Essential Chemistry for Biology

Matter: Elements and Compounds

All living things are composed of matter, which exists in the form of elements and compounds. Understanding the chemical basis of life is essential for studying biology.

• Element: A substance that cannot be broken down into other substances by chemical means. Examples include carbon (C), hydrogen (H), and oxygen (O).

• Compound: A substance consisting of two or more elements combined in a fixed ratio. Example: Water (H2O).

Atoms

Atoms are the smallest units of matter that retain the properties of an element.

• Structure: Atoms consist of a nucleus (protons and neutrons) and electrons orbiting the nucleus.

• Atomic Number: Number of protons in an atom.

• Mass Number: Sum of protons and neutrons.

Chemical Bonding

Atoms combine through chemical bonds to form molecules and compounds.

• Covalent Bonds: Atoms share electrons (e.g., H2O).

• Ionic Bonds: Electrons are transferred from one atom to another, creating charged ions (e.g., NaCl).

• Hydrogen Bonds: Weak attractions between polar molecules, important in water and DNA structure.

Water and Life; Acids, Bases, and pH

Water is vital for life due to its unique properties, and the pH scale measures the acidity or basicity of solutions.

• Properties of Water: Cohesion, adhesion, high specific heat, solvent abilities.

• Acid: Substance that increases H+ concentration in solution.

• Base: Substance that decreases H+ concentration.

• pH Scale: Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral.

Example: Human blood has a pH around 7.4, maintained by buffers.

The Molecules of Life

Carbon Chemistry; Giant Molecules from Smaller Building Blocks

Carbon's ability to form four covalent bonds makes it the backbone of biological molecules.

• Macromolecules: Large molecules built from smaller units (monomers).

• Polymerization: Process of linking monomers to form polymers.

Carbohydrates

Carbohydrates are energy sources and structural materials.

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

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

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

Lipids

Lipids are hydrophobic molecules important for energy storage and membrane structure.

• Fats: Glycerol + fatty acids; store energy.

• Phospholipids: Major component of cell membranes.

• Steroids: Four fused rings (e.g., cholesterol, hormones).

Proteins

Proteins perform a wide range of functions, including catalysis, structure, and transport.

• Amino Acids: Building blocks of proteins (20 types).

• Polypeptides: Chains of amino acids folded into specific shapes.

• Enzymes: Proteins that speed up chemical reactions.

Nucleic Acids

Nucleic acids store and transmit genetic information.

• DNA (Deoxyribonucleic Acid): Stores genetic instructions.

• RNA (Ribonucleic Acid): Involved in protein synthesis.

• Nucleotides: Monomers of nucleic acids (sugar, phosphate, base).

A Tour of the Cell

Microscopes

Microscopes are essential tools for studying cells.

• Light Microscopes: Use light to view living cells.

• Electron Microscopes: Use electrons for higher resolution (TEM, SEM).

The Two Major Categories of Cells

Cells are classified as prokaryotic or eukaryotic.

• Prokaryotic Cells: Lack a nucleus; found in bacteria and archaea.

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles; found in plants, animals, fungi, and protists.

An Overview of Eukaryotic Cells

Eukaryotic cells contain specialized organelles for various functions.

• Nucleus: Contains genetic material (DNA).

• Endoplasmic Reticulum (ER): Synthesis of proteins (rough ER) and lipids (smooth ER).

• Golgi Apparatus: Modifies and ships proteins.

• Lysosomes: Digestion and waste removal.

• Vacuoles: Storage (large in plant cells).

Membrane Structure

The plasma membrane controls the movement of substances in and out of the cell.

• Phospholipid Bilayer: Double layer with hydrophilic heads and hydrophobic tails.

• Proteins: Embedded for transport, signaling, and structure.

The Endomembrane System

This system includes organelles that work together to modify, package, and transport lipids and proteins.

• Includes the nuclear envelope, ER, Golgi apparatus, lysosomes, and vesicles.

Chloroplasts and Mitochondria

These organelles are involved in energy conversion.

• Chloroplasts: Site of photosynthesis in plants and algae.

• Mitochondria: Site of cellular respiration in all eukaryotes.

The Working Cell

Conservation of Energy, Entropy, and Chemical Energy

Cells obey the laws of thermodynamics in energy transformations.

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Every energy transfer increases entropy (disorder).

• Chemical Energy: Stored in the bonds of molecules.

ATP

ATP (adenosine triphosphate) is the main energy currency of the cell.

• ATP stores energy in its phosphate bonds.

• Hydrolysis of ATP releases energy for cellular work.

Equation:

Enzymes

Enzymes are biological catalysts that speed up chemical reactions without being consumed.

• Lower activation energy required for reactions.

• Highly specific for their substrates.

Membrane Function

Cell membranes regulate the passage of materials.

• Passive Transport: Diffusion and facilitated diffusion (no energy required).

• Active Transport: Movement against concentration gradient (requires energy).

Osmosis and Water Balance

Osmosis is the diffusion of water across a selectively permeable membrane.

• Water moves from areas of low solute concentration to high solute concentration.

• Cells must regulate water balance to prevent lysis or shrinkage.

Cellular Respiration

Energy Flow and Chemical Cycling in the Biosphere

Energy flows through ecosystems, while chemicals are recycled.

• Producers convert solar energy to chemical energy.

• Consumers obtain energy by eating other organisms.

Cellular Respiration: Equation and the Role of Oxygen

Cellular respiration releases energy from glucose in the presence of oxygen.

Equation:

• Oxygen acts as the final electron acceptor in the electron transport chain.

Cellular Respiration - An Overview

Cellular respiration consists of multiple stages to efficiently extract energy from food.

• Occurs in both cytoplasm and mitochondria.

Cellular Respiration - The Three Stages

• Glycolysis: Occurs in cytoplasm; breaks glucose into pyruvate.

• Krebs Cycle (Citric Acid Cycle): Occurs in mitochondria; completes breakdown of glucose.

• Electron Transport Chain: Produces most ATP; requires oxygen.

Fermentation

Fermentation allows cells to produce ATP without oxygen.

• Lactic Acid Fermentation: Occurs in muscle cells; produces lactic acid.

• Alcoholic Fermentation: Occurs in yeast; produces ethanol and CO2.

Photosynthesis

The Basics of Photosynthesis

Photosynthesis converts solar energy into chemical energy in plants, algae, and some bacteria.

• Occurs in chloroplasts.

An Overview of Photosynthesis

Photosynthesis consists of two main stages: the light reactions and the Calvin cycle.

Equation:

The Light Reactions

Light reactions capture solar energy and convert it to chemical energy (ATP and NADPH).

• Occur in the thylakoid membranes of chloroplasts.

• Produce O2 as a byproduct.

The Calvin Cycle

The Calvin cycle uses ATP and NADPH to convert CO2 into glucose.

• Occurs in the stroma of chloroplasts.

• Does not require light directly ("dark reactions").

Example: Plants use photosynthesis to produce the glucose needed for cellular respiration.

Additional info: These notes provide foundational concepts for a General Biology midterm, covering essential chemistry, biomolecules, cell structure and function, energy transformations, cellular respiration, and photosynthesis. Students should understand definitions, processes, and the significance of each topic for living organisms.