BIO 3 GENERAL BOTANY LECTURE MANUAL - Hartnell College!!

BIO 3 GENERAL BOTANYLECTURE MANUALSection 5046, Fall 2013Instructor- Dr. Jeffery R. Hughey1

December 2 Plant Genetics Chapter 8GeneticsTopic 10, HandoutDecember 4December 9December 11December 18Field trip to U.S. Agricultural Research Station SalinasPROJECT PRESENTATIONS, PROJECT REPORTS DUEFINAL LABORATORY EXAMINATIONFINAL LECTURE EXAMINATION (3:00-6:00 PM)HERBARIA DUECOURSE DESCRIPTIONIntroduction to the principles of plant biology with an emphasis on cytology, energetics, structure,function, reproduction, genetics, systematics, and plant growth. Detailed morphological study ofcyanobacteria, fungi, photosynthetic and heterotrophic protists, bryophytes, and vascular plants.STUDENT LEARNING OUTCOMES1) Given any plant phylum, the student will be able to describe the characteristics that define the phylumas well as illustrate the life history of one of its representatives.2) Given any plant response, the student will be able to explain the physiological basis for the plant'scondition or action.3) Given images of plant cells, the student will be able to describe the cell’s structure and function.4) Given microscope slides of any plant body, the student will be able to demonstrate knowledge of itsstructure and development.COURSE OBJECTIVES1. Develop an appreciation for the botanical contributions of early explorers.2. Investigate the commercial and ethnobotanical applications of plants.3. Compare and contrast cellular plant diversity.4. Identify the basic features of all plant cells.5. Investigate the vital relationship between plants and the flow of energy.6. Compare and contrast the photosynthetic pathways.7. Examine the chromosomal basis for Mendelian genetics.8. Investigate the structure of macromolecules and their role in plant function.9. Isolate genetic material and analyze DNA sequences from lower and higher plants.10. Investigate natural selection and its affects on populations.11. Infer hypotheses by analyzing morphological and molecular phylogenetic data.12. Investigate life histories of photosynthetic eukaryotes.13. Identify diagnostic morphological characteristics of the major plant phyla.14. Collect and curate botanical specimens from aquatic and terrestrial habitats.15. Develop microscopy skills necessary for the examination of plant structures.16. Investigate the affects of hormones on plant processes.17. Examine the affects of macro and micronutrients on plant growth.18. Investigate the interactions between plants and other organisms.19. Investigate plant community and ecosystem development.20. Investigate the adaptations plants have evolved to particular biomes.21. Analyze the role of agriculture on human history and predict its role in the future.5

INSTRUCTOR INFORMATIONInstructor- Dr. Jeffery R. HugheyOffice- Building N, Room 26COffice Telephone- (831) 770-7054Email- jhughey@hartnell.eduWeb Address- http://www.hartnell.edu/faculty/jhughey/course_doc.htmOffice Hours- Monday 12:30-1:30 PM, Tuesday 5:00-6:00 PM, Thursday 5:00-6:00 PMREQUIRED TEXTBOOKSEvert, R.F. and Eichhorn, S.E. Raven Biology of Plants: 8 th Ed. W.H. Freeman, New York, 2013.Evert, R.F. and Eichhorn, S.E. Laboratory Topics in Botany: 8 th Ed. W.H. Freeman, New York, 2013.Hughey, J. Bio 3- General Botany Lecture Manual: Section 5046, Fall 2013.RECOMMENDED MANUALRushforth et al. A Photographic Atlas for the Sixth Edition of Botany Laboratory. Morton Publishing,Englewood, 2012.GRADINGDetermination of grades in this course will be based on your performance on the following:First Examination100 pts. (50 pts. Lecture/50 pts. Laboratory)Second Examination 100 pts. (50 pts. Lecture/50 pts. Laboratory)Final Laboratory Examination 100 pts.Final Lecture Examination 100 pts.Herbarium100 pts.Research Project100 pts.Total600 pts.Grade Total Points Earned (Percentage) Definition Grade PointsA 540-600 pts. (90-100%) Excellent 4B 480-539 pts. (80-89%) Good 3C 420-479 pts. (70-79%) Satisfactory 2D 360-419 pts. (60-69%) Barely Passing 1F 359 or fewer (59% or less) Failing 0EXAMINATIONSThe Lecture portion of the examinations will consist of a combination of multiple choice, true or false,matching, short answer, and essay questions. Questions will come mainly from the lecture material, butwill also be derived from assigned readings. Supply your own Scantron 882-E form and a number 2pencil. The Laboratory portion of the examinations will focus on material in the lab manual andinformation from lab exercises and field trips. Laboratory questions generally require you to 1) identifyplant structures and 2) name plant specimens.6

MAKE UP EXAMINATION POLICYIf you are unable to attend an examination please notify me by telephone, email, or in person prior to thetest. If you fail to contact me in advance and you miss the examination, submit a written letter signed bythe authority involved (doctor, policeman) that includes their phone number and an explanation. If youhave a valid excuse, I will schedule an intellectually comparable make up oral or essay examination. Nomake ups will be granted for the final examination without prior approval from Dr. Hughey.HERBARIUMA herbarium is a collection of pressed, boxed, or enveloped plant specimens. During scheduled field tripsyou will have the opportunity to collect specimens. You are required to assemble a herbarium ofrepresentative specimens of the major phyla. Herbarium grades will be based on comprehensiveness,identification accuracy, label correctness, aesthetics, and effort in comparison to your peers. The labelshould include the phylum, family, genus and species, location and date of collection, and the name of thecollector.RESEARCH PROJECTSBotanical projects involve four steps. They can be performed individually or in groups of two.1) Submit a research proposal (30 pts.). Proposals are due on October 23 rd , 2013 and should be typed.Your proposal needs to include: 1) title; 2) testable hypothesis; 3) what is known and unknown aboutyour hypothesis; 4) the purpose of performing your experiment; 5) prediction of the results fromyour experiment; 6) materials you need to conduct the study and the methods you will use; 7)illustration/s of your methods; 8) a list of five or more references. Your proposal should be 2-3pages. ALL STUDENTS ARE REQUIRED TO SUBMIT A RESEARCH PROPOSAL.2) Perform the research project. If you need equipment or reagents that you do not have, ask Joni Blackour biology technician or check with me and we may be able to locate or order them for you.3) Write a paper on the research project (35 pts.). Manuscripts are due on December 9 th , 2013. Theyshould include an abstract, introduction, materials and methods, results, discussion, conclusion, andreference sections. See Appendix A in your lab book for a description of these sections. ALLSTUDENTS ARE REQUIRED TO SUBMIT A RESEARCH PAPER.4) Present your research project to the class (35 pts.). Presentations will be given on December 9 th , 2013.They can be presented using the chalkboard, PowerPoint slides, video, and/or the overheadprojector. Presentations will be 5-10 minutes in length, and you will be timed. Students working ingroups should present as a group. THERE ARE NO MAKE UP PRESENTATIONS. IF YOU DONOT PRESENT, YOU WILL NOT EARN POINTS.7

ATTENDANCE POLICYRegular attendance and consistent study are your responsibility and the two factors that contribute most toa successful college experience. I expect you to attend all class sessions. Absences in excess of twoweeks (consecutive or non-consecutive) will result in dismissal. What does that mean? IF YOU MISSFIVE CLASSES, YOU WILL BE DROPPED FROM THE COURSE.DROPPING THE COURSEIt is your responsibility to drop the course. Do not assume that I will submit the drop for you if youdecide to stop coming to class. The last day to drop for a “W” is November 22 nd . Students that do notofficially drop the course by November 22 nd will receive a letter grade based on their Total Points Earned.CLASSROOM VISITORSNo one is permitted to attend this class unless he or she is a registered student.CONDUCTPlease show respect for your peers and your instructor. If I observe any student performing or aiding inany of the types of misconduct listed under “Codes of Student Conduct” on page 31 of the HartnellCatalog, that student will be dropped from the course. Disruptive behavior will not be tolerated (thisincludes text messaging during class).INSTRUCTIONAL SUGGESTIONSCourse suggestions that will improve comprehension, retention, and cognition are warmly welcomed.Requests for less information, postponement of examinations, or easier examinations are not welcomed.SUGGESTIONS FOR DOING WELL IN BIOLOGY 31) Review your lecture and laboratory notes before coming to class2) Study for examinations with a partner or in a group3) Attend class and take complete notes4) Outside of class study at least 10 hours per week8

Why Study Plants?- Chapters 1, 2, 7, 21•Why not?“To be ________________, _______________, and _________________ is sufficient recommendationof a science to make it pleasing to me.” _______________ _______________ (1811-1866)How do humans use plants?Agricultural product as fodder•Fodder- food that is fed to ____________________ ______________________.•________________ (Zea mays) is the most important crop in the United States.–________% of this crop is consumed by animals.What is the role of the photosynthetic organism in the carbon cycle?Global O 2 from photosynthesis•_______% comes from marine cyanobacteria.–Synechococcus–Synechocystis•_______% comes from terrestrial systems.–_______ % of this comes from tropical rainforests.Photosynthetic organisms evolved 3.4 BYA and are responsible for the biological revolution•Increases in O 2 from photosynthesis had 2 consequences:–1) _______________________________- O 2 molecules in atmosphere converted to ozone (O 3 ).•2.5 BYA–2) ________________________________•Respiration- break down of molecules by oxidation.•Eukaryotic cells- appearance and proliferation of cells.–2.1 BYA9

Photosynthesis10

Nitrogen CyclePhosphorus CycleHow do animals use plants?Primary Producers (Food webs and chains)11

Phytoremediation•The _____________ of pollutants or waste by the use of _______ to break down undesirable substances.–________________________–________________________–_________________________________________________ _______________________•Lemna gibba- duckweed.•Eichornia crassipes- water hyacinth.Biodiesel and Bioethanol from PlantsPlants in Space•_______________- a unicellular green alga.–__________________ ____________________.–Process _______________ (urine).–Life support system, _________________ .Medicine in Ancient Times•____________ (3,350-3,140 BC)- frozen in ice, found in the Alps on the Italian-Austrian border.–__________ _____________ used as a laxative and as a natural antibiotic.•The ________________ ________________ used in Ancient Greece:–Anise, black hellebore, cassia, cucumber, wild root of (squirting cucumber), cumin, cyclamen,root of frankincense, germander, lettuce, wild myrrh, olive oil, opium, poppy, parsnip.Hippocrates (460-380 BC) _________________ of medicine•Ancient Greek physician for the Medical School at _____________.•Wrote ___________________ _______________________Medicine in Modern Times•___________% of the _____________________ on the market is derived directly from plants.•Drugs made from ___________ prevent the rejection of transplanted hearts and other organs.•The active ingredient in ______________ was originally derived from ______________ bark.•Paclitaxel, a compound found in the Pacific yew tree, assists in the treatment of some _____________.•The rosy periwinkle helps treat _________________.•______________________ _________________. Ginkgo biloba is prescribed for depression, mentalweakness or confusion, loss of memory, ringing of the ears.Egyptian Papyrus12

The Molecular Composition of Plant Cells - Chapter 2Chemical ElementsMetabolites__________________ Metabolites- molecules ______________________________________________.__________________ Metabolites- molecules __________________________ in their distribution, bothwithin the plant and among different plants; important for ________________________________ and___________________________________.Macromolecule Synthesis and Splitting13

CarbohydratesLipidsProteins14

Nucleic AcidsAlkaloidsTerpenoidsPhenolics15

Systematics- The Science Of Biological Diversity Chapter 12•Systematics- the scientific study of biological ____________________ and its evolutionary history.Theophrastus (370-285 B.C.)•Father of ______________, student of Aristotle.•Classified plants based on form.–_________________–_________________–_________________–_________________Carol von Linné (1707-1778)•Swedish naturalist.•____________________ ____________________.–Plant descriptions.–Plant ____________________ - a two-term system of nomenclature.•____________________ and ____________________ (specific epithet).•Example- catnip.–Nepeta cataria L.–“Nepeta floribus interrupte spicatus pedunculatis”Taxonomy•Taxonomy- (gr. taxis- ________________________, nomos- __________) the science of theclassification of organisms.–Identifying, naming, classifying organisms.•Domain•Kingdom•____________________- phyta•____________________- phyceae•Order- ales•____________________- aceae•Genus•____________________Prokaryotes and Eukaryotes16

3 Domains and 6 KingdomsEukaryote LineagesOrigin of Cells17

Origin of Eukaryotic CellsSpecies ConceptsBiological Species Concept-Phylogenetic Species Concept-Genomic Species Concept-International Code of Botanical Nomenclature (_________________)•Aim- to provide a ____________________ method of naming taxonomic groups.–Principle I- botanical nomenclature is _______________________ of zoological andbacteriological nomenclature.–Principle II- names of taxonomic groups are determined by means of nomenclatural_______________.–Principle III- nomenclature of a taxonomic group is based upon _______ of publication.•Naming- the purpose of giving a name to a taxonomic group is not to indicate its characters or history,but to ___________________________________ and to indicate its_______________.18

Taxonomic Terminology•________________- a taxonomic group of any rank (plural: taxa).•________________- two or more names that apply to the same taxon.•________________- the original name of a taxon.•Author/s- the ________________ person or persons to ________________ a taxon.•Revisionary author/s- the person or persons that _________________________________.•________________- the derivation, origin, or history of a word.•Type Specimen- a specimen designated to serve as a reference point for a scientific name.–Holotype- _________________________________________________________.–Lectotype- ________________________________________________________.Chondracanthus exasperatus (Harvey et Bailey) Hughey 1996Gigartina exasperata Harvey et Bailey 1851Mazzaella laminarioides (Bory) Fredericq et Hommersand 1993Iridaea laminarioides Bory 1828Iridaea cornucopiae Postels et Ruprecht 1840Iridaea boryanum Setchell et Gardner 1936Mazzaella parksii (Setchell et Gardner) Hughey, Silva, et Hommersand 2001Iridophycus parksii Setchell et Gardner 1937Taxonomic Names•Species names consist of the genus name, plus the specific epithet.•Members of a species may be grouped into ________________ or ________________.How do you identify plants?•Ask an _______________________.•Use a _______________________.•Compare plant with a written _______________________.•Use books to picture I.D. specimens.–Photographs and _______________________.•Use a __________________________ ________________.Dichotomous Keys•A method employed for _______________________________________________________.•A dichotomous key is constructed of a series of ____________________, each consisting of twoseparate statements.1. Flowers white .................. Plant A1. Flowers __________ or ____________ ..... 22. Petals red ............ Plant B2. ________________ white ........ Plant C19

Biology 3- General BotanyHartnell CollegeDr. Jeffery HugheyWriting Dichotomous Keys1) Start each statement with a subject.CorrectWrong1. Leaves opposite. 1. Opposite leaves.1. Leaves alternate. 1. Alternate leaves.2) Avoid unnecessary words.CorrectWrong1. Leaves opposite. 1. Plants with opposite leaves.1. Leaves alternate. 1. Plants with alternate leaves.3) Avoid negatives.CorrectWrong1. Flowers purple. 1. Flowers purple.1. Flowers white or pink. 1. Flowers not purple.4) Use absent in place of “not present.” Use “without” in place of “not with.”5) Use measurements rather than “large”, “small”, “tall”, “short”, “big”, “small.”6) Use features that are constant in preference to variable or overlapping features.GoodBad1. Flowers purple. 1. Leaves 8-12 cm long.1. Flowers white. 1. Leaves 6-10 cm long.7) No trichotomies!CorrectWrong1. Flowers white .................. Plant A 1. Flowers white ............ Plant A1. Flowers red or yellow ..... 2 1. Flowers red ................ Plant B2. Petals red ............ Plant B 1. Flowers yellow .......... Plant C2. Petals white ........ Plant C8) Use different words to start successive pairs of key statements. See above #7 use of Flowersand Petals.Using Dichotomous Keys1. Always read both choices.2. Be sure you understand the meaning of the terms involved, do not guess.3. When measurements are given, use a calibrated scale, do not guess.4. Do not base your conclusion on a single observation, if possible examine other specimens.5. If you get stuck, try both divisions and see which one makes sense.6. After arriving at an answer in a key, read the description to see if your plant is in agreement.20

Write a dichotomous key based on the following 10 species. Once you complete yourdichotomous key show it to Dr. Hughey. The following terms will help you construct your key,if you do not know the definition of these terms ask the instructor or use your textbook glossary:leaves, roots, tap root, tuber, rhizome, elongate, lanceolate, simple, compound, stem, sepals,petals, dichotomous, and corymbose.21

Systematics#2- The Science Of Biological Diversity Chapter 12Phylogeny•Phylogeny- the evolutionary relationships among organisms.–Natural classification.•Phylogenetic tree- a _________________ diagram that represents a ____________________ of the____________________ ____________________ of a species or group of related organisms.Hominid Evolutionary TreeTree of Homo sapiens L.Tree TerminologyRoot- _______________________________________________________________________________.Branch- _____________________________________________________________________________.Outgroup- ___________________________________________________________________________.Ingroup- ____________________________________________________________________________.Taxon- _____________________________________________________________________________.Node- ______________________________________________________________________________.Phylogenetic GroupsMonophyletic Paraphyletic Polyphyletic22

Phylogenetic trees•Cladogram–________________________–________________________•________________________- shows divergence distances between taxa.Cladistics•Cladistics- a method of _______________________ organisms on the basis of________________________ characters.–Characters- ____________________, chemical, developmental, and ____________________.•Homologous characters- _____________________ of different species that are similarbecause they were inherited from a ____________________ ____________________.–Outgroup- a closely related taxon ______________________ the group that is being analyzed.–____________________- the branching point on a tree.Molecular Characters (Data)Endosymbiotic Theory and the Evolution of Chloroplasts•Photosynthetic eukaryotes and their ____________________ ____________________ from the____________________ of a ____________________ by a ____________________.–A phagocytotic protozoan took up a cyanobacterium into a food vesicle.–Instead of being digested, the cyanobacterium was retained as an endosymbiont.–The protozoan provided the alga with protection, a stable environment, and mineral nutrients.–The cyanobacterium produced carbohydrates for the protozoan.–The cell wall of the cyanobacterium was lost through evolutionary selection.–Food vesicle membrane= outer chloroplast membrane.–Plasma membrane of cyanobacterium= inner chloroplast membrane.23

Support for the Endosymbiotic Theory•Chloroplasts are about the ____________________ ____________________ as cyanobacteria.•Evolve ____________________ in photosynthesis.•__________S ribosomes.•_________________________ is the primary photosynthetic pigment in cyanobacteria and plants.•Circular prokaryotic DNA without histones.•__________________________Endosymbiosis in _________________________ and _________________________The current plant classification suggests that red algae are __________________________.24

Biology 3- General BotanyHartnell CollegeDr. Jeffery HugheyCladisticsThis laboratory provides a brief introduction to the philosophy, methodology, and implications ofcladistic analysis. Cladistics is a method of organizing organisms on the basis of synapomorphiccharacters.Cladistics is a method used to hypothesize relationships among organisms. Like other methods, it has itsown set of assumptions, procedures, and limitations. The idea behind cladistics is that members of agroup share a common evolutionary history, and are "closely related", more so to members of the samegroup, than to other organisms. These groups are recognized by sharing unique features (anatomical,chemical, molecular traits) which were not present in distant ancestors. These shared derivedcharacteristics (traits) are called synapomorphies.Note that it is not enough for organisms to share characteristics; in fact two organisms may share a greatmany characteristics and not be considered members of the same group. For example, consider ajellyfish, starfish, and a human; which two are most closely related? The jellyfish and starfish live in thewater, have radial symmetry, and are invertebrates, so you might guess that they belong together in agroup. This would be incorrect because this arrangement does not reflect evolutionary relationships. Thestarfish and human are deuterostomes (they have radial, indeterminate cleavage) and coelomates (theyhave true coeloms). Jellyfish are cnidarians.It is not just the presence of shared characteristics that is important, but the presence of shared derivedcharacteristics. In the example above, all three characteristics are believed to have been present in thecommon ancestor of all animals, and so are trivial in determining relationships, since all three organismsin question belong to the group "animals." While humans are different from the other two organisms,they differ only in characteristics which arose newly in an ancestor which is not shared with the othertwo. As you shall see, choosing the right characters is one of the most important steps in a cladisticanalysis.There are three basic assumptions in cladistics:1. Groups of organisms are related by descent from a common ancestor (= organism at node).2. There is a bifurcating pattern of cladogenesis.3. Change in characteristics occurs in lineages over time.25

The first assumption is a general assumption made for all evolutionary biology. It suggests life arose onearth only once, and therefore all organisms are related. We can take any collection of organisms anddetermine a pattern of relationships, provided we have the right kind of information. Again, theassumption states that all the diversity of life on earth has been produced through the reproduction ofexisting organisms.The second assumption is perhaps the most controversial; that is, that new kinds of organisms may arisewhen existing species or populations divide into exactly two groups. There are many biologists who holdthat multiple new lineages can arise from a single originating population at the same time, or near enoughin time to be indistinguishable from such an event. The other objection raised against this assumption isthe possibility of hybridization (interbreeding) between distinct groups. This, however, is a generalproblem of reconstructing evolutionary history, and although it cannot currently be handled well bycladistic methods, no other system has yet been devised which accounts for it.The third assumption that characteristics of organisms change over time is the most important assumptionin cladistics. When characteristics change we are able to recognize different lineages or groups. Theconvention is to call the "original" state of the characteristic plesiomorphic and the "changed" stateapomorphic. The terms "primitive" and "derived" have also been used for these states.HOW TO CONSTRUCT CLADOGRAMSImagine four species, A, B, C, and D. These four species are related to each other, but we are not surehow. Perhaps A and B are more closely related to each other than A and C, A and D, B and C, B and D,or C and D. Maybe all four are equally related.26

Outline of the steps necessary for completing a cladistic analysis.1. List the taxa. The taxa (species) in this example will be A, B, C, and D.2. Determine the characters. Chlorophyll A, Starch stored in the chloroplasts, and roots.3. Determine the character states for your taxa. Construct a data matrix, like the one shown below.CharactersTaxon Chlorophyll A Starch in chloroplast RootsA - - -B + - -C + + -D + + ++ indicates presence of a trait- indicates absence of a trait4. Determine the polarity of characters (whether each character state is original or derived in each taxon).The best technique for determining polarity is to use an outgroup (which in this example is taxon A).5. Group taxa by synapomorphies (shared derived characteristics) not plesiomorphies (original or"primitive" characteristics) or autapomorphies (traits unique to a single taxon).6. Work out conflicts that arise by some clearly stated method, usually parsimony (minimizing thenumber of conflicts).27

Construct a cladogram given the following morphological data:CharactersTaxon Xylem/Phloem Wood Seeds FlowersMosses - - - -Ferns + - - -Gymnosperms + + + -Angiosperms + + + ++ indicates presence of a trait- indicates absence of a traitConstruct a cladogram given the following DNA sequences:CharactersTaxon 1 2 3 4 5 6 7 8 9 10A A T T G C C C G T AB A A T C C G C C T AC A T T G C C C G T AD A T T G C C C C T AOutgroup A A T C C G C C T A28

Construct a cladogram given the following data:CharactersTaxon Vessel Elements Motile Sperm Pollen Tube 2nd FertilizationCycads - + - -Ginkgos - + - -Conifers - - + -Gnetophytes + - + +Angiosperms + - + +Construct a cladogram given the following distance matrix. Use Taxon 3 as your outgroup:Taxon1 Taxon2 Taxon3 Taxon4 Taxon5Taxon1 0.00000Taxon2 0.01045 0.00000Taxon3 0.12744 0.06768 0.00000Taxon4 0.09867 0.08679 0.00401 0.00000Taxon5 0.00498 0.00978 0.09542 0.09392 0.00000PAUP (Phylogenetic Analysis Using Parsimony) is the most widely used software package for theinference of evolutionary trees.An example of the data matrix in Nexus format#NEXUS[angiosperm evolution]begin taxa;dimensions ntax=6;taxlabelsANCEST cycads ginkgos conifers gnetophytes angiosperms;end;begin characters;dimensions nchar=4;format symbols = "+-";matrixANCEST ----cycads -+--ginkgos -+--conifers --+gnetophytes+-++angiosperms +-++;end;29

Search Methods1. Maximum likelihood evaluates a hypothesis about evolutionary history in terms of the probability thatthe proposed model and the hypothesized history would give rise to the observed data set. Thesupposition is that a history with a higher probability of reaching the observed state is preferred to ahistory with a lower probability. The method searches for the tree with the highest probability orlikelihood.2. Bayesian analysis attempts to assess the probability of a model, bipartition or range of a parametervalue, which is in contrast to ML, which assesses the probability of the data given a model. Under someconditions the biased sampling of tree and parameter space converges on the posterior probability. Theapproach most often used in recent months is Markov Chain Monte Carlo (MCMC) sampling.3. Maximum parsimony is character-based and uses information itself rather than distance information.The information content used by this method is not necessarily larger than for the distance matrixmethods, since there are only a limited number of informative (synapomorphic) sites. Calculates for allpossible trees the tree that represents the minimum number of substitutions at each informative site. Doesnot assume an evolutionary model.4. Distance matrix uses distance values and a sequential clustering algorithm. This method of treeconstruction is sensitive to differences in branch length or unequal rates of evolution. Therefore, it shouldonly be used with closely related taxa, or when there is constancy of evolutionary rate. The method isoften used in combination with isoenzyme or restriction site data or with morphological criteria. Itassumes an evolutionary model.Definitions of Cladistic TermsAncestor -- Any organism, population, or species from which some other organism, population, or speciesis descended by reproduction.Basal group -- The earliest diverging group within a clade.Character -- Heritable trait possessed by an organism; characters are usually described in terms of theirstates, for example: "xylem present" vs. "xylem absent," where "xylem " is the character, and "present" (=+) and "absent" (=-) are its states.Clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor ofall of its members and all of the descendants of that most recent common ancestor. From the Greek word"klados", meaning branch or twig.Cladogram -- A diagram, resulting from a cladistic analysis, which depicts a hypothetical branchingsequence of lineages leading to the taxa under consideration. The points of branching within a cladogramare called nodes. All taxa occur at the endpoints of the cladogram.Derived -- A character to have arisen later in the evolution of the clade. For example, "presence ofChlorophyll B" is a primitive character state for all angiosperms, whereas the "presence of flowers" is aderived state.Evolutionary tree -- A diagram which depicts the hypothetical phylogeny of the taxa under consideration.The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminalpoints of the cladogram.30

Homology -- Two structures are considered homologous when they are inherited from a common ancestorwhich possessed the structure.Ingroup -- In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to eachother than any are to the outgroup.Lineage -- Any continuous line of descent; any series of organisms connected by reproduction by parentof offspring.Monophyletic -- Term applied to a group of organisms which includes the most recent common ancestorof all of its members and all of the descendants of that most recent common ancestor. A monophyleticgroup is called a clade.Outgroup -- In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which ishypothesized to be less closely related to each of the taxa under consideration than any are to each other.Parsimony -- Refers to a rule used to choose among possible cladograms, which states that the cladogramimplying the least number of changes in character states is the best.Phylogenetics -- Field of biology that deals with the relationships between organisms.Phylogeny -- The evolutionary relationships among organisms; the patterns of lineage branchingproduced by the true evolutionary history of the organisms being considered.Plesiomorphy -- A primitive character state for the taxa under consideration.Polarity of characters -- The states of characters used in a cladistic analysis, either original or derived.Original characters are those acquired by an ancestor deeper in the phylogeny than the most recentcommon ancestor of the taxa under consideration. Derived characters are those acquired by the mostrecent common ancestor of the taxa under consideration.Polyphyletic -- Term applied to a group of organisms which does not include the most recent commonancestor of those organisms; the ancestor does not possess the character shared by members of the group.Primitive -- Describes a character state that is present in the common ancestor of a clade. A primitivecharacter state is inferred to be the original condition of that character within the clade underconsideration.Sister group -- The two clades resulting from the splitting of a single lineage.Synapomorphy -- A character which is derived, and because it is shared by the taxa under consideration,is used to infer common ancestry.31

Group the following plant species into clades based on the parsimony method.Outgroups:32

Photosynthetic Prokaryotes- Chapter 13•Kingdom- Bacteria–Phylum- ____________________________Cyanobacteria- Gram ____________________________ Bacteria•Gram positive- peptidoglycan layer; stains with crystal violet.•Gram negative- peptidoglycan layer sandwiched by ____________________________ and__________________ layers; does not stain with __________________ __________________.Cyanobacteria•Characteristics–Chlorophyll _________–___________________________–Thylakoids occur __________________–70s ribosomes–DNA microfibrils __________________–Polyhedral bodies–____________ __________________–Habitat- __________________.–Examples- __________________, Nostoc, __________________, __________________,Synechococcus, Synechocystis.Habits•Unicells–__________________ - Synechocystis–__________________ of unicells- Aphanothece•Rows of cells–__________________ filaments w/out sheath (trichome)- Oscillatoria33

–Many __________________ in 1 large sheath- Microcoleus–__________________ filaments with sheath- Lyngbya–__________________ branched filaments- Mastigocladus–__________________ branched filaments- Stigonema–__________________ -branched filaments- ScytonemaAsexual Reproduction•__________________ - internal division of the protoplast results in a mass of spores.•__________________ - filament breaks into 2 parts, each of which forms a new thallus.•__________________ - short sections of a trichome detach and form a new thallus.•__________________ - resting spores; cells that are resistant to unfavorable conditions.•__________________ - division of a single-celled individual into two new single-celled individuals.Heterocyst•Heterocyst- a __________________ -walled large cell that __________________ atmospheric__________________ (diazotroph).–Photosynthetically inactive.–Their formation is __________________ related to nitrogen concentration.–__________________ - cytoplasmic connections that transfer metabolites and ammonium.Movement in the Cyanobacteria•__________________ - active movement of an organism in contact with a solid substrate.–Mechanism- mucilaginous layer of microfibrils generates waves.•__________________ - active movement of an organism without contact with a substrate.–Mechanism- unknown.•Why?–Positively phototactic- ____________________________________.–Positively chemotactic- ___________________________________.34

Symbiotic Associations•__________________ - cyanobacteria occur in about 8% of the species.•__________________ - the water fern; contains Anabaena in the dorsal lobe of its leaf.•Colonial ascidian- sea squirt.•Amoeba, protozoa, diatoms, green algae, mosses, liverworts, water molds, and __________________.Prochlorophyceae•Characteristics–Chlorophylls _________ & __________–_________ phycobilisomes–Thylakoids in stacks of ______–DNA microfibrils ________________________–Habitat•1) Obligate symbionts, live within ____________ ______________; 2) Planktonicfilaments in ___________________ lakes.–Example- ________________________Stromatolites•Stromatolite- _____________ -like deposition of __________________ and trapped__________________; formed by __________________ and diatoms.•Age- ____________ ____________.•________________-__________________-growth-deposition.•_______-shaped in growth= ______ year.•________________, Bahamas, _________________.Cyanobacteria Produce Cyanotoxins•_______________________- alkaloids that target the nervous system.–Anatoxin and saxitoxin.–_________________- staggering, muscle twitching, gasping, and convulsions.–Anabaena, Aphanizomenon, Oscillatoria.•_______________________- large compounds that target the liver.–Microcystins and nodularins.–_________________- weakness, vomiting, diarrhea.–Anabaena, Microcystis, Oscillatoria, Nodularia, Nostoc.35

Fungi- Chapter 14Fungi•Eukaryotic•_________________________ and ______________________________•Most are composed of _________________________ (fungal filaments)•Nuclei occur in continuous _________________________•Heterotrophic ____________________________•Cell wall _________________________ and predominantly made of _________________________•Reproduction is _________________________ and sexual•Life cycles are _____________________________•Numbers- ~__________________ species described•Habitat- ubiquitous, but _________________________ _________________________•Size- ________________scopic and _________________scopic.•Storage product- _________________________Phylum Cryptomycota•_________________________•__________________ chitin.•~1000 species•Habitat- __________________, __________________, and __________________.•Example- _________________________.Phylum Chytridiomycota•_________________________•~__________________ species.•Habitat–Soil from desert, ditches, and banks of ______________ and streams, rumen of large mammals.•Motile ________________________ and ______________________ with a single whiplash flagellum.•Example- _________________________.•Sexual reproduction involves the formation of a _________________________.•Asexual by zoospores.Life Histories36

Allomyces life historyPhylum Microsporidia•Spore forming ________cellular ____________________________________.•~__________________ species.•Lack _____________________, ______________________, and peroxisomes.•Reproduce by forming _________________ that shoot ________________________ into host cells.37

•Example- _________________________.Phylum Glomeromycota•Arbuscular _________________________________.•~_____________ species so far.•Occur in about ______% of vascular plants•_________________________, ____________________________.•Asexual, large __________________________________________•Example- _________________________.Phylum Zygomycota•Aseptate•~_________________________ species.•Habitat–Plant and animal tissue in soil, some are ___________ on plants, insects, and small soil animals.•_________________________.•Example- _________________________ stolonifer (common _________________________ mold).•Sexual reproduction involves the formation of a _________________________.•Asexual by nonmotile spores.Rhizopus life history38

Phylum Ascomycota•_________________________•~32,000 species.•Habitat–________________________, ________________________, plant _____________________.•_________________________.•Examples- Neurospora (powdery mildew), Morchella (morel), Saccharomyces (yeast).•Sexual reproduction involves the formation of ___________ on an _________________________.•Asexual by budding, _________________________, _________________________.Phylum Basidiomycota•_________________________•~22,000 species.•Habitat–_________________________ litter.•_________________________.•Examples- _________________________ (mushroom), Puccinia (rusts), Ustilago (smuts).•Sexual reproduction involves the formation of __________________ on an ____________________.•Asexual by budding, conidiospores, fragmentation.Gilled mushroom life history39

Lichens•___________________biont and ___________________biont.•Mycobiont= part Ascomycota & Basidiomycota.•~13,000 species.•Habitat–From the desert to the poles.•___________________.•Examples- Caloplaca (________________), Parmelia (_______________), Usnea (________________).•Reproduction is by ___________________.40

Kingdom ‘Protista’ Part 1- Chapter 15Heterotrophic Phyla•Oomycota- ________________________________________________.•Myxomycota- _____________________________________________.•Dictyosteliomycota- ________________________________________.Oomycota- water molds•Characteristics–__________cellular, __________________________ and filamentous.–_____________________________ and parasitic.–Food reserve- __________________________.–________karyotic nucleus.–Zoospores- 1 __________________________ and 1 __________________________.–Cell wall __________________________/cellulose-like.•Habitat- marine, freshwater, terrestrial.•_____________ species.•Examples- __________________________ and __________________________.Saprolegnia life historyPhytophthora- sudden ____________ disease, Ireland ____________ famine, crop destruction.41

Myxomycota- plasmodial slime molds•Characteristics–Streaming ______________________________.–Saprophytic and _______________ bacteria, yeast, fungal spores.–Food reserve- __________________________.–_______karyotic nucleus.–Gametes- 2 unequal, apical, __________________________.–_____________ cell wall.•Habitat- __________________________.•700 species.•Examples- __________________________.Physarum life cycleDictyosteliomycota- cellular slime molds•Characteristics–______________-like cells that form ________________.–__________________________ bacteria.–Food reserve- __________________________.–______karyotic nucleus.–Flagella- __________________________.–Cell wall __________________________.•Habitat- terrestrial.•50 species.•Examples- __________________________.Dictyostelium- cellular slime moldDictyostelium42

Photosynthetic Phyla (the algae)•Myzozoa- __________________________.•Euglenozoa- __________________________.•Cryptophyta- __________________________.•Haptophyta- __________________________.•Chlorophyta- __________________________ algae.•Rhodophyta- __________________________ algae.•Heterokontophyta- heterokont algae.–Phaeophyceae- __________________________ algae.–Chrysophyceae- __________________-________________algae.–Bacillariophyceae- __________________________.Myzozoa- dinoflagellates•Characteristics–__________________________, colonial.–Chlorophylls ____ and _____, __________________________.–Food reserve- __________________________ in cytoplasm.–Thylakoids in ________.–___________karyotic nucleus.–Flagella- 1 __________________________ and 1 __________________________.–Cell wall with __________________________ in thecal plates.•Habitat- marine and freshwater.•4,000 species.•Examples- __________________________, __________________________, Dinophysis,__________________________, Pfiesteria.Euglenozoa- euglenoids•Characteristics–__________________________.–Chlorophylls _______ and _______, __________________________.–Food reserve- __________________________ in cytoplasm.–Thylakoids _______-3.–____________karyotic nucleus.–2 unequal flagella, long one with ______________.–No cell wall, ________________________ __________________________.–__________________________.•Habitat- marine and __________________________; puddles, ditches, ponds, streams, lakes, rivers.•1,000 species.•Example- __________________________.43

Kingdom ‘Protista’ Part 2- Chapter 15Cryptophyta- cryptomonads•Characteristics–_________cellular.–Chlorophylls A & C, ______________________.–Food reserve- _________________ within 2 chloroplast membranes.–Thylakoids in _________.–Eukaryotic nucleus.–2 flagella, ________________________________________ (dbl. & single).–______________________________, proteinaceous periplast plates.•Habitat- marine & freshwater.•200 species.•Examples- _____________________________.Haptophyta- haptophytes•Characteristics–Unicellular.–Chlorophylls A & C, _____________________________.–Food reserve- ____________________________ in vesicles.–Thylakoids in 3.–Eukaryotic nucleus.–2 whiplash flagella and 1 _____________________________.–_________________________, covered with scales of cellulose or calcium carbonate.•Habitat- marine & freshwater.•300 species.•Examples- _____________________________ & Phaeocystis.Chlorophyta- green algae•Characteristics–_________cellular and ____________________cellular.–Chlorophylls A & ________, carotenoids.–Food reserve- ____________________ in chloroplast.–Thylakoids in 3-6.–Eukaryotic nucleus.–Highly variable; _____, _____, _____, _______________-flagellated; whiplash when present.–Cell wall cellulosic.•Habitat- marine & _________________________.•17,000 species.•Examples- Ulva, _________________, Chlorella, Volvox, Chara, ____________________, Closterium.44

Ulva life historyCharales- ColeochaeteRhodophyta- red algae•Characteristics–__________________cellular.–Chlorophylls A & _________, phycobilins.–Food reserve- __________________ __________________in cytoplasm.–Thylakoids occur __________________.–Eukaryotic nucleus.–___________ flagella.–____________________________________.–Cell wall with cellulose & galactans.•Habitat- __________________& freshwater.•6,000 species.•Examples- Polysiphonia, __________________, Batrachospermum, __________________.45

Heterokontophyta- heterokontsPhaeophyceae- __________________ algae•Characteristics–__________________cellular.–Chlorophylls A & C, _______________________________.–Food reserve- mannitol & laminarin in __________________.–Thylakoids in 3.–Eukaryotic nucleus.–2 flagella, 1 tinsel & 1 whiplash.–Cell wall cellulosic with _______________________________.•Habitat- __________________.•2,000 species.•Examples- Fucus, __________________, Laminaria, Nereocystis, Ectocarpus, __________________.Laminaria life history46

Chrysophyceae- golden-brown algae•Characteristics–_________cellular, colonial.–Chlorophylls A & C, __________________________.–Food reserve- chrysolaminarin in _________________________.–Thylakoids in 3.–Eukaryotic nucleus.–Most= 2 flagella, 1 tinsel & 1 whiplash.–Cell wall cellulosic, silica, or none.•Habitat- marine and __________________.•1,000 species.•Examples- Dinobryon, _______________________.Bacillariophyceae- _______________________•Characteristics–__________cellular, ___________________________.–Chlorophylls A & C, ______________________.–Food reserve- chrysolaminarin in __________________.–Thylakoids in 3.–Eukaryotic nucleus.–No flagella, __________ 1 tinsel on male gamete.–Cell wall is silica and made of _____ ________________________.•Habitat- ______________________ and freshwater.•100,000 species.•Examples- Acnanthes, Bacillaria, Licmophora, ____________________, _______________________.Frustule Morphology47

Bryophytes- Chapter 16•What is the name of the group we are studying today and tomorrow?–A) flowering plants–B) fungi–C) bacteria–D) mosses–E) don’t care, where are the snacks?•True or false._______ Bryophytes are plants._______ Bryophytes grow only in the water, but not on land.•Which of the following is not true of plants?–A) they are mostly autotrophic–B) they are primarily terrestrial–C) they have the same photosynthetic pigments as brown and red algae–D) they are multicellular–E) still don’t care, where is the popcorn?Kingdom Plantae- ________________________________•___________________trophic (mostly).•________________________________ with advanced tissue differentiation.•________________________________ alternation of generations, where the–Diploid phase (_________________phyte) includes an embryo.–Haploid phase (_________________phyte) produces gametes by mitosis.•Chlorophylls _____ & ______, carotenoids.•Starch stored inside chloroplasts.•Habitat- primarily ________________________________.•________________________________present.•Male and female gametangia present.•Photosynthetic tissues produced by an _________________________ meristem.•Sporangia with a __________________ __________________ .•_________________________ present.•~330,000 species.•True or false._______ ‘Bryo’ is greek for moss._______ Liverworts and hornworts are bryophytes._______ The moss sporophyte is nutritionally dependent on the female gametophyte._______ Water is not required for fertilization in mosses.48

Bryophytes•Bryo- gr. _________________________.•Liverworts, hornworts, and mosses.•_________________________ dominant.•Sporophyte matrotrophic and _____________ _______________ (6-16 weeks).•_________________________ required for fertilization.•Sexual reproduction involves _________________________ and _________________________.•Biflagellated sperm.•Asexual reproduction by _________________________ and _________________________.•Plasmodesmata present.•Rhizoids in most.•_________________________ in most (not the hornworts).•_________________________ or stomata-like structures present.•~16,000 species.•True or false._______ Liverworts because they are shaped like a liver and look glandular were used to treat liverdisease in earlier times._______ The specimen marked ‘A’ is a leafy liverwort and the one marked ‘B’ a thalloid liverwort.Marchantiophyta- ________________________________•Sporophytes _________________________ stomata, but have pores.•Specialized conducting tissue _________________________.•Gametophytes thalloid or leafy.•Rhizoids _________________________ celled.•_________________________ of all living plants.•Sporangium with _________________________ capsule, elaters present in some to disperse spores.•Most cells contain _________________________ chloroplasts.•Habitat- _________________________, some aquatic, temperate and tropical.•6,000 species.•Examples- Marchantia and _________________________.Marchantia AntheridiaMarchantia Archegonia•True or false._______ Below you can see male gametophytes.49

Life history of MarchantiaAnthocerotophyta- ________________________________•Antho- gr. _________________________, keras- gr. _________________________.•Sporophytes _________________________ stomata.•Specialized conducting tissue _________________________.•Gametophytes _________________________.•Rhizoids _________________________ celled.•Sporangia dehisce to disperse spores, elater-like structures present.•Most cells contain a _________________________ chloroplast.•Sporophyte with basal intercalary _________________________.•Habitat- moist temperate and tropical.•100 species.•Example- _________________________50

•Hornwort sporophytes _____________________.–A) are nutritionally dependent on the female gametophyte–B) are primarily terrestrial–C) lack stomata–D) contain a sporangium–E) all of the above•True or false._______ Anthoceros is an example of a true moss (Phylum Bryophyta)._______ Hornwort gametophytes are thalloid.Bryophyta- ________________________________•Sporophytes _________________________ stomata.•Specialized conducting tissue- _____________________ and nonlignified _______________________.•Gametophytes _________________________.•Rhizoids _________________________.•Sporangia with dehiscent capsules.•Most cells with _________________________ chloroplasts.•Habitat- _________________________ and _______________, temperate and tropical, some aquatic.•9,500 species.•Example- Polytrichum, Sphagnum, _________________________.3 Moss Classes•Bryidae- _________________________ mosses, Polytrichum.–Protonema with a _________________________ of cells with slanted cross walls.–Leafy gametophytes develop from minute budlike structures.•Sphagnidae- _________________________ mosses, Sphagnum.–Protonema with _________________________ of cells that is one layer thick.–Gametophytes with clusters of branches, 5 per node.–_________________________ capsular operculum.•Andreaeidae- _________________________ mosses, Andreaea.–Protonema with _________________________ of cells.–Capsule dehisces by splitting in four.–Rhizoids occur in 2 rows.–_________________________ or _________________________ regions on ___________.51

Moss life history•Moss sporophytes _______________________.–A) are nutritionally dependent on the female gametophyte–B) are aquatic and terrestrial–C) have multicellular rhizoids–D) include Polytrichum, Sphagnum, and Mnium–E) all of the above•True or false._______ Moss sporophytes contain stomata._______ Moss gametophytes are thalloid and leafy.52

Seedless Vascular Plants- Chapter 17•True or False.–Nonvascular plants include the algae and bryophytes.–Vascular plants include lycophytes, ferns, gymnosperms, and flowering plants.–Xylem and phloem are the names of musical instruments from Istanbul.Vascular Tissue System•_____________________- plant tissue that conducts water and minerals.–Tracheary elements•___________________________•___________________________ ___________________________•_____________________- plant tissue that conducts food (mainly ___________________________).–___________________________elementsVascular Plant Terminology #1•Leaves- photosynthetic, principal ______________________ ______________________ of the stem.–______________________- small leaves that contain a single strand of vascular tissue.–______________________- large leaves that contain multiple strands of vascular tissue.Vascular Plant Terminology #2•Homosporous- production of one type of spore from _____________ kind of sporangium.•Heterosporous- production of two types of spores from _____________ different kinds of sporangia.Vascular Plant Terminology #3•____________________________- a modified leaf that bears sporangia.–____________________________- a structure that produces spores.Vascular Plant Terminology #4•____________________________- a modified leaf that bears microsporangia.–Microsporangia- a ____________________________________________________________.•____________________________- a modified leaf that bears megasporangia.–Megasporangia- a sporangium that produces ____________________________.Vascular Plant Terminology #5•_____________- a reproductive structure consisting of nonphotosynthetic sporophylls; a ____________.–____________________________- a microsporangiate cone.–____________________________- a megasporangiate cone.______________________________Seedless Vascular Plants•Representatives (425-370 MYA)–______________________________–______________________________–______________________________53

______________________________Seedless Vascular Plants•Phyla (Living today)–______________________________- club mosses, resurrection plant, quillworts.–______________________________- ferns and the fern allies (whisk ferns and horsetails).Lycopodiophyta- lycophytes•Lykos- gr. ______________________________, pous- gr. ______________________________.•______________________________present.•Plants + or - ______________________________ branched.•Sporangia on or in the _________________________ of sporophylls on strobili.•________________sporous & ________________sporous.•Distribution- global.•Habitat- ________________________________, deserts, aquatic.•~1,200 species.•Examples- Lycopodium, _______________________, __________________________.Lycopodium (Lycopodiaceae) life history54

Selaginella- the resurrection plant (Selaginellaceae) is _______________________sporous.Isoetes- the quillwort (Isoetaceae) is ________________________________sporous.•Match spore type on the right to lycophyte family on the left.1. Lycopodiaceae (Lycopodium) a. Homosporous2. Selaginellaceae (Selaginella) b. Heterosporous3. Isoetaceae (Isoetes)55

Monilophyta- ferns and fern allies.•Monilo- gr. _______________________________.•Leaves- ________________phylls, scalelike, & ________________phyll-like.•________________branching patterns.•Sporangia in ________________, lateral, or on sporangiophores in strobili.•Heterosporous & homosporous.•Distribution- global, ___________________.•Habitat- all habitats, > species in ________________.•~11,000 species.•Examples- Polypodium, ____________________, _____________________.Spore development- two types___________________________-___________________________-Class PsilotopsidaOrder Psilotales- ______________________________.•Psilos- gr. ________________.•Leaves- __________________-like or _______________________-like.•Eusporangiate.•Sporangia lateral.•______________________________________________branched.•Homosporous.•_____________ roots, but they have aerial stems.•Distribution- ________________ & subtropical.–Alabama, ________________________________, Florida, Louisiana.•Habitat- epiphytic or on rich soils.•Example- ___________________ (2 spp.), and ________________________ (13 spp.).TmesipterisClass PsilotopsidaOrder Ophioglossales- _____________________.•Ophio- gr. ___________________. Gloss- gr. _______________________.•Leaves- ________________ phylls.•_____________________________ in 2 rows.•Sporangia on ___________________________ or ________________________.•________________________ or __ branched.•___________________________•Roots, stems, and leaves.•Distribution- tropical and _______________________.•Habitat- epiphytic or ___________________________.56

•~____________ species.•Examples- ______________________and _________________________.Class MarattiopsidaMarattio- gr. ____________________________.•Leaves- ________________ phylls, complex, pinnately branched.•Sporangia __________sporangiate, __________________________.•Sporangia on ___________________________ of ________________________.•Distribution- tropical and _______________________.•Habitat- epiphytic and ___________________________.•~____________ species.•Example- _______________________.Class Polypodiosida- ferns•Poly- L. ___________________. podio- gr. ______________________.•Leaves- ________________phylls, fronds.•Sporangia ________________sporangiate, homosporous and heterosporous.•Sporangia usually in ____________________.•______________________________ branching, but not dichotomous.•Roots, stems, and _______________________.•Distribution- global, ___________________.•Habitat- all habitats, > species in ________________.•~_______________________ species.•Examples- Polypodium.Polypodium life history57

Class Equisetopsida- horsetails•Equus- L. ______________________, saeta- L. ______________________.•Leaves- microphyll-like, scaly.•Homosporous.•Sporangia on sporangiophores in a strobilus.•______________________ leaves, but not dichotomous.•Roots and stems (ribbed and jointed).•Distribution- global.•Habitat- along streams in moist sites.•~___________ species.•Example- ______________________.Equisetum life history58

Gymnosperms- Chapter 18Naked versus Enclosed Seed Plants•Gymnosperms–Gymno- gr. ________________________.–Sperma- gr. ________________________.•Angiosperms–Angeion- gr. ________________________.–___________________- gr. seed.Extant Gymnosperms•Match the common name on the right to the phylum on the left.–1) Cycadophyta a. ginkgo–2) Ginkgophyta b. conifers–3) Coniferophyta c. cycads–4) Gnetophyta d. gnetophytesCycadophyta•Cycas- gr. ________________________.•________________________, but ____________ vessel elements.•Sperm present, ________________________.•________________________ leaves.•Pollen tube ________________________ with the egg cell.•Ovulate (megasporangiate) & microsporangiate cones simple & on _________________ plants.•11 genera & 140 species.•Examples- ________________________ & ________________________.Ginkgophyta•Yin- ch. ________________________, hing- ch. ________________________.•________________________, but _____________ vessel elements.•Sperm present, ________________________.•________________________ leaves.•Pollen tube ________________________ with the egg cell.•Ovulate & microsporangiate cones on __________________ plants; ____________________ seeds.•____ genus & _______ species.•Examples- ________________________ = maidenhair tree.Coniferophyta•Con- gr. ________________________, fer- L. ________________________.•________________________, but no vessel elements.•________________________________________________.•________________________ like or ________________________ like leaves.•Pollen tube ________________________ with egg cell.59

•Ovulate & microsporangiate cones on ________________________ plant; ovulate cones compound.•70 genera & 630 species.•Examples- ________________________, Picea, ________________________, Abies, Cupressus.Pinus- pine (Pinaceae), life history.60

Metasequoia- ________________________________________________.Wollemia nobilis- ________________________________________________.Gnetophyta•Gneto- Malay gnenom.•________________________ and ________________________ elements.•Sperm ________________________ motile.•Scalelike, leaflike, broad and ________________________ leaves.•Pollen tube ________________________ with egg cell.•Ovulate & microsporangiate cones compound & mostly borne on separate plants.•3 genera & 70 species.•Examples- ________________________, ________________________, Welwitschia.GnetumEphedra________________________61

Introduction to the Angiosperms- Chapter 19Angiosperms- Anthophyta•_______________________________, but parasitic and saprophytic representatives.•Enclosure of ovules within _______________________________.•Ovule- the structure in seed plants that contains the _______________________________, with__________________ cell; including nucellus and integuments.•Presence of _______________________________ in seeds.•Flower present with _________________ (microsporophylls) & ___________ _____(megasporophylls).•Species- 300,000-450,000Class Monocotyledonae- _______________________________•Flower parts- __________s.•Pollen- ____________________aperturate.•Cotyledons- _________________.•Leaf venation- _______________________________.•1° vascular bundles in stem- _______________________________.•2° growth _______________________________ vascular cambium.•Examples- ____________________, lilies, irises, _______________________________, cattails, palms.Class Eudicotyledonae- _______________________________•Flower parts- __________s & ___________s.•Pollen- ___________aperturate.•Cotyledons- _____________.•Leaf venation- _______________________________.•1° vascular bundles in stem- _______________________________.•2° growth _____________________ vascular cambium.•Examples- _____________________, _____________________, _____________________.Flower AnatomySepals-Petals-Pedicel-Stigma-Style-Ovary-Receptacle-Anther and filament-62

Ovary Position•_____________________ - whorls attached below the ovary.•_____________________ - stamens and petals adnate to the calyx, forming a tube (hypanthium) at thebase of the ovary.•_____________________ - whorls attached above the ovary.Epigyny in Malus (apple) flowerMature Anther with 4 MicrosporangiaMature Embryo Sac- 8 nuclei, 7 celled structureDouble Fertilization63

Glycine- soybean lifecycle._____________________- tissue that contains stored food that is digested by the sporophyte beforeor after maturation of the seed.64

Evolution of Angiosperms- Chapter 20Rafflesia arnoldii•Flower- the reproductive structure of angiosperms; a __________________ shoot that bears sporophylls.Evolutionary Trends Among Flowers•Flowers have gone from __________ indefinite parts to having ______ parts that are definite in number.•Floral __________________ have ____________________ over time.•Floral parts have become ____________________.•Floral ____________________ has become __________________________________.•Carpels have gone from ____________________ and incompletely closed to pistil-shaped and sealed.•Ovary has gone from ____________________ to ____________________.•Perianth has gone from having indistinct sepals and petals to having a distinct calyx and corolla.•Flowers have gone from ____________________ (actinomorphic) to ____________________(zygomorphic) symmetry.Floral Evolution•____________________ and ____________________ have coevolved.–Coevolution- the ____________________ ____________________ of adaptations in 2 or moreinteracting populations.•Insect pollination is ____________________ efficient than passive pollination.•____________________, flies, ____________________.•____________________ are the most important group of visiting insects.Bird and bat-pollinated flowers•Produce copious ____________________.•Usually bright ____________________ and ____________________ in color.–Birds have a good sense of color.•Flowers usually have very ____________________ ____________________.–Smell not developed in birds.Flavonoids•________ soluble phenolic compounds with two six-carbon rings linked by a three-carbon unit.•Occur in the ______________________ of plant cells.•The most important pigments in floral coloration are the _____________________ (red, violet, andblue) and the _____________________________.Wind pollinated flowers ____________________ produce nectar._______________________________•Water soluble _________________ compounds with two six-carbon rings linked by a three-carbon unit.•Occur in the ____________________ of plant cells.•The most important pigments in floral coloration are the ____________________ (red, violet, and blue)and the ____________________.65

Asteraceae and Orchidaceae•Asteraceae–____________________ have flowers closely bunched together in a head.•____________________ species.•Ovary with ______________ ovule•____________________ and ____________________ flowers.•Orchidaceae–Orchid flowers are showy and zygomorphic.•____________________ species.•Ovary with ____________________ of ovules.•Cuplike lower petal.Fruit Related Terminology•Fruit- a ________________________________________.•____________________ - the enlarged basal portion of a carpel.•____________________ - the vessel that encloses the ovule/s; forms the gynoecium.•____________________ - the structure that contains the female gametophyte with egg cell, includingthe nucellus and integuments.•____________________ - a mature ovule.•____________________ - chambers in the ovary that contain the ovules.3 types of PlacentationFruit Classification•Fruit derived from ____________________ than 1 pistil–____________________ fruit- develop from a cluster of mature ovaries produced by a clusterof mature flowers.•____________________.–____________________ fruit- develop from several separate carpels of a single flower.66

•Raspberry, strawberry, ______________________________.Simple Fruit Types- fruit derived from ____________ pistil•________________________________________–Berries- fleshy inner layer. Tomatoes, banana, grapes.•____________________ - a berry with a thick, leathery, inseparable rind.Cucurbitaceae.•____________________ - a berry with a thick, leathery, separable rind. Citrus.–____________________ - fleshy hypanthium. Pear, apple.–____________________ - stony endocarp. Peach, cherry, olive.•____________________–____________________ - tissue of the mature ovary wall splits open, freeing the seeds.•Legume- dehisces along 2 sutures.–____________________ - tissue of the mature ovary wall remains sealed with seeds remainingin the fruit.•Nut- hard pericarp, usually one-seeded.•Achene- small. dandelion.Fruits and seeds have evolved in relation to their dispersal agents•Wind-borne fruits & seeds.•_____________________________.•Fleshy for animal dispersal.•Attachment to ________________________________.67

Early Development of the Plant Body- Chapter 22True or False_______ Embryogenesis is the formation of an embryo._______ The developing embryo in angiosperms is photosynthetic.Embryogenesis•Embryogenesis- formation of an embryo.•The first two divisions are ____________________ and establish embryo _______________________.–____________________ - chalazal pole.•Consists of an ______________ _____________ that gives rise to an ___________________________________, which will eventually give rise to the mature embryo.–____________________ - micropylar pole.•Consists of a ____________ _____________ that gives rise to a __________________.•Establishment of polarity fixes the structural axis on which the lateral appendages will be later arranged.Embryo Proper and the Primary Meristems•The embryo proper is tissue that differentiates to form _______ primary meristems.•Primary Meristems–_______________________- forms the epidermis of the plant by periclinal divisions of theouter cells of embryo proper.–______________________- forms the vascular tissue of the plant by vertical divisions.–_____________ _______________- forms the ground tissue of the plant by vertical divisions.68

_______ The apical meristem in angiosperms _______________________________________________.A) is a region of tissue at the tip of shoots and roots that is responsible for programmed cell death.B) is a region of tissue at the tip of shoots and roots that forms new cells.C) coordinates hormone production much like the brain in mammalsD) produces the bark we see on treesE) none of the aboveApical Meristems•Apical Meristem- ____________________________________________________________________.•As the embryo matures new cell formation gradually becomes restricted to the apical meristems.•Shoot Apical Meristem- positioned ________________ the two embryonic leaves in________________ and ________________ in ________________.•_______________________ - embryonic root.Seed Terms•Hypocotyl- _________________________________________________________________________.•Hypocotyl-root axis- an undistinguished radicle.•_______________________- stemlike axis above the cotyledons.•_______________________- the first bud of an embryonic shoot.•_______________________- the fruit wall, which develops from the wall of the ovary.Garden Bean- food is stored in _____________________________.Castor Bean- food is stored in ______________________________.Onion and Maize- food is stored in __________________________._______ Which of the following effects seed germination?A) waterB) oxygenC) light and temperatureD) hormonesE) all of the above69

Seed Germination•Dependent on ____________________________ and ____________________________ factors.–External (____________________________)•Water•Oxygen•Temperature•Light–Internal (____________________________)•Hormones- gibberellins.•____________________________ - cotyledon/s are carried above ground level.•____________________________ - cotyledon/s remain underground.Examples-True or False_______ The onion has an epigeous type of seed germination.70

Cells and Tissues of the Plant Body- Chapter 23Origin of Primary Tissues•Primary growth- formation of ________________________ ________________________.–Primary plant body.Growth and Development•________________________- the sum total of events that lead to the formation of the plant body.•Growth- an ________________________ ________________________ in size.–Cell ________________________–Cell ________________________•____________ _______________- regions of tissue at the tips of shoots and roots that forms new cells.–Meristematic tissue.•Much of the plant undergoes unlimited or prolonged growth of the apical meristems=_______________.Morphogenesis and Differentiation•Morphogenesis- the ________________________________________________.•________________________- a process by which a relatively unspecialized cell undergoes aprogressive change to form a more ________________________ cell.71

Internal Organization of the Plant Body•Tissue- a group of ___________________ ___________ organized into a structural and functional unit.•Tissue System- a tissue or ______________________________________ organized into a structuraland functional unit; larger units of the plant body.•There are ______ Tissue Systems–________________________–________________________–________________________Ground Tissue•__________________________–Polyhedral to round in shape.–Occur throughout the plant body.–Photosynthesis, storage, and secretion.•__________________________–Elongate in shape.–Occur beneath the epidermis in young stems.–Support young growing tissues.•__________________________- fibers and sclereids.–Long or stellate in shape.–Occur throughout the plant body.–Support (strengthen) and storage.Vascular Tissue #1•Xylem- principal __________________________tissue in vascular plants; ______ at maturity; lignified.•Tracheary Elements–__________________________- elongate and tapering; pits, but no perforations; seedlessvascular plants, gymnosperms, and some angiosperms.–__________ ____element- elongate; pits and perforations; angiosperms.72

Vascular Tissue #2•Phloem- principal _______________________ tissue in vascular plants; living at maturity; not lignified.•Gymnosperm Sieve Elements–Sieve cell- elongate & tapering; with sieve areas.–__________________________cell- elongate & tapering; delivers substances to sieve cells.•Angiosperm Sieve Elements–Sieve-tube element- elongate & tapering; with a sieve plate.–__________________________cell- variable; delivers substances to sieve-tube elements.Dermal Tissue•__________________________- outermost cell layer of the _________________________ plant body.–Variable in shape; guard cells and trichomes.–____________________________________________________of plant body.–Protective (cuticle and water loss) and aeration (stomata).•__________________________- __________________________ protective tissues.–Rectangular in shape; cork cells.–__________________________epidermis.–Protective and aeration (lenticels); replaces epidermis.73

The Root: Structure and Development- Chapter 24Roots•Root- the _________________________________________________, normally occurs below ground.•Root Functions–_______________________.–_______________________ of water, minerals, inorganic ions.–_______________________.–_______________________.•Two types of root systems–____________________- a stout, tapering main root from which smaller lateral roots arise;deep; gymnosperms & dicots.–____________________- arise from stem similar to lateral roots; shallow; monocots.Root Penetration•Root depth and distance depend on ______________________:–__________________________–__________________________–__________________________•__________________________- those involved in uptake of water and minerals occur usually in theupper 1 meter of the soil.•Rootcap- a thimble like mass of __________________________ cells that covers the root and__________________________ mucigel.•The __________________________ in young roots absorbs _____________ and _________________.•Root Hairs- ______________ ______________________ of epidermal hairs that facilitate absorption.Primary Development of the Root Tip•Region of cell ___________________–~1 mm in length.–Apical meristem.•Region of cell ___________________–~2 mm in length.–Cells elongate, functional xylem starts to develop and phloem is mature.•Region of ______________________–~2 mm-variable in length.–Root hairs are produced, functional xylem and phloem are present.74

Name the 3 primary meristems scene on this slide: _____________, _____________, _____________Eudicot versus Monocot Roots•Eudicots–Vascular cylinder ________________.–Cortical cells sometimes retained for life, but some shed due to secondary growth.•Monocots–Vascular cylinder in _____________ with _____________________.–Cortical cells retained for life, because they lack secondary growth.Cortex and Vascular CylinderMatch the following cortical and vascular terminology to their definitions.1. Cortex a. 1 or more layers of nonvascular cells surrounding the vascular tissue of the root.2. Vascular cylinder b. empty spaces among cortical cells; essential for aeration of the root cells.3. Pericycle c. a region of the primary wall containing suberin that is impermeable to water and ions.4. Intercellular spaces d. the innermost layer of the cortex.5. Epidermis e. contains xylem, phloem, and pericycle.6. Exodermis f. consists mostly of ground tissue that occupies the greatest area of the root.7. Endodermis g. the outermost layer of cells.8. Casparian Strip h. the outermost layer of the cortex that is one or more cell layers in depth.75

Lateral Roots Arise from the ___________________________Effects of Secondary Growth on the Primary Body of the Root•Secondary Growth in roots consists of:–1) Secondary vascular tissues (secondary xylem and phloem) from ______________________.–2) Periderm, mostly cork tissue from ________________________________.Root Modifications•__________________________- roots produced from aboveground structures.•__________________________- negatively gravitropic roots that aerate the root system.•__________________________- specialized storage organs consisting of parenchyma and vasculartissue. Carrot, sweet potato, sugarbeet.76

The Shoot: Primary Structure and Development- Chapter 25The Shoot•Shoot- the _________________________________________________, consisting of stem and leaves.–Stem- the above ground ____________ of vascular plants.–Leaf- the principle _________________ _______________________ of the stem.•Foliage leaf- photosynthetic organ.•______________________- the part of the stem where one or more leaves are attached.•______________________- the region of the stem between two successive nodes.•__________________- an embryonic shoot protected by young leaves.Primordium- _________________________________________________________________________Pith- ________________________________________________________________________________Modified Stems•__________________- modified leaves that spirally coil and aid in stem support.•__________________- runners; stems that grow horizontally on the soil surface, often giving rise to newplants at the nodes.•__________________- hard, woody, sharp-pointed modified stems, arise from the axils of leaves.•__________________- hard, woody, sharp-pointed modified leaves or leaf-parts.•__________________- a small non-woody, sharp-pointed outgrowth of bark or the epidermis.77

Underground Stems•__________________- a horizontal stem that grows at or below the soil surface.•______________- an enlarged, short, fleshy underground stem, forms at the tip of a rhizome. i.e. Potato.•_______- a shortened underground stem covered by enlarged fleshy storage leaves. i.e. Onion and garlic.•________________- a thickened underground stem with small papery leaves. i.e. Gladiolus and Crocus.Leaf Arrangement•__________________- the arrangement of leaves on a stem.–__________________- leaves are attached to an underground stem or rhizome.–__________________- 2 leaves attached at each node, borne on opposite sides of the stem.–__________________- 1 leaf attached at each node.–__________________- 3 or more leaves at each node.Leaf Morphology•Blade- __________________.•Petiole- __________________ portion.•__________________- scalelike or leaflike appendages at the base of leaves.•_____________________ vs. ____________________ Leaves–Simple- blades __________________.–Compound- blades _______________________ into leaflets.•____________________compound- leaflets arising from both sides of the axis.•____________________ compound- leaflets diverge from the tip of the petiole.78

Leaf Histology•_____________________- the _______________ tissue of the leaf specialized for photosynthesis.–__________________________ parenchyma- upper cells.–__________________________ parenchyma- lower cells.Leaf Abscission•Abscission- _______________________________________________________________________.•Structural and chemical (ethylene) changes result in the formation of an abscission zone:–__________________________ layer–__________________________ layer•Magnesium ions, sugars, amino acids.79

Secondary Growth in Stems- Chapter 26Seasonal Growth Cycles•__________________- a plant whose life cycle is completed in a single growing season.•__________________- a plant whose life cycle is completed in two growing seasons; flowering andfruiting occurs in the second year.•__________________- a plant whose vegetative portion of the life cycle lives year after year.Secondary Growth•At the beginning of each growing season primary growth is resumed and secondary tissues __________.•Secondary Growth- an ____________________ in thickness (_____________) to the plant body as aresult of the activity of ___________ lateral meristems:–____________________ Cambium–____________________ CambiumVascular Cambium•Vascular cambium- a cylindrical sheath of ___________ cells that produces secondary xylem & phloem.•Consists of two forms of highly vacuolated cells:–____________________ initials–____________________ initials•Vascular rays–Pathways for the movement of ______________ substances and water.–Storage of starch, protein, and lipids.80

Wood- Secondary Xylem•Wood uses- shelter, fire, weapons, furniture, tools, paper, boats, wheels.•Wood is classified as:–_________________wood- magnoliids and eudicots.–_________________wood- ___________________.Conifers- softwoods•Tracheary elements- ____________________ only.Magnoliids and Eudicots- hardwoods•Tracheary elements- tracheids and __________________ ____________________.Periderm•Periderm- outer tissue that replaces the epidermis as the protective covering of the plant.–____________________ - meristem that produces the periderm.–____________________ (phellem)- secondary tissue that cuts toward the outside of the corkcambium; dead at maturity; suberin; impermeable to water and gases.–____________________ - secondary tissue that is cut towards the inside of the cork cambium;living at maturity; no suberin; permeable.•Lenticel- spongy regions on the cork surfaces of stems, ____________________, and other plant partsthat allow for ___________ exchange.•Bark- collective term for all tissues outside the ____________________ cambium.–____________________ phloem–____________________External Features of Woody Stems81

Heartwood vs. Sapwood•Heartwood- the part of the wood in a living tree that contains __________ cells; nonconducting wood.•Sapwood- the part of the wood in a living tree that contains ____________ cells and reserve materials;______________________ wood.Growth Rings Result from the Periodic Activity of the Vascular Cambium•_______________ rings- a layer of growth in secondary xylem or phloem.•_______________ rings- a growth layer that represents one season’s growth.•Early wood–Less dense than late wood.–Produced during period of rapid growth.–Wide cells with thin walls.•__________________ wood–___________________.–Produced during periods of _________________ growth.–____________________ cells with __________________ walls.Bristlecone Pine (Pinus longaeva)•Oldest living tree–_____________ years in age- oldest living.–_____________ years in age- oldest.•Native to the White Mountains of eastern California.•The bristlecone pine is a sensitive ________________ gauge.–3,500 B.C.- 1,300 B.C. warm summers.–1,300 B.C.- 200 B.C. cold summers.•_____________________________- the study of growth rings and historical time.82

Ecology- Chapters 31 and 32Environmental Science-Ecological Definitions•Ecology- the study of the __________________ between _______________ and the _______________.–Interactions (or ________________) determine the abundance and distribution of organisms.•______________________- the size, shape, and location that a population occupies.•______________________- the number of individuals in a given area and their density.Quadrat-Transect-GIS and GPSEcology Deals with 4 Levels•____________________- a single organism.•____________________- a group of individuals of the same species occupying a given area.•______________- all the organisms inhabiting a common environment and interacting with one another.•___________________- a community and its physical environment.Population Distributions_______________ _______________________- How many in California? ______________•Coastal Sage Scrub= CSCR (Little summer heat), 12-25 inches of precipitation.–Summer fog/overcast is common. Summer temperatures from 80-100°F. Winter temperaturesdrop to 27-30°F.–Common Plants•Buckwheat (Eriogonum spp., notably E. fasciculatum), California Lilac (Ceanothus spp.),Manzanita (Arctostaphylos spp.), Monkey flowers (Diplacus spp., the drought tolerant types),Gooseberry and Currant (Ribes spp.), Coyote Brush (Baccharis spp.).–Soil and climate notes•A mixture of diverse soils, from acidic sand on hard pan (Manzanita country) to alkaline clays(largely converted to annual weeds).83

•Ecosystem- _______________________________________________________________________.•________________- the major regional ecosystems.Abiotic and Biotic Factors•Abiotic- characterized by the absence of life; _____________________________.–_________________________–_________________________–_________________________–_________________________–_________________________- ph, texture, gas exchange, salinity, leaching.–_________________________•Biotic- of or relating to life; ____________________________.–_________________________- space, substrate, light, nutrients.–_________________________LatitudeElevationPrinciple of Competitive ExclusionPlant-Herbivore InteractionsSuccession•Succession- _______________________________________________________________________.–_______________________ succession- the initial ____________________ of ____________________________ or bedrock by pioneer species (lichens, mosses, ferns, herbaceous plants).–_______________________ succession- __________________________ in the plants andanimals that live in a community after the initial colonization.Opportunistic vs. Late Successional Forms•r-selected–Colonizers on newly-cleared surfaces.–Life history- ephemerals, annuals,simple veg. life history.–Size- ________________.–Growth- ______________.–Reproduction- high output, ________offspring, low cost/unit.–Energy storage- uniform throughout.Population Growth•K-selected–Invade pioneer communities onpredicatable basis.–Life History- complex, perennials, seasonalreproduction.–Size- ______________.–Growth- ______________.–Reproduction- low output, _________offspring, high cost/unit.–Energy storage- ____________ distributedPopulation Explosions84

Regulating Growth and Development- Chapter 27Hormones•Hormone- gr. to ____________________. ____________________ substances produced in _________amounts that regulate and coordinate metabolism, growth, and morphogenesis.Darwin and DarwinBoysen-Jensen____________________ Major Classes of Plant Hormones•____________________–Leaf primordia, young leaves, developing seeds.–Polarly (unidirectionally) and nonpolarly.•____________________–Root tips.–From roots to shoots via xylem.•____________________–Most tissues in response to stress.–Diffusion from site of synthesis.•____________________ acid–Mature leaves and roots, seeds.–From leaves in phloem and from the roots in the xylem.•____________________–Young tissues of the shoot and developing seeds.–Xylem and phloem.•____________________–Young tissues and throughout the plant.–They act locally.•____________________ is the only plant hormone known to be transported polarly.•Polar transport is ____________________ (toward the base).Auxin Provides Chemical Signals That Communicate Information Over Long Distances•____________________ ________________- inhibitory influence of the apical bud upon lateral buds.Auxin Plays a Role in the ____________________ and ____________________ of Vascular TissueAuxin ____________________ ____________________ Development85

Auxin ____________________ the Formation of Lateral and Adventitious ____________________Auxin ____________________ Abscission____________________ Auxins Kill Weeds- HerbicidesEthylene Plays a Role in ____________________ ____________________Ethylene May ____________________ or ____________________ Cell ExpansionCytokinins ____________________ Cell DivisionCytokinins ____________________ Leaf SenescenceCytokinins ________________________ the Growth of Lateral BudsAbscisic Acid (ABA) __________________________ Seed GerminationAbscisic Acid Plays a Role as a ________________-to-___________________ SignalAbscisic Acid is Responsible for __________________ __________________•Gibberellin (GA) causes __________________ mutants to grow __________________.•Gibberellin causes __________________ of __________________ by stimulating cell division andelongation.86

Gibberellin Plays Multiple Roles in1) Breaking __________________ __________________2) In _____________________________Gibberellin Can Cause ____________________________Gibberellin Affects ____________________________ DevelopmentBrassinosteroidsAdditional Chemical Signals•____________________- signal in defense responses to plant pathogens.•____________________- plant growth regulation and defense.•____________________- growth and development; mitosis and meiosis.•____________________- long-distance signal that activates chemical defenses against herbivores.•____________________- signal in hormonal and defense responses.87

External Factors and Plant Growth- Chapter 28•Tropism- ____________________________________________________________________.•Phototropism- the curving of a growing shoot ______________ _____________________.–_____________________?•Gravitropism- the response of shoot or root to ________________________.–1st __________________________–2nd __________________________•Thigmotropism- the response to _____________________ with a solid object.•Heliotropism- the orientation of _______________ and ________________ to the __________.–Turgor pressure changes of the ________________________.•Pulvinus- ____________________ thickening at the base of the petiole or petiolule.Growth response unrelated to the direction of the external stimulus•__________________ Movement- gr. nastos= closed-pressed.–__________________________–__________________________•__________________________morphogenesis•Nyctinasty- the _____________ and ________________ movement of leaves in response todaily rhythms (night and day).•Thigmomorphogenesis- the __________________________________________________ inresponse to mechanical stimuli.88

Plant Nutrition, Soils, and Disease- Chapters 13 and 29Plant Nutrition•Plant Nutrition- _________________ from ______________________________ of all raw materialsrequired for essential biochemical processes.•More than _____________ _________________ have been identified in plants.•1880s- ten chemical elements were designated as _________________________ for plant growth.–Carbon, hydrogen, oxygen, potassium, calcium, magnesium, nitrogen, phosphorus, sulfur, iron.•1900s- manganese, zinc, copper, chlorine, boron, molybdenum, and finally nickel.Essential ElementsThree criteria are used to judge essentiality1) If it is needed for the plant to ___________________________________________________.2) If it is part of _____ ___________________ or constituent of the plant that is itself essential.a. Magnesium in chlorophyll molecule.b. Nitrogen in proteins.3) If ____________________ ______________________ appear in the absence of the element.2 Types of Essential Elements•_____________________________- required in large amounts.______________ mg/kg or > of dry matter.•____________________________ (trace elements)- required in very small amounts.100 mg/kg of dry matter.Certain plants contain unusually high and low amounts of specific elements.Macronutrient Functions______ Sulfura. ATP, nucleic acids, phospholipids.______ Phosphorusb. chlorophyll molecule.______ Magnesium c. amino acids and coenzyme A.______ Calciumd. cell walls, cofactors, cellular membrane.______ Potassiume. almost all chemical molecules, 96% of the plant.______ Nitrogenf. amino acids, proteins, nucleotides, nucleic acids, chlorophylls.______ Oxygen, Carbon, g. osmosis and ionic balance, stomatal activity.and HydrogenMicronutrient Functions•____________________- nitrogen fixation and nitrate reduction.•____________________- enzyme functioning in nitrogen metabolism.•____________________- involved in some REDOX reactions.•____________________- activator or component of many enzymes.•____________________- enzyme activator, membrane integrity, oxygen release in PSN.•____________________- Ca 2+ utilization, nucleic acid synthesis, membrane integrity.•____________________- chlorophyll synthesis.•____________________- osmosis and ionic balance.SulfurPhosphorus89

MagnesiumCalciumPotassiumNitrogenMolybdenumCopperChlorineZincManganeseBoronIronGlobal Nitrogen and Phosphorus UseNitrogen LossesEutrophicationSoil•Soil- primary ________________ (inorganic ions), ________________, suitable ___________________________________, and ____________________ ____________________ for plants.–Provides a chemical and physical environment for plant growth.–Minerals- naturally occuring inorganic compounds that are usually composed of two or moreelements. i.e.- Quartz (SiO 2 ), Calcite (CaCO 3 ).90

Soil Layers (Horizons)•Soils consists of at least 3 ____________________ (layers)A Horizon= ______________soil.B Horizon= ______________soil.C Horizon= ____________________________.____________________________= below the horizon layers.Soils Are Composed of Solid Matter and Pore Space•Solid Matter- fragments of rock and minerals in the soil.__________ 1. Coarse Sand a. < 2 µm__________ 2. Fine Sand b. 2-20 µm__________ 3. Silt c. 200-2000 µm__________ 4. Clay d. 20-200 µm•Pore Space- the space around the soil particles.–___________________–___________________Plant Pathology- bacteriaPlant Pathology- virusesPlant Pathology- fungi91

Genetics- Chapter 8Mendel Studied 7 Characters in the Garden Pea (Pisum sativum)•Flower _______________________•Flower _______________________•Seed _______________________•Seed _______________________Pod _______________________Pod _______________________Stem _______________________Mendel’s Methods•Cross-pollination- the transfer of _____________ from one plant to the _________________ of another.–Self-pollination–Artificial cross-pollination•Monohybrid crosses- an experimental cross between individuals that ____________________________.•First (_____________) and second (________________) generations.Mendel’s F 1 Observations•One of the traits could be seen in the F 1 generation= __________________________•One of the traits could not be seen in the F 1 generation= __________________________Genetic Terminology•__________________________- an organisms traits.•__________________________- an organisms genetic makeup.•__________________________- identical alleles for a gene.•__________________________- two different alleles for a gene.Genetic Terminology #2•__________________________- one of 2 or more alternative forms of the same gene.•__________________________- a sequence of DNA that codes for a protein.•__________________________- the position on a chromosome occupied by a gene.Mendel’s F 2 Observations•Flower color–Purple:white 705:224 __________________Mendel’s Dihybrid Cross•315:108:101:32 = ________________________92

Mendel’s Work Yielded These Genetic Rules•Alternative versions of genes (different ______________) account for variations in inherited characters.•For each character an organism inherits ____________ alleles, ___________ from each parent.•If two alleles differ, then one, the _____________ allele is fully expressed in the organism’s appearance.•The two alleles for each character ________________________ during gamete production.•Alleles of a gene segregate ____________________________ of the alleles of other genes.Punnett Squares and the Testcross•Punnett square- a ___________________________________________________________________.•Testcross- a genetic experiment used to determine an organisms genotype.Codominance• Codominance- the effects of both alleles are apparent.Incomplete Dominance•Incomplete dominance- type of inheritance in which the F 1 is _______________________ in phenotypebetween the parents.•Neither allele is dominant.•Self-pollination of the F 1 yields a ______________________ F 2 population.Continuous Variation•Continuous variation- a _______________________ in phenotype; indicates that a trait is controlled by________________ or more genes.–__________________________ __________________________Linkage•Linkage- the tendency for certain genes to be ________________________ ____________________,owing to the fact that they are located on the same chromosome.•Linked genes- genes that are inherited __________________________.Genetically Engineered Rice- what does it contain? _________________________93

Genetic Engineering•Genetic Engineering- the technique of ______________________, ____________________, or____________________ genes to a DNA molecule.–Improvements in crops•__________________________•Resistance to __________________________•Resistance to __________________________Transgenic Plants•Tomato with __________________________ and without.•Transgenic tomatoes with and without __________________________.•Petunia with and without __________________________.•Tobacco with and without a __________________________.Transfer of GenesTissue CultureAgrobacterium tumaefaciens•Genomics- a field of genetics that attempts to understand the ______________________,_______________________, function, and _______________________ of genetic information in awhole organism.Arabidopsis thaliana•Genome- all of the genetic information of an organism.94

Dr. Jeffery R. Hughey General Botany-BIO 3Mutant Arabidopsis LaboratoryArabidopsis thaliana (L.) Heynh. is a flowering plant in the mustard family Brassicaceae and is native toEurope, Asia, and northwestern Africa. It is an annual that typically grows to 20–25 cm in height. Theleaves form a rosette at the base of the plant, with a few leaves also on the flowering stem. The basalleaves are green to slightly purplish in color, 1.5–5.0 cm long and 2–10 mm broad, with an entire tocoarsely serrated margin; the stem leaves are smaller, unstalked, usually with an entire margin. Leavesare covered with small unicellular trichomes. The flowers are 3 mm in diameter, arranged in a corymbosefashion; their structure is that of the typical Brassicaceae. The fruit is a siliqua 5–20 mm long, containing20–30 seeds. Roots are simple in structure, with a single primary root, and smaller lateral roots.Arabidopsis completes its life cycle in six weeks. The central stem that produces flowers grows afterabout three weeks, and the flowers naturally self-pollinate. In the lab Arabidopsis may be grown in petridishes or pots, under fluorescent lights or in a greenhouse.Use as a model organismBy the beginning of 1900s, A. thaliana had begun to be used in developmental studies. The firstcollection of its mutants was made around 1945. The species is now widely used for studying plantsciences, including genetics, evolution, population genetics, and plant development. Arabidopsis playsthe role for agricultural sciences that mice and fruit flies (Drosophila) play in animal biology. AlthoughA. thaliana has little direct significance for agriculture, it has several traits that make it a useful model forunderstanding the genetic, cellular, and molecular biology of flowering plants.The small size of its genome makes A. thaliana useful for genetic mapping and sequencing, with 125million base pairs and 5 chromosomes, Arabidopsis has one of the smallest genomes among plants. Itwas the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative.The current version of the genome is maintained by The Arabidopsis Information Resource (TAIR).Much work has been done to assign functions to its 25,498 genes and the 35,000 proteins they encode.The plant's small size and rapid life cycle are also advantageous for research. Having specialized as aspring ephemeral, it has been used to found several laboratory strains that take about six weeks fromgermination to mature seed. The small size of the plant is convenient for cultivation in a small space andit produces many seeds. Further, the selfing nature of this plant assists genetic experiments. Individualplants produce several thousand seeds.Plant transformation in Arabidopsis is routine, using Agrobacterium tumefaciens to transfer DNA to theplant genome. The current protocol, termed "floral-dip", involves simply dipping a flower into a solutioncontaining Agrobacterium, the DNA of interest, and a detergent. This method avoids the need for tissueculture or plant regeneration.The Arabidopsis gene knockout (a technique in which one of an organism's gene is made inoperative)collections are a unique resource for plant biology made possible by the availability of high-throughputtransformations. The site of T-DNA insertions has been determined for over 300,000 independenttransgenic lines, with the information and seeds accessible through online T-DNA databases. Throughthese collections, insertional mutants are available for most genes in Arabidopsis.Finally, the plant is well suited for light microscopy analysis. Young seedlings on the whole, and theirroots in particular, are relatively translucent. This, together with their small size, facilitates live cellimaging using both fluorescence and confocal laser scanning microscopy. By mounting seedlings inwater or in culture media, plants may be imaged uninvasively, eliminating the need for fixation andsectioning and allowing time-lapse measurements. Fluorescent protein constructs can be introducedthrough transformation as well. The developmental stage of each cell can be inferred from its location inthe plant or by using fluorescent protein markers, allowing detailed developmental analysis.95

TAIR and NASC (Nottingham Arabidopsis Stock Centre) are curated sources for diverse Arabidopsisgenetic and molecular information, and also provide numerous links, for example, to databases that storethe results of hundreds of genome-wide gene expression profile experiments. Seed and DNA stocks canbe obtained from NASC or the Arabidopsis Biological Resource Center.History of Arabidopsis researchThe first mutant in Arabidopsis was documented in 1873 by Alexander Braun, describing a double flowerphenotype (the mutated gene was likely Agamous (without stamens or carpels), cloned and characterizedin 1990). However, it was not until 1943 that Friedrich Laibach (who had published the chromosomenumber in earlier proposed Arabidopsis as a model organism. His student Erna Reinholz published herthesis on Arabidopsis in 1945, describing the first collection of Arabidopsis mutants that they generatedusing x-ray mutagenesis. Laibach continued his research by collecting a large number of ecotypes. Withthe help of Albert Kranz, these were organized into the current ecotype collection of 750 naturalaccessions of A. thaliana from around the world.In the 1950s and 1960s John Langridge and George Rédei played an important role in establishingArabidopsis as a useful organism for biological laboratory experiments. Rédei wrote several scholarlyreviews introducing this model to the scientific community. The start of the Arabidopsis researchcommunity dates to a newsletter called Arabidopsis Information Service (AIS), established in 1964. Thefirst International Arabidopsis Conference was held in 1965, in Göttingen, Germany.In the 1980s Arabidopsis started to become widely used in plant research laboratories around the world. Itwas one of several candidates that included maize, petunia, and tobacco. The latter two were attractivesince they were easily transformable with current technologies, while maize was a well establishedgenetic model for plant biology. The breakthrough year for Arabidopsis as the preferred model plantcame in 1986 when T-DNA mediated transformation was first published and this coincided with the firstgene to be cloned and published.Characterized ecotypes and mutant lines of Arabidopsis serve as experimental material in laboratorystudies. The most commonly used background lines are Ler, or Landsberg erecta, and Col, or Columbia.Series of mutants, named Ler-x, Col-x, have been obtained and characterized; mutant lines are generallyavailable through stock centers, of which best known are the NASC and the Arabidopsis BiologicalResource Center in Ohio, USA. The Col or Columbia ecotype was selected, as an agronomicallyperformant line, by Rédei, within a (nonirradiated) population of seeds named Landsberg he receivedfrom Laibach. Columbia is the ecotype sequenced in the Arabidopsis Genome Initiative. The Ler orLandsberg erecta line was selected by Rédei from within a Landsberg population on which he hadperformed some X-ray mutagenesis experiments.Curiosity Kit with five known Arabidopsis mutantsToday you will be identifying five Arabidopsis mutants based on your examination or comparison withthe wild type (Ler, Landsberg erecta). The mutants include the following:1) brevipedicellus- short, downward-pointing flowers and a compact inflorescence architecture2) eceriferum- brighter green stems and siliques3) chlorina- pale green in color, plant does not produce Chlorophyll b4) clavata- excess undifferentiated cells in the shoot and floral meristem, bigger shoot meristems5) glabra- trichomes absentIdentify the mutants above and present your answers to Hughey for confirmation that you matched themaccurately.Most of the above text was taken verbatim from the following resource:http://en.wikipedia.org/wiki/Arabidopsis_thaliana, accessioned online 2011 April 5.96

General Botany, BIO 3Hartnell CollegeLynn “Rip” Van Winkle FungiDr. Jeffery HugheyKingdom FungiPhylum- BasidiomycotaClass- Basidiomycetes (Hymenomycetes)Order- AgaricalesAgaricus hondensisAmanita ocreata- death angel, or destroying angel.Amanita phalloides- death cap.Boletus zelleriChroogomphus vinicolorClitocybe nudaCortinarius sp.Dermocybe phoeniceaDermocybe sanguineaGymnopilus ventricosusHebeloma crustuliniforme- poison pie.Hygrophoropsis aurantiacaHygrophorus subalpinusLactarius fragilisLactarius xanthogalactusNaematoloma fasciculare- sulfur tuft.Russula albidula- white cap.Russula emetica- red cap.Suillus caerulescensSuillus granulatusSuillus tomentosusOrder- AphyllophoralesCrytoporus volvatus- cryptic globe fungus.Laetiporus sulphureusStereum hirsutumTrametes versicolor- turkey tail.Trichaptum abietinus- violet-pored bracket fungus.Order- TremellalesTremella mesentericaPhylum- AscomycotaClass- AscomycetesOrder- PezizalesHelvella lacunosaLichens- symbiotic fungi that contain a fungal component, mycobiont (basidomycete and ascomycete)and a photosynthetic component, the photobiont (green algae or cyanobacterium). They arephotosynthetic.Fruticose- Ramalina farinacea, R. menziesii, Usnea arizonica, U. rubicunda, Hypogymnia imshaugii.Foliose- Peltigera canina, Xanthoparmelia, Parmotrema chinense.Crustose- Xanthoria elegans, Caloplaca, Rhizocarpon.97

General Botany, BIO 3Hartnell CollegeChecklist of Mission Point SeaweedsKingdom PlantaePhylum Anthophyta- flowering plants.Class Monocotyledones- monocots.Phyllospadix scouleri- surf grass.Dr. Jeffery HugheyKingdom ProtistaPhylum Chlorophyta- green algae.Grass green in color.Chaetomorpha linum- no common name.Cladophora columbiana- no common name.Codium fragile- dead man’s fingers.Enteromorpha intestinalis- no common name.Ulva lactuca- sea lettuce.Phylum Heterokontophyta- heterokonts.Class Phaeophyceae- brown algae.Yellow, brown, to black in color due to carotenoid (fucoxanthin) and tannins.Costaria costata- no common name.Egregia menziesii- feather boa.Fucus gardneri- rock weed.Laminaria setchellii- no common name.Macrocystis pyrifera- kelp.Nereocystis luetkeana- bull-whip kelp.Pelvetiopsis limitata & P. arborescens- no common names.Silvetia compressa- no common name.Phylum Rhodophyta- red algae.Green, brown, black, blue, and red in color.Calliarthron cheilosporioides- coralline algae.Calliarthron tuberculosum- coralline algae.Chondracanthus corymbiferus- turkish towel.Chondracanthus exasperatus- turkish towel.Corallina officinalis- no common name.Corallina vancouveriensis- coral weed.Endocladia muricata- sea moss.Mastocarpus jardinii- no common name.Mastocarpus papillatus- turkish washcloth.Mazzaella flaccida- no common name.Mazzaella oregona- no common name.Mazzaella splendens- no common name.Microcladia coulteri- no common name.Palmaria mollis- dulse.Porphyra perforata- nori.Prionitis andersonii- bleach weed.Prionitis lyallii- bleach weed.Prionitis sternbergii- bleach weed.How To Press Marine Algaeblotter papercardboardwax paperseaweedherbarium paperblotter papercardboard98

General Botany, BIO 3Hartnell CollegeDr. Jeffery HugheyGymnosperms of Hartnell CollegeKingdom Plantae- ginkgos, conifers, gnethophytes, cycads.Phylum- ConiferophytaFamily- PodocarpaceaeSpecies- Afrocarpus graciliorCommon name- fern pine.Family- TaxaceaeSpecies- Taxus brevifoliaCommon name- yew tree.Family- CupressaceaeSpecies- Cupressus macrocarpaCommon name- monterey cypress.Species- Juniperus chinensisCommon name- chinese juniper.Species- Thuja occidentalisCommon name- american arborvitae or eastern white cedar.Species- Sequoia sempervirensCommon name- redwood.Family- PinaceaeSpecies- Pinus densifloraCommon name- japanese red pine.Species- Pinus densiflora ‘umbraculifera’Common name- tanyosho pine.Species- Pinus canariensisCommon name- canary islands pine.Species- Pinus radiataCommon name- monterey pine.Species- Picea pungensCommon name- colorado blue spruce.Species- Larix deciduaCommon name- larch.Species- Abies albaCommon name- European silver fir.Phylum- GinkgophytaFamily- GinkgoaceaeSpecies- Ginkgo bilobaCommon name- maidenhair tree.Phylum- CycadophytaFamily- CycadaceaeSpecies- Cycas revolutaCommon name- sago palm.99

General Botany, BIO 3Hartnell CollegeDr. Jeffery HugheyKingdom PlantaePhylum- AnthophytaClass- DicotyledonesFamily- HamamelidaceaeSpecies- Liquidambar styracifluaCommon name- sweetgum tree.Family- BetulaceaeSpecies- Alnus rhombifoliaCommon name- white alder.Family- Sterculiaceae (chocolate family)Species- Brachychiton diversifoliusCommon name- bottle tree.Family- ApocyanaceaeSpecies- Trachelospermum jasminoidesCommon name- star jasmine.Family- Fabaceae (Leguminosae)Species- Robinia ambiguaCommon name- purple robe locust.Family- OleaceaeSpecies- Olea europeaCommon name- olive tree.Family- MyrtaceaeSpecies- Melaleuca quinquenerviaCommon name- paperbark tree.Species- Eucalyptus polyanthemosCommon name- silver dollar gum.Family- CelestraceaeSpecies- Maytenus boariaCommon name- mayten tree.Family- RosaceaeSpecies- Prunus serrulataCommon name- flowering cherry.Species- Prunus blireanaCommon name- purple leaf plum.Species- Pyrus kawakamiiCommon name- evergreen pear.Species- Rosa spp.Common name- rose.Species- Rhaphiolepis indicaCommon name- India HawthornSpecies- Photinia serrulataCommon name- red tips.Family- MagnoliaceaeSpecies- Magnolia grandifloraCommon name- southern magnolia.Family- FagaceaeSpecies- Quercus ilexCommon name- holly oak.Family- BerberidaceaeSpecies- Nandina domesticaCommon name- heavenly bamboo.Family- LauraceaeSpecies- Cinnamomum camphoraCommon name- camphor tree.Family- SolanaceaeSpecies- Solanum aviculareCommon name- kangaroo apple.Family- MalvaceaeSpecies- Zauschneria californicaCommon name- California fuchsia.Respresentative Angiosperms of Hartnell CollegeFamily- PittosporaceaeSpecies- Pittosporum undulatumCommon name- sweet PittosporumFamily- AraceaeSpecies- Philodendron selloumCommon name- lacy treePhilodendronFamily- AraliaceaeSpecies- Fatsia japonicaCommon name- fatsiFamily- ElaeagnaceaeSpecies- Elaeagnus pungensCommon name- silverthornFamily- AsteraceaeSpecies- Senecio cinerariaCommon name- dusty miller.Family- SalicaceaeSpecies- Xylosma congestumCommon name- shiny leavedXylosma.Family- CaprifoliaceaeSpecies- Abelia grandifloraCommon name- glossy Abelia.Family- TheaceaeSpecies- Camellia japonicaCommon name- Japanese CamelliaFamily- LamiaceaeSpecies- Salvia leucanthaCommon name- Mexican sageClass- MonocotyledonesFamily- LiliaceaeSpecies- Cordyline australisCommon name- cabbage palm.Family- ArecaceaeSpecies- Trachycarpus fortuneiCommon name- windmill palm.Family- StrelitziaceaeSpecies- Strelitzia reginaeCommon name- bird of paradise.Family- AgapanthaceaeSpecies- Agapanthus africanusCommon name- lily of the nile.Family- AsparagaceaeSpecies- Asparagus densiflorusCommon name- asparagus fernFamily- AraceaeSpecies- Zantedeschia aethiopicaCommon name- calla lily.Family- StrelitziaceaeSpecies- Strelitzia reginaeCommon name- bird of paradise.Family- AlliaceaeSpecies- Tulbaghia violaceaCommon name- society garlic.100