Alberts - Essential Cell Biology (4th ed.)

Introduction to Proteins

• Proteins are the main building blocks of cells, comprising a significant portion of the cell's dry mass.

• They provide essential shape and structure to the cell and perform nearly all cellular functions, including:

  • Promoting Chemical Reactions (Enzymes): Proteins serve as biological catalysts that accelerate chemical reactions necessary for cellular processes.

  • Transporting Molecules Across Membranes: They facilitate the movement of various substances in and out of the cell, ensuring proper cellular function.

  • Serving as Signals and Receptors in Communication: Proteins are vital in cellular signaling, allowing cells to communicate and respond to their environment.

  • Providing Mechanical Support and Movement: They play a critical role in maintaining cell integrity and enabling motility.

  • Functioning as Antibodies and Hormones: Proteins are involved in immune response and regulatory functions within the body.

The Role of Proteins in Cells

Key Functions:

• Enzymes: Facilitate biochemical reactions by creating conducive environments for reactions to occur. Examples include:

  • Tryptophan Synthetase: Catalyzes the synthesis of the amino acid tryptophan.

  • Pepsin: A digestive enzyme that breaks down proteins in the stomach.

  • DNA Polymerase: Critical for DNA replication, synthesizing new strands of DNA.

• Structural Proteins: Provide shape and support to cells and tissues. Notable examples include:

  • Collagen: A primary structural protein in connective tissues.

  • Elastin: Provides elasticity to tissues, allowing them to stretch.

  • Keratin: A fibrous protein found in hair, nails, and skin.

• Transport Proteins: Essential for transporting molecules across cell membranes. Examples include:

  • Hemoglobin: Carries oxygen in red blood cells.

  • Glucose Transporters: Facilitate the uptake of glucose by cells.

• Motor Proteins: Enable cellular movement and transport of cellular components. Example:

  • Myosin: Involved in muscle contraction and intracellular motility.

• Storage Proteins: Store amino acids or ions required for various cellular activities. Example:

  • Ferritin: Stores iron and releases it when needed.

• Signal Proteins: Relay information between cells. Example:

  • Insulin: A hormone that regulates glucose levels in the blood.

• Receptor Proteins: Detect and transmit signals from the environment to elicit a cellular response. Example:

  • Insulin Receptor: Binds insulin and initiates metabolic processes.

• Gene Regulatory Proteins: Bind to DNA and control gene expression, influencing cellular function. Example:

  • Lactose Repressor: Regulates the metabolism of lactose in bacteria.

The Complexity of Protein Structure

1. Basic Structure of Proteins

• Proteins are composed of 20 different amino acids linked by peptide bonds, forming polypeptide chains.

• Amino Acid Structure: Each of the 20 amino acids has a unique side chain (R group) that determines its chemical properties, classifying them as polar, nonpolar, or charged.

2. Folding and Stability

• Proteins can fold into various three-dimensional shapes, critical for their function, determined by noncovalent interactions like hydrogen bonds and hydrophobic interactions.

• Folding Stability: The stability of a protein's folded state is reliant on weak interactions; improper folding can result in various diseases (e.g., prion diseases).

3. Levels of Protein Organization

• Primary Structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary Structure: Regular local patterns formed by hydrogen bonding along the polypeptide backbone, such as alpha helices and beta sheets.

• Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, determined by interactions among various amino acids and R groups.

• Quaternary Structure: The assembly of multiple polypeptide chains into a functional protein complex.

• Protein Domains: Distinct folding units within larger proteins, often associated with specific functional roles, enhancing functional diversity.

Proteins in Action

Mechanisms of Protein Function

• Proteins perform their functions by specifically binding to other molecules (ligands), relying on their shape and chemical compatibility.

• Binding interactions can vary in strength and specificity, but maintaining specificity is crucial for functionality.

Enzyme Activity

• Enzymes accelerate chemical reactions by lowering the activation energy required. They exhibit a high degree of specificity for their substrates, leading to efficient biochemical processes.

• Example: Lysozyme hydrolyzes polysaccharide bonds in bacterial cell walls, facilitating bacterial cell lysis.

Regulation of Enzyme Activity

• Enzymes can be regulated through various mechanisms, including:

  • Feedback Inhibition: End products of metabolic pathways inhibit early enzymes, preventing overproduction.

  • Allosteric Regulation: The binding of regulatory molecules at sites distinct from the active site causes conformational changes impacting enzyme activity.

  • Covalent Modifications: Changes like phosphorylation can activate or deactivate specific proteins, altering their functions.

Visualizing and Studying Proteins

Techniques for Protein Purification

• Proteins can be extracted from cells or tissues by breaking down the cellular structure and fractionating the components, typically involving various biochemical techniques.

• Advanced Techniques: These allow for high-yield protein purification, enabling detailed structural and functional studies.

• Structural Analysis: Techniques such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are commonly employed to elucidate protein structures at the atomic level.

Conclusion

• Understanding proteins is crucial for grasping cellular processes, as they are central to life and perform a myriad of diverse functions in organisms.