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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)
88
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
1313
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
1616
Transaminations:Transaminations:
2.2 Aspartate and Alanine2.2 Aspartate and Alanine
1717
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
2222
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
3333
2.10 Tryptophan2.10 Tryptophan
3434
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
4141
Enzyme multiplicityExample: Aspartokinase
ThreonineMethionineLysine
Enzyme multiplicityExample: Aspartokinase
ThreonineMethionineLysine
3.1 Regulation of Branched Pathways3.1 Regulation of Branched Pathways
4242
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
4646
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