BSCI 1511 Exam #1 PDF

There is no more biology to study. All I have in common with the chemists and the physicists, the HOD majors and the blair students, all the amino acids I have memorized and my utter indifference toward it I have now surpassed. My stress is constant and sharp and I do not hope for a better grade for...

There is no more biology to study. All I have in common with the chemists and the physicists, the HOD majors and the blair students, all the amino acids I have memorized and my utter indifference toward it I have now surpassed. My stress is constant and sharp and I do not hope for a better grade for anyone. In fact, I want my stress to be inflicted on others. I want no one to escape, but even after admitting this, there is no catharsis. My cumulative grade continues to elude me and I gain no deeper knowledge of myself. No new knowledge can be extracted from my telling. This confession has meant nothing. Day 1: Evolutionary Dating Fossil Record: Shows progression of evolution; reveals transitions among extinct and living species ​ Gradualism: Rate of evolution is linear/constant ​ Punctuated Equilibrium: Rate of evolution varies ○​ Organisms may develop new traits/characteristics due to environmental pressures, natural selection, or mutations ○​ New adaptations allow organisms to thrive in environments previously unavailable to them ○​ Adaptive radiations: Evolution of bats (powered flight and echolocation) leads to wide range of diets and lifestyles (insectivory, frugivory, etc.) ​ Gaps: Period of time where no fossils have been found for particular species Radiometric Dating: Measure Carbon-14 or Potassium-40 present to determine age ​ Carbon-14 effective for more recent samples (~50k yrs); organic samples ​ Potassium-40 effective for rocks/volcanic minerals (NOT fossils); very old samples (hundreds of thousands to billions of years old) ○​ Potassium-40 decays into Argon-40 ○​ When volcanic rock forms, argon escapes, leaving potassium behind to form more argon ○​ Measure ratio of Potassium-40 to Argon-40 to determine age Artifical Selection: Humans selectively choose traits/characteristics ​ Breeding certain wolves to achieve the variety of dog breeds we now have ​ Breeding double-comb chickens produce triple and quadruple combs instead of single Natural Selection: Better adapted organisms are more likely to survive ​ Without mortality, reproduction occurs at rates that would result in huge populations ​ Offspring inherit traits, but there is variability among individuals ​ Variations that increase survival & reproduction are more likely to be passed to offspring Day 2 & 3: Cell Communication ​ Direct vs indirect signaling: ○​ Direct (by gap jct): Small signal molecules pass easily between cells that are connected by gap junctions w/o crossing plasma membrane ○​ Indirect (cytoplasmic receptors): ​ Autocrine: Signal molecule sent and received by same cell ​ Paracrine: Receiving cell is near sender (nitric oxide, histamine, EGF) ​ Hormonal: Hormones released by endocrine cells (insulin, adrenaline, testosterone, cortisol); travel through circulatory system (long-distance) ​ Synaptic: Electrical signals stimulate release of neurotransmitter ​ Kinases and phosphatases regulate signaling (add/remove PO4) 1.​ Reception ​ Cytoplasmic (hydrophilic signals): Signal molecules permeate plasma membrane easily; bind to receptor in cytoplasm and activates it then enters nucleus to bind to specific genes (can act as tsn factor) ​ Transmembrane (hydrophobic signals): Move signal molecules from outside to inside of cell ○​ GPCRs: ​ GPCRs activated by reception of hormones 1.​ Signal / ligand binds to extracellular GPCR, causing a conformational change 2.​ 7-transmembrane region of GPCR undergoes conformation change 3.​ GPCR activates G-protein (GDP → GTP), then G-protein dissociates into α subunit + ß and γ subunit 4.​ Αctivated α subunit binds to adenylyl cyclase; activates it 5.​ ATP → cAMP (second messenger for other cell func.) 6.​ α subunit eventually hydrolyzes (GDP → GTP) and returns to ß + γ subunit ○​ Enzyme linked receptors (e.g. RTK): ​ RTKs activated by reception of growth factors 1.​ Ligand binds to 1 transmembrane monomer to form dimer a.​ Ligand mediated: Single paired ligand join monomers together b.​ Receptor mediated: Unpaired single ligand joins monomer, causing conformation change that allows monomers to dimerize 2.​ Cross-linked dimer – single RTK monomers phosporylates opposite RTK 3.​ SH2-containing proteins bind to individual phosphorylated tyrosines, which is why multiple different proteins can bind to one RTK ​ EXAMPLE: Ras/MAP pathway ○​ Ras (single g-protein subunit) activate=cell division ○​ Beginning ligand(s) amplify; many response molecules produced ​ Ras mutated in ~30% of cancers, preventing GTP from hydrolyzing to GDP and causing continuous cell division  ○​ Ligand-gated ion channels 1.​ Signal molecule (e.g. acetylcholine/ACh) binds to receptor 2.​ Receptor changes shape to open, allowing a gradient to drive ion flow 2.​ Transduction: Converts signal into something target can respond to ​ Small secondary messengers (e.g. cAMP, Ca2+, IP3) ○​ Ca2+: Ions flow from outside cell or within different intracellular compartment into cytosol ​ Certain proteins in cell have binding sites for the released Ca2+ ions, which attach and cause change in shape (and thus, activity) ​ Plants regulate H2O/CO2 movement in stomata via guard cells, which cause stomata to open/close ​ If plant cells are losing H2O, abscisic acid (ABA) is released by nearby cells to bind to ABA receptor, creating Ca2+ gradient that forces salts/H2O to leave and stomata to close  ​ H2O follows salts (K+, Cl–) into guard cells, which allows pores (stomata) to open ○​ cAMP: Produced when adenylyl cyclase is activated by G-proteins in response to external stimuli binding to receptors ​ Adenylyl cyclase removes 2 PO4 from ATP → cAMP ​ cAMP activates protein kinase A (PKA), allowing phosphorylation of target to pass signal ​ cAMP is deactivated by phosphodiesterases  ○​ Inositol Phosphates: Produced when phosphatidylinositols (phospholipids) are phosphorylated and cleaved in half ​ PIP2 splits into DAG & IP3 (second messengers) in response to phospholipase C (PLC; cleaves PIP2) ​ DAG stays in plasma membrane; activates PKC, allowing it to phosphorylate own targets ​ IP3 diffuses into cytoplasm and binds to Ca2+ channels to release Ca2+ to continue signal cascade 3.​ Response: Activity in response to signal ​ cAMP/PKA pathway ○​ Different cell types can release various proteins/receptors to respond to different signals or respond differently to same signals ○​ Active PKA activates CREB (cAMP bind protein), binds to CRE (specific sequence), activates gluconeogenesis genes in liver 4.​ Termination of Signals: What turns off certain signals? ​ cAMP: cAMP phosphodiesterase breaks down cAMP ​ G-Proteins (Hydrolysis): α-subunit hydrolyzes GTP to GDP via GTPase, becoming inactive; α-subunit reassociates with βγ-subunits ​ GPCRs (two possible terminations) 1.​ Ligand dissociates from receptor altogether 2.​ GRK (kinase) phosphorylates receptor; give recognition site for arrestin protein to bind; GPCRs are internalized to be recycled or degraded by lysosomes (see diagram) → ​ Ca2+: Signals terminate through active reuptake into ER/SER Day 3 & 4: Hormones ​ Chemical cell signals secreted by endocrine cells; regulate bodily functions ​ Secreted locally or into circulatory system (long-distance) ​ Pheromones = Long-distance signaling chemicals (aerosolizes) ​ Pathways w/ more steps = greater regulation Posterior Pituitary (PP) Gland ○​ Extension of brain; originated as neural tissue ○​ Hormones synthesized in hypothalamus (in cell bodies) then transported down to axon terminals in posterior pituitary ○​ Oxytocin: Stimulates labor contractions and milk release ○​ ADH (Antidiruetic hormone; vasopressin): Regulates H2O reabsorption in kidney ​ Blood too salty → ADH produced & thirsty ​ Ethanol alcohol blocks ADH release and H2O reabsorption in kidneys Anterior Pituitary (AP) Gland: ​ Originated as tissue in roof of mouth; migrated to fuse w/ posterior pituitary ​ Many hormones synthesized/stored in AP are regulated by separate hormones from hypothalamus being released into blood (via portal blood vessels) ​ Tropic Hormones: Stimulate other endocrine glands to release hormones with specific effects (indirect); directly secreted by pituitary ○​ Thyroxine: Regulates cell metabolism, fat breakdown, protein sythensis, body temp ​ T3: 3 Iodine atoms; less common but more active form ​ T4: 4 Iodine atoms; more common but less active; converts to T3 form ​ Non-tropic Hormones: Directly influence the target tissues (not other endocrine glands) ○​ Prolactin ​ Mammalian Females: Breast development and milk production ​ Mammalian Males: Endocrine function of testes ​ Birds: Fat metabolism and reproduction ​ Amphibians: Timing of metamorphosis (tadpol → frog) ​ Fish: Salt and water balance ○​ Endorphins ​ Natural human opiates; dulls perception of pain when stress/pain in body reaches critical levels (just like morphine/opium/heroin) ​ Growth Hormone ○​ Both tropic & non-tropic ○​ Underproduction = Pituitary dwarfism ○​ Overproduction = Gigantism Adrenal Hormones: Stress response ​ Adrenal cortex uses cholesterol as backbone for cortisol, aldosterone, sex steroids ​ Cortisol (cortex): Blocks non-critical cells from using glucose; reduces inflammation & allergy but blocks immune system ​ Epinephrine/Norepinephrine (medulla): ○​ Medulla is directly stimulated by nervous system (works faster) ○​ Beta Blockers: Block ß-adrenergic GPCR receptors to prevent activation of adenylyl cyclase and production of cAMP (blocks fight-or-flight) ​ Reduces heart rate w/o reducing blood pressure (doesn’t affect α receptors) ○​ Tyrosine → L-Dihydroxyphenylalanine (L-dopa) → Dopamine → Norepinephrine → Epinephrine Sex Hormones ​ Produced in gonads (testes/ovaries), synthesized from cholesterol ​ Mammals: Y-chromo cause gonads to produce androgens (testosterone) @7 weeks (male) Male Sex Hormones: ​ GnRH increased during puberty to stimulate more LH & FSH ​ LH stimulates Leydig cells → Testosterone ​ FSH & Testosterone stimulate Sertoli cells → promote spermatogenesis ​ Inhibin: Regulates FSH production ○​ Male: Produced by sertoli cells ○​ Female: Produced by granulosa cells Blood Glucose Regulation (Pancreas) & Rhythmic Hormones (Biological Clock) ​ α cells produce glucagon ​ ß cells produce insulin ○​ Blood glucose levels stimulate release of insulin ○​ Insulin stimulates cells to move glucose inside and convert to glycogen ​ T1 Diabetes: Lack insulin ​ T2 Diabetes: Lack insulin receptors  ​ Melatonin (pineal gland): Released in dark; causes many animals to change based on season (due to length of day called photoperiod) ○​ Fur/coat changes colors, reproduction (and organs) during specific seasons Termination of Hormonal Signals 1.​ Hormones degraded/inactivated by enzymes in liver, blood, or lymph 2.​ Removal from blood via kidneys and urine excretion Day 5: Meiosis ​ Chromosome pairs numbered by size (1 largest, 22 smallest; x large, y small) ​ Homologous chromosomes: Pair of chromosomes that have same genes (1 from mother, 1 from father) ○​ Females (XX): 23 homologous chromosome pairs ○​ Males (XY): 22 homologous chromosome pairs and X+Y non-homologous pair ​ Down syndrome = Additional copy of chromosome 21 (has 3 instead of 2) ​ Mendel’s Law of Segregation ensure that only one allele exists per trait ○​ Ensures a “reductive division” that prevents chromosomes from multiplying when reproducing (goes from diploid to haploid) ​ Mendel’s Law of Independent Assortment ensures that genes on non-homologous chromosomes are completely separate (maternal allele for one chromosome won’t influence the whether others are maternal or paternal) Stages of Meiosis: 1.​ Early Prophase I: Individual chromatids replicate and condense into pair, creating 2 sister chromatids/chromosomes 2.​ Late Prophase I: 2 individual chromosome pairs come together to form tetrad (4 chromatids) a.​ Recombination possible when maternal and paternal chromosomes have segments of DNA from one another (needed for genetic diversity) 3.​ Metaphase I: Condensed tetrads line up on equatorial plate a.​ If homologous chromosomes fail to separate → down syndrome 4.​ Anaphase I: Centromere “eat” at microtubules that connect to poles, causing separation a.​ Separated chromosomes contain mostly mother or father genetic material but may have some residual from other side (mother or father) 5.​ Telophase I: Chromosomes at separate poles; cell begins to divide (cytokinesis) 6.​ Propase II: Divided cells; nuclear envelope breakdown, new spindles form 7.​ Metaphase II: Condensed sister chromatids line up along equatorial plate 8.​ Anaphase II: Sister chromatids/dyads separate into individual chromatids towards poles 9.​ Telophase II: Individual chromatids at separate poles; cells divide Day 6: Gametogenesis & Fertilization ​ Gametes: Sperm or egg cell ​ Male germ cell → Meiosis (2 divisions) → 4 sperm cells (haploid; viable) ​ Female germ cell → Meiosis (1 division) → 2 unequal size cells (secondary oocyte & first polar body) ○​ Primary oocytes enter meiosis prophase I and stop ○​ All energy put into making high quality cell (thus 1 bigger/better than other) ​ Sperm motility is low in acidic conditions (better when neutral or basic) ​ Production of sperm in testes outside body ensures optimal temp (slight below body temp) Step 1: Spermatogenesis ​ Occurs in seminiferous tubules protected by Sertoli cells (also produce FSH) ​ Spermatids develop moving inward → lumen of tubules → storage in epididymis ○​ Nucleus becomes head; cytoplasm is lost ○​ Acrosome cap forms over head; made of digestive enzymes to penetrate egg ​ Testosterone produces by Leydig cells between seminiferous tubules Step 2: Sperm Transport 1.​ Epididymis via Vas deferens → Seminal vesicle (mucus, protein, fructose) 2.​ Prostate produces milky fluid; makes less fluid 3.​ Bulbourethral gland → Fluid neutralizes urethra acidity Oogenesis ​ 3 Ovulation control methods 1.​ Intercourse-stimulated (rabbits) 2.​ Estrus (heat): Animal only receptive to intercourse when uterus is ready 3.​ Menstrual cycle (most primates) Menstruation Cycle ​ Menstrual Phase (Day 1–5) ○​ Day 1: Uterine lining sheds; bleeding due to low progesterone and estrogen ○​ Day 2–5: GnRH stimulates LH & FSH release to start new cycle  ​ Follicular Phase (Day 1–12) ○​ Day 1–4: LH & FSH stimulates follicle growth in ovaries (primary oocyte development pauses in prophase I) ○​ Day 5–12: 1 dominant follicle develops (produces estrogen, inhibiting LH/FSH) ​ Ovulation (Day 12-14) ○​ Day 12-14: LH surge completes Meiosis I, forming & releasing secondary oocyte (haploid) + polar body into oviduct ​ Rapid estrogen rise triggers LH & thickens endometrium ​ Oocyte viable for ~24 hours; cervical mucus becomes sperm-friendly ​ Luteal Phase (Day 15–28) ○​ Day 15–22: Corpus luteum forms; secretes progest to maintain endometrium ○​ Day 25–28: No fertilization: Corpus luteum degenerates → progest & estro drop ○​ Day 25-28: If fertilized in oviduct: Secondary oocyte completes Meiosis II → Form mature ovum (egg) ​ Sperm + Egg = Zygote (diploid) ​ Zygote divide → blastocyst (cell cluster) → attach to endometrium ​ Implanted blastocyst secretes hCG, preserving corpus luteum ​ Cycle Reset (Day 28) ○​ GnRH stimulates FSH and LH release to restart cycle ​ During pregnancy, high levels of estrogen/progesterone prevent FSH/LH from pituitary, pausing ovarian cycle (the “pill” works same way) Fertilization ​ Polyspermy (multiple sperm fertilize 1 egg) = bad ○​ Additional chromosome/DNA interferes w/ spindle fiber formation ​ Sea urchins are model system for fertilization ○​ Acrosomal process (powered by actin filaments) → Bindin-coated head of sperm extends to fuse with vitelline envelope (VE) on egg  ○​ Jelly coat on egg protects egg fertilization from other species and initiate acrosome reaction to prepare for fertilization ​ FAST polyspermy: Sperm enters egg, immediate influx of Na+ ions depolarize egg plasma membrane to prevent binding of other sperm ​ SLOW polyspermy: Ca2+ levels increase then spread via CICR to stimulate fusion of cortical granules to plasma mem; expand/harden VE ○​ After binding w/ egg plasma membrane, sperm nucleus released into egg cytosol ​ Mammalian fertilization = very similar to sea urchin 1.​ Sperm binds to receptors on zona 2.​ Acrosome rxn induced; release of hydrolytic enzymes to digest hole in zona 3.​ Sperm reaches/fuses to oocyte plasma mem; cortical rxn initiates 4.​ Sperm nucleus enters oocyte 5.​ Enzymes from cortical reaction raise slightly to harden zona ○​ Egg surrounded by thick layer of nurse cells (cumulus) w/ zona pellucida below ○​ Zona glycoprotein binds w/ sperm head; trigger acrosome rxn & digest enzymes Day 7: Conceptual & Genetic Bases of Development ​ Preformation hypothesis: Homonucleus; within sperm is pre-formed embryo ○​ In embryo is another embryo, which has another embryo, etc. ​ Epigenesis hypothesis: Form of animal emerges gradually ​ Housekeeping proteins: Proteins all cells need ​ Determination: The point that cells commit to becoming certain cell type but may not be visible yet ​ Differentiation: The point when cells become measurably different; involves synthesis of cell-specific proteins ​ Morphogenesis: Process by which cells develop shape ​ How does zygote know which species to develop from its genetic information? ○​ Chromosomes/DNA is species-specific ​ How do we turn on genes to make cell-type specific proteins in the correct place? ○​ ? ​ Weismann’s Hypothesis (1892): Determination is caused by segregation of developmental determinants by cell mitoses ​ John Gurdon’s Nuclear Transplantation in Frogs (1968): Determinants could be due to different genes being segregated to different cells by cleavage ○​ Removed nucleus from fully differentiated frog tadpole cell → Transplanted into frog egg cell w/o nucleus ○​ Results = Full tadpole eventually grew; thus, genes are not segregated to different cell types during development ​ Was first example of reproductive cloning of a vertebrate (replicated tadpole was genetically identical to original tadpole) ​ Ian Wilmut Sheep Experiment (1997): 2 different sheep cloned to make one  ​ Totipotency: Cells have the potential to differentiate into any other cell type ○​ Differentiated plant cells are more easily reversed than differentiated animal cells ​ Stem cells = Undifferentiated, dividing cells in adult mammals; pluripotent (can become several, but not all, cell types Early Events of Differentiation ​ Cytoplasmic determinants: Invisible cytoplasmic molecules (proteins, mRNAs, etc.) that determine cell fate Later Events of Differentiation ​ Cell movement/shape changes (morphogenesis) ○​ Gastrulation & neurulation ​ Induction: Communication between diff cell types that leads to increasingly specific developmental fates ○​ Signal molecules/cell contact can induce the fate of cell development ​ Programmed cell death: Cells willingly die (apoptosis), leading to modeling of morphology of organs, limbs, etc Pattern Formation ​ Segmentation: Patterns form as result of gradients of morphogens (signal molecules that determine shape, size, pattern) ○​ mRNA produces biocoid + nanos proteins (pattern gradient in Drosophila) ○​ Gradients from morphogens induce 3 types of segmentation activated sequentially 1.​ Gap genes: Define broad areas that regulate pair rule genes 2.​ Pair Rule genes refine segment location & regulate segment polarity genes 3.​ Segment polarity genes determine final boundaries of each segment then homeotic genes define the role of each segment ​ Mutations in homeotic genes disrupts role of individual segments (e.g. more wings, legs) ​ Homeotic genes control differentiation on posterior/anterior axis ​ Epigenetic Landscape: Developmental events determine final differentiation cell fate ​ Darwin: Similarities among embryos of diff species may be used to infer relationships among groups of organisms ​ Neoteny: Retention of juvenile characteristics into adulthood