Chem 454: Regulatory Mechanisms in Biochemistry

University of Wisconsin-Eau Claire

Chem 454: Regulatory Mechanisms in Biochemistry

University of Wisconsin-Eau Claire

Lecture 11 - Biosynthesis of Amino Acids

Lecture 11 - Biosynthesis of Amino Acids

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Biosynthetic pathways for amino acids, nucleotides and lipids are very old

Biosynthetic (anabolic) pathways share common intermediates with the degradative (catabolic) pathways.

The amino acids are the building blocks for proteins and other nitrogen-containing compounds

Biosynthetic pathways for amino acids, nucleotides and lipids are very old

Biosynthetic (anabolic) pathways share common intermediates with the degradative (catabolic) pathways.

The amino acids are the building blocks for proteins and other nitrogen-containing compounds

IntroductionIntroduction

33

Nitrogen Fixation

Reducing atmospheric N2 to NH3

Amino acid biosynthesis pathways

Regulation of amino acid biosynthesis.

Amino acids as precursors to other biological molecules.

e.g., Nucleotides and porphoryns

Nitrogen Fixation

Reducing atmospheric N2 to NH3

Amino acid biosynthesis pathways

Regulation of amino acid biosynthesis.

Amino acids as precursors to other biological molecules.

e.g., Nucleotides and porphoryns

IntroductionIntroduction

44

Nitrogen fixation is carried out by a few select anaerobic micororganisms

The carbon backbones for amino acids come from glycolysis, the citric acid cycle and the pentose phosphate pathway.

The L–stereochemistry is enforced by transamination of α–keto acids

Nitrogen fixation is carried out by a few select anaerobic micororganisms

The carbon backbones for amino acids come from glycolysis, the citric acid cycle and the pentose phosphate pathway.

The L–stereochemistry is enforced by transamination of α–keto acids

IntroductionIntroduction

55

Microorganisms use ATP and ferredoxin to reduce atmospheric nitrogen to ammonia.

60% of nitrogen fixation is done by these microorganisms15% of nitrogen fixation is done by lighting and UV radiation.25% by industrial processes

Fritz Habers (500°C, 300 atm)

Microorganisms use ATP and ferredoxin to reduce atmospheric nitrogen to ammonia.

60% of nitrogen fixation is done by these microorganisms15% of nitrogen fixation is done by lighting and UV radiation.25% by industrial processes

Fritz Habers (500°C, 300 atm)

1. Nitrogen Fixation1. Nitrogen Fixation

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Enzyme has both a reductase and a nitrogenase activity.

Enzyme has both a reductase and a nitrogenase activity.

1. Nitrogen Fixation1. Nitrogen Fixation

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Contains a 4Fe-4S center

Hydrolysis of ATP causes a conformational change that aids the transfer of the electrons to the nitrogenase domain (MoFe protein)

Contains a 4Fe-4S center

Hydrolysis of ATP causes a conformational change that aids the transfer of the electrons to the nitrogenase domain (MoFe protein)

1.1 The Reductase (Fe protein)1.1 The Reductase (Fe protein)

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The nitrogenase component is an α2β2

tetramer (240 kD)

Electrons enter the P-cluster

The nitrogenase component is an α2β2

tetramer (240 kD)

Electrons enter the P-cluster

1.1 The Nitrogenase (MoFe Protein)1.1 The Nitrogenase (MoFe Protein)

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An Iron-Molybdenum cofactor for the nitrogenase binds and reduces the atmospheric nitrogen.

An Iron-Molybdenum cofactor for the nitrogenase binds and reduces the atmospheric nitrogen.

1.1 The Nitrogenase (MoFe Protein)1.1 The Nitrogenase (MoFe Protein)

1010

The ammonium ion is assimilated into an amino acid through glutamate and glutamine

Most amino acids obtain their α–amino group from glutamate by transamination.

The sidechain nitrogen of glutamine is the nitrogen source for the sidechain nitrogens of tryptophan and histidine.

The ammonium ion is assimilated into an amino acid through glutamate and glutamine

Most amino acids obtain their α–amino group from glutamate by transamination.

The sidechain nitrogen of glutamine is the nitrogen source for the sidechain nitrogens of tryptophan and histidine.

1.2 Assimilation of Ammonium Ion1.2 Assimilation of Ammonium Ion

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Glutamate dehydrogenaseGlutamate dehydrogenase

1.2 Assimilation of Ammonium Ion1.2 Assimilation of Ammonium Ion

1212

Glutamine synthetaseGlutamine synthetase

1.2 Assimilation of Ammonium Ion1.2 Assimilation of Ammonium Ion

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The biosynthetic pathways can be grouped into families:

The biosynthetic pathways can be grouped into families:

2. Amino Acid Biosynthesis2. Amino Acid Biosynthesis

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2.1 Essential Amino Acids2.1 Essential Amino Acids

1515

2.1 Essential Amino Acids2.1 Essential Amino Acids

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Transaminations:Transaminations:

2.2 Aspartate and Alanine2.2 Aspartate and Alanine

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Transaminations:Transaminations:

2.2 Aspartate and Alanine2.2 Aspartate and Alanine

1818

Amidation of aspartateAmidation of aspartate

2.3 Asparagine2.3 Asparagine

1919

Reduction of GlutamateReduction of Glutamate

2.4 Proline and Arginine2.4 Proline and Arginine

2020

Oxidation of 3–phosphoglycerateOxidation of 3–phosphoglycerate

2.5 Serine and Glycine2.5 Serine and Glycine

2121

Serine transhydroxymethylase produces glycine from serine

Serine transhydroxymethylase produces glycine from serine

2.5 Serine and Glycine2.5 Serine and Glycine

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2.6 Tetrahydrofolate2.6 Tetrahydrofolate

2323

2.5 Tetrahydrofolate2.5 Tetrahydrofolate

2424

2.5 Tetrahydro

-folate

2.5 Tetrahydro

-folate

2525

2.6 Methionine2.6 Methionine

Methylation of homocysteineMethylation of homocysteine

2626

Tetrahydrofolate does not have sufficient methyl transfer potential for many biosynthetic methylation reactions

Tetrahydrofolate does not have sufficient methyl transfer potential for many biosynthetic methylation reactions

2.7 S-Adenosylmethionine (SAM)2.7 S-Adenosylmethionine (SAM)

2727

2.7 Activated Methyl Cycle2.7 Activated Methyl Cycle

2828

DNA methylationDNA methylation

2.7 S-Adenosylmethionine2.7 S-Adenosylmethionine

2929

2.8 and 2.9 (skip)2.8 and 2.9 (skip)

3030

Example of essential amino acid synthesis

Involve Shikimate and Chorismate intermediates

Example of essential amino acid synthesis

Involve Shikimate and Chorismate intermediates

2.10 Aromatic Amino Acids2.10 Aromatic Amino Acids

3131

Chorismate:Chorismate:

2.10 Aromatic Amino Acids2.10 Aromatic Amino Acids

3232

2.10 Tyrosine and Phenylalanine2.10 Tyrosine and Phenylalanine

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2.10 Tryptophan2.10 Tryptophan

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Glycophate inhibites the enzyme that converts 5-Enolpyruvylshikimate 3–phosphate to chorismate.

Glycophate inhibites the enzyme that converts 5-Enolpyruvylshikimate 3–phosphate to chorismate.

2.10 Roundup2.10 Roundup

3535

2.11 Substrate Channeling (skip)2.11 Substrate Channeling (skip)

3636

Amino acid biosynthesis is regulated by feedback inhibition.

The first committed step in a biosynthetic pathway is usually to the one that is regulated.

Amino acid biosynthesis is regulated by feedback inhibition.

The first committed step in a biosynthetic pathway is usually to the one that is regulated.

3. Regulation of Amino Acid Biosynthesis

3. Regulation of Amino Acid Biosynthesis

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Example: Serine biosynthesis3–Phosphoglycerate dehydrogenase is inhibited by serine.

Example: Serine biosynthesis3–Phosphoglycerate dehydrogenase is inhibited by serine.

3. Regulation of Amino Acid Biosynthesis

3. Regulation of Amino Acid Biosynthesis

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Example: Serine biosynthesis

3–Phosphoglycerate dehydrogenase

Example: Serine biosynthesis

3–Phosphoglycerate dehydrogenase

3. Regulation of Amino Acid Biosynthesis

3. Regulation of Amino Acid Biosynthesis

3939

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

Combination of feedback inhibition and activation

Combination of feedback inhibition and activation

4040

The regulatory binding domain for threonine deaminase is similar to that found in 3–phosphoglycerate dehydrogenase.

The regulatory binding domain for threonine deaminase is similar to that found in 3–phosphoglycerate dehydrogenase.

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

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Enzyme multiplicityExample: Aspartokinase

ThreonineMethionineLysine

Enzyme multiplicityExample: Aspartokinase

ThreonineMethionineLysine

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

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Cumulative feedback inhibitionExample: Glutamine Synthetase

Glutamine is the sources for nitrogen in the synthesis of

tryptophan histidinecarbamoyl phsphateglucosamine 6–phosphatecytidine triphosphateadenosine monophosphate

Cumulative feedback inhibitionExample: Glutamine Synthetase

Glutamine is the sources for nitrogen in the synthesis of

tryptophan histidinecarbamoyl phsphateglucosamine 6–phosphatecytidine triphosphateadenosine monophosphate

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

4343

Cumulative feedback inhibitionExample: Glutamine Synthetase

Cumulative feedback inhibitionExample: Glutamine Synthetase

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

4444

Cumulative feedback inhibitionGlutamine Synthetase activity is also modulated by and enzymatic cascade

Cumulative feedback inhibitionGlutamine Synthetase activity is also modulated by and enzymatic cascade

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

4545

Cumulative feedback inhibitionGlutamine Synthetase activity is also modulated by and enzymatic cascade

Cumulative feedback inhibitionGlutamine Synthetase activity is also modulated by and enzymatic cascade

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

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Cumulative feedback inhibitionThe regulatory protein P (PA or PD)

Cumulative feedback inhibitionThe regulatory protein P (PA or PD)

3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways

4747

Amino acids are precursors for many biomolecules

Amino acids are precursors for many biomolecules

4. Amino Acid Derivatives4. Amino Acid Derivatives

4848

GlutathioneSulfhydryl buffer and antioxiidant

GlutathioneSulfhydryl buffer and antioxiidant

4.1 Glutathione4.1 Glutathione

4949

Nitric oxide is a short-lived signal molecule.

Formed from arginine

Nitric oxide is a short-lived signal molecule.

Formed from arginine

4.2 Nitric Oxide4.2 Nitric Oxide

5050

Porphyrins are synthesized from glycine an succinyl coenzyme A

Porphyrins are synthesized from glycine an succinyl coenzyme A

4.3 Porphyrins4.3 Porphyrins

5151

4.3 Porphyrins4.3 Porphyrins