Proteins: Structure, Function, and Diversity

Abundance and Importance of Proteins

Proteins are essential macromolecules that account for more than 50% of the dry mass of most cells. They play a central role in nearly every biological process within organisms.

• Structural support

• Storage

• Transport

• Cellular communication

• Movement

• Defense against foreign substances

Functions of Proteins

Proteins perform a wide variety of functions, each determined by their unique structure.

• Enzymatic Role: Protein enzymes act as catalysts in cells, regulating metabolism by selectively accelerating chemical reactions. Importantly, enzymes are not consumed in the reactions they catalyze.

• Diversity and Specificity: Humans have tens of thousands of different proteins, each with a specific structure and function.

Major Types of Proteins and Their Functions

Structural Complexity of Proteins

Proteins are the most structurally complex biological molecules, each possessing a unique three-dimensional shape necessary for its function.

• Unbranched polymers: All proteins are made from the same 20 amino acid monomers.

• Polypeptides: Chains of amino acids linked by peptide bonds.

• Conformation: A protein is a functional molecule made of one or more polypeptides folded into a specific shape.

Amino Acids: The Building Blocks of Proteins

Basic Structure of Amino Acids

Amino acids are the monomers from which proteins are constructed. Each amino acid contains both a carboxyl group (-COOH) and an amino group (-NH2), attached to a central (alpha) carbon.

• Alpha (α) Carbon: The central asymmetric carbon atom in every amino acid.

• Four Components Attached to the α-Carbon:

  1. A hydrogen atom

  2. A carboxyl group

  3. An amino group

  4. A variable R group (side chain)

Role of the R Group

• The R group (side chain) is what makes each of the 20 amino acids unique.

• The simplest R group is a hydrogen atom (as in glycine).

• More complex R groups can be carbon skeletons with various functional groups (as in glutamine).

Diagram: The general structure of an amino acid:

Alpha carbon bonded to:

• Amino group (NH2)

• Carboxyl group (COOH)

• Hydrogen atom (H)

• R group (side chain)

Classification of Amino Acids

Amino acids are classified based on the properties of their R groups:

• Nonpolar R groups: Hydrophobic amino acids

• Polar R groups: Hydrophilic amino acids

• Charged R groups: Can be acidic (negatively charged, due to carboxyl group) or basic (positively charged, due to amino group)

Note: The terms "acidic" and "basic" refer only to the properties of the R group, not the backbone groups shared by all amino acids.

Polypeptides: Amino Acid Polymers

Formation of Peptide Bonds

Amino acids are linked together by peptide bonds through a dehydration reaction:

• A hydroxyl group (-OH) is removed from the carboxyl end of one amino acid.

• A hydrogen atom (-H) is removed from the amino group of another amino acid.

• The resulting covalent bond is called a peptide bond.

This process repeats to form a polypeptide chain, which can range from a few to thousands of amino acids in length.

• N-terminus: End with a free amino group

• C-terminus: End with a free carboxyl group

Levels of Protein Structure

Primary Structure

The primary structure of a protein is its unique sequence of amino acids. This sequence determines all higher levels of structure and ultimately the protein's function.

Secondary Structure

The secondary structure consists of regular coils and folds in the polypeptide chain, stabilized by hydrogen bonds between backbone atoms.

• Alpha (α) helix: A delicate coil held together by hydrogen bonds every fourth amino acid. Common in fibrous proteins like keratin.

• Beta (β) pleated sheet: Regions of the chain lie side by side, forming hydrogen bonds between parallel segments. Found in proteins like spider silk and transthyretin.

Tertiary Structure

The tertiary structure is the overall three-dimensional shape of a single polypeptide, determined by interactions among R groups:

• Hydrogen bonds: Between polar/charged R groups

• Ionic bonds: Between oppositely charged R groups

• Hydrophobic interactions: Nonpolar R groups cluster away from water

• van der Waals interactions: Weak attractions between hydrophobic R groups

• Disulfide bridges: Covalent bonds between sulfhydryl groups of cysteine residues

Quaternary Structure

The quaternary structure arises when a protein consists of two or more polypeptide chains (subunits) aggregated together.

• Examples:

  • Transthyretin: Four identical polypeptides

  • Collagen: Three polypeptides supercoiled into a triple helix

  • Hemoglobin: Four subunits (two α and two β chains), each with α-helical secondary structure

Summary Table: Levels of Protein Structure

Key Equations and Concepts

• Peptide bond formation:

• Levels of protein structure (from simple to complex): Primary → Secondary → Tertiary → Quaternary

Example Exam Questions

• If you wanted to design a new industrial catalyst based on something biological, which molecule would you use? Answer: protein

• Write the four levels of protein structure in the correct order (from simple to complex): Primary, Secondary, Tertiary, Quaternary

Additional info: These notes expand on the original slides and images by providing definitions, examples, and a summary table for clarity and completeness.