BIO 101 Exam 1 Study Guide: Chapters 1-6 (Themes of Biology, Chemistry of Life, Water, Carbon, Macromolecules, Cells)

Chapter 1: Themes of Biology and Evolution

Five Themes of Biology

• Organization: Life is structured in a hierarchy from molecules to the biosphere. Emergent properties arise at each level due to the arrangement and interactions of parts.

• Information: Genetic information is stored in DNA and transmitted from parent to offspring. DNA encodes instructions for building proteins and regulating cellular activities.

• Energy and Matter: Life requires energy transfer and transformation. Producers (e.g., plants) convert solar energy to chemical energy; consumers obtain energy by eating other organisms. Energy flows through ecosystems, while chemicals cycle within them.

• Interactions: Organisms interact with each other and their environment, affecting both. Feedback regulation (especially negative feedback) maintains homeostasis.

• Evolution: Explains the unity and diversity of life. All living things share common features due to descent from a common ancestor, but have diversified through adaptation.

Cells: Eukaryotic vs. Prokaryotic

• Prokaryotic cells: Lack a nucleus and membrane-bound organelles (e.g., Bacteria, Archaea).

• Eukaryotic cells: Have a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Genetic Information and DNA

• DNA: Deoxyribonucleic acid, the molecule that stores genetic information.

• Transmission: DNA is replicated and passed to offspring during reproduction.

Scientific Inquiry

• Inductive reasoning: Drawing generalizations from specific observations.

• Deductive reasoning: Making predictions based on general principles.

• Hypothesis: A testable explanation for an observation.

• Theory: A broad, well-supported explanation of natural phenomena.

• Variables: Independent variable is manipulated; dependent variable is measured.

Evolution and Natural Selection

• Charles Darwin: Proposed natural selection as the mechanism of evolution.

• Natural selection: Individuals with advantageous traits survive and reproduce more successfully.

Classification of Life

• Three domains: Bacteria, Archaea, Eukarya.

Climate Change

• Causes: Human activities (e.g., burning fossil fuels) increase greenhouse gases, altering Earth's climate.

Chapter 2: The Chemical Context of Life

Elements and Compounds

• Element: A substance that cannot be broken down by chemical means (e.g., C, H, O, N).

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

• Essential elements: Elements required for life (C, H, O, N make up ~96% of living matter).

Atomic Structure

• Atom: Smallest unit of an element, composed of protons, neutrons, and electrons.

• Atomic number: Number of protons in the nucleus.

• Atomic mass: Total mass of protons and neutrons.

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

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

Chemical Bonds

• Covalent bonds: Atoms share electron pairs. Nonpolar (equal sharing), polar (unequal sharing).

• Ionic bonds: Transfer of electrons from one atom to another, forming ions.

• Hydrogen bonds: Weak attractions between a hydrogen atom and an electronegative atom (e.g., O or N).

• Van der Waals interactions: Weak, transient attractions between molecules.

Chemical Reactions

• Making and breaking of chemical bonds, leading to changes in the composition of matter.

Chapter 3: Water and Life

Structure and Properties of Water

• Polar covalent bonds: Oxygen is more electronegative than hydrogen, creating a polar molecule.

• Hydrogen bonds: Form between water molecules, leading to unique properties.

Four Key Properties of Water

• Cohesion: Water molecules stick together via hydrogen bonds, contributing to surface tension.

• Moderation of temperature: Water has a high specific heat, buffering temperature changes.

• Floating of ice: Ice is less dense than liquid water due to hydrogen bond arrangement.

• Universal solvent: Water dissolves many substances due to its polarity.

Other Properties

• Adhesion: Water molecules stick to other substances.

• Evaporative cooling: As water evaporates, it removes heat, cooling surfaces.

Solutions and pH

• Solution: Homogeneous mixture of two or more substances.

• Solvent: Dissolving agent (e.g., water).

• Solute: Substance dissolved.

• Hydrophilic: Water-loving; substances that dissolve in water.

• Hydrophobic: Water-fearing; substances that do not dissolve in water.

• pH: Measure of hydrogen ion concentration. $\mathrm{pH} = -\log_{10}[\mathrm{H}^+]$

• Acids: Increase H+ concentration; Bases: Decrease H+ concentration.

• Buffers: Substances that minimize changes in pH.

Chapter 4: Carbon and Life

Organic Chemistry and Carbon

• Organic chemistry: Study of carbon-containing compounds.

• Stanley Miller's experiment: Demonstrated abiotic synthesis of organic molecules.

• Carbon: Can form four covalent bonds, allowing for diverse molecules.

• Major elements: C, H, O, N, S, P.

• Unpaired electrons: Determine bonding capacity.

Hydrocarbons and Isomers

• Hydrocarbons: Molecules consisting only of C and H; nonpolar and hydrophobic.

• 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-image isomers; important in pharmaceuticals.

Chemical Groups and ATP

• Chemical groups: Functional groups (e.g., hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl) affect molecular function.

• ATP (Adenosine triphosphate): Main energy currency of the cell.

Chapter 5: Large Biological Macromolecules

Polymers and Monomers

• Macromolecules: Large molecules (carbohydrates, lipids, proteins, nucleic acids).

• Polymers: Long chains of monomers joined by covalent bonds.

• Monomers: Building blocks of polymers.

• Enzymes: Catalyze reactions, including polymerization and breakdown.

• Dehydration reaction: Joins monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Carbohydrates

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

• Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose).

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

• Functions: Energy storage (starch, glycogen), structural support (cellulose, chitin).

Lipids

• Fats and oils: Glycerol + fatty acids. Saturated (no double bonds), unsaturated (one or more double bonds).

• Phospholipids: Major component of cell membranes; amphipathic.

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

• Functions: Energy storage, membrane structure, signaling.

Proteins

• Amino acids: Monomers of proteins; 20 types with different R groups (side chains).

• Peptide bonds: Link amino acids.

• Levels of structure: Primary (sequence), secondary (α-helix, β-sheet), tertiary (3D shape), quaternary (multiple polypeptides).

• Denaturation: Loss of structure and function due to environmental changes.

• Sickle cell disease: Caused by a single amino acid substitution in hemoglobin.

Nucleic Acids

• DNA vs. RNA: DNA stores genetic information; RNA involved in gene expression.

• Structure: DNA is a double helix, antiparallel strands.

• Monomers: Nucleotides (adenine, guanine, cytosine, thymine in DNA; uracil replaces thymine in RNA).

• Pyrimidines: Cytosine, thymine, uracil; Purines: Adenine, guanine.

Chapter 6: A Tour of the Cell

Microscopy

• Light microscopes: Use visible light to observe cells; limited resolution.

• Electron microscopes: Use electron beams; higher resolution for ultrastructure.

Cell Types and Features

• All cells: Surrounded by plasma membrane, contain cytosol, chromosomes, and ribosomes.

• Prokaryotic cells: No nucleus, DNA in nucleoid region.

• Eukaryotic cells: Nucleus, membrane-bound organelles.

Cell Structures

• Nucleus: Contains DNA, surrounded by nuclear envelope.

• Ribosomes: Synthesize proteins.

• Chromosomes: DNA molecules with associated proteins.

• Chromatin: DNA + proteins in a less condensed form.

• Nucleolus: Site of ribosome synthesis.

Endomembrane System

• Nuclear envelope: Double membrane around nucleus.

• Endoplasmic reticulum (ER): Rough ER (with ribosomes, protein synthesis), Smooth ER (lipid synthesis, detoxification).

• Golgi apparatus: Modifies, sorts, and ships proteins and lipids.

• Lysosomes: Digestive organelles.

• Vacuoles: Storage and support (large in plant cells).

• Plasma membrane: Selective barrier for the cell.

Energy Organelles

• Mitochondria: Site of cellular respiration; produces ATP.

• Chloroplasts: Site of photosynthesis in plants and algae.

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

Cytoskeleton

• Microtubules: Hollow rods; shape, support, and movement.

• Microfilaments: Thin rods; cell shape, muscle contraction.

• Intermediate filaments: Fibrous proteins; structural support.

Cell Walls and Extracellular Structures

• Cell wall: Rigid structure outside plasma membrane (plants, fungi, some protists).

• Extracellular matrix (ECM): Network of proteins and carbohydrates outside animal cells.

Cell Junctions

• Plasmodesmata: Channels between plant cells.

• Tight junctions: Prevent leakage between animal cells.

• Desmosomes: Anchor cells together.

• Gap junctions: Allow communication between animal cells.