Biochemistry Foundations - Complete Interactive Lesson
Part 1: Amino Acids & Protein Structure
Biochemistry Foundations
Part 1 of 7 โ Amino Acids & Protein Structure
The 20 Amino Acids โ Classify by Side Chain
| Category | Amino Acids | Key Feature |
|---|---|---|
| Nonpolar/Hydrophobic | G, A, V, L, I, P, F, W, M | Interior of proteins |
| Polar uncharged | S, T, C, Y, N, Q | H-bonding |
| Positively charged (pH 7) | K, R, H | Basic side chains |
| Negatively charged (pH 7) | D, E | Acidic side chains |
Protein Structure Levels
| Level | Held together by | Description |
|---|---|---|
| Primary (1ยฐ) | Peptide bonds (covalent) | Amino acid sequence |
| Secondary (2ยฐ) | H-bonds (backbone N-H to C=O) | -helix, -sheet |
| Tertiary (3ยฐ) | Hydrophobic, ionic, disulfide, H-bonds | 3D shape of one polypeptide |
| Quaternary (4ยฐ) | Same as tertiary | Multiple subunit assembly |
Disulfide Bonds
Cysteine + Cysteine โ Cystine (C-S-S-C), covalent bond stabilizing tertiary structure.
Isoelectric Point (pI) Logic
- At pH < pI, amino acids/proteins tend to carry net positive charge.
- At pH > pI, they tend to carry net negative charge.
This is heavily tested in electrophoresis and separation contexts.
Amino Acids & Protein Structure ๐ฏ
Key Takeaways โ Part 1
- Know amino acid categories cold (nonpolar, polar, positive, negative)
- Proline = helix breaker (rigid ring); Glycine = most flexible (no side chain)
- Primary: sequence. Secondary: -helix/-sheet. Tertiary: 3D fold. Quaternary: subunits.
- Disulfide bonds (Cys-Cys) = only COVALENT bond in tertiary structure
Worked Examples โ Amino Acids & Protein Structure
<details> <summary><b>Example 1: Classify amino acid by charge at different pH values</b></summary>Question: Aspartic acid (Asp, D) has a side chain with a carboxylic acid (pKa โ 3.9). Is aspartic acid positively, negatively, or neutrally charged at pH 7?
Solution:
- At pH 7 > pKa (3.9), the carboxylic acid is deprotonated: โCOOโป
- The -carboxylic acid (backbone, pKa โ 2) is also deprotonated: โCOOโป
- The -amino group (pKa โ 9.6) is protonated: โNHโโบ
- Net charge: (โ1 from side chain) + (โ1 from backbone) + (+1 from backbone NHโ) = โ1 (negatively charged)
MCAT Strategy: At physiological pH (~7), acidic amino acids (D, E) are negative; basic amino acids (K, R, H) are positive because their pKa values are far from 7.
</details> <details> <summary><b>Example 2: Determine protein behavior in electrophoresis</b></summary>Question: A protein has an isoelectric point (pI) of 5.5. At pH 7, will it migrate toward the positive or negative electrode during electrophoresis?
Solution:
- At pH 7 > pI (5.5), the protein is above its isoelectric point
- Above pI, the protein carries a net negative charge (more deprotonation than protonation)
- Negative proteins migrate toward the positive electrode (anode)
Part 2: Enzyme Kinetics
Biochemistry Foundations
Part 2 of 7 โ Enzyme Kinetics (ULTRA HIGH YIELD)
Michaelis-Menten Equation
Part 3: Carbohydrate Metabolism
Biochemistry Foundations
Part 3 of 7 โ Glycolysis & Gluconeogenesis
Glycolysis (Cytoplasm, Anaerobic)
Net yield per glucose: 2 ATP, 2 NADH, 2 Pyruvate
Part 4: Lipids & Membranes
Biochemistry Foundations
Part 4 of 7 โ TCA Cycle & Oxidative Phosphorylation
TCA Cycle (Mitochondrial Matrix)
Per acetyl-CoA: 3 NADH, 1 FADH, 1 GTP
Part 5: Nucleic Acids & DNA
Biochemistry Foundations
Part 5 of 7 โ Lipids & Fatty Acid Metabolism
Lipid Classification
| Type | Structure | Function |
|---|---|---|
| Triglycerides | 3 fatty acids + glycerol | Energy storage |
| Phospholipids | 2 fatty acids + glycerol + phosphate head | Membranes |
| Steroids | 4 fused rings | Hormones (cholesterol, testosterone, estrogen) |
| Sphingolipids | Sphingosine backbone | Myelin, cell signaling |
-Oxidation (Mitochondrial Matrix)
Each cycle removes 2 carbons and produces:
- 1 NADH, 1 FADH, 1 Acetyl-CoA
Part 6: Bioenergetics & ATP
Biochemistry Foundations
Part 6 of 7 โ Nucleic Acids & Molecular Biology
DNA vs RNA
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose () |
| Bases | A, T, G, C | A, U, G, C |
| Structure | Double-stranded | Usually single-stranded |
| Stability | More stable | Less stable ( makes it prone to hydrolysis) |
Part 7: Review & MCAT Practice
Biochemistry Foundations
Part 7 of 7 โ Metabolic Regulation & Integration
Fed vs. Fasting State
| State | Insulin | Glucagon | Active Pathways |
|---|---|---|---|
| Fed | High | Low | Glycolysis, glycogenesis, lipogenesis, protein synthesis |
| Fasting | Low | High | Gluconeogenesis, glycogenolysis, -oxidation, ketogenesis |
Key Regulatory Hormones
- Insulin: promotes anabolism (storage). Activates PFK-1, pyruvate kinase, glycogen synthase.
- Glucagon: promotes catabolism (mobilization). Activates glycogen phosphorylase, lipase.
- Epinephrine: fight-or-flight. Similar to glucagon + increases heart rate.
Metabolic Integration
- High ATP/NADH โ inhibits TCA, glycolysis (feedback)
- Acetyl-CoA activates pyruvate carboxylase (gluconeogenesis) and inhibits PDH
- Malonyl-CoA (from fatty acid synthesis) inhibits CPT-I (blocks -oxidation)