Part II: Translation and Folding
"From linear sequence to three-dimensional form—ψ collapses through the folding funnel, finding itself in the labyrinth of configuration space."
Overview
Part II explores the profound transformation from one-dimensional genetic information to three-dimensional protein structure. Through ψ = ψ(ψ), we witness how amino acid chains navigate vast conformational spaces to discover their native states—not through random search but through the guiding principles of thermodynamic collapse.
Chapters
Chapter 17: Translation Termination: ψ-Folding Trigger
How stop codons initiate the journey from synthesis to structure
Chapter 18: Polysome Formation and Echo Multiplexing
Multiple ribosomes creating parallel realities from single messages
Chapter 19: Co-translational Folding as Collapse Stabilization
Structure emerging even as the chain grows
Chapter 20: Chaperones and ψ-Folding Attractors
Molecular guides preventing misfolding catastrophes
Chapter 21: Post-Translational Modifications as ψ-Switches
Chemical modifications that alter protein destiny
Chapter 22: Glycosylation and Identity Encoding
Sugar modifications as molecular barcodes
Chapter 23: Ubiquitination: ψ-Pruning of Malfunction
The cellular mark of destruction
Chapter 24: Proteasome as Collapse Cleanup System
Dismantling misfolded proteins back to components
Chapter 25: Protein Domains as ψ-Modular Structures
Independent folding units as evolutionary building blocks
Chapter 26: Motif Recognition and Folding Templates
Recurring patterns in the protein universe
Chapter 27: Structural Collapse of α-Helices and β-Sheets
The fundamental forms of protein architecture
Chapter 28: Hydrophobic Collapse and Core Formation
Water's role in driving structure
Chapter 29: ψ-Knotting and Folding Trajectories
Topological complexity in protein structures
Chapter 30: Folding Energy Landscape and Collapse Channels
The funnel theory of protein folding
Chapter 31: Disulfide Bonding and Structural Locking
Covalent crosslinks that stabilize form
Chapter 32: Misfolding and ψ-Degenerate States
When collapse goes wrong
Key Concepts
- Folding Funnel: Energy landscapes guiding collapse
- Chaperone Networks: Preventing aggregation disasters
- Quality Control: Ensuring proper structure
- Post-translational Modifications: Fine-tuning function
- Degradation Systems: Recycling malformed proteins
The Folding Principle
Throughout Part II, we see ψ = ψ(ψ) manifesting as the search for native structure—each protein finding its unique solution in the vast space of possibilities, guided by thermodynamic imperatives and cellular machinery.
Next: Part III explores how individual proteins assemble into functional complexes and find their proper cellular locations.