Amino Acids and Proteins: Structure, Properties, and Classification

Les Protéines (Proteins)

Introduction

Proteins are essential macromolecules in living organisms, functioning as polymers with amino acids as their monomeric units. Each protein has a genetically determined structure, which defines its size, sequence, and structural organization.

• Proteins are polymers of amino acids.

• Each protein has a unique sequence and structure, determined by genetic information.

Objectives

• Understand the structure of amino acids (AAs) and proteins.

• Study the physical and chemical properties of AAs.

• Learn peptide sequencing.

• Know the different protein structures.

Functions of Proteins

• Structure: Provide shape and support to cells and tissues.

• Transport: Carry molecules across membranes and within the body (e.g., hemoglobin).

• Hormones: Act as signaling molecules (e.g., insulin).

• Movement: Enable muscle contraction and cellular movement (e.g., actin, myosin).

• Energy substrate: Provide energy (4 kcal/g).

• Catalysts: Enzymes accelerate biochemical reactions.

• Identity and defense: Antibodies and immune proteins.

• Toxins: Some proteins act as toxins.

• Medicines: Many drugs are protein-based.

• Food: Dietary proteins are essential for nutrition.

• Clothing: Proteins like wool and silk are used in textiles.

Origin of Proteins

Food is a primary source of protein. The digestive system breaks down dietary proteins into amino acids, which are absorbed into the blood and distributed to cells for the synthesis of new proteins.

Generalities

• Polymers with 2-10 amino acids: dipeptides, tripeptides, oligopeptides.

• Polymers with many amino acids: polypeptides.

• Proteins are composed of one or more polypeptide chains.

Basic Structure of Amino Acids

All amino acids share a common structure:

• Central (alpha) carbon (Cα).

• Amino group (–NH2 or –NH3+).

• Carboxyl group (–COOH or –COO–).

• Hydrogen atom.

• Variable side chain (R group).

General formula:

$\mathrm{H_2N{-}CHR{-}COOH}$

Stereochemistry – Chirality

• The alpha carbon is asymmetric (chiral) if all four groups are different.

• Amino acids are chiral molecules (except glycine).

• Two possible isomers: D-series and L-series (biological proteins use L-amino acids).

• Threonine and isoleucine have a second chiral center.

• Racemization: Conversion between enantiomers; some microorganisms can use or produce D-amino acids.

Description and Classification of Amino Acids

Aliphatic Amino Acids

• Glycine (Gly, G): Simplest side chain (H), non-chiral, smallest molecular mass, non-essential.

• Alanine (Ala, A): Methyl side chain, non-essential.

• Valine (Val, V): Isopropyl side chain, essential, hydrophobic, found inside proteins or membrane helices.

• Leucine (Leu, L): Isobutyl side chain, essential, hydrophobic, major membrane protein constituent.

• Isoleucine (Ile, I): Isobutyl side chain, leucine isomer, second asymmetric carbon, essential.

Hydroxylated Amino Acids

• Serine (Ser, S): Hydroxyl group, phosphorylation site, non-essential, found in membrane proteins and enzyme active sites.

• Threonine (Thr, T): Hydroxyl group, phosphorylation site, two asymmetric carbons, essential, can be glycosylated.

Sulfur-Containing Amino Acids

• Cysteine (Cys, C): Sulfhydryl (thiol) group, can form disulfide bonds, redox-active, non-essential.

• Methionine (Met, M): Thioether group, non-reactive sulfur, important as N-terminal amino acid, essential.

Dicarboxylic (Acidic) Amino Acids

• Aspartate (Asp, D): Acidic side chain, negatively charged at physiological pH, non-essential.

• Glutamate (Glu, E): Acidic side chain, negatively charged at physiological pH, neurotransmitter, non-essential.

Amidated Amino Acids

• Asparagine (Asn, N): Amide group (non-protonable), non-essential.

• Glutamine (Gln, Q): Amide group (non-protonable), most abundant in blood, non-essential.

Dibasic (Basic) Amino Acids

• Lysine (Lys, K): Basic ionizable side chain (pK = 10.8), polar, hydrophilic, essential.

• Arginine (Arg, R): Guanidyl group, pK = 12.5, most basic and hydrophilic, involved in urea cycle, essential.

• Histidine (His, H): Imidazole side chain, pKa = 6.0, essential, decarboxylation produces histamine.

Summary Table: Amino Acid Classification

Class	Examples	Key Properties
Aliphatic	Gly, Ala, Val, Leu, Ile	Hydrophobic, non-polar
Hydroxylated	Ser, Thr	Polar, can be phosphorylated
Sulfur-containing	Cys, Met	Redox-active (Cys), non-reactive (Met)
Acidic	Asp, Glu	Negatively charged at physiological pH
Amidated	Asn, Gln	Polar, non-ionizable amide group
Basic	Lys, Arg, His	Positively charged at physiological pH

Essential vs. Non-Essential Amino Acids

• Essential amino acids must be obtained from the diet (e.g., Val, Leu, Ile, Met, Lys, Thr, Phe, Trp, His, Arg*).

• Non-essential amino acids can be synthesized by the body.

• *Arginine and histidine are semi-essential (required in certain conditions).

Key Concepts and Examples

• Chirality: All amino acids except glycine are chiral; only L-amino acids are found in proteins.

• Protein function: Enzymes, structural proteins, transporters, hormones, antibodies, toxins, and more.

• Classification: Based on side chain properties (aliphatic, aromatic, sulfur-containing, acidic, basic, etc.).

Additional info: This summary covers the structure, classification, and properties of amino acids, as well as the general functions and origins of proteins, suitable for introductory biochemistry studies.