Amino Acids and Proteins Lesson: Structure, Types, and Functions

Lesson Overview

• General Structure of Amino Acids
• Chirality in Amino Acids
• Zwitterionic Nature of Amino Acids
• Classification of Amino Acids
• Formation of Peptides and Proteins
• Levels of Protein Structure
• Alpha-Helix Structure
• Amphipathic Alpha-Helix
• Standard vs. Non-Standard Amino Acids
• Serine in Protease Enzymes
• Protein Folding and Chaperone Proteins

Amino acids and proteins are fundamental to all biological systems. They play a critical role in nearly every cellular process, from structural support to enzyme activity, signal transmission, immune response, and metabolic regulation. Proteins are composed of long chains of amino acids, each uniquely structured to determine the protein's final shape and function. 

This lesson explains the structure of amino acids, how they form peptides and proteins, the different types of amino acids, the hierarchical organization of protein structures, and the functional roles of specific residues. It also introduces key principles such as chirality, zwitterionic properties, peptide bond formation, alpha-helical arrangements, and the role of molecular chaperones in protein folding. These concepts form the foundation for advanced study in biological and medical sciences.

General Structure of Amino Acids

Each amino acid shares a common structure with four components attached to a central alpha carbon.

• One amino group (–NH₂)
  
• One carboxyl group (–COOH)
  
• A hydrogen atom
  
• A unique R group (side chain)

The R group determines the identity and chemical properties of each amino acid. There are 20 standard amino acids, each with a different R group.

The following table outlines the four components bonded to the alpha carbon of an amino acid:

Chirality in Amino Acids

Chirality refers to a molecule having a non-superimposable mirror image. Most amino acids are chiral because the central carbon is attached to four different groups.

• The alpha carbon is chiral in all amino acids except glycine.
  
• Glycine has two hydrogen atoms attached to the alpha carbon, making it achiral.
  
• Chiral amino acids exist as enantiomers, but proteins only use the L-form.

The table below compares chirality between glycine and other amino acids:

Zwitterionic Nature of Amino Acids

Amino acids exist as zwitterions at physiological pH, meaning they have both a positive and a negative charge.

• The amino group is protonated (–NH₃⁺).
  
• The carboxyl group is deprotonated (–COO⁻).
  
• The molecule has no net charge overall.

This form enhances solubility in water and enables amino acids to act as buffers.

The table illustrates the charge status of amino acids at various pH levels:

Classification of Amino Acids

Amino acids are categorized based on the nature of their R groups.

• Non-polar (hydrophobic): Valine, Leucine, Isoleucine
  
• Polar uncharged: Serine, Threonine, Asparagine
  
• Acidic (negatively charged): Aspartate, Glutamate
  
• Basic (positively charged): Lysine, Arginine, Histidine
  
• Aromatic: Phenylalanine, Tyrosine, Tryptophan

The table organizes amino acids by category and properties:

Take This Quiz:

Quiz: Test Your Knowledge of Amino Acids and Proteins!

Formation of Peptides and Proteins

Amino acids link through peptide bonds to form proteins.

• A peptide bond forms between the carboxyl group of one amino acid and the amino group of another.
  
• Water is released in the process (condensation reaction).
  
• Proteins have directionality: the chain starts at the N-terminus and ends at the C-terminus.

The following table describes peptide bond formation and directionality:

Levels of Protein Structure

Proteins fold into specific structures that determine their function. There are four levels of structure.

• Primary Structure: Linear sequence of amino acids
  
• Secondary Structure: Local folding into alpha-helices or beta-sheets
  
• Tertiary Structure: 3D folding of a single chain
  
• Quaternary Structure: Arrangement of multiple polypeptide chains

This table outlines the four hierarchical levels of protein structure:

Alpha-Helix Structure

The alpha-helix is a common form of secondary structure in proteins.

• Stabilized by hydrogen bonds between nearby amino acids.
  
• The R groups extend outward from the helix.
  
• This structure helps in protein stability and function.

The table below highlights the key features of an alpha-helix:

Amphipathic Alpha-Helix

Some alpha-helices are amphipathic, containing both hydrophilic and hydrophobic regions.

• One side of the helix has polar residues.
  
• The other side has non-polar residues.
  
• This allows interaction with both aqueous and lipid environments.

This table summarizes the properties of amphipathic alpha-helices:

Standard vs. Non-Standard Amino Acids

Proteins are made from standard amino acids, but some non-standard amino acids are also important.

• Standard amino acids: Encoded directly by genetic code.
  
• Non-standard amino acids: Formed through post-translational modification.
  
• Example: Hydroxyproline, derived from proline, found in collagen.

The table compares the characteristics of standard and non-standard amino acids:

Serine in Protease Enzymes

Certain amino acids play key roles in enzyme activity.

• Serine is commonly found in the active sites of serine proteases.
  
• It acts as a nucleophile, attacking the peptide bond of the substrate.
  
• Essential for catalytic function.

This table presents the function of serine in enzymatic reactions:

Protein Folding and Chaperone Proteins

Proteins must fold properly to function. Molecular chaperones assist in the folding process.

• Prevent incorrect folding and aggregation.
  
• Bind to unfolded or partially folded proteins.
  
• Do not become part of the final protein.

The table outlines the main roles of molecular chaperones: