📘 Understanding Proteins: Structure, Homology, and Evolution – Full Study Notes
🔹1. Protein Domains: The Modular Building Blocks of Proteins
Proteins are not just long chains of amino acids; they are composed of structurally and
functionally distinct regions called domains. These domains are like “modules” or “Lego
blocks,” each with specific roles and independently stable structures.
✅ Key Features:
A domain folds into a compact, stable three-dimensional structure.
Domains are often reused in different proteins, contributing to evolution through
domain shuffling.
Modular design means different domains in a single protein can perform multiple
tasks—such as binding DNA, catalyzing reactions, or spanning membranes.
🔬 Importance:
Studying domains can help scientists predict protein function based on structure.
Common domains (e.g., SH2, kinase, immunoglobulin) are cataloged in databases
like Pfam and SMART.
🧪 Biophysical Principle:
When two domains interact, the interface is typically hydrophobic, shielding the protein’s
interior from water. This makes the overall structure more stable and functionally active in
biological systems.
, 🔹2. Membrane Proteins: Adapting to the Cell’s Hydrophobic Barrier
The cell membrane is made up of a phospholipid bilayer, which creates a hydrophobic
environment inside the membrane and a hydrophilic environment outside.
✅ Characteristics of Membrane Proteins:
Transmembrane regions contain hydrophobic amino acids that can insert into
the oily core of the membrane.
Extracellular/intracellular regions have polar, charged, or hydrophilic
residues.
Some proteins span the membrane multiple times (e.g., G-protein-coupled
receptors), while others are anchored by lipids.
🧠 Why This Matters:
Membrane proteins are critical drug targets (e.g., ion channels, receptors).
Their structure determines how they interact with drugs, hormones, and other
cells.
🔹3. Protein Structure and Folding: Precision from Sequence
The ability of a protein to fold into a specific 3D structure is essential for its function.
🧬 Protein Folding Principles:
Hydrophobic core: Inside of the protein where water is excluded.
🔹1. Protein Domains: The Modular Building Blocks of Proteins
Proteins are not just long chains of amino acids; they are composed of structurally and
functionally distinct regions called domains. These domains are like “modules” or “Lego
blocks,” each with specific roles and independently stable structures.
✅ Key Features:
A domain folds into a compact, stable three-dimensional structure.
Domains are often reused in different proteins, contributing to evolution through
domain shuffling.
Modular design means different domains in a single protein can perform multiple
tasks—such as binding DNA, catalyzing reactions, or spanning membranes.
🔬 Importance:
Studying domains can help scientists predict protein function based on structure.
Common domains (e.g., SH2, kinase, immunoglobulin) are cataloged in databases
like Pfam and SMART.
🧪 Biophysical Principle:
When two domains interact, the interface is typically hydrophobic, shielding the protein’s
interior from water. This makes the overall structure more stable and functionally active in
biological systems.
, 🔹2. Membrane Proteins: Adapting to the Cell’s Hydrophobic Barrier
The cell membrane is made up of a phospholipid bilayer, which creates a hydrophobic
environment inside the membrane and a hydrophilic environment outside.
✅ Characteristics of Membrane Proteins:
Transmembrane regions contain hydrophobic amino acids that can insert into
the oily core of the membrane.
Extracellular/intracellular regions have polar, charged, or hydrophilic
residues.
Some proteins span the membrane multiple times (e.g., G-protein-coupled
receptors), while others are anchored by lipids.
🧠 Why This Matters:
Membrane proteins are critical drug targets (e.g., ion channels, receptors).
Their structure determines how they interact with drugs, hormones, and other
cells.
🔹3. Protein Structure and Folding: Precision from Sequence
The ability of a protein to fold into a specific 3D structure is essential for its function.
🧬 Protein Folding Principles:
Hydrophobic core: Inside of the protein where water is excluded.
