Unit 4: Amino Acids and Proteins

Amino Acids: Structure and Properties

Amino acids are the monomers (building blocks) of proteins. There are 20 standard amino acids used to build proteins in humans.

General Structure

Every amino acid has a central alpha-carbon (α-carbon) bonded to four different groups:

1. A Hydrogen Atom (H)
2. An Amino Group (-NH2), which is basic.
3. A Carboxyl Group (-COOH), which is acidic.
4. A Side Chain (R-group), which is different for every amino acid and determines its properties.

Chemical Properties

• Zwitterions: At neutral pH (pH 7.4), the amino group is protonated (NH3+) and the carboxyl group is deprotonated (COO-). This doubly-charged ion is called a zwitterion.
• Amphoteric: Because they have both an acidic and a basic group, they can act as either an acid (donate H+) or a base (accept H+). This makes them excellent buffers.

Classification

Amino acids are classified based on the properties of their R-group.

Proteins: Structure and Function

Proteins are large, complex polymers of amino acids linked together. They perform almost all functions in a cell.

The Peptide Bond

• Formation: Amino acids are linked by a peptide bond.
• Reaction: This is a dehydration (condensation) reaction where the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of the next, releasing a molecule of water (H2O).
• Chain: A chain of amino acids is called a polypeptide.

Levels of Protein Structure

A protein's function depends on its unique 3D shape, which is described in four levels:

1. Primary (1°) Structure:
   • Definition: The unique sequence (order) of amino acids in the polypeptide chain.
   • Example: ...-Ala-Gly-Leu-Val-...
   • Stabilized by: Peptide bonds (strong covalent bonds).
2. Secondary (2°) Structure:
   • Definition: Local, repeating folding patterns of the polypeptide backbone.
   • Examples: The α-helix (a coil) and the β-pleated sheet (folded strands).
   • Stabilized by: Hydrogen bonds between the C=O and N-H groups of the backbone (not the R-groups).
3. Tertiary (3°) Structure:
   • Definition: The overall 3D folding of a single polypeptide chain, bringing distant R-groups together.
   • This is the final, functional shape for many proteins.
4. Quaternary (4°) Structure:
   • Definition: The assembly of two or more separate polypeptide chains (subunits) to form a larger, functional protein complex.
   • Example: Hemoglobin is made of four subunits (two alpha, two beta).

Stabilizing Bonds in Protein Structure

The Tertiary (and Quaternary) structures are stabilized by several types of interactions, all involving the R-groups:

• Hydrogen Bonds: Between polar R-groups.
• Hydrophobic Interactions: Nonpolar R-groups cluster together in the protein's core, away from water.
• Ionic Bonds (Salt Bridges): Between acidic (-) and basic (+) R-groups.
• Disulfide Bridges: A strong covalent bond (S-S) that forms between the R-groups of two Cysteine amino acids.

Carbohydrates

Carbohydrates are biomolecules consisting of carbon, hydrogen, and oxygen, usually with a hydrogen-oxygen ratio of 2:1 (like water, C_n(H2O)_n). They are the primary energy source for most organisms.

Structure, Properties, and Function of Monosaccharides

• Definition: The simplest carbohydrates ("simple sugars"). They are the monomers for larger carbohydrates.
• Structure: Can be classified by the number of carbons (e.g., Triose-3C, Pentose-5C, Hexose-6C) or by their functional group (Aldose = aldehyde, Ketose = ketone).
  • Glucose: An aldohexose, the main energy fuel for cells.
  • Fructose: A ketohexose, found in fruit.
  • Galactose: An aldohexose, part of milk sugar.
• Properties: They are sweet, soluble in water, and can form ring structures in solution.
• Function:
  • Primary energy source: Broken down in glycolysis.
  • Building blocks: Used to build larger molecules.

Disaccharides and Polysaccharides

• Disaccharides: Two monosaccharides joined by a glycosidic bond.
  • Sucrose (Table Sugar) = Glucose + Fructose
  • Lactose (Milk Sugar) = Glucose + Galactose
  • Maltose (Malt Sugar) = Glucose + Glucose
• Polysaccharides: Long chains (polymers) of monosaccharides.
  • Starch: (Storage in Plants) A polymer of glucose.
  • Glycogen: (Storage in Animals) A highly branched polymer of glucose, stored in the liver and muscles.
  • Cellulose: (Structure in Plants) A polymer of glucose that forms plant cell walls. Humans cannot digest it (fiber).