General Biology: Foundations, Chemistry, and Molecules of Life

Life and the Scientific Method

Properties of Living Organisms

Living organisms share several key characteristics that distinguish them from non-living matter.

• Order: Organisms have organized structures and systems, allowing for repair and maintenance.

• Reproduction: Ability to produce offspring, ensuring species survival.

• Growth and Development: Organisms grow and develop according to specific instructions coded in their DNA.

• Response to Environment: Ability to sense and respond to stimuli.

• Energy Processing: Organisms take in energy (e.g., food) and release waste.

• Regulation: Maintenance of internal stability (homeostasis).

• Evolutionary Adaptation: Populations evolve over generations to adapt to their environment.

Viruses and Life

Viruses are not considered living organisms because they cannot reproduce or process energy independently; they require a host cell.

The Three Domains of Life

All living organisms are classified into three domains based on molecular and cellular differences.

• Bacteria: Domain Bacteria

• Archaea: Domain Archaea

• Eukarya: Domain Eukarya (includes Animals, Fungi, Protists, Plants)

Levels of Biological Study

Biology can be studied at various levels, from biosphere to molecular.

The Scientific Method

The scientific method is a systematic approach to understanding natural phenomena.

• Hypothesis: A proposed explanation for a set of observations. Must be testable and falsifiable.

• Theory: A well-substantiated explanation that is comprehensive and predictive.

• Fact: A verifiable piece of information that is objectively true.

Example: Termite Study

• Hypothesis: Termites are drawn to ink because it is a similar color to other markers.

• Test: Use different colored markers to observe termite behavior.

Characteristics of a Good Experiment

• Change only one variable at a time (independent variable).

• Dependent variable: the outcome measured.

• Use large sample sizes and repeatable methods.

Graphs: Representing and Interpreting Data

• Components: Title, axes (X: independent variable, Y: dependent variable), labels, units.

• Line Graphs: Show data over a range (e.g., temperature over time).

• Scatter Plots: Relate two variables to show positive or negative relationships.

• Bar Graphs: Compare results for qualitative variables.

Statistics: P-Values

• Null Hypothesis (H0): No real difference between populations.

• Alternative Hypothesis (HA): There is a real difference.

• P-value: Probability of obtaining a result as extreme as observed, assuming H0 is true. If $p < 0.05$, results are statistically significant.

Chemistry Basics

Compounds and Elements

Compounds are molecules made up of two or more elements. Essential elements are required for life.

• Big 4 Elements: Oxygen, Carbon, Hydrogen, Nitrogen

• Trace Elements: Required in small amounts (e.g., Fluorine, Iron, Boron, Chromium, Copper, Zinc)

Atoms

• Atomic Number: Number of protons

• Mass Number: Number of protons + neutrons

• Isotopes: Atoms of the same element with different numbers of neutrons

Radioactive Isotopes

• Used in medical imaging (e.g., PET scans)

Electron Distribution and Chemical Bonds

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

• Covalent Bonds: Atoms share electrons.

• Polar Covalent Bonds: Electrons are shared unequally due to differences in electronegativity (e.g., H2O).

• Nonpolar Covalent Bonds: Electrons are shared equally (e.g., CH4).

• Ionic Bonds: Electrons are transferred from one atom to another.

Intermolecular Interactions

• Weak interactions between molecules (e.g., hydrogen bonds between water molecules).

Chemistry of Water

Cohesion and Adhesion

Water molecules interact through hydrogen bonding, leading to unique properties.

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other surfaces.

• Creates high surface tension (e.g., bugs walking on water).

Thermal Regulation

• Water has a high specific heat due to hydrogen bonding.

• Helps regulate temperature in organisms and environments.

• Sweating: Energy is used to break hydrogen bonds, cooling the body.

Floating Solid Phase

• Ice is less dense than liquid water due to crystal structure.

• Allows aquatic life to survive under ice in winter.

Water as a Solvent

• Solution: Homogeneous mixture of two or more substances.

• Aqueous Solution: Water-based solution (e.g., saltwater).

• Solvent: Substance that dissolves other substances.

• Solute: Substance that is dissolved.

Acidic and Basic Solutions

• pH: Measure of H+ concentration in a solution. $pH = -\log[H^+]$

• Low pH = high acidity; high pH = basic.

• Biological molecules can be affected by changes in pH.

• Buffers: Help stabilize pH in solutions.

pH Balance in Aquatic Ecosystems

• Carbonate concentration affects coral calcification rates.

Chemistry of Carbon

Organic Molecules

Carbon is the backbone of organic molecules due to its ability to form four covalent bonds.

• Can form chains, branches, rings, double bonds.

• Hydrocarbons: simplest organic molecules (e.g., CH4).

Isomers

• Compounds with the same formula but different structures.

• Structural Isomers: Different covalent arrangements.

• Geometric Isomers: Different spatial arrangements (cis/trans).

• Enantiomers: Mirror images, non-superimposable.

Functional Groups

• Specific groupings of atoms that confer particular properties.

• Hydroxyl (-OH): Alcohols

• Carboxyl (-COOH): Acids

• Carbonyl (C=O): Ketones, aldehydes

• Amino (-NH2): Amines

• Phosphate (-PO4): Energy transfer

• Methyl (-CH3): Nonpolar

Polymers and Monomers

• Polymer: Chain of smaller subunits (monomers).

• Dehydration Reaction: Forms polymers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Thalidomide Example

• Enantiomers can have different biological effects.

• Thalidomide: C13H10N2O4

Molecules of Life

Carbohydrates

Carbohydrates are energy sources and structural components.

• Monomer: Monosaccharide (simple sugar)

• Polymer: Polysaccharide (e.g., starch, cellulose, glycogen)

• Glycosidic Linkage: Bond between two monosaccharides

• Probiotics: Live bacteria and yeasts beneficial to health

Lipids

Lipids are hydrophobic molecules, including fats, oils, and steroids.

• Fats: Large lipid molecules composed of glycerol and three fatty acids

• Ester Linkage: Bond formed by dehydration between glycerol and fatty acids

• Saturated Fat: No double bonds, solid at room temperature

• Unsaturated Fat: One or more double bonds, liquid at room temperature

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; amphipathic

• Steroids: Carbon skeleton with four fused rings (e.g., cholesterol, hormones)

Proteins

Proteins perform many cellular functions and are composed of amino acids.

• Monomer: Amino acid

• Polymer: Polypeptide (protein)

• Peptide Bond: Covalent bond between amino acids

Protein Structure

• Primary: Sequence of amino acids

• Secondary: Alpha helix and beta sheet, stabilized by hydrogen bonds

• Tertiary: 3D shape, stabilized by R group interactions

• Quaternary: Multiple polypeptides assembled together

Denaturation

• Loss of protein structure due to heat, chemicals, or salt concentration

Nucleic Acids

Nucleic acids store and transmit genetic information.

• Monomer: Nucleotide (sugar, phosphate, nitrogenous base)

• Polymer: DNA and RNA

• Phosphodiester Bond: Links nucleotides in a chain

• DNA: Double helix, two strands held by hydrogen bonds (A-T, C-G)

• RNA: Single-stranded

Gene Expression

• Gene (DNA) → Transcription (RNA copy) → Translation (Protein)

HTML Table: Comparison of Major Biological Molecules

Type	Monomer	Polymer	Bond Type	Main Function
Carbohydrate	Monosaccharide	Polysaccharide	Glycosidic linkage	Energy, structure
Lipid	Fatty acid, glycerol	Triglyceride, phospholipid	Ester linkage	Energy storage, membranes
Protein	Amino acid	Polypeptide	Peptide bond	Catalysis, structure, transport
Nucleic Acid	Nucleotide	DNA, RNA	Phosphodiester bond	Genetic information

Additional info: Academic context and definitions have been expanded for clarity and completeness. Table entries and some explanations have been logically inferred and supplemented for a self-contained study guide.