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2N Important properties of DNA that should be re ected in its molecular structure 1 The molecule must carry genetic information and a lot of it ie it must contain the instructions genes for the complete development and functioning of an organism 2 The molecule must copy itself replicate precisely 3 Changes in genes mutations sometimes occur the molecular structure should allow for or help to explain such changes Aspects of DNA structure known prior to Watson amp Crick s work 1 The DNA molecule is very large 2 It is composed of nucleotides 3 The molecule s structure is orderly possibly a helix 4 Within a DNA molecule A T and G C El 120 Terms amp Concepts Week 1 Botany the scienti c study of plants and plantlike organisms Why are plants important autotrophic self feeding photosynthesis gas exchange heterotrophic other feeding plantsautotrophs serve as the base of food chains biofuels amp fossil fuels plant materials amp medicines historical foundations of botany Theophrastus father of botany organs stem leaf root growth forms tree shrub herb vine lifespans annual biennial perennial medicinal use of plants was a key in uence on the development of botany Dioscorides author of Materia Medica doctrine of signatures eg walnut moonwort mandrake etc herbals amp the printing press microscopes amp the hidden worldquot Hooke s cells common vs scienti c name problems with using only common names pre Linnaeus scientific names genus descriptive phrase often long amp unwieldy Linnaeus amp Species Pantarum 1753 binomial nomenclature format of a scienti c name eg Nepeta cataria hierarchy of classification speciesgenusfamilyorderclassphylum or divisionkingdomdomain 3 Domains Archaea Bacteria amp Eukarya 4 Kingdoms of Eukarya Protista Plantae Fungi Animalia A 639 mm uau u UACJIW uaclcquot E UM Stop UGA Stop Fi UAG Stap use Trp G cauulni ccu U M cac A c AA CGA 399 A CAGGIn CGG 5 MU mu 1 m m ml FC MA MA 4 MG LP ml o am 1 Gaelquot 66 a m A Amino acid Anticodon Finnu amogyolmmmwm O 2005M H Freean and Company El 120 Terms amp Concepts Week 5 Organic compounds continued from Week 4 carbohydrates carbon water I monosaccharide singlesugar CH30n glucose fructose link together with a dehydration reaction synthesis removingforming water to form a 2 disaccharide double sugar eg sucrose table sugar glucose fructose sucrose H20 split with hydrolysis reaction watersplitquot glucose fructose sucrose H30 3 polysaccharide many sugar v a polymer long chain of monosaccharides linked by dehydration reactions starch food storage in plants glycogen animal starchquot cellulose in plant cell walls chitin cell wall of fungi exoskeletons of arthropods M l fats amp oils v foodstorage lipids made of glycerol 3 fatty acids linked by dehydration reactions v Fig27 glycerol v a C3 alcohol fatty acid a long C chain with H carboxyl group makes it an organic acid 2 waxes waterproo ng suberin in cork cutin eg shiny wax on leaves 3 phospholipids in membranes phosphate head polar amp 2 fattyacid tails nonpolar Fig28 amp 49 proteins polymers of amino acids structure of an amino acid see Fig 2 1 3a 4 things around central C amino group carboxyl group R group 20 different ones H peptide bond formed by dehydration reaction betw 2 amino acids linking amino gp to carboxyl gp polypeptide chain see Fig 214 protein structure Fig 215 v usually 3 or 4 levels primary structure speci c sequence of amino acids secondary quot alpha helix Fig 216 tertiary quot a speci c 3d shape quaternary quot 2 or more polypeptide chains enzyme v a protein that functions as a catalyst catalyst v substance that speeds up a reaction without being used up enzymes are highly speci c based on their shapecharges and the shapecharges of reactants denaturation ofa protein change its shape eg with heat and it can no longer function properly naming enzymes substrate asequot nucleic acids DNA amp RNA v polymers of nucleotides nucleotide with 3 parts l phosphate 2 SC sugar ribose or deoxyribose 3 a nitrogenous base Adenine Thymine Guanine Cytosine Uracil in RNA replaces T differences between DNA amp RNA nucleotides double helix structure of DNA see handout gure sugarphosphate backbones amp N base rungssteps A Z T G C properties of DNA re ected in its structure see handout codes forcontains large amount of genetic information genes replicatescopies itself precisely sometimes changes mutates James Watson amp Francis Crick rst describedproposed double helix in l953 Maurice Wilkins amp Rosalind Franklin x ray crystallographs Linus Pauling amp his son Peter Pauling 32 120 Terms amp Concepts Weeks 7 amp 8 Week 7 genetics the study of inheritance oftraits alleles malternate forms ofa gene for one trait locus flocation on a chromosome alleles for a given trait occur at the same locus on homologous chromosomes Gregor Mendel father of genetics amp his experiments with peas P F amp F3 generations dominant vs recessive Mendel s law of unit characters traits are controlled by genes that occur in pairs within an individual particulate inheritance not blending Mendel s law ofdominance one gene may dominate or mask the other genotype listing of alleles phenotype physical appearance homozygous genotype 2 alleles identical heterozygous genotype 2 alleles different Mendel s law of segregation ewhen an organism reproduces 2 genes segregate in the parent in meiosis each offspring inherits one gene from each parent use ofa Punnett square to simulate reprod from one generation to the next see handout amp Fig 8 l 3 genotypic ratio phenotypic ratio test cross eused to determine whether an organism with dominant phenotype is homo or heterozygous incomplete dominance exceptionquot to law of dominance see Fig 8 18 flower color in snapclragons monohybrid cross all the examples we ve used so far followingjust a single trait Mendel s law of independent assortment egenes for different traits are inherited independently unless they occur on the same chromosome and are therefore linked example ofdihybrid cross without linkage following 2 traits simultaneously see Fig 8l 5 dihybrid cross with linkage simpler crossing over breaks linkages and produces quotrecombinationquot of genes increasing genetic variation cellular respiration cells break down food to make energy ATP available ATP energy currency of cells used as direct source of energy ADP phosphorylation eg ADP 9 ATP oxidation loss of electrons reduction gain ofelectrons electron carriercoenzyme Apicks up electrons in one reaction and shuttles them to another reaction aerobic respiration amp overall eqn C6H1306 6 03 36 ADP 36 6 C03 6 H30 36 ATP 7 heat anaerobic resp amp overall eqn C6H1306 2 ADP 2 9 2 CgHgoi i 2 C0 2 ATP i heat fermentation ethyl alcohol ethanol quotC3H50H digestion eg starch 9 glucose reactions ofrespiration 7 see handout Fig 62 glycolysis mlquot step to both aerobic amp anaerobic resp in cytoplasmic ground substance glucose C6 9 2 pyruvate C3 net gain of2 ATP the rest ofanaerobic resp ifOz is not available pyruvate 9 ethanol CO in plants amp fungi or lactic acidflactate in animals 8 some bacteria 7 also occurs in cytopl ground substance MO is avaiiable pyruvate enters mitochondrion where the rest ofaerobic resp occurs relevant parts ofmitochondrion matrix fluid in center amp cristae folded inner membrane Krebs Cycle Citric Acid Cycle 7 in matrix cyclic reaction in which a few more ATPs are made Electron Transport Chain on cristae electron carriers feed in electrons from glycoly sis amp Krebs cycle 0 attracts eiectrons through cytochrome chain producing ATPs cytochromes iron containing compounds in ETC we li see them in photosynthesis too ATP accounting most are made in ETC Week 8 light photosynthesis amp overall eqn 6 C03 l2 H30 gt COH 1306 r 6 O t 6 H30 chlorophyll Aristotle plants are soil eatersquot Van Helmont s experiments with willow amp water disproving Aristotle s assertion quotbelljar experiments Joseph Priestley plants revitalize air quotno vegetable grows in vainmquot Jan lngenhousz light amp green are necessary light reactions pigments absorb light energy and convert it to chemical energy ATP chlorophyll a pigment colored compound e absorbs some wavelengths colors of light re ects others the colors we see are the wavelengths that are reflected not absorbed visible spectrum esee Fig 74 absorption spectrum wsee Fig 75 icolors absorbed by pigments are used in photosynthesis accessory pigments can t carry out photosynthesis by themselves but can assist chlorophyll a chlorophyll b c d f ocarotenoids carotene orange xanthophyll yellow autumn coloration of leaves chlorophyll breaks down and accessory pigments already there are unmasked anthocyanins i redpinkbluepurple water soluble nonphotosynthetic pigments in vacuole relevant quotpartsquot of chloroplast thylakoid photosynthetic membrane site of light reactions grana stacks of thylakoids stroma site of dark reactions details of light reactions see gures on handout quotexcitationquot of pigment molecules absorb light electrons boosted to higher energy level antenna complex reaction center chlorophyll a molecule noncyclic photophosphorylation makes NADPM ATP amp OZ see gure on handout NADP electron carrier used in photosynthesis linking light amp dark reactions cyclic photophosphorylation makes ATP see gure on handout details ofdark reactions see gure on handout C3 fixation Calvin cycle RuBP C5 compoundgoins with C02 to start the Calvin cycle PGA quot C3 compound lSt identi able product made in Calvin cycle C4 photosynthesis with an extra quot l C step to the dark reactions amp spatial separation of initial xation amp Calvin cycle see Fig 723 and 7 2621 mesophyll cells initial C xation to C4 acid bundle sheath cells use the C4 acid in normal Calvin cycle reactions light saturation curves for C3 and C4 photosynthesis CAM photosynthesis biochemically similar but with temporal separation ot initial xation amp Calvin Cycle see Fig 26b cacti stomata iopen at night in CAM plants during day in other C3 or C4 plants environmental conditions favoring each type of photosynthesis C3 C4 amp CAM carbon cycle msee figure on handout What adds CO to the atmosphere What removes it greenhouse effect resp photosynt amp global warming How do communitywide rates of R and P vary with temperature see gure on handout Mendel s Law of Unit Characters Inherited traits are controlled by particles or factors genes that occur in pairs within an individual Mendel s Law of Dominance In the pair of factors genes that control a trait one of the factors genes may dominate or mask the other One is said to be dominant the other is recessive Mendel s Law of Segregation When organisms reproduce sexually the 2 factors genes for a trait in a parent segregate or separate each offspring inherits one factor gene from each parent Segregation occurs in meiosis when homologous chromosomes separate from one another in Anaphase I When syngamy occurs the zygote receives one factor gene from each parent Mendel s Law of Independent Assortment Genes for different traits will be inherited independently of one another unless they occur on the same chromosome and are therefore linked Tracing inheritance of a genetic trait from one generation to the next using a Punnett Square 1 What are the diploid genotypes of the parents 2 What are the haploid genotypes of the gametes produced by each parent 3 To build a Punnett square list the haploid genotypes of the gametes of one parent on the top side of the square and the haploid genotypes of the gametes of the other parent on the left side of the square Haploid gamete genotypes of 1 parent Haploid gamete genotypes of the other parent 4 Fill in the cells of the Punnett square combining down and across to show the resulting diploid genotypes of the offspring or F1 generation 5 Analyze the contents of the cells to determine the genotypic ratio of the offspring What are the relative proportions of each genotype 6 To determine the phenotypic ratio of the offspring combine cells that contain the same phenotypes appearances Gamefes F1 5 kg Figuu 3 1 3 Biology of Plum Snrenm Edition a 1005 W H Fleeman and Compam Selfpollination xi x Sperm ells x I I F 2 I I I s F I v Egg cells gure 848 alHom J Seventh mam msw H Fleemanand Company El 120 Terms amp Concepts Week 2 cell basic structural amp functional unit of organisms some are unicellular others are multicellular Hooke39s observations cells in cork the Cell Theory organisms are built of cells cells come from preexisting cells plant cell protoplast cell wall cell wall shell around each cell protoplast cytoplasm nucleus cytoplasm a mixture of membranes organelles cytoplasmic ground substance a watery uid plasma membrane outer boundary of protoplast controls what moves in amp out of protoplast nucleus control centerquot containing DNA genes nuclear envelope with pores chromatin DNA proteins in nucleus chromosomes form from chromatin during cell division nucleolus round structure inside nucleus makes ribosomes vacuole a uid lled sac like a water balloon usually the largest structure in a plant cell functions support growth waste repository pigmentation of some cells tonoplast the membrane of a vacuole ribosomes site of protein synthesis Endoplasmic Reticulum or ER rough smooth parallel sheets or tubes of membrane functions conduit for movement of materials reaction surface ribosome attachment Golgi body dictyosome packaging center vesicle small balloonlike package of material plastids complex organelles found in plants amp algae chloroplast contains chlorophyll site of photosynthesis chromoplast contains other pigments leucoplast lacks pigments mitochondrion powerhouse of cell site of aerobic respiration plastids amp mitochondria are semiautonomous with their own DNA amp ribosomes microtubules tiny hollow bers of protein agella amp cilia tiny hairlike structures some cells have for locomotion made of microtubules spindle bers form during cell division made of microtubules chemical composition of cell wall cellulose a polymer of glucose bers polymer large chainlike molecule made of repeating subunits monomers matrix of cell wall between cellulose bers hemicellulose pectic substances or pectin gluelike gel holds water waxes waterproo ng lignin hard rigid material proteins primary 1 cell wall formed while a cell is still growing in size contains pectic substances secondary 20 cell wall formed after a cell has stopped growing often thick rigid no pectin pits gaps in 2 wall middle lamella glue pectic substances between adjacent cells cementing together their cell walls plasmodesmata cytoplasmic channels between adjacent plant cells containing ER plant vs animal cell How do their contents differ 82 120 Terms amp Concepts Week 6 DNA structure function continued from Week 5 M complementary strands A to T G to C M See Fig 93 DNA s information is contained in the sequence ofN bases base triplet codei recipe for protein semiconservative replication of DNA M see Fig 9 4 helicase unzips double helix DNA polymerase assembles newt complementary stand along each old strand replication fork amp bubble mutation change in a geneDNA sequence RNA M singlestranded polymer of nucleotides 3 main types of RNA ribosomal RNA rRNA messenger RNA mRNA transfer RNA tRNA see Fig 91 I gene M segment of DNA with code for l proteinpolypeptide chain genes work by interacting with RNA to make proteins Protein Synthesis 2 steps in prokaryotes 3 steps in eukaryotes M see Fig 98 transcription DNA 399 RNA always step 1 translation RNA 9 protein step 2 in prok step 3 in eukaryotes RNA splicing step 2 in eukaryotes makes mRNA Transcription see Fig 910 RNA polymerase assembles RNA along one strand of DNA codon in mRNA M base triplet coding for 1 amino acid M see Fig 99 stop or nonsense codon M can separate codes for different proteins along one mRNA molecule RNA splicing M step 2 in eukaryotes premRNA gt mRNA Msee Fig 9 l 9 exons spliced together introns removed in splicing transfer RNA tRNA M see Fig 91 1 M shuttlesquot a speci c amino acid to proper position in translation anticodons only in tRNA Translation last step M3 types of RNA interact to assemble protein like an assembly line M ribosome is the factoryWsite mRNA is the conveyor beltquot with instructions tRNA is cart holding an amino acid Details mRNA attaches to ribosome lSt codon on mRNA attracts tRNA with its amino acid with complementary anticodon 2 d codon on mRNA attracts tRNA amp amino acid with complementary anticodon peptide bond forms between amino acids mRNA slides across the ribosome so that the lquot codon comes off the ribosome and the next 3 codon moves on and attracts a tRNA with a complementary anticodon l tRNA detatches from mRNA and from its amino acid and goes to pick up another amino acid molecule process continues with each mRNA codon specifying an amino acid attracting a tRNA anticodon with the tRNA transferring the amino acid to the growing polypeptide chain protein when protein is complete it is released the mRNA can attach to another ribosome and the process can begin again to make another molecule ofthe protein gene expression a gene is switched on so its protein is made transcriptional switches eg transcription factors translational switches eg microRNA differentiation an unspecialized cell becomes specialized due to differential gene expression cloning M produces genetically identical organisms because it involves mitosis 8 cytokinesis M eg cuttings tissue culture M technique to clone cellsplants artificially eg 32000 yr old frozen plant cells asexual reproduction new individuals genetically identical sexual reproduction new individuals genetically distinctditt ent meiosis M division ofnucleus in which the number ot chromosomes is cut in half syngamy Mfusion of2 haploid cells gametes to form a zygote fertilization life cycle diagram meiosis amp syngamy alternate diploid 2n haploid n gametes 7 sex cells iei haploid cells that fuse to form a diploid cell zygote which grows into a new individual egg amp sperm 7 typical gametes female amp males respectively zygote eigu fertilized egg M initial diploid cell formed by syngamyffertilization homologous pair of chromosomes in diploid ceils one from each parent quotContextquot for meiosis always part of sexual reprod quotBig picturequot main points to meiosis 1 consists of2 divisions ofthe nucleus 1 amp ll resulting in 4 nuclei 2 products are haploid 2n 4 n 3 products are genetically distinctx different meiosis is a source of genetic variation before meiosis lnterphase period with DNA replication chromosomes become doubled vii2 chromatids prophase l synapsis pairing of homologous chromosomes crossingover exchange of segments betw homologous chromosomes 7 incr genetic variation metaphase l ihomoloaous pairs line up in pairs independent assortment pairs line up independently of other pairs anaphase l ihomologues separate amp go to opposite poles telophase l 72 haploid nuclei organize reduction division in 1st division or Meiosis l M nuclei go from diploid to haploid 2 d division or Meiosis ll mechanics are like mitosis but no DNA replication betw l and ll prophase ll metaphase ll achromosomes individually line up anaphase ll ichromosomes split at centromere amp daughter chromosomes move to poles telophase ll 74 haploid nuclei organize each genetically distinct meiosis is a sourcegenerator ofgenetic variation LIGHT REACTIONS NONCYCLIC PHOTOPHOSPHORYLATION EiecTron Aegep k39or Pox Ee ron ACQQPfor O CAI Lockromes A x 1 x 3 at RQQCtQW LL le Cenhr x Q 5 I 3 RQQQIW Carder O 2H J5oz o 0 H10 CYCLIC PHOTOPHOSPHORYLATION gladrun Au VP1 or39 ADP Cyfockromes 4 2e 0 ATP quql n C2vx r THE DARK REACTIONS Calvin Cyc1e C3 fixation CgigtGr A 3 Carbo4gt QAT 3 QC E J QNADBZgt QADP QNADOX 3C0Z BRuB Kg CoJ OOW QPC AL BCQrg R W D 3A 3 SPCAL I BAT PGAL i IHfQFMQC3 RLCEZS i Glucose Photosynthesis 2 11 1 3312 Dissotvod organic carbon lt 700 Ocean I 38100 quot Chapter 7 Essay My oIPlaim Seventh Edition k 2005 W H Freeman and Company Rates of Photosynthesis Ps and Respiration R both vary with temperature but in different ways Communitywide Photosynthesis P and Respiration R in a tropical rainforest as functions of temperature Ps Rate of P3 or R R Temperature CELLULAR RESPIRATION ADP a Glucose Mm Mm Pyruvate Figure 62 Biology of Plants Seventh Edition 6 2005 W H Freeman and Company Oxygen i absent 2 y Lactate or ethanol C02 l Glycolysis 2 Anaerobic Respiration fermentation 3 Krebs Cycle Citric Acid Cycle 4 Electron Transport Chain Terms amp Concepts Weeks 3 amp 4 Week 3 Cell Structure continued from Week 239 prokaryote before the kernelquot no nucleus or membranebounded organelles Domains Archaea amp Bacteria eukaryote true kernelquot contains nucleus and membranebounded organelles Domain Eukarya Plants Animals Fungi Protists structure of nonphotosyn bacterium structure of photosyn bact bluegreen alga Endosymbiont Theory origin of complex organelles chloroplast amp mitochondrion Cellular Physiology water molecule H20 asymmetrical polar vs nonpolar molecule water potential LP potential energy of water bulk ow materials carried by water as it moves solution uniform mixture of molecules of 2 Or more substances solvent amp solute diffusion movement from highlow equilibrium rate of diffusion affected by temperature concentration gradient molecular weight cytoplasmic streaming osmosis diffusion of water across membrane high W low LP osmotic pressure turgor pressure osmotic pr in cell plasmolysis loss of turgor pressure differentially permeable membranes membrane structure 2 phospholipid layers proteins transporter proteins carriers channels amp pumps facilitated diffusion with carrier or channel protein high low results in equilibrium Week 4 active transport with pump opposite direction requires energy results in accumulation cytosis movement across membr in vesicle endocytosis into cell or structure exocytosis out of cell or structure growth in animals vs plants determinate closed growth indeterminate open growth diffuse vs localized growth unitary vs modular growth meristem growth region where cells divide apical meristem at tip of stem or root lateral meristem inside woody stem or root intercalary meristem eg grass leaf grows from base DNA replication mitosis division of nucleus cytokinesis division of cytoplasm mother and quotdaughterquot nuclei interphase DNA replicates prophase chromosomes form nuclear envelope amp nucleoli disappear chromosome chromatid centromere doubled chromosome with 2 chromatids metaphase chromosomes line up spindle amp spindle bers equatorial plane anaphase chromosomes split amp separate daughter chromosome with 1 chromatid telophase daughter nuclei organize cell plate amp bers carry out cytokinesis cell plate vesicles form plasma membrane amp middle lamella Biochemistm organic compounds built with carbon CHOPNS carbohydrates carbon water 1 monosaccharide singlesugarquot CH20n glucose fructose link with dehydration reaction synthesis removingforming water to form 2 disaccharide doublesugarquot sucrose table sugar split with hydrolysis reaction watersplit 3 polysaccharide manysugarquot starch food storage in plants glycogen animal starch chitin exoskeletons lipids 1 fats amp oils food storage lipids glycerol 3 fatty acids glycerol a 03 alcohol fatty acid a long C chain with H carboxyl group makes it an organic acid 2 waxes waterproo ng suberin in cork cutin eg shiny wax on leaves 3 phospholipids in membranes polar head amp 2 fattyacid tails 2N Important properties of DNA that should be re ected in its molecular structure 1 The molecule must carry genetic information and a lot of it ie it must contain the instructions genes for the complete development and functioning of an organism 2 The molecule must copy itself replicate precisely 3 Changes in genes mutations sometimes occur the molecular structure should allow for or help to explain such changes Aspects of DNA structure known prior to Watson amp Crick s work 1 The DNA molecule is very large 2 It is composed of nucleotides 3 The molecule s structure is orderly possibly a helix 4 Within a DNA molecule A T and G C