There are two classes of amino acids: essential and non-essential. Non-essential amino acids can be synthesized by tissues, while essential amino acids must be obtained through diet. Nitrogen, a key component of amino acids, comes from atmospheric nitrogen fixed by bacteria or algae. This nitrogen is converted to ammonia and incorporated into amino acids like glutamate and glutamine, which act as carriers to synthesize other amino acids. Amino acids are also precursors to important biomolecules and can be broken down through pathways like the urea cycle. Defects in amino acid synthesis or breakdown can cause medical issues.

1. Amino acid biosynthesis
• There are 2 classes of amino acids; Essential and non-
essential.
• All tissues can synthesize the non-essential amino acids.
• The nitrogen that makes up amino acids, purines, pyrimidines
and other biological molecules comes from atmospheric
nitrogen.
• Nitrogen is fixed by the action of nitrogen fixing bacteria and
blue green algae (cyanobacteria).
• Rhizobium bacteria invade the roots of leguminous plants and
form root nodules where nitrogen fixation takes place.

2. Amino acid biosynthesis
• During fixation nitrogen (N2) is converted to ammonia (NH3) by
a nitrogenase complex.
• When animals feed on plants, the ammonia is assimilated into
amino acids by way of glutamate and glutamine.
• These amino acids act as carriers of the amino group for the
synthesis of other amino acids.
• Glutamate is synthesized from NH4
+ and α-ketoglutarate by
the action of glutamate dehydrogenase
• Glutamine is synthesized from NH4
+ and glutamate by
glutamine synthetase

3. Amino acid biosynthesis

4. Amino acid synthesis
-Pyruvate + glutamate- alanine (alanine aminotransferase)
-Oxalo acetate + glutamate – aspartate (aspartate amino
transferase
- Asparagine- Amidation of aspartate (asparagine synthetase)
- Ribose-5-phosphate- histidine
- 3-Phosphoglycerate- Serine

5. Amino acid synthesis
• Phosphoenol pyruvate ; erythrose-4-phosphate-
phenylalanine, tyrosine and tryptophan
• Tyrosine-Hydroxylation of phenylalanine
• Aspartate- methionine, lysine, threonine, isoleucine
• Serine- cysteine and glycine

6. Regulation of amino acid synthesis
• Occurs in the fed state
• Activated by insulin
• Feed back inhibition in case of excess product

7. Amino acid derivatives
• Antioxidants-glutathione
• Neurotransmitters and signalling molecules e.g serotonin,
histamine, nitric oxide
• The pigment melanin
• Hormones- peptide hormones
• Porphyrin rings in heme
• And many more

8. Amino acid degradation

9. The urea cycle

10. Defects
• Hyperammonemia- carbamoylphosphate synthetase (lethal;
presents with lethargy, periodic vomiting, coma and
irreversible brain damage)
• Phenylketonuria- phenylalanine hydroxylase
• Albinism- Tyrosinase
• Marple syrup urine disease- error in metabolism of
branched-chain amino acids (evident in the first week of extra
uterine life
• Histidemia- Histidase (enzyme converts histidine to
ammonia)- causes speech defects

11. Porphyrin synthesis

12. Porphyrias
• Inherited or acquired disorders caused by a deficiency of an
enzyme in the heme biosynthetic pathway
• Commonly is congenital erythropoietic porphyria due to a
deficiency in uroporphyrinogen III synthase (cosynthase).
• Erythrocytes are prematurely destroyed; there is excretion of large
amounts of uroporphyrinogen turning urine red.
• Teeth also show strong red fluorescence when exposed to ultra
violet light due to deposition of porphrins.
• The skin is also very light sensitive because porphyrins are quite
reactive when exposed to light.

13. Heme degradation
•Occurs in the reticulo endothelial cells of the liver, spleen and
bone marrow.

14. Heme degradation
• Bilirubin is transported to the liver bound to plasma albumin.
• In the liver parenchymal cells, bilirubin undergoes conjugation with
glucuronate to convert it into a polar form done by the enzyme
glucuronyl transferase
• Conjugated bilirubin is secreted into bile and transported into the
intestines (illeum and large intestines) where it is further reduced
into urobilinogens.
• A small amount of urobilinogen is re absorbed and re-excreted
thru the liver

15. Detection of bile pigments
Serum bilirubin Urine
urobilinogen
Urine
Bilirubin
Fecal
urobilinogen
Normal Direct /conjugated
(0.1-0.4 mg/dL)
0-4mg/24h Absent 40-280mg/hr
Indirect/free (0.2-
0.7 mg/dL)
Absent
Hemolytic
jaundice
Indirect ↑ ↑ Absent ↑
Hepatic Both direct and
indirect ↑
↓ if micro
obstruction is
present
Present with
micro
obstruction
↓
Obstructive Direct ↑ absent Present Trace or
absent

16. Hyperbilirubinemia
• The urolibilinogen in the intestines can be reduced to
stercobilinogen.
• Normally, most of the colorless urobilinogens/stercobilinogens are
oxidized to colored urobilins and stercobilins that are excreted in
urine and feaces, respectively
• Under abnormal circumstances, urobilinogen may also be
excreted in the urine
• Hyperbilirubinemia occurs when bilirubin conc exceed 2-2.5mg/dL.
Bilirubin diffuses into the tissues causing the yellow discoloration
(Jaundice); causes are many