Chemical Foundations and Cell Structure: Study Notes for Introductory Biology

Chapter 2: Chemical Context of Life

Elements and Compounds

Matter is composed of chemical elements, which can exist in pure form or combine to form compounds. Understanding the nature of elements and compounds is fundamental to biology.

• Element: A substance that cannot be broken down into other substances by chemical means. There are 92 naturally occurring elements.

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

• Trace Elements: Elements required by an organism in only minute quantities (e.g., iron, iodine).

Atomic Structure

The properties of elements are determined by the structure of their atoms.

• Subatomic Particles: Atoms are composed of neutrons (neutral), protons (positive), and electrons (negative).

• Atomic Number: Number of protons in the nucleus; defines the element.

• Atomic Mass: Sum of protons and neutrons in the nucleus.

• Isotopes: Atoms of the same element with different numbers of neutrons. Radioactive isotopes are unstable and decay over time, emitting radiation.

Energy Levels and Electron Arrangement

Electrons occupy energy levels (shells) around the nucleus, influencing chemical behavior.

• Potential Energy: Energy stored due to position or structure.

• Kinetic Energy: Energy of motion.

• Valence Electrons: Electrons in the outermost shell; determine chemical reactivity.

• Orbitals: Regions where electrons are likely to be found.

Chemical Bonds

Atoms form molecules through chemical bonds, which are essential for biological structure and function.

• Covalent Bonds: Atoms share electrons. Can be single, double, non-polar (equal sharing), or polar (unequal sharing).

• Ionic Bonds: Electrons are transferred from one atom to another, forming charged ions (cation = positive, anion = negative).

• Weak Chemical Bonds: Include hydrogen bonds (attraction between a hydrogen atom and an electronegative atom) and van der Waals interactions (weak attractions due to transient charges).

• Molecular Shape: The shape of a molecule determines its function in biological systems.

Chemical Reactions

Chemical reactions involve making and breaking bonds, transforming reactants into products.

• Reactant: Starting material in a reaction.

• Product: Substance formed from a reaction.

• Chemical Equilibrium: The point at which the forward and reverse reactions occur at the same rate.

• Example Equation:

$\mathrm{C_6H_{12}O_6 + O_2 \rightleftharpoons CO_2 + H_2O}$

Chapter 3: Water and Life

Structure and Properties of Water

Water's unique properties arise from its polar covalent bonds and ability to form hydrogen bonds.

• Polarity: Oxygen is more electronegative than hydrogen, creating a partial negative charge near oxygen and partial positive near hydrogens.

• Hydrogen Bonding: Attraction between the hydrogen of one water molecule and the oxygen of another.

Emergent Properties of Water

Water's properties make Earth suitable for life.

• Cohesion: Water molecules stick together due to hydrogen bonding, leading to high surface tension.

• Moderation of Temperature: Water absorbs and releases heat with minimal temperature change due to high specific heat. Calorie: The amount of heat needed to raise 1g of water by 1°C.

• Evaporative Cooling: As water evaporates, it removes heat from surfaces. Heat of vaporization is the energy required to convert liquid to gas.

• Density Differences: Water is less dense as a solid (ice) than as a liquid, allowing ice to float.

• Solvent Properties: Water dissolves many substances due to its polarity. Hydrophilic substances dissolve easily; hydrophobic substances do not.

Acids, Bases, and pH

Acidic and basic conditions affect living organisms.

• Acid: Increases hydrogen ion (H+) concentration in solution.

• Base: Reduces hydrogen ion concentration, often by increasing hydroxide ions (OH-).

• pH Scale: Measures hydrogen ion concentration; ranges from 0 (acidic) to 14 (basic), with 7 as neutral.

• Buffer: Substance that minimizes changes in pH by accepting or donating H+ ions.

Chapter 4: Carbon and the Molecular Diversity of Life

Carbon: The Backbone of Life

Carbon's ability to form four covalent bonds makes it uniquely suited to form diverse organic molecules.

• Major Elements of Life: C, H, O, N, S, P are found in similar proportions in all organisms.

• Miller Experiment: Demonstrated that organic molecules could form under early Earth conditions, supporting the idea of abiotic synthesis of life's building blocks.

Molecular Diversity from Carbon Skeletons

• Variation in Carbon Skeletons: Length, branching, double bond position, and ring structures contribute to molecular diversity.

• Hydrocarbons: Molecules consisting only of carbon and hydrogen; serve as energy sources.

• Isomers: Compounds with the same formula but different structures.

  • Structural Isomers: Differ in covalent arrangement.

  • Cis-Trans Isomers: Differ in spatial arrangement around double bonds.

  • Enantiomers: Mirror images due to asymmetric carbon.

Functional Groups

Certain chemical groups are key to molecular function.

• Functional Groups: Seven groups are most important: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.

• ATP (Adenosine Triphosphate): Main energy currency of the cell. When ATP is hydrolyzed, it releases energy and forms ADP (adenosine diphosphate) and inorganic phosphate.

Chapter 5: The Structure and Function of Large Biological Molecules

Macromolecules: Polymers and Monomers

Large biological molecules (macromolecules) are polymers built from monomers. Their synthesis and breakdown are essential for life.

• Enzymes: Proteins that catalyze chemical reactions, including the synthesis and hydrolysis of polymers.

• Dehydration Synthesis: Monomers are joined by removing water; one product is always water.

• Hydrolysis: Polymers are broken down by adding water.

Types of Macromolecules

• Carbohydrates: Serve as fuel and building material.

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

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

  • Polysaccharides: Many monosaccharides (e.g., starch, cellulose, glycogen, chitin).

• Lipids: Hydrophobic molecules including fats, phospholipids, and steroids.

  • Fats (Triglycerides): Glycerol + 3 fatty acids. Can be saturated (no double bonds) or unsaturated (one or more double bonds).

  • Phospholipids: Major component of cell membranes; have hydrophilic heads and hydrophobic tails.

  • Steroids: Lipids with four fused rings (e.g., cholesterol).

• Proteins: Polymers of amino acids; diverse in structure and function.

  • Polypeptides: Chains of amino acids.

  • Protein Structure: Four levels—primary (sequence), secondary (alpha helix, beta sheet), tertiary (3D folding), quaternary (multiple polypeptides).

  • Protein Folding: Assisted by chaperonins; environment affects folding.

• Nucleic Acids: DNA and RNA store and transmit genetic information; ATP is an energy carrier.

  • Building Blocks: Sugar (deoxyribose or ribose), phosphate group, nitrogenous base (purine or pyrimidine).

  • Genomics and Proteomics: Study of genomes and proteins, respectively.

Chapter 6: A Tour of the Cell

Studying Cells

Cells are studied using various microscopy techniques and cell fractionation.

• Microscopy: Includes light, electron, and confocal microscopy for visualizing cell structures.

• Cell Fractionation: Separates cellular components for study.

Cell Types and Organization

• Prokaryotic vs. Eukaryotic Cells: Eukaryotes have internal membranes and organelles; prokaryotes do not.

• Surface Area: Limits cell size; larger cells have less surface area relative to volume.

• Mitochondria and Chloroplasts: Eukaryotes have mitochondria; plants and algae also have chloroplasts.

Genetic Information and Protein Synthesis

• Nucleus: Houses genetic material (DNA).

• Ribosomes: Sites of protein synthesis; found in cytoplasm and on rough ER.

Endomembrane System

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

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.

• Lysosomes: Digestive organelles; break down macromolecules.

• Vacuoles: Storage and structural support (especially in plants).

Energy Conversion Organelles

• Mitochondria: Site of cellular respiration; converts glucose to ATP.

• Chloroplasts: Site of photosynthesis in plants and algae.

• Peroxisomes: Break down fatty acids and detoxify harmful substances.

Cytoskeleton

• Structure: Network of fibers (microtubules, microfilaments, intermediate filaments) that support cell shape, movement, and division.

• Motility and Signal Transduction: Cytoskeleton aids in cell movement and communication.

Extracellular Components and Cell Connections

• Cellulose: Main component of plant cell walls; provides structural support.

• Extracellular Matrix (ECM): In animals, composed of glycoproteins and proteoglycans; supports, adheres, and regulates cells.

• Cell Junctions:

  • Plants: Plasmodesmata connect cells.

  • Animals: Tight junctions (seal cells), desmosomes (anchor cells), gap junctions (communicate between cells).