BY-110 Biology Lecture Review: Chapters 1–17 Study Guide

Chapter 1: Evolution, Themes of Biology, and Scientific Inquiry

Theme of Biology

Biology is the scientific study of life, encompassing a wide range of themes that unify the discipline.

• Evolution: The process by which species change over time, accounting for both the unity and diversity of life.

• Scientific Inquiry: The method by which biologists ask questions and seek answers through observation and experimentation.

Properties of Life

Living organisms share several fundamental properties:

• Order: Highly organized structures.

• Regulation: Homeostasis and internal balance.

• Growth and Development: Controlled by genetic information.

• Energy Processing: Use of energy to power activities.

• Response to Environment: Reacting to stimuli.

• Reproduction: Ability to produce offspring.

• Evolutionary Adaptation: Traits that enhance survival.

Hierarchy of Organization

Biological organization ranges from molecules to the biosphere:

• Atoms & Molecules

• Organelles

• Cells

• Tissues

• Organs & Organ Systems

• Organisms

• Populations

• Communities

• Ecosystems

• Biosphere

Three Domains of Life

All life is classified into three domains:

• Bacteria

• Archaea

• Eukarya

Chapter 2: The Chemical Context of Life

Matter and Elements

Matter is composed of elements, which are substances that cannot be broken down by chemical means.

• Periodic Table: Organizes elements by atomic number.

• Elements Important to Life: C, H, O, N, P, S, Ca, K, Na, Cl, Mg.

Atomic Structure

• Atom: Smallest unit of an element.

• Atomic Number: Number of protons.

• Mass Number: Protons + neutrons.

• Atomic Mass: Average mass of isotopes.

• Isotopes: Atoms with same protons, different neutrons.

• Radioactive Isotopes: Unstable, decay over time; used in dating and medical imaging.

Energy of Electrons

• Electron Shells: Energy levels where electrons reside.

• Reactivity: Determined by electron configuration.

Bonds

• Covalent Bonds: Sharing electrons; can be polar or non-polar.

• Ionic Bonds: Transfer of electrons.

• Weak Bonds: Hydrogen bonds, van der Waals interactions.

• Shape: Molecular shape affects function.

Chemical Reactions

• Atoms combine or break apart to form new substances.

Terminology Table

Term	Definition
Atom	Smallest unit of matter
Element	Pure substance of one type of atom
Molecule	Two or more atoms bonded
Compound	Substance with two or more elements

Chapter 3: Water and Life

Water Forms and Structure

Water exists as solid, liquid, and gas. Its polarity and hydrogen bonding are crucial for life.

• Polar Molecule: Unequal sharing of electrons.

• Hydrogen Bonding: Attraction between water molecules.

Properties of Water

• Cohesion: Water molecules stick together.

• Temperature Stabilization: High specific heat; resists temperature change.

• Expansion Upon Freezing: Ice is less dense than liquid water.

• Versatility as a Solvent: Dissolves many substances.

Heat vs. Temperature

• Heat: Total kinetic energy.

• Temperature: Average kinetic energy.

• Specific Heat: Amount of heat to change 1g by 1°C.

Dissociation of Water and pH

• Dissociation: Water splits into H+ and OH-.

• pH: Measures H+ concentration; $\text{pH} = -\log_{10}[\text{H}^+]$

• Acid Rain: Rain with low pH due to pollutants.

• Ocean Acidification: CO2 lowers ocean pH.

Chapter 4: Carbon and the Molecular Diversity of Life

Organic Chemistry and Carbon

Carbon's tetravalence allows it to form diverse molecules.

• Hydrocarbons: Molecules of only C and H.

Isomers

• Structural Isomers: Different covalent arrangements.

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

• Enantiomers: Mirror images; important in pharmaceuticals.

Functional Groups

Group	Structure	Properties	Cellular Function
Hydroxyl	-OH	Polar	Alcohols
Carbonyl	CO	Polar	Ketones, aldehydes
Carboxyl	-COOH	Acidic	Amino acids, fatty acids
Amino	-NH2	Basic	Amino acids
Sulfhydryl	-SH	Polar	Proteins
Phosphate	-PO4	Negative charge	ATP, nucleic acids
Methyl	-CH3	Non-polar	Gene expression

Chapter 5: The Structure and Function of Large Biological Molecules

Polymers and Monomers

• Polymers: Long chains of monomers.

• Monomers: Building blocks (e.g., monosaccharides, amino acids, nucleotides).

• Dehydration: Forms polymers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Carbohydrates

• Monosaccharides: Simple sugars (glucose).

• Polysaccharides: Storage (starch, glycogen) and structural (cellulose, chitin).

Lipids

• Fats: Saturated (solid), unsaturated (liquid), trans fats.

• Phospholipids: Major component of membranes.

• Steroids: Hormones, cholesterol.

Proteins

• Amino Acids: 20 types, differing by R group.

• Protein Structure: Primary, secondary, tertiary, quaternary.

Nucleic Acids

• Nucleotides: Sugar, phosphate, nitrogenous base.

• DNA and RNA: Store and transmit genetic information.

Chapter 6: A Tour of the Cell

Cell as the Basic Unit of Life

• Prokaryotes: No nucleus, few organelles.

• Eukaryotes: Nucleus, many organelles.

Features and Organelles

• Nucleus: Contains DNA.

• Ribosomes: Protein synthesis.

• Mitochondria: ATP production.

• Chloroplasts: Photosynthesis.

• Peroxisomes: Metabolism of hydrogen peroxide.

• Cytoskeleton: Microtubules, microfilaments, intermediate filaments.

• Cell Wall: Plant cells.

• Extracellular Matrix (ECM): Animal cells.

• Intracellular Junctions: Plasmodesmata (plants), tight junctions, desmosomes, gap junctions (animals).

Chapter 7: Membrane Structure and Function

Membrane Structure

• Phospholipid Bilayer: Hydrophobic tails, hydrophilic heads.

• Fluid Mosaic Model: Proteins and lipids move within the membrane.

• Membrane Proteins: Transport, signaling, structure.

• Membrane Carbohydrates: Cell recognition.

Transport Across Membranes

• Passive Transport: Diffusion, facilitated diffusion, osmosis.

• Active Transport: Requires ATP; pumps, co-transport.

• Transport of Large Molecules: Exocytosis, endocytosis.

Solution Types Table

Type	Definition
Hypotonic	Lower solute outside cell
Hypertonic	Higher solute outside cell
Isotonic	Equal solute

Chapter 8: An Introduction to Metabolism

Metabolic Pathways

• Catabolic: Break down molecules, release energy.

• Anabolic: Build molecules, require energy.

Energy Types and Laws

• Kinetic Energy: Motion.

• Potential Energy: Stored.

• Chemical Energy: In bonds.

• First Law: Energy cannot be created or destroyed.

• Second Law: Entropy increases.

Free Energy and Metabolism

• Free Energy (G): Usable energy.

• Exergonic: Releases energy ($\Delta G < 0$).

• Endergonic: Requires energy ($\Delta G > 0$).

ATP and Enzymes

• ATP: Powers cellular work.

• Enzymes: Lower activation energy, substrate-specific.

• Regulation: Competitive/non-competitive inhibitors, allosteric regulation, feedback inhibition.

Chapter 9: Cellular Respiration and Fermentation

Cellular Respiration Overview

• Catabolic Reactions: Breakdown of glucose.

• Redox Reactions: Electron transfer.

• Activation Energy: Required to start.

Stages of Cellular Respiration

• Glycolysis: Glucose to pyruvate; occurs in cytosol.

• Krebs Cycle: Acetyl CoA enters; produces NADH, FADH2, ATP.

• Electron Transport Chain (ETC): Inner mitochondrial membrane; produces most ATP.

Fermentation

• Alcohol Fermentation: Produces ethanol.

• Lactic Acid Fermentation: Produces lactate.

• Facultative Anaerobes: Can use both respiration and fermentation.

Chapter 10: Photosynthesis

Overview and Reactions

• Light Reactions: Convert light energy to chemical energy (ATP, NADPH).

• Photosystems: PS II and PS I; absorb light, transfer electrons.

• Electron Flow: Linear (produces ATP, NADPH), cyclic (produces ATP).

• Calvin Cycle: Fixes CO2, produces sugars.

Phases of Calvin Cycle

• Carbon Fixation

• Reduction

• Regeneration of CO2 Acceptor

Chapter 11: Cell Communication

Overview of Cell Communication

• Direct Contact: Cells touch.

• Secreted Molecules: Signal molecules released.

Cell Signaling

• Reception: Signal detected.

• Transduction: Signal relayed/amplified.

• Response: Cellular change.

Chapter 12: The Cell Cycle

Cell Division

• Mitosis: Diploid cells; growth and repair.

• Meiosis: Haploid cells; sexual reproduction.

Regulation of Cell Cycle

• Checkpoints: Control progression.

• Cyclins and CDKs: Regulatory proteins.

• Internal/External Cues: Influence division.

• Cancer Cells: Lack normal controls.

Phases Table

Phase	Description
Interphase	G1, S, G2; cell growth, DNA replication
Mitosis	Prophase, metaphase, anaphase, telophase
Cytokinesis	Division of cytoplasm

Chapter 13: Meiosis and Sexual Life Cycles

Reproduction

• Asexual: One parent, identical offspring.

• Sexual: Two parents, genetic variation.

Meiosis

• Meiosis I: Reduction division.

• Meiosis II: Equatorial division.

Genetic Variation

• Independent Assortment: Random distribution of chromosomes.

• Crossing Over: Exchange of genetic material.

• Random Fertilization: Increases diversity.

Chapter 14: Mendel and the Gene Idea

History and Terms

• Gregor Mendel: Father of genetics; used pea plants.

• Alleles: Different forms of a gene.

• Dominant vs Recessive: Dominant masks recessive.

• Genotype: Genetic makeup.

• Phenotype: Physical traits.

Mendelian Laws

• Law of Segregation: Alleles separate during gamete formation.

• Law of Independent Assortment: Genes on different chromosomes assort independently.

Exceptions to Mendel

• Linkage: Genes close together inherited together.

• Incomplete Dominance: Blended phenotype.

• Codominance: Both alleles expressed.

• Polygenic Traits: Multiple genes affect trait.

• Multifactorial Traits: Genes and environment.

Chapter 16: The Molecular Basis of Inheritance

DNA as Genetic Material

• Griffith's Experiment: Transformation principle.

• Hershey and Chase: DNA is genetic material.

• Chargaff's Rules: A=T, G=C.

• Watson & Crick: Double helix structure.

DNA Structure and Replication

• Nucleotides: Sugar, phosphate, base.

• Replication: Semi-conservative; leading and lagging strands.

• DNA Repair: Corrects errors.

• Telomeres and Telomerase: Protect chromosome ends.

Chapter 17: Gene Expression: From Gene to Protein

Central Dogma

• DNA → RNA → Protein

Transcription

• Initiation: RNA polymerase binds promoter.

• Elongation: RNA strand synthesized.

• Termination: RNA polymerase releases.

• RNA Processing: Splicing, capping, poly-A tail (eukaryotes).

Translation

• mRNA: Carries code.

• tRNA: Brings amino acids.

• Ribosomes: Site of protein synthesis.

• Initiation, Elongation, Termination: Steps of translation.

Comparison Table: Prokaryote vs Eukaryote Gene Expression

Feature	Prokaryote	Eukaryote
Transcription Location	Cytoplasm	Nucleus
RNA Processing	None	Splicing, capping, poly-A tail
Translation Location	Cytoplasm	Cytoplasm