Life 103; Week 1-2
Life 103; Week 1-2 Life 103
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This 12 page Class Notes was uploaded by Addy Carroll on Monday January 25, 2016. The Class Notes belongs to Life 103 at Colorado State University taught by Dr. Dale Lockwood and Dr. Tanya Dewey in Winter 2016. Since its upload, it has received 49 views. For similar materials see Biology of organisms-animals and plants in Biology at Colorado State University.
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Date Created: 01/25/16
Life 103 Notes adapted from the lecture slides of Dr Dale Lockwood thlggeny Terminology Evoution The change in allele frequencies in a population over time As an allele is a specific version of a gene this definition means that certain gene versions become moreless prominent in a population as time progresses Four ways evolution can occur 1 Selection Changes in allele frequencies due to organisms with advantageous alleles reproducing more successfully than organisms with other alleles This simply means that certain organisms with one version of the gene reproduce more frequentlywith more success than other organisms 2 Genetic Drift Random changes in allele frequencies in a population In addition to just knowing this simple definition it might be helpful to note that these changes are completely based on chance for example if a natural disaster happened to take out more organisms with one allele than the organisms with a different allele 3 Mutation The source of all new allelic diversity This is an evolutionary change that occurs on a more molecular level The actual gene sequence of an organism has to change 4 Migration Movement of alleles between populations This could happen for example if an organism having a certain allele reproduces with an organism from another population where the allele is never found to be present Thus this would introduce the allele to the population Adaptation A trait that evolves by selection for a particular function because it increases fitness from an ancestor that did not have that trait Adaptations can be morphological behavioral or molecular Adaptations solve problems faced by populations and different populations may have different solutions to similar problems Phylogeny The evolutionary relationships of a group of organisms species level and higher Phylogenetic tree Diagram of the ancestral relationships among species see Phylogenetic trees section below for more details Describe patterns Provide information about when certain large events may have occurred Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms In the 18th century Carl Linnaeus published a system of taxonomy based on resemblances Two key features of his system remain useful today twopart names for species see binomial nomenclature section below and hierarchical classification see Hierarchical Classification section below Binomial Nomenclature The twopart scientific name of a species is called a binomial The first part of the name is the genus The second part called the specific epithet is unique for each species within the genus The first letter of the genus is capitalized and the entire species name is italicized Ex Homo sapiens human Both parts together name the species not the specific epithet alone Hierarchical Classification see textbook figure 263 Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups from broad most inclusive to narrow least inclusive are domain kingdom phylum class order family genus and species A taxonomic unit at any level of hierarchy is called a taxon Phylogenetic trees DanNin used the metaphor of a tree to explain the relationship between similar species How do we build these trees What type of evidencedata can we use to reconstruct a tree see textbook figure 2612 1 Morphological traits 2 Behavior 3 Chemical composition 4 Chromosome number 5 DNA These types of data are called characters It may be important to note characters are not the same as characteristics A characteristic is a specific character For example In observing the character of hair color in the classroom we saw that 69 of the students had the characteristic of blonde hair color Character state variation among characters Phylogenetic Tree Terminology see textbook figures 265 2610 Each branch point represents the divergence split of two species Sister taxa are groups that share an immediate common ancestor A rooted tree includes a branch to represent the last common ancestor of all the taxa in the tree A polytomy is a branch from which more than two groups emerge A simplified tree of life The tree of life suggests that animals and fungi are more closely related to each other than plants The tree of life is based largely on rRNA ribosomal RNA genes as these have evolved slowly 599199 Ecology ecohouse ologystudy of The study of the distribution and interaction of organisms with other organisms and the environment Word coined by Ernst Haeckel Most interdisciplinary involving two or more areas of knowledge discipline in biology Organismal Ecology The study of the interaction of an organism and its environment Behavioral Ecology Response to stimulus Foraging Group interaction Evoutionary Ecology Adaptations to the environment see phylogeny notes for adaptations Events in ecological time the length of time an organism experiences influence evolutionary time processes Population Ecology A population is a group of individuals of the same species living in the same area Popuation Ecology focuses on factors affecting how many individuals of a species live in an area Most mathematically based subdivision of ecology Community Ecology A community is a group of interacting populations of different species in an area Community ecology deals with the whole array of interacting species in a community Ecosystem Ecology An ecosystem is the community of organisms in an area and the physical factors with which they interact Ecosystem ecology emphasizes energy flow and chemical cycling among the various biotic and abiotic components Movement of carbon nitrogen and other chemicals through the ecosystem Climate change Ecological interactions Organisms and Environment Species Distributions Range limitations Environment is composed of 1 Biotic factors living see Biotic Factors section below 2 Abiotic factors nonliving see Abiotic Factors section below Biotic Factors Organisms interacting with other species nteractions can be positive negative or neutral Ex plantpollinator predatorprey herbivoreplant competition Abiotic Factors Nonliving parts of the environment Chemical Ex pH salinity Physical Ex weather temperature moisture soil light nutrients 02 N2 Dispersal The movement of individuals One way trip while migration is a round trip Dispersal is natural Bacteria and Archaea Prokaryotes are made up of two domains 1 Bacteria 2 Archaea The problem with prokaryotes Biologically prokaryotes are a nonmonophyletic group see textbook figure 2610a andor phylogeny notes Thus the term prokaryote is not a biologically sensible term Bacteria and Archaea Life is mostly singlecelled Highly adaptable see adaptation in phylogeny notes live just about everywhere hot cold acid sulphurous salty conditions Vast numbers More bacteria in a cup of soil than the number of humans that have ever existed Very high genetic diversity Bacteria are unicellular although some species form colonies Most bacteria are 055 micrometers much smaller than the 10100 micrometers of many eukaryotic cells Bacterial cells have a variety of shapes see textbook figure 272 The three most common shapes are spheres cocci rods bacilli and spirals Cell Walls Most bacteria have them Maintains shape Physica protection Prevents bursting in hypotonic environment Bacterial cell walls contain peptidoglycan a network of sugar polymers crosslinked by polypeptides Both eukaryotes and archaea contain polysaccharides and proteins but lack peptidoglycan Gram Stain see textbook figure 273 Used to make bacteria visible Cassifies many bacterial species Grampositive Gramnegative Gramnegative bacteria Have less peptidoglycan Have outer membrane Can be toxic More likely to be antibiotic resistant Some prokaryotes have fimbriae also called attachment pili see textbook figure 276 which allow them to stick to their substrate or other individuals in a colony Most motile bacteria propel themselves by flagella see textbook figure 277 Structuray and functionally different from eukaryotic flagella Aows for taxis the ability to move in response to stimuli Both bacteria and archaea ces usually lack complex compartmentalization No organelles Some bacteria and archaea have specialized membranes that perform metabolic functions Respiratory membranes in aerobic bacteria Thyakoid membranes in photosynthetic bacteria Bacteria DNA The genome of bacteria is smaller than eukaryotic genomes Most of the genome consists of a circular chromosome Some species of bacteria also have smaller rings of DNA called plasmids The typical bacterial genome is a ring of DNA that is not surrounded by a membrane and that is located in a nucleoid region Bacteria can form exospores or endospores Endospores lnternal to the bacterium Resistant to UV radiation desiccation alcohol and chemicals Can survive for extended periods of time Exospores Formed differently Less robust Reproduction Bacteria reproduce quickly by binary fission and can divide every 13 hours Generay each offspring is identical genetically Mutations can cause variation in offspring Mutations are rare but reproduction is very fast Genetic variation Bacteria and archaea have considerable genetic variation Three factors contribute to this genetic diversity 1 Rapid reproduction 2 Mutation 3 Genetic recombination Genetic recombination Bacterial DNA from different individuals can be brought together by transformation transduction and conjugation A bacterial cell can take up and incorporate foreign DNA from the surrounding environment in a process called transformation Transduction see textbook figure 2711 is the movement of genes between bacteria by bacteriophages viruses that infect bacteria Transformation First shown in 1928 Bacteria that can transform are competent about 1 of bacteria species are naturally competent under laboratory conditions Techniques can make bacteria artificially competent Conjugation see textbook figures 2712 2713 The process where genetic material is transferred between bacterial cells Sex pili aow cells to connect and pull together for DNA transfer A piece of DNA called the F factor is required for the production of sex pili The F factor can exist as a separate plasmid or as DNA within the bacterial chromosome R plasmids carry genes for antibiotic resistance Antibiotics select for bacteria with genes that are resistant to the antibiotics Antibiotic resistant strains of bacteria are becoming more common Antibiotic Resistance Misuse and overuse of antibiotics Agricultura uses Patients demanding antibiotics for nonbacterial infections Majority of ear and sinus infections are viral Patients not using antibiotics properly Antibiotic products soaps toys treated with antibiotics etc Latera gene transfer allows multiple resistance Ex MRSA Methicillin resistant Staphylococcus aureus First appeared in 1961 2 years after methicillin was first used Now resistant to penicillin oxacillin and amoxicillin tetracycline erythromycin and clindamycin 85 of infections occur in hospitals Over 18000 deaths in 2005 Most are skin infections Can spread to other organs Bacterial nutritional adaptations Phototrophs obtain energy from light Chemotrophs obtain energy from chemicals Autotrophs require C02 as a carbon source Heterotrophs require an organic nutrient to make organic compounds Chemoautotrophs Black smoker deep sea vents Major primary producers The role of oxygen in metabolism Bacteria metabolism varies with respect to 02 Obigate aerobes require 02 for cellular respiration Obigate anaerobes are poisoned by 02 and use fermentation or anaerobic respiration Facultative anaerobes can survive with or without 02 Nitrogen metabolism Bacteria can metabolize nitrogen in a variety of ways In nitrogen fixation some bacteria convert atmospheric nitrogen N2 to ammonia NH3 Metabolic cooperation Cooperation between bacteria allows them to use environmental resources they could not use as individual cells In the cynobacterium Anabaena photosynthetic cells and nitrogenfixing cells called heterocytes exchange metabolic products see textbook figure 2714 Proteobacteria These gramnegative bacteria include photoautotrophs chemoautotrophs and heterotrophs Some are anaerobic and others aerobic Subgroup Alpha Proteobacteria Many species are closely associated with eukaryotic hosts Scientists hypothesize that mitochondria evolved from aerobic alpha proteobacteria through endosymbiosis Exampe Rhizobium which forms root nodules in legumes and fixes atmospheric N2 Exampe Agrobacterium which produces tumors in plants and is used in genetic engineering Subgroup Gamma Proteobacteria Examples include sulfur bacteria such as chromatium and pathogens such as legionella salmonella and vibrio cholera Escherichia coli resides in the intestines of many mammals and is not normally pathogenic Subgroup Epsilon Proteobacteria This group contains many pathogens including campylobacter which causes stomach ulcers Ulcers and their history Drs Marshall and Warren Nobel Prize in 2005 Helped define the concept of don t try this at home 0 Grampositive bacteria Grampositive bacteria include Actinobacteria which decompose soil Bacillus anthracis the cause of anthrax Clostridium botulinum the cause of botulism Some staphylococcus and streptococcus which can be pathogenic Mycoplasms the smallest known cells Steptomyces the source of many antibiotics Ecological relationships and bacteria Symbiosis is an ecological relationship in which two species live in close contact a larger host and smaller symbiont Prokaryotes often form symbiotic relationships with larger organisms Parasites that cause disease are called pathogens 0 Benefits of Bacteria Fermentation Waste management Toxic spill cleanup Genetic engineering Antibiotics o Archaea Archaea share certain traits with bacteria and other traits with eukaryotes see textbook table 272 Some archaea live in extreme environments ad are called extremophiles Extreme halophiles live in highly saline environments Extreme thermophiles thrive in very hot environments Methanogens live in swamps and marshes and produce methane as a waste product Methanogens are strict anaerobes and are poisoned by 02 Protists and Algae o Protists Protista is the informal name of the kingdom of mostly unicellular eukaryotes Advances in eukaryotic systematics have caused the classification of protists to change significantly Protists constitute a paraphyletic group see phylogeny notes andor textbook figure 2610 and protista is no longer valid as a kingdom Protists are eukaryotes and thus have organelles and are more complex than prokaryotes Most protists are unicellular but there are some colonial and multicellular species Basic Protist Biology Protists exhibit more structural and functional diversity than any other group of eukaryotes Singlecelled protists can be very complex as all biological functions are carried out by organelles in each individual cell Protists the most nutritionally diverse of all eukaryotes include Photoautotrophs which contain chloroplasts Heterotrophs which absorb organic molecules or ingest larger food particles Mixotrophs which combine photosynthesis and heterotrophic nutrition Protists can reproduce asexually or sexually Mutualisms in Protists There is now considerable evidence that much protist diversity has its origins in endosymbiosis a type of symbiosis in which a symbiont dwells within the body of its symbiotic partner Mitochondria evolve by endosymbiosis of an aerobic prokaryote Plastids evolved by endosymbiosis of a photosynthetic cyanobacterium The plastidbearing lineage of protists evolved into red algae and green algae On several occasions during eukaryotic evolution red and green algae undenNent secondary endosymbiosis see textbook figure 283 in which they were ingested by a heterotrophic eukaryote Five Supergroups of Eukaryotes see textbook figure 282 It is no longer thought that amitochondriates lacking mitochondria are the oldest lineage of eukaryotes Our understanding of the relationships among protist groups continues to change rapidly One hypothesis divides all eukaryotes including protists into five supergroups Excavata The clade excavata is characterized by its cytoskeleton Some members have a feeding groove This controversial group includes diplomonads parabasalids and euglenozoans Dipomonads Have modified mitochondria called mitosomes Are often parasites for example Giardia intestinalis Parabasaids Have reduced mitochondria called hydrogenosomes Include Trichomonas vaginalis the pathogen that causes yeast infections in human females Euglenozoa Diverse clade that all have a spiral or crystalline rod of unknown function inside their flagella Kinetoplastids have a single mitochondrion with an organized mass of DNA called a kinetoplast Euglenids have one or two flagella that emerge from a pocket at one end of the cell Chromalveolata Clade is monophyletic and originated by a secondary endosymbiosis event with red algae This clade is controversial and includes the alveolates and the stramenopiles Superphyum Alveolata protists have membrane bounded sacs alveoli just under the plasma membrane Alveolata includes the dinoflagellates apicomplexans and ciliates Phyum Dinoflagellates are a diverse group of aquatic mixotrophs and heterotrophs They are abundant components of both marine and freshwater phytoplankton Each has a characteristic shape that in many species is reinforced by internal plates of cellulose Dinoflagellate blooms are the cause of toxic red tide Not all red tides are red Not all red tides are harmful Phyum Apicomplexa are parasites of animals and some cause serious human diseases One end the apex contains a complex of organelles specialized for penetrating a host Most have sexual and asexual stages that require two or more different host species for completion The apicomplexan Plasmodium is the parasite that causes malaria see textbook figure 2816 for life cycle Plasmodium requires both mosquitoes and humans to complete its life cycle Approximately 2 million people die each year from malaria Sicklecell anemia confers some protection Phylum Stramenopila or Heterokonts Diatoms are unicellular algae with a unique twopart glasslike wall of hydrated silica Golden algae are unicellular some colonial named for their color which results form their yellow and brown carotenoids Brown algae are the largest and most complex algae A are multicellular and most are marine Brown algae include many species commonly called seaweed Brown algae see textbook figure 2813 for life cycle The algal body is plantlike but lacks true roots stems and leaves and is called a thallus The rootlike holdfast anchors the stemlike stipe which in turn supports the leaflike blades Alternation of Generations A variety of life cycles have evolved among the multicellular algae The most complex life cycles include an alternation of generations the alternation of multicellular haploid and diploid forms Heteromorphic generations are structurally different while isomorphic generations look similar Rhizaria DNA evidence supports Rhizaria as a monophyletic clade Amoebas move and feed by pseudopodia some but not all belong to the clade Rhizaria Rhizarians include forams and radiolarians Both groups have hard shells called tests Pseudopodia extend through holes in the test On the way to Plants Archaeplastida is a supergroup used by some scientists and includes red algae green algae and land plants Over a billion years ago a heterotrophic protist acquired a cyanobacterial endosymbiont The photosynthetic descendants of this ancient protist evolved into red algae and green algae Land plants are descended from the green algae Red Algae Red algae are reddish in color due to an accessory pigment called phycoerythrin which masks the green of chlorophyll Red algae are usually multicellular the largest are seaweeds Green Algae Named for their grassgreen chloroplasts Pants are descended from the green algae The two main groups are chlorphytes and charophyceans see textbook figure 2823 for life cycle of chlorphyte Most chlorophytes live in fresh water although many are marine Other chlorophytes live in damp soil as symbionts in lichens or in snow Watermelon Snow Chlamydomonas nivalis Pink comes from carotenoid astaxanthin Extracted from krill Used as a dye in farmed salmon Unikonts Proposed supergroup of eukaryotes lncludes animals fungi and closely related protists Amoehozoans We supported clade Amoebas Slime molds see textbook figures 2825 2826
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