Chapter 13: Energetics and Catabolism

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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.

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TABLE 13.1

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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 

G

0 '. This is expressed in kilojoules. Catabolic reaction = exergonic Anabolic reactions = endergonic 4

Gibbs Free Energy Change

A+B C + D

 G  G =  = G o ’  G o ’ +

RT ln

[C] [D]/[A][B] + 2.303

RT log

[C] [D]/[A][B] At equilibrium  G = 0 

G o ’ =

-

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,



G

.

- If G o ’ - If G o ’ < 0, the process may go forward.

> 0, the reaction will go in reverse.

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In living cells, The standard conditions for 

G o ’

are as follows: - Temperature = 298 K (25 ° C) - Pressure = 1 atm - Concentrations = 1 M - pH = 7 6

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.

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Adenosine Triphosphate

ATP

contains a base, sugar, and three phosphates.

Under physiological conditions, ATP always forms a complex with Mg 2+ .

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Adenosine Triphosphate

ATP

can transfer energy to cell processes in three different ways: - Hydrolysis releasing phosphate (P i ) - Hydrolysis releasing pyrophosphate (PP i ) - Phosphorylation of an organic molecule Note that besides ATP other nucleotides carry energy.

- For example, guanosine triphosphate (GTP) provides energy for protein synthesis.

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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 +  G o ’ = 62 KJ/mol Reaction requires energy input from food molecules.

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Figure 13.7A

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FADH

Flavine adenine dinucleotide (FAD)

is another related coenzyme that can transfer electrons.

- FADH 2 : reduced form - FAD: oxidized form Unlike NAD + , FAD is reduced by two electrons and

two

protons.

Figure 13.7B

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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 13

Enzymes

Enzymes catalyze biological reactions. - Lower the

activation energy

allowing rapid conversion of reactants to products

H

2

+ 1/2 O

2 

H

2

O

 G o ’ = -237 kJ/mole 14

Enzyme Properties

• Very specific • Large proteins (10 4 to 10 6) • 3-D determines the activity and specificity •

Very efficient: rates increased 10 8 to 10 10 fold

• Subjected to cellular controls 15

Enzyme activity

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

Enzymes

The turnover number is generally 1-10,000 molecules per second .

17 Figure 5.4

Factors

• Temperature • pH • Substrate concentration 18

Factors influencing enzyme activity

Competitive inhibition 19 Figure 5.7a, b

Factors influencing enzyme activity

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Enzymes

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

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Factors influencing enzyme activity

Noncompetitive inhibition 22 Figure 5.7a, c

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 O 2 -

Photoheterotrophy

: Catabolism is conducted with a “boost” from light 23

Microbes catalyze many different kinds of substrates or catabolites.

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Starch

Cellulose 25

Polysaccharides

are broken down to disaccharides, and then to monosaccharides.

- Sugar and sugar derivatives, such as amines and acids, are catabolized to pyruvate.

Pyruvate

catabolism are fermented or further catabolized to CO 2 and other intermediary products of sugar and H 2 O 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.

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Glucose Breakdown

Glucose is catabolized via three main routes.

Figure 13.15

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Embden-Meyerhoff-Parnas Pathway

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

Figure 13.16

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Embden-Meyerhoff-Parnas Pathway

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 O 2 .

- It involves ten distinct reactions that are divided into two stages.

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Stage 1: Glucose activation stage

• 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 32

Stage 2. Energy-yielding stage

• 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 .

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Figure 13.17

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Summary: Embden-Meyerhoff Parnas Pathway

glucose  2 pyruvate 2ATP 2NADH + 2H + 35

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.

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Figure 13.19

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The Entner-Doudoroff Pathway

reactions of pentose phosphate pathway reactions of glycolytic pathway reactions of Embden Meyerhoff pathway Figure 9.8

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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.

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Summary: Entner-Doudoroff Pathway glucose 1 ATP 1 NADPH 1 NADH

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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.

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Fermentation Pathways

Homolactic fermentation

- Produces two molecules of lactic acid

Ethanolic fermentation

- Produces two molecules of ethanol and two CO 2

Heterolactic fermentation

- Produces one molecule of lactic acid, one ethanol, and one CO 2

Mixed-acid fermentation

- Produces acetate, formate, lactate, and succinate, as well as ethanol, H 2 , and CO 2 42

Figure 13.21

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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 CO 2 .

- Acetyl-CoA enters the TCA cycle by condensing with the 4-C oxaloacetate to form citrate.

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Figure 13.24

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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 + CO 2 + NADH + H +

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The Tricarboxylic Acid Cycle

For each pyruvate oxidized: - 3 CO 2 are produced by decarboxylation - 4 NADH and 1 FADH 2 redox reactions are produced by - 1 ATP is produced by substrate-level phosphorylation - Some cells make GTP instead.

- However, GTP and ATP are equivalent in stored energy.

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After the completion of the TCA cycle, all the carbons of glucose have been released as waste CO 2 .

- However, the metabolic pathway is not completed until the electrons carried by the coenzymes (NADH and FADH 2 ) are donated to a

terminal electron acceptor .

The overall process of

electron transport

and ATP generation is termed

oxidative phosphorylation

.

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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  •Oxaloacetate  Glutamate and glutamine aspartate Amphibolic pathway 50

Summary: TCA Cycle

Glucose 10 NADH + H + 2 FADH 2 4 ATP 10 NADH + H + + 2FADH 2  10 NAD + + 2FAD + + 24H + + 24e 51