Amino Acid Catabolism

Digestion and Absorption of Proteins

H
R1 C COO

R2

Transaminases
(aminotransferases)
catalyze the
reversible reaction
at right.

NH3

C COO

O
Transaminase
H

R1 C COO
O

R2

C COO

NH3

There are multiple transaminase enzymes which vary in

substrate specificity.
Some show preference for particular amino acids or
classes of amino acids as amino group donors, and/or for
particular -keto acid acceptors.

COO

COO

COO

CH2

COO

CH2

CH2

CH2

CH2

CH2

HC

NH3+

COO

COO

COO

HC

NH3+

COO

aspartate -ketoglutarate oxaloacetate glutamate

Aminotransferase (Transaminase)

Example of a Transaminase reaction:

Aspartate donates its amino group, becoming the
-keto acid oxaloacetate.
-Ketoglutarate accepts the amino group,
becoming the amino acid glutamate.

CH3
HC

COO

COO

CH2

CH2

CH2
NH3+

COO

alanine

CH3
O

COO

-ketoglutarate

CH2
O

COO

pyruvate

HC

NH3+

COO

glutamate

Aminotransferase (Transaminase)

In another example, alanine becomes pyruvate as

the amino group is transferred to -ketoglutarate.

Common -Keto Acids Used

Pyruvate, oxaloacetate (OAA), -ketoglutarate (most
common acceptors of amino group)
Ala pyruvate
Glu -ketoglutarate
Asp oxaloacetate
e.g. of transamination:

glutamate + pyruvate -ketoglutarate +

alanine
Note: above rxn is reversible; reversibility links protein metab
with the metab of carbohydrates and proteins

Transaminases equilibrate amino groups among

available -keto acids.
This permits synthesis of non-essential amino acids,
using amino groups from other amino acids & carbon
skeletons synthesized in a cell.
Thus a balance of different amino acids is maintained,
as proteins of varied amino acid contents are
synthesized.
Although the amino N of one amino acid can be used
to synthesize another amino acid, N must be
obtained in the diet as amino acids (proteins).

Essential amino acids must be consumed in the diet.

Mammalian cells lack enzymes to synthesize their
carbon skeletons (-keto acids). These include:
Isoleucine, leucine, & valine
Lysine
Threonine
Tryptophan
Phenylalanine (Tyr can be made from Phe.)
Methionine (Cys can be made from Met.)
Histidine (Essential for infants.)

H
O

P
O

H2
C

O
OH

N
H

CH3

pyridoxal phosphate (PLP)

The prosthetic group of Transaminase is

pyridoxal phosphate (PLP), a derivative of
vitamin B6.

H
C

COO

Enz
(CH2)4

NH2

Amino acid
O

P
O

HC
H2
C

N+

H
O

N
H

CH3

Enzyme (Lys)-PLP Schiff base

In the resting state, the aldehyde group of pyridoxal

phosphate is in a Schiff base linkage to the -amino
group of an enzyme lysine side-chain.

EnzLysNH2

The -amino group

of a substrate amino
acid displaces the
enzyme lysine, to
form a Schiff base
linkage to PLP.

P
O

R
HC

H2
C

H
C
N+

COO
H
O

N
H

CH3

Amino acid-PLP Shiff base (aldimine)

The active site lysine extracts H+, promoting

tautomerization, followed by reprotonation &
hydrolysis.

O
EnzLysNH2
O

What was an
amino acid
leaves as an
-keto acid.

P
O

H2
C

NH2
CH2

COO
-keto acid
C

OH

N
CH3
H
Pyridoxamine phosphate (PMP)

The amino group remains on what is now pyridoxamine

phosphate (PMP).
A different -keto acid reacts with PMP and the process
reverses, to complete the reaction.

EnzLysNH2

P
O

R
HC

H2
C

H
C
N+

COO
H
O

N
H

CH3

Amino acid-PLP Shiff base (aldimine)

Several other enzymes that catalyze metabolism or

synthesis of amino acids also utilize PLP as prosthetic
group, and have mechanisms involving a Schiff base
linkage of the amino group to PLP.

In addition to equilibrating amino groups among

available -keto acids, transaminases funnel amino
groups from excess dietary amino acids to those amino
acids (e.g., glutamate) that can be deaminated.
Carbon skeletons of deaminated amino acids can be
catabolized for energy, or used to synthesize glucose or
fatty acids for energy storage.
Only a few amino acids are deaminated directly.

NH3+

H2 H2
OOC C C C
glutamate
H

Glutamate
Dehydrogenase
catalyzes a major
reaction that effects
net removal of N
from the amino
acid pool.

H2O

COO
NAD(P)+
NAD(P)H

H2 H2
OOC C C C
-ketoglutarate

COO + NH4+

Glutamate Dehydrogenase

It is one of the few enzymes that can use NAD+ or NADP+

as e acceptor.
Oxidation at the -carbon is followed by hydrolysis,
releasing NH4+.

Amino acid

-ketoglutarate

-keto acid

glutamate

Transaminase

NADH + NH4+

NAD+ + H2O

Glutamate
Dehydrogenase

Summarized above:
The role of transaminases in funneling amino N to
glutamate, which is deaminated via Glutamate
Dehydrogenase, producing NH4+.

+
H2O NH4

H2O
HO

CH2

H
C

COO

NH3+

serine

H2C

COO

NH3+

aminoacrylate

H3C

COO

pyruvate

Serine Dehydratase

Some other pathways for deamination of amino acids:

1. Serine Dehydratase catalyzes:
serine pyruvate + NH4+
2. Peroxisomal L- and D-amino acid oxidases catalyze:
amino acid + FAD + H2O
-keto acid + NH4+ + FADH2
FADH2 + O2 FAD + H2O2
Catalase catalyzes: 2 H2O2 2 H2O + O2

O
H2N

NH2

urea

Most terrestrial land animals convert excess nitrogen to

urea, prior to excreting it.
Urea is less toxic than ammonia.
The Urea Cycle occurs mainly in liver.
The 2 nitrogen atoms of urea enter the Urea Cycle as NH3
(produced mainly via Glutamate Dehydrogenase) and as
the amino N of aspartate.
The NH3 and HCO3 (carbonyl C) that will be part of urea
are incorporated first into carbamoyl phosphate.

HCO3

Carbamoyl Phosphate
Synthase (Type I) catalyzes
a 3-step reaction, with
carbonyl phosphate and
carbamate intermediates.

ATP
ADP
O
HO
NH3
Pi

Ammonia is the N input.

The reaction, which
involves cleavage of 2 ~P
bonds of ATP, is essentially
irreversible.

H2N

OPO32

carbonyl phosphate

O
C

ATP
ADP

carbamate

O
H2N

OPO32

carbamoyl phosphate

HCO3 + NH3 + 2 ATP

O
H2N

Carbamoyl Phosphate
Synthase
OPO32 + 2 ADP + Pi

carbamoyl phosphate

Carbamoyl Phosphate Synthase is the committed step of

the Urea Cycle, and is subject to regulation.

O
NH3+

Urea Cycle

CH2

NH3+

COO

ornithine
4

O
H2N

urea

NH

NH2

H2O

CH2

COO
CH2

HC

H
N

COO
COO

CH2

HC

CH2
HC

ATP
AMP + PPi

NH

arginine

CH
NH3+

COO

CH2

COO

CH2

COO

NH3+

HC

NH2+

H2N

citrulline

CH2

Pi

Urea Cycle

NH2

CH2

CH2
HC

OPO32

carbamoyl
phosphate

CH2

Enzymes in
mitochondria:
1. Ornithine
Transcarbamylase
Enzymes in
cytosol:
2. ArgininoSuccinate
Synthase
3. Argininosuccinase
4. Arginase.

H2N

COO

fumarate

HC

NH2

COO

aspartate
C

NH2+

NH
CH2
CH2

argininosuccinate

CH2
HC

NH3+

COO

cytosol
mitochondrial matrix
carbamoyl phosphate
Pi
ornithine
ornithine
urea
arginine

citrulline
citrulline
aspartate
argininosuccinate

fumarate

For each cycle, citrulline must leave the mitochondria, and

ornithine must enter the mitochondrial matrix.
An ornithine/citrulline transporter in the inner
mitochondrial membrane facilitates transmembrane fluxes of
citrulline & ornithine.

cytosol
mitochondrial matrix
carbamoyl phosphate
Pi
ornithine
ornithine
urea
arginine

citrulline
citrulline
aspartate
argininosuccinate

fumarate

A complete Krebs Cycle functions only within

mitochondria.
But cytosolic isozymes of some Krebs Cycle enzymes are
involved in regenerating aspartate from fumarate.

COO

COO

COO

CH2

COO

CH2

CH2

CH2

CH2

CH2

HC

NH3+

COO

COO

COO

HC

NH3+

COO

aspartate -ketoglutarate oxaloacetate glutamate

Aminotransferase (Transaminase)

Fumarate is converted to oxaloacetate via Krebs Cycle

enzymes Fumarase & Malate Dehydrogenase.
Oxaloacetate is converted to aspartate via
transamination (e.g., from glutamate).
Aspartate then reenters Urea Cycle, carrying an amino
group derived from another amino acid.

Hereditary deficiency of any of the Urea Cycle

enzymes leads to hyperammonemia - elevated
[ammonia] in blood.
Total lack of any Urea Cycle enzyme is lethal.
Elevated ammonia is toxic, especially to the brain.
If not treated immediately after birth, severe mental
retardation results.

Treatment of deficiency of Urea Cycle enzymes

(depends on which enzyme is deficient):
limiting protein intake to the amount barely
adequate to supply amino acids for growth, while
adding to the diet the -keto acid analogs of
essential amino acids.
Liver transplantation has also been used, since
liver is the organ that carries out Urea Cycle.

cytosol

The complete
Urea Cycle is
significantly only
in liver.

mitochondrial matrix
carbamoyl phosphate
Pi
ornithine
citrulline

ornithine
citrulline
However some
urea
aspartate
enzymes of the
arginine
argininosuccinate
pathway are in
fumarate
other cells and
tissues where they generate arginine & ornithine, which are
precursors for other important molecules.
E.g., Argininosuccinate Synthase, which catalyzes
synthesis of the precursor to arginine, is in most tissues.
Mitochondrial Arginase II, distinct from the cytosolic Urea
Cycle Arginase, cleaves arginine to yield ornithine.

Fates of the Carbon Skeletons of Amino

Acids Glucogenic amino acids are shaded pink, and ketogenic
amino acids are shaded yellow. Most amino acids are both glucogenic and
ketogenic.

Nucleotide catabolism

Purine Catabolism and Salvage

All purine degradation leads to uric acid (but it might not stop
there)
Ingested nucleic acids are degraded to nucleotides by pancreatic
nucleases, and intestinal phosphodiesterases in the intestine
Group-specific nucleotidases and non-specific phosphatases
degrade nucleotides into nucleosides
Direct absorption of nucleosides
Further degradation
Nucleoside + H2O base + ribose (nucleosidase)
Nucleoside + Pi base + r-1-phosphate (n. phosphorylase)
NOTE: MOST INGESTED NUCLEIC ACIDS ARE DEGRADED AND
EXCRETED.

Intracellular Purine Catabolism

Nucleotides broken into nucleosides by action of
5-nucleotidase (hydrolysis reactions)
Purine nucleoside phosphorylase (PNP)

Inosine Hypoxanthine
Xanthosine Xanthine
Guanosine Guanine
Ribose-1-phosphate splits off
Can be isomerized to ribose-5-phosphate

Adenosine is deaminated to Inosine (ADA)

Degradation of Pyrimidines
CMP and UMP degraded to bases similarly
to purines
Dephosphorylation
Deamination
Glycosidic bond cleavage

Uracil reduced in liver, forming -alanine

Converted to malonyl-CoA fatty acid
synthesis for energy metabolism