Metabolism :

MetabolismMetabolism::

Key wordsKey words• Metabolism – definition• Catabolism and anabolism – definition, example• Identify/distinguish structure of coenzymes• Identify structure of ATP

What is Metabolism?What is Metabolism?

• Definition: Metabolism is the sum total of the chemical reactions of biomolecules in an organism

• Metabolism consists of 1.1. catabolism:catabolism: the breakdown of larger molecules into

smaller ones; an oxidative process that releases energy2.2. anabolism:anabolism: the synthesis of larger molecules from

smaller ones; a reductive process that requires energy

• Catabolism:Catabolism: the oxidative breakdown of nutrients

• Anabolism:Anabolism: the reductive synthesis of biomolecules

The study of the biochemical reactions in an organism, including the coordination, regulation and

energy needs

Terminology in MetabolismTerminology in Metabolism

• Metabolic pathway: A sequence of reactions, where the product of one reaction becomes the substrate for the next reaction.- either linear pathway or cyclic pathway- metabolic pathways proceed in many stages, allowing for efficient use of energy

• Metabolites: intermediates in metabolic pathway

Eg. 6 CO2(g) + 6 H2O(l) → C6H12O6(aq) + 6 O2(g)

Anabolism Anabolism

C6H12O6 (aq) + 6O2 (g) → 6CO2 (g) + 6H2O

CatabolismCatabolism

light

photosynthesis

respiration

Metabolic Metabolic pathwaypathway

Metabolic pathway: linear or cyclicMetabolic pathway: linear or cyclic

A Comparison of Catabolism and A Comparison of Catabolism and AnabolismAnabolism

• Metabolism is the sum total of the chemical reactions of biomolecules in an organism

MetabolismMetabolism• Metabolism involves the energy flow in the cell• Photoautotroph via photosynthesis transfers the

energy to heterotrophs• Heterotrophs obtain the energy through

oxidation/reduction of organic compounds (carbohydrate, lipid and proteins)

• Food supplies the energy• Energy = ATP

The Role of Oxidation and Reduction in The Role of Oxidation and Reduction in MetabolismMetabolism

• Oxidation-Reduction (redox) reactions are those in which electrons are transferred from a donor to an acceptor– oxidation:oxidation: the loss of electrons; the substance that loses

the electrons is called a reducing agentreducing agent– reduction:reduction: the gain of electrons; the substance that gains

the electrons is called an oxidizing agentoxidizing agent• Carbon in most reduced form- alkane• Carbon in most oxidized form- CO2 (final product of

catabolism)Reduced Oxidized

Oxidation and Reduction in MetabolismOxidation and Reduction in Metabolism

CH3CH2OH + 2H+ + 2e-

Ethanol Acetaldehyde

NAD+ + H+ + 2e- NADH

CH3CH2OH + NAD+ + NADH +H+

CH3CHO

CH3CHO

CH3CHCOO-OH

+ 2H+ + 2e-

Pyruvate Lactate

NAD+NADH + H+ + 2e-

+ H++ NADH CH3CHCOO-OH

+ NAD+

CH3CCOO-O

CH3CCOO-O

Oxidation of ethanol by NAD+

Reduction of pyruvate by NADH

Oxidation – less e

Reduction – gain e

Oxidizing agent – e acceptor

reducing agent – e donor

Metabolism: FeaturesMetabolism: Features

Metabolic pathway:1. Enzymes – multienzymes 2. Coenzymes3. ATP – produced or used

Regulation of metabolic pathway:– Feedback inhibition or – Feed-forward activation

A group of noncovalently associated enzymes that catalyze 2 or more sequential steps in metabolic/biochemical pathway

Metabolism: RegulationMetabolism: Regulation

• Regulation of metabolic pathway: 1. Feedback inhibition = product (usually ultimate product)

of a pathway controls the rate of synthesis through inhibition of an early step (usually the first step)

A B C D E P

2. Feed-forward activation = metabolite produced early in pathway activates enzyme that catalyzes a reaction further down the pathway

A B C D E P

E1 E2 E3 E4 E5

E1 E2 E3 E4 E5

—

+

CoenzymesCoenzymes

Coenzymes in metabolism:• NAD+/NADH • NADP+/NADPH• FAD+/FADH2

• Coenzyme A (CoASH) – activation of metabolites

Electron carriers

NADNAD++/NADH: An Important Coenzyme/NADH: An Important Coenzyme• Nicotinamide adenine

dinucleotide (NAD+) is an important coenzyme

• Acts as a biological oxidizing agent

• The structure of NAD+/NADH is comprised of a nicotinamide portion.

• It is a derivative of nicotinic acid

• NAD+ is a two-electron oxidizing agent, and is reduced to NADH

Reduced form, NADH carries 2 electrons

NADPNADP++/NADPH: /NADPH: Also comprised of nicotinamide portionAlso comprised of nicotinamide portion

• Nicotinamide adenine dinucleotide phosphate (NADP+) – oxidizing agent

• NADPH involves in reductive biosynthesis

• Differ with NAD+ at ribose (C2 contain a phosphoryl group, PO3

2-

• As electron carrier in photosythesis and pentose phosphate pathway

Reduced form, NADPH carries 2 electrons Anabolism

The Structures Flavin Adenine The Structures Flavin Adenine Dinucleotide (FAD)Dinucleotide (FAD)

• FAD is also a biological oxidizing agent

• FAD – can accept one-electron or two-electron

FADH carries 1 electron, FADH2 carries 2 electrons

The terminal e acceptor (O2) can accept only unpaired e (e must be transferred to O2 one at a time)

FAD/FADHFAD/FADH22

• FADH (semiquinone form) carries 1 electron,

• FADH2 (fully reduced hydroquinone form) carries 2 electrons

1

1

*

Formation of fully reduced hydroquinone form bypass the semiquinone form

Coenzyme A in Activation of Metabolic Coenzyme A in Activation of Metabolic PathwaysPathways

• A step frequently encountered in metabolism is activation– activationactivation:: the formation of a more reactive

substance – A metabolite is bonded to some other molecule

and the free-energy change for breaking the new bond is negative.

– Causes next reaction to be exergonic

Coenzyme A (CoASH)Coenzyme A (CoASH)• Coenzyme A – functions as a

carrier of acetyl and other acyl groups

• Has sulfhydryl/thiol group

Thioester bond

Acetyl-CoA: is a “high-energy” compound because of the presence of thioester bond – hydrolysis will release energy

CoASH

• ATP is essential high energy bond-containing compound

• Phosphorylation of ADP to ATP requires energy

• Hydrolysis of ATP to

ADP releases energyPhosphorylation: the addition of phosphoryl (PO3

2-) group/Pi (inorganic phosphate)

ATP- high energy compoundATP- high energy compound

nucleotide

MetabolismMetabolism::

(2)(2)






ATP- high energy compoundATP- high energy compound

nucleotide

• “High Energy” bonds- bonds that require or release convenient amounts of energy, depending on the direction of the reaction

• Couple reactions: the energy released by one reaction, such as ATP hydrolysis, provides energy for another reactions to completion – in metabolic pathway

The Phosphoric Anhydride Bonds in ATP are The Phosphoric Anhydride Bonds in ATP are “High Energy” Bonds“High Energy” Bonds

Phosphoanhydride /

Couple reaction: exampleCouple reaction: example

Role of ATP as Energy CurrencyRole of ATP as Energy Currency

Phosphorylation of ADP requires energy from breakdown of nutrients (catabolism)

The energy from hydrolysis of ATP will be used in the formation of products (anabolism)

Metabolism of CarbohydrateMetabolism of Carbohydrate

Catabolism

Anabolism

Major pathways of carbohydrate metabolism.

Fig 8.1 3rd ed

Key wordsKey words• Glycolysis, the fate for pyruvate• Substrate-level phosphorylation and oxidative

phosphorylation

GlycolysisGlycolysis• Glycolysis is the first stage of glucose

metabolism

• Glycolysis converts 1 molecule of glucose to 2 units of pyruvate (three C units) and the process involves the synthesis of ATP and reduction of NAD+ (to NADH)

• The pathway has 10 steps/reactions

• Glycolysis are divided into 2 stages/phases, Phase 1=1st 5 reactionsPhase 2=2nd 5 reactions

Linear pathway

GlycolysisGlycolysis• Glycolysis are divided into 2 stages/phases,

1. Phase 1=1st 5 reactions Energy investment – A hexose sugar (glucose) is split into

2 molecules of three-C metabolite (glyceraldehyde-3-phosphate = GAP). The process consume 2 ATP

2. Phase 2=2nd 5 reactions Energy recovery – The two molecules of GAP are converted to

2 molecules of pyruvate with the generation of 4 ATP and 2 NADH.

Overall equation –Glucose + 2 NAD+ + 2 ADP + 2Pi

2 pyruvate + 2 NADH + 2 ATP + 2 H2O + 4H+

Glycolysis has a net “profit” of 2 ATP per glucose

The Reactions of The Reactions of GlycolysisGlycolysis1. Phosphorylation of glucose to give

glucose-6-phosphate2. Isomerization of glucose-6-

phosphate to give fructose-6-phosphate

3. Phosphorylation of fructose-6-phosphate to yield fructose-1,6-bisphosphate

4. Cleavage of fructose-1,6,-bisphosphate to give glyceraldehyde-3-phosphate and dihydroxyacetone phosphate

5. Isomerization of dihydroxyacetone phosphate to give glyceraldehyde-3-phosphate – isomerase enzyme

1

2

3

4

5

Use ATP

Use ATP

glucokinase

phosphofructokinase

The Reactions of Glycolysis (Cont’d)The Reactions of Glycolysis (Cont’d)6. Oxidation of glyceraldehyde-3-

phosphate to give 1,3-bisphosphoglycerate

7. Transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP to give 3-phosphoglycerate

8. Isomerization of 3-phosphoglycerate to give 2-phosphoglycerate

9. Dehydration of 2-phosphoglycerate to give phosphoenolpyruvate

10. Transfer of a phosphate group from phosphoenolpyruvate to ADP to give pyruvate

oxidation

transfer

isomerization

dehydration

transfer

Phosphorylation of ADP to ATP

Phosphorylation of ADP to ATP

6

7

8

9

10

Electron acceptor – NAD+

Glyceraldehyde-3-P dehydrogenase

GlycolysisGlycolysis• Dephosphorylation of ATP• Phosphorylation of ADP

• Oxidation of intermediates and reduction of NAD+ to NADH by dehydrogenase reactions- step 6 - glyceraldehyde-3-phosphate dehydrogenase

By kinase enzyme at step 1, 3, 7 and 10

ATP productionATP production• ATP is produced by phosphorylation of ADP - is

through substrate-level phosphorylation• Substrate-level phosphorylation – the process of

forming ATP by phosphoryl group transfer from reactive intermediates to ADP

• 1,3-bisphosphoglycerate and phosphoenolpyruvate – “high-energy” intermediates/compounds

• Oxidative phosphorylation – the process of forming ATP via the pH gradient as a result of the electron transport chain.

Glycolysis - Step 7 and 10

Fates of Pyruvate From GlycolysisFates of Pyruvate From Glycolysis• Once pyruvate is formed, it

has one of several fates

• In aerobic metabolism-

pyruvate will enter the citric acid cycle, end product in aerobic metabolism CO2 and H2O

• In anaerobic metabolism- the pyruvate loses CO2

produce ethanol = alcoholic fermentation

produce lactate = anaerobic glycolysis

Anaerobic Metabolism of PyruvateAnaerobic Metabolism of Pyruvate• Under anaerobic conditions, the most important pathway for the

regeneration of NAD+ is reduction of pyruvate to lactate• Lactate dehydrogenase (LDH) is a tetrameric isoenzyme consisting

of H and M subunits; H4 predominates in heart muscle, and M4 in skeletal muscle In muscle, during vigorous exercise –

demand of ATP but O2 is in short supply is largely synthesized via anaerobic glycolysis which rapidly generates ATP rather than through slower oxidative phosphorylation

Alcoholic Fermentation Alcoholic Fermentation • Two reactions lead to the production of ethanol:

– Decarboxylation of pyruvate to acetaldehyde

– Reduction of acetaldehyde to ethanol

• Pyruvate decarboxylase is the enzyme that catalyzes the first reaction

• This enzyme require Mg2+ and the cofactor, thiamine pyrophosphate (TPP)

• Alcohol dehydrogenase catalyzes the conversion of acetaldehyde to ethanol

In anaerobic bacteria

NADNAD++ Needs to be Recycled to Prevent Decrease in Needs to be Recycled to Prevent Decrease in Oxidation ReactionsOxidation Reactions

Structure of cell Structure of cell

Cytoplasm/

Cytosol

TYPICAL PROKARYOTIC CELL

Cytosol

Where does the Glycolysis Take Place?Where does the Glycolysis Take Place?

Glycolysis is universal!

Citric Acid Cycle

= Krebs Cycle, Tricarboxylic acid Cycle

(TCA)

Metabolism: FeaturesMetabolism: Features

Metabolic pathway:1. Enzymes – multienzymes 2. Coenzymes3. ATP – produced or used

A group of noncovalently associated enzymes that catalyze 2 or more sequential steps in metabolic/biochemical pathway

Couple reaction: exampleCouple reaction: example

CoenzymesCoenzymes

Coenzymes in metabolism:• NAD+/NADH • NADP+/NADPH• FAD+/FADH2

• Coenzyme A (CoASH) – activation of metabolites

Electron carriers

GlycolysisGlycolysis• Glycolysis are divided into 2 stages/phases,

1. Phase 1=1st 5 reactions Energy investment – A hexose sugar (glucose) is split into

2 molecules of three-C metabolite (glyceraldehyde-3-phosphate = GAP). The process consume 2 ATP

2. Phase 2=2nd 5 reactions Energy recovery – The two molecules of GAP are converted to

2 molecules of pyruvate with the generation of 4 ATP and 2 NADH.

Overall equation –Glucose + 2 NAD+ + 2 ADP + 2Pi

2 pyruvate + 2 NADH + 2 ATP + 2 H2O + 4H+

Glycolysis has a net “profit” of 2 ATP per glucose








Glycolysis – in cytoplasm

Key wordsKey words• Definition – citric acid cycle• Explain the citric acid cycle• Distinguish between glycolysis and citric acid cycle• Understand -oxidation – catabolism of lipid

Citric acid cycle Citric acid cycle • Requires aerobic condition• Amphibolic (both catabolic & anabolic)

• Serves 2 purposes:1. Oxidize Acetyl-CoA to CO2 to produce energy

(ATP & reducing power of NADH & FADH2)-involved in the aerobic catabolism of carbohydrates, lipids and amino acids

2. Supply precursors for biosynthesis of carbohydrates, lipids, amino acids, nucleotides and porphyrins

Citric Acid Cycle

= Krebs Cycle

= Tricarboxylic acid Cycle

(TCA)

TCATCA• Circular pathway• Two-carbon unit

needed at the start of the citric acid cycle

• The two-carbon unit is acetyl-CoA

• Involves 8 reactions• The overall reaction

from 1 acetyl-CoA produce 3 NADH, 1 FADH2, 2 CO2 and 1 GTP (equivalent to 1 ATP)

Pyruvate is converted to Acetyl-CoA – Pyruvate is converted to Acetyl-CoA – activation of pyruvateactivation of pyruvate

• Pyruvate dehydrogenase complex is responsible for the conversion of pyruvate to acetyl-CoA

• Five enzymes in complex• Requires the presence of cofactors TPP (thymine

pyrophosphate), FAD, NAD+, and lipoic acid and coenzyme A (CoA-SH)

• The overall reaction of the pyruvate dehydrogenase complex is the conversion of pyruvate, NAD+, and CoA-SH to acetyl-CoA, NADH + H+, and CO2

Thioester, high energy compound

Oxidation of pyruvate and reduction of NAD+

3C

2CPyruvate = pyruvic acid




Thioester bond


CoASH

Features of TCAFeatures of TCA• Circular pathway• Two-carbon unit needed

at the start of the citric acid cycle


• Involves 8 reactions• The overall reaction from

1 acetyl-CoA produce 3 NADH, 1 FADH2, 2 CO2

and 1 GTP (equivalent to 1 ATP)

How about 1 molecule of glucose?

X 2

Electron acceptor – NAD+ and FAD

Mitochondrial matrix

Citric acid cycle - featuresCitric acid cycle - features• Oxidation decarboxylation

- CO2 leaves at step 3 and 4

• Oxidation of intermediates and reduction of NAD+ to NADH by dehydrogenase reactions- step 3, 4 and 8- isocitrate dehydrogenase- α-ketoglutarate dehydrogenase- malate dehydrogenase

• Oxidation of intermediates and reduction of FAD+ to FADH2 by succinate dehydrogenase reaction- step 6

• Phosphorylation of GDP to GTP – step 5

Where does the Citric Acid Cycle Take Place?Where does the Citric Acid Cycle Take Place?

• In eukaryotes, cycle takes place in the mitochondrial matrix

In prokaryotes? Cytoplasm

The Central Relationship of the Citric The Central Relationship of the Citric Acid Cycle to CatabolismAcid Cycle to Catabolism

• TCA involves 8 series of reactions that oxidizes the acetyl group of acetyl-CoA to 2 molecules of CO2

and the energy is conserves in NADH, FADH2 and “high-energy” compound, GTP

• Acetyl-CoA – synthesize from pyruvate (glycolysis product)

Guanosine – Tri-Phosphate

Aerobic catabolismAerobic catabolism

• NADH, FADH2 from glycolysis and TCA will enter the Electron Transport Chain (ETC) to produce more ATP (oxidative phosphorylation)

• 1 NADH = 2.5 ATP,

• 1 FADH2 = 1.5 ATP

• ETC take place in mitochondria - inner membrane (eukaryotes)

In prokaryotes?

Plasma membrane

In ETC

Oxidation of Pyruvate Forms COOxidation of Pyruvate Forms CO22 and ATP and ATP

Aerobic metabolism is more efficient than anaerobic metabolism

Citric acid cycle - amphibolic Citric acid cycle - amphibolic • Amphibolic (both catabolic

& anabolic)• Serves 2 purposes:

1. Oxidize Acetyl-CoA to CO2 to produce energy (ATP & reducing power of NADH & FADH2)-involved in the aerobic catabolism of carbohydrates, lipids and amino acids

2. Supply precursors for biosynthesis (anabolism) of carbohydrates, lipids, amino acids, nucleotides and porphyrins

Replenish TCA- catabolism of amino a. and fatty a.

Anabolic pathway

Require aerobic condition

Differences between glycolysis & TCA Differences between glycolysis & TCA cyclecycle

• Glycolysis is a linear pathway; TCA cycle is cyclic

• Glycolysis occurs in the cytosol and TCA is in the mitochondrial matrix

• Glycolysis does / does not require oxygen; TCA requires oxygen (aerobic)

Lipids are Involved in Generation and Lipids are Involved in Generation and Storage of EnergyStorage of Energy

• The oxidation of fatty acids (FA)in triacylglycerols are the principal storage form of energy for most organisms– Their carbon chains are in a highly reduced form– The energy yield per gram of fatty acid oxidized is greater

than that per gram of carbohydrate oxidized

C6H12O6 + 6O2

CH3(CH2)14COOH + 23O2

6CO2 + 6H2O

16CO2 +16H2O

-15.9

-38.9Palmitic acid

Glucose

Energy(kJ•mol-1)

Catabolism of Lipids - triacylglycerolCatabolism of Lipids - triacylglycerol• Lipases catalyze hydrolysis of bonds between fatty acid and

the rest of triacylglycerols• Phospholipases catalyze hydrolysis of bonds between fatty

acid and the rest of phosphoacylglycerols • May have multiple sites of action

Catabolism of fatty acid - Catabolism of fatty acid - -Oxidation-Oxidation• -Oxidation:-Oxidation: a series

of reactions that cleaves carbon atoms two at a time from the carboxyl end of a fatty acid

• The complete cycle of one -oxidation requires four enzymes/steps

• Take place in mitochondria matrix

1 round of -oxidation = yield 1 NADH, 1 FADH2 and 1 acetyl-CoA

Spiral pathway

METABOLISM

REVISION

– Catabolism:Catabolism: the oxidative breakdown of nutrients

– Anabolism:Anabolism: the reductive synthesis of biomolecules• Catabolism – features

1. Release energy (ADP ATP)

2. Oxidizing agent (NAD+, FAD)

• Anabolism – features

1. Use energy (ATP ADP)

2. Reducing agent (NADH ,FADH2)

Metabolism – the sum total of biochemical reaction carried out by organism

MetabolismMetabolism• Metabolism involves the energy flow in the cell• Photoautotroph via photosynthesis transfers the

energy to heterotrophs• Heterotrophs obtain the energy through

oxidation/reduction of organic compounds (carbohydrate, lipid and proteins)

• Food supplies the energy• Energy = ATP

Major pathways of carbohydrate metabolism.

Fig 8.1 3rd ed

GlycolysisGlycolysis• Glycolysis is the first stage of glucose

metabolism

• Glycolysis converts 1 molecule of glucose to 2 units of pyruvate (three C units) and the process involves the synthesis of ATP and reduction of NAD+ (to NADH)

• The pathway has 10 steps/reactions

• Glycolysis are divided into 2 stages/phases, Phase 1=1st 5 reactionsPhase 2=2nd 5 reactions

Linear pathway








Glycolysis – in cytoplasm






ATP- high energy compoundATP- high energy compound ATP – energy carrier / an

energy transfer agent

nucleotide




Thioester bond


CoASH

TCATCA• Circular pathway• Two-carbon unit

needed at the start of the citric acid cycle


• Involves 8 reactions• The overall reaction

from 1 acetyl-CoA produce 3 NADH, 1 FADH2, 2 CO2 and 1 GTP (equivalent to 1 ATP)

Citric acid cycle - amphibolic Citric acid cycle - amphibolic • Amphibolic (both catabolic

& anabolic)• Serves 2 purposes:

1. Oxidize Acetyl-CoA to CO2 to produce energy (ATP & reducing power of NADH & FADH2)-involved in the aerobic catabolism of carbohydrates, lipids and amino acids

2. Supply precursors for biosynthesis (anabolism) of carbohydrates, lipids, amino acids, nucleotides and porphyrins

Replenish TCA- catabolism of amino a. and fatty a.

Anabolic pathway

Require aerobic condition

Where does the Citric Acid Cycle Take Place?Where does the Citric Acid Cycle Take Place?

• In eukaryotes, cycle takes place in the mitochondrial matrix

In prokaryotes? Cytoplasm

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Metabolism :