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8.1: Catabolism of Carbohydrates - Biology


Learning Objectives

  • Describe why glycolysis is not oxygen dependent
  • Define and describe the net yield of three-carbon molecules, ATP, and NADH from glycolysis
  • Explain how three-carbon pyruvate molecules are converted into two-carbon acetyl groups that can be funneled into the Krebs cycle.
  • Define and describe the net yield of CO2, GTP/ATP, FADH2, and NADH from the Krebs cycle
  • Explain how intermediate carbon molecules of the Krebs cycle can be used in a cell

Extensive enzyme pathways exist for breaking down carbohydrates to capture energy in ATP bonds. In addition, many catabolic pathways produce intermediate molecules that are also used as building blocks for anabolism. Understanding these processes is important for several reasons. First, because the main metabolic processes involved are common to a wide range of chemoheterotrophic organisms, we can learn a great deal about human metabolism by studying metabolism in more easily manipulated bacteria like E. coli. Second, because animal and human pathogens are also chemoheterotrophs, learning about the details of metabolism in these bacteria, including possible differences between bacterial and human pathways, is useful for the diagnosis of pathogens as well as for the discovery of antimicrobial therapies targeting specific pathogens. Last, learning specifically about the pathways involved in chemoheterotrophic metabolism also serves as a basis for comparing other more unusual metabolic strategies used by microbes. Although the chemical source of electrons initiating electron transfer is different between chemoheterorophs and chemoautotrophs, many similar processes are used in both types of organisms.

The typical example used to introduce concepts of metabolism to students is carbohydrate catabolism. For chemoheterotrophs, our examples of metabolism start with the catabolism of polysaccharides such as glycogen, starch, or cellulose. Enzymes such as amylase, which breaks down glycogen or starch, and cellulases, which break down cellulose, can cause the hydrolysis of glycosidic bonds between the glucose monomers in these polymers, releasing glucose for further catabolism.

Glycolysis

For bacteria, eukaryotes, and most archaea, glycolysis is the most common pathway for the catabolism of glucose; it produces energy, reduced electron carriers, and precursor molecules for cellular metabolism. Every living organism carries out some form of glycolysis, suggesting this mechanism is an ancient universal metabolic process. The process itself does not use oxygen; however, glycolysis can be coupled with additional metabolic processes that are either aerobic or anaerobic. Glycolysis takes place in the cytoplasm of prokaryotic and eukaryotic cells. It begins with a single six-carbon glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Pyruvate may be broken down further after glycolysis to harness more energy through aerobic or anaerobic respiration, but many organisms, including many microbes, may be unable to respire; for these organisms, glycolysis may be their only source of generating ATP.

The type of glycolysis found in animals and that is most common in microbes is the Embden-Meyerhof-Parnas (EMP) pathway, named after Gustav Embden (1874–1933), Otto Meyerhof (1884–1951), and Jakub Parnas (1884–1949). Glycolysis using the EMP pathway consists of two distinct phases (Figure (PageIndex{1})). The first part of the pathway, called the energy investment phase, uses energy from two ATP molecules to modify a glucose molecule so that the six-carbon sugar molecule can be split evenly into two phosphorylated three-carbon molecules called glyceraldehyde 3-phosphate (G3P). The second part of the pathway, called the energy payoff phase, extracts energy by oxidizing G3P to pyruvate, producing four ATP molecules and reducing two molecules of NAD+ to two molecules of NADH, using electrons that originated from glucose. (A discussion and illustration of the full EMP pathway with chemical structures and enzyme names appear in Appendix C.)

The ATP molecules produced during the energy payoff phase of glycolysis are formed by substrate-level phosphorylation (Figure (PageIndex{1})), one of two mechanisms for producing ATP. In substrate-level phosphorylation, a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP. During glycolysis, high-energy phosphate groups from the intermediate molecules are added to ADP to make ATP.

Overall, in this process of glycolysis, the net gain from the breakdown of a single glucose molecule is:

  • two ATP molecules
  • two NADH molecule, and
  • two pyruvate molecules.

Other Glycolytic Pathways

When we refer to glycolysis, unless otherwise indicated, we are referring to the EMP pathway used by animals and many bacteria. However, some prokaryotes use alternative glycolytic pathways. One important alternative is the Entner-Doudoroff (ED) pathway, named after its discoverers Nathan Entner and Michael Doudoroff (1911–1975). Although some bacteria, including the opportunistic gram-negative pathogen Pseudomonas aeruginosa, contain only the ED pathway for glycolysis, other bacteria, like E. coli, have the ability to use either the ED pathway or the EMP pathway.

A third type of glycolytic pathway that occurs in all cells, which is quite different from the previous two pathways, is the pentose phosphate pathway (PPP) also called the phosphogluconate pathway or the hexose monophosphate shunt. Evidence suggests that the PPP may be the most ancient universal glycolytic pathway. The intermediates from the PPP are used for the biosynthesis of nucleotides and amino acids. Therefore, this glycolytic pathway may be favored when the cell has need for nucleic acid and/or protein synthesis, respectively. A discussion and illustration of the complete ED pathway and PPP with chemical structures and enzyme names appear in Appendix C.

Exercise (PageIndex{1})

When might an organism use the ED pathway or the PPP for glycolysis?

Transition Reaction, Coenzyme A, and the Krebs Cycle

Glycolysis produces pyruvate, which can be further oxidized to capture more energy. For pyruvate to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group in the transition reaction, also called the bridge reaction (see Appendix C and Figure (PageIndex{3})). In the transition reaction, electrons are also transferred to NAD+ to form NADH. To proceed to the next phase of this metabolic process, the comparatively tiny two-carbon acetyl must be attached to a very large carrier compound called coenzyme A (CoA). The transition reaction occurs in the mitochondrial matrix of eukaryotes; in prokaryotes, it occurs in the cytoplasm because prokaryotes lack membrane-enclosed organelles.

The Krebs cycle transfers remaining electrons from the acetyl group produced during the transition reaction to electron carrier molecules, thus reducing them. The Krebs cycle also occurs in the cytoplasm of prokaryotes along with glycolysis and the transition reaction, but it takes place in the mitochondrial matrix of eukaryotic cells where the transition reaction also occurs. The Krebs cycle is named after its discoverer, British scientist Hans Adolf Krebs (1900–1981) and is also called the citric acid cycle, or the tricarboxylic acid cycle (TCA) because citric acid has three carboxyl groups in its structure. Unlike glycolysis, the Krebs cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step (Figure (PageIndex{4})). The eight steps of the cycle are a series of chemical reactions that capture the two-carbon acetyl group (the CoA carrier does not enter the Krebs cycle) from the transition reaction, which is added to a four-carbon intermediate in the Krebs cycle, producing the six-carbon intermediate citric acid (giving the alternate name for this cycle). As one turn of the cycle returns to the starting point of the four-carbon intermediate, the cycle produces two CO2 molecules, one ATP molecule (or an equivalent, such as guanosine triphosphate [GTP]) produced by substrate-level phosphorylation, and three molecules of NADH and one of FADH2. (A discussion and detailed illustration of the full Krebs cycle appear in Appendix C.)

Although many organisms use the Krebs cycle as described as part of glucose metabolism, several of the intermediate compounds in the Krebs cycle can be used in synthesizing a wide variety of important cellular molecules, including amino acids, chlorophylls, fatty acids, and nucleotides; therefore, the cycle is both anabolic and catabolic (Figure (PageIndex{5})).

Key Concepts and Summary

  • Glycolysis is the first step in the breakdown of glucose, resulting in the formation of ATP, which is produced by substrate-level phosphorylation; NADH; and two pyruvate molecules. Glycolysis does not use oxygen and is not oxygen dependent.
  • After glycolysis, a three-carbon pyruvate is decarboxylated to form a two-carbon acetyl group, coupled with the formation of NADH. The acetyl group is attached to a large carrier compound called coenzyme A.
  • After the transition step, coenzyme A transports the two-carbon acetyl to the Krebs cycle, where the two carbons enter the cycle. Per turn of the cycle, one acetyl group derived from glycolysis is further oxidized, producing three NADH molecules, one FADH2, and one ATP by substrate-level phosphorylation, and releasing two CO2molecules.
  • The Krebs cycle may be used for other purposes. Many of the intermediates are used to synthesize important cellular molecules, including amino acids, chlorophylls, fatty acids, and nucleotides.

Multiple Choice

During which of the following is ATP not made by substrate-level phosphorylation?

A. Embden-Meyerhof pathway
B. Transition reaction
C. Krebs cycle
D. Entner-Doudoroff pathway

B

Which of the following products is made during Embden-Meyerhof glycolysis?

A. NAD+
B. pyruvate
C. CO2
D. two-carbon acetyl

B

During the catabolism of glucose, which of the following is produced only in the Krebs cycle?

A. ATP
B. NADH
C. NADPH
D. FADH2

D

Which of the following is not a name for the cycle resulting in the conversion of a two-carbon acetyl to one ATP, two CO2, one FADH2, and three NADH molecules?

A. Krebs cycle
B. tricarboxylic acid cycle
C. Calvin cycle
D. citric acid cycle

C

True/False

Glycolysis requires oxygen or another inorganic final electron acceptor to proceed.

False

Fill in the Blank

Per turn of the Krebs cycle, one acetyl is oxidized, forming ____ CO2, ____ ATP, ____ NADH, and ____ FADH2molecules.

2; 1; 3; 1

Most commonly, glycolysis occurs by the ________ pathway.

Embden-Meyerhof

Short Answer

What is substrate-level phosphorylation? When does it occur during the breakdown of glucose to CO2?

Why is the Krebs cycle important in both catabolism and anabolism?

Critical Thinking

What would be the consequences to a cell of having a mutation that knocks out coenzyme A synthesis?


8.2 Catabolism of Carbohydrates

Extensive enzyme pathways exist for breaking down carbohydrate s to capture energy in ATP bonds. In addition, many catabolic pathways produce intermediate molecules that are also used as building blocks for anabolism . Understanding these processes is important for several reasons. First, because the main metabolic processes involved are common to a wide range of chemoheterotrophic organisms, we can learn a great deal about human metabolism by studying metabolism in more easily manipulated bacteria like E. coli. Second, because animal and human pathogens are also chemoheterotroph s, learning about the details of metabolism in these bacteria, including possible differences between bacterial and human pathways, is useful for the diagnosis of pathogens as well as for the discovery of antimicrobial therapies targeting specific pathogens. Last, learning specifically about the pathways involved in chemoheterotrophic metabolism also serves as a basis for comparing other more unusual metabolic strategies used by microbes. Although the chemical source of electrons initiating electron transfer is different between chemoheterorophs and chemoautotroph s, many similar processes are used in both types of organisms.

The typical example used to introduce concepts of metabolism to students is carbohydrate catabolism. For chemoheterotrophs, our examples of metabolism start with the catabolism of polysaccharides such as glycogen, starch, or cellulose. Enzymes such as amylase, which breaks down glycogen or starch, and cellulases, which break down cellulose, can cause the hydrolysis of glycosidic bonds between the glucose monomers in these polymers, releasing glucose for further catabolism.

Glycolysis

For bacteria, eukaryotes, and most archaea, glycolysis is the most common pathway for the catabolism of glucose it produces energy, reduced electron carriers, and precursor molecules for cellular metabolism. Every living organism carries out some form of glycolysis, suggesting this mechanism is an ancient universal metabolic process. The process itself does not use oxygen however, glycolysis can be coupled with additional metabolic processes that are either aerobic or anaerobic. Glycolysis takes place in the cytoplasm of prokaryotic and eukaryotic cells. It begins with a single six-carbon glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Pyruvate may be broken down further after glycolysis to harness more energy through aerobic or anaerobic respiration, but many organisms, including many microbes, may be unable to respire for these organisms, glycolysis may be their only source of generating ATP.

The type of glycolysis found in animals and that is most common in microbes is the Embden-Meyerhof-Parnas (EMP) pathway , named after Gustav Embden (1874–1933), Otto Meyerhof (1884–1951), and Jakub Parnas (1884–1949). Glycolysis using the EMP pathway consists of two distinct phases (Figure 8.10). The first part of the pathway, called the energy investment phase, uses energy from two ATP molecules to modify a glucose molecule so that the six-carbon sugar molecule can be split evenly into two phosphorylated three-carbon molecules called glyceraldehyde 3-phosphate (G3P). The second part of the pathway, called the energy payoff phase, extracts energy by oxidizing G3P to pyruvate, producing four ATP molecules and reducing two molecules of NAD + to two molecules of NADH, using electrons that originated from glucose. (A discussion and illustration of the full EMP pathway with chemical structures and enzyme names appear in Appendix C.)

The ATP molecules produced during the energy payoff phase of glycolysis are formed by substrate-level phosphorylation (Figure 8.11), one of two mechanisms for producing ATP. In substrate-level phosphorylation, a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP. During glycolysis, high-energy phosphate groups from the intermediate molecules are added to ADP to make ATP.

Overall, in this process of glycolysis, the net gain from the breakdown of a single glucose molecule is:

Other Glycolytic Pathways

When we refer to glycolysis, unless otherwise indicated, we are referring to the EMP pathway used by animals and many bacteria. However, some prokaryotes use alternative glycolytic pathways. One important alternative is the Entner-Doudoroff (ED) pathway , named after its discoverers Nathan Entner and Michael Doudoroff (1911–1975). Although some bacteria, including the opportunistic gram-negative pathogen Pseudomonas aeruginosa , contain only the ED pathway for glycolysis, other bacteria, like E. coli, have the ability to use either the ED pathway or the EMP pathway.

A third type of glycolytic pathway that occurs in all cells, which is quite different from the previous two pathways, is the pentose phosphate pathway ( PPP ) also called the phosphogluconate pathway or the hexose monophosphate shunt . Evidence suggests that the PPP may be the most ancient universal glycolytic pathway. The intermediates from the PPP are used for the biosynthesis of nucleotides and amino acids. Therefore, this glycolytic pathway may be favored when the cell has need for nucleic acid and/or protein synthesis, respectively. A discussion and illustration of the complete ED pathway and PPP with chemical structures and enzyme names appear in Appendix C.

Check Your Understanding

Transition Reaction, Coenzyme A, and the Krebs Cycle

Glycolysis produces pyruvate, which can be further oxidized to capture more energy. For pyruvate to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group in the transition reaction , also called the bridge reaction (see Appendix C and Figure 8.12). In the transition reaction, electrons are also transferred to NAD + to form NADH. To proceed to the next phase of this metabolic process, the comparatively tiny two-carbon acetyl must be attached to a very large carrier compound called coenzyme A (CoA) . The transition reaction occurs in the mitochondrial matrix of eukaryotes in prokaryotes, it occurs in the cytoplasm because prokaryotes lack membrane-enclosed organelles.

The Krebs cycle transfers remaining electrons from the acetyl group produced during the transition reaction to electron carrier molecules, thus reducing them. The Krebs cycle also occurs in the cytoplasm of prokaryotes along with glycolysis and the transition reaction, but it takes place in the mitochondrial matrix of eukaryotic cells where the transition reaction also occurs. The Krebs cycle is named after its discoverer, British scientist Hans Adolf Krebs (1900–1981) and is also called the citric acid cycle , or the tricarboxylic acid cycle (TCA) because citric acid has three carboxyl groups in its structure. Unlike glycolysis, the Krebs cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step (Figure 8.13). The eight steps of the cycle are a series of chemical reactions that capture the two-carbon acetyl group (the CoA carrier does not enter the Krebs cycle) from the transition reaction, which is added to a four-carbon intermediate in the Krebs cycle, producing the six-carbon intermediate citric acid (giving the alternate name for this cycle). As one turn of the cycle returns to the starting point of the four-carbon intermediate, the cycle produces two CO2 molecules, one ATP molecule (or an equivalent, such as guanosine triphosphate [GTP]) produced by substrate-level phosphorylation, and three molecules of NADH and one of FADH2. (A discussion and detailed illustration of the full Krebs cycle appear in Appendix C.)

Although many organisms use the Krebs cycle as described as part of glucose metabolism, several of the intermediate compounds in the Krebs cycle can be used in synthesizing a wide variety of important cellular molecules, including amino acids, chlorophylls, fatty acids, and nucleotides therefore, the cycle is both anabolic and catabolic (Figure 8.14).


Contents

Glycolysis, which means “sugar splitting,” is the initial process in the cellular respiration pathway. Glycolysis can be either an aerobic or anaerobic process. When oxygen is present, glycolysis continues along the aerobic respiration pathway. If oxygen is not present, then ATP production is restricted to anaerobic respiration. The location where glycolysis, aerobic or anaerobic, occurs is in the cytosol of the cell. In glycolysis, a six-carbon glucose molecule is split into two three-carbon molecules called pyruvate. These carbon molecules are oxidized into NADH and ATP. For the glucose molecule to oxidize into pyruvate, an input of ATP molecules is required. This is known as the investment phase, in which a total of two ATP molecules are consumed. At the end of glycolysis, the total yield of ATP is four molecules, but the net gain is two ATP molecules. Even though ATP is synthesized, the two ATP molecules produced are few compared to the second and third pathways, Krebs cycle and oxidative phosphorylation. [3]

Even if there is no oxygen present, glycolysis can continue to generate ATP. However, for glycolysis to continue to produce ATP, there must be NAD+ present, which is responsible for oxidizing glucose. This is achieved by recycling NADH back to NAD+. When NAD+ is reduced to NADH, the electrons from NADH are eventually transferred to a separate organic molecule, transforming NADH back to NAD+. This process of renewing the supply of NAD+ is called fermentation, which falls into two categories. [3]

Alcohol Fermentation Edit

In alcohol fermentation, when a glucose molecule is oxidized, ethanol (ethyl alcohol) and carbon dioxide are byproducts. The organic molecule that is responsible for renewing the NAD+ supply in this type of fermentation is the pyruvate from glycolysis. Each pyruvate releases a carbon dioxide molecule, turning into acetaldehyde. The acetaldehyde is then reduced by the NADH produced from glycolysis, forming the alcohol waste product, ethanol, and forming NAD+, thereby replenishing its supply for glycolysis to continue producing ATP. [3]

Lactic Acid Fermentation Edit

In lactic acid fermentation, each pyruvate molecule is directly reduced by NADH. The only byproduct from this type of fermentation is lactate. Lactic acid fermentation is used by human muscle cells as a means of generating ATP during strenuous exercise where oxygen consumption is higher than the supplied oxygen. As this process progresses, the surplus of lactate is brought to the liver, which converts it back to pyruvate. [3]

The Citric acid cycle (also known as the Krebs cycle) Edit

If oxygen is present, then following glycolysis, the two pyruvate molecules are brought into the mitochondrion itself to go through the Krebs cycle. In this cycle, the pyruvate molecules from glycolysis are further broken down to harness the remaining energy. Each pyruvate goes through a series of reactions that converts it to acetyl coenzyme A. From here, only the acetyl group participates in the Krebs cycle—in which it goes through a series of redox reactions, catalyzed by enzymes, to further harness the energy from the acetyl group. The energy from the acetyl group, in the form of electrons, is used to reduce NAD+ and FAD to NADH and FADH2, respectively. NADH and FADH2 contain the stored energy harnessed from the initial glucose molecule and is used in the electron transport chain where the bulk of the ATP is produced. [3]

Oxidative phosphorylation Edit

The last process in aerobic respiration is oxidative phosphorylation, also known as the electron transport chain. Here NADH and FADH2 deliver their electrons to oxygen and protons at the inner membranes of the mitochondrion, facilitating the production of ATP. Oxidative phosphorylation contributes the majority of the ATP produced, compared to glycolysis and the Krebs cycle. While the ATP count is glycolysis and the Krebs cycle is two ATP molecules, the electron transport chain contributes, at most, twenty-eight ATP molecules. A contributing factor is due to the energy potentials of NADH and FADH2. As they are brought from the initial process, glycolysis, to the electron transport chain, they unlock the energy stored in the relatively weak double bonds of O2. [2] A second contributing factor is that cristae, the inner membranes of mitochondria, increase the surface area and therefore the amount of proteins in the membrane that assist in the synthesis of ATP. Along the electron transport chain, there are separate compartments, each with their own concentration gradient of H + ions, which are the power source of ATP synthesis. To convert ADP to ATP, energy must be provided. That energy is provided by the H+ gradient. On one side of the membrane compartment, there is a high concentration of H+ ions compared to the other. The shuttling of H+ to one side of the membrane is driven by the exergonic flow of electrons throughout the membrane. These electrons are supplied by NADH and FADH2 as they transfer their potential energy. Once the H+ concentration gradient is established, a proton-motive force is established, which provides the energy to convert ADP to ATP. The H+ ions that were initially forced to one side of the mitochondrion membrane now naturally flow through a membrane protein called ATP synthase, a protein that converts ADP to ATP with the help of H+ ions. [3]


8.1 Overview of Photosynthesis

Photosynthesis is essential to all life on earth both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago.

Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis (Figure 8.2). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds hence, they are referred to as chemoautotrophs .

The importance of photosynthesis is not just that it can capture sunlight’s energy. A lizard sunning itself on a cold day can use the sun’s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer (Figure 8.3), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf.

Main Structures and Summary of Photosynthesis

Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure 8.4). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.

The following is the chemical equation for photosynthesis (Figure 8.5):

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved.

In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll . The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.

In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast . For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). Within the chloroplast are stacked, disc-shaped structures called thylakoids . Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen . As shown in Figure 8.6, a stack of thylakoids is called a granum , and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis).

Visual Connection

On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

The Two Parts of Photosynthesis

Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light independent-reactions. In the light-dependent reactions , energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions , the chemical energy harvested during the light-dependent reactions drive the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. Figure 8.7 illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.

Link to Learning

Click the link to learn more about photosynthesis.

Everyday Connection

Photosynthesis at the Grocery Store

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle (Figure 8.8) contains hundreds, if not thousands, of different products for customers to buy and consume.

Although there is a large variety, each item links back to photosynthesis. Meats and dairy link, because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from starchy grains, which are the seeds of photosynthesis-dependent plants. What about desserts and drinks? All of these products contain sugar—sucrose is a plant product, a disaccharide, a carbohydrate molecule, which is built directly from photosynthesis. Moreover, many items are less obviously derived from plants: For instance, paper goods are generally plant products, and many plastics (abundant as products and packaging) are derived from algae. Virtually every spice and flavoring in the spice aisle was produced by a plant as a leaf, root, bark, flower, fruit, or stem. Ultimately, photosynthesis connects to every meal and every food a person consumes.

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    8.1: Introduction to Glycolysis - Energy Storage

    • Contributed by Chris Schaller
    • Professor (Chemistry) at College of Saint Benedict/Saint John's University

    Glycolysis is a biochemical pathway in which glucose is consumed and ATP is produced. This pathway is an example of catabolism, in which larger molecules are broken down in the cell to make smaller ones. The opposite kind of pathway is anabolism, in which larger molecules are synthesized from smaller ones in the cell.

    From the biologist's perspective, catabolism is associated with the breakdown of larger molecules to release energy. For example, in grade school science, you may have learned that most organisms derive their energy from the breakdown of carbohydrates. You may have seen the process of respiration expressed through the following equation of reaction:

    That idea gives rise to the slightly misleading paradigm that energy is stored in chemical bonds. The idea goes that, for example, when the single sugar molecule represented by the formula, C6H12O6 , is broken down to make six carbon dioxide molecules, the energy from all of those broken bonds is released for the benefit of the organism.

    You may also have learned about another important energy-storage molecule, ATP. Like the breakdown of sugar, the breakdown of ATP is used to power other processes in the cell. That process might be expressed in the following expression:

    Once again, this can be considered a breaking-down process, in which an ATP molecule is split into a smaller ADP molecule and an inorganic phosphate.

    From the chemist's perspective, it is wrong to suggest that energy is stored in chemical bonds. Instead, energy is released when bonds are formed. This chemical perspective is more than an idea it represents physical reality. It can be demonstrated in a number of ways that energy is released when bonds are made, and energy must be used up in order to break bonds apparently, this situation is the opposite of the biological viewpoint.

    Some authors have suggested that this apparent disagreement is something like a difference of perspective. Think of an observer standing on the shore of the ocean, watching a ship sail away. From the observer's viewpoint, the ship eventually sinks below the ocean. After a while its hull is no longer visible only its masts remain, and finally they, too, slip down and are gone. To a passenger on the ship, however, the ship is still sailing along on the surface of the ocean. Biologists and chemists think about bonding differently because they are looking at it from a different viewpoint.

    Biologists say that energy is stored in chemical bonds because thinking about things that way is useful to them. It is useful to think of catabolic processes, such as the breakdown of sugars, as energy-releasing. It is useful to think of anabolic processes, such as photosynthesis or the synthesis of complex natural products, as energy-intensive.

    Biologists are looking at things purely from the point of view of the biomolecule. Either it is breaking down into smaller pieces (its bonds are breaking), releasing energy, or else it is getting built up into something bigger (its bonds are being made), costing energy.

    In a very loose sense, it is as if the reaction of carbohydrate breakdown is pared down to:

    And the reaction of ATP breakdown is abbreviated to:

    In other words, part of the reaction is ignored. That viewpoint allows a focus on the biomolecule, but it neglects some important things. For example, in the breakdown of carbohydrates, it isn't the C-C bond breaking of the carbohydrates that is the source of energy. It is the formation of strong, new O-H and C=O bonds, and other, more subtle changes, that release the energy.

    As always, we get more insight into a reaction by looking at the structural formulae in the equation, rather than condensed formulae. This way, we can actually see what bonds are being made and broken.

    Figure (PageIndex<1>): An equation of reaction for respiration, or the combustion of glucose, with structures.

    The case of ATP is a little different. The bonds made and broken are pretty much the same in the breakdown of ATP loosely, we just trade in one P-O bond for another. This case is more complicated, but the simplest explanation is that ATP cleavage relieves repulsion between the multiple negative charges in the ATP molecule. Energy decreases in the resulting molecules, and the rest of the energy that used to be in the reactants is released.

    Figure (PageIndex<2>): An equation of reaction for the hydrolysis of ATP, with structures.

    In the reverse, when ADP is phosphorylated to make ATP, the system goes up in energy (the system just means everything in the reaction it is everything on one side of the arrow or the other). That energy, however, is not really stored in any chemical bonds. It is distributed throughout the system, for example, in the motions of all of those atoms. The bonds may stretch, getting longer and shorter, but in addition the groups on the ends of the bonds can spin, and the molecules can tumble and zip around through space. There are lots of ways to distribute that energy throughout that entire collection of atoms it isn't forced to sit in that one bond that was newly formed between two atoms.

    So, although the idea of energy being stored in chemical bonds may be very useful in the biology classroom, it is only going to get in your way in the chemistry classroom. You need to be able to take off your biologist's hat and put on your chemist's lab coat when you need it.

    Our economy is driven largely by the consumption of fossil fuels, such as heptane. Given the following reaction for the breakdown of heptane:

    Use the table of bond strengths to determine how much energy is released when a mol of heptane is consumed.

    1. Start by determining the energy needed to break bonds.
    2. Determine the energy released when new bonds are made.
    3. Determine the overall energy change.

    C-C 6 x 80 kcal/mol = 480 kcal/mol

    C-H 16 x 100 kcal/mol = 1,600 kcal/mol

    O=O 7 x 120 kcal/mol = 840 kcal/mol

    C=O 14 x (- 190 kcal/mol) = - 2,660 kcal/mol

    O-H 16 x (- 110 kcal/mol) = -1,760 kcal/mol

    Overall: 1,240 - 4,420 kcal/mol = -1,500 kcal/mol

    Use the table of bond strengths to determine how much energy is released when a mol of octane is consumed.

    C-C 7 x 80 kcal/mol = 560 kcal/mol

    C-H 18 x 100 kcal/mol = 1,800 kcal/mol

    O=O 12.5 x 120 kcal/mol = 1,500 kcal/mol

    C=O 16 x (- 190 kcal/mol) = - 3,040 kcal/mol

    O-H 18 x (- 110 kcal/mol) = -1,980 kcal/mol

    Overall: 3,860 - 5,020 kcal/mol = -1,160 kcal/mol

    Given an approximate C-O bond strength of 85 kcal/mol, use the table of bond strengths to determine how much energy is released when a mol of glucose is consumed.

    C-C 6 x 80 kcal/mol = 480 kcal/mol

    C-H 7 x 100 kcal/mol = 700 kcal/mol

    C-O 7 x 85 kcal/mol = 595 kcal/mol

    O-H 5 x 110 kcal/mol = 550 kcal/mol

    O=O 6 x 120 kcal/mol = 840 kcal/mol

    C=O 12 x (- 190 kcal/mol) = - 2,280 kcal/mol

    O-H 12 x (- 110 kcal/mol) = -1,320 kcal/mol

    Overall: 3,165 - 3,600 kcal/mol = -435 kcal/mol

    Provide a mechanism for the hydrolysis of ATP to ADP.

    Suggest a possible role for magnesium ion in the hydrolysis of ATP.

    In the mechanism for hydrolysis, water acts as a nucleophile and ATP acts as an electrophile. That's a problem because ATP is negatively charged. It will not attract electrons very easily. By binding to magnesium ion (Mg 2+ ), the charge on the ATP will be lowered, accelerating the reaction with water.


    Molecules to metabolism 2.1

    The structure of living organisms can be partly explained by the molecules which they are made from. Live is based on carbon because the way in which carbon atoms form covalent bonds is central to the structure of the molecules which make up the bodies of all animals, plants and bacteria.

    Key concepts

    Learn and test your biological vocabulary for topic 2.1 molecules to metabolism using these flashcards.

    Essentials - quick revision through the whole topic

    These slides summarise the essential understanding and skills in this topic.
    They contain short explanations in text and images - good revision for all students.

    Read the slides and look up any words or details you find difficult to understand.

    Exam style question about molecule structure.

    The ability to draw monosaccharide molecules is an important skill in this topic.

    Answer the question below, on a piece of paper, then check your answer against the model answer below.

    The image shows a diagram of deoxyribose which is a molecule made from five carbon molecules.

    Outline the structure of deoxyribose and how it is different from the structure of &alphaD-glucose.
    (A labelled diagram may be used in the answer). [4]

    Click the + icon to see a model answer.

    Model answer

    Outline how the structure of deoxyribose is different for the structure of &alphaD-glucose.
    (A labelled diagram may be used in the answer). [4]

    This diagram shows the structure of &alphaD-glucose.

    There is an OH group on the number 2 carbon in glucose but not in deoxyribose

    Deoxyribose has five carbon atoms but glucose has six carbon molecules .

    The ring arrangement in glucose has a hexagonal shape whereas in ribose it has five points, like a pentagon.

    Summary list for 2.1 Molecules to metabolism

    • Molecular biology is explaining biological processes in terms of the chemicals involved.
    • There is a diversity of Carbon based compounds in living things because carbon atoms can form four covalent bonds.
      e.g. carbohydrates, lipids, proteins & nucleic acids.
    • All the enzyme-catalysed reactions in a cell make up its metabolism. There are two types:
      • Anabolism: forming macromolecules from monomers by condensation.
      • Catabolism: breaking complex macromolecules into simpler molecules by hydrolysis.

      Skills in drawing molecules

      • Draw diagrams of:
        • &alphaD-glucose & &betaD-glucose.
        • D-ribose.
        • a fatty acid.
        • an amino acid with generalised R-group.
        • monosaccharides.
        • disaccharides.
        • lipids (triglycerides, phospholipids and steroids)
        • amino acids.
        • polypeptides and peptide bonds.

        Mindmaps

        This diagram summaries the main sections of topic 2.1.
        Test if you can draw something like these concept maps from memory.
        Even better, design your own.

        Test yourself - multiple choice questions

        This is a self marking quiz containing questions covering the topic outlined above.
        Try the questions to check your understanding.

        2.1 Molecules to metabolism 1 / 1

        Which of the following processes could be described as catabolism?

        The digestion of starch into maltose in digestion.

        The production of a large DNA molecule from nucleotide monomers.

        The synthesis of glycogen in the liver from glucose.

        The production of polypeptides from amino acids by the action of enzymes.

        Anabolism is building up of large complex molecules from smaller simple units (Hint to remember: anacondas are long snakes).

        Catabolism is the breakdown of large complex molecules into smaller ones.


        8.1: Catabolism of Carbohydrates - Biology

        Glucose, glycogen, and ATP concentrations were measured in the peripheral and central layers of the sebaceous glands as well as in the epidermis. Both carbohydrates exhibited a decreasing gradient of concentration from the periphery to the center of the glands. No differential distribution of ATP content was found in the sebaceous glands. The periphery of the glands contained 8 m moles glucose, 22 m moles glycogen, and 10 m moles ATP per kg dry weight tissue. The glucose and ATP concentrations were comparable to those in epidermis, whereas on the basis of lipid-free dry weight the amount of glycogen at the periphery was 6.3 times that of epidermis. The total NADP concentration in sebaceous glands was 0.5 m moles/kg dry weight, 78 percent of which was in the reduced form the total NAD concentration was 1.4 m moles/kg dry weight, 34 percent of which was in the reduced state. Sebaceous glands contained 3 times more NADP nucleotides than epidermis. The ratios of the NAD nucleotides to NADP nucleotides were 3: 1 in the sebaceous glands and 8: 1 in the epidermis. Of the 29 enzymes assayed, the most prominent in the sebaceous glands were α-glycerophosphate dehydrogenase, malic enzyme, alanine amino-transferase, glucose-6-phosphate dehydrogenase, and phosphorylase. Enzyme analyses also demonstrated increased contributions of the pentose phosphate pathway and tricarboxylic acid cycle, a significant role for glycogen metabolism and active glycolysis. The high activities of α-glycerophosphate dehydrogenase and triosephosphate isomerase suggest that triosephosphate is being shifted into α-glycerophosphate for the acylglycerol formation. The high aminotransferase activities suggested an important contribution of amino acid metabolism to the sebaceous glands. The conspicuously high activity of alanine aminotrans-ferase indicates a tissue potential to convert amino acids to pyruvate in sebaceous glands. High malic enzyme and malate dehydrogenase activities suggest a malate shunt, by means of which an ATP-driven transhydrogenation between NADP and cytoplasmic NADH occurs to produce NADPH. Isocitrate dehydrogenase was the most active among the NADP-dependent enzymes and appeared to participate in NADPH production in the sebaceous glands. Acid phosphatase activity was 5 to 7 times greated in the central portion than in the peripheral layers of the sebaceous glands. Three β-glycosidases were distributed more in the center than in the periphery of the glands. High acid phosphatase activity in the central portion of sebaceous glands may reflect its involvement in holocrine secretion.


        Glycogenesis

        Glycogenesis is the process of glycogen synthesis. Glycogen is a polymer of glucose residues that is linked by α-1,4 and α-1,6 glycosidic bonds. Therefore, it is the glucose storage molecule in the hepatocytes and skeletal muscle cells. The total amount of glycogen storage among these two tissues depends on the mass of the hepatocytes and skeletal muscle cells. Glycogen amount per mass unit of the liver is higher than the skeletal muscle however, since in body the total mass of the skeletal


        38 Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

        By the end of this section, you will be able to do the following:

        • Discuss the ways in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways
        • Explain why metabolic pathways are not considered closed systems

        You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume organic compounds other than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (see (Figure)). Metabolic pathways should be thought of as porous and interconnecting—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems! Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways.

        Connections of Other Sugars to Glucose Metabolism

        Glycogen , a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is stored as glycogen in both liver and muscle cells. The glycogen will be hydrolyzed into glucose 1-phosphate monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into glucose-1-phosphate (G-1-P) and converted into glucose-6-phosphate (G-6-P) in both muscle and liver cells, and this product enters the glycolytic pathway.

        Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. Fructose is one of the three “dietary” monosaccharides, along with glucose and galactose (part of the milk sugar dissacharide lactose), which are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.

        Connections of Proteins to Glucose Metabolism

        Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism ((Figure)). It is very important to note that each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals, produced from the nitrogen originating in amino acids, and it leaves the body in urine. It should be noted that amino acids can be synthesized from the intermediates and reactants in the cellular respiration cycle.


        Connections of Lipid and Glucose Metabolisms

        The lipids connected to the glucose pathway include cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl groups and proceeds in only one direction. The process cannot be reversed.

        Triglycerides—made from the bonding of glycerol and three fatty acids—are a form of long-term energy storage in animals. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated to glycerol-3-phosphate, which continues through glycolysis. Fatty acids are catabolized in a process called beta-oxidation, which takes place in the matrix of the mitochondria and converts their fatty acid chains into two-carbon units of acetyl groups. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle.


        Pathways of Photosynthesis and Cellular Metabolism The processes of photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a “soup” of nutrients—possibly on the surface of some porous clays, perhaps in warm marine environments. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived as they shifted the nutrients into the components of their own bodies. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access.

        An early form of photosynthesis developed that harnessed the sun’s energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Another type of anoxygenic photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions instead, it used materials such as hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced but that these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the “primeval soup.” A later form of photosynthesis used water as a source of electrons and hydrogen and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a “rust” layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation.

        Section Summary

        The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate.


        Watch the video: Carbohydrate Metabolism (January 2022).