Notes/Study Prep for Foundations of Biology 1
Notes/Study Prep for Foundations of Biology 1 BIOSC 0150
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This 111 page Bundle was uploaded by Kelly Cary on Thursday February 5, 2015. The Bundle belongs to BIOSC 0150 at University of Pittsburgh taught by in Winter2015. Since its upload, it has received 61 views. For similar materials see Foundations of Biology 1 in Biology at University of Pittsburgh.
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Living Organisms Consist of 5 Fundamental Characteristics 0 made up of cells processes information has the ability to reproduce consumes and uses energy is a product of evolution theory explanation for a very general group of observations that are supported by a lot of evidence 0 something that occurs regularly pattern 0 something is responsible for that pattern process 1 Cell Theory the theory that all organisms are made of cells and that all cells come from preexisting cells Robert Hooke and Anton van Leeuwenhoek pattern 0 all organisms are made of cells Rudolph Virchow process 0 all cells come from preexisting cells Louis Pasteur evidence 0 disproved spontaneous generation 0 proved Virchow s hypothesis 2 Theory of Evolution by Natural Selection species are related by common ancestry and characteristics of these species can be modified from generation to generation evolution natural selection occurs when individual organisms with certain heritable traits tend to produce more surviving offspring than individuals without these traits Chemical Foundations of Life basic principles of life all basic biology is chemistry all atoms consist of protons and electrons along with some neutrons o protons and neutrons in the nucleus 0 electrons float around the outside 0 electrons are in orbitals atoms are the smallest part of an element you can have 0 atomic number protons neutrons 0 atoms with the same atomic are the same element with same chemical properties four elements that make up 96 of all living matter Carbon Hydrogen Oxygen Nitrogen 0 structure affects function 0 looking at them you can tell what bonds they can form 0 bonding is dependent on electrons Electrons 0 each orbital can hold two electrons o orbitals are groups in levels called electron shells 0 each electron shell contains a specific number of orbitals 0 first 1 2 electrons o the rest 4 8 electrons 0 atoms are most stable when all orbitals are filled Noble Gases vaence the number of unpaired electrons in the outermost electron shell of an atom o unfilled electron orbitals allow the formation of chemical bonds Covalent Bonds 0 works by sharing electrons 0 makes the elements more stable m atoms 1 m atoms Carbon four covalent bonds 39V I V39 Hydrogen one covalent bond Oxygen two covalent bonds Nitrogen three covalent bonds SWINE BF TWSFER DF ELEIZTE39IIINS ELEIZTE39IIIN lonic Bonds 0 works by transferring electrons 0 one element has one too many Q electrons one has one too little v mm me at 0 moves the electron from one to mam 10 gm the other E t il ntb WWW 1993 EFlFlLFlHEI PUBLISHING 0 also makes the elements more stable electronegativity measure of how strongly an atom attracts electrons o in other words how much does that atom want to hold on to their electrons 0 highly electronegative atom gt has a partial negative charge because it holds electrons tightly 0 gives the other atom a partial positive charge 0 unequal sharing of electrons polar covalent bonds 0 H20 best example of this 0 nonpolar covalent bonds equally sharing of the electrons o no partial charges scaled on a continuum O 0 Nonpola Covalent Bond Polar Covalent Bond Ionic Bond nEN 004 nEN 0420 nENgt 20 Water H20 0 makes up about 70 of organisms 0 super super important water is unique because it has a unique structure 0 pretty small two Hydrogen one Oxygen o bentshape 0 highly polar because the Oxygen is very electronegative and pulls the electrons towards it 0 makes Hydrogen slightly positive the whole structure is overall polar has the ability to form hydrogen bonds 0 not really a bond more of an attraction electrostatic interactions 0 partial negative charge of one molecule is attracted to the partial positive charge of another molecule 0 one water molecule can form four hydrogen bonds at a time water m lmle 0 really good solvent 0 hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in water hydrophilic o uncharged and nonpolar molecules do not dissolve in water they are hydrophobic 0 really high specific heat 0 energy is takes to raise a gram by one hydrogen bond degree Celsius WerEHEKHEEMWWHWMM o cohesive surface tension V mmh mng if i o adheres to any surface that is charged quot n 0 high heat of vaporization F l u a 0 liquid water is denser than solid H20 H m mmlimwmmm water has a slight tendency to ionize p lgar A H20 gt 0H H cavalent mi free protons are never by themselves so this is more accurate Ella H 39 gt OH WEEErm iiil ui u water is both an acid and a base pH of a solution determines whether it is acidic or basic 0 life can only live in a specific pH range 0 buffers are compounds that minimize changes in pH 0 act as acids and bases 0 carbonic acidbicarbonate system is super important 0 acids pH gt 7 bases pH lt 7 neutral pH 7 equa ons pH log H H 10quotpH unit Molars M buffers are compounds that minimize changes in pH 0 the carbonic acidbicarbonate system is an important buffer in blood 0 can accept or donate protons in response to changes in blood pH uni d l In Le s E r am It in HI in Fig Hen qu t we limit 7 net an aetelylease reamien Carbon 0 most versatile element on Earth because it has four unpaired valence electrons 0 can have up to four covalent bonds 0 carboncontaining molecules are called carbon molecules can form an almost limitless array of shapes 0 linear ring branching etc simplest molecule you can make with carbon is Methane carbon with four hydrogens o tetrahedral shape carbon can form single double cl quotH and triple bonds l H H H 7 3 Ethane Propane H H 1Butene a Length c Double bonds Hl H H H H H 39H a r a 7 1 39 Hi xxJ H H H H H H Butane EMethylpropane commonly called isobutane Cyclohexane b Branching d Rings 355 Formula I 3wa Alcohols Ema functional groups know these groups 0 the chemical behavior of an organic molecule 0 Carbonyl Aldah deg R ICZ frequently depends on groups of atoms attached 1 y to the C skeleton 3 usually contain H C N O P or S RT the arrangement gives the groups certain 0 properties 53233311 iii 32 39 0 SH polar team was Rmbk NH H O Phosphate organic RMOM 3 0 DIPQBCz Phosphates Sul 39lydxyl Thiols R SH SH E xample H H Hl Benzene t 3 H Hemparm I I lli Ethanol H O If HM C if H Acetaldehyde HUB EBEI H 39C C C E l H H Acetone H O l 1quot H fif m E DH Acetic Acid 1 Pi H C Wquot N l H H Methylamine HO O a C i H CHOP 0 E ll FE w 0 m h 1 5r PEIE HMC E SH 1 HM Mercapto ethanol H 0 3 Phosphog1ycexic acid chemical reactions involve the making andor breaking of chemical bonds 0 can happen when substances are combined 0 atoms are rearranged or small molecules combine to form large molecules 0 can happen when substance is broken down 0 molecules are split into atoms or smaller molecules during changes in connections change the behavior and structure of the molecule Chemical Equation 0 reactants are written on the left 0 products are written on the right 0 double arrow between them means the rxn is reversible o can reach equilibrium Chemical Equilibrium 0 does NOT mean you have equal amount of products and reactants o no net change 0 quantities remain constant 0 rate of fonNard rxn rate of backward rxn o equilibrium can be altered o changing the concentrations 0 changing the temp not as common in biology changing pH moves buffering systems away from equilibrium all chemical rxns require energy don tjust happen spontaneously 0 energy capacity to do work or supply heat First Law of Thermodynamics 0 energy cannot be created or destroyed 0 energy is constant but can be changed or transformed 0 always requires energy to break a bond sometimes get energy from breaking bonds kinetic energy of motion and potential energy stored energy 0 potential energy is chemical energy in the bonds eectrons on outer shells have more potential energy than those near the nucleus 0 kinetic energy is molecular motion 0 also called thermal energy 0 increasing energy increases speed 0 heat is the thermal energy transferred between objects 0 the temperature of a system is a measure of the average molecular motion of that system Second Law of Thermodynamics 0 systems tend to proceed from a state of order to a state of disorder 0 entropy aka measure of randomness chemical reactions are spontaneous if they can occur without an outside influence energy 0 if entropy increases reactions tend to be spontaneous 0 product is less ordered than the reactants o spontaneous if they go from high PE to low PE chemical processes proceed in the direction that results in increased entropy and lower PE Chemical Evolution 0 early in Earth s history inputs of energy led to simple molecules combining to form increasingly complex carboncontaining substances 1 Prebiotic Soup Model 0 molecules in the atmosphere combined because of intense energy inputs 0 combined with stuff in the ocean 2 Surface Metabolism Metal 0 energy is coming from hydrothermal vents 0 being catalyzed from minerals in the vents Proteins 4 major classes of macromolecules aka large molecules that are essential for life 1 nucleotides 2 complex carbs 3 proteins 4 lipids 13 are polymers a bunch of monomers or chemical subunits covalently bonded together Monomers nucleotide simple sugar amino acid Polymers nucleic acid complex carbs protein amino acid basic structure 0 amino group is positively charged and the ar3im carboxyl group is negatively charged when its at pH 7 Gt carban V o no net charge because the charges cancel each I a hydragen other out V i1 l R side chain H31 CH c 0 makes each amino acid unique 1 amjna ngbax Frauu graup o 20 common amino acids E H lll H m H quotIII 339 II I I I g I I 3399 I E quotEl HEMLc cgfp HarILIE cf HEHL ij HQNL39IE E IllgrdLEII E ngK c cg A IN EllI3I 39 fatal mg 339 IIgc CII a 342 39 EH3 quot3 It Elllg EH EL 3 x V 39 Hla ll13 Ellla a 2 I 33quot ID Glycine Emir Alanine Allail 1IIEEIIliIIIEI1I39f Il E H I ngf Ec lll ML C H LE C I H 3 I quotEa I RID Elll 1542 ng I SHE 39 39 1 EH J it In mag 5 l Ellll Saline HEW ll it mainline Il ll iltr twatcine st Tyrosine Il ll m Mpraragiine Want a Haw c cg Haw c cg Haw c cg Hart c R E I 5339 I ID39 I i I I E m EH2 lle fit1E I I A Lil I EH lvllya cm s b 39339 it c m EH2 m 1quot A or 39Elnllgf NH 51 7 I Nina 5 1 vall F m 3 I 2 39 MIME m I ci ic aasii mpartiic Acid Map IEllutaumiic Illicit Elm List iiim 39Lwll vminine Mall LELIlEliIl39IEIUL ElJl l ulmcineIlllllej llllethiumiinE39Illl et 39ll39IryIlmtuphlamllTrpt Fheny llalamiineflllhe Praline Iij Histidine His 0 side chains determine the reactivity and the solubility of the amino acids 0 hydrophobic I waterresisting not soluble o hydrophilic I waterloving soluble 0 proteins are formed when amino acids polymerize through condensation aka dehydration reaction 0 removing a water molecule to create a covalent bond between monomers 0 bond is called a peptide bond that forms between the carboxyl group of one amino acid to the amino group of another amino acid 0 electron sharing that acts like a double bond Peptide vs Protein 0 peptide is a short amino acid chain with less than 50 monomers o polypeptide is a long amino acid chain with more than 50 monomer o more specifically a protein is one or more amino acid chains that are folded and functional poypeptide chain always starts with the amino group on the left Nterminus and ends with the carboxyl group on the right Cterminus o R groups extend from the backbone which is essentially everything but the R group 0 backbone is flexible to some degree order of amino acids dictates how the protein will fold 4 Basic Levels Primary 0 string of amino acids in a unique sequence Secondary 0 two shapes alpha helix and beta pleated sheets 0 side chains do not contribute to secondary structure at all just the backbone everything else 0 in helix shapes hydrogen bonding occurs every four amino acids to keep the shape stabilized o in the sheets hydrogen bonds are present across the same plane to keep the shape stabilized Tertiary 0 overall folded shape of the protein helices and pleated sheets fold together 0 interactions between R groups and R groups and backbone atoms keep the structure together 0 R groups interactions hydrogen bonding hydrophobic interactions van der Waals interactions disulfide bonds and ionic bonds 1 hydrophobic interactions occur between nonpolar side chains that fold in towards each other because they want to stay away from water 2 hydrogen bonds form between Hydrogen atoms that are attached to an electronegative atom N or O and another electronegative atom 3 van der Waals interactions are weak attractive forces between two uncharged atoms short range 4 disulfide bonds are covalent that form between two cysteine side chains that create a bridge 5 ionic bonds form between a negatively charged side chain and a positively charged side chain Quaternary 0 multiple polypeptide chains that twist together 0 most famous one hemoglobin o hydrophobic interactions mainly hold the structure together 0 proteins are in solution and these side chains want to stay away from water so they fold together structure determines function when a protein is denatured unfolded it can no longer perform its function proteins can spontaneously fold into their active form 0 primary sequence determines how they fold doesn t need energy to fold o it is energetically favorable for hydrophobic amino acids to fold into the center of the protein where they have limited exposure to water 0 it is energetically favorable for hydrophilic amino acids to be on the exterior of the protein where they can interact with water some proteins require molecular chaperons to fold into their fully functional form take picture from powerpoint ions and small molecules can act as regulators that allow proper folding of proteins in response to cellular signals 0 goes from inactive form to active form simply because a certain molecule attached to its structure misfolded proteins can be detrimental 0 most times your body will get rid of the misfolded protein 0 prions are infectious proteins I transferred by consuming brain tissue with this protein I causes neural degeneration o amyloid plaques are another type misfolded proteins I as we age the mechanism that destroys misfolded proteins weakens I proteins start to unravel and combine with other proteins forming fibers called amyloid plaques I cause of things like Alzheimer39s disease and Huntington s disease Protein s Functions 0 catalysis o ability to speed up a reaction by bringing molecules together in a precise orientation so that they can react I enzymes bind to reactant molecules called substrates at a specific place called the active site 0 protein called an enzyme not all proteins are enzymes 0 defense 0 in the form of antibodies and MHC proteins 0 adaptive immune system is based on interactions between specific immune system cells and a specific antigen I your system builds up a memory of everything that attacks your body I antigen foreign molecule that initiates an immune response I antibodies proteins that bind to a specific part of an antigen called the ep ope MHC proteins antigen presenting proteins on the surface of B cells that bind small peptide fragments of antigens and present them to T cells 0 mostly beta sheets T cell is then activated and release cytokines cytokines signal the B cells to reproduce itself and produce antibodies 0 antibodies then attach to the antigen and mark them for destruction B Cell receptors and their antibodies 0 have two identical light chains smaller peptides 0 two identical heavy chains twice the size of light chains 0 shaped like a Y with two antigen bonding site 0 also has transmembrane domains that anchor the heavy chains al B cells have a segment that is common constant region but every B cell also has a unique segment variable region 0 the V regions allows each protein to bind to a unique epitope 0 allows for a lot of variety lmmunoglobulin lgG Structure 0 chains are linked together by disulfide bonds covalent bond between two cysteine amino acids 0 has primary secondary tertiary and quaternary structure 0 transport 0 hemoglobin is in red blood cells and its sole purpose is to transport oxygen 0 gas exchange oxygen and carbon dioxide is essential in vertebrates I cells must obtain oxygen and expel carbon dioxide continuously to support ATP production by mitochondria I ventilation gas exchange circulation and cellular respiration 0 oxygen moves from areas of high partial pressure to areas of low partial pressure aka concentration I in mammals 02 moves from the lungs high partial pressure to blood low partial pressure I oxygen is not soluble in water so it depends on the protein hemoglobin to transport it o hemoglobin made of almost all alpha helices I is a tetramer which is four polypeptide chains twisted together 0 each subunit has one nonprotein group called a heme molecule 0 each heme contains an iron ion Fe 2 that can bind to oxygen 0 this each hemoglobin can bind up to four molecules of oxygen I has all four levels of protein structure 0 oxygen binding to hemoglobin can be shown on a oxygenhemoglobin curve I S shaped curve 0 this is because it can do cooperative bonding look up definition 0 makes it very sensitive to changes in the partial pressures of tissues knows when to deliver oxygen I when a hemoglobin is fully saturated its bonded to four oxygen molecules 0 at rest its bonded to a little more than two oxygen molecules 0 in exercising tissues its bonded to a little less than two oxygen molecules the hemoglobin is giving your tissue the oxygen I when the partial pressure is high the pH of blood drops 0 this is because using oxygen produces carbon dioxide which increases the H concentration which drops the pH 0 the drop in pH makes hemoglobin more likely to release oxygen 0 this is known as the Bohr shift on a graph 0 movement 0 signaling 0 structure Nucleic Acids polymers of nucleotides 0 nucleotides are composed of a phosphate group fivecarbon sugar and a nitrogenous base o the five carbon sugar is either ribose or deoxyribose o ribose in RNA oxygen on the 2 carbon 0 deoxyribose in DNA no oxygen on the 2 carbon 0 two types of nitrogenous bases 0 pyrimidines six atom ring structure I cytosine I uracil RNA I thymine DNA 0 purines nine atom ring structure I guanine I adenine O 0 nucleotides polymerize by 3 NA 5 H N HN CH3 condensationhydrolysis reactions U I N 2 RN 5 0 LN I I Hi 0 form phosphodiester bonds linkages o IT 0 y 1 between the 3 carbon hydroxyl and the H H Pyrimidine Uracil U Tlhymilne T Cytosine C 5 carbon phosphate RNA only DNAonly both DNAand RNA NH2 0 DNA polymer of deoxyribonucleotides 5 7 I Ill 5 N 0 can have A G C T as nitrogenous WEI gt8 NENgt H NAIP S bases 2 N 4 39T39s KN N KN N 3 H quot IL HZlN IL 0 deoxyribose sugar RNA ribonucleotides 0 can have bases A G C U o ribose sugar backbone is directional 5 on one end 3 on the other end Purine Adenine A Guanine G the energy of polymerization comes from nucleoside triphosphates 0 nucleotides can have up to 3 phosphates 0 most common form is ATP 0 when you break down ATP to ADP it releases energy primary structure of nucleic acid is the sequences of nucleotides on the sugarphosphate backbone o secondary structure EnNin Chargaff39s Rules 0 the number of purines is ALWAYS equal to the number of pyrimidines 0 amount of adenine is always equal to thymine and cytosine is always equal to guanine Rosalind Franklin and Maurice Wilkins 0 Xray diffraction shows the shape of something by bouncing Xrays off 0 determined it was a repeating helical shape 0 said the phosphate was the backbone Watson and Crick 0 built a physical model to determine actual shape of DNA 0 suggested that it was a double helix 0 the two strands were antiparallel with the phosphates on the outside 0 5 gt3 3 gt5 o nitrogenous bases face the interior hydrophobic and van der Waals interactions help stabilize the interior 0 bonds between complementary bases are hydrogen bonds 0 3 between G and C o 2 between A and T 0 DNA has a major groove and a minor groove DNA can store and transmit biological information o carries the information required for the growth and reproduction of all cells and organisms the information is contained in the sequence of the bases this ability is a direct result of its structure DNA Replication 0 each strand serves as a template for the formation of a new complementary strand 1 strand separates unwinds 2 base pairing occurs with the template 3 polymerization occurs and the strands rewind to create two helical structures 5 AGTCCTGGAACGCTA 3 3 TCAGGACCTTGCGAT 5 RNA ribonucleic acid 0 nucleotide is always added to the 3 c has an OH group on the 2 Carbon where oxygen only has an H 0 makes it much more reactive and less stable 0 secondary structure results from complementary base pairing however RNA is single stranded o the bases form hydrogen bonds IQE with complementary bases on the SAME g a strand stabilized by hydrogen bonds Loop hydrophobic interactions van der Waals C I Jquot interactions and phosphate backbones E 3N1 single strand region forms a loop double strand forms the stem still antiparallel 0 whole thing is called a hairpin 0 can form tertiary structure unlike DNA 0 no proteins just amino acids 0 RNA is an information containing molecule 0 messenger RNA mRNA is synthesized from a DNA template and carries the genetic information to the ribosome for protein production 0 RNA has the ability to replicate itself 0 look up picturediagram from AP Bio 0 RNA can function as a catalytic molecule 0 ribozymes are enzymelike RNAs capable of catalyzing a number of chemical reactions have an active site just like enzymes riboswitches turn things on and off siRNA miRNA lincRNA snRNA antisense RNA RNA World Hypothesis 0 chemical evolution led to the formation of a molecule that could replicate itself 0 the most likely candidate is RNA not as complex or stable as proteins and DNA The Central Dogma 0 gene expression is the process of translating the information in DNA into functioning molecules within cells 0 Beadle and Tatum developed the onegene one enzyme hypothesis 0 took bread mold and observed the defects that radiation would cause 0 prevented the mold from producing specific compounds 0 proposed that each gene contains the information needed to make an enzyme Srb and Horowitz tested this hypothesis 0 knew that organisms synthesized arginine amino acids in a metabolic pathway made of multiple steps 0 grew bread mold on arginine 0 took the mutants and grew them on 4 different types of mediums one was the control genes contain information for all of the proteins in an organism notjust enzymes 0 changed to onegene onepolypeptide protein hypothesis Crick proposed that the DNA sequences coded for the 20 amino acids that make up proteins Jacob amp Monod suggested that RNA molecules act as a link between genes found in the cell s nucleus and the proteinmanufacturing centers located in the cytoplasm Messenger RNA mRNA carries information from DNA to site of protein synthesis o the enzyme RNA polymerase synthesizes RNA according to the information provided by the sequence of bases Central Dogma DNA gttranscription RNA gttranslation proteins 0 the sequence of DNA specifies the sequence of bases in RNA which specifies the sequence of amino acids in a protein 0 genetic code contains the rules that specify the relationship between a sequences of DNA or RNA bases and the Second base G corres ondin amino acids in a 77 7 39 p g ujuu Wellyquot F USU UAUJ TymsineY USUGysteine protelns U UUG alanine LIGB SE ne UAC IJGG 39 UUA GA A um Stop 30an LIGA Stop cordon 0 AUG IS the start codon UGLE C39quotE IL um 3 MAG Stop coan um 39fl39r yptopl lan O UAA UAG UGA are all cu ccu EAUH m H cau39 H quot7 39 Ell ll E V stop COdOhS C Leucine L Proline GAE w Arginine m GUA can P EMGM I can R 1 redundant 33 GUG GG E me Emmi EGG 2 unambIguous Edeum r r ghepaaragiine igl Serine S 0 each codon only codes for one A mm ABA a N Am v 1 vethionine Acts 7 j Lysine I Argininer amIno acnd Auamanmdm MG K AGE R 3 uniVersal ELM EDDquot Gnu Aspart39lc Gay 0 all organisms have this G g EVaIine V Alanin Emmi Egg GiycineG 4 conservative GU 963 GAG acid El EGG o the first two bases of the codons are identical 0 helps to prevent mutations and mistakes DNA gt 5 to 3 is the coding strand 3 to 5 is the template for RNA Viruses virus an obligate intracellular parasite o enters host cell and use the host s biosynthetic machinery to reproduce and synthesis viral proteins 0 each type of virus infects a specific unicellular species or cell type c virtually every system in the human body can be infected by at least one kind of virus viruses cause the most devastating epidemics 0 Spanish flu 0 HIV that causes AIDS 0 HIV infects T cells and destroys them 0 you don t die from HIV you die from secondary infections because your immune system is so weak and cannot produce antibodies 0 acute phase chronic phase AIDS viruses are very small munInc GJ UF39GC EDIDC my 35ml FIJI39LIJ 0 much smaller than a red blood cell or bacterial cell a virus particle virion consists of the viral genome 0 genetic material DNA or RNA 0 may be linear or circular 0 may consist of a single molecule or have several different segments 0 single stranded or double stranded a protein coat called a capsid some have an envelope which is a membrane taken from the host cell come in a variety of shapes Two Ways Viruses Attack Cells 1 Replicative growth lytic cycle 0 produces the next generation of virions using host cells machinery 0 most often kills the host cell 2 Dormancy lysogency 0 virus coexists with the host cell for a period of time until it is activated 0 host cell replicates the viral DNA each time is divides viruses gain entry to cells by binding to a specific molecule on the cell wall or plasma membrane 0 viral proteins attach to certain things on membranes that act as markers 0 the viral genome then uncoats at the cell surface and it enters the host cell c or the viral genome is engulfed by the host cell and the endosome uncoats it Daughter cell with popl39iage Cell divisions produce 39 population of bacteria infected f Phage DNA Phage 39 d r r quot 39 V circularizes 7 7 with the prophage 39 f f me A Occasionally a prophage 33 7 exits the bacterial isquot U 39 chromosome 39 quot quotquotquoti 7 initiating a lytic cycle r o 2 I v x l Lysogenic cycle l 39Lysogenic cycle Prophage Ly tic cycle The cell lyses releasing phages The acterium reproduces copying the prophage and transmitting it to daughter cells Ly tic cycle is induced l or J is entered it g V 77 quotW o 7 New phage DNA and proteins are synthesized and assembled into phages Phage DNA integrates into the bacterial chromosome becoming a prophage Influenza A virus infects a host cell Hemagglutinin Glycan chain of host cell Membrane of host cell Protein 0 enveloped viruses bud from a cell through the membrane gets a new envelope membrane 0 nonenveloped viruses burst out of the cell and breaks it viruses cannot make their own proteins quot f enveloped virus 2 capsid O a r elrldosome 3951 5 i a 39 m nucleic 7 sarivi is acid I envelope quotaquot protein 39 progeny vi rus in addition to transcription and translation to make proteins viruses also has to copy 0 their genetic material to make a new generation they depend on the host cell for nucleotides 0 most RNA viruses use a viral RNA polymerase called RNA replicase O retroviruses the RNA genome is transcribed to DNA by a viral enzyme called reverse transcriptase 0 they break the central dogma of molecular biology because it goes RNA gt DNA gt RNA gt proteins Reverse transcriptase Doubleistranded GD l llti ill illll lili 39llt illl Reverse transcriptase Singleastranded cDNA 17 xi viiiiiill lllliiiiiiirliillililil39it mRNA OI l 39llillll39quot lil39llll lill Q r i 39 Primer roublegstranded cDNA DNA polymerase 2011 Pearson Education Inc first it makes a single stranded cDNA from a single stranded viral RNA template then it removes that RNA strand and synthesizes the cDNA strand resulting in double stranded DNA that can be inserted into the host cell genome Ebola enveloped linear RNA virus that uses RNA replicase to replicate has already claimed 2000 lives transmitted through direct contact cannot be spread through the air 0 can only be spread after symptoms begin incubation period 2 21 days time between infection and onset of symptoms 0 0 Symptoms fever severe headache muscle pain diarrhea vomiting abdominal pain 0 internal and external bleeding some cases currently no cures or vaccines immune system does not recognize it affects every area of the body Carbohydrates simple carbs all have the same molecular formula CH20n 0 glucose and fructose share the same molecular formula C6H1206 but they differ structurally 0 their carbonyl group is in different places glucose is an aldose end and fructose is a ketose middle 0 carbs can also differ in the length of their carbon skeleton o carbs tend to form ring structure in aqueous solutions alpha and beta form 0 hydroxyl on the end bends around and attacks the aldose simple sugars monosaccharides 0 each one has a unique structure and function 0 joined together make polysaccharides complex carbohydrate disaccharides two monomers simplest form of polysaccharides o lactose sucrose trehalose o joined by a glycosidic linkage formed by condensation because water is a by product 0 form between any two hydroxyl group 0 the location and geometry of these bonds vary widely among polysaccharides o the types of glycosidic bonds determine the structure function and stability of polysaccharides H OH D glucosc D glucnsc starch plants and glycogen animals 0 polymers of glucose used as storage H20 HVO HiOH HOAH HCOH HlOH HiOH H GLUCO SE Fig u re 76 impinges i CELLOJBIOSIE o starch is a mixture of branched amylopectin and unbranched amylose alpha polymers H H C OH l c 0 HO c H l H C OH H 3 OH l H C OH H FRUCTO SE quotVa 2 l szc ratGlucose quotC ll aH C 2 l on i l aDGluc opyranose oH quot quot39 H a nomerllc ciquot 1quot Sc o TI quot C SH H K mll I n 3c It I H V on 3D Gl ucopylralnose Dam pksdl iothemiil mm Edition mu muwnmny glycogen is a highly branched alpha glucose polymer cellulose plants Chitin structural polymer of beta glucose monomers located in cell walls makes long parallel chains that connect by hydrogen bonds structural polysaccharide found in fungi cell walls and animal exoskeletons comprised of Nacetylglucosamine NAc monomers o has a nitrogen group 0 beta 14 linkages create long parallel chains that connect by hydrogen bonds and peptide bonds 0 very very stable peptidoglycan structural polysaccharide found in bacteria long backbone of two alternating monosaccharides one has a chain of amino acids a ached when adjacent strands align peptide bonds form between amino acids carbs indicate cell identity 0 outer surface of cells contain glycoproteins proteins joined to carbs by covalent bonds 0 key molecules in cell to cell recognition and cell Carbohydrates Integral Phospholipid Protein y i quot r1 1 r 739 n iil in H my l lri 1quot l l l l r l y l l i f l l l i l l i i l l l i39 l l l l l l i l l l l J i l l l l l l quot 39 l l to cell signaling n w 1 ca rbs serve as storage for energy if 3 guy y 71quot Ll i4 Fl L4 Vi l4 i VF Ni l Lilla o provrde chemical energy for cells y y y V y g o glycogen and starch can be broken down into glucose Peripheral Protein Cholesterol for cells to use 0 phosphorylase enzyme that hydrolyzes the glycosidic linkages in glycogen o amylase enzyme that hydrolyzes the glycosidic linkages in starch 0 energy stored in glucoseother carbs is used to make adenosine triphosphate ATP 0 CH20n 02 ADP Pi gt C02 H20 ATP 0 Pi inorganic phosphate Adenosi ne triphosp h ate ATP H2O n i EMMY Inorganic phosphate Adenth i ne diphosphate ADP 332 39quot1 photosynthesis plants convert the chemical energy of sunlight into the chemical energy of carbs Photosynthesis Equation gt 361 11202 602 carbs have more free energy than C02 because CH and CC bonds have much higher PE than CO bonds 0 the more CH and CC bonds you have the more energy you can store fats are also good for energy storage 0 have double the CH bonds than carbs 0 store twice as much energy per gram than carbohydrates fats are a type of lipid o unlike other biological molecules lipids do not have a common structure and are not polymers 0 they are hydrophobic and contain carbon types of important lipids 1 fats triacylglycerols 2 steroids 3 phospholipids fatty aCId hydrocarbon chaIn bonded to a carboxyl functional W Saturated famdd m dfatwd group H J O 7 I 0 major component of fats and phospholipids either saturated or unsaturated o saturated only single bonds between the carbons 0 solid at room temperature pack really close I39 2 1 393 g 393 s n 539 H quot39y A h nwr e I I IJ N h r l I39l r l 139 I I I I IJ NI IJ MI 1 I F 0 nr together 2 0 when the chains are really really long they form g Ham a wax at room temp Pamggm o unsaturated one or more double bonds in the hydrocarbon chain Umleic cid I 2001 Sinauer Associates Inc 0 liquid at room temp not as packed closely together because of the kinks caused by double bonds fats are composed of three fatty acids linked to glycerol 0 glycerol hydrophilic fatty acid chains hydrophobic o linked together by Ester linkages 0 form via condensation dehydration between a hydroxyl group of glycerol and the carboxyl group of a fatty acid steroids are a family of lipids that can be distinguished by a bulky fourringed structure 0 have different functional groups attached to different carbons cholesterol steroid that is important part of cell membranes membrane lipids are amphipathic polar and nonpolar region 0 phospholipids have two regions the head and the tail head hydrophilic interacts with water tail hydrophobic cannot interact with water 0 when placed in water they ll create a lipid bHayer hydrophobic a hardm hiiic o polar heads will face the water and the nonpolar tails will face towards each other in order to get away from the water 0 occurs spontaneously in aqueous solutions does not need energy hydrophobic effect Selective Permeability o smallnonpolar molecules move across the bilayer rather quickly 0 oxygen nitrogen carbon dioxide etc o largepolar molecules move across very slowly sometimes not at all 0 glucose sucrose etc all polar 0 ions will not go through because of their charge 0 nucleotides and amino acids factors that affect permeability 0 number of double bonds in the hydrocarbon tails o the more double bonds unsaturated the easier it is for something to go through 0 temperature 0 look up graph 0 when temp increases the permeability increases 0 increases KE molecular motion so the molecules want to spread apart length of tail shorter tails higher permeability number of cholesterol molecules in the membrane 0 more cholesterol the lower the permeability o cholesterol stiffens the membrane Cholesterol H0 Fluidity in Membranes 0 individual phospholipids can move laterally throughout a layer of the bilayer but rarely flip from one layer to another lateral diffusion o the fluidity of a membrane depends on temperature the structure of hydrocarbon tails and the presence of cholesterol 0 cholesterol maintains the fluidity doesn t let it reach extremes of falling apart and being glued together solutes small molecules and ions in solution 0 have thermal energy and are in constant random motion 0 movement of solutes that results from their kinetic energy random motion is diffusion Diffusion 0 occurs spontaneously down a concentration gradient until equilibrium is reached 0 move from areas of high concentration to low concentration 0 diffusion of water osmosis the concentration of a solution outside the cell may differ from inside the cell c hypotonic the solution has a lower solute concentration than the cell so water moves into the cell causing plant cells to swell and animal cells to swell and burst o isotonic the concentration of solutes is equal inside and outside the cell so water moves across the membrane in both directions maintaining cell size 0 hypertonic the solution has a higher solute concentration than the cell so water moves out of the cell and into the solution causing the cell to plasmolyze H 39F ll39HllE l t i ll lH39 39EE 39 MllE E39ELLITIEH Em lml l Cell membranes contain almost as much protein as phospholipids 0 early models of the cell membrane suggested that the phospholipid bilayer was sandwiched between proteins a Sandwich model Bell exterior Singer and Nicolson challenged the sandwich Membrane 39 39 39 ra teinspn e 9 7 model and proposed that amphIpathIc proteins EBquot Mari H f w whimEyfiwmhfiNW7 ill lllllllllllllll llllll could span the membrane Fh s mm id Fir l ll lillllllllll a a ll llill l l 3 Proteins can he amphipathic I 739 39 The polar ahd charged fil l3911ll lllj Eli lltll FE39lEliJE39 Ell brine hiricir gihi li 39 quot539 Framing l quot 39 39 39 39 7 r 39 39 cell interior Eelquot Ini l l no 31 Humm Eux iwwm quotuTll jr igl39llmgfi ESWUEE Singer and Nicolson s FIUId Mosaic Model are 3r rap no If 1972 IS the current model of cell membrane b Amhilp hi proteins can integrate into lipid bilayers Structu re utslda oellll ll will if in i l 2 l I l l Peripheral a i In J Integral 5555 Il39l39 39llll 39 39 39 9mm BYTDPLASMIC SHE 0F MEMBRANE OE39I M WIWW w There are two main types of membrane proteins i 39 GEIIEIterior Peripheral 1 Integral proteins are embedded Within the f r hydrophobic interior of lipid bilayers quotr j they are amphipathic with a hydrophobic mm M 1 mg region that may cross the entire membrane or quotHEW quot WWW MAJ ll proteun extend only part way Into the bilayer i I 39 M quot y f V transmembrane proteins are integral 1 I 39A 39 proteins that span the entire membrane and cell inferior V prunein lll39 nm MICE he have hydrophilic segments both inside and outside the cell 2 Peripheral membrane proteins bind to the membrane without passing into the membrane 0 found only on one side of the membrane bind through noncovalent interactions hydrophobic effect often attached to integral membrane proteins Integral membrane proteins can be isolated from membranes with detergents Mums IlstlLATilliE MEMBRANE Plilll39TElllilE detergents are amphipathic molecules that tend to IE 3 form micelles in water they break up membranes by if yf leefdfi ft m coating hydrophobic portions of the membrane and ff J E EEquot 5 membrane proteins 0 dissolve membrane to isolate the protein 0 don t need to do this for a peripheral 2 Binding b membrane because they re not embedded instead detergrants you would I li l at proteins membrane proteins have many functions 0 enzymatic activity attachment to the cytoskeleton and extracellular matrix cellcell recognition intercellularjoining signal transduction transport transport proteins are transmembrane proteins that transport ions and molecules three broad classes of transport proteins 1 channels 2 carrier proteins or transporters 3 pumps 1 channels 0 act as tunnels for ions or small molecules to cross a membrane 0 highly selective o the structure of the proteins allows only a particular type of ion or molecule to pass through 6 0 0 V i o mgmmm onMa eectrochemIcal gradients occur when Ions bqu up on one side of a plasma membrane 0 combination of both a concentration gradient and a charge gradient Nettij charge O O 1 llllllll inside cellll H V r 39 39 a at El charge Low concentration of INEF Outside cell ion channels are specialized membrane proteins that circumvent the plasma membrane s impermeability to small charged compounds 0 ions diffuse through channels down their electrochemical gradients CFTR is an example of an ion channel 0 CFTR is a protein that allows chloride ions to move across plasma membranes defective in cystic fibrosis 0 if you can t move chloride ions in or out of the cells the water doesn t move out and the mucus thickens Membrane with Illllem rene withut EFTH f William eiFr wen ElFll Eu 39 t i l l EJMEI Curr1e nt eterte i iime llen flw lien flew aquaporins are water channels that allow water to cross the cell membrane faster than it would by simple diffusion Key residues allow water to pass but bllloclvt inns and larger moleegules Outside cell the flow of ions and small molecules through 39 139 membrane channels is carefully controlled V m 39 o gated channels open and close in response 1 1 39 l ll llll 39 la 7 I l l l l r v ir39 v r v r 39 39 gt Vrv 7 v r V 1 V quotI ll l I Ig l i V I r I 1 l amp Tl lllll ill 0 Le a change in charge on one side of the quotwe o r in all membrane inside eell II rr39ne39EIrihril Ht tili39mr z i1 i5139I11FI IdE39I r 5r W 1EI i Hm l r39lll39uirljli39 l1 l39lilDlEr39vllquoti i5 l1tgil quot39flll la39 7 i5 itea39ereeel ehennel e ee n5 merged re la llee te1he euleielem enan nelie eleeeel quot F illgrgr gallirjewuu xnrnlglr r Erie ewe tev eee utteiiele eel 39 p l 45 liirI39Ia n3ii ilill39I39E39i 7 fiein entering nen lfllillll li39li lII39IiIEIlE Bill leend Elmiii Friar ire the movement of substances through channels does not require an input of energy 0 passive transport is diffusion of a substance across a membrane along an electrochemical gradient with no energy investment 0 facilitated diffusion is the passive transport of substances that would not othenNise cross the membrane 0 can occur through channels or through carrier proteins Di u imii Faeillitata amuslinn Anthea lr r LHU 39 39 y largo m f 39I39 D I E r GMEME r cull li39islluln Hal imi li l i li Eliazgl39uti imutirutn l null il l39lillL Furjam It39luwz itwnl of ftctm u nmwrmm l or iVIiTliZEIT I39E IfEI nmllnmulna i ili a am will E IFDCIlEIi39iiEJ hl gimmith litri u li lituill39yr iiu Fmt lnisfl l 5E i vnlliu 3234 Pinarm Eaucugm we Carrier proteins or transporters change shape during the transport process 0 only move molecules down a concentration gradient high to low passive transport GLUT1 is a glucose transporter that increases membrane permeability to glucose 7 lF HElEEEE lHWF lTHlEEIE Fl HEW ELUT IFEEILlIlTHTE39S ELUEE EE E IFFUEI39EH ut ide cell i 39 if l i Glucose W i l l l lm daca 1a ul hnuln pramIla 2a Elliui r Binding Em mrmtli nal Rampage change 39quot I EG A EiEI39JM Pumps are membrane proteins that transport molecules across the membrane against their electrochemical gradient 0 movement against an electrochemical gradient requires energy in the form of ATP active transport The sodium potassium pump NaKATPase uses ATP to transport Na and K against their concentration gradients o ase shows there is an enzyme in the pump that helps break down ATPs 1 binding sites with a high affinity for Na ions available 2 3 Na ions from inside the cell bind and activate ATPase activity of pump 3 phosphate from ATP attaches to the pump and changes pump shape so the Na ions have less affinity 4 Na ions leave outside cell 5 this conformation has a higher affinity for K ions 6 two K ions bind 7 phosphate is cleaved from the pump and shape changes 8 low affinity K and then the cycle repeats PH BEE 3 lll39lll39 THE El ilLuH F l li EEIiuH FILIHllF rlratllitETPEIEEZI 39lil39lllFl E3 amp llin milmus EL Ethane ttings 7 7 a unbound pmhlm Eu PalIlsllum kindling 1quot Elhinpi clump Hill Secondary active transport or cotransport uses an electrochemical gradient set up by a pump to power the movement of a different molecule against its concentration gradient w w w quota a Na 7 Ha 31 Nail H N 3m mgquot 5 quot5 M J a Na Vi Hav gant Had 393 lumssev a l v H K quot3 39H I l Hahn ggg Mini quot3 K I lHaglurmse 7 symptom Iiquot W Glucose 3 I N 4 Gimme m Ho J lTIPr lH1 2 Ki mm PI GIU39EWSE Baum mmhmu39rirqr shnrn erilFint Enlil39um low M iris2mquot and linmuNrr Water is Essential to Plants transpiration is water loss via evaporation from the aerial parts of a plant 0 transpiration occurs when stomata are open and the air surrounding the leaves is drier than the air inside the leaves water flows from roots to leaves without an input of energy due to water potential water potential LP is the potential energy that water has in a particular environment compared to the potential energy of pure water at room temperature and atmospheric pressure 0 LP for pure water 0 water flows from areas of high potential energy to areas of areas of low potential energy 0 two factors affect water potential 0 solute potential LIJS 0 pressure potential LIJP o WWSWP Solute potential is the tendency of water to move solute potential the potential of water to move by osmosis byosmosis the presence of solutes decreases the solute Solute potential inside Cell is placed in pure water cell and in surrounding Its solute potential is low potential below that Of water the CllfoSlon Of water solution is the same No relative to its surroundings net movement of water Water moves into cell via osmosis as solute concentration increases LIJS decreases hypotonic because water is flowing into the cell Pure water Pressure potential is the tendency of water to move in response to pressure Water movement Turgor pressure is an important source of pressure on water in cells v Inside of cell Expanding volume of cell pushes membrane out Turgor pressure Figure 364a Biological Scieince 2 2005 Pearson Prentice Hall Inc u pressure potential the tendency of water to move in response to pressure 0 cell does not burst because of Wall pressure Stiff cell wall pushes back with equal and opposite force Solute potentials differ Outside of cell cell wall in the absence of pressure water moves from areas of high solute potential Pure Wale s 39quotquot quot to areas of low solute potential 39l 0MPa is 0MPa 1 0 MP 0 no pressure potential In this Situation 0 measured in megapascals gt 10MPa Water moves left to right from area with high water potential to area with low water potential Figure 36gt2a Biological Science Zle 2005 earson Prentice Hall Inc b Solute and pressure potentials differ the potential energy of water in a particular location is the sum of pressure potential and solute potential that it experiences 0 no movement of water Pure water Turgid cell a water potential gradient exists between soil plants and the Purewater Solution atmosphere goes from high to low quot MPa 53335 W 333352 0 atmosphere has a very low water potential i 00MPa w time Water potentials are equal Water potentials are equal no net movement no net movement mi mm mm is o roots and soil have a very high water potential if soil is salty it would lose water Low water potential Atmosphere il1952 MPa Changes with humidity usually very low I39llllil f H Tllll arganiinullirnla line myunllI germ Ea Leaf4143 MPa gm Depends on transpiration rate h low when stomata are open 39i39i iilfill39lifl minerals r Thoway ll w39 Root lll 06 MPa Mediumhigh Soil ll o3 MPa 1 High if moist low if extremely dry phlthem 39HE39SEElll High water potential Figure 3623 Biological Science Zle 2005 Pearson Prentice Hall Inc water moves along a steep waterpressure gradient from root to shoot upwards in vascular tissue called xylem dead cells with two cell walls to make it extra stiff no organelles o tracheids long tapered and vessel elements short and wide the other type of vascular tissue is phloem which conducts sugar and other substances in two directions from roots to shoots and shoots to roots i Trmslmlion I Hershi mm Wail translocation the movement of sugars through a plant from sources to sinks 0 source tissue where sugar enters the phloem o sink tissue where sugar exits the phloem 0 sugar sucrose concentrations are high sources and low in sinks Milanler Bewa phloem is made up of two types of living specialized cells sievetube elements and companion cells 0 sievetube elements are connected to one another end to end by perforated structures called sieve plates this is where the sugars flow 0 have no nuclei and very few organelles get them through the companion cells 0 these pores in the plates create a direct connection between the cytoplasms of adjacent cells PressureFlow Model 0 phloem sap moves down a waterpotential gradient created by changes in pressure potential 3 o differences in turgor pressure in the phloem near source tissues and the phloem near sink tissues generate the force 0 generating the pressure differences requires 7 ATP 5 E E lJl ElE leaf cell Companion nail IIg E high turgor pressure in the phloem at the source is created by movement of sugars into phloem phloem loading low turgor pressure in the phloem at the sink is created by movement of sugars out of phloem phloem unloading Walter Communion W slur cell root salt the difference in pressure potential drives phloem f sap from source to sink 0 there is a oneway flow of sucrose and a continuous loop of water movement as water is supplied to and from the xylem High proton Low sucrose concentration concentration Involves passwe and active transport H H HH Sucrose Proton pump Hl Sucroseproton o proton pumps and protonsucrose HATPase W H cotransporter symporters are necessary for E quot p s 39 quot E phloem loading ook up antiporter both molecules are 3 moving in the same direction and g 39 a p 39 quot 39 Sucrose g symporter one is going one way on is ATP H1 39 H n gOing the Other lnsicle phloem cell 0 gO against concentration Low proton High sucrose concentration concentration gradient aka require energy Figure 36 22 Biological Science 212 2005 Pearson Prentice Halllnc the unloading of phloem can Phloem quot loading into QI OWing leaves Phloem unloading into roots of sugar beets either be passive or active ofsugarioeets s lavetube Companion cell Root cell 0 immature leaves need 53 Suciose sucrose energy In the form of 7 I sucrose to grow so they u lzazizztzzi 39 5 2 E mm quot quot J Hum QED eaSIly take up the sugar Passwe transport across 7 membrane then use of Active transport Into tonoplast ATP wi tllnin cell indirectly requiring cllirect use of ATP Figure 364 Biologialiiience ie Figure36725b Biolugical Edenroam In In flowing into it therefore do not need energy 0 mature leaves already have vacuoles full of sucrose so you need energy to move even more sucrose into it Homeostasis in Animals homeostasis the stability in the chemical and physical conditions within an animal s cells tissues and organs 0 body temperature 986 F blood glucose level etc cells require precise concentrations of solutes to function properly 0 solution osmolarity the concentration of dissolved substances in a solution 0 electrolyte a compound ie Na amp K that dissociates into ions when dissolved in water electrolytes and water move through organisms by diffusion and osmosis down the gradient concentration osmotic stress occurs when the concentration of dissolved substances in a cell or tissue is abnormal o minimizing water loss excretion of wastes and blood composition are all related to maintaining homeostasis and avoiding osmotic stress excretion of nitrogenous wastes varies between species 0 look up chart 0 our bodies have to get rid of ammonia because it is toxic to us different animals do this in different ways osmoregulation the control of water and solutes within cells 0 animals must maintain waterand electrolyte balance in three environments 0 marine o freshwater o terrestrial land 0 osmoconformers organisms that do not need to osmoregulate 0 Le sponges and jellyfish 0 their blood is isotonic to seawater salty 33233 osmoregulation is required in most marine vertebrates because their tissues are hypotonic to salt water gt 0 they lose water by osmosis and gain electrolytes by m diffusion meansport centraled osmoregulators maintain balance by taking water and WWW 333332 transporting electrolytes out I333332Ei g m i im c this includes marine bony fish osmoconformers maintain high urea content which increases osmolarity and makes their blood isotonic with seawater water loss is less 0 this includes cartilaginous fish like sharks 0 don t lose water through osmosis sharks still maintain relatively low concentrations of salt in their blood 0 excrete NaCl to counteract the diffusion of NaCl into their gills from seawater o excrete salt through the rectal gland aka poop out da ass ook up diagram freshwater animals are under osmotic stress because they gain lots of water and lose salt 0 the electrolytes are replaced in two ways 0 as nutrients from food sources 0 active transport from the water ook up diagram land animals constantly lose water to the environment but they lose it by evaporation rather than osmosis ook up diagram Left Kidney ll39IfEleT in crosssection 39lul39ena Caua t v Descending in landdwelling vertebrates osmoregulation occurs primarily in the kidney 0 the kidney is responsible for water and electrolyte balance as well as the excretion of nitrogenous wastes ureters connects kidney to bladder o the nephron is the basic unit of function of the kidney 0 water cannot be transported actively in the nephron it moves only by osmosis o to move water cells in the kidney setup strong osmotic gradients o by regulating these gradients and specific channel proteins kidney cells exert precise control over loss or retention of water and electrolytes a nephron has four parts and is closely associated with a collecting duct 0 the blood vessels associated with the nephron bring dirty blood into the nephron and transport molecules and ions that are reabsorbed over a million per kidney Peluie of Kidney EIEEIEIEI WebMD LLC 3VA quot quot1quoti H I39 ggza Proximaltubule ni starmbul e I j anal quot a 39 7 y l corpusclg 1 39 Cortex m Medlulla r Final urine to ureter Cortex Med ulla the renal corpuscle filters blood forming a preurine consisting of ions nutrients wastes and water 0 collection of capillaries 0 proteins red blood cells etc are too big to get through the filter in the proximal tubule epithelial cells reabsorb nutrients vitamins valuable ions and water 0 glucose ions etc were small even to get through the filter but the body wants to reabsorb it into the blood because they re important Medial 0139 water and solute rumormien Lumen of proximal tubule Apical membrane N a Glueeae I 2 Half Of Naif Vitamins BIDDH vessel near proximal tubule iRenal Corpuscle and the Filtration Membrane Glomerular Efferent L 7 c sularspace arteriole 7 39 Afferent arteriole Cvtoplasmlc extensmns of podocytes Proximal Filtration slits spaces 39 g convoluted en foot processes Podocytes are the epithelial cells or 939 l39a capsule temple that make up visceral layer of glomerular capsule squamous epithelium Feneslrations lPoresl a Renal corpuscle Glomerular capillary endo nelium lpodocyte covering and basement membrane removed b Gliomerular capillary surrounded by podoqytes Foot processes of podocyte b Walter and ion movement differ in me three regierie a Passive w l transportiggmi y y el Active transport Usmelarity of uid inside limp ef Henle milliiesmell L Descending limb is highly Aseeeding limb is nearly permeable to water but impermeable tr weter but impermeable to solutes highly pelnmea b lje to Na and G Tauma the loop of Henle establishes a strong osmotic gradient in the tissues outside the loop and osmolarity increases as the loop descends o permeability ranges throughout the tupe 0 taking out the good stuff and concentrating it down to ureawaste once the filtrate has passed through the Loop of Henle the major solutes it contains are urea other wastes and a low concentration of ions 0 in the distal tubule ions and water are reabsorbed o the collecting duct may reabsorb more water to maintain homeostasis o urea leaves the base of the collecting duct and contributes to the osmotic gradient set up by the Loop of Henle hormones regulate water and electrolyte balancein the distal tubule and collecting duct 0 presence of ADH makes the collecting duct high permeable to water Small mumaquot urlm homeostasis of blood glucose is controlled by hormones o insulin is secreted by the pancreas when blood glucose is high 0 stimulates muscle and liver cells to import glucose 0 glucagon is secreted by the pancreas when blood glucose levels fall 0 stimulates the liver to break down glycogen and make glucose mlmm mqu 0 use as fuel or store it for later Diabetes Mellitus disrupts glucose homeostasis 0 Type 1 Diabetes lnsulin Dependent e g ge Immature 39 L lUEE EE39 o IndIVIduals do not produce Insulin emigre a5 nguguu 0 cells that produce Insulin In pancreas are destroyed aquot a 39 quotwquot Humewlaa ia 0 Type 2 Diabetes NonInsulin Dependent Pancreas Emilia calla insulin 5quot3 EllElma glmoaei HIE mL llng 0 individuals make insulin but they are 3 3 resistant to it 0 does not bind properly to receptors on target cells Prokaryotes All cells have i 39 Lilweir treats own QIEEJ39QJEI39I l a intagluicma Bland gimmm level drops anal Funlint J i r 539quot Psalrereaa ffr r 3 WEJEBEEE v Qlllli39 n l nl39i A t l nucleic acids store and transmit information proteins perform most of the cell s functions carbohydrates chemical energy carbon support identity 0 plasma membrane selectively permeable membrane barrier Prokaryotes are organisms without a membranebound nucleus 0 there are two domains of prokaryotes bacteria and Bacteria archaea Prokaryotes have structural similarities 0 plasma membrane 0 a single chromosome 0 ribosomes to synthesize proteins 0 stiff cell wall hypertonic inside need cell wall to keep them from bursting iiiii quotr Archaea Common ancestor of all species living today Eukarya Plasmid I Cyloplasrn Chromosome l Plasma P membrane quot 39 Cell wall I t 39 bacteria and archaea are distinguished by c the types of molecules that make up their plasma membranes and cell walls 0 the machinery they use to transcribe DNA and translate mRNA into proteins SIU MMEFW isms as Eharastsriisiiss sf Eastsriia archasa and Eli karya Eactsn is Amhasa Euitarys Eilhli ii ranclnssd lby a nuislsair l tln his Yes snuslspxa u 7 Eirsulair summitsums present i ss but linsar in snrns itss Nils linear spssiss rganslllss snslsssd by maimhiranss his his r39ss present r i I a H t l l Q agella present r ss i39fss Np agella and cilia undulatsji Mlultissiliiiiar spssiss Na with same ssssptio nst his r39ss Plasma rnarnbrans lipids ssrnpssa sf Vss His inransi isti i ss lglyssrsll banded ts uinbranshasl asids lipids bonded by ester linkass u l i H lby stl39isr linkagss Gall walls when prassnit ssni39taiiin lies his this pantidsgliycsn l u Firm p lyl lll l llf ssr npssad sf 21lEl suihiiinits No any 5 subunits es 39i39ss Translatisn ilnitisitsd with msthismins ND li i39TlElE Wit 35 35 l l a Nisrmylms ihisnins Wrist most prokaryotic species have one supercoiled circular chromosome in the nucleoid region of the cell 0 many bacteria contain small circular DNA molecules called plasmids o plasmids are physically independent of the cellularchromosome gives an advantage to that organism a Grampositive cells stain more than Gramnegative cells most prokaryotes have a cell wall 0 within bacteria two general types ofcell wall exist that can be distinguished by treatment with a dye called the Gram stain o Grampositive cells gt purple o Gramnegative cells gt pink Gram positive cells contain an extensive amount of peptidoglycan that s what holds onto the stain o peptidoglycan has a long backbone of two alternating monosaccharides one has a chain of amino acids attached 0 when adjacent strands align peptide bonds form b Grampositive cell wall Lg I kiwi a 2 s between amino aCIds U 0 makes them super strong and stiff peptidoghcan Plasma membrane Proitein Gramnegative cells have a cell wall with a thin peptidoglycan layer surrounded by an outer phospholipid bilayer 0 have polysaccharides to identify and communicate with other cells c Gram negative cell wall Polyseccharides Cell wall Pelpltiidogllycan 7 Plasma quotj quota in membrane Lg p y 3 w I J 39 Protein quotAsome prokaryotes have taillike flagella for movement or needlelike projections called fimbriae to attach to other surfaces many prokaryotes have internal photosynthetic membranes c recently simple organelles have been discovered in many bacterial species 0 storing calcium ions or other key molecules 0 holding crystals of the mineral magnetic o organizing and sequestering enzymes bacteria and archaea show extensive morphological diversity in terms of size shape and mobility a Size veri es h Shape veri es e Metiillity vanities mettl ititareztzrgtrm 39quot iEntertae rrgiszesmequot 333 iSE39El et ml ll l39me Bacteria and arChaea haVe a great deal of diversity in habitat o extremophiles are bacteria or archaea that live in extreme habitats hydrothermal vents with water as hot as 121 C at a pH less than 10 at temperatures of 0 C under Antarctic ice in water virtually saturated with salt halophiles Smallest J39Ii39ycoplasmri nrynsofdes Heels chains of spheres compost bacterial Iquot Swi niiri ni rig Psc LI IEI39DH39 one s aerugr39nosa j Comps re sizes Largest Thismargarita namib enSst Spirals Cairnpylobacter r39ejunr Gliding Oscillazorla limosal bacteria and archaea may use one of three sources of energy for ATP production 0 light organic molecules inorganic molecules Phototrophs use light energy to produce ATP by photophosphorylation o cyanobacteria were the first organisms to produce oxygen through photosynthesis responsible for aerobic respiration Chemoorganotrophs oxidize organic molecules with high potential energy carbohydrates 0 they produce ATP by cellularrespiration or fermentation pathways Chemolithotrophs oxidize inorganic molecules with high potential energy ammoniaNH3 0 they produce ATP by cellular respiration bacteria and archaea obtain buildingblock compounds containing carboncarbon bonds in two ways 1 autotrophs synthesize their own from simple starting materials 2 heterotrophs acquire them from their environment Autetreipll39ie Hetemtmpl e eelfeeyntheeieee frern 302 EH35 er frem rnelleeulee emeticzed by ether ether eimple rnelleeulee ergenierne Phletertrepahe pheteeutetrephe pheteheteretrephe fr em Sunlight Ghem eer39genetreplhne ehemeergieneeutetrephe einermeergenelheteretrephe rem ergenie meleeulee hemelithetrephe ehemelithmeete trephe ehemei thetrephie heteretrephe frem inrgenie meleeulee Robert Koch hypothesized that bacteria might be responsible for causing infectious diseases 0 Koch s experimental results were the first test of the germ theory of disease 0 certain diseases are infectious 0 these diseases result from the transmission and growth of certain bacteria and viruses pathogenic bacteria gt cause disease 0 only a tiny fraction of bacterial species living on and in the human body are pathogenic bacteria in the gut are essential to human health antibiotics are molecules that kill bacteria or stop them from growing 0 produced naturally by certain soildwelling bacteria or fungi 0 act as a defense mechanism do not work against viruses 0 penicillin was the first discovered antibiotic o overuse of antibiotics have resulted in antibiotic resistant strains of bacteria bioremediation is the use of bacteria and archaea to clean up sites polluted with organic solvents certain bacteria and archaea are theonly organisms capable of converting molecular nitrogen to ammonia c this process is called nitrogen fixation 0 take gas from atmosphere and convert it into mainlitphm iFteduction Fixation by bacteria archaea ammonia andor nitrate mime airI haea Organic compounds with aminagroupe lNlH21 Decompositii on by bacteria archaea fungi nus ammonia 03 if r r NHst ammonium ions nitrate Oxidation Oxidation by bacteria quot02 by bacteria nitrite archaea Eukaryotic Cells Plants and Animals unlike prOkaryOteS eUKaryOteS have 3 TABLE 42 Principal D39ill39rtenences Between Prokaryofic and Eukaryotic Celts membrane bound nucleus titanium o prokaryotes have DNARNA in 39 the nucleoid Size of call Typically 052 10 nm in diameter Typically lCI lQU rum in diameter cytoplasm Nucleus No nuclear membrane or nucleoli True nucleus consisting ol nuclear membrane and nucleoli Membraneenclosed Absent Present examples include lysosomes Golgi organelles compileci endoplasmic reliculurrii mitochondria and chloroplasts Nuclear pore i Flagella Consist at are protein building block39s Complex consist at mullipla micronbolas Cytoplasmatic ring Central granule Glycocahrx Present as a capsule or slime layer Present in some cells that lack a cell wall Nuclear envelope ISell wall Usuallyi present chemicallyI complex When presentr chemicallyr simple typical bacterial cell wall includes poplidoglyconl A FlaSma membrane No carbohydrates and generally lacks slerols Sierols and carbohydrates that score as receplors c i i 39 Fraser ff 39 Cyloplasm No cyloslreleton ar cytoplasmic streaming Cyloslreletan cytoplasmic streaming Fwd Eibosarnes Smaller size 705 larger size 13051 smaller size 705 in organelles lChromosome lDNA Single circular chromosome lacks histories Multiple linear chromosomes with histories arrangement NUCleal lamma Chroma Cell division Binorgr lission Mitosis Soxuol reproduction No meiosis Ironsler at DNA hogments carIii Involves meiosis lNucIeius ccccc iaht 2006 byThe McGraerill Companies Inc GownghtEa i Pearson Eduoa1ionmpsblishing as Beriarnin Gummings All ri eeeeeeeeee d quotAtraffic across the nuclear envelope occurs through nuclear pores 0 nuclear membrane has two plasma membranes inner and outer nuclear proteins are synthesized by ribosomes in the cytosol and contain a common amino acid sequence that marks them for transport into the nucleus 0 this 17 amino acid sequence is called the nuclear localization signal NLS 0 special signal sequences on other proteins direct them for transport from the cytosol into specific organelles nucleus peroxisomes mitochondria and chloroplast endomembrane system synthesizes processes transports and recycles proteins and lipids o secretory pathway hypothesis proposes that proteins intended for secretion from the cell are synthesized and processed in smooth ER rough ER and Golgi apparatus PulseChase experiments support the PHUB ESS 39lI39HE SEGHETDRY P THWAY A MODEL secretory pathway model 0 common experiment to show molecular movement in a cell 0 put labeled molecules in a system of cells for a while which then attach to 3321 mm the proteins being made quot o dilute out the label and look at where the labeled proteins are moving data shows that proteins start off in rough ER then travel to Golgi apparatus and then secretory vesicles 1 Hillbosome deposits protein in EFL 2 Protein exits ER 3 Protein enters Gelgi for processing 4 Pretein exits Golgi Plasma membrane 5 Protein exits cell proteins bound for the endomembrane system have a 20aminoacidlong ER sign sequence 39 7011 Pearson Emmian Inn on Nterminus o as the protein is being synthesized on the ribosome a signal recognition particle SRP in the cytoplasm binds to the ER signal sequence 0 the SRP binds to a SRP receptor in the ER membrane the interaction of the SRP and its receptor directs the rest of the synthesis of the protein into the ER PROCESS THE SIGNAL HYP DTHESIS RNA Flibosome Signal sequence Cytosol SRP receptor I Lumen of rough EFI 4quot 1 Signal sequence 2 Signal binds 3 SRP binds to 4 Protein is 5 Protein is synthesized to SRP receptor synthesized synthesis into EFL is complete 2011 Pearson Education INC in the RER lumen proteins are folded and glycosylated o proteinfolding occurs with the help of chaperone proteins 0 glycosylation is catalyzed by enzymes 0 glycosylation is the process of putting a carbohydrates on it proteins are transported from the ER to the Golgi apparatus in vesicles Golgi cisternae move in a cis to trans direction carrying and modifying their cargo as they move cisternal maturation cis is near ER cis is away from ER after proteins fuse with membrane whole cis moves through the Golgi cis face l receiving side of Golgi apparatus Vesicles coalesce to Vesiclles move form new crs Golly crsternae from ER to Golgi Vesicles also transport certain proteins back to E R Cisternall maturation Golgi cisternae move in a cis tottrains direction Vesicles form and leave Golgi carrying speci c proteins to other locations or to the pllasma mem brane for secretion trans face shipping side of Golgi apparatus Vesicles transport speci c proteins baclmlarrl to newer Golgi cisternae each protein that comes out of the Golgi apparatus has a molecular tag that places it in a particular type of transport vesicle Lumen of Golgi apparatus 5 forsecretion PROCESS FR TEIN SDRTG AESiCLE TRANSPDRT To plasma membrane 1 Proteins are ta ed 3 a e as 99 w a Ku gs j a i glgems are is ReceptorsI 3Ve5Icles bud quot e I 7 Transportsff vesicles 391 Return to the EH 4 Proteins interact with receptors 5 Delivery 2011 Pearson Education Inc some vesicles are sent to the cell surface where they fuse with the plasma membrane and release the contents to the exterior of the cell exocytosis VS endocytosis refers to the pinching off of the plasma membrane resulting in the uptake of material from outside the cell receptor mediated endosome lowers the pH through hydrogen ion pumps Formation of coated ipit Formation of coated vesiclle Receptor Dynamin 9 Adaptin o 0 0 0 Clathrin 4 U ncoaied vesicle V ready to use Vestcle Veg iysosome uncoallng Koeopal Er Stanton Berna and Levy Physiology 6th Edition Copyright 2008 by l rosby an imprint of E sevier Inc All rights reserved Exocytosis of waste 1239 Products of digestion j I by endloyto 39Fond particles Fusion forms secondary I lysosome autophagy is the process by which damaged organelles are surrounded by a membrane and delivered to a lysosome to be recycled vs in phagocytosis the cell plasma membrane surrounds another cell or food particle and engulfs it o the structure formed is called a phagosome o it is delivered to a lysosome where it is digested Lysosome Lysosomalhydrolase Autolysosome 1 391 L J 39 1 Isolation membrane 63 t VESICLE VESICLE DOCKING VESICLE BREAKDOWN NUCLEATION ELONGATION amp FUSION amp DEGRADATION cytoskeleton is a dense and complex network of fibers inside the cell 0 three types of cytoskeletal proteins actin filaments intermediate filaments and microtubules 1 actin filaments are the smallest cytoskeletal elements 0 they are formed by polymerization of individual actin molecules monomers o actin filaments are grouped together into long bundles or dense networks just inside the plasma membrane 0 actin interacts with the motor protein myosin to cause cellular movement 2 intermediate filaments provide structural support to the cell 0 many types exist each consisting of a different protein 0 these filaments are not involved in movement 3 microtubules are large hollow tubes made of tubulin dimers subunits o tubulin dimers are made of an dtubulin polypeptide subunit and a Btubulin polypeptide subunit 0 microtubules originate from microtubule organizing centers MTOC and radiate throughout the cell in animal cells the MTOC is called the centrosome and contains two bundles of microtubules called centrioles o microtubules can act as railroad tracks transport vesicles move through the cell along these tracks in an energydependent process 0 kinesin hydrolyzes ATP to walk along a microtubule track a Structure of kinesin Stalk m r I 1 r w l VFiLIleTT iologicallcience2le b Kinesinquotwallksquot along a microtubule track Transport I Q 47 239 gt cu M Iquot v I x vesicle Kinesin Microtubule 2003 Pearson Prentice Hall Inc eukaryotic flagella and cilia move the entire cell 0 they consist of several microtubule that form an axoneme Receptor for mmf protein 7 Ifquot I 1 a u 4 Motor protein hilar tuhu la ATP powered off cytoskeleton o movement occurs when the motor protein dynein uses ATP and walks up the microtubules Protists Radial microtubules spokes Inner B tubule Atubule Doublet microtubule eukaryotes are diverse yet share fundamental features that distinguish them from bacteria and archaea most are large have more organelles and a cytoskeleton a nuclear envelope multicellularityis common 0 asexual and sexual reproduction protists are a group of organisms that include all eukaryotes except the land plants fungi and animals protests are amazingly diverse size from bacteriasized to giant kelp habitat from open ocean to the guts of termites unicellular or multicellular morphology the shape and appearance of an organism s body and its component pans the common feature among protists is that they tend to live in environments where they are surrounded by water seven major groups of eukaryotes have been identified on the basis of morphological characteristics amoebozoa opisthokonta excavata plantae rhizaria alveolata and O stramenopila earliest eukaryotes were probably singlecelled organisms with o mitochondria o a nucleus 0 an endomembrane system 0 a cytoskeleton o no cell wall 0 a novel type of flagellum for swimming Endosymbiosis Theory 0 mitochondria originated when a bacterial cell took up residence inside another cell about 2 billion years ago 0 mitochondria are about the size of an average bacteria mitochondria replicate by fission as do bacteria mitochondria have their own ribosomes and manufacture their own proteins mitochondria have double membranes consistent with the engulfing mechanism mitochondria have their Nuclear envelope Endoplasmic reticulum Nucleus T Mitochondrion Ancestral photnaynthetic Infolding of plasma 4 a Call with quotV II E mam brana K 39 wa eukaryote p nucleus and 39 Hf if M r endomembrane I n mastic i39 quot system ll uh 2quot est no F k c339 a r J N a II x x 1 l u tyquot F gti t L 1 a prolaaryote q f gt Hm 5 Engulfing of n 39 photosynthetic F Engull39ing I of aerobic ll h 2 heterotrophiclx m Plasma membrane an M M39tochondr on 5 I 39 Ancestral hetemtmphic euka ryc e Copy guth Pearson Education Inc publlshlng as Bentlamln Cummings own genomes organized as circular molecules like bacterial chromosomes the leading hypothesis for the origination of the nuclear envelope is that it is derived from the infoldings of the plasma membrane infoldings would have given rise to the endoplasmic reticulum ER at the same time protists feed in various ways ingesting packets of food o absorbing organic molecules directly from the environment 0 performing photosynthesis phagocytosis using pseudopodia to engulf food 0 other ingestive feeders attach themselves to a surface and feed by sweeping food particles into their mouth with cilia absorptive feeding occurs when nutrients are taken up across the plasma membrane directly from the environment 0 some absorptive feeders are decomposers feeding on dead organic matter or detritus 0 many absorptive feeders live inside other organisms o if an absorptive species damages its host it is called a parasite the endosymbiosis theory contends that the eukaryotic chloroplast originated when a protist engulfed a cyanobacterium o the photosynthetic bacterium provided its host with oxygen and glucose in exchange for protection and access to light evidence 0 chloroplasts have bacterialike characteristics 0 many animal and protist cells have endosymbiotic cyanobacteria o chloroplasts have a circular DNA molecule containing genes that are similar to cyanobacterial genes 0 one group of protists has a chloroplast with an outer layer of peptidoglycan which is found in the cell walls of cyanobacteria the chloroplasts found in some protists have four membranes and are hypothesized to be the result of secondary endosymbiosis secondary endosymbiosis Eukaryotic cell Nuclei I b d H I seconda endo mbiont y Tl39i emem rane c are last W W Quadrg gg raned Nucleomo rph p 0 secoma endomb o m Secondary endosymbiont39s fig a 7 nucleus ilwgg 7797 quots b39 I W 5 i 5 quot him 4 7777 r quotV r t Vquot v 7 3 wa L7 QM quot I J g g 9 fa a a x Peri plastid membrane 7 m Secon daryendosymbiortt39s cell membrane Epiplastid membrane EPiPIaFtld membrane Doublemembraned chloroplast phagosomal membrane primary endlosyrnbiondt amoeboid motion is a sliding movement observed in Direction of motion some protists that is accomplished by streaming of pseudopodia 0 requires ATP the other major mode of locomotion involves swimming via flagella or cilia a Flagella Direction of motion b Cilia Inc plikli hinn sexual reproduction originated in protists o asexual reproduction is based on mitosis and cell division in eukaryotic organisms 0 results in daughter cells that are genetically identical to the parent 0 sexual reproduction is based on meiosis and fusion of gametes 0 results in daughter cells that are genetically different from their parents and from each other a life cycle describes the sequence of events that occur as individuals grow mature and reproduce 0 some protists have life cycles dominated by haploid cells one copy of each chromosomes 0 some protists have life cycles dominated by diploid cell two copies of each chromosome 0 some protists have life cycles that alternate between haploid and diploidforms known as alternation of generations protists play a key role in aquatic food chains 0 diatoms and other small organisms that drift in the open oceans or lakesare called plankton o photosynthetic plankton are called phytoplankton o phytoplankton form the base of food chains in aquatic environments Trophlic level protists play a key role in the global carbon cycle Quaternary lHa k consumers 39 K39IIW h IV and act as carbon smks that could help reduce w a 399 3quot global climate change z Snake Tertiary 7 f V Tuna congaera Mouse Herring Grasshopper Zooplankton Plant Producers 42 Phytoplankton Aterrestrtal food chain An aquattc food chain a 1 J t harmful algal blooms are caused by photosynthetic I I toxinproducing protists called dinoflagellates o a bloom occurs when a unicellular species population grows rapidly and reaches high densities in an aquatic environment IEWhth Heading 3 3 km trillstaid tt39w39suuitt g puawssymuwitca through its mum into J a human victim i I H mammal spam call mt39ttltms snag call Ln the gm oil39s mosquito The parasite calted a aporrazoita is burn wave m nmm v v I v v J u mites mmajna V Xquot m l i mate and quotquotquotquot quot 39 39 E mun 39 Ta 1 3 female sea malts 139 i 39 t J a 39 r 4 J a watch EL mlizs m Eli 39 i ge aw H II nmxtauibu s 39 39 39 law39s i uLquubluwi quot E39T39hmugh i i quot ittli a39lSE t1thiF39LhE 39 quot r gt I ERNIE m39eragaln 39 7 7 7 H a 7 rs l asexualrepru f E Packed with quickLv ductinn Ltu multiplying nunamau tca I36W OLLOamp Ltnl Klimt 1113 bdrm mtiltiinlija39 maul messing chemicals ME the liitf ti39 it ll 39 CEHSE KEMI IS raver E fllptllfg5 l HOlfUJE ttlf Willi anagram I 39 WE39RE IQITm I lLiIIBr quot 39 39 I11nrmltaa3t TIEYW bani tn the blond 51mm bagtnm attach one Lna V 73 a malaria is highly infectious and caused by the protist Plasmodium i Eukaryotes are diverse yet share fundamental features that distinguish them most are large nuclear envelope membrane bound organelles Protists are a group of organisms that include all eukaryotes except the land plants fungi and animals Protists are amazingly diverse habitat size unicellular multicellular morphology shape appearance of its body Vary in the way the obtain food ingesting packets of food absorbing organic molecules directly from the environment performing photosynthesis absorptive feeding nutrients taken through the plasma membrane through channels Energy and Reactions chemical reactions require energy aka the capacity to do work or supply heat 0 two types of energy 0 kinetic energy energy of motion I in molecular systems this is molecular motion or thermal energy measured as temperature 0 potential energy stored energy I in molecular systems this is stored in chemical bonds chemical energy First Law of Thermodynamics 0 energy cannot be created or destroyed but it can be transferred or transformed from one type of energy to another 0 the total energy of the universe is constant Second Law of Thermodynamics 0 systems tend to proceed from a state of order to a state of disorder randomness o the entropy of the universe is always increasing eectron position and configuration is the most important y source of chemical potential energy in a molecule 39 39quotquota x x o electrons in an outer shell farther from the m charged nucleus have more potential energy than do electrons in an inner shell 11 quotl I 0 potential energy stored in atoms or molecules may I be transformed into kinetic energy by a change in fl in Q electron position closer to the nucleus law 2 2p 35yquot 33 Elsa in a biological system or molecule the total energy is referred to as enthalpy H o enthalpy H includes 0 the potential energy of the molecule heat content 0 effect of the molecule on surrounding pressure and volume not big changes in enthalpy are represented by AH a measure of the difference in heat content start to finish of a reaction 0 exothermic reactions release heat energy 0 AH lt 0 negative H o in an endothermic reaction heat energy is taken up 0 AH gt 0 positive H entropy S is a measure of the amount of disorder in a system 0 when the products of a chemical reaction become less ordered than the reactant molecules entropy increases 0 AS gt O Gibbs free energy of a reaction is the amount of energy available to do work usable energy 0 the Gibbs free energy change AG takes into account the change in total energy AH and the change in entropy AS AG AH TAS AG Gibbs free energy change 0 units kcalmol AH change in enthalpy AS change in entropy T temperature Kelvin add 273 to Celcius the change in free energy of any reaction is equal to the difference in free energy between the products and the reactants AGreaction Gproducts Greactants 0 AG determines whether a reaction requires added energy to proceed mzzmimzazcu nal if the free energy of the products is lower than the free energy of the reactants the reaction is exergonic I n lt 0 mm l o spontaneous reaction in o no energy is needed for the reaction to proceed Em in if the free energy of the products is higher than the free energy of the reactants the reaction is endergonic 0 AG gt O 0 not spontaneous 0 energy must be added for the reaction to proceed fii39rmhlih gim mr39s ijiWumwam energetic coupling between exergonic and endergonic reactions allows the chemical energy released from one reaction to drive another reaction II Hicti3939a39cflquot 5tli lra39i39 Biz I lib ADP 3 E A BP Ill E m i quot e ADP LL AB AG ll 3 Energy 3939 7quot quotllll I if t ET39i39rthesize h Reactants Frog trees of reaction Pmducts o exergonic reactions can be coupled to endergonic reactions making the sum of reactions exergonic 0 coupling unfavorable nonspontaneous reactions to ATP hydrolysis enables the reactions to proceed graph above the hydrolysis Of ATP iS highly exergonic Energy is released when ATP is hydrolyzed H20 Water HO PEO Iquot I 1 Iquot 43 ADP Inorganic Energy phosphate Figuire 92b Biologicall Science 2Ie 2005 Pearson Prentice ll39lalll Inc reduction oxidation reactions redox reactions are chemical reactions that involve electron transfer remember OIL RIG 0 when an atom or molecule gains an electron it is reduced 0 reduction gain of one or more electrons 0 when an atom or molecule loses an electron it is oxidized 0 oxidation the loss of one or more e oxidation and reduction events are always coupled o electron donors are always paired with Reduction Gain o electrons A electron acceptors 39 iritlation j CEH IEDE E 03 ll E71 SiDE E HED K v l T Oxidation Loss of electrons 39 EEdU Eiii l IE1 I WLJ inst an L39L E39JLT quotA39l39lquotl 1ll39l 39Jnnalm c ailin I3939il391 El n A oxidized B reduced J each electron transferred from one molecule to another during a redox reaction is usually accompanied by a proton H 0 reduced molecule gains a proton and has higher potentialenergy o oxidized molecule loses a proton and has lower potential energy two important electron carriers involved in redox reactions are FADH2 and NADH Enzymes and Reactions a negative AG indicates a spontaneous reaction but it tells you nothing about the rate of the reac on o spontaneous reactions do not necessarily occur quickly 0 the rate of a spontaneous reaction can be increased by increasing the temperature 0 the rate of a spontaneous reaction can be increased by increasing the concentration of reactants the rates of reactions in biological systems are increased by the action of enzymes enzymes catalyze reactions by c bringing reactants together in precise orientations o stabilizing the transition states of chemical reactions substrates bind to the enzyme s active site 0 many enzymes undergo a conformational change when the substrates are bound to the active site aka induced fit Substrate 4 glucose A 1 Enzyme hexokinase 2011 Pearson Education IHG When the substrate binds to the enzyme39s active site the enzyme changes shape slightly This induced fitquot results in tighter binding of the substrate to the active site the activation energy Ea of a reaction is the amount of free energy required to reach the intermediate condition or transition state 0 interactions between the enzyme and the substrate stabilize the transition state and lower the activation energy required for the reaction to proceed enzymes are not changed or used up in the reaction Product En 731m e Su bstrate Enzyme complex 2001 Sinauer Associates Inc all enzymes show this type of saturation kinetics enzymes are saturable 0 active sites cannot accept substrates any 2391 faster no matter how large the concentration of substrates gets Flats of reaction many enzymes require additional atoms or molecules to function 0 cofactors n o inorganic ions Zn2Mg2and Fe2 o reversibly interact with enzymes 0 coenzymes 0 organic molecules such as NADH and FADH2 o reversibly interact with enzymes 0 prosthetic groups without enzyme activation energy without enzyme Zyme activation gtI energy with enzyme SJ reaCtantS overall energy eg CD2 H20 released during reaction products HZCO3 gt Reaction coordinate t r frl HEPf f I 1 5 1II 1 5D EDI Concentration of substrate 0 nonamino acid molecules such as heme and retinal o permanently bound to proteins enzymes have an optimal temperature and pH enzymes are often regulated activated or inactivated in response to cellular conditions 0 three common types of regulation are a Competitive inhibition 0 competitive Inhibition I occurs when a molecule similar in size and Substrates Q shape to the substrate competes with the 39 r substrate for access to the active site or Enzyme molecule o alloste ric regulation E TJS Q 333iil ie 22239 n 8tquot bind when a regulatory I occurs when a molecule causes a change g n g jgmfjetgittge in enzyme shape by binding to the enzyme at a location other than the active site b Allosteric regulation 0 covalent modification 39 I a chemical change to the enzymes primary structure that alters the function of an or enzyme 22m 22 Allosteric activation Allosteric deactivation phosphorylation the addition of one or more Theac vesnebecomes Theacmesnebecomes available to the substrates unavailable to the substrates when a regulatory molecule When a regulatory molecule phosphate groups is the most common modification bindsmadmerentsueon bindstoadmeremsneon I these modifications are reversible theenzyme phosphorylation changes the shape and activity of proteins Metabolism and Cellular Respiration metabolism is the sum of all the chemical reactions in a cell or organism 0 consists of a large number of metabolic pathways metabolic pathway a series of reactions each catalyzed by a different enzyme to form a biological molecule 0 has a distinctive starting Enzfm Enzyme 2 Enzyme 3 molecule 39 A quot l Reaction 1 Reaction 2 7 Reaction 3 o characteristic products Staf ng Prdu o B amp C are malesum intermediates because they serve as reactants and products 0 D will have the highest concentration at equilibrium catabolic pathways break down large complex molecules into smaller ones releasing energy into the process ie polysaccharides starch glycogen etc fats lipids proteins etc o cellular respiration vs anabolic pathways synthesize large molecules from smaller ones and usually requires an input of energy 0 photosynthesis anabolier l E2 Elli E3 iim1i E4 r Emma Int armE latehlintenmadlam li intermediate 39 Gamma 39 re 3 mummies 1 4 3 inf i1 3 all z mniecule i39 j Eatah lism Inhibition halts bath anahulism and afahnlism ll metabolic pathways are regulated 0 they can be turned on or off in response to the metabolic needs of the cell m 5343351 0 by regulating key reactions in catabolic and anabolic 135153 k m in active site pathways cells can maintain homeostasis 3 feedback inhibition occurs when an enzyme in a pathway is inhibited by the product of that pathway V H 1 limitian damninmll coil informed law A used up by camme fl no 39 o if there is an abundance of products it will signal back to quotquotlm m B switchguilt Emma the first enzyme to stop 7 l39n39telrmmj lam E Isrolcruclmc s binds to all l li site Enigma a l39ntermadiam El r x End product Y isol euci nei Em glucose metabolism is central to all metabolism 0 all organisms use glucose to build fats carbs and other compounds either consume or produce them 0 sources of energy in order of importance I carbs I fats I proteins 0 cells recover glucose by breaking down these molecules 0 glucose is used to make ATP through cellular respiration or fermentation 0 through enzymecatalyzed rxns cells can produce glucose from glycogen starch and most simple sugars 0 cell only contains enough ATP very unstable to last a max of 2 minutes cellular respiration oxidizes glucose to make ATP 0 carbon atoms of glucose are oxidized to form carbon dioxide 0 carbs are hydrolyzed into glucose monomers 0 oxygen atoms in oxygen are reduced to form water 0 the resulting change in free energy is used to synthesize ATP from ADP and Pi C6H1206 602 gt 6CO2 6H2O energy 685 kcal of heat cellular respiration has 4 steps 1 glycolysis 2 pyruvate processing 3 citric acid cycle 4 electron transport and oxidative hos ho lation GLEWEIE Tm gggggt m p p ry cm 39 cellular respiration any suite of rxns IWQWL Mmmm m that use e harvested from high energy molecules to produce ATP via the ETC if y a substmteallauell aubstrt lbuel oxidative phosphorylatlan phosphorylatlun phosphoryilaltlion 1C1553v g ziisuliw er Wynn in glycolysis glucose is broken down into two molecules of pyruvate o glycolysis is a metabolic pathway consisting of 10 steps 0 the potential energy released is used to phosphorylate ADP to ATP 0 all reactions of glycolysis occur in the cytosol of eukaryotic cells the ancestor of all living organisms made ATP by glycolysis total gain 4 ATPs 2 NADH and 2 Pyruvate net gain 2 ATPs 2 NADH and 2 Pyruvate first part energy investment phase 0 phosphorylating molecules All 10 reactions of glycolysis occur in cytosol Wha oesin A P requIres energy 9 ATP T 903 coma OCH 2 l 0 H2 392 0 020 uses up 2 ATP molecules to H o quot 2 m 3 c o T 2404 break down a 6carbon molecule Mil390quot E T quot T quotT 390 E lt i DH H OH HO H HO H H Glucose Enzyme Glucose chtose Fructose if 6pfmosphate 6 pl nosphate 16bispl nosphate fie py Glycolysis begins with an HCOH What comes out HADP IIIIIIIIIIIIIII P z r fingggsp IIIIIIIIIIIIIIII 1 ADP H200 second phase energy payoff phase The quot2 indicates that glucose has been split into two 3carbon sugars only one is shown 2 NAD 2 ADP 2 ADP 2 2 2 2 O D D 039 i0 iD CD iii HclmlI E H oe ogt o to Hzco HZCOH CH2 CH3 Pyruvate During the energy payoff phase 4 ATP 4quotquot are produced fora net gain of 2 ATP A NAD H 2 ATP 2 ATP in glycolysis ATP is produced through substratelevel phosphorylation not a proton gradient 0 this is the enzymecatalyzed transfer of a phosphate group from an intermediate substrate to ADP to form ATP 0 each step is catalyzed by a different enzyme an important site of regulation in glycolysis is the step catalyzed by the enzyme phosphofructokinase 0 high levels of ATP liGJI 3142 ltdllmolliie ems1s 1E3lkdfmoln inhibit the enzyme 9 thrgligh feedbaCk u iiLu at new emigre ll Lima Hzfz a i m InthItIon an a 3 DH 1 99 Inll notI 51 mmquot oIl chtoseaphosphate Hostess1 lhisphosphate phosphofructokinase has two binding sites for ATP the active site and a regulatory site 0 catalyzes a very early step in the in glycolysis because the steps before it can be used for other AT 3 regulatory purposes making it a good regulation spot site 7quot 0 example of feedback Inhibition When ATP binds here the quot reaction rate slows dramatically Fructose6a phosphate 7 at r at active site actlve Slte Cellular Respiration Part 2 Pyruvate Processing Citric Acid Cycle and Electron Transport Chain pyruvate from glycolysis is transported from the ATPWhampmmsxi cytosol into mitochondria imarmembm 39 39 quot o intermembrane space is extremely important Matrix h cristae Ribosome x 39 inner membrane 1 Outer membrane lD NlA pyruvate processing is catalyzed by the enzyme pyruvate dehydrogenase in the mitochondrial matrix E Ei quot Egg 0 in the presence of 02 I qu 39g ll pyruvate dehydrogenase 29 1 pig Egg Idahidmge e 4 If 9 13 results in the production of EH3 EH3 one molecule of acetyl Pwu te Hi i Mimiin Mew Egg A Lhmrtbaritidllqurlpqiilm FLn r mii39lhiachrlr mimii J EliI213 Munr F MIlm quotIquot lnr pyruvate processing is under both positive and negative control 0 pyruvate dehydrogenase is inhibited by high levels of products 0 high levels of ATP three phosphates 0 high levels of acetyl CoA and NADH stops when pyruvate dehydrogenase is phosphorylated and changes shape 0 pyruvate dehydrogenase is stimulated by high levels of reactants 0 high levels of AMP only one phosphate group 0 high levels of coenzyme A CoA and NAD the acetyl CoA enters the citric acid cycle aka the Kreb cycle where it is oxidized to two molecules of C02 0 substrate phosphorylation occurs in mitochondrial matrix 0 acetyl CoA comes in and produces o 3 NADH 1 FADH2 1 GTP o for every glucose molecule you get 6 NADH 2 FADH2 2 GTP the citric acid cycle can be turned off at multiple points by feedback inhibition 0 Le high levels of ATP slows the cycle down before ETC C6H1206 10 NAD 2 FAD 4 ADP 4 Pi gt 6 C02 10 NADH FADH2 4 ATP most of glucoses original energy is in the electrons transferred to NADH and FADH2 o NADH and FADH2 carry two electrons each 0 during the fourth stepin cellular respiration the high potential energy of the electrons carried by NADH and FADH2 is gradually decreased as they move through a series of redox reac ons 0 oxygen really electronegative has the high affinity for electrons so it s the final acceptor o electrons are transferred to 02 which is reduced to form H20 the proteins involved in these reactions make up the electron transport chain ETC the cycle a A l I i2quot Acetyl CoA NADlH The two red carbons enter IH gtGOD39 PRUCESS GITHI G ACID CYCLE r N 39 I A wa acety Co OH I 1gr gt H 20 H 0 7 Ge C00 vi 0H2 l coo V Citrate In each turn of the cycle the 1 two blue 1 carbons are HS COA All 8 reactiorls of the citric acid cycle occur in the mitochondrial HG 420339 HQ 7 OH NADH coo Ea V llsocitrate 00 NAD matrix outside the cristae 00 converted to I l C02 The EIITBIB AEID runs twice for each glucose precursor BOD ocKetugilutaratekv co NAD E NlADH HlSCoA l CYCLE Change in free energy AG in kcallmol 211 Pearson E u ahum Inc GIuc 100 200 300 400 500 600 In each of these drops energy is transferred to energystoring molecules ATP NADH and FADH2 o the proteins are embedded within the inner mitochondrial membranes 0 in prokayrotes oxidation of NADH occurs in the plasma membrane 0 the ETC proteins contain chemical groups that facilitate redox reactions mobile electron carriers shuttle electrons between the proteins in the ETC Ubiquinone Coenzyme Q o hydrophobic and lipid soluable toenzyme 11B in the next cycle 20 I 2 this red carbon HS CoA S CDA if Pg gmesalmue SucdnleoA 5 carbon 7 Matate r can coo GTP I I FAD Fig2 GDP H20 H clmz orATP quot TH GOO ADP Each reaction is catalyzed coo by a different enzyme F Succmate umarate FADHg 2011 Pearson Educati nnnnn c GLYCDLYSIS PYRUVATE PROCESSING 100 AND GITRIG ACID GYGLE ATP TP 0 k Oxaloacetate Cytochrome C 02 is the final electron acceptor o the transfer of electrons along with protons to oxygen forms water 002 electron acceptor only found in is the most efficient final aerobic respiration the energy released as electrons move through the ETC is used to pump protons across the mitochondrial inner membrane into the intermembrane space 0 complex I III and N do this active transport 0 complex ll does not contribute to the proton gradient The electron transport clnain occurs in the inner membrane of the mitochondrion membranes of cristae PROCESS ELECTRON TRANSPORT CHAIN H r H Hf lntermembrane H H H H H space quot4 W I r Mitochondrial matrix FADH2 2quot 2H 11202 MAD FAD Comlplex I Complex Ill NADH H Complex Ill Complex IV What goes in What comes out quotquotproteins contain very distinctive cofactors and prosthetic groups flavins cytochromes etc The Reactions of the ETC no substrate level phosphorylation ETC component descriptive name reaction complex I NADH dehydrogenase oxidizes NADH and transfers two electrons through a protein to reduce an oxidized form of Q four H are pumped into the intermembrane space complex ll succinate dehydrogenase oxidizes FADH2 and transfers two electrons through a protein to reduce an oxidized form of Q Q ubiquinone after being reduced by complexes l and II it moves through the hydrophobic interior of the ETC membrane where it is oxidized by complex lll complex lll cytochrome c reductase oxidizes Q and transfers one electron at a time through proteins in order to reduce cytochrome c four H for each pair of electrons is transported to the intermembrane space cyt c cytochrome c reduced when it accepts an electron from complex Ill and then moves along the surface of the ETC membrane where it is oxidized by complex IV complex IV cytochrome c oxidase oxidizes cyt c and transfers each electron through proteins to reduce 02 which picks up two H from the matrix to produce water two additional H are pumped in the intermembrane space oxidation of glucose is now complete 0 all the complexes differ in their tendency to hold electrons aka electronegativity o electrons go from low electronegativity complex I to high electronegativity complex IV 0 oxidation of 10 molecules of NADH produced from each glucose molecules accounts for about 80 of total energy released from sugar ATP synthase uses the proton gradient established by the electron transport chain to make ATP ATP synthesis catalyzed by ATP synthase is called oxidative phosphorylation enzyme complex in the inner mitochondrial membrane that is made up of two components ATPase knob F1 unit a membrane bound protein transporting base F0 acts as a molecular motor 1 protons flowing through the F0 unit spin the rotor 2 the rotor spins the F1 unit 3 as the F1 unit spins its subunits change shape and catalyze the phosphorylation of ADP to ATP direction of spin can be reveresed hydrolyzing ATP and pumping protons into intermembrane space Cellular Respiration and Fermentation A rotor within the membrane spins clockwise when H flows past it down the H gradient A stator anchored in the membrane holds the knob stationary A rod or stalk extending into the knob also spins activating catalytic sites in the knob Three catalytic sites in the stationary knob join inorganic Phosphate to ADP to make ATP Peter Mitchell s chemiosmosis hypothesis people still oppose this proposed a link between the ETC and ATP synthase the real job of the ETC is to pump protons across the inner membrane of mitochondria from the matrix to the intermembrane space synthase synthesizes ATP from ADP and Pi oxidative phosphorylation is the production of ATP by ATP synthase using the proton established via redox reactions of an electron transport chain the vast majority of the ATP from glucose oxidation occurs via oxidative phosphorylation chemiosmosis was likely to have arisen early in evolution alkaline fluids released from hydrothermal vents may be evidence natural electrochemical gradient all eukaryotes and many prokaryotes use oxygen as the final electron acceptor of electron transport chains in aerobic respiration O O 0 allows the generation of a large protonmotive force for ATP production after a proton gradient is established an enzyme in the inner membrane like ATP gradient oxygen is the most effective electron acceptor because it is highly electronegative a large difference between the potential energy of NADH and 02 electrons some prokaryotes use other electron acceptors in anaerobic respiration o ETC and ATP synthase occurs in the plasma membrane 0 cells that do not use oxygen as an electron acceptor cannot generate such a large potential energy difference 0 uses electron acceptors like nitrate NO3 sulfate 8042 H2 H28 CH4 0 make less ATP than cells that use aerobic respiration glycolysis can produce ATP in the absence of oxygen 0 NAD is needed for glycolysis to occur without it ATP cannot be produced which is fatal 0 grow much more slowly than aerobic respiration facultative anaerobes organisms that can switch between fermentation and cellular respka on fermentation is the metabolic pathway that regenerates NAD from NADH in the absence of oxygen 0 because the ETC shuts down without 02 and isn t supplying the NAD for glycolysis 0 does not fully oxidize glucose in lactic acid fermentation occurs in muscle cells pyruvate accepts electrons from NADH and lactate and NAD are produced vs in alcohol fermentation pyruvate is enzymatically converted to acetaldehyde and C02 and acetaldehyde accepts electrons from NADH to produce ethanol and NAD 239 fermentation is extremely inefficient compared to cellular respiration o organisms never use fermentation if an appropriate electron acceptor is available for cellular respiration tons of bacteria and archaea live in oxygenfree environments like our small intestines 0 Le cattle eat grass to feed the bacteria living in their stomach and then use the fermentation byproducts as energy Photosynthesis photosynthesis is the process of using sunlight to produce carbohydrates 0 requires sunlight carbon dioxide and water produces oxygen as a byproduct converting electromagnetic energy of sunlight to chemical energy in CCCH bonds of carbs o the overall reaction when glucose is the carbohydrate 6 C02 6 H20 light energy gt gt gt C6H1206 6 02 photosynthesis contrasts with cellular respiration o cellular respiration is exergonic o oxidizes sugarto C02 0 photosynthesis is endergonic 0 reduces CO2 to sugar photosynthesis consists of two linked sets of reactions 0 lightdependent reactions produce 02 from H20 0 calvin cycle reactions produce sugar from CO2 the lightdependent reactions and the Calvin cycle are linked by electrons o electrons released in the lightdependent reactions when water is split to form oxygen gas are transferred to the electron carrier NADP forming NADPH o the Calvin cycle then uses these electrons and the potential energy in ATP to reduce CO2 to make sugars Cornelius van Niel s experiments shows that H20 and CO2 do not combine directly and that the oxygen atoms in CO2 are not released as 02 are instead released through H20 Outer boundary Inner boundary photosynthesis occurs in the chloroplasts of green plants membrane algae and other photosynthetic organisms o thylakoid membranes contain large quantities of pigments that absorb certain wavelengths of light 0 most common pigment is chlorophyll which absorbs every color except green light which is what we see plants oxidize their sugars in their mitochondria Thylakoid space Partition solvent front Intermcmbrane can determine what pigments space 61395th mdhrmtem are in a plant using thin layer chromatography mmmmmh ph s chloroplasts have two membranes inside of a thylakoid is lumen d tmmdh m m h 1 one leaf cell has about 4050 4d tmemdhycmmph 3 chloroplasts that s a lot 1 grind leaves and add solvent pigments from leaves move to the solvent D imfpi mm 2 spot pigments on a thin layer of porous material 3 separate pigments in solvent Mmigration of solvent light is a type of electromagnetic radiation a type Gamma Ultraviolet Infrared of Rays XRays Rays Rays Radar RM TV Shortwave AM 0 light has both particlelike and wavelike 1x10 1x10 1st 1x104 1x102 1x102 1x104 Wavelength in meters characteristics 0 as a particle light exists in H V1s1ble L1ght discrete packets called photons o as a wave light can be characterized by its wavelength the range of wavelengths is called the 4m 5x104 6x104 7x104 Wavelength in meters electromagnetic spectrum 1 L o VISIble light ranges In wavelength from Highgnergy LowEnergy about 400710 nanometers pigments absorb only certain wavelengths of light 0 the color we see is the color that is reflected by the pigment the other wavelengths of light are absorbed o shorter wavelengths contain more energy than long wavelengths 0 blue high energy red low energy sunlight white light aka all wavelengths in the visible light section 0 if a pigment absorbs all wavelengths it will appear black because no visible light is reflected back to your eye there are two major classes of pigment in plant leaves 1 chlorophylls chlorophyll a and chlorophyll b o absorb red and blue light 0 reflect and transmit green light 2 carotenoids carotenes and xanthophylls o absorb blue and green light 0 reflect and transmit yellow orange and red light the absorption spectra for pigments correlates with the action spectrum of photosynthesis o violetblue amp red regions of the spectrum are associated with high 02 concentrations it it 393 Chlorophyll a all f39 a L j f a E 3 a F E 15 a E E Wavelength of light um Wwili rgfh 6F Ugh Absarptiun Spectrum ii Spectrum absorption spectrum measures how the wavelength of photons influences the amount of light absorbed by a pigment 1 chlorophylls have a long tail made of isoprene units and a head consisting of a large ring structure with a magnesium atom in the middle 0 tail interacts with proteins embedded in the thylakoid membrane head absorbs light I39ZI i HL chemphyll a H i i a H H f C C CC l C E C E C iii C Hi lll H H IIHLB H3 H1 H5 SHE H Hi Hi l H3 H3 H3 ring 2 carotenoids are accessory pigments that absorb light and pass the energy on to chlorophyll 0 two rings are responsible from absorbing light 0 in the fall leaves chlorophyll degrades first leaving carotenoids to absorb and reflect light 0 extend the range of wavelengths that can drive photosynthesis 0 also protect chlorophyll molecules from being degraded corn and carrots get their color from this difference between them is a hydroxyl group electrons become excited when photons are absorbed by pigments o fluorescence or heat occurs when a pigment absorbs a photon and the excited electron falls back to its ground state 0 the radiation given off during fluorescence has lower energy and a longer wavelength than the original Rx photon only about 2 of excited electrons c an electron s state is incremental not continuous chlorophyll does not absorb green light because there is no discrete step for it no difference in possible energy states for its electrons pigments work together in groups in a complex called a photosystem o photosystems consist of two major components 0 an antenna complex composed of 200300 chlorophyll molecules and accessory pigments organized in an array of proteins 0 photosystems also contain proteins that capture and process excited electrons energy is transferred inside the antenna complex y from one molecule to the next until it reaches the 7 reaction center in a process called resonance 0 when a red or blue photon strikes a pigment in the antenna complex electrons are excited c this energy is passed to an adjacent pigment molecule exciting another electron Thylakoid membrane Photosystems and Chlorophyll I Electron and energy tre nsfer Reaction center for chlorophyll PSSL LPFOCIJ Electron ameptor cHo in chlorophyll r ph i n39 H2C CH H CH5In chlmophyil a 500 nm Photon CH CH 450 nm 2 r 3 l Carotenoid 39 Whee39system Chlorophyll when a chlorophyll molecule is excited in the reaction center the excited electron is transferred to an electron acceptor in a redox reaction 0 resonance energy is only possible between pigments that are able to absorb different wavelengths of photons so that the potential energy drops at every step 0 when the acceptor becomes reduced electromagnetic energy is transformed to chemical energy only in the presence of light there are two photosystems that differ in their response to red light 0 photosystem I 0 reaction center chlorophyll is called P700 responds to far red light of 700 nm 0 photosystem II 0 reaction center chlorophyll is called P680 responds to red light of 680 nm together they contribute to the enhancement effect rate of photosynthesis increases if exposed to red and farred wavelengths photosystem II triggers chemiosmosis and ATP synthesis in the chloroplast 0 when energy reaches the P680 reaction center the chlorophyll is oxidized when a highenergy electron is donated to the electron acceptor pheophytin Energy or mleetrana nutmegtern II the m CH 11 25 H34 KEH NH Nll 39 3 k 5 l r 1 Hr HEBw fillNEHE CH3 i ch5 70H Disiiflso quot 1 HnCa ka A a 42 electrons are passed from the reduced pheophytin to an electron transport chain in the thylakoid membrane 0 plastoquinone PO is a hydrophobic molecule that shuttles electrons from pheophytin across the thylakoid membrane to a very electronegative cytochrome complex 0 PE released allows protons to be picked up from stroma and dropped off at the lumen area making the pH of the lumen 1000 times higher than the stroma 0 both in structure and function this ETC is similar to mitochondrial ETC 0 both contain quinones and cytochromes 0 both use a protonmotive force that drives ATP production via ATP synthase redox reactions in an ETC provide the energy for the cytochrome complex to pump protons in the thylakoid lumen o the proton gradient exergonic process provides the protonmotive force for ATP synthase to produce ATP endergonic process 0 ATP synthase in chloroplasts is almost exactly the same as in mitochondria photophosphorylation is the production of ATP through the proton gradient established by the capture of light energy in Photosystem II o lumen has high concentration of H ADP FL39 and low pH I R LE m39P Light 0 occurs In mitochondria and depends energy on ChemIOSmOSIS title ansmr A Strum I oxygenic photosynthesis is the process in which Photosystem ll oxidizes water to replace the electrons passed to pheophytin o 2H20 gt 4H 4e 02 0 only protein complex that can 1 I 1 split water 3 0 when excited electrons leave quot photosystem II and enter the ETC the photosystem becomes so electronegative that enzymes can remove electrons from water leaving the protons amp 02 what we breathe oxygenic photosynthesis when oxygen is generated as a byproduct anoxygenic photosynthesis when organisms only have a single photosystem and therefore do not oxidize waterproduce 02 gas studied heliobacteria to study photosystem I purple bacteria to study photosystem II Photosystem l produces NADPH E o excited electrons from the P700 reaction center in Photosystem l are passed down an ETC to the protein ferredoxin 0 has a bunch of Cystine AA Lag 0 contain SH the enzyme NADP reductase transfers a proton and two electrons from ferredoxin to NADP forming NADPH photosystem I and NADP reductase are in the thylakoid membrane ferredoxin is in the stroma HADFFquot r4 Hquot Photosystem I lF39rE Ill the NADPH and ATP produced by the photosystems light reactions is used by the Calvin cycle to make carbohydrates dark reactions several groups of bacteria have just one of the two photosystems o purple photosynthetic bacteria and purple sulfur bacteria do not have Photosystem II 0 these bacteria perform anoxygenic photosynthesis with only Photosystem l 0 does not have oxygen for PM to split cyanobacteria algae and plants have both photosystems 0 these photosystems work together to produce an enhancement effect 0 photosynthesis increases dramatically when cells are exposed to both red 680nm and farred 700nm light 0 produce chemical energy in ATP and NADPH Z scheme is a model of how Photosystems l and II interact and explains the enhancement effect 4equot re 0300 It N2 NADP 2w Ferredoxin Higher ED 66Gb J Ilv ly in V 7 1391 J YIIr 1 a quotquotI quot re a ll 391 39 I i g H W l I 3quot a 4 Photons 2 NADPH Energy of electron produced via protonamotive force Photosystem E Lower at the end of the ETC the electron is passed to a protein called plastocyanin o plastocyanin PC carries the electron back across the thylakoid membrane and donates it to the reaction center pigment in Photosystem l physically linking the two photosystems 0 one PC molecule can shuttle 1000 electrons per second 0 electrons from PC replace electrons from the P700 chlorophyll molecules in the Photosystem l reaction center photosynthesis is more efficient when both 680nm and 700nm wavelengths are available 0 aka white light allows both photosystems to run at maximum rates in the mitochondrial ETC electron PE starts high and then steadily drops as the electrons are transferred to the final acceptor 02 which has low potential energy vs in the chloroplast s ETC the final electron acceptor has a higher PE than the electron donor H20 cyclic electron flow cyclic photosynthesis occurs when 6 Photosystem l passes electrons to Photosystem ll Higher n o if it has enough NADPH it produces additional ATP instead of using the electrons to reduce NADP g o coexists with noncyclic electron flow and is used to Ph ton reduce C02 and produce sugars g E produced via protonmotive force Lower Photosystem l amp ATP synthase abundant in the exterior unstacked membranes of grana Photosystem ll amp cytochrome complex abundant in the interior stacked membranes of grana the reactions that produce sugar from carbon dioxide in the Calvin cycle are lightindependent 0 even though light is not involved the Calvin cycle is more active in the day 0 the reactions require the ATP and NADPH produced by the lightdependent reactions the Calvin Cycle occurs in the stroma of the chloroplast and consists of three phases a The Calvin cycle has three phases b The reaction occurs in a cycle I 7 77 V g Carbons are symbolized as 39 i redl balls to help you foliow 3 902 them through the cycle 3 1 6 i t r RuBP Fixation of 3phosphoglycerate 39 All three phases of the 3 Amp 3 pi i carbon diOXide Calvin cycle take place in j M s 6 the stroma of chloroplasts 3 2 6 ADP 6 ini Regeneration of i Reduction of RuBP from 33P E Bphospho glycerate to GSP 1 Fixation 3 RulBP 3 co gt e SiphOSpl mgllyceirate 6 NADPH 2 Reduction 39 5 313 to step 3 6 NADP 6 H a 3Phoslphoglycerate 6 ATP a MADPH 6 39 i 7 1 63 View 5 Gap GSF 3 Regeneration to giluco seffructose 5 G3P 3 Iquot 3 RuBP 1 333 Glucose fructose 2011 Pearson Education inc carbon fixation is the addition of C02 to an organic compound redox reaction 0 C02 reacts with ribulose bisphosphate RuBP and produces two 3phosphoglycerate 3PGA molecules 0 three turns of the cycle fixes three molecules of C02 which yields one molecule of G3P and fully regenerated RuBP each mole of C02 requires energy from 3 moles of ATP and 2 moles of NADPH to fix it and reduce it to sugar 0 conversion of C02 to carbs is definitely worth the energy investment the 3phosphoglycerate is phosphorylated by ATP and reduced by NADPH in the reduction phase 0 the product is glyceraldehyde 3phosphate esp which is used to z H quot I gt v a e 1 17 Hi 77 quota 7 I133 Si o synthesnze hexoses glucose fmml Tquot me 1 if 5 PP 39IE H i T43 riri tizm and fructose 1 G3P H DH iztzizti lgn o reform RuBP the other 5 G3P 1 9H I li H a all f j H n E quotDH Enwwu 0 during regeneration the remaining mmi mum 95JDFQf G3P is used in reactions that Ribuimcmtgg Encaalf h f Enk l f blnil BPhosphog lytmatc bit p h oi nale ll h tsp hosp l mm synthesnze RuBP one turn of the Calvin cycle fixes one molecule of C02 0 need 3 turns of the cycle 3 C02 to make one new G3P the C02fixing enzyme is ribulose 15bisphosphate carboxylaseoxygenase Rubisco 0 one of the oldest and most abundant enzymes on Earth if carbon fixation F ho torespir ation ET 0 kinda slow and IneffICIent ATE H MDFH 0 found in all photosynthetic Fluff 7 to organisms that use the EU Cl N WUIEP H l i fifth Calvin cycle 0 has 16 subunits 16 separate it polypeptide chains HM 39 WMquot 0 8 active sites i 1 NM 77 z F wm o catalyzes 3 reactions per MESH Nitg second really slow C02 and 02 compete for Rubisco s active site extremely inefficient 0 when 02 level is high there is competition between molecules photorespiration undoes photosynthesis o it consumes energy and releases fixed C02 0 when photorespiration occurs the rate of photosynthesis declines drastically 0 appears to be maladaptive reduces the fitness of individuals 0 however some products from photorespiration are known to be involved in plant signaling and development Stomata C02 enters leaves through stomata pore surrounded by two guard cells that regulate the opening and closing 0 open during the day to provide for photosynthesis 0 a strong concentration gradient for favoring entry of C02 is 3m maintained by the Calvin cycle which constantly uses up the C02 in chloroplasts Guard Cell Nucleus 1 toma H20 Exit quot quot 393 f H20 Enter Closed Open BUT plants must balance C02 delivery with water loss 0 on hot dry days leaf cells lose a great deal of water to evaporation through their stomata 0 closing the stomata stops C02 delivery and photosynthesis while increasing photorespiration because of high 02 levels plants in dry hot environments have mechanisms to increase C02 and limit photorespiration 0 C4 photosynthesis carbon fixation and the Calvin cycle occur in separate cells C4 plants incorporate C02 into 4carbon C4 organic acids instead of 3PGA o PEP carboxylase fixes C02 to a 3 C molecule phosphoenolpyruvate PEP in mesophyll cells 0 the 4C organic acids that result are Liane 7 7 7 7 7 mp cm W transported to bundlesheath cells via will capitalism 39 1 plasmodesmata call into l mn r g g gm 7 o the 4C organic aCIds releases a C02 molecule that rubisco uses to make 3PGA in the 3977 BillEZSEEST Calvin cycle initiates the Calvin cycle Calvin cycle o the remaining 3C molecule IS returned to KaiEpalialuparatianmstEpa u1l1uTempmHI3Epama l n Mantegna THE 84 llil lillesophyll V C4 pathway reqUIres 30 ATP molecules but Increases pathway sell PEP carbmwase l z the amount of C02 so that less 02 binds to rubisco very 7 7 efficient 39I roxalpacatam 4c F Elff 002 is stored at night and usedl during the day 7 M late 43 1 I a I quot 3977 2011 Pearson Education Inc Crassulacean acid metabolism CAM plants fix carbon at night and perform the Calvin cycle during the day 0 during the night CAM plants take in C02 and temporarily fix it into organic acids 0 during the day C02 is released from the stored organic acids and used by the Calvin cycle occurs in cacti and other plants that keep their stomata closed during the day due to heat C4 and CAM photosynthesis function as C02 pumps 0 they minimize photorespiration when stomata are closed and C02 cannot diffuse in from the atmosphere 0 in C4 plants the reactions catalyzed by PEP and rubisco are separated in space while in CAM plants the reactions are separated in time o in tropical climates C4 photosynthesis is more efficient than C3 the rate of photosynthesis is finely tuned to reflect changes in environmental conditions and use resources efficiently light triggers synthesis of photosynthetic proteins high sugar levels inhibit synthesis of photosynthetic proteins high sugar levels stimulate production of proteins required for sugar processing and storage 0 rubisco is activated by regulatory molecules but inhibited by low C02 availability plants use the G3P produced in the Calvin cycle to make glucose and fructose gluconeogenesis 0 glucose and fructose are combined to form sucrose which is transported in phloem 0 sucrose is water soluble and readily transported to other parts of the plant 0 sucrose synthesis occurs in the cytosol o in photosynthesizing cells where sucrose is abundant glucose is temporarily stored in the chloroplast as starch 0 glucose is polymerized inside the chloroplast o starch is broken down at night and used to make more sucrose which is used to fuel cellular respiration CellCell Interactions purpose of plasma membrane create an environment inside the cell that is different from outside the cell by regulating the transport of substances most cells possess a protective layer or wall that forms in addition to the plasma membrane 0 this layer generally consists of a fiber composite made of two parts 0 a crosslinked network of long filaments or fibers to resist tension stretching and straining forces 0 a stiff ground substance that surrounds the fibers to resist compression Middle wall is dynamic if they are damaged they can Lama release signals that trigger the reinforcement of 52m walls in nearby cells Pectin Cellulose Microfibril Plasma Hemicellulose Membrane Soluble Protein when fruits ripen cell walls are degraded in a controlled way to make them digestible when new plant cells form they secrete a cellulose fiber composite called a primary cell wall that defines the shape of the cell 0 consists of long strands of cellulose which are bundled into structures called microfibrils and then crosslinked by other polysaccharide filaments 0 space between the microfibrils is filled with gelatinous polysaccharides such as pectins which are hydrophilic and hold large amounts of water to keep the cell moist 0 synthesized in the rough ERGolgi and secreted to the extracellular space young plants secrete proteins that disrupt hydrogen bonds that crosslink microfibrils called expansins see later with auxin and cell elongation some cells secrete a secondary cell wall inside the primary cell wall usually as they age 0 the secondary cell wall structure correlates with the specific cell s function 0 in cells that form wood the secondary cell wall contains lignin exceptionally rigid o in leaf cells the secondary cell wall contains waxes most animal cells secrete a fiber composite called the extracellular matrix ECM that provides structural support 0 very flexible gives cells shape and helped them stick together 0 lots of polysaccharides and proteins 0 surrounding matrix contains gelforming proteoglycans with polysaccharides attached the ECM and cytoskeleton are directly linked o collagens cablelike protein stretch across the ECM and anchor into the protein laminin which is connected to Awnmamem transmembrane proteins which are then connected to Pmtmlmmmplex actin filaments in the cytoskeleton Carbohydrates 0 this linkage is critical because it keeps cells in I place and helps them adhere to each other Extracellular matrix ECM Plasma Cytoskeleton membrane Collagen fiber most ECM components are synthesized in the rough ER processed in the Golgi and secreted via exocytosis o the amount and composition of EMC varies among different types of cells 0 skin cells have little EMC bone and cartilage have large EMC o lung tissue contains large amounts of a quot rubberlike protein called elastin Plasma quotHtegrm Micro lments membrane of the cytoskeleton integrins membrane proteins that bind to extracellular proteins 0 transmit signals that inform the cell if it is in the right spot and anchored properly laminins EMC crosslinking proteins the basis of multicellularity is physical connections between cells 0 cells of multicellular organisms adhere to each other 0 the structures that hold cells together vary among multicellular organisms epithelium a tissue that forms external and internal surfaces act as a barrier extracellular space between adjacent cells is comprised of 3 layers primary wall sandwiches the middle lamella primarily gelatinous pectins the middle lamella connects adjacent plant cells if degraded the cells will separate Plasma membrane M15151ng lamella Secondatywa s a middlelamellalike layer made of gelatinous polysaccharides exists between cells in many animal tissues 0 the polysaccharide glue may be reinforced by cablelike proteins that span the ECM to connect adjacent cells epithelial tissue is composed of sheets of cells that cover organs and line body cavities 0 many types of structures connect neighboring epithelial cells tightjunctions are composed of specialized proteins in the plasma membranes of adjacent animal cells that bind to each other and Threedimensional view oftight junctions form a watertight seal in a quilted pattern r 0 dynamic some are easily torn apart some are really tightly held together 0 changes due to changes in the environment Tight junction Pl b 0 found In areas where you want a barrier bladder 333233quot 0 only selected nutrients enter and leave via Membrane proteins speCIaIIzed transport proteins and channels thatformtight junctions desmosomes are made of proteins that link the cytoskeletons of adjacent Cells Desmosome o cadherins are the adhesion proteins in desmosomes x v 32quotquot39 0 can only bind to a cadherin of the same type of cell fl me o integral membrane proteins that form bridges between I anchoring proteins InSIde adjacent cells 3 ix Intermediate Linker filament I glycoproteins keratin b Desmosromes Anchoring junctions bind adjacent cells together and help form an internal tensionreducing network of fibers 0 intermediate filaments help reinforce these connections by attaching to the anchoring proteins in the cytoplasm selective adhesion is the tendency of cells of one tissue to adhere to other cells of the same type 0 there are several classes of cell adhesion proteins 0 each major cell type has its own cell adhesion proteins 0 these cell cell connections are also species and tissue specific 0 experiment to prove this involved antibodies direct connections between cells in the same tissue allow cells to communicate and work together in a coordinated fashion 0 plant cells are connected by plasmodesmata as seen in the sieve tube elements and companion cells in the phloem 0 animal cells are connected by gap junctions signals either regulate gene expression or deactivate an already existing protein plasmodesmata are gaps in the cell wall where the plasma membranes cytoplasm and smooth ER of two cells connect Plasmodesmata create gaps that connect plant cells communication portal where small molecules may be j I smgsmk transported through plant tissues within 1 o symplast shared cytoplasm eJ 39f 39iaes r Jic o apoplast region outside membrane pasgfgl39mngh plasmodesmata j 0 Includes lamella Membrane r E ofcell1 IgureSIBa part2 BiologicalScIence 22 ofcel2 gap junctions connect adjacent cells by forming channels that allow the flow of small molecules between cells Gapjunctions create gaps that connect animal cells 0 communication portals cell cell signaling occurs in four steps 1 signal reception 2 signal processing junccifigns 3 signal response 4 signal deactivation hormones are information carrying molecules used in longdistance cellcell signaling 0 secreted in small concentrations but have a huge impact Membrane proteins from adjacent cells line up to form a channel Figure 813l2 part 2 Biological Science2le 2005 Pearson Prentice Hall Inlc hormone information containing molecule that is secreted by one cell type and is circulated around the body until it acts on a different part of the body ie auxin estrogens ethylene insulin thyroxine T4 etc lipidsoluble hormones usually diffuse across the plasma membrane on a protein receptor and enter the target cells cytoplasm ie steroids 0 lipidinsoluble hormones bind to protein receptors on the cell membrane and initiates signal transduction pathways 0 Gproteincouple receptors are often found in signal transduction o G proteins bind to GDP inactive or GTP active 0 turns on an enzyme that makes a molecule called a second messenger nonprotein signaling molecule 0 enzymelinked receptors results in a phosphorylation cascade o enzymes involved are called mitogenactivated protein kinases MAPK o activated enzymes at a given stage exist in greater numbers than the activated enzymes that preceded them so the original signal is amplified many many times I usually held in close proximity by scaffolding proteins ll Neurotransmitter 39 Gvprotei n rcoupled Merrillrane I39EC EWDF spanning i Phosphorylation 7 39 cascade Extracellular aide l F i 39 mmquot both receptors can do illltllilnl llrlililltilillll 7 b thph sp 39a y mmm r fame cascade and second g 5mg messengers k G l in J 5 receptors are dynamic and can be blocked o ability to bind to a hormone tightly may decline is over stimulated for a long period of time 0 drugs can be used to clog receptors so signaling molecules cannot bind to them second messengers often activate protein kinases which are enzymes that activate or deactivate other proteins by adding a phosphate group to them 0 are not restricted to one role the same messenger can initiate different reactions in different cell types 0 it is common for more than one second messenger to be involved in triggering a cell s response to the same extracellular signaling molecule cells have builtin systems for turning of intercellular signals 0 enzymes called phosphatase remove phosphate groups from cascade proteins 0 signal transduction pathways trigger a quick response and can be shut down just as quickly making them extremely sensitive to small changes 0 when signal transductions systems do notjust down properly bad things like cancer can happen 0 signal transduction pathways form a complex network that allows an integrated response to an array of extracellular signals changes gene expression which affects proteins 0 crosstalk integrates the diverse signals that cell receives 0 organizes the signals so that the cell always knows what is going on possible situations 1 products from one pathway may inhibit steps of a different pathway 2 response from one pathway may stimulate a greater response in a different pathway 3 the presence of multiple steps in each signaling pathway provides a series of points where crosstalk can regulate the flow of info and everything can happen at once unicellular organisms interact with each other via cell signaling 0 pheromone sensing o yeast cells respond to pheromone signals from the opposite mating type by growing toward the source of the signal during sexual reproduction actin I use both phosphorylation cascades and Gproteincoupled receptors 0 they have receptors that will only bind to the opposite sex s signals 0 quorum sensing o in quorum sensing bacteria and other microorganisms release speciesspecific signaling molecules that responds to population density 0 when they reach a certain quorum or threshold their activity changes drastically Signaling In Plants plants gather process and respond to the information they monitor in a series of three steps 1 receptor cell perceives external stimulus and transduces the information to an internal signal 2 a cellcell hormone signal released by the receptor cell travels throughout the body 3 responder cells receive the cellcell hormonal signal transduce it to an internal signal and change activity receptor proteins change shape in response to a stimulus o the change in shape may be caused by wavelength of light pressure binding to a molecule 0 this change of shape results in an intracellular signal signal transduction 0 once the information has been transduced to an intracellular form it travels down a signal transduction pathway phosphorylation cascade is triggered when the change in the receptor protein s shape leads to the transfer of a phosphate group from ATP to the receptor vs second messengers are produced when receptor proteins trigger the production of intracellular signals or their release ie Calcium ions Ca2 mmquot factor I V 39 a 39 NUCLEUS 39 inactive 39 Active transcriptle l RESPOJEQ I transcription n39 signal transduction changes an external signal into an internal signal 0 often results in the release of a hormone that carries information to responder cells 0 these hormones bind to receptors and start additional signal transduction pathways because plants perceive a wide variety of stimuli they have a wide array of hormones o auxin o phototropic hormone I later identified as indoleacetic acid IAA CHE color o leadsto asymmetriccellelongationandthusthe 1 ll bending response called phototropism N plays a key role in controlling growth via phototropism IL and gravitropism indole aaacetic acid 0 fruit development from auxin produced by the llM seed o in the abscission of the leaves and in the aging process 0 the differentiation of xylem and phloem o cytokinins gibberellins GAS abscisic acid ABA brassinosteroids and ethylene hormones can only elicit a response if the cell has the correct receptor for it to bind to 0 plants have a wide variety of hormones that can be transmitted through the xylemphloem sap or by simple diffusion hormone binding can have two results 1 activation of membrane transport proteins produces a change in the membrane s electrical potential or the cell wall s pH 2 changes in gene expression that result in new combinations of proteins or RNAs in the cell DanVin and DanVin discovered that plants exhibit phototropism growth in a particular direction in response to light 0 plants exhibit a phototropic response only if blue wavelengths of light are present 0 photoreceptors are pigments that detect blue light 0 first discovered gene that encodes for a blue photoreceptor was PHOT1 o encodes for a membrane protein PHOT1 that is phosphorylated in response to blue light 0 phototropins are blue light receptors that cause the phototropic response and trigger signal transduction that results in I movement of chloroplasts inside leaf cells so that they can receive optimal sunlight I opening of the stomata so that C02 can diffuse into the cell blue light is sensed at the tip of a coleoptile and a signal is then transmitted to lower cells 0 later experiments by Peter BoysenJensen and Fritz Went supported the hormone hypothesis 0 concluded that the signal was chemical and that it was water soluble o coleoptile a modified leaf that forms a sheath protecting emerging shoots of young grasses Light as I39E Q39H l39 i a M r 3955 1 x I m l l r r a g t a nth Trnuquotj39y quot t t 1R g 1 rl il39 i v if E a an 1 L H l by l39 Ha quot v 399 39 a i u 39 I Hnn II 5 II I39v l l l I 391 39v I d r 39 i 4 k3 t l i a t l l l I i I u a i L 1 M I L it r l h i a 9 quotI J a m a quot F see quot 1quot trip TilI 1 covered d y r f a H 4 l by trans ff Enu m Sgp rmg TL separated quot 7me39de 339 PETE gimme 1 by grailmin bill Militia in i l j I r F 39 El nlEl hquot 39 y I I v u EAHWIIH AND l WllHl 1533 E l EEHKJEHEEH MEWS El tIEiEiEi Addison Wesley Loughpan Inc N O Cholodny and Went independently proposed that phototropism results from an asymmetric distribution of auxin o the CholodnyWent Hypothesis makes three predictions 1 auxin produced at the tips moves from the light side to the dark side 2 auxin is transported down one side of the coleoptile 3 this asymmetric distribution causes cells on the shaded side to elongate more than cells on the illuminated side resulting in bending auxin binds to auxinbinding proteins in the stem and leaf 0 the signal transduction cascade that follows increase the number of membrane proton pumps HATPases in the plasma membrane o the acidgrowth hypothesis explains how cells elongate in response to the pH change x x 395 395 395 for cells to get larger the cell wall must expand and water I v has to enter the cell and generate turgor pressure to increase 397 volume 0 when proton pumps lower the pH of the wall to 45 proteins called expansins are activated 0 unzip hydrogen bonds loosening the cell wall structure 0 as protons are pumped out of the cell a gradient is established with eExp nsinssepm the inside being more negative i l l g l il f ii Cell wall loosening Crosslinking enzymes 0 concentration of solutes increases polysaccharids Figure 398 Cell elongation in responseto auxm the add growth hypotheSis Expansin inside the cell as does the water CELLWALL omeavmgauows 0 cells don t move water 33333 39 quot quot 39 5quotde39 directly they create an 7 osmotic gradient that favors g f mange water movement quot 39 id 39 39 quot a igr e39 blue light receptors trigger a number of mm c 39i llll Plasma membran39 r Nucleus swam other responses in plants mom mmxmgm an o poisoning of the chloroplasts stem elongation flower production 0 opening of the stomata 0 activation of PHOT by blue light allows water to enter the guard cells and stomata to open 0 the plant hormone ABA abscisic acid overrides the blue light response and leads to stomatal closing when there is limited water http a39bcs wh freern an comsth eli fewi rerco me ntrch p38 3802003 html plants also have pigment receptors for red light called phytochromes o phytochromes regulate germination stem elongation and flowering Signaling in Animals animals use electrical signaling along neurons for internal communication there are two basic types of nervous systems 1 the diffuse arrangement of cells called a nerve net 0 found in cnidarians jellyfish hydra anemones and ctenophores comb jellies aka simple animals 2 central nervous system CNS 0 includes large numbers of neurons aggregated into clusters called ganglia aka for advanced animals 0 most animals with a CNS have a large ganglia or brain sensory cells respond to light sound touch or other stimuli o sensory receptors in the skin eyes ears tongue and nose transmit information about the external environment 0 sensory cells inside the body monitor conditions that are important in homeostasis such as blood pH and oxygen levels 0 the information is transmitted by nerve cells called sensory neurons the central nervous system CNS made up of the brain Brain and spinal cord integrates information from many sensory quot3F 3939Tquot339 EWES neurons mmquot 0 most neurons have the same three parts a 3533 dendrite a cell body soma and an axon F39sripherai I IEfia39EIIfE T 862 Figure 422b 535 How DOES Information Flow in a Neuron information flow through neurons Spinal HE H39ES Dendrites Cell body Axon Collect Contains Passes electrical signals electrical nucleus and on to dendrites of another signals organelles cell or to an effector cell each neuron makes many connections with other neurons at synapses Membrane potential mV 30 the unequal separation of charges across a plasma membrane is called a membrane potential 0 membrane potentials are measured in millivolts mV there are generally more negative ions on the inside of the plasma membrane than the outside 0 this gives the membrane potential a negative sign in neurons membrane potentials are typically about 70 to 80 mV when a neuron is at rest not communicating with other neurons its membrane has a voltage called the resting potential 0 NaKATPase imports K ions and exports Na ions Key 939 Na 3 diu39quot if 7 39 Potassium Sodium resulting In the concentration of K Ions being higher inSIde K 1 ggtggs39um 39 Wham l chem the cell and Na being higher outside the cell lQUTSIoee 390 a lCELL no 9 0 neurons communicate with action potentials rapid temporary changes in membrane potential 0 action potentials propagate rapidly along the length of axons causing electrical signaling an action potential has three phases 1 depolarization gt membrane potential becomes less negative and moves toward a positive charge repolarization gt membrane potential changes back to a negative charge hyperpolarization gt membrane potential slightly more negative than the res3ng potential INSIDE g CELL o 2 3 Plasma membrane Action potential Outside o l belt a E Depolarization lnaidle of call Pepolarization i ll 7 Na 39 i o The membrane do polariiaa as Na ion rush iln The inside otthe oell becomes positive compared to the outside 3 W Action potential a a a a n Hyperpolanzation a E K 9 F he action potential triggers Ned channels to open in the 39 next area of membrane Meanwhile ti channels open in the tira1areaand K39 ions dilf39use out at Action potential Time ll Fleeting potential K 1 Na l 3 I in the action potential consists of a strong inward flow of Na followed by a strong outward flow of K o the action potential depends on a voltagegated channel ion channels that open and close in response to changes in membrane a As the nerve signal moves along the neutron the resting potential lie restored behind it o the action potential is propagated down the axon as charge spreads down the membrane 0 the action potential is propagated as a wave of depolarization Direction of travel of action potential at In response to a signal the electrical information action potential is Eif laiife l eaquot e mes transduced into chemical information l3w g m neurotransmitters at the synapse o neurotransmitters are often proteins mmEa e 39a z ga 39 c The action potential continues to travel down the axon Resting neurotransmitters are chemical messengers that transmit information from neurons to other neurons or target cells 0 many neurotransmitters function as ligands that bind to receptors called ligandgated ion channels 0 ligandgated ion channels in the postsynaptic membrane open and admits a flow of ions along an electrochemical gradient opening of ligand gated channels can lead to depolarization inflow of Na or hyperpolarization outflow of K and inflow of Cl of postsynaptic cell membrane Neurotransmitter other neurotransmitters bind to receptors that activate enzymes for production of a second messenger 0 second messengers are chemical signals produced inside the cell when a chemical signal arrives at the cell surface 0 may trigger changes in gene expression enzyme activity or membrane potential the nervous system works with the endocrine system to regulate body functions and respond to the environment 0 the endocrine systemis a collection of organs and cells that secrete chemical signals into the bloodstream there are five major categories of chemical signals in animals 1 autocrine signals 0 act on the same cell that secretes them 2 paracrine signals 0 diffuse locally and act on nearby cells 3 endocrine signals 0 hormones carried between cells by blood or other body fluids 4 neural signals 0 diffuse short distances between neurons 5 neuroendocrine signals 0 hormones neurohormones are released from neurons hormones act via three pathways 1 endocrine pathway Pathway Example Pathway Example Pathway Exam pile 2 neuroendocrine pathway 3 neuroendocrinetoendocrine pathway all three steps lead to a feedback response and the shutting down of the hormone o hormones produced by effector cells feed back to the endocrine cells lowering hormone production 0 the effector hormone also feeds back to the neuroendocrine and i neuroendocrineto endocrine pathways 0 endocrine signals are released in response to electrical signals which modulate the signal from the nervous system a Simple endanrine pathway b Simple neuraharmana pathway most animal hormones belong to one of three chemical families 1 peptides and polypeptides c not lipid soluble bind to receptors on the Polypeptides IAminogtflciltl Steaoicds CH3 surface of the target cell MHZ CH 2 amino acid derivatives H affirm 0 most are not lipid soluble bind to receptors on e um mil Ho Cc39 CH surface of the target cell l L L Secretin Epinephrine o ll l39llll39llllll quot 39s t wa Hlllllltlllltm ll Most not lipid soluble bind to receptors on surface of target cell one ll D k we I lpld soluble often bind to receptors inside target cell Not lipid soluble bind to receptors on surface of target cell Figure 473 Biological Science 2Ie 2005 Pearson Prentice Hall Inc 3 steroids 0 lipid soluble bind to receptors on the inside of the target cell steroid hormones bind to intracellular receptors and affect gene expression STEROII 7 774 VftIORMONE ACTWON Proteingcw 39 a F E l Iago A v Steroid hormone IJ I Hormone Promoter response element 1 Steroid hormone 2 Hormone binds 3 Hormone 4 Many mRNA 5 Each transcript enters target cell to receptor receptor complex transcripts is translated many induces binds to DNA are produced times further conformational induces start amplifying amplifying the change of transcription the signal signal Figure 4714 Biological Science Zle 2005 Pearson Prentice Hall39 Inc most polypeptide hormones and amIno aCId derived hormones MODEL FOR EPINEPllRllNE ACTION 1 Epinephrine bl nd to cell su rface recepto rs binds to receptorl Epinephrine o trigger signal transduction cascades a 2 Activation 7 3 Adenylyl of G protein cyclase Ti ansmission CAMP 332quot 0 message i 7 f 39 from celll 0f CAMP surface 4 Activation of cAMPdependent protein klnase A ADP 5 Activation of phosphoryiase kinase ADP 6 Activation of phosphorylase Amplification 7 Prodluction of glucose from glycogen Figure 474 7 Bio iogical Science Zle 2005 Pearson Prentice Hall Inc Cell Cycle cell division the process by which existing cells divide to form new cells 0 two types of cell division 1 meiosis leads to the production of gametes eggs and sperm 0 daughter cells have half the amount of genetic material as the parent cell 2 mitosis leads to the production of all other cell types somatic cells aka anything but gametes 0 daughter cells are genetically identical to the parent cell mitosis and cytokinesis are responsible for three key events in eukaryotes 0 growth 0 wound repair 0 asexual reproduction l ir 39l til l l lll 39E l i l Ehmmns ome Eifu tuf 39Il39ellnmere Solenoid I a cell s genetic material DNA is organized into chromosomes V 33 39Eligmgi n i o chromosomes contain a single long double quot 39 helix of DNA wrapped around proteins called histones o in eukaryotes this DNAprotein material is called chromatin chromosomes change before and during mitosis 0 before single thread like structure 0 during double stranded condensed structure i 39 v Eentromere 39 Chromatin condensed l hmmomme Fiure 1 Sigh gimp each of the DNA copies in a replicated Ehmmatid h39fmatidf Gh39 matidi chromosome is called a chromatid o chromatids from the same l I I 1339 A r f chromosome are referred to as sister 15 REPLICATIUH 134 ch r O m ati d S 3 I if J l o a replicated chromosome consists of L r will two chromatids but it is still considered a V single chromosome i Centromere Homelog I romosomes centromere a specialized region where chromatids are joined together growing cells cycle between two phases 1 dividing phase called the mitotic M phase 2 nondividing phase called interphase chromosome replication occurs only during interphase o the stage in which DNA replication occurs is called the synthesis 8 phase pulsechase experiments revealed that interphase also includes two gap phases during which no DNA synthesis occurs 0 radioactively label thymidine cause it is the only nucleotides exclusive to DNA during the gap phases organelles are synthesized and additional cytoplasm is made 0 this ensures that daughter cells will have the organelles they need and be normal in size and function W PHASE the cell cycle consists of four phases mlit sis I TIME EEI gt g 0 M phase 1 di v iginm Icytoklnems icytoplasmlc mdi39ViSiUln quot o interphase made of G1 gap phase 8 phase and G2 gap phase chromosomes are replicated in S phase and divided into daughter cells in M phase Mitosis M phase is a continuous process with five subphases 1 Prophase SPHASE 2 Prometaphase lDMAreplicatiohl 3 Metaphase 4 Anaphase 5 Telophase G1 PHASE Figure 17 3 Molecular Biology oi the Cell 4th Edition ll Ll From atmhlna I G5 of l39niierzphue nuup 727 1 115 71 L I A 1 in rqisum nm 7 39Ehl arnmillrl x Hing megma 1 w a H tMu malt155 Emplic h igdf Egll fgll c u whammy J gammy dggyg quot V r A 39 quot u a 39 39 quot Ill39r vilt39 i39 lquot quot 39grh iIii h Val Wquot39quot rr39Ig m a i Hu l h l Huglam 5mm IN 39IijuIiriiliitslziillilii ixiz was amrhmm rrniltlrlml39Iulic Epill il Hinuluit39l39ltrm WE juntaPH n7 ll3939il l2lrur 39 ill1lEPIIIIIIIElilillli Elll39 llil il39l39i Twmm a Hill ma H 1 H1th diam clwmn i quotDmglmr wall pewsLei EquotalFFcR Ina prophase Microtubules o chromosomes condense and the mitotic spindle apparatus begins around a hollow core to form 0 the spindle apparatus is made of microtubules called spindle fibers 0 there are two types of spindle fibers I polar microtubules push the poles of the cell away from each other during mitosis I kinetochore microtubules pull chromosomes to the poles of the cell during mitosis o the spindle fibers originate from a microtubuleorganizing center MTOC I I in animal cells the MTOC is called a Pr USQeSa39 9quotsz centrosome I each centrosome contains a pair of centrioles pair of centrioles A B microtubules growing from nucleating sites on centrosome prometaphase o the nuclear envelope dissolves and microtubules attach to chromosomes 0 kinetochore microtubules from each mitotic spindle attach to the sister chromatids of each chromosome 0 attachment occurs in the centromere region at the kinetochore 0 each sister chromatid has its own kinetochore o kinesin and dynein motors on the kinetochores walk the chromosomes along microtubules Ce ntrom39ere with ki netochore Metaphase late metaphase 0 formation of the spindle is complete and chromosomes migrate to the middle of the cell c the imaginary plane formed between spindle poles on which chromosomes line upis called the metaphase plate MiCrotubule attached t kinetochre anaphase o centromeres split sister chromatids are pulled by the spindle fibers toward opposite poles of the cell 0 as soon as they are no longer attached at the centromere sister chromatids become Ki n atoc bar 5 separate daughter chromosomes Fibers I kinetochore microtubules shorten because tubuIIn subunits of the microtubules are lost from their plus ends at the kinetochore o dyneins and other kinetochore motor 3 quothrnmnsomes proteins are attached to the kinetochore s Anaphase fibrous crown and walk toward the minus 7 end of the spindle fiber telophase o a new nuclear envelope begins to form around each set of chromosomes and they decondense o mitosisis complete when two independent nuclei have formed cytokinesis o typically occurs immediately after mitosis o the cytoplasm divides to form two daughter cells 0 each daughter cell has its own nucleus and complete set of organelles cytokinesis in plants occurs as vesicles are transported to the middle of the dividing cell and fuse to form a cell plate vs cytokinesis in animals fungi and slime molds occurs when a ring of actin and myosin filaments contracts inside the cell membrane forming a cleavage furrow 17 mu mm 1 Cleavage furrow Vesicles Walll of 1 pm 39 forming parent call Ll lt f cell plate m v r 39 Cell plate New cell wall 5 I A A f NB 7 39 gt 39 39 i 1 r l I f 39 I r I J i a a or J l 39 quot I 39 l it l at Contractile mining of Daughter cellist r 39 x microfillamenta Daughter cells at Cleavage of an animal call SEM in Call plate formation in a plant cell TEM bacteria do not undergo mitosis instead they divide by binary fission Brigier of truncation g 5 2 I Summosome replication begins Enron thereafter one cup of the origin moves rapidly toward the other and of the mill E ll WE ifquot Plasma A membrane Bacterial chromosome LE coirearl Two DEWFEES Hoplication continues aquot main 7 ne copy of the origin is new at each end of E line will Replication finishes The plasma l39l39lEllTl39hr l lE grows i nwamj and GEM wall is deposited a Two aughtm calls froemit cellcycle length can vary greatly among cell types 0 variation in the length of G1 phase is responsible for differences 0 G1 phase is essentially eliminated in rapidly dividing cells I I G V I The cell fdloubie chxecksfthe if 39duplicatedloriromosomesfor f quot enrol making any needed quot repairs 15 at 5 Jr 57 o nondividing ces get permanently stuck in I 2 G1 phase ii x V I ertter an arrested stage called the GO lquot f lt 39ff39a39f f j f39f S a e is v ff the rate of cell division can also respond to changes C iricai Toots in in environmental conditions 0 variations in cellcycle length suggest o the cell cycle is regulated o regulation varies among cells and organisms MPhase promoting factor MPF induces mitosis in all eukaryotes o MPF is present in the cytoplasm of Mphase cells 0 consists of two distinct subunits aka a dimer 0 a protein kinase that phosphorylates target molecules initiating mitosis o a regulatory protein called cycin mm MPF protein kinase is a cyclindependent kinase Cdk o Cdk is active only when bound to the cycin subunit l Eelll cycle arrest him H upl39wbsirala floatan mortise 39 39 pondlam p I Cdk is further regulated by two 2 G1 S GZ G1 8 GZ M phosphorylation events g 39 1 after it binds to cyclin MPF s Cdk g I subunit becomes phosphorylated g MPF aet39v39ty at two sites 5 this makes Cdk inactive 3 MitoFic allows the concentration of dimer cydm to increase without immediately 33 turning on mitosis 2 late In the G2 phase enzymes Time dephosphorylate one of the phosphate groups on the Cdk subun 0 makes Cdk active initiating mitosis during anaphase an enzyme complex begins degrading MPF s cyclin subunit 0 the enzyme complex is activated by events in mitosis o the complex attaches small proteins called ubiquitins to MPF s cyclin subunit which marks it for destruction there are cellcycle checkpoints in three phases of the cell cycle 0 checkpoints are critical regulation points 0 interactions among regulatory molecules at each checkpoint allow a cell to decide whether to proceed with division the first and most important checkpoint occurs late in G1 0 four factors affect whether cells pass the G1 checkpoint 1 cell size 2 nutrient availability 3 social signals from other cells 4 health of DNA whether it is degradeddamaged or not the p53 protein regulates the cell cycle through gene expression in G1 if DNA is damaged 0 p53 can activate genes that stop the cell cycle until the DNA damage is repaired o othenNise p53 initiates apoptosis programmed cell death the second checkpoint is between the G2 and M phases 0 cells stop growing if chromosome replication has not proceeded properly or if DNA is damaged 0 both conditions prevent the removal of the inactivating phosphate from MPF keeping MPF from functioning there are two checkpoints in M phase 0 one regulates the start of anaphase o if chromosomes are not properly attached to the mitotic spindle apparatus in metaphase cell growth stops 0 one regulates progression through anaphase o if chromosomes do not fully separate in anaphase MPF cyclins are not degraded o MPF remains active and prevents the cell from existing the M phase Resting State EspindteAssemblyCheckpoint Mi Check that the cell cycle checkpoints prevent cell division of m Chmkwim Chm1 i 39 C tirrmuUEumt tittt tEljment damaged cells or mature cells am Hi g m Spindle thOSe in DNArcplimtit1n Gil CHISECkPDiiHE Check 39Fm Ilf illi izc i Nu lrients Grn W li li tictnrs l tibia amingo when cell cycle checkpoints fail uncontrolled cell growth can occur 0 a mass of cells formed by uncontrolled cell growth is called a tumor 39VR ctiting State GU some tumors are benign 0 they grow in a single location and are not Ema We Mailgmnt mm l cancerous 3 lliftoiiiiimi liit 33th ESEE ig tf ig dmans invasion or metastasis and metastasiie to di emnt sites 0 malignant tumors are cancerous cancers are thought to arise from cells with defects in the G1 checkpoint o cancerous cells have two types of defects 1 defects that make the proteins required for cell growth active when they should not be 2 defects that prevent tumor suppressor genes from shutting down the cell cycle cells respond to signals from other cells and divide only when their growth benefits the whole organism c this process is called social control which is based on growth factors small proteins released by cells that stimulate division in other cells Rb is a tumor suppressor protein that prevents progression to the S phase 0 different than MPF but acts similarly e noollos iomo pmtelnl lib in some human cancers G1 cyclin is overproduced because of excessive growth factors or because of other defects p16 Ilorrn r mommar Eli t will ll oron FIE blocked iEEF Jill many different types of defects can cause the G1 checkpoint to fail um pIIE 7 Edi itElmo 0 most cancers result from multiple defects in cellcycle regulation 0 rh liifi bonito to Drilling l romwllnu ohorsohon39lotion offal Elli E IianIiEItlb mui lrElIIE HitW5 If afloatilli isquot lrn ltlrillte lrlf l lzllznlte cancer develops only after several genes mm Hawme F have been damaged 0 each type of cancer is caused by a unique combination of errors Mitosis vs Meiosis Table 131 0 every organism has a characteristic number of chromosomes called a karyotype 0 sex chromosomes determine the sex of the individual XX XY all other chromosomes are autosomes chromosomes carry genes 0 a gene is a section of DNA that influences one or more hereditary traits O Homologous chromosomes different versions of a specific gene are called alleles O chromosomes of the same type are called homologous chromosomes or homologs hollow olwtiwitim d with Centrornere homologs carry the same genes in the same locations but each one may contain different alleles omitlo IKinetochoro quotlilommolmi mm a cell s ploidy indicates the number of each type of chromosome present 0 Sister chromatidls the haploid number n indicates the number of distinct types of chromosomes present 0 O organisms with just one of each type of chromosome are called haploid n O organisms with two of each type of chromosome are termed diploid 2n polyploid 3n 4n etc organisms with three or more versions of each type of chromosome are called of each type diploid cells have one paternal chromosome of each type and one maternal chromosome meiosis is nuclear division that precedes the formation of gametes eggs and sperm 0 meiosis reduces the number of chromosomes in half 0 in diploid organisms meiosis makes haploid cells before meiosis begins each chromosome in the diploid 2n parent cell is replicated 0 when replication is complete each chromosome has two identical sister chromatids attached at the centromere mingle III ll39 ll 39ili lh ll i a Pii39q h lll Balls have one chromosomal 1mm each homologous palr meiosis consists of two cell divisions Meiosis l o the diploid 2n parent cell produces two haploid n daughter cells Meiosis II o the sister chromatids of each chromosome separate and go to different daughter cells 0 four haploid daughter cells are produced 0 now sexual reproduction can occur trimmings Ill Eliromosumes align at ma nmlaphasa39 plate Ana mm Ill DELIQIWIIQT chmmosmms move 39I lf39JE39lI HE IllES 39ll39 a39l plfl ll Spindle dlsappaars nucim Imm and cytolilrmsis lakes place Daughter Gall Maioals ruesuns In1our haploid daughter culls in sexual reproduction egg and sperm unite forming a new individual and restoring the chromosome number fertilization an animal s life cycle summarizes life from fertilization through offspring production 0 meiosis produces haploid gametes that combine during fertilization to form a diploid zygote o zygote develops through mitosis into an adult of the next generation 3 Diploid 2n E1 I Haploid n Grows into adult male or a adultfemale Meiosis l is a continuous process with five distinct phases 1 early prophase l 2 late prophase l 3 metaphase l 4 anaphasel 5 telophasel rm haploid Egg Fertilization haploid n Zygote diploid 2n early prophase l o the homolog pairs come together in a imitate dumpster pairing process called synapsns Fatima GFITITEITJHEITE EVENT 53119 o the structure that results from synapSIs l 39 consists of two homologs and is called a bivalent or tetrad late prophase l o the nonsister chromatids begin to separate at several points but remain connected at chiasmata crossover points in prophase l crossing over occurs when chromosomal segments are swapped between adjacent homologs o synaptonemal complex binds them together El ltf l l l f a a ma hill39l llllllivgl lls Asthetllmmtlsnrnes39 Ehmmatunls tllmmusume rrlmra clutter tugelhet and ganglia ll39lfilfl39lll llllll lair synausis occurs is exchangedquot 1 E 1 to E E EaiEllEl chromatids metaphase l o the bivalents tetrads finish migrating to the metaphase plate anaphasel o the paired homologs separate and begin to migrate to opposite ends of the cell telophase l o the homologs finish migrating to the poles of the cell c then the cell divides in the process of cytokinesis at the end of Meiosis I one chromosome of each homologous pair is distributed to a different daughter cell 0 a reduction division has occurred 0 the daughter cells of meiosisl are haploid but still in the form of sister chromatids like meiosis l meiosis II is a continuous process but with four distinct phases 0 prophase ll metaphase ll anaphase ll telophase ll prophase II o the spindle apparatus forms and one spindle fiber attaches to the kinetochore of each sister chromatid at the centromere metaphase II o the chromosomes line up at the metaphase plate anaphasell o sister chromatids separate and the resulting daughter chromosomes begin moving to opposite sides of the cell telophase II o chromosomes arrive at opposite sides of the cell and a nuclear envelope forms around each haploid set of chromosomes 0 each cell undergoes cytokinesis meiosis ll results in four haploid cells 0 each has one daughter chromosome of each type in the chromosome set the key difference between the two types of cell division 0 homologs pair in meiosis o homologs do not pair in mitosis Meiosis offspring produced during asexual reproduction are genetically identical to the parent 0 clones are genetically identical to one another vs sexual reproduction leads to greater variation 0 offspring produced by sexual reproduction the fusion of gametes have a chromosome makeup different from that of one another and from that of either parent 0 genetic variation in sexual reproduction results from 0 independent assortment o crossing over 0 random combination of egg and sperm outcrossing independent assortment separation and distribution of homologous chromosomes during meiosis results in a variety of combinations of maternal and paternal chromosomes 0 humans have a haploid number of 23 0 there are about 84 million different p gsmmw minim combinations of chromosomes in gametes mm gth mlcvawa V so chromosomes probable a i L I arrangements of 7 7 VaHV ohmmooumes at Ifw zr 39 motoohooo i homologous ohromooomea x 5quot RR U i H r ff mvr Meta hr 2 fKq o 11313313 V Hquot fix R n 1 1 a quotr i if 1 I H E 1 if 1 L r i L 39 39 39 39 J x 39quotxf 1quot V kx 39xr rx 1 rr Bombina iion 1 Combination 2 or obino iion 3 Combination vi crossing over form of genetic recombination 0 produces new combinations of alleles on the same WWI chromosome if 0 these combinations did not exist in either parent o crossing over increases the genetic variability of gametes 1mm produced by meiosis beyond that produced by the random assortment of chromosomes quot 39l39ctr ad quot39339 l Spindlje n1 39 l a Z 1 N quot quot quoti Motaphasc l selffertilization occurs when gametes from the same individual combine 1 0 genetic variation introduced during meiosis ensures that offspring will be genetically different from the parent Glamates 7 Heterozygous Yer diploid cell from a plant with round yellow seeds Recombinant chromosomes Metaphase l Anaphase ll l39elop hase I lFr39opha39se ll Metaphase Anaphase ll Telophase II lPossible haploid gametes outcrossing occurs when gametes from different individuals combine to form offspring 0 increases the genetic diversity of the offspring because chromosomes from two different parents are combined example two human parents can potentially produce 84 million x 84 million 706 x 1012 genetically distinct offspring c this does not take into account crossing over two things must occur for a gamete to get one complete set of chromosomes 1 each pair of homologous chromosomes must separate from each other during the first meiotic division 2 the sister chromatids must separate from each other and move to opposite poles during meiosis ll if both homologs or both sister chromatids move to the same pole of the parent cell the products of meiosis will be abnormal 0 aka nondisjunction may occur in as many as 10 of meiotic divisions o aneuploid zygotes those with too few or too many chromosomes typically do not surviveto produce viable offspring mistakes in meiosis are the leading cause of spontaneous abortion miscarriage if nondisjunction occurs in meiosis l the 7 Helmets chromosomes from the parent cells are not properly distributed to each daughter cell 0 two gametes WI have an extra Wilmam lialmats 39I copy of a chromosome causmg E x a condition called trisomy o can result in Down Hmmmmnrx syndrome on 21 0 two gametes will lack that chromosome causing a condition x A v i all t I 1 n1 nit a1 nm net n n called monosomy Number of chmmmomes my Hon iajumtlm of homologous m Hun iajiunctitm of slate meiotic e quot0 rs ap pe ar to b e a CCi d ental chromosomes In meloaia 39I chromatids ln meiosis ti 4 higher Inst EiJ HIJ 4m o no genetic predisposition o maternal age is an important factor in the frequency of trisomy Meiosis and Sexual Reproduction the reproductive systems of animals are highly variable 0 organisms in most lineages of the tree of life undergo asexual reproduction 0 three main mechanisms of asexual reproduction budding fission and parthenogenesis 0 sexual reproduction is common among multicellular organisms 0 some species switch between asexual and sexual reproduction budding when the offspring forms within or on the parent and breaks away when fully developed hall llimam Parent bacteria doquot 39IBINARY FISSIQ in BACTEIEE parthenogenesis when the female produces an offspring without fertilization from a male 0 the offspring are genetically identical to the mother 0 eggs can be produced by mitosis or meiosis asexual reproduction is much more efficient than sexual reproduction because no males are prOdUCEd Asexual reproduction Sexual reproduction Generation 1 two hypotheses that may explain the paradox of sex 0 the purifying selection hypothesis 0 the changing environment hypothesis FemaleR Generation 2 Q llr39lale Generation 3 o Generaiti 4 purifying selection natural selection against deleterious alleles o in asexual reproduction a damaged gene will be inherited by all of that individual s offspring o in sexually reproducing individuals it is more likelyfor them to have offspring that lack deleterious alleles present in the parent 0 over time purifying selection should steadily reduce the numerical advantage of asexual reproduction changingenvironment hypothesis idea that sexual reproduction increases the fitness of individuals in certain environments 0 if the environment changes offspring that are genetically different from their parents are more likely to survive and produce offspring than offspring that are genetically identical to their parents studies on Caenorhabditis elegans tested the changingenvironment hypothesis 0 C elegans can reproduce by either selffertilization or by outcrossing 0 studies showed that when exposed to pathogens outcrossing will be favored Daphnia crustaceans that live in freshwater habitats are an example of organisms that reproduce both asexually and sexually in a typical year 0 throughout the spring and summer Daphnia produce only diploid female offspring by parthenogenesis o in late summerearly fall many females begin producing male offspring o haploid sperm produced by meiosis in the males fertilize haploid eggs that females produce by meiosis o fertilized eggs are released in a casing that survives on the bottom of the lakepond during winter o in spring the sexually produced offspring hatch and reproduce asexually Daphnia switched to sexual reproduction only if they were exposed to poorquality water low food availability and short day lengths all three things had to happen gametogenesis the production of male and female gametes o spermatogenesis is the formation of sperm 0 oogenesis is the formation of eggs in the vast majority of animals gametogenesis occurs in a sex organ or gonad o testes male gonads o ovaries female gonads spermatogenesis occurs continuously throughout the male s ZED Spermatogonluml adult lIfe F l l lMliltOSlS 0 there are four components to the mammalian sperm Meiosis ll 4 0 head n e C k Secondary spermatocyle O O Meiosis ll 0 tail Spermalld filled with mitochondria so that it can swim quickly Differentiation o o o o i if l SparIf cell in oogenesis the production of primary oocytes stops early in development in many mammals before birth in humans 0 when primary oocytes undergo meiosis only one of the four haploid products matures into an egg ovum First polar body milv clwitla gt a lhapkncl gt an egg cell contains a yolk and a 1 gt Domes vntelline envelope outSIde the cell a membrane 7 V x l 7 39 7 V 39521 3 le wiltmuw sews I quot x 7 fiir39ljemlnzarllion A a I Plasvmamcrnbranc C gomum IA Emmy I lrlinloitll g x Co rijcalgranu Pr39mm f V 7 a I 7 Dvum eggl Mitochondrjon n 7 39 A Malure gg 1 i Secondary an Quayle 39 ihap39ioid l qunn g m body the plaid fertilization is the joining of a sperm and an egg to form a diploid zygote o in many animal species individuals release their gametes into their environment and external fertilization occurs 0 in other animals males deposit sperm into the reproductive tracts of females and internal fertilization occurs Genetics genetics is the branch of biology that focuses on inheritance o in 1865 Gregor Mendel worked out the rules of inheritance through a series of brilliant experiments on garden peas 0 early in the 20th century Walter SuPon and Theodor Boveri formulated the chromosome theory of inheritance hereditary the transmission of traits from parents to their offspring o a trait is any characteristic of an individual 0 Mendel was addressing two basic questions 0 why do offspring resemble their parents 0 how does the transmission of traits occur there were two prevalent hypotheses of inheritance at the time of Mendel 1 blending inheritance o parental traits blend such that their offspring have intermediate traits 0 white rabbit black rabbit grey rabbit a mix of the two 2 inheritance of acquired characteristics 0 parental traits are modified then passed on to their offspring Mendel chose the common garden pea Pisum sativum as his model organism 0 easy to grow 0 short reproductive cycle 0 normally pollinate themselves through selffertilization produces large numbers of seeds matings are easy to control E f flifl39itf if qn easily recognizable traits used crosspollination to control mating Mendel worked with pea varieties that differed in seven easily recognizable traits 0 seed shape seed color pod shape pod color flower color flower and pod position and stem length 0 Mendel s pea population had two distinct phenotypes observable features for each of the seven traits Mendel s first experiments involved crossing pure lines that differed in just one trait o the adults in the cross were the parental generation and the offspring are the F1 generation Seed Shape Seed color Mendel first crossed plants that had round seeds with plants that had wrinkled seeds 0 F1 generation all round seeds r wrinkled trait seemed to disappear j m 0 F2 formed from selfpollination of F1 wrinkled seeds reappeared 7 Mendel s worked contradicted the hypothesis of blending inheritance Mendel invented terminology to describe the traits in his crosses o dominant traits were visible in the hybrids F1 0 doesn t necessarily mean that it is the most commonstronger o recessive traits disappeared in the F1 generation and reappeared in the F2 generation Mendel repeated these experiments with each of the other traits o in each case the dominant trait was present in a 31 ratio over the recessive trait in the F2 generation 3 39 l l li l a 39 eneratitiin Mendel performed a reciprocal cross to determine if gender quot35 at g tPi influenced inheritance it doesn t attirtiiwmmw Qtnemwn o the mother s phenotype in the first cross is the father s V f f phenotype in the second cross and vice versa f39 39JF I r EH 7 AH Eist lWit7539 i at 7 F i F distant ll Eit i i Mad 1 mata all of Mendel s monohybrid reCIprocal crosses showed w I I similar results 35 Mb quotTiff tiff F3 gananatttn o the F1 progeny showed only the dominant trait 3 a5 9315 magi p 3 o reciprocal crosses produced the same results quot o the ratio of F2 individuals with dominant and 5 aaati39 adtie recessive phenotypes was about 3 to 1 Mendel proposed the particulate inheritance hypothesis 0 Mendel suggested that hereditary determinants now called genes maintain their integrity from generation to generation 0 Mendel also proposed that each individual has two versions of each gene 0 alleles different versions of a gene 0 different alleles are responsible for the variation in the traits that Mendel studied genotype the alleles found in an individual 0 each individual has two versions or alleles of each gene 0 an individual s genotype has a profound effect on its phenotype to explain the reappearance of the recessive phenotype in F2 Mendel developed the principle of segregation o the two members of each gene pair must segregate separate into different gamete cells during the formation of eggs and sperm in the parents 0 as a result each gamete contains one allele of each gene Mendel used a letter to indicate the gene for a particular trait o R represented the gene for seed shape uppercase R indicated a dominant allele round owercase r was for a recessive allele wrinkled 0 individuals that have two copies of the same allele are homozygous 0 RR or rr 0 individuals that have different alleles are heterozygous o Rr a mating cross between two pure line individuals that differ in one trait RR and rr results in offspring that all have a F anemti n r a Plant gl o quotn from Palm gm 391 font heterozygous genotype Rr and a dominant mm gmwm wmmwg mg Fm phenotype for that trait E quotfquot Gametes it 1139 a monohybrid cross is a mating of two parents that are heterozygous for a smgle F1 Emmi M Siam a traIt RF I I g j mm d tarry 0 results In offspring that are 1A l gaitfertilization in 1 plants RR 12 Rr and A rr 0 produces a 31 ratio of Fi anam un Fourdifferent quoti r l quot phen types G 939 3 1 new It Punnett square is now used to predict the genotypes and phenotypes ofthe offspring from a cross 0 male gametes on the side Funnel Stilleremf Dilhyhrid tress ametes from l39i39rf39jr females gametes on top rr new A arr A E Hr 1 ET e r 7 139s n E g 3 F1 cross rt39yx Hr ije E u 1 rau rid yel lover WV L rou rid green wrinkled gellew wrinkled green Mendel developed his model of inheritance by studying single traits 0 used dihybrid crosses to determine whether the principle of segregation holds true if parents differ in more than one trait o a dihybrid cross is a mating parents that are both heterozygous for two traits Mendel s experiments tested two contrasting hypotheses 0 independent assortment o alleles of different genes are transmitted independently of each other 0 dependent assortment o the transmission of one allele depends on the transmission of another if dependent assortment occurs there should be 4 genotypes and 2 phenotypes in a 31 ratio in the F2 offspring if independent assortment occurs there should be 9 genotypes and 4 phenotypes in a 9331 ratio in the F2 offspring 0 his results supported this FigW8 39 ii i f i25ir h otheSIs y p P Generation WRR e Wquot t t Gametes F1 Generation T t er Hypothesis of V Hypothesis of Predictions dependent independent assortment assortment P d39 t d r W Sperm re It 3 ll 1139l lv offspring of Sperm m h 4 M Fzgeneration 113263 lz t4 a wee WRr YyRR Yer i o 7 I WRR 1 er U4 0 Eggs 39 39 rooow nes Vii9r wrr m YyRR E er nyR nyr 3 14 0 lh i 1quot 0 Phenotyplc ratio 31 A Wm Yyrr ny r yynquot all 3H6 0 We 1 is a Phenotypic ratio 9331 315 108 1tJ1 372 enotyplc ratloapproxumatey o g i i Ph 39 39 39 I 9331 Mendel used testcrosses to further confirm the principle of independent assortment o in a testcross a parent that is homozygous recessive for a particular trait is mated with a parent that has the dominant phenotype but an unknown genotype Walter Sutton and Theodor Boveri formulated the chromosome theory of inheritance o it states that chromosomes are composed of Mendel s hereditary determinants what we now call genes 0 they determined that meiosis explains the patterns of inheritance that Mendel observed Htmwgaus H i Dominant High Elgar my lmmrdli r i ih l l a l39IIiIII39 r 39V mamaa Wield Era Female armies H 12 r H mmm E 14 H Iatl39iaer n u H E 1 Hm Am a r e quot1 r at n ll apan Q if i lZ Fa Fl39Ff 19 Fl39r V4 J39T Naming panamams 5amp5 n39 undl r Equot w klin the physical separation of alleles during anaphase of meiosis l is responsible for Mendel s principle of segregation o the genes for different traits assort independently of one another at meiosis I because they are located on different nonhomologous chromosomes W i l 39n H m lAIHIEWJHE Iipa39mcbmEIIj zCn39 I picmin 7 I l pllulcll I39Jlplul anl mprodui w ll 21 I gt Thomas Hunt Morgan adopted fruit flies Drosophila melanogaster as a model organism for genetic research 0 small 0 ease of rearing 0 short generation time 10 days 0 abundant offspring Morgan identified red eyes as the wild type most common for eye color and white eyes as a mutation riftrmquot tr 0 when a wildtype female fly was mated with a mutant male fly all F1 progeny had red eyes 0 reciprocal crosses yielded F1 females with red eyes but the F1 males had white eyes Nebe Stevens analyzed beetle and other insect karyotypes and found a difference between males and females 0 female diploid cells contained 20 large chromosomes 0 male diploid cells had 19 large and 1 small Y chromosomes 0 Y chromosomes pair with large X chromosomes during meiosis l rL39IJiE12L39rlj stularips It ll X and Y chromosomes are now called sex chromosomes 0 sex chromosomes determine the sex of the offspring o in beetles likehumans 0 females have two X chromosomes 0 males have an X and Y other species have other systems sex chromosomes pair during meiosis l and segregate during meiosis ll resulting in gametes With either an X or a Y chromosome X chromosome Y chromosome I Meiosis r 7 ll ll Meiosis llll l l s i lll lll 5U of sperm contain 511 of sperm contain X chromosome Y chromosome Sex chromosomes pair at meiosis I Gametes the varied inheritance pattern that can occur when genes are carried on the sex chromosomes is termed sexlinked inheritance or sexlinkage 0 females and males have different numbers of alleles of XLinked Recessive Inheritance that gene Carrier Mother 0 nonsex chromosomes are called autosomes Fairer W other genes on autosomes are said to show autosomal r X Y X X inheritance X x Y x xr X Y g 39 39 1 a Norrnal Normal Carrier Affected Daughter Son lDaughter Son 25 25 25 25 most Ylinked genes help determine sex 0 the human Y chromosome has 78 genes the encode about 25 proteins 0 the Y chromosome is passed along from a father to son Xlinked genes have genes for many characters unrelated to sex 0 the human X chromosome has approximately 1100 genes 0 fathers pass Xlinked alleles to all of their daughters but to none of their sons Common XLinked Disorders 0 redgreen colorblindness o hemophilia A and B o Duchenne muscular dystrophy o Becker s muscular dystrophy Kn T tnv carriora atffatz39tedemal g Etand artji main asffec39tedifemale a tatandard39famala i must chromosomes contain more than one gene 0 the physical association of two or more genes found on the same chromosomes is called linkage linked genes are predicted to always be transmitted together during gamete formation 0 aka they should violate the principle of independent assortment which states they will sort independently of each other 33mm I o to determine whether linked genes behave as EH tt VIE with predicted Morgan mated two flies that were H at tttti ji nt heterozygous for two sexlinked traits r g t 1 results showed that the genes were not completely tit at 13th at El linked but they also didn t have a 11 1 1 ratio that ur aprtrg 39 7 39 proved Independent assortment r 394 tiquotii 3 It quotT 139 J E quottint HEWlme 3 1153 Jmn m aw Flri a Mth n rv d F mt 39EE Morgan referred to the flies with novel phenotypes as recombinant new phenotypegenotype that was not present in parent generation 0 the combination of alleles on their X chromosome was different from the combinations of alleles present in the parental generation 0 Morgan proposed that gametes with recombinant genotypes were generated when crossing over occurred during prophase of meiosis l in females 0 linked genes are inherited together unless crossing over occurs which is when genetic recombination occurs genes are more likely to cross over when they are far apart from each other than when they are close together frequency of crossing over can be used to create a genetic map a diagram showing the relative positions of genes along a particular chromosome all Mannln genetic disdainova mPe lraai WW nuELunUL nmwi a 39E 932 mi in firm ulr u r 13mm 4 1H g Hawaii iinus E T Y F n mamng h Doesn39t mayquot i ruiirag h nerr ramElm quot Eli f Twig N115 r outlaw3 all IL use 1 39 Erwin f I IiTI mgrIra quot f 39lcfii animal 19d 39 3 I Ilaj constructing a genetic map ll WEEK WW quot quot quotT1 W39F hia rm Elli MHIIIIH Immm gunk Inn u Fr i39 i f iil i I an H nial39urlu Hw p 135 3E1 33915 351 m m 341 E 1151 1553 1amp1 ma multiple allelism many genes have more than two alleles VS polymorphic when more than two distinct phenotypes are present in a population due to multiple allelism codominance when a heterozygous organism displays the phenotype of both alleles of a single gene is said to display 0 neither allele is dominant or recessive to the other human blood types are an example of multiple allelism and codominance 715 7 A lth t E Eh HIE BID EA l REE alleles AME E Ai E tnlnsnsdll Exe E A IAIA or lAi A A8 IAIB or lBi m B IBIB o ii 1 in m alleles of a gene are not always clearly dominant or recessive incomplete dominance the heterozygotes have an o E intermediate phenotype pleiotropic gene a single gene that controls more than V in Est one trait s K I Gametee 1quot392F39 1quot392 Trait 391 S v perm f Trait 2 Gene FE s Ew my A hie le at y g 1sz 1rtrr Traf c 3 f f most phenotypes are strongly influenced by the physical environment in addition to their genotypes o the combined effect of genes and environment is referred to as genebyenvironment interaction the human genetic disease phenylketonuria PKU is an example of a genebyenvironment interaction untreated this disease causes phenylalanine to accumulate in the body of affected individuals results in profound mental retardation individuals placed on a low phenylalanine diet develop normally the expression of many genes depends on the presence or absence of other genes these are genebygene interactions the phenotype produced by an allele depends on the action of alleles of other genes genebygene interactions cause comb morphology in chickens F2 Generation FlP Flt rP m HrPF Walnut FIFIPP F p Walen ut Walnut HP rose cornle pea comb rrF P 39Wafmst FirPp H990 Wye n dune tit e 19pr lR ose 7 Fran R p iWE ln ut39 Emmi a rm Fl use rrF39P Pea j nrpp lwalnut H er Walnut quotPP Flaa 1 Her l Wain Lrt rer Pea Hoop nu mun mom Hose lH39rf E VJ Single WP u may 1 ll F2 generation consisted of chickens with tour types of combs 9 walnut 3 rose 3 pea 1 single Bateson andl Punnett reasoned that comb morphology is determinedl by two different genes Mendel worked with discrete traits characteristics that are qualitatively different 0 Le in garden peas seed color is either yellow or green 0 no intermediate phenotypes exist quantitative traits traits that are not discrete but fall into a continuum are called quantitative traits o NilssonEhle proposed that if many genes each contribute a small amount to the value of a quantitative trait the population usually exhibits a normal distribution bellshaped curve for the trait E T E 5 39IliEi H 123 ailIo aaElia AntI raEb MiaI MEI ME MEE MES MEMB U39alua and Een lype wheat kernel color displays a normal distribution 0 three genes that control kernel color assort independently Parentell aa be at V Ari EB DIS generation gure line white x pure line reel F1 le Eb Cr generation nnediiunn red l Selt tertillization F2 V 213 generation 15 Milt or 15 tAAbbeo EMbbDo tAABEee d a bec EAaE Hoc 4MBon a L L m E 39E E taaBE ee Extentch tAAbbCE E E q ta beo Aeabb e EaaHBGr dAaEbDG EMEE EC z E l aa ibee t aabbCC 2 aaBbCG l aaEEEC eeaeeoe 1 r 1 397 1l aalbboe aabblfl o daaEbCe E Aa ib c dea 39 o 2 MEbGE tMB C E increasing redneee L l t 2 3 e 5 E Kemel eolr Number of red pigment allelea A E or G in genotype transmission of quantitative traits results from polygenic inheritance 0 each gene adds a small amount to the value of the phenotype pedigrees family trees used to analyze human crosses that already exist 0 pedigrees record 0 the genetic relationships among the A ectedfemale individuals in a family Narmalfemale I Affected male 0 each person s sex male ET 0 phenotype for the trait being studied i l pedigrees can be used to determine the mode of transmission of a trait i o if a given trait is due to a single gene the pedigree may reveal whether 0 the trait is autosomal or sexlinked o the trait is due to a dominantor recessive allele to analyze the inheritance of a trait that shows discrete variation begin by assuming the simplest case 0 a single autosomal gene is involved 0 the alleles present in the population have a simple dominant recessive relationship when a phenotype is due to an autosomal recessive allele individuals with the trait must be homozygous o unaffected parents of an affected individual are likely to be heterozygous carriers for the trait 0 carriers have the allele and transmit it without exhibiting the phenotype sickle cell disease is an example of an autosomal recessive trait males and females are equally likely to be affected affected offspring often have unaffected parents g unaffected parents of offspring are heterozygous a Affected Carrier affected offspring are homozygous the trait often skips a generation if both parents are heterozygous about 1A of the offspring will be affected autosomal dominant traits are expressed in any individual with at least one dominant allele 0 individuals homozygous or heterozygous for the trait will display the dominant phenotype Huntington39s disease is an example of an autosomal dominant trait males and females are equally likely to be affected affected parent affected offspring are heterozygous if only unaffected offspring are homozygous recessive trait does not skip generations affected offspring have at least one one of their parents is affected if one parent is heterozygous then about KEY of the offspring will be affected Affected Affected Unaffected Unaffected Male Female Male Female pedigrees can indicate whether a trait is sexlinked or not 0 if a trait appears equally often in males and females it is likely to be autosomal o if males are much more likely to have the trait it is usually Xlinked redgreen color blindness is an example of an Xlinked recessive trait REF Normal genre I Ah mmal FEEEEEWE ne males are affected more frequently 3F Htmal gene producing male offspring than females trait is never passed from father to son affected sons are usually born to carrier mothers trait often skips generations a daughters of affected males and unaffectednoncarrier females are carriers Nominal Niected carrier Normal Father Carrier Normal Carrier Nomad Hprmal Normal Earner Affected hypophosphatemia is an example of an Xlinked dominant trait Kll k d f ln t E EEtE f fth males and females are equally likely affected n L an all daughters of affected fathers are affected Una39 eeterl K r Affecterl father A r mether bUt no sons rquot 1 v 1 affected sons always have affected mothers Jill l39I39I i about12 of offspring will be affected if mother quotE is affected E 1 I E trait does not skip generations I Unaffected Detected Unaffeetetl affeetetl A ffeeierl Llriafleetetl aari daughter aen daughter U3 Hatienal Library ef l39uledieine
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