General Biology: Foundations, Chemistry of Life, and Biological Macromolecules

Chapter 1: Introduction – Evolution and the Foundations of Biology

1. The 8 Characteristics of Living Organisms

To be considered "alive," an organism must typically exhibit all eight of the following traits:

• D – DNA: All living things contain genetic material (DNA or RNA) that stores the instructions for building and operating the organism.

• O – Organization: Living things have a specific organization of cells, tissues, and organs.

• G – Growth and Development: Living things grow and develop according to instructions coded in their DNA.

• R – Reproduction: Living things can produce offspring, either sexually (two parents) or asexually (one parent).

• A – Adaptation (Evolution): Over many generations, populations of living things change to better survive in their environments.

• C – Cells: The cell is the fundamental building block of life. An organism can be unicellular (one cell) or multicellular (many cells).

• E – Energy Use: All living things must obtain and use energy to power their biological processes. This is also called metabolism.

• R – Response to Environment: Living things respond to changes in their environment, such as a plant growing toward light or a human pulling the hand away from a hot stove.

2. The Cell: The Fundamental Unit of Life

The cell is the smallest level of organization that can perform all the functions of life. Even a single cell can grow, reproduce, and maintain homeostasis.

3. Evolution: Unity and Diversity

Evolution explains both the similarities and differences among living things:

• Unity: All living things share certain features (like DNA) because they are descended from a common ancestor.

• Diversity: As species adapt to different environments, they evolve unique traits, leading to the diversity of life.

4. The 5 Unifying Themes in Biology

• Organization: Life is organized into a hierarchy, from atoms and cells to ecosystems.

• Information: Genetic information (DNA) acts as a "blueprint" for building and running an organism.

• Energy and Matter: Life requires energy (like sunlight) and matter (like nutrients) to survive.

• Interactions: All forms of life interact with their environment and other organisms.

• Evolution: Explains how life changes over time and creates the diversity of the world.

5. Steps of the Scientific Method

1. Observation: Noticing something interesting.

2. Question: Asking a scientific question about it.

3. Hypothesis: Proposing a testable explanation.

4. Prediction: Making a prediction based on the hypothesis.

5. Experiment: Testing the hypothesis with an experiment.

6. Analysis: Looking at the data to see if the hypothesis was right or wrong.

6. Inductive vs. Deductive Reasoning

• Inductive (Specific → General): Using specific examples to create a general rule. Example: "Every swan I have ever seen is white. Therefore, all swans are white."

• Deductive (General → Specific): Using a general rule and applying it to a specific case. Example: "All mammals have hair. This animal is a mammal, so it must have hair."

7. Variables: Independent vs. Dependent

• Independent Variable: The thing you change on purpose (e.g., the amount of water given to a plant).

• Dependent Variable: The thing you measure (e.g., how tall the plant grows). Its value "depends" on what you did to the independent variable.

8. Control Group vs. Test Group

• Test (Experimental) Group: Gets the special treatment (the independent variable).

• Control Group: Stays under "normal" conditions for comparison.

9. Observation vs. Experimentation

• Observation: Simply watching and recording what happens naturally.

• Experimentation: Actively changing one thing (a variable) to see what happens.

10. Evolution and Natural Selection

• Evolution: The change in traits of a population over time.

• Natural Selection: The process by which individuals with the best traits for survival reproduce more, passing on those traits. Over many generations, this leads to evolution.

Chapter 2: The Chemical Context of Life

1. Atoms: Structure; Protons, Neutrons, and Electrons

Atoms are the basic units of matter, composed of:

• Protons: Located in the nucleus; positive charge.

• Neutrons: Located in the nucleus; no charge (neutral).

• Electrons: Orbit the nucleus in shells; negative charge.

2. Atoms, Elements, Molecules, and Compounds

• Atom: The smallest unit of matter.

• Element: A pure substance made of only one type of atom (e.g., gold).

• Compound: A substance made of atoms of different elements (e.g., H2O).

Predicting Charge: To find the charge, subtract electrons from protons. Proton (+1) + Electron (-1) = Total Charge

3. The Periodic Table & Calculations

• Atomic Number: Number of protons (defines the element).

• Mass Number: Protons + Neutrons.

• Electrons: In a neutral atom, number of electrons equals number of protons.

4. Valence Electrons and Bonding

Valence electrons are found in the outermost shell. Atoms "want" a full outer shell and will form chemical bonds to achieve this.

5. Covalent Bonds: Polar vs. Nonpolar

• Nonpolar: Electrons are shared equally.

• Polar: Electrons are shared unequally, creating slight positive and negative poles.

6. Ionic Bonds

Ionic bonds form when one atom steals an electron from another, creating ions with opposite charges that attract each other.

7. The Polar Nature of Water

Water (H2O) is a polar molecule. Oxygen is highly electronegative, pulling shared electrons closer and making the oxygen end slightly negative and the hydrogen ends slightly positive.

8. Hydrophilic vs. Hydrophobic

• Hydrophilic: Substances that mix well with water (charged or polar).

• Hydrophobic: Substances that do not mix well with water (nonpolar).

9. Hydrogen Bonds and Water's Properties

• Hydrogen Bond: A weak bond between a hydrogen atom and an electronegative atom (like oxygen).

• Polar Covalent Bond: Holds the atoms of a water molecule together.

• Hydrogen Bond: Holds water molecules to each other.

10. Emergent Properties of Water

• Cohesion: Water molecules stick together (surface tension).

• Adhesion: Water molecules stick to other substances (capillary action).

• Temperature Moderation: Water resists temperature changes (high specific heat).

• Universal Solvent: Water dissolves almost anything with a charge.

11. pH Scale and Hydrogen Ions (H+)

The pH scale measures the concentration of hydrogen ions in a solution:

• Acids (pH 0–6): High concentration of H+.

• Bases (pH 8–14): Low concentration of H+ (and more OH- ions).

• Neutral (pH 7): Equal concentrations of H+ and OH-.

Note: Each step on the pH scale is a 10-fold difference.

Chapter 3: Carbon and the Molecular Diversity of Life

1. Carbon: The Backbone of Life

Carbon has four valence electrons, allowing it to form four covalent bonds with other atoms. This enables carbon to create complex, branched, and ring-shaped molecules.

2. The Building Blocks of Life

Biological macromolecules are often polymers made of smaller units called monomers.

Macromolecule	Monomer	Main Functions
Carbohydrates	Monosaccharides	Short-term energy, structure
Lipids	Glycerol & Fatty Acids	Long-term energy, membranes
Proteins	Amino Acids	Enzymes, structure, transport, defense
Nucleic Acids	Nucleotides	Storing and transmitting genetic info

Additional info: Lipids are not true polymers but are built from smaller building blocks.

3. Dehydration Synthesis vs. Hydrolysis

• Dehydration Synthesis: Building a polymer by removing a water molecule to join monomers.

• Hydrolysis: Breaking down a polymer by adding water to break the bond between monomers.

4. Carbohydrates

• Simple Sugars (Monosaccharides): Single sugar molecules like glucose.

• Complex Carbohydrates (Polysaccharides): Long chains of sugars (e.g., starch in plants, glycogen in animals).

• Structural Carbohydrates: Cellulose (plant cell walls), chitin (fungi/insects).

5. Lipids

• Hydrophobic: Lipids do not mix with water due to nonpolar hydrocarbon chains.

• Structure: Triglycerides consist of one glycerol and three fatty acids.

• Saturated Fats: No double bonds; solid at room temperature.

• Unsaturated Fats: One or more double bonds; liquid at room temperature.

6. Proteins

Proteins are made of amino acids joined by peptide bonds. Each amino acid has:

• Amino group (NH2)

• Carboxyl group (COOH)

• Hydrogen atom

• R group (side chain) – determines properties

The 4 Levels of Protein Structure:

1. Primary: Unique sequence of amino acids

2. Secondary: Coils (α-helix) and folds (β-pleated sheet) due to hydrogen bonding

3. Tertiary: 3D shape due to R-group interactions

4. Quaternary: Multiple polypeptide chains join together (e.g., hemoglobin)

7. Nucleic Acids

Nucleic acids (DNA and RNA) are made of nucleotides, each with:

• 5-carbon sugar (deoxyribose in DNA, ribose in RNA)

• Phosphate group

• Nitrogenous base

Key Differences:

• DNA: Double-stranded, bases are A, T, C, G; sugar is deoxyribose

• RNA: Single-stranded, bases are A, U, C, G; sugar is ribose