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Spring_2021_Bis2A_Singer_Lecture_07 - Biology

Spring_2021_Bis2A_Singer_Lecture_07 - Biology


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Metabolism in General Biology

Cellular metabolism represents roughly 1/3 of the General Biology curriculum. You will learn about common chemical reactions thatare associatedwith the transformation of life's molecular building blocks and about different core modes of energy transfer that you will encounter often in biology. The energy story and the design challenge rubrics introduced earlier will become increasingly important in these next few modules and beyond.

What have we learned? How will it relate to metabolism?

  1. We have focused on the identification and chemical properties of common biological functional groups. As we dive into metabolism, this will help you be familiar with and sometimes even predict the chemical nature/reactivity of compounds you have never seen before.
  2. We have practiced recognizing and classifying molecules into four major functional groups. This will help you as we discuss how to build and break down these molecules.
  3. We have learned some basic thermodynamics. This gives us a common set of concepts with which to discuss whether a biochemical reaction or process is likely to occur, and if so in which direction and how fast. This will be critical as we consider some key reactions that take place in metabolism.
  4. We have learned and practiced the energy story rubric. This will allow us to study new biochemical reactions and to discuss them with a common, consistent language and approachwhichalso reinforces the lessons we learned about thermodynamics.

An overview of this section

  • We will introduce an important concept called reductionpotential andyou will be giventhe opportunity to use a redox tower. There is also a discussion on redox chemistry in your discussion manual. Use both resources.
  • We will introduce two major players in metabolism, ATP and NADH. We expect you to recognize their structures if shown on an exam.
  • We will cover the metabolic pathway glycolysis. Keep in mind that we want you to look at any reaction and tell us an energy story of that reaction. You should not try to memorize these pathways (though it will help to remember some big picture things - we will stress these). Often we will give you the pathway as a figure on the exams. Glycolysis produces 2 ATP via a process called substrate level phosphorylation, 2 NADH and 2 pyruvate compounds.
  • We will use the reactions of the TCA cycle to create multiple examples of energy stories. The TCA cycle will also produce more ATP, NADH and oxidize glucose into CO2.
  • We will look at an alternative pathway to that of the TCA cycle, fermentation. Here, for the first time, we will see NADH used as a reactant in a metabolic reaction.
  • We will follow NADH to the end of its journey, as it donates its electrons to the electron transport chain (ETC). In this module, you will need to use a redox tower. The ETC produces a proton gradient. No ATPis directly generatedin this process. However, the proton gradientis then usedby the cell to run an enzyme called ATP synthase, whichcatalyzesthe reaction ADP + Pi --> ATP. This method of ATP production (called oxidative phosphorylation) results in more ATP being produced than through substrate level phosphorylation.
  • And finally, we will go through the process of photosynthesis.

Reduction-Oxidation Reactions

In this class, most of the reduction/oxidation reactions (redox) that we discuss occur in metabolic pathways (connected sets of metabolic reactions). Here the cell breaks down the compounds it consumes into smaller parts and then reassembles them into larger macromolecules. Redox reactions also play critical roles in energy transfer, either from the environment or within the cell, in all known forms of life. For these reasons, it is important to develop at least an intuitive understanding and appreciation for redox reactions in biology.

Most students of biology will also study reduction and oxidation reactions in their chemistry courses; these kinds of reactions are important well beyond biology. Regardless of the order in which students are introduced to this concept (chemistry first or biology first), most will find the topic presented in very different ways in chemistry and biology. That can be confusing.

Chemists often introduce the concepts of oxidation and reduction from the technically more correct and inclusive standpoint of oxidation states. See this link for more information: . Fortunately, there’s no need to go into the details here (most of you will see that in chemistry at some point), just follow the argument for now. It might make things less confusing in both the long and short run. Anyhow, chemists will often ask students to apply a set of rules (see link above) to determine the oxidation states of individual atoms in a reaction. The chemistry formalism defines oxidation as an increase in oxidation state and reduction as a decrease in oxidation state.

All of this, of course, holds true in biology. However, biologists don’t typically think of redox reactions in this way. Why? We suspect it’s because most of the redox reactions encountered in biology involve a change in oxidation state that comes about because electrons are transferred between molecules. So, biologists typically define reduction as a gain of electrons and oxidation as a loss of electrons. The biological concept of redox is entirely consistent with the concept chemists use but it doesn’t account for redox reactions that can happen without the transfer of electrons. The biologist’s definition is therefore not as general as the chemist’s, but it works for most cases encountered in biology.

This is a biology reading for a biology class. We, therefore, approach redox from the “gain/loss of electrons” conceptualization that is commonly taught in biology classes. In our opinion, it’s easier to use (no long list of rules to memorize and apply), more intuitive, and works for almost all cases we care about in undergraduate biology. So, if you had chemistry already and this topic seems a little different in biology, remember that at its core it’s the same thing you learned about before. Biologists just adapted what you learned in chemistry to make more intuitive sense in biology. If you haven’t learned about redox yet don’t worry. If you can understand what we’re trying to do here when you cover this concept in chemistry class you’ll be a few steps ahead. You’ll just need to generalize your thinking a bit instead of seeing the topic for the first time.

Let's start with some generic reactions

Transferring electrons between two compounds results in one of these compounds loosing an electron and one compound gaining an electron. For example, look at the figure below. If we use the energy story rubric to look at the overall reaction, we can compare the before and after characteristics of the reactants and products. What happens to the matter (stuff) before and after the reaction? Compound A starts as neutral and becomes positively charged. Compound B starts as neutral and becomes negatively charged. Because electrons are negatively charged, we can explain this reaction with the movement of an electron from Compound A to B. That is consistent with the changes in charge. Compound A loses an electron (becoming positively charged), and we say that A has become oxidized. For biologists, oxidationis associated with the loss of electron(s). B gains the electron (becoming negatively charged), and we say that B has become reduced. Reductionis associated with the gain of electrons. We also know, since a reaction occurred (something happened), that energy must have been transferred and/or reorganized in this process and we'll consider this shortly.

Figure 1. Generic redox reaction with half-reactions

Attribution: Mary O. Aina

To reiterate: When an electron(s) is lost, or a molecule is oxidized, the electron(s) must then pass to another molecule. We say that the molecule gaining the electron becomes reduced. Together these paired electron gain-loss reactions are known as an oxidation-reduction reaction (also called a redox reaction).

This idea of paired half-reactions is critical to the biological concept of redox. Electrons don’t drop out of the universe for “free” to reduce a molecule or jump off a molecule into the ether. Donated electrons MUST come from a donor molecule and be transferred to some other acceptor molecule. For example in the figure above the electron the reduces molecule B in half-reaction 2 must come from a donor - it just doesn't appear from nowhere! Likewise, the electron that leaves A in half-reaction 1 above just "land" on another molecule - it doesn't just disappear from the universe.

Therefore, oxidation and reduction reactions must ALWAYS be paired. We’ll examine this idea in more detail below when we discuss the idea of “half-reactions”.

  • A tip to help you remember: The mnemonic LEO says GER (Lose Electrons = Oxidation and Gain Electrons = Reduction) can help you remember the biological definitions of oxidation and reduction.

Figure 2. A figure for the mnemonic "LEO the lion says GER." LEO: Loss of Electrons = Oxidation. GER: Gain of Electrons = Reduction

Attribution: Kamali Sripathi

• The vocabulary of redox can be confusing: Students studying redox chemistry can often become confused by the vocabulary used to describe the reactions. Terms like oxidation/oxidant and reduction/reductant look and sound very similar but mean distinctly different things. An electron donor is also sometimes called a reductant because it is the compound that causes the reduction (gain of electrons) of another compound (the oxidant). In other words, the reductant is donating it’s electrons to the oxidant which is gaining those electrons. Conversely, the electron acceptor is called the oxidant because it is the compound that is causing the oxidation (loss of electrons) of the other compound. Again, this simply means the oxidant is gaining electrons from the reductant who is donating those electrons. Confused yet?

Yet another way to think about definitions is to remember that describing a compound as reduced/oxidized is describing the state that the compound itself is in, whereas labeling a compound as a reductant/oxidant describes how the compound can act, to either reduce or oxidize another compound. Keep in mind that the term reductant is also synonymous with reducing agent and oxidant is also synonymous with oxidizing agent. The chemists who developed this vocabulary need to be brought up on charges of "willful thickheadedness" at science trial and then be forced to explain to the rest of us why they needed to be so deliberately obtuse.

The confusing language of redox: quick summary

1. A compound can be described as “reduced” - term used to describe the compound's state

2. A compound can be a “reductant” - term used to describe a compound's capability (it can reduce something else). The synonymous term "reducing agent" can be used to describe the same capability (the term "agent" refers to the thing that can "do something" - in this case reduce another molecule).

3. A compound can be an “oxidant” - term used to describe a compound's capability (it can oxidize something else). The synonymous term "oxidizing agent" can be used to describe the same capability (the term "agent" refers to the thing that can "do something" - in this case oxidize another molecule).

4. A compound can “become reduced” or "become oxidized"- term used to describe the transition to a new state

Since all of these terms are used in biology, in General Biology we expect you to become familiar with this terminology. Try to learn it and use it as soon as possible - we will use the terms frequently and will not have the time to define terms each time.

Knowledge Check Quiz

The Half Reaction

Here we introduce the concept of the half reaction. We can think each half reaction as a description of what happens to one of the two molecules (i.e. the donor and the acceptor) involved in a "full" redox reaction. A "full" redox reaction requires two half reactions. We illustrate this below. In the example below, half reaction #1 depicts the molecule AH becoming losing two electrons and a proton and in the process becoming A+. This reaction depicts the oxidation of AH. Half reaction #2 depicts the molecule B+ gaining two electrons and a proton to become BH. This reaction depicts the reduction of B+. Each of these two half reactions is conceptual and can't happen on their own. The electrons lost in half reaction #1 MUST go somewhere, they can't just disappear. Likewise, the electrons gained in half reaction #2 must come from something. They too just can't appear out of nowhere.

One can imagine that there might be different molecules that can serve as potential acceptors (the place for the electrons to go) for the electrons lost in half reaction #1. Likewise, there might be many potential reduced molecules that can serve as the electron donors (the source of electrons) for half reaction #2. In the example below, we show what happens (the reaction) when molecule AH is the donor of electrons for molecule B+. When we put the donor and acceptor half reactions together, we get a "full" redox reaction that can actually happen. In the figure below we call that reaction "Reaction #1". When this happens we call the two half reactions coupled.

Figure 3. Generic redox reaction where compound AH is being oxidized by compound B+. Each half reaction represents a single species or compound to either lose or gain electrons (and a subsequent proton as shown in the figure above). In half reaction #1 AH loses a proton and 2 electrons: in the second half reaction, B+ gains 2 electrons and a proton. In this example HA is oxidized to A+ while B+ is reduced to BH.

Using this idea, we can theoretically couple and think about any two half reactions, one half reaction serving as the electron donor for the other half reaction that accepts the donated electrons. For instance, using the example above, we could consider coupling the reduction of B+ that happens in half reaction 2 with another half reaction describing the oxidation of the molecule NADH. In that case, the NADH would be the electron donor for B+. Likewise you could couple the oxidation of AH that happens in half reaction #1 with a half reaction describing the the reduction of hypothetical molecule Z+. You can mix-and-match half reactions together as you please provided one half is describing the oxidation of a compound (it's donating electrons) and the reduction of another compound (it's accepting the donated electrons).

  • A note on how we write full reactions versus half reactions: In the example above, when we write Reaction #1 as an equation, the 2 electrons and the H+ that are explicitly described in the underlying half reactions, are not explicitly included in the text of the full reaction. In the reaction above you must infer that an exchange of electrons happens. This can be observed by trying to balance charges between each reactant and it's corresponding product. Reactant AH becomes product A+. In this case, you can infer that some movement of electrons must have taken place. To balance the charges on this compound (make the sum of charges on each side of the equation equal) you need to add 2 electrons to the right side of the equation, one to account for the "+" charge on A+ and a second to go with the H+ that was also lost. The other reactant B+ is converted to BH. It must therefore gain 2 electrons to balance charges, one for B+ and a second for the additional H+ that was added. Together this information leads you to conclude that the most likely thing to have happened is that two electrons were exchanged between AH and B+.

  • This will also be the case for most redox reactions in biology. Fortunately, in most cases, either the context of the reaction, the presence of chemical groups often engaged in redox (e.g. metal ions), or the presence of commonly used electron carriers (e.g. NAD+/NADH, FAD+/FADH2, ferredoxin, etc.) will alert you that the reaction is of class "redox". You will be expected to learn to recognize some of these common molecules.

Reduction Potential

By convention, we quantitatively characterize redox reactions using an measure called reduction potentials. The reduction potential attempts to quantitatively describe the “ability” of a compound or molecule to gain or lose electrons. The specific value of the reduction potential is determined experimentally, but for the purpose of this course we assume that the reader will accept that the values in provided tables are reasonably correct. We can anthropomorphize the reduction potential by saying that it is related to the strength with which a compound can “attract” or “pull” or “capture” electrons. Not surprisingly this is is related to but not identical to electronegativity.

What is this intrinsic property to attract electrons?

Different compounds, based on their structure and atomic composition have intrinsic and distinct attractions for electrons. This quality leads each molecule to have its own standard reduction potential or E0. The reduction potential is a relative quantity (relative to some “standard” reaction). If a test compound has a stronger "attraction" to electrons than the standard (if the two competed, the test compound would "take" electrons from the standard compound), we say that the test compound has a positive reduction potential. The magnitude of the difference in E0’ between any two compounds (including the standard) is proportional to how much more or less the compounds "want" electrons. The relative strength of the reduction potential is measured and reported in units of Volts (V) (sometimes written as electron volts or eV) or milliVolts (mV). The reference compound in most redox towers is H2.


Possible NB Discussion Point

Rephrase for yourself: How do you describe or think about the difference between the concept of electronegativity and red/ox potential?


Redox student misconception alert: The standard redox potential for a compound reports how strongly a substance wants to hold onto an electron in comparison to hydrogen. Since both redox potential and electronegativity are both discussed as measurements for how strongly something "wants" an electron, they are sometimes conflated or confused for one another. However, they are not. While the electronegativity of atoms in a molecule may influence its redox potential, it is not the only factor that does. You don't need to worry about how this works. For now, try to keep them as different and distinct ideas in your mind. The physical relationship between these two concepts is well beyond the scope of this general biology class.

The Redox Tower

All kinds of compounds can take part in redox reactions. Scientists have developed a graphical tool, the redox tower, to tabulate redox half reactions based on their E0' values. This tool can help predict the direction of electron flow between potential electron donors and acceptors and how much free energy change might be expected from a specific reaction. By convention, all half reactions in the table are written in the direction of reduction for each compound listed.

In the biology context, the electron tower usually ranks a variety of common compounds (their half reactions) from most negative E0' (compounds that readily get rid of electrons), to the most positive E0' (compounds most likely to accept electrons). The tower below lists the number of electrons that are transferred in each reaction. For example, the reduction of NAD+ to NADH involves two electrons, written in the table as 2e-.

oxidized form

reduced form

n (electrons)

Eo´ (volts)

PS1* (ox)

PS1* (red)

-

-1.20

Acetate + CO2

pyruvate

2

-0.7

ferredoxin (ox) version 1

ferredoxin (red) version 1

1

-0.7

succinate + CO2 + 2H+

a-ketoglutarate + H2O

2

-0.67

PSII* (ox)

PSII* (red)

-

-0.67

P840* (ox)

PS840* (red)

-

-0.67

acetate

acetaldehyde

2

-0.6

glycerate-3-P

glyceraldehyde-3-P + H2O

2

-0.55

O2

O2-

1

-0.45

ferredoxin (ox) version 2

ferredoxin (red) version 2

1

-0.43

CO2

glucose

24

-0.43

CO2

formate

2

-0.42

2H+

H2

2

-0.42 (at [H+] = 10-7; pH=7)

Note: at [H+] = 1; pH=0 the Eo' for hydrogen is ZERO. You will see this in chemistry class.

α-ketoglutarate + CO2 + 2H+

isocitrate

2

-0.38

acetoacetate

b-hydroxybutyrate

2

-0.35

Cystine

cysteine

2

-0.34

Pyruvate + CO2

malate

2

-0.33

NAD+ + 2H+

NADH + H+

2

-0.32

NADP+ + 2H+

NADPH + H+

2

-0.32

Complex I FMN (enzyme bound)

FMNH2

2

-0.3

Lipoic acid, (ox)

Lipoic acid, (red)

2

-0.29

1,3 bisphosphoglycerate + 2H+

glyceraldehyde-3-P + Pi

2

-0.29

Glutathione, (ox)

Glutathione, (red)

2

-0.23

FAD+ (free) + 2H+

FADH2

2

-0.22

Acetaldehyde + 2H+

ethanol

2

-0.2

Pyruvate + 2H+

lactate

2

-0.19

Oxalacetate + 2H+

malate

2

-0.17

α-ketoglutarate + NH4+

glutamate

2

-0.14

FAD+ + 2H+ (bound)

FADH2 (bound)

2

0.003-0.09

Methylene blue, (ox)

Methylene blue, (red)

2

0.01

Fumarate + 2H+

succinate

2

0.03

CoQ (Ubiquinone - UQ + H+)

UQH.

1

0.031

UQ + 2H+

UQH2

2

0.06

Dehydroascorbic acid

ascorbic acid

2

0.06

Plastoquinone; (ox)

Plastoquinone; (red)

-

0.08

Ubiquinone; (ox)

Ubiquinone; (red)

2

0.1

Complex III Cytochrome b2; Fe3+

Cytochrome b2; Fe2+

1

0.12

Fe3+ (pH = 7)

Fe2+ (pH = 7)

1

0.20

Complex III Cytochrome c1; Fe3+

Cytochrome c1; Fe2+

1

0.22

Cytochrome c; Fe3+

Cytochrome c; Fe2+

1

0.25

Complex IV Cytochrome a; Fe3+

Cytochrome a; Fe2+

1

0.29

1/2 O2 + H2O

H2O2

2

0.3

P840GS (ox)

PS840GS (red)

-

0.33

Complex IV Cytochrome a3; Fe3+

Cytochrome a3; Fe2+

1

0.35

Ferricyanide

ferrocyanide

2

0.36

Cytochrome f; Fe3+

Cytochrome f; Fe2+

1

0.37

PSIGS (ox)

PSIGS (red)

.

0.37

Nitrate

nitrite

1

0.42

Fe3+ (pH = 2)

Fe2+ (pH = 2)

1

0.77

1/2 O2 + 2H+

H2O

2

0.816

PSIIGS (ox)

PSIIGS (red)

-

1.10

* Excited State, after absorbing a photon of light

GS Ground State, state prior to absorbing a photon of light

PS1: Oxygenic photosystem I

P840: Bacterial reaction center containing bacteriochlorophyll (anoxygenic)

PSII: Oxygenic photosystem II

Table 1. Common redox tower used in Bis2A. By convention the tower half reactions are written with the oxidized form of the compound on the left and the reduced form on the right. Compounds that make good electron donors have highly negative reduction potentials. Compounds such as Glucose and Hydrogen gas are excellent electron donors. By contrast compounds that make excellent electron acceptors, such as Oxygen and Nitrite are excellent electron acceptors.

Video on electron tower

For a short video on how to use the electron tower in redox problems click here or below. This video was made by Dr. Easlon for Bis2A students. (This is quite informative.)

What is the relationship between ΔE0' and ΔG?

How do we know if any given redox reaction (the specific combination of two half reactions) is energetically spontaneous or not (exergonic or endergonic)? Moreover, regardless of the direction of spontaneity, how can we determine what the quantitative change in free energy is for a specific redox reaction? The answer lies in the difference in the reduction potentials of the two compounds. The difference in the reduction potential for the reaction (E0'), can be calculated by taking the difference between the E0' for the oxidant (the compound getting the electrons and causing the oxidation of the other compound) and the reductant (the compound losing the electrons). In our generic example below, AH is the reductant and B+ is the oxidant. Electrons are moving from AH to B+. Using the E0' of -0.32 for the reductant and +0.82 for the oxidant the total change in E0' or E0' is 1.14 eV.

Figure 4. Generic red/ox reaction with half reactions written with reduction potential (E0') of the two half reactions indicated.

∆E0' between oxidant and reductant can tell us about the spontaneity of a proposed electron transfer. Intuitively, if electrons are proposed to move from a compound that "wants" electrons less to a compound that "wants" electrons more (i.e. a move from a compound with a lower E0'to a compound with a higher E0', the reaction will be energetically spontaneous). If the electrons are proposed to move from a compound that "wants" electrons more to a compound that "wants" electrons less (i.e. a move from a compound with a higher E0'to a compound with a lower E0', the reaction will be energetically non-spontaneous). Because of the way biological/biochemical redox tables are ordered (small E0' on top and larger E0' on the bottom) transfers of electrons from donors higher on the table to acceptors lower on the table will be spontaneous.

It is also possible to quantify the amount of free energy change associated with a specific redox reaction. The relationship is given by the Nernst equation:

Figure 5. The Nernst equation relates free energy of a redox reaction to the difference in reduction potential between the reduced products of the reaction and oxidized reactant.
Attribution: Marc T. Facciotti

Where:

  • n is the number of moles of electrons transferred
  • F is the Faraday constant of 96.485 kJ/V. Sometimes it is given in units of kcal/V which is 23.062 kcal/V, which is the amount of energy (in kJ or kcal) released when one mole of electrons passes through a potential drop of 1 volt

Note that the signs of ∆E and ∆G are opposite one another. When ∆E is positive, ∆G will be negative. When ∆E is negative, ∆G will be positive.

Glycolysis: An overview

Organisms, whether unicellular or multicellular, need to find ways of getting at least two key things from their environment: (1) matter or raw materials for maintaining a cell and building new cells and (2) energy to help with the work of staying alive and reproducing. Energy and the raw materials may come from different places. For instance, organisms that primarily harvest energy from sunlight will get raw materials for building biomolecules from sources like CO2. By contract, some organisms rely on red/ox reactions with small molecules and/or reduced metals for energy and get their raw materials for building biomolecules from compounds unconnected to the energy source. Meanwhile, some organisms (including ourselves), have evolved to get energy AND the raw materials for building and cellular maintenance from sometimes associated sources.

Glycolysis is the first metabolic pathway discussed in BIS2A;

a

metabolic pathway is a series of linked biochemical reactions. Because of its ubiquity in biology, we hypothesize that glycolysis was probably one of the earliest metabolic pathways to evolve (more on this later). Glycolysis is a ten-step metabolic pathway that

is centered

on the processing of glucose for both energy extraction from chemical fuel and for the processing of the carbons in glucose into various other biomolecules (some of which are key precursors of many much more complicated biomolecules). We will therefore examine our study of glycolysis using the precepts outlined in the energy challenge rubric that ask us

to formally consider

what happens to BOTH matter and energy in this multi-step process.

The energy story and design challenge of glycolysis

Our investigation of glycolysis is a good opportunity to examine a biological process using both the energy story and the design challenge rubrics and perspectives.

The design challenge rubric will try to get you to think actively, and broadly and specifically, about why we are studying this pathway—what is so important about it? What "problems" does the evolution of a glycolytic pathway allow life to solve or overcome? We will also want to think about alternate ways to solve the same problems and why they may or may not have evolved. Later, we will examine a hypothesis for how this pathway—and other linked pathways—may have evolved, and thinking about alternative strategies for satisfying various constraints will come in handy then.

We ask you to think about glycolysis through the lens of an energy story in which you examine the 10-step process as a set of matter and energy inputs and outputs, a process with a beginning and an end. By taking this

approach

you will learn not only about

glycolysis,

but also some skills required to read and interpret other biochemical pathways.


So what isglycolysis? Let's find out.

Figure 1. The ten biochemical reactions ofglycolysisare shown.Enzymes are labeledin blue. The structure of each sugar-derived compoundis depictedas a molecular model;other reactants and products may be abbreviated(e.g., ATP, NAD+, etc.). The box surrounding the reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenaseindicatesthat this reaction is of special interest in the course. Attribution:Marc T. Facciotti (original work)

Table 1. This table shows glycolytic enzymes and measurements of the energy at standard state (ΔG°'/(kJ/mol)) compared with measurements taken from a living cell (ΔG/(kJ/mol)). Under conditions of constant temperature and pressure, (ΔG°'/(kJ/mol)), reactions will occur in the direction that leads to a decrease in the value of the Gibbs free energy. Cellular measurements of ΔG can be dramatically different from ΔG°' measurements because of cellular conditions, such as concentrations of relevant metabolites,etc. There are three large, negative ΔG drops in the cell in the process of glycolysis. We consider these reactions irreversible and are often subject to regulation.

EnzymeStepΔG/(kJ/mol)ΔG°'/(kJ/mol)
Hexokinase1-34-16.7
Phosphoglucose isomerase2-2.91.67
Phosphofructokinase3-19-14.2
Fructose-bisphosphate aldolase4-0.2323.9
Triose phosphate isomerase52.47.56
Glyceraldehyde 3-phosphate dehydrogenase6-1.296.30
Phosphoglycerate kinase70.09-18.9
Phosphoglycerate mutase80.834.4
Enolase91.11.8
Pyruvate kinase10-23.0-31.7

Overall, the glycolytic pathway comprises 10 enzyme-catalyzed steps. The primary input into this pathway is a single molecule of glucose, though we discover that other molecules may enter this pathway at various steps. We will focus our attention on (1) consequences of the overall process, (2) several key reactions that highlight important types of biochemistry and biochemical principles we will want to carry forward to other contexts, and (3) alternative fates of the intermediates and products of this pathway.

Note for reference that glycolysis is an anaerobic process. There is no requirement for molecular oxygen in glycolysis - oxygen gas is not a reactant in any of the chemical reactions in glycolysis. Glycolysis occurs in the cytosol or cytoplasm of cells. For a short (three-minute) overview YouTube video of glycolysis, click here.

First half of glycolysis: energy investment phase

We typically refer the first few steps of glycolysis as an "energy investment phase" of the pathway. This, however, doesn't make much intuitive sense (in the framework of a design challenge; it's not clear what problem this energy investment solves) if one only looks at glycolysis as an "energy-producing" pathway and until these steps of glycolysis are put into a broader metabolic context. We'll try to build that story as we go, so for now just recall that we mentioned that some first steps are often associated with energy investment and ideas like "trapping" and "commitment" that are noted in the figure below.

Step 1 of glycolysis:

The first step in glycolysis, shown below in Figure 2, is glucose being catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase catalyzes the phosphorylation of glucose, where glucose and ATP are substrates for the reaction, producing a molecule called glucose 6-phosphate and ADP as products.

Figure 2. The first half of glycolysis is called the energy investment phase. In this phase, the cell spends two ATPs into the reactions. Attribution: Marc T. Facciotti (original work)

Note:
The paragraph above states that the enzyme hexokinase has "broad specificity." This means that it cancatalyzereactions with different sugars, not just glucose. From a molecular perspective, can you explain why this might be the case? Does this challenge your conception of enzyme specificity? If you Google the term "enzyme promiscuity" (don't worry; it's safe for work), you will hopefully gain a broader appreciation for enzyme selectivity and activity.

The conversion of glucose to the negatively charged glucose 6-phosphate significantly reduces the likelihood that the phosphorylated glucose leaves the cell by diffusion across the hydrophobic interior of the plasma membrane. It also "marks" the glucose in a way that tags it for several possible fates (see Figure 3).

Figure 3. Note that this figure shows that glucose 6-phosphate can, depending on cellular conditions, be directed to multiple fates. While it is a component of the glycolytic pathway, it is not only involved in glycolysis but also in the storage of energy as glycogen (colored in cyan) and in the building of various other molecules like nucleotides (colored in red). Source: Marc T. Facciotti (original work)

As Figure 3 shows, glycolysis is but one fate for glucose 6-phosphate (G6P). Depending on cellular conditions, G6P may be diverted to the biosynthesis of glycogen (for energy storage), or it may be diverted into the pentose phosphate pathway for the biosynthesis of various biomolecules, including nucleotides. This means that G6P, while involved in the glycolytic pathway, is not solely tagged for oxidation at this phase. Perhaps showing the broader context that this molecule is involved in (in addition to the rationale that tagging glucose with a phosphate decreases the likelihood that it will leave the cell) helps to explain the seemingly contradictory (if you only consider glycolysis as an "energy-producing" process) reason for transferring energy from ATP onto glucose if it is only to be oxidized later—that is, glucose is not only used by the cell for harvesting energy and several other metabolic pathways depend on the transfer of the phosphate group.

Step 2 of glycolysis:

In the second step of glycolysis, an isomerase catalyzes the conversion of glucose 6-phosphate into one of its isomers, fructose 6-phosphate. An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers.

Step 3 of glycolysis:

The third step of glycolysis is the phosphorylation of fructose 6-phosphate, catalyzed by the enzyme phosphofructokinase. A second ATP molecule donates a phosphate to fructose 6-phosphate, producing fructose 1,6-bisphosphate and ADP as products. In this pathway, phosphofructokinase is a rate-limiting enzyme, and its activity is tightly regulated. It is allosterically activated by AMP when the concentration of AMP is high and when it is moderately allosterically inhibited by ATP at the same site. Citrate, a compound we'll discuss soon, also acts as a negative allosteric regulator of this enzyme. In this way, phosphofructokinase monitors or senses molecular indicators of the energy status of the cells and can in response act as a switch that turns on or off the flow of the substrate through the rest of the metabolic pathway depending on whether there is “sufficient” ATP in the system. The conversion of fructose 6-phosphate into fructose 1,6-bisphosphate is sometimes referred to as a commitment step by the cell to the oxidation of the molecule in the rest of the glycolytic pathway by creating a substrate for and helping to energetically drive the next highly endergonic (under standard conditions) step of the pathway.

Step 4 of glycolysis:

In the fourth step in glycolysis, an enzyme, fructose-bisphosphate aldolase, cleaves 1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.

Second half: energy payoff phase

If viewed in the absence of other metabolic pathways, glycolysis has so far cost the cell two ATP molecules and produced two small, three-carbon sugar molecules: dihydroxyacetone phosphate (DAP) and glyceraldehyde 3-phosphate (G3P). When viewed in a broader context, this investment of energy to produce a variety of molecules that can be used in a variety of other pathways doesn't seem like such a bad investment.

Both DAP and G3P can proceed through the second half of glycolysis. We now examine these reactions.

Figure 4. The second half of glycolysis is called the energy payoff phase. In this phase, the cell gains two ATP and two NADH compounds. At the end of this phase, glucose has become partially oxidized to form pyruvate. Facciotti (original work).

Step 5 of glycolysis:

In the fifth step of glycolysis, an isomerase transforms the dihydroxyacetone phosphate into its isomer, glyceraldehyde 3-phosphate. The six-carbon glucose has therefore now been converted into two phosphorylated three-carbon molecules of G3P.

Step 6 of glycolysis:

The sixth step is key and one from which we can now leverage our understanding of the several chemical reactions that we've studied so far. If you're energy focused, this is finally a step of glycolysis where some reduced sugar becomes oxidized. The reaction is catalyzed by the enzyme glyceraldehyde 3-phosphate dehydrogenase. This enzyme catalyzes a multi-step reaction between three substrates—glyceraldehyde 3-phosphate, the cofactor NAD+, and inorganic phosphate (Pi)—and produces three products: 1,3-bisphosphoglycerate, NADH, and H+. One can think of this reaction as two reactions: (1) an oxidation/reduction reaction and (2) a condensation reaction in which an inorganic phosphate is transferred onto a molecule. Here, the red/ox reaction, a transfer of electrons off G3P and onto NAD+, is exergonic, and the phosphate transfer is endergonic. The net standard free energy change hovers around zero—more on this later. The enzyme here acts as a molecular coupling agent to couple the energetics of the exergonic reaction to that of the endergonic reaction, thus driving both forward. This processes happens through a multi-step mechanism in the enzyme's active site and involves the chemical activity of a variety of functional groups.

It is important to note that this reaction depends upon the availability of the oxidized form of the electron carrier, NAD+. If we consider that there is a limiting pool of NAD+, we can then conclude that the reduced form of the carrier (NADH) must continuously oxidize back into NAD+ to keep this step going. If NAD+ is not available, the second half of glycolysis slows down or stops.


Possible NB Discussion Point

Can you write an energy story for Step 6 of glycolysis (the reactioncatalyzedby glyceraldehyde 3-phosphate dehydrogenase)? When you discuss energy, just describe whether steps are exergonic or endergonic. As a group, try to build up an increasingly "expert" version that is complete, brief, and uses appropriatevocabulary. Amend one another's texts in a polite and constructive way.


Step 7 of glycolysis:

In the seventh step of glycolysis, catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate transfers a phosphate to ADP, forming one molecule of ATP and a molecule of 3-phosphoglycerate. This reaction is exergonic and is also an example of substrate-level phosphorylation.

Step 8 of glycolysis:

In the eighth step, the remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase).

Step 9 of glycolysis:

Enolase catalyzes the ninth step. This enzyme causes 2-phosphoglycerate to lose water from its structure; this is a dehydration reaction, resulting in the formation of a double bond that increases the potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP).

Step 10 of glycolysis:

The last step in glycolysis is catalyzed by the enzyme pyruvate kinase (the enzyme in this case is named for the reverse reaction of pyruvate’s conversion into PEP) and results in the production of a second ATP molecule by substrate-level phosphorylation and the compound pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic pathways are named for the reverse reactions, since the enzyme can catalyze both forward and reverse reactions (these may have been described initially by the reverse reaction that takes place in vitro, under non-physiological conditions).

Outcomes of glycolysis

Here are a couple of things to consider:

One of the clear outcomes of glycolysis is the biosynthesis of compounds that can enter into a variety of metabolic pathways. Likewise, compounds coming from other metabolic pathways can feed into glycolysis at various points. So, this pathway can be part of a central exchange for carbon flux within the cell.

If glycolysis runs long enough, the constant oxidation of glucose with NAD+ can leave the cell with a problem: how to regenerate NAD+ from the two molecules of NADH produced. If the cell does not regenerate NAD+, nearly all the cell's NAD+ will transform into NADH. So how do cells regenerate NAD+?

Pyruvate is not completely oxidized; There is still some energy to extract. How might this happen? Also, what should the cell do with all of that NADH? Is there any energy there to extract?


Possible NB Discussion Point

To some, that glycolysis is such a complex, multi-step pathway may seem counter-intuitive: “Why wouldn’t evolution lead to a *simpler* way to extract energy from food since energy is an important requirement for life?” Explain the necessity/advantage of having glucose get broken down in many steps.


Substrate-level phosphorylation (SLP)

The simplest route to synthesize ATP is substrate-level phosphorylation. ATP molecules are generated (that is, regenerated from ADP) because of a chemical reaction that occurs in catabolic pathways. A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP. This very direct method of phosphorylation is called substrate-level phosphorylation (SLP). We can find SLP in a variety of catabolic reactions, most notably in two specific reactions in glycolysis (which we will discuss specifically later). What the reaction requires is a high-energy intermediate compound whose free energy of oxidation can drive the synthesis of ATP.

Figure 5. Here is one example of substrate-level phosphorylation occurring in glycolysis. There is a direct transfer of a phosphate group from the carbon compound onto ADP to form ATP. Facciotti (own work)

In this reaction, the reactants are a phosphorylated carbon compound called G3P (from step 6 of glycolysis) and an ADP molecule, and the products are 1,3-BPG and ATP. The transfer of the phosphate from G3P to ADP to form ATP in the active site of the enzyme is substrate-level phosphorylation. This occurs twice in glycolysis and once in the TCA cycle (for a subsequent reading).

Fermentation and regeneration of NAD+

Section summary

This section discusses the process of fermentation. Due to the heavy emphasis in this course on central carbon metabolism, the discussion of fermentation understandably focuses on the fermentation of pyruvate. Nevertheless, some of the core principles that we cover in this section apply equally well to the fermentation of many other small molecules.

The "purpose" of fermentation

The oxidation of a variety of small organic compounds is a process that is utilized by many organisms to garner energy for cellular maintenance and growth. The oxidation of glucose via glycolysis is one such pathway. Several key steps in the oxidation of glucose to pyruvate involve the reduction of the electron/energy shuttle NAD+ to NADH. You were already asked to figure out what options the cell might reasonably have to reoxidize the NADH to NAD+ in order to avoid consuming the available pools of NAD+ and to thus avoid stopping glycolysis. Put differently, during glycolysis, cells can generate large amounts of NADH and slowly exhaust their supplies of NAD+. If glycolysis is to continue, the cell must find a way to regenerate NAD+, either by synthesis or by some form of recycling.

In the absence of any other process—that is, if we consider glycolysis alone—it is not immediately obvious what the cell might do. One choice is to try putting the electrons that were once stripped off of the glucose derivatives right back onto the downstream product, pyruvate, or one of its derivatives. We can generalize the process by describing it as the returning of electrons to the molecule that they were once removed, usually to restore pools of an oxidizing agent. This, in short, is fermentation. As we will discuss in a different section, the process of respiration can also regenerate the pools of NAD+ from NADH. Cells lacking respiratory chains or in conditions where using the respiratory chain is unfavorable may choose fermentation as an alternative mechanism for garnering energy from small molecules.

An example: lactic acid fermentation

An everyday example of a fermentation reaction is the reduction of pyruvate to lactate by the lactic acid fermentation reaction. This reaction should be familiar to you: it occurs in our muscles when we exert ourselves during exercise. When we exert ourselves, our muscles require large amounts of ATP to perform the work we are demanding of them. As the ATP is consumed, the muscle cells are unable to keep up with the demand for respiration, O2 becomes limiting, and NADH accumulates. Cells need to get rid of the excess and regenerate NAD+, so pyruvate serves as an electron acceptor, generating lactate and oxidizing NADH to NAD+. Many bacteria use this pathway as a way to complete the NADH/NAD+ cycle. You may be familiar with this process from products like sauerkraut and yogurt. The chemical reaction of lactic acid fermentation is the following:

Pyruvate + NADH ↔ lactic acid + NAD+

Figure 1. Lactic acid fermentation converts pyruvate (a slightly oxidized carbon compound) to lactic acid. In the process, NADH is oxidized to form NAD+. Facciotti (original work)

Energy story for the fermentation of pyruvate to lactate

An example (if a bit lengthy) energy story for lactic acid fermentation is the following:

The reactants are pyruvate, NADH, and a proton. The products are lactate and NAD+. The process of fermentation results in the reduction of pyruvate to form lactic acid and the oxidation of NADH to form NAD+. Electrons from NADH and a proton are used to reduce pyruvate into lactate. If we examine a table of standard reduction potential, we see under standard conditions that a transfer of electrons from NADH to pyruvate to form lactate is exergonic and thus thermodynamically spontaneous. The reduction and oxidation steps of the reaction are coupled and catalyzed by the enzyme lactate dehydrogenase.

A second example: alcohol fermentation

Another familiar fermentation process is alcohol fermentation, which produces ethanol, an alcohol. The alcohol fermentation reaction is the following:

Figure 2. Ethanol fermentation is a two-step process. Pyruvate (pyruvic acid) is first converted into carbon dioxide and acetaldehyde. The second step converts acetaldehyde to ethanol and oxidizes NADH to NAD+. Facciotti (original work)

In the first reaction, a carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas (some of you may be familiar with this as a key component of various beverages). The second reaction removes electrons from NADH, forming NAD+ and producing ethanol (another familiar compound—usually in the same beverage) from the acetaldehyde, which accepts the electrons.

Fermentation pathways are numerous

While the lactic acid fermentation and alcohol fermentation pathways described above are examples, there are many more reactions (too numerous to go over) that Nature has evolved to complete the NADH/NAD+ cycle. It is important that you understand the general concepts behind these reactions. In general, cells try to maintain a balance or constant ratio between NADH and NAD+; when this ratio becomes unbalanced, the cell compensates by modulating other reactions to compensate. The only requirement for a fermentation reaction is that it uses a small organic compound as an electron acceptor for NADH and regenerates NAD+. Other familiar fermentation reactions include ethanol fermentation (as in beer and bread), propionic fermentation (it's what makes the holes in Swiss cheese), and malolactic fermentation (it's what gives Chardonnay its more mellow flavor—the more conversion of malate to lactate, the softer the wine). In Figure 3, you can see a large variety of fermentation reactions that various bacteria use to reoxidize NADH to NAD+. All of these reactions start with pyruvate or a derivative of pyruvate metabolism, such as oxaloacetate or formate. Pyruvate is produced from the oxidation of sugars (glucose or ribose) or other small, reduced organic molecules. It should also be noted that other compounds can be used as fermentation substrates besides pyruvate and its derivatives. These include methane fermentation, sulfide fermentation, or the fermentation of nitrogenous compounds such as amino acids. You are not expected to memorize all of these pathways. You are, however, expected to recognize a pathway that returns electrons to products of the compounds that were originally oxidized to recycle the NAD+/NADH pool and to associate that process with fermentation.

Figure 3. This figure shows various fermentation pathways using pyruvate as the initial substrate. In the figure, pyruvate is reduced to a variety of products via different and sometimes multistep (dashed arrows represent possible multistep processes) reactions. All details are deliberately not shown. The key point is to appreciate that fermentation is a broad term not solely associated with the conversion of pyruvate to lactic acid or ethanol. Source: Marc T. Facciotti (original work)

A note on the link between substrate-level phosphorylation and fermentation

Fermentation occurs in the absence of molecular oxygen (O2). It is an anaerobic process. Notice there is no O2 in any of the fermentation reactions shown above. Many of these reactions are quite ancient, hypothesized to be some of the first energy-generating metabolic reactions to evolve. This makes sense if we consider the following:

  1. The early atmosphere was highly reduced, with little molecular oxygen readily available.
  2. Small, highly reduced organic molecules were relatively available, arising from a variety of chemical reactions.
  3. These types of reactions, pathways, and enzymes are found in many different types of organisms, including bacteria, archaea, and eukaryotes, suggesting these are very ancient reactions.
  4. The process evolved long before O2 was found in the environment.
  5. The substrates, highly reduced, small organic molecules, like glucose, were readily available.
  6. The end products of many fermentation reactions are small organic acids, produced by the oxidation of the initial substrate.
  7. The process is coupled to substrate-level phosphorylation reactions. That is, small, reduced organic molecules are oxidized, and ATP is generated by first a red/ox reaction followed by the substrate-level phosphorylation.
  8. This suggests that substrate-level phosphorylation and fermentation reactions coevolved.

Consequences of fermentation

Imagine a world where fermentation is the primary mode for extracting energy from small molecules. As populations thrive, they reproduce and consume the abundance of small, reduced organic molecules in the environment, producing acids. One consequence is the acidification (decrease in pH) of the environment, including the internal cellular environment. This can be disruptive, since changes in pH can have a profound influence on the function and interactions among various biomolecules. Therefore, mechanisms needed to evolve that could remove the various acids. Fortunately, in an environment rich in reduced compounds, substrate-level phosphorylation and fermentation can produce large quantities of ATP.

It is hypothesized that this scenario was the beginning of the evolution of the F0F1-ATPase, a molecular machine that hydrolyzes ATP and translocates protons across the membrane (we'll see this again in the next section). With the F0F1-ATPase, the ATP produced from fermentation could now allow for the cell to maintain pH homeostasis by coupling the free energy of hydrolysis of ATP to the transport of protons out of the cell. The downside is that cells are now pumping all of these protons into the environment, which will now start to acidify.

-------------------------------- BONUS READING ON COMMON REDOX CHEMISTRY ISSUES -------------------------------

Alternative View of Some Common Confusing Issues in Basic Redox Chemistry for Biology

This reading tries to break down some of the more challenging topics that students run into when studying redox chemistry in General Biology. This reading is not a substitute for your main reading but rather a complement to it that revisits some of the same topics through a different lens.

Finding ΔE

Students often struggle with finding the ∆E for a given redox reaction. One of the main barriers to developing this skill seems to be associated with developing a picture of the redox reaction itself. From the context of most biological redox reactions it is useful to imagine/picture a redox reaction as a simple exchange of electrons between two molecules, an electron donor and an electron acceptor that accepts electrons from the donor.

An analogy with kiwi fruit: To help build this mental picture we offer an analogy. Two people are standing next to one another. At the start, one person is holding a kiwi fruit in their hand and the second person's hands are empty. In this reaction, person 1 gives the kiwi to person 2. At the end of the reaction person 2 is holding a kiwi and person 1 is not. We can write this exchange as we might a chemical reaction:

person 1(kiwi) + person 2() <-> person 1() + person 2(kiwi).

start/initial state <-> final/end state

If we read this "reaction" from left to right, person 1 is a kiwi donor and person 2 is a kiwi acceptor. We can extend this analogy a little by proposing that person 1 and person 2 have different desire and ability to grab and hold kiwi fruit - we'll call that kiwi-potential. We can then propose to set up a situation where person 1 and person 2 compete for a kiwi. Let's propose that person 2 has a higher "kiwi-potential" than person 1 - that is, person 2 has a stronger desire and ability to grab and hold wiki than person 1.

If we set up a competition where person 1 starts with the kiwi and person 2 competes for it, we should expect that after some time the kiwi will be exchanged to person 2 and stay there most often. At the end of the reaction the kiwi will be with person 2. Due to the difference in "kiwi-potential" between person 1 and person 2, we can say that the spontaneous direction of kiwi flow is from person 1 to person 2. If we ever observed the kiwi flow from person 2 to person 1 we could probably conclude that person 1 required some extra help/energy to make that happen - flow from person 2 to person 1 would be non-spontaneous.

Let's call the "kiwi-potential", Kp. In our analogy, Kpperson 1 < Kpperson 2. We can calculate ∆Kp, the difference in Kp between the two people, and that will tell us something about how likely we can expect to see kiwi exchange hands between these two people. The bigger the difference in Kp the more likely the kiwi will move from the person who has a lower Kp to the person who has the higher Kp.

By definition, to calculate ∆Kp we obtain the solution to ∆Kp = Kpfinal/end - Kpinitial/start. Since the kiwi is with person 2 at the end of the reaction and it starts with person 1 at the beginning of the reaction we would calculate ∆Kp = Kpperson 2 - Kpperson 1.

Doing it with electrons instead of kiwi fruit: To find ∆E for a redox reaction we can translate this analogy to the molecular space. Instead of people we have two molecules. Instead of a kiwi, we have electrons. Different molecules have different inherent abilities to grab and hold electrons and this can be measured by the value E. If two molecules exchange one or more electrons we can imagine that electrons will flow spontaneously from a molecule with lower E0 to one with a higher E0. We can write a familiar reaction with those substitutions.

molecule 1(electron) + molecule 2() <-> person 1() + molecule 2(electron).

start/initial state <-> final/end state

To find ΔE0, you solve for ΔE0 = E0-final/end - E0-initial/start. Alternatively, you can think of it as ΔE0 = E0-acceptor - E0-donor.

When evaluating a redox reaction for ∆E you therefore need to:

  1. First, find which of the reactants is the electron donor. The donor can also be associated with the initial state because it is the molecule that initially (before the start of the reaction) has the electron(s) to donate. This will always be one of the reactants and will be the molecule that gets oxidized (i.e. the molecule that loses electrons).

  2. Second, find which of the reactants is the electron acceptor. This will also always be a reactant and will be the molecule that becomes reduced by the reaction (i.e. gains electrons). This molecule can be also associated with the final state since, in its reduced form, it is the molecule that has the electrons at the end of the reaction.

  3. Third, calculate ΔE0 = E0-acceptor - E0-donor or if you prefer, ΔE0 = E0-final/end - E0-initial/start.

In the example above, we can examine the reactants and determine that NAD+ is the oxidized form of the electron carrier - it can, therefore, not be the donor. This means that H2 must act as the electron donor in this reactant. During the reactantion electrons flow onto NAD+ from the donor H2 creating the reduced product NADH and oxidized product H+. To calculate ∆E0 we say that at the start of the reaction the exchanged electrons are on the donor H2. We say that at the end of the reaction the electrons are found on NADH. Calculating ∆E0 requires us to evaluate the difference:

E0-acceptor - E0-donor

or equivalently,

E0-final/end - E0-initial/start.

Using a redox table to find E0 values for the start and end molecules shows us that NAD+/NADH has an E0 of -0.30 while H+/H2 has an E0 of -0.42.

Therefore, ΔE0 = (-0.30) - (-0.42) = 0.12 V.

We can see intuitively that this reaction is spontaneous: electrons are flowing from a molecule that "wants" electrons less (E0 of H+/H2 = -0.42) to a molecule that wants them more (E0 of NAD+/NADH = -0.30).

Reading Different Looking Redox Towers

Novice students of redox chemistry will all undoubtedly run across different ways of representing a redox tower. These different representations may look different but contain the same information. Without explanation, however, reading these tables - when they look different - can be confusion. We will compare and contrast different common forms of redox towers.

Redox Tower: Type 1

Figure 1. A Generic redox tower with oxidized/reduced couple listed with its reduction potential (E0') .

Attribution: Caidon Iwuagwu

In this type of redox tower, the oxidized and reduced forms of a molecule are separated by a slash. There is a line drawn from each half-reaction to its redox potential E0 reported on the vertical axis.

Redox Tower: Type 2

Electron Acceptor

Electron Donor

E0(eV)

CO2 + 24e-

glucose

- 0.43

2H+ + 2e-

H2

- 0.42

CO2 + 6e-

methanol

- 0.38

NAD+ + 2e-

NADH

- 0.32

CO2 + 8e-

acetate

- 0.28

S0 + 2e-

H2S

- 0.28

SO42- + 8e-

H2S

- 0.22

Pyruvate + 2e-

lactate

- 0.19

S4O62- + 2e-

S2O32-

+ 0.024

Fumarate + 2e-

succinate

+ 0.03

Cytochrome box + 1e-

Cytochrome bred

+ 0.035

Ubiquinoneox + 2e-

Ubiquinonered

+ 0.11

Fe3+ + 1e- → (pH 7)

Fe2+

+ 0.2

Cytochrome cox + 1e-

Cytochrome cred

+ 0.25

Cytochrome aox + 1e-

Cytochrome ared

+ 0.39

NO3- + 2e-

NO2-

+ 0.42

NO3- + 5e-

1/2 N2

+ 0.74

Fe3+ + 1e- → (pH 2)

Fe2+

+ 0.77

1/2 O2 + 2e-

H2O

+ 0.82

In this type of redox tower, each row consists of a half-reaction. The oxidized form of a molecule is shown in the first column, the reduced form of the molecule is shown in the second column. Finally, the E0 value of the molecule is listed in the third column from the left. The number of electrons transferred to reduce the oxidized form of the molecule is shown in column 1. While the format of the table looks different from Type 1 tower, both contain the exact same information.

Redox Tower: Type 3

oxidized form

reduced form

n (electrons)

Eo´ (volts)

CO2

glucose

24

-0.43

2H+

H2

2

-0.42 (at [H+] = 10-7; pH=7)

Note: at [H+] = 1; pH=0 the Eo' for hydrogen is ZERO. You will see this in chemistry class.

CO2

methanol

6

-0.38

NAD+ + 2H+

NADH + H+

2

-0.32

CO2

acetate

8

-0.28

S0

H2S

2

-0.28

SO42-

H2S

8

-0.22

Pyruvate + 2H+

lactate

2

-0.19

S4O62-S4O62-20.024

Fumarate

succinate

2

0.03

Cytochrome boxCytochrome bred10.035

Ubiquinone; (ox)

Ubiquinone; (red)

2

0.1

Fe3+ (pH = 7)

Fe2+ (pH = 7)

1

0.20

Cytochrome c; Fe3+

Cytochrome c; Fe2+

1

0.25

Cytochrome a

Cytochrome a

1

0.39

Nitrate

nitrite

2

0.42

Nitrate

1/2 N2

5

0.74

Fe3+ (pH = 2)

Fe2+ (pH = 2)

1

0.77

1/2 O2 + 2H+

H2O

2

0.816

In this redox tower, the oxidized form of a molecule is in the leftmost column, its reduced form is in the second column from the left, the number of electrons transferred is in the third column from the left, and the E0 is in the far right column.

Again, all of these towers contain the exact same information and are used in an identical manner.

Special note: If you have studied redox chemistry in a formal chemistry course, you might notice two key differences between the towers you use in a biology setting and those used by chemists.

1. In chemistry, the redox towers are flipped relative to those in biology: In chemistry, the molecules with the most positive E0 are listed starting at the top of the table and the compounds with the most negative E0 are listed at the bottom. In bioloigal redox tables molecules with the largest E0 are listed at the bottom while those with the smallest E0 are listed starting at the top. The biology orientation has the advantage of making it easy to picture electrons spontaneously falling down the table from molecules that "want" the electrons less (lower E0) to molecules that "want" electrons more (higher E0).

2. In chemistry, the redox potential for hydrogen (H+/H2) is listed as 0. This is because (a) redox potentials for chemistry are measured under a set of non-biologically relevant standard conditions and (b) hydrogen is being used as the common standard redox potential against which all other redox potentials are measured. In biology, the redox potential for hydrogen (H+/H2) is listed as -0.42. This difference between the chemistry and biology tables comes about because the redox potential for (H+/H2) in biology is measured at a physiological pH of 7.0.

Familiarize yourself with how to read and interpret all three types of redox towers!

Chemistry and Biology Teach Redox Differently

For students who have been taught redox chemistry in a formal chemistry course, biological lessons in redox can sometimes seem like they're talking about something completely different. Not surprisingly, chemists tend to teach the most proper and universally applicable approach to evaluating redox reaction. This approach consists of using a set of rules to formally evaluate whether atoms in a molecule have undergone a change in oxidation state. Meanwhile, biologists tend to approach the discussion of redox reactions by thinking about electron transfers between molecules. It turns out that the approach biologists take is not as rigorous as how chemists approach redox reactions and can sometimes not identify bona fide redox reactions that wouldn't be missed using the chemist's approach. However, since the vast majority of biological redox reactions do involve a transfer of electron (and therefore change in redox states).

Let's look at a specific example to see the differences in approach.

The Chemistry Approach (oxidation numbers):

To evaluate/solve redox reactions in CHEMISTRY, we use the concept of oxidation states/numbers (we will just be saying oxidation number here). The oxidation number of an element refers to how the electrons are shared between atoms in a chemical compound and they tell us about the movement of the electrons in the redox reaction. There are specific rules to assigning oxidation numbers, we will not be going over all of them since they will not be applicable to the redox reactions you will see in General Biology, but here are a few:

  1. A single element has an oxidation number of 0

  2. Fluorine ALWAYS has an oxidation number of -1

  3. Hydrogen has an oxidation number of +1 with nonmetals and -1 with metals.

etc.

For more on calculating oxidation numbers see:

So to find which elements are reduced/oxidized when given a redox reaction, you must track the change of the oxidation numbers between the reactants and the products. Here is an example:

In the unbalanced reaction NO3-+ FADH2⟶ NO2-+ FAD+

  1. Using the rules, we observe that in NO3-, the oxidation number of Nitrogen is +5. In NO2-, the oxidation number of Nitrogen is +3. So because +5 ⟶ +3, N is reduced in this reaction.

  2. We could conduct a similar calculation for key atoms on FAD+ and FADH2 to discover that FADH2 is oxidized in the reaction.

The Biology/Biochemistry Approach (electron flow):

To evaluate/solve redox reactions in biology/biochemistry, we typically do not use or assign oxidation numbers to evaluate redox reactions. Rather we follow the exchange of electrons between molecules. Fortunately, biology tends to reuse a limited number of electron carriers and redox towers tell us which form of a compound is reduced or oxidized. As mentioned above, the basic approach to redox in biology is to define oxidation as: the loss of electrons. Reduction is defined as: the gain of electrons. Here is an example:

NO3-+ FADH2⟶ NO2-+ FAD+

Here we examine the reactants and immediately spot the common electron carrier FADH2, the reduced form of the electron carrier. In the products we observe the oxidized form of the electron carrier FAD+. We conclude that FADH2 lost electrons (became oxidized) in the reaction. Since the electrons had to go somewhere they were likely accepted by NO3- which then became reduced to NO2-. In this case the biologist's model arrives at the same conclusion as the chemist's approach through a more intuitive approach that doesn't require memorizing numerous rules and how to apply them.

In our General Biology class, we take the biology/biochemistry approach to redox. You will not need to know how to calculate redox states in this course.

DISCLAIMER: DO NOT WORRY IF YOU HAVE NOT TAKEN CHEMISTRY YET !! WE WILL NOT BE USING THE CHEMISTRY APPROACH WHEN IT COMES TO REDOX REACTIONS IN OUR CLASS. THE PURPOSE OF THIS IS JUST TO DISTINGUISH AND HOPEFULLY CLARIFY THE TWO APPROACHES FOR STUDENTS THAT MAY HAVE ALREADY TAKEN A CHEMISTRY COURSE!!



Comments:

  1. Tedmond

    I am also worried about this question, where can I find more information on this issue?

  2. Niguel

    Wonderful, very valuable message

  3. Marx

    I ask forgiveness that I intervene, but I propose to go by another way.

  4. Georg

    I heard this story about 7 years ago.

  5. Fletcher

    Ask your calculator



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