Amino Acids (Basic, Acidic), Transamination & Proteins

Proteins are the most abundant macromolecules in living systems, and they play a crucial role in many biological processes. Similarly, amino acids are the building blocks of proteins, and their properties and interactions determine the structure and function of proteins. Therefore, understanding the structure and function of proteins and amino acids is essential for understanding many aspects of biochemistry. 

Moreover, Amino acids and proteins are fundamental concepts in biochemistry, and they are likely to be tested in the NEET PG exam.

Read this blog further and learn more about this important biochemistry topic for NExT/ NEET PG exam preparation.

Basic AA

• Arginine, Lysine and Histidine
• All are positively charged so all are Polar
• Comparison of Polarity
  • Arginine (+++) > Lysine (++) > Histidine (+)
• Essential amino acid category
  • Arginine (semi-essential)
  • Lysine (essential) 
  • Histidine (semi-essential)

Acidic AA

• Aspartate, Asparagine, Glutamate and Glutamine 
• all are negatively charged so all are Polar
• All are Non-essential AA Because all of them can be made from TCA intermediate as
  • OAA → Aspartate → Asparagine
  • α-KG → Glutamate → Glutamine

OH-Containing amino acid

Serine	Threonine	Tyrosine
Non-essential	Essential	Non-essential
Polar	Polar	Polar

Sulfur containing amino acids

1. Methionine

• Sulfur is attached to 2 carbons with strong bond (C–S–C)
• Non-polar (No -SH group)
• Essential AA 
  • Tip: difficult to attach Sulphur with 2 C

2. Cysteine

• Sulfur is attached to 1 carbon (C–SH)
• Polar (due to -SH group)
• Non-essential (can be made from methionine)
  • First methionine is converted to homocysteine
  • Homocysteine is converted to cysteine using serine and vit B₆  

Amino Acid

• Proline
  • NH₂ group is not Free (2^o amine)
  • Amino acid is attached to side chain forming a pyrrolidine ring
  • Non-polar
  • Non-essential (can be synthesized from ornithine in body)

Selenocysteine and Pyrrolysine

• 21st AA → Selenocysteine → Given by UGA
• 22nd AA → Pyrrolysine → Given by UAG
• UGA and UAG are stop codons and usually do not code for aa
• Exceptions: Selenocysteine & Pyrrolysine
  • These AA are formed by Co–translational (during translation) modification (not by Post-translational modification)

Derived amino acids

• Def: AA not coming from codons but obtained from other AAs
• Two types
  • Found in proteins 
    • Hydroxyproline, Hydroxylysine 
  • Not found in proteins
    • present as free amino acids e.g. Ornithine Citrulline (Involved in Urea cycle)
    • Homocysteine (Involved in methionine metabolism)

TRANSAMINATION

• 1st reaction in the catabolism of AA
• Reversible
• Requires B₆ /PLP (pyridoxal phosphate)
• Common AA involved: Glutamate

• Transaminases e.g. SGOT and SGPT
• only α-amino group can take part in transamination 
  • Exception is δ(delta) amino group of ornithine 

• 17 amino acids can take part in transamination 
• Rest 3 Amino acids can't take part in transamination e.g. proline (OH-proline), Lysine and Threonine
• 3 Amino acids that can't take part in transamination: Mnemonic: POLYTHENE
  • PO  -  PrOline
  • LY  -  LYsine
  • THENE - THrEoNinE

Transdeamination: Transamination (peripheral cells) + Oxidative deamination (liver)

PROTEINS

• Protein: polymers of amino acid

Amide bond Formation

• Formed by removal of H₂O when two amino acid joined together
• During this, carboxy gp of one amino acid and amine group of another amino acid reacts to form amide bond (-CONH-).
• If this is present in a protein it is called peptide bond.
• It is a strong covalent bond.
• It has partial double bond character which is in trans-configuration

Note: In fats, double bond is present but in cis-configuration

Structures of Proteins 

Name	Definition
1ᵒ Structure	Sequence of amino acids
2ᵒ structure	Obtained from folding of 1ᵒ structureα Helix (Symmetrical / helical structure)β Sheetsβ Turns
3ᵒ structure	Further folding of 2o structure to form a fully folded 3ᵒ structure
4ᵒ structure	> 1 polypeptide chain e.g. Hb (four polypeptide chains)

Monomeric protein: Those proteins which have only one monomer. They do not have Quaternary structure e.g. myoglobin

Features	1°	2°	3°	4°
Bond	Covalent/ Peptide/ Amide	Hydrogen bond	S~S  Hydrophobic  Hydrogen  Ionic	Hydrophobic  H-bond  Ionic  (Mnemonic- HHI)
Functional activity	Absent	Absent	Present	Present
Denaturation	Retained because peptide bond is very strong	Lost	Lost	Lost
Detection	Mass spectrometry,  Edman’s Technique	X-ray crystallography: Best for crystallizable proteins NMR spectrometry: Best for non-crystallizable proteins

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