Metabolism:

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

What is Metabolism?
Definition: Metabolism is the sum total of the chemical reactions of biomolecules in an organism Metabolism consists of
1. Catabolism: the breakdown of larger molecules into smaller ones, an oxidative process releases energy 2. Anabolism: the synthesis of larger molecules from smaller ones, a reductive process that requires energy

Catabolism: the oxidative breakdown of nutrients Anabolism: the reductive synthesis of biomolecules

Terminology in Metabolism
Eg. 6 CO2(g) + 6 H2O(l) C6H12O6(aq) + 6 O2(g)
photosynthesis

light

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

respiration

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: intermediat es in metabolic pathway

Metabolic pathway

Metabolic pathway: linear or cyclic

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

A Comparison of Catabolism and Anabolism

Metabolism
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 Metabolism

Oxidation-Reduction (redox) reactions are those in which electrons are transferred from a donor to an acceptor oxidation: the loss of electrons; the substance that loses the electrons is called a reducing agent reduction: the gain of electrons; the substance that gains the electrons is called an oxidizing agent Carbon in most reduced form- alkane Carbon in most oxidized form- CO2 (final product of catabolism)
Reduced Oxidized

Oxidation and Reduction in Metabolism

Oxidation of ethanol by NAD + NAD + + H+ + 2 e Oxidizing agent e acceptor Reduction gain e

CH3 CH2 OH

NADH Oxidation less e O CH3 CH + 2 H+ + 2 e O CH3 CH + NADH + H+ Acetaldehyde

reducing agent e donor

+ CH3 CH2 OH + NAD Ethanol

Reduction of pyruvate by NADH NADH O CH3 CCOO - + 2 H+ + 2 e O + CH3 CCOO - + NADH + H Pyruvate

NAD + + H+ + 2 e OH CH3 CHCOOOH CH3 CHCOO- + NAD + Lactate

Metabolism: Features
Metabolic pathway:
1. Enzymes multienzymes 2. Coenzymes 3. ATP produced or used
Regulation of metabolic pathway: Feedback inhibition or Feed-forward activation

Metabolism: 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) ABCDEP
E1 E2 E3 E4 E5

2. Feed-forward activation = metabolite produced early in pathway activates enzyme that catalyzes a reaction further down the pathway
ABCDEP
E1 E2 E3 E4 E5

Coenzymes
Coenzymes in metabolism: NAD+/NADH Electron carriers NADP+/NADPH FAD+/FADH2 Coenzyme A (CoASH) activation of metabolites

NAD+/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

NADP+/NADPH: Also comprised of nicotinamide portion

Reduced form, NADPH carries 2 electrons

Nicotinamide adenine dinucleotide phosphate (NADP+) oxidizing agent NADPH involves in reductive biosynthesis Differ with NAD+ at ribose (C2 contain a phosphoryl group, PO32 As electron carrier in photosythesis and pentose phosphate pathway Anabolism

The Structures Flavin Adenine Dinucleotide (FAD)

FAD is also a biological oxidizing agent FAD can accept oneelectron or twoelectron
The terminal e acceptor (O2) can accept only unpaired e (e must be transferred to O2 one at a time)

FADH carries 1 electron, FADH2 carries 2 electrons

FAD/FADH2
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 Pathways

A step frequently encountered in metabolism is activation
activation: 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 functions as a carrier of acetyl and other acyl groups Has sulfhydryl/thiol group

Thioester bond

CoASH

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

ATP- high energy compound

ATP is essential high energy bondcontaining compound

Phosphorylation of ADP to ATP requires energy

Hydrolysis of ATP to ADP releases energy
nucleotide

Phosphorylation: the addition of phosphoryl (PO32-) group/Pi (inorganic phosphate)

Metabolism:
(2)

ATP- high energy compound

ATP is essential high energy bondcontaining compound

Phosphorylation of ADP to ATP requires energy

Hydrolysis of ATP to ADP releases energy
nucleotide

Phosphorylation: the addition of phosphoryl (PO32-) group/Pi (inorganic phosphate)

The Phosphoric Anhydride Bonds in ATP are High Energy Bonds

Phosphoanhydride /

High Energy bondsbonds 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

Couple reaction: example

Role 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 Carbohydrate

Catabolism Anabolism

Major pathways of carbohydrate metabolism.

Fig 8.1 3rd ed

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

Glycolysis
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 reactions Phase 2=2nd 5 reactions Linear pathway

Glycolysis
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). 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 Glycolysis

1. Phosphorylation of glucose to give glucose-6-phosphate 2. Isomerization of glucose-6phosphate to give fructose-6phosphate 3. Phosphorylation of fructose-6phosphate to yield fructose-1,6bisphosphate 4. Cleavage of fructose-1,6,bisphosphate to give glyceraldehyde-3-phosphate and dihydroxyacetone phosphate 5. Isomerization of dihydroxyacetone phosphate to give glyceraldehyde-3phosphate isomerase enzyme
1

glucokinase
Use ATP

Use ATP 3 phosphofructokinase

4 5

The Reactions of Glycolysis (Contd)

6

10

6. Oxidation of glyceraldehyde-3phosphate to give 1,3bisphosphoglycerate Electron acceptor NAD+ 7. Transfer of a phosphate group transfer from 1,3-bisphosphoglycerate to Phosphorylation of ADP to give 3-phosphoglycerate ADP to ATP 8. Isomerization of 3phosphoglycerate to give 2isomerization phosphoglycerate 9. Dehydration of 2phosphoglycerate to give dehydration phosphoenolpyruvate 10. Transfer of a phosphate group transfer from phosphoenolpyruvate to ADP Phosphorylation of to give pyruvate
Glyceraldehyde-3-P dehydrogenase oxidation
ADP to ATP

Glycolysis
Dephosphorylation of ATP Phosphorylation of ADP
By kinase enzyme at step 1, 3, 7 and 10

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

ATP 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 Glycolysis - Step 7 and 10 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.

Fates of Pyruvate From Glycolysis

Once pyruvate is formed, it has one of several fates In aerobic metabolismpyruvate 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 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
In anaerobic bacteria 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

NAD+ Needs to be Recycled to Prevent Decrease in Oxidation Reactions

Structure of cell

Cytoplasm/ Cytosol

TYPICAL PROKARYOTIC CELL

Where does the Glycolysis Take Place?

Glycolysis is universal! Cytosol

Citric Acid Cycle

= Krebs Cycle, Tricarboxylic acid Cycle (TCA)

Key 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

Requires aerobic condition Amphibolic (both catabolic & anabolic) Serves 2 purposes:

Citric Acid Cycle

= =

Krebs Cycle
Tricarboxylic acid Cycle

(TCA)

TCA
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 activation 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, Oxidation of pyruvate and NADH + H+, and CO2 +
reduction of NAD

3C

Pyruvate = pyruvic acid

2C
Thioester, high energy compound

Features of TCA
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) X2
Electron acceptor NAD+ and FAD

Mitochondrial matrix

How about 1 molecule of glucose?

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 Acid 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 Guanosine Tri-Phosphate

Acetyl-CoA synthesize from pyruvate (glycolysis product)

Aerobic 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 In ETC

ETC take place in mitochondria inner membrane (eukaryotes)

In prokaryotes?

Oxidation of Pyruvate Forms CO2 and ATP

Aerobic metabolism is more efficient than anaerobic metabolism

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 cycle

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 Storage 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
Energy (k Jmol -1) C6 H1 2 O6 + 6 O 2 Glu cose CH3 ( CH2 ) 1 4 COOH + 2 3 O 2 Palmitic acid 6 CO 2 + 6 H 2 O -15.9

1 6 CO 2 + 1 6 H 2 O -38.9

Catabolism 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 - -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

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

METABOLISM
REVISION

 Catabolism: the oxidative breakdown of nutrients 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

Metabolism
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

Glycolysis

Linear pathway

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 reactions Phase 2=2nd 5 reactions

Fates of Pyruvate From Glycolysis

Once pyruvate is formed, it has one of several fates In aerobic metabolismpyruvate 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

Glycolysis in cytoplasm

ATP- high energy compound

ATP energy bondcontaining compound
ATP energy carrier / an is essential high energy transfer agent

Phosphorylation of ADP to ATP requires energy

Hydrolysis of ATP to ADP releases energy
nucleotide

Phosphorylation: the addition of phosphoryl (PO32-) group/Pi (inorganic phosphate)

Coenzyme A (CoASH)
Coenzyme A functions as a carrier of acetyl and other acyl groups Has sulfhydryl/thiol group

Thioester bond

CoASH

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

TCA
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)

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?

In eukaryotes, cycle takes place in the mitochondrial matrix In prokaryotes? Cytoplasm