2020_SS1_Bis2A_Facciotti_Reading_18 - Biology

2020_SS1_Bis2A_Facciotti_Reading_18 - Biology

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Learning goals associated with 2020_SS1_Bis2A_Facciotti_Reading_18

• Properly connect the pentose phosphate pathway (PPP) to glycolysis and explain the PPP's role in supplying NADPH for cellular anabolic reactions and in the biosynthesis of nucleotides and aromatic amino acids (tryptophan, phenylanlanine, tyrosine).
• Diagram the pentose and hexose sugars, be able to number their carbon atoms, and identify the key functional groups on each molecule.
• Identify a nucleotide from its molecular structure and be able to decompose the molecule into three main functional units: nitrogenous base, ribose, and phosphates.
• Be able to classify common biomolecules as a lipid, protein, carbohydrate, or nucleic acid.
• Create illustrations that serve as models of the three-dimensional structures of DNA. These should span several levels of detail and abstraction that include cartoon models of:
a. three nucleotides and their phosphodiester bonds.
b. two antiparallel strands showing hydrogen bonds between nucleotides in opposite strands
c. a zoomed out representation of the polymer’s helical structure.
• Name the nitrogenous bases that form hydrogen bonds to one another and identify complementary base pairing ("base-pairing rules").

Introduction into the pentose phosphate pathway (PPP)

Discussions of metabolism in most introductory biology 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 important and universal metabolic pathways, many courses leave out the pentose phosphate pathway (PPP), also known as the hexose monophosphate shunt. In this class, we consider the PPP important for two key reasons. First, it is the primary route for the formation of pentoses, the five-carbon sugar required for nucleotide biosynthesis and a variety of other essential cellular components. Second, redox reactions in the PPP generate NADPH, the main mobile electron donor used in anabolic (building) reactions.

A note from the instructor

Like the modules on glycolysis and the TCA cycle, we do not expect students to memorize specific compound names or details of molecular structures in the pathway. We provide those details in the reading so you can understand the transformations occurring in this pathway and refer back to them when needed. Rather than memorizing, focus instead on the mastering the assigned learning goals related to the PPP.

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

We call glycolysis, the TCA cycle and the pentose phosphate pathway central carbon metabolism. These three pathways (along with the reaction that converts pyruvate to acetyl-CoA) contain all the chemical precursors required by cells for the biosynthesis of nearly all other biomolecules. The PPP produces pentose phosphates (five-carbon sugars), eyrthrose-phosphate (a four-carbon sugar), and NADPH. The pentose phosphates are key precursors for nucleotide biosynthesis while NADPH serves as the main mobile electron donor for anabolic (building) reactions. The PPP also produces sedoheptulose-phosphate, an essential seven-carbon sugar used in the building of Gram-negative bacteria's outer cell membranes.

Below is a diagram of the pathway. The pathway involves several redox reactions and multiple molecular rearrangement that interconvert molecules of 3-, 4-, 5-, 6-, and 7-carbons. The pathway begins with the oxidation of Glucose-6-phosphate (G6P), a key intermediate of glycolysis, by the enzyme glucose-6-phosphate dehydrogenase (G6PDH). This enzyme oxidizes G6P through the coupled reduction of the electron carrier NADP+ to make NADPH. Enzymes 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 glycolysis.

Figure 1. The Pentose Phosphate Pathway (PPP).

The Pentose Phosphate Pathway diverts the glucose-6-phosphate from glycolysis, oxidizes the sugar to produce NADPH for anabolic reactions, creates ribose-5-phosphate for nucleotide biosynthesis, and other key 3, 4 and 7 carbon intermediates. Two of the products, fructose-6-phosphate and glyceraldehyde-3-phosphate reenter glycolysis. Compound names are blue while enzyme names are red italic font.
Attribution: Marc T. Facciotti

As shown in the figure above, products of the pathway include glyceraldehyde-3-phosphate. This sugar can then be further oxidized via glycolysis. Fructose-6-phosphate that can reenter glycolysis and NADPH, a reductant for many biosynthetic (anabolic) reactions is also made. In addition, the pathway provides a variety of intermediate sugar-phosphates that the cell requires, such as pentose-phosphates (for nucleotides and some amino acids), erythrose-phosphate (for amino acids) and sedohepulose-phosphate (for gram-negative bacteria). The figure below illustrates the input-output relationship between PPP and the "top half" of glycolysis.

Figure 2. The relationship between glycolysis and PPP.

The Pentose Phosphate Pathway is shown as a "shunt" (alternative metabolic pathway) for glucose-6-phosphate.
Attribution: Marc T. Facciotti

Nucleic acids

There are two types of nucleic acids in biology: DNA and RNA. DNA carries the heritable genetic information of the cell andis composedof two antiparallel strands of nucleotides arranged in a helical structure.Each nucleotidesubunitis composedof a pentose sugar (deoxyribose), a nitrogenous base, and a phosphate group. The two strands associate via hydrogen bonds between chemically complementary nitrogenous bases. Interactions known as "base stacking" interactions also help stabilize the double helix.By contrast toDNA, RNA can beeitherbesingle stranded, or double stranded. It toois composedof a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is a molecule ofmanytricks.It is involvedin protein synthesis as a messenger, regulator, and catalyst of the process.RNA is also involvedin various other cellular regulatory processes and helps tocatalyzesome key reactions (more on this later).With respect toRNA, in this course weare primarily interestedin (a) knowing the basic molecular structure of RNA and what distinguishes it from DNA, (b) understanding the basic chemistry of RNA synthesis that occurs during a process called transcription, (c) appreciating the various roles that RNA can have in the cell, and (d) learning the majortypes ofRNA that you will encounter most frequently (i.e.mRNA,rRNA,tRNA,miRNAetc.)andassociating them with the processesthey are involvedwith. In thismodulewe focus primarily on the chemical structures of DNA and RNA and how they canbe distinguishedfrom one another.

Nucleotide structure

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).DNA and RNA are madeup of monomers known as nucleotides. Individual nucleotides condense with one another to form a nucleic acid polymer.Each nucleotide is madeup of three components: a nitrogenous base (for which there are five different types), a pentose sugar, and a phosphate group.These are depictedbelow. The main difference between these two types of nucleic acids is the presence or absence of a hydroxyl group at the C2 position, also called the 2' position (read "two prime"), of the pentose (see Figure 1 legend and the section on the pentose sugar for more on carbon numbering). RNA has a hydroxyl functional group at that 2' position of the pentose sugar; the sugaris calledribose, hence the name ribonucleic acid.By contrast, DNAlacks the hydroxyl group at that position, hence the name, "deoxy" ribonucleic acid. DNA has a hydrogen atom at the 2' position.

Figure 1. A nucleotide is madeup of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups.Carbons in thepentoseare numbered1′ through 5′ (the prime distinguishes these residues from those in thebase,whichare numberedwithout using a prime notation). The baseis attachedto the 1′ position of the ribose, and the phosphateis attachedto the 5′ position. When a polynucleotideis formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain.Two types ofpentoseare foundin nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an -H instead of an -OH at the 2′ position.Bases can be dividedinto two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.
Attribution:Marc T. Facciotti (original work)

The nitrogenous base

The nitrogenous bases of nucleotides are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra


and thus acting as a base by decreasing the hydrogen ion concentration in the local environment. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T).

By contrast, RNA

contains adenine (A), guanine (G) cytosine (C), and uracil (U) instead of thymine (T).

Adenine and guanine are classified

as purines. The primary distinguishing structural feature of a purine is


carbon-nitrogen ring. Cytosine, thymine, and uracil

are classified

as pyrimidines. These

are structurally distinguished

by a single carbon-nitrogen ring.

You will be expected

to recognize that each of these ring structures

is decorated

by functional groups that may

be involved

in a variety of chemistries and interactions.


Take a moment to review the nitrogenous bases in Figure 1. Identify functional groups as described in class. For each functional group identified, describe what type of chemistry you expect it tobe involvedin. Try to identify whether the functional group can act as either a hydrogen bond donor, acceptor, or both?

The pentose sugar

The pentose sugar contains five carbon atoms. Each carbon atom of the sugar molecule

are numbered

as 1′, 2′, 3′, 4′, and 5′ (1′

is read

as “one prime”).

The two main functional groups that are attached to the sugar are often namedin reference to

the carbon to which

they are bound

. For example, the phosphate residue

is attached

to the 5′ carbon of the sugar and the hydroxyl group

is attached

to the 3′ carbon of the sugar. We will often use the carbon number to refer to functional groups on nucleotides so be very familiar with the structure of the pentose sugar.

The pentose sugar in DNA

is called

deoxyribose, and in RNA, the sugar is ribose. The difference between the sugars is

the presence of

the hydroxyl group on the 2' carbon of the ribose and its absence on the 2' carbon of the deoxyribose. You can, therefore, determine if you are looking at a DNA or RNA nucleotide by the presence or absence of the hydroxyl group on the 2' carbon atom—you will probably

be asked

to do so on


occasions, including exams.

The phosphate group

There can be anywhere between one and three phosphate groups bound to the 5' carbon of the sugar. When one phosphateis bound,the nucleotide is referredto as a Nucleotide MonoPhosphate(NMP). Iftwo phosphates are boundthe nucleotide is referredto as Nucleotide DiPhosphate (NDP). When three phosphatesare boundto the nucleotideit is referredto as a Nucleotide TriPhosphate (NTP). Thephosphoanhydridebonds between that link the phosphate groups to each other have specific chemical properties that make them good for various biological functions. The hydrolysis of the bonds between the phosphate groups is thermodynamically exergonic in biological conditions; Nature has evolved many mechanisms to couple this negative change in free energy to help drive many reactions in the cell. Figure 2 shows the structure of the nucleotide triphosphate Adenosine Triphosphate, ATP, which we will discuss in greater detail in other chapters.

Note: "high-energy" bonds

The term "high-energy bond"is usedA LOT in biology. This term is, however, a verbal shortcut that can cause some confusion. The term refers to the amount of negative free energy associated with the hydrolysis of the bond in question. The water (or other equivalent reaction partner) is an important contributor to the energy calculus. In ATP, for instance, simply"breaking" aphosphoanhydridebond - say with imaginary molecular tweezers - by pulling off a phosphate would not be energetically favorable. We must therefore be careful not to say that breaking bonds in ATP is energetically favorable or that it "releases energy". Rather, we should be more specific, noting that the hydrolysis of the bond is energetically favorable.Some of this common misconception is tiedto, in our opinion,the use of the term "high-energy bonds". While in Bis2a we have tried to minimize the use of the vernacular "high energy" when referring to bonds, trying instead to describe biochemical reactions by using more specific terms, as students of biology you will no doubt encounter the potentially misleading - though admittedly useful - shortcut "high-energy bond" as you continue in your studies. So, keep the above in mind when you are reading or listening to various discussions in biology. Heck, use the term yourself. Just make sure that you really understand what it refers to.

Figure2.ATP (adenosine triphosphate) has three phosphate groups that canbe removedby hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate). Attribution:Marc T. Facciotti (original work)

Double helix structure of DNA

DNA has a double helix structure (shown below) created by two strands of covalently linked nucleotide subunits.The sugar and phosphate groups of each strand of nucleotides are positionedon the outside of the helix, forming the backbone of the DNA (highlighted by the orange ribbons in Figure 3). The two strands of the helix run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand (See Figures 4 and 5). We referred to this orientation of the two strands as antiparallel. Note too thatphosphate groups are depictedin Figure 3 as orange and red "sticks" protruding from the ribbon. The phosphatesare negatively chargedat physiologicalpHsand therefore give the backbone of the DNA a strong local negatively charged character.By contrast, thenitrogenous basesare stackedin theinterior of the helix(these are depictedas green, blue, red, and white sticks in Figure 3). Pairs of nucleotides interact with one another through specific hydrogen bonds (shown in Figure 5). Each pair of separated from the next base pair in the ladder by 0.34nmand this close stacking and planar orientation gives rise to energetically favorable base-stacking interactions. The specific chemistry associated with these interactions is beyond the content of Bis2a butis describedin more detail here for the curious or more advanced students. Wedoexpect, however, that studentsare awarethat the stacking of the nitrogenous bases contributes to the stability of the double helix and defer to your upper-division genetics and organic chemistry instructors to fill in the chemical details.

Figure3. Native DNA is an antiparallel double helix. The phosphate backbone (indicatedby the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. Attribution:Marc T. Facciotti (original work)

In a double helix, certain combinations of base pairing are chemically more favored than others based on the types and locations of functional groups on the nitrogenous bases of each nucleotide. Inbiologywe find that:

Adenine (A) is chemically complementary with thymidine (T) (A pairswith T)


Guanine (G) is chemically complementary with cytosine (C) (G pairs with C).

We often refer to this pattern as "base complementarity" and say that the antiparallel strands are complementary to each other. For example, if the sequence of one strand is of DNA is 5'-AATTGGCC-3', the complementary strand would have the sequence 5'-GGCCAATT-3'.

We sometimeschoose torepresent complementary double-helical structures intextby stacking the complementary strands on top ofonanotheras follows:



Note that each strand has its 5' and 3' ends labeled and that if one were to walk along each strand starting from the 5' end to the 3' end that the direction of travel would be opposite the other for each strand; the strands are antiparallel. We commonly say things like "running 5-prime to 3-prime" or "synthesized 5-prime to 3-prime" to refer to the direction we are reading a sequence or the direction of synthesis. Start getting yourself accustomed to this nomenclature.

Figure 4. Panel A. In a double-stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′.Herethe strandsare depictedas blue and green lines pointing in the 5' to 3' orientation.Complementary base pairing is depictedwith a horizontal line between complementary bases. Panel B. The two antiparallel strandsare depictedin double-helical form. Note thatthe orientation of the strands is still represented. Note that the helix is right-handed - the "curl" of the helix, depicted in purple, windsin the direction ofthe fingers of the hand if the right handis usedand the direction of the helix points towards the thumb. Panel C. This representation shows two structural features that arise from the assembly of the two strands called the major and minor grooves.These grooves can also be seenin Figure 3.
Attribution:Marc T. Facciotti (original work)

Figure 5. A zoomed-in molecular-level view of the antiparallel strands in DNA. In a double-stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′.The phosphate backbone is locatedon the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine.
Attribution:Marc T. Facciotti (original work)

Functions and roles of nucleotides and nucleic acids to look out for in Bis2a

Besides their structural roles in DNA and RNA, nucleotides such as ATP and GTP also serve as mobile energy carriers for the cell. It surprises some students when they learn to appreciate that the ATP and GTP molecules we discuss in bioenergetics are the same as those involved in the formation of nucleic acids. We will cover this in more detail when we discuss DNA and RNA synthesis reactions. Nucleotides also play important roles asco-factors in many enzymaticallycatalyzedreactions.

Nucleic acids, RNA in particular, play a variety of roles in incellularprocess besides being information storage molecules. Some roles that you should keep an eye out for as we progress through the course include: (a) Riboprotein complexes - RNA-Protein complexes in which the RNA serves both catalytic and structural roles. Examples of such complexes include, ribosomes (rRNA),RNases,splicesosomecomplexes, and telomerase. (b) Information storage and transfer roles. These roles include molecules like DNA, messenger RNA (mRNA), transfer RNA (tRNA). (c) Regulatory roles. Examples of these include various non-coding (ncRNA). Wikipedia has a comprehensive summary of the different known RNA molecules that we recommend browsing to get a better sense of the great functional diversity of these molecules.

2020_SS1_Bis2A_Facciotti_Reading_18 - Biology

INTRODUCTION 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 (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. Here the remaining two carbons 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

Module 5.3 left off with the end-products of glycolysis: 2 pyruvate molecules, 2 ATPs and 2 NADH molecules. This module and module 5.5 will explore what the cell may now do with the pyruvate, ATP and NADH that were generated. In module 5.5 we will see how pyruvate is the primary starting substrate for fermentation reactions, reactions that allow cells to regenerate NAD + from NADH, to allow for the continued oxidation of glucose and the uninterrupted continuation of glycolysis. In this module, we will explore the continued and complete oxidation of pyruvate all the way to CO2.

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.

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 module 5.5). Alternatively, NADH can be recycled back into NAD + by donating electrons to something known as an electron transport chain (this is covered in module 5.6).

  • Pyruvate can be used as a terminal electron acceptor (either directly or indirectly) in fermentation reactions, and is discussed in Module 5.5.
  • Pyruvate could be secreted from the cell as a waste product.
  • Pyruvate could be further oxidized to extract more free energy from this fuel.

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 5.6). 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

The 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, NAD + is reduced to NADH during this process per molecule of pyruvate oxidized.

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.

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 also called the Krebs cycle

In bacteria and archaea reactions in the citric acid cycle typically happen in the cytosol. In eukaryotes, the citric acid cycle takes place in the matrix of mitochondria. Almost all (but not all) of the enzymes of the citric acid 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 citric acid 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.

In the citric acid 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 citric acid cycle is also the first reactant, the cycle runs continuously in the presence of sufficient reactants. (credit: modification of work by “Yikrazuul”/Wikimedia Commons)

Steps in the Citric Acid 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.

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 (Module 5.6) 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.

Summary 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.

Click through each step of the citric acid cycle here.

Energy Stories

Work on building some energy stories 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 module 5.5, 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".

Additional Links

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

Additional Questions:

What is the primary difference between a circular pathway and a linear pathway?

In a circular pathway, the final product of the reaction is also the initial reactant. The pathway is self-perpetuating, as long as any of the intermediates of the pathway are supplied. Circular pathways are able to accommodate multiple entry and exit points, thus being particularly well suited for amphibolic pathways. In a linear pathway, one trip through the pathway completes the pathway, and a second trip would be an independent event.

MODULE 05.6 Oxidative Phosphorylation and the Electron Transport Chain

INTRODUCTION The electron transport chain (ETC) is the portion of respiration that uses an external electron acceptor as the final/terminal acceptor for the electrons that were removed from the intermediate compounds in glucose catabolism. In eukaryotic cells the ETC is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed from enzyme to enzyme through a series of redox reactions. These reactions are couple the exergonic redox transfers to the endergonic transport of hydrogen ions across the membrane. This process contributes to the creation of a transmembrane electrochemical gradient. The electrons passing through the ETC gradually lose potential energy up until the point they are deposited on the terminal electron acceptor. The free energy difference of this multistep redox process is

-60 kcal/mol when NADH donates electrons or 45 kcal/mol when FADH2 donates, for organisms using oxygen as the final electron acceptor.

Introduction to Red/Ox, oxidative phosphorylation and Electron Transport Chains In modules 5.1, we discussed the general concept of Red/Ox reactions in biology and introduced the Electron Tower, a tool to help you understand Red/Ox chemistry and to estimate the direction and magnitude of potential energy differences for various Red/Ox couples. In modules 5.3 and 5.4 substrate level phosphorylation and fermentation were discussed and we saw how exergonic Red/Ox reactions could be directly coupled by enzymes to the endergonic synthesis of ATP. These processes are hypothesized to be one of the oldest forms of energy production used by cells. In this section we discuss the next evolutionary advancement in cellular energy metabolism, oxidative phosphorylation. First and foremost, oxidative phosphorylation does not imply the use of oxygen, it can, but it does not have to use oxygen. It is called oxidative phosphorylation because it relies on Red/Ox reactions to generate a electrochemical transmembrane potential that can then be used by the cell to do work.

A quick summary of Electron Transport Chains The ETC begins with the addition of electrons, donated from NADH, FADH2 or other reduced compounds. These electrons move through a series of electron transporters, enzymes that are embedded in a membrane, or carriers that undergo Red/Ox reactions. The free energy transferred from these exergonic Red/Ox reactions is coupled to the endergonic movement of protons across a membrane. This unequal accumulation of protons on either side of the membrane "polarizes" or "charges" the membrane, with a net positive (protons) on one side of the membrane and a negative charge on the other side of the membrane. The separation of charge creates an electrical potential . In addition, the accumulation of protons also causes a pH gradient known as a chemical potential across the membrane. Together these two gradients (electrical and chemical) are called an electro-chemical gradient .

Review: The Electron Tower

Since Red/Ox chemistry is so central to the topic we begin with a quick review of the table of reduction potential - sometimes called the "redox tower". As we discussed in Module 5.1, all kinds of compounds can participate in biological Red/Ox reactions. Making sense of all of this information and ranking potential Red/Ox pairs can be confusing. A tool has been developed to rate Red/Ox half reactions based on their reduction potentials or E0 ' values. Whether a particular compound can act as an electron donor (reductant) or electron acceptor (oxidant) depends on what other compound it is interacting with. The redox tower 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 organizes these half reactions based on the ability of electrons to accept electrons. In addition, in many redox towers each half reaction is written by convention with the oxidized form on the left followed by the reduced form to its right. The two forms may be either separated by a slash, for example the half reaction for the reduction of NAD + to NADH is written: NAD + /NADH + 2e - , or by separate columns. An electron tower is shown in figure 1 below.

Common Red/ox tower

Review Red/Ox Tower video from Module 5.1 For a short video on how to use the redox tower in red/ox problems click here. This video was made by Dr. Easlon for Bis2A students.

Using the Red/Ox Tower: A tool to help understand electron transport chains

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. Notice that compounds such as glucose and hydrogen gas are excellent electron donors and have very low reduction potentials E0 ' . Compounds, such as oxygen and nitrite, whose half reactions have relatively high positive reduction potentials (E0 ' ) generally make good electron acceptors are found at the opposite end of the table.

Menaquinone: an example Let's look at menaquinoneox/red. This compound sits in the middle of the redox tower with an half-reaction E0 ' value of -0.074 eV. Menaquinoneox can spontaneously (ΔG<0) accept electrons from reduced forms of compounds with lower half-reaction E0 ' . Such transfers form menaquinonered and the oxidized form of the original electron donor. In the table above, examples of compounds that could act as electron donors to menaquinone include FADH2, an E0 ' value of -0.22, or NADH, with an E0 ' value of -0.32 eV. Remember the reduced forms are on the right hand side of the red/ox pair.

Once menaquinone has been reduced, it can now spontaneously (ΔG<0) donate electrons to any compound with a higher half-reaction E0 ' value. Possible electron acceptors include cytochrome box with an E0 ' value of 0.035 eV or ubiquinoneox with an E0 ' of 0.11 eV. Remember that the oxidized forms lie on the left side of the half reaction.

The Electron Transport Chain

The electron transport chain , or ETC , is composed of a group of protein complexes in and around a membrane that help couple to energetically couple a series of exergonic/spontaneous red/ox reactions to the endergonic pumping of protons across the membrane to generate a an electro-chemical gradient. This electrochemical gradient creates a free energy potential that is termed a proton motive force whose energetically "downhill" exergonic transfer can later be later coupled to a variety of cellular processes.

  1. Electrons enter the ETC from a high energy electron donor, such as NADH or FADH2, which are generated during a variety of catabolic reactions like and including those associated glucose oxidation (review modules 5.3-5.5). Depending on the complexity (number and types of electron carriers) of the ETC being used by an organism, electrons can enter at a variety of places in the electron transport chain - this depends upon the respective reduction potentials of the proposed electron donors and acceptors.
  2. After the first redox reaction, the initial electron donor will become oxidized and the electron acceptor will become reduced. The difference in redox potential between the electron acceptor an donor is related to ΔG by the relationship ΔG = -nFΔE, where n = the number of electrons transferred and F = Faraday's constant. The larger a positive ΔE the more exergonic a reaction.
  3. If sufficient energy transferred during an exergonic redox step the electron carrier may couple this negative change in free energy to the endergonic process of transporting a proton from one side of the membrane to the other.
  4. After multiple redox transfers, the electron is delivered to a molecule known as the terminal electron acceptor. In the case of humans and plants, this is oxygen. However, there are many, many, many, other possible electron acceptors, see below.

What are the complexes of the ETC? ETCs are made up of a series (at least one) of membrane associated red/ox proteins or (some are integral) protein complexes (complex = more than one protein arranged in a quaternary structure) that move electrons from a donor source, such as NADH, to a final terminal electron acceptor, such as oxygen - this donor/terminal acceptor pair is the primary one used in human mitochondria. Each electron transfer in the ETC requires a reduced substrate as an electron donor and an oxidized substrate as the electron acceptor. In most cases the electron acceptor is a member of the enzyme complex. Once the complex is reduced, the complex can serve as an electron donor for the next reaction.

How do ETC complexes transfer electrons? As previously mentioned the ETC is composed of a series of protein complexes that undergo a series of linked red/ox reactions. These complexes are in fact multiprotein enzyme complexes referred to as oxidoreductases or simply reductases . The one exception to this naming convention is the terminal complex in aerobic respiration that uses molecular oxygen as the terminal electron acceptor. That enzyme complex is referred to as an oxidase . Red/Ox reactions in these complexes are typically carried out by a non-protein moiety called a prosthetic group . This is true for all of the electron carriers with the exception of quinones, which are a class of lipids that can directly be reduced or oxidized by the oxidoreductases. In this case, both the Quinonered and the Quinoneox is soluble within the membrane and can move from complex to complex. The prosthetic groups are directly involved in the red/ox reactions being catalyzed by their associated oxidoreductases. In general these prosthetic groups can be divided into two general types: those that carry both electrons and protons and those that only carry electrons.

  • Flavoproteins ( Fp ), these proteins contain an organic prosthetic group called a flavin , which is the actual moiety that undergoes the oxidation/reduction reaction. FADH2 is an example of a Fp.
  • Quinones , are a family of lipids which means they are soluble within the membrane.
  • It should also be noted that NADH and NADPH are considered electron (2e-) and proton (2 H + ) carriers.
  • Cytochromes are proteins that contain a heme prosthetic group. The Heme is capable of carrying a single electron.
  • Iron-Sulfur proteins contain a non-heme iron-sulfur clusters that can carry an electron. The prosthetic group is often abbreviated as Fe-S

Aerobic versus Anaerobic respiration In the world we live in, most of the organisms we interact with breath air, which is approximately 20% oxygen. Oxygen is our terminal electron acceptor . We call this process respiration, specifically aerobic respiration, we breath in oxygen, our cells take it up and transport it into the mitochondria where it is used as the final acceptor of electrons from our electron transport chains. That is aerobic respiration : the process of using oxygen as a terminal electron acceptor in an electron transport chain.

While most of the organisms we interact with use oxygen as the terminal electron acceptor, this process of respiration evolved at time when oxygen was not a major component of the atmosphere. Respiration or oxidative phosphorylation does not require oxygen at all it simply requires a compound with a high reduction potential to act as a terminal electron acceptor accept electrons from one of the complexes within the ETC. Many organisms can use a variety of compounds including nitrate (NO3 - ), nitrite (NO2 - ), even iron (Fe +++ ) as terminal electron acceptors. When oxygen is NOT the terminal electron acceptor, the process is referred to as anaerobic respiration . The ability of an organism to vary its terminal electron acceptor provides metabolic flexibility and can ensure better survival if any given terminal acceptor is in limited supply. Think about this, in the absence of oxygen we die but an organism that can use a different terminal electron acceptor can survive.

A generic example of a simple, 2 complex ETC Figure 2 shows a generic electron transport chain, composed of two integral membrane complexes Complex Iox and Complex IIox. A reduced electron donor, designated DH (such as NADH or FADH2) reduces Complex 1ox giving rise to the oxidized form D (such as NAD or FAD). Simultaneously, a prosthetic group within complex I is now reduced (accepts the electrons). In this example the redox reaction is exergonic and the free energy difference is coupled by the enzymes in Complex I to the endergonic translocation of a proton from one side of the membrane to the other. The net result is that one surface of the membrane becomes more negatively charged, due to an excess of hydroxyl ions (OH - ) and the other side becomes positively charged due to an increase in protons on the other side. Complex Ired can now reduce the prosthetic group in Complex IIred while simultaneously oxidizing Complex Ired. Electrons pass from Complex I to Complex II via thermodynamically spontaneous red/ox reactions, regenerating Complex Iox which can repeat the previous process. Complex IIred reduces A, the terminal electron acceptor to regenerate Complex IIox and create the reduced form of the terminal electron acceptor. In this case, Complex II can also translocate a proton during the process. If A is molecular oxygen, water (AH) will be produced. This reaction would then be considered a model of an aerobic ETC. However, if A is nitrate, NO3 - then Nitrite, NO2 - is produced (AH) and this would be an example of an anaerobic ETC.

Generic 2 complex electron transport chain. In the figure, DH is the electron donor (donor reduced) and D is the donor oxidized. A is the oxidized terminal electron acceptor and AH is the final product, the reduced form of the acceptor. As DH is oxidized to D, protons are translocated across the membrane, leaving an excess of hydroxyl ions (negatively charged) on one side of the membrane and protons (positively charged) on the other side of the membrane. The same reaction occurs in Complex II as the terminal electron acceptor is reduced to AH.

Based on Figure 2 above and using the electron tower in Figure 1, what is the difference in the electrical potential if (A) DH is NADH and A is O2 and (B) DH is NADH and A is NO3 - . Which pairs (A or B) provide the most amount of usable energy?

Detailed look at aerobic respiration The eukaryotic mitochondria has evolved a very efficient ETC. There are four complexes composed of proteins, labeled I through IV in [link], and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of bacteria and arechaea.

The electron transport chain is a series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen. In the process, protons are pumped from the mitochondrial matrix to the intermembrane space, and oxygen is reduced to form water.

Complex I

To start, two electrons are carried to the first complex aboard NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B2, also called riboflavin, is one of several prosthetic groups or co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, non-peptide molecules bound to a protein that facilitate its function prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is a very large protein, containing 45 amino acid chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane.

Q and Complex II

Complex II directly receives FADH2, which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone (Q). The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced, (QH2), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I and the electrons derived from FADH2 from complex II, including succinate dehydrogenase. This enzyme and FADH2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP molecules are made from the FADH2 electrons. As we will see in the following section, the number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane.

Complex III

The third complex is composed of cytochrome b, another Fe-S protein, Rieske center (2Fe-2S center), and cytochrome c proteins this complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe ++ (reduced) and Fe +++ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes (cytochrome c is the acceptor of electrons from Q however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time).

Complex IV

The fourth complex is composed of cytochrome proteins c, a, and a3. This complex contains two heme groups (one in each of the two cytochromes, a, and a3) and three copper ions (a pair of CuA and one CuB in cytochrome a3). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H2O). The removal of the hydrogen ions from the system contributes to the ion gradient used in the process of chemiosmosis.


In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the membrane. The uneven distribution of H + ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane.

If the membrane were open to diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by their electrochemical gradient. Many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane through an integral membrane protein called ATP synthase ([link]). This complex protein acts as a tiny generator, turned by transfer of energy mediated by protons moving down their electrochemical gradient. The movement of this molecular machine (enzyme) serves to lower the activation energy of reaction and couples the exergonic transfer of energy associated with the movement of protons down their electrochemical gradient to the endergonic addition of a phosphate to ADP, forming ATP.

ATP synthase is a complex, molecular machine that uses a proton (H + ) gradient to form ATP from ADP and inorganic phosphate (Pi). (Credit: modification of work by Klaus Hoffmeier)

Chemiosmosis ([link]) is used to generate 90 percent of the ATP made during aerobic glucose catabolism it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. The overall result of these reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium, and water is formed.

In oxidative phosphorylation, the pH gradient formed by the electron transport chain is used by ATP synthase to form ATP in a Gram - bacteria.

A Hypothesis as to how ETC may have evolved

A proposed link between SLP/Fermentation and the evolution of ETCs When we last discussed energy metabolism, it was in context of substrate level phosphorylation (SLP) and fermentation reactions. One of the questions in the Discussion points was what would be the consequences of SLP, both short-term and long-term to the environment? We discussed how cells would need to co-evolve mechanisms to remove protons from the cytosol (interior of the cell), which lead to the evolution of the F0F1ATPase, a multi-subunit enzyme that translocates protons from the inside of the cell to the outside of the cell by hydrolyzing ATP as shown in figure 6 below. This arrangement works as long as small reduced organic molecules are freely available, making SLP and fermentation advantageous. As these biological process continue, the small reduced organic molecules begin to be used up and their concentration decreases, putting a demand on cells to be more efficient. One source of potential "ATP waste" is in the removal of protons from the cell's cytosol, organisms that could find other mechanisms could have a selective advantage. Such selective pressure could have led to the first membrane-bound proteins that could use Red/Ox reactions as their energy source, as depicted in figuire 7 . In other words use the energy from a Red/Ox reaction to move protons. Such enzymes and enzyme complexes exist today in the form of the electron transport complexes, like Complex I, the NADH dehydrogenase.

Proposed evolution of an ATP dependent proton translocator As small reduced organic molecules become limiting organisms that can find alternative mechanisms to remove protons from the cytosol may have had and advantage. The evolution of a proton translocator that uses the energy in a Red/Ox reaction could substitute for the ATAase.

Continuing with this line of logic, there are organisms that can now use Red/Ox reactions to translocate protons across the membrane, instead of an ATP driven proton pump. With protons being being translocated by Red/Ox reactions, this would now cause a build up of protons on the outside of the membrane, separating both charge (positive on the outside and negative on the inside an electrical potential) and pH (low pH outside, higher pH inside). With excess protons on the outside of the cell membrane, and the F0F1ATPase no longer consuming ATP to translocate protons, the pH and charge gradients can be used to drive the F0F1ATPase "backwards" that is to form or produce ATP by using the energy in the charge and pH gradients set up by the Red/Ox pumps as depicted in figure 8 . This arrangement is called an electron transport chain (ETC).

The evolution of the ETC the combination of the Red/Ox driven proton translocators coupled to the production of ATP by the F0F1ATPase.

MODULE 05.7 Pentose Phosphate Pathway

INTRODUCTION In most introductory biology and biochemistry courses focus on glycolysis (oxidation of glucose to pyruvate) and the TCA cycle, the 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 or hexose monophosphate shunt. This pathway, like the TCA cycle is partially cyclic in nature, where 3 glucose molecules enter and 2 glucose and 1 glyceraldyde-3-phosphate leave. The 2 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 Instuctor 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 4-carbon sugar and the latter a 7-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 reactins found in the PPP, the transketolase and transaldolase reactions, thow 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.

Oxidatvie Pentose Phosphate Pathway: AKA 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. Pentose are required precursors for nucleotides and other essential biomolecules. The PPP also generates NADPH instead of NADH, which is required for most anabolic reactions. The PPP, in conjuction with Glycolysis and the TCA cycle make up what we call Central Metabolism. These 3 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 (5 carbon sugars), Eyrthrose-phosphate (four carbon sugars)and NADPH . This pathway is also responsible for the production of Sedoheptulose -phosphate , an essential 7-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 transaldolase and transketalase 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 3 glucose-6-Phosphate (in green) molecules being oxidized to form 3 CO2 molecules, 1 glyceraldehyde-Phosphate (in red), and 2 hexose-phosphates (in red). In this cycle, the formed glyceradehyde-Phosphate feeds into glycolysis and the 2 hexose-Phosphates (glucose-Phosphates) can recycle into the PPP or gycolysis.

Pentose Phosphate Pathway Take home message

As shown in Figure 2, the net result of the pathway is 1 trios-phosphate (glyceraldehyde-3-Phosphate) that can then be further oxidized via glycolysis 2 recycled hexose-phosphates (in the form of either glucose-6-phosphae or fructose-6-phosphate) and NADPH which is 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-Co 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.


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

MODULE 05.8 Photosynthesis and the Calvin Cycle

INTRODUCTION The light dependent reactions of photosynthesis couple the transfer of energy in light into chemical compounds through a series of redox reactions in an electron transport chain (review module 5.6). In the light dependent reactions, both ATP and NADPH are generated. Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO2 from the environment and incorporate it into larger biomolecules. An enzyme, RuBisCO, catalyzes a reaction with CO2 and another molecule, RuBP to produce two three carbon sugars. This process is called carbon fixation. After three cycles, a three-carbon molecule of glyceraldehyde-3-phosphate (G3P), the same one we saw earlier in glycolysis, leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more CO2. Photosynthesis forms an energy cycle with the process of cellular respiration. Plants need both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites. Therefore, plants contain both chloroplasts and mitochondria - more on these organelles soon.

Light Energy

The sun emits an enormous amount of electromagnetic radiation (solar energy). Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation. The human eye can only perceive a small fraction of this energy and this portion of the electromagnetic spectrum is therefore referred to as “visible light.” Visible light constitutes only one of the many types of electromagnetic radiation emitted from the sun and other stars.

The sun emits energy in the form of electromagnetic radiation. This radiation exists at different wavelengths, each of which has its own characteristic energy. All electromagnetic radiation, including visible light, is characterized by its wavelength. Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength (or the more stretched out it appears in the diagram), the less energy it carries. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving a heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.

Light Absorption

Light energy initiates many light dependent biological process when pigments absorb photons of light. Organic pigments, whether in the human retina, chloroplast thylakoid, or microbial membrane often have specific ranges of energy levels or wavelengths that they can absorb that are dependent on their chemical makeup and structure. A pigment like the retinal in our eyes, when coupled with an opsin sensor protein, “sees” (absorbs) light predominantly with wavelengths between 700 nm and 400 nm. Because this range defines the physical limits for what light we can see, we refer to it, as noted above, as the "visible range". For similar reasons, plants pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm plant physiologists refer to this range for plants as photosynthetically active radiation.

The visible light seen by humans as white light is composed of a rainbow of colors, each with a characteristic wavelength. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. In the visible spectrum, violet and blue light have shorter (higher energy) wavelengths while the orange and red light have longer (lower energy) wavelengths.([link]).

The colors of visible light do not carry the same amount of energy. Violet has the shortest wavelength and therefore carries the most energy, whereas red has the longest wavelength and carries the least amount of energy. (credit: modification of work by NASA)

Understanding Pigments

Chlorophylls (including bacteriochlorophylls) and carotenoids are the two major classes of photosynthetic lipid derived pigments found in bacteria, plants and algae each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c, d, and f. Chlorophyll a is related to a class of more ancient molecules found in bacteria called bacteriochlorophylls . Carotenoids are also very ancient molecules, found in bacteria and eukaryotes. They are the red/orange/yellow pigments found in nature. They are found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—which are used as advertisements to attract seed dispersers (animals or insects that may carry seeds elsewhere). In photosynthesis, carotenoids function as photosynthetic pigments. In addition, when a leaf is exposed to full sun, that surface is required to process an enormous amount of energy if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids help absorb excess energy in light and safely dissipate that energy as heat.

Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum . The graph in [link] shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths.

(a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated in the red box, are responsible for the green color of leaves. β-carotene is responsible for the orange color in carrots. Each pigment has (d) a unique absorbance spectrum.

Many photosynthetic organisms have a mixture of pigments which optimizes the organism's ability to absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and available wavelengths decrease and change, respectively, with depth. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees absorb most of the sunlight and scatter the remaining solar radiation ([link]).

Plants that commonly grow in the shade have adapted to low levels of light by changing the relative concentrations of their chlorophyll pigments. (credit: Jason Hollinger)

Photophosphorylation an Overview:

Photophosphorylation is the process of transferring the energy from light into chemicals, in particular ATP and NADPH. The evolutionary roots of photophosphorylation are likely in the anaerobic world, between 3 billion and 1.5 billion years ago, when life was abundant in the absence of molecular oxygen. Photophosphorylation probably evolved relatively shortly after electron transport chains and anaerobic respiration began to provide metabolic diversity. The first step of the process involves the absorption of a photon by a pigment molecule. Light energy is transferred to the pigment and promotes electrons into a higher potential energy state - termed an "excited state". The electrons are colloquially said to be "energized". In the excited state, the pigment now has a very low reduction potential and can donate the "excited" electrons to other carriers with greater reduction potentials. These electron acceptors may in turn become donors to other molecules with greater reduction potentials and in so doing form an electron transport chain. As electrons pass from one electron carrier to another via red/ox reactions, these exergonic transfers can be coupled to the endergonic transport (or pumping) of protons across a membrane to create an electrochemical gradient. This electrochemical gradient generates a proton motive force whose exergonic drive to reach equilibrium can be coupled to the endergonic production of ATP, via ATP synthase. As we will seen in more detail, the electrons involved in this electron transport chain can have one of two fates: (1) they may be returned to their initial source in a process called cyclic photophosphorylation or (2) they can be deposited onto a close relative of NAD + called NADP + . If the electrons are deposited back on the original pigment in a cyclic process, the whole process can start over. If, however, the electron is deposited onto NADP + to form NADPH (**shortcut note - we didn't explicitly mention any protons but assume it is understood that they are also involved**) the original pigment must regain an electron from somewhere else. This electron must come from a source with a smaller reduction potential than the oxidized pigment and depending on the system there are different possible sources, including H2O, reduced sulfur compounds such as SH2 and even elemental S 0 .

What happens when a compound absorbs a photon of light?

When a compound absorbs a photon of light, the compound is said to leave its ground state and become "excited", in the sense that it has this extra energy. This is illustrated in figure 5 schematically.

A diagram of what happens to a molecule that absorbs a photon of light.

What are the fates of the "excited" electron? There are four possible outcomes, which are schematically diagrammed in Figure 6 below. These options are:

  1. The electron can relax to a lower orbital, transferring energy as heat.
  2. The electron can relax to a lower orbital and transfer energy into a photon of light - a process known as fluorescence .
  3. The energy can be transferred by resonance to a neighboring molecule as the e - returns to a lower orbital.
  4. The energy can change the reduction potential such that the molecule can become an e - donor. Linking this excited e - donor to a proper e - acceptor can lead to an exergonic electron transfer. In other words, the excited state can be involved in Red/Ox reactions.

As the excited electron decays back to its original orbit, the energy can be transferred in a variety of ways. While many so called antenna or auxiliary pigments absorb light energy and transfer it to something known as a reaction center (by mechanisms depicted in option III in figure 6) it is what happens at the reaction center that we are most concerned with (option IV in figure 6). Here a chlorophyll or bacteriochlorophyll molecule absorbs a photon's energy and an electron is excited. This energy transfer is sufficient to allow the reaction center to donate the electron in a red/ox reaction to a second molecule. This initiates the photophosphorylation electron transport reactions. The result is an oxidized reaction center that must now be reduced in order to start the process again. How this happens is the basis of electron flow in photophosphorylation and will be described in detail below.

Simple Photophosphorylation Systems: Anoxygenic photophosphorylation

Introduction Early in the evolution of photophosphorylation, these reactions evolved in anaerobic environments where there was very little molecular oxygen available. Two sets of reactions evolved under these conditions, both directly from anaerobic respiratory chains as described above. These are known as the light reactions because they require the activation of an electron (an excited electron) from the absorption of a photon of light by a reaction center pigment, such as bacteriochlorophyll. The light reactions are categorized either as cyclic or as noncyclic photophosphorylation, depending upon the final state of the electron(s) removed from the reaction center pigments. If the electron(s) return to the original pigment reaction center, such as bacteriochlorophyll, this is cyclic photophosphorylation the electrons make a complete circuit and is diagramed in figure 8. If the electron(s) are used to reduce NADP + to NADPH, the electron(s) are removed from the pathway and end up on NADPH, this process is referred to as noncyclic since the electrons are no longer part of the circuit. In this case the reaction center must be re-reduced before the process can happen again. Therefore, an external electron source is required for noncylic photophosphorylation. In these systems reduced forms of Sulfur, such as H2S, which can be used as an electron donor and is diagrammed in figure 9. To help you better understand the similarities of photophosphorylation to respiration, a redox tower (figure 7) has been provided that contains many commonly used compounds involved with photosphosphorylation.

Electron tower that has a variety of common photophosphorylation components. PSI and PSII refer to Photosystems I and II of the oxygenic photophosphorylation pathways. For the examples in Figure 8 and Figure 9 P840 is similar in reduction potential as is PSI.

Cyclic Photophosphorylation In cyclic photophosphorylation the bacteriochlorophyllred molecule absorbs enough light energy to energize and eject an electron to form bacteriochlorophyllox. The electron reduces a carrier molecule in the reaction center which in turn reduces a series of carriers via red/ox reactions. These carriers are the same carriers found in respiration. If the change in reduction potential from the various red/ox reactions are sufficiently large, protons, H + are translocated across the membrane. Eventually the electron is used to reduce bacteriochlorophyllox and the whole process can start again. This is called cyclic photophosphorylation because the electrons make a complete circuit: bacteriochlorophyll is the source of electrons and is the final electron acceptor. ATP is produced via the F1F0 ATPase . The schematic in figure 8 below demonstrates how cyclic photophosphorylation works.

Cyclic Photophosphorylation. The reaction center P840 absorbs light energy and becomes excited, denoted with an *. The excited electron is ejected and used to reduce an FeS protein leaving an oxidized reaction center. The electron its transferred to a quinone, then to a series of cytochromes which in term is reduces the P840 reaction center. The process is cyclical. Note the gray array coming from the FeS protein going to a ferridoxin (Fd), also in gray. This represents an alternative pathway the electron can take and will be discussed below in non-cyclic photophosphorylation. NOTE the same electron that leaves the P480 reaction center is not necessarily the same electron that eventually finds its way back to reduce the oxidized P840.

Non-cyclic photophosphorylation In cyclic photophosphorylation electrons cycle from bacteriochlorophyll (or chlorophyll) to a series of electron carriers and eventually back to bacteriochlorophyll (or chlorophyll): there is no loss of electrons, they stay in the system. In non-cyclic photophosphorylation the electrons are removed from the photosystem and redox chain and they eventually end up on NADPH. That means there needs to be a source of electrons, a source that has a smaller reduction potential than bacteriochlorophyll (or chlorophyll) that can donate electrons to bacteriochlorophyllox to reduce it. An electron tower is proved above so you can see what compounds can be used to reduce the oxidized form of bacteriochlorophyll. The second requirement, is that when bacteriochlorophyll becomes oxidized and the electron is ejected it must reduce a carrier that has a greater reduction potential than NADP/NADPH (see the electron tower). In this case, electrons can flow from energized bacteriochlorophyll to NADP forming NADPH and oxidized bacteriochlorophyll. Electrons are lost from the system and end up on NADPH, to complete the circuit bacteriochlorophyllox is reduced by an external electron donor, such as H2S or elemental S 0 .

Non-cyclic photophosphorylation. In this example, the P840 reaction center absorbs light energy and becomes energized, the emitted electron reduced a FeS protein and in turn reduces ferridoxin. Reduced ferridoxin (Fdred) can now reduce NADP to form NADPH. The electrons are now removed from the system, finding their way to NADPH. The electrons need to be replaced on P840, which requires an external electron donor. In this case, H2S serves as the electron donor.

Possible Discussion It should be noted that for bacterial photophosphorylation pathways, for each electron donated from a reaction center (remember only one electron is actually donated/reaction center (or chlorophyl molecule), the resulting output from that electron transport chain is either the formation of NADPH (requires 2 electrons)or ATP can be made, NOT not both. In other words, the path the electrons take in the ETC can have one or two possible outcomes. This puts limits on the versatility of the bacterial anoxygenic photosynthetic systems. But what would happen if there evolved a process that utilized both systems, that is a cyclic and non-cyclic photosynthetic pathway? That is, if both ATP and NADPH could be formed from from a single input of electrons? A second limitation is that these bacterial systems require compounds such as reduced sulfur to act as electron donors to reduce the oxidized reaction centers, not necessarily widely found compounds. What would happen if a chlorophyllox molecule would have a reduction potential higher (more positive) than that of the molecular the O2/H2O reaction? Answer, a planetary game changer.

Oxygenic Photophosphorylation

Generation of NADPH and ATP The overall function of light-dependent reactions is to transfer solar energy into chemical compounds, largely the the molecules NADPH and ATP. This energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in [link]. Protein complexes and pigment molecules work together to produce NADPH and ATP.

A photosystem consists of a light-harvesting complex and a reaction center. Pigments in the light-harvesting complex pass light energy to two special chlorophyll a molecules in the reaction center. The light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited electron must then be replaced. In (a) photosystem II, the electron comes from the splitting of water, which releases oxygen as a waste product. In (b) photosystem I, the electron comes from the chloroplast electron transport chain discussed below.

The actual step that transfers light energy into the biomolecule takes place in a multiprotein complex called a photosystem , two types of which are found embedded in the thylakoid membrane, photosystem II (PSII) and photosystem I (PSI) ([link]). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons).

Both photosystems have the same basic structure a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by the light-harvesting complex , which passes energy from sunlight to the reaction center it consists of multiple antenna proteins that contain a mixture of 300� chlorophyll a and b molecules as well as other pigments like carotenoids. The absorption of a single photon or distinct quantity or “packet” of light by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured by biological molecules but is not stored in any useful form yet. The energy is transferred from chlorophyll to chlorophyll until eventually (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons.

In the photosystem II (PSII) reaction center, energy from sunlight is used to extract electrons from water. The electrons travel through the chloroplast electron transport chain to photosystem I (PSI), which reduces NADP + to NADPH. The electron transport chain moves protons across the thylakoid membrane into the lumen. At the same time, splitting of water adds protons to the lumen, and reduction of NADPH removes protons from the stroma. The net result is a low pH in the thylakoid lumen, and a high pH in the stroma. ATP synthase uses this electrochemical gradient to make ATP.

The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation they can actually give up an electron in a process called a photo activation . It is at this step in the reaction center, this step in photosynthesis, that light energy is transferred into an excited electron. All of the subsequent steps involve getting that electron onto the energy carrier NADPH for delivery to the Calvin cycle where the electron is deposited onto carbon for long-term storage in the form of a carbohydrate. PSII and PSI are two major components of the photosynthetic electron transport chain , which also includes the cytochrome complex . The cytochrome complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), thus enabling both the transfer of protons across the thylakoid membrane and the transfer of electrons from PSII to PSI.

The reaction center of PSII (called P680 ) delivers its high-energy electrons, one at a time, to the primary electron acceptor , and through the electron transport chain (Pq to cytochrome complex to plastocyanine) to PSI. P680’s missing electron is replaced by extracting an electron from water thus, water is split and PSII is re-reduced after every photoact. Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. Splitting two molecules of water is required to form one molecule of diatomic O2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration.

As electrons move through the proteins that reside between PSII and PSI, they take part in exergonic redox transfers. The free energy associated with the exergonic redox reaction is coupled to the endergonic transport of hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus the ones produced by splitting water, accumulate in the thylakoid lumen and will be used to synthesize ATP in a later step. Since the electrons on PSI now have a greater reduction potential than when they started their trek (it is important to note that PSI unexcited sits lower on the redox tower than NADP+/NADPH), they must be re-energized in PSI. Therefore, another photon is absorbed by the PSI antenna. That energy is transferred to the PSI reaction center (called P700 ). P700 is oxidized and sends an electron through several intermediate redox steps to NADP + to form NADPH. Thus, PSII captures the energy in light and couples its transfer via redox reactions to the creation of a proton gradient. The exergonic and controlled relaxation of this gradient can be coupled to the synthesis of ATP. PSI captures energy in light and couples that, through a series of redox reactions, to reduce NADP + into NADPH. The two photosystems work in concert, in part, to guarantee that the production of NADPH will be in the right proportion to the production of ATP. Other mechanisms exist to fine tune that ratio to exactly match the chloroplast’s constantly changing energy needs.

Additional links

Light Independent Reactions or 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 refereed to as autotrophs , while those organisms that require organic forms of carbon, such as glucose or amino acids, are refereed 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

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 [link]. Ribulose-1,5-bisphosphate (RuBP) is composed of five carbon atoms and includes two phosphates.

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 also is produced 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 molecules 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.

The harsh conditions of the desert have led plants like these cacti to evolve variations of the light-independent reactions of photosynthesis. These variations increase the efficiency of water usage, helping to conserve water and energy. (credit: Piotr Wojtkowski)

Free Response Questions

Why is the third stage of the Calvin cycle called the regeneration stage?

Because RuBP, the molecule needed at the start of the cycle, is regenerated from G3P.

Which part of the light-independent reactions would be affected if a cell could not produce the enzyme RuBisCO?

None of the cycle could take place, because RuBisCO is essential in fixing carbon dioxide. Specifically, RuBisCO catalyzes the reaction between carbon dioxide and RuBP at the start of the cycle.

Why does it take three turns of the Calvin cycle to produce G3P, the initial product of photosynthesis?

Because G3P has three carbon atoms, and each turn of the cycle takes in one carbon atom in the form of carbon dioxide.

Prepare for the Test: Create an energy story for each phase of the Calvin cycle. Classify the reactants and products and pay attention to where the energy is at the beginning of the reaction and the end of the reaction. At this point you should be able to tell if a reaction is a REDOX reaction (does it have NADPH as a reactant or product?) or if the reaction is endergonic or exergonic (is ATP created or used in the reaction?).

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Steps of Noncyclic Electron Pathway Flashcards Quizlet DA: 11 PA: 50 MOZ Rank: 61

  • Steps of Noncyclic Electron Pathway
  • Terms in this set (7) light hits photosystem 2 and pigments absorb solar energy
  • Water splits & O2, H, and e- are released

Photosynthesis Non Cyclic Electron Flow Flashcards Quizlet DA: 11 PA: 50 MOZ Rank: 62

  • Photosynthesis Non Cyclic Electron Flow
  • A photon of light excites a chlorophyl molecule in the light harvesting complex and is tranferred to other pigment molecules until it excites the electrons and P680 molecules.

Cyclic vs. Non-cyclic Electron Flow

  • Under certain conditions, the photoexcited electrons take an alternative path called cyclic electron flow, which uses photosystem I (P700) but not photosystem II (P680)
  • This process produces no NADPH and no O 2, but it does make ATP
  • This is called cyclic photophosphorylation.

Non-cyclic Electron Transport in Photosynthesis

Non-cyclic Electron Transport in Photosynthesis Photophosphorylation refers to the use of light energy to ultimately provide the energy to convert ADP to ATP, thus replenishing the universal energy currency in living things.In the simplest systems in prokaryotes, photosynthesis is used just for the production of energy, and not for the building of any biological molecules.

Noncyclic electron flow biology Britannica DA: 18 PA: 32 MOZ Rank: 54

  • Other articles where Noncyclic electron flow is discussed: photosynthesis: The pathway of electrons: …and intermediate carriers is called noncyclic electron flow
  • Alternatively, electrons may be transferred only by light reaction I, in which case they are recycled from ferredoxin back to the intermediate carriers
  • This process is called cyclic electron flow.

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Non-cyclic Photophosphorylation The photophosphorylation process which results in the movement of the electrons in a non-cyclic manner for synthesizing ATP molecules using the energy from excited electrons provided by photosystem II is called non-cyclic photophosphorylation.

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Electron Acceptor and Donor

  • Electron acceptors are ions or molecules that act as oxidizing agents in chemical reactions. Electron donors are ions or molecules that donate electrons and are reducing agents
  • In the combustion reaction of gaseous hydrogen and oxygen to produce water (H 2 O), two hydrogen atoms donate their electrons to an oxygen atom.

5.9A: Electron Donors and Acceptors in Anaerobic

  • Both inorganic and organic compounds may be used as electron acceptors in anaerobic respiration
  • Inorganic compounds include sulfate (SO 42-), nitrate (NO 3–), and ferric iron (Fe 3+)
  • These molecules have a lower reduction potential than oxygen.

Electronegativity and Electron-donor-acceptor Complexes

  • To provide a better electron-acceptor
  • Molecular orbital diagram for a simple electron-donor-acceptor complex
  • LUMO is the unoccupied molecular orbital of the acceptor molecule and HOMO is the highest occupied molecular orbital of the donor molecule.

Self-organization of electron acceptor molecules on DA: 12 PA: 45 MOZ Rank: 60

  • Graphene grown on Ir(111) electronically decouples adsorbed molecules from the metallic substrate and allows the study of their self-organization on surfaces
  • We study two electron acceptor molecules from the same family
  • The intermolecular interaction, attractive for TCNQ and repulsive for F4-TCNQ, dictates Carbon nanostructures

Theoretical study of new acceptor and donor molecules

  • The calculated electron affinities allow to rate the donor or acceptor character of the molecules
  • They confirm that CHO is a strong acceptor
  • Its high electron affinity (3.5 eV), which characterizes a good acceptor, is almost as large as the affinity of TCNQ (3.62 eV).

Electron carrier molecules (video) Khan Academy DA: 19 PA: 50 MOZ Rank: 74

normally when we talk about the production of energy in the cell glucose and ATP are the main characters of the story but in this video we're going to talk about a behind the scene player called electron carrier molecules that really do play a vital role in this energy production process as well but in order to talk about electron carrier molecules

Which molecule is the final electron acceptor at the DA: 11 PA: 50 MOZ Rank: 67

  • The electron transport chain consists of a series of redox reactions in which electrons are transferred to oxygen as the final electron acceptor

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While those electron acceptors have commonalities in optical bandgap and energy levels, PTIC exhibits exceptional photostabilities in both solution and film, over other studied examples.

Anaerobic Respiration Boundless Microbiology

  • Both inorganic and organic compounds may be used as electron acceptors in anaerobic respiration
  • Inorganic compounds include sulfate (SO 42-), nitrate (NO 3–), and ferric iron (Fe 3+)
  • These molecules have a lower reduction potential than oxygen.

Nonfullerene Acceptor Molecules for Bulk Heterojunction

  • The bulk-heterojunction blend of an electron donor and an electron acceptor material is the key component in a solution-processed organic photovoltaic device
  • In the past decades, a p-type conjugated polymer and an n-type fullerene derivative have been the most commonly used electron donor and electron acceptor, respectively.

What is an electron acceptor in cellular respiration DA: 13 PA: 50 MOZ Rank: 73

  • An electron acceptor is any substance that gains electrons from some thing else
  • For a strictly aerobic organism, the final electron acceptor is oxygen
  • However, each individual component of the electron transport is an electron acceptor for electrons from the previous component.

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  • Electron acceptors are the molecules or chemicals that have high oxidizing ability (like to be reduced) and are able to accept electrons
  • Examples of electron acceptors are oxygen, nitrate, iron

High Hole-Mobility Molecular Layer Made from Strong DA: 12 PA: 32 MOZ Rank: 56

  • These results indicate that strong electron acceptor molecules with metal adatoms can form high hole-mobility molecular layers by controlling the molecule–metal ordered structure and their CT interaction

Biology 150 Ch. 9 Flashcards Quizlet DA: 11 PA: 40 MOZ Rank: 64

  • What kind of molecules serve as electron acceptors in cellular respiration? a
  • molecules with high potential energy b
  • molecules with low potential energy c
  • molecules in an excited state water d
  • How many NADH are produced by glycolysis? a

Controlling electron transfer in donor-bridge-acceptor

  • Molecular conductance calculations on these bridges show that cross-conjugation results in quantum interference effects that greatly alter the through-bridge donor-acceptor electronic coupling as a function of charge injection energy
  • These calculations display trends that agree well with the observed trends in the electron transfer rates.

Delocalization of exciton and electron wavefunction in non DA: 14 PA: 28 MOZ Rank: 57

Among these NFAs, the family of the A-D-A type molecules (where A denotes an electron-poor/acceptor moiety and D, an electron-rich/donor moiety), typically composed of …

Chemoorganotrophy – General Microbiology

  • The best electron acceptor will be the one that is lowest down on the electron tower, in an oxidized form (i.e
  • On the left-hand side of the redox couple)
  • Some common electron acceptors include nitrate (NO3-), ferric iron (Fe3+), sulfate (SO42-), carbonate (CO32 …

Toward control of electron transfer in donor-acceptor

  • Toward control of electron transfer in donor-acceptor molecules by bond-specific infrared excitation Milan Delor, 1Paul A
  • Meijer,1 Michael Towrie,2 *Julia A
  • Weinstein1 Electron transfer (ET) from donor to acceptor is often mediated by nuclear-electronic

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In aerobic respiration, the final electron acceptor (i.e., the one having the most positive redox potential) at the end of the ETS is an oxygen molecule (O 2) that becomes reduced …

What is the final electron acceptor in photosynthesis

  • Electron acceptors are ions or molecules that act as oxidizing agents in chemical reactions
  • Electron donors are ions or molecules that donate electrons and are reducing agents
  • Oxygen is an oxidizing agent (electron acceptor) and hydrogen is a reducing agent (electron donor).

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  • During cellular respiration, electrons move through a series of electron acceptor molecules
  • Which of the following is a TRUE statement about this process? asked Sep 11, 2016 in Biology & Microbiology by perio
  • A) The electrons gain energy as they move from one electron acceptor to another
  • B) Oxygen is eventually reduced by the electrons to

Microbiology Chapter 11: Catabolism Flashcards Quizlet DA: 11 PA: 50 MOZ Rank: 82

  • This generates a proton motive force (PMF), which is used to synthesize most of the ATP by oxidative phosphorylation
  • A small amount of ATP is made from substrate level phosphorylation
  • Respiration can be anaerobic or aerobic (anaerobic- terminal electron acceptors are exogenous molecules other than O2 aerobic- terminal electron acceptor is O2)

End-capped engineering of bipolar diketopyrrolopyrrole

Fused ring electron acceptor molecules having many advantages like effective thermal characteristics, high PCEs. a strong level of absorption in the visible region, long life, photo-chemically stable,.

Toward control of electron transfer in donor-acceptor

  • Electron transfer (ET) from donor to acceptor is often mediated by nuclear-electronic (vibronic) interactions in molecular bridges
  • Using an ultrafast electronic-vibrational-vibrational pulse-sequence, we demonstrate how the outcome of light-induced ET can be radically altered by mode-specific infrared (IR) excitation of vibrations that are coupled to the ET pathway.

Electron Donor-Acceptor Organic Polymers by “Click” Type DA: 18 PA: 50 MOZ Rank: 92

Among these electron-accepting molecules, TCNE is one of the strongest organic electron acceptors, and its high chemical reactivity toward nucleophiles or electron-rich reagents is frequently used to introduce strong acceptor moieties, for example, 1,1,4,4-tetracyanobuta-1,3-diene (TCBD), into organic molecules [27, 28].

Question . Place the following steps of the light DA: 13 PA: 50 MOZ Rank: 88

  • To replace the excited electrons, water molecules are split, creating O2 and H+ ions as byproducts
  • An electron in chlorophyll in the second photosystem is excited when hit by a light photon
  • A primary electron acceptor grabs the excited electrons from the second photosystern and transfers them to the second electron transport chain

Efficient Defect Passivation for Perovskite Solar Cells by

Here, organic donor-π-acceptor (D-π-A) molecules with different electron density distributions are employed to efficiently passivate the defects in the perovskite films.

Why is oxygen the final electron acceptor

  • Electron acceptors are ions or molecules that act as oxidizing agents in chemical reactions
  • In this reaction, the oxygen is reduced to an oxidation state of -2 and each hydrogen is oxidized to +1
  • Oxygen is an oxidizing agent (electron acceptor) and hydrogen is a reducing agent (electron

Systematic Merging of Nonfullerene Acceptor π-Extension DA: 12 PA: 50 MOZ Rank: 90

Herein, a series of new A-D-A (acceptor-donor-acceptor) type small molecule acceptors (ITBTR-C2, ITBTR-C4, ITBTR-C6, and ITBTR-C8) with indacenodithieno[3,2-b]thiophene (IDTT) as the core, benzothiadiazole (BT) as the π bridge, and ethyl-, butyl-, hexyl-, and octyl-substituted 2-(1,1-dicyanomethylene) rhodanine as the end groups, respectively

Delocalization of exciton and electron wavefunction in non DA: 13 PA: 21 MOZ Rank: 63

  • 4c, due to the electron delocalization in a Y6 cluster (with three Y6 molecules, which were observed in above MD simulation), the estimated distance (d e–h) between the hole and electron at the donor/acceptor interface increases from 22 Å (for one Y6 molecule) to 51 Å.

Theoretical study of the interaction of electron donor and

  • Adsorbed molecules and the WS 2 monolayer and acquire the distinctive characteristics of the adsorbed system theoretically
  • In this study, we report first-principles calculations that examine the adsorption of the typical electron donor (NH 3) and acceptor (H 2O) molecules on the WS 2 monolayer

Molecules Free Full-Text Synthesis of Naphthalene DA: 12 PA: 19 MOZ Rank: 62

  • Naphthalene derivatives bearing electron-accepting and electron-donating groups at the 2,6-positions belong to the family of D-π-A push-pull dyes
  • It has been found that these compounds, e.g., 2-(1-(6-((2-(fluoro)ethyl)(methyl)amino)naphthalen-2-yl)ethylidene)malononitrile (FDDNP), show not only interesting optical properties, such as solvatochromism, but they have the potential to label

Electron spin dynamics as a controlling factor for spin

  • Electron spin dynamics as a controlling factor for spin-selective charge recombination in donor - Bridge - Acceptor molecules
  • / Miura, Tomoaki Scott, Amy M. Wasielewski, Michael R
  • In: Journal of Physical Chemistry C, Vol
  • Research output: Contribution to journal › Article › peer-review

Controlling electron transfer in donor-bridge-acceptor

  • Controlling electron transfer in donor-bridge-acceptor molecules using cross-conjugated bridges Annie Butler Ricks, Gemma C

59) Both the electron and the H+ that are now back in DA: 13 PA: 50 MOZ Rank: 97

Question: 59) Both the electron and the H+ that are now back in the matrix are "captured" when they are bonded to _____ (last electron acceptor).60) This process in question 59 forms _____.61) In anaerobic respiration, how many ATP molecules are produced?62) In aerobic respiration, about how many ATP molecules are produced? This sum is the

Photosystem II biology Britannica DA: 18 PA: 23 MOZ Rank: 76

  • The light reaction of photosynthesis
  • The light reaction occurs in two photosystems (units of chlorophyll molecules)
  • Light energy (indicated by wavy arrows) absorbed by photosystem II causes the formation of high-energy electrons, which are transferred along a series of acceptor molecules in an electron transport chain to photosystem I
  • Photosystem II obtains replacement electrons from water

Delocalization of exciton and electron wavefunction in non

molecules (where A denotes an electron-poor/acceptor moiety and D, an electron-rich/donor moiety), typically composed of linearly fused conjugated ring as the middle D core, such as