08 and photosynthesis Metabolism, cell respiration, · 08 Metabolism, cell respiration, and photosynthesis M08_BIO_SB_IBDIP_9007_U08.indd 352 25/11/2014 16:34 The conformational changes

Metabolism, cell respiration,

and photosynthesis08

M08_BIO_SB_IBDIP_9007_U08.indd 350 25/11/2014 16:34

Essential ideas8.1 Metabolic reactions are regulated in response to the cell’s needs.

8.2 Energy is converted to a usable form in cell respiration.

8.3 Light energy is converted into chemical energy.

Metabolic reactions are regulated in response to the cell’s needs.

Energy is a topic of discussion every day in our modern world. We talk about the energy needed to run our modes of transport. We talk about being so tired after a long day at school that we need a short nap. The need for food becomes essential at times to regain the energy levels necessary for us to function. This chapter will look at energy in living systems. The harnessing of energy by plants will be discussed in detail, as well as how both plants and animals may then release this harnessed energy in a form usable by the organism in question. The role of enzymes in these energy processes will be examined � rst.

Organisms on our planet are part of a balanced system in which the products of the metabolic processes of one group of organisms are shared by all organisms. There is a constant interaction amongst all species. We must be ever-mindful of this balance and must continually work towards its maintenance.

8.1 Metabolism

Understandings: ● Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions. ● Enzymes lower the activation energy of the chemical reactions that they catalyse. ● Enzyme inhibitors can be competitive or non-competitive. ● Metabolic pathways can be controlled by end-product inhibition.

Applications and skills: ● Application: End-product inhibition of the pathway that converts threonine to isoleucine. ● Application: Use of databases to identify potential new anti-malarial drugs. ● Skill: Calculating and plotting rates of reactions from raw experimental results. ● Skill: Distinguishing different types of inhibition from graphs at a specifi ed substrate concentration.

Guidance ● Enzyme inhibition should be studied using one specifi c example for competitive and non-competitive inhibition.

MetabolismYour metabolism is the sum of all the chemical reactions that occur within you as a living organism. The type of reaction that uses energy to build complex organic molecules from simpler ones is called anabolism. The type of reaction that breaks down complex organic molecules with the release of energy is called catabolism. Table 8.1 summarizes anabolic and catabolic reactions.

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NATURE OF SCIENCE

Developments in scientifi c research follow improvements in computing: developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways.


Table 8.1 Anabolic and catabolic reactions

Anabolic reactions Catabolic reactions

Build complex molecules Break down complex molecules

Are endergonic Are exergonic

Are biosynthetic Are degradative

Example: photosynthesis Example: cellular respiration

Metabolic pathwaysAlmost all metabolic reactions in organisms are catalysed by enzymes. Many of these reactions occur in speci� c sequences and are called metabolic or biochemical pathways. A very simple, generalized, metabolic pathway is represented in Figure 8.1.

Substrate A Substrate B Final product

Each arrow represents a speci� c enzyme that causes one substrate to be changed to another, until the � nal product of the pathway is formed. Some metabolic pathways consist of cycles of reactions instead of chains of reactions. Others involve both cycles and chains of reactions. Cell respiration and photosynthesis were discussed in Chapter 2, and both are complex pathways with chains and cycles of reactions. Metabolic pathways are usually carried out in designated compartments of the cell where the necessary enzymes are clustered and isolated. The enzymes required to catalyse every reaction in these pathways are determined by the cell’s genetic makeup.

Induced-fi t model of enzyme actionEnzyme–substrate speci� city was discussed in Section 2.5. Enzyme speci� city is made possible by enzyme structure. Enzymes are very complex protein molecules with high molecular weights. The higher levels of protein structure allow enzymes to form unique areas, such as the active site. The active site is the region on the enzyme that binds to a particular substrate or substrates. This binding results in the reaction occurring much faster than would be expected without the enzyme.

In the 1890s Emil Fischer proposed the lock-and-key model of enzyme action. He suggested that substrate molecules � t like a key into a rigid section of the enzyme ‘lock’. At the time this model provided a good explanation of the speci� city of enzyme action. However, as knowledge about enzyme action has increased, Fischer’s model has been modi� ed.

It is now obvious that many enzymes undergo signi� cant changes in their conformation when substrates combine with their active site. The accepted new model for enzyme action is called the induced-� t model. A good way to visualize this model of enzyme action is to think of a hand and glove, the hand being the substrate and the glove being the enzyme. The glove looks a bit like the hand. However, when the hand is actually placed in the glove, there is an interaction that results in a conformational change of the glove, thus providing an induced � t.

Figure 8.1 An example of a

metabolic pathway.

Biological processes and chemical pathways are usually quite complex. When scientists attempt to explain these complex reactions, they usually break them down into smaller, intermediate steps. These intermediate steps are then carefully researched and imitated. The hope is that eventually an understanding of the complete process is obtained. There are many subjects where knowledge is gained in a similar manner. Discuss some examples. Is this manner of understanding complex concepts always successful? What are some of the limitations of this approach?

Enzymes are globular proteins that, as a minimum, have the tertiary level of organization.

Endergonic reactions are said to occur when the products of a chemical reaction have more energy than the reactants or substrates of the reaction. Endergonic reactions tend to occur in biosynthetic reactions in which more complex molecules are produced in the reaction. In contrast, exergonic reactions occur when the products of a chemical reaction have less energy than the reaction’s reactants or substrates. Exergonic reactions tend to occur in degradative reactions or those reactions in which a complex molecule is broken down into simpler materials.

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Metabolism, cell respiration, and photosynthesis08


The conformational changes and induced � t are the result of changes in the R-groups of the amino acids at the active site of the enzyme, as the enzyme interacts with the substrate or substrates.

Activation energyWhen talking about enzyme action, we always refer to activation energy (AE). Activation energy is best understood as the energy necessary to destabilize the existing chemical bonds in the substrate of an enzyme–substrate catalysed reaction. Enzymes work by lowering the activation energy required (see Figure 8.2). This means that the enzymes cause chemical reactions to occur faster because they reduce the amount of energy needed to bring about the chemical reaction.

It is important to note that, even though enzymes lower the activation energy of a particular reaction, they do not alter the proportion of reactants to products.

uncatalysed

product

reactant

activation energyfor uncatalysed reaction

activation energyfor catalysed reaction

ener

gy s

uppl

ied

ener

gy r

elea

sed

catalysed

Mechanism of enzyme actionThe following summarizes the mechanism of enzyme action.

• The surface of the substrate contacts the active site of the enzyme.• The enzyme changes shape to accommodate the substrate.• A temporary complex called the enzyme–substrate complex forms.• The activation energy is lowered and the substrate is altered by the rearrangement of

the existing atoms.• The transformed substrate, the product, is released from the active site.• The unchanged enzyme is then free to combine with other substrate molecules.

Enzyme action can also be summarized by the following equation:

E + S ↔ ES ↔ E + P

where E is the enzyme, S is the substrate, ES is the enzyme–substrate complex, and P is the product.

Figure 8.2 Enzymes accelerate reactions by lowering the activation energy required. This fi gure represents the effect of an enzyme on an exergonic reaction. The activation energy is needed to destabilize the chemical bonds in the reactant. The upper curve shows the activation energy when no enzyme is involved. The lower curve shows the activation energy required when an enzyme is present to catalyse the reaction.

In 1958, Daniel Koshland used a larger body of knowledge than had been available to Fischer, to present the induced-fi t model.

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InhibitionThe effects of pH, temperature, and substrate concentration on the action of enzymes were discussed in Section 2.5. Here, we will discuss the effects of certain types of molecules on enzyme active sites. If a molecule affects an active site in some way, the activity of the enzyme may be altered.

Competitive inhibitionIn competitive inhibition, a molecule called a competitive inhibitor competes directly with the usual substrate for the active site of an enzyme. The result is that the substrate will have fewer encounters with the active site and rate of the chemical reaction will be decreased. The competitive inhibitor must have a structure similar to the substrate to function in this way. An example is the use of sulfanilamide (a sulfa drug) to kill bacteria during an infection. Folic acid is essential to bacteria as a coenzyme. It is produced in bacterial cells by enzyme action on paraminobenzoic acid (PABA). The sulfanilamide competes with the PABA and blocks the enzyme. This prevents the production of folic acid resulting in the death of the bacteria. Because human cells do not use PABA to produce folic acid, they are unaffected by the drug.

Competitive inhibition may be reversible or irreversible. Reversible competitive inhibition may be overcome by increasing the substrate concentration. By doing this, there are more substrate molecules to bind with the active sites as they become available, and the chemical reaction may proceed more rapidly.

Non-competitive inhibitionNon-competitive inhibition involves an inhibitor that does not compete for the enzyme’s active site. In this case, the inhibitor interacts with another site on the enzyme (see Figure 8.4). Non-competitive inhibition is also referred to as allosteric inhibition, and the site the inhibitor binds to is called the allosteric site. Binding at the allosteric site causes a change in the shape of the enzyme’s active site, making it non-functional. Examples of non-competitive inhibition include metallic ions, such as mercury, binding to the sulfur groups of the component amino acids of many enzymes. This results in shape changes of the protein, which causes inhibition of the enzyme.

Again, this type of inhibition may be reversible or irreversible. There are also examples of allosteric interactions activating an enzyme rather than inhibiting it.

End-product inhibitionEnd-product inhibition prevents the cell from wasting chemical resources and energy by making more of a substance than it needs. Many metabolic reactions occur in an assembly-line type of process so that a speci� c end product can be achieved. Each step of the assembly line is catalysed by a speci� c enzyme. When the end product is present in a suf� cient quantity, the assembly line is shut down. This is usually done by inhibiting the action of the enzyme in the � rst step of the pathway. As the existing end product is used up by the cell, the � rst enzyme is reactivated. The enzyme that is inhibited and reactivated is an allosteric enzyme. When present in higher concentrations, the end product binds with the allosteric site of the � rst enzyme, thus bringing about inhibition. Lower concentrations of the end product result in fewer bindings with the allosteric site of the � rst enzyme, and, therefore, activation of the enzyme.

substrate

competitiveinhibitor

enzyme

Figure 8.3 A competitive inhibitor blocks the active site of an enzyme so the substrate

cannot bind to it.

Figure 8.4 An allosteric (non-competitive) inhibitor combines

with the allosteric site of an enzyme, causing the active site to change shape; the substrate

cannot then bind to it.

allosteric inhibitor

substrate

enzyme

A coenzyme is not usually a protein. It has an essential role in the normal actions of an enzyme.

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Ainitial

substrate

intermediateA

intermediateB

end product

enzyme 1

enzyme 2

enzyme 3

Binitial

substrate

intermediateB

end product

endproduct enzyme 1�

enzyme 2

enzyme 3

intermediateA

The bacterium Escherichia coli uses a metabolic pathway to produce the amino acid isoleucine from threonine. It is a � ve-step process. If isoleucine is added to the growth medium of E. coli, it inhibits the � rst enzyme in the pathway and isoleucine will not be synthesized. This situation will exist until the isoleucine is used up.

The inhibition of the � rst enzyme in the pathway prevents the build-up of intermediates in the cell. This is a form of negative feedback.

Figure 8.5 A short pathway of metabolic reactions with a specifi c end product that, when in suffi cient quantity, causes end-product inhibition. This is also a form of negative feedback. The intermediates are essential molecules produced in the step-by-step pathway to achieve the end product. A represents a normal pathway with several enzymes producing intermediate compounds along the way. B represents feedback inhibition. In this condition a large amount of end-product is present. The end-product inhibits enzyme 1 in the pathway. The result is that the pathway is halted.

Many examples of enzyme inhibitors exist in medicine. Two examples of competitive inhibitors are ethanol and fomepizole. Either one of these two may be used as an antidote for ethylene glycol or methanol poisoning. Ethylene glycol and methanol may be used in producing car antifreeze, de-icing solutions, solvents, and cleaners. Fomepizole is a competitive inhibitor of alcohol dehydrogenase, which catalyses the breakdown of ethylene glycol and methanol into toxic metabolites. This allows other catalytic pathways to be activated, which do not result in toxic substances.

Worked example

Competitive and non-competitive inhibitors are examples of reversible enzyme inhibitors. When graphs of their effects are produced, certain characteristics can be seen. When a chemical is a competitive inhibitor, it competes for the active site of an enzyme, and its concentration must be kept high to keep the chemical reaction occurring at a slower rate. Non-competitive inhibitors do not compete for the active site of the enzyme. The result of this is that the rate of reaction will only increase if the enzyme concentration is increased. Examine Figure 8.6.

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Exercises1 Explain why enzymes only work with specific substrates.

2 What determines whether an enzyme is competitively or non-competitively inhibited?

3 Where would the most efficient control of a metabolic pathway involving end-product inhibition occur?

Vmax

V

AB

C

[S]

Curve A represents a chemical reaction catalysed by an enzyme without the effect of an inhibitor. Curves B and C represent chemical reactions catalysed by enzymes affected by inhibitors.

1 Which curve represents the reaction in which a competitive inhibitor is active?2 Which curve represents the effects of a non-competitive inhibitor?3 Explain your answers.

Solutions

1 Curve B.2 Curve C.3 Curve C shows the action of a non-competitive inhibitor because it results

in a lower maximum reaction rate. This occurs because the inhibitor binds to the enzyme present and is not released. The reaction rate will not increase as the substrate increases because there is a limited amount of enzymes still active. Curve B represents competitive inhibition because, as the substrate increases, the rate of the reaction also increases. This is because of the larger concentration of substrate out-competing the inhibitor for the active site of the enzyme. Curve B will eventually equal the maximum reaction when enough substrate is added.

Figure 8.6 Enzyme inhibition. [S] = substrate concentration;

V = reaction rate; Vmax = maximum reaction rate.

When asked to differentiate between competitive and non-competitive inhibition curves on a graph, look to see if Vmax is achieved as the substrate is increased. If it is, then competitive inhibition is being represented. If it is not achieved and is signifi cantly less, non-competitive inhibition is being represented.

NATURE OF SCIENCE

Developments in areas such as bioinformatics have enhanced the research into metabolic pathways. Bioinformatics uses many areas of computer science and mathematics to look for unique events and patterns. This research uses large amounts of data stored in databases. Scientists often develop software to help this type of research. In 2011, an international team from the Genomics Institute of the Novartis Research Foundation and The Scripps Research Institution, by studying databases, discovered a new group of compounds that may lead to a new generation of anti-malarial drugs capable of both preventing the disease and of alleviating symptoms when the disease is already present in an individual.

This discovery came after mining the data for groups of related compounds that showed activity in the liver. They found a cluster of compounds related to imidazolopiperazine that is showing great promise.

To learn more about how enzymes work, go to the hotlinks site, search for the title or ISBN, and click on Chapter 8: Section 8.1.

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8.2 Cell respiration

Understandings: ● Cell respiration involves the oxidation and reduction of electron carriers. ● Phosphorylation of molecules makes them less stable. ● In glycolysis, glucose is converted to pyruvate in the cytoplasm. ● Glycolysis gives a small net gain of ATP without the use of oxygen. ● In aerobic cell respiration pyruvate is decarboxylated and oxidized, and converted into acetyl compound and attached to coenzyme A to form acetyl coenzyme A in the link reaction.

● In the Krebs cycle, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers, liberating carbon dioxide.

● Energy released by oxidation reactions is carried to the cristae of the mitochondria by reduced NAD and FAD.

● Transfer of electrons between carriers in the electron transport chain in the membrane of the cristae is coupled to proton pumping.

● In chemiosmosis protons diffuse through ATP synthase to generate ATP. ● Oxygen is needed to bind with the free protons to form water to maintain the hydrogen gradient, resulting in the formation of water.

● The structure of the mitochondrion is adapted to the function it performs.

Applications and skills: ● Application: Electron tomography used to produce images of active mitochondria. ● Skill: Analysis of diagrams of the pathways of aerobic respiration to deduce where decarboxylation and oxidation reactions occur.

● Skill: Annotation of a diagram of a mitochondrion to indicate the adaptations to its functions.

Guidance ● The names of the intermediate compounds in glycolysis and the Krebs cycle are not required.

Oxidation and reductionIn Chapter 2 the general processes of respiration and photosynthesis were discussed. In this chapter we will consider these aspects of cellular metabolism in detail. It is important to recall that metabolism is the sum total of all the chemical reactions carried out by an organism. These reactions involve:

• catabolic pathways• anabolic pathways.

Catabolic pathways result in the breakdown of complex molecules into smaller molecules. Conversely, anabolic pathways result in the synthesis of more complex molecules from simpler ones. Cellular respiration is an example of a catabolic pathway. Photosynthesis is an example of an anabolic pathway. To understand these complex pathways, it is essential to understand two general types of chemical reactions: oxidation and reduction.

NATURE OF SCIENCE

Paradigm shift: the chemiosmotic theory led to a paradigm shift in the fi eld of bioenergetics.

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Oxidation and reduction can be compared using a table like Table 8.2.

Table 8.2 A comparison of oxidation and reduction

Oxidation Reduction

Loss of electrons Gain of electrons

Gain of oxygen Loss of oxygen

Loss of hydrogen Gain of hydrogen

Results in many C–O bonds Results in many C–H bonds

Results in a compound with lower potential energy

Results in a compound with higher potential energy

A useful way to remember the general meaning of oxidation and reduction is to think of the words ‘oil rig’.

• oil = oxidation is loss (of electrons)• rig = reduction is gain (of electrons).

These two reactions occur together during chemical reactions. Think of it in this way: one compound’s or element’s loss is another compound’s or element’s gain. This is shown by the following equation:

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy

In this equation, glucose is oxidized because electrons are transferred from it to oxygen. The protons follow the electrons to produce water. The oxygen atoms that occur in the oxygen molecules on the reactant side of the equation are reduced. Because of this reaction, there is a large drop in the potential energy of the compounds on the product side of the equation.

Because oxidation and reduction always occur together, these chemical reactions are referred to as redox reactions. When redox reactions take place, the reduced form of a molecule always has more potential energy that the oxidized form of the molecule. Redox reactions play a key role in the � ow of energy through living systems. This is because the electrons that are � owing from one molecule to the next are carrying energy with them. In a similar sort of way, the catabolic and anabolic pathways mentioned earlier are also closely associated with one another. You will see this association as you work through this chapter.

An overview of respirationSection 2.8 provided an introduction to the process of cellular respiration. Three aspects of cellular respiration were discussed:

• glycolysis • anaerobic respiration • aerobic respiration.

As you will recall, glycolysis occurs in the cytoplasm of the cell, produces small amounts of adenosine triphosphate (ATP) and ends with the product known as pyruvate. If no oxygen is available, the pyruvate enters into anaerobic respiration. This occurs in the cytoplasm and it does not result in any further production of ATP. The products of anaerobic respiration are lactate or ethanol and carbon dioxide. If oxygen is available, the pyruvate enters aerobic respiration in the mitochondria of the cell. This process results in the production of a large number of ATPs, carbon dioxide and water.

If asked in an exam to compare oxidation and reduction, using a table like Table 8.2 is an excellent way to structure the answer.

Benedict’s reagent is a chemical reagent commonly used to detect the presence of simple reducing sugars. It contains soluble blue copper (II) ions that may be reduced to copper (I) ions. These copper (I) ions are not soluble in water and will form a red–orange coloured precipitate. The colour of the precipitate indicates the quantity of simple sugar present: a green colour indicates a low sugar concentration and a red colour indicates a high sugar concentration. The electrons to reduce the Benedict’s reagent resulting in the colour change come from the oxidation of the sugar molecules.

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In this section, we will discuss the cellular respiration that involves glycolysis and the three stages of aerobic respiration:

• the link reaction• the Krebs cycle• oxidative phosphorylation.

GlycolysisThe word glycolysis means ‘sugar splitting’ and this pathway is thought to be one of the � rst biochemical pathways to evolve. It uses no oxygen and occurs in the cytosol of the cell. No organelles are required. The sugar splitting proceeds ef� ciently in aerobic and anaerobic environments. Glycolysis occurs in both prokaryotic and eukaryotic cells. A hexose, usually glucose, is split in the process. This splitting actually involves many steps but we can explain it effectively in three stages.

1 Two molecules of ATP are used to begin glycolysis. In the � rst reaction, the phosphates from the ATPs are added to glucose to form fructose-1,6-biphosphate, a process called phosphorylation. The importance of phosphorylation in this step is that it creates a less stable molecule.

6-carbon glucose

fructose-1, 6-bisphosphate

2 ATP

2 ADP

P P

2 The less stable 6-carbon phosphorylated fructose is split into two 3-carbon sugars called glyceraldehyde-3-phosphate (G3P). This splitting process is known as lysis.

fructose-1, 6-bisphosphate

glyceraldehyde-3-phosphate glyceraldehyde-3-phosphate

P

P P

P

Figure 8.7 The fi rst stage of glycolysis; the circles represent carbon atoms.

Figure 8.8 The second stage of glycolysis.

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3 Once the two G3P molecules are formed, they enter an oxidation phase involving ATP formation and the production of the reduced coenzyme NAD. Each G3P or triose phosphate molecule undergoes oxidation to form a reduced molecule of NAD+, which is NADH. As NADH is being formed, released energy is used to add an inorganic phosphate to the remaining 3-carbon compound. This results in a compound with two phosphate groups. Enzymes then remove the phosphate groups so that they can be added to adenosine diphosphate (ADP) to produce ATP. The end result is the formation of four molecules of ATP, two molecules of NADP, and two molecules of pyruvate. Pyruvate is the ionized form of pyruvic acid.

G3P

2

i2

4 ADP

2

pyruvate

4 ATP

2 NAD�

2 NADH

2

P

PP

P

Summary of glycolysis• Two ATPs are used to start the process.• A total of four ATPs are produced: a net gain of two ATPs.• Two molecules of NADH are produced.• The pathway involves substrate-level phosphorylation, lysis, oxidation, and ATP

formation.• The pathway occurs in the cytoplasm of the cell.• This metabolic pathway is controlled by enzymes. Whenever ATP levels in the cell are

high, feedback inhibition will block the � rst enzyme of the pathway. This will slow or stop the process.

• Two pyruvate molecules are present at the end of the pathway.

MitochondriaIt is inside the mitochondria and in the presence of oxygen that the remainder of cellular respiration occurs.

We discussed the structure of the mitochondrion in Chapter 1. You might like to refresh your memory of this because, as we discuss aerobic respiration, which occurs in the mitochondrion, we will refer to parts of this organelle.

Figure 8.9 The third stage of glycolysis.

Once pyruvate is obtained, the next pathway is determined by the presence of oxygen. If oxygen is present, pyruvate enters the mitochondria and aerobic respiration occurs. If oxygen is not present, anaerobic respiration occurs in the cytoplasm. In the latter case, pyruvate is converted to lactase in animals, and ethanol and carbon dioxide in plants.

The way of producing ATP in glycolysis is called substrate-level phosphorylation because the phosphate group is transferred directly to ADP from the original phosphate-bearing molecule.

To learn more about mitochondria, go to the hotlinks site, search for the title or ISBN, and click on Chapter 8: Section 8.2.

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The link reaction and the Krebs cycleOnce glycolysis has occurred and there is oxygen present, pyruvate enters the matrix of the mitochondria via active transport. Inside, pyruvate is decarboxylated, a reaction involving the loss of a carbon in the form of carbon dioxide, to form the 2-carbon acetyl group. This is the link reaction shown in Figure 8.10. The removed carbon is released as carbon dioxide, a waste gas. The acetyl group is then oxidized with the formation of reduced NAD+. Finally, the acetyl group combines with coenzyme A (CoA) to form acetyl CoA.

NAD�

CO2 NADH

coenzyme AC O

C O

O�

CH3

pyruvate transport proteinacetyl CoA

Cytosol Mitochondrion

mitochondrialmembrane

C O

S CoA

CH3

The link reaction is controlled by a system of enzymes. The greatest signi� cance of this reaction is that it produces acetyl CoA. Acetyl CoA may then enter the Krebs cycle to continue the aerobic respiration process.

So far in this discussion, the respiratory substrate has been a hexose. However, in reality, acetyl CoA can be produced from most carbohydrates and fats. Acetyl CoA can be synthesized into a lipid for storage purposes. This occurs when ATP levels in the cell are high.

If cellular ATP levels are low, the acetyl CoA enters the Krebs cycle. This cycle is also called the tricarboxylic acid cycle. It occurs in the matrix of the mitochondrion and is referred to as a cycle because it begins and ends with the same substance. This is a

This false-colour transmission electron micrograph (TEM) of a mitochondrion shows the internal structure. The matrix (blue) is permeated by the membranous cristae (pink).

Figure 8.10 The link reaction.

Decarboxylation is the removal of a carbon atom.

A coenzyme is a molecule that aids an enzyme in its action. Coenzymes usually act as electron donors or acceptors.

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characteristic of all cyclical pathways in metabolism. You do not need to remember the names of all the compounds formed in the Krebs cycle. However, it is important that you understand the overall process.

Let’s consider the cycle as a series of steps.

1 Acetyl CoA from the link reaction combines with a 4-carbon compound called oxaloacetate. The result is a 6-carbon compound called citrate.

oxaloacetate4C

�CoAacetylCoA

CoA

citrate6C

2 Citrate (a 6-carbon compound) is oxidized to form a 5-carbon compound. In this process, the carbon is released from the cell (after combining with oxygen) as carbon dioxide. While the 6-carbon compound is oxidized, NAD+ is reduced to form NADH.

4C 6C

5C

NADH

acetyl CoA

CoA

NAD�

CO2

3 The 5-carbon compound is oxidized and decarboxylated to form a 4-carbon compound. Again, the removed carbon combines with oxygen and is released as carbon dioxide. Another NAD+ is reduced to form NADH.

4C 6C

acetyl CoA

CoA

CO2

5C

4C

NADHNAD�

NADH

NAD�

CO2

Figure 8.11 Acetyl CoA combines with oxaloacetate to

form citrate.

Figure 8.12 Then a 5-carbon compound is formed.

Figure 8.13 Next, a 4-carbon compound is produced.

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4 The 4-carbon compound undergoes various changes resulting in several products. One product is another NADH. The coenzyme FAD is reduced to form FADH2. There is also a reduction of an ADP to form ATP. The 4-carbon compound is changed during these steps to re-form the starting compound of the cycle, oxaloacetate. The oxaloacetate may then begin the cycle again.

acetyl CoA

CoA

4Coxaloacetate 6C

CO2

5C

4C

NADHADP � Pi

ATP

FAD

NAD�

NADH

FADH2

NAD�

NADH

NAD�

CO2

It is important to remember that the Krebs cycle will run twice for each glucose molecule entering cellular respiration. This is because a glucose molecule forms two pyruvate molecules. Each pyruvate produces one acetyl CoA that enters the cycle. Look again at the complete Krebs cycle (Figure 8.14) and note the following products that result from the breakdown of one glucose molecule:

• 2 ATP molecules per molecule of glucose• 6 molecules of NADH (which allow energy storage and transfer)• 2 molecules of FADH2

• 4 molecules of carbon dioxide (released).

Figure 8.14 Finally, the 4-carbon compound is converted to oxaloacetate.

Two carbon dioxides are released for each glucose molecule during the link reaction. Four carbon dioxides are released during the Krebs cycle. This accounts for all six of the carbon atoms that were present in the initial glucose molecule. Glucose is completely catabolized and its original energy is now carried by NADH and FADH2 or is in ATP.

So far, only four ATPs have been gained, six are generated (four from glycolysis and two from the Krebs cycle) but two are used to start the process of glycolysis. Each of these ATPs has been produced by substrate-level phosphorylation.

Ultimately, the breakdown of each glucose molecule results in a net gain of 36 ATPs. Let’s now consider the phase of cellular respiration where most of the ATPs are produced. In this phase oxidative phosphorylation is the means by which the ATPs are produced.

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Electron transport chain and chemiosmosisThe electron transport chain is where most of the ATPs from glucose catabolism are produced. It is the � rst stage of cellular respiration where oxygen is actually needed, and it occurs within the mitochondrion. However, unlike the Krebs cycle, which occurred in the matrix, the electron transport chain occurs on the inner mitochondrial membrane and on the membranes of the cristae.

Embedded in the membranes involved are molecules that are easily reduced and oxidized. These carriers of electrons (energy) are close together and pass the electrons from one to another because of an energy gradient. Each carrier molecule has a slightly different electronegativity, and, therefore, a different attraction for electrons. Most of these carriers are proteins with haem groups and are referred to as cytochromes. One carrier is not a protein and is called coenzyme Q.

In this chain, electrons pass from one carrier to another because the receiving molecule has a higher electronegativity and, therefore, a stronger attraction for electrons. In the process of electron transport, small amounts of energy are released. The sources of the electrons that move down the electron transport chain are the coenzymes NADH and FADH2 from the previous stages of cellular respiration.

CHALLENGE YOURSELF1 Examine Figure 8.15.

acetyl CoA

CoA

4Coxaloacetate 6C

CO2

5C

4C

NADHADP � Pi

ATP

FAD

NAD�

NADH

FADH2

NAD�

NADH

NAD�

CO2

(a) Redraw the fi gure and place an arrow and the letter D at the two locations where decarboxylation occurs. On the same fi gure place an arrow and the letter O at the fi ve locations where oxidation of a cyclic intermediate compound occurs.

(b) How did you determine the two locations where decarboxylation occurred?(c) How did you determine the fi ve locations where oxidation occurred?

The haem group of the carrier is the part that is easily reduced and oxidized.

Figure 8.15

To learn more about the electron transport chain, go to the hotlinks site, search for the title or ISBN, and click on Chapter 8: Section 8.2.

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FMN

NADH

FADH2

Fe·S

Fe·S

Cyt b

Q

Fe·S

Cyt c1

Cyt c

Cyt aCyt a3

O20

reduction–oxidation reactions

free

ene

rgy

rela

tive

to O

2 /

k ca

l mol

�1

This protein carrier hasa flavin-containing group.

FMN:

This protein contains an iron–sulfur complex.

Carriers

Fe·S:

These are cytochromes (iron-containing proteins).

Cyt:

This is coenzyme Q, also calledubiquinone; it is not a protein.

Q:

10

20

30

40

50

5

15

25

35

45

55

12

In Figure 8.16 it is clear that the electrons are stepping down in potential energy as they pass from one carrier to another. It is important to note that:

• FADH2 enters the electron transport chain at a lower free energy level than NADH, thus FADH2 allows the production of two ATPs while NADH allows the production of three ATPs

• at the very end of the chain, the de-energized electrons combine with available oxygen.

Oxygen is the � nal electron acceptor because it has a very high electronegativity and, therefore, a strong attraction for electrons. When the electrons combine with the oxygen, so do two hydrogen ions from the aqueous surroundings. The result is water. Because of the way this water is formed, it is referred to as water of metabolism.

It is also clear from Figure 8.16 that there is a fairly large number of electron carriers. Because of the larger number, the electronegativity difference between adjacent carriers is not as great. This means that lower amounts of energy are lost at each exchange. These lower amounts of energy are effectively harnessed by the cell to carry out phosphorylation. If the amount of energy lost at each exchange was high, much of it could not be used and the cell could even be damaged.

Figure 8.16 The oxidation–reduction reactions of the electron transport chain. It is not necessary for you to remember all the names of the carriers.

The kangaroo rat from a desert region of the USA gets 90% of its daily water intake from water of metabolism. In contrast, a typical human only gets 12% of his or her daily water intake from metabolism.

No ATPs are produced directly by the electron transport chain. However, this chain is essential to chemiosmosis, which does produce the ATP.

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So energy is now available as a result of the electron transport chain. This is the energy that allows the addition of phosphate and energy to ADP to form ATP. The process by which this occurs is called chemiosmosis. Chemiosmosis involves the movement of protons (hydrogen ions) to provide energy so that phosphorylation can occur. Because this type of phosphorylation utilizes an electron transport chain, it is called oxidative phosphorylation. Substrate-level phosphorylation, mentioned in the earlier phases of cellular respiration, does not involve an electron transport chain.

Before continuing, it is essential to review the interior structure of the mitochondrion. In the process of cellular respiration, the structure of the mitochondrion is very closely linked to its function. The matrix is the area where the Krebs cycle occurs. The cristae provide a large surface area for the electron transport chain to function on. The membranes also provide a barrier, allowing proton accumulation on one side. Embedded in the membranes are the enzymes and other compounds necessary for the processes of the electron transport chain and chemiosmosis to occur.

The inner membranes of the mitochondria have numerous copies of an enzyme called ATP synthase. This enzyme uses the energy of an ion gradient to allow the phosphorylation of ADP. The ion gradient is created by a hydrogen ion concentration difference that occurs across the cristae membranes. Figure 8.17 shows oxidative phosphorylation.

H�

H�

H�

H�

H�

H�

H�H�

H�H�

H�

H�

H�

H�

H�

H�H�

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H�

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electroncarrier

Q

Cyt c

NAD�

NADH � H�

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FADH2 FAD

protein complexof electroncarriers

intermembranespace

mitochondrialmatrix

innermitochondrialmembrane

(carrying electrons from food)

12

P iADP �

Electron transport chain Chemiosmosis

2 H� � O2 H2O

In Figure 8.17, note the three labelled areas on the left: the intermembrane space, inner mitochondrial membrane, and mitochondrial matrix. Also, note that hydrogen ions are being pumped out of the matrix into the intermembrane space. The energy for this pumping action is provided by the electrons as they are de-energized moving through the electron transport chain. This creates the different hydrogen ion concentration on the two sides of the cristae membranes, mentioned above. With the higher hydrogen ion concentration in the intermembrane space, these ions begin to move passively through a channel in ATP synthase back into the mitochondrial matrix. As the hydrogen ions move through the ATP synthase channel, the enzyme harnesses the available energy, thus allowing the phosphorylation of ADP.

Using any diagram or photomicrograph of a mitochondrion, practise annotating where the processes of aerobic respiration occur.

Figure 8.17 Oxidative phosphorylation occurs at

the inner membranes of the mitochondria of a cell.

The pumping actions of the carriers result in a high

concentration of hydrogen ions in the intermembrane space.

This accumulation allows movement of the hydrogen

ions through the enzyme ATP synthase. The enzyme uses the energy from the hydrogen fl ow to couple phosphate with ADP

to produce ATP.

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Summary of ATP production in cellular respirationWe have now described the complete catabolism of one molecule of glucose. The raw materials were glucose and oxygen. Many enzymes, carriers, and other molecules are involved in the process. The products are carbon dioxide, water, and ATP. The ATPs are essential because they provide the energy by which life is maintained. We can describe the energy � ow in the general process as shown in Figure 8.18.

Glucose → NADH or FADH2 → Electron transport chain → Chemiosmosis → ATP

To account for the production of ATP in cellular respiration, let’s look at the three main processes, glycolysis, the Krebs cycle, and the electron transport chain, in a table.

Table 8.3 The processes of cellular respiration

Process ATP used ATP produced

Net ATP gain

Glycolysis 2 4 2

Krebs cycle 0 2 2

Electron transport chain and chemiosmosis 0 32 32

Total 2 38 36

Theoretically 36 ATPs are produced by cellular respiration, but in reality the number is closer to 30. This is thought to be because some hydrogen ions move back to the matrix without going through the ATP synthase channel. Also, some of the energy from hydrogen ion movement is used to transport pyruvate into the mitochondria. The 30 ATPs generated by cellular respiration account for approximately 30% of the energy present in the chemical bonds of glucose. The remainder of the energy is lost from the cell as heat.

A fi nal look at respiration and the mitochondrionCellular respiration is the process by which ATP is provided to the organism so that it can live. It is a very complex series of chemical reactions, most of which occur in the mitochondrion. Let’s end our discussion of this essential-to-life process by looking at a table showing the parts of the mitochondrion and how those parts allow cellular respiration.

Because of the hydrophobic region of the membrane, the hydrogen ions can only pass through the ATP synthase channel. Some poisons that affect metabolism act by establishing alternative pathways through the membrane, thus preventing ATP production.

Figure 8.18

Unfortunately, since the beginning of scientifi c experimentation, there have been instances of improper presentation of results. These improper presentations have included improper data reporting or even data fabrication. In the scientifi c community, this misconduct is extremely frowned upon. Discuss the possible repercussions to science research as a whole when such misconduct occurs. Continue your discussion to include reasons why scientists sometimes present improper or fabricated data.

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Table 8.4 The role of the mitochondrion in cellular respiration

Feature Role

Outer mitochondrial membrane

A membrane that separates the contents of the mitochondrion from the rest of the cell

Matrix An internal cytosol-like area that contains the enzymes for the link reaction and the Krebs cycle

Cristae Tubular regions surrounded by membranes that increase the surface area for oxidative phosphorylation

Inner mitochondrial membrane

A membrane that contains the carriers for the electron transport chain and ATP synthase for chemiosmosis

Space between inner and outer membranes

A reservoir for hydrogen ions (protons)

The overall equation for cellular respiration is:

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy (as heat or ATP)

All organisms need the ability to produce ATP for energy, so all organisms carry out respiration.

Exercises4 Using ideal ATP production numbers, how many ATPs would an individual generate if he or she

consumed only pyruvate and carried one pyruvate molecule through cellular respiration?

5 Striated or voluntary muscles that occur in humans generally have a larger number of mitochondria than other cell types. Why is this important?

6 If both NAD and FAD are reduced, which would allow the greater production of ATPs via the electron transport chain and chemiosmosis?

7 If an individual took a chemical that increased the ability of hydrogen ions to move through the phospholipid bilayer of the mitochondrial membranes, what would the effect be on ATP production?

8 If ATP synthase was not present in the cristae of a mitochondrion, what would be the effect?

CHALLENGE YOURSELF2 Annotate the diagram of a

mitochondrion provided in Figure 8.19 to indicate the adaptations that allow the mitochondrion to carry out its essential functions.

Figure 8.19

8.3 Photosynthesis

Understandings: ● Light-dependent reactions take place in the intermembrane space of the thylakoids. ● Light-independent reactions take place in the stroma. ● Reduced NADP and ATP are produced in the light-dependent reactions. ● Absorption of light by photosystems generates excited electrons. ● Photolysis of water generates electrons for use in the light-dependent reactions. ● Transfer of excited electrons occurs between carriers in thylakoid membranes. ● Excited electrons from Photosystem II are used to contribute to generate a proton gradient. ● ATP synthase in thylakoids generates ATP using the proton gradient. ● Excited electrons from Photosystem I are used to reduce NADP. ● In the light-independent reactions a carboxylase catalyses the carboxylation of ribulose bisphosphate.

● Glycerate 3-phosphate is reduced to triose phosphate using reduced NADP and ATP. ● Triose phosphate is used to regenerate RuBP and produce carbohydrates. ● Ribulose bisphosphate is reformed using ATP. ● The structure of the chloroplast is adapted to its function in photosynthesis.

NATURE OF SCIENCE

Developments in scientifi c research follow improvements in apparatus: sources of 14C and autoradiography enabled Calvin to elucidate the pathways of carbon fi xation.

To see an introduction to photosynthesis, go to the hotlinks site, search for the title or ISBN, and click on Chapter 8: Section 8.3.

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Applications and skills: ● Application: Calvin’s experiment to elucidate the carboxylation of RuBP. ● Skill: Annotation of a diagram to indicate the adaptations of a chloroplast to its function.

The chloroplastSome people refer to the chloroplast as a photosynthetic machine. They are not wrong. Unlike respiration, where some of the steps occur outside the mitochondrion, all of the photosynthetic process occurs within the chloroplast. Chloroplasts, along with mitochondria, represent possible evidence for the theory of endosymbiosis, discussed in Chapter 1, Section 1.5. Both organelles have an extra outer membrane (indicating a need for protection in a potentially hostile environment), their own DNA, and they are very near in size to a typical prokaryotic cell.

outer membrane

inner membrane

granum of severalthylakoids

1 thylakoid

stroma

The structure of the chloroplast was discussed in Chapter 1. You may want to return to that chapter for a brief refresher. Chloroplasts occur mostly within the cells of the photosynthetic factory of the plant, the leaves. However, some plants have chloroplasts in cells of other organs.

Figure 8.20 This false-colour TEM and drawing show the structure of a chloroplast. Can you fi nd as many parts in the TEM as are labelled in the drawing?

Plastids are a group of closely related organelles that occur in photosynthetic eukaryotic cells.There are three types of plastid that occur in plant cells:

• chloroplasts, which are green and involved in photosynthesis

• leucoplasts, which are white or ‘clear’ and function as energy storehouses

• chromoplasts, which are brightly coloured and synthesize and store large amounts of orange, red, or yellow pigments.

All these plastids develop from a common proplastid.

The overall process of photosynthesisDuring the discussion on respiration, we considered the means by which the cell breaks down chemical bonds in glucose to produce ATP. In this section, the discussion centres on the establishment of chemical bonds to produce organic compounds. Using light energy, the raw materials of photosynthesis are carbon dioxide and water. Many enzymes are involved to enable the formation of products that include glucose, more water, and oxygen. The overall equation is:

light 6 CO2 + 12 H2O → C6H12O6 + 6 H2O + 6 O2

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Water occurs on both sides because 12 molecules are consumed and 6 molecules are produced. Clearly, photosynthesis is essentially the reverse of respiration. Whereas respiration is, in general, a catabolic process, photosynthesis is, in general, an anabolic process. Photosynthesis occurs in organisms referred to as autotrophs. These organisms make their own food. Non-photosynthetic and non-chemosynthetic organisms are referred to as heterotrophs. They must obtain their food (which is necessary for energy) from other organisms.

Photosynthesis involves two major stages:

• the light-dependent reaction• the light-independent reaction.

The light-dependent reactionThe light-dependent reaction occurs in the thylakoids or grana of the chloroplast. A stack of thylakoids make up a granum (plural grana). Light supplies the energy for this reaction to occur. The ultimate source of light is the Sun. Even though plants may survive quite well when they receive light from sources other than the Sun, most plants on our planet rely on the Sun for the energy necessary to drive photosynthesis.

To absorb light, plants have special molecules called pigments. There are several different pigments in plants, and each effectively absorbs photons of light at different wavelengths. The two major groups are the chlorophylls and the carotenoids. These pigments are organized on the membranes of the thylakoids. The regions of organization are called photosystems and include:

• chlorophyll a molecules• accessory pigments• a protein matrix.

The reaction centre is the portion of the photosystem that contains:

• a pair of chlorophyll a molecules• a matrix of protein• a primary electron acceptor.

Bacteria that carry out photosynthesis have only one type of photosystem. However, modern-day plants have two types of photosystem. Each absorbs light most ef� ciently at a different wavelength. Photosystem I is most ef� cient at 700 nanometres (nm) and is labelled as P700. Photosystem II is most ef� cient at 680 nm and is labelled as P680. These two photosystems work together to bring about a non-cyclical electron transfer. Figure 8.21 shows the overall light-dependent reaction of photosynthesis involving non-cyclic photophosphorylation (non-cyclic electron � ow).

The numbered descriptions that follow refer to the numbered steps in Figure 8.21.

1 A photon of light is absorbed by a pigment in Photosystem II and is transferred to other pigment molecules until it reaches one of the chlorophyll a (P680) molecules in the reaction centre. The photon energy excites one of the chlorophyll a electrons to a higher energy state.

2 This electron is captured by the primary acceptor of the reaction centre.3 Water is split by an enzyme to produce electrons, hydrogen ions, and an oxygen

atom. This process is driven by the energy from light and is called photolysis. The electrons are supplied one by one to the chlorophyll a molecules of the reaction centre.

Light energy behaves as if it exists in discrete packets called photons. Shorter wavelengths of light have greater energy within their photons than longer wavelengths. Photons can transfer their energy upon interaction with other particles. This transfer of energy occurs many times in photosynthesis.

370



4 The excited electrons pass from the primary acceptor down an electron transport chain, losing energy at each exchange. The � rst of the three carriers is plastoquinone (PQ). The middle carrier is a cytochrome complex.

5 The energy lost from the electrons moving down the electron transport chain drives chemiosmosis (similar to that in respiration) to bring about phosphorylation of ADP to produce ATP.

6 A photon of light is absorbed by a pigment in Photosystem I. This energy is transferred through several accessory pigments until received by a chlorophyll a (P700) molecule. This results in an electron with a higher energy state being transferred to the primary electron acceptor. The de-energized electron from Photosystem II � lls the void left by the newly energized electron.

7 The electron with the higher energy state is then passed down a second electron transport chain that involves the carrier ferredoxin.

8 The enzyme NADP reductase catalyses the transfer of the electron from ferredoxin to the energy carrier NADP+. Two electrons are required to reduce NADP+ fully to NADPH.

NADPH and ATP are the � nal products of the light-dependent reaction. They supply chemical energy for the light-independent reaction to occur. The explanation above also shows the origin of the oxygen released by photosynthesizing plants (step 3). However, you need to know more detail about the production of ATP.

ATP production in photosynthesis is very similar to ATP production in respiration. Chemiosmosis allows the process of phosphorylation of ADP. In this case, the energy to drive chemiosmosis comes from light. As a result, we refer to the production of ATP in photosynthesis as photophosphorylation.

NADPreductase

photon

photon

water-splittingenzyme

2H�

NADP� � H�

H�

H2O

12� O2

(P680)reactioncentre

e�

electron carrier (PQ)

e�

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ns

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(P700)reactioncentre

excitedelectronacceptor

excitedelectronacceptor

electron carrier

ferredoxin (electron carrier)

cytochromecomplex

(electron carrier)

NADPH

Figure 8.21 The light-dependent reaction of photosynthesis.

371


A comparison of chemiosmosis in respiration and photosynthesis is shown in Table 8.5.

Table 8.5 A comparison of chemiosmosis

Respiration chemiosmosis Photosynthesis chemiosmosis

Involves an electron transport chain embedded in the membranes of the cristae

Involves an electron transport chain embedded in the membranes of the thylakoids

Energy is released when electrons are exchanged from one carrier to another

Energy is released when electrons are exchanged from one carrier to another

Released energy is used to pump hydrogen ions actively into the intermembrane space

Released energy is used to pump hydrogen ions actively into the thylakoid space

Hydrogen ions come from the matrix Hydrogen ions come from the stroma

Hydrogen ions diffuse back into the matrix through the channels of ATP synthase

Hydrogen ions diffuse back into the stroma through the channels of ATP synthase

ATP synthase catalyses the phosphorylation of ADP to form ATP

ATP synthase catalyses the photophosphorylation of ADP to form ATP

In both cases ATP synthase is embedded along with the carriers of the electron transport chain in the membranes involved.

In photosynthesis, the production of ATP occurs between Photosystem II and Photosystem I. Study Figure 8.22. Notice that the b6–f complex, which is a cytochrome complex, pumps the hydrogen ions into the thylakoid space. This increases the concentration of these ions, which then move passively through the ATP synthase channel, providing the energy to phosphorylate ADP.

photon

Stroma

H2O

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thylakoidmembrane

b6�f complex ATP synthase

PQ

Pi

Besides the non-cyclic electron pathway used to produce ATP by photophosphorylation, there is an alternative pathway involving a cyclic pathway. This cyclic pathway is discussed on the following page.

Figure 8.22 Chemiosmosis in a plant cell chloroplast.

372



The process just described is also known as non-cyclic photophosphorylation. There is another way the light-dependent reaction of photosynthesis may produce ATP. It is called cyclic photophosphorylation. It proceeds only when light is not a limiting factor and when there is an accumulation of NADPH in the chloroplast. In this process, light-energized electrons from Photosystem I fl ow back to the cytochrome complex of the electron transport chain between Photosystem II and Photosystem I (see Figure 8.21). From the cytochrome complex, the electrons move down the remaining electron transport chain allowing ATP production via chemiosmosis. These ATPs are then shuttled to the Calvin cycle so that it can proceed more rapidly.

Experiment to demonstrate electron transfer in chloroplasts *Safety alerts: Use safety goggles and lab aprons. Be cautious in the use of chemicals and glassware. Be careful of light sources as they may be hot. Dispose of chemicals as directed by your teacher. Wash your hands thoroughly upon completion of the activity.*

Electrons energized by light allow the production of ATP and NADPH in the light-dependent reaction of photosynthesis. In this experiment, DCPIP or DPIP (2,6-dichlorophenol-indophenol) will be used to replace NADP in the light-dependent reaction. DCPIP is a blue colour, but turns colourless when reduced. There is a direct relationship between the rate of photosynthesis and the change in colour from blue DCPIP to its reduced, clear form.

Full details with a worksheet of how to carry out this experiment are available on your eBook.

Worksheets

Data and observations

Table 8.6

Experimental cuvette

Start colour/absorbance

Finish colour/absorbance

Dark/unboiled

Light/unboiled

Light/boiled

Questions

1 What was the control in this experiment?

2 What product would have received the energized electrons if DCPIP had not been added?

3 What is the actual source of the electrons that reduced the DCPIP?

4 What was the effect of darkness on the reduction of DCPIP? Explain.

5 What was the effect of boiling the chloroplasts on this experiment? Explain.

The light-independent reactionThe light-independent reaction occurs within the stroma or cytosol-like region of the chloroplast.

The ATP and NADPH produced by the light-dependent reaction provide the energy and reducing power for the light-independent reaction to occur. Up to this point there has been no mention of carbohydrate production. Therefore, as we know glucose is a product of photosynthesis, the result of the light-independent reaction must be the production of glucose.

The light-independent reaction involves the Calvin cycle (see Figure 8.23), which occurs in the stroma of the chloroplast. Because it is a cycle, it begins and ends with the same substance. You should recall that a similar cyclic metabolic pathway occurred in respiration: the Krebs cycle.

373


6

carbon dioxide fixationrubisco

CO2 from the air

RuBP unstable intermediate6

6 ADP

ATP

4 P i

P i

P

6

10

12triosephosphate

triosephosphate

6

12glycerate-3-phosphate

2triosephosphate

sugar phosphatecomplex carbohydrates

�

�

�

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12 NADPH

12 ADP

12 P i12 NADP�

Refer to Figure 8.23 as you read about the steps of the Calvin cycle.

1 Ribulose bisphosphate (RuBP), a 5-carbon compound, binds to an incoming carbon dioxide molecule in a process called carbon � xation. This � xation is catalysed by an enzyme called RuBP carboxylase (rubisco). The result is an unstable 6-carbon compound.

2 The unstable 6-carbon compound breaks down into two 3-carbon compounds called glycerate 3-phosphate (GP).

3 The 3-carbon molecules of GP are acted upon by ATP and NADPH from the light-dependent reaction to form two other 3-carbon molecules called triose phosphate (TP). This is a reduction reaction.

4 The molecules of TP may then go in either of two directions. Some leave the cycle to become sugar phosphates that may become more complex carbohydrates. Most, however, continue in the cycle to reproduce the originating compound of the cycle, RuBP.

5 In order to regain RuBP molecules from TP, the cycle uses ATP.

In Figure 8.23, spheres are used to represent the carbon atoms so that they can be tracked through the cycle. The coef� cients (numbers) in front of each compound involved show what it takes to produce one molecule of a 6-carbon sugar. It is clear that for every 12 TP molecules, the cycle produces one 6-carbon sugar and six molecules of the 5-carbon compound RuBP. All the carbons are accounted for, and the law of conservation of mass is demonstrated. Also, it is important to note that 18 ATPs

Figure 8.23 The Calvin cycle. The numbered steps are

described in the text.

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and 12 NADPH are necessary to produce six RuBP molecules and one molecule of a 6-carbon sugar.

TP is the pivotal compound in the Calvin cycle. It may be used to produce simple sugars such as glucose, disaccharides such as sucrose, or polysaccharides such as cellulose or starch. However, most of it is used to regain the starting compound of the Calvin cycle, RuBP.

A team led by Melvin Calvin in the late 1940s and early 1950s worked on experiments to fi nd the early products of photosynthesis. The fi nal products were already well known. His research involved the creation of the now famous ‘lollipop’ apparatus. This specially designed apparatus was actually a fl attened fl ask that was used to house algal cells carrying out photosynthesis. By using radioactive tracer experiments with this apparatus, Calvin was successful in his studies. Discuss the role of creativity in scientifi c investigations as well as in art.

NATURE OF SCIENCE

As mentioned earlier, Calvin and his team worked out the details of carbon fi xation. In order to do this, Calvin used improvements in apparatus design and recent developments in radioactive tracers and autoradiography. Calvin devised the ‘lollipop’ apparatus. This is a thin, almost bulb-shaped, glass vessel with a supporting stem. The vessel was designed to mimic the shape of a leaf: thin and broad. He then carried out the following procedures.

• Chlorella (a type of green algae) was placed inside the lollipop.

• The algae cells were then exposed to 14C (radioactive carbon) and light.

• Samples of the Chlorella were then released from the apparatus at short time intervals.

• Each removed sample was immediately placed into a boiling methanol solution to denature the enzymes and stop the photosynthetic process.

• The compounds within the algae were then separated. Two-way paper chromatography was used for this separation. This process used one solvent to separate the fi rst set of components. Then the paper was turned and placed in a different solvent to obtain a further separation of components.

• The fi nal radioactive products were identifi ed using autoradiography.

Because Calvin carried out this procedure with algae released at different time intervals, he obtained different products at different times. This allowed him to sequence the steps of the overall process and to elucidate the pathways of carbon fi xation (the Calvin cycle).

Summary of photosynthesisIn summary, the process of photosynthesis includes the light-dependent and the light-independent reactions. The products of the light-dependent reaction are ATP and NADPH, which are needed to allow the light-independent reaction to proceed. Thus it is clear that light is needed for the light-independent reaction to occur, but not directly. A summary of the two reactions is shown in Figure 8.24.

O2

Light-dependent reactions

CO2

Light-independent reaction(Calvin cycle)

glucose

cellulose

stroma

TP

GPRuBP

ADP� P i

NADP�

NADPH starch(storage)

ATP

chloroplast

thylakoid

photosystem II

electron transport chain

photosystem I

H2Olight

Figure 8.24 A summary of the complete process of photosynthesis.

To learn more about photosynthesis, go to the hotlinks site, search for the title or ISBN, and click on Chapter 8: Section 8.3

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Note that NADP+ and ATP move back and forth in the chloroplast from the thylakoids to the stroma in their reduced and oxidized forms. A � nal summary of the two reactions is shown in Table 8.7.

Table 8.7 Photosynthesis

Light-dependent reaction Light-independent reaction

Occurs in the thylakoids Occurs in the stroma

Uses light energy to form ATP and NADPH Uses ATP and NADPH to form triose phosphate

Splits water in photolysis to provide replacement electrons and H+, and to release oxygen to the atmosphere

Returns ADP, inorganic phosphate, and NADP to the light-dependent reaction

Includes two electron transport chains and Photosystems I and II

Involves the Calvin cycle

The chloroplast and photosynthesisFrom the explanation of photosynthesis, it is clear how important the chloroplast is to the overall process. The structure of the chloroplast allows the light-dependent and light-independent reactions to proceed ef� ciently. In biology, the relationship of structure to function is a universal theme. The chloroplast and photosynthesis are no exception to this, as shown in Table 8.8.

Chloroplast structure Function allowed

Extensive membrane surface area of the thylakoids

Allows greater absorption of light by photosystems

Small space (lumen) within the thylakoids

Allows for faster accumulation of protons to create a concentration gradient

Stroma region similar to the cytosol of the cell

Allows an area for the enzymes necessary for the Calvin cycle to work in

Double membrane on the outside

Isolates the working parts and enzymes of the chloroplast from the surrounding cytosol

Table 8.8 The structure and function of a chloroplast

376



CHALLENGE YOURSELF3 Examine the diagram of a typical chloroplast (Figure 8.25). Answer the questions below the diagram

with the appropriate letter.A

D

B

C

(a) Which letter represents the stroma where all the enzymes necessary for the light-independent reaction occur?

(b) Which letter represents the double membrane that controls the entry and exit of materials for the chloroplast?

(c) What is the letter of the thylakoid that contains the photosystems?(d) Which letter represents a granum, which is where the light-dependent reaction occurs?(e) Which two letters represent the areas of the chloroplasts that cause the green colour of

chloroplasts? Why do these areas create this colour?(f) The chloroplasts within some plant cells can often be seen moving in a cyclical pattern near the

periphery of the cell. This is called cyclosis or cytoplasmic streaming. What might be the value of such movement to the process of photosynthesis?

Once you understand the details of photosynthesis, return to Section 2.8. Look again at the section about limiting factors of photosynthesis. You should now be able to explain more fully how temperature, light intensity, and carbon dioxide concentration may limit the rate of photosynthesis.

Exercises 9 Why do plants need both mitochondria and chloroplasts?

10 You have a leaf from each of two very different plants. One leaf has more pigments than the other. Which leaf would have the greater photosynthetic rate, assuming all affecting factors are equal? Why?

11 Explain the final products of the two photosystems involved in the light-dependent reaction of photosynthesis.

12 Many scientists state that the enzyme RuBP carboxylase (rubisco) is the most ubiquitous protein on Earth. Why is there a very good chance that this is true?

13 How are the products of the light-dependent reaction important to the light-independent reaction?

To become more confi dent in your understanding of the chloroplast, obtain some electron micrographs of chloroplasts from several different plants. On these micrographs, annotate names of structures and their functions.

Figure 8.25

Scientists in laboratories located around the world are presently working on the development of an artifi cial leaf. This laboratory-developed leaf would be capable of carrying out photosynthesis. The efforts of these research facilities may one day greatly increase the availability of food resources for the world’s hungry human populations.

The fi rst international conference dedicated to the creation of an artifi cial leaf was held in 2011. This conference addressed the goals of the Global Artifi cial Photosynthesis (GAP) project. Research centres are active in this area of study throughout the world, and the objective of this conference was to allow the researchers to share their discoveries. Energy capture, energy conversion and storage, and carbon fi xation using modifi ed and synthetic biological processes, were all addressed. From the GAP project, it is hoped that enhanced crop production, reduced atmospheric CO2 levels, and increased availability of fuels for heating and cooking may be realized.

377


Practice questions

1 Where is carbon dioxide produced in the mitochondrion?

A

B C

D

(Total 1 mark)

2 In the mitochondrial electron transport chain, what is the last electron acceptor?

A CO2

B H2O

C O2

D NAD(Total 1 mark)

3 Which of the following statements is true about enzymes?

A They are used up in the reactions they catalyse.

B Allosteric inhibitors bind to the active site.

C They lower the energy of activation for a reaction.

D They supply the energy of activation for a reaction.(Total 1 mark)

4 What is the role of NADH + H+ in aerobic cell respiration?

A To transfer hydrogen to the electron transport chain.

B To reduce intermediates in the Krebs cycle.

C To accept electrons from the electron transport chain.

D To combine with oxygen to produce water.(Total 1 mark)

5 What reaction, involving glycerate 3-phosphate, is part of the light-independent reactions of photosynthesis?

A Glycerate 3-phosphate is carboxylated using carbon dioxide.

B Two glycerate 3-phosphates are linked together to form one hexose phosphate.

C Glycerate 3-phosphate is reduced to triose phosphate.

D Five glycerate 3-phosphates are converted to three ribulose 5-phosphates.(Total 1 mark)

6 What is the advantage of having a small volume inside the thylakoids of the chloroplast?

A High proton concentrations are rapidly developed.

B High electron concentrations are rapidly developed.

C Photosynthetic pigments are highly concentrated.

D Enzymes of the Calvin cycle are highly concentrated.(Total 1 mark)

Practice questions

1 Where is carbon dioxide produced in the mitochondrion?

2 In the mitochondrial electron transport chain, what is the last electron acceptor?

A

B

3 Which of the following statements is

A

B

C

D

4 What is the role of NADH + H

A

B

C

D

5 What reaction, involving glycerate 3-phosphate, is part of the light-independent reactions of photosynthesis?

A

B

C

D

6 What is the advantage of having a small volume inside the thylakoids of the chloroplast?

A

B

C

D

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7 During glycolysis a hexose sugar is broken down to two pyruvate molecules. What is the correct sequence of stages?

A Phosphorylation → oxidation → lysis

B Oxidation → phosphorylation → lysis

C Phosphorylation → lysis → oxidation

D Lysis → oxidation → phosphorylation(Total 1 mark)

8 Which is correct for the non-competitive inhibition of enzymes?

Inhibitor resemblessubstrate

Inhibitor binds toactive site

A yes yes

B yes no

C no yes

D no no

(Total 1 mark)

9 Where are the light-dependent and light-independent reactions taking place in the diagram below?

I II

IIIIV

Light dependent Light independent

A I IV

B II III

C III II

D IV I

(Total 1 mark)

10 What is the link reaction in aerobic respiration?

A Pyruvate is carboxylated, acetyl reacts with coenzyme A, reducing NADH + H+

B Pyruvate is decarboxylated, acetyl reacts with coenzyme A, forming NADH + H+

C Pyruvate reacts with coenzyme A, forming NADH + H+

D Pyruvate is decarboxylated, reacting with coenzyme A, reducing NADH + H+

(Total 1 mark)

During glycolysis a hexose sugar is broken down to two pyruvate molecules. What is the correct

Total 1 mark)

Total 1 mark)

Total 1 mark)

Total 1 mark)

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08 and photosynthesis Metabolism, cell respiration, · 08 Metabolism, cell respiration, and photosynthesis M08_BIO_SB_IBDIP_9007_U08.indd 352 25/11/2014 16:34 The conformational changes