exam 6 concepts

Retroviruses

• Single-stranded RNA viruses that use reverse transcriptase to make DNA from RNA.

• DNA can be used to make mRNA or integrate into host DNA (lysogenic cycle).

• HIV

Lichens

• Lichens are symbiotic associations between fungi + algae/cyanobacteria.

• Fungi provide protection, water, and nitrogen; algae/cyanobacteria provide carbohydrates via photosynthesis.

• Fungi are eukaryotic, unlike viruses, which are non-cellular.

Archaebacteria

• Archaebacteria are living prokaryotes, survive independently, and have polysaccharide cell walls.

• bacteria have peptidoglycan cell wallsare non-living, lack metabolism, and must hijack a host cell to replicate.

X-linked Genetic Disorders

• Found on the X chromosome, not the Y.

• Males (XY) with the allele = fully affected.

• Females (XX) with 1 affected X = carriers, may show partial or no symptoms.

• Example: X-linked retinoschisis → causes partial/complete blindness by degrading the retina.

Y-linked disorders

• Y-linked disorders affect only males; females can’t be affected (no Y chromosome).

• X-linked disorders can affect both sexes:

  • Males with 1 affected X = fully affected

  • Females with 1 affected X = carriers, may show partial or no symptoms

• Partial symptoms in females indicate the disorder is X-linked, not autosomal or Y-linked.

Ductus Venosus

• Oxygenated blood from placenta returns via umbilical vein.

• Half bypasses liver through ductus venosus directly to the heart.

• Blood bypasses liver because fetal liver is not fully functional (filtering/detoxifying).

• Other half flows through portal vein into the liver.

ductus venosus

foramen ovale

ductus arteriosus

• Ductus venosus: Bypasses liver by directing half of umbilical vein blood to heart (fetal liver not fully functional).

• Foramen ovale: Small opening between right and left atria; allows blood to bypass lungs by moving directly to left atrium (no fetal lung gas exchange).

• Ductus arteriosus: Vessel connecting pulmonary artery to aorta; bypasses lungs by diverting blood away from pulmonary circulation.

Sperm Structure and Acrosome Function

• Sperm parts: Head (contains acrosome), mid-piece (energy), tail (motility).

• Acrosome: Lysosome-like organelle with enzymes that digest the zona pellucida.

• Zona pellucida: Glycoprotein membrane around the oocyte with ZP3 receptor proteins.

• Acrosome reaction: Triggered by sperm binding to ZP3, releasing enzymes to penetrate zona pellucida.

• Importance: Without acrosome, sperm cannot penetrate zona pellucida or fertilize the egg.

Antibody Structure & Classes

• Structure: Y-shaped proteins with constant & variable regions; 2 heavy + 2 light chains linked by disulfide bonds.

• Classes: IgA, IgD, IgE, IgG, IgM.

• IgG: Most abundant in serum, monomeric, can cross placenta to protect fetus.

• IgM: Pentameric structure, unique among antibodies.

Classes: IgA, IgD, IgE, IgG, IgM.

Menstrual Cycle Hormonal Regulation

• Low estrogen & progesterone → Hypothalamus releases GnRH → Anterior pituitary releases FSH & LH.

• FSH stimulates follicles → Follicles secrete estrogen → Estrogen causes positive feedback → More GnRH & LH surge.

• LH surge triggers ovulation → Follicles secrete estrogen & progesterone → Thickening of endometrium for implantation.

Hormones in Lactation

• Prolactin: Stimulates milk production in mammary glands.

• Oxytocin: Causes milk ejection by contracting mammary smooth muscle.

• Together, they enable feeding and provide nutrients plus antibodies to the baby.

Meiosis I vs Meiosis II

• Meiosis I: Homologous chromosomes separate → daughter cells become haploid (half chromosome number).

• Meiosis II: Sister chromatids separate → chromosome number stays haploid; no further reduction.

Gastrulation & Germ Layers

• Gastrulation: Invagination of cells in blastula → forms gastrula with 3 germ layers: ectoderm (outer), mesoderm (middle), endoderm (inner).

• Ectoderm: Nervous system, epidermis/hair, sensory structures (eye lens/retina), neural tube, facial bones, adrenal medulla.

• Mesoderm: Musculoskeletal, circulatory/lymphatic, excretory, gonads, connective tissue, parts of digestive/respiratory, notochord, dermis, adrenal cortex.

• Endoderm: Epithelial lining of digestive/respiratory tracts, liver, pancreas, gall bladder, thyroid/parathyroid, thymus, urinary bladder lining.

Lac Operon Regulation

• Operon: DNA region with structural & regulatory genes controlled by promoter & operator.

• Lac Operon (E. coli): Controls lactose breakdown via genes lacZ, lacY, lacA.

• Regulation: Repressor protein binds operator, blocking RNA polymerase.

• Lactose presence: LacZ converts lactose → allolactose, which binds repressor, inactivating it → RNA polymerase transcribes lactose digestion genes.

• Result: Lactose enzymes made only when lactose/allolactose present.

Plant Energy Storage and Photosynthesis

• Light-dependent reactions: Use sunlight to produce ATP & NADPH.

• Dark reactions (Calvin cycle): Use ATP & NADPH to produce glucose.

• Glucose use: Fuel for aerobic respiration in plant cells.

• Energy storage: Excess glucose stored as starch (polymer of alpha-glucose).

• Storage location: Starch stored in vacuoles and plastids called leucoplasts.

Alternative Splicing

• Selective removal of introns and joining of exons in pre-mRNA to create different mRNA variants.

• Allows one gene to produce multiple different proteins.

• Only occurs in eukaryotes (prokaryotes lack introns and splicing machinery).

• Increases protein diversity beyond the number of genes.

Role of hCG in Early Pregnancy

• hCG is secreted by the placenta after implantation to maintain the corpus luteum.

• The corpus luteum secretes estrogen and progesterone to maintain the endometrium for embryo support.

• Without hCG, the corpus luteum degrades, progesterone and estrogen drop, and menstruation occurs.

• Later in pregnancy, the placenta takes over progesterone production directly.

TSH

• TRH from the hypothalamus stimulates the anterior pituitary to produce TSH.

• TSH (Thyroid-Stimulating Hormone) stimulates the thyroid gland to grow and secrete thyroid hormones T3 (triiodothyronine) and T4 (thyroxine).

• TSH regulates metabolism, not reproduction.

Species Diversity

• Species diversity = species richness + relative abundance.

• Species richness = total number of different species in a community.

• Relative abundance = number of individuals per species.

Island Biogeography

• Species richness increases with island size due to more habitats and resources.

• Species richness decreases with greater distance from the mainland because of less immigration and more local extinctions.

• When distance is unknown, island size is the key factor for predicting species richness.

Gastrin and HCl in Digestion

• G cells (stomach) secrete gastrin, a peptide hormone absorbed into blood.

• Gastrin stimulates parietal cells to secrete hydrochloric acid (HCl).

• HCl keeps stomach pH very acidic (~2), killing bacteria and activating pepsin.

• Pepsinogen (from chief cells) is converted to pepsin by HCl for protein digestion.

• HCl also helps absorb vitamin B-12 in the ileum.

• Gastrin is secreted and acts within the same organ (stomach).

Role of T3 (Triiodothyronine)

• Secreted by the thyroid gland.

• Targets most cells in the body (not a specific organ).

• Essential for growth and neurological development in children.

• Increases basal metabolic rate (BMR) by boosting cellular metabolism.

Insulin

• Secreted by beta cells of the pancreas.

• Targets liver, muscle cells, and adipose (fat) tissue.

• Stimulates glucose absorption and storage, lowering blood glucose levels.

• Does not target the pancreas itself.

• Works alongside glucagon to regulate blood sugar

Epinephrine

• Secreted by the adrenal medulla.

• Targets multiple tissues throughout the body, not the adrenal medulla itself.

• Activates the sympathetic nervous system — triggers “fight or flight” response.

Epinephrine effects

• Increases blood glucose, blood pressure, and heart rate.

• Increases blood flow to skeletal muscles.

• Dilates pupils.

• Bronchodilation (relaxes airway smooth muscles).

• Decreases blood flow to non-essential organs (intestines, bladder).

• Increases overall metabolic activity.

Luteinizing Hormone (LH)

• Secreted by the anterior pituitary.

• Targets the ovaries (females) and testes (males).

• In females:

  • Stimulates formation of the corpus luteum.

  • LH surge triggers ovulation (release of secondary oocyte).

• In males:

  • Stimulates Leydig cells in testes to produce testosterone.

Prokaryotic vs. Eukaryotic Transcription and Translation

• Lack membrane-bound organelles and a nuclear membrane.

• Genetic material is in the nucleoid (no nucleus).

• Transcription and translation occur simultaneously in the cytoplasm.

• Ribosomes can begin translating mRNA immediately after transcription starts.

• bacteria/archae kingdoms

Prokaryotic vs. Eukaryotic Transcription and Translation

• Have a nucleus separating DNA from cytoplasm.

• Transcription occurs inside the nucleus.

• mRNA must be exported to cytoplasm for translation by ribosomes

• animalia, plantae, fungi, protists kingdoms

Steroid Hormones

• Synthesis: Made from cholesterol in smooth ER.

• Structure: Retain cholesterol’s 4-ring backbone; variations arise from diff functional groups.

• Types:

  • Sex hormones: Androgens (testosterone), estrogens (estradiol), progestogens (progesterone).

  • Others: Mineralocorticoids, glucocorticoids.

• Functions: Regulate sexual dev (puberty, menstruation, pregnancy, sperm prod), physiological processes.

Hormones Derived from Tyrosine

• Synthesized from AA tyrosine.

• Include melatonin, epinephrine, norepinephrine, dopamine, serotonin.

• Mostly function as neurotransmitters or hormones affecting mood, stress response, and circadian rhythms.

Hormones Derived from Polypeptides

• Synthesized by ribosomes, coded by genes in the genome.

• Examples: FSH, LH, ACTH, hGH, TSH, prolactin, ADH, PTH, glucagon, insulin.

• Typically water-soluble, act via membrane receptors to trigger cell signaling cascades.

Coevolution

• Coevolution is when two species reciprocally influence each other’s evolution.

• Seen in relationships like predator-prey (e.g., faster predators → faster prey).

• Coevolution involves adaptive changes in both species due to close interactions.

Coevolution EX

• Also occurs in mutualistic relationships, like:

  • Hummingbirds & trumpet creeper flowers:

    • Hummingbirds evolved long beaks for tubular flowers.

    • Flowers evolved long petals to match beak shape → improves pollination.

Carbon Cycle

• Carbon reservoirs include the atmosphere (CO₂), producers, consumers, and decomposers.

• Producers absorb CO₂ via photosynthesis and convert it to organic carbon.

• Consumers eat producers and release CO₂ back through cellular respiration.

Decomposers in the Carbon Cycle

• Decomposers/saprophytes (fungi, bacteria) break down dead matter using cellular respiration.

• They secrete enzymes to digest organic compounds into absorbable units.

• Their respiration releases CO₂ into the atmosphere & supply C for plants photosynthesis

• Fossil fuel combustion also contributes CO₂ to the air.

Voltage-Gated Ion Channels & Neuron Transmission

• Voltage-gated ion channels open in response to membrane potential changes.

• Na⁺ influx depolarizes the axon; K⁺ efflux repolarizes it.

• An action potential triggers sequential opening of these channels along the axon.

Motor End Plate & Muscle Fiber Activation

• Acetylcholine at neuromuscular junction opens ligand-gated Na⁺ channels.

• Sufficient depolarization activates voltage-gated channels in sarcolemma.

• Action potential travels via T-tubules, triggering Ca²⁺ release from sarcoplasmic reticulum.

Calcium & Muscle Contraction

• Ca²⁺ binds troponin, enabling myosin-actin crossbridge formation.

• Sarcomeres shorten → muscle contracts.

• Ca²⁺ is actively pumped back into sarcoplasmic reticulum to end contraction.

Ligand-Gated and Mechanically-Gated Ion Channels

• Ligand-gated channels open in response to neurotransmitter binding (e.g. acetylcholine).

• Mechanically-gated channels open in response to physical stimuli (pressure, vibration).

• Both types generate graded potentials that may trigger an action potential if threshold is reached.

DNA Microarray

• Detects gene expression by hybridizing cDNA to gene-specific wells.

• mRNA is isolated and converted to cDNA via reverse transcriptase.

• Fluorescence indicates gene expression; intensity reflects expression level.

• Only expressed genes produce signal—unexpressed genes show no binding.

Polymerase Chain Reaction (PCR)

• Amplifies DNA (not RNA or gene expression).

• Involves 3 steps: denaturation, annealing, and elongation.

• Uses primers and DNA polymerase to replicate target DNA.

• DNA amount increases exponentially with each cycle.

Karyotyping

• Used to visualize number and structure of chromosomes.

• Can detect large chromosomal abnormalities (e.g. trisomy 21 in Down Syndrome).

• Involves staining and photographing chromosomes.

• Cannot assess gene expression.

Gel Electrophoresis

• Separates DNA, RNA, or proteins by size and charge.

• Smaller molecules migrate farther through the gel.

• Used before sequencing or probing for specific sequences.

• Does not measure gene expression.

Thyroid Hormones (T3 & T4)

• Lipid-soluble tyrosine derivatives made by the thyroid gland.

• Increase basal metabolic rate; needed for growth & brain development in children.

• Iodine is required for their synthesis.

Thyroid Disorders

• Hypothyroidism: ↓ metabolism, HR, RR; leads to fatigue, weight gain, decrease in gastric motility

• Hyperthyroidism: ↑ metabolism, sweating; causes weight loss, thinness.

• Both can cause goiter (thyroid enlargement).

Calcitonin vs Parathyroid Hormone (PTH)

• Calcitonin: lowers blood Ca²⁺ by stimulating osteoblasts (build bone) and inhibiting osteoclasts (break down bone).

• PTH: raises blood Ca²⁺ by stimulating osteoclasts (release Ca²⁺ from bone) and increasing osteocyte calcium absorption.

Homeotic (HOX) Genes

• Homeotic genes control body structure development during embryogenesis by regulating gene expression in body segments.

• HOX genes specifically determine segmentation and anatomic placement by turning genes on/off in each segment via the homeobox DNA sequence.

• Small changes in HOX gene expression lead to major structural differences between related species (e.g., shrimp vs. grasshopper).

• Mutations in HOX genes can cause misplacement of structures (e.g., leg growing on head) and often cause developmental failure due to their conserved nature.

lac Operon and lacZ Gene

• The lac operon regulates lactose metabolism in prokaryotes

• lacZ codes for β-galactosidase, an enzyme that breaks lactose into glucose and galactose.

• Regulatory genes produce a repressor protein that binds the operator, blocking RNA polymerase and preventing transcription.

• When lactose is present, it binds the repressor, inactivating it and allowing transcription of lac genes for lactose metabolism.

p53 gene

• tumor suppressor gene encoding a protein that regulates cell repair and apoptosis.

• Downregulation or mutation of p53 impairs its ability to control abnormal cell growth.

• Loss of p53 function can lead to unchecked cell proliferation and cancer development.

SRY gene

• located on the Y chromosome and produces the testis-determining factor protein.

• It is essential for male sexual development, especially Sertoli cell formation.

• Sertoli cells secrete signals that inhibit the development of Müllerian ducts (which form female reproductive structures).

• Without SRY, the embryo develops ovaries and female reproductive organs.

trp operon

• trpE is a part of

• controls tryptophan synthesis in prokaryotes by producing enzymes needed for tryptophan production.

• Regulatory genes produce an inactive repressor allowing RNA polymerase to transcribe tryptophan genes.

• When tryptophan is abundant, it binds to the repressor, activating it.

• The active repressor binds the operator, blocking RNA polymerase and stopping tryptophan synthesis (negative feedback).

Resting & Graded Potential

• Resting potential = -70mV (normal polarized neuron state)

• Stimulus opens gated Na⁺ channels → Na⁺ enters → depolarization begins

• Graded potential = small, local change in membrane potential (Graph A)

Action Potential & Threshold

• Threshold: -50 to -55mV → triggers action potential

• Action potential = rapid depolarization from voltage-gated Na⁺ channels opening along axon (Graph B, peak = Graph C)

• At peak, voltage-gated Na⁺ channels close

Repolarization & Hyperpolarization

• Repolarization: voltage-gated K⁺ channels open → K⁺ leaves cell → membrane potential returns toward resting (Graph D)

• Hyperpolarization: K⁺ channels slow to close → excess K⁺ leaves → membrane potential dips below resting (Graph E)

Refractory Period & Ion Restoration

• Refractory period: neuron temporarily unresponsive to new stimulus

• Sodium-potassium pumps restore resting ion balance and membrane potential

Aposematic Coloration

• Bright, conspicuous colors/patterns warning predators to avoid the animal

• Example: Poisonous frogs use bright colors to signal toxicity

Chitin Function & Organisms

• Chitin = β-glucose polymer used for structural support

• Found in fungal cell walls & arthropod exoskeletons

• Yeast (unicellular fungus) has a chitin-containing cell wall

• Enzymes degrading chitin would damage yeast the most

Diatoms

• Plant-like protists that perform photosynthesis

• Cell walls made of silica (not chitin)

Segmentation in Animals

• Segmentation = division of body into repetitive segments

• Seen in: arthropods, annelids, and chordates

Cnidarians (e.g., Jellyfish)

• No body segmentation

• Two body forms:

  • Medusa: free-floating, umbrella-shaped with tentacles

  • Polyp: immobile, cylindrical with upward tentacles

• Life cycle may alternate between medusa (sexual) and polyp (asexual) stages

Analogous vs. Homologous Structures

• Analogous: similar function, different ancestry → from convergent evolution

• Homologous: similar ancestry, may differ in function → from divergent evolution

Bird vs. Bat Wings (DAT Tip

• Bird & bat wings = analogous (flight, different ancestors)

• Their forelimbs = homologous (inherited from a common ancestor)

Smooth ER vs. Rough ER

• Smooth ER: no ribosomes; synthesizes lipids & steroid hormones, detoxifies

• Rough ER: has ribosomes; folds, modifies, and transports proteins

• Rough ER performs post-translational modifications (e.g., adding chemical groups)

Lysosomes

• Contain hydrolytic enzymes for digestion of biomolecules

• Functions: apoptosis, autophagy, and pathogen breakdown (e.g., in phagocytes)

• Formed from the Golgi apparatus

Phospholipids

• Made of: 2 fatty acids (hydrophobic) + 1 phosphate group (hydrophilic) on a glycerol backbone

• Hydrophobic tails: nonpolar hydrocarbons

• Hydrophilic head: glycerol + negatively charged phosphate

• Amphipathic → form bilayers: hydrophobic interior, hydrophilic exterio

Albumins

• Simple, water-soluble functional proteins

• Act as carriers for fatty acids, hormones, ions, and vitamins

• Help maintain blood osmotic pressure

Recessive vs. Dominant Inheritance

• A recessive trait is likely if two unaffected parents have an affected child.

• A dominant trait usually does not skip generations; at least one parent is affected.

• A skipped generation (e.g., affected grandparent → unaffected parent → affected child) suggests recessive inheritance.

Autosomal vs. X-linked Recessive Inheritance

• X-linked recessive traits: Affected mothers will have all affected sons.

• If an affected mother has an unaffected son, the trait is not X-linked recessive.

• Autosomal traits affect males and females equally; X-linked recessive traits affect more males.

• Y-linked traits occur only in males (never in females).

Centrifugation

• most to least dense: 1st pellet: Nuclei

• 2nd pellet: Mitochondria & chloroplasts

• 3rd pellet: Microsomes & small vesicles

• 4th pellet: Ribosomes, viruses, macromolecules

• Denser components pellet first; lighter components pellet after repeated spins

Key Transcription Facts

• RNA polymerase reads DNA 3′→5′; synthesizes RNA 5′→3′

• Uracil (U) replaces thymine (T) in RNA

• Transcription occurs in the nucleus

• Uracil is used in RNA because it’s less energetically costly than thymine

Transcription Example

• DNA (coding strand): 5′ – ATATATGCGCACGC – 3′

• Template strand: 3′ – TATATACGCGTGCG – 5′

• mRNA (5′→3′): GCGUGCGCAUAUAU

Parallel Evolution

• Occurs in related species with a common ancestor

• Species evolve similar traits independently

• Example: Two monkey species with similar features

Convergent Evolution

• Occurs in unrelated species

• Similar traits evolve due to similar environments/functions

• Example: Insect wings vs. bat wings (flight, no shared ancestor)

Divergent Evolution

• Occurs in related species that become increasingly different

• Caused by speciation and different environmental pressures

• Example: Galapagos finches’ beaks evolving for different food sources

Open vs. Closed Circulatory Systems

• Open system: Blood (hemolymph) pumped into hemocoel, bathes organs; returns via ostia

  • arthropods, insects, mollusks have this

• Closed system: Blood circulates in vessels (arteries, veins, capillaries)

Efficiency of Closed Circulatory Systems

• Higher blood pressure → faster flow

• Separates oxygenated & deoxygenated blood

• Greater oxygen-carrying capacity (more hemoglobin)

• More efficient oxygen transport → supports higher metabolism

Feathery Gills

• Feathery gills = large surface area for gas exchange

• Important for aquatic organisms due to low dissolved oxygen in water

• Maximized surface area improves respiratory efficiency

Moist skin

• Moist skin or tracheal endings enhance gas diffusion

• Found in annelids (mucus-secreting skin) and arthropods (e.g., grasshoppers)

• Moisture helps O₂ and CO₂ dissolve and diffuse more easily

Miller–Urey Experiment

• Simulated early Earth using CH₄, NH₃, H₂, H₂O, and electric sparks (lightning)

• Produced organic molecules (e.g., amino acids, fatty acids, aldehydes) from inorganic components

• Demonstrated possible chemical origin of life in a closed system