General Biology 2 - Lecture notes All PDF

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This is a whole set of notes for the full semester of Bio 155 (now known as Bio 2610) from Ivana Mali. This is about general ecology, evolution and diversity....

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What is Biology Themes and Concepts of Biology  Definition: science of life or living matter in all its forms and phenomena o Origin o Growth o Reproduction o Structure  It also deals with how organisms interact with one another and with their environment  Biologists study life in many ways Properties of Life Main attributes of life  Order: hierarchical organization of things  Sensitivity: respond to stimuli  Growth, development and reproduction  Regulation: have regulatory mechanisms to co-ordinate functions  Homeostasis: maintain constant internal conditions  Energy processing: all organisms use a source of energy for their metabolic activities 1. Levels of Organization Cellular organization  Atoms>> molecules>> organelles>> cell>> o **The cell is the basic unit of life  Tissues>> organs>> system>> organism  Organism>> population>> species>> community>> ecosystem   

Sensitivity Light: plants grow towards light; eye pupils change size Migration: animals respond to cold or less daylight

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Growth, development and reproduction Hereditary molecules (DNA) passed to offspring Ensures offspring are in the right species

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Regulation Cells supplies with nutrients Substances transported through organism Many other functions highly regulated

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Homeostasis Homeostasis= steady state External environment often different from their environment Keeping internal body temp related for example

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Energy Processing Some organisms capture energy from the sun

Others use chemical energy (molecules they take as food)

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Biology  

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Very important natural science: helps to explain what our world is like Affects our daily lives and our futures o Population growth o Resource depletion o Diseases o Climate change Fundamental to managing world's resources in a suitable manner Basic tools of biologists are thought and observation

Biology is a Science  Definition of science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method Scientific Reasoning  An ultimate goal= to know  Two methods of logical thinking  Inductive reasoning o Uses related observations to arrive at a general conclusion  Deductive reasoning o Hypothesis based science o Uses general principle or law to forecast specific -----------------------------------------------------------------------------------------------------Two main pathways of scientific study  Descriptive science o Observe, explore, discover  Hypothesis based science o Begins with a specific question or problem and a potential solution that one can test o NEVER say I "proved" my hypothesis  Not a clear line between the two  I.e. observation can easily lead to a specific question Scientific Method  Testing hypotheses by means of repeatable experiments  Hypothesis= suggested explanation for event, that one can test o An educated guess  Don’t use scientific method to define science o Sometimes it is difficult to repeat experiments, but you can still test the hypothesis o i.e. archeology, geology etc. o Usually, scientific process starts with an observation that leads to a question o Hypothesis must be testable and falsifiable

Testing a Hypothesis  Conducting one or more experiments designed to eliminate one or more hypotheses  Variables o Any part of the experiment that you all to vary throughout the experiment  Controls o Contain every feature of the experimental group except it is not manipulated o If experimental group results are not equal the control's the difference must be the manipulation o SOMETIMES REJECTING ONE HYPOTHESIS DOES NOT DETERMINE WHETHER OR NOT ONE CAN ACCEPT THE OTHER HYPOTHESIS  Science does not claim to "prove" anything  Scientific understandings are always subject to modification with further information  Openness to falsifying ideas distinguishes sciences from non-sciences  Reject hypothesis if inconsistent with results, conditionally accept if consistent with results  New ideas are constantly replacing old ones Using predictions  Most useful hypotheses make predictions  Prediction that is rejected may cause rejection of hypothesis  Example: Einstein's theory of relativity (E=MC2)-sun would bend path of light passing by it o Accepted provisionally because no invalidating experiment o Light bent in eclipse corroborated prediction, supported hypothesis Developing Theories  Theory implies certainty to scientist (built upon rigorous testing and experimentation)  Theory implies "guess" to general public Theory vs. Law  A scientific theory is a well-substantiated explanation of some aspect of the natural world  A scientific law is simply an observation that the theory attempts to explain  ON A LAW IS AN OBSERVATION, A THEORY IS AN EXPLANATION THE EXAM Research and Scientific Method  Insight and investigation play a role in scientific knowledge o Not always orderly sequence of logical steps  Basic research: extends boundaries of scientific knowledge

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Not focused on developing a product or service Applied research: usually affects scientific industry Use science to solve real-world problems Disease cures, increase crop yield, drought resistance in crops etc.

Communication  All scientific work must be communicated via papers in scientific journals  Can be either very general, or very specific

Chapter 17   o o

It is the unifying theory of biology Most organisms have different genetic compositions: Provide raw material for evolution Variation exists in natural populations

Natural Selection  Charles Darwin  Alfred Russel Wallace  Independently conceived and described the mechanism for evolution  Darwin postulated that ancestral species beaks had adapted over time to equip the finches to acquire different food sources  Survival of the fittest  More prolific reproduction of individuals with favorable traits  Better chance of survival because of those traits  This leads to evolutionary change 3 principles  Most characteristics of organisms are inherited  More offspring is produced that able to survive (limited resources)  Offspring vary among one another (the ones that have characteristics that allow them to best compete will survive and have more offspring o Decent of modification (change in populations over generations) Natural selection is not the only process that leads to changes in population in genetic makeup o Mutations o New alleles introduced through immigration o Random changes in small populations  Gene variation in nature o Very high in natural healthy populations o Variation within species is the raw material for selection and evolution Adaptation  Hereditable trait that helps an organism's survival and reproduction in its present environment  Webbed feet  Thich fur  Fast speed 

Types of Evolution  Divergent o Two species that evolve from a common ancestor in diverse directions  Convergent

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Similar phenotypes evolve independently is distantly related species

Evidence of evolution  Natural selection can produce evolutionary change  Fossil record shows that evolution has occurred o Were around in Darwin's day but were very spotty o Organisms buried in sediment o Calcium in bone and hard tissue is mineralized o Sediment surrounding the specimen converts into rock Types of Fossils  Whole soft bodies o Probably the rarest type o Mammoths/mastodons preserved in ice o Embryos in eggs  Hard parts only o Mollusk shells o Bones and teeth of vertebrates  Trace fossils o Indicate "work" of that organism o Footprints, animal tracks, burrows o Coprolites (fossil dung) o Gastroliths (stones in stomach from grinding food) o Middens (nesting materials, esp. packrats)  Special types o Amber (fossilized tree sap) o May contain fossils of insects, frogs, or bird feathers etc o Fossils within a fossil Fossilization  Fossilization if a rare occurrence o Remains will decay quickly or are scavenged o Death must occur in appropriate habitat o Usually only creatures with hard parts preserved as fossils, with some notable exceptions (like organisms trapped in ice)  Finding them is even more difficult! o Fossils destroyed by erosion o Rocks holding the fossils are not always accessible  Dating fossils can be problematic o Date of surrounding rock matrix reflects age of fossils contained within o Done by relative dating in Darwin's day o Position of rocks with respect to one another o Deeper strata holds older rocks  Provides fairly accurate results  Index fossils: specific species found only at certain levels  Recent dating uses more accurate techniques  Measures rate of decay of isotopes in rocks

Isotopes are unstable forms of elements with extra

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neutrons Decay rates are constant over time =the half life o Can use rocks like an internal clock o Measures dates in millions of years  Gaps still exist in fossil record, but far better than in Darwin's day o Recent finds of missing links o Eg. Fossils snakes with legs o Eg. Fossil whales with hind pelvis (rudiments of hind legs)  Examples of evolution in animals o Many examples come from fossil records o Shows change over (long) tome, as environment changed o Those groups that were able to adapt survived o Those groups that could not adapt died/ went extinct o Romer's gap 360-345million BC  Archaeopteryx o Critical and iconic piece of evolutionary history o One of the oldest and first in split o First fossil evidence was in 1861 o 1877 a complete specimen was found o Crow sized, bipedal reptile o Both primitive reptilian and derived avian features o Small reptilian teeth o Long bony tail o Free belly ribs o 1st toe pointing backwards o Strong running o Short flights between trees o Absent of modern birds shoulder joint o Primary wing feathers asymmetrical  Horses changed over time from small mammals to bigger mammals  Climactic change produced more grasslands o Forests disappeared (too dry) o High speed became very important to escape predators o Adapted to eat grasses (more complex teeth) o Horse species gradually evolved these features in response to environmental change  We have evidence that natural selection has produced evolutionary change o From both natural and from human altered situations o Environmental changes due to humans changes organisms o Organisms attempt to adapt to new conditions o IE Peppered moth  Industrial revolution influenced the coloring  Before there were more white  After there were more dark Artificial Selection  Humans have selected certain phenotypes in plants and animals o

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Preferred traits for specific purposes, or for colorful, ornate appearance  Has occurred in lab, agriculture and domestication o Diversity of dogs is far greater than that of the wild Canidae  Artificial selection does indeed produce substantial change (in a short amount of time) Other Evidence of Evolution  Homology o Forelimb bones of animal o May different purposes but exhibit similarities o Natural selection modified initial structures in ancestor  Development (ontogeny) o Follows the evolution of that organism o Evolutionary history reflected in development of embryo o They exhibit characteristics of ancestors o Human examples  Gill slits  Rudimentary tail  Fine "Fur" (during the 5th month) o Developmental similarities show decent from a common ancestor o Adults have diverged based upon environmental pressure  Vestigial structures o Structures with no apparent function o Resemble features of presumed ancestors  Ear wiggling  Tail  Appendix  Wisdom teeth  Biogeography o Geographic distribution patterns o Before supercontinent Pangea broke up animals were distributed world wide o Groups evolved since the breakup appear uniquely in different regions of the planet  Molecular record o Traces of evolutionary past exist at molecular level o Evolutionary change implies change within DNA o Genotype controls phenotype o Distant relatives have a greater number of differences in DNA sequence (or amino acids) than more recent relatives  Close match between genetic similarity and external characters exhibited by fossils  Convergent evolution o Different geographic areas have groups of plants and animals that are strikingly similar  Organisms find themselves only distantly related  Coincidence? o Natural selection favored similar evolutionary adaptations in similar environments 

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Convergence of phenotypes in separate lineages

Chapter 18 Species and the Ability to Reproduce  Species- a group of individual organisms that interbreed and produce and produce fertile, viable offspring  Share external and internal characteristics o Develop from their DNA  The closer the relationship two organisms share, the more DNA they have in common  Appearance can be misleading o Dogs  Some appear similar, but are different species Hybrids  Offspring of cross genetically different individuals  Form rarely, but will be unhealthy or sterile  Horse and donkey (M/F Donkey) (F/M Hinny) o These two species are in the same genus Gene Pool  A collection of all gene variants in the species  Basis to any change must be genetic o The only way to share and pass on traits  2 ways to pass on the variation o Asexual reproduction o Sexual reproduction (sperm and egg)  Only heritable traits can evolve Sympatric Species  Species that overlap in geographical range  Regularly occur together o Distinctive, different phenotypes o Utilize different parts of habitat o Exhibit different behaviors Sibling Species  Occur together, assumed to be identical species  Bias of observer and observations  Often different in mating call, chemicals etc.  Animals themselves have no problem making distinctions Geographic Variations  Populations of a single species in different areas may be distinct from one another  Classified as a subspecies or varieties  Intermediate forms in regions where populations overlap slightly  May have characteristics of both populations  Geographically distant populations share genes via gene flow o Keeps members of isolated populations within same population Speciation  Darwin; branching effect o As one species changes over time, it branches to form more than one new species  Two new populations must form from one original population  Impossible for those individuals to interbreed

Speciation= split of one ancestral species into two descendant species Allopatric Speciation  Allo= other  Patric= homeland  Populations becoming isolated geographically  Differentiation occurs  Subsequent reproductive isolation  Completely separated (no gene flow)  Two categories o Dispersal  Few members of a species moved to a new geographical area o Variance  When natural situation arises to physically divide organisms  One might expect isolated populations to diverge over time  But, it geographic isolation required for speciation to occur Sympatric speciation  Speciation without being geographically separated population o Disruptive selection can cause population to exhibit two or more different phenotypes  These phenotypes could evolve into different species  However, some barrier would still have to be present, could be ecological rather than geographical  Can happen if there is a serious chromosomal error during cell division/gamete production  Aneuploidy o Too many or to few chromosomes during meiosis  Polyploidy o Extra set of chromosomes  Auto polyploidy and allopolyploidy occur in plants Adaptive radiations  Evolution into a number of different ecological roles or modes of life  Usually over relatively short time period  Leads to variety of new forms and species  A population of one disperses throughout an area  Each finds a distinct niche or isolated habitat  Many adaptations evolve from a single point of origin; thus, causing the species to radiate into several new ones Reproductive isolation  Genes of one species cannot easily the gene pool of another  Vicious barriers developed to prevent this from happening o Reproductive isolation - barriers to reproduction  Some kind of courtship  Copulation  Fertilization o Barriers are essential or maintenance of species identity  Keeps species intact and prevents homogenization of life  Two major categories 

Prezygotic isolation Prevents formation of fertilized egg Prevents mating/fertilization from occurring Avoidance of costly mistakes o Postzygotic isolation  Hybrids unhealthy or sterile Prezygotic mechanisms o Ecological isolation  Two species in the same area  Utilize different portions of habitat  Do not normally encounter one another  Therefore, not a chance of mating o Behavioral isolation  Different courtship rituals o Breeding periods  Different times  Seasonal component o Mechanical isolation  General structural differences (reproductive organs)  Size  "Lock and key", wrong key the lock stays locked Postzygotic isolation o Prevents function or development of normal zygote o Hybrids are weaker o Usually sterile Diversity of life o Did not increase substantially until about 550 million years ago o "Cambrian explosion"  Many evolutionary experiments documented fossil record  Nearly all major animal body plans can be seen in Cambrian rock (543-525 million years ago)  Most major animal phyla appeared in the fossil record  Divergence of most modern metazoan phyla  Implies that earliest branches of animal family tree arose before Cambrian Mass extinctions o Number of species risen steadily since the Cambrian explosion o Five major setbacks (mass extinctions)(MEMORIZE ALL 5 FOR EXTRA CREDIT) o

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Permian extinction (250 million years ago) o Half the families and marine organisms and over 90% of species went extinct o Catastrophic hypothesis (volcanic eruption) o Gradual hypothesis (sea level change, increase in anoxia, increased aridity)  KT Boundary (65 mya) o Triggered by large asteroid slamming into earth o The boundary separated by an iridium-rich layer o Caused fires and obscured the sun for many months o Killed off plants and caused far-reaching results Diversity tends to rebound quickly after mass extinction o New vacancies in the environment o Creates new round of adaptations o Organisms making up new diversity not the same as those who existed o During the age of dinosaurs, mammals were small and insignificant o Extinction of dinosaurs created many new niches and allowed mammals to become larger and diversify A SIXTH EXTINCTION?? o Human activities may lead to the latest mass extinction 

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Only extinction that is caused primarily by a single species (homo sapiens) Began thousands of years ago Extermination of large mammals in North America Accelerated as humans moved over the earth  Habitat destruction  Introduction of foreign species Rebound from this extinction may be minimal

Chapter 19 

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Gene: a unit of heredity that is transferred from parent to offspring and is held to determine some characteristic of the offspring A distinct sequence of nucleotides forming part of a chromosome Allele: any of the different forms of a gene occupying the same position (locus) on a chromosome o Get one allele from dad and one from mom o A gene may have several alleles that code for different traits Diploid organisms can only carry 2 alleles for a particular gene, but more than two may be present in the individuals that comprise the population o Alleles are either dominant or recessive (for now) Dominant Allele: determines the phenotype of a heterozygote o Masks the recessive allele Recessive allele: not expressed in phenotype unless it is homozygous Allele frequency: rate at which allele appears within a population o The number of copies for that allele divided by all the copies Gen...