1. What are Lipids?
Lipids are a diverse group of hydrophobic or amphipathic biomolecules that are insoluble in water but soluble in non-polar organic solvents such as chloroform, ether, and benzene. They are essential components of cell membranes, energy storage molecules, and signaling molecules.
Key Characteristics
- Hydrophobic or amphipathic in nature
- Insoluble in water
- Soluble in organic solvents
- Rich in C, H, and small amount of O
- High energy density (~9 kcal/g)
2. Fatty Acids
Fatty acids are long-chain carboxylic acids that are fundamental building blocks of most lipids.
General Structure
Comprehensive Table of Saturated Fatty Acids
Saturated fatty acids contain NO double bonds. They pack tightly and are solid at room temperature.
| Common Name | Carbon Skeleton | Systematic Name | Melting Point (°C) |
|---|---|---|---|
| Lauric Acid | 12:0 | n-Dodecanoic acid | 44.2 |
| Myristic Acid | 14:0 | n-Tetradecanoic acid | 53.9 |
| Palmitic Acid | 16:0 | n-Hexadecanoic acid | 63.1 |
| Stearic Acid | 18:0 | n-Octadecanoic acid | 69.6 |
| Arachidic Acid | 20:0 | n-Eicosanoic acid | 76.5 |
Comprehensive Table of Unsaturated Fatty Acids
Unsaturated fatty acids contain one or more double bonds (usually in cis configuration), which creates kinks in the chain, lowering their melting point.
| Common Name | Carbon Skeleton | Systematic Name | Melting Point (°C) |
|---|---|---|---|
| Palmitoleic Acid | 16:1(Δ9) | cis-9-Hexadecenoic acid | -0.5 |
| Oleic Acid | 18:1(Δ9) | cis-9-Octadecenoic acid | 13.4 |
| Linoleic Acid | 18:2(Δ9,12) | cis-,cis-9,12-Octadecadienoic acid | -5 |
| α-Linolenic Acid | 18:3(Δ9,12,15) | all-cis-9,12,15-Octadecatrienoic acid | -11 |
| Arachidonic Acid | 20:4(Δ5,8,11,14) | all-cis-5,8,11,14-Eicosatetraenoic acid | -49.5 |
- Double bonds in natural fatty acids are mostly in the cis configuration.
- Double bonds usually occur every 3 carbons (e.g., Δ9, 12, 15).
- Rule of Thumb: Melting point DECREASES as the number of double bonds INCREASES. Melting point INCREASES as chain length INCREASES.
3. Simple Lipids
Simple lipids are esters of fatty acids with alcohols.
- Triacylglycerols (Triglycerides): Glycerol + 3 fatty acids. Major energy storage.
- Waxes: Long chain fatty acid + long chain alcohol. Waterproof coating.
4. Glycerol Based Lipids
These lipids contain a glycerol backbone and are major components of cell membranes.
- Phosphoglycerides: Glycerol, 2 fatty acids, Phosphate group, Alcohol group.
- Examples: Phosphatidylcholine (lecithin), Phosphatidylethanolamine, Phosphatidylserine.
5. Sphingosine Based Lipids
Contain a sphingosine backbone instead of glycerol. Sphingosine is an 18-carbon amino alcohol.
- Ceramide: Sphingosine + Fatty acid (amide linkage). Structural parent of all sphingolipids.
- Sphingomyelin: Ceramide + Phosphate + Choline. Found in myelin sheath.
- Glycosphingolipids: Contain sugar molecules (Cerebrosides, Gangliosides).
6. Cholesterol
Cholesterol is a sterol lipid present in animal cell membranes. It consists of four fused rings (Steroid nucleus).
- Maintains membrane fluidity.
- Precursor of Steroid hormones (Cortisol, Testosterone) and Vitamin D.
7. Nitrogenous Bases
Heterocyclic aromatic molecules containing nitrogen. They strongly absorb UV light at 260 nm.
- Purines (Double Ring): Adenine (A), Guanine (G).
- Pyrimidines (Single Ring): Cytosine (C), Thymine (T), Uracil (U).
8. Nucleotide & Watson & Crick DNA Model Structure
Proposed by James Watson and Francis Crick in 1953, based on X-ray diffraction data from Rosalind Franklin, this is the most common physiological conformation: B-DNA. A comprehensive understanding requires looking from the fundamental monomer level to complex chromosomal packaging.
Key Labeled Features of Watson-Crick Model (B-Form)
- Major Groove (Wide & Deep) ~12 Å
- Minor Groove (Narrow & Deep) ~6 Å
- Helix Diameter (Width) 20 Å (2.0 nm)
- Rise per bp (Distance between bases) 3.4 Å
- Pitch (Length of one complete turn) 34 Å
- Base Pairs per Turn (Exactly) 10.5 bp
- Twist Angle (Per bp rotation) 36°
- Right-Handed Helix Conformation
A. Nucleotide Structure & Bond Formation
The entire DNA molecule is structurally held together by specific types of chemical bonds:
- β-N-Glycosidic Bond (Covalent): Connects the nitrogenous base to the pentose sugar. It is formed via a condensation reaction between the 1'-OH of the sugar and the N1 of a pyrimidine (or N9 of a purine).
- Phosphoester Bond (Covalent): Connects the 5'-carbon of the sugar to the first phosphate group.
- Phosphodiester Bond (Covalent): This forms the "sugar-phosphate backbone". It occurs when the 3'-OH group of one nucleotide's sugar attacks the 5'-phosphate group of the next nucleotide, releasing a water molecule.
- Hydrogen Bonds (Non-Covalent): These connect the two antiparallel strands together across the helix. Adenine pairs with Thymine (2 H-bonds) and Guanine pairs with Cytosine (3 H-bonds).
Comparison of Different DNA Structures (A, B, Z Forms)
| Feature | A-DNA | B-DNA (Standard) | Z-DNA |
|---|---|---|---|
| Helical Sense | Right-handed | Right-handed | Left-handed |
| Diameter | ~26 Å | ~20 Å | ~18 Å |
| bp per Turn | 11 | 10.5 | 12 |
| Major Groove | Narrow & Deep | Wide & Deep | Flat / Unclear |
| Physiological Condition | Dehydrated environments | Normal physiological conditions | High Salt / Alternating GCGC |
B. Tertiary Structure (DNA Supercoiling & Strand Breaking)
To fit inside the cell, DNA twists upon itself. Supercoiling is quantitatively described by the following topological equation:
- Linking Number (Lk): The total number of times one strand of DNA crosses the other. Crucial Point: Lk is an invariant topological property. As long as the circular DNA remains intact, Lk cannot change.
- Twist (Tw): The number of helical turns in the DNA strand.
- Writhe (Wr): The number of times the double helix crosses over its own central axis (the actual supercoils).
How Bonds Break to Change Supercoiling:
Because the Linking Number (Lk) is constant in a closed loop, the cell must physically cut the DNA backbone (break the phosphodiester bonds) to relieve tension during replication or transcription. This is done by Topoisomerases:
- Topoisomerase I: Cuts only one strand of the DNA, allows it to unwind, and reseals the break. Changes Lk by increments of ±1. Does not require ATP.
- Topoisomerase II (e.g., DNA Gyrase): Cuts both strands of the DNA, passes another segment of the double helix through the break, and reseals it. Changes Lk by increments of ±2. Requires ATP.
C. Quaternary Structure (Chromatin Packaging)
In eukaryotes, DNA is highly condensed into chromatin to fit within the nucleus.
- Nucleosome (10 nm fiber): "Beads on a string". Consists of ~147 bp of DNA wrapped 1.67 times around a histone octamer (two each of H2A, H2B, H3, and H4).
- Solenoid (30 nm fiber): Formed by the coiling of nucleosomes, stabilized by the linker histone H1.
- Looped Domains & Chromosome: The 30 nm fibers form loops attached to a protein scaffold, ultimately condensing into a metaphase chromosome.
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