General Biology Study Guide: Chemistry Essentials, Biological Molecules, and Cell Structure

Chemistry Essentials

Atoms and Atomic Structure

Understanding atoms is fundamental to biology, as all matter is composed of atoms. This section covers the structure, properties, and organization of atoms.

• Atomic Structure: Atoms consist of subatomic particles: protons (positive charge), neutrons (neutral), and electrons (negative charge). The atomic number equals the number of protons, and the mass number is the sum of protons and neutrons.

• Isotopes: Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers.

• Electron Configuration: Electrons are arranged in shells around the nucleus. The arrangement affects chemical reactivity and bonding.

• Periodic Table: Elements are organized by increasing atomic number. Groups (columns) share similar chemical properties due to valence electrons.

• Valence Electrons: The electrons in the outermost shell determine how atoms interact and bond with each other.

Example: Carbon has 6 protons, 6 neutrons (in its most common isotope), and 6 electrons. Its atomic number is 6, and its mass number is 12.

Chemical Bonds

Chemical bonds hold atoms together in molecules and compounds. The type of bond affects the properties of the substance.

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent Bonds: Formed when atoms share pairs of electrons. These bonds can be single, double, or triple.

• Polar Covalent Bonds: Electrons are shared unequally, creating partial charges within the molecule.

• Hydrogen Bonds: Weak attractions between a hydrogen atom (attached to a highly electronegative atom like oxygen or nitrogen) and another electronegative atom.

Example: Table salt (NaCl) is formed by ionic bonding between sodium and chloride ions.

Polarity and Polar Bonds (Hydrogen Bonds)

Polarity refers to the distribution of electrical charge over atoms in a molecule. Polar molecules have regions of partial positive and negative charge.

• Electronegativity: The tendency of an atom to attract electrons. Differences in electronegativity lead to polar covalent bonds.

• Hydrogen Bonds: Important in water, DNA, and proteins. They contribute to the unique properties of water, such as cohesion and adhesion.

Example: Water ($H_2O$) is a polar molecule; hydrogen bonds between water molecules give it high surface tension.

Chemistry of Biological Molecules

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

• Common Functional Groups: Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), and methyl (-CH3).

• Functional groups are key to the structure and function of biological molecules.

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined together (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, cellulose, glycogen).

• Hydrolysis and Dehydration Reactions: Hydrolysis breaks polymers into monomers by adding water; dehydration synthesis joins monomers by removing water.

Example: Starch is a polysaccharide used by plants for energy storage.

Lipids

Lipids are hydrophobic molecules, including fats, oils, and steroids. They are important for energy storage, membrane structure, and signaling.

• Fatty Acids: Long hydrocarbon chains with a carboxyl group. Saturated fatty acids have no double bonds; unsaturated have one or more double bonds.

• Triglycerides: Composed of three fatty acids and one glycerol molecule.

• Steroids: Lipids with a four-ring structure (e.g., cholesterol).

• Phospholipids: Major component of cell membranes, with hydrophilic heads and hydrophobic tails.

Example: Phospholipids form the bilayer of cell membranes.

Proteins

Proteins are polymers of amino acids and perform a wide variety of functions in cells.

• Amino Acids: Building blocks of proteins, each with a central carbon, amino group, carboxyl group, and side chain (R group).

• Peptide Bonds: Covalent bonds joining amino acids in a protein.

• Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Local folding (alpha helices, beta sheets).

  • Tertiary: Overall 3D shape.

  • Quaternary: Association of multiple polypeptide chains.

Example: Hemoglobin is a protein with quaternary structure, composed of four polypeptide chains.

The Cell Part I: Cell Membranes and Material Transport

Cell Membranes

Cell membranes are composed of a phospholipid bilayer with embedded proteins, providing structure and regulating transport.

• Membrane Proteins: Serve as channels, receptors, enzymes, and structural components.

• Selective Permeability: Membranes allow certain substances to pass while blocking others.

• Fluid Mosaic Model: Describes the dynamic arrangement of lipids and proteins in the membrane.

Material Transport

Cells transport materials across membranes by passive and active mechanisms.

• Passive Transport: Movement of substances down their concentration gradient (e.g., diffusion, osmosis).

• Active Transport: Movement against the gradient, requiring energy (ATP).

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Thermodynamics: Transport is influenced by energy changes (Second Law of Thermodynamics).

Example: Sodium-potassium pump uses ATP to move Na+ and K+ ions across the membrane.

The Cell Part II: Cell Structures, Types, and Functions

Cell Types

Cells are classified as prokaryotic or eukaryotic based on their structure.

• Prokaryotic Cells: Lack a nucleus and membrane-bound organelles (e.g., bacteria).

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles (e.g., plants, animals, fungi).

Cell Organelles

Organelles are specialized structures within eukaryotic cells that perform specific functions.

Organelle	Function
Cytoplasm	Gel-like substance where cellular processes occur
Mitochondria	Site of cellular respiration and energy (ATP) production
Nucleus	Contains genetic material (DNA); controls cell activities
Rough ER	Protein synthesis and processing
Golgi Apparatus	Modifies, sorts, and packages proteins and lipids
Endomembrane System	Network of membranes involved in transport within the cell
Ribosomes	Protein synthesis
Vacuoles	Storage of substances; large central vacuole in plant cells
Chloroplasts (plants)	Site of photosynthesis

Example: The mitochondria are often called the "powerhouse" of the cell because they generate ATP.

Additional info: Some details about the fluid mosaic model, the sodium-potassium pump, and the classification of organelles were inferred for completeness and clarity.