Amino acids are classified based on the properties of their R groups, which influence their behavior in proteins. The main categories include nonpolar (hydrophobic) amino acids like valine and leucine, which repel water and are usually found in the protein core. Polar uncharged amino acids, such as serine and threonine, can form hydrogen bonds and are often found on protein surfaces. Acidic amino acids like aspartic acid and glutamic acid carry a negative charge, while basic amino acids such as lysine and arginine carry a positive charge at physiological pH. This classification helps predict amino acid interactions, protein folding, and function. Understanding these properties is key in biochemistry, molecular biology, and drug design. This article is about Classification of Amino Acids PPT.
Biochemistry Notes | Biochemistry PPT
Classification of Amino Acids PPT
Classification of Amino Acids: Handouts
- Amino Acids: Building blocks of protein.
- Proteins: Bio-macromolecules of cells. Polymers of amino acids.
- Peptide Bond: Special covalent bond that joins amino acids.
- 20 Common Amino Acids: Proteins are made from combinations of 20 amino acids.
- Classification Criteria:
- Based on NH2 group location (α, β, γ, δ amino acids)
- Based on charge (Positive and Negative)
- Based on nutrition (Essential and Nonessential)
- Based on metabolic fate (Glucogenic and Ketogenic)
- Based on R group properties (Polarity, Aliphatic/Aromatic, Acidic/Basic)
- Classification by R Group Properties: Five classes:
- Non-polar Aliphatic R-groups
- Aromatic R-groups
- Polar uncharged R-groups
- Positively charged (Basic) R-groups
- Negatively charged (Acidic) R-groups
(1). Non-polar Aliphatic R-Groups
- R-groups are non-polar and hydrophobic.
- Examples: Glycine, Alanine, Proline, Valine, Leucine, Isoleucine & Methionine.
- Glycine: Simplest amino acid, side chain is H, α-carbon is achiral.
- Proline: Cyclic structure, amino group in rigid conformation, is an “Imino acid”.
- Proline’s cyclic structure reduces polypeptide flexibility and causes bends.
- Methionine: Sulfur-containing, has a nonpolar thioether group.
(2). Aromatic R-Groups
- Aromatic side chain.
- Examples: Phenylalanine, Tyrosine, Tryptophan.
- Side chains are relatively nonpolar (hydrophobic).
- Can contribute to both hydrophobic and hydrophilic interactions.
- Tyrosine’s –OH group can form hydrogen bonds.
- Tyrosine is an important functional group in some enzymes.
- Tryptophan has an indole ring.
- Tyrosine and Tryptophan are more polar than phenylalanine (due to hydroxyl and nitrogen groups).
- Tryptophan and Tyrosine absorb ultraviolet light at 280 nm.
- Protein quantification by spectrophotometry uses 280 nm wavelength.
(3). Polar Uncharged R-Groups
- Polar and soluble in water.
- Side chains are uncharged.
- Examples: Serine, Threonine, Cysteine, Asparagine & Glutamine.
- Hydrophilic, form hydrogen bonds with water.
- Polarity provided by:
- Serine & Threonine: Hydroxyl group
- Cysteine: Sulfhydryl group (SH)
- Asparagine & Glutamine: Amide group
- Asparagine and Glutamine are amides of Aspartate and Glutamate.
- Cysteine is a sulfur-containing amino acid and is readily oxidizable.
- Two Cysteine molecules can oxidize to form Cystine, a covalently linked dimer, joined by a disulfide bond.
- Disulfide bonds are strongly hydrophobic (nonpolar).
- Disulfide bonds are important in protein structure, forming covalent bonds within or between polypeptide chains.
(4). Positively Charged R-Groups
- Most hydrophilic R-groups.
- R group contains basic groups.
- Also called Basic Amino Acids.
- Examples: Lysine, Arginine and Histidine.
- Lysine has a secondary amino-group at the ε (epsilon) position.
- Arginine has a positively charged guanidino group.
- Histidine has an imidazole ring.
- Histidine has an ionizable side chain with pKa near neutral pH (7.0) or biological pH (7.4).
- Histidine residues often act as proton donors or acceptors in enzyme catalytic sites (e.g., RNase).
(5). Negatively Charged R-Groups
- Negatively charged.
- Examples: Aspartate (Aspartic acid) and Glutamate (Glutamic acid).
- Have a second carboxyl group on the side chain, contributing extra negative charge.
Modified Amino Acids
- Many proteins contain modified amino acids (post-translational modification).
- These modifications do not have tRNA or specific codons.
- Examples:
- 4-Hydroxyproline: Derivative of Proline, found in plant cell wall proteins and collagen.
- 5-hydroxylysine: Lysine derivative found in collagen.
Essential Amino Acids
- Cannot be made by the body, must come from the diet.
- Nine Essential Amino Acids: Histidine, Threonine, Isoleucine, Leucine, Phenylalanine, Valine, Tryptophan, Methionine and Lysine.
- Conditionally essential amino acids: Synthesis can be limited under certain conditions (e.g., Arginine, Cysteine, Glycine, Glutamine, Proline and Tyrosine).
- Nonessential Amino Acids: Body can synthesize these (e.g., Alanine, Aspartic Acid, Asparagine, Glutamic Acid, Serine and Selenocysteine).
References
- Berg, J.M. and Tymoczko, J.L., 2018. Stryer biochemie (Vol. 8). Heidelberg: Springer Spektrum.
- Nelson, D.L., Lehninger, A.L. and Cox, M.M., 2008. Lehninger principles of biochemistry. Macmillan.
- Voet, D. and Voet, J.G., 2010. Biochemistry. John Wiley & Sons.
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