Biochemistry Second Year

1. AMINO ACID
METABOLISM
(part 1)

2. OVERVIEW OF CENTRAL AMINO ACID METABOLISM
ENVIRONMENT ORGANISM
Ingested
Diatary
proteins
70-100g/d
Bio-
synthesis Body
Proteins
35-200g/d
AMINO
ACIDS
Nitrogen
(NH3)
Carbon
skeletons
(Keto- acids)
Urea
Degradation
(required)
1 2 3
a
b
Purines
Pyrimidines
Porphyrins (heme)
Niacin
Neurotansmitters
Polyamines
c c
Used for energy
pyruvate
α-ketoglutarate
succinyl-CoA
fumarate
oxaloacetate
acetoacetate
acetyl CoA
(glucogenic)
(ketogenic)
CO2
+
Water

3. Metabolic Classification of the Amino Acids
• Based on synthesis:
Essential and Non-essential
• Based on degradation (Fate):
Glucogenic and Ketogenic
Essential Amino Acids in Humans
• Required in diet
• Human is incapable of forming their requisite carbon skeleton
Non-essential Amino Acids in Humans
• Not required in diet
• Can be formed from α-keto acids by transamination and subsequent
reactions
• Valine
• Leucine
• Isoleucine
• Methionine
• Phenylalanine
•Tryptophan
• Threonine
•Histidine*
• Lysine
•Glycine
•Alanine
•Proline
•Tyrosine* •Serine
•Cysteine*
•Glutamine
•Asparagine
•Glutamate
•Aspartate
•Arginine*

4. DEGRADATION (FATE) OF THE CARBON SKELETONS
Carbon skeletons are used for energy.
Glucogenic Amino Acids: degradead to TCA cycle intermediates Oxaloacetate,
Fumarate,Succinyl CoA, α-ketoglutarate,
or pyruvate (gluconeogensis).
Ketogenic Amino Acids: degraded to acetyl CoA, acetoacetyl CoA, or
acetoacetate ( form ketone bodies).

5. AMINO ACID DEGRADATION INTERMEDIATESAMINO ACID DEGRADATION INTERMEDIATES
CO2
CO2
Pyruvate
Acetyl-CoA Acetoacetate
Citrate
Isocitrate
-ketoglutarate
Succinyl-CoA
Fumarate
Oxaloacetate
Citric
Acid
Cycle
CO2
Glucose
Ala Ser
Cys Thr*
Gly Trp*
Ile*
Leu•
Lys•
Thr*
Leu• Trp*
Lys• Tyr*
Phe*
Asn
Asp
Asp
Phe*
Tyr*
Ile*
Met
Val
Arg His
Glu Pro
Gln
Glucogenic
Ketogenic
* Both Glucogenic and Ketogenic
• Purely Ketogenic
PEP
Malate
Succinate

6. Incorporation of NH4
+
Into
Organic Compounds
1) NH4
+
+ HCO3
-
+ 2 ATP NH2CO2PO3
-2
+ 2 ADP +
Carbamoyl Phosphate Pi + 2 H+
2) NH4
+
+
Carbamoyl
Phosphate
Synthetase I
(CPS-I)
Glutamate
dehydrogenase
O
-
O2CCH2CH2CCO 2
-
-Ketoglutarate
Glutamate
NADP +NADPH +
H+
NH3
+
-
O2CCH2CH2CHCO 2
-
TCA Cycle
Incorporation of NH4
+
Into
Organic Compounds (Cont.)
NH3
+
-
O2CCH2CH2CHCO 2
- + NH4
+
+ 2 ATP
NH3
+O
H2NCCH2CH2CHCO 2
-
Glutamine
Glutamate Glutamine
Synthetase
Mg++
N of glutamine donated to other compounds
in synthesis of purines, pyrimidines,
and other amino acids
3)

7. Biosynthesis of Amino Acids
*Transaminations:
Amino Acid1 +α-Keto Acid2  Amino Acid2 +α-Keto Acid1
+
O
R-CCO 2
-
Glutamate
Pyridoxal phosphate (PLP)-
Dependent Aminotransferase
+
α- Ketoglutarate
Biosynthesis of Essential Amino Acids
Their -ketoacids are not common intermediates (enzymes needed to form them
are lacking) so transamination is not an option.
Biosynthesis of Non-essential Amino Acids
Transamination of -ketoacids that are available as common intermediates.
(treatment of hyperamonemia)
All (except Tyr) synthesized from the common intermediates synthesized in cell :
• Pyruvate
• Oxaloacetate
• -ketoglutarate
• 3-phosphoglycerate
NH3
+
-
O2CCH2CH2CHCO 2
-
NH2
R-CHCO 2
-
O
-
O2CCH2CH2CCO 2
-

8. Transamination Reactions : One Step
Pyruvate + AA  Alanine + -ketoacid
Oxaloacetate + AA Aspartate + -ketoacid
-ketoglutarate + AA Glutamate + -ketoacid
Transaminases: Equilibrate amino groups among -ketos. Require pyridoxal
phosphte (PLP).
Blood transaminases has a diagnostic value. (AST or GOT , ALT or GPT)
All AAs, except Lys and Thr, can be transaminated. Most transaminases
generate Glu or Asp.
*ATP-dependent amidation of Glu, Asp:
 GLU + ATP + NH3  GLN + ADP + Pi
By the nnzyme glutamine synthetase Where NH3 is toxic ; stored
as Gln.
Gln donates amino gps in many reactions
 ASP + ATP + GLN  ASN + AMP + PPi + GLU
By the enzyme Asparagine synthetase.
Low in some cell tumor types. ( Asparaginase treatment ) .

9. Transaminations
Glutamate -Ketoglutarate
+ +
Pyruvate Alanine
Glutamate -Ketoglutarate
+ +
Oxaloacetate Aspartate
Glutamate-Pyruvate
Aminotransferase
(Alanine Transferase ALT)
Glutamate-Oxaloacetate
Aminotransferase
(Aspartate Transferase AST)
Blood levels of these aminotransferases, also called transaminases,
are important indicators of liver disease

10. AAMMIINNOO AACCIIDD CCAATTAABBOOLLIISSMM
AA.. NNiittrrooggeenn ((NNHH3))
H2N C
O
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 excreted by kidney.
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.

11. Carbamoyl Phosphate Synthetase
is the committed step of the Urea
Cycle, and is subject to regulation.
H2N C OPO3
2
O
HCO3

+ NH3 + 2 ATP
+ 2 ADP + Pi
Carbamoyl Phosphate
Synthetase
carbamoyl phosphate
N
H
C COO
CH2
CH2
COO
H
CH3C
O
N-acetylglutamate
H3N+
C COO
CH2
CH2
COO
H
glutamate (Glu)
Carbamoyl Phosphate Synthetase has
an absolute requirement for an allosteric
activator N-acetylglutamate.
This derivative of glutamate is
synthesized from acetyl-CoA &
glutamate when cellular [glutamate] is
high, signaling an excess of free amino
acids due to protein breakdown or
dietary intake.

12. H2N C OPO3
2
O
CH2
CH2
CH2
HC
COO
NH3
+
NH3
+
CH2
CH2
CH2
HC
COO
NH3
+
NH
CO NH2
COO
CH2
HC
COO
NH2
CH2
CH2
CH2
HC
COO
NH3
+
NH
C NH2
+
COO
CH2
HC
COO
H
N
AMP + PPi
ATP
CH2
CH2
CH2
HC
COO
NH3
+
NH
C
NH2
+
H2N
COO
HC
CH
COO

C NH2H2N
O H2O
Pi
ornithine
urea
citrulline
aspartate
arginino-
succinate
fumarate
arginine
carbamoyl
phosphate
Urea Cycle
1
2
3
4
Urea Cycle
-Enzymes in
mitochondria:
1. Ornithine
Trans-
carbamylase
-Enzymes in
cytosol:
2. Arginino-
Succinate
Synthetase
3. Arginino-
succinase
4. Arginase.

13. Fumarate is converted to oxaloacetate via Krebs Cycle.
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.
aspartate -ketoglutarate oxaloacetate glutamate
Aminotransferase (Transaminase)
COO
CH2
CH2
C
COO
O
COO
CH2
HC
COO
NH3
+
COO
CH2
CH2
HC
COO
NH3
+
COO
CH2
C
COO
O+ +

14. 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.
Postulated mechanisms for toxicity of high [ammonia]:
1. High [NH3] would drive Glutamine Synthetase:
glutamate + ATP + NH3  glutamine + ADP + Pi
This would deplete glutamate – a neurotransmitter & precursor for
synthesis of the neurotransmitter GABA (later) .
2. Depletion of glutamate & high ammonia level would drive Glutamate
Dehydrogenase reaction to reverse:
glutamate + NAD(P)+
α-ketoglutarate +
NAD(P)H + NH4
+
The resulting depletion of α-ketoglutarate, an essential Krebs Cycle
intermediate, could impair energy metabolism in the brain.
Deficiencies related to Urea Cycle
Carbamoyl Phosphate Synthetase Deficiency
and N-acetylglutamate synthetase Deficiency
Ornithine Transcarbamoylase Dificiency
Argininosuccinate Synthetase and Lyase Deficiencies
Arginase Deficiency

15. • Blood Urea Nitrogen (BUN)
• Normal range: 7-18 mg./dL
Elevated in ↑amino acid catabolism
↑Glutamate  ↑N-acetylglutamate 
↑CPS-1 activation
Elevated in renal insufficiency
Decreased in hepatic failure