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Final Exam Keywords part 2

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Jon Houseman

Biology biologists and biosciences Ages of sand - A model created by Douglas Adams (1952-2001) - Divides the progress of modern science into four stages of sand - Telescope, microscope, the silica chip, and fibre optic cables are the four ages Analogy - Two structures which perform the same function but evolved differently - They may have evolved together through a process called “convergent evolution” - An example of analogous structures is the wings of a bird vs the wings of a butterfly Binomen - System used to names organisms - Consists of two names, the Genus (capitalized, italics or underlined) - And the species (lowercase, italics or underlined) Binomial nomenclature - The system of nomenclature for animals - Species are named by their "binomen": a generic name and a specific name - Subspecies have a name composed of three names, a "trinomen" Biogeography - The study of the distribution of biodiversity over space and time - It aims to reveal where organisms live, and at what abundance - Through works of Wallace, Darwin, etc. it became the basis for modern biology Catastrophe theory - Punctuated equilibrium: evolution occurs rapidly from catastrophic events Georges Cuvier (1769-1832) - Catastrophes include volcanic activity, floods, and meteors - Species which can survive are only ones who live on, evidence: Burgess Shale fossils Cell theory - All organisms are composed of cells Schleiden and - Individual cells have all the characteristics of life Schwann (1860) - All cells come from the division of other cells Chronological prediction - A prediction of what will happen in the future - Not necessarily based on logic, trends, or reason - Differs from a scientific logical prediction Cladogram - A branching diagram to classify living organisms on the basis of shared ancestry - Endpoints of branches represent different species of organisms - Divergent points indicate common ancestor: illustrates phylogenic relationships Common ancestry - The concept that all organisms evolved from a common ancestral organism - Proposed by Georges-Louis Leclerc, Comte de Buffon (1707-1788) Constancy of species - The belief that all species are unique, unchanging, and placed on earth by God - Evidence appears to challenge this belief leading to a theory by Charles Darwin Control - Treatment that tests the result with no experimental manipulation - Also includes methods of control such as: Control of variables, Sampling error (precision), Repeat the test Convergent evolution - This occurs when species evolve by separate pathways to the same result - Result is “homoplasy” - Example: analogous structures Cuvier (Georges) - Lived from 1769-1832 - Proposed the catastrophe theory - Explained extinction of species Darwin (Charles) - Lived from 1808-1882 - Travelled for 5 years on the S.S. Beagal, collecting species from various islands - 5 theories and the book “On the Origin of Species by Means of Natural Selection” Darwin (Erasmus) - Lived from 1731-1802, grandfather of Charles Darwin - Writings on botany and zoology suggested a “common descent” - Ideas based on: developmental changes, artificial selection, and vestigial structures Deduction - Conclusions drawn from general cases to the specific examples - Realistically done through experiments and law and reason - Used primarily in the physical sciences Descent with modification - Essentially biological evolution - Some individuals in the population experience changes to their DNA - Successful mutations are passed on to future generation, unsuccessful ones die off Divergent evolution - This occurs when a species split-evolves by separate pathways - Result is “homology” - Homologous structures: same structure, different function, likely common ancestor Domain - The highest taxonomic category - Separated by ribosomal differences - Three categories are: archaea, eubacteria, and eukarya Empirical observation - Information gained by means of observation, experience, or experiment - The central basis of the scientific method is attaining empirical evidence Essentialism - The idea that a species is unchangeable, permanent, and perfect - The “essence” in all beings is the life force that drives them to be what they are Eukaryotes - A cell with a membrane-bound nucleus - All multicellular life is composed of eukaryote cells, though there are unicellular too - A domain in Linnaeus’ Taxonomic Hierarchy is the eukarya Evolutionary tree - A branching diagram illustrating the evolution of a common ancestor - The diagram depicts all (or some) species which diverged from that ancestor Extinction - When all individuals of a species die, that species is extinct - Causes: catastrophe, human intervention, sexual selection, natural selection Fact - A theory which has been tested beyond a doubt by various hypotheses - Rare in the natural sciences due to the variability of the subject Finalism - Teleology is the philosophical study of design and purpose - Holds all things to be designed for or directed toward a final result - Argued by Darwin that survival is only observable, final good Fitness - The capability of a species to survive better than others - Specifically to survive long enough to reproduce Fossil record - The remains or traces of an organism of a past geological era - Embedded in the earth’s crust, capable of being identified and aged - The record is the catalogue of all pre-existing organisms, named and dated Germ theory - Idea opposing spontaneous generation of life Pasteur (1822-1895) - Proposes that micro-organisms exist in the air - Evidence: meat in sterile environment grows no maggots, meat in open air does Historical narrative - Telling of the past, usually with some form of explanation for the witnessed events - The study of biology takes the form of historical narratives - Research in biology hopes to provide an explanation for them Homology - Two similar structures which perform the different functions but evolved differently - May have evolved from a common ancestor through “divergent evolution” - An example of homologous structures is the various forelimbs seen today Homoplasy - Characteristics shared by a set of species - Often a product of convergent evolution (environment) - Not resembling of a common ancestor Huxley (Julian) - Lived from 1887-1975 - Proposed a synthetic theory of evolution - Natural selection based on Mendelian genetics to explain population genetics Hypothesis - A testable prediction of how something works or behaves - Observations of the natural world prove or disprove a hypothesis Induction - Conclusions drawn from specific examples to the general cases - Requires multiple observations - Used in natural sciences due to variability, defies the physical sciences Lamarck (Jean-Baptiste) - Lived from 1744-1829 - Proposed transmutation of species through environment - All species started the same, then evolved through environmental changes Law - A universal theory, there are few of these in the biological sciences Leclerc (George-Louis - Buffon) - Lived from 1707-1788; proposed common ancestor & biogeography Linnaean taxonomy - Hierarchy of all living things based on structure - Though slightly changed, still in use today - Branched into: domain, kingdom, phylum, class, order, family, genus, species Linnaeus (Carolus) - Lived from 1735 - Detailed a Systema naturae to catalogue all living things (cell wall and how they eat) Logical prediction - A prediction based on logic, trends, facts, or reason - Used in natural and physical sciences to develop hypotheses - Differs from a non-scientific chronological prediction Lyell (Charles) - Lived from 1797- 1875 - Proposed gradualism: Earth is subject to slow but continuous change - Extreme geological changes have occurred, evidence that earth is very old Mendel (Gregor) - Lived from 1822-1884 - Presented the behaviour of genetic ‘factors’ - The Law of segregation of characters, and the Law of independent assortment th Modern biology - Biological discoveries and research of the 20 century - Much more the focus of scientific community than ever before - Technological advancements (ages of sand) allowed for significant experiments Natural sciences - The study of animae objects, with variability and multiple theories and laws - Based on historical narratives, induction is the most used method - Single falsification will not result in abandonment of a theory Natural selection - The evolutionary process of survival of the fittest - The alleles which give an organism a higher chance to reproduce stay in gene pool - The alleles differ and change from random mutations Null hypothesis - A statement of what will be observed should the hypothesis be wrong Organicists - Merge of the two ideologies of “vitalists” and “physicalists” - Idea of the “essence” replaced by the genetic code - The importance of emergence: simple interactions yield complex outcomes Pasteur (Louis) - Lived from 1822-1895 - Proposed the “germ theory” that life comes from life - Developed a process of sterilizing medium still used today (pasteurization) Physical sciences - The study of inanimate objects, single theories of physical and chemical laws - Based on empirical measurements, experiments are most used method - Single falsification is enough to abandon a theory Physicalists - Ideology that living things (except humans) are machines - All complex processes can be divided into many simple functions - 17 century ideology so God’s will was still a key-point Prokaryotes - A single celled organism with a DNA suspended in cytoplasm - All bacteria (eubacteria and archaea) are prokaryotes - It is believed that eukaryote cells came from prokaryote cells Proximate causes - Physical science-like biology (Example: Phenotype – morphology and behaviour) - Usually have predictable outcomes which are intrinsically mechanical - They deal with the “here and now” and can be tested by experiments Sampling error - A concern with experiments dealing with sample choice or size - Caused by disproportionate group, not representative of the whole population - Sample group may be similar but supposed to be representative of diversity Scala naturae - A theological catalogue of organisms based on closeness to God - Created by Aristotle - Gods, man, and birds were high; worms, inert earth, and elements were low Schleiden and Schwann - In 1860 their independent work developed the cell theory - Schleiden observed through a microscope that all plant tissue are composed of cells - Schwann observed through similar methods the same about animal tissue th th Scientific revolution - After the Dark Ages, 16 century to 18 century, burst of scientific interest - Knowledge of how the world functions, discoveries in math, physics, and chemistry - Paved the way for greater discoveries for the natural world with physical basics Special creation - Concept that God, or some creator, created and put all species on the earth as is - Therefore species are perfect and not subject to change - This idea was debated and evidence suggests other methods of diversifying earth Synthetic theory of evolution - Union of ideas from several biological specialties Julian Huxley (1887-1975) - Stimulated by population genetics, also called modern evolutionary theory - Forms a logical account of evolution - Shows how Mendelian genetics is consistent with natural selection and gradual evolution Taxon (taxa) - A name designating a group of organisms - Category of the Linnaean taxonomic hierarchy Taxonomy - The science of the classification of organisms - An ordered system of that indicated natural relationships Theory - A model that explains events in the natural world - Makes predictions on how they will occur - Based on, and tested by, various hypotheses; usually best result in natural science Transitional forms - “Missing links” - Fossilized remains of intermediary forms that illustrate an evolutionary transition - According to modern evolutionary theory, all populations of organisms are in transition Transmutation - Change of an organism due to the random mutation of its DNA - Occurs fast and is unpredictable - May be beneficial to that organism’s survival, may be detrimental Transmutation of species - The altering of one species into another; Jean Baptiste Lamarck (1809) - Commonly used for evolutionary ideas in the 19th century before Charles Darwin - Occurs through environmental pressures on organisms Ultimate causes - Natural science-like biology (Example: Genotype - genes and history) - Usually have probabilistic outcomes and are intrinsically variable - They deal with the evolutionary past and can be explained through historical narratives Uniformitarian theory - Gradualism: Species change slowly from one form to another Charles Lyell (1797- 1875) - Geological changes are the same today as they have been throughout earth’s history - Stratigraphy and a geological time-scale were the basis of this theory Vestigial structures - Reduced anatomical structures with no practical function in certain species - Consistent, and evidence for, evolution by common ancestry - Used by many scientists including Darwin(s) as basis for evolution Vitalists - Ideology that living things operate by common physical and chemical laws - But living things have unique vital forces (essence) which make them what they are Hadean and Archaean eons Hadean key words: Adhesion - Behaviour of molecules to adhere (stick) to other molecules - Classic example of the behaviour of water due to polarity of the molecule Archaean eon - Second major eon of earth’s history (3,800 – 2,500 Ma) - Anaerobic bacterial life, oxygen starts to accumulate in oceans and atmosphere - Liquid water prevalent by end Biomonomers - Amino acids, pyruvate, basic hydrocarbons, glucose, nucleotides etc. - Believe to be created from “Interstellar organics” or “Prebiotic soup” - “Miller-Urey Apparatus” proved that it is possible to produce these organic compounds Biopolymers - Macromolecules: proteins, lipids, carbohydrates, nucleic acids - Created through chemical evolution: the binding of biomonomers - Questions: “panspermia”, ribozymes, importance of clays (+ive and –ive charged) Carbon - Essential element in all organic compounds, very abundant - Perfectly symmetrical, stable tetrahedral bonds - Excellent for forming chains, only other candidate is less abundant silicon Central dogma (of biology) 1) Replication  DNA copies itself to make more DNA 2) Transcription  Parts of DNA copied into RNA strands 3) Translation  RNA codes translated by ribosome to produce a protein Chemical evolution - Development of simple chemicals into more complex compounds - Cooling of primitive earth lead to creation of inorganic compounds - Through energy capture (lightning, thermal vents) small organic were created Cohesion - Behaviour of water molecules to stick together - Result of the polarity of the molecule, hydrogen bonds form between molecules - Creates a surface tension across surface of water (can support some insects) Crystal lattice of water - Solid 2 O (ice) has a crystalline structure and a lower density than liquid 2 O (water) - At 4 C, water arranges itself with neighbouring molecules into a honeycomb shape - This is due to hydrogen bonds, in liquid the lattice breaks, in ice the lattice is solid - Biological importance: Ice (less dense) forms at tops of bodies allowing the lower volume of liquid water to continue supporting life Emergence - Complex systems and patterns arise out of relatively simple interactions - Examples: swarming of animals, chemical bonds to produce complex organics - Life is a major source of complexity, and evolution is the major principle or driving force behind life Evaporation - The change of state from liquid water to gaseous vapour through heat transfer Geological time scale - A chronologic schema relating stratigraphy to time - Describes relationships between events throughout the history of the Earth. - Age of earth is estimated to be 4.6 Ga, the start of the “Hadean eon” Green house gases - Water vapour, carbon dioxide, methane, nitrous oxide, and ozone - These gases foster the accumulation of heat in the lower atmosphere - These gases are also believed to be the building blocks of organic systems today Hadean eon - First major eon of earth’s history (4,600 – 3,800 Ma) - Formation of the solar system and planet; ends with origin of life - Consisted of a building phase and a stabilizing phase Hydrogen bond - The strongest of van der Waals forces (intermolecular forces) - Occurs from high differences in electronegativities, specifically H – N, O, or F - Allows for various properties: adhesion, cohesion, surface tension, crystal lattice Hydrophilic - A substance (or end of a substance) which interacts with water (polar) Hydrophobic - A substance (or end of a substance) which does not interact with water (non- polar) Hydrothermal vents - Vents at the bottom of ocean that spew out hot noxious gases, such at SO 2 - Contingent for the origin of life due to high energy and presence of organics Interstellar organic compounds - Organic compounds believed to come from “interstellar space dust” - Contingent for origin of life due to possible introduction of organics Interstellar space dust - Meteorites and smaller particles from space - Focus on materials from space that landed on earth - Certain interstellar space dust may have organic compounds on them Micelles - A sphere composed of a single layer of lipid molecules - Micelles may replicate if inner aqueous environment contains reactants which produce a hydrophobic product  accumulating in the surface of the micelle until division Δ Miller experiment - CO2+ H 2 + CH + 4O + o2her inorganics →organic compounds - Evidence of how life may have originated, “pre-biotic soup” Non-polar compound - Hydrophobic compound with no polar asymmetry - Does not interact with water, but does interact with other non-polars Panspermia - The hypothesis that "seeds" of life exist already all over the Universe - Life on Earth may have originated through these "seeds" - Other habitable bodies may have had life delivered to them as well Phanerozoic eon - Fourth major eon in earth’s history (543 Ma – Present) - Introduction, and explosion of multicellular organisms - Consists of various eras, separated by mass extinctions by means of catastrophes Polar compound - Hydrophilic compound with polar asymmetry - Results from a difference in electronegativity between bonded atoms Prebiotic soup - The hypothesis that the oceans were full of ingredients for life - The Miller-Urey apparatus provided evidence that organics can rise from inorganics - Origin of life may have stemmed from prebiotic soup on the young, hostile earth Proteins first hypothesis - The hypothesis that various proteins were created in prebiotic soups - Miller-Urey experiment provided some evidence since only L-proteins were found - Proteins then bind to clays as heterogeneous catalysts and other organic compounds (enzymes or RNA) to be produced from this protein stencil Proterozoic eon - Third major eon in earth’s history (2,500 – 543 Ma) - Oxygen atmosphere, single celled aerobic organisms - Introduction of first eukarya, the protists Protocells - A primitive cell-like structure with some properties of life - Taking micelles one step further, metabolic reaction may occur inside - Potential precursor of first prokaryotic cells Reducing atmosphere - Condition preventing oxidation by removal of oxygen and other oxidizing agents - Before oxygen filled earth’s atmosphere, this was believed to be the case - With no oxygen, clays and other iron minerals had a different appearance RNA world - The hypothesis that RNA molecules were created in prebiotic soups - Miller-Urey experiment provided some evidence since RNA was found - Since RNA can self replicate, translate proteins, and work backwards to transcribe DNA, it is a candidate for origin of life (ribozymes, RNA-viruses, etc) Specific heat - The amount of thermal energy required to increase the temperature of a certain mass of substance (usually water) Spontaneous origins - The idea that life spontaneously was created by no physical-chemical means Surface tension - Force created by the cohesion of water more so than underlying molecules - Hydrogen bonds cause the surface molecules of water to interact with each other - Certain insects can stand on water, water curves up the sides of a glass, etc Surfactant - Wetting agents that lower the surface tension of a liquid, amphiphilic - Allows for easier spreading, and lower the interfacial tension between two liquids Vesicles - A small, membrane-bound compartment that transfers substances - Act throughout the endomembrane system as well as with the plasma membrane - Produced by the endoplasmic reticulum and the Golgi apparatus Volcanic out-gassing - Volcanic activity which produced mainly gases such are CO 2 - Important during the period of “snow ball earth” where temperatures on the surface were very cold yet volcanic activity was prevalent Archaean key words: Aerobic - Requirement of oxygen - Usual necessity for oxygen is in the respiration processes - Oxygen acts as an electron acceptor Anaerobic - No requirement of oxygen - Usual dependence on oxygen is from the organism’s metabolic processes - Other inorganic molecules, such as sulphur, can be used as electron acceptors Archaea - One of the three domains, from Linnaeus’ taxonomic hierarchy - These prokaryotic organisms can survive in extreme conditions, “extremophiles” - Survives as either “Halophiles”, “Thermophiles”, can also be “methanogens” ATP sythetase (synthase) - Membrane-spanning protein complex, couples reactions: - Energetically favouring transport of protons across a membrane with the synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and a phosphate group Autotroph - An organism that produces its own food from CO , 2imple inorganics, and energy - The energy could come from the sun, “photo”, or from the oxidation of other organic, “organo”, or inorganic “litho” compounds Bacteria (Eubacteria) - One of the three domains, from Linneaus’ taxonomic hierarchy - These prokaryotic organisms are the most metabolically diverse - All six -troph options are possible Binary fission - One mode of prokaryotic reproduction - DNA replicates in cell, and cell splits in half - This method yields no genetic variation from parent to daughter cells Cellular respiration - The process by which high-energy molecules are converted to ATP - Takes place aerobically or anaerobically, depending on organism and environment - Takes place in all living organisms Chemolithotrophic heterotrophs - Class of organisms that consume other organisms as a source of carbon - These organisms get energy from the oxidation of inorganic compounds - These organisms can only be bacteria Chemolithotrophs - Class of organisms that fix their own source of carbon - These organisms get energy from the oxidation of inorganic compounds - These organisms can only be bacteria Chemoorganoheterotrophs - Class of organisms that consume other organisms as a source of carbon - These organisms get energy from the oxidation of organic compounds - These organisms can be bacteria, some protists, fungi, or animals Chemoorganotrophs - Class of organisms that fix their own source of carbon - These organisms get energy from the oxidation of organic compounds - These organisms can only be bacteria Conjugation - One mode of prokaryotic reproduction - Part of DNA of a donor cell moves through a cytoplasmic bridge into recipient cell - Genetic recombination occurs and yields genetic variation - In ciliate protozoa, this is the form of sexual reproduction Cyanobacteria - A phylum of bacteria that obtain their energy through “photosynthesis” - Due to its high efficiency, these bacteria flourished filling the atmosphere with O 2 - Involved in the marine nitrogen cycle and a primary producer in areas of the ocean Electron donor - A molecule which has easily relievable electrons (electron pair) - This is caused by an accessible atom of low electronegativity, usually H + + - - Useful in biochemical redox reactions such as NADH  NAD + H + 2e Electron receptor - A molecule which has a high affinity for electron pairs - This is caused by an accessible atom with a high electronegativity, usually O + - - Useful in the “electron transport chain”: 2H + 2e + ½O  2 O 2 Electron transport chain - Stage in cellular respiration where high-energy electrons are used to make ATP - Occurs in mitochondria as well as chloroplasts of eukaryotic cells - Electrons pass through a protein complex creating an electrochemical gradient - As H diffuses back across membrane, ATP-synthase generates ATP Extremophiles - Another name for archaea bacteria - Can survive in hypertonic solutions (salt water) as halophiles - Can survive in very hot conditions (hydrothermal vents) as thermophiles Fermentation - Process by in which NADH reduces organic molecules instead of the ETC - Less efficient production of ATP than the ETC - Occurs in anaerobic conditions in some eukaryotic and prokaryotic cells Gram-negative - Description of bacterial cell walls - Capsule may not be present, if present it is curved - Peptidoglycan layer is thin, does not show on test, outer membrane present - This is the form of most pathogen bacteria Gram-positive - Description of bacterial cell walls - Capsule present, not curved - Peptidoglycan layer is large, thick, shows up on test, no outer membrane Heterotroph - An organism that consumes its own food and energy from other organisms - Additional energy could come from the sun, “photo”, or from the oxidation of other organic, “organo”, or inorganic “litho” compounds Nitrogen fixation - A metabolic process in which molecular nitrogen is converted to ammonia - Certain bacteria, specifically cyanobacteria, perform this - Can take form of a symbiotic relationship with a plant that uses the ammonia Nucleoid - The central region of a prokaryotic cell where DNA is located - No membrane bounds this region - Replication and transcription occur here Oxidized - Process of a substance losing electrons - Occurs during oxidation reactions - These substances are called reducing agents Pathogen - a biological agent that causes disease or illness to its host - could be viral, bacterial, fungal, or prionic - Not all pathogens are negative Peptidoglycan - The primary structural molecule of bacterial cell walls - A polymeric substance formed from a polysaccharide backbone + short polypeptides Photoheterotrophs - Class of organisms that consume other organisms as a source of carbon - These organisms get energy from the sun - These organisms can only be bacteria Photosynthesis - Highest efficiency method of carbon fixation and energy capture - CO 2 H O2 Δ→gh(CH 2) n H O2+ O 2 - Used in plants and cyanobacteria Phototrophs - Class of organisms that fix their own source of carbon - These organisms get energy from the sun - These organisms can be bacteria, certain protists, or plants Plasmid - Separate DNA molecule in certain prokaryotes, usually circular or double stranded - Often contains gene which supplement those in the nucleoid - Replicates independent of nucleoid DNA Reduced - Process of a substance gaining electrons - Occurs during reduction reactions - These substances are called oxidizing agents Transduction - One mode of prokaryotic reproduction - DNA is transferred from a donor to a recipient by means of a “bacteriophage” - This method yields variable genetic variation - The DNA may kill the bacteria and reproduce more bacteriophages or - The DNA may combine with host cell DNA and the message will be passed on Transformation - One mode of prokaryotic gene transfer - Bacterial cell can intake DNA from the surrounding environment - The DNA may prove useful or useless and be passed on or - The DNA may prove detrimental and kill the bacteria - This method yields genetic variation depending on survival of bacteria Eukaryote cell architecture Bilipid layer - Construction of cell membranes - Composed of two layers of lipids, hydrophobic heads point in, hydrophilic tails out - Fluid Mosaic structure Binary fission - Prokaryote method of asexual reproduction - Cell simply splits – dividing into two parts - No genetic variation occurs this way Cell theory - Cells are the small unit of living life - All organisms are composed of cells - All life (cells) came from pre-existing cells Cell wall - Rigid external layer surrounding cell membrane - Plants, fungi, bacteria, and some protists have cell walls - Provides cell protection and support Central vacuole - Centriole Chloroplast Chromatin Cristae Cytoskeleton Cytosol (or cyotplasma) Endomembrane system Endoplasmic reticulum Endosymbiosis Eukaryote Golgi apparatus Histone Lysosomal vesicles Micelle Microtubules Mitochondria Nuclear envelope Nuclear pores Nucleic acid Nucleolus Nucleoplasm Nucleus Organelles Phospholipid bilayer Plasma membrane Ribosomes Rough endoplasmic reticulum Smooth endoplasmic reticulum Thylakoids Tubulin Vesicle Proterozoic eon 9+2 organization - Orientation of cilia and flagella in eukaryotes - Position of 9 microtubules surrounding two central ones - Differs from prokaryotic flagella which acts as a micro motor Alternation of generations - Life cycle that switches between haploid and diploid between generations - Haploid generation: haploid spores undergo mitosis making haploid gametophytes - Diploid generation: gametophytes fertilize  zygote  sporophyte  meiosis Amoeboid movement - Type of protist locomotion where pseudopods use actin and myocin to move - ATP can change the density of the protein solution to solid or liquid states - The solid ectoplasm makes the outer structure of the pseudopod for liquid endoplasm channel to flow through causing movement Antibody - Type of protein found in the blood plasma - Binds to specific antigens found of cell surfaces, or foreign invaders - Destroys the cells with the antigen markers as a part of our immune system Antigen - Substances which prompt the production of antibodies
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