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Amino Acids (Basic, Acidic), Transamination & Proteins

Feb 17, 2023

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Selenocysteine and Pyrrolysine

Derived amino acids



Amide bond Formation

Structures of Proteins

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 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


Important Information

  1. Which AA has max. tendency to bind phosphate? 
  2. Which AA is site for covalent modification? 
  3. Which AA is involved in O–Glycosidic bonds?

Answer for all of these 3 questions is OH containing AA. 

  • So, in option choose option of OH containing AA. 
  • If 2 or more OH containing AA are given, SERINE is the best option to mark.

      4. Which AA is involved in N–Glycosidic bonds?

Ans: Asparagine (has CONH which can provide N for N-glycosidic bond)

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 (2o amine)
    • Amino acid is attached to side chain forming a pyrrolidine ring
    • Non-polar
    • Non-essential (can be synthesized from ornithine in body)

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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)
amino acids selenocysteine

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)


  • 1st reaction in the catabolism of AA
  • Reversible
  • Requires B6 /PLP (pyridoxal phosphate)
  • Common AA involved: Glutamate
general scheme of transamination reaction
  • Transaminases e.g. SGOT and SGPT
  • only α-amino group can take part in transamination 
    • Exception is δ(delta) amino group of ornithine 
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

Important Information

Transport form of NH3?

  • From body and brain – Glutamine
  • From Muscles - Alanine (via Cahill cycle)
glucose alanine cycle
generation and transport of ammonia from peripheral cells

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


  • Protein: polymers of amino acid
formation of peptide bond

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 

1 StructureSequence of amino acids
2 structureObtained from folding of 1ᵒ structureα Helix (Symmetrical / helical structure)β Sheetsβ Turns
3 structureFurther folding of 2o structure to form a fully folded 3ᵒ structure
4 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

Important Information

AA not found in α-helix

  • Proline and glycine  create ‘bend’ in α helix
  • Tryptophan  due to bulky side chain
  • Aspartate, Glutamate and Valine



Covalent/ Peptide/ Amide 

Hydrogen bond

  • S~S 
  • Hydrophobic 
  • Hydrogen 
  • Ionic
  • Hydrophobic 
  • H-bond 
  • Ionic 

(Mnemonic- HHI)

Functional activity






Retained because peptide bond is very strong 





Mass spectrometry, 

Edman’s Technique 

  • X-ray crystallography: Best for crystallizable proteins
  • NMR spectrometry: Best for non-crystallizable proteins

Important Information

  • Bonds in Enzyme-Substrate interactions (Mnemonic: HHI)
  • H - Hydrophobic
  • H - Hydrogen
  • I - Ionic
  • Sometimes covalent but Never Vander Waals Forces
  • Bonds in Protein-DNA interactions (Mnemonic: HIV)
  • H - Hydrophobic
  • I - Ionic
  • V - Vander Waals Forces
  • Never Covalent bond

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