Camp 1

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Metabolism
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Key words

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

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What is Metabolism?
The study of the biochemical reactions in an
organism, including the coordination, regulation
and energy needs

• Definition Metabolism is the sum total of the
  chemical reactions of biomolecules in an organism
• Metabolism consists of
• catabolism the breakdown of larger molecules
  into smaller ones an oxidative process that
  releases energy
• 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

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Terminology 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

light
Eg. 6 CO2(g) 6 H2O(l) ? C6H12O6(aq) 6
O2(g) Anabolism
photosynthesis
C6H12O6 (aq) 6O2 (g) ? 6CO2 (g)
6H2O Catabolism
respiration
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Metabolic pathway
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Metabolic pathway linear or cyclic
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A Comparison of Catabolism and Anabolism

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

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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

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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
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Oxidation and Reduction in Metabolism
Reduction gain e
Oxidation less e
Oxidizing agent e acceptor
reducing agent e donor
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Metabolism Features
A group of noncovalently associated enzymes that
catalyze 2 or more sequential steps in
metabolic/biochemical pathway

• Metabolic pathway
• Enzymes multienzymes
• Coenzymes
• ATP produced or used
• Regulation of metabolic pathway
• Feedback inhibition or
• Feed-forward activation

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Metabolism Regulation

• Regulation of metabolic pathway
• 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
• 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

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Coenzymes

• Coenzymes in metabolism
• NAD/NADH
• NADP/NADPH
• FAD/FADH2
• Coenzyme A (CoASH) activation of metabolites

Electron carriers
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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
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NADP/NADPH Also 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, PO32-
• As electron carrier in photosythesis and pentose
  phosphate pathway

Reduced form, NADPH carries 2 electrons
Anabolism
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The Structures Flavin Adenine Dinucleotide (FAD)

• FAD is also a biological oxidizing agent
• FAD can accept one-electron or two-electron

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
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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
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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

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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
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ATP- high energy compound

• ATP is essential high energy bond-containing
  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)
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Metabolism (2)
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ATP- high energy compound

• ATP is essential high energy bond-containing
  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)
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The Phosphoric Anhydride Bonds in ATP are High
Energy Bonds

• 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

Phosphoanhydride /
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Couple reaction example
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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)
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Metabolism of Carbohydrate
Catabolism Anabolism
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Major pathways of carbohydrate metabolism.
Fig 8.1 3rd ed
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Key words

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

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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 11st 5 reactions
• Phase 22nd 5 reactions

Linear pathway
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Glycolysis

• Glycolysis are divided into 2 stages/phases,
• Phase 11st 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
• Phase 22nd 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
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The Reactions of Glycolysis
glucokinase
1

1. Phosphorylation of glucose to give
   glucose-6-phosphate
2. 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

Use ATP
2
Use ATP
3
phosphofructokinase
4
5
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The Reactions of Glycolysis (Contd)

1. Oxidation of glyceraldehyde-3-phosphate to give
   1,3-bisphosphoglycerate
2. Transfer of a phosphate group from
   1,3-bisphosphoglycerate to ADP to give
   3-phosphoglycerate
3. Isomerization of 3-phosphoglycerate to give
   2-phosphoglycerate
4. Dehydration of 2-phosphoglycerate to give
   phosphoenolpyruvate
5. Transfer of a phosphate group from
   phosphoenolpyruvate to ADP to give pyruvate

Glyceraldehyde-3-P dehydrogenase
oxidation
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Electron acceptor NAD
transfer
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Phosphorylation of ADP to ATP
isomerization
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dehydration
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transfer
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Phosphorylation of ADP to ATP
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Glycolysis

• 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
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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
• 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
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Fates 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

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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
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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

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NAD Needs to be Recycled to Prevent Decrease in
Oxidation Reactions
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Structure of cell
Cytoplasm/ Cytosol
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Where does the Glycolysis Take Place?
Cytosol
Glycolysis is universal!
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Citric Acid Cycle Krebs Cycle, Tricarboxylic
acid Cycle (TCA)
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Metabolism Features
A group of noncovalently associated enzymes that
catalyze 2 or more sequential steps in
metabolic/biochemical pathway

• Metabolic pathway
• Enzymes multienzymes
• Coenzymes
• ATP produced or used

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Couple reaction example
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Coenzymes

• Coenzymes in metabolism
• NAD/NADH
• NADP/NADPH
• FAD/FADH2
• Coenzyme A (CoASH) activation of metabolites

Electron carriers
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Glycolysis

• Glycolysis are divided into 2 stages/phases,
• Phase 11st 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
• Phase 22nd 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
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Fates 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

Glycolysis in cytoplasm
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Key words

• Definition citric acid cycle
• Explain the citric acid cycle
• Distinguish between glycolysis and citric acid
  cycle
• Understand ?-oxidation catabolism of lipid

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Citric acid cycle

• Requires aerobic condition
• Amphibolic (both catabolic anabolic)
• Serves 2 purposes
• 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
• Supply precursors for biosynthesis of
  carbohydrates, lipids, amino acids, nucleotides
  and porphyrins

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Citric Acid Cycle Krebs Cycle Tricarboxylic
acid Cycle (TCA)
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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)

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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, NADH
  H, and CO2

Oxidation of pyruvate and reduction of NAD
3C
Pyruvate pyruvic acid
2C
Thioester, high energy compound
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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
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Features of TCA
Mitochondrial matrix
Electron acceptor NAD and FAD

• 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)

X 2
How about 1 molecule of glucose?
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Citric 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
• - a-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

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Where does the Citric Acid Cycle Take Place?

• In eukaryotes, cycle takes place in the
  mitochondrial matrix

In prokaryotes?
Cytoplasm
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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
• Acetyl-CoA synthesize from pyruvate
  (glycolysis product)

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

In ETC
In prokaryotes?
Plasma membrane
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Oxidation of Pyruvate Forms CO2 and ATP
Aerobic metabolism is more efficient than
anaerobic metabolism
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Citric acid cycle - amphibolic

• Amphibolic (both catabolic anabolic)
• Serves 2 purposes
• 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
• 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
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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)

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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

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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

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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
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• METABOLISM

REVISION
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• Catabolism the oxidative breakdown of nutrients
• Anabolism the reductive synthesis of biomolecules

• Catabolism features
• Release energy (ADP? ATP)
• Oxidizing agent (NAD, FAD)
• Anabolism features
• Use energy (ATP ? ADP)
• Reducing agent (NADH ,FADH2)

Metabolism the sum total of biochemical
reaction carried out by organism
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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

68
Major pathways of carbohydrate metabolism.
Fig 8.1 3rd ed
69
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 11st 5 reactions
• Phase 22nd 5 reactions

70
Fates 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

Glycolysis in cytoplasm
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ATP- high energy compound
ATP energy carrier / an energy transfer agent

• ATP is essential high energy bond-containing
  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)
72
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
73
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)

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Citric acid cycle - amphibolic

• Amphibolic (both catabolic anabolic)
• Serves 2 purposes
• 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
• 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
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Where does the Citric Acid Cycle Take Place?

• In eukaryotes, cycle takes place in the
  mitochondrial matrix

In prokaryotes?
Cytoplasm