Study Guide for Trimester 3 Finals

Bond Structures and Molecular Stability

  • Covalent Bonds:
    • Double bonds, such as carbon-carbon double bonds (C=C), influence molecular stability and shape.
    • Double bonds are stronger and shorter than single bonds, affecting reactivity and molecular function.

Difference Between DNA and RNA

  • DNA:

    • Structure: Double-stranded.
    • Sugar: Deoxyribose.
    • Bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
    • Function: Stores genetic information.

  • RNA:

    • Structure: Single-stranded.
    • Sugar: Ribose.
    • Bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G).
    • Function: Used in protein synthesis (mRNA, tRNA, rRNA).

Properties of Water

  • Cohesion: Water molecules stick to each other due to hydrogen bonding, which allows for surface tension.
  • Adhesion: Water molecules stick to other substances, helping water climb structures like plant vessels (capillary action).
  • High Specific Heat: Water resists changes in temperature, maintaining stable internal temperatures for organisms and environments.
  • Universal Solvent: Water can dissolve many polar and charged substances, making it essential for transporting nutrients and waste in cells.

Hydrolysis and Dehydration Synthesis

  • Dehydration Synthesis: Builds macromolecules by removing water.
  • Hydrolysis: Breaks macromolecules by adding water.

Photosynthesis and Cellular Respiration

  • Photosynthesis (in chloroplasts):

    • Converts CO₂ and sunlight into glucose and O₂.
    • Light-dependent Reactions: Use sunlight and water to produce ATP and NADPH, releasing oxygen as a byproduct.
    • Calvin Cycle: Uses ATP, NADPH, and CO₂ to produce glucose.

  • Cellular Respiration (in mitochondria):

    • Converts glucose into ATP.
    • Glycolysis (in cytoplasm): Breaks glucose into 2 pyruvate molecules, producing ATP and NADH.
    • Krebs Cycle (mitochondrial matrix): Breaks down pyruvate into CO₂, generating NADH and FADH2.
    • Electron Transport Chain (ETC) & Chemiosmosis: Uses electrons from NADH and FADH2 to pump protons, producing ATP.

Eukaryotes vs. Prokaryotes

  • Eukaryotes:
    • Have membrane-bound organelles (nucleus, mitochondria).
  • Prokaryotes:
    • No nucleus or organelles; simpler structure.

Organelles and Their Functions

  • Nucleus: Stores DNA.
  • Mitochondria: Produces ATP.
  • Ribosomes: Sites of protein synthesis.
  • Endoplasmic Reticulum (ER), Golgi Apparatus, Lysosomes: Involved in processing and transport of biomolecules.

Active Transport

  • Definition: Movement of molecules against their concentration gradient, requiring energy (ATP).
  • Examples: Sodium-potassium pump, proton pump.

Osmosis and Tonicity

  • Osmosis: Water moves across membranes toward areas of higher solute concentration.
  • Tonicity: Effects of solutions on cell shape:
    • Hypotonic: Water moves into the cell; cell swells and may burst.
    • Hypertonic: Water moves out of cell; cell shrinks.
    • Isotonic: Equal water movement; cell remains the same size.

Enzymes and Their Roles

  • Biological Catalysts: Speed up reactions by lowering activation energy.
  • Enzyme-Substrate Interactions: Governed by lock-and-key or induced fit models.
  • Denaturation: Disruptions from high heat, extreme pH, or salinity deactivate enzymes.

Experimental Design

  • Identifying Variables: Include controls and constants.
  • Control Group: A group not receiving the experimental treatment; used for comparison.

Evolution of O₂ on Earth

  • Photosynthetic Organisms: Began producing O₂ ~2.5 billion years ago during the Great Oxygenation Event, changing Earth's atmosphere and enabling aerobic respiration.

Positive Feedback Mechanisms

  • Definition: Amplify changes that are not homeostatic.
  • Example: Oxytocin during childbirth intensifies contractions.

Cell Communication

  • Involves: Ligands, receptors, and signal transduction pathways.
  • Significance: Essential for coordination of cell functions.

Cell Cycle and Checkpoints

  • Phases: Interphase (G₁, S, G₂), Mitosis, Cytokinesis.
  • Checkpoints: G₁ (growth), G₂ (DNA replication), M (spindle attachment).
    • Controlled by cyclins and CDKs: Regulate cell cycle progression; unchecked cyclin production can lead to cancer.

Inheritance Patterns and Chi-Square Test

  • Chi-Square Test: Compares observed vs. expected data.
    • Null Hypothesis: Suggests no significant difference between observed and expected data.
    • Chi-square value: Used to evaluate significance, rejecting when greater than the critical value.
Trait Types: Autosomal and X-linked

  • Autosomal Dominant:

    • Inheritance: One mutated allele is sufficient.
    • Example: Huntington’s disease.
    • Risk to offspring: 50% chance if one parent is affected.

  • Autosomal Recessive:

    • Inheritance: Two mutated alleles needed.
    • Parents: Often both carriers but unaffected.
    • Example: Cystic fibrosis, sickle cell anemia.

  • X-linked Dominant:

    • Inheritance: One mutated X chromosome causes the trait.
    • Affects both sexes but usually more severe in males.
    • Example: Rett syndrome.

  • X-linked Recessive:

    • Inheritance: Males need one copy, females need two.
    • Mostly affects males, with females as carriers.
    • Example: Hemophilia, red-green color blindness.

Macromolecules

  • Carbohydrates (C, H, O): Energy sources (e.g., glucose, starch).
  • Proteins (C, H, O, N, S): Structural and functional roles (e.g., enzymes).
  • Lipids (C, H, O): Membranes and energy storage.
  • Nucleic Acids (C, H, O, N, P): Genetic information (DNA, RNA).

Meiosis

  • Definition: Cell division creating 4 genetically unique haploid gametes via crossing over and independent assortment.

Protein Folding

  • Functional 3D Structure: Achieved through distinct levels:
    • Primary Structure: Amino acid sequence.
    • Secondary: Local folding into alpha-helices and beta-pleated sheets.
    • Tertiary: Overall 3D shape from R-group interactions.
    • Quaternary: Formation of functional proteins from multiple polypeptide chains.

Transcription and Translation

  • Transcription (in Nucleus): DNA → mRNA.
  • Translation (in Cytoplasm/Ribosome): mRNA → Protein, involving tRNA, ribosomes, codons, and amino acids.

Lac Operon

  • Gene Regulation System in E. coli: Activates lactose-digesting enzymes when lactose is present and glucose is low.
  • Components: Promoter, operator, repressor, and genes (lacZ, lacY, lacA).

DNA Replication

  • Process: Semi-conservative.
  • Involves: Enzymes such as helicase, DNA polymerase, ligase; occurs during the S phase of interphase.

Alternative Splicing

  • Definition: Allows one gene to produce multiple proteins by rearranging exons after introns are removed.

Gel Electrophoresis

  • Technique: Separates DNA, RNA, or proteins based on size and charge.
  • Mechanism: DNA, negatively charged, moves towards positive end; smaller fragments move faster.

Hardy-Weinberg Equation

  • Purpose: Describes allele/genotype frequencies in a non-evolving population.
  • Conditions: No mutation, migration, selection, random mating, large population.

Common Ancestry

  • Concept: All organisms share a common ancestor, supported by DNA, fossil records, embryology, and homologous structures.

Reproductive Isolation

  • Definition: Prevents gene flow between species.
  • Types:
    • Temporal: Different breeding times.
    • Behavioral: Differences in mating behaviors.
    • Mechanical: Structural differences preventing mating.
    • Gametic: Incompatibilities between sperm and egg.
    • Habitat: Same area, but occupying different habitats.

Symbiotic Relationships Between Species

  • Mutualism: Both benefit (e.g., bees and flowers).
  • Commensalism: One benefits, the other is unaffected.
  • Parasitism: One benefits and one is harmed.
  • Predation: One benefits from harming the other.
  • Competition: Both are harmed by limited resources.

Keystone Species

  • Definition: A species with a disproportionately large impact on its ecosystem.
  • Examples: Sea otters controlling sea urchin populations, wolves in Yellowstone.

Genetic Drift

  • Definition: Random changes in allele frequency, especially in small populations.
  • Bottleneck Effect: Population drastically reduced.
  • Founder Effect: New population founded by few individuals.

Density-Dependent vs. Density-Independent Factors

  • Density-Dependent: Influenced by population size (e.g., disease, competition).
  • Density-Independent: Not affected by population size (e.g., natural disasters).

Mitosis

  • Definition: Produces two identical diploid daughter cells through phases: Prophase, Metaphase, Anaphase, Telophase.
  • Function: Used for growth, repair, and asexual reproduction.

Artificial Selection vs. Natural Selection

  • Artificial Selection: Human-directed trait selection (e.g., dog breeds).
  • Natural Selection: Environmental pressures favor traits enhancing survival and reproduction.