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Bio 181 Biosphere collection of ecosystems Ecosystem Population all organisms that belong to the same groupspecies and live in same geographical area Society smaller groups with similar traits ex greek life Organismal biology study of structure function ecology and evolution at the level of the organism Phylogemy mapgraph of evolutionary relationships history of organismal lineages as they change through time Cell structure of all organisms Organelle specialized subunit within a cell that has a speci c fxn Usually separately enclosed within own lipid bilayer living and nonliving worlds share the same chemical foundations and obey the same physical laws C O H Four key aspects of all living things 1 complexity with precise spatial organization on several scales 2 the ability to change in response to the environment 3 the ability to reproduce and 4 the capacity to evolve Laws of Thermo energy cant be created or destroyedcan only be transformed the degree of disorder entropy in the universe tends to inc Energy comes from 1 the sun and 2 chemical compounds Essential Features of a Cell 1 store and transit info DNA goes to RNA to protein gtgtgtgttranscription copying bc DNARNA are similar to translation different quotlanguagequot 2 has a plasma membrane contros exchange of material with the nonliving environ some cells have internal plasma membranes nucleus eukaryotes with a nucleus and prokaryotes without 3 can harness energy from the environment Viruses are NOT living organismsthey cant harness energy They need a cell for this Hydrogen bonding bw 2 strands of DNA and 1 strand of protein Cation positive anion negative Proteins polypeptide amino acids are strung together my peptide bonds carboxyl amino group a carbon and different R group Nucleic Acids nucleotides RNA and DNA phosphate group negatively charged sugar base pyrimidine bases thymine DNA cytosine uracil RNA purine Adenine thymineand guanine cytosine sugar and a base nucleoside sugar base and phosphate nucleotide WatsonCrick structure right handed helix backbone will be on outside Chargaff s rule A T G C Hydrogen bonds base stacking slight attraction bases adjacent to each othernot opposite from stability of the DNA double helix hydrogen bonding between the bases Implications of DNA structure four nucleotides at a given position if DNA is 10 nucleotides long 4quot10 possible nucleotide sequences repication copying of genetic info from one DNA to another DNA based on complementary double stranded nature of double helix DNA is able to specify exact copies of itself errors mutations Chromatin histones proteins which DNA are wrapped around rich in amino acids lygine and arginine DNA whistones chromatin four histone proteins occur as an eight protein complex two of each histone molecule type known as a nucleosome DNA is wrapped twice around each nucleosome DNA wraps around histones nucleosome Transcription RNA polymerase transcribes DNA to produce RNA transcript tempate strand is the DNA strand you read from read from 3 to 5 RNA is synthesized 5 to 3 Carbssugars gucose galactose fructose Lipids attach to glycerol head lt and long chains fatty acids phospholipidd building blocks of membranes phosphate group and choline charge DNA stores and transmits genetic infobioogica fxn polymer of nucleotides and forms double helix Transcription process by which RNA is synthesized from a DNA templategene expression Primary transcript is processed to become messenger RNA mRNA RNA Polymerase in Prokaryotes simultaneous transcription and translation poycystronic multiple proteins from one strand Three Chemical Modi cation 5 cap polyadenylation polyA tail to the 3 end introns are excised from RNA strand exons are spliced together Alternative splicing two proteins isoforms from one strand Ribosoma RNA rRNA found in all ribosomes that aid in translation Transfer RNA tRNA carries individual amino acids for use in translation Small Nuclear RNAsnRNA found in eukaryotes and involved in splicing polyadenyltation and other processes in the nucleus smal regulatory RNA molecules that can inhibit translation microRNA or miRNA or cause destruction of an RNA transcript small interfering RNA Amino Acid monomer of proteins Structure corners of the structure forms tetrahedral shape around alpha carbon there are 20 HYDROPHOBC HYDROPHLC basic or acidic and charged or uncharged but polar SPECAL AMINO ACIDS glycine small not symmetric free rotation around CN bond more exible polypeptide bond Proline kink in chain from R group linked back to amino group restricts rotation decrease polypeptide structure Peptide Bond Formation forms through condensation rxn liberates water molecule hods together peptide bonds amino group Nterminus to Cterminus the energy comes from breaking of the high energy bonds of GTP with elongation factors FOUR levels of protein structure primary sequence of amino acids secondary interactions of nearby amino acids apha sheets backbone beta sheets adjacent structures parallel and antiparallel tertiary structure 3D shape of protein single polypeptide bond fxn amino acid side chain intxns quaternary structure polypeptide subunits that bind to each other tRNA has own unique self pairing structure has nucleotide CCA at 3 end 3 hydroxyl of the A is attachment site for amino acid Translation initiation prokaryotes polycistronic mRNA at any shinedalgarno sequence so mRNA an be poly mRNA that codes for several polypeptides eukaryotes monocistronic mRNA initiation is at the 5 cap and the rst AUG is the start codon eongation keeps going termination reease factor binds to the A site bond between the polypeptide and tRNA breaks primary structure sequence Chapter 5 Robert Hooke 1665 coins the term cell Cell Theory 1 All organisms are made up of cells 2 The cell is the fundamental unit of life 3 Cells come from preexisting cells Phospholipids hydrophiic and phobic components Lipids naturally organize to from micele ball like structure formed by lipids with a bulky hydrophilic head and single fatty acid tail biayer two layers of phospholipidspolar head groups on outside and nonpolar on inside liposome closed structure with an inner space phosphoipids can move laterally throughout lipid bilayer how quickly they move within and across membranes depends on temp and structure of fatty acid tail saturated fatty acid chain lack double bonds have a straight structure and favor tight packing unsat fatty acids have 1 double bonds Cholesterol choestero is an amphipathic both hydrophobic and hydrophilic propertiesphosphoipids are also amphipathic molecule that affects membrane uidity choestero can increase of decrease membrane uidity based on temp norma temp reduced mobility low temp increases uidity microenvironment known as lipid rafts can assemble in membrane Protein membranes contain this membrane proteins can be integral permanently associated with cell membranes include transmembrane proteins or peripheral temporarily associated with the lipid bilayer The uidmosaic model of membrane structure membranes are a dynamic and uid mosaic of phospholipids diff types of proteins and carbs Going across a membrane passive transport doesn39t require input of energy active transport req energy to move soutes are in constant random motion and have thermal energythis random motion diffusion high to low concentration phospholipid bilayer shows selective permeability ions are hard to get through osmosis diffusion of water if solute cant get through then water is going to move until concentration of solute is similar Primary active transport permits molecules to move against their concentration low to high sodium potassium pump is a membrane protein that uses energy to use energy used in ATP Secondary active transport using one gradient to drive transport against another the antiporter moves after primary active transport moves protein and an electrochemical thingy is created Plant cells have walls and vacuoles animal cells will burst with too much water but plant cells wont amino terminal chloroplast or mitochondria interna signal to nucleus Endoplasmic reticulum smooth er has no ribosomes and is primary site for lipid synthesis proteins not synthesized here bigger in cells specialized to produce lipids rough er has ribosomes and many proteins including those that are destined for secretion proteins produced end up in the lumen of the endomembrane system embedded in its membrane or secreted out of the cell signal recognition particle binds to ribosome and protein and tethers cytoplasmic ribosomes to RER signa anchor sequence are threaded through channel in the ER membrane until sequence is encountered ER channel releases protein into membrane stays embedded Golgi apparatus functions further modify proteins and lipids produced in ER to sort proteins and lipids as they move to their nal destinations to synthesize the cell s carbohydrates lysosomes speciaized vesicles derived from golgi apparatus that degrade damaged or unneeded macromolecules gogi delivers enzymes that break down macromolecules to a lysosome vesicle with macromolecules also merges with lysosome mitochondria not part of the endomembrane system harness energy for the cell contain own genomes and grow and multiply independently of other membrane compartments Synthesis of RNA is from 5 to 3 DNA from which RNA is synthesized is 3 to 5 uracil is in RNA thymine is in DNA RNA polymerase synthesizes RNA from DNA hydrogen bonds are being formed between two strands with matching 3 between GC 2 between AUpyrine and purine phosphodiester bonds connect RNA monomers together transcription occurs in nucleus which is full of RNA nucleotides only in eukaryotes energy comes from release of two phosphates it was 3 formation of phosphodiester bonds Protein synthesis peptide bond condensation release of water Exons code for proteins introns are removed by the splicing important for forming many proteins depending on how primary transcript is spliced after DNA is capped tailed and spliced mature mRNA polyA tail stabilizes the mRNARNA is very weak open to destruction by enzymesA s keep coding bits secure 5 cap in eukaryotes important for ribosomal recognition No 5 cap in prokaryotesanalogous thing is the shine dalgarnotransation initiation in prokaryotes Also in prokaryotes translation and transcription happen simultaneous prokaryote mRNA is polycystronic mRNA can have more than 1 protein multiple starts and stops proteins formation starts at the Nterminus amino terminus to the C carboxyl terminus start codonAUG encodes mathymine tRNA attaches to the RNA due to base pairings and the amino acids string together by peptide bonds the last tRNA old is ejected charged attached to amino acids tRNA don39t become proteins anUcodonloops free 3 end amino acid attachment site aminoacy tRNA synthetase the enzyme used to attach uncharged tRNA to free amino acids knows which is the correct because of theanUcodon secondary alpha helixbeta sheets can have bothmade by hydrogen bonds 100 tertiary 3D structure some hydrogen bonds quaternary multiple subunits golgi does this after proteins come from ER excreted bound contained in lipid sac if signal sequence is at amino terminus on a protein goet to mitochondria or chloroplast if there is an internal signal goes back to the nucleus important for maintaining tertiary structure Making Life work Capturing and Using Energy 1 Cellular Respiration I Requirements of the cell a way to encodetransmit info a membrane separating inside from out energy ATP universal currency of all cells Provides energy in a form that all cells can readily use to perform work Contains energy in its chemical bonds that is readily accessible to the cell Metabolic classi cation organisms have two ways to harvest energy from their environment and two sources of carbon Metabolism building and breaking down of carbon sources to harness of release energy Cascading sets of chemical rxnsproducts of one are reactants of next Chemotrophs energy from chemical compounds Heterotrophs carbon from organic compounds get from other sources Autotrophs carbon from C02 self feeders make their own organic sources of carbon Phototrophs energy from sunlight Heterotrophs heliobacteria non sulfur bacteria and autotrophs plants and cyanobacteria Catabolism and Anabolism Ca tabolism breaking down producing ATP macromolecules to subunits Anabolism building subunits to macromolecules requiring ATP input of energy Energy of a System system39s ability to do work Types of Energy Potential stored energy Kinetic energy of motion Energy in electrons chemical energy is a form of potential energy When electrons are far from both atoms nuclei large amount of potential energy Organic molecules with many covalent bonds carry potential energy in their chemical bonds Gibbs Free Energy the amount of energy in a system available to do work Endergonic non spontaneous requires energy input G Exergonic spontaneous releases energy 6 G H TS Enthalpy H total energy available Forming bonds inc chemical energy in bonds Entropy s the degree of disorder ATP Hydrolysis the reaction of ATP with water is exergonic and releases energy G G for ATP hydrolysis is intermediate compared to G of hydrolysis Rate of a Reaction chemical reactions in cells are catalyzed by proteins called enzymes Enzymes lower the activation energy for a reaction but delta G stays the same The transition state or peak of Ea is the only thing affected Enzyme catalyzed reactions Substrate gt Products 5 Enzyme gt ES gt EP gt E P Substrate forms complex with enzyme substrate is converted to product while still part of a complex Enzyme active site binds substrate and converts it to the product Intxns between substrate and active site are weak noncovalent intxns or transient covalent bonds that stabilize the transition state and dec the activation energy Enzyme activity can be in uenced by inhibitors and activators Inhibitors Irreversible inhibitors form covalent bonds Wenzymes and irreversibly inactivate them Reversible inhibitors form weaks bonds With enzymes and easily dissociate from them a competitive bind to active site and prevent substrate from binding They compete with the substrate for the active site binds either inhibitor or substrate b noncompetitive bind to diff site from active site binding sites of inhibitor and substrate are diff causes dec in rate of rxn Enzyme threonine dehydratase is an example of an allosteric enzyme Activated or inhibited when binding to another molecule changes its shape Activators Cofactorsbind and induce t of substrate to active site and coenzymes can cause an enzyme to change shape when binding a substrate Cellular Respiration Four steps 1 glycolysis cytoplasm 2 acetylCoA synthesis cystoplasm STAGES 12 fuel molecules are broken down into ATP 3 citric acid cycle mitochondria 4 oxidative phosphorylation Oxidation Reduction Rxns OIL RIG Catabolism of carbohydrate Carbs and lipds have high PE because electrons shared are far from nuclei electron carriers are NAD NADH and FADH and FAD energy released in stored as ATP and electron carriers Making ATP Substrate level phosphorylation transfers a phosphate group to ADP to produce ATP Occurs during stage 1 and 3 glycolysis and citric acid cycle Glycolysis Glucose is the starting molecule 6 carbon End product 3 carbon pyruvate 2 produced Anaerobic oxygen not consumed Phase 1 glucose is prepared for the next two phases by addition of two phosphate groups costs 2 ATPs Phase 2 two molecules of glyceraldehyde 3 phosphate are produced Phase 3 two molecules of pyruvate are formed and two molecules of the electron carrier NADH are produced production of 4 ATP and 2NADHspent 2 so NET is 2 Acetyl CoA Synthesis Pyruvate from glycolysis is transported into mitochondria where it is converted to acetyl CoA one molecule of pyruvate produces 1 C02 1 NADH 1 Acetyl Coatotal is two because there are 2 glucose molecules Citric Acid Cycle in mitochondria Fuel molecules are completely oxidized Both substrate level phosphorylation and reduction of electron carriers occur Eight reactionsoxaloacetate is regenerated Acetyl CoA is totally oxidized2 ATP 6 NADH 2FADH2for 1 glucose molecules Electron transport chain is located in the mitochondrial inner membrane Electrons that come in with NADH have more energy Complex 1 is for NADH electrons oxidized to NAD complex 2 gets 2 electrons from FADH2 become oxidized to FAD FADH 2 coenzyme Q 3 cytochrome c 4 oxygen and make water OR NADH coenzyme Q 3 cytochrome c 4 oxygen and make water coenzymeQ is hydrophobic in membrane and transports electrons to next complex Dropping off those electrons able to pump protons against the gradient only complex 1 4 protons 3 protons 4 2 protons complex 2 cannot Energy is released as electrons are passed from high energy electron carriers NADH and FADH2 to the nal low energy accepter oxygen Every NAHD 25 atp FADH 15because of the amount of protons are pumped through ATP Synthase protons able to diffuse down their electrical and concentration gradients through a transmembrane protein channel ATP synthase into mitochondrial matrix uses potential energy to make ATP FERMENTATION what to do when no 02 is present as a nal electron acceptor in ETC Eukaryotes do it by lactic acid fermentation Two p yru va te turns into two lactic acid molecules turns NAD in to NADH to produce pyru va te Prokaryotes ethanol 2 pyruvate break off C02 acetaldehyde 2 ethanol also recycles NAD to NADH to keep pyruvate formation going Where do organisms store glucose Glycogen animals liver and starch granules inside cells The branches are cleaved on at a time Boxidization lipids as energy Lipids cant be used by all cell types but provide a lot of energy Produces 106 molecules of ATP from 16 carbon FADHZ and NADH will be taken to ETC AcetyIcoA molecule cleaved after oxidation How is respiration regulated Level of ATP in cell is indicator of energy available When ATP levels are high cell has a lot of free energy and path ways are down regulated or slowed down When low cell activates path ways that lead to ATP syn thesis Phosphofructokinasel catalyzes step 3 in GLYCOLISIS and is allosterically regulated ATP levels are low PFK1 is activated allowing glycolysis to continue When high citrate PFK1 is inhibited and glycolysis is slowed Photosynthesis I biochemical process for building carbs from sunglight and coZ from air Major pathway by which energy and carbon are incorporated into carbs 6C02 reduction 6H20 oxidation e donor gt C6H206 reduction protons 602 oxidation byproduct Calvin cycle 3 step process that results in incorporation of C02 into carbs Light harvesting rxns use sunlight to produce ATP and NADPH required by calvin cycle Photosynthesis faces challenges to its ef ciency Takes place in chloroplast light dependent rxns Calvin Cycle Carboxylation reduction regeneration steps Doesn39t need sunlight gets energy from ATP and NADH Input C02 then added to RuBP carboxylation RuBP is catalyzed by rubisco 3 PGA consumption of ATP Reduction NADPH transfers high energy electrons 2 triose phosphate carb output exist as 3 carbon compounds regeneration after getting 15 carbons reassembled carbons to RuBP 5 carbons molecules instead of 3carbon molecules Need 3 ATP for each C02 Rubisco is a slow enzyme and must be produced in large quantities Nadph reducing agent Starch granules in a chloroplast Excess carbs at stored as starch in plants Formation of starch allowed plants with a source of carbs to use during the night without suanht Pigments molecules that absorbs some wavelengths of visible light re ect light that we do not see Chlorophyll photosynthetic pigments anchored in thylakoid membrane Carotenoids orange yellow absorb in visible spectrum that are poorly absorbed by chlorophyll When light is absorbed electrons get excited and produce light The energy is passed from chlorophyll to chlorophyll until reaches reaction center RC transfers abs light energy and a high energy e to next molecule it becomes oxidized Two Photosystems Photosystem 2 donating electrons and gets replacement electrons from water produces protons inside thylakoid membrane Photosystem 1 e is excited yet again NADPH is produced for the calvin cycle Electron transport chain connects two photosystems and e pass bw P52 and 1 through cytochrome b6f complex serves as a Pump During e transport protons are pumped from stroma to thylakoid lumen Protons ow back into stroma through ATP synthase during synthesis of ATP ZScheme Absorption of light energy by P52 energizes electrons from water and they enter the chain second input of light energy by PSl raises e to an even higher level so they can reduce NADP Cyclic electron transport when variation in light in tensity In high light calvin cycle isn39t able to use all NADPH produced and if there is not return of NADP then the high e can damage ce e are shunted and this increases ATP while decreasing NADPH es from PSl re redirected from ferredoxin to ETC plastoquinone challenges to photosynthetic ef ciency reactive oxygen species xanthophylls convert excess light energy to heat reducing rate at which energy and e enter ETC antioxidants detoxify reactive oxygen species Photorespiration challenge Input rubisco can fxn as oxygenase Oxygenation rubisco adds 2 to RUBP 1 molecule of 3 phosphoglycerate and 1 of 2 phosphoglycerate C02 loss 2 PG cant be used by calvin cycle The conversion of 2 pg into 3 pga results in net loss of reduced carbon Fewer carbs are outputted Speculation trade off Through evolution to change a inity of rubisco for 02 or C02 produces tradeoffsilte selectivity and speed Rubisco s slow rate is counteracted by the amount of it made Cell Communication Essential Elements Signaling cell signaling molecule receptor cell receptor molecule Once signaling molecule binds to speci c receptor there is receptor activation and signal transduction signal transmitted to interior of cell by signal transduction pathway response and termination Different distances Endocrine estrogentestosterone horomones travel through circulatory system LONGEST Paracrine shorter 20 cell diametersautocrine self signaling embryonic development antibodies Growth factors are small soluble molecules PDGF platelet derived growth factors Juxtacrine signaling transmembrane protein acts as signaling molecule and transmembrane protein on adjacent cell is the receptor Notch expressing supporting glial cells Delta expressing neuron Ligand signaling molecule Ligand binding site location on the receptor to which the ligand binds Cell surface receptors Polar signaling moleculeligand the conformation of the receptor changeslike a light bulb G Protein Coupled Receptors GT P active GDP inactive When a ligand binds to G Protein coupled receptor it binds to and activates G protein by replacing GDP with GT P Activation Alpha binds to GTP and dissociates from beta and gammait also interacts with the active effector protein and this gets response Second Messengers Small nonprotein water soluble molecule Cyclic AMP from ATP and adenyy cycase enzyme Amplify signal Protein Kinase A After activation of adenyy cycase activates and phosphorya tion of kinase A Termination 3 phases Adrenaline detaches from receptor after a certain amount of time inactivating receptor G Protein also inactivates itself and goes to GDP Phosphodiesterase converts cyclic AMP to AMP Phosphatase strips phosphate from active kinase and turns to inactive Receptor Kinase enzyme that ends phosphate group Once phosphorylated by kinase active Dim eriza tion cross ph osph oryliza tion signaling proteins bind to receptors Only active when there is a RAS protein Kinase is ampli ed from kinase to kinase Inactive one GT P bound RAS is converted to GDP Ex insulin signaling armslegs wound helaing kit feathers and skin pigment LiganGated ion channels receptors that alter the ow of ions across plasma membrane During muscle contraction neuron send signal ace tylch oline Sodium ions rush in to cell when acetylcholine receptor conformation changes Intracellular receptors Small nonpolar signaling molecule ANGINE Cell Signaling and Cancer Increased receptors Low levels of signaling more receptors more binding gt abnormal gene expressionexcess cell division Overproductionaltered signaling molecule More chances of binding gt abnormal gene expression RAS Mutations Account for 30 human cancers Prevent RAS from converting GT P to GDP causing protein to always be on Cell Form and Fxn Fxn of cell is re ected in its shape and internal structures Tissues and Organs Tissue collection of cells that work together to perform speci c fxn two or more tissues combine to make up an organ Cytoskeleton Supports and maintains cell shape Holds organelles in position and moves them Cytoplasmic streaming Three components made of proteins Microtubules largest Alpha tubulin and beta tubulin subunit gt dimerize Radiate outward to cell periphery from a centrosome Make up cilia and agella propels movement requires ATP Also found in Spindle apparatussplit chromosomes Micro laments small Polymers of actin monomers and are in helix Various locations in cytoplasm branched and beneath plasma membrane Organize proteins associated with it In epithelial cells of small intestine Transport materials in cells Shortening of muscle cell during contraction Separation of daughter cells at end of mitosis Intermediate laments only animals Polymers of intermediate lament proteins that combine to form cable like structures un cells providing mechanical strength Over 100 different kinds of intermediate laments ln epithelial cells kera tins Fibroblasts vimentins Neurons neuro laments Inside nucleus lamins Connect cellular junctions like desmosomes Defects Epidermolysis bulosa defective keratin genes doesn39t build connections between cells Causes outer layer of epidermis to detach fragile slltin Check for spread of cancer Intermediate laments in places they don 39t belong Microtubles and Micro lamen ts are always changing Become longer and shorter Faster growing end faster polymerization plus end slower growing end minus end Minus ends of microtubules are positioned at centrosome and plus end is toward plasma membrane Microtubules undergo rapid shrinkage depolymerization and slower growth polymerization these cycles dynamic instability Dramatic shrinkage microtubule catastrophe plus end is unstable This process of reaching out and shrinking is good bc it allows microtubules to explore cellular space Muscle Contraction relies on actin and m yosin Shortening of cell is by motor protein myosin and actin micro lament Myosin binds to actin and undergoes conformational change gt actin micro laments slide to each other Vesicle movement within cells requires mf Myosin attaches to transport vesicles and it uses mfs as tracks Myosin moves towards plus end of mfs ATP provides energy Movement also by mts Also fxn as tracks Motor proteins kinesin and dynein Kinesin moves cargo towards plus end and dynein moves toward minus end Energy by conformational change in motor proteins and ATP Mts in cilia are arranged 92 Energy harvested by hydrolysis of ATP powers motion of cilia and agella Cells can crawl using motion of micro laments Iamellipodium Extracellular matrix polysaccharides and proteins that cells in tissues and organs are connected to Cell adhesion molecules There are various cell adhesion molecules in cell membrane that allows them to sort themselves Cadherins are important to cell to cell adhesion Different types of cadherins and they only attach to the speci c type Cadherins are trasnmembrane proteins Extracellular domain of cadherin binds to exc domain of same type of cadherin Cytoplasm of cadherin linked to internal cytoskeleton Increases strength of tissues and organs by cytoskeleton linkage Integrins enable cells to adhere to ECM This attachment provides structural reinforcement of tissues under physical stress Transmembrane proteins with cytop Adherens juctions cadherins to actin Desmosome cadherins to intermediate laments Tight junction plasma membrane of one cell to plasma membrane of another cell Gap junctions allows small molecules and uid passing from one cell to another proteins embedded in plasma membrane of a cell and another cellallows for channel in cytoplasm to be created Only in animal cells In PLANTS Plasmodesma ta transfer of RNA and proteins because they are much larger than hap juxns The plasma membrane bW two cells are continuous Connects plant cells 50 substances can move from cell to cell Without having to be transported through lipid biayen Cytoplasm to cytoplasm Smooth ER runs through this Specialized proteins control protein tra ic Hemidesmosomes integrinsconnection to exc matrix and to intermediate laments Binds intermediate laments to in tegrin to basal lamina exc matrix NOT cell to cell binding locking cell in place Extra cellular matrix in plants Cell Wall 1 middle lamina middle lamella loose and gooey 2 primary cell wall more rigid bc of cellulose 3 secondary cell wall no intermediate laments because they have cell wall more rigid In animals Secreted by cells in a mix of proteins and polysacch Large brous proteins like collagen elastin laminin Found in gel polysacch matrix Cb agen most abundant animal protein three polypeptides in helix ECM and Cytoplasm Integrins span plasma membrane and connect actin laments inside cell to ECM lntegrins bind bronectin in ECM which bind to collagen Basal Lamina Special layer of ECM beneath epitheia tissue ECM and Cancer When cells form strong cnxn to basal lamina it can move through basal lamina across the circulatory system in and out which the integrins facilitate Cell shape is in uenced by structure of ecm and by composition of it ECM in uence on cell shape neurons and broblasts ECM and gene expression Different amount of proteins production in laminin albumine inc in presence of laminin REVIEW Can make ATP in 2 ways Oxidative phosphoryla tion makes more Carrier molecule NADH and NADH2 Substrate Ie vel phosphoryla tion Takes place in two places glycolysis and krebslcitric acid cycle makes 2 ATP one for each Acoafor each acetyl coa 3 Nadh 6 for each glucose FADH 2 for each glucose Glycolysis NET 2 ATP because use 2 and make 4 every glucose 2 NADH and 2 ATP by substrate Ie vel phosphorylation C02 is produced oxidation off glucose molecule 2 Intermediate product pyruvates gt 2 NADH made Acetyl Coa 2 carbons Made gt oxaloacetate 4 carbons combins with acoa and has 6 carbons citrate oxaloacetate is regenerated 4 carbons Every time carbon is oxidized NAD is reduced Phosphofructokinase1 allosterically regulated it changes shape based on what its bound to 3ml step of glycolysis with other parts of respiration should I or should I not break down sugar ADPAMP gt turn up fructose 6 phosphate makes fructose 1 6biphosphate citrateATP gt turn down glucose production Regulates glycolysis Chapter 1 Cell Division Mitotis Cell Division Single cell becomes two daughter cells Eukaryotes genome is linear and large DNA is in nucleus Prokaryotes genome is small and circular DNA is in cytoplasm Prokaryotes binary ssion A cell replicated its DNA increases in size divides in to 2 daughter cells and each daughter cell receives one copy of the replicated parental DNA Eukaryotes mitotic division Meiosis leads to gametes Daughter cells have HALF of genetic material as parental cells Reductive Mitosis leads to somatic cells general cells in body Genetic material is divided equally and daughter cells are identical to parental cells Purpose is to distribute chromosomes equally to daughter cells Interphase 31 phase cell grows and protein content inc and waits for a signal to divide S phase synthesis of DNA replication 32 or gap phase more growth M phase mitosis and cytokinesis GO cells that are not actively dividing nerve cells lens cells etc DNA organization into chromosomes Histones and other proteins chromatin Chromatin looped and packaged chromosomes Human karyotype has 46 homologous chromosomes Homologous chromosomes carry same set of genes in the same order but version is different one from mother and one from father After replication homologous chromosomes are composed of sister chromatids Mitosis in ve stages Prophase Chromosomes condense and centrosomes radiate microtubues and migrate to opposite poles Have to also replicate centrosomes Prometaphase Microtubules attach to chromosomes Nuclear membrane dissolves Microtubes reach outretract until they nd a centromere to attach to Microtub ues attach to kinetochores of centromeres Two protein complexes kinetochores which are on each side of centromere and associated with each sister chromatids The tension on the kinetochore is what allows it to know when to separate Meta phase Chromosomes line up in middle Ana phase Proper tension on each side of kinetochore to pull sister chromatids apart as soon as they separate the sister chromatids are noW chromosomes and go to each pole Telophase Complete set of chromosones arrives at a spindle pole and cystolic changes occur in preparation for the cell 5 division to occur Chromosomes begin to decondense and microtubules start to break down nuclear membrane starts to reform Cytokineses animal Actin bers building up With m yosin and making contractile ring so to pinch off Cytokineses plants Phragmoplast is built in middle of cell Where cell wallcell plate Will be built The phragmoplast consists of overlapping microtubules and guide the quotmaterialsquot to build cell wall Meiotic Cell division Two rounds of division Results in 4 daughter cells Each cell contains half the number of chromosome and is genetically unique 23 chromosomes each Prophase 1 Meiosis 1 DNA is replica ted before In synapsis homologous chromosomes pair with each other side by side gene for gene Each pair of chromosomes four stranded structure called bivalent tetrads Within these are cross like structures called chiasmata visible cross overs between non sister chromatids Chiasmata allows homo chromosomes of maternal and paternal origin to undergo an exchange of DNA segments Basically linkage and occurs between non sister chroma tids Essential for proper distribution They become recombinant chromatids Metaphase lining up Ana phase Homologous chromosomes separate but sister chromatids do notreductional division Telophase split apart and start to reform nucleus Meiosis 2 no DNA synthesis between the two meiosis phases Prophase 2 breakdown of envelope attachment of mts Metaphase lining up Anaphase pull apart sister chromatids Telophase Nuclear envelope reforms The division of cytoplasm can be unequal Sperm fairly equal cytoplasmic division all form functional sperm Egg very unequally divided cytoplasm One overloaded oocyte and the three other haploids are polar bodies that will eventually disintegrate Fertilization gametes fuse to form zygote restores diploid Tim Hunt coined term cyclin a protein in a cell during division Saw a spike and decrease in cyclin during cell division and hypothesized that it must be tied to cell division Cyclin essential for cell cycle regulation promote cell cycle movement They binds and activate cyclin dependent kinases to control progression throughout cycle CDKs always present unlike cyclin phosphorylate target proteins involved in promoting cell division Several different cyclins and CDKs for speci c steps of cell cycle GlS cyclinCDK complex prepares cell for DNA replication S cyclinCDK help initiate DNA synthesis Mcyclin CDK helps prepare the cell for mitosis Many checkpoints to see if everything is set to go Inhibits progression until 100 ready DNA replication checkpoint At end of 62 checks for unreplicated DNA before mitosis DNA damage checkpoint checks for damaged DNA before entering 5 phase Genes that inhibit cell cycle are OFF P53 mostly exported from nucleus and degraded in cytoplasm Inhibition occurs when high concentration of p53 in nucleus from 31 to S Requires repair rst and then allowed to proceed Phosphorylation occurs only when there is damage to DNA bc damage activates protein kinases that phosphorylate p53 blocking export and degredation Spindle assembly checkpoint checks all chromosome being attached to spindle before anaphase Cancer Oncogene cancer causing gene Promoting replication Protooncogene normal genes important in cell division that have potential to become cancerous if mutated Tumor suppressors encode proteins whose normal activities inhibit cell division GI checkpoint is subject to social control 1 growth factors arrive from other cells 2 cause increase in cyclin and E2F concentrations 3 cyclin binds to CDK cdk is phosphorylated Rb inactivates E2F by binding to it gtltgtltgtltgtltgtlt multiple mutation model inactivation of rst tumor suppressor gene activation of oncogene inactivation of second tumor suppressor gene now malignant inactivation of third tumor suppressor gene metastatic caner multiple mutations over a period of years can be correlated with the progression of cancer Chapter 2 DNA Replication and Manipulation Hypothetical Models for Replication Semiconservative one parent strand and one daughter strand after replication Conservative after replication the new duplex consists of two daughter strands leaving parent strand intact Dispersive two helix with old and new interspersed throughout strands MeselsonStahl experiment Bacterial DNA replication is semiconservative After two rounds of replication the daughter DNA molecules therefore form two bands one intermediate in density and the other light Experiments with uorescently labeled DNA led to the discovery that eukaryotic cells also replicate semi conservatively Replication Replication occurs 5 to 3 Unwinding of the DNA duplex results in replication fork The daughter strand on top elongates from left to right 3 to 5 and that on the bottom from right to left Replication of top strand is discontinuous fragmented whereas bottom is con nuous Primers are removed and replaced with DNA and fragments of discontinuous lagging strand are ligated where they meet Can begin at any origin or replication Pro have only one Eu have many At ea replication fork new strand with the free 3 end is leading strand and with free 5 end is lagging strand DNA Synthesis and RNA Primers DNA polymerase enzyme for DNA replication cannot begin a new strand on its own it can only elongate an existing piece of RNA or DNA Each DNA strand must begin with short RNA that serves as primer for DNA synthesis Primer is made by RNA polymerase called RNA primase Most DNA polymerases can correct their own errors in a process called proofreading If an error is detected DNA poly activates a cleavage fxn and removes incorrect nucleotide and inserts correct one DNA polymerase extends an RNA primer One on leading strand progression is going same way as fork Lagging strand 5 to 3 but opposite direction of fork Helicase unwinds the DNA duplex Topoisomerase ll relieves the stress of unwinding Single stranded binding proteins stabilize single strands of DNA Replication Forks see origin of replication from the middle starting point you have one fork for each bubble going in opposite directions at each replication fork the new strand with free 3 end is leading strand and with the free 5 end is the lagging strand Replication of Circular DNA Bacteria mitochondria chloroplasts Only one bubble The End Replication Problem Eukaryotic cells have ends The last RNA primer on lagging strand sits near the end of the parent strand Rna primer is removed and a section of template DNA remains unreplicated So each replication it gets shorter In adult somatic cells miotic division can only occur about 50 times before the telomeres are so short that cells stop dividing Hypothesis that this is unregulated check for cancer prevention Eukaryotes have developed solution to this for germ line cells Telomerase reverse transcriptase RNA to DNA telomerase RNA folds up and binds to complementary bases that will then generate DNA bases that are complementary to it template strand T TAGGG DNA Manipulation Polymerase Chain Rxn PCR Common method for making copies of a piece of DNA Allows a targeted region of DNA to be replicated into as many copies 1 denaturation heat separates two strands 2 annealing Use DNA primers to match portion of DNA by comp base pairing and serve them starting point for polymerase 3 extension temperature that is most favorable for DNA polymerase to come in and extend off primer to synthesis daughter strand Components for PCR Template DNA DNA polymerase TAQ ATGC nucleotides two primers short stretches of DNA Electrophoresis Large one move slowly small move faster Big fragments at start of well small at end because of speed Can analyze for target sequence Move toward opposite electrodes Restriction enzymes cut DNA at speci c sequences Allows recombinant DNA technology Or can cut large genomes into small for analysis Opposite cuts on two diff strands are sticky Blunt ended are cut in the same spot right down middle Restriction enzymes recognize and cleave nucleotide sequences called restriction sites Top strand is 5 to 3 and the bottom is 3 to 5 Restriction fragments Each tick mark represents cleavage site Use tools in combination Southern Blot Restriction enzyme is added to solution containing DNA The resulting fragments are separated by size by gel electrophoresis DNA fragments in gel are denatured and then blotted onto lter paper Filter paper is places into plastic bag containing solution with radioactively labeled DNA strand probe and this matches and stick to complementary fragments Can visualize which areas on blot are radioactive Each of these lanes is a well Sanger Sequencing Most reliable type of sequencing PCR with one major difference use special type at some frequency that is a terminator nucleotide Terminator nucleotide dideoxynucleotide Lacks 3 hydroxyl group and cannot be elongated because there is no h ydroxyl group to attack an incoming nucleotide triph osphate Dideoxynucleotide incorporation addition of terminator nucleotide The sequence want to separate DNA by size so use electrophoresis Use polyacrylomide gel can separate out DNA at single nucleotide length differences ie bw 3 bases and 4 bases Recombinant DNA GMO Donor DNA that you want is obtained by restriction enzymes which is also used on the vector DNA where its going Sticky cuts overhanging They are perfectly complementary Fragments are mixed together and joined by DNA ligase Genomic and vector fragments have complementary ends Transformation Introduced into bacteria cell by transformation Chemically induced to suck up DNA from outside the cell also replicated recombinant DNA as it replicates
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