UNIT 1: Amino Acids and Their Properties: Structure, Classification, and Identification

Amino Acids and Their Properties

Introduction to Amino Acids

Amino acids are the building blocks of proteins, each consisting of a central carbon atom (the alpha carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group). The properties of amino acids are determined by the chemical nature of their side chains, which influence protein structure and function.

• Amino acids are organic compounds containing both amino (-NH2) and carboxyl (-COOH) functional groups.

• There are 20 standard amino acids found in proteins.

• The side chain (R group) determines the chemical characteristics and classification of each amino acid.

Classification of Amino Acids

Amino acids are classified based on the properties of their side chains, such as polarity, charge, and hydrophobicity. These classifications are important for understanding protein folding and interactions.

• Nonpolar (Hydrophobic) Amino Acids: Side chains are typically hydrocarbons, making them insoluble in water. Examples: Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Phenylalanine (Phe), Proline (Pro), Tryptophan (Trp).

• Polar (Uncharged) Amino Acids: Side chains contain groups that can form hydrogen bonds, increasing solubility in water. Examples: Serine (Ser), Threonine (Thr), Cysteine (Cys), Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln).

• Acidic (Negatively Charged) Amino Acids: Side chains contain a carboxyl group that is deprotonated at physiological pH. Examples: Aspartic acid (Asp), Glutamic acid (Glu).

• Basic (Positively Charged) Amino Acids: Side chains contain an amino group that is protonated at physiological pH. Examples: Lysine (Lys), Arginine (Arg), Histidine (His).

Structural Formulas of Amino Acids

Each amino acid has a distinct side chain (R group) attached to the alpha carbon. The general structure is:

• General formula: $\mathrm{NH_2{-}CHR{-}COOH}$

• Example: For Alanine, R = CH3

Identification of Amino Acid Properties

The properties of amino acids can be identified by examining the functional groups present in their side chains:

• Polar Identification: Presence of oxygen, nitrogen, or sulfur bound to hydrogen at the end of the R group.

• Basic Identification: NH2 attached to a carbonyl (C=O) is considered basic.

• Acidic/Charged Identification: Presence of a carboxyl group (COOH or COO-) at the end of the R group.

• Basic/Charged Identification: Presence of NH2, NH, NH2, NH3+ at the end of the R group. NH2 not attached to a carbonyl (C=O) is considered basic; otherwise, it is considered polar.

Table: Classification of Amino Acids by Properties

Amino Acid	Abbreviation	Side Chain Type	Property
Alanine	Ala	CH3	Nonpolar
Valine	Val	Isopropyl	Nonpolar
Leucine	Leu	Isobutyl	Nonpolar
Isoleucine	Ile	Sec-butyl	Nonpolar
Methionine	Met	Thioether	Nonpolar
Phenylalanine	Phe	Benzyl	Nonpolar
Proline	Pro	Pyrrolidine ring	Nonpolar
Serine	Ser	Hydroxymethyl	Polar
Threonine	Thr	Hydroxyethyl	Polar
Cysteine	Cys	Thiol	Polar
Tyrosine	Tyr	Phenol	Polar
Asparagine	Asn	Amide	Polar
Glutamine	Gln	Amide	Polar
Aspartic Acid	Asp	Carboxyl	Acidic
Glutamic Acid	Glu	Carboxyl	Acidic
Lysine	Lys	Amino	Basic
Arginine	Arg	Guanidino	Basic
Histidine	His	Imidazole	Basic
Tryptophan	Trp	Indole	Nonpolar

Examples and Applications

• Protein Structure: The sequence and properties of amino acids determine the folding and function of proteins.

• Enzyme Activity: Acidic and basic amino acids often participate in catalysis due to their ability to donate or accept protons.

• Genetic Code: Each amino acid is encoded by specific codons in DNA and RNA.

Summary Table: Amino Acid Properties

Property	Identification	Examples
Nonpolar	Hydrocarbon side chains, absence of polar groups	Ala, Val, Leu, Ile, Met, Phe, Pro, Trp
Polar	Presence of O, N, or S bound to H at end of R group	Ser, Thr, Cys, Tyr, Asn, Gln
Acidic	Carboxyl group (COOH or COO-) at end of R group	Asp, Glu
Basic	NH2, NH, NH2, NH3+ at end of R group	Lys, Arg, His

Additional info: The identification rules for amino acid properties are inferred from standard biochemistry conventions and the provided chart. The table entries are expanded for clarity and completeness.