C Interaction and Interdependence

• Enzymes are mostly protein biological catalysts, with some RNA examples • They work in small amounts and remain unchanged after catalysis

• Metabolism is all enzyme-controlled chemical reactions in cells • Specific enzymes control which metabolic reactions occur and when

• Anabolism builds complex molecules by condensation and requires energy • Catabolism breaks molecules by hydrolysis or oxidation and releases energy

• Enzymes are usually globular proteins with a small active-site pocket • The active site binds substrate, forms an ES complex, and catalyses reaction

• Substrate binding induces shape changes in both enzyme and substrate • Induced fit aligns catalytic groups and raises substrate toward transition state

• Molecular motion brings substrates and active sites into collision • Higher kinetic energy increases successful active-site collisions

• Active-site amino acid arrangement determines substrate specificity • Denaturation changes tertiary structure and active-site shape, not peptide bonds

• Temperature increases rate to an optimum, then denaturation lowers activity • pH changes active-site bonding; substrate concentration rises to saturation plateau

• Measure substrate loss or product formation per unit time • Use initial rate, replicates, controls, and graphs from amylase or catalase assays

• Enzymes lower activation energy by providing an alternative pathway • They stabilize transition states but do not remove the energy barrier

• Intracellular enzymes act in cytoplasm, organelles, or membranes • Extracellular enzymes are secreted and act outside cells, such as digestion enzymes

• Exergonic metabolic reactions inevitably release some energy as heat • Endotherms use metabolic heat to maintain body temperature

• Linear pathways run from substrate to product, such as glycolysis • Cyclical pathways regenerate an acceptor, such as Krebs and Calvin cycles

• Non-competitive inhibitors bind away from the active site at allosteric sites • Binding changes enzyme shape and reduces activity despite substrate presence

• Competitive inhibitors resemble the substrate and bind reversibly to active sites • Increasing substrate concentration can reduce their effect

• End products inhibit earlier pathway enzymes when product accumulates • Feedback inhibition regulates pathway output, such as isoleucine synthesis

• Mechanism-based inhibitors become irreversible after active-site reaction starts • Penicillin inhibits transpeptidase and prevents bacterial wall cross-linking

• ATP is a small soluble nucleotide and universal energy currency • It links energy-yielding respiration to energy-requiring cellular processes

• ATP supplies active transport, anabolic synthesis, and movement • Examples include membrane pumps, macromolecule synthesis, and chromosome movement

• ATP hydrolysis to ADP and phosphate releases energy for coupled reactions • Respiration phosphorylates ADP to ATP; ATP is recycled rather than stored

• Cell respiration is enzyme-controlled release of energy from organic compounds • Carbon compounds are oxidized stepwise so energy can be transferred to ATP

• Aerobic respiration uses oxygen and mitochondria, producing CO₂, water, and high ATP • Anaerobic respiration in human cytoplasm produces lactate and low ATP

• Rate depends on metabolic demand, organism size, oxygen, substrate, temperature, and pH • Respirometers measure oxygen uptake while soda lime absorbs CO₂

• NAD accepts hydrogen during oxidation/dehydrogenation reactions • Reduced NAD carries electrons and protons to the electron transport chain

• Glycolysis converts glucose to two pyruvate molecules in the cytoplasm • It is a linear pathway with substrate-level ATP and reduced NAD net yield

• Pyruvate accepts hydrogen from reduced NAD to form lactate • Regenerated NAD allows glycolysis to continue

• Yeast converts pyruvate to ethanol and CO₂ during alcoholic fermentation • Fermentation regenerates NAD for glycolysis and is used in baking and brewing

• Pyruvate is oxidized and decarboxylated in the mitochondrial matrix • Acetyl groups join coenzyme A to form acetyl-CoA for the Krebs cycle

• Acetyl-CoA combines with oxaloacetate to form citrate • The cycle regenerates oxaloacetate and yields CO₂, ATP, reduced NAD, and reduced FAD

• Reduced NAD and FAD donate electrons to carriers in the inner mitochondrial membrane • Electron transfers release energy while coenzymes are reoxidized

• Electron transport energy pumps protons from matrix to intermembrane space • The inner membrane maintains a proton gradient and membrane potential

• Protons flow through ATP synthase back into the matrix • ATP synthase couples proton flow to ADP phosphorylation by chemiosmosis

• Oxygen is the terminal electron acceptor at the end of the chain • Oxygen combines with electrons and protons to form metabolic water

• Lipids yield more ATP and metabolic water per gram because they are more reduced • Carbohydrates are easier to hydrolyse and enter glycolysis quickly

• Photosynthesis converts light energy into chemical energy in carbon compounds • Photoautotrophs use chlorophyll in chloroplasts or cyanobacterial membranes

• Carbon dioxide is reduced to carbohydrate using hydrogen from water • Glucose represents the main stored product, though many compounds are synthesized

• Oxygen is released from photolysis of water, not directly from CO₂ • Oxygenic photosynthesis occurs in plants, algae, and cyanobacteria

• Paper chromatography separates chlorophylls and accessory pigments • Rf values compare pigment movement relative to solvent front

• Chlorophyll and accessory pigments absorb specific wavelengths • Absorbed light excites electrons for light-dependent reactions

• Absorption spectra show wavelengths absorbed by pigments • Action spectra show wavelengths most effective for photosynthesis rate

• Light intensity, CO₂ concentration, and temperature can limit photosynthesis • Investigations change one variable and estimate rate from O₂ production or CO₂ uptake

• CO₂ enrichment tests whether increased CO₂ raises photosynthesis or growth • Greenhouse and FACE experiments compare realistic crop and ecosystem responses

• Photosystems are pigment-protein arrays in thylakoid membranes • Antenna pigments pass energy to reaction-centre chlorophyll

• Pigment arrays broaden wavelength absorption and funnel energy efficiently • A single chlorophyll molecule cannot sustain the full light reaction system

• Photosystem II uses light energy to split water • Photolysis supplies replacement electrons, protons, and oxygen

• Electron transport pumps protons into the thylakoid space • Proton flow through ATP synthase produces ATP by photophosphorylation

• Photosystem I re-excites electrons for NADP reduction • NADP accepts electrons and H⁺ to form reduced NADP/NADPH

• Thylakoids organize photosystems, electron carriers, and ATP synthase • Key outputs on the stromal side are ATP and reduced NADP

• Rubisco fixes CO₂ to RuBP, forming glycerate 3-phosphate • Rubisco is abundant but slow and limited by low CO₂

• Glycerate 3-phosphate is reduced to triose phosphate • ATP supplies energy and reduced NADP supplies hydrogen

• Most triose phosphate regenerates RuBP so the Calvin cycle continues • ATP is required for regeneration of the CO₂ acceptor

• Triose phosphate is converted into sugars, starch, lipids, and organic acids • Mineral nutrients allow synthesis of amino acids and other compounds

• Light-dependent reactions supply ATP and reduced NADP for the Calvin cycle • The Calvin cycle returns ADP and NADP and depends on CO₂/hydrogen carbonate availability

• Receptor proteins have binding sites specific to signalling ligands • Ligand binding starts signal transduction in target cells

• Autoinducers allow bacteria to detect population density thresholds • Vibrio fischeri bioluminescence and biofilm formation are key examples

• Animal signals include hormones, neurotransmitters, cytokines, and Ca²⁺ ions • They differ in source, distance, speed, and target-cell response

• Hormones include protein/peptide, steroid, and amine classes • Neurotransmitters include acetylcholine, amino acids, peptides, amines, and nitric oxide

• Neurotransmitters act locally across narrow synaptic clefts • Hormones travel through blood to distant cells with matching receptors

• Hydrophilic ligands bind transmembrane receptors and use intracellular relays • Steroid and thyroid hormones cross membranes and bind cytoplasmic or nuclear receptors

• Signal transduction relays, amplifies, integrates, and distributes ligand signals • Pathways use relay proteins, second messengers, phosphorylation cascades, and effectors

• Acetylcholine can bind ligand-gated sodium channels • Sodium influx changes membrane potential and can depolarize the postsynaptic membrane

• GPCRs are seven-helix transmembrane receptors linked to G proteins • Ligand binding causes GDP-GTP exchange and activation of effector proteins

• Epinephrine binds adrenergic GPCRs and activates G protein signalling • Adenylyl cyclase forms cAMP, activating kinase cascades for glycogen breakdown

• RTK ligand binding causes dimerisation and autophosphorylation • Insulin signalling moves GLUT4 vesicles to membranes and promotes glycogenesis

• Steroid and thyroid hormones bind intracellular receptor proteins • Hormone-receptor complexes enter or act in the nucleus as transcription factors

• Oestradiol regulates female sex characteristics and hypothalamus-pituitary targets • Progesterone from corpus luteum or placenta maintains endometrium and pregnancy

• Positive feedback amplifies responses, such as ethylene in fruit ripening • Negative feedback restores stability, such as insulin lowering blood glucose

• Neurons carry electrical impulses in the nervous system • Motor, sensory, and relay neurons differ in axon, dendrite, and cell body arrangement

• Sodium-potassium pumps use ATP to move 3 Na⁺ out and 2 K⁺ in • Ion gradients make the resting axon polarized at about -70 mV

• A nerve impulse is a propagated action potential along a nerve fibre • Stimulus-triggered sodium influx reverses membrane polarity

• Larger axon diameter lowers resistance and increases impulse speed • Myelin sheaths and nodes of Ranvier enable faster saltatory conduction

• Synapses connect neurons to neurons, muscles, or glands • Chemical synapses transmit one way across a narrow synaptic cleft

• Action potentials open voltage-gated Ca²⁺ channels in presynaptic terminals • Ca²⁺ causes vesicle fusion and neurotransmitter exocytosis into the cleft

• Neurotransmitters diffuse and bind receptors on the postsynaptic membrane • EPSPs depolarize the membrane and make threshold more likely

• Threshold opens voltage-gated Na⁺ channels, causing rapid depolarization • Voltage-gated K⁺ channels then repolarize or briefly hyperpolarize the axon

• Local currents from Na⁺ diffusion depolarize the next axon region • Refractory regions behind the impulse help ensure one-way propagation

• Oscilloscope traces show resting potential, threshold, and action potential phases • Stimulus intensity is encoded by impulse frequency, not action potential size

• Myelin insulates axons and ion exchange occurs mainly at nodes of Ranvier • Saltatory conduction jumps node to node and greatly increases speed

• Exogenous chemicals can mimic, block, or prolong neurotransmitter effects • Neonicotinoids bind insect acetylcholine receptors; cocaine blocks dopamine reuptake

• Inhibitory neurotransmitters open Cl⁻ entry or K⁺ exit channels • Hyperpolarization makes threshold harder to reach

• Postsynaptic neurons integrate EPSPs and IPSPs from many synapses • Temporal and spatial summation determine whether threshold is reached

• Pain uses free nerve endings with TRP ion channels in skin and other tissues • Heat, acid, capsaicin, or tissue damage can trigger impulses perceived as pain

• Consciousness emerges from coordinated activity across interacting brain regions • EEG, MRI, and fMRI provide evidence for neural correlates of conscious processing

• Integration lets interacting parts coordinate an overall biological function • Systems interact across molecular, cellular, organ, organism, and ecosystem levels

• Cells form tissues, organs, organ systems, and whole organisms • Emergent properties arise when subsystems interact, such as gut peristalsis and absorption

• Organs are integrated by nervous signals, hormones, and blood transport • Transport links nutrients, gases, wastes, hormones, and energy substrates between organs

• The brain integrates sensory input and coordinates complex responses • Cerebral hemispheres, cerebellum, hypothalamus, and medulla have distinct roles

• The spinal cord links brain and peripheral nervous system • It integrates unconscious processes such as reflex arcs

• Sensory neurons carry impulses from receptors to spinal cord and brain • Inputs may reach cerebral hemispheres for conscious perception

• Motor neurons carry impulses from CNS to skeletal muscle effectors • Voluntary muscle contraction is coordinated through cerebral hemispheres

• Nerves are bundles of sensory and motor nerve fibres in connective tissue • Mixed nerves carry impulses both to and from the CNS

• Pain reflexes are rapid involuntary withdrawal responses • Reflex arcs use receptors, sensory neurons, relay neurons, motor neurons, and skeletal muscle

• The cerebellum coordinates timing and force of skeletal muscle contractions • It maintains balance, posture, and smooth learned movements

• The pineal gland secretes melatonin according to light-dark cycles • Melatonin modulates sleep timing as part of circadian rhythms

• Adrenal glands secrete epinephrine during stress or danger • It increases heart rate, ventilation, and respiratory substrate availability

• The hypothalamus links nervous inputs to endocrine control • Pituitary hormones regulate glands including thyroid, gonads, adrenals, and mammary glands

• Baroreceptors monitor blood pressure; chemoreceptors monitor CO₂, pH, and O₂ • The medulla adjusts sinoatrial node activity by sympathetic and parasympathetic nerves

• Chemoreceptors detect CO₂-driven pH changes in blood and cerebrospinal fluid • The medulla alters diaphragm and intercostal muscle activity to change ventilation rate

• The CNS controls voluntary swallowing and egestion • The enteric nervous system coordinates involuntary peristalsis in gut smooth muscle

• Tropisms are directional growth responses in seedlings • Experiments compare shoot or root growth under lateral light or gravity stimuli

• Shoots show positive phototropism toward lateral light • Auxin redistribution causes greater elongation on the shaded side

• Phytohormones are plant signalling chemicals controlling growth and development • Auxin, cytokinin, and ethylene coordinate responses to stimuli and internal state

• PIN auxin efflux carriers actively move auxin between plant cells • Asymmetric carrier placement maintains auxin gradients during tropic responses

• Auxin activates proton pumping into the apoplast • Acidified cell walls loosen, allowing water uptake, elongation, and bending

• Auxin generally promotes root formation; cytokinin promotes shoot formation and division • Their ratio coordinates root-shoot growth and plant tissue culture outcomes

• Ethylene is a gaseous phytohormone that promotes fruit ripening • Ripening fruit releases more ethylene, creating positive feedback in nearby fruit

• Pathogens are disease-causing viruses, bacteria, fungi, protists, or parasites • Archaea are not currently known to cause human infectious diseases

• Keratinized skin, shedding, lysozyme, mucus, and cilia are primary defences • Mucous membranes protect respiratory and digestive surfaces

• Platelets and damaged tissue release clotting factors at wounds • Thrombin converts fibrinogen to fibrin, trapping blood cells and sealing entry points

• Innate immunity is broad, rapid, and does not become more specific over life • Adaptive immunity is antigen-specific and produces memory cells

• Phagocytes use amoeboid movement to reach infection sites • They recognize, engulf, and digest pathogens using lysosomal enzymes

• B-cells produce antibodies after activation; T-cells assist or destroy infected cells • Lymphocytes originate in bone marrow and circulate through blood, lymph, and lymph nodes

• Antigens are non-self molecules that trigger specific immune responses • They are often proteins or glycoproteins recognized by antibodies or lymphocyte receptors

• B-cells bind antigen, internalize it, and present it with MHC proteins • Helper T-cells activated by the same antigen stimulate B-cell activation

• Activated B-cells divide by mitosis through clonal selection • Plasma cells rich in rough ER secrete large amounts of one specific antibody

• Memory B- and T-cells remain after the primary response declines • Re-exposure triggers faster, stronger secondary immunity

• HIV is transmitted through infected blood, semen, vaginal fluids, or breast milk • Transmission risk depends on fluid exchange, barriers, and viral load

• HIV infects helper T-cells using CD4 receptors and reverse transcriptase • AIDS results when helper T-cell loss weakens antibody production and immune coordination

• Antibiotics block bacterial processes absent from eukaryotic cells • They do not treat viruses; antivirals target viral replication processes

• Antibiotic use selects resistant variants that survive and reproduce • Multi-resistant strains arise through mutation, plasmids, and overuse of antibiotics

• Zoonoses transfer from animal reservoirs to humans, sometimes through vectors • Examples include rabies, tuberculosis, Japanese encephalitis, and COVID-19

• Vaccines contain weakened/inactivated pathogens, antigens, or genetic instructions • Immunization produces active artificial immunity and memory cells

• Herd immunity indirectly protects susceptible people when many are immune • Thresholds depend on transmission route and pathogen contagiousness

• Evaluate COVID-19 data using source reliability, trends, and controlled comparisons • Calculate percentage change, percentage difference, incidence, and vaccine efficacy

C4.1.1Populations

• A population is interacting organisms of the same species in one area • Members have opportunities to interbreed and may be reproductively isolated from others

C4.1.2Population size estimation

• Population size is estimated when full counts are impractical • Random sampling reduces bias; stratified and systematic sampling fit different habitats

C4.1.3Random quadrat sampling

• Quadrats estimate density, frequency, cover, or abundance of sessile organisms • Random coordinates and known quadrat area support representative population estimates

C4.1.4Capture-mark-release-recapture

• Capture-mark-release-recapture estimates motile animal populations • Lincoln index assumes marks persist, mixing occurs, and marking does not affect survival

C4.1.5Carrying capacity

• Carrying capacity is the maximum population an environment can sustain • Limited food, space, mates, and other resources create competition near capacity

C4.1.6Negative feedback control

• Density-dependent factors regulate populations by negative feedback • Competition, predation, waste, and disease intensify as population density rises

C4.1.7Population growth curves

• Exponential growth occurs when resources are abundant and limiting factors are weak • Sigmoid growth slows as resources limit growth near carrying capacity

C4.1.8Modelling sigmoid growth

• Sigmoid curves can be modelled with yeast, duckweed, or other fast-growing organisms • Lag, exponential, transition, and plateau phases show changing growth rate

C4.1.9Competition vs. cooperation

• Intraspecific competition occurs for food, mates, space, or light • Cooperation such as social hunting or parental care can increase survival and reproduction

C4.1.10Community

• A community is all interacting populations in an ecosystem • Species interactions make populations interdependent within the abiotic environment

C4.1.11Interspecific relationships

• Interspecific relationships occur between different species in communities • Categories include herbivory, predation, competition, mutualism, parasitism, and pathogenicity

C4.1.12Mutualism as interspecific relationship

• Mutualism benefits both species through exchanged resources or protection • Examples include legumes and Rhizobium, orchids and mycorrhizae, corals and zooxanthellae

C4.1.13Endemic vs. invasive species

• Endemic species are native to a restricted geographic area • Invasive species can escape controls and compete with endemic species for niche resources

C4.1.14Tests for interspecific competition

• Competition is tested using lab experiments, field observations, or removal studies • Connell's barnacle study links removal experiments to fundamental and realized niches

C4.1.15Chi-squared test

• Chi-squared tests association between two species from quadrat presence/absence data • Compare observed and expected counts, degrees of freedom, and critical values

C4.1.16Predator-prey relationships

• Predator-prey relationships regulate populations through density-dependent feedback • Snowshoe hare and lynx cycles show time-lagged predator and prey changes

C4.1.17Top-down vs. bottom-up control

• Top-down control begins with predators and cascades to lower trophic levels • Bottom-up control begins with producers or resources and affects higher trophic levels

C4.1.18Allelopathy and antibiotics

• Allelopathy releases chemicals that inhibit competitor germination or growth • Antibiotics are microbial allelochemicals, such as penicillin from Penicillium

• Ecosystems are open systems exchanging energy and matter with surroundings • Energy flows through ecosystems while matter can enter, leave, and recycle

• Sunlight is the principal energy source for most ecosystems • Exceptions include caves and deep-ocean vents supported by chemosynthesis

• Chemical energy flows from producers to consumers through feeding • Energy enters as light or chemical energy and leaves ecosystems as heat

• Food chains and food webs model feeding relationships in communities • Arrows point in the direction of energy and biomass transfer

• Decomposers obtain energy from carbon compounds in detritus • Dead organisms, faeces, fallen leaves, and shed tissues supply organic matter

• Autotrophs synthesize carbon compounds from simple inorganic substances • They use external energy sources to fix carbon and build biomass

• Photoautotrophs use light captured by photosynthetic pigments • Chemoautotrophs use oxidation of inorganic substances, such as iron or sulfur compounds

• Heterotrophs obtain carbon compounds from other organisms or organic matter • They use these compounds for respiration and synthesis of their own biomass

• Both autotrophs and heterotrophs release energy by cell respiration • Oxidation of carbon compounds transfers energy to ATP and heat

• Trophic levels classify organisms as producers, primary consumers, and higher consumers • Omnivores and decomposers may feed across more than one trophic level

• Energy pyramids represent energy flow per unit area per unit time • Each bar shows energy available to one trophic level

• Energy availability decreases at each transfer between trophic levels • Losses occur through respiration, heat, egestion, excretion, and uneaten biomass

• Cell respiration converts some chemical energy to heat in all trophic levels • Heat dissipates to the environment, so energy cannot be recycled

• Large energy losses restrict food chains to a few trophic levels • Higher trophic levels usually support less biomass and fewer individuals

• Primary production is accumulation of carbon compounds in autotroph biomass • Gross production minus respiration gives net primary production

• Secondary production is biomass accumulation by heterotrophs • It depends on food intake, assimilation, respiration losses, and biomass conversion

• Carbon cycle diagrams show stores as boxes and fluxes as labelled arrows • Include CO₂, photosynthesis, feeding, respiration, decomposition, fossil fuels, and combustion

• Carbon sinks absorb more carbon than they release, such as forests, soils, and oceans • Carbon sources release more carbon than they absorb, such as fossil fuel combustion

• Combustion of biomass, peat, coal, oil, and natural gas releases CO₂ • Draining peat and forest fires increase carbon flux to the atmosphere

• The Keeling Curve records atmospheric CO₂ at Mauna Loa since the late 1950s • Long-term rise reflects combustion; annual oscillation reflects Northern Hemisphere photosynthesis

• Photosynthesis supplies atmospheric O₂ used in aerobic respiration • Respiration supplies CO₂ used by photosynthesis, linking autotrophs and heterotrophs

• All chemical elements required by organisms are recycled in ecosystems • Decomposers convert detritus and waste into inorganic nutrients for producers