1. Chemotropic Energy:glycolysis and fermentation
Chapter 9
Chemotropic Energy:glycolysis and fermentation

2. Chemotrophic Energy Metabolism: Glycolysis and Fermentation
Cells cannot survive without a source of energy or a source of chemical building blocks
In many organisms these requirements are related
Chemotrophs obtain energy from the food they engulf or ingest 2

3. Metabolic Pathways
To accomplish any task, a cell requires a series of reactions occurring in an ordered sequence
This requires many different enzymes to catalyze each individual reaction
All the chemical reactions in a cell are referred to as its metabolism, which consists of many specific metabolic pathways 3

4. General types of metabolic pathways
Anabolic pathways synthesize cellular components, often polymers such as starch and glycogen
They usually involve an increase in order and a decrease in entropy
So, they are endergonic (energy-requiring)

5. General types of metabolic pathways (continued)
Catabolic pathways are involved in the breakdown of cellular constituents, such as the hydrolysis of glucose
These degradative pathways typically involve a decrease in order and increase in entropy
So, they are exergonic, energy-liberating reactions

6. Catabolic pathways
Catabolic pathways involve the production of metabolites, small organic building blocks
However, the reactions are not just the reversal of an anabolic pathway; enzymes and intermediates may be different
Catabolism can be carried out in the presence (aerobic) or absence (anaerobic) of oxygen

7. ATP: The Universal Energy Coupler
The efficient linking (coupling) of energy-yielding and energy-requiring processes is crucial to cell function
The most common energy intermediate is adenosine triphosphate (ATP)
It is the primary (but not the only) energy currency of the biological world

8. Other high-energy molecules
High-energy molecules such as GTP and creatine phosphate store chemical energy that can be converted to ATP
Chemical energy is also stored as reduced coenzymes such as NADH

9. ATP Contains Two Energy-Rich Phosphoanhydride Bonds
ATP contains the aromatic base, adenine, the five-carbon sugar, ribose, and a chain of three phosphate groups
The phosphate groups are linked by phosphoanhydride bonds
Adenine linked to ribose is adenosine

10. Forms of adenosine
Adenosine occurs in cells in the unphosphorylated form
It can also be phosphorylated up to three times, called adenosine monophosphate (AMP), adenosine diphosphate (ADP), or adenosine triphosphate (ATP)
Hydrolysis of ATP releases energy (DG = –7.3kcal/mol)

11. Figure 9-1

12. Figure 9-1A

13. Figure 9-1B

14. Phosphoanhydride bonds
Phosphoanhydride bonds are referred to as energy-rich bonds
This term is a shorthand way of saying that free energy is released when the bond is hydrolyzed
The energy is a feature of the reaction the molecule is involved in, and not of a particular bond in the molecule

15. ATP Hydrolysis Is Highly Exergonic Because of Charge Repulsion and Resonance Stabilization
Hydrolysis of ATP to ADP and Pi is exergonic because of
Charge repulsion between the adjacent negatively charged phosphate groups
Resonance stabilization of both products of hydrolysis
Increased entropy and solubility of the products of hydrolysis

16. Charge repulsion
The three phosphate groups of ATP each bear at least one negative charge
These negative charges tend to repel each other, straining the covalent bond linking them together
This is called charge repulsion

17. Resonance stabilization
Though the carboxylate group is shown with one C=O and one C–O, there is one electron pair that is delocalized
The electron pair is equally distributed over both of the C bonds to oxygen, so that carboxylate group is an average of the two bonds
This is called a resonance hybrid and the lowest energy configuration is resonance-stabilized

18. Figure 9-2A

19. Resonance stabilization (continued)
The phosphate ion is resonance stabilized too
When a phosphoester bond is formed beween a phosphate and an alcohol group, the extra electrons are only delocalized over three oxygens instead of four
The resulting molecule is less resonance stabilized and thus has higher energy

20. Resonance stabilization in anhydride bonds
When phosphate groups participate in anhydride bond formation, they are also less resonance stabilized and so are higher energy
In this way resonance stabilization contributes to the highly exergonic nature of ATP hydrolysis

21. Increase in entropy
As a phosphate group is removed from ATP it is no longer fixed in position
The spatial randomization of ADP and Pi after hydrolysis decreases their free energy and makes the reaction more exergonic
The ADP and Pi also become more soluble and their increased interactions with water molecules also decreases their free energy

22. ATP and ADP are higher-energy than AMP.
So, ATP and ADP are both higher-energy compounds than is AMP

23. DGo is an underestimate
Because DGo from equation 9-1 is based on equal concentrations of ADP and ATP (1M each), it is an underestimate
This is because under most biological conditions, the concentration of ATP is much larger

24. ATP Is an Important Intermediate in Cellular Energy Metabolism
ATP occupies an intermediate position in the overall spectrum of energy-rich phosphorylated compounds in the cell
Under standard conditions, a compound can phosphorylate a less energy-rich compound, but not a more energy-rich compound

25. ATP is intermediate among the energy-rich phosphorylated compounds in the cell
ATP can be formed from ADP by the transfer of a phosphate group from PEP, but not from glucose-6-phosphate
The reverse is also true; ATP can phosphorylate glucose but not pyruvate

26. Figure 9-3

27. DGotransfer
DGotransfer refers to the standard free energy change that accompanies the transfer of a phosphate from a donor to an acceptor .

28. Group transfer reactions
Reactions that involve the movement of a chemical group from one molecule to another are called group transfer reactions
The phosphate group is one of the most frequently transferred, especially in energy metabolism
It is important that ATP/ADP occupy an intermediate position in terms of bond energy

29. ATP/ADP: intermediate in terms of bond energy
ATP can serve as a phosphate donor in some reactions
Its dephosphorylated form, ADP, can serve as an acceptor in other reactions
That is because there are compounds both above and below the pair in energy

30. ATP/ADP
The ATP/ADP pair represent a reversible means of conserving, transferring, and releasing energy within the cell
As catabolic processes occur in the cell, the energy liberated is used to produce ATP from ADP
Then energy released from hydrolysis of ATP is used for essential processes of life that use energy

31. Chemotrophic Energy Metabolism
Chemotrophic energy metabolism describes the reactions and pathways by which cells catabolize nutrients and conserve the released energy in the form of ATP
Much of chemotrophic energy metabolism involves energy-yielding oxidative reactions (oxidation)

32. Biological Oxidations Usually Involve the Removal of Both Electrons and Protons and Are Highly Exergonic
Substances that are energy sources for cells are oxidizable compounds, the oxidation of which is highly exergonic
Oxidation is the removal of electrons .

33. Oxidation in biological chemistry
In biological systems oxidation involves removal of hydrogen ions (protons) in addition to electrons .
This process is also a dehydrogenation

34. Transfer of electrons
Because oxidation reactions involve the removal (in effect) of two hydrogen atoms, many of the enzymes involved are called dehydrogenases
The electrons must be transferred to another molecule, which is reduced
Reduction, the addition of electrons, is an endergonic process

35. Hydrogenation
In reduction, the electrons that are transferred are frequently accompanied by protons
Therefore, the overall reaction is a hydrogenation .

36. Oxidation and reduction
Equations describing reductions or oxidations are half reactions
In real situations, reduction and oxidation always take place simultaneously
Any time an oxidation occurs, the electrons (and protons) must be added to another molecule in a reduction

37. Coenzymes Such as NAD+ Serve as Electron Acceptors in Biological Oxidations
Usually electrons and hydrogens removed during biological oxidation are transferred to one of several coenzymes
Coenzymes are small molecules that function along with enzymes by serving as carriers of electrons or small functional groups
They are in low concentrations in the cell as they are recycled

38. NAD+
The most common coenzyme involved in energy metabolism is nicotinamide adenine dinucleotide, NAD+
It serves as an electron acceptor, adding two electrons and a proton to its aromatic ring, generating NADH plus a proton .

39. Most Chemotrophs Meet Their Energy Needs by Oxidizing Organic Food Molecules
Most chemotrophs depend on organic food molecules as oxidizable substrates
Oxidation of these organic compounds— carbohydrates, fats, and proteins—produces energy for the cell in the form of ATP and reduced coenzymes

40. Glucose Is One of the Most Important Oxidizable Substrates in Energy Metabolism
The six-carbon sugar glucose is the main energy source for most of the cells in the body
Blood glucose comes mainly from dietary carbohydrates, starch, or sucrose, or from the breakdown of stored glycogen
In plants, glucose is the monosaccharide released upon starch breakdown
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 40

41. The Oxidation of Glucose Is Highly Exergonic
Glucose is a good source of energy because its oxidation is a highly exergonic process
DGo = –686 kcal/mol for complete conversion of glucose to carbon dioxide and water, with oxygen as the final electron acceptor .
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 41

42. Glucose Catabolism Yields Much More Energy in the Presence of Oxygen than in Its Absence
It is not possible to obtain the full 686 kcal/mol for complete oxidation of glucose; energy conversion is not 100% efficient
Complete oxidation of glucose in the presence of oxygen is called aerobic respiration
Many organisms, such as bacteria, carry out anaerobic respiration, using electron acceptors such as S, H+, and Fe3+
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 42

43. Anaerobic respiration
Even in the absence of oxygen, most organisms can extract limited energy from glucose
They do so via glycolysis
Electrons removed during glucose oxidation are returned to an organic molecule later in the same pathway
This is called fermentation
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 43

44. Two types of fermentation
In some animals and many bacteria, the end product of fermentation is lactate, and so anaerobic glucose catabolism is called lactate fermentation
In most plant cells and microorganisms such as yeast the process is termed alcoholic fermentation because the end product is ethanol
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 44

45. Based on Their Need for Oxygen, Organisms Are Aerobic, Anaerobic, or Facultative
Obligate aerobes have an absolute requirement for oxygen
Obligate anaerobes cannot use oxygen as an electron acceptor; oxygen is toxic to these organisms
Facultative organisms can function under aerobic or anaerobic conditions
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 45

46. Glycolysis and Fermentation: ATP Generation Without the Involvement of Oxygen
Anaerobes carry out oxidative reactions without using oxygen as an electron acceptor
Most organisms generate two molecules of ATP for every glucose molecule that is oxidized
However, some organisms are able to produce more ATP molecules per glucose
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 46

47. Glycolysis Generates ATP by Catabolizing Glucose to Pyruvate
Glycolysis (or the glycolytic pathway) is a ten-step reaction sequence that converts one glucose molecule into two molecules of pyruvate
Pyruvate is a three-carbon compound
Both ATP and NADH are produced
Main point could be that glycolysis is almost universally conserved – likely present in last common ancestor of all cells. 47

48. Figure 9-6

49. Glycolysis is present in all organisms
Glycolysis is common to both aerobic and anaerobic organisms
In most cells the enzymes for glycolysis are found in the cytosol
But in some parasitic protozoans called trypanosomes, the first seven enzymes are found in membrane-bounded organelles called glycosomes

50. Glycolysis in Overview
In the absence of oxygen glycolysis leads to fermentation
In the presence of oxygen glycolysis leads to aerobic respiration

51. Important features of the glycolytic pathway are
The initial input of ATP (Gly-1)
The sugar splitting reaction in which glucose is split into two three-carbon molecules
The oxidative event that generates NADH (Gly-6)
The two steps at which the reaction sequence is coupled to ATP generation (Gly-7 and Gly-10)

52. The glycolytic pathway can be divided into three phases
Phase I: the preparatory and cleavage steps
Phase II: the oxidative sequence, which is the first ATP-generating event
Phase III: the second ATP-generating event

53. Phase I: Preparation and Cleavage
The net result of the first three reactions is to convert glucose into a doubly phosphorylated molecule (fructose-1,6-bisphosphate)
The phosphates are transferred to glucose from ATP
ATP hydrolysis is also the driving force that makes the phosphorylation exergonic and thus irreversible

54. The first reaction adds a phosphate to the sixth carbon atom
The bond formed is a phosphodiester bond, a lower-energy bond than the phosphoanhydride bonds in ATP
The enzyme that catalyzes the reaction is hexokinase, and is specific for phosphorylation of other six-carbon sugars as well
Liver cells also have glucokinase, which is specific for just glucose

55. The second phosphate is added to carbon one
The first carbon of glucose is not as easily phosphorylated as the sixth
The Gly-2 reaction first converts glucose-6-phosphate to fructose-6-phosphate, allowing the Gly-3 reaction to add a phosphate to carbon one
This reaction is catalyzed by the enzyme phosphofructokinase-1 (PFK-1)

56. Summary of Gly-1 to Gly-5
The first phase of the glycolytic pathway can be summarized as

57. Phase 2: Oxidation and ATP Generation
The net energy yield of phase one is negative
Two molecules of ATP have been consumed per molecule of glucose
In phase 2, ATP production is linked to an oxidative event, followed by the generation of ATP in phase 3

58. Gly-6 and Gly-7
The oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate is highly exergonic, and drives
the reduction of NAD+ to NADH (Gly-6)
the phosphorylation of ADP with inorganic phosphate, Pi (Gly-7)

59. Important features of Gly-6 and Gly-7
NAD+ is an electron acceptor
The oxidation is coupled to the formation of a high-energy, doubly phosphorylated intermediate, 1,3-bisphosphoglycerate
ATP generation by transferring a phosphate group to ADP from a phosphorylated substrate such as 1,3-bisphosphoglycerate is called substrate-level phosphorylation

60. Summary of Gly-6 and Gly-7
Gly-6 and Gly-7 can be summarized as
Each reaction involving glyceraldehyde-3-phosphate occurs twice per starting molecule of glucose
The two ATPs invested in the first phase are recovered in the second phase, for no net ATP

61. Phase 3: Pyruvate Formation and ATP Generation
The phosphoester bond of 3-phosphoglycerate is converted to a phosphoenol bond
The phosphate group is moved to the adjacent carbon, forming 2-phosphoglycerate (Gly-8)
Water is removed from the 2-phosphoglycerate by the enzyme enolase (Gly-9) generating the high-energy compound phosphoenolpyruvate (PEP)

62. Phosphoenolpyruvate
Hydrolysis of the phosphoenol bond of PEP is one of the most exergonic known in biological systems
PEP hydrolysis drives ATP synthesis by transferring a phosphate to ADP, catalyzed by the enzyme pyruvate kinase (Gly-10)
The transfer is irreversible in the direction of pyruvate and ATP formation

63. Summary of Gly-8 to Gly-1
The third phase of glycolysis can be summarized as

64. Summary of Glycolysis
The two molecules of ATP formed in the second phosphorylation event (Gly-10) represent the net yield of ATP for the glycolytic pathway .
The pathway is highly exergonic in the direction of pyruvate formation; DG in a cell is typically –20 kcal/mol

65. Conservation of Glycolysis
The glycolytic pathway is one of the most common and highly conserved metabolic pathways known
Virtually all cells have the ability to convert glucose to pyruvate, extracting energy in the process
The next steps depend on the availability of oxygen

66. The Fate of Pyruvate Depends on Whether Oxygen Is Available
Pyruvate occupies a key position as a branch point in chemotrophic energy metabolism
In the presence of oxygen, pyruvate undergoes further oxidation to acetyl coenzyme A
Acetyl CoA can be completely oxidized to CO2, generating more than 30 ATP per glucose

67. Figure 9-8A

68. The fate of pyruvate in the absence of oxygen
Under anaerobic conditions no further oxidation of pyruvate occurs
Pyruvate is reduced by accepting the electrons (and protons) that must be removed from NADH
The most common products of pyruvate reduction are lactate or ethanol and CO2

69. Figure 9-8B,C

70. In the Absence of Oxygen, Pyruvate Undergoes Fermentation to Regenerate NAD+
Fermentation must regenerate NAD+ from NADH so that glycolysis can continue
Cells monitor and stabilize the NAD+/NADH ratio, an indicator of the cell’s redox state (general level of oxidation of cellular components)
Electrons are transferred to pyruvate with two possible outcomes

71. Lactate Fermentation
The anaerobic process that culminates with lactate is called lactate fermentation
Lactate is generated by direct transfer of electrons from NADH to pyruvate by lactate dehydrogenase .

72. Overall metabolism of glucose to lactate
The overall metabolism of glucose to lactate in the absence of oxygen can be summarized as
Lactate fermentation is commercially important and also occurs in our muscles during strenuous exertion

73. Gluconeogenesis
Lactate produced in muscles under hypoxic conditions is transferred to the liver
In the liver, it is converted into glucose by the process of gluconeogenesis
It is the reverse of lactate fermentation but with several differences

74. Alcoholic Fermentation
Under anaerobic conditions plant cells carry out alcoholic fermentation, as do yeasts and other microorganisms
Pyruvate loses a carbon (as CO2) and forms the two-carbon compound acetaldehyde (enzyme: pyruvate decarboxylase)
Acetaldehyde reduction by NADH gives rise to ethanol (enzyme: alcohol dehydrogenase)

75. Summary of alcoholic fermentation.
Adding the overall equation for glycolysis

76. Other Fermentation Pathways
In proprionate fermentation, bacteria reduce pyruvate to proprionate
Bacteria that cause food spoilage do so by butylene glycol fermentation
Other processes yield acetone, isopropyl alcohol, or butyrate, all variations on the common theme of reoxidizing NADH by the transfer of electrons to an organic acceptor

77. Fermentation Taps Only a Fraction of the Substrate’s Free Energy but Conserves That Energy Efficiently as ATP
An essential feature of every fermentation process is
no external electron acceptor is involved and no net oxidation occurs
Fermentation gives a modest ATP yield of two ATP per glucose; most of the free energy of the glucose molecule is still present in the lactate or ethanol

78. Free energy of lactate
The two lactate molecules produced from one glucose contain most of the energy present per mole of glucose
Go = –319.5 kcal/mol, or 93% of the original free energy of glucose
Although the energy yield is low, the free energy is conserved as ATP with an efficiency that probably exceeds 40%

79. Alternative Substrates for Glycolysis
Glucose is a major substrate for both fermentations and respiration in a variety of organisms and some tissues
But for some organisms and tissues, glucose is not significant at all
There are a variety of alternatives to glucose, which are often converted into an intermediate in the glucose catabolism pathway

80. Other Sugars and Glycerol Are Also Catabolized by the Glycolytic Pathway
Many sugars are available to cells, either monosaccharides or disaccharides that can be readily hydrolyzed into monosaccharides
The monosaccharides are then converted into a glycolytic intermediate
Glucose and fructose enter most directly after phosphorylation on carbon atom 6; mannose and fructose require more steps

81. Pentoses and glycerol can be channeled into the glycolytic pathway too
Phosphorylated pentoses can enter the glycolytic pathway but must first be converted to hexose phosphates
The conversion takes place via the phosphogluconate pathway, also called the pentose phosphate pathway
Glycerol, a three-carbon molecule resulting from lipid breakdown, enters after conversion to dihydroxyacetone phosphate

82. Polysaccharides Are Cleaved to Form Sugar Phosphates That Also Enter the Glycolytic Pathway
Glucose occurs primarily in the form of storage polysaccharides, most often starch in plants and glycogen in animals
The polysaccharides are mobilized by phophorolysis, using inorganic phosphate to break the (→ 4) bond between glucose units
Glucose is liberated as glucose-1-phosphate

83. Gluconeogenesis
The process of glucose synthesis is called gluconeogenesis
Glucose is synthesized from three- and four- carbon precursors
Pyruvate and lactate are the most common starting materials

84. Gluconeogenesis and glycolysis
Gluconeogenesis occurs by simple reversal of glycolysis using the same enzyme in both directions
But not all the steps are simple reversals of glycolysis: Gly-1, Gly-3, and Gly-10 are accomplished by other means
These are the most exergonic reactions of glycolysis

85. Anabolic and catabolic pathways
The Gly-1, Gly-3, and Gly-10 steps of glycolysis are thermodynamically the most difficult to reverse and so must differ for gluconeogenesis
This illustrates an important principle
Biosynthetic anabolic pathways are seldom just the reversal of the corresponding catabolic pathway

86. Bypass reactions
The Gly-1, Gly-3, and Gly-10 steps of gluconeogenesis occur through bypass reactions at each of those steps
These are alternative reactions that circumvent the three reactions that would be most difficult to drive in the opposite direction

87. The Regulation of Glycolysis and Gluconeogenesis
Cells have enzymes for both glycolysis and gluconeogenesis, so the processes must be regulated
Spatial regulation keeps the two processes confined to separate places in the body
There is also temporal regulation in which the two processes take place at different times in one cell

88. Key Enzymes in the Glycolytic and Gluconeogenic Pathways Are Subject to Alllosteric Regulation
Allosteric regulation involves the interconversion of an enzyme between two forms, one catalytically active and the other inactive
The enzyme will be active or not depending on whether an allosteric effector is bound to the allosteric site
The effector might be an activator or inhibitor

89. Key regulatory enzymes of glycolysis and gluconeogenesis
For glycolysis the enzymes are hexokinase, phosphofructokinase-1 (PFK-1), and pyruvate kinase
For gluconeogenesis they are fructose-1,6-bisphosphatase, and pyruvate carboxylase
Each of the enzymes is unique to its pathway so the pathways can be regulated independently

90. Glycolysis and gluconeogenesis are reciprocally regulated
AMP and acetyl CoA, the two effectors to which both pathways are sensitive, have opposite effects
AMP activates glycolysis and inhibits gluconeogenesis
Acetyl CoA activate gluconeogenesis but inhibits glycolysis

91. Further allosteric regulation of glycolysis and gluconeogenesis
Both pathways are subject to allosteric regulation by compounds involved in respiration
Acetyl CoA and citrate are key intermediates in an aerobic pathway called the tricarboxylic acid cycle
Both have inhibitory effects on glycolysis, decreasing the rate of pyruvate formation

92. Fructose-2,6-Bisphosphate Is an Important Regulator of Glycolysis and Gluconeogenesis
Fructose-2,6-Bisphosphate (F2,6BP) is the most important regulator of both glycolysis and gluconeogenesis
Synthesis of F2,6BP is catalyzed by phosphofructokinase-2 (PFK-2)
F2,6BP activates the glycolytic enzyme (PFK-1) that phosphorylates fructose-6-phosphate and it inhibits FBPase that catalyzes the reverse reaction

93. Figure 9-13

94. Additional role of PFK-2
PFK-2 also has a fructose-2,6-bisphosphatase activity that removes the phosphate group from F2,6BP, converting the compound back to fructose-6-phosphate
PFK-2 is called a bifunctional enzyme because it has two separate catalytic activities

95. Effect of cAMP on F2,6BP
cAMP affects the F2,6BP concentration in two ways
1. It inactivates the PFK-2 kinase activity
2. It stimulates the F2,6BP phosphatase activity
These two effects tend to decrease the concentration of F2,6BP in the cell

96. Effect of cAMP on hormone regulation
cAMP level in cells is controlled primarily by the hormones glucagon and epinephrine (adrenaline)
These cause an increase in cAMP concentration, stimulating gluconeogenesis when more glucose is needed

97. Novel Roles for Glycolytic Enzymes
Glycolysis is connected to other cell processes
Hexokinase (Gly-1) is a transcriptional repressor in yeast cells under high glucose levels
Mammals have four isoforms of hexokinase
One is expressed in highly catabolically active tumor cells
Another binds to mitochondria and helps coordinate glycolysis with mitochondrial functions
Many other examples exist

98. Additional functions of other glycolytic enzymes
Glyceraldehyde-3-phosphate dehydrogenase (Gly-6) and enolase (Gly-9) have DNA-binding abilities
They can act as transcriptional regulators
They connect the glycolytic pathway with processes such as cell division and programmed cell death
Point three of the cells & transport processes summary was not a prominent part of the text, in my opinion. 98

99. Cancer connections
Phosphoglucoisomerase (PGI; Gly-2) is involved in cell motility and migration during cancer cell metastasis
Metastasis: the release of cells from malignant tumors into the bloodstream; these can form secondary tumors throughout the body
PGI stimulates cell proliferation and migration 99