General Biology: Foundations, Chemistry, Water, and Organic Molecules

Chapter 1: Introduction to Biology and the Scientific Method

Key Concepts in Biology

This chapter introduces the foundational principles of biology, the scientific method, and the characteristics of life. Understanding these basics is essential for further study in biology.

• Terms: Hypothesis, Prediction, Experimental Variables, Control Variables, Constants/Controls, Independent Variable, Dependent Variable, Natural Selection, Adaptation, Descent with Modification, Evolution

• Scientific Method: A systematic approach to inquiry involving observation, hypothesis formation, experimentation, and analysis.

• Experiment: A controlled procedure to test a hypothesis.

• Independent Variable: The variable that is changed or controlled in a scientific experiment.

• Dependent Variable: The variable being tested and measured.

• Properties of Life: Organization, metabolism, homeostasis, growth, reproduction, response to stimuli, and adaptation through evolution.

• Charles Darwin: Developed the theory of evolution by natural selection, explaining how species adapt and change over time.

• Natural Selection: The process by which organisms better adapted to their environment tend to survive and produce more offspring.

Example: Darwin's finches on the Galápagos Islands showed variation in beak shape, which was linked to their food sources, illustrating natural selection.

Chapter 2: Chemistry and Biology

Atoms, Elements, and the Periodic Table

This section covers the basic chemical principles underlying biological processes, including atomic structure, isotopes, and the periodic table.

• Terms: Element, Atom, Subatomic Particle, Proton, Neutron, Electron, Atomic Number, Mass Number, Isotope, Radioactive Isotope, Half-life, Radioactive Dating, Energy, Kinetic Energy, Potential Energy, Valence Shell, Valence Electron, Orbital, Electronegativity, Ion, Cation, Anion

• Atoms: The smallest unit of matter, composed of protons, neutrons, and electrons.

• Elements: Pure substances consisting of only one type of atom, defined by atomic number (number of protons).

• Isotopes: Atoms of the same element with different numbers of neutrons. Radioactive isotopes decay over time and are used in dating fossils and medical imaging.

• Periodic Table: Organizes elements by increasing atomic number and similar chemical properties.

• Valence Electrons: Electrons in the outermost shell, important for chemical bonding.

• Electronegativity: The tendency of an atom to attract electrons in a chemical bond.

Example: Carbon-14 is a radioactive isotope used in radiocarbon dating to determine the age of ancient artifacts.

Chemical Bonds and Molecules

Chemical bonds form when atoms share or transfer electrons, resulting in molecules with unique properties.

• Terms: Chemical Bond, Covalent Bond, Polar Covalent Bond, Nonpolar Covalent Bond, Ionic Bond, Hydrogen Bond, Van der Waals Forces, Hydrophobic Interaction, Reactant, Product, Chemical Reaction, Chemical Equilibrium

• Covalent Bonds: Atoms share electrons; can be polar (unequal sharing) or nonpolar (equal sharing).

• Ionic Bonds: Electrons are transferred from one atom to another, creating charged ions.

• Hydrogen Bonds: Weak attractions between a hydrogen atom and an electronegative atom (e.g., oxygen or nitrogen).

• Van der Waals Forces: Weak, temporary attractions between molecules.

• Chemical Reactions: Processes that change reactants into products; can reach chemical equilibrium when forward and reverse reactions occur at the same rate.

Example: Water molecules are held together by hydrogen bonds, giving water its unique properties.

Chapter 3: Water and Its Properties

Properties and Importance of Water

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

• Terms: Kilocalorie, Joule, Specific Heat, Evaporation, Evaporative Cooling, Hydration Shell, Solution, Solvent, Solute, Aqueous Solution, Hydrophilic, Hydrophobic, Molecular Mass, Molarity, Hydrogen Ion, Hydroxide Ion, Hydronium Ion, Acid, Base, Buffer

• States of Water: Solid (ice), liquid, and gas (vapor).

• Cohesion and Adhesion: Cohesion is the attraction between water molecules; adhesion is the attraction between water and other substances.

• Surface Tension: Water has a high surface tension due to hydrogen bonding.

• Specific Heat: Water can absorb or release large amounts of heat with little temperature change.

• Density: Ice is less dense than liquid water, allowing it to float.

• Solvent Properties: Water dissolves many substances, making it the "universal solvent." Hydrophilic substances dissolve easily; hydrophobic substances do not.

• pH and Buffers: Water can dissociate into hydrogen and hydroxide ions. Buffers help maintain stable pH in biological systems.

Example: The high specific heat of water helps regulate Earth's climate and maintain stable temperatures in organisms.

Chapter 4: Organic Chemistry and Biological Molecules

Carbon Chemistry and Functional Groups

Organic chemistry focuses on carbon-based molecules, which form the backbone of all living organisms. Functional groups determine the properties and reactivity of organic molecules.

• Terms: Organic Chemistry, Hydrocarbon, Fat, Structural Isomers, Cis-trans Isomer, Enantiomer, Functional Group, Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydryl, Phosphate, Methyl

• Carbon: Can form four covalent bonds, allowing for a diversity of stable structures (chains, rings, branches).

• Isomers: Molecules with the same molecular formula but different structures (structural, cis-trans, enantiomers).

• Functional Groups: Specific groups of atoms that confer characteristic chemical properties (e.g., hydroxyl, carboxyl, amino).

• ATP (Adenosine Triphosphate): The primary energy carrier in cells. ATP stores energy in its phosphate bonds and releases it during hydrolysis.

Example: The amino group (-NH2) is found in amino acids, which are the building blocks of proteins.

Biological Molecules and Their Functions

Biological molecules such as carbohydrates, lipids, proteins, and nucleic acids are essential for life. Their structure and function are determined by the arrangement of carbon and functional groups.

• Carbohydrates: Provide energy and structural support (e.g., glucose, starch, cellulose).

• Lipids: Store energy, form cell membranes, and act as signaling molecules (e.g., fats, phospholipids, steroids).

• Proteins: Perform a wide range of functions, including catalysis (enzymes), transport, and structural support.

• Nucleic Acids: Store and transmit genetic information (DNA, RNA).

Example: Enzymes are proteins that speed up chemical reactions in the body.

Table: Major Functional Groups in Organic Molecules

This table summarizes the main functional groups, their structure, and their properties.

Functional Group	Structure	Properties	Example
Hydroxyl	-OH	Polar, forms hydrogen bonds	Alcohols (e.g., ethanol)
Carbonyl	>C=O	Polar, found in sugars	Aldehydes, ketones
Carboxyl	-COOH	Acidic, donates H+	Amino acids, fatty acids
Amino	-NH2	Basic, accepts H+	Amino acids
Sulfhydryl	-SH	Forms disulfide bonds	Proteins
Phosphate	-PO4	Negative charge, energy transfer	ATP, nucleic acids
Methyl	-CH3	Nonpolar, affects gene expression	DNA, lipids

Additional info:

• ATP hydrolysis releases energy according to the equation: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

• pH is calculated as: $\text{pH} = -\log_{10}[\text{H}^+]$