Pathways in Amino Acids and Protein Metabolism 2

COLLEGE OF MEDICINE AND HEALTH
SCIENCES
SCHOOL OF MEDICINE AND PHARMACY
MODULE TITLE: BIOCHEMISTRY
Structural Biochemistry:
Pathways in amino acids and protein metabolism
Overview Amino acids and Protein Metabolism
 The metabolism of amino acids comprises a wide array of synthetic and

degradative reactions by which amino acids are
 assembled as precursors of polypeptides or other compounds and
 broken down to recover metabolic energy.
 The chemical transformations of amino acids are distinct from those of
carbohydrates or lipids
 amino acids involve the element nitrogen
 The bulk of the cell’s amino acids are incorporated into proteins, which are
continuously being synthesized and degraded
 Unlike carbohydrates or lipids, there is no true storage form of amino acids which is
analogous to glycogen or triacylglycerols
 Mammals synthesize certain amino acids and obtain the rest from their diets.
Overview Amino acids and Protein Metabolism…
Overview of body Amino acids pool-source utilization

Overview Amino acids Metabolism


• Excess dietary amino acids are not simply excreted but are converted to common
metabolites that are precursors of glucose, fatty acids, and ketone bodies and are
therefore metabolic fuels.
Pathways of amino acid Metabolism
• Pathways of amino acid metabolism can be studied in the following amino acid
metabolism
1. Protein Degradation
• Proteins have lifetimes that range from as short as a few minutes to weeks or more.
• Cells continuously synthesize proteins from and degrade them to amino acids
• The process has three functions:
(1) to store nutrients in the form of proteins and to break them down in times of
metabolic need, processes that are most significant in muscle tissue;
(2) to eliminate abnormal proteins whose accumulation would be harmful to the cell;
and
Pathways of amino acid Metabolism…
(3) to permit the regulation of cellular metabolism by eliminating superfluous enzymes

and regulatory proteins
 Controlling a protein’s rate of degradation is therefore as important to the cellular and
organismal economy as is controlling its rate of synthesis
 The rate of protein degradation in a cell varies with its nutritional and hormonal
state.
 For example, under conditions of nutritional deprivation, cells increase their rate of protein
degradation so as to provide the necessary nutrients for metabolic processes
 Protein degradation is assisted by different enzymatic reaction
a) Protein degradation by Lysosomes
 Lysosomes degrade many Proteins
 Lysosomes contain ∼50 hydrolytic enzymes, including a variety of proteases known
as cathepsins
 Lysosomes degrade substances that the cell takes up via endocytosis

 They also recycle intracellular constituents that are enclosed within vesicles that fuse with
lysosomes, a process called autophagy (Greek: autos, self + phagein, to eat)
 In well-nourished cells, lysosomal protein degradation is nonselective.
 In starving cells, such degradation would deplete essential enzymes and regulatory
proteins.
 Lysosomes therefore also have a selective pathway, which is activated only after a prolonged
fast, that imports and degrades cytosolic proteins containing the pentapeptide Lys-PheGlu-
Arg-Gln (KFERQ) or a closely related sequence
 Such KFERQ proteins are selectively lost from tissues that atrophy in response to fasting
(e.g., liver and kidney) but not from tissues that do not do so (e.g., brain and testes)
 Many normal and pathological processes are associated with increased lysosomal
activity
 for example, the muscle wastage caused by disuse, denervation, or traumatic injury.
b) Lysosomes Independent Protein degradation

 Protein breakdown in eukaryotic cells also occurs in an ATP-requiring process that is
independent of lysosomes.
 This process involves ubiquitin, a 76-residue monomeric protein named for its
ubiquity and abundance.
 It is one of the most highly conserved eukaryotic proteins known (it is identical
in such diverse organisms as humans, trout, and Drosophila), suggesting that it is
uniquely suited for some essential cellular function
 Ubiquitin marks Proteins for degradation (by covalently linking them to ubiquitin)
 This process occurs in three steps
1. In an ATP-requiring reaction, ubiquitin’s terminal carboxyl group is conjugated, via a
thioester bond, to ubiquitin-activating enzyme (E1).
 Most organisms have only one type of E1
b) Lysosomes Independent Protein degradation
2. The ubiquitin is then transferred to a specific

Cys sulfhydryl group on one of numerous
homologous proteins named ubiquitin-
conjugating enzymes (E2s; 11 in yeast and >20
in mammals).
 The various E2s are characterized by an
∼150-residue catalytic core containing the
active site Cys.
3. Ubiquitin-protein ligase (E3) transfers the
activated ubiquitin from E2 to a Lys ε-amino
group of a previously bound protein, thereby
forming an isopeptide bond.
 Cells contain many species of E3s, each of which mediates the ubiquitination of
a specific set of proteins and thereby marks them for degradation.
 Each E3 is served by one or a few specific E2s.
 For a protein to be efficiently degraded, it must be linked to a chain of at least four
tandemly linked ubiquitin molecules in which Lys 48 of each ubiquitin forms an
isopeptide bond with the C-terminal carboxyl group of the following ubiquitin.
 These polyubiquitin chains may contain 50 or more ubiquitin units.
c) Ubiquitinated degradation by Proteasome
 Ubiquitinated proteins are proteolytically degraded in an ATP-dependent process

mediated by a large (∼2500 kD, 26S) multiprotein complex named the 26S
proteasome
 The Proteasome unfolds and hydrolyzes Ubiquitinated Polypeptides
 The 26S proteasome consists of:
 a hollow cylindrical core, known as the 20S proteasome, which is covered at one
or both ends by a 19S cap.
 the quantities “26S,” “20S,” and “19S” refer to the corresponding particles’
sedimentation coefficients in units of Svedbergs (S)
 26S proteasome cleaves its polypeptide substrates into ∼8-residue fragments, which
then diffuse out of the proteasome
 19S caps recognize ubiquitinated proteins, unfold them, and feed them into the 20S
proteasome in an ATP-dependent manner
2. Amino Acid Deamination
 Free amino acids originate from

 the degradation of cellular proteins and
 from the digestion of dietary proteins.

 The gastric protease pepsin, the pancreatic enzymes trypsin, chymotrypsin, and
elastase and a host of other endo- and exopeptidases degrade polypeptides to
oligopeptides and amino acids.
 These substances are absorbed by the intestinal mucosa and transported via the
bloodstream to be absorbed by other tissues
 The further degradation of amino acids takes place intracellularly and includes a step
in which the α-amino group is removed.
 In many cases, the amino group is converted to ammonia, which is then incorporated
into urea for excretion

 The remaining carbon skeleton (α-keto acid) of the amino acid can be broken down to
other compounds
a. Amino Acid Deamination by Transaminases
 Most amino acids are deaminated by transamination, the transfer of their amino group
to an α-keto acid to yield the α-keto acid of the original amino acid and a new amino
acid.
Transamination
 the process by which the α-amino group of the amino acid is first removed prior to the
metabolism of their carbon skeletons into a major metabolic intermediate
 In this process the α-amino group of most amino acids is transferred to α-ketoglutarate
to form glutamate and the corresponding α-keto acid
 The enzymes that catalyze these reactions are called transaminases
(aminotransferases)
 In mammals, these enzymes are found predominantly in the liver and muscle
 For example,
 Aspartate transaminase catalyzes the transfer of the amino group of aspartate to α-
ketoglutarate
Transamination
 The predominant amino group acceptor is α-ketoglutarate, producing glutamate and

the new α-keto acid

 Glutamate’s amino group, in turn, can be transferred to oxaloacetate in a second

transamination reaction, yielding aspartate and re-forming α-ketoglutarate:
Clinical Implication of Transamination
 Although the aminotransferases are in liver and muscle, in pathologic conditions

these enzymes may leak into the blood where they are useful clinical indicators of
damage to liver or muscle
 The two most important aminotransferase reactions are catalyzed and leak into
the blood when the level is elevated
1. Alanine aminotransferase (ALT):

 Present in liver, brain, kidney and heart tissues; predominantly in Liver
 The enzyme catalyzes the transfer of the amino group of alanine to α-
ketoglutarate, resulting in the formation of pyruvate and glutamate.
 The reaction is readily reversible.
 However, during amino acid catabolism, this enzyme functions in the direction of
glutamate synthesis.
 Blood levels of these aminotransferases, also called transaminases, are important
indicators of liver disease
2. Aspartate aminotransferase (AST)
 liver, brain, kidney, heart tissues and muscles
 AST transfers amino groups from glutamate to oxaloacetate, forming aspartate,
which is used as a source of nitrogen in the urea cycle.
Glutamate-Pyruvate
Aminotransferase
Glutamate (Alanine Transferase, a-Ketoglutarate
+ ALT) +
Pyruvate Alanine
Glutamate-
Glutamate Oxaloacetate a-Ketoglutarate
+ Aminotransferase +
Oxaloacetate (Aspartate Transferase, Aspartate
AST)
Role of Pyridoxal phosphate in transamination reactions
 The enzymes that catalyze transamination, called aminotransferases or transaminases,
require the coenzyme pyridoxal-5′-phosphate (PLP)
 The coenzyme of all transaminases is pyridoxal phosphate, which is derived from
pyridoxine (vitamin B6)
 The coenzyme is transiently converted into pyridoxamine phosphate during
transamination
 On addition of substrate, the -amino group of the incoming amino acid displaces the
amino group of the active site lysine
 A new Schiff base (a cpd with general formula R2C=NR1 , subclass of imines, cpd
with C=N) linkage is formed with the amino acid substrate
 The resulting amino acid–pyridoxal phosphate–Schiff base that is formed remains
tightly bound to the enzyme by multiple noncovalent interactions
b. Deamination of Glutamate
 Glutamate can be oxidatively deaminated by glutamate dehydrogenase (GDH),
 yielding ammonia and
 regenerating α-ketoglutarate for use in additional transamination reactions.
 Glutamate dehydrogenase, a mitochondrial enzyme, is the only known enzyme that
can accept either NAD+ or NADP+ as its redox coenzyme.
 Oxidation occur with transfer of a hydride ion from glutamate’s Cα to NAD(P)+,
thereby
 forming α-iminoglutarate, which is hydrolyzed to
 α-ketoglutarate and
 ammonium ion
 The ammonia liberated in the GDH reaction is eventually excreted in the form of
urea.
 Thus, the glutamate dehydrogenase reaction functions to eliminate amino groups
from amino acids that undergo transamination reactions with α-ketoglutarate
3. The Urea Cycle
 Living organisms excrete the excess nitrogen arising from the metabolic breakdown of
amino acids in one of three ways.
 Many aquatic animals simply excrete ammonia.
 Where water is less plentiful, processes have evolved that convert ammonia to less
toxic waste products that require less water for excretion
 One such product is
 Urea which is produced by most terrestrial vertebrates;
 Uric acid which is excreted by birds and terrestrial reptiles
 Urea is synthesized in the liver by the enzymes of the urea cycle
 It is then secreted into the bloodstream and sequestered by the kidneys for excretion
in the urine.
 The overall urea cycle reaction is
 urea’s two nitrogen atoms are

contributed by ammonia and
aspartate,
 whereas its carbon atom comes
from HCO3−.
 Five enzymatic reactions are involved in the urea cycle,

 two of which are mitochondrial and
 three cytosolic
1. Carbamoyl Phosphate Synthetase Acquires the First Urea Nitrogen Atom.

 Carbamoyl phosphate synthetase (CPS) catalyzes the condensation and activation
of NH3 and HCO3− to form carbamoyl phosphate,
 the first of the cycle’s two nitrogen-containing substrates,
 with the concomitant cleavage of 2 ATP.
 Eukaryotes have two forms of CPS:
 Mitochondrial CPS I uses ammonia as its nitrogen donor and participates in
urea biosynthesis,
 Cytosolic CPS II uses glutamine as its nitrogen donor and is involved in
pyrimidine biosynthesis
 Five enzymes participate in

the urea cycle:
(1) carbamoyl phosphate synthetase,
(2) ornithine transcarbamoylase,
(3) argininosuccinate synthetase,
(4) argininosuccinase, and
(5) arginase.
 Enzymes 1 and 2 are
mitochondrial and enzymes 3–5
are cytosolic.
The urea cycle

 CPS I catalyzes an essentially irreversible reaction that is the rate-limiting step of

the urea cycle
1. ATP activates HCO3− to form carboxyphosphate and ADP.
2. Ammonia attacks carboxyphosphate, displacing the phosphate to form carbamate
and Pi.
3. A second ATP phosphorylates carbamate to form carbamoyl phosphate and ADP.
The mechanism of action of CPS I

2. Carbamoylation of Ornithine Produces Citrulline.

 Ornithine transcarbamoylase transfers the carbamoyl group of carbamoyl
phosphate to ornithine, yielding citrulline
 Both ornithine and citrulline are “nonstandard” α-amino acids that do not occur in
proteins.
 The transcarbamoylase reaction occurs in the mitochondrion, so ornithine, which is
produced in the cytosol, must enter the mitochondrion via a specific transport
system.
 since the remaining urea cycle reactions occur in the cytosol, citrulline must be
exported from the mitochondrion
3. Argininosuccinate Synthetase Acquires the Second Urea Nitrogen Atom.
 Urea’s second nitrogen atom is introduced by the condensation of citrulline’s ureido
group with an aspartate amino group by argininosuccinate synthetase
 ATP activates the ureido oxygen atom as a leaving group through

 formation of a citrullyl–AMP intermediate, and
 AMP is subsequently displaced by the aspartate amino group.
 The PPi formed in the reaction is hydrolyzed to 2 Pi, so the reaction consumes two
ATP equivalent
The mechanism of action of argininosuccinate synthetase

4. Argininosuccinase Produces Fumarate and Arginine.

 With the formation of argininosuccinate, all of the urea molecule components have
been assembled.
 the amino group donated by aspartate is still attached to the aspartate carbon
skeleton.
 This situation is remedied by the argininosuccinase catalyzed elimination of
fumarate, leaving arginine
 Arginine is urea’s immediate precursor.
 The fumarate produced in the argininosuccinase reaction is converted to
oxaloacetate by the action of fumarase and malate dehydrogenase.
 The oxaloacetate is then used for gluconeogenesis
5. Arginase Releases Urea
 The urea cycle’s final reaction is the arginase catalyzed hydrolysis of arginine to
yield urea and regenerate ornithine
 Ornithine is then returned to the mitochondrion for another round of the cycle.
 The urea cycle thus converts two amino groups,
 one from ammonia and
 One from aspartate, and
 a carbon atom from HCO3− to the relatively nontoxic product, urea, at the cost of
four “high-energy” phosphate bonds.
c. Substrate Availability Regulate Urea Cycle
 Carbamoyl phosphate synthetase I, which catalyzes the first committed step of the
urea cycle, is allosterically activated by N-acetylglutamate
 This metabolite is synthesized from glutamate and acetyl-CoA by N-acetylglutamate
synthase
 When amino acid breakdown rates increase, the concentration of glutamate
increases as a result of transamination.
 The increased glutamate stimulates N-acetylglutamate synthesis
4. Breakdown of Amino Acids
 Amino acids are degraded to compounds that can be metabolized to CO2 and H2O or
used in gluconeogenesis (Synthesis of glucose from non-carbohydrate precursors).
 Oxidative breakdown of amino acids accounts for 10 to 15% of the metabolic energy
generated by animals
 The -amino group is removed first and the resulting carbon skeleton is converted into
one or more major metabolic intermediates and used as metabolic fuel
 “Standard” 20 amino acids are degraded to one of seven metabolic intermediates:
 pyruvate,  oxaloacetate,
 α-ketoglutarate,  acetyl-CoA, or
 succinyl-CoA,  acetoacetate
 fumarate,
 The amino acids can be divided into two groups based on their catabolic pathways:
1. Glucogenic amino acids, which are degraded to pyruvate, α-ketoglutarate, succinyl-
CoA, fumarate, or oxaloacetate and are therefore glucose precursors
 they can give rise to the net synthesis of glucose

 This is because the citric acid cycle intermediates and pyruvate can be converted into
phosphoenolpyruvate and then into glucose via gluconeogenesis
Fate of carbon skeletons of amino acids

4. Breakdown of Amino Acids…
2. Ketogenic amino acids, which are broken down to acetyl-CoA or acetoacetate and
can thus be converted to fatty acids or ketone bodies
 they give rise to ketone bodies
 The acetyl CoA or acetoacetyl CoA can also be used to synthesize lipids
 Some amino acids are precursors of both carbohydrates and ketone bodies.
 Example: Isoleucine (Ile), Phenylalanine (Phe), Tryptophan (Trp) and Tyrosine
(Tyr) are both ketogenic and glucogenic
 some of their carbon atoms end up in acetyl CoA or acetoacetyl CoA,
whereas others end up in precursors of glucose
 Since animals lack any metabolic pathways for the net conversion of acetyl-CoA or
acetoacetate to gluconeogenic precursors, no net synthesis of carbohydrates is
possible from the purely ketogenic amino acids Lys and Leu.
 Of the standard set of 20 amino acids, only Leu and Lys are solely ketogenic
 The remaining 14 amino acids are classified as solely glucogenic
1. Alanine, Cysteine, Glycine, Serine, and Threonine Are Degraded to Pyruvate
 Five amino acids—alanine, cysteine, glycine, serine, and threonine—are broken down
to yield pyruvate
 Alanine is straightforwardly transaminated to pyruvate.
 Serine is converted to pyruvate through dehydration by serine–threonine
dehydratase.
 Cysteine can be converted to pyruvate via several routes in which the sulfhydryl
group is released as H2S, SO2 3−, or SCN−
 Glycine is converted to pyruvate by first being converted to serine by the enzyme
serine hydroxymethyltransferase
 In mammals other than humans, threonine’s major route of breakdown is through
threonine dehydrogenase producing 𝛂-amino-𝛃-ketobutyrate, which is converted to
 acetyl-CoA and
 glycine by 𝛂-amino-𝛃-ketobutyrate lyase
 threonine is both glucogenic and ketogenic.
 This PLPdependent enzyme catalyzes the elimination of water from serine in six
steps:
(1) formation of a serine-PLP Schiff base,
(2) removal of the α-H atom of serine to form a resonance-stabilized carbanion,
(3) β elimination of OH−,
(4) hydrolysis of the Schiff base to yield the PLP–enzyme and aminoacrylate,
(5) nonenzymatic tautomerization to the imine, and
(6) nonenzymatic hydrolysis to form pyruvate and ammonia.
 Threonine undergoes an analogous series of reactions to yield α-ketobutyrate.
The serine–threonine dehydratase reaction

2. Asparagine and Aspartate Are Degraded to Oxaloacetate
 Transamination of aspartate leads directly to oxaloacetate.

 Asparagine is also converted to oxaloacetate after its hydrolysis to aspartate by
L-asparaginase
 L-asparaginase is an effective chemotherapeutic agent in the treatment of cancers

that must obtain asparagine from the blood, particularly acute lymphoblastic
leukemia (ALL).
3. Arginine, Glutamate, Glutamine, Histidine, and Proline Are Degraded to 𝛂-
Ketoglutarate
 Arginine, glutamine, histidine, and proline are all degraded by conversion to
glutamate which in turn is
 oxidized to α-ketoglutarate by glutamate dehydrogenase
 Conversion of glutamine to glutamate involves only one reaction: hydrolysis by
glutaminase
 In the kidney, the action of glutaminase produces ammonia, which combines with a
proton to form the ammonium ion (NH4+) and is excreted.
 During metabolic acidosis, kidney glutaminase helps eliminate excess acid
 Although free NH3 in the blood could serve acid-absorbing purpose, ammonia is
toxic.
 It is therefore converted to glutamine by glutamine synthetase in the liver
 Glutamine acts as an ammonia transport system between the liver, where much of it is
The degradation of arginine, glutamate,

glutamine, histidine, and proline to 𝛂-
ketoglutarate.
4. Methionine, Threonine, Isoleucine, and Valine Are Degraded to Succinyl-CoA
 Methionine, threonine, isoleucine, and valine have degradative pathways that all yield
propionyl-CoA.
 Propionyl-CoA is converted to succinyl-CoA by a series of reactions requiring biotin
and coenzyme B12
 Methionine degradation begins with its reaction with ATP to form S-
adenosylmethionine (SAM; alternatively AdoMet).
 This sulfonium ion’s highly reactive methyl group makes it an important biological
methylating agent.
 SAM is the methyl donor in the synthesis of phosphatidylcholine from
phosphatidylethanolamine
 Donation of a methyl group from SAM leaves S-adenosylhomocysteine, which is then
hydrolyzed to adenosine and homocysteine.
4. Methionine, Threonine, Isoleucine, and Valine Are Degraded to Succinyl-CoA
 The homocysteine can be methylated to re-form methionine via a reaction in which N5-
methyltetrahydrofolate
 The homocysteine can combine with serine to yield cystathionine, which subsequently
forms cysteine (cysteine biosynthesis) and 𝛂-ketobutyrate.
 The α-ketobutyrate continues along the degradative pathway to propionyl-CoA and
then succinylCoA.
 Threonine is Degraded Mainly to Propionyl-CoA in Humans.
5. Branched-Chain Amino Acid Degradation
 Branched-Chain Amino Acid Degradation Involves Acyl-CoA Oxidation.

 Degradation of the branched-chain amino acids isoleucine, leucine, and valine begin
with three reactions that employ common enzymes
1. Transamination to the corresponding α-keto acid.
2. Oxidative decarboxylation to the corresponding acyl-CoA.
3. Dehydrogenation by FAD to form a double bond.
 The degradation of valine, which contains one less carbon than isoleucine, yields CO2
and propionyl-CoA, which is then converted to succinyl-CoA.
 The further degradation of leucine, which yields acetoacetate instead of propionyl
CoA,
Branched-Chain Amino Acid Degradation
Branched-Chain Amino Acid Degradation Involves Acyl-CoA Oxidation

6. Leucine and Lysine Are Degraded Only to Acetyl-CoA and/or Acetoacetate
 Leucine degradation begins in the same manner as isoleucine and valine

degradation
 but the dehydrogenated CoA adduct β-methylcrotonyl-CoA is converted to
acetyl-CoA and acetoacetate, a ketone body
 The predominant pathway for lysine degradation in mammalian liver produces
 acetoacetate and
 2CO2 via the initial formation of the α-ketoglutarate–lysine adduct
saccharopine
 The saccharopine pathway is thought to predominate in mammals because a genetic
defect in the enzyme that catalyzes Reaction 1 in the sequence results inhyperlysi
nemia and hyperlysinuria (elevated levels of lysine in the blood and urine,
respectively) along with mental and physical retardation.
The pathway of lysine degradation in mammalian liver.

7. Tryptophan Is Degraded to Alanine and Acetoacetate
 the major tryptophan degradation pathway is indicated in the following diagram
 is catalyzed by kynureninase
 The kynureninase reaction follows the same initial steps as transamination but
an enzyme nucleophilic group then attacks Cγ of the resonance stabilized
intermediate, resulting in Cβ—Cγ bond cleavage
8. Phenylalanine and Tyrosine Are Degraded to Fumarate and Acetoacetate
 the first reaction in phenylalanine degradation is its hydroxylation to tyrosine

 a single pathway is responsible for the breakdown of both amino acids.
 The final products of the six-reaction degradation are
 fumarate, a citric acid cycle intermediate, and
 acetoacetate, a ketone body.
5. Amino Acid Biosynthesis
 Many amino acids are synthesized by pathways that are present only in plants and
microorganisms.
 Since mammals must obtain these amino acids in their diets, these substances are
known as essential amino acids.
 The other amino acids, which can be synthesized by mammals from common
intermediates, are termed nonessential amino acids.
 Their α-keto acid carbon skeletons are converted to amino acids by
transamination reactions utilizing the preformed α-amino nitrogen of another
amino acid, usually glutamate
 Arginine is classified as essential, even though it is synthesized by the urea cycle,
 because it is required in greater amounts than can be produced by that route
during the normal growth and development of children
5. Amino Acid Biosynthesis…
Essential vs Nonessential Amino Acids in Humans
 The essential amino acids occur in
animal and vegetable proteins. Different
proteins, however, contain different
proportions of the essential amino
acids.
 Milk proteins, contain them all in
the proportions required for proper
human nutrition.
 Bean protein, on the other hand,
contains an abundance of lysine but
is deficient in methionine,
 wheat is deficient in lysine but
contains ample methionine
Nonessential Amino Acids Biosynthesis
 All the nonessential amino acids except tyrosine are synthesized by simple
pathways from one of :four common metabolic intermediates
 pyruvate,
 oxaloacetate,
 α-ketoglutarate, and
 3-phosphoglycerate
 tyrosine is synthesized by the one-step hydroxylation of the essential amino acid
phenylalanine
 the dietary requirement for phenylalanine reflects the need for tyrosine as well.
 The presence of dietary tyrosine therefore decreases the need for phenylalanine
 Alanine, Asparagine, Aspartate, Glutamate, and Glutamine are Synthesized from
Pyruvate, Oxaloacetate, and 𝛂-Ketoglutarate.
 Pyruvate, oxaloacetate, and α-ketoglutarate are the α-keto acids (the so-called
carbon skeletons) that correspond to alanine, aspartate, and glutamate,
Nonessential Amino Acids Biosynthesis…
 the synthesis of each of the amino acids is a one-step transamination reaction
 The syntheses of
alanine, aspartate,
glutamate, asparagine,
and glutamine
 These reactions involve, respectively, transamination of (1)
pyruvate, (2) oxaloacetate, and (3) α ketoglutarate, and
amidation of (4) aspartate and (5) glutamate.
 Asparagine and glutamine are, respectively, synthesized from aspartate and
glutamate by ATP-dependent amidation.
 In the glutamine synthetase reaction glutamate is first activated by reaction with
ATP to form a 𝛄-glutamylphosphate intermediate.
 NH+4 then displaces the phosphate group to produce glutamine
 Aspartate amidation by asparagine synthetase to form asparagine follows a
different route; it uses glutamine as its amino group donor and cleaves ATP to AMP +
PP
a . Glutamate Is the Precursor of Proline, Ornithine, and Arginine.
 Conversion of glutamate to proline involves the reduction of the γ-carboxyl group
to an aldehyde
 Reduction of the glutamate γ-carboxyl group to an aldehyde is an endergonic
process that is facilitated by first phosphorylating the carboxyl group in a reaction
 The unstable product, glutamate-5-phosphate, has not been isolated from reaction
mixtures but is presumed to be the substrate for the reduction that follows.
 The resulting glutamate-5-semialdehyde (which is also a product of arginine and
proline degradation internal Schiff base Δ1-pyrroline-5-carboxylate.
 The final reduction to proline is catalyzed by pyrroline-5-carboxylate reductase
 In humans, a three-step pathway leads from glutamate to ornithine via a branch from
proline biosynthesis
 Glutamate-5-semialdehyde, which is in equilibrium with Δ1-pyrroline-5-carboxylate,
is directly transaminated to yield ornithine in a reaction catalyzed by ornithine-𝛅-
amino transferase
 Ornithine is converted to arginine by the reactions of the urea cycle
b. Serine, Cysteine, and Glycine Are Derived from 3-Phosphoglycerate

 Serine is formed from the glycolytic intermediate 3-phosphoglycerate in a three-
reaction pathway
1. Conversion of 3-phosphoglycerate’s 2-OH group to a ketone, yielding 3-
phosphohydroxypyruvate, serine’s phosphorylated keto acid analog.
2. Transamination of 3-phosphohydroxypyruvate to phosphoserine.
3. Hydrolysis of phosphoserine to serine
The conversion of 3-phosphoglycerate to serine
 The pathway enzymes are (1) 3-phosphoglycerate dehydrogenase, (2) a PLP

dependent aminotransferase, and (3) phosphoserine phosphatase.
b. Serine, Cysteine, and Glycine Are Derived from 3-Phosphoglycerate…
 Serine participates in glycine synthesis in two ways:

1. Direct conversion of serine to glycine by serine hydroxymethyl transferase in a
reaction that also yields N5,N10-methylene-THF
2. Condensation of the N5,N10-methylene-THF with CO2 and NH4+ by glycine synthase
 In animals, cysteine is synthesized from serine and homocysteine, a breakdown
product of methionine
 Homocysteine combines with serine to yield cystathionine, which subsequently
forms cysteine and α-ketobutyrate.
 Since cysteine’s sulfhydryl group is derived from the essential amino acid
methionine, cysteine can be considered to be an essential amino acid
Clinical Disorders Related Amino acid Metabolism
 Inborn errors of metabolism are commonly caused by mutant genes that generally
result in abnormal proteins, most often enzymes.
 The inherited defects may be expressed as a total loss of enzyme activity or, more
frequently, as a partial deficiency in catalytic activity.
 Without treatment, the inherited defects of amino acid metabolism almost invariably
result in mental retardation or other developmental abnormalities as a result of harmful
accumulation of metabolites.
 Many are rare, occurring in less than 1 per 250,000 in most populations
i. Maple syrup urine disease
 Maple syrup urine disease (MSUD) is a rare condition (1:185,000)
 It is an autosomal recessive disorder in which there is a partial or complete deficiency in
branched-chain α-keto acid dehydrogenase
 This enzyme complex decarboxylates leucine, isoleucine, and valine
i. Maple syrup urine disease…
 These amino acids and their corresponding α-keto acids accumulate in the blood,
causing a toxic effect that interferes with brain functions.
i. Maple syrup urine disease…
The disease is characterized by:

i. Feeding problems
ii. Vomiting
iii. Dehydration
iv. Severe metabolic acidosis
v. A characteristic maple syrup odor to the urine
 If untreated, the disease leads to mental retardation, physical disabilities, and even
death
Treatment
 The disease is treated with a synthetic formula that contains limited amounts of leucine, isoleucine,
and valine.
 The formula is sufficient to provide the branched-chain amino acids necessary for normal growth
and development without producing toxic levels.
 Early diagnosis and lifelong dietary treatment is essential if the child with MSUD is to develop
normally.
ii. Albinism
 Albinism refers to a group of conditions in which a defect in tyrosine metabolism

results in a deficiency in the production of melanin.
 These defects result in the partial or full absence of pigment from the skin, hair, and
eyes.
 Albinism appears in different forms, and it may be inherited by one of several modes:
autosomal recessive (primary mode), autosomal dominant, or X-linked.
 Complete albinism (also called tyrosinase-negative oculocutaneous albinism) results
from a deficiency of tyrosinase activity
 This causes a total absence of pigment from the hair, eyes, and skin.
 It is the most severe form of the condition
 In addition to hypopigmentation, affected individuals have vision defects and
photophobia (sunlight hurts their eyes)
 They are at increased risk for skin cancer.
ii. Albinism
iii. Homocystinuria
 The homocystinurias are a group of disorders involving defects in the metabolism of
homocysteine
 The diseases are inherited as autosomal recessive illnesses, characterized by high
plasma and urinary levels of homocysteine and methionine and low levels of cysteine
 The most common cause of homocystinuria is a defect in the enzyme cystathionine β-
iii. Homocystinuria…
 This enzyme is involved in conversion of homocysteine to cystathionine

 Synthase deficiency exhibit:
 Ectopia lentis (displacement of the lens of the eye)
 Skeletal abnormalities
 Premature arterial disease
 Osteoporosis
 Mental retardation
Treatment includes:
i. Restriction of methionine intake
ii. Supplementation with vitamins B6, B12, and folate
iv. Alkaptonuria
 Alkaptonuria is a rare metabolic disease involving a deficiency in homogentisic acid

oxidase
 This deficiency results in the accumulation of homogentisic acid
 This reaction occurs in the normal degradative pathway of tyrosine
 The illness has three characteristic symptoms:
 Homogentisic aciduria (the patient's urine contains elevated levels of homogentisic
acid, which is oxidized to a dark pigment on standing)
 Large joint arthritis
 Black ochronotic pigmentation of cartilage and collagenous tissue.
 Patients with alkaptonuria are usually asymptomatic until about the age of 40
 Dark staining of the diapers sometimes can indicate the disease in infants, but usually
no symptoms are present until later in life
iv. Alkaptonuria…
 Diets low in protein—especially in phenylalanine and tyrosine—help reduce the

levels of homogentisic acid, and decrease the amount of pigment deposited in body
tissues
 Although alkaptonuria is not life-threatening, the associated arthritis may be severely
crippling
6. Other Products of Amino Acid Metabolism
 Certain amino acids, in addition to their major function as protein building blocks,
are essential precursors of a variety of important biomolecules, including:
 nucleotides and nucleotide coenzymes,
 heme, and
 various hormones and neurotransmitters
Heme Is Synthesized from Glycine and Succinyl-CoA
 Heme is an Fe-containing prosthetic group that is an essential component of many
proteins, such as hemoglobin, myoglobin, and the cytochromes
 Heme biosynthesis takes place partly in the mitochondrion and partly in the cytosol
 Mitochondrial acetate is metabolized via the citric acid cycle to succinyl-CoA, which
condenses with glycine in a reaction that produces CO2 and 𝛅-aminolevulinic acid
(ALA).
 ALA is transported to the cytosol, where it combines with a second ALA to yield
porphobilinogen (PBG).
 The reaction is catalyzed by the Zn-requiring enzyme porphobilinogen synthase
 the condensation of four PBG molecules to form uroporphyrinogen III, the porphyrin
nucleus, in a series of reactions catalyzed by porphobilinogen deaminase (also called
uroporphyrinogen synthase) and uroporphyrinogen III synthase
 Protoporphyrin IX, to which Fe is added to form heme, is produced from
uroporphyrinogen III in a series of reactions catalyzed by
 (1) uroporphyrinogen decarboxylase, which decarboxylates all four acetate side
chains (A) to form methyl groups (M);
 (2) coproporphyrinogen oxidase, which oxidatively decarboxylates two of the
propionate side chains (P) to vinyl groups (V); and
 (3) protoporphyrinogen oxidase,
Amino Acids Are Precursors of Physiologically Active Amines
 Epinephrine (adrenaline), norepinephrine, dopamine, serotonin (5-
hydroxytryptamine), 𝛄-aminobutyric acid (GABA), and histamine are hormones
and/or neurotransmitters derived from amino acids.
 The biosynthesis of each of these physiologically active amines involves
decarboxylation of the corresponding precursor amino acid. Amino acid
decarboxylases are PLP-dependent enzymes that form a PLP–Schiff base with the
substrate so as to stabilize (by delocalization) the Cα carbanion formed on Cα—
COO− bond cleavage
 Formation of histamine (from histidine) and formation of GABA (from glutamate) are
one-step processes; the synthesis of serotonin from tryptophan requires a
hydroxylation step as well as decarboxylation.
 The various catecholamines—dopamine, norepinephrine, and epinephrine—are
related to catechol (at left) and are sequentially synthesized from tyrosine
Amino Acids Are Precursors of Physiologically Active Amines…
1. Tyrosine is hydroxylated to 3,4-dihydroxyphenylalanine (L-DOPA) in a reaction that
requires 5,6,7,8-tetrahydrobiopterin
2. L-DOPA is decarboxylated to dopamine.
3. A second hydroxylation yields norepinephrine.
4. Methylation of norepinephrine’s amino group by S-adenosylmethionine
Nitric Oxide Is Derived from Arginine
 Arginine is the precursor of a substance that was originally called endothelium
derived relaxing factor (EDRF) because
 it was synthesized by vascular endothelial cells and caused the underlying
smooth muscle to relax.
 The reaction that converts arginine to NO and citrulline is catalyzed by nitric oxide
synthase (NOS)
Metabolic pathways in carbohydrates and lipids metabolism
Assignments
 Other Products amino acid metabolism

 Nitrogen Fixation
 Clinical Disorders Related Amino acid Metabolism
Metabolic pathways in carbohydrates and lipids metabolism
Recommended Core Reference

1. Donald Voet, Judith G Voet, Charlotte W. Pratt. (2016). Fundamentals of
Biochemistry: Live at Molecular Level, 5th Edn. Wiley, USA.
2. Other Medical Biochemistry Books

Pathways in Amino Acids and Protein Metabolism 2

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Pathways in Amino Acids and Protein Metabolism 2

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COLLEGE OF MEDICINE AND HEALTH

Overview Amino acids and Protein Metabolism

 The metabolism of amino acids comprises a wide array of synthetic and

Overview Amino acids and Protein Metabolism…

Overview of body Amino acids pool-source utilization

Overview Amino acids and Protein Metabolism…

Overview Amino acids Metabolism

Overview Amino acids and Protein Metabolism…

(3) to permit the regulation of cellular metabolism by eliminating superfluous enzymes

 Lysosomes degrade substances that the cell takes up via endocytosis

b) Lysosomes Independent Protein degradation

b) Lysosomes Independent Protein degradation

2. The ubiquitin is then transferred to a specific

c) Ubiquitinated degradation by Proteasome

 Ubiquitinated proteins are proteolytically degraded in an ATP-dependent process

2. Amino Acid Deamination

 Free amino acids originate from

 from the digestion of dietary proteins.

a. Amino Acid Deamination by Transaminases

 The predominant amino group acceptor is α-ketoglutarate, producing glutamate and

 Glutamate’s amino group, in turn, can be transferred to oxaloacetate in a second

Clinical Implication of Transamination

 Although the aminotransferases are in liver and muscle, in pathologic conditions

1. Alanine aminotransferase (ALT):

 urea’s two nitrogen atoms are

 Five enzymatic reactions are involved in the urea cycle,

1. Carbamoyl Phosphate Synthetase Acquires the First Urea Nitrogen Atom.

 Five enzymes participate in

The urea cycle

 CPS I catalyzes an essentially irreversible reaction that is the rate-limiting step of

The mechanism of action of CPS I

2. Carbamoylation of Ornithine Produces Citrulline.

 ATP activates the ureido oxygen atom as a leaving group through

The mechanism of action of argininosuccinate synthetase

4. Argininosuccinase Produces Fumarate and Arginine.

 they can give rise to the net synthesis of glucose

Fate of carbon skeletons of amino acids

1. Alanine, Cysteine, Glycine, Serine, and Threonine Are Degraded to Pyruvate

The serine–threonine dehydratase reaction

 Transamination of aspartate leads directly to oxaloacetate.

 L-asparaginase is an effective chemotherapeutic agent in the treatment of cancers

The degradation of arginine, glutamate,

4. Methionine, Threonine, Isoleucine, and Valine Are Degraded to Succinyl-CoA

4. Methionine, Threonine, Isoleucine, and Valine Are Degraded to Succinyl-CoA

 Branched-Chain Amino Acid Degradation Involves Acyl-CoA Oxidation.

Branched-Chain Amino Acid Degradation Involves Acyl-CoA Oxidation

 Leucine degradation begins in the same manner as isoleucine and valine

The pathway of lysine degradation in mammalian liver.

 the major tryptophan degradation pathway is indicated in the following diagram

 the first reaction in phenylalanine degradation is its hydroxylation to tyrosine

5. Amino Acid Biosynthesis

b. Serine, Cysteine, and Glycine Are Derived from 3-Phosphoglycerate

The conversion of 3-phosphoglycerate to serine

 The pathway enzymes are (1) 3-phosphoglycerate dehydrogenase, (2) a PLP

b. Serine, Cysteine, and Glycine Are Derived from 3-Phosphoglycerate…

 Serine participates in glycine synthesis in two ways:

i. Maple syrup urine disease…

The disease is characterized by:

 Albinism refers to a group of conditions in which a defect in tyrosine metabolism

 This enzyme is involved in conversion of homocysteine to cystathionine

 Alkaptonuria is a rare metabolic disease involving a deficiency in homogentisic acid

 Diets low in protein—especially in phenylalanine and tyrosine—help reduce the

6. Other Products of Amino Acid Metabolism

 Other Products amino acid metabolism