Final exam/ cumulative

Chapter 2–3: Atoms, Molecules, and Cells

Atoms & Molecules

• Atom: Smallest unit of matter; composed of protons, neutrons, electrons

• Element: Substance made of one kind of atom

• Compound: 2+ elements chemically bonded (e.g., H2O)

• Covalent bonds: Atoms share electrons (polar = unequal; nonpolar = equal)

• Hydrogen bonds: Weak attraction between a hydrogen and an electronegative atom (important in DNA, water)

• Ions: Charged atoms (cation = +, anion = -)

Water Properties

• Cohesion, adhesion, high specific heat, ice floats, solvent

pH & Buffers

• pH = -log[H+]; acidic < 7, basic > 7

• Buffers maintain stable pH (important in homeostasis)

Macromolecules

• Carbohydrates: Monosaccharides → polysaccharides; quick energy & structure (e.g., cellulose)

• Lipids: Fatty acids & glycerol; hydrophobic, used in membranes, energy storage

• Proteins: Amino acids; structure, enzymes, signaling

• Nucleic acids: Nucleotides; store genetic info (DNA, RNA)

Cell Structure

• Prokaryotes: No nucleus or organelles

• Eukaryotes: Nucleus, membrane-bound organelles

• Organelles: Nucleus, ER, Golgi, mitochondria, chloroplasts (plants), lysosomes

• Cell membrane: Phospholipid bilayer, selective permeability

Chapter 4 & 12.5: Nucleic Acids and Genome Packaging

DNA Structure

• Double helix; antiparallel strands

• Sugar-phosphate backbone with nitrogenous bases: A-T (2 bonds), G-C (3 bonds)

• Base pairing maintains consistent width

Genome Organization

• DNA → wrapped around histones → nucleosomes → chromatin → chromosomes

• Euchromatin: Loosely packed, active

• Heterochromatin: Tightly packed, inactive

Chapter 6: Metabolism

Energy

• Kinetic: Motion (e.g., muscle)

• Thermal: Type of kinetic, from movement

• Potential: Stored (chemical bonds)

Thermodynamics

• 1st Law: Energy conserved

• 2nd Law: Entropy increases

Free Energy (G)

• ΔG < 0: Exergonic, releases energy

• ΔG > 0: Endergonic, requires input

• Entropy (S) increases in spontaneous reactions

Metabolism

• Catabolism: Break down, release energy (e.g., respiration)

• Anabolism: Build up, require energy (e.g., synthesis)

• Energy coupling: Catabolism powers anabolism

ATP

• Adenine + ribose + 3 phosphate

• Hydrolysis: ATP → ADP + Pi; releases energy

• Drives mechanical, transport, chemical work

Enzymes

• Catalysts that lower activation energy

• Substrate binds active site

• Specificity depends on shape

• Affected by pH and temperature

• Inhibition:

  • Competitive: Binds active site

  • Noncompetitive: Changes enzyme shape

Chapter 7: Cellular Respiration

Overview

• C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

Redox Reactions

• Oxidation: Loss of electrons (glucose)

• Reduction: Gain of electrons (oxygen → water)

Electron Carriers

• NAD+ → NADH

• FAD → FADH2

• Carry electrons to ETC

Steps

1. Glycolysis (cytoplasm): 2 ATP, 2 NADH, 2 pyruvate

2. Pyruvate Oxidation: Pyruvate → Acetyl-CoA + CO2 + NADH

3. Citric Acid Cycle: 2 ATP, 6 NADH, 2 FADH2, 4 CO2

4. Oxidative Phosphorylation (ETC + chemiosmosis): ~28 ATP

Phosphorylation

• Substrate-level: Direct transfer (glycolysis, citric acid)

• Oxidative: From ETC proton gradient

Chemiosmosis

• H+ flows through ATP synthase → ATP

Fermentation

• Anaerobic; regenerates NAD+

• Lactic acid (animals), alcohol + CO2 (yeast)

Chapter 8: Photosynthesis

Equation

6CO2 + 6H2O + light → C6H12O6 + 6O2

Location

• Chloroplast: Thylakoid (light reactions), stroma (Calvin cycle)

Light Reactions

• Split water → O2 + ATP + NADPH

• Photosystem II → ETC → Photosystem I

Calvin Cycle

• Carbon fixation (RuBisCO)

• Reduction → G3P

• Regeneration of RuBP

• Powered by ATP, NADPH from light reactions

Comparison with Respiration

• Opposite directions of energy and electron flow

• Both involve ETC and chemiosmosis

Chapters 11–13: Cell Division & Genetic Variation

Mitosis

• Somatic cells; identical daughter cells

• Phases: Prophase → Metaphase → Anaphase → Telophase

• Cytokinesis splits cell

Meiosis

• Germ cells; produces 4 non-identical haploid gametes

• Meiosis I (homologs separate), Meiosis II (sister chromatids)

Genetic Variation

• Crossing over (Prophase I)

• Independent assortment (Metaphase I)

• Random fertilization

DNA Replication

• Semi-conservative

• DNA polymerase, helicase, primase, ligase

• Leading vs lagging strand (Okazaki fragments)

Mutations

• Point (silent, missense, nonsense)

• Insertions/deletions (frameshift)

• Causes: Errors, radiation, chemicals

Chapters 14–15, 19: Inheritance

Mendelian Genetics

• Gene: DNA sequence for a trait

• Allele: Variant of a gene

• Homozygous: Same alleles; heterozygous: Different alleles

• Dominant: Expressed if present; recessive: Masked unless homozygous

Laws

• Segregation: Alleles separate during meiosis

• Independent Assortment: Genes on different chromosomes sort independently

Non-Mendelian

• Incomplete dominance: Blend

• Codominance: Both alleles expressed

• Multiple alleles: ABO blood types

• Polygenic: Many genes, one trait (e.g., height)

Sex-linked Traits

• X-linked recessive traits show more in males (e.g., color blindness)

Pedigrees

• Diagram of inheritance through families

Chromosome Mutations

• Deletions, duplications, inversions, translocations

Genetic Variation

• Mutation, recombination, sexual reproduction increase diversity

Connections Across Chapters

• ATP is central in cellular respiration (Ch. 7) and photosynthesis (Ch. 8)

• Enzymes regulate all biochemical processes: metabolism, DNA replication, respiration

• Energy coupling connects catabolic and anabolic reactions

• Genetic variation arises during meiosis, which is critical for inheritance patterns

• Electron carriers (NADH, FADH2) link redox reactions and ATP synthesis

• Mutations and chromosome errors influence phenotypes and inheritance

• Cell membranes, proteins, and nucleic acids work together to allow for gene expression, signal transduction, and metabolism