1. The Citric Acid Cycle
Chapter 16 (Page )

2. Glycolysis Review

3. 1. Summary of Glycolysis
Glycolysis is the catabolic processing of glucose to extract energy.
Glucose + 2 NAD+ + 2 ADP + 2 Pi  2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O
Preparatory
Phase
Payoff
Phase 2 2

4. Glucose Carbons in GAP D- Glucose 1P : 3C
FIGURE 14–7 Fate of the glucose carbons in the formation of glyceraldehyde 3-phosphate. (a) The origin of the carbons in the two threecarbon products of the aldolase and triose phosphate isomerase reactions. The end product of the two reactions is glyceraldehyde 3-phosphate (two molecules). (b) Each carbon of glyceraldehyde 3-phosphate is derived from either of two specific carbons of glucose. Note that the numbering of the carbon atoms of glyceraldehyde 3-phosphate differs from that of the glucose from which it is derived. In glyceraldehyde 3-phosphate, the most complex functional group (the carbonyl) is specified as C-1. This numbering change is important for interpreting experiments with glucose in which a single carbon is labeled with a radioisotope. (See Problems 6 and 9 at the end of this chapter.)

5. Glucose Carbons in GAP D- Glucose 1P : 3C
FIGURE 14–7 Fate of the glucose carbons in the formation of glyceraldehyde 3-phosphate. (a) The origin of the carbons in the two threecarbon products of the aldolase and triose phosphate isomerase reactions. The end product of the two reactions is glyceraldehyde 3-phosphate (two molecules). (b) Each carbon of glyceraldehyde 3-phosphate is derived from either of two specific carbons of glucose. Note that the numbering of the carbon atoms of glyceraldehyde 3-phosphate differs from that of the glucose from which it is derived. In glyceraldehyde 3-phosphate, the most complex functional group (the carbonyl) is specified as C-1. This numbering change is important for interpreting experiments with glucose in which a single carbon is labeled with a radioisotope. (See Problems 6 and 9 at the end of this chapter.)

6. 1. Summary of Glycolysis
Glycolysis is the catabolic processing of glucose to extract energy.
Glucose + 2 NAD+ + 2 ADP + 2 Pi  2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O
Carbon Oxidation States:
Preparatory
Phase
Payoff
Phase +1 +3 +1 +2 2 2 -3
There is a net loss of 4 electrons from. Where did they go? -1 -1
Net Carbon Oxidation States:
2 x +2 = +4

7. 1. Summary of Glycolysis
Glycolysis is the catabolic processing of glucose to extract energy.
Glucose + 2 NAD+ + 2 ADP + 2 Pi  2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O
Where do the four e¯ go?
There is a net loss of 4 electrons from. Where did they go?
NAD H e- → NADH
Energy is conserved in the formation of NADH.

8. 1. Summary of Glycolysis
Glycolysis is the catabolic processing of glucose to extract energy.
Glucose + 2 NAD+ + 2 ADP + 2 Pi  2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O
Standard free energy of the whole process:
Glucose + 2 NAD+  2 Pyruvate + 2 NADH + 2 H+ G1′ = –146 kJ/mol
2 ADP + 2 Pi  2 ATP + 2 H2O G2′ = kJ/mol
Glucose + 2 NAD+ + 2 ADP + 2 Pi 
2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O Gs′ = -85 kJ/mol
There is a net loss of 4 electrons from. Where did they go?
Energy is conserved in the formation of ATP.

9. 2. Fates of Pyruvate
FIGURE 14–4 Three possible catabolic fates of the pyruvate formed in glycolysis. Pyruvate also serves as a precursor in many anabolic reactions, not shown here.

10. Glucose and Cellular Respiration

11. 1. Only a small amount of energy available in glucose is captured in glycolysis2
G′ = –146 kJ/mol
GLUCOSE
Full oxidation (+ 6 O2)
G′ = –2,840 kJ/mol
The full oxidation of glucose is part of the process of cellular respiration.
6 CO2 + 6 H2O
The full oxidation of glucose is part of the process of cellular respiration.

12. 2. Cellular Respiration
Process in which cells consume O2 and produce CO2
Provides more energy (ATP) from glucose than glycolysis
Also captures energy stored in lipids and amino acids
Evolutionary origin: developed about 2.5 billion years ago
Used by animals, plants, and many microorganisms
Occurs in three major stages:
acetyl CoA production
acetyl CoA oxidation
electron transfer and oxidative phosphorylation

13. Generates some: ATP, NADH, FADH2
3A. Respiration: Stage Acetyl-CoA Production
Generates some: ATP, NADH, FADH2
FIGURE 16–1 (part 1) Catabolism of proteins, fats, and carbohydrates in the three stages of cellular respiration. Stage 1: oxidation of fatty acids, glucose, and some amino acids yields acetyl-CoA.

14. Generates more NADH, FADH2, and one GTP
3B. Respiration: Stage Acetyl-CoA oxidation
Generates more NADH, FADH2, and one GTP
FIGURE 16–1 (part 2) Catabolism of proteins, fats, and carbohydrates in the three stages of cellular respiration. Stage 2: oxidation
of acetyl groups in the citric acid cycle includes four steps in which electrons are abstracted.

15. 3C. Respiration: Stage 3 Oxidative Phosphorylation
Generates a lot of ATP
FIGURE 16–1 (part 3) Catabolism of proteins, fats, and carbohydrates in the three stages of cellular respiration. Stage 3: electrons carried by NADH and FADH2 are funneled into a chain of mitochondrial (or, in bacteria, plasma membrane–bound) electron carriers—the respiratory chain—ultimately reducing O2 to H2O. This electron flow drives the production of ATP.

16. 4. Localization of events involved in glucose catabolism and cellular respiration
Cellular respiration involving glucose:
A. Glycolysis occurs in the cytoplasm
B. Citric acid cycle occurs in the mitochondrial matrix
Except the action of succinate dehydrogenase, which is located in the inner membrane
Mostly dealing with soluble proteins
C. Oxidative phosphorylation occurs in the inner membrane

17. 4A. Structure of a Mitochondrion
Double membrane leads to four distinct compartments:
Outer Membrane:
Relatively porous membrane allows passage of metabolites
Intermembrane Space (IMS):
similar environment to cytosol
higher proton concentration (lower pH)
Inner Membrane
Relatively impermeable, with proton gradient across it
Location of electron transport chain complexes
Convolutions called Cristae serve to increase the surface area
Matrix
Location of the citric acid cycle and parts of lipid and amino acid metabolism
Lower proton concentration (higher pH)

18. 4A. Structure of a Mitochondrion
Courtesy of Mariana Ruiz Villareal.

19. The Citric Acid Cycle

20. 1. Conversion of Pyruvate to Acetyl-CoA
Net Reaction:
Oxidative decarboxylation of pyruvate
First carbons of glucose to be fully oxidized
FIGURE 16–2 Overall reaction catalyzed by the pyruvate dehydrogenase complex. The five coenzymes participating in this reaction, and the three enzymes that make up the enzyme complex, are discussed in the text.

21. 1. Conversion of Pyruvate to Acetyl-CoA
Catalyzed by the pyruvate dehydrogenase complex
Requires 5 coenzymes
NAD+ and CoA-SH are co-substrates
TPP, lipoyllysine, and FAD are prosthetic groups
FIGURE 16–2 Overall reaction catalyzed by the pyruvate dehydrogenase complex. The five coenzymes participating in this reaction, and the three enzymes that make up the enzyme complex, are discussed in the text.

22. 1AI. Structure of Coenzyme A
Coenzymes are not a permanent part of the enzymes’ structure.
They associate, fulfill a function, and dissociate
The function of CoA is to accept and carry acetyl groups
FIGURE 16–3 Coenzyme A (CoA). A hydroxyl group of pantothenic acid is joined to a modified ADP moiety by a phosphate ester bond, and its
carboxyl group is attached to β-mercaptoethylamine in amide linkage. The hydroxyl group at the 3’ position of the ADP moiety has a phosphoryl
group not present in free ADP. The —SH group of the mercaptoethylamine moiety forms a thioester with acetate in acetyl-coenzyme A (acetyl-CoA) (lower left).

23. 1AII. Structure of Lipoyllysine
Prosthetic groups are strongly bound to the protein
The lipoic acid is covalently linked to the enzyme via a lysine residue
An acetyl transporter
FIGURE 16–4 Lipoic acid (lipoate) in amide linkage with a Lys residue. The lipoyllysyl moiety is the prosthetic group of dihydrolipoyl transacetylase (E2 of the PDH complex). The lipoyl group occurs in oxidized (disulfide) and reduced (dithiol) forms and acts as a carrier of both hydrogen and an acetyl (or other acyl) group.

24. 1AIII. Structure of TPP Thiamine pyrophosphate (TPP)
FIGURE 16–4 Lipoic acid (lipoate) in amide linkage with a Lys residue. The lipoyllysyl moiety is the prosthetic group of dihydrolipoyl transacetylase (E2 of the PDH complex). The lipoyl group occurs in oxidized (disulfide) and reduced (dithiol) forms and acts as a carrier of both hydrogen and an acetyl (or other acyl) group.

25. 1AIV. Structure of FAD Flavin adenine dinucleotide (FAD)
- An electron carrier.
FIGURE 16–4 Lipoic acid (lipoate) in amide linkage with a Lys residue. The lipoyllysyl moiety is the prosthetic group of dihydrolipoyl transacetylase (E2 of the PDH complex). The lipoyl group occurs in oxidized (disulfide) and reduced (dithiol) forms and acts as a carrier of both hydrogen and an acetyl (or other acyl) group.

26. 1B. Pyruvate Dehydrogenase Complex (PDC)
PDC is a large (up to 10 MDa) multienzyme complex
pyruvate dehydrogenase (E1)
dihydrolipoyl transacetylase (E2)
dihydrolipoyl dehydrogenase (E3)
Advantages of multienzyme complexes:
short distance between catalytic sites allows channeling of substrates from one catalytic site to another
channeling minimizes side reactions
regulation of activity of one subunit affects the entire complex

27. 3D Reconstruction from Cryo-EM data
A cryoelectron micrograph inspired model of PDC shows a core (green) consisting of 60 molecules of E2 arranged in 20 trimers forming a pentagonal dodecahedron
(50 nm in diameter).
pyruvate dehydrogenase (E1)
dihydrolipoyl transacetylase (E2)
dihydrolipoyl dehydrogenase (E3)
FIGURE 16–5b The pyruvate dehydrogenase complex. (b) Three-dimensional image of PDH complex, showing the subunit structure: E1, pyruvate dehydrogenase; E2, dihydrolipoyl transacetylase; and E3, dihydrolipoyl dehydrogenase. This image is reconstructed by analysis of a large number of images such as those in (a), combined with crystallographic studies of individual subunits. The core (green) consists of 60 molecules of E2, arranged in 20 trimers to form a pentagonal dodecahedron. The lipoyl domain of E2 (blue) reaches outward to touch the active sites of E1 molecules (yellow) arranged on the E2 core. Several E3 subunits (red) are also bound to the core, where the swinging arm on E2 can reach their active sites. An asterisk marks the site where a lipoyl group is attached to the lipoyl domain of E2. To make the structure clearer, about half of the complex has been cut away from the front. This model was prepared by Z. H. Zhou and colleagues (2001); in another model, proposed by J. L. S. Milne and colleagues (2002), the E3 subunits are located more toward the periphery (see Further Reading).

28. 1C. Overall Reaction of PDC
FIGURE 16–6 Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex. The fate of pyruvate is traced in red. In step 1 pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1), undergoing decarboxylation to the hydroxyethyl derivative (see Fig. 14–15). Pyruvate dehydrogenase also carries out step 2, the transfer of two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group. Step 3 is a transesterification in which the —SH group of CoA replaces the —SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group. In step 4 dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2. In step 5 the reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle. (Subunit colors correspond to those in Fig. 16–5b.)
Enzyme 1
Step 1: Decarboxylation of pyruvate
Step 2: Oxidation of acetyl-TPP
-Electrons reduce lipoamide and form a thioester

29. 1C. Overall Reaction of PDC+1
FIGURE 16–6 Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex. The fate of pyruvate is traced in red. In step 1 pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1), undergoing decarboxylation to the hydroxyethyl derivative (see Fig. 14–15). Pyruvate dehydrogenase also carries out step 2, the transfer of two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group. Step 3 is a transesterification in which the —SH group of CoA replaces the —SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group. In step 4 dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2. In step 5 the reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle. (Subunit colors correspond to those in Fig. 16–5b.)
Enzyme 1
Step 1: Decarboxylation of pyruvate
Step 2: Oxidation of acetyl-TPP
-Electrons reduce lipoamide and form a thioester

30. 1C. Overall Reaction of PDC+3
FIGURE 16–6 Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex. The fate of pyruvate is traced in red. In step 1 pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1), undergoing decarboxylation to the hydroxyethyl derivative (see Fig. 14–15). Pyruvate dehydrogenase also carries out step 2, the transfer of two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group. Step 3 is a transesterification in which the —SH group of CoA replaces the —SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group. In step 4 dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2. In step 5 the reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle. (Subunit colors correspond to those in Fig. 16–5b.)
Enzyme 1
Step 1: Decarboxylation of pyruvate
Step 2: Oxidation of acetyl-TPP
-Electrons reduce lipoamide and form a thioester

31. 1C. Overall Reaction of PDC+3 +3
FIGURE 16–6 Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex. The fate of pyruvate is traced in red. In step 1 pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1), undergoing decarboxylation to the hydroxyethyl derivative (see Fig. 14–15). Pyruvate dehydrogenase also carries out step 2, the transfer of two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group. Step 3 is a transesterification in which the —SH group of CoA replaces the —SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group. In step 4 dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2. In step 5 the reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle. (Subunit colors correspond to those in Fig. 16–5b.)
Enzyme 2
Step 3: Formation of acetyl-CoA (product 1)

32. 1C. Overall Reaction of PDC+3 +3
FIGURE 16–6 Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex. The fate of pyruvate is traced in red. In step 1 pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1), undergoing decarboxylation to the hydroxyethyl derivative (see Fig. 14–15). Pyruvate dehydrogenase also carries out step 2, the transfer of two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group. Step 3 is a transesterification in which the —SH group of CoA replaces the —SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group. In step 4 dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2. In step 5 the reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle. (Subunit colors correspond to those in Fig. 16–5b.)
Enzyme 3
Step 4: Reoxidation of the lipoamide cofactor
Step 5: Regeneration of the oxidized FAD cofactor
Forming NADH (product 2)