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The Business of Life • Living Things: Parts & Emergent Properties • Self-Organization in the Sea • Reproduction: Asexual & Sexual • The Diversity & Unity of Living Things: Classification & Evolution by Natural Selection Living Things and Levels of Organization • Some biologists study the parts of living things (molecules, cells, etc): Reductionism • Others study the Emergent Properties The sum is greater than the parts: Holism The Chemistry of Life • Living Things are mostly Water: 70-95% • Water is the Biological Solvent • Biochemistry occurs in Aqueous Solution • An Organisms’ Dry Weight consists mostly of Organic Compounds: • Carbon-based Molecules, e.g. Proteins Living Things: Defined • Living Things Consist of Cells • Living Things Use Energy to • Self-Organize • Grow, and • Reproduce (cells make cells) • Populations of living things may Evolve Living Things: Parts & Emergent Properties • Living things contain special molecules; but these molecules are not alive • These molecules (& others) make up a cell • Cells can self-organize & reproduce: Emergent Properties of Life • At each higher level of organization: New Properties Emerge Organic Compounds • Complex & Energy rich • Organisms build them up: - Function & Storage • And break them down - Release stored energy - Re-use their parts 1 Organic Compounds: types • Carbohydrates: energy & structure • sugars, starch, cellulose & chitin • Lipids: energy, membrane & hormones • fats & oils, phospholipids, steroids • Proteins: diverse and abundant • transport, enzymes, receptors, etc. • Nucleic Acids: Genetic material • Deoxyribonucleic acid & Ribonucleic acid Carbohydrates: CH20 • Glucose is an energy molecule: • primary fuel for aerobic respiration • Starch stores energy for later use • Cellulose & Chitin provide structure • Cellulose: cell wall of plants (algae), wood • Chitin: cell wall of fungus, exoskeleton of arthropods - insects and crustaceans Phospholipids are Both Hydrophobic & Hydrophilic - Basis of Biological Membranes Carbohydrates: CH20 • Carbohydrates are made of C, H & O • Monosaccharides are simple sugars e.g. Glucose C6H12O6 • Polysaccharides are complex sugars many glucose molecules bound together e.g. Starch and Cellulose Lipids are mostly Hydrocarbons: H & C • Lipids are Hydrophobic compounds: water is not attracted to lipids • Fats (oils) contain twice the energy per weight of glucose: • Advantageous for mobile organisms e.g. animals • Provides insulation & protection, Example: Blubber Insulates Proteins: Polypeptides of Amino Acids - C, H, O, N & S • The most diverse & abundant organic cpds Other Lipids are Steroids • Steroid Hormones: chemical messengers • e.g. estradiol, testosterone • Create the ‘traits’ of organisms: • The expression of genes • Consist of long chains of Amino Acids • Cholesterol is a steroid used in membranes 2 Proteins: Polypeptides of Amino Acids - C, H, O, N & S • Abundant and Diverse in Function: • Transport (hemoglobin) • Enzymes: catalyze chemical reactions • Hormones • Hormone Receptors • Structure, etc. • Organisms need Nitrogen for Proteins Nucleic Acids & The Flow of Genetic Information • DNA is made of Four Nucleotides: ATGC • Genes are specific Sequences of DNA • Genes code for Proteins - which create the traits of organisms • A specific sequence of DNA nucleotides is transcribed into messenger RNA (mRNA) • The mRNA is then translated to a specific sequence of amino acids => Protein Nucleic Acids: DNA & RNA C, H, O, N & P • Deoxyribonucleic acid & Ribonucleic acid • DNA is is the Genetic Material: • Handed down from cell to cell, and • From generation to generation • Organisms need Phosphorus & Nitrogen • for their nucleic acids The Flow of Genetic Information DNA Inheritance: cellcell, parentoffspring Gene Expression: within cells DNA RNA Proteins Chemical Energy Organisms Use Energy • Organisms must Harvest Energy from the environment, because • Organisms continuously Use Energy (efficiently; Harness Energy) to – • Self-Organize, Grow & Reproduce • Chemical energy is the form of energy used by organisms in their activities • Metabolism: the sum of an organisms chemical reactions 3 Sunlight & Photosynthesis: Energy for Life on Earth • Photosynthesis traps the energy of the sun (photons) and uses that energy to make (synthesize) sugars and other energy compounds Photosynthesis: 6 CO2 & 6 H2O → C6H12O6 & 6 O2 Carbon Dioxide & Water → Sugar & Oxygen Recall: Sugar is an organic compound Giant Kelp: Macrocystis • Photosynthetic organisms are called Autotrophs: self-feeding • They can harvest the energy of the sun and transform it into chemical energy • Plants & Algae are Autotrophs Chemical Energy & Cellular Work: ATP → ADP & Pi • Organisms release the stored energy in their molecules to make ATP: Adenosine Tri-Phosphate • ATP is the energy currency of the cell the right amount of energy for cell movement, transport & chemical synthesis • Organisms use either Anaerobic and/or Aerobic Respiration to make ATP Autotrophs & Heterotrophs • Autotrophs can transform solar energy into chemical energy - the energy contained in chemical bonds • Heterotrophs: Other-feeding, are organisms that must consume ‘others’ for their chemical energy: herbivores, carnivores and decomposers Aerobic Respiration C6H12O6 & 6 O2 → 6 CO2 & 6 H2O Organic Cpd & Oxygen → Carbon Dioxide & Water • Aerobic Respiration: • Requires Oxygen • Produces 18x the ATP vs. anaerobic respiration • Efficient Harnessing of Chemical Energy! 4 The Living Processes of Organisms: Metabolism - Occurs in Cells The Living Processes of Organisms: Metabolism - Occurs in Cells Cell Parts: Plasma membrane, DNA & Cytoplasm • Plasma membrane: a fence with gates - protects the organized living cell from the chaos of the universe • DNA: the genetic material (HQ) - directions to make proteins • Cytoplasm: • Cytosol: semi-liquid matrix • Organelles: cell bodies with special function Prokaryotic Cells Pro-before, Karyo-Nucleus • Prokaryote cells are Ancestral • They lack a nucleus: their DNA is ‘naked’ • They are relatively small & simple, without membrane-bound organelles Eukaryotic Cells: Endosymbionts • Two of the most important organelles in Eukaryotes are: 1. Mitochondria - the site of Aerobic Respiration 2. Chloroplasts - the site of Photosynthesis • These organelles are bacteria! Eukaryotic Cells: Eu-true, Karyo-Nucleus • Eukaryotes are Derived, more recently evolved • Eukaryotic Cells have a true nucleus - their DNA is enclosed in membrane • They are relatively large & complex, with many membrane-bound organelles The Endosymbiotic Theory • An ancestral Eukaryote engulfed an aerobic bacterium & did not completely digest it! • Endosymbiosis evolved • Later: a photosynthetic bacteria, was engulfed e.g. Prochloron • New symbiosis 5 Why are Cells so Small? • Prokaryotic cells average 1-10 microns • Eukaryotic cells average 10-100 microns Cell Size is Limited by Surface Area Levels of Organization: Organismal Biology & Ecology Cells need adequate Membrane (surface area) to meet the needs of their Cytoplasm (volume) • Cells need new sources of energy & nutrients • Cells need to release their wastes • Cells exchange matter & energy across their membranes • As a cell increases in size, volume increases faster than surface area • Eukaryotic cells can be larger due to their abundant internal membranes Sponge: a simple, multicellular animal • Many organisms are unicellular • Larger organisms are multicellular: • Cells make-up tissues • Tissues make-up organs • Organs make-up organ systems • Our Focus: Whole organisms and above • Populations: groups of the same species • Communities: groups of different species • Ecosystems: communities, energy & nutrients Organismal Level Sponge: a simple, multicellular animal Population Level A Population of mussels: Mytilus • Population: members of the same species living in the same area, with the opportunity to interact • Patterns: density & dispersion, age structure, sex ratio, etc. • Processes: density-dependent effects: intraspecific competition, crowding, disease, etc. An Intertidal Community • Community: populations of different species living in the same area, with the opportunity to interact • Patterns: species richness, biodiversity • Processes: interspecific interactions • Competition • Predation • Symbiosis: • Mutualism • Parasitism • Commensalism 6 Limiting Resources • Populations & Communities can be limited by necessary resources that are in short supply • A resource in short supply may: • Affect survival and reproduction • Limit population size or Species richness • Nitrogen and Phosphorus are two limiting nutrients: photosynthetic organisms • Food and Shelter may limit animals Salinity, Diffusion & Osmosis • Diffusion is the passive movement of substances from an area of high activity (concentration) to an area of lower activity (concentration) • Diffusion continues until Equilibrium is reached Osmoregulation & Osmoconformers Self-Organization in the Sea Organisms have two alternate ‘strategies’: 1. Conform to their environment: allow their internal environment (cells) to be determined by the environment outside their body/cells 2. Regulate their internal environment to maintain Homeostasis: a constant internal state, regardless of the environment • Regulation (self-organization) costs energy, but • Provides benefits: better control of metabolism Osmosis: Diffusion of Water • Osmosis is the diffusion of water • Water flows passively across cell membranes • Osmosis can threaten living things Osmoregulators I • Osmoregulation: managing water & salt balance • Osmoconformers allow their internal water & salt concentrations to match the water around them • Hagfish are Osmoconformers: They live on the ocean floor, conditions are fairly constant: internal water concentration equals external water concentration (some salts vary) • Sharks (Class Chondrichthyes) maintain an internal water concentration similar to the external water concentration • But their salt levels are lower than sea water • Sharks retain urea in their blood - to balance their concentrations of salt (NaCl) to water 7 Osmoregulators II • Bony marine fish (Class Osteichthyes) - maintain their internal salts at 14 ppt - vs the 35 ppt salinity of sea water Temperature as Environment • Temperature affects metabolism • Limits survival & distribution of organisms (freeze) • Bony marine fish actively: - drink sea water, - pump NaCl from their gills & - excrete concentrated urine Sea Turtles secrete salty tears Thermoregulation Poikilotherms vs Homeotherms • Temperature affects metabolism: The chemical reactions of living things • An increase of 100C doubles metabolic rates • Poikilotherms (ectotherms)- are conformers, ‘cold-blooded’ (externally heated) • Homeotherms (endotherms) - are regulators, maintain a constant warm body temperature ‘warm-blooded’ (internally heated) • Poikilotherms do not ‘spend’ energy to be warm, but they are less active in cold temperatures vs. homeotherms (e.g. fish vs. otter) • Homeotherms spend 97% of their energy budget on being warm! but their higher body temperature allows for greater activity: feeding, metabolism, etc. • Why does the early bird get the worm? Reproduction Asexual Reproduction • Organisms are made of Cells • Reproduction is the making of new cells - To create a new, separate individual • Asexual reproduction: reproduction without ‘sex’ - Produces Clones: genetically identical • Sexual reproduction: mixes genetic material - Makes new cells/individuals with - Unique Genomes: combinations of genes • Many organisms produce ‘clones’ - offspring with identical genetic material (DNA/chromosomes) 1. A mother cell replicates its DNA (chromosomes) 2. Then divides into two daughter cells 3. Each daughter cell is genetically identical to the mother cell and its ‘sister’ 8 Binary Fission • Prokaryotes (Bacteria & Archaea) reproduce by - Binary Fission ‘split in two’ - Creates two genetically - identical offspring Mitosis • Eukaryotes undergo Mitosis: - Creates two genetically-identical cells • Eukaryotes can be unicellular or multicellular • In multicellular forms the new cell produces more identical cells to become a multicellular individual - genetically-identical to its parent Mitosis & Asexual Reproduction Examples: - Unicellular Dinoflagellate - Budding in a multicellular coral - Rhizomes in a multicellular plant Sexual Reproduction Creates New Genetic Combinations Sexual Reproduction requires a complex life cycle. • At some stage in a sexual life cycle: Cells have two copies of each chromosome: - Diploid cells (2n) - one from each parent via fertilization • At another stage in a sexual life cycle: Cells have only one copy of each chromosome - Haploid cells (n) - via Meiosis Sexual Life Cycles Alternate: Meiosis (2n→n) & Fertilization (n+n→2n) • Meiosis: Is the process in which a diploid cell (2n) divides to produce four haploid cells (n) spores or gametes: eggs & sperm • Fertilization is the coming together of: two haploid cells (n) - egg & sperm creates a new diploid cell (2n) - a zygote Fertilization Creates a Zygote: a Genetically Unique Diploid Cell Diagrams of Human and Algal Life Cycles: with Meiosis & Fertilization • Sexual Life Cycles create new, unique Genomes 9 Three Types of Sexual Life Cycles: - All: Alternate Meiosis & Fertilization - Difference: Mitosis Three Types of Sexual Life Cycles in Multicellular Organisms All Alternate Meiosis & Fertilization Key Haploid (n) n Gametes n Mitosis n n MEIOSIS Spores 2n (a) Animals 2n Mitosis Mitosis n n MEIOSIS Diploid multicellular organism Mitosis n n FERTILIZATION Zygote Haploid unicellular or multicellular organism Haploid multicellular organism (gametophyte) Diploid (2n) Gametes n n Spores Gametes n FERTILIZATION MEIOSIS 2n Diploid multicellular organism (sporophyte) Difference: Mitosis can occur in diploid cells, haploid cells, or both to produce Mitosis n n 2n Zygote 2n Mitosis (b) Plants and some algae FERTILIZATION Zygote (c) Most fungi and some protists Reproduction & Survival Multicellular Diploids (e.g. animals) Multicellular Haploids (e.g. fungi) Multicellular Diploids & Haploids (e.g. plants) Mating Behavior & Anisogamy • In Evolutionary Terms: Survival is meaningless without Reproduction • Many species ‘pair spawn’ - a male & female come together to join their gametes • Natural Selection has strongly influenced: Mating patterns • The differences between the sexes affects their relative mating strategies • Females make eggs: few, large, non-motile, energy rich • Males make sperm: many, small, motile, few added nutrients ‘cheap’ • Many Marine Organisms Broadcast spawn: release many gametes directly into the water often on a daily or lunar cycle, e.g. Tridacna Anisogamy Theory A(n)-not, without; Iso-the same; Gamy-gametes • Anisogamy Theory refers to the different gametes made by the sexes, and predicts ‘syndromes’ of their mating behavior • ‘Female syndrome’: because females make few, large, energy rich eggs - they should be choosy • ‘Male syndrome’: because males make many, small, ‘cheap’ sperm - they should be eager Anisogamy & Sexual Selection • Anisogamy Theory predicts: • Females should be Choosy - pick one best mate • Males should be Eager - mate with anything (nearly) that moves • Sexual Selection refers to this difference in selection on the sexes, due to Anisogamy • Males tend to be large, colorful, armed - To attract females and compete with males • Females tend to be smaller and drab - They can choose from many available males 10 Live Birth & Maternal Care Parental Care Successful reproduction includes offspring survival In pair-spawning species, the fertilized egg, or zygote, may be cared for by a parent. In fishes, fathers often care for eggs until hatching. The Unity and Diversity of Life • Over 2 million living species have been named & many others are known from the fossil record • Despite this great diversity, evidence indicates that all organisms, living & dead, are related. • We all come from a common ancestor! Hierarchical Classification • Internal fertilization occurs in many groups. • Mothers often retain the young until hatching (birth). • Mammals provide much parental care before and after birth, e.g. milk & protection. • Mostly Maternal Care! Classifying Life • Carolus Linneaus introduced a System of Classification that is still used today • It consists of a series of nested sets • From Kingdom to species • Each grouping was made by shared characters: e.g. Chordates have a notochord and Mammals have mammary glands The Classification System today Includes ‘Domain’ Each species has a unique binomial: Genus species e.g Panthera pardus A species is a group of organisms that can successfully reproduce with each other Figure 25.8 11 Classification & Evolution The Theory of Evolution by Natural Selection • Linnaeus grouped organisms by their common characteristics. He did not accept evolution • The Theory of Evolution states that populations of living things change over time • Scientists today see these same groups as relatives - descended from a common ancestor • Darwin called this ‘Descent with Modification’ • Why do mammals share mammary glands? Their common ancestor evolved the trait, so the living descendants share the trait Charles Darwin: Feb. 12, 1812 • Darwin was brought up to be a Doctor • He was also a great Naturalist • He ended up with a degree in Natural Theology: The study of nature to demonstrate how perfectly the world was made by the creator • Many scientists had ideas of evolution prior to Darwin, but Darwin discovered the mechanism: Natural Selection Darwin & the Voyage of the Beagle: 1831-1836 • Darwin knew the organisms of Temperate England • Organisms of Tropical S. America were different • Organisms of Temperate S. America? • Then – Galapagos Islands and Darwin’s Finches • After graduating, he was destined for the clergy, but was hastily placed on board the HMS Beagle just before its departure in the spring of 1831 Darwin’s ‘Dangerous Idea’ • Darwin found groups of similar organisms were found in localized regions: Biogeography • This regionalization suggested they had evolved from a common ancestor in that region • He proposed Natural Selection as a mechanism that could create new, better forms, adapted for their particular environments Darwin’s Theory of Evolution by Natural Selection * Part I. Observation 1. Populations have tremendous reproductive potential. Observation 2. Populations tend to be stable. Observation 3. Resources are limited. (Malthus 1798) Inference 1. Production of excess offspring leads to a struggle for existence; only a fraction of the offspring born will survive to reproduce. • After Ernst Mayr. 1982 12 Darwin’s Theory of Evolution by Natural Selection * Part II. Observation 4. Individuals vary within a population. Observation 5. Much of this variation is heritable. Inference 2. Some variants will be better able to survive and reproduce in their environment. Inference 3. The reproductive differential between variants in the population will lead to a gradual change in the population, with favorable traits (adaptations) accumulating over the generations. * After Ernst Mayr. 1982 Further Support for Evolution • Comparative Anatomy • Comparative Embryology • Artificial Selection • DNA - the hereditary material • Evolution is a fact: e.g. Guppies - 100’s of other published studies • Problems of poor design Adaptation • The Theory of Evolution by Natural Selection suggests a process that creates new types of organisms, better ADAPTED to survive and reproduce in their environments • Adaptations are: • New Features • They provide a performance advantage • They have been shaped by natural selection Evolution • Evolution defined: Any change over time in a population’s appearance or genetic structure Evolution: Theory & Fact • The Theory of Evolution by Natural Selection is the unifying theme of biology • It explains a great deal about living things • It has been well tested and not disproven • It generates ideas in biology • Evolution has also been directly observed by scientists: Populations were observed to change over time. In these cases, evolution is a fact. Phylogenetic Hypotheses • Modern Classification systems hypothesize the branching of descendants from common ancestors: Phylogenetic Hypotheses • Cladistics is a modern school of classification that uses only shared, derived characters (often adaptations) to suggest relationships 13 Convergent Evolution: • Separate evolutionary events shaped by the same selective forces produce similar responses - Torpedo shape for hydrodynamic efficiency We now group organisms into three Domains vs. the old five Kingdom system Domain Bacteria: prokaryotic Domain Archaea: prokaryotic Domain Eukarya: eukaryotic Archaea & Eukarya are sister groups Marine ‘Lifestyles’ • Plankton: wanderers, drift in the water column; unable to swim against currents • Nekton: swimmers, able to direct their movement in the ocean, swim against currents Hierarchical Classification & Systematics Carolus Linnaeus created a classification system (1748) still used today. He grouped species in increasingly broad categories of nested sets Kingdom, Phylum, Class, Order, Family, Genus & specific epithet • Benthos: bottom-dwellers, may be permanently attached to the sea floor, or otherwise bottom-associated Binomial Nomenclature Linnaeus also created the Scientific Binomial the two-part scientific name of a species Genus species (specific epithet) Underlined or italicized: Homo sapiens, or Homo sapiens Phylogentic Systematics Since the time of Darwin, systematists have organized groups (taxa) based on their hypothesized evolutionary relationships Phylogenetic systematics has been shaped by Cladistics: a school of systematics which uses only shared, derived characteristics to identify related groups, or ‘clades’ of organisms (clade = a branch) 14 Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching ‘phylogenetic trees’ Each branch point, or ‘node’ Represents their most recent common ancestor and the divergence of two groups ‘Deeper’ branch points Represent progressively greater amounts (time) of divergence Cladistics Clades Can be nested within larger clades, but not all groupings or organisms qualify as clades A ‘good’ clade consists of a common ancestor and all of its descendants = A Monophyletic Group (one tribe) Pleisiomorphies A shared ancestral character: Pleisiomorphy Is a homologous structure that predates the branching of a particular clade from other members of that clade Is shared beyond the taxon we are trying to define In cladistics, is called a ‘pleisiomorphic character’ or a ‘pleisiomorphy’ Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics A cladogram Is a depiction of patterns of shared characteristics among taxa A clade within a cladogram Is defined as a group of species that includes an ancestral species and all its descendants Cladistics Is the study of resemblances among clades Shared Derived vs. Shared ‘Primitive’ Characteristics In cladistic analysis ‘Clades’ are defined by their evolutionary novelties, or shared derived characters: ‘Synapomorphies’ Synapomorphies are: Evolutionary novelties evolved uniquely within a particular clade: usually an Adaptation Often used to name groups (taxa): e.g. mammary glands define members of Class Mammalia Outgroups Systematists use a method called outgroup comparison To differentiate between shared derived and shared ancestral character states Synapomorhphies vs. Pleisiomorphies 15 As a basis of comparison we need to designate an outgroup A species or group of species that is closely related to the ingroup, the various species we are studying Outgroup comparison Is based on the assumption that homologies present in both the outgroup and ingroup must be ancestral characters - ‘pleisiomorphies’ -that predate the divergence of both groups from a common ancestor The outgroup comparison enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade I.e. Synapomorphies: Shared derived characters Phylogenetic Trees and Timing Any chronology represented by the branching pattern of a phylogenetic tree Is relative rather than absolute in terms of representing the time of divergences Recall: Phylogenetic trees = Phylogenetic Hypotheses Logical, provisional explanations: they attempt to explain the distribution of characters and character states based on evolutionary relationships 16