Lecture 36: Amino Acid Biosynthesis

What is glutamate’s alpha-amino group the source of?

the alpha-amino group in most other amino acids

What catalyzes the transfer of glutamate’s alpha-amino group?

aminotransferase

What do aminotransferases use as a cofactor?

PLP (pyridoxal phosphate)

True or False: Glutamine donates its side-chain N in the biosynthesis of a wide range of compounds.

true

What catalyzes glutamine’s donation of its side chain N?

glutamine amidotransferases 

Specifically, what does glutamine amidotransferases use from glutamine?

ammonia

Glutamine amidotransferases have two domains in the enzyme. Describe the functions of these domains.

domain 1:

• hydrolysis of amide in Gln side-chain

domain 2:

• NH₃ reacts with acceptor substrate

How are the glutamine amidotransferase domains connected?

through the NH₃ channel

What kind of intermediate does the glutamine amidotransferase reaction contain?

a covalent glutamyl-enzyme intermediate

What are the classes of reactions involved in the biosynthesis of amino acids and nucleotides?

• transamination reactions with glutamate

• transfer of amino groups derived from amide N of glutamine

• transfer of 1-carbon units using tetrahydrofolate as a cofactor

True or False: Most bacteria and plants can synthesize all 20 of the common amino acids.

true

True or False: Mammals can synthesize only about half of them; the rest must come from the diet.

true

List the nonessential amino acids.

• alanine

• asparagine

• aspartate

• glutamate

• serine

List the conditionally essential amino acids.

• arginine

• cysteine

• glutamine

• glycine

• proline

• tyrosine

List the essential amino acids.

• histidine

• isoleucine

• leucine

• lysine

• methionine

• phenylalanine

• threonine

• tryptophan

• valine

True or False: Threonine was the last of these 20 amino acids to be discovered—here at UIUC by Prof. William Rose and colleauges.

true

The carbon skeletons for amino acid biosynthesis comes from intermediates in what?

• glycolysis:

  • 3-phosphoglycerate

  • PEP

  • pyruvate

• pentose phosphate pathway:

  • erythrose-4-P

  • ribose-5-P

• TCA cycle

  • OAA

  • a-ketoglutarate

Which amino acid(s) are derived from ribose-5-phosphate?

histidine

Which amino acid(s) are derived from 3-phosphoglycerate?

• serine

• glycine and cysteine

  • derived from serine

Which amino acid(s) are derived from erythose-4-phosphate?

• tryptophan

• phenylalanine

• tyrosine

• serine

  • erythrose-4-phosphate can be interconverted with 3-phosphoglycerate

Which amino acid(s) are derived from PEP?

• tryptophan

• phenylalanine

• tyrosine

Which amino acid(s) are derived from pyruvate?

• alanine

• valine

• leucine

• isoleucine

Which amino acid(s) are derived from OAA?

• aspartate

• asparagine, methionine, threonine, and lysine

  • derived from aspartate

Which amino acid(s) are derived from a-ketoglutarate?

• glutamate

• glutamine, proline, and arginine

  • derived from glutamate

Describe the reaction(s) to produce alanine.

reaction 1:

• substrate(s): pyruvate and glutamate

• coactivator(s): PLP

• enzyme: alanine aminotransferase

• process: transamination 

• product(s): alanine and a-ketoglutarate

Describe the reaction(s) to produce aspartate.

reaction 1:

• substrate(s): OAA and glutamate

• coactivator(s): PLP

• enzyme: aspartate aminotransferase

• process: transamination

• product(s): a-ketoglutarate and aspartate

Describe the reaction(s) to produce asparagine.

reaction 1:

• substrate(s): OAA and glutamate

• coactivator(s): PLP

• enzyme: aspartate aminotransferase

• process: transamination

• product(s): a-ketoglutarate and aspartate

reaction 2:

• substrate(s): aspartate, glutamine, and ATP

• coactivator(s): none

• enzyme: amidotransferase

• product(s): asparagine, glutamate, AMP, and PP_i

Describe the reaction(s) to produce serine.

reaction 1:

• substrate(s): 3-phosphoglycerate and NAD⁺

• coactivator(s): none

• enzyme: phosphoglycerate dehydrogenase

• process: alcohol oxidation

• product(s): 3-phosphohydroxypyruvate

reaction 2:

•  substrate(s): 3-phosphohydroxypyruvate and glutamate

• coactivator(s): none

• enzyme: phosphoserine aminotransferase

• process: transamination

• product(s): 3-phosphoserine and a-ketoglutarate

reaction 3:

• substrate(s): 3-phosphoserine and H₂O

• coactivator(s): none

• enzyme:  phosphoserine phosphatase

• process: phosphate hydrolysis

• product(s): serine and P_i

Describe how glycine is made from serine.

reaction 1:

• substrate(s): serine and tetrahydrofolate

• coactivator(s): PLP

• enzyme: serine hydroxymethyl-transferase

• product(s): glycine, N⁵, N¹⁰-methylene H₄ folate, and H₂O

Which type of carbonyl group is removed in the serine hydroxymethyl transferase? Where does this group go?

formaldehyde, group adds to N⁵, N¹⁰-methylene H₄ folate

What is the most common form of tetrahydrofolate?

N¹⁰-formyl THF

What are the various types of tetrahydrofolates important for?

• N⁵-methyl THF

  • methionine metabolism

• N⁵, N¹⁰-methylene THF

  • glycine biosynthesis and conversion of uridine to thymidine

• N¹⁰-formyl THF

  • purine biosynthesis

What is the most reduced form of tetrahydrofolate?

N⁵-methyl THF

True or False: Glycine is also made from CO₂ and NH₄⁺ by the action of glycine synthase, with N⁵, N¹⁰-methylenetetrahydrofolate as a methyl group donor.

true

What converts N⁵, N¹⁰-methylene THF to N⁵-methyl THF?

MTHFR (N⁵, N¹⁰-methylene THF reductase)

What does homocysteine come from?

methionine metabolism

Describe how cysteine is produced from homocysteine.

reaction 1:

• substrate(s): homocysteine and serine

• coactivator(s): PLP

• enzyme: cystathionine B-synthase

• product(s): cystathionine and H₂O

reaction 2:

• substrate(s): cystathionine and H₂O

• coactivator(s): PLP

• enzyme: cystathionine gamma lyase

• product(s): cysteine, a-ketoglutarate, and NH₄⁺

True or False: The two enzymes needed to convert homocysteine to cysteine utilize PLP as a cofactor.

true

Where does the thiol group on cysteine come from?

homocysteine

Describe how homocysteine is formed from methionine (give me the step by step pathway).

1. methionine makes a nucleophilic attack on ATP

2. methionine is transferred to adenosine and PP_i and P_i are given off; S-adenosyl-methionine (SAM) is formed

3. the methyl group on SAM is transferred to a different R group—forming adenosyl-homocysteine

4. hydrolase removes adenosine from 5-adeosyl-homocysteine; homocysteine is formed

Describe how homocysteine forms methionine.

reaction 1:

• substrate(s): homocysteine and N⁵-methyltetrahydrofolate

• coactivator(s): THF and coenzyme B₁₂

• enzyme: methionine synthase

• product(s): methionine

True or False: SAM is the methyl donor in many methylation reactions.

true

What are some examples of where SAM is the methyl donor?

• DNA

• RNA

• phospholipids

• proteins

What is the active coenzyme in coenzyme B₁₂?

methylcobalamin

True or False: Efficient recycling of S-adenosyl homocysteine back to Met is critical. Hereditary diseases in humans are associated with enzyme and vitamin deficiencies in the Met/Cys pathway.

true

Deficiencies in which enzymes can result in homocystinuria and hyperhomocysteinemia?

• methionine synthase

• cystathionine B-synthase

• MTHFR

Other than enzyme deficiencies, what else can cause homocystinuria and hyperhomocysteinemia?

deficiencies:

• vitamin B₆

• folate

• vitamin B₁₂

What can elevated homocysteine levels cause?

• homocystinuria

• hyperhomocysteinemia

• accelerated atherosclerosis

• thrombosis

• other health problems

What is vitamin B₆ used to make?

PLP

True or False: 3 nonessential and six essential amino acids are made from OAA or pyruvate.

true

What are the aromatic amino acids?

• tryptophan

• phenylalanine

• tyrosine

What is the precursor for the aromatic amino acids?

chorismate

What are the precursors for chorismate?

• 2 PEP

• 1 erythrose-4-P

Describe the synthesis of chorismate.

reaction 1:

• substrate(s): PEP, E-4-P, and H₂O

• coactivator(s): none

• enzyme: 2-keto-3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

• product(s): 2-keto-3-deoxy-D-arabinoheptulosonate-7-phosphate and P_i

reaction 2:

• substrate(s): 2-keto-3-deoxy-D-arabinoheptulosonate-7-phosphate and NAD⁺

• coactivator(s): none

• enzyme: dehydroquinate synthase

• product(s): 3-dehydroquinate and P_i

reaction 3:

• substrate(s): 3-dehydroquinate

• coactivator(s): none

• enzyme: 3-dehydroquinate dehydratase

• product(s): 3-hydroshikimate and H₂O

reaction 4:

• substrate(s): 3-hydroshikimate, NADPH, and H⁺

• coactivator(s): none

• enzyme: shikimate dehydrogenase

• product(s): shikimate and NADP⁺

reaction 5:

• substrate(s): shikimate and ATP

• coactivator(s): none

• enzyme: shikimate kinase

• product(s): ADP and shikimate-3-phosphate

reaction 6:

• substrate(s): shikimate-3-phosphate and PEP

• coactivator(s): none

• enzyme: 5-enolpyruvylshikimate-3-phosphate synthase

• product(s): 5-enolpyruvylshikimate-3-phosphate and P_i

reaction 7:

• substrate(s): 5-enolpyruvyshikimate-3-phosphate

• coactivator(s): none

• enzyme: chorismate synthase

• product(s): chorismate and P_i

Where does the amino acid backbone of Trp come from?

Ser

Where does the amino backbone of Phe and Tyr come from?

chorismate

What is the target of roundup/glyphosate?

the step involving 5-enoylpyruvylshikimate-3-phosphate synthase—inhibiting this reaction will stop the production of essential amino acids for plants

What is the source of the N of Trp’s indole ring?

Gln’s amido-NH

Where do 2 carbons of the indole ring come from?

from PRPP, which comes from the pentose phosphate pathway

What does Ser give trypotphan?

• alpha C

• alpha amino

• alpha-carboxylate

• -CH₂ side chain

Describe the production of tyrosine from chorismate.

reaction 1:

• substrate(s): chorismate

• coactivator(s): none

• enzyme: choismate mutase

• product(s): prephenate

reaction 2:

• substrate(s): prephenate and NAD⁺

• coactivator(s): none

• enzyme: prephenate dehydrogenase

• product(s): 4-hyroxyphenylpyruvate, NADH, H⁺, and CO₂

reaction 3:

• substrate(s): 4-hydroxyphenlypyruvate and glutamate

• coactivator(s): none

• enzyme: aminotransferase

• product(s): a-ketoglutarate and tyrosine

Describe the production of phenylalanine from chorismate.

reaction 1:

• substrate(s): chorismate

• coactivator(s): none

• enzyme: choismate mutase

• product(s): prephenate

reaction 2:

• substrate(s): prephenate

• coactivator(s): none

• enzyme: prephenate dehydratase

• product(s): phenylpyruvate, CO₂, and OH^-

reaction 3:

• substrate(s): phenylpyruvate and glutamate

• coactivator(s): none

• enzyme: aminotransferase

• product(s): a-ketoglutarate and phenylalanine

True or False: Tyrosine and phenylalanine are formed from chorismite in bacteria and plants.

true

When is Tyr conditionally essential?

when dietary Phe is insufficient

What causes phenylketonuria?

a genetic deficiency in phenylalanine hydrolase or dihydrobiopterin reductase

What does dihydrobiopterin do?

converts 7,8-dihydrobiopterin to 5,6,7,8-tetrahydrobiopetrin

What does phenylalanine hydroxylase do?

converts phenylalanine to tyrosine

Deficiencies in which enzymes will cause PKU?

• phenylalanine hydroxylase (majority)

• BH₂ synthetase

• BH₂ reductase

What can PKU cause? 

• hyperphenylalaninemia

• decreased synthesis of catecholamines and serotonin

• CNS symptoms:

  • mental retardation

  • failure to walk or talk

  • seizures

  • hyperactivity

  • tremor

  • microcephaly

  • failure to grow

• hypopigmentation

  • fair hair

  • light skin color

  • blue eyes

  • deficiency in melanin

True or False: PKU is the most common clinically encountered inborn error of amino acid metabolism (1:15,000).

true

What is elevated and deficient in PKU?

elevated:

• Phe

• phenyllactate

• phenylacetate

• phenylpyruvate

deficient:

• Tyr

What is important to know about the diagnosis and treatment for PKU?

diagnosis:

• early diagnosis (within first two days after birth) is essential

treatment:

• lifelong diet low in Phe and avoid aspartame

• pts shouldn’t totally eliminate Phe from the diet

• supplement Tyr

Review the chart describing the biosynthesis of histidine in bacteria and plants.

okay :)

How is GABA synthesized?

• substrate(s): glutamate

• cofactor(s): PLP

• enzyme: glutamate decarboxylase

• product(s): CO₂ and GABA

How is histamine synthesized?

• substrate(s): histidine

• cofactor(s): PLP

• enzyme: histidine decarboxylase

• product(s): CO₂ and histamine

True or False: Glutamate is an amino acid neurotransmitter while GABA and histamine are synthesized by decarboxylating amino acids.

true

Drugs that block the binding of histamine to its cellular receptors are useful in what?

• allergic reactions (antihistamines)

  • competitive inhibitors

• sleep aid (sedation)

• acid reflux (H₂ blockers)

True or False: Histamine released from certain white blood cells (mast cells cause the redness, swelling, and itchiness in allergies.

true

True or False: Acid secretion by stomach cells is controlled by histamine.

true

Describe how serotonin is produced.

reaction 1:

• substrate(s): tryptophan, tetrahydrobiopterin, and O₂

• cofactor(s): none

• enzyme: tryptophan hydroxylase

• product(s): 5-H-T, H₂O, and dihydrobiopterin

reaction 2:

• substrate(s): 5-H-T

• cofactor(s): PLP

• enzyme: aromatic amino acid decarboxylase

• product(s): CO₂ and serotonin

Where is serotonin found?

• human GI tract (about 90% found here)

• platelets

• CNS

What are the functions of serotonin in the CNS?

• pain perception

• affective disorders

• regulation of sleep

• temperature

• blood pressure

What is serotonin derived from?

tryptophan

What are catecholamines derived from?

tyrosine

Describe how dopamine is produced.

reaction 1:

• substrate(s): tyrosine, tetrahydrobiopterin, and O₂

• cofactor(s): none

• enzyme: tyrosine hydroxylase

• product(s): Dopa, H₂O, and dihydrobiopterin

reaction 2:

• substrate(s): Dpa

• cofactor(s): PLP

• enzyme: aromatic amino acid decarboxylase

• product(s): dopamine and CO₂

Describe how norepinephrine is produced.

reaction 1:

• substrate(s): tyrosine, tetrahydrobiopterin, and O₂

• cofactor(s): none

• enzyme: tyrosine hydroxylase

• product(s): Dopa, H₂O, and dihydrobiopterin

reaction 2:

• substrate(s): Dopa

• cofactor(s): PLP

• enzyme: aromatic amino acid decarboxylase

• product(s): dopamine and CO₂

reaction 3:

• substrate(s): dopamine, ascorbate, and O₂

• cofactor(s): none

• enzyme: dopamine B-hydroxylase

• product(s): norepinephrine, H₂O, and dehydroascorbate

Describe how epinephrine is produced.

reaction 1:

• substrate(s): tyrosine, tetrahydrobiopterin, and O₂

• cofactor(s): none

• enzyme: tyrosine hydroxylase

• product(s): Dopa, H₂O, and dihydrobiopterin

reaction 2:

• substrate(s): Dopa

• cofactor(s): PLP

• enzyme: aromatic amino acid decarboxylase

• product(s): dopamine and CO₂

reaction 3:

• substrate(s): dopamine, ascorbate, and O₂

• cofactor(s): none

• enzyme: dopamine B-hydroxylase

• product(s): norepinephrine, H₂O, and dehydroascorbate

reaction 4:

• substrate(s): norepinephrine

• cofactor(s): adoMet

• enzyme: phenylethanolamine-N-methyltransferase

• product(s): epinephrine and adoHcy

What are catecholamines degraded by?

• MAO (monoamine oxidase)

• COMT (catechol-O-methyltransferase)

When catecholamines are broken down, where are they secreted?

in the urine

Where is MAO found?

• neural tissue

• gut tissue

• liver tissue

What does MAO and COMT do to catecholamines?

decreases their half-lifes

True or False: Antidepressant drugs (MAO inhibitors) block monoamine oxidases—allowing neurotransmitters to accumulate to higher concentrations.

true

Which amino acid is melanin and thyroid hormone derived from?

tyrosine

Defects in tryosinase or other enzymes in melanin synthesis can lead to what?

albinism

True or False: Thyroid hormone is an iodinated derivative of tyrosine.

true

What is lignin derived from?

phenylalanine

What is lignin?

an extremely abundant structural component of wood and other plant tissues

Describe tyrosinemia type I.

• due to a deficiency in fumaryl-acetoacetate hydrolase

• accumulation of fumarylacetoacetate and its metabolites, particularly succinylacetone, in the urine

• characteristic cabbage-like odor occurs

• liver failure and renal tubular acidosis result

• treatment includes dietary restriction of phenylalanine and tyrosine

Describe methylamalonyl CoA mutase deciciency.

• the disease is due to a deficiency in methylmalonyl CoA mutase

• elevated levels of methylmalonyl CoA occur in the blood

• metabolic acidosis and developmental problems occur

Describe maple syrup urine disease.

• the disease is due to a deficiency in branched-chain a-keto acid dehydrogenase

• levels of branched-chain a-amino acids and their a-keto analogs are elevated in plasma and urine

• neurologic problems are common; the disease has a high mortality rate

• treatment involves a restricted dietary intake of the branched-chain amino acids