BIO 102 Comprehensive Chapter Notes Summary & Study Notes

🧬 Chromosomal Basis & Genetic Linkage

Genetic linkage occurs when genes are located close together on the same chromosome and tend to be inherited together. Crossing over during meiosis can break linkage and create new allele combinations. The recombination frequency (percent of recombinant offspring) reflects physical distance between genes; 1 map unit (mu) = 1% recombination. A linkage map shows relative gene positions (not absolute distances).

🔗 Mapping & Recombination

Recombination frequency increases with physical distance; very distant genes may appear to assort independently because crossovers almost always occur between them. To detect such relationships, test intermediate genes to infer linkage.

⚧ Sex-Linked Inheritance & SRY

Sex-linked genes are on sex chromosomes and inherit differently in males and females. The human X carries ~2350 genes; the SRY gene on the Y chromosome triggers male developmental pathways by regulating downstream gene expression (testis development and hormone production). Presence of a Y generally determines genetic maleness in humans.

❌ X-Inactivation & Dosage Compensation

In female mammals one X is randomly inactivated early in embryogenesis (dosage compensation). The inactive X condenses (heterochromatin) and is passed to descendant cells, producing mosaic patterns (e.g., calico cats) in heterozygous females.

🌱 Cytoplasmic Inheritance & Genomic Imprinting

Cytoplasmic inheritance (mitochondria, chloroplasts) is usually uniparental (maternal in most multicellular eukaryotes) because zygotes inherit more cytoplasm from the egg. Genomic imprinting is parent-of-origin specific expression: an allele is silenced (often via methylation) depending on whether it was inherited from sperm or egg. Imprints are erased in germ cells so new imprinting appropriate to sex can occur.

🧩 Chromosomal Mutations & Nondisjunction

Chromosomal structure changes arise from DNA breaks (chemicals, radiation, viruses). Nondisjunction (failure of homologs or sister chromatids to separate) yields aneuploidy (extra or missing chromosomes) or polyploidy (more than normal sets). Many autosomal monosomies/trisomies are lethal; some trisomies of small autosomes (e.g., 13, 15, 18, 21, 22) can produce live births with severe effects. Sex-chromosome aneuploidies often have milder phenotypes (e.g., Turner X0, Klinefelter XXY).

🧾 Pedigrees & Genetic Counseling

Human pedigrees track inheritance patterns: autosomal dominant, autosomal recessive, X-linked recessive/dominant patterns have distinctive family distributions. Carriers (heterozygotes) can transmit recessive alleles without showing symptoms. Prenatal diagnostic tools include amniocentesis (around month 4; small miscarriage risk) and chorionic villus sampling (earlier; higher miscarriage risk) to detect chromosomal abnormalities or mutant alleles.

⚙️ Energy, Thermodynamics & Metabolism

Thermodynamics: study of energy transformations. Energy exists as kinetic (motion) and potential (stored). Cells commonly measure energy in terms of free energy changes; biologically, chemical energy in bonds is most convenient to track (e.g., ATP).

🔁 Redox Reactions

Redox: oxidation (loss of electrons) and reduction (gain of electrons) always occur together — electrons removed from one molecule are transferred to another. Example carriers include $NADP^+$/$NADPH$ and $NAD^+$/$NADH$.

⚡ Reaction Rates & Activation Energy

Activation energy is the energy barrier to initiate a reaction; higher activation energy means slower rate. Reaction rates can be increased by raising temperature or by using catalysts. Biological systems rely on enzymes (biological catalysts) because raising temperature broadly would damage cells.

🧪 Enzymes & Catalysis

An enzyme has an active site complementary to substrate(s). Induced fit: substrate binding changes enzyme shape to facilitate catalysis. Catalysis sequence: substrate binding → transition-state stabilization → product formation → product release. Thousands of enzymes are needed because each catalyzes specific reactions under controlled regulation.

🚫 Inhibition & Regulation

Enzyme inhibition: critical for metabolic control. Irreversible inhibitors permanently inactivate enzymes (often bind covalently). Reversible inhibitors can dissociate: competitive inhibitors bind active site; noncompetitive (allosteric) inhibitors bind elsewhere and alter enzyme activity. Allosteric sites mediate regulation; feedback inhibition is common in pathways where end-product inhibits an upstream enzyme.

🧬 Cofactors, Coenzymes & Pathways

Cofactors: inorganic ions (e.g., $Mg^{2+}$). Coenzymes: organic molecules (e.g., vitamins-derived carriers) that assist catalysis. Metabolism: sum of catabolic (breakdown, energy-releasing) and anabolic (biosynthetic, energy-consuming) pathways. Pathways must be coordinated and regulated to balance energy, intermediates, and cellular needs.

🧬 Mendel & Patterns of Inheritance

Gregor Mendel formulated core principles using pea crosses: traits are governed by factors (now genes) with alleles. Dominant alleles mask recessive alleles in heterozygotes. Homozygote (same alleles) vs heterozygote (different alleles). Principle of segregation: allele pairs separate during gamete formation.

🎲 Probability & Punnett Squares

Mendelian predictions use probability rules: product rule for independent events (multiply probabilities) and rule of addition for alternative pathways (sum probabilities). Punnett squares visualize gamete combinations for monohybrid and dihybrid crosses.

🔁 Independent Assortment & Chromosome Theory

Dihybrid crosses (two traits) yield 9:3:3:1 ratios when genes assort independently. The chromosome theory links Mendel's factors to chromosomes: different chromosome pairs segregate independently in meiosis.

🔀 Extensions: Incomplete Dominance & Codominance

Incomplete dominance: heterozygote shows intermediate phenotype (F2 ratios differ from classic 3:1). Codominance: both alleles are fully expressed (e.g., $AB$ blood type).

🅰️ Multiple Alleles & ABO System

Blood type results from three alleles: $I_A$, $I_B$, and $i$. Genotypes: type A = $I_AI_A$ or $I_Ai$; type B = $I_BI_B$ or $I_Bi$; type AB = $I_AI_B$ (codominance); type O = $ii$.

📈 Polygenic Inheritance & Pleiotropy

Polygenic traits involve multiple genes with additive effects, producing continuous variation (bell-shaped distributions). Pleiotropy: a single gene influences multiple phenotypic traits (e.g., sickle-cell allele affects hemoglobin, circulation, and organ function).

🧩 Epistasis

Epistasis: interaction where alleles at one locus mask or modify expression at another locus (e.g., pigment deposition genes in Labrador coat color where one gene can prevent pigment irrespective of color alleles).

🔬 Cell Division Overview

Cell division duplicates and partitions genetic material and cytoplasm. In bacteria, binary fission replicates the circular DNA at an origin and partitions products; septation (protein ring contraction) divides the cell.

🧬 Eukaryotic Chromosomes & Chromatin

Eukaryotic chromosomes are linear DNA molecules packaged with proteins (chromatin) — roughly 40% DNA and 60% protein. Nucleosomes (DNA wrapped around histone octamers) compact DNA. Replicated chromosomes consist of two sister chromatids joined at the centromere.

⏳ Cell Cycle Phases

The cell cycle: interphase (G1, S, G2) and mitotic phase (mitosis + cytokinesis). S phase: DNA replication. Some cells exit to G0 (nondividing) but can re-enter for repair.

🔁 Mitosis & Cytokinesis

Mitosis ensures equal distribution of duplicated chromosomes to daughter nuclei; cytokinesis partitions the cytoplasm, producing two genetically identical diploid daughters (for somatic cells).

✅ Cell Cycle Regulation & Checkpoints

Control points: G1 checkpoint (growth signals, DNA integrity; passing commits cell to division), G2 checkpoint (checks DNA replication), mitotic checkpoint (ensures spindle attachment before anaphase). Regulation involves cyclins and cyclin-dependent kinases (CDKs); internal/external signals modulate progression.

✋ Inhibitory Controls: Senescence, Contact Inhibition & Apoptosis

Contact inhibition halts division when cells touch neighbors. Senescence (telomere shortening) limits replication (~70 divisions). Apoptosis is programmed cell death used to remove damaged or abnormal cells.

⚠️ Cancer & Mutated Control Genes

Cancer arises from accumulated mutations, especially activation of proto-oncogenes into oncogenes (promote uncontrolled division) and loss of tumor suppressor genes (which normally inhibit division, repair DNA, or trigger apoptosis). Inherited high-risk mutations reduce the number of additional hits needed for tumorigenesis.

☀️ Photosynthesis Overview

Photosynthesis converts solar energy into chemical energy stored in carbohydrates. Two linked sets of reactions: light-dependent reactions (capture light to make $ATP$ and reduce $NADP^+$ to $NADPH$, oxidizing $H_2O$ to $O_2$) and light-independent reactions (Calvin cycle: use $ATP$ and $NADPH$ to fix $CO_2$ into carbohydrates).

🌿 Chloroplasts & Photosystems

Photosynthesis occurs in chloroplasts (stroma and thylakoid membranes). Photosystems are pigment–protein complexes (light-harvesting antennae) that funnel energy to reaction-center chlorophylls, initiating electron transfer.

🎯 Pigments & Photoelectric Effect

Pigments absorb specific wavelengths; chlorophylls absorb violet-blue and red, reflecting green. Photons excite electrons (photoelectric effect); short wavelengths carry more energy per photon.

🔋 Light Reactions: Electron Flow & Gradients

Photoexcited electrons from PS II pass through an electron transport chain (ETC), powering proton pumping to generate an $H^+$ gradient used to make $ATP$. Electrons then reach PS I, are re-excited, and ultimately reduce $NADP^+$ to $NADPH$ (via $NADP^+$ reductase).

🧩 Calvin Cycle (Carbon Fixation)

The Calvin cycle fixes $CO_2$ in three phases: (1) carbon fixation — $CO_2$ attaches to $RuBP$ (enzyme rubisco) producing a 6-carbon intermediate that splits into two 3-carbon molecules; (2) reduction — $NADPH$ and $ATP$ supply electrons and energy to convert intermediates to carbohydrate (generalized as $CH_2O$ units); (3) regeneration — $RuBP$ is regenerated so the cycle can continue.

♻️ Photorespiration & Alternative Pathways

Photorespiration consumes $O_2$ and releases $CO_2$, reducing photosynthetic efficiency, especially at high temperatures. Plants evolved alternatives:

• C3: typical Calvin-cycle fixation (most plants).
• C4: spatial separation of initial $CO_2$ fixation and Calvin cycle; effective in hot, sunny environments to reduce photorespiration at cost of extra energy.
• CAM: temporal separation (fix $CO_2$ at night into 4-C acids; run Calvin cycle during day) — conserves water in arid environments but limits daily carbon gain.