B Form and Function

• Carbon forms four strong covalent bonds with C, H, O, N, S, and P • Carbon skeletons form chains, branches, rings, and single or double bonds • Functional groups give carbon compounds distinctive chemical properties

• Condensation links monomers with covalent bonds and releases water • Polysaccharides, polypeptides, and nucleic acids are polymers made this way • Glycosidic, peptide, and phosphodiester bonds are key examples

• Hydrolysis breaks covalent bonds in polymers using water • Water provides -H and -OH groups to form monomers • Amylases, proteases, and nucleases catalyse hydrolysis of major biomolecules

• Pentoses such as ribose and hexoses such as glucose are monosaccharides • Glucose is soluble, transportable, chemically stable, and a direct respiratory substrate • Alpha- and beta-glucose differ at carbon 1 and form different polysaccharides

• Starch stores energy in plants as amylose and amylopectin • Glycogen stores energy in animals and fungi and is more highly branched • Insolubility, compactness, and easy hydrolysis make both effective glucose stores

• Cellulose is made from beta-glucose joined by 1,4 glycosidic bonds • Alternating glucose orientation makes straight, unbranched chains • Hydrogen bonds form fibrils and fibres that strengthen plant cell walls

• Glycoproteins and glycolipids form the external glycocalyx of membranes • Cell-surface carbohydrates enable self/non-self recognition, adhesion, and signalling • ABO blood group antigens show how surface sugars affect immune compatibility

• Lipids are hydrophobic, sparingly soluble in water, and soluble in non-polar solvents • Fats, oils, waxes, phospholipids, and steroids are lipid examples • Lipids are not true polymers because they are not built from repeating identical monomers

• Condensation forms ester bonds between glycerol and fatty acids • Triglycerides contain glycerol plus three fatty acids • Phospholipids contain glycerol, two fatty acids, and an ionized phosphate group

• Saturated fatty acids have no carbon-carbon double bonds • Monounsaturated and polyunsaturated fatty acids have one or multiple double bonds • Double bonds create kinks, lower melting points, and affect membrane and storage properties

• Triglycerides in adipose tissue store concentrated long-term energy • Insoluble fat stores avoid osmotic effects and can provide insulation, protection, and buoyancy • Fat oxidation releases more energy and metabolic water than carbohydrate of the same mass

• Phospholipids are amphipathic with hydrophilic phosphate heads and hydrophobic tails • In water they form monolayers or bilayers with tails away from water • Bilayers are stable barriers and the basic structure of cell membranes

• Steroids are mostly non-polar lipids with four fused carbon rings • Non-polar steroids pass through the hydrophobic core of phospholipid bilayers • Oestradiol and testosterone are cholesterol-derived steroid hormone examples

• Amino acids have an alpha carbon bonded to an amine, carboxyl, hydrogen, and R-group • The R-group varies between amino acids and determines chemical properties • Proteins contain C, H, O, N, and usually S

• Condensation joins the carboxyl group of one amino acid to the amine group of another • A peptide bond forms and water is released • Chains have an N-terminus and C-terminus and are assembled at ribosomes

• Essential amino acids cannot be synthesized and must be obtained from dietary protein • Non-essential amino acids can be made by transamination, mainly in the liver • Deficiency of essential amino acids limits protein synthesis and can cause malnutrition

• Twenty coded amino acids can form vast numbers of sequences • Protein diversity depends on amino acid type, number, and order • Genes encode polypeptide sequences; the proteome is the full protein set expressed

• Protein shape determines function, especially enzyme active sites • High temperature or unsuitable pH disrupts weak bonds and denatures proteins • Denaturation may be reversible in small proteins but often becomes irreversible

• Amphipathic phospholipids have hydrophilic heads and hydrophobic tails • In water they spontaneously form continuous closed bilayers • Lipid bilayers are the structural basis of plasma membranes and vesicles

• Hydrophobic fatty acid tails form a stable membrane core • The core has low permeability to ions and large or hydrophilic molecules • Membranes separate aqueous compartments and control entry and exit

• Diffusion is passive movement down a concentration gradient using kinetic energy • Small non-polar molecules such as oxygen and carbon dioxide diffuse through the bilayer • Diffusion rate depends on factors such as gradient, distance, surface area, and temperature

• Integral proteins are embedded in one or both lipid layers and may span the membrane • Integral proteins can act as channels, carriers, pumps, receptors, enzymes, or antigens • Peripheral proteins attach to membrane surfaces and can act as receptors or scaffolds

• Osmosis is passive net movement of water across a partially permeable membrane • Water moves from lower solute concentration to higher solute concentration • Aquaporins are protein pores that increase water diffusion across membranes

• Channel proteins provide hydrophilic pores for facilitated diffusion • Polar molecules, ions, ADP, ATP, and water use specific channels or transporters • Channels are selective and move substances down gradients without ATP

• Pump proteins use ATP from respiration for active transport • They move specific molecules or ions against concentration gradients • Active transport is selective and uses carrier or pump proteins, not channel proteins

• Simple diffusion depends mainly on particle size and hydrophobic or hydrophilic properties • Facilitated diffusion and active transport use proteins to create selective permeability • Selective transport is essential in roots, intestines, kidneys, and neurons

• Glycoproteins and glycolipids have short carbohydrate chains on the extracellular surface • Together they form the glycocalyx • The glycocalyx supports recognition, adhesion, signalling, and interaction with water

• The fluid mosaic model describes mobile lipids and proteins in a phospholipid bilayer • Membranes include integral proteins, peripheral proteins, cholesterol, glycoproteins, and glycolipids • Freeze-etching, protein extraction, and fluorescent tagging supported the model

B2.2.1Organelles as discrete subunits

• Organelles are discrete cell subunits adapted for specific functions • Nuclei, chloroplasts, mitochondria, vesicles, ribosomes, and plasma membrane are organelles • Cell wall, cytoskeleton, and cytoplasm are not usually considered organelles

B2.2.2Nucleus-cytoplasm separation

• The nuclear envelope protects DNA and separates transcription from translation • Introns can be removed from pre-mRNA by RNA splicing before translation • Nuclear pores regulate mRNA export and protein import using selective transport

B2.2.3Advantages of compartmentalization

• Compartmentalization concentrates enzymes, substrates, and suitable pH for specific reactions • It separates incompatible biochemical processes so they can be controlled • Lysosomes and phagolysosomes contain acidic hydrolytic digestion away from cytoplasm

• A zygote divides to produce unspecialized cells that later differentiate • Differentiation occurs when different genes are activated in different cells • Morphogen gradients control gene expression and body pattern formation

• Stem cells self-renew by repeated division while remaining undifferentiated • Stem cells have potency: the capacity to differentiate into mature cell types • Embryonic stem cells have broader potential than most adult stem cells

• Stem cell niches provide signals that maintain, activate, or differentiate stem cells • Bone marrow niches regulate haematopoietic stem cells that form blood cells • Hair follicle bulge niches contain multipotent stem cells for hair regeneration

• Totipotent cells can form all body cells plus placental cells • Pluripotent cells form all body cell types but not placenta or totipotent cells • Multipotent adult stem cells repair and maintain limited tissues or organs

• Specialized cells vary widely in size according to function • Egg cells are large for nutrient storage; sperm are small with a long flagellum • Neurons can be very long, and striated muscle fibres are extended multinucleate cells

• Surface area controls exchange, while volume controls metabolic demand • As cells grow, volume increases faster than surface area • Low surface area-to-volume ratio limits diffusion and therefore cell size

• Gas exchange supplies respiratory gases between organisms and environment • Animals take in oxygen and release carbon dioxide for aerobic respiration • Larger or active organisms need specialized exchange surfaces because SA:V decreases

• Efficient gas-exchange surfaces are permeable, thin, moist, and large • Large surface area and steep concentration gradients increase diffusion • Short diffusion paths speed movement of oxygen and carbon dioxide

• Dense capillary networks provide large exchange area and rapid transport • Continuous blood flow carries oxygen away and carbon dioxide toward the surface • Ventilation refreshes air or water to maintain steep gas gradients

• Many small alveoli provide large surface area and thin squamous walls • Capillary beds maintain gradients and bring red blood cells close to alveolar air • Surfactant reduces surface tension, while elastic fibres support ventilation and recoil

• Diaphragm and intercostal muscles change thoracic volume and pressure • Inspiration uses diaphragm and external intercostal contraction to draw air in • Expiration reduces thoracic volume; internal intercostals and abdominal muscles aid forced exhalation

• Spirometry records breathing patterns, ventilation rate, and lung volumes • Tidal volume is air moved during normal relaxed breathing • Vital capacity equals tidal volume plus inspiratory and expiratory reserve volumes

• Stomata allow carbon dioxide, oxygen, and water vapour to diffuse • Guard cells open and close stomata by changes in turgor • Waxy cuticle, lower epidermal stomata, air spaces, mesophyll, and veins balance gas exchange with water loss

• Dicot leaves have waxy cuticle, upper and lower epidermis, palisade and spongy mesophyll • Vascular bundles contain xylem and phloem for water and assimilate transport • Spongy mesophyll air spaces and stomata create internal diffusion routes

• Transpiration is evaporation from mesophyll walls followed by diffusion of water vapour through stomata • Temperature, humidity, wind, and light alter concentration gradients and stomatal opening • Potometers estimate transpiration indirectly by measuring water uptake

• Stomatal density is the number of stomata per unit leaf area • Higher density can increase carbon dioxide uptake and water loss • Leaf casts or micrographs allow stomatal counts and comparisons between species

• Capillaries are narrow, highly branched, and close to cells • One-cell-thick endothelial walls reduce diffusion distance • Fenestrations in some capillaries allow rapid exchange and tissue fluid formation

• Arteries and veins have endothelium, smooth muscle, elastic tissue, and collagen • Arteries have thicker walls and smaller lumens to withstand high pressure • Veins have wider lumens and thinner walls for low-pressure return

• Thick artery walls and collagen prevent rupture under high pressure • Elastic fibres stretch and recoil to even out pulse pressure and maintain flow • Smooth muscle in arteries and arterioles regulates blood distribution

• Ventricular contraction creates a pressure wave felt as a pulse • Pulse rate can be measured at radial or carotid arteries • Counting for a full minute is most accurate; shorter counts can be scaled

• Veins have valves that prevent backflow toward capillaries • Thin flexible walls allow surrounding muscles to compress veins • Large lumens reduce friction during low-pressure blood return

• Atherosclerosis forms plaques beneath damaged coronary artery endothelium • Plaque rupture can trigger thrombosis and occlude coronary arteries • Reduced oxygen supply can kill cardiac muscle and cause myocardial infarction

• Transpiration from leaf mesophyll creates tension in xylem water columns • Cohesion between water molecules transmits tension from leaves to roots • Adhesion to xylem walls helps maintain an unbroken transpiration stream

• Mature xylem vessels are dead, hollow tubes with absent or perforated end walls • Lignified walls resist collapse under negative pressure and waterproof the vessel • Pits allow lateral movement of water between vessels and surrounding tissues

• Dicot stems have epidermis, cortex, pith, and vascular bundles in a ring • Each vascular bundle contains xylem, phloem, cambium, and supporting fibres • Plan diagrams show tissue positions without drawing individual cells

• Dicot roots have epidermis with root hairs, cortex, endodermis, and central vascular tissue • Xylem forms a central cross with phloem between its arms • The Casparian strip blocks apoplast flow and forces selective symplast entry to xylem

• Habitat is the place where an organism, population, species, or community lives • Habitat descriptions can include geographic location, physical position, and ecosystem type • Microhabitats are small areas with conditions different from the surrounding habitat

• Adaptations improve survival under abiotic conditions such as water availability, salinity, oxygen, and wind • Marram grass has rolled, hairy leaves and thick cuticle to reduce water loss in dunes • Mangroves use aerial roots, pneumatophores, salt exclusion, or salt excretion in saline low-oxygen swamps

• Species distribution depends on abiotic variables such as temperature, salinity, pH, light, rainfall, humidity, and substratum • Limiting factors can restrict survival, growth, reproduction, or activity by deficiency or excess • Plant limiting factors include light, water, nutrients, carbon dioxide, and temperature

• A range of tolerance lies between critical minimum and maximum limits • The optimum zone supports highest survival, growth, abundance, and reproduction • Zones of stress and intolerance explain reduced abundance or absence along environmental gradients

• Coral reefs need warm, shallow, clear, sunlit, saline water with suitable pH • Reef-building corals rely on photosynthetic symbiotic algae • Low nutrients, sediment, cold water, or reduced light can limit reef formation

• Terrestrial biome distribution is mainly determined by temperature, rainfall, and insolation • Productivity depends strongly on water availability and photosynthesis rate • Latitude and seasonal variation help explain rainforest, temperate forest, taiga, grassland, tundra, and desert distribution

• Biomes are groups of ecosystems with similar communities due to similar abiotic conditions • Similar biomes can evolve similar forms through convergent evolution • Examples include tropical rainforest, temperate forest, taiga, grassland, tundra, and hot desert

• Hot desert strategies include expire, evade, or endure under heat and water scarcity • Camels, cacti, scorpions, and kangaroo rats show water-saving, heat-avoidance, or storage adaptations • Tropical rainforest adaptations include pitcher plant nutrient capture, gibbon brachiation, flying lizard gliding, and orchid mantis mimicry

• A niche is the role of a species in a community • It includes habitat, activity, feeding, reproduction, and biotic and abiotic interactions • Cormorants and shags illustrate different niches through diet and behaviour despite similar habitat

• Oxygen availability shapes microbial niches and respiration strategy • Obligate aerobes require oxygen, such as Mycobacterium tuberculosis • Obligate anaerobes are poisoned by oxygen; facultative anaerobes such as E. coli can switch pathways

• Photoautotrophs use light energy to make organic molecules from carbon dioxide • Plants, algae, and cyanobacteria contain photosynthetic pigments • Cyanobacteria were early oxygen-producing photosynthetic organisms

• Holozoic nutrition is heterotrophic feeding by ingestion of organic matter • Food is digested internally, absorbed, and assimilated • Herbivores, carnivores, and omnivores are consumers with holozoic nutrition

• Mixotrophs combine autotrophic and heterotrophic nutrition • Euglena photosynthesizes using chloroplasts and can ingest bacteria by phagocytosis • Mixotrophy may be obligate or facultative, including some plankton and symbioses

• Saprotrophs secrete enzymes onto dead organic matter and absorb digestion products • Many fungi and bacteria are saprotrophic decomposers • Saprotrophs recycle inorganic nutrients, but energy is lost as heat through respiration

• Archaea include photoheterotrophic, chemoautotrophic, and heterotrophic nutrition • Halobacteria use light-driven ion pumps rather than oxygenic photosynthesis • Methanogens and hydrogen-dependent archaea illustrate chemosynthesis and anaerobic niches

• Incisors slice, canines tear, and premolars and molars grind food • Gorillas and Paranthropus robustus have robust jaws and large grinding teeth for tough vegetation • Humans have smaller canines, smaller molars, and more gracile skulls linked to omnivorous diet

• Herbivores have adaptations such as chewing mouthparts, aphid stylets, or detoxifying gut bacteria • Plants resist herbivory with spines, stinging hairs, or toxic compounds • Examples include cacti, stinging nettles, deadly nightshade, oleander, and cassava

• Predators use binocular vision, specialized senses, speed, stealth, or venom to find and kill prey • Prey use wide fields of view, camouflage, mimicry, armour, aposematic colouration, or toxins • Examples include peregrine falcons, hedgehogs, chameleons, coral snake mimicry, poison dart frogs, and bombardier beetles

• Forest strata create intense competition for light from canopy to ground layer • Canopy trees, lianas, epiphytes, and strangler figs reach light using different forms • Shade-tolerant plants may have large leaves, different pigments, bright flowers, or strong scent

• Fundamental niche is where a species could live based on adaptations and tolerance limits • Realized niche is where it actually lives after biotic and abiotic interactions • Competition, predation, mutualism, dispersal, and climate can narrow realized niches

• Competitive exclusion occurs when one species outcompetes another for the same limiting resource • Niche overlap increases interspecific competition • Gause's Paramecium experiments showed P. aurelia excluding P. caudatum in mixed culture