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Amino Acids
2.1.1 Definition
Amino acids are the monomeric units of peptides and proteins, composed of a central carbon atom (α-carbon) bonded to four substituents:
Amino group (-NH₂)
Carboxyl group (-COOH)
Hydrogen atom (-H)
Side chain (R group) – unique for each amino acid and responsible for its chemical properties.
At physiological pH (~7.4), amino acids typically exist as zwitterions, where the amino group is protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO⁻).
2.1.2 Chirality and Stereochemistry
Most amino acids (except glycine) are chiral molecules, meaning the α-carbon has four distinct substituents.
In biological systems, L-amino acids predominate, which are incorporated into peptides and proteins during ribosomal synthesis.
D-amino acids also occur naturally (e.g., in bacterial cell walls and some non-ribosomal peptides), often conferring structural stability and resistance to proteases.
2.1.3 Essential vs Non-Essential Amino Acids
Amino acids are classified into two broad categories based on whether the human body can synthesize them:
Essential amino acids (must be obtained from diet):
Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine.
Non-essential amino acids (synthesized endogenously):
Alanine, Asparagine, Aspartic acid, Glutamic acid, Serine.
Conditionally essential (required in special circumstances such as illness or rapid growth):
Arginine, Cysteine, Glutamine, Glycine, Proline, Tyrosine.
2.1.4 Classification by Side Chain Properties
The R group (side chain) determines the chemical behavior of each amino acid. They are classified as follows:
1. Nonpolar, Aliphatic (Hydrophobic)
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline (Pro, P).
Role: Hydrophobic interactions stabilize peptide folding; often found in protein cores or membranes.
2. Aromatic
Phenylalanine (Phe, F), Tyrosine (Tyr, Y), Tryptophan (Trp, W).
Role: Participate in π–π stacking, absorb UV light (useful for spectroscopic quantification).
3. Polar, Uncharged
Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), Glutamine (Gln, Q).
Role: Hydrogen bonding, enzymatic catalysis, disulfide bond formation (Cys).
4. Positively Charged (Basic)
Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H).
Role: Electrostatic interactions, DNA/RNA binding, pH-sensitive catalysis (His is key in enzyme active sites).
5. Negatively Charged (Acidic)
Aspartic acid (Asp, D), Glutamic acid (Glu, E).
Role: Ionic interactions, metal ion coordination, active sites of enzymes.
2.1.5 Chemical Properties of Amino Acids
pKa values: Each amino acid has characteristic pKa values for its amino, carboxyl, and side chain groups, which determine its ionization state at different pH levels.
Isoelectric point (pI): The pH at which the amino acid (or peptide) carries no net charge. This is critical for peptide purification by isoelectric focusing.
Hydrophobicity scale: Amino acids differ in their tendency to associate with water, influencing peptide folding and membrane association.
2.1.6 Post-Translational Modifications (PTMs) of Amino Acids
In peptides and proteins, amino acids frequently undergo covalent modifications that regulate structure and function:
Phosphorylation (Ser, Thr, Tyr): Key in signaling cascades.
Methylation (Lys, Arg, His): Regulates gene expression, histone modification.
Acetylation (Lys, N-terminus): Modulates protein stability and DNA binding.
Hydroxylation (Pro, Lys): Important in collagen stability.
Glycosylation (Asn, Ser, Thr): Adds carbohydrate chains, affecting stability and recognition.
Disulfide bond formation (Cys): Provides structural stability in peptides and proteins.
2.1.7 Biological Importance
Amino acids are precursors of neurotransmitters (e.g., tryptophan → serotonin, tyrosine → dopamine).
Serve as metabolic intermediates in gluconeogenesis, urea cycle, and Krebs cycle.
Dictate secondary and tertiary structures of peptides via hydrogen bonding, hydrophobic effects, and electrostatics.
Define biological specificity through side chain interactions in enzyme active sites and receptor binding.
2.1.8 Summary
Amino acids are the fundamental determinants of peptide structure and function. Their diverse chemical properties, stereochemistry, and capacity for modification enable the immense variety of biological activities observed in peptides. Understanding amino acid classification, ionization behavior, and functional contributions provides the foundation for comprehending peptide folding, synthesis, and applications.
2.1.1 Definition
Amino acids are the monomeric units of peptides and proteins, composed of a central carbon atom (α-carbon) bonded to four substituents:
Amino group (-NH₂)
Carboxyl group (-COOH)
Hydrogen atom (-H)
Side chain (R group) – unique for each amino acid and responsible for its chemical properties.
At physiological pH (~7.4), amino acids typically exist as zwitterions, where the amino group is protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO⁻).
2.1.2 Chirality and Stereochemistry
Most amino acids (except glycine) are chiral molecules, meaning the α-carbon has four distinct substituents.
In biological systems, L-amino acids predominate, which are incorporated into peptides and proteins during ribosomal synthesis.
D-amino acids also occur naturally (e.g., in bacterial cell walls and some non-ribosomal peptides), often conferring structural stability and resistance to proteases.
2.1.3 Essential vs Non-Essential Amino Acids
Amino acids are classified into two broad categories based on whether the human body can synthesize them:
Essential amino acids (must be obtained from diet):
Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine.
Non-essential amino acids (synthesized endogenously):
Alanine, Asparagine, Aspartic acid, Glutamic acid, Serine.
Conditionally essential (required in special circumstances such as illness or rapid growth):
Arginine, Cysteine, Glutamine, Glycine, Proline, Tyrosine.
2.1.4 Classification by Side Chain Properties
The R group (side chain) determines the chemical behavior of each amino acid. They are classified as follows:
1. Nonpolar, Aliphatic (Hydrophobic)
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline (Pro, P).
Role: Hydrophobic interactions stabilize peptide folding; often found in protein cores or membranes.
2. Aromatic
Phenylalanine (Phe, F), Tyrosine (Tyr, Y), Tryptophan (Trp, W).
Role: Participate in π–π stacking, absorb UV light (useful for spectroscopic quantification).
3. Polar, Uncharged
Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), Glutamine (Gln, Q).
Role: Hydrogen bonding, enzymatic catalysis, disulfide bond formation (Cys).
4. Positively Charged (Basic)
Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H).
Role: Electrostatic interactions, DNA/RNA binding, pH-sensitive catalysis (His is key in enzyme active sites).
5. Negatively Charged (Acidic)
Aspartic acid (Asp, D), Glutamic acid (Glu, E).
Role: Ionic interactions, metal ion coordination, active sites of enzymes.
2.1.5 Chemical Properties of Amino Acids
pKa values: Each amino acid has characteristic pKa values for its amino, carboxyl, and side chain groups, which determine its ionization state at different pH levels.
Isoelectric point (pI): The pH at which the amino acid (or peptide) carries no net charge. This is critical for peptide purification by isoelectric focusing.
Hydrophobicity scale: Amino acids differ in their tendency to associate with water, influencing peptide folding and membrane association.
2.1.6 Post-Translational Modifications (PTMs) of Amino Acids
In peptides and proteins, amino acids frequently undergo covalent modifications that regulate structure and function:
Phosphorylation (Ser, Thr, Tyr): Key in signaling cascades.
Methylation (Lys, Arg, His): Regulates gene expression, histone modification.
Acetylation (Lys, N-terminus): Modulates protein stability and DNA binding.
Hydroxylation (Pro, Lys): Important in collagen stability.
Glycosylation (Asn, Ser, Thr): Adds carbohydrate chains, affecting stability and recognition.
Disulfide bond formation (Cys): Provides structural stability in peptides and proteins.
2.1.7 Biological Importance
Amino acids are precursors of neurotransmitters (e.g., tryptophan → serotonin, tyrosine → dopamine).
Serve as metabolic intermediates in gluconeogenesis, urea cycle, and Krebs cycle.
Dictate secondary and tertiary structures of peptides via hydrogen bonding, hydrophobic effects, and electrostatics.
Define biological specificity through side chain interactions in enzyme active sites and receptor binding.
2.1.8 Summary
Amino acids are the fundamental determinants of peptide structure and function. Their diverse chemical properties, stereochemistry, and capacity for modification enable the immense variety of biological activities observed in peptides. Understanding amino acid classification, ionization behavior, and functional contributions provides the foundation for comprehending peptide folding, synthesis, and applications.