Chapter 13: Energetics and Catabolism

1. Chapter 13: Energetics and Catabolism

2. Chapter 13:Introduction • All living cells need energy to move and grow • The energy to build cells comes from chemical reactions. • - Catabolism: Breakdown of complex molecules into smaller ones • - Anabolism: Reactions that build cells • Catabolism provides energy & intermediates for anabolism. • - However, some of the energy is released as heat.

3. TABLE 13.1

4. Free energy (G) Free energy is the energy in a chemical reaction that is available to do useful work. The change in free energy during a reaction is G0'. This is expressed in kilojoules. Catabolic reaction = exergonic Anabolic reactions = endergonic

5. A+B C + D DG=DGo’ + RTln [C] [D]/[A][B] DG =DGo’ + 2.303 RT log [C] [D]/[A][B] At equilibrium DG = 0 DGo’ =- 2.303 RT log [C] [D]/[A][B] The direction of a reaction can be predicted by a thermodynamic quantity called Gibbs free energy change, DG. - If Go’ < 0, the process may go forward. - If Go’ > 0, the reaction will go in reverse. Gibbs Free Energy Change

6. In living cells, The standard conditions for DGo’ are as follows: - Temperature = 298 K (25° C) - Pressure = 1 atm - Concentrations = 1 M - pH = 7

7. Many of the cell’s energy transfer reactions involve energy carriers. - Molecules that gain or release small amounts of energy in reversible reactions. - Examples: NADH and ATP Some energy carriers also transfer electrons. - Electron donor is a reducing agent. - Electron acceptor is an oxidizing agent. Energy Carriers

8. ATP contains a base, sugar, and three phosphates. Under physiological conditions, ATP always forms a complex with Mg2+. Adenosine Triphosphate

9. ATP can transfer energy to cell processes in three different ways: - Hydrolysis releasing phosphate (Pi) - Hydrolysis releasing pyrophosphate (PPi) - Phosphorylation of an organic molecule Note that besides ATP other nucleotides carry energy. - For example, guanosine triphosphate (GTP) provides energy for protein synthesis. Adenosine Triphosphate

10. Nicotinamide adenine dinucleotide (NADH) carries two or three times as much energy as ATP. - It also donates and accepts electrons. - NADH is the reduced form. - NAD+ is the oxidized form. Overall reduction of NAD+ consumes two hydrogen atoms to make NADH. NAD+ + 2H+ + 2e–→ NADH + H+DGo’ = 62 KJ/mol Reaction requires energy input from food molecules. NADH

11. Figure 13.7A

12. Flavine adenine dinucleotide (FAD) is another related coenzyme that can transfer electrons. - FADH2: reduced form - FAD: oxidized form Unlike NAD+, FAD is reduced by two electrons and two protons. FADH Figure 13.7B

13. Enzymes Enzymes are catalytic proteins (or RNA) that speed up the rate of biochemical reactions by lowering the activation energy. Enzymes are highly specific in the reactions they catalyze and this specificity is found in the three dimensional structure of the polypeptide (s) in the protein

14. Enzymes catalyze biological reactions. - Lower the activation energy allowing rapid conversion of reactants to products Enzymes H2 + 1/2 O2 H2O DGo’ = -237 kJ/mole

15. Enzyme Properties • Very specific • Large proteins (104 to 106) • 3-D determines the activity and specificity • Very efficient: rates increased 108 to 1010 fold • Subjected to cellular controls

16. Enzyme activity • Active site • Enzyme-substrate complex • Tranformation • Release of products and original enzyme

17. Enzymes The turnover number is generally 1-10,000 molecules per second. Figure 5.4

18. Factors • Temperature • pH • Substrate concentration

19. Factors influencing enzyme activity Competitive inhibition Figure 5.7a, b

20. Factors influencing enzyme activity

21. Enzymes couple specific energy-yielding reactions with energy-requiring reactions. Enzymes

22. Factors influencing enzyme activity Noncompetitive inhibition Figure 5.7a, c

23. There are three main catabolic pathways: - Fermentation: Partial breakdown of organic food without net electron transfer to an inorganic terminal electron acceptor - Respiration: Complete breakdown of organic molecules with electron transfer to a terminal electron acceptor such as O2 - Photoheterotrophy: Catabolism is conducted with a “boost” from light Catabolism: The Microbial Buffet

24. Microbes catalyze many different kinds of substrates or catabolites.

25. Starch Cellulose

26. Polysaccharides are broken down to disaccharides, and then to monosaccharides. - Sugar and sugar derivatives, such as amines and acids, are catabolized to pyruvate. Pyruvate and other intermediary products of sugar catabolism are fermented or further catabolized to CO2 and H2O via the TCA cycle. Lipids and amino acids are catabolized to glycerol and acetate, as well as other metabolic intermediates. Aromatic compounds, such as lignin and benzoate derivatives, are catabolized to acetate through different pathways, such as the catechol pathway.

29. Glucose is catabolized via three main routes. Glucose Breakdown Figure 13.15

30. In the EMP pathway, a glucose molecule undergoes a stepwise breakdown to two pyruvate molecules. Embden-Meyerhoff-Parnas Pathway Figure 13.16

31. The EMP pathway is the most common form of glycolysis. - It occurs in the cytoplasm of the cell. - It functions in the presence or absence of O2. - It involves ten distinct reactions that are divided into two stages. Embden-Meyerhoff-Parnas Pathway

32. Glucose is “activated” by phosphorylations that ultimately convert it into fructose-1,6- bisphosphate. Two ATPs are expended. Fructose-1,6-bisphosphate is cleaved into two 3-carbon-phosphate isomers. -Dihydroxyacetone phosphate -Gyceraldehyde-3-phosphate Dihydroxyacetone phosphate Gyceraldehyde-3-phosphate Stage 1: Glucose activation stage

33. Each glyceraldehyde-3-phosphate molecule is ultimately converted to pyruvate. Redox reactions produce two molecules of nicotinamide adenine dinucleotide (NADH). Four ATP molecules are produced by substrate-level phosphorylation. Stage 2. Energy-yielding stage

34. Figure 13.17

35. Summary: Embden-Meyerhoff-Parnas Pathway glucose  2 pyruvate 2ATP 2NADH + 2H+ 35

36. Probably evolved earlier than EMP pathway. Glucose is activated by one phosphorylation reaction, and then dehydrogenated to 6-phosphogluconate. - Then dehydrated and cleaved to pyruvate and glyceraldedyde-3-P, which enters the EMP pathway to form pyruvate The ED pathway produces 1 ATP, 1 NADH, and 1 NADPH. The Entner-Doudoroff Pathway

37. Figure 13.19

38. The Entner-Doudoroff Pathway reactions of pentose phosphate pathway reactions of Embden-Meyerhoff pathway reactions of glycolytic pathway Figure 9.8 38

39. Many gut flora use the ED pathway as their primary glycolytic pathway. - E. coli feeds on gluconate from mucus secretion (Fig. 13.18A). - Bacteroides thetaiotaomicron actually induce colonic production of the mucus. - They literally “farm” it. Another bacterium, Zymomonas, ferments the blue agave plant. - A product is the Mexican beverage pulque.

40. Summary: Entner-Doudoroff Pathway • glucose • 1 ATP • 1 NADPH • 1 NADH

41. Fermentation Fermentation is the completion of catabolism without the electron transport system and a terminal electron acceptor. - The hydrogens from NADH + H+ are transferred back onto the products of pyruvate, forming partly oxidized fermentation products. Most fermentations do not generate ATP beyond that produced by substrate-level phosphorylation. - Microbes compensate for the low efficiency of fermentation by consuming large quantities of substrate and excreting large quantities of products.

42. Fermentation Pathways Homolactic fermentation - Produces two molecules of lactic acid Ethanolic fermentation - Produces two molecules of ethanol and two CO2 Heterolactic fermentation - Produces one molecule of lactic acid, one ethanol, and one CO2 Mixed-acid fermentation - Produces acetate, formate, lactate, and succinate, as well as ethanol, H2,and CO2

43. Figure 13.21

44. The Tricarboxylic Acid Cycle The TCA cycle is also known as the Krebs cycle or citric acid cycle. - In prokaryotes, it occurs in the cytoplasm. - In eukaryotes, it occurs in the mitochondria. Glucose catabolism connects with the TCA cycle through pyruvate breakdown to acetyl-COA and CO2. - Acetyl-CoA enters the TCA cycle by condensing with the 4-C oxaloacetate to form citrate.

45. Figure 13.24

46. Conversion of pyruvate to acetyl-CoA is catalyzed by a very large multisubunit enzyme called the pyruvate dehydrogenase complex (PDC). - The net reaction is: Pyruvate + NAD+ + CoA Acetyl-CoA + CO2 + NADH + H+

48. The Tricarboxylic Acid Cycle For each pyruvate oxidized: - 3 CO2 are produced by decarboxylation - 4 NADH and 1 FADH2 are produced by redox reactions - 1 ATP is produced by substrate-level phosphorylation - Some cells make GTP instead. - However, GTP and ATP are equivalent in stored energy.

49. After the completion of the TCA cycle, all the carbons of glucose have been released as waste CO2. - However, the metabolic pathway is not completed until the electrons carried by the coenzymes (NADH and FADH2) are donated to a terminal electron acceptor. The overall process of electron transport and ATP generation is termed oxidative phosphorylation.

50. The TCA Cycle • Overall process of oxidative breakdown of substrate to oxidative phophorylation is called respiration • The TCA cycle was originally developed to provide intermediates to biosynthetic pathways • a-ketoglutarate  Glutamate and glutamine • Oxaloacetate  aspartate • Amphibolic pathway