Unit 4: Amino Acids, Proteins, and Carbohydrates

1. Amino Acids: Structure and Properties

Amino acids are the fundamental building blocks (monomers) of proteins. Each amino acid has a central alpha-carbon (α-carbon) bonded to four groups:

• An amino group (—NH₂)
• A carboxyl group (—COOH)
• A hydrogen atom (—H)
• A variable side chain or R-group

[Image of the general structure of an L-amino acid]

Properties of Amino Acids

• Zwitterions: At physiological pH (~7.4), the amino group is protonated (—NH₃⁺) and the carboxyl group is deprotonated (—COO⁻). This molecule with both positive and negative charges is called a zwitterion.
• Amphoteric: Because they can act as both an acid (donate H⁺) and a base (accept H⁺), amino acids are amphoteric.
• Classification (Based on R-Group): The 20 standard amino acids are classified by their R-group properties as nonpolar (hydrophobic), polar uncharged (hydrophilic), acidic (negatively charged), or basic (positively charged).

2. Physical and Chemical Properties of Proteins

Proteins are polymers of amino acids linked by peptide bonds. Their properties are determined by their amino acid composition and 3D structure.

a) Physical Properties

• Solubility: Varies greatly. Globular proteins are generally soluble; fibrous proteins are insoluble. Solubility is lowest at the isoelectric point (pI), the pH at which the protein has no net charge.
• Denaturation: The loss of a protein's native 3D structure (secondary, tertiary, and quaternary), leading to a loss of function.
  • Agents: Heat, extreme pH, organic solvents, detergents.

b) Chemical Properties

• Peptide Bond Formation: Formed by a dehydration (condensation) reaction between the carboxyl group of one amino acid and the amino group of the next.
• Hydrolysis: Peptide bonds can be broken by hydrolysis (adding water), catalyzed by acids, bases, or enzymes (proteases).

3. Different Levels of Structural Organization of Proteins

Protein structure is described at four distinct levels:

a) Primary (1°) Structure

The primary structure is the unique, linear sequence of amino acids in a polypeptide chain, held together by peptide bonds.

b) Secondary (2°) Structure

The secondary structure refers to the local, repetitive folding of the polypeptide backbone, stabilized by hydrogen bonds between the C=O and N-H groups of the backbone.

• Alpha-Helix (α-helix): A right-handed coil.
• Beta-Pleated Sheet (β-sheet): Formed from two or more polypeptide segments lying side-by-side.

c) Tertiary (3°) Structure

The tertiary structure is the overall three-dimensional folding of a single polypeptide chain, stabilized by interactions between the R-groups (side chains).

d) Quaternary (4°) Structure

The quaternary structure is the assembly of two or more separate polypeptide chains (subunits) into a single, functional protein complex (e.g., Hemoglobin).

[Image showing the four levels of protein structure]

4. Forces Stabilizing Protein Structure

These forces are primarily responsible for the 3° and 4° structures.

1. Covalent Bonds:
   • Disulfide Bonds (—S—S—): A strong bond between two cysteine residues.
2. Non-Covalent Interactions:
   • Hydrogen Bonds: Between polar R-groups, and between R-groups and water.
   • Hydrophobic Interactions: The primary driving force. Nonpolar R-groups cluster in the protein's core, away from water.
   • Electrostatic Interactions (Salt Bridges): Attractions between oppositely charged R-groups.
   • Van der Waals Forces: Weak attractions between all atoms.

5. Carbohydrates: Introduction

Carbohydrates are biological molecules (biomacromolecules) consisting of carbon (C), hydrogen (H), and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water). They are the most abundant biomolecules on Earth.

6. Monosaccharides: Structure, Properties, and Function

a) Structure

Monosaccharides (simple sugars) are the simplest carbohydrates and the monomers for larger ones. They are polyhydroxy aldehydes (aldoses) or polyhydroxy ketones (ketoses).

• Examples: Glucose (an aldohexose), Fructose (a ketohexose), Ribose (an aldopentose).
• Ring Structures: In solution, they form stable ring structures (e.g., α-Glucose, β-Glucose).

b) Properties

• Isomerism: They can exist as isomers (e.g., Glucose, Fructose, and Galactose are all C₆H₁₂O₆).
• Reducing Sugars: All monosaccharides are reducing sugars, meaning they can donate electrons and be detected by Benedict's test.

c) Function

• Primary Energy Source: Glucose is the main fuel for cellular respiration.
• Building Blocks: Monomers for di- and polysaccharides.

7. Disaccharides: Structure, Properties, and Function

a) Structure

Disaccharides consist of two monosaccharide units joined by a glycosidic bond.

• Sucrose (Table Sugar) = Glucose + Fructose
• Lactose (Milk Sugar) = Galactose + Glucose
• Maltose (Malt Sugar) = Glucose + Glucose

b) Properties

• Reducing vs. Non-reducing:
  • Reducing: Lactose, Maltose (have a free anomeric carbon).
  • Non-reducing: Sucrose (anomeric carbons of both units are in the bond).

c) Function

• Energy: Easily hydrolyzed to monosaccharides for quick energy.
• Transport: Sucrose is the transport sugar in plants.

8. Polysaccharides: Structure, Properties, and Function

a) Structure

Polysaccharides are long-chain polymers (macromolecules) of monosaccharides. They can be linear or branched.

b) Properties and Functions

They are generally not sweet and are insoluble in water.