4: Protein Structure
- Page ID
- 150156
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Proteins are polymers of the bifunctional monomer, amino acids. The twenty common naturally-occurring amino acids each contain an α-carbon, an α-amino group, an α-carboxylic acid group, and an α-side chain or side group. These side chains (or R groups) may be either nonpolar, polar and uncharged, or charged, depending on the pH and pKa of the ionizable group. Two other amino acids occasionally appear in proteins. One is selenocysteine, which is found in Archaea, eubacteria, and animals and just recently found is pyrrolysine, found in Archaea. We will concentrate on only the 20 abundant, naturally-occurring amino acids.
- 4.1: Amino Acids
- A1. Amino Acid Structure
- Structure and Property of the Naturally-Occurring Amino Acids
- A10. General Links and References
- A2. Amino Acid Stereochemistry
- A3. Amino Acid Charges
- A4. Introduction to Amino Acid Reactivity
- A5. Reactions of Lysine
- A6. Reactions of Cysteine
- A7. Cysteine Chemistry
- Oxidation
- Reduction (Redox) Reactions and Oxidation Numbers
- A8. Reactions of Histidine
- A9. In Vivo Post Translational Modification of Amino Acids
- 4.4: Protein Folding - in Vivo and in Vitro
- D1. Introduction
- D2. Protein Folding In Vitro
- D3. Folding of Single Protein Molecules
- D4. The Denatured State
- D5. Multiple Conformations from The Same Sequence
- D6. Protein Folding In Vivo
- Do you find biochemistry amazing?
- D7. Redox Chemistry and Protein Folding
- D8. Protein Transport Across Membranes
- D9. Recent References
- 4.6: Thermodynamics and IMF's in Protein Stability
- It is clear that proteins are not all that stable, and many contributions of varying magnitudes must sum to give the proteins marginal stability under physiological conditions.Hydrophobic interaction, defined in the new sense, must play a major role in stability. Also, since proteins are so highly packed compared to a lose denatured state, London Forces must also play a significant part. (Remember dispersion forces are short range and become most significant under conditions of closest packing.)
- F1. Introduction to Protein Stability
- F10. Protein Stability in Thermophilic Organisms
- F11. General Links and References
- F2. Ion - Ion Interactions
- F3. Hydrogen Bonding
- F5. Additives and Their Interactions with Protein Surfaces
- F6. The Hydrophobic Effect and Change in Heat Capacity
- F7. Hydrophobic Effect and Protein Denaturation
- F8. Mutagenesis and Protein Stability
- F9. Protein Stability and Molecular Orbitals
- Introduction
- 4.7: G. Predicting Protein Properties From Sequences
- G1. Introduction to Bioinformatics, Computational Biology and Proteomics
- G2. Prediction of Secondary Structure
- G3. Prediction of Hydrophobicity
- G4. Prediction of Membrane Protein Structure
- G5. Prediction of Protein Tertiary Structure
- G6. Proteomics Problem Set 1
- G7. Proteomics Problem Set 2
- G8. General Links and References