1. Metabolism
Chapter 5

2. Types of work carried out by organisms
chemical work
synthesis of complex molecules
transport work
take up of nutrients, elimination of wastes, and maintenance of ion balances
mechanical work
movement of organisms or cells and movement of internal structures

3. Figure: 05-24
Caption:
Scheme of anabolism and catabolism showing the key role of ATP and the proton motive force in integrating the processes. Monomers can come preformed as nutrients from the environment or from catabolic pathways like glycolysis and the citric acid cycle.

4. Energy currency of cells
ATP
used to transfer energy from cell’s energy-conserving systems to the systems that carry out cellular work
Figure 8.2

5. Figure: 05-12
Caption:
High-energy bonds. The table shows the free energy of hydrolysis of some of the key phosphate esters and anhydrides, indicating that some of the phosphate ester bonds are of higher energy than others. Structures of four of the compounds are given to indicate the position of low-energy and high-energy bonds. ATP contains three phosphates, but only two of them are high energy (shown in blue). ADP contains two phosphates of which only one is high energy. AMP does not contain a high-energy phosphate bond. Also shown is the structure of the coenzyme acetyl-CoA. The C–S bond between the acetyl portion and the b-mercaptoethylamine portion is a high-energy thioester bond (Table 3.1). The “R” group of acetyl-CoA is a 39 phospho ADP group.

6. Oxidation-Reduction Reactions and Electron Carriers
many metabolic processes involve oxidation-reduction reactions (electron transfers)
electron carriers are often used to transfer electrons from an electron donor to an electron acceptor

7. Oxidation-reduction (redox) reactions
transfer of electrons from a donor to an acceptor
can result in energy release, which can be conserved and used to form ATP

8. Standard reduction potential (E0)
equilibrium constant for an oxidation-reduction reaction
a measure of the tendency of the reducing agent to lose electrons
more negative E0  better electron donor
more positive E0  better electron acceptor

10. The greater the
difference
between the E0
of the donor and
the E0 of the
acceptor 
the more
negative
the Go´

11. Energy and electron flow in metabolism
flow of electrons down the tower releases energy
light energy is used to drive electrons up the tower during photosynthesis

12. Electron carriers NAD NADP nicotinamide adenine dinucleotide
nicotinamide adenine dinucleotide phosphate

13. NAD can accept electrons and a hydrogen from a reduced substrate (e. g
NAD can accept electrons and a hydrogen from a reduced substrate (e.g. SH2). These are carried on the nicotinamide ring.

14. Electron carriers FAD FMN flavin adenine dinucleotide
flavin mononucleotide
riboflavin phosphate
Riboflavin, a vitamin, is composed of the isoalloxazine ring and its attached circle (circled). Portion of the ring that is directly involved in oxidation-reactions is in color.
riboflavin

15. Electron carriers
coenzyme Q (CoQ)
a quinone
also called ubiquinone

16. Electron carriers cytochromes use iron to transfer electrons
iron is part of a heme group

17. Electron carriers nonheme iron proteins e.g., ferrodoxin
use iron to transport electrons
iron is not part of a heme group

18. Balancing Oxidation-Reduction Reactions
 1. Identify redox elements and determine the oxidation state. Note: only one element is allowed to have its oxidation state changed in each half reaction.
2. Write the half-reactions.
3. Balance the redox elements.
4. Balance the electrons.
5. Balance the other elements.
  a. Balance O by addition of water (H2O).
b. Balance H by addition of H+.
6. Check charge balance.
7. Add two half reactions making sure the electrons cancel.

19. Figure: 05-13a-b
Caption:
Energy conservation in fermentation and respiration. (a) In fermentation, ATP synthesis occurs as a result of substrate-level phosphorylation; a phosphate group gets added to some intermediate in the biochemical pathway where it becomes a “high-energy” phosphate group and eventually gets transferred to ADP to form ATP. (b) In respiration, the cytoplasmic membrane, energized by the proton motive force, dissipates some of that energy in the formation of ATP from ADP and inorganic phosphate (Pi) in the process called oxidative phosphorylation. The coupling of the proton motive force to ATP synthesis occurs by way of a membrane protein enzyme complex called ATP synthase (ATPase) (see Section 5.12 and Figure 5.21).

20. Glycolysis Figure: 05-14a Caption:
Embden-Meyerhof pathway (glycolysis), the sequence of enzymatic reactions in the conversion of glucose to pyruvate and then to fermentation products (enzymes are shown in small type). The product of aldolase is actually glyceraldehyde 3-P and dihydroxyacetone P, but the latter is converted to glyceraldehyde 3-P. Note how pyruvate is the central “hub” of glycolysis, all fermentation products are made from pyruvate, and just a few common examples are given.

21. Figure: 05-14b
Caption:
Embden-Meyerhof pathway (glycolysis), the sequence of enzymatic reactions in the conversion of glucose to pyruvate and then to fermentation products (enzymes are shown in small type). The product of aldolase is actually glyceraldehyde 3-P and dihydroxyacetone P, but the latter is converted to glyceraldehyde 3-P. Note how pyruvate is the central “hub” of glycolysis, all fermentation products are made from pyruvate, and just a few common examples are given.

22. Proton Motive Force Figure: 05-20 Caption:
Generation of the proton motive force during aerobic respiration. The figure shows the orientation of key electron carriers in the membrane of an organism like Paracoccus denitrificans, a model prokaryote for studies of respiration. The + and – charges across the membrane represent H+ and OH-, respectively. Abbreviations are as follows: FMN, flavoprotein; Q, quinone; Fe/S, iron sulfur protein; cyt a, b, c, cytochromes (bL and bH, low and high potential b-type cytochromes, respectively). At the quinone site a recycling of electrons occurs during the “Q cycle.” This is because electrons from QH2 can be split in the bc1 complex (Complex III) between the Fe/S protein and the b-type cytochromes. Electrons that travel through the latter reduce Q (in two, one-electron steps) back to QH2, thus increasing the number of protons pumped at the Q-bc1 site. Electrons that travel to Fe/S proceed to reduce cytochrome c1 and then cytochrome c, and then a-type cytochromes in Complex IV, eventually reducing O2 to H2O (two hydrogen atoms are required to reduce For simplicity, protein Complex II, the succinate dehydrogenase complex, is not shown in this scheme. The numbers of the complexes shown are those used by convention by scientists in the field of membrane bioenergetics. Compare this electron transport chain with that of Escherichia coli, shown in Figure

23. Citric Acid Cycle Figure: 05-22a Caption:
The citric acid cycle (CAC). (a)The CAC begins when the two-carbon compound acetyl-CoA (formed from pyruvate) condenses with the four-carbon compound oxalacetate to form the six-carbon compound citrate. Through a series of oxidations and transformations, this six-carbon compound is ultimately converted back to the four-carbon compound oxalacetate, which then begins another cycle with addition of the next molecule of acetyl-CoA.

24. Figure: 05-22b
Caption:
The citric acid cycle (CAC). (b) The overall balance sheet of fuel (NADH/FADH) for the electron transport chain and CO2 generated in the CAC. Compare with Figure 5.14 and note the major energy difference between fermenting and respiring glucose.

25. Catabolic Diversity Figure: 05-23a Caption:
Energetics and carbon flow in (a) chemoorganotrophic respiratory metabolism. Note the importance of electron transport leading to proton motive force formation.

26. Catabolic Diversity Figure: 05-23b Caption:
Energetics and carbon flow in (b) chemolithotrophic metabolism. Note the importance of electron transport leading to proton motive force formation.

27. Catabolic Diversity Figure: 05-23c Caption:
Energetics and carbon flow in (c) phototrophic metabolism. Note how in phototrophic metabolism carbon for biosynthesis can come from CO2 (photoautotrophy) or organic compounds (photoheterotrophy). Note also the importance of electron transport leading to proton motive force formation.

28. Figure: 02-08
Caption:
Metabolic options for obtaining energy. The organic and inorganic chemicals listed here are just a few of the many different chemicals used by various chemotrophic organisms. Oxidation of the organic or inorganic chemicals yields ATP in chemotrophic organisms while conversion of solar energy to chemical energy (again, in the form of ATP) occurs in phototrophic organisms.