Microbiology

Ch. 13: Energetics and Catabolism

Prof. Pyung Cheon Lee

1 Chapter Overview

● Energy and entropy: Building a cell ● Energy and entropy in biochemical reactions ● Energy carriers and electron transfer ● Catabolism: The microbial buffet ● Glucose breakdown ● Fermentation ● The tricarboxylic acid (TCA) cycle

2 Metabolism: relationship between catabolism and anabolism

3 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 for anabolism. - However, some of the energy is released as heat.

4 TABLE 13.1

5 Energy and Entropy

Energy is the ability to do work. Entropy is a measure of the disorder or randomness of a system. Cells use energy to assemble simple, disordered molecules into complex, ordered forms.

Figure 13.2

6 Energy and Entropy

The local, temporary gain of energy enables the cell to grow. :Continued growth requires a continual gain of energy and continual radiation of heat. What is true of the cell holds as well for the entire biosphere. :On Earth, the total metabolism of all life-forms must ultimately dissipate most energy as heat. :So overall, Earth’s biosphere behaves as a giant thermal reactor.

7 Solar Energy

Figure 13.3

8 Gibbs Free Energy Change

The direction of a reaction can be predicted by a thermodynamic quantity called Gibbs free energy change, ∆G.

∆G includes enthalpy and entropy.

∆G = ∆H – T∆S - ∆H: Change in enthalpy, the heat energy absorbed or released - T∆S: Product of temperature and entropy change

- If ∆G < 0, the process may go forward. - If ∆G > 0, the reaction will go in reverse.

9 The standard conditions for ∆Go are as follows:

- Temperature = 298 K (25C) - Pressure = 1 atm - Concentrations = 1 M

In living cells, the conditions for ∆Go’ are the same plus the additional standard condition of pH = 7.

10 Energy Carriers 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.

11 Adenosine Triphosphate (ATP)

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

Figure 13.6

12 Adenosine Triphosphate

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.

13 NADH 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+ ∆Go’ = 62 KJ/mol

Reaction requires energy input from food molecules.

14 Figure 13.7A

15 FADH 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.

Figure 13.7B

16 Catabolism: The Microbial Buffet

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

17 Microbes catalyze many different kinds of substrates or catabolites

Figure 13.11

18 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.

19 Figure 13.13

20 Glucose Breakdown

Glucose is catabolized via three main routes.

Figure 13.15

21 Embden-Meyerhoff-Parnas Pathway

In the EMP pathway, a glucose molecule undergoes a stepwise breakdown to two pyruvate molecules.

22 Embden-Meyerhoff-Parnas Pathway - It occurs in the cytoplasm of the cell.

- It functions in the presence or absence of O2. - It involves 10 reactions that are divided into two stages.

1) Glucose activation stage - Glucose is “activated” by phosphorylations that ultimately convert it into fructose-1,6-bisphosphate.

2) Energy-yielding stage - Glyceraldehyde-3-phosphate is ultimately converted to pyruvate.

- Redox reactions produce two molecules of NADH.

- Four ATP molecules are produced by substrate-level phosphorylation.

23 Substrate-level phosphorylation

24 The Entner-Doudoroff Pathway

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.

25 26 The Pentose Phosphate Shunt

Like the ED pathway, the pentose phosphate shunt forms 6-phosphogluconate.

It is then converted to the key intermediate pentose ribulose-5-phosphate, which in turn produces a series of sugars, each containing three to seven carbons.

This pathway produces 1 ATP and no NADH, but two NADPHs for biosynthesis (eg. Fatty acid).

27 28 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.

29 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

30 31 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 4C oxaloacetate to form citrate.

32 33 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

34 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.

35 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.

36 37 When glucose is absent, cells can catabolize acetate or fatty acids using a modified TCA cycle called the glyoxylate shunt (pathway). - Consists of two enzymes that divert isocitrate to glyoxylate and incorporate a second acetyl- CoA to form malate.

38