Biology Study Guide: Chemistry Foundations, Biomolecules, Cells, and Molecular Processes

CHAPTER 2 - Chemistry Foundations, Water, & Carbon

Atoms and Subatomic Particles

An atom is the smallest unit of matter that retains the properties of an element. Atoms are composed of three main subatomic particles:

• Protons: Positively charged, located in the nucleus.

• Neutrons: No charge, located in the nucleus.

• Electrons: Negatively charged, orbit the nucleus in electron shells.

Valence electrons are electrons in the outermost shell; they determine an atom's chemical reactivity.

Ions and Chemical Bonds

• Ion: An atom or molecule with a net electric charge due to loss or gain of electrons.

• Ionic bond: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent bond: Formed when two atoms share one or more pairs of electrons.

• Polar covalent bond: Unequal sharing of electrons, resulting in partial charges (e.g., in water).

• Non-polar covalent bond: Equal sharing of electrons, no charge separation (e.g., O2).

Water Molecule Structure and Properties

The water molecule (H2O) has a bent shape due to polar covalent bonds between oxygen and hydrogen. This results in polarity and enables hydrogen bonding between water molecules.

• Cohesion: Water molecules stick together.

• Adhesion: Water molecules stick to other surfaces.

• High specific heat: Water resists temperature changes.

• Solvent properties: Water dissolves many substances.

• Ice floats: Solid water is less dense than liquid water.

These properties are essential for life, such as temperature regulation and nutrient transport.

Acids, Bases, and pH

• Acid: Substance that increases H+ concentration in solution (pH < 7).

• Base: Substance that decreases H+ concentration (pH > 7).

• pH scale: Measures acidity/alkalinity; logarithmic scale.

Carbon and Functional Groups

Carbon forms four covalent bonds, allowing for diverse organic molecules. Functional groups (e.g., hydroxyl, carboxyl, amino, phosphate) determine chemical properties and reactivity.

• Hydroxyl (-OH): Polar, forms hydrogen bonds.

• Carboxyl (-COOH): Acidic, can donate H+.

• Amino (-NH2): Basic, can accept H+.

• Phosphate (-PO4): Contributes negative charge.

Condensation/Dehydration and Hydrolysis Reactions

• Condensation (Dehydration) reaction: Joins monomers by removing water.

• Hydrolysis reaction: Breaks polymers by adding water.

• These reactions build and break down organic molecules.

CHAPTER 3 - Proteins

Amino Acid Structure

Amino acids are the building blocks of proteins. Each has a central carbon, an amino group, a carboxyl group, a hydrogen atom, and a variable R group.

• General formula: $\mathrm{H_2N{-}CHR{-}COOH}$

Levels of Protein Structure

• Primary: Sequence of amino acids.

• Secondary: Alpha helices and beta sheets formed by hydrogen bonding.

• Tertiary: 3D folding due to interactions among R groups.

• Quaternary: Multiple polypeptide chains assembled together.

CHAPTER 4 - Nucleic Acids

Nucleotide Structure

Nucleotides consist of a phosphate group, a five-carbon sugar, and a nitrogenous base.

• DNA: Deoxyribose sugar, bases A, T, C, G.

• RNA: Ribose sugar, bases A, U, C, G.

Levels of DNA Structure

• Primary: Linear sequence of nucleotides.

• Secondary: Double helix formed by base pairing.

• Tertiary: Higher-order folding and packaging.

CHAPTER 5 - Carbohydrates

Monosaccharide Structure and Variation

Monosaccharides are simple sugars (e.g., glucose, fructose). They differ in carbon number, arrangement, and functional groups.

Disaccharides and Glycosidic Linkages

• Disaccharide: Formed by joining two monosaccharides via a glycosidic bond.

• Alpha linkage: Bond below the plane of the ring.

• Beta linkage: Bond above the plane of the ring.

Polysaccharide Structure

• Storage polysaccharides: Starch (plants), glycogen (animals).

• Structural polysaccharides: Cellulose (plants), chitin (fungi, insects).

CHAPTER 6 - Lipids, Membranes, and Transport

Saturated vs. Unsaturated Hydrocarbons

• Saturated: No double bonds, straight chains, solid at room temperature.

• Unsaturated: One or more double bonds, kinked chains, liquid at room temperature.

Phospholipids and Membrane Structure

• Phospholipids: Amphipathic molecules with hydrophilic heads and hydrophobic tails; form bilayers.

• Semi-permeable: Membranes allow some substances to pass, restrict others.

Steroids

• Steroids: Four-ring structure, amphipathic, function as hormones and membrane components.

Osmosis and Tonicity

• Hypertonic: Higher solute outside; cell loses water.

• Hypotonic: Lower solute outside; cell gains water.

• Isotonic: Equal solute; no net water movement.

Plant cells: turgid (hypotonic), flaccid (isotonic), plasmolyzed (hypertonic). Animal cells: lysed (hypotonic), normal (isotonic), shriveled (hypertonic).

Active Transport

• Active transport: Movement of substances against concentration gradient using energy (ATP).

CHAPTER 7 - Cells and Cell Systems

Microscopy

• Light microscope: Uses visible light; lower resolution.

• Electron microscope: Uses electron beams; higher resolution.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic: No nucleus, simple structure, e.g., bacteria.

• Eukaryotic: Nucleus, complex organelles, e.g., plants, animals.

• Both have plasma membrane, cytoplasm, ribosomes.

Eukaryotic Organelles

• Nucleus: Stores genetic material.

• Mitochondria: Energy production.

• Endoplasmic reticulum: Protein and lipid synthesis.

• Golgi apparatus: Processing and packaging.

• Lysosomes: Digestion.

• Chloroplasts: Photosynthesis (plants).

CHAPTER 8 - Energy, REDOX, and Enzymes

Energy Utilization and Thermodynamics

• First law: Energy cannot be created or destroyed.

• Second law: Entropy (disorder) increases.

ATP and Cellular Energy

• ATP: Main energy currency; energy stored in phosphate bonds.

• Energy released by hydrolysis: $\mathrm{ATP + H_2O \rightarrow ADP + P_i + energy}$

• Each ATP molecule releases about 7.3 kcal/mol.

Coenzymes and REDOX

• Coenzymes: Assist in electron transfer during REDOX reactions (e.g., NAD+, FAD).

Enzyme Function and Regulation

• Active site: Region where substrate binds.

• Substrate: Molecule acted upon by enzyme.

• Activation energy: Energy required to start a reaction; enzymes lower this.

• Feedback inhibition: End product inhibits enzyme activity.

• Competitive inhibitor: Binds active site, blocks substrate.

• Allosteric (non-competitive) inhibitor: Binds elsewhere, changes enzyme shape.

CHAPTER 9 - Cell Respiration

Phosphorylation Types

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

• Oxidative phosphorylation: ATP synthesis via electron transport chain and chemiosmosis.

Stages of Cellular Respiration

• Glycolysis: Occurs in cytoplasm; produces pyruvate, NADH, ATP.

• Pyruvate oxidation: Occurs in mitochondria; produces acetyl-CoA, NADH, CO2.

• Citric acid cycle: Occurs in mitochondria; produces NADH, FADH2, ATP, CO2.

• Electron transport chain: Electrons move through complexes, energy used to pump H+ across membrane.

• ATP synthase: Uses H+ gradient to convert ADP to ATP.

• Oxygen: Final electron acceptor; essential for aerobic respiration.

Fermentation

• Lactic acid fermentation: Pyruvate converted to lactate.

• Alcohol fermentation: Pyruvate converted to ethanol and CO2.

CHAPTER 10 - Photosynthesis

Pigments and Light Absorption

• Pigments: Absorb specific wavelengths (photons); reflected/transmitted wavelengths determine color.

• Absorbance spectrum: Shows which wavelengths are absorbed.

Light Reactions and Calvin Cycle

• Light reactions: Inputs: light, water; outputs: ATP, NADPH, O2.

• Calvin cycle: Inputs: CO2, ATP, NADPH; outputs: glucose.

• Products of light reactions fuel the Calvin cycle.

CHAPTER 12: The Cell Cycle, Mitosis, and Cancer

Cell Cycle and Interphase

• Cell cycle: Sequence of growth and division.

• Interphase: G1 (growth), S (DNA synthesis), G2 (preparation).

Chromatin and Chromosomes

• Chromatin: DNA + proteins; present during interphase.

• Chromosomes: Condensed chromatin; present during mitosis.

Mitosis Phases

• Prophase: Chromosomes condense.

• Metaphase: Chromosomes align at center.

• Anaphase: Sister chromatids separate.

• Telophase: Nuclear envelope reforms.

• Cytokinesis: Cell divides.

Checkpoints and Cancer

• Checkpoints: Control cell cycle progression.

• G0 phase: Non-dividing state.

• Benign tumor: Non-invasive.

• Malignant tumor: Invasive, cancerous.

CHAPTER 13: Meiosis and Genes

Ploidy and Chromosome Structure

• Ploidy: Number of sets of chromosomes (haploid, diploid).

• Sister chromatids: Identical copies of a chromosome.

Meiosis Phases

• Meiosis I: Homologous chromosomes separate.

• Meiosis II: Sister chromatids separate.

Nondisjunction

• Nondisjunction: Failure of chromosomes to separate; leads to aneuploidy.

CHAPTER 14: Mendel and Beyond

Mendel’s Experiments and Principles

• Principle of segregation: Alleles separate during gamete formation.

• Principle of independent assortment: Genes on different chromosomes assort independently.

Dominance Relationships

• Complete dominance: One allele masks the other.

• Incomplete dominance: Heterozygote shows intermediate phenotype.

• Codominance: Both alleles expressed in heterozygote.

CHAPTER 15: DNA Replication

Replication Bubble and Strand Synthesis

• Replication bubble: DNA unwinds at origin.

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized in Okazaki fragments.

CHAPTERS 16 & 17: Central Dogma

Central Dogma and Genetic Code

• Central dogma: DNA → RNA → Protein.

• Triplet code: Three nucleotides code for one amino acid.

• Transcription: DNA to RNA.

• Translation: RNA to protein.

Elongation in transcription: RNA polymerase adds nucleotides. Elongation in translation: Ribosome adds amino acids to polypeptide chain.