proteins- janice smith

Definition: Naturally occurring amino acids have both an amino group (NH₂) and a carboxyl group (COOH) attached to the same carbon atom, known as the α-carbon. Hence, they are called α-amino acids. Side Chain (R group): This is the variable group attached to the α-carbon that determines the identity and properties of each amino acid.

Proteins are polyamides: long chains formed by joining amino acids through amide bonds (also known as peptide bonds). A portion of a protein shows repeating units of amino acids linked by peptide bonds.

Number of Naturally Occurring Amino Acids: 20 Glycine is the simplest amino acid, where R = H. It is the only amino acid without a stereogenic (chiral) center. All other amino acids (R ≠ H) are chiral due to the α-carbon having four different groups attached.

Chiral Center: All amino acids (except glycine) are chiral. D and L system: Like sugars, amino acids are classified using D (right) and L (left) prefixes. Naturally occurring amino acids in proteins are L-amino acids. D-amino acids are rare in nature. R/S Configuration: Based on CIP rules: Most L-amino acids have S configuration. Exception: Cysteine (due to the sulfur-containing side chain), which has R configuration despite being an L-amino acid.

Amino acids have common names. They can be represented by either: A one-letter abbreviation, or A three-letter abbreviation.

A: An amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and an R group (side chain).

A: Glycine has R = H and lacks a stereogenic center; it is not chiral.

A: Polyamides are chains formed by linking amino acids via amide (peptide) bonds, forming proteins.

A: The R group attached to the α-carbon; it determines the amino acid’s identity and properties.

20.

A: They are L-amino acids and most have the S configuration, except cysteine (which has R).

A: Glycine is the only one.

A: L-amino acids occur naturally in proteins; D-amino acids are rare and not commonly found in nature.

A: Using either a one-letter or three-letter code.

A: The amino group and carboxyl group are both attached to the same α-carbon.

These amino acids are classified as “neutral” because their side chains (R groups) are neither strongly acidic nor basic under physiological pH.

These amino acids have carboxylic acid (-COOH) groups in their side chains that lose a proton (H⁺) at physiological pH (~7.4), making the side chains negatively charged (–COO⁻).

These amino acids have basic (positively charged) side chains at physiological pH due to the presence of amine or imidazole groups.

Acidic Amino Acids: Contain an additional –COOH group in the side chain Examples: Aspartic acid, Glutamic acid Basic Amino Acids: Contain an additional basic nitrogen atom Examples: Lysine, Arginine, Histidine Neutral Amino Acids: All others (hydrophobic, polar uncharged, etc.)

Unique because its nitrogen is part of a five-membered ring. Unlike other amino acids that are primary amines, proline is a secondary amine (2°). The ring structure restricts flexibility, often found in turns or kinks in protein chains.

Each has two stereogenic centers: the α-carbon and an additional β-carbon. This leads to 4 stereoisomers, but only one is found in proteins (L-isomer with specific configuration). These are among the few amino acids that are diastereomers due to multiple chiral centers.

Humans can synthesize only 10 of the 20 standard amino acids. The other 10 are essential amino acids — they must be obtained through the diet. In diagrams like this, they are often marked with an asterisk (*).

A: Proline – its nitrogen is part of a five-membered ring.

A: Isoleucine and Threonine