Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Chapter 10 Catabolism: Energy Release and Conservation

Barny Whitman: Office hours: Thursdays 9-11am 541 Biological Sciences Building For appointments: whitman@uga.edu
1

Feel challenged? Convert equations to sentences. Review freshman chemistry. On the quiz, you will have to use these equations, but you will not have to remember them.
3

How large must the DE be to make ATP?

[no calculators, please]

Figure 10.10 Mitochondria and Paracoccus electron transport

-200 mV +35 mV +385 mV

+50 mV Eo of carriers (mV): NADH, -320; FADH, -220; succinate, +31; Q, +100; cyt c +230; H2O, +820
5

Figure 10.13-Q cycle

The only mechanism of H+ pumping that is really understood

Find the typo!

Figure 10.15 What types of energy conversions are catalyzed by the ATP synthase?

What types of energy conversions are catalyzed by the ATP synthase? Conversion of chemiosmotic energy, ie. the energy stored in a gradient across a membrane, into conformational energy , ie. the energy stored in the structure of a macromolecule, as well as the conversion of conformational energy into covalent bond energy, ie. in a small molecule such as ATP

Variations in respiration typical among prokaryotes 1. Aerobic respiration- modifications of the electron transport chain are typical; especially common are a wide variety of terminal oxidases
2. Anaerobic respiration- use of an electron acceptor other than O2. 3. Different entry points into electron transport chain depends upon Eo of electron donorlithotrophy
9

Figure 10.12 Electron Transport Chain of E. coli

Branched pathway
Different cytochromes used than in the mitochondria Notice different numbers of protons are pumped

10

Figure 10.9Tower of Power In anaerobic respiration, different components of the electron transport chain are used depending upon the Eo of the acceptor

11

Denitrification- nitrate is the electron acceptor. Which components of the electron transport chain are used?

-200 mV

+35 mV

+385 mV

+50 mV
12

Electron transport chain in Paracoccus during denitrification.

Denitrification occurs in a sequential series of reactions Reactions NO3-/NO2NO2- /NO NO/N2O N2O/N2 Eo (Mv) +430 +360 +1180 +1360

NO3- is nitrate NO2- is nitrite NO is nitric oxide N2O is nitrous oxide

13

Sulfur reduction- sulfur is the electron acceptor. Which components of the electron transport chain are used?

-200 mV

+35 mV

+385 mV

+50 mV
14

Table 10.1Eo of acceptors

+820 mV +360 mV +740 mV (N2)

-220 mV -240 mV -280 mV -270 mV

+770 mV but ~+200 mV at pH 7 +140 mV +475 mV
15

+ 33 mV

Why are prokaryotic electron transport chains so diverse?

16

Figure 10.9Tower of Power For lithotrophs, different entry points into electron transport chain depend upon Eo of electron donor

17

Nitrification- ammonia and nitrite are the electron donors. Which components of the electron transport chain are used?
-200 mV +35 mV +385 mV

+50 mV
18

Figure 10.26- Nitrobacter electron transport chain. Reverse electron transport is used to reduce NAD for biosynthesis.

19

Tables 10.3/10.4

Homework: Calculate the changes in midpoint potential (Eo) from the changes in free energy. Do your values make sense?
20

Photosynthesis Chlorophyll-based photosynthesis uses light energy to make good electron donors from poor electron donors. It then uses the electron transport chain to generate a PMF or reduce NAD(P).

Bacteriorhodopsin-based photosynthesis uses light energy to generate a PMF directly. The major pigment is retinal instead of chlorophyll. Electron transport is not involved.
21

Chlorophyll based photosynthesis: Light is captured by the light-harvesting complex, transferred to the reaction center, which is the site of the photochemical event. Extensive diversity of the LHC in prokaryotes allows for capturing light of a variety of wavelengths and conditions. In contrast, the RCs are more conserved- there being only two types, RCI and RCII.

The LHC is the site of photon capture, ie. the conversion of light energy to the excited state of the pigment molecules.
The RC is the site of the photochemical event, ie. energy conversion from the excited state of the pigment molecules to covalent bond energy in generation of a strong reductant and strong oxidant. A charge separation Always associated with membranes.
22

Organization of the phototrophic apparatus in different groups of phototrophic bacteria. OM = outer membrane, CW = cell wall, CM = cytoplasmic membrane, RC = reaction center, LHC = light-harvesting complex. Question marks indicate that the organization of the cell envelope and the organization of the photosynthetic apparatus in Heliothrix oregonensis is not exactly known. From: JRG OVERMANN and FERRAU GARCIA-PICHEL (2003) The Phototrophic Way of Life. M. Dworkin (ed.) The Prokaryotes, 3rd edition, available on-line.
23

Phycobilisome- primary LHC to both RCI and RCII

Photosynthetic apparatus in the cyanobacteria. Cyt = cytochrome; P840 and P870 reaction center special pair = primary electron donor; B800, B850, B875 = bacteriochlorophyll molecules bound to light-harvesting complexes II and I; A 0 = primary electron acceptor in green sulfur bacteria = Chl a; A 1 = secondary electron acceptor in green sulfur bacteria = menaquinone; Q A, Q B = ubiquinone; FX, FA, FB = FeS-clusters bound to the reaction center; Fd = ferredoxin; FMO = Fenna-Matthews-Olson protein; FNR = ferredoxin NADP+ reductase; PQ = plastoquinone; PC = plastocyanin; PS = photosystem. From: OVERMANN and GARCIA PICHEL (2003) The Phototrophic Way of Life. M. Dworkin (ed.) The 24 Prokaryotes, 3rd edition, available on-line.

Photosynthesis in the cyanobacteria is very similar to that in the chloroplast. Major differences are in the LHC. Otherwise, the both have two RCs and generate a PMF for ATP biosynthesis and NADPH for CO2 reduction.

Why are two RCs necessary to reduce NADP with H2O as the electron donor?
25

Oxygenic photosynthesis appear to have evolved about 2.3 billion years ago, corresponding to the Great Oxidation Event of the earths atmosphere. Microbial life is at least 3.8 billion years old. Why do you think it took so long for oxygenic photosynthesis to evolve?

26

Photosynthetic apparatus in the purple bacteria. CM = cytoplasmic membrane; Cyt = cytochrome; P840 and P870 reaction center special pair = primary electron donor; B800, B850, B875 = bacteriochlorophyll molecules bound to lightharvesting complexes II and I; QA, QB = ubiquinone; FX, FA, FB = FeS-clusters bound to the reaction center; Fd = ferredoxin; From: OVERMANN and GARCIAPICHEL (2003) The Phototrophic Way of Life. M. Dworkin (ed.) The Prokaryotes, 3rd edition, available on-line.
27

Anoxygenic phototrophs use two ways to make NAD(P)H.

In the green bacteria, NAD is reduced by ferredoxin produced by the photosynthetic electron transport chain. Electrons are returned to the reaction center by electron donors such as sulfide or thiosulfate. Noncyclic photosynthesis. In the purple bacteria, photosynthesis generates an PMF. Reverse electron transport then reduces NAD with poor electron donors such as succinate (but also sulfide and thiosulfate). Cyclic photosynthesis.
28

Heterotrophy- the dark side of life

many different energy sources are funneled into common degradative pathways many pathways generate glucose or intermediates of the pathways used in glucose metabolism Using common degradative pathways greatly increases metabolic efficiency for generalist organisms- what might specialists do?

29

Figure 10.2Heterotrophy- the dark side of life

many different energy sources are funneled into common degradative pathways Using common degradative pathways greatly increases metabolic efficiency for generalist organismswhat might specialists do?
30

Figure 10.3Prokaryotic cells are usually not compartmentalized, so catabolism and anabolism occur simultaneously in the cytoplasm. Amphibolic pathway: many of the reactions function in both catabolism and anabolism. A few enzymes that catalyze irreversible reactions serve as the gate keepers. How do you prevent a futile cycle? Name some common amphibolic pathways:

31

Figure 10.4Embden-Meyerhof Pathway. Most common pathway for glucose degradation to pyruvate. Look for the addition of phosphates to activate the sugar, oxidation steps to generate NADH, biosynthesis of highenergy molecules for making ATP by substrate-level phosphorylation

32

Summary of Embden-Meyerhof Pathway.

glucose + 2ADP + 2Pi + 2NAD+

2 pyruvate + 2ATP + 2NADH + 2H+ Note that 2 ATPs are invested in the activation and 4 ATPs are produced, for a net of 2 ATPs.

33

Figure 10.5Entner-Duodoroff Pathway. Less common that EM pathway but still widely distributed in bacteria and archaea.

Net yield per glucose molecule: 1 ATP 1 NADPH 1 NADH

Why use this pathway if the net yield of ATP is less?

34

Figure 10.6Pentose phosphate Pathway. Can operate at same time as Embden-Meyerhof or Entner-Duodoroff pathways; an amphibolic pathway, esp. for ribose biosynthesis; Over all yield: glucose-6-P + 12NADP+ + 7H2O 6CO2 + 12NADPH + 12H+ Pi Note that EMP reactions generate 2 ATP + NADH per pyruvate made.
35

Why use the Pentose phosphate Pathway?

1. Production of NADPH for biosynthesis. 2. Production of ribose-5-phosphate for nucleic acid biosynthesis and erythrose-4-phosphate for aromatic amino acid biosynthesis. 3. Yields some ATP. 4. Allows for catabolism of pentoses.

36

Use your general knowledge to estimate (or guestimate):

How many genes in a prokaryotic cell?

How many proteins are present at any one time? How many enzymes are present at any one time? How many enzymes are active at any one time? How many of these enzymes catalyze reversible reactions?

So what does it all mean?

37

Figure 10.7Tricarboxylic acid cycle. The best pathway on earth. Probably the most widely distributed pathway in prokaryotes. yield per acetyl-CoA molecule: 1 GTP 3 NADH 1 FADH2 2 CO2 Also a major source of intermediates for amino acid biosynthesis.

38

Figure 10.16Total yield of ATP during aerobic respiration.

Assumes a P/O ratio of 2.5 for NADH oxidation and 1.5 for FADH2 oxidation. P= 1 ATP = 4 H+ O = 1/2O2 = 2e- =1 NADH = 10 H+ for FADH2, 2e- = 6 H+ Prokaryotes often have a lower yield because their electron transport chains translocate fewer H+ per 2e- and the PMF is used for more than ATP biosynthesis.
39

Figure 10.19Fermentation, an alternative to aerobic respiration.

In the absence of an external electron acceptor, cells reduce pyruvate produced from glycolysis to regenerate NAD+ for glucose oxidation. A wide variety of different pathways are found in different prokaryotes. Growth is then possible from the ATP generated by substrate level phosphorylation. How do these cells make their PMF?
40

Simple sugars and other monomers are rare in nature. Most of the carbon is in polymers such as cellulose, hemicellulose, chitin, lignin, proteins, fatty acids, etc. How do cells get this material?

1.
2.

Production of extracellular enzymes to degrade polymers too large to be taken up by cells, such as proteases Attachment to polymers and production of cell-associated degradative complexes, such as the cellulosome

Roy H. Doi & Akihiko Kosugi Nature Reviews Microbiology 2, 541-551 (July 2004)
41

Figure 10.20-Uptake of other sugars. Hexoses are converted to intermediates of glycolytic pathways, such as glucose-6-P. Disaccharides are converted to monosaccharides. Reserve polymers, such as glycogen and starch, also cleaved by phosphorylases: (glucose)n + Pi (glucose)n-1 + glucose-1-P

42

Figure 10.21-22-Lipid catabolism

Triglycerides hydrolyzed to glycerol and fatty acids by lipases, glycerol then degraded via the glycolytic pathway, and fatty acids often oxidized via oxidation pathway. The reserve material, poly(b-OH butyrate) also metabolized in this fashion.
43

Figure 10.23-Protein and amino acid catabolism

1. 2. 3. 4. Proteases hydrolyze proteins to peptides and amino acids, which are taken up by the cell Amino group is removed from the amino acid by deaminations or tranaminations. Resulting organic acids are converted to pyruvate, acetyl-CoA, or TCA cycle intermediate Oxidized by TCA cycle

What is the other keto acid in the TCA cycle?

What amino acid does it form?

44

Aromatic degradation
Lignin is one of the most abundant organic compound on earth. Produced by woody plants, it is very recalcitrant and accumulates in soil. Many other aromatic compounds are important xenobiotics and pollutants.

45

Aromatic degradation
Degradation proceeds stepwise: 1. Polymers converted to monomers 2. In aerobes, monomers converted to catechol or protocatechuate and then to TCA cycle intermediates by the bketoadipate pathway 3. In anaerobes, monomers are degraded to benzoate and acetyl-CoA

46