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Central metabolic pathways:Pathways that provide precursor

metabolites to all other pathways

Carbohydrates metabolic pathways

and carboxylic acids

☺Embden – Meyerhof –

Parnas Pathway= EMP = glycolysis☺Pentose phosphate pathway(PPP)☺Entner Doudoroff pathway(ED)

Similarities of the three pathways:

• Convert glucose to phosphoglycer-

aldehyde

• Phosphoglyceraldehyde is

converted to pyruvate through the

same reactions

Carbohydrates pathways and

Krebs Cycle

Central metabolic pathways:Three substrate level

phosphorylations

Six oxidation reactions → NADH

and FADH2

Pyruvate → depends on cell

Respiration → oxidized to acetyl-

CoA → CO2

Fermentation → alcohol, organicacids, solvents.

The oxidation of NADH and FADH2

Respiration → oxidized viaelectron transport → formation of∆P

Fermentation → oxidized incytosol by an organic acceptor →no production of ATP

Glucose 6-P-GluconateATP

G6P

NADPHATP

PPP ED

ATP

CO2 NADPH

Pentoses

Pi

H2O

F6PATP

FBP

Gluconate

Fumarate

Succinate

ATP, NADH

ATP

CO2 NADH

citrate

Cis- aconitate

Isocitrate

FADH2

ATP

succinyl CoA

CO2 NADH

2

α-ketoglutarate

NADPH

oxalosuccinate

CO2

PGLAD

PEP

Pyruvate

Acetyl-CoA

Oxaloacetate

Malate

NADH

Citric Acid Cycle

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Embden – Meyerhof – ParnasPathway

Catalyzes the splitting of the

glucose molecule (C6) into two

phosphoglyceraldehyde (C3)molecules

Catalyzes the oxidation of

phosphoglyceraldehyde (C3) topyruvate

Figure 1. Glycolysis

Glycolysis as an anabolic pathway

The glycolytic pathway serves not onlyto oxidize carbohydrate to pyruvate and tophosphorylate ADP, but also providesprecursor metabolites for many otherpathways.

G6P → polysaccharides, aromatic aminoacids, pentosa phosphates

F6P → amino sugars (muramic acid andglucosamine)

DHAP → phospholipids

PGA → serine, glycine, cystein

PEP → aromatic amino acids, muramicacid

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Glycolytic pathway can be reversed

from PEP only to F 1,6 bP (not at all to

pyruvate).

This is due to the pyruvate kinase and

phosphofructokinase reactions are

physiologically irreversible → high free

energy in the phosphoryl donors

Regulation of glycolysis pathway:

Two key enzymes :

1. phosphofructokinase

2. fructose 1,6 bisphosphate

phosphatase

♣phosphofructokinase activity will

be stimulated when the ADP levels

are high (ATP levels are low) →

glycolysis is stimulated

♣phosphofructokinase activity is

inhibited by PEP (end - product

inhibition).

When glycolysis is stimulated by ADP,

the reversal of glycolysis is slowed by

high levels of AMP → AMP inhibits the

fructose 1,6 bisphosphate reaction

Fructose 1,6 bisphosphatase regulates

pyruvate kinase

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Pentose Phosphate Pathway

In this pathway:

Producing pentose phosphate

→ precursors to the ribose and

deoxyribose in the nucleic acid

Providing erythrose phosphate

→ precursors to the aromatic

amino acids

Reactions of Pentose phosphatepathway:

�Oxidation-decarboxylation reactions

products : CO2, 2 NADPH, 5 carbon

sugar (ribulose –5– phosphate).

�Isomerization reactions → precursors

to the stage 3

• some of the ribulose-5-phosphate

is isomerized to ribose-5-phosphate

and to xylulose-5-phosphate

Two type of reactions:

Transfer of two-carbon fragment

from ketose to an aldose →

transketolase

Transfer of three-carbon fragment

from ketose to an aldose →

transaldolase

The rule : the donor is always a ketoseand the acceptor is always analdose

�Sugar rearrangement reactions →

glyceraldehyde phosphate.

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Thiobacillus novellus and Brucella

abortus use only an oxidative

pentose phosphate pathway to

grow on glucose

Stage 2 and 3 of the pentose phosphate

pathway are reversible synthesize

pentose phosphates from

phosphoglyceraldehyde

The pentose phosphate pathway and

glycolysis interconnect at

phosphoglyceraldehyde and F6P

organisms growing on pentoses can

make hexose phosphates

Figure 3. Pentose phosphate pathway

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Entner--Doudoroff Pathway

♣Only found in prokaryotes.widespread, particularly amonggram-negative bacteria, aerobic

♣Yield of the pathway: 1 molglucose 2 pyruvate, 1 ATP, 1NADH and 1 NADPH.

♣Difference to pentose phosphate= some of 6P–gluconates aredehydrated to 2 keto-3-deoxy-6-P-gluconate (KDPG) instead of toribulose-5-phosphate.

Figure 4. Entner-Doudoroff pathway

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The Citric acid cycle:

This cycle is present in most

heterotrophic bacteria growing

aerobically, but organisms that

grow on C1 compounds (methan,

methanol and so on) carry out a

reductive pathway

They are 4 oxidations per acetyl-

CoA producing 2 NADH, 1

CITRIC ACID CYCLE

NADPH and 1 FADH2, and 1

substrate-level phosphorylation

producing ATP.

CoA

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The Citric acid cycle is feedback

inhibited by several end product:

♠In Gram – bacteria: citrate

synthase is allosterically

inhibited by NADH.

♠In facultativ anaerob by α-

ketoglutarat.

♠In Gram + the citrate synthase is

inhibited by ATP

The Citric acid cycle provide

precursors to 10 of the 20 amino

acid found in protein:

Succinyl-CoA: L- lysine and L-

methionin, tetrapyroles

(prosthetic group in several

protein, Cyt & Chlorophylls)

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Oxaloacetate : aspartate, which

itself is the precursor to five

other amino acid.

Fumarate: aspartate

α-ketoglutarat :glutamate, which

itself is the precursor to three

other amino acid.

Modification of the citric acid cycleinto a reductive cycle duringfermentation Growth.

The solution is to convert the citricacid cycle from an oxidative into areductive pathway.

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Pyruvate

Acetyl-CoA

Oxaloacetate Citrate

malate

Fumarate

succinate

Succinyl~CoA

[cis-akonitate]

isocitrate

oxalosuccinate

α-ketoglutarat

Glucose-6-P

The Glyoxylate Cycle

Phosphoenolpyruvate

The Glyoxylate cycle is required by

aerobic bacteria to grow on fatty

acids and acetate (Plants and

protozoa also have this cycle)

What regulates the fate of the

isocitrate?

In E. coli: the isocitrate hydrogenase

activity is partially inactivated by

phosphorylation when cell are grown

on acetate.

Acetate also induces the enzymes ofGlyoxylate cycle.

Isocitrate lyase requires a highintracellular concentration of isocitrate

Gluconeogenesis

Growing microorganisms on poor

carbon source, such as L-malate,

succinate, acetate or glycerol

requires the ability to synthesize

hexoses needed for the production of

cell wall mucopeptides, storage

glycogen and other compounds

derived from hexose, such as

pentoses, for nucleic acid

biosynthesis

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Hexose synthesis involves a reversal

of carbon flow from pyruvat

(gluconeogenesis).

It is not allow a carbon flow from

pyruvat to hexoses directly because:

1. Pyruvat kinase is not reversible

because the free-energy

requirement is to great. PEP is

formed by PEP-carboxykinase (Mg2+

dependent, with GTP as phosphate

donor)

2. Reaction with phosphofructokinase

is irreversible. Fructose-1,6-

bisphophatase dephosphorylates

FBP to yield F-6-P and Pi.

3. Glucose – 6- phosphatase removes

Pi from G-6-P to yield glucose.

2 pyruvate + 4ATP + 2GTP + 2NADH

+ 2H+ + 4H2O

→Glucose + 2NAD+ + 4ADP + 2GDP

+ 6Pi

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Gluconeogenesis enzymes

1. Pyruvate carboxylase: pyruvat →

OAA

2. PEP carboxykinase: OAA + GTP →

pyruvat

3. Fructose-1,6-bisphosphatase

4. Glucose-6-phosphatase

5. ATP-glucose pyrophosphorylase: G-

1-P +ATP →ADP-glucose

6. Glycogen Synthase: α-1,4-glycan +

ADP-glucose →glycogen / starch

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Regulation:

carboxykinase, which is regulated

by catabolite repression (inhibited

when glucose or other carbohydrate

carbon source are available).

PEP carboxykinase is induced at the

stationary phase of growth and

requires cAMP and regulatory

signal.

Regulation:

1. Allosteric Control of enzymes activity

in Catabolic PathwaysThe major regulatory step is PEP

Alosteric regulation in Emden-Meyerhof-

Parnas, Gluconeogenesis and TCA is

predominantly effected by

intermediates.

This is due, in part,to the interrelation of

the Emden-Meyerhof-Parnas, pentose

phosphate and TCA pathways at the

level of intermediates of Emden-

Meyerhof-Parnas

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♣The effector intermediates may

either be inhibitors, activators, or

both (affecting different enzymes)

♣accumulation of Fru 1,6 biP

serves to activate both ADP-

glucose pyrophosphorylase and

pyruvate kinase

♣accumulation of PEP serves to

inhibit phosphofructokinase but

activates pyruvate dehydrogenase

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2. Posttranslational Covalent

Modification of proteins

♠Covalent modification of prokaryotic

proteins involves phosphorylation at

various residues, uridylylation,

adenylylation, methylation, fatty

acylation and proteolysis

♠Example: Isositrat Dehydrogenase

For growth on acetate or fatty

acids, E.coli require the functioning

of the glyoxylate bypass.

During growing on acetate, isocitrate

dehidrogenase is inhibited by

approximately 75% compared to during

growth on most other carbon.

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This inhibition is caused by the

phosphorylation of a single serine

residue of isocitrate dehydrogenase,

which completely inactivates the

enzyme.

Phosphorylation of isocitrate

dehydrogenase is carried out by an

ATP-dependent IDH kinase/

phosphatase, which also catalyzes

dephosphorylation of phospho-

isocitrate dehydrogenase.