AP Biology Semester 2 Final Exam Study Guide: Structured Study Notes

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Regulation of Gene Expression

Feedback Inhibition and Operon Model

Gene expression in prokaryotes and eukaryotes is tightly regulated to ensure proper cellular function. Feedback inhibition and operon models are key mechanisms in prokaryotic gene regulation.

Feedback Inhibition: A process where the end product of a metabolic pathway inhibits an enzyme involved earlier in the pathway, preventing overproduction.
Operon: A cluster of genes under the control of a single promoter, allowing coordinated expression.
Operator: DNA segment where a repressor binds to regulate transcription.
Repressor: Protein that binds to the operator to block transcription.
Corepressor: Molecule that activates a repressor.
Inducer: Molecule that inactivates a repressor, allowing transcription.
Activator: Protein that increases transcription by binding to DNA.
Trp Operon: Repressible operon; tryptophan acts as a corepressor.
Lac Operon: Inducible operon; lactose acts as an inducer. CRP (cAMP receptor protein) is a stimulatory activator.

Example: The lac operon is activated in the presence of lactose and low glucose, allowing E. coli to metabolize lactose.

Eukaryotic Gene Expression

Eukaryotic gene expression is regulated at multiple levels, including chromatin modification, transcription, RNA processing, and translation.

Chromatin Modification: Histone acetylation and DNA methylation affect gene accessibility.
Transcription Control Elements: Enhancers and promoters regulate transcription initiation.
RNA Processing: Includes splicing, capping, and polyadenylation.
mRNA Degradation: Determines mRNA lifespan and protein production.
Translation Initiation Factors: Control the start of protein synthesis.
Protein Processing and Degradation: Post-translational modifications and proteasome-mediated degradation.

Example: Alternative splicing of pre-mRNA allows production of different proteins from a single gene.

The Cell Cycle and Mitosis

Genome Organization and Cell Division

The cell cycle is the series of events that cells go through as they grow and divide. It includes interphase and mitosis.

Genome: The complete set of genetic material in a cell.
Chromosomes: Structures that carry genetic information.
Chromatin: DNA and protein complex forming chromosomes.
Haploid Cells: Cells with one set of chromosomes (n).
Diploid Cells: Cells with two sets of chromosomes (2n).
Sister Chromatids: Identical copies of a chromosome connected at the centromere.
Centromere: Region where sister chromatids are joined.

Phases of the Cell Cycle

Interphase: Consists of G1 (growth), S (DNA synthesis), and G2 (preparation for mitosis).
Mitosis: Divided into five stages:
- Prophase: Chromosomes condense, spindle forms.
- Prometaphase: Nuclear envelope breaks down, spindle attaches to chromosomes.
- Metaphase: Chromosomes align at the metaphase plate.
- Anaphase: Sister chromatids separate.
- Telophase: Nuclear envelope reforms, chromosomes decondense.
Mitotic Spindle: Structure that separates chromosomes.
Centrosomes: Organize spindle fibers.

Cell Cycle Regulation

Cell Cycle Control System: Regulates progression through the cell cycle.
Checkpoints: G1, G2, and M checkpoints ensure proper division.
Density Dependent Inhibition: Cells stop dividing when crowded.
Anchorage Dependence: Cells require attachment to a surface to divide.
Malignant Tumors: Cancerous growths that invade tissues.
Metastasis: Spread of cancer cells to other parts of the body.

Meiosis and Genetic Variation

Meiosis and Fertilization

Meiosis is the process by which gametes are produced, reducing chromosome number by half and increasing genetic diversity.

Fertilization: Fusion of gametes restores diploid number.
Meiosis: Two consecutive divisions (Meiosis I and II) produce four haploid cells.
Autosomes: Non-sex chromosomes.
Sex Chromosomes: Determine sex (X and Y).

Stages and Genetic Variation

Key Events: Crossing over, independent assortment, and random fertilization.
Benefits: Genetic variation increases adaptability and survival.

Cancer Genetics

Oncogenes and Tumor Suppressor Genes

Cancer arises from mutations in genes that regulate cell growth and division.

Oncogenes: Mutated genes that promote uncontrolled cell division.
Proto-oncogenes: Normal genes that can become oncogenes.
Tumor Suppressor Genes: Genes that inhibit cell division; loss leads to cancer.

Mendelian Genetics

Mendel’s Laws and Patterns of Inheritance

Gregor Mendel discovered fundamental laws of inheritance through experiments with pea plants.

Law of Segregation: Each individual has two alleles for each gene, which segregate during gamete formation.
Law of Independent Assortment: Genes for different traits assort independently.
Monohybrid Cross: Cross involving one trait.
Dihybrid Cross: Cross involving two traits.
Multiplication Rule: Probability of two independent events occurring together.
Addition Rule: Probability of either of two mutually exclusive events occurring.
Incomplete Dominance: Heterozygote shows intermediate phenotype.
Codominance: Both alleles are fully expressed.
Multiple Alleles: More than two alleles for a gene.
Pleiotropy: One gene affects multiple traits.
Epistasis: One gene affects expression of another.
Polygenic Inheritance: Multiple genes contribute to a trait.
Pedigrees: Diagrams showing inheritance patterns.
Recessive/Dominant Disorders: Genetic diseases caused by recessive or dominant alleles.
Sickle Cell: Example of pleiotropy and heterozygote advantage.

Chromosomal Genetics

Gene Linkage and Sex-Linked Traits

Genes located on chromosomes can be linked or sex-linked, affecting inheritance patterns.

Chromosome/Gene Connection: Genes are located on chromosomes.
Sex-Linked Genes: Genes on sex chromosomes, often X-linked.
X Gene Inactivation: In females, one X chromosome is inactivated.
Recombinant Frequencies: Measure of crossing over between genes.
Gene Linkage Maps: Diagrams showing gene positions based on recombination.

Developmental Biology

Cytoplasmic Determinants and Induction

Cell fate is influenced by cytoplasmic determinants and signals from neighboring cells.

Cytoplasmic Determinants: Molecules in egg cytoplasm that influence development.
Induction: Process where one cell influences the fate of another.

Nuclear Transplantation and Cloning

Nuclear Transplantation: Replacing the nucleus of an egg with a nucleus from another cell.
Cloning: Producing genetically identical organisms.

Evolution and Natural Selection

Darwin’s Theory and Evidence

Charles Darwin developed the theory of natural selection, influenced by other scientists and observations.

Influences: Linnaeus, Malthus, Hutton, Lyell, Cuvier, Lamarck, Artificial Selection.
Observations: Variation, overproduction, competition, differential survival.
Natural Selection: Process where organisms with favorable traits survive and reproduce.
Evidence: Direct observations, homology, vestigial structures, convergent evolution, analogies, fossil record, biogeography.
Examples: Peppered moths, MRSA, finches, soapberry beetles, sickle cell.

Population Genetics

Genetic Variation and Hardy-Weinberg Equilibrium

Population genetics studies genetic variation and evolutionary forces.

Genetic Variation: Differences among individuals in a population.
Sources: Mutation, recombination, gene flow.
Hardy-Weinberg Theorem: Describes allele and genotype frequencies in a non-evolving population.

Hardy-Weinberg Equation:

Methods of Evolution: Mutation, gene flow, genetic drift, natural selection, non-random mating.
Genetic Drift: Random changes in allele frequencies.
Gene Flow: Movement of alleles between populations.
Founder Effect: Small group starts new population.
Bottleneck Effect: Population size drastically reduced.
Selection Types: Directional, disruptive, stabilizing.
Heterozygote Advantage: Heterozygotes have higher fitness.
Frequency Dependent Selection: Fitness depends on frequency of phenotype.

Phylogeny and Classification

Phylogenetic Trees and Homologies

Phylogenetic trees depict evolutionary relationships among organisms.

Basal Taxon: Earliest diverging group.
Polytomy: Branch with more than two descendants.
Sister Taxa: Closest relatives.
Morphological Homologies: Similar structures due to common ancestry.
Molecular Homologies: Similar DNA or protein sequences.

Speciation

Species Concepts and Reproductive Isolation

Speciation is the process by which new species arise.

Biological Species Concept: Species are groups of interbreeding populations.
Reproductive Isolation: Prevents gene flow between species.
Prezygotic Barriers: Prevent fertilization (e.g., habitat, temporal, behavioral isolation).
Postzygotic Barriers: Prevent viable offspring (e.g., hybrid inviability).
Allopatric Speciation: Occurs with geographic isolation.
Sympatric Speciation: Occurs without geographic isolation.
Factors in Sympatric Speciation: Polyploidy, habitat differentiation, sexual selection.

Macroevolution and Early Life

Fossil Record and Continental Drift

The fossil record and geological events provide evidence for macroevolution.

Fossil Record: Chronological collection of life's remains.
Radiometric Dating: Determines age of fossils using isotopes.
Continental Drift: Movement of Earth's plates affects evolution.
Adaptive Radiation: Rapid diversification after mass extinctions.

Prokaryotes and Eukaryotes

Stromatolites and Cyanobacteria

Stromatolites and cyanobacteria are among the earliest life forms.

Stromatolites: Layered structures formed by microbial activity.
Cyanobacteria: Photosynthetic prokaryotes.

Endosymbiotic Theory

The endosymbiotic theory explains the origin of eukaryotic organelles.

Endosymbiotic Theory: Mitochondria and chloroplasts originated from engulfed prokaryotes.

Viruses

Viral Structure and Replication

Viruses are infectious agents with diverse structures and replication cycles.

Viral Structure: Composed of nucleic acid and protein coat (capsid).
Replicative Cycle: Includes attachment, entry, replication, assembly, and release.
Lytic Cycle: Virus destroys host cell.
Lysogenic Cycle: Viral DNA integrates into host genome.
Retroviruses: Use reverse transcriptase to copy RNA into DNA.

The Immune System

Innate and Adaptive Immunity

The immune system protects against pathogens through innate and adaptive responses.

Innate Immunity: Non-specific, immediate defense.
Adaptive Immunity: Specific, slower response.
Humoral Response: B-cells produce antibodies.
Cell-Mediated Response: Cytotoxic T-cells destroy infected cells.
Helper T-cells: Activate B and T cells.
MHC: Major histocompatibility complex, presents antigens.

Photosynthesis

Main Reactions and Plant Adaptations

Photosynthesis converts light energy into chemical energy in plants.

Chlorophyll: Pigment that absorbs light.
Chloroplast Structure: Contains thylakoids, stroma.
Linear Electron Flow: Produces ATP and NADPH.
Cyclic Electron Flow: Produces ATP only.
Calvin Cycle: Fixes carbon dioxide into sugars.
CAM and C4 Plants: Adaptations to minimize water loss.

Ecology

Population Growth

Population growth describes how populations change in size over time.

Exponential Growth: Population increases rapidly under ideal conditions.
Logistic Growth: Population growth slows as it approaches carrying capacity.

Population Growth Equation:

where N is population size, r is growth rate, and K is carrying capacity.

Fetal Pig Dissection

Reference Materials

For detailed anatomy and physiology, refer to the document posted on Google Classroom.

Additional info:

Some topics were expanded with academic context to ensure completeness and clarity for exam preparation.