BSC1010 Exam 1 Comprehensive Study Notes (Chapters 1–3)

Chapter 1: Introduction to Biology

Characteristics of Life

• Organization: Living things are made of one or more cells and have an ordered structure.
• Metabolism / Energy Use: Organisms obtain and transform energy and matter to power life processes.
• Homeostasis / Regulation: Living things maintain relatively stable internal conditions despite external change.
• Growth, Development, and Reproduction: Organisms grow and develop according to genetic instructions and produce offspring sexually or asexually.
• Response and Evolution: Organisms respond to stimuli; populations change over generations through evolution/adaptation.

Levels of Organization and Emergent Properties

• Atom $\rightarrow$ Molecule: Atoms combine into molecules; molecules can have new chemical properties not present in individual atoms.
• Organelle: Specialized structures inside cells perform particular jobs.
• Cell: Smallest unit of life; life functions emerge from interacting molecules and organelles.
• Tissue: Groups of similar cells cooperate for a common function.
• Organ: Multiple tissue types work together for a specific task.
• Organ System: Several organs coordinate major body functions.
• Organism: A complete living individual.
• Population: Members of the same species living in the same area.
• Community: All populations of different species in an area.
• Ecosystem: A community plus the nonliving environment and energy/matter interactions.
• Biosphere: All ecosystems and regions of Earth where life exists.
• Emergent Property: A new property that appears at a higher level because parts interact; it is not obvious from the parts alone.

Domains and Kingdoms of Life

• Domain Bacteria: Prokaryotic, unicellular; cell walls usually contain peptidoglycan. Belongs to Kingdom Bacteria/Eubacteria.
• Domain Archaea: Prokaryotic, unicellular; cell walls lack peptidoglycan; many have unique membrane chemistry. Belongs to Kingdom Archaea/Archaebacteria.
• Domain Eukarya: Cells have a nucleus and membrane-bound organelles. Includes Protists, Fungi, Plantae, and Animalia.
• Kingdom Protista: Mostly unicellular eukaryotes; diverse nutrition and movement.
• Kingdom Fungi: Eukaryotic heterotrophs that absorb nutrients; cell walls contain chitin.
• Kingdom Plantae: Multicellular photosynthetic eukaryotes; cellulose cell walls and chloroplasts.
• Kingdom Animalia: Multicellular heterotrophic eukaryotes; no cell wall; usually ingest food.

Modes of Reproduction

• Asexual Reproduction: One parent; no fusion of gametes; offspring are usually genetically very similar to the parent. Fast and efficient, but produces less genetic variation.
• Sexual Reproduction: Usually involves two gametes produced by meiosis; fertilization combines genetic material. Slower, but creates more genetic variation in offspring.

Chapter 2: Chemistry of Life

Essential Biological Elements

• CHONPS: Carbon ($\text{C}$), Hydrogen ($\text{H}$), Oxygen ($\text{O}$), Nitrogen ($\text{N}$), Phosphorus ($\text{P}$), Sulfur ($\text{S}$) are the major elements in biological molecules.
• Na (Sodium): Important ion for fluid balance, nerve impulses, and muscle function.
• Cl (Chloride): Major negative ion; contributes to fluid balance and stomach acid.
• K (Potassium): Major intracellular positive ion; important for nerve and muscle function.

Atomic Structure and Chemical Concepts

• Atomic Number: Number of protons; identifies the element.
• Proton: Positive charge; located in the nucleus.
• Neutron: No charge; located in the nucleus.
• Electron: Negative charge; occupies orbitals/electron shells around the nucleus.
• Mass Number: Protons + neutrons ($\text{protons} + \text{neutrons}$).
• Isotope: Same element (same number of protons) with a different number of neutrons.
• Valence Electrons: Electrons in the outermost shell; determine how an atom bonds and reacts.

Types of Chemical Bonds

• Nonpolar Covalent Bond: Electrons are shared approximately equally; no strong partial charges.
• Polar Covalent Bond: Electrons are shared unequally because one atom is more electronegative; creates partial positive and negative ends.
• Ionic Bond: Electrons are transferred, creating oppositely charged ions that attract.
• Hydrogen Bond: Weak attraction between a partially positive $\text{H}$ atom and an electronegative atom (often $\text{O}$ or $\text{N}$) on another molecule or another part of a molecule.

Properties of Water

• Polarity: Oxygen pulls shared electrons more strongly, giving water partial charges.
• Hydrogen Bonding: Neighboring water molecules are held together by hydrogen bonds.
• Cohesion: Water sticks to water; contributes to surface tension.
• Adhesion: Water sticks to other polar surfaces; helps capillary action.
• High Specific Heat: Water resists temperature change, stabilizing organisms and environments.
• High Heat of Vaporization: Evaporation removes substantial heat, helping cool organisms.
• Excellent Solvent: Dissolves many ionic and polar substances.
• Ice Density: Ice is less dense than liquid water because hydrogen bonds form a more open crystal lattice in ice, so ice floats.

Functional Groups

• Amino Group ($-\text{NH}_2 / -\text{NH}_3^+$): Acts as a base by accepting $\text{H}^+$; found in amino acids.
• Carboxyl Group ($-\text{COOH} / -\text{COO}^-$): Acts as an acid by donating $\text{H}^+$; found in amino acids and fatty acids.
• Phosphate Group ($-\text{PO}_4$): Negatively charged/polar; important in ATP, nucleic acids, and phospholipids.

Nucleosides vs. Nucleotides

• Nucleoside: Composed of a nitrogenous base + pentose sugar.
• Nucleotide: Composed of a nitrogenous base + pentose sugar + phosphate group.
• DNA Sugar: Deoxyribose.
• RNA Sugar: Ribose.

Biological Macromolecules and Metabolism

• Metabolism: All chemical reactions in a cell/organism.
• Catabolic Reactions: Break molecules down and release energy.
• Anabolic Reactions: Build molecules and require energy.
• Carbohydrates:
  • Main Function: Quick energy; short-term storage; structure.
  • Building Block: Monosaccharide.
  • Polymer / Large Form: Polysaccharide.
  • Examples: Glucose, starch, glycogen, cellulose.
  • Key Notes: Usually ratio of $\text{C}:\text{H}:\text{O}$ near $1:2:1$.
• Proteins:
  • Main Function: Enzymes, structure, transport, signaling, movement.
  • Building Block: Amino acid.
  • Polymer / Large Form: Polypeptide/protein.
  • Examples: Amylase, hemoglobin, collagen.
  • Key Notes: Joined by peptide bonds; shape determines function.
• Nucleic Acids:
  • Main Function: Store/use genetic information.
  • Building Block: Nucleotide.
  • Polymer / Large Form: DNA or RNA.
  • Examples: DNA, RNA.
  • Key Notes: Sugar-phosphate backbone; bases carry information.
• Lipids:
  • Main Function: Long-term energy, membranes, insulation, hormones.
  • Building Block: No single true monomer.
  • Polymer / Large Form: Not a true polymer.
  • Examples: Fats, oils, phospholipids, steroids.
  • Key Notes: Mostly hydrophobic; rich in $\text{C}$ and $\text{H}$.

Protein Structure and Denaturation

• Amino Acid Structure: Central carbon bonded to an amino group, carboxyl group, $\text{H}$, and variable R group.
• Primary Structure: Amino-acid sequence held together by peptide bonds.
• Secondary Structure: Local $\alpha$-helices and $\beta$-pleated sheets formed mainly by hydrogen bonds in the backbone.
• Tertiary Structure: Overall 3-D shape of one polypeptide; influenced by R-group interactions including hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bonds.
• Quaternary Structure: Two or more polypeptide subunits assembled into one functional protein; stabilized by the same kinds of interactions as tertiary structure.
• Denaturation: Heat, pH, or chemicals can disrupt protein shape and function, usually without breaking primary peptide bonds.

Carbohydrate Monomers, Polymers, and Reactions

• Monomer: Monosaccharide, such as glucose.
• Polymer: Polysaccharide, such as starch, glycogen, or cellulose.
• Dehydration Synthesis: Builds a larger molecule by removing water as a covalent bond forms.
• Hydrolysis: Breaks a larger molecule by adding water to split a covalent bond.

Nucleic Acids and DNA Structure

• Monomer: Nucleotide.
• Three Nucleotide Parts: Phosphate group + pentose sugar + nitrogenous base.
• DNA Bases: A, T, G, C. A pairs with T using $2$ hydrogen bonds; G pairs with C using $3$ hydrogen bonds.
• Antiparallel: The two DNA strands run in opposite directions: one $5' \rightarrow 3'$ and the other $3' \rightarrow 5'$.
• Complementary Sequence Example: For $3'\text{-ATGGTAGATC-}5'$, the complementary strand is $5'\text{-TACCATCTAG-}3'$.
• Hydrogen-Bond Count Calculation:
  • $\text{A--T}$ or $\text{T--A}$ pairs = $2$ H bonds.
  • $\text{G--C}$ or $\text{C--G}$ pairs = $3$ H bonds.
  • Sequence $3'\text{-ATGGTAGATC-}5'$ has $6\text{ A/T pairs}$ and $4\text{ G/C pairs}$.
  • Total hydrogen bonds: $(6 \times 2) + (4 \times 3) = 12 + 12 = 24\text{ H bonds}$.

Lipid Biochemistry and Types

• Common Features: Mostly nonpolar/hydrophobic and rich in carbon and hydrogen; generally insoluble in water.
• True Monomer Status: Lipids do not have one repeating monomer and are not true polymers.
• Triglyceride: Glycerol + $3$ fatty acids; major long-term energy-storage lipid.
• Saturated Fatty Acid: No $\text{C=C}$ double bonds; straighter chains, often solid at room temperature.
• Unsaturated Fatty Acid: One or more $\text{C=C}$ double bonds; bends/kinks, often liquid at room temperature.
• Phospholipid: Glycerol + $2$ fatty acid tails + phosphate-containing polar head.
• Amphipathic: Phospholipids have a hydrophilic head and hydrophobic tails, so they spontaneously form bilayers in water.

Chapter 3: Cells

Cell Size Limitations

• Surface-Area-to-Volume Ratio: As a cell grows, volume increases faster than surface area. Small cells have more membrane surface relative to volume, allowing faster exchange of nutrients, gases, wastes, and signals.
• Diffusion Distance: Shorter internal distances make transport and signaling more efficient.

Microscopy Types and Applications

• Light Microscope (LM): Uses visible light and glass lenses; can view living cells; lower resolution than electron microscopes.
• Scanning Electron Microscope (SEM): Scans the surface with electrons; produces detailed 3-D-like images of external surface structures.
• Transmission Electron Microscope (TEM): Electrons pass through a thin specimen; shows detailed internal ultrastructure in 2-D. Specimen must be dead.

Cell Structures and Organelle Functions

• Plasma Membrane: Selective barrier; phospholipid bilayer with proteins; controls transport and communication.
• Cytoplasm/Cytosol: Fluid region where many metabolic reactions occur; organelles are suspended here.
• Nucleus: Stores DNA; controls gene expression; surrounded by nuclear envelope with pores.
• Nucleolus: Makes rRNA and assembles ribosomal subunits.
• Ribosome: Site of protein synthesis; free ribosomes make cytosolic proteins, bound ribosomes make secreted/membrane/endomembrane proteins.
• Rough ER: Has ribosomes; synthesizes and folds many proteins for secretion/membranes.
• Smooth ER: Lipid synthesis, detoxification, carbohydrate metabolism, $\text{Ca}^{2+}$ storage.
• Golgi Apparatus: Modifies, sorts, and packages proteins/lipids into vesicles.
• Lysosome: Acidic digestive organelle; breaks down macromolecules, pathogens, and worn organelles.
• Peroxisome: Oxidizes fatty acids and detoxifies harmful compounds; breaks down $\text{H}_2\text{O}_2$ with catalase.
• Mitochondrion: Cellular respiration and ATP production; double membrane; own DNA and ribosomes.
• Chloroplast: Photosynthesis in plants/algae; double membrane; thylakoids and chlorophyll; own DNA and ribosomes.
• Central Vacuole: Large plant organelle for storage, digestion, and maintaining turgor pressure.