Chapter 24 Biosynthetic Pathways Chemistry 203. Catabolic reactions: Anabolic reactions:Biosynthetic...

Chapter 24

Biosynthetic Pathways

Chemistry 203

Catabolic reactions:

Anabolic reactions: Biosynthetic reactions

Complex molecules Simple molecules + Energy

Simple molecules + Energy (in cell) Complex molecules

Metabolism

Biosynthetic pathways

Anabolic and catabolic reactions have different pathways.

1. Flexibility: if a normal biosynthetic pathway is blocked, the organism can often use the reverse of the catabolic pathway for synthesis.

Complex Molecule Simple MoleculesCatabolic

Biosynthetic

(Glucose)n +Pi

Glycogen

phosphorylase(Glucose)n-1

Glycogen(one unit smaller)

+Glucose 1-phosphate

(Glucose)n-1 +UDP-glucose (Glucose)nGlycogen

(one unit larger)

+ UDP

2. Overcoming Le Chatelier’s principle:

Biosynthetic pathways

If a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium moves to counteract the change.

Biosynthetic pathways

Anabolic and catabolic reactions need different energy.

Anabolic and catabolic reactions take place in different locations.

Catabolic reactions

Anabolic reactions

Mitochondria

Cytoplasm

Biosynthetic pathways

1. Biosynthesis of Carbohydrates

2. Biosynthesis of Lipids

Biosynthesis of Fatty acids

Biosynthesis of Membrane Lipids

3. Biosynthesis of Amino acids

Glycolysis

Glucose is converted to two molecules of pyruvate.

An anaerobic reaction in cytoplasm.

10 Reactions

Glycolysis

Steps [1] – [5] energy investment phase:

The 6-carbon glucose molecule is converted into two 3-carbon segments.

2 ATP molecules are hydrolyzed.

Glycolysis

Steps [6] – [10] energy-generating phase:

producing 1 NADH and 2 ATPs for each pyruvate formed.

Glycolysis

Enzymes:

Step [1] begins with the phosphorylation of glucose into glucose 6-phosphate, using an ATP and a kinase enzyme.

Glycolysis

Step [2] isomerizes glucose 6-phosphate to fructose 6-phosphate with an isomerase enzyme.

Glycolysis

Step [3] is the phosphorylation of fructose 6-phosphate into fructose 1,6-bisphosphate with a kinase enzyme.

Glycolysis

Glycolysis

Overall, the first three steps of glycolysis:

1.2 phosphate groups is added.

2.A 6-membered glucose ring is isomerized into a 5-membered fructose ring.

3. The energy stored in 2 ATP molecules is utilized to modify the structure of glucose

Glycolysis

Step [4] cleaves the fructose ring into a dihydroxy-acetone phosphate and a glyceraldehyde 3-phosphate.

Step [5] isomerizes the dihydroxyacetone phosphate into another glyceraldehyde 3-phosphate.

Glycolysis

Thus, the first phase of glycolysis converts glucose into 2 glyceraldehyde 3-phosphate units and 2 ATP is used.

In step [6] the aldehyde end of the molecule is oxidized and phosphorylated by a dehydrogenase enzyme and NAD+;this produces 1,3-bisphospho-glycerate and NADH.

Glycolysis

Glycolysis

In step [7], the phosphate group is transferred onto an ADP with a kinase enzyme, forming 3-phosphoglycerate and ATP.

In step [8], the phosphate group is isomerized to a new position in 2-phosphoglycerate.

Glycolysis

In step [9], water is lost to form phosphoenol-pyruvate.

Glycolysis

Glycolysis

In step [10], the phosphate is transferred to an ADP,yielding pyruvate and ATP with a kinase enzyme.

The 2 glyceraldehyde 3-phosphate units are converted into 2 pyruvate units in phase two of glycolysis.

Overall, the energy-generating phase forms 2 NADHs and 4 ATPs.

Glycolysis

Glycolysis

Overall of glycolysis

2 ATPs are used in phase one of glycolysis, and 4 ATPs are made in phase two of glycolysis.

The net result is the synthesis of 2 ATPs from glycolysis.

The 2 NADHs formed are made in the cytoplasm and must be transported to the mitochondria to join the electron transport chain and make ATP.

under aerobicconditions

under anaerobicconditions

in fermentationby microorganisms

The fate of pyruvate

Aerobic conditions

The NADH formed needs O2 to return to NAD+, so without O2 no additional pyruvate can be oxidized.

Pyruvate must diffuse across the outer and inner membrane of mitochondria into the matrix.

Fermentation is the anaerobic conversion of glucose to ethanol and CO2 by yeast and other microorganisms.

Fermentation

1. Biosynthesis of Carbohydrates

6H2O 6H2O C6H12O6 6H2O+ +energy chlorophyll +(from

sun light)Glucose(from sun)

In plants

6CO2

Photosynthesis

1. Biosynthesis of Carbohydrates

In animals

When both glucose and stored glycogen are depleted, glucose can be synthesis by gluconeogenesis.

Intermediates of Glycolysis and Citric acid cycle are used to produce glucose.

Gluconeogenesis is not the exact reversal of glycolysis: pyruvate to glucose does not occur by reversing the steps of glucose to pyruvate.

(in liver)

1. Biosynthesis of Carbohydrates

Only four enzymes are unique.

(compare to glycolysis)

ATP is produced in glycolysis and used up in gluconeogenesis.

Lactate from glycolysis in muscle is transported to the liver,

where gluconeogenesis converts it back to glucose.

Cori Cycle

Gluconeogenesis

Glucose is the main source of energy for cells and the only source of energy used by the brain.

Gluconeogenesis is a mechanism that ensures that the brain has a supply of glucose when a diet is low in carbohydrates.

Conversion of glucose to other Carbohydrates (in animals)

Conversion of glucose to other hexoses (isomers) and synthesis ofdi- or polysaccharides.

Activation of glucose by Uridine Triphosphate (UTP) to form UDP-glucose.

OH

HO

H

O-P-O-P-OCH2

H

OHH

OH

CH2OH

H

O-

O

O-

O

HHHO OH

H HO

HN

N

O

O

Uridine diphosphate glucose (UDP-glucose)

(Similar to ATP)

UTP

UTP

UDP

UDP

pyrophosphate

pyrophosphate

Glucose 1-phosphate + UDP-glucose +

(Glucose)n +UDP-glucose (Glucose)n+1 +

Glucose 1-phosphate + + (Glucose)n

(Glucose)n+1 + +

OH

HO

H

O-P-O-P-OCH2

H

OHH

OH

CH2OH

H

O-

O

O-

O

HHHO OH

H HO

HN

N

O

O

Uridine diphosphate glucose (UDP-glucose)

OH

HO

H

O-P-O-P-OCH2

H

OHH

OH

CH2OH

H

O-

O

O-

O

HHHO OH

H HO

HN

N

O

O

Uridine diphosphate glucose (UDP-glucose)

- -

OH

HO

H

O-P-O-P-OCH2

H

OHH

OH

CH2OH

H

O-

O

O-

O

HHHO OH

H HO

HN

N

O

O

Uridine diphosphate glucose (UDP-glucose)

OH

HO

H

O-P-O-P-OCH2

H

OHH

OH

CH2OH

H

O-

O

O-

O

HHHO OH

H HO

HN

N

O

O

Uridine diphosphate glucose (UDP-glucose)

- -

Enzyme

Conversion of glucose to other Carbohydrates (in animals)

Glycogenesis: conversion of glucose to glycogen.

Exess glucose is stored in form of glycogen.

Same process to produce di- and polysaccharides.

2. Biosynthesis of Fatty acids

Our body can produce all the fatty acids except essential fatty acids.

Acetyl CoA

Fatty acids synthesis: in cytoplasm

Degeradation of fatty acids: in mitochondria

They build up two C at a time.

Excess food Acetyl CoA Fatty acids Lipid (fat)

2. Biosynthesis of Fatty acids

ACP has a side chain that

carries the growing fatty acid

ACP rotates counterclockwise,

and its side chain sweeps over

the multienzyme system (empty spheres).

Acyl Carrier Protein (ACP)

At each enzyme, one reaction of chain is catalyzed.

CH3C-SCoAO

+ HS-ACP

+ HS-synthase

+ HS-synthase

CH3C-S-ACPO

CH3C-SCoAO

CH3C-S-ACPO

CH3C-S-synthaseO

CH3C-S-SynthaseO

+ HS-CoA

+

+ HS-ACP

HS-CoA

Acetyl-CoA Acetyl-ACP

Acetyl-ACP Acetyl-synthase

Acetyl-synthaseAcetyl-CoA

2. Biosynthesis of Fatty acids

Step 1: ACP picks up an acetyl group from acetyl CoA and delivers to the first enzyme:

2. Biosynthesis of Fatty acids

Step 2: ACP-malonyltransferase reaction:

Step 3: condensation reaction:

CH2C-SCoA

COO-

O+ HS-ACP CH2C-S-ACP

COO-

O+ HS-CoA

Malonyl-CoA Malonyl-ACP

CH3C-S-synthaseO

+ CH2C-ACPCOO-

O

CH3C-CH2-C-S-ACPO O

+ CO2 + HS-synthase

Acetyl-synthaseMalonyl-ACP

Acetoacetyl-ACP

Step 4: the first reduction:

Step 5: dehydration:

2. Biosynthesis of Fatty acids

CH3C-CH2-C-S-ACP

O

Acetoacetyl-ACP

+ NADPH + H+

D--Hydroxybutyryl-ACP

C

OH

CH2-C-S-ACPHH3C

O+ NADP+

O

D--Hydroxybutyryl-ACP

OH

C CC-S-ACP

H3C H

+ H2O

Crotonyl-ACP

C

OH

CH2-C-S-ACPHH3C

O

CH3-CH2-CH2-C-S-ACP

O

Butyryl-ACP

+ NADPH + H+

OH

C C

C-S-ACP

H3C HCrotonyl-ACP

+ NADP+

Step 6: the second reduction:

2. Biosynthesis of Fatty acids

One cycle of merry-go-round.

Maximum 16C (Palmitic acid). For 18C (Stearic acid) another system and enzyme.

+ CH2C-S-ACPCO2

-

Malonyl-ACP

CH3CH2CH2C-S-ACPO

CH3CH2CH2CH2CH2C-S-ACP

Butyryl-ACP

Hexanoyl-ACP

3. condensation4. reduction

6. reduction5. dehydration

O

O

2. Biosynthesis of Fatty acids

Second cycle:

3. Biosynthesis of Membrane Lipids

1- Glycerophospholipid

2- Cholesterol

3. Biosynthesis of Membrane Lipids

Glycerol 1-phosphate, which is obtained by reduction of

dihydroxyacetone phosphate (from glycolysis).

CH2-OHC=OCH2-OPO3

2-NADH + H+

CH2-OHCHCH2-OPO3

2-HO NAD+

Dihydroxyacetonephosphate

Glycerol1-phosphate

+ +

A vehicle for transporting electrons in and out of mitochondria.

3. Biosynthesis of Membrane Lipids

CH2-OHCHCH2-OPO3

2-HO 2RC-S-CoA

O CH2-OCR

CH

CH2-OPO32-

RCOO

O

2CoA-SH+ +

Acyl CoA A phosphatidateGlycerol1-phosphate

Fatty acids are activated by CoA, forming Fatty Acyl CoA.

An amino alcohol is added to phosphate by phosphate ester bond.

Is activated by CTP (like UTP but cytosine instead of uracil)

3. Biosynthesis of Membrane Lipids

Cholesterol is made of acetyl CoA (all of the C atoms).

3CH3CSCoAO

-O SCoA

OO OH

Acetyl CoA 3-Hydroxy-3-methylglutaryl-CoA

-O OH

O OH

Mevalonate

HMG-CoAreductase

First reaction of three acetyl CoA to form the six-carbon compound

3-hydroxy-3-methylglutaryl CoA (HMG-CoA).

-2CoA-SH

-1CoA-SH

In Liver

Mevalonate undergoes phosporylation and decarboxylation to give the C5 compound, isopentenyl pyrophosphate.

3. Biosynthesis of Membrane Lipids

-CO2

ATP ADP-O OH

O OH

MevalonateOP2O6

3-

Isopentenylpyrophosphate

Isoprene

Building block

Isopentenyl pyrophosphate (C5) is the building block for the synthesis of

geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15).

3. Biosynthesis of Membrane Lipids

OP2O63-

OP2O63-

Geranyl pyrophosphate Farnesyl pyrophosphate

3. Biosynthesis of Membrane Lipids

HOCholesterol

Two farnesyl pyrophosphate (C15) units are joined to form squalene (C30) and, in a series of at least 25 steps, squalene is converted to cholesterol (C27).

4. Biosynthesis of Amino Acids

All 20 amino acids are found in a normal diet.

Essential amino acids: cannot be synthesis in our body.

Nonessential amino acids: can be synthesis in our body.

Most nonessential amino acids are synthesized from

intermediates of either glycolysis or the citric acid cycle.

4. Biosynthesis of Amino Acids

-O-C-CH2-CH2-C-COO-

-Ketoglutarate

+ NH4+

-O-C-CH2-CH2-CH-COO-

NH3+

Glutamate

NADPH + H+

NADP+

O

O O

Amination and reduction

Reverse of oxidative deamination reaction (degradation in catabolism).

4. Biosynthesis of Amino Acids

Glutamate in turn serves as an intermediate in the synthesis of

several amino acids by the transfer of its amino group by transamination.

COO-

C=OCH3

COO-

CH-NH3+

CH2CH2COO-

COO-

CH-NH3+

CH3

COO-

C=OCH2CH2COO-

-KetoglutaratePyruvate

+

AlanineGlutamate

+