Download Energetics and Catabolism

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 G0'. This is expressed in
kilojoules.
Catabolic reaction = exergonic
Anabolic reactions = endergonic
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Gibbs Free Energy Change
A+B
C+D
G = Go’ + RT ln [C] [D]/[A][B]
G = Go’ + 2.303 RT log [C] [D]/[A][B]
At equilibrium G = 0
Go’ = - 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 Go’ < 0, the process may go forward.
- If Go’ > 0, the reaction will go in reverse.
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In living cells,
The standard conditions for Go’ are as follows:
- Temperature = 298 K (25° C)
- Pressure = 1 atm
- Concentrations = 1 M
- pH = 7
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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 Mg2+.
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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.
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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+ Go’ = 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.
- FADH2: 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
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Enzymes
Enzymes catalyze biological reactions.
- Lower the activation energy allowing
rapid conversion of reactants to products
H2 + 1/2 O2  H2O
Go’ = -237 kJ/mole
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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
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Enzyme activity
• Active site
• Enzyme-substrate complex
• Tranformation
• Release of products and original
enzyme
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Enzymes
The turnover number is generally 1-10,000 molecules per second.
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Figure 5.4
Factors
• Temperature
• pH
• Substrate concentration
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Factors influencing enzyme activity
Competitive inhibition
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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
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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 O2
- Photoheterotrophy: Catabolism is
conducted with a “boost” from light
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Microbes catalyze many different kinds of
substrates or catabolites.
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Starch
Cellulose
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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.
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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
O2.
- 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-1,6bisphosphate.
• 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
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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-MeyerhoffParnas Pathway
glucose

2 pyruvate
2ATP
2NADH + 2H+
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The Entner-Doudoroff Pathway
Probably evolved earlier than EMP pathway.
Glucose is activated by one phosphorylation
reaction, and then dehydrogenated to 6phosphogluconate.
- 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
EmbdenMeyerhoff
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 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
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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 CO2.
- 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 + CO2 + NADH + H+
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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.
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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.
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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  Glutamate and glutamine
•Oxaloacetate  aspartate
Amphibolic pathway
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Glucose
Protons
Summary: TCA Cycle
10 NADH + H+
2 FADH2
4 ATP
10 NADH + H+ + 2FADH2  10 NAD+ + 2FAD+ + 24H+ + 24e-
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