ERT 211/1 Biochemical Engineeringportal.unimap.edu.my/portal/page/portal30/Lecturer...

CHAPTER 3: METABOLIC STOICHIOMETRY

AND ENERGETICS IN MICROORGANISMS

ERT 211/1 Biochemical Engineering

BY:

EN. MOHD. FAHRURRAZI TOMPANG

Introduction

Metabolism is the collection of enzyme catalyzed reactions that convert substrates that are external to the cell into various internal products.

ERT 211/1 - Chapter 3

Characteristics of Metabolisms

1. Varies from organisms to organism

2. Many common characteristics

3. Affected by environmental conditions

a) O2 availability: Saccharomyces cerevisiae

i. Aerobic growth on glucose → more yeast cells

ii. Anaerobic growth on glucose → ethanol

b) Control of metabolism is important in bioprocesses


Types of Metabolism

Catabolism

Metabolic reactions in the cell that degrade a substrate into smaller / simpler products.

Glucose → CO2

Anabolism

Metabolic reactions that result in the synthesis of larger / more complex molecules.


Figure 3.1: Classes of Reactions


Classification based on Metabolism

Where microbes get their energy?

Sunlight vs. Chemical

Photo- vs. Chemo- trophs

How do they obtain carbon?

Carbon Dioxide (or inorganic cmpds.) vs. Organic Compounds (sugars, amino acids)

Auto- vs. Hetero- trophs

Examples

Photoautotrophs vs. Photoheterotrophs

Chemoautotrophs vs. Chemoheterotrophs


Table 3.1:Types of -trophs

Type Energy C source Example

Photoauto- Sun CO2 Purple and green sulfur bacteria

Photohetero- Sun Organic compounds

Purple and green non-sulfur bacteria

Chemoauto- Chemical bonds

CO2 H, S, Fe, N bacteria

Chemohetero- Chemical bonds

Organic Most bacteria, fungi, protozoa, animals


Bioenergetics

The source of energy to fuel cellular metabolsim is “reduced” forms of carbon (sugars, hydrocarbons, etc.)

The Sun is the ultimate source via the process of

Photosynthesis in plants:

CO2 + H2O + hv → CH2O + O2


ATP - Adenosine Triphosphate

Catabolism of carbon-containing substrates generates high energy biomolecules


Thermodynamic principles

Free-energy change ∆G’ of single chemical reaction:

αA+βB→γC+δD (3.1)

∆G’= ∆G°’ +RT ln (cγdδ/aαbβ) (3.2)

∆G°’ = -RT ln K’eq (3.3)

K’eq = (cγdδ/aαbβ) (3.4)


Example:

Consider a typical cell with [ATP] = 3.0 mM, [ADP] = 0.8 mM, and [Pi] = 4.0 mM. Free energy at 37°C.

Solution:

∆G’= ∆G°’ +RT ln ([ADP][Pi]/[ATP])

= -30.5 kJ/mol + (8.3145 J/Kmol)(310 K) ln (0.8 E-3 M x 4.0 E-3 M/3.0 E-3 M)

= -30.5 KJ/mol – 17.6 kJ/mol

=-48.1 kJ/mol


Metabolic Reaction Coupling: ATP and Other Phosphate Compounds

Enzymatic hydrolysis of ATP yielding ADP andinorganic phosphate (Pi) as well as releasing (-) largefree-energy and reversing the reaction with addition ofphosphate to ADP, free energy can be stored (+) forlater use.


Metabolic Reaction Coupling: ATP and Other Phosphate Compounds


Metabolic Reaction Coupling: Oxidation and reduction coupling via NAD

Recall

Oxidation = Loses electrons e.g dehydrogenation

Reduction = Addition electrons e.g hydrogenation

Example: Reduction of pyruvic acid and oxidation of lactic acid


Metabolic Reaction Coupling: Oxidation and reduction coupling via NAD

Pairs of hydrogen atoms freed duringoxidation or required in reduction are carriedby nucleotide derivatives, NAD andphophorylated form NADP


NAD+ and NADP +

Nucleotide derivatives that accept H+ and e during oxidation /reduction reactions


Thermodynamic Principle

Oxidation-reduction reaction:

Aox + Bred Aox + Bred

∆E°’= E°’(Aox/Ared) - E°’(Box/Bred) (3.5)

Standard half-cell potential

Aox + 2e → Ared (3.6)

The hydrogen half cell (pH=0)

2H + 2e → H2 E0 = 0.00 V (3.7)

Free-energy:

∆G°’ = -n F ∆E’ (3.8)


Carbon Catabolism

Embden- Meyerhof-Parnas (EMP) Pathway

Pentose Phosphate Pathway

Entner Doudoroff (ED) Pathway

Overview of Glucose Metabolism

• Under aerobic conditions glucose is converted to pyruvate by glycolysis while generating two ATPs

• Under aerobic conditions, pyruvate is further oxidized by the citric acid cycle and oxidative phosphorylation to generate CO2 and H2O

• Under anaerobic conditions, pyruvate is instead converted to a reduced end product, that is,

In muscle: lactate - homolactic fermentation In yeast: ethanol + CO2 - alcoholic fermentation

(note: fermentation is an anaerobic biological reaction process)


Glucose Metabolism


Glycolysis

• Glycolysis is the breakdown (catabolism) of glucose to pyruvate under aerobic conditions

To understand the pathway at 4 levels:

1. The chemical interconversion steps or the sequence of reactions by which glucose is converted to the pathway end’s product , i.e., pyruvate

2. The mechanism of the enzymatic conversion of each pathway intermediates and its successor

3. The energetics of the conversion, ∆G and ∆

4. The mechanisms controlling the flux (rate of flow) of metabolites through the pathway

• Glycolysis converts C6 glucose to two C3 pyruvate

• The free energy released in this process is harvested to synthesise ATP from ADP and Pi

• They are 10 reactions involved in the glycolysis, all catalaysed by 10 specific enzymes

• The enzymes of glycolysis are located in the cytosol where they are only loosely associated

Glycolysis can be divided into two stages:

Stage 1:

Energy investment

Reactions 1-5 of the pathway are involved

Hexose (C6)glucose is phosphorylated and cleaved to yield 2 molecules of triose

(C3) glyceraldehydes -3-phosphate (GAP)

The process consumes 2 ATPs

Stage 2:

Energy recovery

Reactions 6-10 of the pathway are involved

The two molecules of GAP are converted to pyruvate

The process generates 4 ATPs

Glycolysis


The reactions of glycolysis


• There are 10 reactions catalyzed by 10 different enzymes

1. Hexokinase: First ATP Utilization

2. Phosphoglucose Isomerase

3. Phosphofructokinase: Second ATP Utilization

4. Aldolase

5. Triose Phosphate Isomerase

6. Glyceraldehyde-3-Phosphate Dehydrogenase: First “High Energy” Intermediate Formation

7. Phosphoglycerate Kinase: First ATP Generation

8. Phosphoglycerate Mutase

9. Enolase: Second “High energy” Intermediate Formation

10. Pyruvate Kinase: Second ATP Generation

Glycolysis: Reaction 1

• The reaction is the conversion of glucose to form glucose-6-phosphate (G6P)

• First ATP Utilization

• The reaction involves the transfer of a phosphoryl group from ATP to glucose to form glucose-6-phosphate (G6P)

• The reaction is catalyzed by hexokinase (HK)

• The reaction needs Mg2+ ion

• Uncomplex ATP is inhibitory

Note: Kinase enzyme catalyzes the transfer of phosphoryl groups between ATP and other molecules


Why is Mg2+ required in any kinase enzyme activity?

Mg2+ complexed with ATP at the phosphate oxygen atoms

This shield their negative charges, making the γ-phosphorous atom of ATP more accessible for the nucleophilic attack by the C6-OH group of glucose

Other divalent ions which can replace Mg2+ is Mn2+

α β γ

1

23

4

5

6



• The reaction is the conversion of glucose-6-phosphate (G6P) to form fructose-6-phosphate (F6P)

• The reaction is catalyzed by phosphoglucose isomerase(PGI)

• This reaction is the isomerization of an aldose to a ketose

• The proposed mechanism for the PGI reaction involves the general acid-base catalysis by the enzyme

• Involves ring opening and ring closure between C1 and O

aldose

ketose


Glycolysis: Reaction 3• The reaction is the conversion of fructose-6-phosphate

(F6P) to form fructose-1,6-bisphosphate (FBP)

• The reaction is catalyzed by phosphofructokinase(PFK)

• Second ATP Utilization

• Reaction is similar to hexokinase

reaction, catalyzing the nucleophilic attack by C1-OH group of F6P on the electrophilic γ-phosphorous atom of Mg2+-ATP complex

• PFK catalyzes one of the pathway’s rate-determining reaction, it function with large negative free energy changes

• One of the 3 non-equilibrium rxn in glycolysis (others are HK and PK)

Mechanisms that control PFK activity:

ATP is both a substrate and also an allosteric inhibitor of enzyme

ADP, AMP reverse the inhibitory effect of enzyme, therefore they are activators



• The reaction is the cleavage of fructose-1,6-bisphosphate (FBP) to form the two trioses, glyceraldehyde -3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP)

• Bisphosphate, not diphosphate as the phosphoryl gp are not linked

• The reaction is catalyzed by aldolase

• This reaction is an aldol cleavage between C3 and C4 which requires carbonyl at C2 and hydroxyl at C4

• The two trioses are interconvertible and thus can enter a common degradative path

• Each trioses has a phosphoryl gp

• Carbon atoms of 1, 2 and 3 of glucose become atom 3, 2 and 1 of DHAP and 4, 5 and 6 of glucose become 1, 2 and 3 of GAP


Mechanism for base-catalysed aldol cleavage

The presence of enolate intermediates



• Reaction 4 results in the production of glyceraldehyde -3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP), which are ketose-aldoseisomers

• Only GAP will continue to be degraded in the glycolysis

• Reaction 5 is the interconversionof GAP to DHAP, occurs via an enediol or enediolate intermediate

• This reaction is catalyzed by triose phosphate isomerase(TIM)



• Involves the oxidation and phosphorylationof glyceraldehyde -3-phosphate (GAP) by NAD+ and Pi to form 1,3-bisphosphoglycerate (1,3-BPG)

• The reaction is catalyzed by glyceraldehyde-3-phosphate dehydrogenase

• The reaction is very exergonic and this drives the synthesis of “high energy” compound, 1,3-BPG

• 1,3-BPG is one of the phosphate compounds with high standard free energy, higher than ATP



Table 3.2: Standard Free Energies of Phosphate Hydrolysis of some biological compound


• The reaction is the conversion of 1,3 bisphosphoglycerate (1,3-BPG)to form 3-phosphoglycerate (3PG)

• The reaction is catalyzed by phosphoglycerate kinase (PGK)

• The reaction results in a generation of its first ATP molecules in the presence of ADP and Mg2+


Mechanism of phosphoglycerate kinase (PGK) reaction



• The reaction is the conversion of 3-phosphoglycerate (3PG) to form 2-phosphoglycerate (2-PG)

• The reaction is catalyzed by phosphoglycerate mutase(PGM)

• Note: a mutase catalyzes the transfer of a functional group from one position to the another on a molecule

• The reaction is a necessary preparation for the next reaction which generates a “high energy” phosphoryl compound for use in the ATP synthesis


Proposed reaction mechanism for phosphoglycerate mutase (PGM)

•The active form of the enzyme contains Phos-His residue at the active site

Step 1: 3-PG binds to PGM in which His is phosphorylated

Step 2: The phosphoryl gp is transferred to the substrate, resulting in an intermediate 2,3-PG.enzyme complex

Steps 3 and 4: The complex decomposes to form 2-PG with regeneration of the phosphoenzyme

•Occasionally, 2,3-BPG dissociates from enzyme leaving an inactive dephosphoenzymelike in Step 5



• The reaction is the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate(PEP)

• This reaction is catalyzed by enolase

• The reaction generate a second “High energy” intermediate compound, PEP (refer to Table 13-2)


Remember

Table 13-2, Page 362-Standard Free Energies of Phosphate Hydrolysis of some biological

cpds



• The final reaction in glycolysis is the conversion of phosphoenolpyruvate(PEP) to form pyruvate

• The reaction is catalyzed by pyruvatekinase (PK)

• One of the 3 non-equilibrium rxn in glycolysis (others are HK and PFK)

• This reaction involves the coupling of PEP hydrolysis to pyruvate to the synthesis of ATP from ADP

• Thus the reaction generates the second ATP molecules


Mechanism of the Reaction Catalyzed by PyruvateKinase (PK)

• Reaction requires both monovalent (K+) and divalent ions (Mg+)

Step 1: Nucleophilic attack of phosphorus atom of PEP by β-phosphoryloxygen of ADP, thus displacing enolpyruvate and forming ATP; the reaction is endergonic

Step 2: Enolpyruvate converts to pyruvate, and this is a very exergonicreaction

• Overall reaction of PEP to pyruvate is exergonic


Summary on Glycolysis

• The overall reaction of glycolysis is:

Glucose + 2NAD+ + 2ADP + Pi → 2NADH + 2Pyruvate + 2ATP + 2H2O + 4H+

• The reaction occurs in 10 enzymatically catalysed reactions

• The mechanisms of the 10 glycolytic enzymes have been elucidated through chemical and kinetic measurements combined with X-ray structural studies

• 3 of the 10 reactions are non-equilibrium, which ensure the pathway go forward:

Reaction 1: Glucose to G6P by HK

Reaction 3: F6P to FBP by PFK

Reaction 10: PEP to pyruvate by PK


The Three Products of Glycolysis

1. ATP2. NADH3. PYRUVATE

1. ATP

• 2 ATP per molecule of glucose were invested and subsequently 4ATP were generated by substrate-level phosphorylation, giving a net yield of 2ATP per glucose

• ATP produced satisfies most of the cell’s energy needs.

2. NADH

• 2 NAD+ are reduced to 2 NADH

• Reduced NADH represent a source of free energy that can be recovered by subsequent oxidation

• Under aerobic condition, electron pass from reduced coenzymes thru’ a series of electron carriers to the final oxidizing agent, O2, in a process known as electron transport

• The free energy of electron transport drives the synthesis of ATP from ADP

• In aerobic organism, the sequence of events also serves to regenerate oxidized NAD+

• Under anaerobic conditions, NADH must be reoxidized by other means in order to keep the glycolytic pathway supplied with NAD+


The Three Products of Glycolysis (cont…)

3. PYRUVATE

• 2 pyruvate molecules are produced

• Under aerobic condition, complete oxidation of pyruvate to CO2 and H2O via citric acid cycle and oxidative phosphorylation, where ATP is generated

• In anaerobic metabolism, pyruvate is metabolized to a lesser extent to regenerate NAD+, via a process known as fermentation


THE PENTOSE PHOSPHATE PATHWAY

•Why the Pentose Phosphate Pathway (The PPP)

An alternative mode of glucose oxidation where G6P is converted to R5P or hexosesto pentoses, and R5P and its derivatives are required for the synthesis of RNA, DNA, etc.

The production of NADPH

•Tissues most heavily involved in lipid biosynthesis (liver, mammary gland, adipose tissue and adrenal cortex) are rich in the PPP enzymes

•About 30% of the glucose oxidation in liver occurs via the PPP


THE PENTOSE PHOSPHATE PATHWAY (continue…)

•NADH vs NADPH

They are not metabolically interchangeable

NADH uses the free energy of metabolite oxidation to synthesise ATP (oxidative phosphorylation), whereas NADPH uses the free energy of metabolite oxidation for reductive biosynthesis (eg. biosynthesis of fatty acid and cholesterol require NADPH in addition to ATP)

This differentiations is possible because the dehydrogenases involved in oxidative and reductive metabolism are highly specific for their respective coenzymes, NADH or NADPH


Nicotinamide nucleotides in catabolism and biosynthesis

• NAD+ is the cofactor for most enzymes that act in the direction of substrate oxidation (dehydrogenases) whereas NADPH usually functions as a cofactor for reductases, enzymes that catalyze substrate reduction

• NADPH is synthesized either from NADP+ in the PPP or from NADH through the action of mitochondrial energy-linked transhydrogenase

• NADP+ is synthesized from NAD+ by an ATP-dependent kinase reaction



Overall rxn:

3 G6P + 6 NADP+ + 3 H2O 6 NADPH + 6 H+ + 3 CO2 + 2 F6P + GAP

Occurs in 3 stages:

Stage 1: Oxidative rxn (Rxn 1-3) which yield NADPH and ribulose-5-phosphate (Ru5P)

3 G6P + 6 NADP+ + 3 H2O 6 NADPH + 6 H+ + 3 CO2 + 3 Ru5P

G6P generated from hexokinase on glucose (glycolysis) or glycogen breakdownOnly Rxn 1-3 of pathway are involved in the production of NADPH2 molecules of NADPH are generated per 1 molecule of G6P that enter pathway

Stage 2: Isomerization and epimerization rxn (Rxn 4 and 5) which transform Ru5P either to ribose-5-phosphate (R5P) or xylose-5-phosphate (Xu5P)

3 Ru5P R5P + 2 Xu5P



Stage 3: A series of C-C bond cleavage and formation rxn (Rxn 6-8) that convert 2 molecules of Xu5P and one molecule of R5P to 2 molecules of F6P and one molecule of GAP

transketolase

transaldolase

transketolase

2 Xu5P + 1 R5P 2 F6P 1 GAP



1. Gluco-6-phosphate dehydrogenase (G6PD)

2. 6-phospho-glucono-lactonase

3. 6-phospho-gluconate dehydrogenase

4. Ribulose-5-phosphate isomerase

5. Ribulose-5-phosphate epimerase

6. Transketolase

7. Transaldolase

8. Transketolase

Note: Epimers are sugars that differ only by the configuration at one carbon atom



Relationship between

Glycolysis and The Pentose

Phosphate Pathway

•The PPP starts with G6P produces in

Step 2 of Glycolysis

•It generates NADPH for use in

reductive biosynthesis and R5P for

nucleotide biosynthesis

•Excess R5P is converted to glycolytic

intermediates by a sequence of reactions

that can operate in reverse to generate

additional R5P, if needed


Entner Doudoroff (ED) Pathway

Overall stoichiometry of the reaction:

Glucose + ATP + NADP + → glyceralde 3-phosphate + pyruvicacid + ADP + NADPH + H+

2 moles of ADP were phosphorylated by reacting one mole of GA-3P to pyruvate through the same reaction as used for this conversion in EMP pathway

Energy yield: onemole of ATP per mole glucose processed


Summary of Carbon Catabolism

3 Glucose molecules enter glycolysis (EMP pathway), produce 6 ATP

3 Glucose molecules through the Pentose Phosphate Pathway and then reenter glycolysis, produce 5 ATP

3 Glucose molecules enter ED pathway, produce 3 ATP


FERMENTATION

1. Homolactic Fermentation

•In muscle, under anaerobic condition e.g., during vigorous activity when the demand for ATP is high and O2 is in short supply:

NADH is oxidised by pyruvate to generate NAD+ and lactate by lactate dehydrogenase(LDH)

The reaction is reversible, so pyruvate and lactate level are readily equilibrated

The reaction is also known as anaerobic glycolysis, the stage where the conversion of pyruvateto lactate is classified as Reaction 11

The overall process of an anaerobic glycolysis in muscle can be represented as:

Glucose + 2 ADP + 2Pi 2 Lactate + 2 ATP

The lactate may be:

exported out of the cell by blood to the liver where it is used to synthesise glucose, or

converted back to pyruvate, to enter the pathway for further degradation


1. Homolactic Fermentation (continue…)


FERMENTATION (continue..)

2. Alcoholic Fermentation

• In yeast, under anaerobic condition, pyruvate is converted to ethanol and CO2 while regenerating

NAD+

• Yeast produces ethanol and CO2 via 2 consecutive reactions:

The carboxylation of pyruvate to form acetaldehyde and CO2 as catalyzed by pyruvate

decarboxylase (enzyme not present in animals), then

The reduction of acetaldehyde to ethanol by NADH as catalysed by alcohol dehydrogenase,

thereby generating NAD+


Alcoholic Fermentation (continue…..)

The two reactions of alcoholic fermentation:

Thiamin

diphosphate (TPP)-

essential cofactor of

pyruvate

decarboylase

1. Pyruvate

decarboxylase

2. Alcohol

dehydrogenase


Fermentation (continue..)

The Energetics of Fermentation

•Overall Reaction in alcoholic fermentation (from glucose)

Glucose + 2Pi +2ADP 2 Ethanol + 2CO2 + 2ATP ∆G = -196 kJ.mol-1

•Overall Reaction in homolactic fermentation (from glucose)

Glucose + 2Pi +2ADP 2 Lactate + 2ATP ∆G = -235 kJ.mol-1

•Each of these processes is coupled to the net formation of 2ATP molecules


Fermentation (continue..)

The Energetics of Fermentation (continue…)

•They are non-oxidative process

•No net oxidation and reduction

•NAD+ and NADH do not appear in the overall net reaction

•NADH formed in the oxidation of GAP is consumed in the reduction of pyruvate

•The regeneration of NAD+ in the reduction of pyruvate to lactate or ethanol sustains the continued operation of glycolysis under anaerobic conditions

•Only a small fraction of the energy of glucose is released in the anaerobic conversion to lactate or ethanol (2ATP per glucose vs. 38ATP per glucose in ox. phos.)

•The rate of ATP production is higher in anaerobic than in aerobic glycolysis

•Much more energy can be extracted aerobically via citric acid cycle and oxidative phosphorylation step


METABOLISM OF OTHER HEXOSES

• Three other hexoses apart from

glucose are:

1. Fructose

2. Galactose

3. Mannose

• After digestion monosaccharides

enter the blood stream, which carries

them to various tissues

• Fructose, galactose and mannose are

converted to glycolytic intermediates

then metabolized in the glycolytic

pathway


METABOLISM OF OTHER HEXOSES (continue..)

1. Fructose

• From fruits and sucrose (a disaccharides of fructose and glucose)

• 2 pathways for the metabolism of sucrose because of the presence of different enzymes in different

tissues

• In muscle, fructose converts to F6P which then enter the glycolytic pathway. This only require 1

step, thus 1 enzyme,HK

• In liver, fructose converts to intermediates and finally GAP which then enter the glycolytic

pathway. This require 7 steps thus 7 enzymes


METABOLISM OF OTHER HEXOSES (continue…)

Metabolism of

fructose

1. fructokinase

2. 2 Fructose-1-

phosphate aldolase

3. Glyceraldehyde

kinase

4. Alcohol

dehydrogenase

5. Glycerol kinase

6. Glycerol phosphate

dehydrogenase

7. Triose phosphate

isomerase

METABOLISM OF OTHER HEXOSES (continue..)

1. Fructose (continue…)

•In muscle, after Rxn 4, there are 2 pathway leading from glyceraldehyde to GAP, before entering the

pathway, both consume ATP

•NADH is oxidized in in Rxn 4 but is being reduced again in Rxn 6

•What happens when there is an excessive fructose in blood, eg. In IV feeds?

•Fructose intolerance-a genetic diseases with deficiency in Fructose-1-phosphate aldolase

Fructose-1-phosphate may be produced faster than aldolase can cleave, accumulation of

fructose-1-phosphate depletes Pi in liver, ATP drops, glycolysis and production of lactate is

activated, high concentration of lactate in blood is deadly


Metabolism of other HEXOSES (continue..)

2. Galactose

•Obtained from the hydrolysis of lactose from dairy products

•Lactose is disaccharide of galactose and glucose

•Hexokinase only recognise glucose, fructose and mannose but not galactose

•Epimerization rxn must occur before galactose enter glycolysis

•Galactose is converted to G6P which then enter the glycolytic pathway. This require 4 steps and 4 enzymes



Metabolism of

galactose

1. Galactokinase

2. Galactose-1-phosphate

uridyl transferase

3. UDP-galactose-4-

epimerase

4. phosphoglucomutase



2. Galactose (continue…)

•Galactosemia- a genetic disease characterized by the inability to convert galactose to glucose

•Involve the deficiency of enzyme of Rxn 2

•Symptoms:

Failure to grow well

Mental retardation

Death from liver damage

•Treatment- galactose free diet



3. Mannose

•A product of digestion of polysaccharides and glycoprotein

•A C2 epimer of glucose (Epimer is sugars that differ only by the configuration at one C atom)

•Mannose enter the glycolytic pathway after its conversion to F6P. It need 2 steps thus 2 enzymes



Metabolism of mannose

1. hexokinase

2. Phosphomannose isomerase


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