The Properties of Water

1. Water Molecules

• Polar Molecule:

  • Oxygen is more electronegative than hydrogen, leading to an unequal sharing of electrons.

  • Results in oxygen being partially negative and hydrogen partially positive.

• Hydrogen Bonding:

  • Each water molecule can form hydrogen bonds with four neighboring water molecules (tetrahedral shape).

2. Emergent Properties of Water Due to Hydrogen Bonding

• Cohesive Behavior:

  • Water molecules stick together, creating surface tension.

• Versatility as a Solvent:

  • Water can dissolve many substances due to its polarity.

• Expansion Upon Freezing:

  • Ice is less dense than liquid water, allowing it to float.

• Ability to Moderate Temperature:

  • Water can absorb and release heat with minimal temperature change due to high specific heat.

3. Cohesion and Adhesion

• Definitions:

  • Cohesion: Ability of water molecules to stick to themselves.

  • Adhesion: Ability of water molecules to stick to other surfaces.

• Contribution to Water Movement:

  • Water travels from roots to leaves in trees through cohesive forces connecting water molecules and adhesive forces allowing water to adhere to plant cell walls.

4. Heat vs. Temperature

• Heat: Total energy in a substance. (e.g., boiling water)

• Temperature: Average kinetic energy of a substance. (e.g., 100°C boiling point)

5. Specific Heat of Water

• High specific heat is attributed to the need for energy to break hydrogen bonds and reform them, allowing water to absorb and release heat slowly.

6. Water's Climate Influence

• Water's high specific heat moderates temperatures, leading to milder coastal climates compared to inland areas.

The Solvent of Life

1. Definitions

• Solution: A homogeneous mixture of substances.

• Solvent: The dissolving agent in a solution.

• Solute: The substance that is dissolved.

2. Hydrophobic vs. Hydrophilic Substances

• Hydrophilic: Substances that have an affinity for water.

• Hydrophobic: Substances that do not have an affinity for water.

The Dissociation of Water Molecules

1. Products of Dissociation

• Water dissociates into hydrogen ions (H⁺) and hydroxide ions (OH⁻).

2. Acids, Bases, and pH

• Acid: Increases H⁺ ion concentration in a solution.

• Base: Absorbs H⁺ ions in a solution.

• pH: Measure of hydrogen ion concentration.

3. Altering Hydrogen Ion Concentration

• Acids release H⁺ ions, making solutions more acidic, while bases absorb H⁺ ions, making solutions more basic.

4. Buffers in Biological Systems

• Bicarbonate Buffer System: Maintains blood pH around 7.4 by releasing or absorbing H⁺ as needed.

5. Effects of Fossil Fuel Burning

• Acid Precipitation: SO₂ and NOₓ released react with water vapor, forming acids.

• Ocean Acidification: CO₂ increases in oceans forms carbonic acid, lowering ocean pH.

The Importance of Carbon

1. Carbon's Electron Configuration

• Carbon’s four valence electrons allow formation of complex and diverse organic molecules through covalent bonding.

2. Variation in Carbon Skeletons

• Carbon skeletons can differ in length, branching, and presence of double bonds, contributing to molecular diversity.

3. Hydrocarbons

• Hydrocarbons consist of carbon and hydrogen and are non-polar, making them hydrophobic.

4. Types of Isomers

• Structural Isomers: Differ in atom arrangements.

• Geometric Isomers: Differ in spatial arrangements due to double bonds.

• Enantiomers: Non-superimposable mirror images.

Functional Groups

1. Major Functional Groups and Their Properties

• Hydroxyl (-OH): Polar, enhances solubility.

• Carbonyl (C=O): Important for sugar structure.

• Carboxyl (-COOH): Acidic, donates H⁺ ions.

• Amino (-NH₂): Base, found in amino acids.

• Sulfhydryl (-SH): Crucial for protein structure.

• Phosphate (-PO₄³⁻): Involved in energy transfer.

• Methyl (-CH₃): Affects gene expression.

ATP and Macromolecules

1. Role of ATP

• ATP stores energy in phosphate bonds and releases it when hydrolyzed to ADP, driving cellular processes.

2. Major Classes of Macromolecules

• Carbohydrates, lipids, proteins, and nucleic acids.

3. Monomers vs. Polymers

• Monomers are small molecules; polymers are large, linked molecules.

Carbohydrates

1. Types of Carbohydrates

• Monosaccharides: Simple sugars (glucose).

• Disaccharides: Two monosaccharides (sucrose).

• Polysaccharides: Many monosaccharides (starch).

2. Glycosidic Linkage Formation

• Formed by dehydration; broken down by hydrolysis.

3. Importance of Glycosidic Linkage Variations

• Starch (α-linkages) digestible by animals; cellulose (β-linkages) is not without microbes.

Lipids

1. Structure and Importance

• Fats: Glycerol + 3 fatty acids, for energy storage.

• Phospholipids: Glycerol + 2 fatty acids + phosphate, form cell membranes.

• Steroids: Four fused rings, serve as hormones.

• Lipids are not monomers as they aren't made from repeating subunits.

2. Ester Linkage

• Formed by condensation; broken by hydrolysis.

3. Saturated vs. Unsaturated Fats

• Saturated: No double bonds, solid at room temp.

• Unsaturated: At least one double bond, liquid at room temp.

Proteins

1. Protein vs. Polypeptide

• Protein: One or more polypeptides folded into a specific structure.

• Polypeptide: Linear chain of amino acids.

2. Peptide Bond Formation

• Forms between the amino group of one amino acid and the carboxyl group of another; broken by hydrolysis.

3. Amino Acid Structure

• Composed of amino group, carboxyl group, hydrogen atom, and R group.

4. Importance of Protein Structure

• Structure determines function; formed by the sequence of amino acids.

5. Secondary Structure Types

• α-helix and β-pleated sheet, both stabilized by hydrogen bonds.

6. Tertiary Structure Maintenance

• Stabilized through weak interactions and disulfide bridges.

7. Denaturation Conditions

• Caused by heat, pH changes, salt concentration, or chemicals.

8. Sickle Cell Anemia

• Genetic disorder leading to misshaped hemoglobin causing symptoms like pain and organ damage; provides a heterozygote advantage for malaria resistance.

Nucleic Acids

1. Nucleotide Components

• Composed of a sugar, phosphate group, and nitrogenous base; linked via phosphodiester bonds to form DNA/RNA.

2. Nucleotide Differences

• Pyrimidine: Single ring (C, T, U) vs. Purine: Double ring (A, G).

• Nucleotide: Base + sugar + phosphate vs. Nucleoside: Base + sugar.

• Ribose (RNA) vs. Deoxyribose (DNA).

3. DNA Structure

• Exists as a double helix with complementary base pairing (A-T, G-C).

4. Evolutionary Relationships

• DNA and protein comparisons can show evolutionary relationships, with similarities indicating closer kinship.

Personal Notes and Predictions

• Emphasis on protein importance, structure analysis, and roles of macromolecules in functions.

• Potential focus areas: dehydrating synthesis vs. hydrolysis, sickle cell genetics, effects of water in enzyme data, etc.