wikimedia Commons (modified)

Steps in the TCA Cycle

Step 1: 

The first step of the cycle is a condensation reaction involving the two-carbon acetyl group of acetyl-CoA with one four-carbon molecule of oxaloacetate. The products of this reaction are the six-carbon molecule citrate and free co-enzyme A. This step is considered irreversible because it is so highly exergonic. Moreover, the rate of this reaction is controlled through negative feedback by ATP. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases. If not already, the reason will become evident shortly.

Step 2: 

In step two, citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate.

Step 3: 

In step three, isocitrate is oxidized by NAD+ and decarboxylated. Keep track of the carbons! This carbon now more than likely leaves the cell as waste and is no longer available for building new biomolecules. The oxidation of isocitrate therefore produces a five-carbon molecule, α-ketoglutarate, a molecule of CO2 and reduced NADH. This step is also regulated by negative feedback from ATP and NADH, and a positive effect from ADP.

Step 4: 

Step 4 is catalyzed by the enzyme succinate dehydrogenase. Here, α-ketoglutarate is further oxidized by NAD+. This oxidation again leads to a decarboxylation and thus the loss of another carbon as waste.  So far two carbons have come into the cycle from acetyl-CoA and two have left as CO2. At this stage, There is no net gain of carbons assimilated from the glucose molecules that are oxidized to this stage of metabolism. Unlike the previous step however succinate dehydrogenase - like pyruvate dehydrogenase before it - couples the free energy of the exergonic redox and decarboxylation reaction to drive the formation of a thioester bond between the substrate co-enzyme A and succinate (what is left after the decarboxylation). Succinate dehydrogenase is regulated by feedback inhibition of ATP, succinyl-CoA, and NADH.

Suggested discussion

We have seen several steps in this and other pathways that are regulated by allosteric feedback mechanisms. Is there something(s) in common about these reactions? Why might these be good steps to regulate?

Suggested discussion 

The thioester bond has reappeared! Use the terms we've been learning (e.g. reduction, oxidation, coupling, exergonic, endergonic etc.) to describe the formation of this bond and below its hydrolysis.


Step 5: 

In step five, There is a substrate level phosphorylation event, where inorganic phosphate (Pi) is added to GDP or ADP to form GTP (an ATP equivalent for our purposes)or ATP. The energy that drives this substrate level phosphorylation event comes from the hydrolysis of the CoA molecule from succinyl~CoA to form succinate. Why is either GTP or ATP produced? In animal cells there are two isoenzymes (different forms of an enzyme that carries out the same reaction), for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, the process of protein synthesis primarily uses GTP. Most bacterial systems produce GTP in this reaction. 

Step 6: 

Step six is another redox reactions in which succinate is oxidized by FAD+ into fumarate. Two hydrogen atoms are transferred to FAD+, producing FADH2. The difference in reduction potential between the fumarate/succinate and NAD+/NADH half reactions is insufficient to make NAD+ a suitable reagent for oxidizing succinate with NAD+ under cellular conditions. However, the difference in reduction potential with the FAD+/FADH2 half reaction is adequate to oxidize succinate and reduce FAD+. Unlike NAD+, FAD+ remains attached to the enzyme and transfers electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion or plasma membrane (depending on whether the organism in question is eukaryotic or not).

Step 7:

Water is added to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate with NAD+. Another molecule of NADH is produced in the process.


Note that this process completely oxidizes 1 molecule of pyruvate, a 3 carbon organic acid, to 3 molecules of CO2. During this process, 4 molecules of NADH, 1 molecule of FADH2, and 1 molecule of GTP (or ATP) are produced. For respiring organisms this is a significant source of energy, since each molecule of NADH and FAD2 can feed directly into the electron transport chain, and as we will soon see, the subsequent redox reactions will indirectly energetically drive the synthesis of additional ATP. This suggests that the TCA cycle is primarily an energy generating mechanism; evolved to extract or convert as much potential energy form the original energy source to a form cells can use, ATP (or the equivalent) or an energized membrane. However, - and let us not forget - the other important outcome of evolving this pathway is the ability to produce several precursor or substrate molecules necessary for various catabolic reactions (this pathway provides some of the early building blocks to make bigger molecules). As we will discuss below, there is a strong link between carbon metabolism and energy metabolism.

Link to Learning

Click through each step of the citric acid cycle here.


Energy Stories

Work on building some energy stories yourself 

There are a few interesting reactions that involve large transfers of energy and rearrangements of matter. Pick a few. Rewrite a reaction in your notes, and practice constructing an energy story. You now have the tools to discuss the energy redistribution in the context of broad ideas and terms like exergonic and endergonic. You also have the ability to begin discussing mechanism (how these reactions happen) by invoking enzyme catalysts. See your instructor and/or TA and check with you classmates to self-test on how you're doing.

Connections to Carbon Flow

One hypothesis that we have started exploring in this reading and in class is the idea that "central metabolism" evolved as a means of generating carbon precursors for catabolic reactions. Our hypothesis also states that as cells evolved, these reactions became linked into pathways: glycolysis and the TCA cycle, as a means to maximize their effectiveness for the cell. A side benefit to this evolving metabolic pathway was the generation of NADH from the complete oxidation of glucose - we saw the beginning of this idea when we discussed fermentation. We have already discussed how glycolysis not only provides ATP from substrate level phosphorylation, but also yields a net of 2 NADH molecules and 6 essential precursores: glucose-6-P, fructose-6-P, trios-P, 3-phosphoglycerate, phosphoenolphyruvate, and of course pyruvate. While ATP can be used by the cell directly as an energy source, NADH posses a problem and must be recycled back into NAD+, to keep the cycle in balance. As we see in detail in the fermentation module, the most ancient way cells deal with this poblem is to use fermentation reactions to regenerate NAD+

During the process of pyruvate oxidation via the TCA cycle 4 additional essential precursors are formed: acetyle~CoA, alpha-ketoglutarate, oxaloacetate, and succinyl~CoA. Three molecules of CO2 are lost and this represents a net loss of mass for the cell. These precursors, however, are substrates for a variety of catabolic reactions including the production of amino acids, fatty acids, and various co-factors, such as heme. This means that the rate of reaction through the TCA cycle will be sensitive to the concentrations of each metabolic intermediate (more on the thermodynamics in class). A metabolic intermediate is a compound that is produced by one reaction (a product) and then acts as a substrate for the next reaction. This also means that metabolic intermediates, in particular the 4 essential precursors, can be removed at any time for catabolic reactions, if there is a demand. 

Not all cells have a functional TCA cycle

Since all cells require the ability of make these precursor molecules, one might expect that all organisms would have a fully functional TCA cycle. In fact, the cells of many organisms DO NOT have a the enzymes to form a complete cycle - all cells, however, DO have the capability of making the 4 TCA cycle precursors noted in the previous paragraph. How can the cells make precursors and not have a full cycle? Remember that most of these reactions are freely reversible, so, if NAD+ is required to for the oxidation of pyruvate or acetyl~CoA, then the reverse reactions would require NADH. This process is often referred to as the reductive TCA cycle. To drive these reactions in reverse (with respect to the direction discussed above) requires energy, in this case carried by ATP and NADH. If you get ATP and NADH driving a pathway one direction, it stands to reason that driving it in reverse will require ATP and NADH as "inputs".

Suggested discussion

Why might some organisms not have evolved a fully oxidative TCA cycle? Remember, cells need to keep a balance in the NAD+ to NADH ratio as well as the [ATP]/[AMP]/[ADP] ratios.

Here are some additional links to videos and pages that you may find useful.


Introduction into the pentose phosphate pathway

Most introductory biology and biochemistry courses focus on glycolysis (oxidation of glucose to pyruvate) and the TCA cycle (oxidation of pyruvate to acetyl-CoA and the eventual complete oxidation to CO2). While these are extremely important and universal reactions, most courses leave out the pentose phosphate pathway (PPP) or hexose monophosphate shunt. This pathway, like the TCA cycle, is partially cyclic in nature in which three glucose molecules enter and two glucose and one glyceraldyde-3-phosphate (G3P) leave. The two glucose molecules can recycle, and the G3P enters glycolysis. Its an important pathway because it is the primary mechanism for the formation of pentoses, the five-carbon sugar required for nucleotide biosynthesis as well as the formation of a variety of other essential cellular components and NADPH, the cellular reductant primarily used in anabolic reactions. 

A note from the Instructor

As with the modules on glycolysis and the TCA cycle, there is a lot of material in this module. As with the other modules, I do not expect you to memorize specific names of compounds or enzymes. However, I will give you those names for completeness. For exams, I will always provide you with the pathways we discuss in class and in the BioStax Biology text modules. What you need to be able to do is understand what is going on in each reaction. We will go over in lecture problems that will be similar to those I will ask of you on exams. Do not be overwhelmed with specific enzyme names and specific structures. What you should know are the general types of enzymes used and the types of structures found. For example, you do not need to memorize the structures of eyrthose or sedoheptulose. You will need to know that both are sugars, the former a four-carbon sugar and the latter a seven-carbon sugar. Remember the ending "ose" identifies the compound as a sugar. In addition, you will not need to know the details of the two unique reactions found in the PPP, the transketolase and transaldolase reactions, though you do need to be able to identify a ketone containing sugar versus an aldehyde containing sugar. Finally, you will not be expected to memorize enzyme names, but like in glycolysis and the TCA cycle, you will be expected to know the various types of reactions a type of enzyme can catalyze, for example, a transaldolase moves aldehyde groups from one compound to another. This is the level of understanding I expect. If you have any questions please ask. 

Oxidative pentose phosphate pathway: a.k.a., the hexose monophosphate shunt

While glycolysis has evolved to oxidize hexoses to form carbon precursors for biosynthesis, energy (ATP), and reducing power (NADH), the Pentose Phosphate Pathway (PPP) has evolved to utilize pentoses or five-carbon sugars. Pentoses are required precursors for nucleotides and other essential biomolecules. Instead of NADH, the PPP also generates NADPH which is required for most anabolic reactions. The PPP, in conjunction with glycolysis and the TCA cycle, make up what we call Central Metabolism. These three central pathways (along with the reaction pyruvate to Acetyl-CoA) are responsible for producing all of the necessary precursor molecules required by all cells. The PPP is responsible for producing pentos-phosphates (give carbon sugars), eyrthrose-phosphate (four-carbon sugars), and NADPH. This pathway is also responsible for the production of sedoheptulose-phosphate, an essential seven-carbon sugar used in the outer cell membranes of Gram-negative bacteria. 

Below is a diagram of the pathway. The pathway is complex and involves a variety of novel rearrangement reactions that move two and three carbon units around. These reactions called transaldolases and transketalases are used to produce the intermediates within the pathway. The net result is oxidation and subsequent decarboxylation of glucose to form a pentose. The total reaction involves three glucose-6-phosphate (in green) molecules being oxidized to form three CO2 molecules, one glyceraldehyde-phosphate (in red), and two hexose-phosphates (in red). In this cycle, the formed glyceradehyde-phosphate feeds into glycolysis and the two hexose-phosphates (e.g., glucose-phosphates) can recycle into the PPP or gycolysis.

Figure 1. Pentose Phosphate Pathway
Take home message

As shown in Figure 1, the net result of the pathway is one trios-phosphate (glyceraldehyde-3-phosphate) that can then be further oxidized via glycolysis, two recycled hexose-phosphates (in the form of either glucose-6-phosphate or fructose-6-phosphate), and NADPH which is a required reductant for many biosynthetic (anabolic) reactions. The pathway provides a variety of intermediate sugar-phosphates that the cell may require, such as pentose-phosphates (for nucleotides and some amino acids), erythrose-phosphate (for amino acids) and sedohepulose-phosphate (for gram-negative bacteria). 

The PPP along with glycolysis, the TCA cycle, and the oxidation of pyruvate to acetyl-CoA makes up the major pathways of central metabolism and is required to some degree of all organisms to construct the basic substrates to create the building blocks of life.

Section summary

By the end of this module you should be able to describe the role the pentose phosphate pathway plays in central metabolism and determine the end products of the pathway.


Light Independent Reactions and Carbon Fixation

A short introduction

The general principle of carbon fixation is that some cells under certain conditions can take inorganic carbon, CO2 (also referred to as mineralized carbon), and reduce it to a usable cellular form. Most of us are aware that green plants can take up CO2 and produce O2 in a process known as photosynthesis. We have already discussed photophosphorylation, the ability of a cell to transfer light energy onto chemicals and ultimately to produce the energy carriers ATP and NADPH in a process known as the light reactions. In photosynthesis, the plant cells use the ATP and NADPH formed during photophosphorylation to reduce CO2 to sugar, (as we will see, specifically G3P) in what are called the dark reactions. While we appreciate that this process happens in green plants, photosynthesis had its evolutionary origins in the bacterial world. In this module we will go over the general reactions of the Calvin Cycle, a reductive pathway that incorporates CO2 into cellular material. 

In photosynthetic bacteria, such as Cyanobacteria and purple non-sulfur bacteria, as well plants, the energy (ATP) and reducing power (NADPH) - a term used to describe electron carriers in their reduced state - obtained from photophosphorylation is coupled to "Carbon Fixation", the incorporation of inorganic carbon (CO2) into organic molecules; initially as glyceraldehyde-3-phosphate (G3P) and eventually into glucose. Organisms that can obtain all of their required carbon from an inorganic source (CO2) are referred to as autotrophs, while those organisms that require organic forms of carbon, such as glucose or amino acids, are referred to as heterotrophs. The biological pathway that leads to carbon fixation is called the Calvin Cycle and is a reductive pathway (consumes energy/uses electrons) which leads to the reduction of CO2 to G3P. 

The Calvin Cycle: the reduction of CO2 to Glyceraldehyde 3-Phosphate

Figure 1. Light reactions harness energy from the sun to produce chemical bonds, ATP, and NADPH. These energy-carrying molecules are made in the stroma where carbon fixation takes place.

In plant cells, the Calvin cycle is located in the chloroplasts. While the process is similar in bacteria, there are no specific organelles that house the Calvin Cycle and the reactions occur in the cytoplasm around a complex membrane system derived from the plasma membrane. This intracellular membrane system can be quite complex and highly regulated. There is strong evidence that supports the hypothesis that the origin of chloroplasts from a symbiosis between cyanobacteria and early plant cells.

Stage 1: Carbon Fixation

In the stroma of plant chloroplasts, in addition to CO2, two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose bisphosphate (RuBP), as shown in the figure below. Ribulose-1,5-bisphosphate (RuBP) is composed of five carbon atoms and includes two phosphates.

Figure 2. The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule, 3-PGA. In stage 2, the organic molecule is reduced using electrons supplied by NADPH. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue. Only one carbon dioxide molecule is incorporated at a time, so the cycle must be completed three times to produce a single three-carbon GA3P molecule, and six times to produce a six-carbon glucose molecule.

RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation, because CO2 is “fixed” from an inorganic form into an organic molecule.

Stage 2: Reduction

ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P) - a carbon compound that is also found in glycolysis. Six molecules of both ATP and NADPH are used in the process. The exergonic process of ATP hydrolysis is in effect driving the endergonic redox reactions, creating ADP and NADP+. Both of these "spent" molecules (ADP and NADP+) return to the nearby light-dependent reactions to be recycled back into ATP and NADPH.

Stage 3: Regeneration

Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle to contribute to the formation of other compounds needed by the organism. In plants, because the G3P exported from the Calvin cycle has three carbon atoms, it takes three “turns” of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions.