Metabolism of Amino Acids and other Nitrogenous Compounds

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Metabolism of Amino Acids and otherNitrogenous
Compounds

• The Nitrogen Cycle
• Amino Acid Biosynthesis
• Catabolism of Amino Acids
• Elimination of Ammonium Ion
• Amino Acids as Precursors of other Biomolecules

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• Nitrogen is found in many different organic and
  inorganic forms in the atmosphere and biosphere.

Inorganic
organic
nitrate NO3- nitrite NO2-
hyponitrite N2O22- nitrogen N2 (80of air)
ammonia NH3
amino acids protein purines pyrimidines biogenic
amines
Inorganic nitrogen can be used by plants and
bacteria. Nitrogen used by animals exists in
organic forms.
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The nitrogen cycle

• Soil bacteria play a significant role in cycling
  nitrogen through the biosphere
• Nitrogenase containing bacteria N2 NH3
• Nitrite bacteria (Nitrosomonas) NH3 NO2-
• Nitrate bacteria (Nitrobacter) NO2- NO3-
• Denitrifying bacteria NO3- N2

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• Biological Nitrogen Fixation
• N2 is converted by some bacteria into ammonia
• (NH3) that can be used by plants.
•  

• N N 3 H2 2 NH3

A bond very difficult to break.

• This is a reduction reaction of N2, and is
• thermodynamically unfavorable.
• 16 ATP is required to fix one molecule of N2.

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Nitrogen fixation occurs in dinitrogen
complex . It requires a strong reducing agent
and a large amount of energy.
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Dinitrogenasecomplex
AH2
A
ferredoxin or flavodoxin
ferredoxin or flavodoxin
dinitrogenase reductase
dinitrogenase reductase
Mo-Fe protein
16 ADP 16 Pi
16 ATP
dinitrogenase reductase 16 ATP
dinitrogenase reductase 16 ATP
Fe-S protein
dinitrogenase
dinitrogenase
2 NH4
H2
N2 2 H
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• Essential materials for nitrogen fixation
• Strong reducing agent as electron source (H2S,
  H2 )
• Large amount of ATP
• Electron transfer proteins such as Mo-Fe
  protein
• (dinitrogenase reductase) and non-heme Fe-S
  protein
• (dinitrogenase)
• Final electron acceptor like nitrogen.
• Overall reaction
• N2 10H 8e- 16 ATP ? 2NH4 16ADP 16Pi
  H2

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Biological significance of nitrogen fixation - a
self fertilization system for plants. Some
bacteria can develop specific association with
certain plants. Legume plants, after being
infected by bacteria (Clostridia) will form
tumor-like nodules on their roots, which allows
cooperative association between bacteria and
plants. The plants produce carbohydrate for
bacteria and bacteria provide ammonia to plants
by carrying out N fixation.
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For example, soy bean plants.
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Biosynthesis of amino acids

• While each amino acids has a unique biosynthetic
  pathway, each shares several common features
• There are six biosynthetic families based on
  common precursors.
• Amino acids obtain their carbon skeletons from an
  intermediate of glycolysis, citric acid cycle or
  phosphogluconate pathway.
• -NH2 usually comes from glutamate.

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Six biosynthetic families based on common
precursors.
Pyruvate Alanine Valine
Leucine Oxaloacetate Aspartate
Asparagine Methionine
Lysine Threonine
Isoleucine Ribose-5-phosphate Histidine
?-Ketoglutarate Glutamate
Glutamine Proline
Arginine 3-Phosphoglycerate Serine
Cysteine Glycine Phosphoenolpyruva
te Tryptophan Phenylalanine
Tyrosine
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• pyruvate glutamate alanine
  ?-ketoglutarate
• oxaloacetate glutamate aspartate
  ?-ketoglutarate

alanine aminotransferase
aspartate aminotransferase
Alanine can be synthesized from the interaction
between pyruvate and glutamate. Pyruvate gains
an amino group to become alanine, and glutamate
loses NH2 and oxidized to become
a-ketoglutarate.
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Glutamate synthesis
C
O
C
H


NH
NADPH H
4
?-ketoglutarate
glutamate
The process of amino group addition is called
amination. ?-ketoglutarate ties this process to
the citric acid cycle.
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Glutamine synthesis
Glutamate can be further aminated to form
glutamine.
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Glutamate and glutamine

• All life has the glutamate dehydrogenase and
  glutamine synthetase.
• In addition, higher plants and prokaryotes have
  glutamate synthase.
• ?-ketoglutarate glutamine NADPH H
• 2 glutamate NADP

glutamate synthase
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Nonessential amino acids

• Those that can be produced by animals.
• Pathways are relatively straightforward.
• pyruvate glutamate alanine
  ?-ketoglutarate
• oxaloacetate glutamate
  aspartate ??-ketoglutarate
• Some pathways are more complex, like the one for
  serine.

alanine aminotransferase
aspartate aminotransferase
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Biosynthesis of serine
3-phospho- hydroxy- pyruvate
3-phosphoglycerate
3-phospho- serine
serine
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Biosynthesis of glycine

• Glycine is synthesized from serine.
• It uses an unusual process - a one carbon
  transfer.
• Tetrahydrofolate (FH4) is an essential cofactor
  for this reaction.

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Biosynthesis of glycine
Serine
Tetrahydrofolate
C
H

C
Glycine
N5,N10-Methylene- tetrahydrofolate

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Biosynthesis of amino acids

• While each amino acids has a unique biosynthetic
  pathway, each shares several common features
• There are six biosynthetic families based on
  common precursors.
• Amino acids obtain their carbon skeletons from an
  intermediate of glycolysis, citric acid cycle or
  phosphogluconate pathway.
• -NH2 usually comes from glutamate.

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Six biosynthetic families based on common
precursors.
Pyruvate Alanine Valine
Leucine Oxaloacetate Aspartate
Asparagine Methionine
Lysine Threonine
Isoleucine Ribose-5-phosphate Histidine
?-Ketoglutarate Glutamate
Glutamine Proline
Arginine 3-Phosphoglycerate Serine
Cysteine Glycine Phosphoenolpyruva
te Tryptophan Phenylalanine
Tyrosine
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Essential amino acids

• Produced by plants and bacteria.
• Biosynthesis involves longer and more complex
  pathways.
• Example
• Synthesis of phenylalanine, tyrosine and
  tryptophan.
• They share two to three common steps.

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Essential amino acids
erythrose 4-phosphate
OH
OH
O
C
C
C
2 Pi
H
H
H

several steps
C
Chorismate
phosphoenol- pyruvate
to tryptophan
to tyrosine phenylalanine
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Phenylpyruvate
Phenylalanine
Chorismate
p-Hydroxyphenyl pyruvate
Tyrosine
Anthranilate
Tryptophan
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Production of intermediates
glucose
nucleosides
ribose-p
glucose-6-p
erythrose-4-p
glyceraldehyde-3-p
serine
3-phosphoglycerate
chorismate
glycine cysteine purines
phosphoenolpyruvate
tyrosine
pyruvate
alanine valine lucine
acetyl CoA
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Production of intermediates
pyrimidines
oxaloacetate
citrate
aspartate
asparagine
?-ketoglutarate
succinyl CoA
glutamate
glutamine proline arginine
porphyrins
heme
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Major metabolic pathwaysof amino acids
Body protein
citric acid cycle
turnover
carbon skeleton
Dietary protein
Amino acid pool
digestion
catabolism
NH4
urea cycle
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Protein Turnover

• In animals, about 75 of all amino acids are used
  for the production of protein.
• Because of the constant degradation of cellular
  structure, proteins in the body are constantly
  being replaced - protein turnover.
• Old proteins are constantly degraded. New
  proteins have to be synthesized for tissue growth
  and cell repairing.

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Examples of proteinturnover in the body

• Protein turnover rate (half-life)
• enzymes 7-10 minutes
• in liver 10 days
• in plasma 10 days
• hemoglobin 120 days
• muscle 180 days
• collagen 1000 days

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Amino acid Catabolism

• Amino acids cannot be stored.
• If there is an excess of amino acids or a lack of
  other energy sources, the body will use them for
  energy production.
• Amino acid degradation requires the removal of
  the amino group as ammonium.
• Ammonium must then be disposed of as it is toxic
  to the body.

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• Amino acids are only used as fuel when
• Too much protein is ingested
• Normal recycling of protein
• Starvation/diabetes.
• Catabolic pathways
• Each amino acid has a unique pathway.
• All are converted to mainstream metabolites.

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Catabolism of amino acids starts
with deamination.   After losing the amino
group the rest of the carbon skeleton can
usually enter TCA cycle as intermediate
molecules for energy production.
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• Removal of amino group is a two step process.
• Transamination reaction
• Aminotransferase moves the amino group to
• to a ?-Keto acid to form another amino acid.
• The amino group receiver is usually ?-
  ketoglutarate to produce glutamate.
• Oxidative deamination
• Removal of the amino group from glutamate
  producing an ammonium ion.

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For example
O C-COO- H-C-H
H-C-H COO-
NH3 H-C-COO- H-C-H
H-C-H COO-
NH3 H-C-COO- H-C-H H
O C-COO- H-C-H
H
alanine aminotransferase


alanine ?-ketoglutarate
pyruvate glutamate
to the citric acid cycle
on to the next step
The amino group receiver is usually
?-ketoglutarate.
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The purpose of transamination is to transfer the
amino groups to one species of a.a. (glutamate)
that can be used for further nitrogen
metabolism, either synthesis of other amino acid
or elimination of NH4.
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Oxidative deamination example
Energy
NADH H NH4

off to the urea cycle
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Summary
oxidative deamination
transamination
?-amino acid ?-keto acid
?-ketoglutarate glutamate
NAD H2O NADH NH4
(1)
(2)
oxaloacetate aspartate
To the urea cycle
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NH3 and NH4 produced from deamination are
both toxic, even in small amount (major drawback
for protein to be used as energy source). NH3
and NH4 have to be transformed into organic
molecules or to be removed from the body.
NH4 can either used for the biosynthesis of
glutamate (NH4 a-ketoglutarate) or to enter
urea cycle for excretion.  
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Catabolism of the carbon skeleton

• Ketogenic amino acids (Isoleucine, leucine,
  isolucine and tyrosine)
• Degraded to acetyl CoA or acetoacetyl CoA
• Produce ketone bodies.
• Glucogenic amino acids (argenine, glutamate,
  valine aspartate)
• Degraded to pyruvate, ?-ketoglutarate, succinyl
  CoA, fumarate or oxaloacetate.
• They can then be used for glucose synthesis.

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• Isoleucine, leucine and valine share some steps
  in their catabolism.
• Transamination is catalyzed by branched-chain
  aminotransferase.
• After transamination, ? ketoproducts are then
  decarboxylated via a complex similar to the
  pyruvate dehydrogenase complex.
• Their catabolism then proceeds in different
  directions.

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valine
CoASH CO2
?-keto acid dehydrogenase complex
isoleucine
branched- chain amino transferase
leucine
Acyl-CoA derivatives
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Maple syrup urine disease
Genetic disease caused by deficiency of
branched -chain aminotransferase. Alpha keto
amino acids, valine, isolucine and lucine will
accumulated in the blood and excreted in the
urine (smells like maple syrup). If untreated,
mental retardation and early death.
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• Phenylalanine catabolism
• Transamination does not occur as the first step.
  It is initially hydroxylated to tyrosine

Transamination
p-hydroxyphenypyruvate
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homogentisate
homogentisate oxidase
p-hydroxyphenypyruvate
4-maleylacetoacetate
4-fumarylacetoacetate
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Phenylketonuria (PKU)

• Genetic defect of the enzyme phenylalanine
  hydroxylase.
• Affects about 1 baby per 13,000.
• Phenylalanine Phenylpyruvate
• (affect developing brain)
• Can result in mental retardation and early death.
• Treatment - restrict phenylalanine until age 10
  (brain is developed).

aminotransferase
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Where amino acids enter cycle
isoleucine leucine tryptophan
alanine, glycine serine, threonine tryptophan
acetyl CoA
acetoacetyl CoA
pyruvate
asparagine aspartate
oxaloacetate
leucine lysine phenylalanine tryosine tryptophan
citrate
tyrosine phenylalanine aspartate
fumarate
?-ketoglutarate
isoleucine methionine valine
succinyl CoA
glutamate, glutamine proline, arginine
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Elimination of ammonium ion

• NH4 is produced from amino acid catabolism is
  toxic and must be eliminated.
• NH4 is eliminated through the urea cycle
• that occurs in the liver.
• The urea cycle
• Occurs in the liver.
• Results in the formation of urea.
• Urea is eliminated by excretion (urine).

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•  
• Urea cycle is a five-step pathway carried out by
  
• liver cells.
• The strategy is to synthesize arginine that is
• then hydrolyzed to release urea and L-ornithine.
  
• (Fig. 19.16).

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2 ATP 2 H2O
NH4 CO2
carbamoyl phosphate
O O
H2N-C-O-P-O-
O-
2 ADP Pi
O
H2N-C-NH2 urea
NH3
H3N-(CH2)3CH-COO
- L-ornithine
Pi
H2O
O NH3

H2N-C-NH-(CH2)3CH-COO-
L-citrulline
NH2 NH3

H2NC-NH-(CH2)3CH-COO-
L-arginine
Urea Cycle
ATP
COO- NH2
COO-

-OOC-CH2CH-NC-NH
-(CH2)3CH L-argininosuccinate
AMP PPi
NH3
-OOCCH2CH-COO-
L-aspartate
-OOC-CHCH-COO- fumarate
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• A complete block of any step of the urea cycle is
  incompatible with life.
• No alternate pathway for NH4 elimination.
• Some genetic disorders will affect arginase
  carbamoyl phosphate synthase ornithine
  transcarbamoylase

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NH4 CO2
carbamoyl-phosphate synthase I
2 ATP
2 ADP Pi
urea
L-ornithine
carbamoyl phosphate
arginase
ornithine transcarbamoylase
H2O
Pi
L-arginine
mitochondrial matrix
L-citrulline
argininosuccinate lyase
argininosuccinate synthase
ATP
L-arginino- succinate
AMP PPi
fumarate
L- aspartate
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As one important group of nutrients, the main
functions of proteins and amino acids are for
making new cellular structure, making hormones
and enzymes.
A small portion of amino acids serves
as precursors of important biomolecules such as
porphyrins, nucleic acids, nucleotide bases and
biogenic amines.
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Amino acids as precursors of other biomolecules

• Porphyrins
• Important part of all pigment proteins (heme,
  chlorophyll, cytochromes) as prosthetic groups
• Porphyrin combination of succinyl CoA
• and glycine.
• Heme Fe porphyrin.
• chlorophyll Mg porphyrin.
• An average adult produces about 900 trillion
  hemoglobin molecules each second. With 4 heme
  per hemoglobin, its easy to see how porphyrin
  production is important.

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Porphyrin biosynthesis

• The first step is the condensation of glycine and
  succinyl CoA to produce ?-aminolevulinate (ALA).

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• Next, two molecules of ALA are used to produce
  porphobilinogen.

2
ALA
porphobilinogen
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• Four porphobilinogen molecules are then condensed
  to produce protophorphyrin IX.

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• Finally, for heme, an Fe2 is inserted.

Fe2
ferrochelatase
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Biogenic amines Histamine, serotonin,
melatonin, dopamine, norepinephrine etc. - A
group of biologically active molecules with
small size. Most of them are the products of
decarboxylation of amino acids.
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  Histamine - decarboxylated form of histidine
GABA, a neurotransmitter is from glutamate
Serotonin, melatonin are the derivatives of
tryptophan Dopamine and epinephrine are
converted from tyrosine.   Aspartate, glycine
and glutamine are precursors for making purines
and pyrimidines.
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Tryptophan
Serotonin
Melatonin
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Purine and pyrimidine nucleotides

• Where the nitrogen base parts come from.

CO2
glycine
aspartate
NH4
formate
formate
CO2
amide N of glutamine
aspartate
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