Chemistry of Life: Study Notes for General Biology

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Chemistry of Life

Introduction

The chemistry of life explores the molecular foundations that enable biological processes. Understanding the structure and properties of water, biomolecules, and their interactions is essential for studying living organisms.

Properties of Water

Polarity and Hydrogen Bonding

Water is a unique molecule due to its polar covalent bonds and ability to form hydrogen bonds.

Polar Covalent Bonds: In water (H2O), electrons are shared unequally between oxygen and hydrogen, making the molecule polar.
Hydrogen Bonds: Weak attractions between the positive hydrogen end of one water molecule and the negative oxygen end of another. These are not true chemical bonds but stabilize molecular structures.
Importance: Hydrogen bonds give water its unique properties that sustain life.

Example: Water molecules form hydrogen bonds with each other and with other polar molecules.

Cohesion, Adhesion, and Surface Tension

Water molecules interact through cohesion and adhesion, leading to phenomena like surface tension.

Cohesion: Water molecules stick to each other due to hydrogen bonding.
Adhesion: Water molecules stick to other surfaces (e.g., water on a car window).
Surface Tension: The cohesive forces at the surface of water create a 'skin' that resists external force.

Example: Water can be drawn up small tubes in plants (capillary action).

Temperature Regulation

Water has a high specific heat and heat of vaporization, allowing it to regulate temperature.

Specific Heat: The amount of heat required to raise the temperature of water is higher than most liquids.
Heat of Vaporization: Water requires more energy to evaporate, aiding in cooling (e.g., sweating).
Ice Density: Ice is less dense than liquid water due to hydrogen bond spacing, allowing it to float and insulate aquatic life.

Example: Bodies of water resist rapid temperature changes, protecting organisms.

Water as a Solvent

Water's polarity makes it an excellent solvent for many substances.

Hydrophilic Substances: Polar and ionic compounds dissolve easily in water.
Hydrophobic Substances: Non-polar substances (e.g., oil) do not dissolve in water.

Example: Water dissolves salts and sugars, facilitating transport in biological systems.

Biomolecules

Introduction to Biomolecules

Living organisms are primarily composed of carbon, hydrogen, and oxygen. Organic molecules contain carbon and are essential for life.

Versatile Bonding: Carbon forms four covalent bonds, allowing for diverse molecular structures (chains, rings).
Functional Groups: Clusters of atoms that determine molecule properties (e.g., polarity, acidity).

Example: Amino acids have amine and carboxyl functional groups.

Macromolecules and Monomers

Large biological molecules (macromolecules) are built from smaller subunits (monomers).

Carbohydrates: Monosaccharides (simple sugars) joined by glycosidic bonds.
Lipids: Fatty acids and glycerol joined by ester bonds.
Proteins: Amino acids joined by peptide bonds.
Nucleic Acids: Nucleotides joined by phosphodiester bonds.

Example: Glucose is a monosaccharide; starch is a polysaccharide.

Dehydration Synthesis and Hydrolysis

Macromolecules are assembled and disassembled by specific reactions.

Dehydration Synthesis: Monomers are joined by covalent bonds, releasing water.
Hydrolysis: Macromolecules are broken down by adding water.

Example: Formation of sucrose from glucose and fructose by dehydration synthesis.

Proteins

Structure and Function

Proteins are the most diverse biomolecules, involved in structure, nutrition, enzymes, transport, communication, and defense.

Amino Acids: Building blocks of proteins, each with a central carbon, amine group, carboxyl group, and variable R group.
Peptide Bonds: Link amino acids in a chain.

Example: Hemoglobin is a protein that transports oxygen in blood.

Levels of Protein Structure

Primary Structure: Unique sequence of amino acids.
Secondary Structure: Folding into alpha helices and beta sheets due to hydrogen bonding.
Tertiary Structure: Overall 3D shape formed by interactions among R groups (hydrogen bonds, hydrophobic interactions, disulfide bridges).
Quaternary Structure: Association of multiple polypeptide chains.

Example: Hemoglobin has four subunits (quaternary structure).

Denaturation

Proteins lose function if their shape is disrupted by changes in pH, temperature, or chemicals.

Denaturation: Loss of protein structure and function.

Example: Cooking an egg denatures its proteins.

Carbohydrates

Types and Functions

Carbohydrates are composed of carbon, hydrogen, and oxygen, often in a 1:2:1 ratio. They serve as energy sources and structural materials.

Monosaccharides: Simple sugars (e.g., glucose, fructose).
Disaccharides: Two monosaccharides joined (e.g., sucrose).
Polysaccharides: Long chains (e.g., starch, glycogen, cellulose, chitin).

Example: Starch stores energy in plants; glycogen stores energy in animals.

Lipids

Types and Properties

Lipids are nonpolar molecules used for energy storage, cell structure, and insulation.

Fatty Acids: Long hydrocarbon chains with a carboxyl group.
Saturated Fatty Acids: No double bonds; solid at room temperature.
Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature.
Triglycerides: Three fatty acids bonded to glycerol.
Phospholipids: Two fatty acids, glycerol, and a phosphate group; major component of cell membranes.
Waxes: Long fatty acid chains bonded to alcohols or carbon rings; protective coatings.
Steroids: Four fused carbon rings; include cholesterol and hormones.

Example: Phospholipids form the bilayer of cell membranes.

Nucleic Acids

Structure and Function

Nucleic acids store and transmit genetic information. They are polymers of nucleotides.

Nucleotide Structure: Phosphate group, five-carbon sugar (ribose or deoxyribose), nitrogenous base (A, T, C, G, U).
DNA: Double-stranded, contains deoxyribose, bases A, T, C, G.
RNA: Single-stranded, contains ribose, bases A, U, C, G.
Base Pairing: Purines (A, G) pair with pyrimidines (T/U, C).
Phosphodiester Bonds: Link nucleotides in a chain.

Example: DNA stores genetic instructions; RNA helps in protein synthesis.

DNA Structure

Antiparallel Strands: DNA strands run in opposite directions (5' to 3' and 3' to 5').
Hydrogen Bonds: Hold complementary bases together (A-T: 2 bonds, C-G: 3 bonds).

Example: The double helix structure of DNA enables replication and information storage.

Functional Groups in Biomolecules

Common Functional Groups

Functional groups determine the chemical properties and reactivity of biomolecules.

Functional Group	Structure	Found In	Properties
Amino	–NH2	Amino acids, nucleotide bases	Basic
Carboxyl	–COOH	Amino acids, fatty acids	Acidic
Phosphate	–PO4	Nucleotides, phospholipids	Polar, reactive

Key Formulas and Equations

General Carbohydrate Formula:
Dehydration Synthesis (Example):
Hydrolysis (Example):

Summary Table: Macromolecules

Macromolecule	Monomer	Bond Type	Function
Carbohydrates	Monosaccharides	Glycosidic	Energy, structure
Lipids	Fatty acids, glycerol	Ester	Energy storage, membranes
Proteins	Amino acids	Peptide	Structure, enzymes, transport
Nucleic Acids	Nucleotides	Phosphodiester	Genetic information

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