GenBio 1 Full Semester Notes
GenBio 1 Full Semester Notes 01:119:115
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Lecture 1 The Process of Science Sect 17 Science 09052012 Not causes for phenomena Allows to measure in a systematic manner Observation 2 main approaches in biology Discoverv science 0 O O 0 Based on gathering data stuff you can observe and measure Inductive reasoning Begin with a set of observations then draw conclusions Ex Human genome Hypothesis Driven science 0 0000000 Hypothesis proposed explanation for a set of observations TENTATIVE Not a theory Falsifiable Leads to predications Deductive Reasoning Starts with General premisis I extrapalates I Specific results Ex If all organisms are mad of cells Premise 1 and humans are organisms Premise 2 Then humans are composed of cells Deduction Prediction Scientific Method used in driven science 0 O O 0 Used to test predictions Observations Critical questions Develop hypotheses 0 Test predictions Ex Process of Science ProblemObservations Collect Information State hypothesis Use inductive reasoning Predictions ifthen statement Use deductive reasoning Test predictions Controlled experiments Draw conclusions analyze data Report conclusions Emergence The whole is more than the sum of the parts Biology lots of facts Figure 16 0 Chemical Level 0 Atom 0 Smallest unit of element Subatomic particles n Protons n Neutrons n Electrons o Molecules o Emergent properties 0 Cellular level Multicellular Organisms o Tissues I Organs I Organ Systems I Organism Population 0 Individuals of a species living in the same place at the same time 0 Community 0 Populations of different organisms living in the same place at the same time Ecosystem o The community and nonliving environment Biosphere o The earth and all of the ecosystems Diabetes 0 Major health problem Tiein to the Gen Bio topics Emergence l gives understanding of disease Helps understand scientific process1 Lecture 2 Evolution 1amp18 09072012 Evolution process by which organisms change over time 0 Genes for new traits are passed from one generation to the next 0 This causes differences in populations Evolution is important in every aspect of biology Comes from Theodosius Dobzhausky 0 quotNothing in biology makes sense except in the light of evolutionquot 0 Evolution links together biology into uni ed body of knowledge EMERGENCE Biology tries to understand 0 Structure 0 Function 0 Behavior Interactions Biodiversity 0 Biological diversity 18 x 10quot6 species identi ed 0 Total estimate is between 4100 million Systematics l scienti c study of diversity of organisms and evolutionary relationships 0 2 PARTS 0 Taxonomy l describing naming and classifying 0 Phylogeny l Evolutionary listing Taxonomy 0 Species basic unit of classi cation 0 How to de ne species 0 Morphospecies Anatomical features 0 Biological Species Concept Members of the same species can produce offspring that in turn can also reproduce 0 Proposed by Ernst Ma yr in 1942 Binomial System of Nomenclature 0 Used to name species 0 Carolus Linnaeus Swedish physician 18005 0 Genus speci c epithetname EX Homo Sapiens o RULES Latin Genus Name capitalized Epithet is not capitalized Italicized or underlined Genus can be abbreviated Genus is unique Can be used alone to specify all the species within the genus 7 Speci c epithet is not necessarily unique 0 Classi cation 0 Species basic level PWP I SUNE I 0 Everything above species creates a hierarchy Domain Kingdom Phylum Class Order Family Genus Species Each level is more inclusive than the one below it 0 Taxon l Grouping of organisms at any one level Plural Taxa TREE OF LIFE Fig 111 Domains Bacteria and Archaea o Prokaryotes 0 Single cell 0 Lack nucleus and organees Euka rya o Euka ryotes Gene cs Gene l fundamental physical and functional unit of heredity Chromosome l physical structure that carries the genes Locus place on chromosome at which gene for a given trait occurs Allele l alternate forms of gene 0 Dominant aee l Expressed trait Recessive aee l Unexpressed trait Genotype Complete genetic make up of an individual Expressed and unexpressed o Phenotype Physical or chemical expression of an individual s genes 0 Population Group of individuals of one species that live in the same area at the same time 0 Evolution accumulation of genetic changes within a population over time 0 Change in allele frequencies in a population 0 NOT changes in an individual in hisherits lifetime PreDarwinian Ideas 0 Aristotle 384322 BC 0 Scale of Nature Very simple l very complex 0 No changeevolution JudeoChristian Cultures 0 Old Testament creation All species were created by God No evolution Natural Theology l study nature in order to discover God s plan 0 Jean Baptist DeLamarck 0 French naturalist 17441829 0 First scientist to propose that organisms undergo change over time as a result of some natural phenomena rather than divine intervention 0 Suggested that changing environment causes organisms to change behavior Inheritance of acquired characteristics l Organisms pass characteristics that are acquired during their lifetime to next generation 0 Provided mechanism of evolution Darwin amp Evolution 0 Background 0 English 18091882 0 Christ college Clergyman Natural theology 0 Voyage on Beagle 18311836 Naturalist on ship 0 Evidence for evolution 0 Earth very old Charles Lye l Geologist u Had evidence that earth was undergoing SLOW change 0 Arti cial selection Selective Breeding Humans have modi ed many species a Only allow certain characteristics to reproduce Agriculture 0 Rev Thomas Malthus 17661834 Critical to Darwin s thinking 0 Clergyman and economist 0 Essay on human population and growth Human populations have capacity to increase in size geometrically Food supply grows only arithmetically War disease and famine are necessary to slow down population growth Capacity to overproduce is applicable to all species Only a fraction of individuals need to survive to reproduce Struggle for existence among species lnherited variations favorable to survival are PRESERVED and PASSED ON Adaptation l evolutionary modi cation that improves the chances of survival and reproductive success in a particular environment quotSurvival of the Fittestquot 0 Fitness organisms ability to produce offspring Natural Selection mechanism of evolution 0 Better adapted organisms are more likely to survive and reproduce 0 As a result the population changes over time EVOLUTION 0 Frequency of favorable traitsalleles increases over generations 0 Less favorable traitsalleles become scarce or disappear 4 Mechanisms of Evolution by Natural Selection 0 Variation l individuals in a population exhibit variation 0 Overproduction all species have such great potential fertility that population size would increase exponentially if all individuals reproduced successfully Most populations are relatively constant in size Limits on population growth a Natural resources are limited I Predators a Disease a Weather Differential Reproductive Success In Individuals with most favorable characteristics are the one who will survive and reproduce KEY POINTS Mechanism by which evolution occurs No foresight Acts on variation Selection acts on individual 0 INDIVIDUALS DO NOT EVOLVE Evolution is the process of adaptation of successive generations of individual organisms to their environment 0 l characteristics of species will change Lecture 3 Cell Structure 09122012 Cell smallest unit that can carry out all of the activities associated with life Exchanges materials with the environment Capable of metabolism Capable of growth and development Responsive to environmental stimuli Capable of movement 0 Has information storage system DNA Reproduction Categories of cells TWO MAJOR ONES Prokaryotes 0 Fig 46 0 Exist in domains bacteria and Achaea 0 1st appeared about 3538 billion years ago Earth 46 billion years ago 0 Characteristics Plasma membrane Lack membrane Have nucleoid nuclear area DNA not enclosed by membrane Lack membrane bound organelles Size 110 um micrometers Eukaryotes 0 Fig 47 to 410 0 Exist in Domain Eukarya 0 1st appeared about 1921 billion years ago 0 Characteristics Plasma Membrane Contain membrane bound nucleus Contain membrane bound organelles Size 10 30 um micrometers Cell Size 0 Critical to cell function 0 Everything enters and leaves the cell throughacross the plasma membrane 0 Inside cell transport 0 Waste products removed 0 Most cells are small 0 Fig 41 0 Cells 1 30 um 0 Small molecules 10 um Cells need to maximize their cell membrane surface area in relation to volume Surface Area to Volume Ratio SAVoI Fig 42 0 Box 1 Each side 2cm 0 SA 24 cmquot2 0 Vol 8 cmquot3 o SAVo 248 31 0 Box 2 Each side 1 cm 0 SA 6 cmquot2 0 Vol 1 cmquot3 o SAVo 61 0 TABLE 41 Endomembrane System Membrane l a general term for a thin sheet 0 Lipid bilayer Double layer of fat 0 Form compartments do not have free ends 0 Membranes separate internal environment from external environment 0 Divides up inside of cell into compartments 0 Include Plasma membrane Cell membrane Nucleus Endoplasmic Reticulum ER Golgi complexes Lysosomes Vacuoles 0 Communicate Direct physical continuity They touch By transfer of membrane segments intercourse 1 Budding 2 When bud comes off called VESICLE 3 Vesicle joins another membrane 0 Plasma Membrane 0 Structure that encloses cell inside away from outside 0 Controls passage of materials in and out o Selectively permeable 0 NOT A CELL WALL Cell wall l outside of plasma membrane of certain cells plants fungi bacteria Organelles Nucleus 0 Fig 413 Visible organelle 5 um diameter Almost all DNA is located here Nuclear envelope l membrane surrounds nucleus OOOO Separates nucleoplasm from cytoplasm Nucleoplasm inside of nucleus Cytoplasm quotliquid likequot stuff in rest of cell a 2 concentric membranes a 2040 nm between them a Two membranes fused at intervals 0 Where they fuse it forms nuclear pores 0 Nuclear pores have protein complexes 0 They regulate passage of materials between nucleoplasm and cytoplasm o Nucleolus Consists of RNA and proteins I Found within nucleus No membrane surrounding Location where ribosomes are made a Ribosomes l Site of protein synthesis n Leave nucleus via nuclear pores I Some free 0 in cytoplasm No membrane a Others Membrane bound 0 Associated with Endoplasmic Reticulam o Endoplasmic Reticulum O O O 0 Fig 414 ER Lumen inside of ER Single internal compartment ER Membrane Connected to outer nuclear membrane Site of chemical reactions 2 Types of ER Rough ER ribosomes attached and Smooth ER Membranes connected lnternal spaces continuous Rough ER Proteins from ribosomes travel through translocan pore into ER lumen lnside ER protein folded and modi ed Protein transferred to other places in cell Smooth ER No ribosomes attached Primary site of lipid synthesis and metabolism Lots in liver In Breaks down glycogen n Important in regulating blood glucose n Lots of detoxifying enzymes Breaks down chemicals 0 Abuse of drugs stimulates liver to make more SER in order to break down toxins o Leads to increase tolerance to drugs Golgi ComplexApparatus 0 Fig 415 0 Stacks of membranous sacs cisternae Each sac has own lumen Not continuous space like ER 0 Each stack Cis face a part that is nearest nucleus n receives materials from transport vesicles from ER Trans Face n Closest to plasma membrane a Packages molecules in vesicles and transports those vesicles out of the Golgi to other organelles The Medial region n In between Cis and Trans faces 0 Modi es proteins Once modi ed leaves Golgi via vesicles Fig 416 protein transport Lysosomes O 0000 Fig 417 Lysis l loosening some quotbodyquot Only exists in animal cells in cytoplasm Powerful hydrolytic enzymes digestive enzymes Primary Lysosome Processed in Golgi and buds off Secondary Lysosome Forms when primary lysosome fuses with vesicle containing ingested material if enzymes are released into cytoplasm it will destroy cell Prevented by lysosome membrane Some Human diseases Rheumatoid arthritis a One partial cause is leaky lysosomes n Damage to cartilage cells in joints TaySachs disease a Rare genetic disorder a Askenazi Jewish population a Infant born amp appears normal and continues 5 months of age n Then deterioration starts Blindness deafness feeding difficulty paralysis Death usually before age of 5 n Missing the enzyme Hexosaminidase o This enzyme breaks down a normal membrane lipid in brain cells 0 ln disease it is missing from lysosome which causes accumulation in lysosomes 0 Starts to interfere with cellular activities a Example of lysosomal storage disease Vacuoles 00000 0 Empty Membrane bound Filled with uid uid lled sacs Membrane l Tonoplast Found in protozoa algae fungi and plants not necessarily in animal cells Plants Functions n Storage waste products a Maintains water balance a Stores toxins n Plant cell growth 0 Young cells have many small vacuoles With age they coalesce 0 Become central vacuole Cell increases in size by adding water to central vacuole Cytoskeleton 0 Function Holds organelles in place Maintain cell shape Allows cell to change shape Motility 0 Three Major FilamentsFibers Micro lamentActin laments n 7 nm diameter a Actin protein a Rapidly assemble and disassemble 0 Important in movement Intermediate laments n 10 nm diameter a Stable and tough don t disassemble n Maintain Cell shape a Forms nuclear amina l ines nuclear side of nuclear envelope Microtubues n 25 nm diameter a consists of alpha tubuin and beta tubuin Can easin assemble and disassemble FuncUons Structural framework Chromosome movement during cell division 0 Form tracks for organees Part of ciia and agella used for movement Organizing centers MTOC Function as anchors for microtubues Comprise of centrioes El El El Lecture 4 Mitosis Chapter 10 09142012 Intro 0 Cell theory 0 Cells are the basic living units of organization and function in all organisms o All cells come from other cells 0 Some cells are terminally differentiated do not divide 0 Ex Blood cells nerve cells 0 Cell division 0 Singlecelled organism l Produces new organism o Multicellular organism Allows organism to grow and develop from a single cell Allows for renewal and repair 0 Genetic Material 0 Genome l Cell s total genetic material Chromosomes chromocolor somebody 0 DNA doublehelix that s wrapped around proteins Histones proteins found in eukaryotic cells which associate with DNA Nucleosomes beadlike consists of 8 histones Wrapped around those 8 histones are 146 nucleotide pairs of DNA Adjacent nucleosomes are linked by 60 nucleotide pairs of DNA a Called linker DNA O O O 0 FIG 102a Gene Informational unit responsible for structure of proteins 1005 10005 of genes on each chromosome Locus location on a chromosome where a gene is located Linear sequence of genetic information on chromosome Humans 20000 genes Chromatin O DNAprotein in disperse state looks like thread bers 0 Only during cell division does it coil up and condense Each chromosome 0 has a unique shape and size 0 Has a centromere constricted area where spindles attach o Telomeres tips of chromosomes 0 The number of chromosomes 0 Haploid number n of distinct or different chromosomes Gametes reproductive cells 0 Diploid Number 2n Two copies of each chromosome in each cell one from mother and one from father Somatic cell body cell The copies are homologous chromosomes n Homologous Chromosomes Have same length 0 Same centromere placement 0 Same gene locus n and Zn cells undergo mitosis Cell Cycle Mitosis l 61 1st gap phase l S synthesis phase l 62 2ncl gap phase FIG 105 61 S 62 lnterphase T generation time o Varies 0 Between 820 hours lnterphase 0 Intro Time between successive cell division Synthesis and growing Metabolic activity Longest phase in cell Genetic material in form of chromatin o 3 Stages Gl a No DNA synthesis n Metabolic activities a Growth amp Development a Preparation for S phase begins S synthesis Phase a Genetic material is being synthesized n Chromosomes replicate a DNA amp proteins synthesize a Cell after replication 0 Each chromosome consists of 2 sister chromatids Sister chromatids are exact copies of each other 0 Each has centromere 2 sister chromatids attach to each other Kinetochore protein structure attached to each centromere o Microtubules bind during mitosis 0 Move chromosomes to new cells 62 n Metabolic Activities n Preps for mitosis protein synthesis E Short M Phase Mitosis amp Cytokinesis about 10 of cell cycle n Mitosis Nuclear division associated with the division of the somatic cells not sex cells Continuous Process 5 stages 0 Prophase o Prometaphase o Metaphase o Anaphase o Telophase n Chromosomes Early chromatin Condense shorter thicker amp becomes visible Late prophase structure is evident formation of mitotic spindle takes place orientation 2 poles equatorial plane met plate microtubules in cytoplasm disassembling used from microtubulesnear nucleus amp reassemble MTOC Microtubule Organizing Center at each pole in plants and animals main MTOC cell center ceutrosome Microtubules relocate out from MTOC Microtubules organize into mitotic spindles lnterphase Prometa phase Ceutrile found in animal cells 9 sets of 3 microtubules arranged like a cyHnder 9x3 structure pair of ceutriles 1 pair during interphase at right angles of each other they duplicate amp becomes 2 pairs Each pair is found in MTOC function in organizing spindle Mitotic Spindle responsible for the separation of chromosomes during anaphase 0 Nuclear membrane Meta phase Anaphase Breaks down fragments stored in vesicles used later for daughter nuclear envelopes Nucleus disappears Spindle microtubules grow attach to kinetochores Chromosomes move to metaphase plate Sister chromosomes oriented to opposite poles Mitotic spindle complete spindle ber microtubules Kinetochore microtubules connect chromatid to the poles Polar microtubules additional spindle bers Sister chromatids separate at their ceutromes move to opposite poles Microtubules consists of tublin subunits easily assembleddisassembled Disassemble in region of ceutromere but doesn t let go microtuble shortens Each sister chromatid is now an independent chromosome Telophase Chromosomes de condense Nuclear envelope forms around each daughter nucleus 0 Each of nuclei Genetically identical 0 Figure 106 Cytokinesis Cytoplasms divides 2 daughter cells 0 Cell Organelles Randomly each cell gets enough Expect centrioles each daughter cell gets one pair Plant Cells 0 Cell plate forms in region of old metaphase plate Vesicles from Golgi line up 0 Contain material 0 Create primary cell wall for each daughter cell 0 Middle lamella This will center primary cell walls of adjacent cells together Vesicle membranes fuse together 0 Create plasma membrane for each daughter cell FIG 10118 In all cells the cell cycle is regulated Internal and external signals to regulate Cancer Cell Escaped from cell cycle control 0 Growing out of control Lecture 5 Chapter 10 meiosis 09192012 Types of Reproduction 0 Asexual 0 Single parent 0 Produces either by splitting budding fragmentation etc o Offspring are identical to parent clones 0 Result of mitotic division 0 Advantages Rapid process Organism doesn t expend time or energy nding a mate Organisms and offspring will be well adapted to current environment 0 The parent 1 diploid 2n parent 2 diploid offspring 1 haploid n parent 2 haploid offspring Sexual 0 Union of gametes sex cells to form zygote Referred to ass egg and sperm Gamete n gamete n l zygote 2n Called fertilization syngamy o Offspring are not genetically identical to parents 0 Problem lf gametes have same number of chromosomes as parent then zygotes would have doubled the chromosome number 0 Solution MEIOSIS Cell undergoes 2 successive divisions Starts with 1 diploid cell l 2 haploid cells Chromosome Somatic cell in higher plants and animals 0 2 sets of chromosomes 0 One from mother and one from father Together make diploid number Humans 2n 46 Gametes 0 Always haploid n o 1 set of chromosomes 0 No homologous pairs 0 Zygote 0 Always diploid 2n 0 2 sets of chromosomes Meiosis 1 Interphase 2 Meiosisl 3 Interkinesis 4 Meiosis Interphase Chromosomes duplicate Centrioles duplicate Each chromosome consist of 2 sister chromatids Genetic material is still chromatin Meiosis Prophase o Synapsis Homologous chromosomes align and pair up One is maternal homologue and one is paternal Synaptonemal complex forms a Protein structure Tetrad 4 member structure 4 chromatids o Crossing over Enzymes break and rejoin DNA molecules Occurs between nonsister homologous chromatids Genetic recombination cause for genetic variation Chromatin condenses n Centromeres and kinetochores of homologous chromosomes separate a Centromeres of the sister chromatids are still attached a Chiasma location where homologous chromosomes are still attached Lecture 6 Chemistry Element 09212012 0 Can t be changedbroken down by ordinary chemical reactions 0 All elements have chemical symbol 0 00000000 0 O oxygen C carbon H hydrogen N nitrogen P phosphorous S sulfure Na Sodium Cl chlorine Fe ron C H O amp N z 96 of most organisms Atomic Structure 0 Atom 0 Smallest part of element that retains chemical properties Subatomic Particles O O O Protons 1 unit of positive charge found in nucleus Neutrons no charge and found in nucleus Electrons 1 unit of negative charge found outside of nucleus 0 Atom is neutral in charge e p 0 Atomic number 0 Based on number of protons Atomic mass 0 Protons and neutrons 17 x 10quot24 9 o 1 amu atomic mass unit Dalton o e 11800 mass of proton 0 atomic mass protons neutrons Isotopes 0 Form of an element with different of neutrons but same protons amp e Ex 2H deuterium Ex 3H tritium Radioisotope l o Unstable Nucleus breaks down decays During decay it emits radiation Defected Radioactivity can be measured OOOO Molecules Compound in which 2 or more atoms combined in xed ratio and joined strongly to form stable particles 0 Chemical formula 0 Type of atoms 0 How many of each atom 0 Ex H20 ratio 21 and 2 H and 1 O 0 Molecular Masses 0 Sum of atomic masses of atoms 0 EX H20 H 1 amu O 16 amu H20 18 amu Chemical Equations 0 Description of a chemical reaction 0 Left side reactants Right side products Reactants products Chemical Bonds Electrons 0 Move around nucleus in orbitals o Valence electrons Outer most e Occupy the valence shell O O H amp He have full valence shells when 2 e occupy All other atoms have full valence shells when 8 e occupy o Bonds 0 Result of how atoms share electrons 0 Bond Energy 0 O O Represents a certain amount of chemical energy By forming bonds cells store energy endothermic By breaking bonds cells release energy exothermic Electronegativity O O O O O O 0 Measure of an atom s attraction for electrons in chemical bonds The more electronegative an atom is the more strongly it pulls electrons toward itself 0 is most electronegative Difference in electronegativity between 2 atoms determines the type of bond which forms If same or very similar electronegativity then e shared equally l nonpolar covalent bond lf difference lt2 then e shared unequally l polar covalent bond If different gt2 then e is captured by one of atoms Covalent Bond 0 Sharing of e between atoms 0 Results in each atom having a lled valence shell 0 Strong bond 0 of bonds 0 Covalent bonding properties Element Valence e e needed covalent to ll shell bonds Carbon 4 4 4 single double and triple Oxygen 6 2 2 single and double Sulfur 6 2 2 single and double Hydrogen 1 1 1 single Nitrogen 5 3 3 single double triple 0 Types of covalent bonds 0 Nonpolar covalent bond Shared equally 39 EX 02 Ex CH4 methane similar electronegativities shape 0 Polar Covalent Bond One part of molecule has e more than the other Ex H20 2 Hs sharing e with O lonic Bond 0 Ion electrically charged atom or group of atoms Anion one or more units of negative charge Cation One of more units of positive charge 0 Like charges repel anol opposites attract lonic bond o Formed between anion and cation 0 Ex Sodium Chloride NaCl 0 Hydrophilic o Dissolve in H20 0 Fig 210 Hydrogen Bonds 0 Forms when H combines with an electronegative atom it acquires a partial positive 0 H then tends to bond with atoms that has partial negative charge 0 Ex 0 N S F 0 Fig 211 0 H20 molecules interact with one another via H bonds 0 Fig 213 0 Each H20 molecule can from H bonds with 4 other H20 molecules 0 Liquid H20 H bonds are constantly being broken and reformed Hydrogen bonds are not very strong but collectively they are strong Water Cohesion something sticks to itself 0 Surface tension measure of how difficult it is to stretch or break the surface of a liquid 0 Greater surface tension than most liquids at surface between water and air Water molecules are very ordered H bonds between each other and also molecules below Fig 215 Adhesion sticks to some other substance 0 Capillary actin tendency of water to rise in small spaces of hydrophilic material Ex thin glass tube a Adhesion glass and water a Cohesion water to water Helps maintain stable temperatures 0 High speci c heat amount of heat that has to absorbed in order to raise lg of a substance by 1 C 0 Raising temperature Adding heat to make molecules move faster l bonds break 0 High speci c heat l relatively large amount of heat energy has to be supplied to raise temperature Lots of E needed to break H bonds between water molecules 0 H20 has high heat of vaporization quantity of heat that liquid must absorb for lg to be converted from liquid to gas 0 Due to H bonding water molecules must have lots of E to escape from surface of liquid 0 Molecules that escape take a lot of heat with them Leaves surface liquid cooler 0 Ice oats Each H20 molecule forms up to 4 H bonds In Liquid water z 15 of molecules bond to 4 partners I Many molecules are close to each other lce 0 a All molecules are bonded to 4 partners I Molecules have moved apart a Water expands when freezes n Ice is less dense then liquid water Fig 216 Van de Waals interactions Occurs between nonpolar molecules 0 Electrically neutral 0 Can still have regions of very weak and charge bc e are constantly in motion Adjacent molecules can interact over short distances 0 Very weak 0 Lecture 7 Carbon Chemistry 09262012 Organic Compounds CC CH Carbon Bonds Covalent bonds 4 bonds 0 Chains insert image of bonds Single Double Triple 0 Branches CCC 39 l C 0 Rings insert image of ring CC bond strength 0 Strong enough to keep molecules together 0 Weak enough to break under right conditions Hydrocarbon Composed of C and H o Nonpolar covalent bonds Nonpolar and uncharged o Hydrophobic o Insoluble 0 Functional Group A group or groups of atoms that replace 1 or more H on the C skeleton Functional group R remains of molecule Table 31 1 Hydroxyl Group ROH 0 Ex ethane OH group ethanol ethyl alcohol 0 OH makes it polar because 0 is electronegative Hydrophilic 2 Carbonyl o CO C atom double bonded to O o Aldehyde RCHO Has terminal carbonyl group Ketone 0 Has internal carbonyl group 0 Polar hydrophilic 3 Carboxyl RCOOH C joined by double bond to O and single bond to OH 0 Non ionized form 0 2 0 5 are very close very electronegative 0 Polar hydrophilic molecule H proton released 0 Ionized form 0 Acidic because it releases a proton 4 Amino Group RNH2 Amines Accepts H to become NH3 0 Proton acceptor l base 0 Hydrophilic 5 Phosphate o RPO4H2 Releases 1 or both protons o Acidic o Hydrophilic Phopholipids and nucleic acids 6 Sulfhydryl o RSH Proteins 0 EX thiols 7 Methyl RCH3 o Nonpolar Hydrophobic Macromolecules 10005 of atoms comprise one 4 classes 0 Carbohydrates O O O Lipids Proteins Nucleic Acids Polymer O O Macromolecule produced by linking monomers Monomers identicalsimilar to each other linked by covalent bonds Fig 34 Condensation reaction connect monomers dehydration reaction Dehydration reaction results in a loss of H20 molecule Speci c Enzymes needed to cause reaction Ex HOXOH HOXOH n quotOHH come off n HOXOXOH H20 l dimer n Dimer molecule made up of two monomers o Hydrolysis breaks down polymers and controlled by speci c enzymes Carbohydrates CH20 Sugars Building blocks 0 They are the monomers 3 to 7 C OH groups Carbonyl groups Hydrophilic o ose Monosaccharides 0 Fig 36 0 Single sugars glucose fructose o Glucose 6carbon aldehyde sugar C6H1206 2 forms a Chain g 36c a Ring more typical g 37b O O O O n Alpha glucose and beta glucose are isomers Disaccharides o Glycosidic linkage bond between two monosaccharides o Maltose Glucose glucose 0 Sucrose Glucose fructose o Lactose Glucose galactosemilk sugar Lactase enzyme for hydrolysis of galactose Polysaccharide o 100510005 of sugars joined 0 Storage polysaccharides Food reserves l ex Starch I Found only in plants a Comprised of alphaglucose Fig 39 Glycogen I Found only in animals n Comprised of alphaglucose a Larger and more highly branched than starch a Can be known as animal starch I Found in muscles and liver 0 Structural polysaccharides Cellulose cell walls a Fig 310 a Most abundant carbohydrate on earth a Betaglucose subunits n Dif cult to hydrolyze a Few organisms can digest cellulose 0 Ex Fungi snails microorganisms n Cellulose is ber Chitin n Fig 311 I Monomer Nacetyl glucosamine a Beta glucose with a N containing group I Found in Arthropods insects spiders crustaceans 0 Their exoskeleton Fungi 0 Their cell wall Lipids not polymer Hydrophobic do not dissolve in polar solvents Dissolve in nonpolar solvents o Fats o o 0 Ex Chloroform Most abundant lipid Energy source lg of fat 9cal of energy Consists of glycerojoined to 1 2 or 3 fatty acids ester anage Glycerol n 3 carbon alcohol a 3 OH groups Fatty Acid I Has carboxyl group a Long unbranched hydrocarbon a 1422 carbons n Hydrophobic Fatty acids are attached to glycerol during condensation reaction Ester linkage covalent bond between fatty acid and glycerol Triacylglycerol triglyceride o Glycerol 3 fatty acids 0 Main storage for fat Saturated fatty acids O O 0 Each C completely associated with H Solid at room temperature Most animal fats are saturated Unsaturated fatty acids 0 O O 0000 H removed from chain and C double bonds with C Monounsaturated One double bond Polyunsaturated 2 or more double bonds Tend to be liquid at room temperature Oils Plants and sh have unsaturated Fig 312b Phospholipids O O O O Amphipathic Hydrophilic and hydrophobic regions Glycerol attached to 2 fatty acids hydrophobic part plus phosphate group Phosphate group negatively charged hydrophilic Fig 313 Steroids 0 Carbon skeleton in form of 4 fused rings 3 rings have 6 Cs and one has 5Cs 0 Different steroids are going to differ in side chains or functional groups attached 0 Ex Cholesterol Fig 315a In animals Synthesized in liver Membranes Precursor for synthesis of other steroids Proteins polymer Monomer Amino acids 0 Same fundamental structure Alpha carbon attached to hydrogen amino group carboxyl group and R group 0 20 amino acids found Different R groups Different properties polarity and charge Fig 317 0 Characteristics Some Non polar n R groups are hydrocarbons n Hydrophobic Some are polar a Most have hydroxyl groups n Hydrophilic Electrically charged a Hydrophilic n Acidic carboxyl group or basic amino group amino acids 0 Essential amino acid Ones we must get from diet 0 Peptide Bond Join amino acids in a linear sequence Occurs between carboxyl group OHCO of one amino acid to the amino group HNH of another amino acid a Water released a Fig 318 Polypeptide n Linear sequence of amino acids 0 Protein Structure 0 Primary structure Fig 319 One Polypeptide linear sequence of amino acids 0 Secondary structure Fig 320 H bonds occur at regular intervals between amino acids that are close together in a polypeptide chain R groups do not participate Alpha helix n Helix spiral coil exible elastic Beta pleated sheet a Rigid strength 0 Tertiary structure Fig 321 Interconnections between R groups in different regions of the same polypeptide 3D shape Ex H bonds ionic bonds covalent bonds hydrophobic interactions disul de bond l These bonds can lead to tertiary structure 0 Quaternary structure Fig 322 Several polypeptide chains Ex hemoglobin o Denaturation Lost conformation Ex pH temperature salt concentration they have to be in proper levels to keep protein from denaturing Nucleic Acids Monomers Nucleotides 0 Two classes DNA RNA 0 Function Transmit hereditary information and determine what polypeptides are produced in the cell Lecture 8 Membranes and Transport ch 5 09282012 Structure Plasma Membrane o Phospholipid 0 Principal component of membranes 0 Form bilayers CyHndncalshape Amphipathic nature part hydrophilic and part hydrophobic Van der waals interactions keep membrane together Membrane always in a closed vesicle shape 0 No free ends FluidMosaic model 0 Fig 52b 0 Singer and Nicolson 1972 0 Fluid Temperature solidify if too cold Fatty acid chain length not tightly packed due to different length Degree of fatty acid saturation n Unsaturated double bonds Cholesterol n Mainly hydrophobic 0 Inner portion of membrane n Hydrophilic OH 0 Associated with membrane heads a Stabilizes uidity o Interferes with interactions between tais o Prevents membrane from solidifying at low temperatures 0 Interacts with head region 0 Prevents membrane from become unstable at high temperatures 0 Mosaic Proteins embedded in membrane I Some held in place by cytoskeleton a Others move ateray in uid within single layer Fig 54 Fig 57 Proteins o Membrane functions a Amphipathic Different types 0 lst type integral protein it is deeply inserted in and may span the entire protein 0 2nd type peripheral proteins Not embedded Only hydrophilic components Fig 510 Attachment to cytoskeleton Transport Enzymatic activity 0 Catalyze reaction 0 Signal transduction 0 Binding site for chemical messenger relays message into cell 0 Ex hormone o Intercellularjoining Carbohydrates 0 Attached to 0 Protein gycoprotein 0 Lipid gycoipid Transport 0 Intro 0 Selectively permeable 0 2 Basic types Passive a no metabolic E involved a E Comes from concentration gradient stored energy Diffusion Type of passive transport Tendency for molecules to spread out into available space Net movement always occurs from lower concentration to higher concentration until equilibrium is reached Fig 511 What diffuses across a membrane by simple diffusion 0 0 0 Osmosis 0 Intro Active a Metabolic E used Gases oxygen Small nonpolar molecules hydrophobic Small polar molecules that are uncharged hydrophilic a EX Water Special case of diffusion Passive Solvent n Substance capable of dissolving other substances Solute n Dissolved substance Direction of osmosis is determined only by the difference in total solute concentration type of solute doesn t matter Comparison of two solutions a lsotonic Same solute concentration a Hypertonic 0 Higher concentration of solute lower water concentration a Hypotonic Lower concentration of solute higher water concentration 0 Cells Animal cells No cell wall a Hypotonic environment 0 Inside of cell is hypertonic 0 Water moves from environment to inside cell 0 Cell will swell up until it can lyse burst n Hypertonic environment 0 Inside of cell is hypotonic Water moves out of cell 0 Cell will shrink until it can shrivel and die cremated cell Plant cells fungi and some protists have cell wall a Hypotonic environment 0 Water moves from environment to inside cell 0 Cell will swell up but cell wall prevents lysis 0 Pressure inside cell Turgor pressure 0 Cell is considered turgid n Hypertonic environment 0 Water moves out of cell Cell will shrivel up until plasmolysis occurs Plasmolysis kills cell c Fig 514 0 Not everything can cross by passive transport 0 EX Large molecules Polar molecules lons charged U EX H 0 Carrier mediated transport lntro n Transport proteins carrier proteins a Span membrane a Allow speci c molecules to avoid contact with tails and cross membrane Passive and active types of mediated transport a Facilitated diffusion 0 Energy from concentration gradient is not expended Passive Solute binds to transport protein Protein changes shape due to binding 0 Opens channel through membrane 0 EX aquaporins water transport Glut 1 glucose transport glucose into RBC g 516 Potassium ion channels K transport Fig 515 B Active transport Cells expend energy Trasport protein required integral changes shape Works against concentration gradient Allows cell to stockpile materials Ex Sodiumpotassium pump 0 In animal cells 0 Pumps 3 Na out of cell and 2 K into cell Fig 517 Transport of large molecules 0 Cell energy input ATP 0 Active transport 0 Not carriermediated o Exocytosis b Uses Vesicles El El El El El Wastes secretory product 0 Ex hormone Vesicle fuses with plasma membrane Contents released from cell Growth of plasma membrane Fig 520 0 Endocytosis Material taken into cell by forming vesicles that derive from plasma membrane Phagocytosis El El El Folds of plasma membrane enclose large particles and form vacuole around it Vacuole pinches off inside cell Fuses with lysosome which digests the particles 0 Ex white blood cell l engulfs bacterial cell c Fig 521 Pinocytosis El El Cell takes in uid and dissolved materials in uid Tiny droplets trapped by folds of plasma membrane Pinch off into cytoplasm Go into pincocytotic versicles Contents slowly transferred into cytoplasm Very unspeci c Fig 522 Chemical Reactions ch 7 10032012 Energy the capacity to do work 0 2 forms 1 Kinetic 2 Potential 0 Laws of Thermodynamics 1 Energy cannot be created or destroyed It can be converted 2 When energy converted from 1 form to another some energy converted into heat Heat Kinetic E of randomly moving particles cannot perform work 0 Total amount of E in universe is not changing but total amount of E available to do work is decreasing over time o Entropy S 0 Measure of disorder 0 Organized Energy is usable low entropy o Disorganized energy heat is less usable high entropy o Entropy is continually increasing in universe over time o S and heat are inversely proportional 0 Energy conversion 0 Heat which increases entropy 0 Cars 20 30 efficient the rest is heat 0 Cells 40 efficient Sun Cellular work 0 Mechanical agella and cilia moving 0 Transport 0 Chemical breaks chemical bonds to release energy that is stored in bonds How does ce supply E 1 2 3 4 Potential E stored in covalent bonds of quothigh Equot molecules Kinetic E released when bonds are broken Metabolism chemical reactions that change arrangement of atoms Enthalpy H Total bond energy of a system Total potential energy in a cell Free Energy G Amount of energy that is available to do work under the conditions of a biochemical reaction Only E that do cellular work Related to entropy and enthalpy HGTSGH TS Enthalpy Free E TempEntropy A any change that occurs in a system between initial state before reaction and the nal state after reaction AG AH T AS a Temperature is held constant during reaction a As temperature increases there is an increase in random molecular motion n Temperature contributes to disorder and multiplies effect of entropy n AG amp AH l kilojoules o kl unit of E per mole n T l Kelvin n AS l kJK This equation predicts whether a chemical reaction will release E or absorb E Metabolism Sum of all chemical reactions and E transformation in organism Homeostasis balanced internal environment even if external conditions change Types of Metabolic Reactions 0 Anabolism o Catabolism Exergonic reaction E outward 0 Chemical reaction in which reactants have more potential E than the products 0 R l P energy energy released 0 Spontaneous reaction Goes from higher to lower free energy Total free energy in nal state is less than G in initial state AG is negative Catabolic Reaction 0 Breakdown OOOOO Large molecules l small molecules Complex simple Used to get E Used to recycle products Ex molecules with lots of potential energy l broken down Kinetic E to do work heat 0 Endergonic Reaction E inward O 0000 Reactants have less potential E than the products Total Free energy G in the nal state is more than the initial AG is positive Require addition of E to proceed Anabolic Reaction simple l complex E storage Growth Ex small molecules with low potential E energy large molecules with lots of potential energy Coupled Reactions 0 Endergonic Reactions requires E coupled with exergonic reaction provides E o Page 158155 ATP adenosine triphosphate Main molecules for energy storage 0 High energy compound 0 Structure o Nitrogen containing organic base 0 Ribose ve carbon sugar 0 3 phosphate groups Phosphate bonds 0 Stores lots of potential E 0 Terminal P can be removed 0 Hydrolysis reaction 0 Involves addition of water 0 ATP water ADP Pi Releases lots of E exergonic reaction Fig 75 Energy released is used to start endergonic reaction somewhere else 0 ATP links exergonic and endergonic reaction 0 Coupled reactions 0 Phosphorylation reaction enzyme Removes a phosphate group from ATP Moves phosphate to another molecule substrate Substrate starts as low energy and when phosphate attaches substrate becomes high energy 0 EX glucose fructose l sucrose H20 n AG 27 kJmol endergonic a Not spontaneous ATP H20 l ADP Pi n AG 32 kJmol exergonic Glucose ATP l glucoseP ADP GlucoseP fructose l sucrose Pi Glucose fructose ATP l sucrose ADP Pi n AG 27 32 5 kJmol exergonic n This is the equation to use don t need to show all steps 0 when electrons move E is released Oxidation Reduction reaction Redox Results in movement of e away from one atom toward another 0 Oxidation quotActed upon by oxygenquot Loss of e 0 Reduction quotReducing positive chargequot Gain of e o Redox e cannot exist in a free state in a cell 0 Oxidizing agent An e acceptor Becomes reduced in a redox reaction 0 Reducing agent An e donor Becomes oxidized in a redox reaction 0 Molecule can be oxidized by losing H atom takes e o What does electron movement have to do with energy 0 Energy associated with e is transferred to acceptor molecule 0 Ex Enzymes NAD nicctinamide adenine dinudotide H acceptor Oxidizing agent becomes reduced NAD XH2 l NADH X H n X was oxidized loss of W n NAD was reduced The electron that is carried by NADH can be passed to other substrates can donate energy NADH participates in coupling reaction 0 All reactions in a cell require Ea activation energy even exergonic reactions 0 Biological Catalysts 0 Speed up reactions by lowered Ea 0 Fig 710 0 Affect rate but don t get used up O O O Lowers Ea by bringing reacting substances together Weaken chemical bonds of reactants Enzyme cannot cause reaction to happen that wouldn t have happened anyway it only speeds it up Most names end in ase Iactase sucrase etc Globular protein 0 3D tertiary quaternary structure causes cleftsgrooves Active site a Region that can interact with substrate Substrate substance acted upon by enzyme Ex sucrase will only split sucrose 0 Enzyme substrate complex 0 O 0 Fig 711 lnduced t between enzyme and substrate Substrate binds to enzyme and changes shape of enzyme in order to t This causes strain which breaks bonds 0 Optimal pH and temperature 0 O O 0 Fig 712 The point where rate of reaction is fastest Change in pH and temp will destroy shape of enzyme and change side chains EX Humans enzymes optimal is 3540 C Too high will denature Metabolic Pathways o Enzymes are in teams 0 Work in sequence 0 Product of one reaction is the substrate for the next reaction 0 A l enzyme 1 l B l enzyme 2 l C 0 Enzyme inhibition 0 Chemicals can inhibit or destroy enzymes 0 Can be reversible or irreversible o Reversible inhibition Competitive Fig 717A n Inhibitor structurally similar to substrate a Competes for active site a Temporary situation a Does not damage the enzyme Noncompetitive n Inhibitor binds to enzyme at site other than the active site a Causes enzyme to change shape a Substrate can t bind to enzyme 0 Irreversible inhibition Permanent inactivation of enzyme Ex poisons work this way El Lecture 11 Photosynthesis Ch 9 10102012 Ultimate source of oxygen is C02 Plants Can convert light E l chemical bond E Light 0 Form of electromagnetic energy Range of radiation 0 O O 0 Travel 5 in waves Wavelength lamda A FIG 9 o Photon 1 Gamma rays short wavelength high E X Rays UV Visible n Violet 380 nm most energy a Red 760 nm least energy Infrared Microwaves Radio waves longest wavelength low E 0 Small particle of light E 0 Amount of E in photon is inversely proportional to A Shorter A more Energyphoton Longer A less Energyphoton Biological processes 0 Use visible light 0 When a molecule absorbs a photon of light energy 0 An electron is energized and then Energized Shift of e from lower E orbital to higher E orbital 0 Electron may either return to lower E orbital ground state or either Energy dissipates as heat or Emission of light with larger A than absorbed light uorescence 0 Or energized e may leave atom and be captured by an acceptor 0 FIG 93 Chloroplasts Conversion of light into chemical bond E simple sugars They are eukaryotes 3 membrane system 0 Outer membrane 0 Inner membrane 0 Stroma uid lled space within inner membrane Enzymes within stroma o Thylakoid disklike structure within stroma Made up of thylakoid membrane 0 Granum Stack of thylakoids Orientation maximizes light absorption 0 FIG 94b 0 When light meets matter it may be 0 Transmitted l light goes through matter 0 Re ected l light gets reemitted from surface 0 Absorbed o Photosynthetic pigments o Pigment l substance that absorbs visible light 0 Photosynthetic pigments Embedded in thylakoid membranes Capture light energy will be used in photosynthesis o Chlorophyll main pigment FIG 95 Long hydrocarbon tail hydrophobic Embedded in thylakoid membrane Porphyrin rings a Absorbs light energy a Carbon Nitrogen and Magnesium atom a Alternating single and double bonds within rings which allows for absorption of light 0 Chlorophyll a Primary pigment Has CH3 on ring Bright green color 0 Accessory pigments absorb Aof light not absorbed by chlorophyll a Pass energy to chlorophyll Ex chlorophyll b n Instead of methyl group it has a terminal carbonyl aldehyde a Yellow green Ex catotenoids yellow orange 0 Each pigment absorbs light E at different A from other pigments o Spectrophotometer measures light intensity Can create absorption spectrum 0 absorption spectrum Absorption of light of different wavelengths 0 Action spectrum Determines which wavelengths are more efficient for photosynthesis 0 FIG 96 Photosynthesis E I C6H1206 602 o Lightdependent reactions photo part 0 Thylakoids Carbon xation reactions synthesis part 0 Stroma Light dependent Reactions 0 Convert light E to chemical E ATP amp NADPH Summary 0 12 H20 12 NADP 18 ADP 18 Pi light l 602 12NADPH 18 ATP 0 2 types 0 Noncyclic 0 Cyclic Photosystem l amp Photosystem II 0 Found in thylakoid membrane 0 Capture light energy 0 Transfer excited electron 0 Together produce ATP and NADPH o Antenna complex light gathering unites o z 250 chlorophyll accessory pigments proteins 0 Reaction center 0 Location where chlorophyll a molecules transfer electrons to primary electron acceptors o Photosystem best absorption at z 700 nm Chlorophyll within photosystem Called P700 0 Photosystem best absorption at z 680 nm Chlorophyll within photosystem Called P680 Noncyclic photophosphorylation Production of ATP through energy from light 0 Photosystem Antenna complex absorbs photon E funneled to reaction center Reaction center a Energy causes electron in P680 to move to higher E level P680 excited I Energized electron is accepted by a primary electron acceptor called pheophytin n Electron moves down electron transport chain until it is donated to P700 that is in Photosystem n Turns to P680 not excited but extremely strong oxidizing agent 0 Photosystem Causes water to split to electrons e are donated to P680 to bring it back to neutrality H moved into thylakoid lumen Oxygen released Splitting of water photolysis FIG 911 Absorb photons O Energy is transferred to reaction center P700 Energized e transferred to primary e acceptor Passed down from ETC to ferredoxin Ferredoxin n Transfers e to NADP l NADPH NADPH n Released into stroma When P700 gives up e I P700 n Missing electron is replaced by Photosystem ll Noncyclic Zscheme As e move down ETC in photosystem II and photosystem I H ions pumped across thylakoid membrane from stroma into thylakoid lumen Summary 0 Light 0 Continuous oneway ow of electron 0 Water is the source of the electrons o NADP terminal electron acceptor which reduces it to NADPH 0 Pumps H 0 ATP amp NADPH are released into stroma Energy required for C xation reactions Cyclic energy transport O O O 0 Light dependent reaction Only photosystem I P700 absorbs light l P700 Electron passes down ETC until goes back to P700 Energy pumps H into thylakoid lumen Summary 0 O O O 0 Only in P700 Electrons are cycled through system H pumped ATP eventually produced No NADPH produced ATP Synthesis chemiosmosis Results from noncyclic and cyclic electron transport 0 E from electrons in ETC is used to pump H o Thylakoid lumen becomes acidic O pH of 5 Stroma is basic pH of 8 I There is proton gradient across thylakoid membrane 0 ATP Synthase o Transmembrane protein 0 Forms channels H move through channels Movement provides energy which is used in phosphorylation ADP Pi ATP Photophosphorylation a Result of chemiosmosis Carbon xation reactions 0 ATP amp NADPH o 6 C02 12 NADPH 18 ATP l C6H1206 12 NADP 18 ADP 18 Pi H20 0 Calvin Cycle C3 0 Most plants use this Stroma is location of cycle Does not require light directly Needs ATP amp NADPH 13 reactions 13 enzymes in stroma 3 main phases C02 uptake C reduction Rqu regeneration 0 C02 uptake C02 ribulose biphosphate Rqu 5c Enzyme rubisco n Unstable 6 C compound a 2 x PGA phosphoglycerate 3 C compound C from C02 now xed into organic compound 0 C reduction 0 Rqu regeneration o PGA I ATP used and turned into ADP amp NADPH turned into NADP l G3P glyceraldehyde 3phosphate 0 Turned into glucose or fructose 0 Or turned into Rqu 0000 O Respiration 10052012 Intro 0 Food source of energy Digestive system Break down food 0 Carbs Sugars amino acids 0 Proteins l Glycerol Blood stream Cells 0 Fats Fatty acids 0 Cellular respiration o Converts E of chemical bonds to chemical E stored in ATP 0 Aerobic uses oxygen 0 Anaerobic doesn t use oxygen Aerobic respiration of Eukaryotes o Catabolize break down nutrients into C02 and H20 0 Series of redox reactions e from nutrients transferred 0 z 30 steps different enzymes 0 Glucose common material for most cells Ex Brain uses ONLY glucose not only energy storage though 0 C6H1206 602 6H20 l 6C02 12H20 E Reactants Products 02 used aerobic Redox reaction a Glucose is oxidized H is removed l C02 n 02 is reduced 0 H added l H20 n Exergonic AG is negative I Table 81 Glycolysis quotsugar splittingquot Glucose enters cell via GLU71 Cytosol uid component of cell 0 2 Phases 0 1 Energy investment Glucose molecule gets 2P groups and splits into 3GP Phosphorylation reaction moves P group from ATP to the glucose molecule 0 2 Energy capture Substratelevel phosphorylation transfer of a P from a phosphorylated intermediate to form ATP Two pyruvates form chain of three carbons Summary 0 Phase 1 Glucose 2ATP l 2G3P 2ADP 0 Phase 2 ZG3P 2NAD 2Pi 4ADP l 2 pyruvate 2NADH 4ATP 0 Total Used 2ADP l 4ATP Net 2ATP l 2NADH Fig 83 Pyruvate conversion to acetyl CoA Mitochondrial structure 0 Outer membrane 0 Inside of outer is Inner membrane 0 Fold in inner membrane is cristae 0 Inside inner membrane is matrix 0 Between inner and outer membrane is intermembrane space Pyruvate from glycolysis o Diffuses through small pores in outer membrane into matrix Requires E Membrane protein pyruvate carrier 0 Reactions catalyzed by pyruvate dehydrogenase o Pyruvate undergoes oxidative decarboxylation reaction A carboxyl group is removed Coenzyme A binds to pyruvate dehydrogenase from panthothenic acid aBuit n Contains sulfur atom Acetyl CoA n Acetyl group activated easily transferred to an acceptor molecule a High E 0 FIG 85 0 Summary of pyruvate to acetyl CoA 2 pyruvate 2NAD 2CoA l 2 acetyle CoA 2NADH 2 CoA Total after glycolysis and pyruvate conversion 0 2 ATP 0 4 NADH Citric Acid Cyle Krebs Cyle Tricarbocylic acid TCA cycle 0 Matrix 0 Acetyle CoA 2C oxaloacetate 4C l Citrate 6C 0 Citrate reduces NAD to NADH and takes out C02 and ends up with 5 carbon compound 0 5 C compound reduces NAD to NADH and takes out C02 and ends up with 4 carbon compound 0 4 C compound reduces FAD avin adenine dinucleotide to FADH2 and reduces NAD to NADH 0 FIG 86 0 Summary of Citric Acid Cycle 0 2 cycles of CACglucose molecule 0 No ATP used 0 Produced 4 C02 6 NADH 2 FADH2 2 ATP 0 Now glucose completely oxidized End of 3 stages of aerobic respiration 4 ATP 0 Most of E from glucose in form of high E e in NADH and FADH2 o This E used to synthesis more ATP through e transport chain and chemiosmosis Electron Transport Chain ETC series of electron carriers embedded in inner mitochondria membrane 0 Function to transfer e from NADH and FADH2 to 02 c Fig 88 Carriers 0 Mostly proteins 0 Lipids 0 Can exist in oxidized and reduced forms 0 e passed down the chain in a series of redox reactions Carriers grouped into 4 distinct complexes 0 Complex l Accepts e from NADH and produces ubiquinone 0 Complex II Accept e from FADH and produces ubiquinone 0 Complex III Accepts e from ubiquinone and passes those e to cytochrome C 0 Complex IV Cytochrome C oxidase accepts e from cytochrome C to reduce 02 to form H20 0 Complexes I III and IV pump H from matrix into intermembrane space 0 Creates proton gradient 0 Matrix has higher pH than intermembrane space intermembrane space has lower pH because of more H 0 FIG 89 0 Complex V ATP synthase 0 Forms channels for H to diffuse through from intermembrane space into the matrix 0 H movement causes rotation and provides E for ADP Pi l ATP Chemiosmosis Model Explains coupling of ATP synthesis to e transport in aerobic respiration 0 Energy from H diffusion o Oxidative phosphorylation synthesis of ATP which occurs by chemiosmosis 0 FIG 811 Oxygen is terminal e acceptor l if oxygen is not available then ETC stops all steps of aerobic respiration ATP not produces Summer of aerobic respiration of one glucose molecule How many ATPs were used 0 TWO E investment phase What is produced 0 Glycolysis ATP 2 NADH 2 FADH2 0 o Pyruvate conversion ATP 0 NADH 2 FADH2 0 ATP 2 NADH 6 FADH2 2 0 Total ADP 4 NADH 10 FADH2 2 ln ETC 0 NADH o 28 ATP total Oxidation of FADH2 o 4 ATP total Grand Total 0 Glycolysis 2 ATP 0 CAC 2 ATP 0 ETC 28432ATP o 36 total Prokaryotes o No mitochondria o Aerobic resp cytosol o Phases same as eukaryotes o ETC 0 Plasma membrane 0 38 ATPglucose 16 October 2012 Chapter 24 amp 25 Prokaryotes 0 Prokaryotes Intro 0 Domains Bacteria Archae 0 Dominant 0 body 70 trillion cells 0 bacterial cells 700 trillion Pervasive Morphology Fig 251 0 Size 0 51 micrometer 0 Volume 11000 of eukaryotic cell 0 Shape 0 coccus cocci balls diplococcus group of two 0 streptococcus chain 0 staphylococcus clump 0 bacillusbacilli rods 0 spirals 0 spirillum rigid 0 spirochete exible 0 vibrilo short Cell structure 0 Lack membranebound organelles Have a nuclear area nucleoid 0 No mitochondria 0 No chloroplast Cytoplasm ribosomes 0 storage granules enzymes 0 Plasma membrane foldingsinward enzymes embedded Cell wall Fig 253 surrounds plasma membrane 0 functions 0 shape 0 provides physical protection prevents bursting in hypotonic environment 0 in a hypertonic environment cell will still plasmolyze 0 peptidoglycan 0 major component of cell wall 0 2 amino sugars linked by short polypeptides only in domain Bacteria differences in cell wall composition bases of Gram Stain 0 Gram positive 0 thick cell wall 0 made of peptidoglycan pick up and retain lots of crystal violet stain penicillin interferes with peptidoglycan synthesis most effective against gram positive bacteria 0 Gram negative 0 cell wall thin peptidoglycan layer 0 do not retain the crystal violet stain 0 outer membrane 0 thick lipopolysaccharides LPS toxic results in fevers 0 Cell Surface Structures 0 Capsule or slime layer 0 Capsule 0 surrounds cell wall 0 polysaccharides or protein 0 capsule organized tightly associated 0 Slime layer loosely attached 0 Provide protection against phagocytosis 0 Fimbriae and pili 0 hairlike 0 comprised of protein fimbriae shorter more numerous 0 used in attachment Flagella and cilia important in locomotion 0 Endospore Dormant stage 0 Survive unfavorable environmental conditions 0 Reproduction Genetical material 0 found in nuclear area 0 single circular DNA molecule 0 in addition may also have plasmids 0 plasmids 0 comprised of DNA 0 smaller circular replicate independently contains nonessential genes 0 ex resistance to antibiotics ex catabolic enzymes 0 gives them an advantage Binary Fission mechanism of reproduction asexual DNA replicates 0 wall forms between two cellsgt one cell divides into two cells Gene transfer 0 Exchange of genetic material between bacterial cells 0 Horizontal gene transfer occurs from one organism to another organism that is not its offspring 0 Transformation Fig 256 0 bacterial cell dies lyses DNA released 0 another cell takes up some of this DNA incorporates it into its own genome Transduction Fig 257 phage 0 type of Virus infects a bacterial cell 0 takes up some of the host cell s DNA unintentionally 0 phage carries bacterial DNA to another bacterial cell 0 gt DNA gets incorporated into new host cell s genome Conjugation Fig 258 0 two bacterial cells of different mating types 0 genetic material transferred from one type to the other Nutrition and E capture Table 251 0 C source 0 autotroph self feeder 0 can manufacture its own organic molecules 0 use inorganic C02 0 heterotroph obtains organic compounds from other organisms 0 E source 0 phototroph light E 0 chemotroph E from chem compounds from enVironment 0 ex photoautotroph ex cyanobacteria plants Archaea 0 Characteristics 0 cell walls lack peptidoglycan 0 plasma membrane strong lipids lipids lack fatty acids 0 have isoprene branched hydrocarbon isoprene chains 0 bonded to glycerol 0 attached by ether linkages glycerol attached to COH2 ether linkage between C and O Archaea in Eukaryotes glycerol attached to C02 double bond ester bond between C and single bonded O gt weaker ester linkage because 0 is electronegative and atoms are fighting for electrons Live in extreme habitats 0 early Earthgt extremophiles 0 thermophiles 45110 degrees C 0 proteins don t denature 0 halophiles 0 salty conditions 0 ex salt pond 20 salt methanogens produce CH4 gas 0 strict anaerobes 0 poisoned by 02 0 ex sewage marshswamps digestive tracts Bacteria 0 Ecological cyanobacteria 0 bluegreen algae gramnegative endosymbiantsgt chloroplasts 0 aquatic environments photosynthesis rhizobial bacteria mutualistic relationship with legumes live in nodules on roots 0 bacteria supply N to plant 0 plant supplies organic compounds to the bacteria 0 Disease spirochetes ex Lyme disease syphilis 0 rickettsias ex Rocky Mountain spotted fever 0 streptococci ex strep throat 0 Viruses 0 Characteristics 0 Nonliving particles 0 not cells 0 no nucleus 0 no cytoplasm no organelles 0 cannot carry out metabolic activities on their own 0 cannot reproduce on their own either DNA or RNA NOT both Genetic material Very small 0 20300 nm 0 need an electro microscope to see Obligate intracellular parasites invade susceptible host cells 0 survive only by using host cell s resources Do not grow and divide instead replicate multiply inside living host cell 0 Components Nucleic acids 0 DNA or RNA 0 information to allow virus to replicate Within the host cell 0 can be SS single stranded or DS double stranded 0 can be linear circular or segmented Capsid 0 protein coat 0 surrounds nucleic acid 0 determines shape of virus 0 attachment by some viruses to host cell Envelope some Viruses 0 acquire from moving through host plasma membrane lipid bilayer surrounds capsid Evolution of viruses 0 Cellular origin hypothesis 0 nucleic acids escaped from cellular organisms 0 ex plasmids explains specificity of Viruses 0 supported by genetic similarities between Viruses and host cells 0 Coevolution hypothesis 0 appeared before 3 domains diverged 0 originated from precells 0 Viral replication 0 Bacteriophages phage Virus that infects bacteria Lytic cycle 0 Virus destroys host cell 0 5 steps 0 attachment attaches to specific receptors on host cell 0 penetration through cell wall and plasma membrane into cytoplasm replication and synthesis Viral genome all information for making new Viruses 0 degrades host cell nucleic acids 0 gt Viral components synthesized instead 0 assembly Viral components assembled into new Viruses release lytic enzymes produced by the Virus 0 destroy the host plasma membrane 0 all steps take 2060 minutes 0 Lysogenic cycle 0 Viral genome integrated into host bacterial DNA prophage provirus integrated Virus 0 Viral proteinsgt responsible for repression replicates along with host chromosome harmful external enVironmental conditions are present harmful to the host 0 Virus reverts to lytic cycle 0 replicates and destroys host cell Lecture 12 Origin of Life ch21 10122012 Chemical Evolution 0 Life developed from nonliving matter 0 4 Requirements 0 1 Little or no free oxygen Oxygen oxidizes breaks bonds n Early Earth 0 Atmosphere used to be low in free oxygen 0 Atmosphere was strongly reducing l made bonds 0 2 Source of energy Simple inorganic molecules l biological molecules n Early Earth Thunderstorms Volcanoes o Meteorite Radiation no ozone lots of UV 0 3 Chemical building blocks 39 H20 Dissolved inorganic molecules Atmosphere C02 H20 vapor CO H2 N2 NH3 H25 CH4 0 4 Time Earth 46 billion years ago Life arose 35 billion years ago Lifeless Life Small organic molecules formed spontaneously l combined l organic macromolecules l combined l complex structures l gained functions l metabolism amp reproduction Formation of Small Organic Molecules o Prebiotic Soup Hypothesis OparinHaldane hypothesis 0 Hypothesis Life formed near Earth s surface Conditions favored spontaneous formation of simple organic molecules 0 Test of hypothesis Miller and Urey 19505 Designed closed apparatus a Conditions of early earth represented in apparatus H20 CH4 NH3 H2 0 Created energy in electrical spark lightning When compounds examined they found amino acids and other organic molecules I FIG 212 0 Recent Development Miller amp Urey s experiments have been repeated and have produced all nucleic acids all amino acids and a variety of lipids and sugars and even ATP 0 Does not work if Oxygen is added 0 Organic molecules accumulated in the seas quotOrganic soupquot lron Sulfur World Hypothesis 0 Cracks of ocean oor hydrothermal vents Protected from meteorite bombardment at surface Hot H20 CO minerals iron and nickel sul de Formation of Polymers Clay or rock surfaces 0 Negative ions attract and bind monomers o Particularly Zn and Fe2 are catalysts o In lab 0 Take amino acid solutions and drip onto hot rocks l forms polypeptides Complex Structures 0 Polymers selfassemble into protobionts under certain conditions 0 Protobiont 0 Aggregate of abioticallywithout life produced organic polymers 0 Ex microsphere Probiont formed by adding water to polypeptide Trap materials inside Characteristics n Electrical potential across surface n Absorb materials Undergo osmotic swelling and shrinking 0 Internal environment is different from external environment 0 Divide in 12 D No mechanism of heredity Living Cells 0 Metabolism First Hypothesis O 0000 0 Chemical reactions between simple molecules occurred in an enclosed space Use source of energy to drive reactions lnternal environment different from external environment Precell became organized and capable of growth Eventually precell developed ability to reproduce FIG 214 0 Origin of Heredity 0 Living cells Genetic information in form of DNA DNA is transcribed into molecule called mRNA messenger RNA mRNA translated into protein DNA l RNA l protein 0 RNA world hypothesis Prebiotic earth gave rise to RNA molecules capable of n Catalyze synthesis of RNA l RNA can replicate a Catalyze peptide bond formation l protein synthesis Ribozymes a RNA that have catalytic properties a RNA was 1st genetic material DNA evolved later a Perhaps RNA made doublestranded copies evolved into DNA Advantage Doublestrand more stable Evidence 0 No fossils that trace nonlife to life Nonfossil 0 Carbon isotopes in rocks 0 Represent metabolic activity 0 Cells developed approximately 38 billion years ago 0 Theory CONTROVERSIAL Microfossils 0 Ancient remains of microscopic life 0 Cells developed approximately 35 billion years ago 0 Theory CONTROVERSIAL Stromatolites 0 Rock like columns layers of dead cells 0 Slimy bacteria 00000 O Sediment sticks l mineralized New layers of cells grow over dead cells Repeated layering Found in Southern Africa Western Australia Apprx 35 billion years ago is when living cells evolved FIG 216 First cells proka ryotes o Heterotrophs 1 O 0 Obtain organic molecules from environment Do not synthesize molecules on own Fermentation anaerobic breakdown of organic compounds ATP yield is less than aerobic respiration Supply of spontaneously generated molecules declined o Photosynthetic Autotrophs 2nd 0 0 Use E from sunlight to produce their own food 1st ones probably used light E to split H rich molecules such as H25 H2S easy to split because S is not very electronegative Cyanobacteria type of photosynthetic autotrophs 0 Obtain electrons by splitting H20 Because H20 is abundant Oxygen is released Aerobes 3rd 0 As oxygen lives in atmosphere increased evolution of aerobic respiration occurred 0 Advantage over fermentation l extract more ATP Eukaryotes Appeared 22 billion years ago 0 Serial endosymbiosis O O 0 FIG 218 Main hypothesis to explain how eukaryotes arose from prokarytoes Mitochondria and chloroplasts Originated from a relationship between 2 prokaryotic organisms Smaller prokaryote was ingested by host larger prokaryote Smaller one survive digestion by host Evolved into mutually advantageous relationship Endosymbiant prokaryote on inside a Lost ability to survive on its own Host cell a Lost ability to live without endosymbiant Chloroplasts From photosynthetic bacteria cyanobacteria that lived inside larger heterotrophic bacteria Mitochondria From aerobic bacteria that lived inside larger anaerobic bacteria 0 Evidence 0 Mitochondria and chloroplasts Double membranes In lnner from endocymbiants plasma membrane a Outer from invagination of hosts of plasma membrane Size similar to bacteria Enzymes similarto bacteria DNA they have their own and similar to bacteria Ribosomes have their own and similar to prokaryotes Undergo binary ssion similar to bacteria 0 Problems 0 Doesn t explain how other membranebound organelles evolved History of Life 0 Carl Woese 1970 s 0 First to suggest that there are 3 major branches of organisms DOMAINS Recorded in rocks and fossils Earth s crust o 5 major rock strata o Mud and sand 0 Strata older on bottom younger at top 0 Characteristic fossils in each layer 0 Earth s history in units of time 0 Based on major events 0 Divisions of time Eons largest time scale a Eras Periods o Epochs Table 211 0 Three eons o Archaean eon 46 25 billion years ago When life originated on earth Little known about this time o Proterozoic eon 2500 542 million years ago More known Periods n Early Proterozoic Eukaryotes evolved a Ediacaran period 0 Evolution of multicellular softbodied animals 0 Phanerozoic eon Eras n Paleozoic Era Ex Cambrian period Cambrian radiation l rapid evolution of animals n Mesozoic Era Dinosaurs and other reptiles n Cenozoic Era 0 Age of mammals Lecture 14 Protists Ch 26 10192012 Intro 0 quotvery rstquot evolved 15 16 billion years ago 0 1st eukaryotic cells 0 Classi cation 0 Not a kingdom Classi cation of Eykaryotes o 5 super groups Archiplastids protists Chromalveolates protists Excavates protists Alveolates protists n Kingdom Plantae Unikants protists n Kingdom Fungi n Kingdom Animalia o Evolutionary relationships among eukaryotes FIG 263 0 Protists Eukaryotic o Nucleus and membrane bound organelles 0 Multiple chromosomes made of DNA and proteins 0 Variation among protists 0 Structure Unicellular Colonial n Loosely connected group of cells Multicellular a Simple body forms do not have specialized Ussues 0 Nutrition Most are Photoautotrophic n Chlorophyll Heterotrophic n Absorb food a Ingest food Mixotrophs o Locomotion Pseudopodia n Using cytoplasmic extensions of cells Gliding over surfaces In Over slime they produce Cilia of agella n Structure o 9 pairs of microtubules in ring 0 2 singlet microtubules in center 0 Photosynthetic protists o Algae o quotplantlike protistsquot Chlorphylla 0 Not plants because lack a cuticle waxy covering Lack true roots stems and leaves Lack multicellular reproductive organs 0 Many protists in plankton Free oating Mainly microscopic organisms ln upper layers of water Foundation of most marine and many fresh water food chains Excavates o Diverse only protists o Excavated deep oral groove Euglenoids FIG 265a amp b o Unicellular o Modi ed mitochondria Disc shaped cristae o Paramylon Polysaccharide Energy stoarage Pellicle exible outer covering Flagella 0 13 of them are photosynthetic Mixotrophs n Chlorophyll a Caratenoids u If grown in dark they lose chorophy and become heterotrophic O 0 Habitat Fresh water ponds and puddles Water with lots of organic material They are good indicators of organic pollution o Reproduction Asexually n Longitudinal division a split in half along long axis Chromoalveolates 0 Only protists Dino agellates FIG 266 0 O O 0 Most unicellular some in colonies Intracellular shell inside plasma membrane Cellulose plates Silicates 2 agella Groove in center of cell One agella wrapped within groove 2nol agella projects behind cell a Allows cell to spin and move forward Photosynthetic Chlorophyll Carotenoids n Fucoxanthin yellowbrown color Habitat Plankton Endosymbiants a Live inside bodies of marine invertebrates n Ex mollusks jelly sh coral n Zooxanthellae photosynthesis Asexual reproduction 0 Bloom population explosion Occur occasionally in some dino agellates Color water a Ex red tide xanthophyll red pigment Coastal pollution Some produce neurotoxins Diatoms o Unicellular Cell wall looks like petri dish 2 shells overlap and sealed together Lots of silica in shells n Silica causes glasslike appearance a 10005 of small perforations in walls a FIG 2610 0 No agella Move by secreting slimy substance 0 Photosynthetic Have chlorophyll Carotenoids 0 Fresh water Cool ocean water o Reproduction Most often reproduce asexually by cell division 2 halves of shell separate each half becomes larger half for new cell Once cell gets very small it produces shellless gamete Then gametes come together and produce zygote Zygote grows and then produces a shell FIG 2610b o Diatoms die Shells fall to ocean oor Diatomaceous earth used for n Filters n Scouring powders a Used to be in toothpaste too abrasive 0 Brown algae FIG 2611 0 Most complex protists o Multicellular o Largest of algae few cm to 75m Seaweed 0 Ex kelp Structure n Blade leaf like u Stripe stem like u Holdfast root like 0 Flagella bi agellate Reproductive cells 0 Photosynthetic Chlorophyll Carotenoids fucoxanthin 0 Marine Cold northern waters Kelp from under water forests o Reproduction Asexual and sexual alternation of generations n Spends portion of life cycle as haploid and portion as diploid o Align Polysaccharide In cell walls Holds water Thickener in pudding salad dressing hand lotion Golden Algae FIG 2612 0 Unicellular Covered with tiny scales of either a Silica or n Calcium carbonate 0 Bi agellate cells 0 Photosynthetic Chlorophyll Carotenoids n Yellowbrown n Xanthophyll o Freshwaterand marine Nanplankton 210 micrometers o Asexual reproduction Rhizarians o Protists o Forams o Actinopods Not photosynthetic Archaeplastids Supergroupincludes 0 Plants O Protists Red algae and green algae Red algae FIG 2614 0 O O Multicellular Highly branched No agella Photosynthetic Chlorophyll a Phyoerythrin Red accessory pigment n Phycocyanin 0 Blue I Carotenoids Yellowgreen Warm tropical waters Ocean Reproduction Alternation of generations Commercial importance Porphyra a Used to wrap sushi Agar n Polysaccharide found in cell wall D Gelforming lab culture Carrageenan n Polysaccharide a Food additive Stabilize foods 0 Green Algae FIG 2615 0 Cell wall Cellulose Starch is main food reserve Flagella present 0 Photosynthetic Chlorophyll Carotenoids 0 Fresh water some marine o Reproduction Varied sexual or asexual 0 Land plants arose from ancestral green algae Unkikants 0 Kingdom Fungi o Kindom Animalia o Protists O Lecture 15 Fungi Ch 29 10242012 Intro 0 Multicellularmosty Not photosynthetic Absorptive heterotrophs o No ingestion o No internal digestion 0 Resource acquisition Secrete Hydrolases into surrounding medium Polymers broken into monomers Absorb monomers Need moist environment 0 3 types Saprotrophs n Nutrients from nonliving organic material a They are decomposers Parasites n Absorb food from cells of living hosts 0 Ex athlete s foot 0 Cell wall chitin o Nitrogen containing polysaccharide Strong Flexible Durable o In contrast Prokaryotes n Gram pepticloglycan n Gram l pepticloglycan LPS Plants cellulose Habitats o Terrestrial 0 pH optimal 56 Range 29 0 Temperature wide range 0 Hypertonic environments saltsugar Body organization FIG 291 0 Nonreproductive Hypha e basic unit a Long branched laments n Grow Secrete Hydrolases Myceliam mycelia n Tangled mass of hypae Types of hypae n Coenocytic No individual cells 0 One cell gt 1005 10005 nuclei Called a septate n Septate hypae Cross walls Monokaryotic 0 Cells are haploid n o Dikaryotic nn 0 Each cell has 2 nuclei 0 Each nuclei is not identical Because each one came from opposite mating strains 0 Functionally similar to diploid Perferate o Septa has a pore o Organelles and cytoplasm move between cells not nuclei 0 Reproductive Spores n Produced by either 0 Aerial hyphae allows for dispersal of spores Fruiting bodies l mushrooms 0 Complex 0 Multicellular Reproduction 0 Spore Reproductive cell Haploid Not motile no agella Produced either at end of hypha or in fruiting body a Produced either asexually or sexually n Then germinates and grows a FIG 292 0 Meiosis Making gametes only in diploid cells 0 Gametangia Structures in which gametes form 0 Sporangia Structures in which spore are produced 0 Canidiophores Specialized hypae Produce conidia asexual spores FIG 294 0 Classi cation 0 O O O 0 Spore and fruiting body characteristics and molecular data Eukarya Supergroup unikant Kingdom Fungi 100000 species 5 phyla Table 291 FIG 295 Evolution of important characteristics Chytridiomycotachytridiomyceteschytrids Decomposers 0 Most primitive group O Earliest to evolve from protest ancestor Flagellated cells 0 Primitive characteristic 0 Chitin in cell wall 0 Absorptive heterotrophs Zygomycota 0 Intro o Decomposers in soil Hyphae coenocytic Septa 0 Separate non reproductive hyphae from reproductive structures Zygospores 0 Sexual spores Ex rhizopus stolonifer black bread mold 0 Black bread mold life cycle 0 FIG 299 Asexual reproduction n Spore falls on food resource bread 0 Starts to germinate grow a Hyphae grow Mycelium forms a Certain hyphae grow upward aerial hyphae Sporangia 0 Spore sacs at tips of aerial hyphae o Spores produced here Spores o 50000 produced within each sporangia o Produced by mitosis l asexually 0 Released when sporangium rupture Sexual reproduction n 2 mating types of hyphae and Heterothallic selfsterile o Hyphae mate only with opposite mating type and grow close together and each forms gametangium Gametangia fuse which is called plasmogamy o Plasmogamy fusion of cytoplasm but not nuclei and nuclei fuse l karyogamy o Karyogamy union of gametes sexual reproduction Zygote develops into zygospore Zygospore o Zygosporangium thick layer protects Resistant o Meiosis 2n l n o Germinate Aerial hyphae sporangium at tip 0 Sporangium Mitosis spores Sexual spores l released l germinate l hyphae Why have sexual reproduction n Favorable conditions asexual reproduction n Unfavorable conditions 0 Sexual meiosis Ascomycota 0 Intro 0 Singlecelled yeasts o Filamentas hyphae 0 Ex Yeasts Food spoilage molds Chestnut blight Truf es o Morels Hyphae o Perferate septa Life Cycle 0 Asexual reproduction Produce conidia haploid n Spores produced in conidiphores OOOO n Conidia break off germinate through mitosis l more hyphae a FIG 2912 0 Sexual reproduction and hyphae fuse n Nuclei of one hyphae migrate to other hypa n Plasmogamy cytoplasm fuse nuclei do not a Karyogamy does not occur right away cells stay in this phase New hyphae grow from fused structure U dikaryotic n n n Branching occurs a Asci ascus singular produced at tips of hyphae Ascocarp n Fruiting body a Produced by intertwining of monokaryotic and dikaryotic hyphae Within ascus n Karyogamy nuclei fuse n Zygote 2n n Zygote nucleus undergoes meiosis right away l 4 haploid nuclei a Each nucleus undergoes a mitotic division l 8 haploid nucleus a Each nucleus becomes incorporated into an ascospore 8 ascospores within each ascus Ascospores n Released through opening at top of ascus n Dispersed n Germinate n Go through mitosis 0 FIG 2913 0 FIG 2914 Yeasts o Unicellular o Asexual reproduction Budding No spores 0 Sexual reproduction 2 yeast cells fuse l produce zygote Zygote undergoes meiosis l 4 haploid nuclei l ascospores o Breads beverages Basidiomycota o Edible mushrooms braket fungi puff balls plant parasites wheat rust corn smut No asexual reproduction Sexual 0 Primary mycelium O Monokaryotic hyphae n and hyphae fuse l plasmogamy n n n Produce secondary mycelium l dikaryotic hyphae n n Primary and secondary mycelium underground most of mass Buttons produced n n compact masses of hypae each button l fruiting body mushroom basidicarp n n Basidicarp Stalk and cap Lower surface of cap has many gills n Gills lined with basidia Basidia enlarged hypal ce Karyogamy Zygote goes through mitosis l 4 haploid nuclei l nuclei move to edge of basidium Projectius form n Nucleus and cytoplasm move into each Each projection l basidiospore n Basidiospores sexual spores Outside of basidium 0 FIG 2917 0 FIG 2916 Glomeromycota Sexual reproduction don t know not documented Symbiants associations with roots of trees and herbaceous plants Ecological o Lichen FIG 2910 0 Symbiosis Fungus Ascomycota phototroph green algae cyanobacteria o Soredia Dispersal unite Both species 0 Mutualism Both species bene t 0 Mycorrhizae o Mutualism o Fungus zygomycote root Fungus bene t a Food from plant Root bene t a Water and minerals from fungus Lecture 16 Colonization of Land Ch 27 10262012 Intro 0 Until 440 million years ago all life on earth in oceans 0 Between 410440 million years ago plants 1st colonize land 0 Common ancestor of all plants charophytes stoneworts 0 FIG 2615d 0 Type of green algae protest 0 Shares characteristics with plants Photosynthetic pigments Cellulose Starch Cytokinesis cell plate formed 0 DNA amp RNA sequences 0 Plant characteristics 0 Eukaryotic o Photosynthetic autotrophs 0 Complex multicellular bodies 0 FIG 274FIG 275 Land adaptations Cuticle o Waxy covering o Prevent drying out 0 Does not allow for gas exchange Stomata is solution Stomata stoma 0 Tiny openings 0 Gas exchange Gametangia o Multicellular sex organs Layer of nonreproductive cells that surrounds and protects gametes o 2 types archegonium a Female n Produces single egg Antheridium a Male n Produces many sperm 0 Adaptation Gametes dispersed through air or by animals not by water Protect gametes and embryos from drying out o In comparison 0 Algae No cuticle No stomato Unicellulargametangia FIG 271 Gametes dispersed in water Reproduction Alternation of Generations 0 Part of life cycle in multicellular haploid stage and part in multicellular diploid stage 0 Life Cycle 0 FIG 272 0 Gametophyten haploid Antheridia male sperm produced Archegonia female egg produced a When sperm and egg come together FERTILIZATION l zygote formed within archegonia l becomes multicellular embryo l embryo is young sporophyte plant a Sporophyte mature plant 0 2n diploid Sporogenous cells 0 Spores are produced by meiosis o Spores go through mitosis o Becomes multicellular gametophyte 0 NOW WEquotVE GONE FULL CIRCLE D Major plant groups TABLE 271 10 extant plant phyla Bryophytes o Mosses o Liverworts o Hornworts 0 Lack specialized vascular system nonvascular plants 0 Evolved 400460 million years ago Seedless Vascular Plants 0 Ferns horsetails whisk ferns and club mosses 0 Need water to reproduce o Evolved 420 million years ago Gymnosperms 0 Seed plants 0 Evolved 360 million years ago 0 Vascular plants 0 Ex conifers Angiosperms o Flowering plants 0 Flowers form seeds that are enclosed in fruit o Evolved 130 million years ago 0 Vascular 0 Dominant today 0 Vascular Plants 0 Vasculartissue Specialized system for transporting substances through plant body Xylem water and mineral conduction Phloem dissolved organic molecule conduction o Lignin Key step in evolution of vascular plants Found in cell wall of cells that function in support and conducUon Allows plant to grow tall n Maximizes light interception Bryophytes Intro 0 Most closely related to 1st land plants 0 Only nonvascular plants Very small no extensive means of internal transport Diffusion and osmosis is mode of transport U Need to live in moist environment a Water allows for reproduction sperm agella movement Mosses o Morphology Plant El rhizoids hairlike structure functions in absorption upright stemlike structure with leaf like blades at top No vascular system so El Do not have true roots stems or leaves Life cycle FIG 277 El El Alternation of Generations Many species separate male and female other species have one plant male and female gametangia Gametophyte n 0 Dominant generation 0 Because can live independently of the sporophyte generation 0 At tip of gametophyte shoot 0 Antheridium sperm 0 Archegonium one egg 0 Fertilization o Sperm has two agella bi agellate o Transported from antheridium to archegonia through water or insects o Sperms lands on archegonia swims in and fuses with egg Zygote 2n o Grow by mitosis o Multicellular embryo l develops into mature sporophyte plant Sporophyte o Grows out of female gametophyte 0 But remains attached and nutrionally dependent on gametophyte 0 Initially green but at maturity it s brown Sporophyte 0 Foot anchors to gametophyte 0 Materials are absorbed through gametophyte o Seta stalk o Capsule Bit of photosynthesis Sporoganeous cells 0 Calyptra In some species of mosses Covers capsule Derived from archegonia Sporogenous cells 0 Undergo meiosis 0 Form haploid spores 0 Main function of sporophyte is to produce spores Mature spores Capsule opens up and spores released 0 If spore lands in suitable location weather it will germinate 0 1st a lament of cells l protonema n 0 Forms buds Each bud grows unto a gametophyte green 0 Plants that are NOT mosses Spanish moss owering plant lrish moss algae Reindeer moss lichen Liverworts FIG 279 Nonvascular 0 Dominant gametophyte generation Thallus body of gametophyte o Flattened lobed o Underside of thallus rhizoids anchor plant to soil 0 Damp environments 0 Life cycle 0 Similar to mosses Hornwarts FIG 2710 o Thallus plus hornlike structure 0 Horn like structures sprophyte Seedless Vascular Plants 0 Intro 0 Vascular system xylem and phloem o All have true stems with vascular tissue 0 Most also have true roots and leaves 0 Whisk fern FIG 2717 0 No true roots or leaves 0 Rhizome Horizontal underground stem covered with rhizoids Horse tail FIG 2718 0 True roots stems and leaves 0 Ancient plants coal deposits 0 Club mosses 0 Not moss 0 True roots leaves and stems o Temperate woodlands o Ferns 0 Most numerous today of seedless plants 0 Mainly tropics o Fern life cycle FIG 2716 Sporophyte generation dominant n Rhizome bears true roots and fronds leaves 0 As frond rst emerges very tightly coiled o Called ddlehead o Fiddlehead grows l expands l unros l becomes frond n Sori On underside of frond Each sorus is a cluster of sporangia Sporangia contain sporogenous ces 2n 0 Sporogenous cells undergo meiosis l haploid spores n Spores released and then germinate Undergo mitosis to become gametophyte which is called prothallus o Prothaus is tiny independent lacks vascular tissue produces both archegonium and antheridium 0 Water transports sperm to egg n Fertilization occurs Produces zygote 2n 0 Goes through mitosis and becomes muticeuar embryo which is attached to and dependent on gametophyte Sporophyte pants becomes independent and kills gametophyte Homosporous vs Heterosporous Plants Homospory o All spores are same 0 bryophytes horsetails whisk ferns and most ferns and club mosses Heterospory O O 0 Some types of ferns and club mosses and all seed plants Production of 2 different kinds of spores Megaspore and microspore Sporangium On sporophyte Spore case in which spores are formed Megasporangium produces megasporocytes Megasporocytes goes through meiosis l turns to megaspores l produces gametophyte l produces an egg in archegonium Microsporangium produces microsporocytes Microsporocytes goes through meiosis l turns to microspores l goes through mitosis l produces gametophyte l produces sperm within antheridium Microspores in seed plants Evolved into pollen which disperses through air This is signi cant development in plant evolution because it was forerunner of seed evolution FIG 2719 Lecture 17 Seed Plants Ch28 Intro 0 Alternation of generations 0 O O O Sporophyte l dominant 2n Gametophyte Reduced in size Heterosporous Sperm no agella Pollination Vascular tissue Xylem Phloem Seeds 11072012 Multicellular welldeveloped plant inside sporophyte I Has embryonic root stem and leaves a baby Food supply Seed coat protective Types Gymnosperms naked seeds I Seeds are either totally exposed or on scales of cone a Most are evergreen Angiosperms contained seeds n Flowering plants a Seeds within fruit Gymnosperms o 4 phyla FIG 282 Conifers o Woody plants seeds in cone 0 Ex pines spruces rs o Characterized by needles Needles n are considered leaves a are adapted to dry conditions a thick cuticle n stomata in pits reduces water loss 0 Most are evergreen 0 Pine Life Cycle FIG 284 0 Pine tree sporophyte o Produces microspores and megaspores in separate cones FIG 285 Most pine trees are monecious male and female cones on same tree 0 Male cone pollen cone Small and on lower branches than female cones Sporophylls leaflike scales 2 microsporangia at base of each sporophyll Each sporophyll contains microsporocytes Each microsporocyte 2n l undergoes meiosis l haploid microspores l mitosis l reduced immature male gametophyte l pollen grains Pollen grain n 4 main cells Generative cells l produce sperm 0 One tube cell l produces pollen tube 0 2 remaining cells degenerate Also 2 large air sacs on pollen grain a Used for wind dissemination 0 Female cones seed cones Upper branches of tree 2 megasporangia or ovules on upper surface of each cone scale a Within each megasporangium is a megasporocyte 2n Megasporocyte l meisosis l 4 haploid megaspores one megaspore undergoes mitosis l megagametophyte l produces an egg Gametophyte a Female a Reduced a Not photosynthetic n Dependent on sporophyte for nutrition Pollination pollen grain carried by wind and lands on scales of female cone U Tube cell grows pollen tube 0 NOW have mature male gametophyte mature microgametophyte Pollen tube digests through megasporangium to the egg in archegonium n 2 sperm formed from generative cell and travel down pollen tube 1 sperm degenerates n Fertilization Egg sperm occurs 1 year after pollination l produces zygote 2n Seed develops from ovule megasporangium any enclosed structures a Embryo 2n root and leaves a Surrounded by female gametophyte n food a Seed coat develops from integuments layers of sporophyte tissue Surrounds megasporangium Seed germinates l sporophyte 2n pine tree 0 Other gymnosperm phyla o Cycads FIG 286 0 Gingko FIG 287 0 Gnetophytes FIG 288 Angiosperms owering plants 0 Intro o Evolved 130 million years ago 0 Most successful group of plants today 300000 species 0 2 classes monocots eudicots Table 282 0 Flower 0 Intro Reproductive structure a Involved in sexual reproduction Various forms 4 basic parts a Complete ower has all 4 parts a Incomplete ower is missing 1 or more parts 0 Flower parts Sepal outermost part of ower n Leaflike a Green usually a Covers and protects the bud n Sterile ower part not directly involved in reproduction n Leaflike u If petal is brightly colored it functions to attract animal pollinators u If petal is dull they are wind pollinated n Sterile ower part Stamen male organ n 2 parts anther and lament n Anther meiosis takes place here Pistil female organ n Stigma at top Sticky 0 Location where pollen lands a Style long quotstemquot of pistil o Pollen goes through style a Ovary quotsacquot at base of pistil Single or compound ovary Each compartment is carpel o Carpels bear ovules n Ovule megasporangium Contains gametophyte l produces egg Ovule eventually developing into seed El El El Ovule surrounded by integuments layers of sporophyte tissue 0 Developes in the two parts Perfect ower Stamens AND pistis Imperfect ower stamen or pistis but not both FIG 2810 FIG 2811 FIG 2812 Plant reproduction CH 28 amp 37 0 Life cycle 0 Development of female gametophytes o Ovary 1 or more ovules inside Each megaspore into contains megasporocyte Undergoes meiosis to produce l o 4 haploid megaspores 3 megaspores are disintegrate 1 min which undergoes 2 mitotic divisions Created 8 haploid nuclei 0 Develop into mature family gametophyte Known as embryo sac 7 cells 8 nuclei n Our cell egg cell 3 cells antipodals disintegrate 2 cells submerged Central cell a 2 nude polar nuclei n Eggs and central cell directly matured in fertilization Ga meotphye O O O O O O O Anther contains microsporangia Each microsporangia has many microsporocyte Microsporocyte l undergoes meiosis l 4 haploid microspores Microsporocyte bursts open Releases microspores Each microspore develops in an immature male gametophyte AKA pollen grain Pollen grain Tube cell Generative cell Another splits open This sheds pollen FIG 373 Pollination 0 Transfer of pollen grains from another to stigma o Selfpollination Within same ower or Occurs between different owers on same plant 0 Crosspollination Transfer of pollen to ower on different plant Prevents inbreeding incest Cross pollinators have selfincompatibility n Selfincompatible pollen can t fertilize ower on same plant Abiotic wind or water a Many owers a Flowers are inconspicuous a No nectaries Nectaries structures that produce nectar sugary solution a Separate male and female owers a Ex corn oak trees grasses ragweed Biotic animals n Mutualistic relationships between plant and animal 0 Both partners bene t 0 Plant gets transport service 0 Animal some sort of reward 0 Ex food nectar pollen or breeding site mating or brood site where animal s offspring develops a Coevolution 2 species interact so closely that both become adapted to each other and undergo evolutionary change a FIG 374 a Table 371 0 Pollen grain lands on stigma Germinates U Tube cell l produces pollen tube a Pollen tube grows down the style a Down the style into the ovary n Syngerids release LUREs LUREs are two polypeptides that direct pollen toward ovary Released when synergids disintegrate n Germinated pollen grain pollen tube mature male gametophyte Generative cell a Goes through mitosis l which moves down pollen tube into embryo sac n Both sperm involved in fertilization double fertilization o Doublefertilization One sperm fuses with egg l produces zygote 2n Other sperm fuses with 2 haploid polar nuclei of central cell l produces 3n cell triploid n This triploid grows by mitosis n Produces endosperm triploid tissue has lots of nutrients o This nourishes growing embryo FIG 377 0 Mature seed Seed coat from integuments outermost layers of ovule Embryo 2n n Radicle consists of embryonic root n Cotyledons Seed leaves Monocots 1 cotyledon Eudicots 2 cotyledon n Hypocotyl This connects radicle and cotyledons o Develops into stem n Plumlule 1st true leaves Endosperm 0 Fruit 0 Function Protect seed Aid in dispersal of seeds 0 4 types Simple a single ovary several fused carpels n Ex peach green bean tomato Aggregate FIG 3711 a Single ower with several separate carpels n Ex raspberry Multiple a Group of several owers a Walls of ovaries fuse together a Ex pinapple Accesorry D Other plant tissues in addition to ovary n Ex apples pears Plant Anatomy Ch33 11092012 Plant Cell Nucleus and organelles Central vacuole 0 90 of volume of cell is water 0 Tonoplast 0 Functions Growth a Water added to vacuole which leads to increase in size of cell a Hydrostatic turger caused by pressure from all the water Storage D Ex proteins toxic chemicals Lysosomal break down of molecules 0 Plastids o Membranebound organelles 0 Functions Chloroplasts Anyloplast n Starch storage Chromoplast n Pigments 0 Cell Wall 0 Primary cell wall All plant cells Cellulose polysaccharides protein Hydrogen bonding n Bundles of ber formed from Hbonding Growing cell a Thin exible primary cell wall Mature cell a Either primary cell wall thickens and solidi es or secondary cell wall forms 0 Secondary cell wall not in all plants Forms between plasma membrane and primary cell wall Polysaccharides and lignin Lignin strengthening polymer In Not carbohydrate a May be composed of amino acid monomers Support and protection Wood I Made up mostly of secondary cell walls 0 Middle lamella Zone between primary cell walls of adjacent cells Comprised of pectin cementing polysaccharide like glue holding cell together As food ripens pectin dissolves Thickening agent in making jams and jellies Plant Body 0 2 systems 0 Root system below ground 0 Shoot system above ground 0 Cells tissues and organs 0 Cell Basic functional unit of a plant Variety of types Organized into tissues 0 Tissue Group of cells that are associated and function together 0 Simple tissue only one type of cell 0 Complex tissue two or more types of cells 0 Tissue systems in owering plants TABLE 331 Ground Tissue system a Photosynthesis storage and support Vascular n Conduction support Dermal U Covering Organs Each organ is composed of all three tissue systems 0 Roots stems leaves ower parts and fruits 0 Ex crosssection of herbaceous eudicot FIG 323 Ground Tissue System Composed of 3 simple tissue TABLE 332 and Fig 333 Parenchyma cells 0 Characteristics Thin exible primary cell wall Most cells do not have secondary cell wall Cells are alive at maturity They are the least specialized of all cells They can differentiate into other cell types Most common cell type 0 Form parenchyma tissue 0 Functions Photosynthesis Storage Secretion n Hormones n Enzymes n Nectar n Tannins Soft parts of plant Collenchyma cell 0 Characteristics Primary cell walls are unevenly thickened corners are thickest Elongated Alive at maturity Found near stem surfaces and along leaf veins Extremely exible 0 Form coenchyma tissue 0 Functions Purely structural No metabolic tissue Grouped in stands l provides support 0 No secondary cell wall 0 No lignin 0 Ex ceery strands are coenchyma tissue Sclerenchyma cells 0 Characteristics Have secondary cell walls Lignin Hard strong Used in structural support Dead at maturity o 2 types sclereid cell a Short cuboidal thick secondary cell wall lots of lignin n Ex Grit in pears or peach pit is comprised of sclereid cells Fiber cell a Long slender tapered at ends a Occur in bundles I Found in wood and bark of owering plants a Important in protecting and supporting stems and roots and leaves Vascular Characteristics 0 Embedded in ground tissue 0 Transports materials through xylem and phloem 0 Functions in support 0 Xylem 0 Function Conduct water and dissolve minerals Direction From roots l stems and leaves Structural support 0 Composition in angiosperms Complex tissue Comprised of 4 cell types a Tracheids n Vessel elements a Xylem parenchyma cells function in storage a Fiber cells function in support 0 Tracheids Dead and hollow at maturity only cell wall remains Have secondary cell walls Long tapered cells Important in support Function in conduction from roots to shoots a Water passes from 1 tracheid to another through pits Pit n Thin area in tracheid cell wall I Has primary cell wall but no secondary cell wall a NOT a hole just a thin area n Pits slow down water movement results in inefficient conduction 0 But if air gets in tracheid cell traps it away from system makes system safe for water Tracheids are chief water conduction cells in gymnosperms and seedless vascular plants 0 Vessel Elements Phloem Dead and hollow at maturity Has secondary cell wall lots of lignin Short Have perforations holes at either end of cell Pits inside side wall a This allows for lateral conduction Vessel n Stack of vessel elements acts as pipeline High speed conduction l efficient Need continuous column of water is need conduction will shut down NOT safe 0 Function Conducts dissolved CHzO throughout plant Structural support 0 Composition in angiosperms Complex tissue 4 different cell types n Sieve tube elements a companion cells n phloem parenchyma cells storage a Fiber cells support 0 Sieve Tube elements Alive at maturity but lost many organelles Do NOT have a nucleus mitochondria ribosomes and tonoplast vacuole DO have ER plastids plasma membrane primary cell wall Elongated On end walls a Sieve plates tiny pores at either end Stacked to form sieve tubes n Cytoplasm extends from cell to cell through sieve plats Conducts dissolved sugar 0 Companion cells At least one companion cell adjacent to each sieve tube element Living at maturity with all organelles n Nucleus controls activity in sieve tube element as well Moves sugar into and out of sieve tube elements a Load and unload sugar I Can do this against concentration gradient Requires lots of metabolic E 0 So there are lots of mitochondria for ATP 0 Plasmodesmata Cytoplasmic connections between companion cells and sieve tube elements Organelles can t pass through 0 TABLE 333 and FIG 334 Dermal Tissue system 0 Characteristics 0 2 complex tissues epidermis Periderm 0 Function in protective covering Herbaceous plant non woody plant 0 Dermal tissue Single layer of cells l called epidermis n Outermost layer of plant 0 Epidermal cells No chloroplasts Transparent Those covering aerial parts of plant stems leaves owers fruits Minimize water loss by secreting waxy cuticle El El El Cuticle covers surface of exterior walls Prevents water loss Slows down gas exchange 0 Stomata minute pores Each surrounded by 2 guard cells Carbon dioxide water vapor oxygen passes through by diffusion o Trichomes Outgrowths hairs Functions El Ex in salty environment trichomes will be one leaves and function will be to remove excess salt Ex in desert plants trichomes on aerial parts of plants and function will be to increase re ection of light to keep internal tissues cool and reduce water loss 0 No periderm Woody plants 0 As plant increase in girth epidermis sloughed off and replaced by periderm o Periderm outer bark of older stems and roots of plant Plant Growth 0 When plant grows cell divide only in speci c areas the meristems Meristems composed of cells whose primary function is to form new cells mitosis 0 Primary growth Increase in stem and root length 0 All plants undergo primary growth 0 Results of activity in apical meristems Apical meristems at tips of roots and shoots O 0 Secondary growth OOOO Increases in girth Only in gymnosperms and woody angiosperms Lateral meristems Responsible for production of wood and bark Lecture 20 Plant Transport 11162012 Leaf Photosynthesis 0 Thin and ax max absorption of light 0 C02 and 02 can undergo internal diffusion in the leaf Dermal Tissue o Epidermis on upper and lower surfaces Covered by cuticle waxy layer which prevents water loss 0 Stomata More stomata on lower surface of leaf Open during day Closed at night amp during drought Controlled by guard shell shape which results from movement of water a into the guard cells l They become turgid and produce pore u out of guard cell collapse against each other and become accid close pore o Mechanism of stomatal opening FIG 3410 Blue light 400500 nm a Triggers H pumps in guard cell membrane a Pump H out of cell create gradient n H gradient drives facilitated diffusion of K into guard cells n Chlorine ions and other negative ions also enter guard cell maintains electrical balance Solute concentration is now higher inside cell 0 Water moves into guard cell 0 So turgidity of guard cell increases 0 And now pore opens During the day K concentration in guard cell decreases Sucrose levels goes up 0 Because hydrolysis of starch is occurring 0 Sucrose is osmotically active it dissolves This increases solute concentration inside cell Pore stays open By evening Sucrose concentration goes down 0 Cell is converting back to starch Starch is not osmotically active does not dissolve So water moves out of cell 0 Cell then becomes accid Pore closes El El El GroundTissue o Mesophyll Photosynthetic tissue Parenchyma cells I Has chloroplasts n Loosely packed a Gas exchange 0 Two sublayers Palisade mesophyll n Columnar n Toward upper epidermis a Main site of photosynthesis Spongy Mesophyll a Lower epidermis n Loosely arranged a Gas exchange 0 Vascular Tissue 0 Vascular bundles Extend through mesophyll 0 Each vein contains Xylem toward upper epidermis Phloem toward lower epidermis Eudicot vs Monocot leaves o Eudicot Blade broad at part of leaf Petiole stalk that attaches the blade to the stem Netted venation Separate palisade and spongy mesophyll layers 0 Monocot Narrow Often lack petiole n lnstead base of leaf wraps around stem Parallel venation Palisade and spongy layers are usually not in separate layers 0 Modi ed leaves FIG 3414 0 Spines Found in cacti Function is protection 0 Tendrils Found in vines Climbing o Bud scales Protect tip of shoot 0 Bulbs Storage of food Large eshy leaves attached to short underground stem Ex onion 0 Succulent leaves Water storage Ex jade plants Stem Functions 0 Support 0 Internal transport 0 Produce new tissues Buds develop into stems with leaves or reproductive structures 0 Stem external structure FIG 357 0 Bud undeveloped embryonic shoot Can develop into owers stems or leaves 0 Bud scales Outer protective layer 0 Node Area where leaf is attached 0 lnternode Region between nodes 0 Leaf scar Where leaf WAS attached 0 Bundle scar Within leaf scar where vascular tissue used to extend from stem to leaf 0 Lenticle Loosely arranged cells in the bark of woody twigs Oxygen and other gases and can diffuse through entices 0 Stem internal structure 0 Dermal Tissue epidermis covered with cutice and stomata 0 Ground tissue Cortext n Parenchyma cells Photosynthesis Storage D Collenchyma amp scerenchyma Support Pith n In center of stem n Parenchyma cells n Storage 0 Vasculartissue Embedded in ground tissue Conduction amp support Vascular bundles n In circle around edge of stem n Xylem towards inside a Phloem towards outside Support a Xylem tracheids and vessel elements and bers n Phloem bers a FIG 351 0 Stem internal structure monocot O O O O Dermal epidermis cuticle Ground tissue No distinct cortex or pith Vascular bundles Scattered throughout stem Each bundle enclosed in sheath Comprised of sclerenchyma cells FIG 352 Monocot stems No lateral meristems Primary gravity only 0 Secondary growth in stems 0 Vascular cambrium between primary phloem and primary xylem They divide and produce secondary xylem wood and replaces primary xylem And secondary phloem inner bark replaces primary phloem o Cork cambrium Divide and produce cork cells and cork parenchyma Periderm outer bark n Formed from Cork cambrium Cork cells Cork parenchyma Transport 0 Water and minerals 0 Overview Water is taken up by roots into xylem l to stem l to leaf n Unidirectional a Water and mineral transport 0 NO ENERGY REQUIRED 0 Water potential Psi W Free E of water a Amount of E available to do work Measure of cell s ability to absorb water Water s tendency to evaporate Reference point pure water at sea level W 0 mega pascas MPa unit of pressure a Higher W the more potential E is available to perform work when water moves a W decreases when solute dissolves in water a Solute molecules and ions associate with water molecules which causes motion of water moleucles and W lowers more negative a Water moves from region of higher less negative W to region of lower more negative n In other words W a Water moves from hypotonic to hypertonic Solution 1 Solution 2 Less solute More solute Hypotonic Hypertonic Les negative W More negative W EX 1 EX 2 Net movement of water From solution 1 l solution 2 Transport of water and minerals Unidirectional n Soil l root l stem l leaf Large amounts of water moved fast Table 351 Uptake of water and minerals by roots U Soil W Varies depending on how much water in soil 0 Extremely dry relatively more solute hypertonic o W is very low very negative 0 Soil is most hypotonic o W is higher less negative I Root W 0 Negative because of dissolves olutes n Movement of water 0 ln dry soil 0 Soil has higher solute concentration soil is hypertonic to root so water moves from root to soil Moist soil 0 Roots hypertonic to soil roots more negative W water moves from soil to roots Root pressure a Pushes water from roots up through stem to top of plant a Minerals from soil pumped into xylem Decreases W in xylem So more water enters into xylem from root n Guttation Results from root pressure Occurs when soil moisture is high and transpiration is low Transpiration Loss of water through stomata Water forced out of hydathodes in leaves a Tensioncohesion model transpiration cohesion model Long distance movement of water Soil l root l root xylem l stem xylem l leaf xylem l leaf mesophyll l exit in stomata Photosynthesis begins at start of day 0 Stomata open 0 Water diffuses out transpiration Transpiration o Evaporation of water 99 of absorbed water 0 Bene cial Mineral transport Evaporative cooling sweating Maple tree a Loses 200Lhour Transpiration pull 0 Unbroken chain of water molecules 0 Cohesion Sticking to each other o Adhesion Sticking to walls of xylem cells 0 Sugar Translocation o Photosynthetic Sugar 0 Sucrose glucose fructose o Phloemconducts dissolved sucrose Bidirectional n Sugar made in leaves photosynthesis l down to roots I Sugar stored in roots up to other parts of plant Slower than xylem o Translocation transport of food in plant Source area with excess sugar Sink area of storage or metabolism Movement is from source sink Variable movement one thing could sometimes be a source or be a sink 0 PressureFlow Hypothesis Pressure gradient n Between source where sugar is loaded into phloem and sink where sugar is unloaded ln source a Ex leaf sucrose Sucrose moves into companion cells n Loading 0 Movement of sucrose from companion cells into STE of phloem 0 Active transport ATP 0 lncse concentration of solute in sieve tube elements water potential decbeomes more negative 0 STE solution hypertonic relative to xylem o I water moves from xylem into STE this causes hypostatic pressure in sieve tubes 0 Pressure pushes sugar solution through phloem from region of high pressure to region of low pressure ln sink a Unloading Sugar moves out of STE and into sink cell a Ex root cortex parenchyma cell Requires ATP active transport STE water potential increases less negative STE hypotonic relative to xylem Water moves out of sieve tubes and into xylem FIG 3512 Lecture 21 Hormonal Control 11212012 Intro Hormone 0 Organic compounds 0 Signal or chemical messenger o Elicits physiological response 0 Animals 0 Produced in one part of body and transported long distances 0 Large and complex 0 Many kinds Each has very speci c effect 0 Plants 0 Effect in body close to were produced 0 Small molecules 0 Few types Responsible for regulating almost all aspects of a plant s life Each can have many different effects Interact with one another Concentration 0 Hormonal balance 0 Ropisms Directional growth response that is produced by an environmental stimulus Directional a Positive grows toward stimulus a Negative grows away from stimulus Ex phototrophism a Light a Phototropins yellow pigment Absorbs blue light a Trigger responses El a FIG 381 0 6 Major classes of plant hormones Table 381 Auxin 1st plant hormone discovered o Darwin s experiments 18705 0 Phototrophism o Canary Grass Coleoptile protective sheath that surrounds stem a First part of grass seeding to emerge from soil When exposed to light from only one direction l plant bends toward light 0 Experiments FIG 383 Shieldedremoved coleoptile at tip then bend DID NOT occur Shielded below tip then bend DID occur Conclusion n Something from upper part of coleoptile is in uences lower part and causes stem to bend 0 19205 auxin is responsible for bending o Auxin Group of natural and arti cial hormones IAA indolacetic acid a Most common and physiologically important natural auxin Main site of production is the shoot apical meristem Transport is polar unidirectional It is down shootroot axis 0 Active requires ATP 0 Functions 0 Elongation of stems and coleoptiles Elongation of cell wall Cell wall a Primary 0 Has cellulose bers plastic a Secondary Cellulose and lignin 0 Unable to expand a Auxin works only on primary cell walls Mechanism n IAA involved in pumping H into cell wall 0 l cell wall is acidic l activates an enzyme 0 l enzymes breaks crosslinks between cellulose bers 0 l makes cell wall more plastic a Cell takes up more water by osmosis l causes elongation Why does cell elongate rather than grow in all directions I Has to do with orientation of cellulose bers 0 Phototrophism When plant is exposed to light from one direction I plant bends towards light Auxin travels laterally to shaded side of stem then moves down stem by polar transport Cells on shaded side are exposed to higher concentrations of auxin that light side 0 Fruit Development Auxin released by seeds Apply to certain owers in which fertilization has not yet occurred l ovary englarges n Fruit seedless Ex seedless tomatos o Apical dominance Herbicides o 24D and 245T These are synthetic auxins Function as selective herbicides Kills plants with broad leaves weeds but not grasses Strucutre lAA l disrupts growth 245 T not allowed in US dioxins produced Agent orange 5050 mix Gibberellin o Promotes stem elongation 0 Causes cells to divide and elongate 0 Molecular rearrangement of polysaccharides in cell wall 0 Ex corn Apply gibberellin to n Dwarf corn 0 Make this grow as tall as normal com a Normal corn Often no response 0 Seed Germination o Barley seeds o Imbibition process by which seed absorbs water and becomes activated 0 Embryo releases gibberellin into endosperm outer layer 3n 0 Gibberellin triggers synthesis of alphaamylase l secreted into inner endosperm layer very starchy o Breaks down into glucose l absorbed by embryo o Flowering 0 Ex biennials lives for 2 years 1st year no owers 2ncl year produces owers 0 If gibberellin applied in 1st year owers will develop 0 Bolting 0 Rapid elongation of a stalk with a ower 0 Fruit Development 0 Ex spray on grapes l gibberellin makes it get larger Cytokinins Promote cell division and cell differentiation Apical dominance 0 Growth in plant is almost all from apical meristem rather than the axillary buds o Controlled by interaction between cytokinins and auxins Antogonistic Auxin produced in apical meristem and inhibits growth of axillary buds form lateral branches Cytokinin n Promote growth of axillary buds 0 Plants with apical dominance get ta NOT branch out Pinch off tips of plant a Remaining is apical meristems No auxin o Axillary buds are not inhibited Causes full bushy plant Senescence 0 Slow aging process 0 Cytokinins produced in roots 0 Cut a plant at stem no more cytokinins Ethylene C2H4 Gas 0 Role in senescence 0 Fruit ripening 0 Middle amea Pectin dissolves 0 Color changes 0 Acidity and avor changes 0 Fruit produces ethylene Commercial Use 0 Ex tomatoes Picked before ethylene triggered Put into environment where there is no ethylene n Cold air movement C02 Gassed with ethylene l stimulates ripening don t taste good because it s not natural 0 Functions 0 Inhibits cell elongation o Promotes seed germination o Promotes apical dominance o Involved in responses to wounds and invasion ABA abscisic acid 0 Nothing to do with abscission leaves falling quotStress signal hormonequot 0 Ex doughts Water loss Wind Leaf produce ABA a Close stomata 0 Ex onset of winter Domancy in plants ABA produced in terminal buds n Shoots make bud scales n Inhibits primary growth in shoots a Inhibits cell division in vascular cambria n Dormancy in seeds 0 Seeds high levels of ABA 0 Can t germinate until ABA is washed out BR brassinosteroids 0 19905 0 Group of steroids 0 Functions Cell division Cell elongation Vascular development Seed germination OOOO Lecture 22 Genetics 11282012 Heredity 0 Transmission of genetic info from parent to offspring patterns Gregor Mendel 0 18221884 0 Studied patterns of inheritance in eukaryotes 0 Published work in 1865 0 Work rediscovered in 1900 Genetics 0 Genes and transmission Gene Chromosome 0 Expression of genetic information Genotype all genetic traits Phenotype traits that are physically shown Mendel s Experiments Organism o Pea pisum sativum 0 Advantages of pea lnexpengve Varieties Easy to grow Clearly identi able traits Easy to control pollination n Selffertilize has stamen and pistil o Pollen grains move from stamen and land on pistil of same ower a Cross pollination He removed anthers before pollen matured which prevented selffertilization Characters 0 Speci c property of an organism that is inherited o Traits each variant of a character 0 He selected 7 contrasting pairs of characters Character Traits dom vs rec Flower color Purple vs white Seed color Yellow vs green Pod color Pod shape Stem height Flower position 0 Applied quantitative methods 0 Experimental approach Planned experiments Recorded data 0 Mathematical analysis Truebreeding lines 0 Express same trait generation after generation of self fertilization 0 There are no exceptions 0 Same phenotype Tested blending inheritance hypothesis Previously widely thought that sperm and egg contained a sampling of uids from various parts of the body reproduction uids blend and produce offspring offspring would be intermediate between mother and father Crossed truebreeding plants with contrasting traits 0 Examples Pod color greendominant or yellowrecessive P parental generations truebreeding He crossed green with yellow B Offspring were all green not an intermediate n Offspring called F1 1st lial generation a He allowed for F1 to undergo selffertilization F2 generation 34 green and 14 yellow Explanation o Mendel Particulateinheritance Characters of an organism are determined by heritable factors Each character is controlled by 2 factors Factor from one parent was able to mask the expression of the factor from the other parent 0 Genes Allele alternate form of gene Dominant n Parental type found in offspring Recessive a Not expressed Locus a Place on chromosome where gene is located Diploid cells n 2 alleles for each gene Haploid cells n 1 allele for each gene 0 Monohybrid cross Follows behavior of alleles of a single locus 0 Ex Mendel s pod color experiment Green Dominant G Yellow Recessive g Truebreeding homozygous at particular locus 66 x gg 66 Gg Gg gg Inheritance of a single character explained by Medel s principle of segregation o A sperm or egg carries only 1 allele for each inherited character because allele pairs separate from each other during gamete production 0 Diploid individual 0 Homologous chromosomes Same size and shape Same genes but may be different alleles o Homozygous Has 2 identical alleles at locus n Ex 66 or gg o Heterozygous 2 different alleles at locus U EX Gg a Not truebreeding because not all offspring are identical 0 Ex pod color 0 F1 Gg o Meiosis l replication l splitting of chromatids 0 Each gamete which is formed during meiosis contains only one allele from each pair 0 This is segregation o Gametes formed by F1 generation 12 G and 12 g 0 FIG 114 Punnett Square 0 Sir Reginald Punnett Determine possible offspring genotypes o Combinations of egg and sperm 0 Gametes and expected frequencies at top of square Monohybrid F2 phenotypic ration Monohybrid cross 0 Inheritance of 2 different alleles at a single locus 0 Parents are truebreeding F1 a heterozygous o Gg 0 Green phenotype 0 F2 Genotype 14 66 12 Gg 14 gg Phenotype 34 green 14 yellow Mendel s 31 monohybrid F2 phenotypic ratio 0 FIG 116 Test cross backcross 0 Identify genotype of dominant phenotype 0 Take individual with dom Phenotype and mate to an individual with recessive phenotype 0 FIG 117 000 What happens if we follow two or more genes on different chromosomes Principle of independent assortment Members of any gene pair will segregate from one another independently of members of other gene pairs Genetic recombination Only works if alleles are on different pairs of homologous chromosomes Meiosis o How homologous pairs line up 0 FIG 119 Dihybrid Cross different alleles at two different loci Ex crossed peas that varies in both pod color and pod shape 0 Color Green G yeow g 0 Shape In ated I constricted i 0 Parent green in ated x yellow constricted GGII x ggii Parent gametes produced GI gi 0 F1 generation Gin green in ated F1 gametes produced GI Gi gI gi 0 F2 generation gure out with Punnett square GI Gi gI gi G GGII GGIi GgII Gin Gi GGIi GGii Gin Ggii g GgII Gin ggII gin gi Gin Ggii gin ggii Phenotype Genotype Green in ated GGII Gin GGIi GgII Total 9 Green and constricted GGii Ggii Total 3 Yellow in ated ggII 9in Total 3 Yellow constricted Ggii Total 1 9331 F2 dihybrid phenotypic ratio 0 Test cross to determine genotype of dominant phenotype Mate with homozygous recessive at both loci Lecture 24 DNA 12052012 Hereditary material 0 Genes 0 Located on chromosomes 0 Store information o Transmitted o Mutation gene is converted to another form Chromosomes 0 DNA deoxyribonucleic acid 4 nucleotides 0 Proteins 20 amino acids 0 Which DNA or protein are genes 0 Early hypothesis Genes made of proteins 0 Fredrick Grif th 1928 0 Evidence to reject protein hypothesis Streptococcus pneumoniae bacterium Humans develop pneumonia Mice lethal in mice a Smooth strain S strain 0 Smooth shiny colony on agar Cells enclosed in polysaccharide capsule o Virulent killed mice n Rough strain R strain 0 Rough surface colony on agar Because they do not have capsule So they are easy for immune cells to engulf and destroy o avirulent did not kill mice 0 Experiments 0 Took live S strain l injected into mice l mice died Took live R strain l injected into mice l mice lived He heatkilled S strain l injected into mice l mice lived Took live R strain heatkilled S strain l injected into mice l mice died l recover live S cells This is called transformation l genetic change in which properties of strain of dead cells is conferred to a strain of living cells FIG 121 Transforming principle Avery MacLeod and McCarty 1944 O O O O Lysed S cells And separated cell contents into fractions Lipids proteins polysaccharides nucleic acids Tested each of the fractions for transforming ability DNA Only fraction that could transform o Heritable 0 Some still skeptical Hershey and Chase 1952 0 T2 bacteriophage FIG 122 Virus that infects bacteria DNA core and protein coat Infection a Only part of virus enter the bacterial cell l that must be genetic material 0 Purpose of experiments To determine whether protein or DNA is the hereditary material that enters cell 0 Trace protein and DNA through virus cycle Sulfur n Cysteine and methiaine amino acids a Not present in DNA a Labeled one batch of virus with radioactive 35S Phosphorus n In nucleic acids of DNA a Not present in proteins a Labeled batch of virus with radioactive 32P 0 Results Viral progeny contained 32P but no 35S DNA is hereditary material FIG 123 Structure of DNA Nucleotides 0 Basic building blocks of DNA 0 Each contains Phosphate Sugar deoxyribose One of four nitrogenous bases n Adenine n Guanine n Cytosine n Thiamine FIG 124 0 Nitrogenous bases Purine n 2 rings 5sides bonded to 6sided ring a adenine A and guanine G Pyrimidines n One ring 6sided n Cytosine and thymine 0 Evidence for DNA structure 0 James Watson and Francis Crick 1953 o Rosalind Franklin 19511953 Studied xray diffraction of DNA FIG 126 a Method for determining the 3D structure of a molecule Her studies show a DNA is helical spiral n Width of helix a Distance between turns a Nucleotide bases were stacked o Erwin Chargaff Studied DNA composition from many different organisms Came up with 2 rules a Total purine content total pyrimidine content a Amount of T amount of A AND amount of C amount of G D But AT CG 0 Watson and Crick model Structure of DNA Explained how DNA could carry genetic information Explained how information could be replicated 0 Features of Watson amp Crick Model 0 Double helix 2 strands of DNA wound around each other On unduplicated chromosome n 2 strands of DNA One chromosome in prophase is composed of two sister chromatids m Now there are 4 strands of DNA Each strand has 2 n Sugar phosphate group is back bone outside of helix n Phosphate and sugar phosphodiester linkages D No variability o Nitrogenous bases Point toward center of helix Attached to backbone sugar by covalent bonds Lots of variability Carry genetic information in sequence of bases 0 2 strands are held together by H bonds between bases As and Ts pair up by 2 H bonds Gs and Cs pair up by 3 H bonds 0 2 strands run antiparallel run in opposite directions direction of polynucleotide n De ned by phosphodiester bonds between adjacent nucleotides ln backbone a Each carbon in sugar is numbered by prime designation n Phosphate group connects to 3 carbon of one sugar and 5 carbon of the next sugar I This is 3 5 phosphate linkage a FIG 129 0 Speci c Base pairing rules Purine always pairs with a pyrimidine A T complementing with 2 H bonds C G complementing with 3 H bonds Strands are complimentary DNA Replication Semiconservative 0 Each new DNA molecule contains One parental strand old And one newly synthesized strand FIG 1210 Semiconservative model 0 1st prepared by Watson amp Crick 0 later con rmed by Meselson amp Stahl 0 FIG 1211 0 Process 0 Initiation 2 strands of helix have to be unwound 3 requirements for unwinding a DNA helicases Enzymes Break H bonds between bases and separate 2 strands a Single strand binding proteins 0 Bind to single DNA strands o Prevent reformation of double helix n Topoisomerases Breaks in backbone and then rejoin strands Relieve strain from unwinding l relaxed con guration 0 l prevent knots Origin of replication a Location of replication in DNA molecule a Eukaryotic chromosome linear Does not being at ends of chromosomes 0 Several origins l each is bubble Each bubble has 2 replication fork n Replication fork Both stands of helix synthesize at same time o Bidirectional o Occurs in opposite directions on 2 strands o Elongation nucleotide monomers added 5 l 3 direction a linkage of 5 phosphate group of next nucleotide subunit added to n 3 OH group of sugar at end of preexisting strand Nucleoside triphosphate monomers n Nucleoside base sugar attached to 3 phosphate groups n 2 phosphates removed l E needed to drive reaction DNA polymerase I Use complementary as template Synthesize in 5 to 3 direction Reads template 3 to 5 a Can only add to an existing strand RNA primer short piece of RNA n Synthesized at location where the DNA is unwound at fork n Complementary to DNA template a Synthesized by primase Does not require free 3 end 0 Makes new piece of RNA opposite the DNA a RNA primer degraded l space lled in with DNA Origin of replication a Leading strand 0 Growing toward replication fork Smooth and continuous n Lagging strand 0 Short discontinuous segments 0 I Okazaki fragments 0 Within a fragment direction of synthesis is away from replication fork 0 Overall direction of lagging strand synthesis is toward the fork 0 DNA ligase joins inear fragments by covalent bonds a FIG 1214 a FIG 1215 a FIG 1212 Lecture 16 Control of Gene Expression 12122012 Molecular Genetics Intro 0 All cells have the same genetic information but they are not all identical 0 Gene expression is regulated 0 Only a subset of genetic info Constitutive genes housekeeping genes 0 Encode proteins that are always needed 0 Constantly transcribed Bacterial gene regulation 0 Mainly at transcriptional level 0 DNA l RNA transcribe Lac Operon Intro 0 Jacob amp Monod 1961 First to demonstrate gene regulation Lactose metabolism in E coli 0 E Coli Escherichia coli Human intestine Adjust to changes in chemical environment Host drinks milk then EColi needs to digest lactose For lactose to be useful to E Coli Taken into cell lactose permease transport carrier Hydrolyzed by Bgal l glucose galactose Galactoside transacetylase enzyme In culture Grow Ecoi on medium with no lactose I levels of all 3 proteins very low Grow E Coli with lots of lactose n Synthesis of 3 proteins Terms lnducUon n Turning on of gene expression lnducer n Compound that stimulates synthesis of an enzyme lnducible enzyme a Coded for by an inducible gene a Produced in response to an inducer 3 Genes in E coli lactose metabolism Next to each other on chromosome Share a single promoter a DNA nucleotide sequence a RNA polymerase binds l transcription Info transcribed into single continuous mRNA Either all 3 genes are on or all 3 are off Genes are part of operon Operon O O 0 Only in prokaryotes Complex constitutes of group of structural genes with related functions closely related DNA sequence that control them Consists at Promoter Operator short stretch of DNA l switch Structural genes protein coding sequences Operator and promoter act as binding sites Not transcribed Repressor genes Not part of operon Codes for a repressor protein Repressor protein lactose repressor Always made l constitutive In absence of lactose n Repressor protein has binding site on lac operator a RNA polymerase binds to promorter l blocked I Cannot transcribe structural genes If lactose present lactose goes into cell l allele lactose n Allolactose binds to 2nCI binding site allosteric on repressor protein a Changes conformation of repressor protein l protein can no longer bing to operator Allolactose n Induces lac operon genes by inactivating o Transcript 1 mRNA all 3 genes Each gene has own translation start and stop codons 3 proteins no nucleus in prokaryotes n Transcription and translation are simultaneous 0 FIG 142 0 2 ways to control operons 0 Negative control Regulatory protein repressor Turns operon off so that transcription occurs only when repressor fails to bind If sequence of operator changes a l repressor cannot bind a l genes constantly transcribed 0 Positive control regulative by activator proteins that bind to DNA and stimulate transcription o Lac operon positive control More efficient to use glucose Lac operon promote a l inefficient by itself a l law affinity for RNA polymerase Catabolite activator protein CAP n Promotes affinity for RNA polymerase CAP 2 forms a lnactive form by itself a Active form when bound to cAMP cyclic adenosine monophosphate n Levels of cAMP increases when glucose depleted CAP cAMP complex a Binds to CAP binding site next to RNA polymerase binding site CAP binding site and RNA polymerase binding site are promoters l bends DNA helix n l increases affinity of promoter region for RNA polymerase I Glucose Present cAMP decreases 0 CAP inactive o Promoter is inefficient Glucose depleted El El El CAMP increases 0 CAP active 0 Promoter is ef cient a FIG 145 Gene Regulation in Eukaryotes Intro 0 O O O 0 They respond to environment Multicellular organisms There is specialization of cells Control of gene regulation is mostly transcriptional level but also post transcriptional and post translation levels Do not have operons Gene expression controlled by chromosome organization and speci c regulatory sequences Chromosome organization 0 O 1 m of DNA fits in 5 pm nucleus DNA packaging ch 10 Chromatin interphase Histones Nucleosome n 146 base pairs of DNA wound around 8 histones a linker DNA a FIG 102a l fold nucleosomes to form a ber Fiber form loops scaffolding proteins a Loop and coil l condensed chromosomes 0 Transcription can occur only in regions where chromatin are extended Euchromatin loosely packed sites of active genes Heterochromatin tightly coiled even during interphase Ex Barr body a Inactive x chromosome condensed no transcription 0 Control of transcription Ch 14 o Transcription requires A transcription initiation site a All genes a Base pair begins Promoter a RNA polymerase binds a More complex than in prokaryotes n Contains TATA box 0 Located 2535 base pairs upstream from transcription initiation site 0 Tandemly one after the other repeated gene sequences Some genes present as multiple copies 0 Rate of transcription UPE upstream promoter elemenets a 812 bases 1 or several regulatory proteins bind l regulate gene expression a The more UPEs the more actively gene expressed Enhancers n Sequences which are 10005 of base pairs away from promoters n Regulate promoter bind to enhancers n lncrease rate of RNA synthesis after initiation transcription Silencers n Decrease transcription 0 Posttranscriptional control Interrupted coding sequences a mRNA contain long sequences of bases that do not code for amino acid lntrons n lntervening sequences a Transcribed not translated Exons expressed sequences a Coding regions a Transcribed and translated PremRNA n lncludes introns and exons lntrons must be removed n snRNPs Small nucleus ribonucleoprotein particles bind to pre mRNA Splice of boundaries n Exons put together a Mature mRNA moves to cytloplasm 0 Post translation Modi cation of protein EX glycosylation phosphorylation Recombinant DNA technology ch 151 0 Intro 0 Recombinant DNA 0 Restriction enzymes Produced by bacteria n Cut up foreign DNA trying to incorporate into genome Cut DNA at restriction sites a Cleavage Ex Hindlll 5 AAGCT T 3 3 T T CGAA 5 n Palindromes Sticky ends n Bases not Hbonded n Bind to complementary 55 DNA sequences a FIG 151 0 Vector Carrier molecule fragment of foreign DNA required to transfer genes from one organization to another EX plasmid a Small circular o Recombinant DNA technology methods 0 00 Ex cloning Larger of copies of DNA segments Foreign DNA into microorganism Cut foreign DNA and plasmid DNA with same restriction enzyme Two types of DNA mixed together Complementary sticky ends l H bonds Ligase Links DNA fragments l DNA spliced into vector l recombinant DNA Transformation Cell acquires plasmid across cell membranes Plasmid replicates l many copies of foreign DNA produced cloning ampli cation 0 Applications 0 0 Basic research DNA sequences Forensics Biotechnology the use of organisms to develop useful products Pharmaceutical proteins Ex insulin n E coli Transgenic organisms Ex agriculture resistance to pesticides Medicine Gene therapy deliver normal genes to affected tissue
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