Core Principles of Biology: Evolution, Cell Division, Genetics, and Gene Expression

Chapter 1: Themes of Biology and Evolution

Major Themes in Biology

• Organization: Biological systems are structured in a hierarchy from molecules to the biosphere. Emergent properties arise at each level due to the arrangement and interactions of parts.

• Information: Life processes depend on the transmission and expression of genetic information, primarily through DNA.

• Energy and Matter: Living organisms require energy to maintain order, grow, and reproduce. Energy flows through ecosystems (e.g., sunlight to chemical energy), while chemicals cycle within them.

• Interactions: Organisms interact with each other and their environment, affecting both their own survival and the ecosystem's dynamics. Feedback regulation (e.g., negative feedback) maintains homeostasis.

• Evolution: The process by which populations change over generations, explaining both the unity and diversity of life.

Cell Types and Genetic Information

• Eukaryotic cells have membrane-bound organelles, including a nucleus; prokaryotic cells lack a nucleus.

• DNA encodes genetic information and is transmitted during cell division.

Producers vs. Consumers

• Producers (e.g., plants) convert energy from sunlight into chemical energy.

• Consumers (e.g., animals) obtain energy by eating other organisms.

Scientific Inquiry

• Inductive reasoning: Deriving general principles from specific observations.

• Deductive reasoning: Making specific predictions from general principles.

• Hypothesis: A testable explanation for observations.

• Theory: A broad explanation supported by a large body of evidence.

• Variables: Independent variable is manipulated; dependent variable is measured.

Evolution and Diversity of Life

• Charles Darwin proposed natural selection as the mechanism of evolution.

• Life is classified into three domains: Bacteria, Archaea, and Eukarya.

Climate Change

• Human activities (e.g., burning fossil fuels) contribute to climate change by increasing greenhouse gases.

Chapter 12: The Cell Cycle and Mitosis

Overview of Cell Division

• Cell division is essential for growth, development, and repair.

• Results in genetically identical daughter cells (in mitosis).

Key Terms

• Genome: The complete set of an organism's DNA.

• Chromosomes: DNA molecules packaged with proteins.

• Chromatin: DNA-protein complex in non-dividing cells.

• Somatic cells: Body cells (diploid); gametes: reproductive cells (haploid).

• Sister chromatids: Identical copies of a chromosome, joined at the centromere.

Phases of the Cell Cycle

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

• Mitosis: Division of the nucleus; stages include:

  • Prophase: Chromosomes condense, spindle forms.

  • Prometaphase: Nuclear envelope fragments, spindle fibers attach to kinetochores.

  • Metaphase: Chromosomes align at the metaphase plate.

  • Anaphase: Sister chromatids separate and move to opposite poles.

  • Telophase: Nuclear envelopes reform, chromosomes decondense.

• Cytokinesis: Division of the cytoplasm.

  • In animal cells: cleavage furrow forms.

  • In plant cells: cell plate forms.

Other Concepts

• Binary fission: Cell division in bacteria.

• Cancer cells: Exhibit uncontrolled division due to faulty cell cycle control.

• Checkpoints: Control points in the cell cycle (e.g., G1, G2, M).

• G0 phase: Non-dividing state.

• Benign vs. malignant tumors: Benign do not spread; malignant can metastasize.

Chapter 13: Meiosis and Sexual Life Cycles

Key Concepts

• Genes: Units of heredity located on chromosomes.

• Gametes: Reproductive cells (sperm and egg); somatic cells: all other body cells.

• Locus: Specific location of a gene on a chromosome.

• Asexual vs. sexual reproduction: Asexual produces identical offspring; sexual combines genes from two parents.

• Karyotype: Ordered display of chromosomes.

• Homologous chromosomes: Chromosome pairs, one from each parent.

• Autosomes: Non-sex chromosomes; sex chromosomes: X and Y.

• Diploid (2n): Two sets of chromosomes; haploid (n): one set.

Meiosis

• Occurs in germ cells to produce gametes.

• Two divisions: Meiosis I and II, resulting in four haploid, genetically unique daughter cells.

• Prophase I: Homologous chromosomes pair and exchange segments (crossing over at chiasmata).

• Metaphase I: Homologous pairs align randomly at the metaphase plate.

• Anaphase I: Homologous chromosomes separate.

Comparison: Mitosis vs. Meiosis

• Mitosis: One division, two identical diploid cells.

• Meiosis: Two divisions, four non-identical haploid cells.

Genetic Variation Mechanisms

• Independent assortment of chromosomes.

• Crossing over during Prophase I.

• Random fertilization of gametes.

Chapter 14: Mendel and the Gene Idea

Mendel's Experiments

• Gregor Mendel studied inheritance using pea plants.

• Characters: Heritable features (e.g., flower color); traits: variants of characters.

• True-breeding: Offspring identical to parents.

• P, F1, F2 generations: Parental, first filial, and second filial generations.

• Crossing true-breeding plants yields all dominant trait in F1; F2 shows 3:1 ratio (dominant:recessive).

Mendel's Concepts

• Alleles: Alternative forms of a gene.

• Law of segregation: Alleles separate during gamete formation.

• Homozygous: Two identical alleles; heterozygous: two different alleles.

• Phenotype: Physical appearance; genotype: genetic makeup.

• Testcross: Determines genotype by crossing with homozygous recessive.

• Dihybrid cross: Involves two traits; shows independent assortment.

Deviations from Mendelian Genetics

• Incomplete dominance: Heterozygote shows intermediate phenotype (e.g., pink flowers).

• Codominance: Both alleles expressed (e.g., AB blood type).

• Multiple alleles: More than two alleles exist (e.g., ABO blood group).

• Pleiotropy: One gene affects multiple traits (e.g., sickle cell disease).

• Epistasis: One gene affects expression of another (e.g., coat color in mice).

• Polygenic inheritance: Multiple genes affect a trait (e.g., skin color).

• Environmental impact: Phenotype influenced by environment.

Inherited Disorders

• Recessive disorders: Require two copies of mutant allele (e.g., cystic fibrosis, sickle cell).

• Carriers: Heterozygotes for recessive disorders.

• Dominant disorders: Only one mutant allele needed (e.g., Huntington's disease).

• Multifactorial disorders: Influenced by genes and environment.

Chapter 15: Chromosomal Basis of Inheritance

Key Discoveries

• Thomas Hunt Morgan used fruit flies to show genes are on chromosomes.

• Wild type: Most common phenotype; mutants: alternative phenotypes.

Sex Determination and Sex-Linked Genes

• XY system: Males (XY), females (XX).

• Sex-linked genes: Located on X or Y chromosomes.

• X-linked disorders (e.g., color blindness, hemophilia) are more common in males due to having only one X chromosome.

• Barr body: Inactivated X chromosome in females; leads to mosaicism.

Linked Genes and Chromosomal Alterations

• Linked genes: Genes located close together on the same chromosome.

• Nondisjunction: Failure of chromosomes to separate properly.

• Aneuploidy: Abnormal number of chromosomes (e.g., monosomic, trisomic).

• Polyploidy: More than two sets of chromosomes (common in plants).

• Structural changes: Deletion, duplication, inversion, translocation.

Human Disorders

Disorder	Chromosomal Change	Features
Down Syndrome	Trisomy 21	Intellectual disability, characteristic facial features
Klinefelter Syndrome	XXY	Male with extra X, sterile
Triple X Syndrome	XXX	Female, usually normal
Turner Syndrome	Monosomy X	Female, sterile, short stature
Cri du chat	Deletion on chromosome 5	Cry sounds like a cat, intellectual disability

Genomic Imprinting and Extranuclear Genes

• Genomic imprinting: Expression of an allele depends on parent of origin.

• Extranuclear genes: Found in mitochondria and chloroplasts; inherited maternally.

Chapter 16: Molecular Basis of Inheritance

Key Experiments

• Morgan: Genes are on chromosomes.

• Griffith: Discovered transformation in bacteria.

• Avery, McCarty, MacLeod: DNA is the transforming molecule.

• Hershey and Chase: DNA, not protein, is genetic material (using bacteriophages).

• Chargaff: Base pairing rules (A=T, G=C).

• Rosalind Franklin: X-ray diffraction images revealed DNA's helical structure.

• Watson and Crick: Proposed double helix model of DNA.

DNA Structure and Replication

• Double helix: Two antiparallel strands.

• Semiconservative replication: Each new DNA has one old and one new strand.

• Origins of replication: Sites where DNA replication begins.

• Replication fork: Y-shaped region where DNA is unwound.

Enzymes and Proteins in DNA Replication

• Helicase: Unwinds DNA.

• Single-Strand Binding Proteins: Stabilize unwound DNA.

• Topoisomerase: Relieves strain ahead of fork.

• Primase: Synthesizes RNA primer.

• DNA Polymerases: Add nucleotides to new strand.

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized in Okazaki fragments.

• DNA Ligase: Joins Okazaki fragments.

DNA Repair and Chromatin Structure

• Mismatch repair: Corrects errors after replication.

• Nucleotide excision repair: Removes and replaces damaged DNA.

• Telomeres: Repetitive DNA at chromosome ends; protect from degradation.

• Chromatin: DNA and protein complex; histones are main proteins.

• Nucleosome: DNA wrapped around histone core.

Chapter 17: Gene Expression: From Gene to Protein

Central Dogma and Gene Expression

• Central Dogma: Information flows from DNA → RNA → Protein.

• Transcription: Synthesis of RNA from DNA template.

• Translation: Synthesis of protein from mRNA.

• In eukaryotes, transcription occurs in the nucleus; translation in the cytoplasm. In prokaryotes, both occur in the cytoplasm.

Genetic Code

• 20 amino acids, encoded by triplet codons (3 nucleotides).

• 64 codons: 61 code for amino acids, 3 are stop codons.

• Start codon: AUG (methionine).

• Code is redundant (multiple codons per amino acid) but not ambiguous (each codon specifies only one amino acid).

• Genetic code is universal (shared by almost all organisms).

Transcription and mRNA Processing

• RNA polymerase: Synthesizes RNA.

• mRNA modifications (eukaryotes): 5’ cap, poly-A tail, RNA splicing (removal of introns, joining of exons).

• Alternative splicing: Allows one gene to code for multiple proteins.

Translation and Protein Synthesis

• tRNA: Transfers amino acids to ribosome; has anticodon complementary to mRNA codon.

• Ribosome: Site of protein synthesis; has A, P, E sites for tRNA binding.

• Translation occurs in three stages: initiation, elongation, termination.

• Polyribosomes: Multiple ribosomes translating one mRNA simultaneously.

• Proteins may undergo folding and post-translational modifications.

Mutations and Gene Editing

• Point mutations: Single nucleotide changes.

• Types: Silent (no effect), missense (changes amino acid), nonsense (introduces stop codon).

• Insertions/deletions: May cause frameshifts.

• Mutagens: Physical or chemical agents causing mutations.

• CRISPR: Tool for gene editing.

• Gene: Region of DNA that can be expressed to produce a functional product.