Structure of Water and Hydrogen Bonding
Water is the most abundant molecule in living organisms. Its unique properties arise from its polar covalent bonds and ability to form hydrogen bonds.
Oxygen is more electronegative than hydrogen, so it pulls shared electrons closer. This creates a partial negative charge (δ⁻) on oxygen and partial positive charges (δ⁺) on the hydrogens.
Result: Water is a polar molecule with unequal charge distribution.
| Property | Explanation | Biological Significance |
|---|---|---|
| Cohesion | Water molecules stick to each other via H-bonds | Pulls water up through plant xylem (transpiration) |
| Adhesion | Water sticks to other polar surfaces | Water climbs vessel walls; capillary action |
| High Specific Heat | Takes a lot of energy to change water's temperature | Moderates climate; stabilizes body temperature |
| High Heat of Vaporization | Takes a lot of energy to evaporate water | Evaporative cooling (sweating) |
| Ice Floats | Solid water is less dense than liquid water | Insulates lakes; aquatic life survives winter |
Elements of Life
Living organisms are composed primarily of just a few elements, with carbon being the most important for building biological molecules.
These six elements make up ~98% of living matter:
Carbon
Backbone of all organic molecules
Hydrogen
In water, carbs, lipids, proteins
Nitrogen
In proteins & nucleic acids
Oxygen
In water & all macromolecules
Phosphorus
In ATP, DNA, phospholipids
Sulfur
In some amino acids (cysteine)
Carbon has 4 valence electrons, allowing it to form up to 4 covalent bonds. This makes it incredibly versatile:
- Can bond with other carbons → long chains and rings
- Can form single, double, or triple bonds
- Creates diverse 3D shapes essential for molecular function
- Bonds are strong but not too strong → molecules can be modified
Some elements are needed in small amounts but are still essential: Fe (iron in hemoglobin), Ca (bones, signaling), K (nerve impulses), Mg (chlorophyll), I (thyroid hormones).
Introduction to Macromolecules
Biological macromolecules are large polymers built from smaller monomers. Understanding how they're assembled and broken down is fundamental.
| Macromolecule | Monomer | Elements | Key Functions |
|---|---|---|---|
| Carbohydrates | Monosaccharides | C, H, O | Energy, structure |
| Lipids | Glycerol + fatty acids | C, H, O | Energy storage, membranes |
| Proteins | Amino acids | C, H, O, N, (S) | Enzymes, structure, transport |
| Nucleic Acids | Nucleotides | C, H, O, N, P | Genetic info, energy (ATP) |
Carbohydrates
Carbohydrates are the primary source of quick energy and also serve structural roles. They follow the formula (CH₂O)n.
Single sugars
Glucose, Fructose, Galactose
2 sugars linked
Sucrose, Lactose, Maltose
Many sugars linked
Starch, Glycogen, Cellulose
| Polysaccharide | Found In | Function | Structure |
|---|---|---|---|
| Starch | Plants | Energy storage | α-glucose, helical, branched (amylopectin) |
| Glycogen | Animals | Energy storage | α-glucose, highly branched |
| Cellulose | Plant cell walls | Structure | β-glucose, unbranched, H-bonded fibers |
| Chitin | Fungi, arthropods | Structure (exoskeleton) | Modified glucose with nitrogen |
Lipids
Lipids are hydrophobic (water-fearing) molecules that include fats, phospholipids, and steroids. Unlike other macromolecules, they are NOT true polymers.
Glycerol + 3 fatty acids
Long-term energy storage
Glycerol + 2 FA + phosphate
Cell membranes
4 fused carbon rings
Hormones, cholesterol
Saturated Fats
No double bonds → straight chains → pack tightly → SOLID at room temp
Examples: Butter, animal fat
Unsaturated Fats
Has double bonds → kinks in chain → can't pack tightly → LIQUID at room temp
Examples: Olive oil, fish oil
Nucleic Acids
Nucleic acids store and transmit genetic information. The two types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
Each nucleotide has three parts:
Deoxyribose (DNA)
Ribose (RNA)
PO₄³⁻
Forms backbone
A, T, G, C (DNA)
A, U, G, C (RNA)
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Strands | Double-stranded (helix) | Single-stranded |
| Bases | A, T, G, C | A, U, G, C |
| Function | Long-term genetic storage | Protein synthesis, regulation |
| Location | Nucleus (mostly) | Nucleus and cytoplasm |
DNA: A pairs with T (2 H-bonds) | G pairs with C (3 H-bonds)
RNA: A pairs with U | G pairs with C
Memory trick: "Apple Tree" (A-T) and "Good Cat" (G-C)
Proteins
Proteins are the most diverse macromolecules, performing nearly every function in cells. They are polymers of amino acids linked by peptide bonds.
All 20 amino acids share a common structure:
The R group (side chain) is different for each amino acid and determines its properties (polar, nonpolar, charged, etc.).
| Level | Description | Bonds/Forces |
|---|---|---|
| Primary (1°) | Linear sequence of amino acids | Peptide bonds (covalent) |
| Secondary (2°) | Local folding: α-helix or β-pleated sheet | Hydrogen bonds (backbone) |
| Tertiary (3°) | Overall 3D shape of single polypeptide | H-bonds, ionic, disulfide, hydrophobic |
| Quaternary (4°) | Multiple polypeptides assembled | Same as tertiary (between subunits) |
Denaturation
When proteins lose their 3D shape due to:
- High temperature (heat)
- Extreme pH (acids/bases)
- High salt concentration
Result: Loss of function (protein "unravels")
Why Shape Matters
Structure determines function.
Enzymes have active sites that fit specific substrates. A single amino acid change can alter shape and cause disease (e.g., sickle cell anemia).