(2) IB Biology HL Study Guide 2024-2026 - cells, organisms, ecosystems

A2.3 AHL Viruses

Definition and Shared Features: Viruses share relatively few features across their immense diversity. These common characteristics include: * Small, fixed size. * Genetic material consisting of nucleic acids, which can be either DNA or RNA. * An outer protein coat known as a capsid. * No cytoplasm. * Few or no enzymes.
Diversity of Structure: * Viruses vary significantly in shape and structure. * Genetic material can be single-stranded or double-stranded RNA or DNA. * Envelopment: Some viruses are enveloped in host cell membrane, while others are not enveloped. * Specific examples include bacteriophage lambda, coronaviruses, and Human Immunodeficiency Virus (HIV).
Life Cycle and Host Dependence: Viruses rely entirely on a host cell for essential life functions, including energy supply, nutrition, and protein synthesis. * Lytic Cycle: Using bacteriophage lambda as the example, the lytic cycle involves phases of infection, replication, and the eventual bursting of the host cell to release new virions. * Lysogenic Cycle: Bacteriophage lambda can also enter a lysogenic cycle, where the viral DNA is integrated into the host genome and replicated without destroying the cell immediately.
Origins and Evolution: * The diversity of viruses suggests several distinct origins from other organisms rather than a single common ancestor. * Viruses represent an extreme form of obligate parasitism. * Convergent Evolution: Shared structural features among viruses may be the result of convergent evolution due to their similar parasitic lifestyles. * Shared Genetic Code: The fact that the universal genetic code is shared between viruses and living organisms points to their evolutionary links.
Rapid Evolution: * Some viruses evolve at extremely high rates. Notable examples include influenza viruses and HIV. * Reasons for rapid evolution include high mutation rates (especially in RNA viruses) and short generation times. * Consequences: Rapid evolution poses significant challenges for the treatment of diseases, as viruses can quickly develop resistance to drugs or evade the immune system.

C2.1 AHL Chemical Signaling

Receptors and Ligands: Signaling chemicals are referred to as "ligands." Receptors are proteins with specific binding sites for these ligands.
Quorum Sensing in Bacteria: Bacteria use cell signaling to coordinate group behavior. A primary example is bioluminescence in the marine bacterium Vibrio fischeri.
Functional Categories of Signaling Chemicals in Animals: * Hormones: Transported long distances via the blood system. * Neurotransmitters: Diffuse across synaptic gaps for localized effects. * Cytokines. * Calcium ions ( $Ca^{2+}$ ).
Chemical Diversity: * Hormones can be amines, proteins, or steroids. * Neurotransmitters include amino acids, peptides, amines, and nitrous oxide.
Receptor Locations and Signal Transduction: * Transmembrane Receptors: Located in the plasma membrane. These typically interact with hydrophilic ligands that cannot penetrate the cell membrane. * Intracellular Receptors: Located in the cytoplasm or nucleus. These interact with hydrophobic ligands (like steroids) that can cross the plasma membrane. * Signal Transduction Pathways: Binding of a ligand to a receptor initiates a sequence of internal cellular responses.
Specific Signaling Mechanisms: * Neurotransmitter Receptors: The acetylcholine receptor is a transmembrane protein. Binding causes the opening of an ion channel, allowing positively charged ions to diffuse into the cell, changing the membrane potential ( $V_m$ ). * G Protein-Coupled Receptors (GPCRs): These receptors convey signals into the cell by activating G proteins. There are many such receptors in the human body. * Epinephrine (Adrenaline) Mechanism: Involves G proteins and cyclic AMP (cAMP) acting as a second messenger. * Tyrosine Kinase Receptors (Insulin): Binding of insulin to the receptor causes phosphorylation of tyrosine residues inside the cell. This triggers a cascade that moves vesicles containing glucose transporters to the plasma membrane. * Intracellular Gene Expression (Steroids): Steroid hormones like oestradiol, progesterone, and testosterone bind to and activate intracellular receptors. The activated receptor-hormone complex binds to specific DNA sequences to promote gene transcription.
Feedback Regulation: * Oestradiol: Affects cells in the hypothalamus that secrete gonadotropin-releasing hormone (GnRH). * Progesterone: Affects cells in the endometrium. * Feedback Loops: Signaling pathways are regulated by both positive and negative feedback mechanisms.

D3.3 SL Homeostasis

Definition: Homeostasis is the maintenance of the internal environment within preset limits, regardless of external fluctuations.
Human Homeostatic Variables: Body temperature, blood $pH$ , blood glucose concentration, and blood osmotic concentration.
Negative Feedback Loops: * Negative feedback is the primary mechanism for homeostasis because it returns variables to a set point from values either above or below that point.
Regulation of Blood Glucose: * Controlled by pancreatic endocrine cells that secrete insulin and glucagon. * These hormones are transported in the blood to target cells to maintain steady glucose levels.
Diabetes Mellitus: * Type 1 Diabetes: Physiological changes resulting in a lack of insulin production. * Type 2 Diabetes: Often linked to risk factors like diet and lack of exercise, characterized by reduced sensitivity to insulin.
Thermoregulation: * Example of negative feedback control. * Involves peripheral thermoreceptors, the hypothalamus, and the pituitary gland. * Effectors: Thyroxin, muscle tissue (shivering), and adipose tissue. * Human Mechanisms: Vasodilation (to lose heat), vasoconstriction (to conserve heat), shivering, sweating, uncoupled respiration in brown adipose tissue, and hair erection.

C3.1 SL Integration of Body Systems

System Integration: Multicellular organisms are organized in a hierarchy (cells, tissues, organs, systems). Integration allows component parts to perform collective functions, resulting in emergent properties (e.g., a cheetah's speed).
Signaling Systems: Integration is achieved through hormonal signaling, nervous signaling, and the transport of materials/energy.
Nervous System Organs: * The Brain: Central information integration organ. It processes multiple inputs and is responsible for learning and memory. * The Spinal Cord: Center for unconscious processes.
Neurons and Nerves: * Sensory Neurons: Convey messages from receptors to the Central Nervous System (CNS). * Motor Neurons: Carry output from the cerebral hemispheres to muscles to stimulate contraction. * Nerve Structure: Bundles of nerve fibers (myelinated and unmyelinated) surrounded by a protective sheath.
Reflex Arcs: The pain reflex arc is an involuntary response. It involves a free sensory nerve ending, a single interneuron in the grey matter of the spinal cord, and skeletal muscle as the effector.
The Cerebellum: Coordinates skeletal muscle contraction and balance.
Circadian Rhythms: Sleep patterns are modulated by the pineal gland's secretion of melatonin in a diurnal pattern.
Epinephrine (Adrenaline): Secreted by adrenal glands to facilitate intense muscle contraction for vigorous activity.
Hypothalamus and Pituitary: Control the endocrine system.
Feedback Control of Vital Signs: * Heart Rate: Monitored by baroreceptors (blood pressure) and chemoreceptors (blood $pH$ , $O_2$ , and $CO_2$ levels). The medulla coordinates changes to stroke volume and heart rate. * Ventilation Rate: Chemoreceptors in the brainstem monitor blood $pH$ changes. The medulla sends signals to the diaphragm and intercostal muscles.

D3.2 Inheritance (SL and AHL)

Fundamentals of Inheritance: * Involves the production of haploid gametes and their fusion into a diploid zygote. * Diploid cells have two copies of each autosomal gene.
Genotype vs. Phenotype: * Genotype: The combination of alleles inherited. * Phenotype: Observable traits resulting from the interaction of genotype and environment.
Allele Interactions: * Dominant and Recessive: Dominant alleles mask the effect of recessive ones in heterozygotes. * Codominance: Heterozygotes have a dual phenotype (e.g., AB blood type). * Incomplete Dominance: Heterozygotes show an intermediate phenotype (e.g., Mirabilis jalapa).
Specific Genetic Conditions: * Phenylketonuria (PKU): An autosomal recessive disease caused by a mutation in a gene for an enzyme that converts phenylalanine to tyrosine. * ABO Blood Groups: Example of multiple alleles ( $I^A$ , $I^B$ , and $i$ ). * Haemophilia: A sex-linked genetic disorder carried on the X chromosome.
AHL Patterns of Inheritance: * Independent Assortment: Unlinked genes segregate independently during meiosis. * Dihybrid Crosses: Predict genotypic/phenotypic ratios. Unlinked autosomal genes typically yield a $9:3:3:1$ ratio for double heterozygotes cross and $1:1:1:1$ for a test cross. * Autosomal Gene Linkage: Genes located close together on the same chromosome do not assort independently. The notation uses vertical lines for homologous chromosomes. * Recombinants: Offspring with different allele combinations than the parents due to crossing over.
Chi-squared ( $\chi^2$ ) Test: Used on dihybrid cross data to determine if observed results match expected outcomes. Statistical significance is usually tested at the $p=0.05$ level.
Variation and Representation: * Polygenic Inheritance: Causes continuous variation (e.g., human skin color). * Box-and-Whisker Plots: Displays: minimum, first quartile ( $Q1$ ), median, third quartile ( $Q3$ ), maximum, and outliers. * Outlier Formula: Defined as a point more than $1.5 \times IQR$ (interquartile range) away from the quartiles.

A4.1 SL Evolution

Definition: Evolution is the change in the heritable characteristics of a population. This excludes acquired changes (distinguishing it from Lamarckism).

Evidence for Evolution:

* Molecular Evidence: Similarity in base sequences of DNA/RNA and amino acid sequences in proteins indicate common ancestry.
* Selective Breeding: Rapid evolutionary changes in domesticated animals and crop plants provide evidence of selection.
* Homologous Structures: Structures derived from a common ancestor, such as the pentadactyl limb (divergent evolution).

Convergent Evolution: The origin of analogous structures, which have the same function but different evolutionary origins.

Speciation: The splitting of a pre-existing species. Speciation increases the total number of species, while extinction decreases it.

* Gradual evolutionary change within a single lineage is not speciation.
* Isolation: Reproductive isolation (often via geographic isolation) and differential selection drive speciation.
* Example: The Congo River separated bonobos from common chimpanzees, leading to divergence.

B3.2 AHL Transport

Tissue Fluid: Formed by pressure filtration of plasma in capillaries, particularly at the arteriole end due to high blood pressure. Excess tissue fluid drains into lymph ducts, which feature valves and thin walls, before returning to total circulation.
Circulation Systems: * Bony Fish: Single circulation. * Mammals: Double circulation.
Mammalian Heart Adaptations: Features include cardiac muscle, pacemaker (sinoatrial node), atria, ventricles, septum, coronary vessels, and atrioventricular/semilunar valves to ensure unidirectional flow.
Cardiac Cycle: Sequence of events in the left side of the heart initiated by the sinoatrial node. Measured via systolic and diastolic pressure.
Plant Transport: * Root Pressure: Positive pressure potential generated by active transport of mineral ions into xylem, pushing water up when transpiration is low (e.g., high humidity). * Phloem Translocation: Sieve tube elements have reduced cytoplasm, no nucleus, and sieve plates to ease flow. Companion cells have many mitochondria and are connected to sieve tubes via plasmodesmata for loading carbon compounds at sources and unloading at sinks.

D3.1 SL Reproduction

Asexual vs. Sexual: * Asexual: Faster, produces genetically identical offspring adapted to stable environments. * Sexual: Produces variation via meiosis and fertilization, allowing for adaptation to changing environments.
Male vs. Female Gametes: Male gametes are smaller and motile; female gametes are larger with food reserves.
Menstrual Cycle: Ovarian and uterine cycles regulated by FSH, LH, oestradiol, and progesterone via feedback loops.
Human Fertilization: Entry of a sperm nucleus into the egg, destruction of the sperm's tail and mitochondria, and the joint mitosis of combined chromosomes to form two diploid nuclei.
In Vitro Fertilization (IVF): Uses artificial hormones to induce superovulation.
Flowering Plant Reproduction: * Sexual reproduction involving pollination and fertilization within ovules. * Insect-pollinated flowers: Specific adaptations for attracting pollinators. * Cross-pollination: Promoted by separate maturation times for pollen and stigma or separate male/female flowers to increase genetic diversity. * Self-incompatibility: Genetic mechanisms to prevent inbreeding. * Seed Dispersal: Distinct from pollination; involves the movement of seeds and the subsequent mobilization of food reserves for germination.

C2.2 SL Neural Signaling

Neuron Structure: Cell body (cytoplasm and nucleus), dendrites (short fibers), and a single long axon.
Resting Potential: Established by pumping sodium ( $Na^+$ ) and potassium ( $K^+$ ) ions across the plasma membrane using ATP. The resting potential is negative.
Action Potential: Propagation of electrical impulses along nerve fibers involving the movement of positively charged ions (depolarization/repolarization).
Transmission Speed: Faster in myelinated fibers compared to non-myelinated, and faster in giant axons (e.g., squid) compared to smaller ones.
Synaptic Transmission: * Depolarization of the presynaptic membrane triggers calcium ( $Ca^{2+root}$ ) uptake. * Neurotransmitters (e.g., acetylcholine) are released into the synaptic cleft. * Binding to receptors on the postsynaptic membrane generates an excitatory postsynaptic potential.

B3.1 SL Gas Exchange

Principles: Gas exchange is vital but becomes challenging as size increases and surface area-to-volume ratio ( $SA:V$ ) decreases.
Surface Adaptations: Permeable, thin tissue layer, moist, and large surface area.
Mammalian Lungs: Alveolar structure with surfactants (prevent collapse), branched bronchioles, and dense capillary networks.
Ventilation: Driven by the diaphragm, intercostal muscles, abdominal muscles, and ribs.
Plant Gas Exchange: * Leaves: Adapted with a waxy cuticle, epidermis, air spaces within spongy mesophyll, stomatal guard cells, and veins. * Transpiration: Water loss as a consequence of gas exchange; affected by various environmental factors. * Stomatal Density: Determined using micrographs or leaf casts.

A4.2 SL Conservation of Biodiversity

Levels of Biodiversity: Ecosystem diversity, species diversity, and genetic diversity.
Biodiversity Crisis: We are currently in a sixth mass extinction. Unlike past non-anthropogenic extinctions, this one is driven by human activity.
Causes of Extinction: * Terrestrial Megafauna loss: North Island giant moas (Dinornis novae zealandiae). * Marine species loss: Caribbean monk seals (Neomonachus tropicalis). * General causes: Human population growth, over-hunting, urbanization, deforestation, pollution, and invasive species.
Ecosystem Loss: Loss of mixed dipterocarp forest in Southeast Asia.
Conservation Approaches: * In situ: Nature reserves, rewilding. * Ex situ: Zoos, botanic gardens, seed banks. * EDGE Programme: Prioritizes evolutionarily distinct and globally endangered species.

D4.1 AHL Natural Selection

Gene Pool: Consists of all genes and their alleles in a population.
Neo-Darwinism: The integration of Darwinian natural selection with genetics.
Selection Types: * Directional Selection: Favors one extreme phenotype. * Disruptive Selection: Favors both extremes over the intermediate. * Stabilizing Selection: Favors the intermediate phenotype.
Hardy-Weinberg Principle: * Equation for alleles: $p + q = 1$ * Equation for genotypes: $p^2 + 2pq + q^2 = 1$ * Equilibrium requires random mating and equal survival rates.
Artificial Selection: Selective breeding for desirable traits in crops or animals.
Variation Sources: Mutation (new alleles) and sexual reproduction (new combinations).
Selection Pressures: Abiotic factors (temperature, $pH$ ) and biotic factors (competition, predation, disease).
Sexual Selection: Differential success in attracting mates based on physical or behavioral traits (e.g., plumage of birds of paradise).

B3.3 AHL Muscles and Motility

Sarcomere Contraction: Described by the sliding filament model involving actin and myosin filaments.
Protein Titin: Helps sarcomeres recoil after stretching and prevents overstretching.
Motor Units: A single motor neuron and all the muscle fibers it innervates via neuromuscular junctions.
Skeletal Systems: Exoskeletons (arthropods) or endoskeletons (vertebrates) providing anchorage for muscles and acting as levers.
Synovial Joints: Example: Human hip joint. Includes bones (femur, pelvis), cartilage, synovial fluid, ligaments, and tendons.
Antagonistic Muscles: Because muscles only exert force when contracting (shortening), they must work in pairs (e.g., internal and external intercostal muscles pulling the ribcage in opposite directions).
Locomotion: Driven by the need to forage, escape danger, find mates, or migrate.
Marine Mammal Adaptations: Streamlining, limbs converted to flippers, tails forming a fluke (up-and-down movement), and airway changes for periodic breathing.