Biochemistry Ultimate Cheat Sheet
1000+ words of pure high-yield facts. Master Enzyme Kinetics, Ramachandran Plots, Metabolic Pathways, and Bioenergetics to secure top marks in DBT BET Section B.
1. Amino Acids & Protein Structure
Proteins and their building blocks are heavily tested. You must know the structural properties, pI (Isoelectric point) calculations, and the Ramachandran Plot inside out.
Key Amino Acid Properties
- Glycine: The simplest, optically inactive (achiral). Because it lacks a side chain, it has high conformational flexibility and populates a large area on the Ramachandran plot.
- Proline: An imino acid. It creates a rigid "kink" in the peptide chain, making it an alpha-helix breaker.
- Cysteine: Contains a sulfhydryl (-SH) group. Two cysteines oxidize to form a Disulfide bond (Cystine), which strongly stabilizes tertiary structure.
- Tryptophan, Tyrosine, Phenylalanine: Aromatic amino acids. They absorb UV light at 280 nm, which is used to quantify protein concentration. Tryptophan has the highest absorbance.
• Top Left Quadrant: Beta-sheets.
• Bottom Left Quadrant: Right-handed Alpha-helices.
• Top Right Quadrant: Left-handed Alpha-helices.
| Classification | Amino Acids | Key Exam Note |
|---|---|---|
| Acidic (Negative) | Aspartate (D), Glutamate (E) | Carboxylate groups; pKa around 4.0. |
| Basic (Positive) | Lysine (K), Arginine (R), Histidine (H) | Histidine is the physiological buffer (pKa ~ 6.0). |
| Hydroxyl-containing | Serine (S), Threonine (T), Tyrosine (Y) | Primary targets for Kinase phosphorylation. |
| Sulfur-containing | Cysteine (C), Methionine (M) | Methionine is the start codon (AUG) residue. |
2. Enzyme Kinetics & Inhibition
Every single DBT JRF paper has a numerical or graph based on Michaelis-Menten kinetics and the Lineweaver-Burk plot. You must know how Vmax and Km change under different inhibitions.
Michaelis-Menten Equation
The equation is: V = (Vmax [S]) / (Km + [S]).
Km (Michaelis Constant) is the substrate concentration at which the reaction velocity is half of Vmax. A lower Km indicates higher affinity of the enzyme for the substrate.
Fig: Lineweaver-Burk Plot showing Competitive Inhibition (Lines cross at Y-axis)
| Inhibition Type | Effect on Vmax | Effect on Km | Lineweaver-Burk Plot Feature |
|---|---|---|---|
| Competitive | Unchanged | Increases (apparent) | Lines intersect at the Y-axis (1/Vmax). Inhibitor resembles substrate. |
| Uncompetitive | Decreases | Decreases | Lines are parallel. Inhibitor binds only to the ES complex. |
| Non-Competitive (Mixed) | Decreases | Unchanged | Lines intersect at the X-axis (-1/Km). Binds E and ES equally. |
3. Metabolism & Bioenergetics
Metabolic pathways are interconnected. DBT examiners love to test the regulatory enzymes, the energetic yield (ATP/NADH), and specific pathway inhibitors.
Glycolysis & Regulation
Glycolysis converts one molecule of Glucose into two molecules of Pyruvate, generating a net of 2 ATP and 2 NADH. The most critical regulatory step is catalyzed by Phosphofructokinase-1 (PFK-1). PFK-1 is allosterically activated by AMP and Fructose-2,6-bisphosphate, and inhibited by ATP and Citrate. Note: Hexokinase is found in most tissues (low Km, high affinity), while Glucokinase is found in the liver (high Km, functions only when glucose is high).
Electron Transport Chain (ETC) & Oxidative Phosphorylation
The ETC creates a proton gradient across the inner mitochondrial membrane, which ATP Synthase uses to make ATP. Blocking this chain stops ATP production and can be fatal.
| ETC Complex | Name / Function | Specific Inhibitors (Highly Tested) |
|---|---|---|
| Complex I | NADH Dehydrogenase | Rotenone, Amytal, Piericidin A |
| Complex II | Succinate Dehydrogenase (TCA enzyme) | Malonate (Competitive inhibitor) |
| Complex III | Cytochrome bc1 Complex | Antimycin A |
| Complex IV | Cytochrome C Oxidase | Cyanide (CN⁻), Carbon Monoxide (CO), Azide |
| Complex V | ATP Synthase | Oligomycin (Blocks proton channel F0) |
4. Nucleic Acids & Topology
DNA structure isn't just A binding to T. You must understand the biophysical properties of DNA, including melting temperature and topological constraints.
DNA Forms and Tm
- B-DNA: The most common, right-handed helix discovered by Watson and Crick. It has ~10.4 base pairs per turn.
- A-DNA: Right-handed, but wider and more compressed. Forms in dehydrated conditions or in DNA-RNA hybrids.
- Z-DNA: Left-handed helix. Usually forms in regions with alternating purine-pyrimidine sequences (like CGCGCG).
Melting Temperature (Tm): The temperature at which 50% of the DNA double helix is denatured into single strands. Tm is directly proportional to the GC content (because G-C pairs have 3 hydrogen bonds, making them stronger than A-T pairs which have 2). When DNA denatures, its UV absorbance at 260 nm increases—this is called the Hyperchromic Effect.
Guaranteed Exam Hits
- Uncoupling Agents: 2,4-Dinitrophenol (2,4-DNP) and Thermogenin (UCP1 in brown fat) are uncouplers. They destroy the proton gradient. Electron transport continues rapidly, oxygen is consumed, but NO ATP is formed. The energy is released as pure heat.
- Fatty Acid Oxidation Energetics: Beta-oxidation of Palmitic Acid (16-Carbon) requires 7 cycles, producing 8 Acetyl-CoA, 7 NADH, and 7 FADH2, yielding a net of 106 ATP.
- Gluconeogenesis Bypass: The three irreversible steps of Glycolysis are bypassed in Gluconeogenesis using four unique enzymes: Pyruvate Carboxylase, PEP Carboxykinase, Fructose-1,6-bisphosphatase, and Glucose-6-phosphatase.
- Enzyme Efficiency: The catalytic perfection of an enzyme is measured by the ratio Kcat / Km (Specificity Constant). The upper limit is restricted only by the diffusion rate of the substrate.
- Edman Degradation: Used for protein sequencing. The chemical Phenylisothiocyanate (PITC) is used to sequentially cleave the N-terminal amino acid without breaking the rest of the peptide chain.
- Vitamin Coenzymes: Vitamin B1 (Thiamine) is active as TPP (required for Pyruvate Dehydrogenase). Vitamin B6 (Pyridoxine) is active as PLP (required for all Transamination reactions).
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