General Biology Study Guide: Chemistry of Life, Macromolecules, and Cell Structure

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Chapter 2: Chemistry of Life

Atomic Structure and Chemical Bonds

The structure and properties of atoms and their interactions form the foundation of biological molecules and processes. Understanding atomic structure and chemical bonding is essential for grasping how molecules behave in biological systems.

Atoms are composed of protons, neutrons, and electrons. The arrangement of these subatomic particles determines the atom's identity and chemical behavior.
Covalent bonds involve the sharing of electron pairs between atoms, resulting in stable molecules. Ionic bonds occur when electrons are transferred from one atom to another, creating charged ions that attract each other. Hydrogen bonds are weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.
Bond strength and polarity are influenced by the difference in electronegativity between atoms. Polar covalent bonds have unequal sharing of electrons, leading to partial charges on atoms.
Electronegativity is a measure of an atom's ability to attract electrons in a bond. Differences in electronegativity determine bond polarity.

Special Properties of Water

Water is essential for life due to its unique chemical and physical properties, which arise from its molecular structure and hydrogen bonding.

Cohesion: Water molecules stick to each other due to hydrogen bonding, contributing to surface tension.
Adhesion: Water molecules can also stick to other polar or charged surfaces.
High specific heat: Water can absorb or release large amounts of heat with little temperature change, helping to stabilize environmental and organismal temperatures.
Solvent properties: Water's polarity allows it to dissolve many ionic and polar substances, making it the universal solvent in biological systems.
Example: Water's cohesive and adhesive properties enable capillary action, which is critical for water transport in plants.

Acids, Bases, and pH

Acids and bases are substances that alter the concentration of hydrogen ions (H+) in a solution, affecting pH and biological processes.

Acids donate H+ ions, increasing the concentration of hydrogen ions in solution.
Bases accept H+ ions or donate OH- ions, decreasing the concentration of hydrogen ions.
pH scale: Measures the concentration of H+ ions; lower pH indicates higher acidity, higher pH indicates higher basicity.
Equation:

Functional Groups and Chemical Properties of Carbon

Carbon's ability to form four covalent bonds allows for a diversity of stable organic molecules. Functional groups attached to carbon skeletons determine the chemical reactivity and properties of molecules.

Functional groups include hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups.
These groups confer specific chemical properties, such as polarity, acidity, or basicity, and influence molecular interactions.
Example: The carboxyl group (-COOH) acts as an acid, while the amino group (-NH2) acts as a base.

Polymers and Dehydration Synthesis

Biological macromolecules are often polymers, formed by linking monomers through dehydration synthesis reactions.

Dehydration synthesis (condensation reaction): Monomers are joined by covalent bonds with the removal of a water molecule.
Hydrolysis: The reverse process, where polymers are broken down into monomers by the addition of water.
Equation:

Chapter 3: Proteins

Protein Structure and Function

Proteins are polymers of amino acids that perform a vast array of functions in cells, including catalysis, structure, transport, and regulation.

Amino acids are the monomers of proteins, each containing an amino group, carboxyl group, hydrogen atom, and a unique side chain (R group).
Peptide bonds are covalent bonds that link amino acids together in a polypeptide chain.
Levels of protein structure:
- Primary structure: Sequence of amino acids.
- Secondary structure: Local folding into alpha-helices and beta-sheets, stabilized by hydrogen bonds.
- Tertiary structure: Overall 3D shape of a polypeptide, determined by interactions among side chains.
- Quaternary structure: Association of multiple polypeptide subunits.
Protein denaturation: Loss of structure and function due to disruption of non-covalent interactions (e.g., by heat, pH changes, or chemicals).
Chaperone proteins assist in proper protein folding and prevent misfolding.

Chapter 4: Nucleic Acids

Structure and Function of Nucleic Acids

Nucleic acids, including DNA and RNA, store and transmit genetic information in cells.

Nucleotides are the monomers of nucleic acids, each consisting of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.
DNA is typically double-stranded, with complementary base pairing (A-T, G-C) and a double helix structure.
RNA is usually single-stranded and plays roles in protein synthesis and gene regulation.
Phosphodiester bonds link nucleotides together in a strand.
Base pairing is essential for DNA replication and transcription.

Chapter 5: Carbohydrates

Structure and Function of Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, serving as energy sources and structural components in cells.

Monosaccharides are simple sugars (e.g., glucose, fructose).
Disaccharides are formed by joining two monosaccharides (e.g., sucrose, lactose).
Polysaccharides are long chains of monosaccharides (e.g., starch, glycogen, cellulose).
Glycosidic bonds link monosaccharides in polysaccharides.
Functions: Energy storage (starch in plants, glycogen in animals), structural support (cellulose in plants, chitin in fungi and arthropods).

Chapter 6: Lipids and Membranes

Structure and Function of Lipids

Lipids are hydrophobic molecules that play key roles in energy storage, membrane structure, and signaling.

Fats (triglycerides) are composed of glycerol and three fatty acids. They store energy and provide insulation.
Phospholipids have a hydrophilic head and two hydrophobic tails, forming the basis of cell membranes.
Steroids are lipids with a characteristic four-ring structure (e.g., cholesterol, hormones).
Saturated fatty acids have no double bonds; unsaturated fatty acids have one or more double bonds, affecting membrane fluidity.

Biological Membranes

Cell membranes are composed primarily of a phospholipid bilayer with embedded proteins, cholesterol, and carbohydrates, providing selective permeability and compartmentalization.

Phospholipid bilayer: Hydrophilic heads face outward, hydrophobic tails face inward, creating a semi-permeable barrier.
Membrane proteins include integral (span the membrane) and peripheral (attached to the surface) proteins, each with specific functions (transport, signaling, structural support).
Cholesterol modulates membrane fluidity and stability.
Selective permeability: Only certain molecules can cross the membrane freely; others require transport proteins.

Transport Across Membranes

Cells regulate the movement of substances across membranes through various transport mechanisms.

Passive transport: Movement of molecules down their concentration gradient without energy input (e.g., diffusion, osmosis, facilitated diffusion).
Active transport: Movement of molecules against their concentration gradient, requiring energy (usually ATP).
Example: The sodium-potassium pump actively transports Na+ and K+ ions across the plasma membrane.

Chapter 7: The Cell

Prokaryotic vs. Eukaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on their structural features.

Prokaryotic cells lack a nucleus and membrane-bound organelles; their DNA is located in the nucleoid region (e.g., bacteria, archaea).
Eukaryotic cells have a nucleus and various membrane-bound organelles (e.g., animals, plants, fungi, protists).
Comparison Table:

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	Absent	Present
Organelles	Absent	Present
Size	Small (1-10 μm)	Larger (10-100 μm)
Examples	Bacteria, Archaea	Animals, Plants, Fungi, Protists

Organelles in eukaryotic cells include the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and others, each with specialized functions.

Cellular Transport and Communication

Cells use various mechanisms to transport materials and communicate with their environment and other cells.

Vesicular transport: Endocytosis and exocytosis move large molecules or particles into and out of cells.
Cell signaling: Involves receptors, signal transduction pathways, and cellular responses.

Macromolecules Overview

Comparison of Biological Macromolecules

Biological macromolecules include proteins, nucleic acids, carbohydrates, and lipids, each with distinct monomers, bonds, and functions.

Macromolecule	Monomer	Bond Type	Main Functions
Proteins	Amino acids	Peptide bonds	Catalysis, structure, transport, regulation
Nucleic acids	Nucleotides	Phosphodiester bonds	Genetic information storage and transfer
Carbohydrates	Monosaccharides	Glycosidic bonds	Energy storage, structure
Lipids	Glycerol, fatty acids	Ester bonds	Energy storage, membranes, signaling

Form and function: The structure of each macromolecule is closely related to its biological role.

Additional info: Some explanations and examples were expanded for clarity and completeness based on standard General Biology curriculum.