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Amino acids, protein structure, and functions of proteins
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Proteins are polymers of amino acids with diverse functions.
Functions:
Structure:
20 different amino acids with different R groups:
Describe the four levels of protein structure (primary, secondary, tertiary, quaternary). For each level, identify: (a) the type of bonds or interactions involved, and (b) give a specific example.
Four Levels of Protein Structure:
1. Primary Structure
(a) Bonds: Peptide bonds (covalent) linking amino acids
(b) Example: Insulin A-chain: 21 amino acids starting with Gly-Ile-Val-Glu...
2. Secondary Structure
| Section | Format | Questions | Time | Weight | Calculator |
|---|---|---|---|---|---|
| Multiple Choice | MCQ | 60 | 90 min | 50% | š« |
| Free Response (Long) | FRQ | 2 | 50 min | 30% | š« |
| Free Response (Short) | FRQ | 4 | 40 min | 20% | š« |
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Regular folding patterns due to hydrogen bonding:
Denaturation:
Chaperone proteins:
(a) Bonds/Interactions: Hydrogen bonds between backbone atoms (C=O and N-H)
Two main types:
(b) Example:
3. Tertiary Structure
(a) Bonds/Interactions:
Overall 3D shape of single polypeptide
(b) Example:
4. Quaternary Structure
(a) Bonds/Interactions: Same as tertiary (H-bonds, ionic, hydrophobic, van der Waals)
(b) Example:
Summary Table:
| Level | Bond/Interaction | Example |
|---|---|---|
| 1Ā° | Peptide bonds | Amino acid sequence |
| 2Ā° | H-bonds (backbone) | Ī±-helix, Ī²-sheet |
| 3Ā° | Multiple (R-groups) | Myoglobin (3D fold) |
| 4Ā° | Multiple (subunits) | Hemoglobin (4 subunits) |
Key Concept: Structure determines function! Denaturation (loss of 3D structure) ā loss of function.
An enzyme has optimal activity at pH 7.0 and temperature 37Ā°C. Predict and explain what happens to enzyme activity when: (a) pH is changed to 3.0, (b) temperature is increased to 80Ā°C, and (c) a competitive inhibitor is added. Include discussion of protein structure changes.
Enzyme Conditions: Optimal at pH 7.0 and 37Ā°C
(a) pH changed to 3.0 (strongly acidic):
Prediction: ā ļø Enzyme activity greatly reduced or eliminated
Explanation:
Protonation of amino acids:
Disruption of ionic bonds:
Tertiary structure denaturation:
Result: Loss of catalytic activity (may be reversible if pH restored quickly)
(b) Temperature increased to 80Ā°C (far above optimum):
Prediction: ā ļø Enzyme denatured, activity lost permanently
Explanation:
Increased kinetic energy:
Progressive unfolding:
Permanent denaturation:
Activity-Temperature Relationship:
Activity
^
| /\
| / \
| / \_____ (denaturation)
| /
|_/________________> Temperature
37Ā°C 80Ā°C
Why irreversible: Unlike pH change, heat breaks so many bonds simultaneously that protein cannot refold to native state.
(c) Competitive inhibitor added:
Prediction: š½ Enzyme activity reduced but NOT eliminated
Explanation:
Competitive inhibition mechanism:
Effect on protein structure:
Kinetic effects:
Equation:
Comparison:
| Condition | Structure Change | Activity | Reversible? |
|---|---|---|---|
| Low pH | Tertiary disrupted | Very low | Yes (if quick) |
| High temp | Complete denaturation | Zero | No |
| Competitive inh. | None | Reduced | Yes (ā substrate) |
where [I] = inhibitor concentration, K_i = inhibitor constant
Key difference: