FOB-II Biology Essentials

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1. Cellular Signaling and Communication 1.1 Introduction to Cell Signaling Definition: Process by which cells communicate with each other, enabling coordinated activities and responses to environmental stimuli. Importance: Essential for multicellular organisms to function, coordinate, and respond appropriately. Biological Example: Hawaiian bobtail squid and Aliivibrio fischeri bacteria use quorum sensing for light production, allowing the squid to hunt. 1.2 Types of Cell Signaling Autocrine Signaling: Cell targets itself . Releases signal and has receptors to receive it. Paracrine Signaling: Cell signals nearby cells . Messengers travel short distances, often unstable or quickly degraded. Endocrine Signaling: Cell signals distant cells throughout the body. Messengers ( hormones ) travel via the bloodstream to reach targets. 1.3 Signal Transmission Routes When an extracellular messenger binds to a receptor, it causes a conformational change that relays the signal internally. Route 1: Second Messengers Receptor activates an effector enzyme . Effector generates small molecules called second messengers (e.g., cAMP, Ca$^{2+}$, IP$_3$). Second messengers activate/inactivate other proteins, carrying the signal forward. Route 2: Protein Recruitment Receptor's internal domain directly attracts and activates cellular signaling proteins. 1.4 Regulation of Signaling: Phosphorylation Key "On/Off" Switch: Adding or removing phosphate groups changes protein shape and activity. Protein Kinases: Enzymes that add phosphate groups ($\text{PO}_4^{3-}$), usually activating proteins. Often target serine, threonine, or tyrosine amino acids. Can be cytoplasmic or membrane-bound. Protein Phosphatases: Enzymes that remove phosphate groups, often deactivating proteins. Typically more complex, with catalytic and regulatory subunits for specificity. Effects of Phosphorylation: Activate/inactivate enzymes, alter protein-protein interactions, change protein localization, mark for degradation. 1.5 Types of Cellular Messengers Amino Acids & Derivatives: Glutamate, acetylcholine, epinephrine (neurotransmitters, hormones). Gases: Nitric Oxide (NO), Carbon Monoxide (CO). Steroids: Cholesterol-derived, regulate sexual differentiation, metabolism. Eicosanoids: Fatty acid derivatives, regulate pain, inflammation (e.g., blocked by aspirin). Proteins & Polypeptides: Diverse group regulating cell division, differentiation, immune responses. 1.6 Receptors for Cellular Messengers G Protein-Coupled Receptors (GPCRs): Seven transmembrane $\alpha$-helices. Ligand binding causes conformational change, activating an internal G protein . Structure: N-terminus outside, C-terminus inside, loops for ligand/G protein binding. Activation: Ligand binding $\rightarrow$ disrupts noncovalent bonds $\rightarrow$ transmembrane helices shift $\rightarrow$ cytoplasmic loops change shape $\rightarrow$ high affinity for G protein $\rightarrow$ G protein releases GDP, binds GTP ("on" state). Amplification: Single activated GPCR can activate many G proteins. Receptor Protein-Tyrosine Kinases (RTKs): Ligand binding causes receptors to dimerize and activate their intrinsic kinase domain. Phosphorylate tyrosine residues on other proteins. Ligand-Gated Channels: Receptors are also ion channels. Ligand binding directly opens channel, allowing ion flow (e.g., nerve impulses). Steroid Hormone Receptors: Located inside the cell (cytoplasm). Steroid hormones diffuse through membrane, bind receptor $\rightarrow$ complex moves to nucleus $\rightarrow$ directly controls gene transcription. 1.7 GPCR Desensitization and Recycling Desensitization: Prevents overstimulation while messenger is present. Phosphorylation: GPCR kinase (GRK) phosphorylates activated GPCR. Arrestin Binding: Arrestin binds to phosphorylated GPCR, blocking G protein interaction. Fate of Internalized Receptor (via endocytosis): New Signaling Platform: Receptor-arrestin complex can activate other pathways (e.g., MAPK). Degradation: Sent to lysosome and destroyed (long-term desensitization). Recycling (Resensitization): Dephosphorylated and returned to cell surface, restoring sensitivity. 1.8 Second Messengers Definition: Small, internal signaling molecules rapidly produced/released after first messenger (e.g., hormone) binds to receptor. Function: Amplify and distribute signals. First messenger is specific to one receptor. Second messenger can stimulate a wide variety of cellular activities. Examples: Cyclic AMP (cAMP), $\text{Ca}^{2+}$ (calcium ions), Phosphoinositides, Inositol trisphosphate ($\text{IP}_3$), Diacylglycerol (DAG), Cyclic GMP (cGMP), Nitric Oxide (NO). Discovery of cAMP (Earl Sutherland): Epinephrine needed membrane fraction to activate glycogen phosphorylase; membrane released a heat-stable substance (cAMP) that then activated the enzyme in the soluble fraction. Phospholipids as Precursors: Phosphatidylinositol is a source for lipid second messengers (modified by phospholipases, kinases, phosphatases). 1.9 Hormonal Regulation of Blood Glucose Glucagon: Pancreas, low blood sugar $\rightarrow$ stimulates glycogen breakdown. Insulin: Pancreas, high blood sugar $\rightarrow$ stimulates glucose uptake/storage. Epinephrine: Adrenal gland (stress), raises blood glucose for energy. Signaling Mechanisms: Insulin: Receptor Protein-Tyrosine Kinase (RTK). Glucagon & Epinephrine: G Protein-Coupled Receptors (GPCRs). Convergent Signaling: Glucagon and Epinephrine are different but cause the same response (glycogen breakdown, inhibit synthesis) by activating different GPCRs that both lead to increased cAMP. 2. Molecular Genetics: DNA Repair and Recombination 2.1 Introduction to Cancer Cells HeLa Cells: First immortal human cell line, derived non-consensually from Henrietta Lacks in 1951. Fundamental to biological research. Defining Trait: Loss of Growth Control Normal Cells: Grow as monolayer, exhibit contact inhibition, require external growth factors. Cancer Cells: Ignore inhibitory signals, form multilayered foci, often proliferate without external growth factors. Genetic Instability: Cancer cells are aneuploid (abnormal chromosome number/structure), often due to defective cell cycle checkpoints. Resistance to Apoptosis: Evade programmed cell death despite genetic damage. Cells of Origin: Malignant tumors arise from tissue stem cells or progenitor cells; specific cell type influences cancer type. 2.2 DNA Variation DNA Sequence Variation: Human-to-human $\approx 0.1\%$ difference ($\approx 3 \times 10^6$ common variants). Polymorphism: Existence of a gene/species in several allelic/different forms. Any difference in nucleotide sequence between individuals. Types of DNA Polymorphisms: STR (Short Tandem Repeats): Repeats of short DNA sequences. SNP (Single Nucleotide Polymorphisms): Most common type, single base pair change (e.g., C vs. T at a locus). CNV (Copy Number Variations): Differences in the number of copies of a DNA segment. Distinguishing Mutations: Crucial to differentiate disease-causing mutations from neutral variations. 2.3 DNA Mutations Point Mutations: Change in a single nucleotide. Silent: Changes codon but not amino acid (due to redundancy of genetic code). Missense: Changes codon, resulting in different amino acid. Nonsense: Changes codon to a stop codon, leading to truncated protein. Frameshift: Insertion or deletion of nucleotides not in multiples of three, altering reading frame (often severe). Splicing: Affects RNA splicing sites. Regulatory: Affects gene expression regulation. Insertions/Deletions (Indels): Addition or removal of nucleotides. Can cause frameshifts if not in multiples of 3. Detected by chromatograms (shifts in peaks). Can result from strand slippage during replication or unequal crossing over. Rearrangements: Large-scale changes (e.g., inversions, translocations). Transitions vs. Transversions: Transition: Purine to purine (A $\leftrightarrow$ G) or pyrimidine to pyrimidine (C $\leftrightarrow$ T). Transversion: Purine to pyrimidine or pyrimidine to purine (A/G $\leftrightarrow$ C/T). Fragile X Chromosome: Associated with a characteristic constriction (fragile site) on the long arm, often due to repeat expansions. Forward Mutation: Wild-type to mutant. Reverse Mutation: Mutant to wild-type. Suppressor Mutation: A second mutation that masks or compensates for the effect of an earlier mutation. 2.4 Mutation Rate Definition: Frequency with which a wild-type allele changes into a mutant allele. Expressed per cell division, gamete, or replication round. Example: Achondroplasia (hereditary dwarfism) has a mutation rate of $4 \times 10^{-5}$ per gamete. Factors Affecting Mutation Rate: Frequency of DNA Change: Spontaneous molecular changes or induced by environmental agents (chemicals, radiation). Repair Efficiency: Effective repair systems lower rates; faulty systems elevate them. Recognition & Recording: Probability of detecting and recording the mutation. 2.5 Spontaneous Mutations Tautomeric Shifts: Purine and pyrimidine bases can exist in different tautomeric forms (e.g., keto $\leftrightarrow$ enol, amino $\leftrightarrow$ imino). Rare tautomeric forms can lead to incorrect base pairing during replication (e.g., G-T, A-C), causing replicated errors. Wobble Base Pairing: Non-standard base pairs (e.g., G-T, A-C) can form due to flexibility, leading to replication errors. Strand Slippage: Occurs in repetitive sequences (e.g., STRs) during replication, leading to insertions or deletions. Unequal Crossing Over: Misalignment of homologous chromosomes during meiosis can cause insertions and deletions. Depurination: Loss of a purine base (A or G) from a nucleotide, creating an apurinic site. This site can be bypassed by DNA polymerase, often leading to insertion of an incorrect base. 2.6 Chemically Induced Mutations Base Analogs: Chemicals similar to normal bases, incorporated into DNA, then mispair. 5-Bromouracil (5-BU): Analog of thymine. Can tautomerize to pair with G instead of A. Alkylating Agents: Add alkyl groups to bases, altering their pairing properties. Deaminating Agents: Remove amino groups from bases (e.g., cytosine to uracil, adenine to hypoxanthine), leading to mispairing. Oxidative Radicals: Reactive oxygen species (ROS) modify bases (e.g., guanine to 8-oxy-7,8-dihydrodeoxyguanine, which pairs with A). Intercalating Agents: Flat planar molecules that insert themselves between base pairs, distorting the helix and causing insertions/deletions during replication. 2.7 Radiation-Induced Mutations Ultraviolet (UV) Light: Causes formation of pyrimidine dimers (e.g., thymine dimers), distorting the DNA helix and blocking replication/transcription. Ionizing Radiation: (X-rays, gamma rays) High energy, causes double-strand breaks, base damage, and chromosome aberrations. 2.8 DNA Repair Mechanisms Ames Test: Used to identify chemical mutagens by testing their ability to revert mutations in bacteria (e.g., Salmonella unable to synthesize histidine). Mismatch Repair (MMR): Corrects incorrectly inserted nucleotides that escape proofreading during replication. Recognizes mispaired bases or small loops. Distinguishes new strand from old (e.g., via methylation in bacteria) to ensure correct base is chosen. Direct Repair: Reverts altered bases to their original structure without removing the base or nucleotide. Photoreactivation: Photolyase uses visible light energy to break pyrimidine dimers. Methyltransferase: Removes alkyl groups from bases. Base-Excision Repair (BER): Removes a single damaged base. DNA glycosylase: Recognizes and removes specific damaged base, creating an AP (apurinic/apyrimidinic) site. AP endonuclease: Cleaves phosphodiester backbone at AP site. DNA polymerase: Fills gap. DNA ligase: Seals nick. Nucleotide-Excision Repair (NER): Removes bulky lesions that distort the DNA helix (e.g., pyrimidine dimers, large chemical adducts). Recognizes distortion. Excision nucleases cut phosphodiester backbone on both sides of the lesion. Helicase removes segment. DNA polymerase fills gap. DNA ligase seals nick. 2.9 Homologous Recombination Definition: Exchange of genetic material between homologous DNA molecules. Important for DNA repair (esp. double-strand breaks) and genetic diversity during meiosis. Holliday Model: Homologous DNA molecules align. Nicks occur in one strand of each DNA molecule. Strand invasion and exchange, forming a Holliday junction . Branch migration extends the region of heteroduplex DNA. Resolution (cleavage) of the Holliday junction yields either non-recombinant or recombinant products. Double-Strand-Break (DSB) Model: Initiated by a double-strand break in one DNA molecule. Exonuclease degradation creates 3' overhangs. One 3' end invades homologous chromosome. DNA synthesis and formation of two Holliday junctions. Resolution leads to recombinant products. 3. Epigenetics and Gene Regulation 3.1 What is Epigenetics? C.H. Waddington's original definition: "Above or in addition to genetics" to explain differentiation. Modern Definition: Non-sequence dependent inheritance of phenotypic traits. Changes in gene expression without altering the underlying DNA sequence. Example: Identical twins can have different phenotypes (e.g., hair color) due to epigenetic differences. Mechanism: Explains how differentiated cells (muscle, skin, blood) with identical DNA sequences acquire and maintain distinct identities. 3.2 Epigenetic Mechanisms DNA Methylation: Covalent addition of a methyl group ($\text{CH}_3$) to a cytosine base, typically at CpG dinucleotides (Cytosine-phosphate-Guanine). Often occurs in CpG islands near gene promoters. Effect: Cytosine methylation typically maintains inactive-condensed chromatin state and represses gene transcription. Location: Found in heterochromatic regions (tightly packed DNA). Establishment & Maintenance: Established by de novo methyltransferases and maintained across cell divisions by maintenance methyltransferases (e.g., DNMT1) that recognize hemi-methylated DNA. Essential Role: Some DNA methyltransferases are essential for development. Differentiation: DNA methylation patterns differentiate totipotent embryonic stem cells from unipotent adult stem cells. Histone Modifications: Histones are proteins around which DNA is wound to form chromatin. Modifications (e.g., acetylation, methylation, phosphorylation, ubiquitination) to histone tails alter chromatin structure and accessibility. Histone Acetylation: Generally associated with open chromatin (euchromatin) and active gene transcription. Acetyl groups neutralize positive charges on histones, loosening DNA-histone interaction. Histone Methylation: Can be associated with either gene activation or repression, depending on the specific residue and number of methyl groups. Euchromatin: Open, less condensed, gene-rich, actively transcribed. Characterized by histone acetylation. Heterochromatin: Condensed, gene-poor (or silenced), transcriptionally inactive. Characterized by DNA methylation and specific histone methylations. 3.3 X-Chromosome Inactivation (Lyonization) Barr Bodies: Inactivated X chromosome in somatic cells of female mammals. Mechanism: XIST gene on one X chromosome is activated. XIST RNA is produced and coats the active XIST chromosome. Binding of XIST RNA leads to epigenetic silencing (e.g., DNA methylation, histone modifications) of that entire X chromosome. Result: Dosage compensation in females, ensuring they have one functional X chromosome like males. 3.4 Differentiated Cells and Totipotency Totipotency: Ability of a single cell to differentiate and develop into a complete organism (e.g., zygote). Differentiated cells can become totipotent: Demonstrated by induced pluripotent stem cells (iPSCs), where epigenetic reprogramming can revert specialized cells to a stem cell-like state. 4. Biotechnology and Genetic Engineering 4.1 Recombinant DNA Technology (RDT) Definition: Artificially combining DNA from two different sources into a single molecule. Pioneers: Boyer and Cohen (1973). Goal: To reproduce the artificially created DNA (DNA Cloning) or express genes for desired products. Basic Principles: Generation & Selection of DNA fragments: Obtain desired gene. Insertion into Cloning Vector: Create recombinant DNA (rDNA). Introduction into Host Cells: Transformation. Multiplication & Selection of Clones: Amplify rDNA. Expression of Gene: Produce desired product. 4.2 Key Components of RDT Vectors: DNA molecules capable of self-replication in a host cell and carrying foreign DNA. Characteristics: Self-replicating origin (ori), convenient restriction enzyme sites, selectable marker genes, small size, easy isolation. Plasmids: Common vectors. Example: pBR322 (contains ori, rop gene, ampicillin and tetracycline resistance genes, unique restriction sites). Restriction Enzymes (Restriction Endonucleases): Naturally occurring enzymes that cut DNA at specific recognition sequences ( restriction sites ). Produce either "sticky ends" (overhangs) or "blunt ends." Essential for cutting both the foreign DNA and the vector DNA, creating compatible ends for ligation. DNA Ligase: Enzyme that forms phosphodiester bonds to join DNA fragments (e.g., insert into vector). 4.3 Steps of Recombinant DNA Technology Isolation of DNA: Extract and purify DNA from source organism and vector. Restriction Digestion: Cut target DNA and vector DNA with appropriate restriction enzymes. Ligation: Join target DNA into the vector using DNA ligase, forming recombinant plasmid. Transformation: Introduce recombinant plasmid into host cells (e.g., E. coli treated with $\text{CaCl}_2$ and heat shock). Multiplication/Cloning: Host cells replicate, amplifying the recombinant DNA. Selection Strategies (using Marker Genes): Selectable Markers: Genes whose presence can be easily detected (e.g., antibiotic resistance like $amp^R$). Only cells with plasmid grow on selective media. Insertional Inactivation: Insert foreign DNA into a marker gene (e.g., $amp^R$ in pBR322). Disruption of the gene means cells with insert will be sensitive to that antibiotic, while those without insert remain resistant. Differential screening with two antibiotics (e.g., ampicillin and tetracycline) identifies recombinant clones. 4.4 Applications of RDT Production of insulin, growth hormone, vaccines, gene therapy, genetically modified organisms (GMOs). 4.5 CRISPR-Cas9 System (Nobel Prize 2020) Origin: Bacterial adaptive immune system against viral attacks. CRISPR: C lustered R egularly I nterspaced S hort P alindromic R epeats. Bacterial genome contains repeating DNA segments separated by unique "spacer" sequences derived from viral DNA. Spacers act as a "database" of past infections. Cas9: CRISPR-associated protein 9, an endonuclease (DNA-cutting enzyme). Mechanism: Viral DNA sequences are transcribed into CRISPR RNAs (crRNA) . crRNA binds to a complementary sequence in invading viral DNA. Cas9 (guided by crRNA) digests the viral DNA, preventing replication. 4.6 Guide RNA (gRNA) Anatomy CRISPR gRNA Complex: Composed of two parts: crRNA (CRISPR RNA): Contains the 17-20 nucleotide sequence complementary to the target DNA. tracrRNA (trans-activating crRNA): Folds into a secondary structure to recruit Cas9 protein. Single Guide RNA (sgRNA): A synthetic RNA molecule combining crRNA and tracrRNA into one hybrid molecule for easier use. 4.7 Protospacer Adjacent Motif (PAM) Sequences Definition: Short DNA sequences adjacent to the target sequence that are recognized by specific Cas proteins. Importance: Cas9 will only cut if the target sequence is immediately followed by a specific PAM sequence. Cas9 PAM: 5'-NGG-3' (where N is any nucleotide). Designing gRNA: Must have a PAM site immediately downstream (3') of the target DNA sequence, and the crRNA sequence must be complementary to the target. 4.8 Using CRISPR for Gene Editing Gene Knockout: CRISPR-Cas9 creates a double-stranded break (DSB) in target DNA. Cell's repair mechanism: Non-Homologous End Joining (NHEJ) . This pathway is efficient but error-prone, often introducing small insertions or deletions (indels) that disrupt the gene's coding sequence, leading to a functional knockout. Gene Knock-in/Correction: Cell's repair mechanism: Homology-Directed Repair (HDR) . Scientists provide a "correct" DNA template with homologous sequences flanking the desired edit. The cell uses this template to repair the DSB, precisely inserting the new sequence. 5. Phylogenetics and Systematics 5.1 What is Phylogeny? Definition: Study of evolutionary relationships among groups of organisms and their development. Goal: Trace the evolutionary history of all life, based on the hypothesis that all living organisms share a common ancestry. Visualization: Relationships are depicted in a phylogenetic tree (analogous to a family tree). Challenge: Evolution happens over millions of years and cannot be observed directly; relationships are inferred from extant organisms. 5.2 Sources of Evidence for Phylogeny Fossil Record: Pros: Direct evidence of ancestral organisms. Cons: Often incomplete, many gaps. Phenotypic Characteristics (Classic Method): Based on observable traits, especially anatomical structures (e.g., bone structure). Molecular Data (Modern Method): Most common. Compares protein and DNA sequences. Greater sequence similarity $\rightarrow$ more closely related organisms. 5.3 Homologous Characteristics Definition: Traits shared by related species due to inheritance from a common ancestor . Strong evidence of shared evolutionary history. Anatomical Homology: Example: Front leg of a mouse and wing of a bat. Different function/appearance, but underlying bone structure and development show common mammalian forelimb origin. Molecular Homology: DNA sequences in different species are homologous if they evolved from a single ancestral DNA sequence. 5.4 Building a Phylogenetic Tree with DNA Sequence Alignment: Identify homologous genes in different organisms. Line up nucleotide sequences to identify similarities and differences (substitutions, insertions/deletions). Gaps (–) represent indels. Principle of Parsimony: The simplest explanation (requiring fewest evolutionary changes) is often preferred. Computer programs are used for complex alignments. Quantifying Evolutionary Distance: Count differences between aligned sequences. More differences $\rightarrow$ more distant evolutionary relationship. Results organized into a distance matrix . 5.5 Rates of Molecular Evolution Nonsynonymous Substitutions: Nucleotide changes that alter the amino acid sequence of the protein. Impact: Affects protein function and organism's traits. Rate: Varies dramatically; constrained genes (e.g., $\alpha$-actin) evolve slowly, less constrained genes (e.g., interferon $\gamma$) evolve faster. Synonymous Substitutions (Silent Mutations): Nucleotide changes that do not alter the amino acid sequence (due to genetic code redundancy, often in 3rd codon position). Impact: No change to protein. Rate: Generally faster than nonsynonymous substitutions. Guiding Principle: Highest rates of nucleotide substitution are found in sequences with the least effect on organism's function. Application: Fast-evolving genes for closely related species; slow-evolving, conserved genes for ancient relationships. 6. Population Genetics 6.1 Gene Pool Description Variability: Life exhibits pervasive genetic variability. Genetic vs. Phenotypic Variation: Genetic variation is more complex; different DNA sequences can yield same protein, and non-coding regions vary with little phenotypic effect. Frequency: Proportion or percentage, usually as a decimal fraction. Sampling: For large populations, genotypic and allelic frequencies are calculated from a sample. 6.2 Calculating Genotypic Frequencies For genotypes AA, Aa, aa in a sample of N individuals: $f(\text{AA}) = \frac{\text{Number of AA individuals}}{\text{N}}$ $f(\text{Aa}) = \frac{\text{Number of Aa individuals}}{\text{N}}$ $f(\text{aa}) = \frac{\text{Number of aa individuals}}{\text{N}}$ Sum of all genotypic frequencies equals 1: $f(\text{AA}) + f(\text{Aa}) + f(\text{aa}) = 1$. 6.3 Calculating Allelic Frequencies Fewer alleles than genotypes; simpler description of gene pool. Can be calculated from number of genotypes or genotypic frequencies. For two alleles A and a (frequencies p and q): From numbers of genotypes: $p = f(\text{A}) = \frac{(2 \times \text{Number of AA}) + (\text{Number of Aa})}{2 \times \text{Total number of individuals}}$ $q = f(\text{a}) = \frac{(2 \times \text{Number of aa}) + (\text{Number of Aa})}{2 \times \text{Total number of individuals}}$ From genotypic frequencies: $p = f(\text{A}) = f(\text{AA}) + \frac{1}{2}f(\text{Aa})$ $q = f(\text{a}) = f(\text{aa}) + \frac{1}{2}f(\text{Aa})$ Sum of allelic frequencies equals 1: $p + q = 1$. 6.4 Hardy-Weinberg Law Mathematical Model: Evaluates the effect of reproduction on genotypic and allelic frequencies. Assumptions: Population is large, randomly mating, and not affected by mutation, migration, or natural selection. Predictions (if assumptions met): Prediction 1: Allelic frequencies of a population do not change from generation to generation. Prediction 2: Genotypic frequencies stabilize after one generation in the proportions: $f(\text{AA}) = p^2$ $f(\text{Aa}) = 2pq$ $f(\text{aa}) = q^2$ where $p$ is frequency of allele A and $q$ is frequency of allele a. Implication: Under Hardy-Weinberg conditions, reproduction alone does not alter allelic or genotypic frequencies; allelic frequencies determine genotypic frequencies. 7. Evolutionary Developmental Biology (Evo-Devo) 7.1 What is Evo-Devo? Definition: Interdisciplinary field investigating the interplay between evolutionary processes and developmental mechanisms. Core Questions: How do developmental processes themselves evolve? How do developmental processes influence the path and possibilities of evolution? Origin: Emerged to address the neglect of development in the "Modern Synthesis" of evolutionary theory (which focused heavily on population genetics). "Blot Seen Round the World": Discovery of the homeobox ($\approx 180$ bp DNA sequence coding for transcription factors) in the 1980s. Highly conserved across diverse animals (flies, mice, humans). Revealed a common, ancient "genetic toolkit" for building bodies. 7.2 Evo-Devo's Place in Evolutionary Theory Complements Traditional Evolutionary Biology: Traditional (e.g., Population Genetics): Explains the fate of variation in populations (e.g., via natural selection). Evo-Devo: Explains the origin and introduction of phenotypic variation through changes in development. Asks how developmental biases and constraints channel evolution. 7.3 Model Organisms in Evo-Devo Chosen for: Representation: How well they represent a broader taxonomic group (e.g., mice for mammals). Manipulation: Ease of study (short generation time, genetic tools). Example: Starlet sea anemone ( Nematostella vectensis ) chosen for phylogenetic position. 7.4 Conserved Mechanisms Definition: Organized sets of genes and proteins (e.g., Wnt, Hedgehog signaling pathways) that perform specific developmental tasks across many species. Conceptual Puzzle: Homology is about structure; mechanisms are about function. Solution: A conserved mechanism is a shared, derived trait with specific parts, organization, and context, producing a stereotypical outcome with some variation. 7.5 Evolutionary Novelty Definition: A new anatomical structure not homologous to any structure in ancestral species. Examples: Turtle shell, insect wings, tetrapod limb. Origin: Rarely from brand-new genes; usually by "tinkering" with existing developmental tools. Key Mechanisms: Co-option: Re-use of existing gene/genetic network in a new place or time during development. Changes in Gene Regulation: Altering when and where genes are switched on/off (via cis-regulatory elements), rather than changing the protein itself. Developmental Plasticity: Environment triggers new phenotype, which can later become genetically fixed. 7.6 The Genetic Toolkit Central Mystery: How does a single fertilized egg (with full DNA) produce diverse cell types and complex structures? Answer: Gene Regulation: Not all genes active in all cells. Regulatory genes act as master switches. Chain Reactions: Single regulatory gene can trigger cascades of genetic activity to build complex structures. Hox Genes: Famous set of regulatory genes acting as "master architects." Define body plan from head to tail. Errors cause dramatic changes (e.g., leg where antenna should be). Universal Toolkit (Deep Homology): Same families of master control genes (Hox) found in insects, mice, humans. Common ancestor (>$600$ MYA) evolved core genetic toolkit. Evolution works by tinkering with these toolkits; small changes in regulatory genes lead to major body form changes. Example: Mouse eye-building gene can trigger fly eye formation in a fly. Cell Fate Determination: Differential Gene Expression: Different cell types express different sets of genes from the same DNA blueprint. Role of Signals: Chemical signals from environment/neighboring cells provide instructions for gene activation and cell type specification. 8. Immunology and Host-Pathogen Interactions 8.1 The Genetic Exception: Immune System Gene Rearrangement Fundamental Rule: All somatic cells have identical DNA. Immune System Exception: Immune cells deliberately rearrange, mutate, and lose specific gene segments to create diversity. Process: Somatic DNA recombination shuffles V(D)J gene segments in developing lymphocytes (B and T cells). Result: Vast repertoire of unique receptors and antibodies, each recognizing a different antigen. Critical Balance: Self vs. Non-Self: Immune system must distinguish self-antigens from foreign ones. Failure leads to autoimmune disease. 8.2 Two Branches of Adaptive Immunity Humoral Immunity (B cells): Mediated by antibodies (immunoglobulins). Targets extracellular pathogens and toxins. Antibodies recognize antigens directly. Cellular Immunity (T cells): Mediated by T cells . Targets intracellular pathogens (e.g., viruses), cancer cells. T cells recognize antigen fragments presented on MHC molecules by other cells. 8.3 The Unifying Principle: Clonal Selection Immense Pre-existing Diversity: Body pre-makes vast pool of lymphocytes, each specific for one antigen. "Select and Expand": Antigen enters body, selects the specific lymphocyte that recognizes it. Clonal Expansion: Selected lymphocyte activates and rapidly divides, creating a large clone of identical cells. Immunological Memory: After infection, memory cells remain, providing long-lasting, faster, stronger response upon re-exposure (basis for vaccination). 8.4 Antibody Structure (Immunoglobulins, Ig) Function: Primary effector molecules of humoral immunity, bind antigens to neutralize or mark for destruction. Molecular Architecture: Y-shaped molecule, composed of four polypeptide chains. Two identical Heavy Chains . Two identical Light Chains ($\kappa$ or $\lambda$, never one of each). Chains held together by disulfide bonds. Key Functional Regions: Variable Region (V): At tips of Y-arms, formed by variable ends of light and heavy chains. Forms the Antigen-Binding Site , determining antigen specificity. Constant Region (C): Forms stem and lower parts of arms. Determines antibody's effector function (e.g., complement activation, interaction with immune cells). 8.5 Generating Antibody Diversity The human genome has $\approx 20,000$ genes, but immune system produces up to $10^{15}$ different antibodies. Solution: Antibody genes are assembled from a library of segments. Mechanism 1: Somatic Recombination ("Mix and Match") Segments: V (Variable), D (Diversity - heavy chain only), J (Joining), C (Constant). Process: In developing B cells, a random V segment is permanently joined to a random J (and D for heavy chain) segment via DNA rearrangement. Intervening DNA is excised. Transcription & Translation: Recombined DNA transcribed, spliced into mRNA, translated into unique light/heavy chain protein. Example: Human Kappa Light Chain: $\approx 35$ V segments $\times 5$ J segments $\times 1$ C segment $\approx 175$ combinations. Mechanism 2: Combinatorial Diversity Any unique heavy chain can pair with any unique light chain, multiplying total diversity. Mechanism 3: Junctional Diversity Imprecise joining of V, D, J segments. Random nucleotides are often deleted or inserted at junctions by enzymes like TdT. Drastically increases variation in antigen-binding site. Mechanism 4: Somatic Hypermutation After antigen exposure, B cells undergo high rate of point mutation in variable regions. Creates minor variations, allowing for "affinity maturation" (selection of higher affinity antibodies). 8.6 T-Cell Receptors (TCRs) Function: Each mature T cell recognizes one specific antigen presented on MHC molecules on the surface of other cells. Structure: Cell-surface protein complex with two chains: One Alpha ($\alpha$) chain, One Beta ($\beta$) chain. (Some have $\gamma/\delta$ chains). Held by disulfide bonds. Constant Region: Anchors receptor. Variable Region: Antigen-binding site, determines specificity. Diversity Generation (similar to antibodies): Somatic Recombination: Genes for $\alpha$ and $\beta$ chains assembled from V(D)J segments. Combinatorial Diversity: Any $\alpha$ chain can pair with any $\beta$ chain. Junctional Diversity: Imprecise V(D)J joining. Key Difference from Antibodies: T cells do not undergo somatic hypermutation after maturation. This prevents reactivity against self-tissues. 8.7 Major Histocompatibility Complex (MHC) & Self-Recognition Definition: Cluster of genes coding for histocompatibility antigens (proteins) displayed on surface of most cells. Function: Act as unique "self" ID badge for each individual (except identical twins). Dual-Signal Rule for T-Cell Activation: A T cell activates only if its TCR binds BOTH a foreign antigen fragment (peptide) AND a self MHC molecule simultaneously. Ensures T cells attack only compromised self cells, not healthy cells or free-floating pathogens. MHC presents the antigen. 8.8 The Transplant Challenge: Genetics & Immune Rejection Core Problem: Transplanted organs are recognized as "foreign" due to mismatched MHC antigens, leading to rejection. Genetic Keys to Compatibility: Major Histocompatibility Complex (MHC): Primary trigger of rejection. Maximize matched MHC antigens between donor/recipient. ABO Blood Group Antigens: Also elicit strong immune reaction. Donor/recipient must have compatible ABO blood types. Managing Immune Response: Immunosuppressive Drugs: Suppress entire immune system, preventing rejection but increasing vulnerability to infection. Meticulous Genetic Matching: Reduces "foreignness," lessens need for high drug doses. Best Outcome: Combination of both strategies. 9. Neurobiology and Behavior 9.1 The Neuron: Basic Unit of Communication Definition: Nerve cell processing and transmitting information via electrical and chemical signals. Components: Cell Body (Soma): Core of neuron, maintains cell, contains nucleus, synthesizes proteins. Dendrites: Tree-root shaped, receive information from other neurons, transmit electrical signals to cell body. Covered in synapses. Axon (Nerve Fiber): Tail-like structure, carries signals away from cell body to terminal buttons. Myelin Sheath: Fatty layer covering axons. Function 1: Insulates nerve cells, prevents interference. Function 2: Speeds up nerve impulse conduction. Synaptic Connections: Allow communication between neurons (via synapse). 9.2 Neural Signaling: The Action Potential Synapse: Tiny gap between neurons. Action Potential: Electrical nerve impulse that travels along a neuron's axon. Transient, all-or-nothing electrical current. Importance: Fundamental for nerve functions, processing information, muscle contraction, sensory detection, reflexes. Location: Typically generated in axon hillock when membrane potential reaches "threshold of excitation." All-or-Nothing Principle: Once threshold is reached, action potential fires with full strength; below threshold, it doesn't fire. Phases of an Action Potential: Depolarization (Rising Phase): Resting potential $\approx -70 \text{mV}$ (high $\text{Na}^+$ outside, $\text{K}^+$ inside). Stimulation opens voltage-gated $\text{Na}^+$ channels. $\text{Na}^+$ rushes into cell, making inside more positive. If threshold ($\approx -55 \text{mV}$) reached, massive $\text{Na}^+$ influx, positive spike. Repolarization (Falling Phase): $\text{Na}^+$ channels close. $\text{K}^+$ channels open, $\text{K}^+$ rushes out of cell. Inside of cell becomes negative again. Hyperpolarization (Undershoot): $\text{K}^+$ channels close slowly, slight excess $\text{K}^+$ leaves, making membrane potential even more negative (e.g., $-80 \text{mV}$). Contributes to relative refractory period (harder for neuron to fire again). $\text{Na}^+$-$\text{K}^+$ pump restores resting concentrations. 9.3 Synaptic Transmission Definition: Process by which one neuron communicates with another across the synapse. Steps: Action potential reaches presynaptic terminal. Triggers release of neurotransmitters (chemical messengers) from synaptic vesicles into synaptic cleft. Neurotransmitters diffuse across cleft and bind to specific postsynaptic receptor sites on postsynaptic neuron. Binding triggers electrical impulse (or inhibition) in postsynaptic neuron. Structures: Presynaptic membrane, postsynaptic membrane, synaptic cleft, neurotransmitters (in vesicles), postsynaptic receptor sites. Neurotransmitters: Brain chemicals communicating information. Examples: Acetylcholine (muscle contraction), Dopamine (schizophrenia link), Serotonin (depression link), Adrenaline, GABA. Each has specific function; defines synaptic connections. 10. Endocrinology and Hormonal Regulation 10.1 Introduction Coordination: Nervous and endocrine systems work together to coordinate body functions. Nervous System: Acts via nerve impulses (action potentials) and neurotransmitters. Endocrine System: Controls body activities by releasing hormones (mediators). Difference: Means of control are very different (electrical vs. chemical, fast vs. slower/widespread). 10.2 The Hormones Definition: Chemical messengers created by the body. Function: Transfer information from one set of cells to another to coordinate functions. Mechanism: Made and stored in originating organ (endocrine gland). Sent to a target (cells/organs with specific receptors). Trigger events at target. 10.3 Endocrine Glands (Examples) Pituitary Gland: "Master gland," regulated by hypothalamus. Secretes many hormones controlling other glands. Hypothalamus: Controls pituitary gland, links nervous and endocrine systems. Thyroid Gland: Produces thyroid hormones (metabolism). Adrenal Glands: Produce adrenaline, cortisol (stress response). Pancreas: Produces insulin, glucagon (blood glucose regulation). Gonads (Testes/Ovaries): Produce sex hormones.