PRINCIPLES OF BIO I
PRINCIPLES OF BIO I BIOL 1107
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Date Created: 09/12/15
Cellular respiration the process is exergonic carbon and hydrogen atoms of the sugar are oxidized lose in their sharing of e39 oxygen atoms are reduced gain in their sharing o e39 e39 lose energy as they travel downthe e39 transport chain energy is used to produce ATP Water is formed from oxygen electrons from sugar s carbon and hydrogen atoms lose potential energy oxidation as they are transferred to oxygen the process is endergonic requires light eneIgy carbon and hydrogen atoms from carbon dioxide and Water are reduced gain in their sharing of e39 oxygen atoms of Water are oxidized lose in their sharing of e39 e39 gain energy from light energy as they tmvel up the e39 tmnsport c ain energy is used to produce sugar and ATP oxygen is formed from Water e39 from Water s hydrogen atoms and carbon dioxide s carbon atoms gain potential energy reduction as the are tran Femad toward n ar Photos thesis autotroph producers of the biosphere an organism that produces complex organic compounds ns from simple organic molecules using energy from light or inorganic chemical 1x amost all plants are autotrop most use Water as a reducing agent converts physical energy from sun light into chemical energy in the form of reduced carbon canbe phototrophs or lithotrophs photo use light as an energy source 1itho oxidize inorganic compounds photo and litho use aponion of ATP produced during photosynthesis or oxidation of inorganic compounds to reduce NADP to NADPH to form energy rich organic compounds such as carbs heterotroph consumers of the biosphere unable to make organic material by photosynthesis live on cmpds produced by other organisms decomposers consume remains of dead organisms most fungi and some prokaryotes get iel this Way dependent on photoautotrophs for food and also for 02 l n mm Humelm Chloroplasts chloroplasts are the major site of photosynthesis in most plants color of the leaf is from chlorophyll a green pigment in the chloroplast light energy absorbed by chlorophyll drives synthesis of organic molecules in a chloroplast chloroplasts are found in the mesophyll the tissue in the interior of the leaf COZ enters the leaf Oz exits through stomata pores water absorbed by the roots is delivered to the veins str0ma dense uid within the chloroplast enclosed by an envelope of two membranes stroma is separated from in the thylakoid space interior of the thylakoids by a system of interconnected membranous sacs called thylakoids Thylakaid Light dependant Outer cumgznment reactions take lntemem rane space place here 7 5mm Granum stack of thylakoids Chloroplast Stages two stages are light rxns photo part and the Calvin cycle synthesis part light rxns converts solar energy to chemical energy water is split providing a source of protons H and e39 light absorbed by chlorophyll drives transfer of e39 and H4r from water to an acceptor NADP where they are temporarily stored light rxns use solar power to reduce NADPJr to NADPH by adding a pair of e39 along with an Hir they also generate ATP ph0t0phosph0rylati0n use of chemiosmosis to power addition of phosphate to ADP so light energy is initially converted to chemical energy as two compounds NADPH a source of e39 for reducing that can be passed on to an e39 acceptor reducing it ATP light rxns don t produce sugar thylakoids of the chloroplast are sites of light rxns molecules of NADPJr and ADP pick up e39 and phosphate then NADPH and ATP are released to the stroma where they play an important role in the calvin cycle calvin cycle begins by carbon xation incorporating C02 from the air into organic molecules already present in the chloroplast then the fixed carbon to carbs by the addition of e39 steps of calvin cycle are sometimes called dark or light independent rxns because none of the steps require light directly for most plants this process still occurs in daylight because then light rxns can provide the NADPH and ATP that the cycle needs occurs in the stroma PhotosystemsMechanism ph0t0system units of protein complexes involved in photosynthesis that carry out absorption of light and transfer of energy and e39 found in the thylakoid membranes of plants algae and some bacteria rxn center an enzyme that uses light to reduce molecules inside the photosystem surrounded by light harvesting complexes that aid absorption of light and transfers energy to rxn centers each light harvesting complex consists of various pigment molecules contains a molecule able to accept e39 being reduced called the primary e39 acceptor light harvesting and rxn center complexes are membrane protein complexes thylakoid membrane has photosystem I and photosystem II photosystem II fns first in light rxns contain different pigments each absorbing a different wavelength of light light drives synthesis of ATP and NADPH by energizing the two photosystems in the thylakoid membranes of chloroplasts key to this is linear e ow ow of e39 through the photosystems and other components built into the thylakoid membrane linear e39 ow occurs during the light rxns of photosynthesis cycic e flow usues photosystem I but not photosystem II e39 cycle back from ferredoxin Fd to the cytochrome complex and then continue to PS I no production of NADPH and no release of 02 does generate ATP gt Pigment malemla phmsystem II PS I Phakosystem 1 PS 1 Linear e39 ow Cyclic e39 ow excited e39 from each of the photosystems can be donated to a 1 electron acceptor both photosystems active e39 flow from one e39 carrier to the next a light excites electrons in PS H b e39transferred to the l e39 acceptor c e39 flow down the e39 transport chain at e39transferred to PS l e light excites e39 inPS I f e39 transferred to the 1 e39 acceptor g e39 transferred to NADP e39 and reducing power are stored in NADPH e39 from the splitting of H20 replace the e39 lost from PS 11 and generate 02 as a byproduct e39 are gaining ener the flow of e39 and the splitting of water also creates a Hl gradient across the thylakoid membrane which then is used to synthesize ATP by chem iosmosis This process is known as linear photophosphorylation only photosystem I is active e39 ow from one e39 carrier to the next a light excites electrons in PSI 17 e39 transferred to the l e39 acceptor c e39 ow down the electron transport chain 51 e39 transferred to PS I e39 from the electron transport chain replace electrons lost from PS no H20 split and no 02 generated flow of e39 creates a H gradient across the thylakoid membrane which is used to synthesize ATP by chemiosm osis cyclic photophosphorylation Chemiosmosis mito and chloro both generate ATP by this method an e39 transport chain assembled in the membrane pumps protons across the membrane as e39 are passed through a bunch of carriers that get progressively more electronegative transform redox energy stored as an H gradient across a membrane ATP synthase is also in the membrane it couples diffusion of hydrogen ions down their gradient with phosphorylation of ADP Respiration mito both Photosynthesis chloro e39 come from food by NADH chemical energy from food e39 pumped across the inner mito membrane e39 transport chains move protons across membrane as e39 are moving down the chain ATP synthase is in the same e39 come from H20 or PS I energy is light e39 pumped across the thylakoid space membrane as the e39transport chain diffusion of H is coupled to ATP production many components are very similar in structure Calvin Cycle uses ATP and NADPH to convert C02 to sugar occurs in the chloroplast stroma incorporates C02 into organic molecules by carbon xation and then reduces the xed carbon to carbohydrate carb0n xation no direct light energy required ATP and NADPH from the light reaction NADPH provides the reducing power and ATP provides the chemical energy cycle produces a 3carbon sugar glyceraldehyde3phosphate G3P cycle has 3 phases 1 Input phase C02 is xed by rubisc0enzyme that catalyzes the rst step C02 is incorporated one at atime by attaching to ribulosebiphosphate RuBP pdt is a 6 C intermediate that is unstable and splits in half two moleculesphosphoglycerate per C02 xed 2 Reduction phase ATP is used for phosphorylation NADPH is used for reduction 3 Regeneration of CO2 Acceptor RuBP sugar carbons are shuf ed around to make 3 5carbon sugars RuBP from 5 3carbon sugars spends three ATP RuBP can take C02 again and cycle continues to produce one molecule of glyceraldehyde 3phosphate 3 C02 molecules are xed two molecules of glyceraldehyde 3phosphate are required to make one molecule of glucose mm to llanq p to I unset anon xilmn nun quotand Winn ations environmental conditions that promote photorespiration hot bright dry days in these climates A A I 39 L 39 39 39 39 39 the two most important ofthese adaptations are exhibited by CA and CAM c4 lants when their stomata close on hot days c3 plants produce less sugarbecause the declining level ofCOz starves the calvin cycle as co2 becomes scarce in the leaf rubisco adds 02 to the calvin cycle instead of co2 pdt splits and a 2 c cmpd leaves the chloro r u u u A While producing col produces no ATP consumes ATP r A 4 r the calvin cycle and releases col that would otherwise be xed 02 and more co2 than today 39 39 39 w 39 02 an photorespiration is inevitable to some extent probability thatRuBisCO reacts with oxygen vs col depends on the relative concentrations of the two molecules at the site ofthe reaction g3 c02 is initially xed to the 3 carbon sugar phosphoenolpyvuvate PEP forming a4 carbon compound oxaloacetate rxn catalyzed by PEPcarboxylase which is better at distinguishing between 02 and C02 than ru isco is PEP carboxylase is only in mesophyll cells ofC4 plants rubisco is more concentrated in cells of surrounding leaf veins bundle sheath cells C02 enrichment allows C4 plants to sustain higher rates of photosynthesis than non C4 plants especially at higher temperatures concentration of C02 relative to 02 in bundle sheath cells is higher mesophyll cells of a C4 plant pumpC02 into the bundle sheath keeping the C02 concentration in the bundle sheath cells high enough for rubisco to bind carbon dioxide rather than oxygen reactions with PEP carboxylase and the regeneration ofPEP can be thought of as a C02 concentrating pump powered by ATP rates of photorespiration in C4 plants are lower than in C3 plants ef cient use of C02 allows C4 plants to grow better at higher temperatures and use less water C4 plants operate these two processes in separate cell es CAM plants operate these two pathways at different times of day CAM CAM plants close their stomata during the day and usually only open them at night stomatabeing closed prevents C02 from entering leaves and also prevents water loss C02colected at night through the open stomata stored as organic acids until the day during the day the C02 is released from these organic acids inside the leaf and functions to drive the calvin cycle carbon xation C02 is xed to RuBP Light rections that produce the NADPH and ATP for the reduction of C and the regeneration of RuBP occur all day CAM plants truly have light reactions and dark reactions C4 0 co Mesnnhyll o 0 mmmeu 397 Night cell Orgalvlrduu llllufmllrtamun orgal llc Edd lLaV JOll x llml Bundle m 0 Day sheath x quotl39 a lgallll aids l leleAS 0 lo Lalle rytle Sugar Sugar Spatial separation ol steps Temporal separation ol steps lrl Cl lanls non llxalmn anll m AM 1 am rallmn llxalwl ll l9 Calm Lycle mull ll39l dlllerev ll and ll Calvll39l Lycle urcul ll ille typeset lull Same LEM mlllmmume Photosgthesis Summag lightrxns capture solar energy and use it to make ATP and transfer e39 from water to NADP forming NADPH calvin cycle uses ATP and NADPH to produce sugar from C02 Fquot 3 4 Make a diagram of a DNA molecule that accurately depicts the relationship and polarity of each DNA strand in the molecule hydrophobic nitrogenous bases in the molecule s interior away from surrounding aqueous solution negatively charged phosphate groups wouldn t be forced together in the interior hydrogen bonds between two strands wnucleotide bases 5 end phosphate new nucleotides added to 3 end primer which is OH side Describe how cells replicate their DNA and predict how replication would be affected if one of the major enzymes involved was missing from the cell Compare and contrast DNA replication an Origin of replication9Parental template strand9Daughter new strand9 Replicationforkbubble Enzymes o Helicases untwist the double helix at the replication forks separating the two parental strands and making them template strands o singlestrand binding proteins bind to unpaired DNA strands keeping them from repairing o topoisomerase relieves strain from untvvisting by breaking swiveling and rejoining DNA strands RNA chain is primer primase starts complementary RNA chain from single RNA nucleotide 0 new DNA strand starts from 3 end of RNA primer DNA polymerases catalyze synthesis of new DNA by adding nucleotides to preexisting chain Helicase unwinds the parental double helix Molecules of singlestrand binding protein stabilize unwound template strands Leading strand is synthesized in 5 93 direction by DNA pol Ill Primase begins synthesis of RNA primer for the Okazaki fragment DNA pol III is completing synthesis of other Okazaki fragments when it reaches the leading primer it will detach and begin adding DNA nucleotides to the 3 end DNA pol I removes primer om the 5 end and replaces it with DNA nucleotides 7 DNA ligase joins the 3 end of one fragment to the 5 end of the rst fragment V eP Nt ox Polymerase Chain Reaction PCR amplifying DNA in vitro by incubating it with speci c primers a heat resistant DNA polymerase and nucleotides Polymerase Chain Reaction 0 mimicking natural DNA replication with the technique of Polymerase Chain Reaction 0 A key difference between natural replication and PCR is that natural replication copies all of the DNA in a cell while PCR copies speci c targeted fragments 0 DNA strands are separated using heat rather than helicase enzyme 0 Synthetic DNA primers are used to provide a starting point for DNA polymerase The primers are complementary to a speci c sequence of DNA and in this manner can target a speci c stretch of DNA for replication Primers are allowed to anneal to the template DNA by lowering the temperature 0 A special heatstable DNA polymerase is used 0 By successively raising and lowering the temperature DNA replication can be automated and takes place in a short period of time It is possible to have several replication PCR cycles producing tens of millions of copies of a speci c DNA fragment in less than an hour 0 complementary DNA carries complete coding of genes but no introns o 5 93 Explain how gel electrophoresis is used to analyze DNA separates macromolecules on rate of movement through an agarose gel in an electric eld distance DNA molecule travels is inversely proportional to its length fragments restriction enzyme digestioncutting or PCR amplication is separated into bands bands can be analyzed to determine whether normalabnormal Gel electrophoresis Gels are usually made from agarose long chains of carbohydrate extracted om seaweed When heated in water agarose is a liquid and can be poured into a mold As it cools it solidi es like jello and forms a three dimensional porous network of bers DNA has a net electrical charge39 if DNA fragments are placed at one end of the gel and exposed to an electric current the agments will migrate towards the positive electrode cathode Smaller fragments are able to t through the pores more easily and migrate faster than larger agments Once the gel has run the DNA is stained using a uorescent dye such as ethidiurn bromide and the agments show up as bands on the gel 5 Interpret gel electrophoresis results 0 Read band S are more copies of the fragment in the brighter band than in the lighter band 6 Explain how DNA can vary from one individual to the next and how these differences can be used to create a DNA ngerprint Individuals have different genes on their chromosomes by evaluating many different genes people cannot have the same genes so the band will be different 7 Evaluate DNA ngerprint data 0 Evaluate bands 0 Short Tandem Repeats DNA that differ for people analyze this 0 Every cell in a person contains the exact same DNA with a small number of exceptions and that most DNA is the same from person to person However differences do exist in small regions of DNA between people and that no two people other than identical twins have the exact same DNA Scientists can look at these small differences to try to identify individuals 8 Describe how DNA mRNA tRNA RNA polymerase and ribosomes act together to produce a protein Predict the outcome if one of these components did not function correctly 0 O 0 mRNA fully processed mRNA is used and have mRNA read by more than one ribosome at a time lots of proteins very quickly mRNA and tRNA form with hydrogen bonds tRNA each one binds to speci c amino acid sequence at bottom called anticodon o t RNA and amino acid match up by using arninoacyltRNA synthesis enzyme anticodon recognizes and translates to mRNA recognizes codon anticodon ACG recognizes codon UGC complementary translation tool to convert nucleotide language into amino acid O 0 protein factory ribosome rRNA 7 most abundant type of cellular RNA 0 O O O s one amino acid to others in a particular sequence small subunit large subunit grabs onto RNA pulls it through and reads it one codon at a time tRNA comes in and for each codon it reads it brings in an amino acid and joins it EPA sites A site new amino acids brought in I P site growing protein is held I E site used tRNA is expelledexited polyribosomes strings of ribosomes 9 If given a double stranded DNA fragment predict the sequence of the protein that might be produced triplet code 3 letter code startMET use RNA sequence thus convert DNA fragment to RNA sequence 593 10 Predict how a speci c mutation might affect the function of a protein produced by gene nucleotidepair substitution replacement of one nucleotide and its partner with another pair of nucleotides 0 silent mutation no observable effect on phenotype rnissense mutation little effect on the proteinnew amino acid has similar properties se mutation codes for a stop codon terminating prematurely o nonsen insertionsdeletions additionslosses of nucleotide pairs in a ene O ameshi mutation occur whenever number of nucleotides inserteddeleted is not a multiple of ee 1 1 Describe the advantage of using RNA for translation of a protein rather than DNA DNA wouldn t be damaged and wouldn t have to leave the cell worried about damage can be thrown away disposable many copies can be ma e there are only 2 chromosomes so 2 copies of gene if one is damaged unable to replenish 12 Compare and contrast the process of DNA replication and Transcription Transcrip O 0000 000 0 tion RNA polymerase pries two strand of DNA apart and joins together RNA nucleotides complementary to DNA template strand elongating RNA polynucleotide in the 593 direction DNA sequence where RNA polymerase attaches and initiates transcription is known as promoter bacteria signals end of transcription r 39nator UNLIKE DNA POLYMEREASES RNA polymerases are able to start from anywhere don t need a primer I TATA box 25 nucleotides upstream from transcriptional start point hints for start Several transcription factors one must recognize TATA box and bind to DNA before RNA polymerase II can bind in the correct location transcription initiation complex transcription factors bind to DNA along with RNA polymerase II RNA polymerase II unwinds DNA double strand helix initiates RNA synthesis at the start point of the template strand unwound DNA creates RNA transcriptitranscription unit Elongation I polymerase moves downstream unwinding DNA and elongating RNA 5 93 I DNA strands reform a double helix Termination RNA transcript is released polymerase detaches from RNA produced completed RNA transcript O Distinct differences OOOOO RNA copy not DNA so T9U only short stretch are copied genes are not that many nucleotides when you replicate DNA you replicate both strands transcription only one strand is template the other does not complementary of ONE strand Transcription doesn t need primase or helicase or ligase or single stranded binding proteins 13 Draw a diagram illustrating how DNA from two different sources could be recombined into a single molecule including the tools that would be used and how they function Restriction enzyme cuts sugar phosphate backbones creating sticky ends protect the bacterial cell by cutting up foreign DNA from other organisms or phages DNA fragment from another source is added Base pairing of sticky ends produce various combinations Fragment from different DNA molecule cut by the same restriction enzyme to get same sticky end DNA ligase seals the strands and a recombinant DNA molecule is produced cloning vector original plasmid DNA molecule that can carry foreign DNA into a host cell and replicate there 14 Describe the advantages and potential risks of genetic engineering and transgenic organisms Disadvantages 0 law of unintended consequences something else happened that you did not expect could be ful harm o dangerous strand of something could be created 0 allergic reactions 0 pollen rnix with natural plants and create superweeds Advantages 0 easy not costly fast 0 produces more plantsanimals 15 Explain the basis of genetic testing to a nonscientist complementary antiparallel single stranded binding proteinsholds them apart Ligase connects 3 end DNA ngerprinting template daughter strands Primer RNA chain complementary strands regulatory contains a nucleotide sequence promoter that helps recruit RNA coding region of DNAenable gene expression to be turned up or down lntron exon Promotor RNA polymerase attaches and initiates transcription T Terminator polyribosome 539 339 ends 3OH 5 phosphate group DNA polymerase grabs on template and reads them making complementary semiconservative get original back replication fork bubble Y shaped region on replication DNA molecule where parental strands strands are being unwound and new are being synthesized gel electrophoresis molecular weight marker approximate size ofmolecule run on a e mRNA tRNA rRNA anticodon Transcription translation Spliceosomes releases intron ribosome helicase gyrase relieves strain while unwound by helicase Primase starting poinUprimer antiparallel leading lagging strands PCR polymerase chain reaction simple tandom repeat STR are short stretches of DNA that are repeated several times one a er another in a region of chromosome The exact number of times the sequence is repeated can vary from chromosome to chromosome and can be used to distinguish between individuals Gene region of DNA that can be expressed to produce a nal functional product that is either a polypeptide or an RNA molecule two components coding information for what protein looks like regulatory when info to be used codon triplet code genetic code messenger transfer ribosomal RNA start stop codon A P and E sites mutation Silent nonsense missense frame shi PKU reading frame Plasmid small circular DNA molecules that replicate separately from bacterial GMO genetically modi ed organism restriction enzymes chromosome small number of genes binant DNA DNA that comes om sticky ends stick through hydrogen recom bonds and hgase joins it back together two different sources plasmidamphuman DNA cloning palindromic sequence same forward and Genetically modi ed DNA ngerprinting same backward organism directly modifying DNA vector expression vectortool used to holdtransportcarry molecules of DNA transgenic organism Transcription The RNA polymerase reads the code from the template strand in the 339 to 539 direction and thus produces the mRNA strand in the 539 to 339 direction RNA processing both ends of primary transcript are altered 5 end synthesized rst 57cap modi ed form of G nucleotide added onto 5 end a er transcription of the rst 2040 nucleotides 3 end modi ed before exits 0 50250 A nucleotides forming poly A tail 0 facilities expdrt of mature mRNA frOm nucleus 0 help ribosomes attach to 5 end of mRNA in cytoplasm intervening sequences introns exons expressed by being translated into amino acid sequences RNA polymerase II transcribes both introns and exons from DNA but mRN A that enters cytoplasm only has eXons RNA splicing 0 small nuclear ribonucleotproteins snRNPs recognize splice sites 0 spliceosome like ribosome releases introndegraded and joins together the two exons Importance of Introns single gene can encode for more than one kind of polypeptide 0 rise to two or more diff polypeptides depending on which segments are treated as exons during RNA processing alternative RNA splicing Wobble exible base pair in third codon position Building a Polypeptide 0 three stages close to transcription 0 hydrolysis of guanosine triphosphate GTP energy required for initiatonelongation I 39 eases accuracy and ef ciency of this step Proteins in the ERspeci c locations signal peptide targets protein to the ER 0 signal peptide 20 aminoa cids near or at leading end N terminus recognized by signal recognition particle SRP I escort that brings ribosome to a receptor proteinbuilt into the ERmembrane I signalpeptide removed by enzyme I secreted from the cell into ER lumen Bacteria and Eukaryotes o compartrnental organization bacteria uses streamlined operation simultaneously transcribe and translate at the same 39 o Eukaryote nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing to clone pieces of DNA 0 obtain plasmid and insert DNA from another source foreign DNA recombindant DNA 0 single cell reproduces through repeated cell divisions to form a clone of cells apopulation of genetically identical cells Biology 8e Campbell Chapter 33 Invertebrates MultipleChoice Questions 1 Which cells in a sponge are primarily responsible for trapping and removing food particles from circulating water A choanocytes B mesoglea cells C pore cells porocytes D epidermal cells Answer A Topic Concept 331 Skill KnowledgeComprehension 2 Which of the following is correctly associated with sponges A osculum B body cavity C cnidocytes D spicules made of chitin E muscle cells and nerve cells Answer A Topic Concept 331 Skill KnowledgeComprehension 3 A sponge s structural materials spicules spongin are manufactured by the A pore cells B epidermal cells C choanocytes D zygotes E amoebocytes Answer E Topic Concept 331 Skill KnowledgeComprehension 4 Which of these can be observed in the mesohyl of various undisturbed sponges at one time or another amoebocytes spicules spongin zygotes choanocytes A 1 only Elk WP B l and 2 C l 2 and 3 D l 2 3 and 4 E all ve of these Answer D Topic Concept 331 Skill KnowledgeComprehension 5 Which chemical is synthesized by some sponges and acts as an antibiotic A streptomycin B spongin C calcium carbonate D silica E cribrostatin Answer E Topic Concept 331 Skill KnowledgeComprehension Purity of Water Exiting Osculum Figure 331 6 Which of these factors when used to label the horizontal axis of the graph in Figure 33 1 would account most directly for the shape of the plot A spongin concentration gmunit volume B rate of cribrostatin synthesis moleculesunit time C number of pores per sponge D number of spicules per sponge E number of choanocytes per sponge Answer E Topic Concept 331 Skill SynthesisEvaluation 7 In terms of food capture which sponge cell is most similar to the cnidocyte of a Cnidarian A zygote B choanocyte C gamete D epidermal cell E pore cell Answer B Topic Concepts 331332 Skill KnowledgeComprehension 8 A radially symmetrical animal that has two embryonic tissue layers probably belongs to which phylum A Porifera B Cnidaria C Platyhelminthes D Nematoda E Echinodermata Answer B Topic Concept 332 Skill KnowledgeComprehension 9 Which of the following are characteristics of the phylum Cnidaria a gastrovascular caVity a polyp stage a medusa stage cnidocytes a pseudocoelom A l and 4 B 2 and 3 C 2 3 and 4 D l 2 3 and 4 E all five of these Elk WP Answer D Topic Concept 332 Skill KnowledgeComprehension 10 Which of the following is true of members of the phylum Cnidaria A They are not capable of locomotion because they lack true muscle tissue B They are primarily lter feeders C They have either or both of two body forms mobile polyps and sessile medusae D They may use a gastrovascular caVity as a hydrostatic skeleton E They are the simplest organisms with a complete alimentary canal two openings Answer D Topic Concept 332 Skill KnowledgeComprehension 11 The members of which class of the phylum Cnidaria occur only as polyps A Hydrozoa B Scyphozoa C Anthozoa D Cubozoa E both B and D Answer C Topic Concept 332 Skill KnowledgeComprehension 12 Which class of the phylum Cnidaria includes quotjelliesquot with rounded as opposed to boxlike medusae A Hydrozoa B Scyphozoa C Anthozoa D Cubozoa E Both A and C are referred to as quotjelliesquot Answer B Topic Concept 332 Skill KnowledgeComprehension l3 Corals are most closely related to which group A jellies B freshwater hydras C sea anemones D sponges E bamacles Answer C Topic Concept 332 Skill KnowledgeComprehension 14 Which characteristic is shared by both cnidarians and atworms A dorsoventrally attened bodies B ame bulbs C radial symmetry D a digestive system with a single opening E both A and D Answer D Topic Concepts 332 333 Skill KnowledgeComprehension 15 Generally members of which atworm classes are nonparasitic A Turbellaria B Trematoda C Cestoda D Monogenea E A C and D Answer A Topic Concept 333 Skill KnowledgeComprehension 16 In a small stream you pick up a rock and observe many small attened worms crawling on its undersurface You decide that they belong to the phylum Platyhelminthes To which class do they probably belong A Cestoda B Monogenea C Turbellaria D Trematoda Answer C Topic Concept 333 Skill ApplicationAnalysis 17 What would be the most effective method of reducing the incidence of blood ukes in a human population A Reduce the mosquito population B Reduce the freshwater snail population C Purify all drinking water D Avoid contact with rodent droppings E Carefully wash all raw fruits and vegetables Answer B Topic Concept 333 Skill ApplicationAnalysis 18 The larvae of many common tapeworm species that infect humans are usually found A encysted in freshwater snails B encysted in the muscles of an animal such as a cow or pig C crawling in the abdominal blood vessels of cows and pigs D encysted in the human brain E crawling in the intestines of cows and pigs Answer B Topic Concept 333 Skill KnowledgeComprehension 19 While vacationing in a country that lacks adequate meat inspection a student ate undercooked ground beef Sometime later the student became easily fatigued and lost body 5 weight At about the same time whitish attened rectangular objects full of small white spheres started appearing in his feces Administration of niclosamide cured the problem The student had probably been infected by a A pinworm B hookworm C nematode D tapeworm E proboscis worm Answer D Topic Concept 333 Skill ApplicationAnalysis 20 Which of the following correctly characterizes the phylum Rotifera A a singleopening digestive tract B a pair of mandibles made of chitin C parthenogenic reproduction D inability to persist in environments where they might undergo desiccation E a relatively large size Answer C Topic Concept 333 Skill KnowledgeComprehension 21 Which of the following statements about tapeworm feeding methods is correct A They have complete digestive tracts B They use degenerate mouths to ingest some of their food C As adults they live and feed in the host39s bloodstream D They are autotrophic E They absorb nutrients across their body walls Answer E Topic Concept 333 Skill KnowledgeComprehension 22 While sampling marine plankton in a lab a student encounters large numbers of fertilized eggs The student rears some of the eggs in the laboratory for further study and finds that the blastopore becomes the mouth The embryo develops into a trochophore larva and eventually has a true coelom These eggs probably belonged to an A chordate B echinoderm C mollusc D nematode E arthropod Answer C Topic Concept 333 Skill ApplicationAnalysis 23 A lophophore is used by ectoprocts and brachiopods A for locomotion B at a larval stage C for feeding D for sensory reception E as a skeletal system Answer C Topic Concept 333 Skill KnowledgeComprehension 24 A brachiopod can be distinguished from a bivalve by the presence of A two hinged shells B a digestive system with separate mouth and anus C a lophophore D suspension feeding E a distinct head Answer C Topic Concept 333 Skill KnowledgeComprehension 25 If a lung were to be found in a mollusc where would it be located A mantle cavity B coelom C foot D visceral mass E excurrent siphon Answer A Topic Concept 333 Skill KnowledgeComprehension 26 Which molluscan class includes members that undergo embryonic torsion A chitons B bivalves C gastropods D cephalopods Answer D Topic Concept 333 Skill KnowledgeComprehension 27 A terrestrial mollusc without a shell belongs to which class A chitons B bivalves C gastropods D cephalopods Answer C Topic Concept 333 Skill KnowledgeComprehension 28 Which molluscan class includes marine organisms whose shell consists of eight plates A chitons B bivalves C gastropods D cephalopods Answer A Topic Concept 333 Skill KnowledgeComprehension 29 A radula is present in members of which classes A chitons B bivalves C gastropods D cephalopods Answer C Topic Concept 333 Skill KnowledgeComprehension 30 While snorkeling a student observes an active marine animal that has a series of muscular tentacles bearing suckers associated with its head Segmentation is not observed but a pair of large welldeveloped eyes is evident The student is observing an animal belonging to which class A chitons B bivalves C gastropods D cephalopods Answer B Topic Concept 333 Skill KnowledgeComprehension 31 Which molluscan class includes organisms that are primarily suspension feeders A chitons B bivalves C gastropods D cephalopods Answer B Topic Concept 333 Skill KnowledgeComprehension 32 Of the annelid classes below which have parapodia A Oligochaeta B Polychaeta C Hirudinea leeches D all three of these E two of these Answer B Topic Concept 333 Skill KnowledgeComprehension 33 Many of which of the following annelid classes are parasites A Oligochaeta B Polychaeta C Hirudinea leeches D all three of these E two of these Answer C Topic Concept 333 Skill KnowledgeComprehension 34 Of the annelid classes below which have externally segmented bodies A Oligochaeta B Polychaeta C Hirudinea leeches D all three of these E two ofthese Answer D Topic Concept 333 Skill KnowledgeComprehension 35 Of the annelid classes below which make castings that are agriculturally important A Oligochaeta B Polychaeta C Hirudinea leeches D all three of these E two of these Answer A Topic Concept 333 Skill KnowledgeComprehension 36 The name of which of the following annelid classes indicates the relative number of bristles chaetae its members have A Oligochaeta B Polychaeta C Hirudinea leeches D all three of these E two of these Answer E Topic Concept 333 Skill KnowledgeComprehension 37 Some species of which of the following annelid classes release an anticoagulant that is of medical signi cance A Oligochaeta B Polychaeta C Hirudinea leeches D all three of these E two of these Answer C Topic Concept 333 Skill KnowledgeComprehension 38 Which of the following is found only among annelids A a hydrostatic skeleton B segmentation C a clitellum D a closed circulatory system E a cuticle made of chitin Answer C Topic Concept 333 Skill KnowledgeComprehension 39 Which of the following is a characteristic of nematodes A All species can be characterized either as scavengers or as decomposers B They have only longitudinal muscles C They have atrue coelom D They have a gastrovascular caVity E Many species are diploblastic Answer B Topic Concept 334 Skill KnowledgeComprehension 40 Humans most frequently acquire trichinosis by A having sexual contact with an infected partner B eating undercooked pork C inhaling the eggs of worms D eating undercooked beef E being bitten by tsetse ies Answer B Topic Concept 334 Skill KnowledgeComprehension 41 Which of the following can be used to distinguish a nematode worm from an annelid worm 1 type of body cavity 2 number of muscle layers in the body wall 3 presence of segmentation 4 number of embryonic tissue layers 5 shape of worm in crosssectional view A 2 only B 2 and 3 C l 2 and 3 D l 2 3 and 5 E all five ofthese Answer C Topic Concept 334 Skill KnowledgeComprehension 42 Nematode worms and annelid worms share which of the following features A use of uid in the body cavity as a hydrostatic skeleton B ecdysis C presence of a circulatory system D presence of segmentation E absence of species with parasitic lifestyles Answer A Topic Concept 334 Skill KnowledgeComprehension 43 A student observes a wormlike organism crawling about on dead organic matter Later the organism sheds its outer covering One possibility is that the organism is a larval insect like a maggot On the other hand it might be a member of which phylum and one way to distinguish between the two possibilities is by looking for the presence of A Platyhelminthes a cuticle of chitin B Nematoda an alimentary canal C Annelida a body cavity D Nematoda a circulatory system E Annelida muscle in the body wall Answer D Topic Concept 334 Skill ApplicationAnalysis 44 The hea1tworms that can accumulate within the hearts of dogs and other mammals have a pseudocoelom an alimentary canal and an outer covering that is occasionally shed To which phylum does the heartworm belong A Platyhelminthes B Arthropoda C Nematoda D Acoela E Annelida Answer C Topic Concept 334 Skill ApplicationAnalysis 45 Infection with which parasite might cause excessive elasticity in human skeletal muscles A trichinella worms B tapeworms C copepods D blood ukes E rotifers Answer A Topic Concept 334 Skill KnowledgeComprehension 46 Which of the following are entirely or partly composed of calcium carbonate A spicules of siliceous sponges B coral animals exoskeletons C molluscs39 mantles D insects cuticles E nematodes39 cuticles Answer B Topic Concepts 331334 Skill KnowledgeComprehension 47 Which of the following are characteristics of arthropods l protostome development 2 bilateral symmetry 3 a pseudocoelom 4 three embryonic germ layers 5 a closed circulatory system A l and 2 B 2 and 3 C l 2 and 4 D 2 3 and 5 E 3 4 and 5 Answer C Topic Concept 334 Skill KnowledgeComprehension 48 Among the invertebrate phyla phylum AIthropoda is unique in possessing members that have A a cuticle B a ventral nerve cord C open circulation D wings E segmented bodies Answer D Topic Concept 334 Skill KnowledgeComprehension 49 A shared derived characteristic for members of the arthropod subgroup that includes spiders would be the presence of A chelicerae B an open circulatory system C an exoskeleton D a cuticle E a cephalothoraX Answer A Topic Concept 334 Skill KnowledgeComprehension 50 You nd a small animal with eight legs crawling up your bedroom wall Closer examination will probably reveal that this animal has A antennae B no antennae C chelicerae D A and C E B and C Answer E Topic Concept 334 Skill KnowledgeComprehension 51 While working in your garden you discover a wormlike segmented animal with two pairs of jointed legs per segment The animal is probably a A millipede B caterpillar C centipede D polychaete worm E sow bug Answer A Topic Concept 334 Skill KnowledgeComprehension 52 Which of the following characteristics most likely explains why insects are so successful at dispersing to distant environments A hemocoel B wings C jointed appendages D chewing mandibles E internal fertilization Answer B Topic Concept 334 Skill KnowledgeComprehension 53 What distinguishes complete metamorphosis from incomplete metamorphosis in insects A presence of wings in the adult but not in earlier life stages B presence of sex organs in the adult but not in earlier life stages C radically different appearance between adults and earlier life stages D only A and B E A B and C Answer C Topic Concept 334 Skill KnowledgeComprehension 54 A terrestrial animal species is discovered with the following larval characteristics exoskeleton system of tubes for gas exchange and modi ed segmentation A knowledgeable zoologist should predict that its adults would also feature A eight legs B two pairs of antennae C a sessile lifestyle D an open circulatory system E parapodia Answer D Topic Concept 334 Skill ApplicationAnalysis 55 The possession of two pairs of antennae is a characteristic of A spiders B insects C centipedes D millipedes E crustaceans Answer E Topic Concept 334 Skill KnowledgeComprehension 56 One should expect to nd the quot9 2 patternquot of microtubules in association with the feeding apparatus of which of the following A annelids B coral animals C tapeworms D sponges E terrestrial insects Answer D Topic Concepts 331334 Skill ApplicationAnalysis 57 Which of the following is a characteristic of adult echinoderms A secondary radial symmetry B spiral cleavage C gastrovascular cavity D exoskeleton E lophophore Answer A Topic Concept 335 Skill KnowledgeComprehension 58 Which of the following can extend the stomach through their mouth to feed A class Crinoidea sea lilies and feather stars B class Asteroidea sea stars C class Ophiuroidea brittle stars D class Echinoidea sea urchins and sand dollars E class Holothuroidea sea cucumbers Answer B Topic Concept 335 Skill KnowledgeComprehension 59 Which of the following have distinct central disks and long exible arms A class Crinoidea sea lilies and feather stars B class Asteroidea sea stars C class Ophiuroidea brittle stars D class Echinoidea sea urchins and sand dollars E class Holothuroidea sea cucumbers Answer C Topic Concept 335 Skill KnowledgeComprehension 60 Which of the following are elongated in the oralaboral axis 15 A class Crinoidea sea lilies and feather stars B class Asteroidea sea stars C class Ophiuroidea brittle stars D class Echinoidea sea urchins and sand dollars E class Holothuroidea sea cucumbers Answer E Topic Concept 335 Skill KnowledgeComprehension 61 Which of the following have a mouth that is directed upward A class Crinoidea sea lilies and feather stars B class Asteroidea sea stars C class Ophiuroidea brittle stars D class Echinoidea sea urchins and sand dollars E class Holothuroidea sea cucumbers Answer A Topic Concept 335 Skill KnowledgeComprehension 62 Which of the following can have long movable spines A class Crinoidea sea lilies and feather stars B class Asteroidea sea stars C class Ophiuroidea brittle stars D class Echinoidea sea urchins and sand dollars E class Holothuroidea sea cucumbers Answer D Topic Concept 335 Skill KnowledgeComprehension 63 Which of the following describes echinoderms A They have an endoskeleton of hard calcareous plates B Tube feet provide motility in most species C They have a pseudocoelom D Only A and B are true E A B and C are true Answer D Topic Concept 335 Skill KnowledgeComprehension 64 An organism is able to extend its feeding structures through a hole in its body wall If the organism were a sea star it would extend its A stomach B lophophore C pharynx D mandibles E tentacles Answer A Topic Concept 335 Skill KnowledgeComprehension The following questions refer to the paragraph below A farm pond usually dry during winter has plenty of water and aquatic pond life during the summer One summer Sarah returns to the family farm from college Observing the pond she is fascinated by some sixlegged organisms that can crawl about on submerged surfaces or when disturbed seemingly quotje quot through the water Watching further she is able to conclude that the quotmystery organismsquot are ambush predators and their prey includes everything from insects to small fish and tadpoles 65 From this description one can conclude that the organisms that have caught Sarah s attention are A insects B crustaceans C aquatic spiders D myriapods E eurypterids Answer A Topic Concept 335 Skill ApplicationAnalysis 66 Sarah noticed the presence of many empty exoskeletons attached to emergent vegetation These exoskeletons looked exactly like those of the largest of the quotmystery organismsquot she had seen in the pond They also looked similar to the bodies of the dragon ies that patrolled the surface of the pond If Sarah had learned a lot from her college biology class what should she have concluded about the mysterious pond organisms A They are larval dragon ies destined to undergo incomplete metamorphosis B They are larval dragon ies destined to undergo complete metamorphosis C They are adult dragon ies so old that they can no longer y have fallen into the pond but have not yet drowned D They are adult dragon ies that must like many amphibian species return to water in order to mate Answer A Topic Concept 335 Skill ApplicationAnalysis 67 If the pond organisms are larvae rather than adults Sarah should expect them to have all of the following structures except A antennae B an open circulatory system C an exoskeleton of chitin D complex eyes E sex organs Answer E Topic Concept 335 Skill ApplicationAnalysis 68 Sarah observed that the mystery pond organisms never come up to the ponds surface Ifshe catches one of these organisms and observes closely perhaps dissecting the organism she should find 1 gills 2 spiracles 3 tracheae A 1 only B 3 only C l and 3 D 2 and 3 E l 2 and 3 Answer A Topic Concept 335 Skill ApplicationAnalysis 69 Sarah had learned that ancestral Carboniferous era dragon y species were much larger than extant dragon y species are with wingspans of 70 cm This struck her as odd because she had also learned that one of the things that keeps insects small is their relatively inefficient respiratory system Which two hypotheses might help account for the large size of ancestral dragon ies l Ifthe atmosphere during the Carboniferous had featured a higher oxygen content than the modern atmosphere then tracheae might have been sufficient means for oxygen delivery to the interior tissues 2 Iflarge size was a drawback then the large dragon ies underwent extinction which explains why all extant dragon ies are smaller 3 Ifthe ancestral dragon ies had possessed muscles that permitted effective ventilation of the tracheae then the tracheae might have been sufficient means for oxygen delivery to the interior tissues 4 If ancestral dragon ies existed during greenhouse conditions then they must have survived by decreasing their activity levels no longer capturing prey in ight Thus for them an ineffective respiratory system was sufficient A l and 2 B l and 3 C l and 4 D 2 and 3 E 2 and 4 Answer A Topic Concept 335 Skill SynthesisEvaluation 70 A stalked sessile marine organism has several feathery feeding structures surrounding an opening through which food enters The organism could potentially be a cnidarian a lophophorate a tubedwelling worm a crustacean or an echinoderm Finding which of the following in this organism would allow the greatest certainty of identi cation A the presence of what seems to be radial symmetry B a hard covering made partly of calcium carbonate C a digestive system with mouth and anus separate from each other D a water vascular system E a nervous system Answer D Topic Concepts 332335 Skill ApplicationAnalysis 71 Which of the following animal groups is entirely aquatic A Mollusca B Crustacea C Echinodermata D Arthropoda E Annelida Answer C Topic Concepts 332 7335 Skill KnowledgeComprehension 72 In a tide pool a student encounters an organism with a hard outer covering that contains much calcium carbonate an open circulatory system and gills The organism could potentially be a crab a shrimp a bamacle or a bivalve Which structure below would allow for the most certain identi cation A a mantle B a heart C a body cavity D a lophophore E eyes Answer A Topic Concepts 332 7335 Skill ApplicationAnalysis 73 Protostomes that have an open circulatory system and an exoskeleton of chitin are part of which phylum A Cnidaria B Annelida C Mollusca D Arthropoda E Echinodermata Answer D Topic Concepts 332 7335 Skill KnowledgeComprehension 74 Protostomes with a unique drape of tissue that may secrete a shell are part of which phylum A Cnidaria B Annelida C Mollusca D Arthropoda E Echinodermata Answer C Topic Concepts 332 7335 Skill KnowledgeComprehension 75 Which of the following is a diploblastic phylum of aquatic predators A Cnidaria B Annelida C Mollusca D Arthropoda E Echinodermata Answer A Topic Concepts 3327335 Skill KnowledgeComprehension 76 Deuterostomes that have an endoskeleton are part of which phylum A Cnidaria B Annelida C Mollusca D Arthropoda E Echinodermata Answer E Topic Concepts 3327335 Skill KnowledgeComprehension 77 Protostomes that have a closed circulatory system and obvious segmentation are part of which phylum A Cnidaria B Annelida C Mollusca D Arthropoda E Echinodermata Answer B Topic Concepts 3327335 Skill KnowledgeComprehension The following questions refer to the paragraph below An elementary school science teacher decided to liven up the classroom with a saltwater aquarium Knowing that saltwater aquaria can be quite a hassle the teacher proceeded stepwise First the teacher conditioned the water Next the teacher decided to stock the tank with various marine invertebrates including a polychaete a siliceous sponge several bivalves a shrimp several sea anemones of different types a colonial hydra a few coral species an ectoproct a sea star and several gastropod varieties Lastly some vertebratesia parrotf1sh and a clownfishiwere added She arranged for daily feedings of copepods and feeder fish 78 One day little Tommy a student in an undersupervised class of 40 fth graders got the urge to pet Nemo the clown sh who was swimming among the waving petals of a pretty underwater quot owerquot that had a big hole in the midst of the petals Tommy giggled upon finding that these petals were sticky feeling A few hours later Tommy was in the nurse s office with nausea and cramps Microscopic examination of his fingers would probably have revealed the presence of A teeth marks B spines C spicules D nematocysts E a radula Answer D Topic Concepts 3327335 Skill ApplicationAnalysis 79 Parrotflsh have mouths adapted to scrape algae off of coral and can even munch on coral The aquarium s corals rapidly dwindled in their place were shards of A chitin B calcium carbonate C silica D bone E chitin impregnated with calcium carbonate Answer B Topic Concepts 3327335 Skill ApplicationAnalysis 80 The species in the aquarium that possess true bilateral symmetry include the l sponges 2 molluscs 3 echinoderm 4 sea anemones 5 B l and 4 C2and5 D 2 3 and5 E 2 34 and5 Answer C Topic Concepts 3327335 Skill ApplicationAnalysis 81 If the teacher wanted to show the students what a lophophore is and how it works the teacher would point out a feeding A hydra B sponge C bivalve D gastropod E ectoproct Answer E Topic Concepts 3327335 Skill ApplicationAnalysis 82 The bivalves started to die one by one only the undamaged shells remained To keep the remaining bilvalves alive the teacher would have had to remove the A sea anemones B sea star C gastropods D ectoprocts E parrotf1sh Answer B Topic Concepts 3327335 Skill ApplicationAnalysis 83 If the teacher had used a dissecting microscope to examine the outer surfaces of the empty bivalve shells the teacher would probably have seen marks that had been left by A jaws B nematocysts C tube feet D a lophophore E a madreporite Answer C Topic Concepts 3327335 Skill ApplicationAnalysis 84 The teacher was unaware of the difference between suspension feeding and predation The teacher thought that by providing live copepods 2 mm long and feeder fish 2 cm long the dietary needs of all of the organisms would be satis ed Consequently which two organisms 22 would have been among the rst to starve to death assuming they lack photosynthetic endosymbionts l sponges 2 coral animals 3 bivalves 4 sea stars 5 shrimp A l and 2 B l and 3 C 2 and 5 D 3 and 4 E 4 and 5 Answer B Topic Concepts 3327335 Skill ApplicationAnalysis 85 If the teacher had wanted to demonstrate that some invertebrates possess a closed circulatory system the teacher should have removed and dissected a A mollusc B sea star C shrimp D polychaete E parrot sh Answer D Topic Concepts 332335 Skill ApplicationAnalysis 86 Had the teacher wanted to point out organisms that belong to the most successful animal phylum the teacher should have chosen the l bivalves 2 sea anemones 3 shrimp 4 polychaete 5 copepods A 1 only B 4 only C 3 and 5 D 4 and 5 E l 2 and 3 Answer C Topic Concepts 332335 Skill ApplicationAnalysis 87 The clown sh readily swims among the tentacles of the sea anemones the parrot sh avoids them One hypothesis for the clown sh39s apparent immunity is that these sh slowly build a 23 tolerance to the sea anemone39s toxin A second hypothesis is that a chemical in the mucus that coats the clown sh prevents the nematocysts from being triggered Which of the following graphs supports the rst but not the second of these hypotheses T he clown sh which had never before been in the presence of a sea anemone and sea anemones were introduced to the same aquarium at Time 0 A Percenl 0t lime clownlish spends amon sea anemone tentacles Time B Percem of llme Iquot clownlish spends x among 555 z anemone tentacles 11 Time C Percent of me clown sh spends among sea anemane tentacles D Percent of me clown sh spends amen sea anemane tentacles Time Answer B Topic Concepts 332 7335 Skill SynthesisEvaluation 88 The clown sh readily swims among the tentacles of the sea anemones the parrot sh avoids them One hypothesis for the clown sh39s apparent immunity is that they slowly build a tolerance 24 to the sea anemone39s toxin A second hypothesis is that a chemical in the mucus that coats the clown sh prevents the nematocysts from being triggered Which of these ndings would lend the greatest support to the second hypothesis Upon close examination clown sh maneuverability is so precise as to allow it to avoid contacting any tentacles B Clown shes can eat the dead tentacles of the sea anemones C Clown shes are immune to the toxins of not just one but many species of sea anemone D Clown sh mucus contains a chemical very similar to one found in the trigger mechanism of sea anemone nematocysts Answer D Topic Concepts 332 7335 Skill SynthesisEvaluation 89 The clown sh readily swims among the tentacles of the sea anemones the parrot sh avoids them One hypothesis for the clown sh39s apparent immunity is that they slowly build a tolerance to the sea anemone39s toxin A second hypothesis is that a chemical in the mucus that coats the clown sh prevents the nematocysts from being triggered Which of the following graphs supports the second but not the rst of these hypotheses A tenlacle after contact wilh iile Parrothsh Clowntish Nematocvsts per mil surface area of tentacle after contact will sh Parromsh Clownftsh o tentacle after contact will fish Parrottlsh Clownftsh D mber of nunrdischarged Nematucysts pm unl surface area 0 tentacle ailev Contact wilh lish Payrollish Clown sh Answer C Topic Concept 332 7335 Skill SynthesisEvaluation 90 The clown sh and parrot sh died on the same day Autopsies revealed the presence of many small atworms using tiny suckers to attach to the sh gills Most likely these worms were members of which phylum and which class A Annelida Hirudinea B Annelida Polychaetae C Platyhelminthes Cestoda D Platyhelminthes Monogenea E Platyhelminthes Turbellaria Answer D Topic Concepts 332 7335 Skill ApplicationAnalysis 91 If the worms discovered during the autopsies have all features characteristic of their phylum dissection of the worms should reveal the presence of 4 a gastrovascular cavity 5 the acoelomate condition A 5 only B 1 and 2 C 4 and 5 D 1 2 and 3 E 3 4 and 5 Answer C Topic Concepts 332 7335 Skill ApplicationAnalysis 92 The teacher and class were especially saddened when the colonial hydrozoan died They had watched it carefully and the unfortunate creature never even got to produce offspring by budding Yet everyone was elated when Tommy now recovered noticed a small colonial hydrozoan growing in a part of the tank far from the location of the original colony The teacher who proclaimed a miracle was apparently unaware that these hydrozoans exhibit A spontaneous generation B abiogenesis C alternation of generations D ecdysis E a medusa stage Answer E Topic Concepts 332 7335 Skill ApplicationAnalysis SelfQuiz Questions 1 Which two main clades branch from the most recent common ancestor of the eumetazoans A Calcarea and Silicea B Lophotrochozoa and Ecdysozoa C Cnidaria and Bilateria D Rotifera and Deuterostomia E Deuterostomia and Bilateria Answer C 2 A land snail a clam and an octopus all share A a mantle B a radula C gills D embryonic torsion E distinct cephalization Answer A 3 Which phylum is characterized by animals that have a segmented body A Cnidaria B Platyhelminthes C Silicea D Arthropoda E Mollusca Answer D 4 Which of the following characteristics is probably most responsible for the great diversi cation of insects on land A segmentation B antennae C eyes D bilateral symmetry E exoskeleton Answer E 5 The water vascular system of echinoderms 391 s N m a 5 e D m E O o N 1 o 2 Replication Cell Ionizing Errors Metabolism Radiation UV Light Chemicals DNA repair Apoptosis Gene Cell Expression Division Mutation is a permanent change to DNA Apoptosis CELL SUICIDE cell eats itseli What are mutants DNA intercalating agent red Mutation Most mutations occur when DNA replicated 3 T0335 iACGGCT 5 5 AGACTGCCGA 3 WRO Not all mutations are bad What is a gene i Regulatory I i Coding I DNA Transcription RNA Polymerase Promoter marks the stat of a gene messenger RNA mRNA5 Transcription Similar to DNA replication but different Template antisense Strand 39 I I I I I l I I I RNA Transcript TAI TG TAGT GG GTT G Nontemplate Sense Strand A work in progress Initial RNA produced is un nished 5 Introns Introns 3 IMWI W EXOII 1 Exon 2 Exon 3 5 Cap E1 E2 E3 lPolyA tail 39AAAA How is processing helpful Gena Domain 3 Domain 2 Domain 1 Polypeptide Pyruvate ase Regulation Substrate binding ADP binding Domains tend to fold separately Different domains can be combined to make new proteins 9 30 of human genes can be spliced in different ways IgM antibody gene 1 2 3 4 5 6 7 8 ll D l D l l Recognize Interact Insert into pathogens with other membrane proteins recruit other proteins or cells to destroy pathogens when a cell is attached Reading the code tRNA quot 0 I in I t NA quotI d l v I I I I E J i I I K anticodon ACG mRNA 539E 3r codons Translation quotU3 V quot 3711 115 32 ltf0af 439 I I I L IIIillill aoilalIilllatllllluigcllctib I tlallbiatiullSWf 12 Triplet code Codon Table Second Base U C A G UUU Phe F UCU UAU UGU U UUC UCC 8 MS UAC Tyrm UGC CySC C UUA Leu L UCA e UAA UGA A UUG UCG UAG UGG Trp W G CUU CCU CAU His H CGU U CUC CCC CAC CGC C 1 CUA LCML CCA Pro P CAA Gm Q CGA Argm A Di a CUG CCG CAG CGG G 39 AUU ACU AAU AGU U CL 8 AUC 1161 ACC AAC AS N AGC Se C 5 AUA ACA Thr T AAA AGA A 3 AUG Met M ACG AAG Lys K AGG Arg R G 0 GUU GCU GAU Asp D GGU U GUC GCC GAC GGC C GUA V3107 GCA AMA GAA G1 E GGA Gly G A GUG GCG GAG 1 GGG G H This RNA sequence was transcribed from a gene How many amino acids does this mRNA code for 5 GCGAUGCCUCAUCGAUAACCG 3 csAdaksjde asdaisdf Raise your hand if you can read thisaksdjfjasdkjaskklasDjfkkjajdin dlskj Need punctuation to make the correct protein Start Stop Bases in DNARNA form triplet code Codon Table Second Base U C A Phe F A Tyr Y Leu L His H Leu L G111 Q 116 1 AS N quot11 p u quot3 m F U Q m D 99W PJWL Lys K Asp D Glu This RNA sequence was isolated from the beginning of a gene How many amino acids does this fragment probably code for 5 GCGAUGCCUCAUCGAUAACCG 3 4 Typical 5 UAAcchGhAGIACUirUchUUFCUtIUG 3 Strain 1 5 UAACCAUijGGhCUAUCAUUGCUUUG 3 How is the protein produced by the Strain 1 different from a typical protein Missense or Substitution There are three additional strains that have different mutations Typical 5 UAACCAUGAAGACUAUCAUUGCUpUGl 3 Strain 2 5 UAACCAUGAAGACUAUCAUUGCUPAGI 3 This mutation is called a nonsense because instead of the mutation just changing the amino acid it inserts a stop protein Typical 5 UAACCAUGAAGACUAUCAUUGCUUUG 3 Strain 3 5 UAACCAUGAAGACCAUCAUUGCUUUG 3 20 Typical 5 UAACCAUGAAGACUAUCAUUGCUUUG 3 Strain 4 5 UAACCAUGAAGACAUCAUUGCUUUGA 3 21 ab c d wequot 3 ill i l The RNA sequence above contains the complete coding region for a small protein Imagine you have found five different individuals each with a different mutation in this gene These five mutations ae are indicated above by the red arrows Which ofthese five mutations is MOST likely to have a significant impact on the function ofthe protein that is produced 22 Challenge Questions The DNA fragment below contains the complete coding region for a gene What is the amino acid sequence of the protein 37 AGCCGGCTCTTACTTTTGATAATAACGAGAAAGAATTTAAGAAACA 57 57 TCGGCCGAGAATGAAAACTATTATTGCTCTTTCTTAAATTCTTTGT 37 6 Cells ProkagoticEukagotic only bacteria and Archea are made of prokaryotic cells protists fungi animals and plants are euk all cells have in common 1 plasma membrane cytosol jellylike is contained there as well as organelles and other components 2 chromosomes carry genes in the form of DNA 3 ribosomes tiny complexes that make proteins according to instructions from genes in a euk most of the DNA is in the nucleus which is bound by a double membrane in a prok DNA is concentrated to a region but not enclosed by a membrane region is the nucleoid interior here is called cytoplasm in a euk organelles are suspended in cytosol in the cytoplasm presence of a true nucleus is the diff between proldeuk euks are much larger size relates to fn metabolic requirements impose upper limits on a size that s practical for the cell plasma membrane selective barrier allows sufficient passage of Oz nutrients and waste for each unit of surface area on the membrane a limited amount of something can cross per second ratio of surface area to volume as a cell gets bigger its V increases proportionally more than surface area a smaller object has a larger ratio of surface area to V need for surface area is large to accommodate V explains why cells are so small larger organisms don t have bigger cells they just have more a high ratio of surface area to V is important proks and euks have in common ribosomes plasma membrane and cytoplasm Eukaryotic also have internal membranes that divide cell into compartments that provide different local environments to facilitate specific metabolic fns allows for incompatible processes to go on simultaneously plasma and organelle membranes also directly participate in cell metabolism because many enzymes are built right into membranes each membrane has a unique composition of lipids and proteins suited to that membranes fn in euks the first step in protein synthesis is transferring information from DNA to mRNA transcription which is the rst of the two main steps of protein synthesis Eukaryotic RibosNucleus ribosomes and nucleus are cell components involved in genetic control of the cell nucleus houses most cell DNA 139ib0s use into from DNA to make proteins nucleus is generally the biggest organelle nuclear envelope encloses the nucleus separating contents from the cytoplasm envelope is a double membrane each membrane composed of a lipid bilayer perforated by pores at everywhere but the pores the nuclear side of the envelope is lined by the nuclear lamina netlike array of protein laments maintains shape of nucleus by supporting the nuclear envelope in the nucleus DNA is organized into chromosomes carry genetic info chromosomes are made of chromatin chr0matin complex of protiens and DNA nucleolus in the nondividing nucleus adj oins part of the chromatin ribosomal subunits are manufactured by nucleolus has chromosomal regions with ribosomal RNA rRNA genes and ribosomal proteins that are imported from the cytoplasm site of ribosomal subunit assembly from DNA instructions a large and small subunit exit into the cytoplasm where they assemble into a ribosome the nucleus directs protein synthesis by making mRNA based on instructions provided by DNA mRNA is then transported to the cytoplasm through nuclear pores once mRNA reaches the cytoplasm ribos translate mRNA s genetic message into the primary structure of a speci c polypeptide Nucleus and Ribosomes nucleus houses most of the cells DNA in chromosomes chromosomes only appear as the cell is about to divide 139ib0s0mes use info from DNA to make proteins nucleus has most of the genes some are in mitochondria and chloroplasts nuclear envelope separates nuclear contents from the cytoplasm double lipid bilayer encloses genetic material in eukaryotic cells pe1forated by pores complex lines each pore and regulates entryexit of most proteins and RNAs but also large complexes of macromolecules the nuclear membrane is impermeable to most things but the nuclear pores allow passage of small molecules and ions nuclear membrane encloses the nucleus and separates cell material from the cytoplasm ba1rier to prevent macromolecules from diffusing between the nucleoplasm and the cytoplasm each membrane of the nuclear envelope has a lipid bilayer outer is continuous with the RER and has ribos attached inner has several inner nuclear membrane proteins membranes are connected at pore sites nuclear side of the envelope except at the pores is lined by the nuclear lamina netlike arrangement of protein filaments maintains shape of nucleus by supporting nuclear envelope evidence also suggests a nuclear matrix framework of bers extending throughout the interior in the nucleus DNA is organized into chromosomes carry genetic info each chromosome is made up of chromatin complex of proteins and DNA nucleolus structure within the nondividing nucleus adjoins part of the chromatin in the nucleolus ribosomal RNA rRNA is synthesized proteins taken in from the cytoplasm are put together with rRNA into large and small ribosomal subunits which exist in the nucleus through the nuclear pores to the cytoplasm when it gets back to the cytoplasm a large and small unit can assemble into a ribosome there can be 2 or more nucleoli it depends functional connection between nucleolus nuclear pores and nuclear membrane is subunits of ribosomes are assembled in the nucleolus and pass through the nuclear membrane via nuclear pores ex a dish of animal cells was grown in the presence of radioactive phosphorus The phosphorus largely ended up in nucleotides inside actively growing animal cells In which structure would you expect the majority of radioactive phosphorus to accumulate the nucleus because it needs large numbers of nucleotides to perform its fns ex consider a protein that is made in the ER You observe that when protein synthesis is completed the protein is in the ER membrane Where else would it be found embedded in the plasma membrane fning in the transport of molecules into the cell Ribosomes complexes of rRNA that carry out protein synthesis cells active in protein synthesis also have prominent nucleoli ribosomes build proteins in 2 cytoplasm locations complexes made of rRNA and protein work in 2 places 1 free ribosomes suspended in the cytosol most protein by free ribos fn within the cytosol ex enzymes that catalyze rst steps of sugar breakdown most proteins that function in the cytosol such as actin or in the nucleus such as DNA polymerase are synthesized by free ribosomes 2 bound ribosomes attaches to the outside of the ER or nuclear envelope usually make proteins a destined for insertion into membranes b for packaging within certain organelles such as lysosomes c export or secretion ex lysosomal enzyme insulin ER protein are synthesized by bound ribosomes ex what is most likely to be involved in the process of producing proteins for a chloro or mito free cytoplasmic ribos at any time free ribosomes are suspended in the cytosol bound ribosomes are attached to the outside of the ER or nuclear envelope bound and free ribos are identical they can alternate between the 2 roles most proteins made by free ribos function within the cytosol ex enzymes that catalyze the first steps in sugar breakdown bound membranes generally make proteins for insertion into membrane for packaging with certain organelles ex with lysosomes or for export secretion cells that specialize in secretion like in the pancreas which secrete digestive enzymes have high proportions of bound ribos as they are being synthesized secretory proteins enter the lumen of the endoplasmic reticulum from the ER vesicles transport these proteins to the Golgi where they are sequentially modi ed and concentrated in a cistotrans direction secretory vesicles bud from the Golgi and move along cytoskeletal laments to eventually fuse with the plasma membrane secreting their protein cargo Endomembrane System membranes of this system are related either by physical continuity or by transfer of membrane segments as vesicles sacs made of membrane segment thickness molecular composition and types of rxns in a given membrane vary and can be modi ed several times end0 system nuclear envelope golgi apparatus lysosomes various kinds of vacuoles and plasma membrane regulates protein traf c and performs metabolic fns in the cell plasma membrane isn t really in the right place but is similar enough to be included factors that limitaffect cell size all raw materials needed for reaction have to enter through the cell membrane each unit of volume requires a speci c amount of surface area to supply it when the SNV ratio becomes so small that the SA cannot import enough raw material the cell will not grow any larger Endoplasmic Reticulum eXtensive network or membranes accounts for half the total membrane in eukaryotic cells has a network of membranous tubules and sacs called cistemae reservoir for liquid ER membrane separates the inside area the ER lumen cavity or cistemal space from cytosol ER membrane is continuous with the nuclear envelope so space between 2 membranes of the envelope is continuous with the lumen of the ER 2 distinct but connected regions smooth and rough Smooth Endoplasmic Reticulum outer surface lacks ribosomes functions in many metabolic processes such as synthesis of lipids metabolism of carbs and detox of drugspoisons enzymes of the smooth ER are important in synthesis of lipids including oils phospholipids and steroids enzymes involved in detox are typically in the liver involves adding OH groups to drug molecules to make it more soluble so the body can ush it out of the system also stores Ca2 ions in muscle cells special smooth ER pushes calcium ions from the cytosol to the ER lumen responsible for the process stimulation 9 contraction of a muscle cell Rougl1 Endoplasmic Reticulum many types of cells secrete proteins by ribos attached to the rough ER as a polypeptide chain goes from a bound ribo it s threaded into the ER lumen through a pore formed by a protein complex in the ER membrane as the protein enters the ER lumen it folds into its proper shape glyc0pr0teins proteins with carbohydrates covalently bonded to them secretory protein manufactures cellular membranes by adding membrane proteins and phospholipids to its own membrane after secretory proteins are formed ER membrane keeps them separate from proteins produced by free ribosomes depart from ER wrapped in membranes of vesicles bud like bubbles from a different region called the transitional ER transp0rt vesicles go from one part of the cell to another rough ER is also a membrane factory grows in one place by adding membrane proteins and phospholipids to its own membrane polypeptides that are going to be membrane proteins come from ribosomes are inserted into the ER membrane and anchored by hydrophobic portions rough ER can also make its own phospholipids enzymes built into the ER membrane put together phospholipids from precursors in cytosol ER membrane is transferred in the form of transport vesicles to other components to the endo system Golgi Apparatus after leaving the ER many transport vesicles go to the golgi center of manufacturing sorting and shipping products of the ER like proteins are modified stored and sent to other locations golgi is very extensive in cells specialized for secretion consists of at membranous sacs cistemae cell may have hundreds of them membrane of the cistemae in a stack separates internal space from cytosol vesicles near the golgi are used in the transfer of stuff between parts of the golgi and other functions a stack has structural polarity 2 poles are the cis face and trans face cis is usually near the ER trans vesicles move stuff between the golgi and ER vesicle buds from the ER and adds its membrane and contents of its lumen to cis face by fusing with the golgi trans face gives rise to vesicles pinch off and travel products of ER are modi ed in their transit from the cis to trans region golgi nishes stuff but also makes macromolecules many secreted polysaccs are golgi products including pectin nonproteingolgi products depart from the trans face inside transport vesicles that eventually fuse with the plasma membrane golgi manufactures and refines in stages with different cistemae containing unique groups of enzymes cistemal maturation model suggests the cistemae of the golgi progress forward from the cis to the trans face of the golgi carry and modify cargo as they move before a golgi stack releases product from the trans face it sorts and targets them molecular ID tags like phosphate groups added to golgi products are like ZIP codes Lysosomes digestive compartments membranes sac of hydrolytic enzymes an animal uses to digest macromolecules enzymes work best in acidic environments of lysosomes if a lysosome breaks open enzymes aren t very active because cytosol has a neutral pH excessive leaks can destroy the cell hydrolytic enzymes and lysosomal membrane are made by the RER and transported to the golgi some proteins come by budding from the trans face of the golgi proteins in the inner surface of the lysosomal membrane and digestive enzymes are then spared from destruction because they have 3D shapes protecting vulnerable bonds from the enzymatic attack lysosomes carry out intracellular digestion pref1X lyso means decomposition phag0cyt0sis amoebas and other protists eat by engulfing smaller organismsfood particles a food vacuole forms this way and then fuses with a lysosome lysosomal enzymes digest the food digestion products simple sugars amino acids and other monomers pass into cytosol and become cell nutrients some human cells can do phagocytosis too ex macrophages a type of white blood cell lysosomes also use hydrolytic enzymes to recycle cell material aut0phagy damaged organelle or small amount of cytosol surrounded by a double membrane of unknown origin and lysosome fuses with outer membrane of this vesicle lysosomal enzymes break up material and organic monomers are returned to cytosol membrane around a lysosome allows the digestive enzymes to work at the 45 pH they require pH within a lysosome is about 5 so all the enzymes in one work best in an acidic environment Vacuoles maintenance compartments membrane bound food vacs formed by phagocytosis contractile vacuoles found in many protists pump H20 out of the cell maintains concentrations of ions and molecules plants and fungi don t have lysosomes so vacuoles carry out hydrolysis central vacuole in mature plant cells smaller vacs fuse together solution in it is called cell sap which is different from cytoplasm regulates cytoplasm composition creates internal pressure and stores cell compounds many plant cells use vacuoles as disposal for metabolic by products some contain pigment some contain compounds poisonous to predators major role in growth of plant cells enlarge as vacuoles absorb H20 lets cell grow with little investment into new cytoplasm cytosol occupies athin layer between central vacuole and plasma membrane ratio of plasma membrane surface to cytosolic surface is large Mitochondria amp Chloroplasts change energy from one form to another organisms transform the energy they get from their surroundings done by the mito and chloros mit0ch0nd139ia site of cell respiration cell respiration process that generates ATP by extracting energy from sugars fats and other fuels with the help of oxygen in euks but not proks chlor0plasts found in plants and algae sites of photosynthesis convert solar energy to chemical energy by absorbing sunlight and using it to direct construction of organic compounds ex39 sugars from C02 and H 20 both are enclosed by membranes but not part of the endomembrane system membrane proteins of the mito and chloros are made by free ribos in the cytosol and ribos contained within the organelles themselves they also contain a small amount of DNA with a program of the construction of proteins made by the organelles ribos mitos and chloros reproduce and grow within the cell per0xis0me oxidative organelle also imports proteins from the cytosol Mitochondria in almost all euks including plant animal fungi and most protists some cells have one big mito but it is more common to have 100 s or even 1000 s number correlates with the cells level of metabolic activity has 2 membranes each a phospholipid with a unique collection of embedded proteins ribosomes in the mito are in the mito matrix not the intermembrane outer membrane is smooth inner membrane is complicates has foldings called cristae inner membrane divides the mitochondria into 2 compartments 1 narrow region dividing the inner and outer 2 mitochondrial matrix enclosed by inner membrane contains many enzymes also has mitochondrial DNA and ribos enzymes here catalyze some steps in cell respiration cristae has lots of folds giving the inner membrane a high surface area increased surface area increased productivity of cell respiration Chloroplasts specialized member of a family of related plant organelles called plastids contain chlorophyll a green pigment also contains enzymes and other things that fn in photosynthetically producing sugar contents separated off from the cytosol by an envelope envelope made up of 2 membranes separated by a very narrow intermembrane space thylak0ids inside chloros membrane system attened interconnected sacs surrounded by a uid called stroma granum uid outside thylakoids contains chloro DNA and ribos and enzymes membranes of a choloro divide it into 1 intermembrane system 2 stroma 3 thylakoid space chloros change shape grow and sometimes split in 2 Peroxisomes fn in oxidation lack membrane as part of its structure contain enzymes that transfer H from various things to O2 produce H202 some peros use 0 to break fatty acids down into molecules that can be transported to the mito where they can be used for cell resp peros in the liver detox alcohol the H202 it forms is toxic but enzymes that break it down are in the same area away from other cellular components that could be damaged allowing incompatible processes to occur gly0xys0mes special peros in fat storing tissues of plant seeds contain enzymes that start conversion of fatty acids to sugar peros do not bud from the endomembrane system unlike lysosomes grow larger by incorporating proteins in the cytosol lipids made in the ER and lipids synthesized in itself may split in 2 when they reach a certain size do not contain DNA Cytoskeleton network of fibers extending throughout the cytoplasm dynamic network of fibers that can be quickly dismantled and reassembled to change cell shape and the position of cell components major role in organizing structure and activity of the cell gives mechanical support and maintains shape important for animal cells because they lack cell walls cell motility movement changes in all location and limited movements in parts of cells usually requires interaction of cytoskeleton with motor proteins m0t0r proteins attach to receptors on cell walls produce movement of cell or parts of the cell cytoskeleton and motor proteins work together with the plasma membrane to allow movement along bers along the cell they bend cilia and agella by gripping microtubules within them and sliding the tubules against each other cilia and agella move due to the interaction of the cytoskeleton with motor proteins vesicles that bud off from the ER travel to the golgi along cytoskeletal tracks manipulates plasma membrane to form food vacuoles or other phagocytic vesicles streaming of cytoplasm that circulates materials within a large plant cell is another type of cell movement brought on by the cytoskeleton also involved in regulating biochemical activities in the cell in response to mechanical stimulation signal transmission Components Microtubules hollow tubes 25nm wall consists of 13 columns of tubulin molecules protein subunit is tubulin a dimer made of or tubulin and Btubulin maintain shape fns in cell motility but are the only cytoskeletal bers not associated with intracellular movement or whole cell locomotion they also guide organelle movement and separate chromosomes track that proteins move along microtubs grow out from a centrosome centr0s0me near the nucleus considered a microtub organizing center where protein dimers assemble into microtubules compression resistant in the centrosome there is a pair of centrioles centrioles are composed of 9 sets of triplet microtubs arranged in a ring only in animal cells before a cell divides the centrioles replicate specialized arrangement of microtubules make agella and cilia beat which are extensions from the cell that contain microtubs lots of cilia on surface of a cell one or few agella per cell cilia and agella differ in their beating patterns agella wave around and generate power perpendicular to the cilia aXis cilia might also act as a signal receiving antenna for the cell but ones that usually don t move and usually one per cell similarity between cilia and agella both have a core of microtubules sheathed in an extension of the plasma membrane rmltrutubule assembly ufcllla Dr t1agellars anelmred m a eell by abasal budy rbasal budtes and cantrmles arerdentaeal m strueture nther and tn the z eentxal mterntubules nergrlmnng duublet reach enmpnsed ufseveral pnlypeptades rrespunslble fur tlre bendmg mnyements energy fur tlns rfurces exerted by dynem vn1hng39 causethe duubletstu eurye J r r magma Mremdlaments rsulld mds 7nm m drameter ralsu ealled aetan laments because they are bullt 39nm aetan glubulzr pmtern rmltru lzment ls a tynsted duuble enatn nfaetan subumts srde uf an aetan lament Vallest anew lament tn extend as a branch rln ead nfresrstang cumpressmn llke mlcmtubules mtemdlaments heartenslun rpullm fumes rcnnzx nuter eytnplasmte layer ufa eell rhas ennsrsteney uf gel acrnss the membrane ralsu tncrease eell surface area and are rnterlnelred wth thcker laments uf apmtern ealled mynsin ralsu aets as amntnrpmtern racunmyusm aggregates are respunslble fur lnealrzed enntraetanns ufcells rpszln lnpndia cellular extenstnns tempurary mtreal tn pnagneytnsrs farmed by mlcmtub and lzmem struetures uwmg rntn pseudnpndra mltru lzmems laments near tlre eells end rnteraet wnh myusm wlnelr eanses a enntraetann rthepssudupud extendsrtselfuntal tlre anmreassambles rtselfrntn anetwurk lntermedtate Ftlaments named for their diameter between the other two 10nm larger than micro laments smaller than microtubules specialized for bearing tension each type is made of a diff molecule subunit belonging to a family of proteins including keratins more permanent in nature not disassembled like microtubules and micro laments chemical treatments that remove micro laments and microtubules leave a web of intermediate laments that retain its original shape especially important in reinforcing cell shape and x organelles in place nucleus often sits in a cage made of intermediate laments xed in location by branches other intermediate laments line the interior of the nuclear envelope Cell Wall protects maintains shape and prevents excessive uptake of H20 much thicker than plasma membrane made of cellulose bers embedded in other polysaccs and proteins synthesized in the RER and golgi young plant cells secrete a relatively thin and exible wall called the primary cell wall in growing cells cellulose brils are oriented at right angles to direction of cell expansion middle lamella thin layer rich in sticky polysaccs called pectins glues adjacent cells together when the cell matures and stops growing it strengthens its wall some plant cells strengthen their wall by secreting hardening substances into the 1 cell wall other cells add secondary cell wall between the plasma membrane and primary wall often deposited in several layers has a strong and durable matrix plant cell walls are usually perforated by channels between adjacent cells called plasmodesmata Extracellular Matrix main ingredients are glycoproteins secreted by the cells most abundant is collagen forms strong bers outside cells animal cells secrete glycoproteins that form the ECM collagen bers are embedded in a network of proteoglycan complexes proteoglycans are a major component of the ECM it is a ller substance existing between cells in an organism proteoglycan consists of small core protein with carb chains noncovalently attached some cells are attached to the ECM by other ECM glycoproteins ex39 bronectz39n attaches ECM to integrins embedded in the cell membrane bronectin and other ECM glycoproteins bind to the cell surface proteins called integrins integrins are built into the plasma membrane one side binds to the ECM and the other side is associated with micro laments integrins span the membrane and bind on their cytoplasmic side to associated proteins attached to micro laments of the cytoskeleton they are in a position to transmit signals between the ECM and the cytoskeleton by communicating with a cell through integrins the ECM can regulate a cells behavior 1 mechanical signaling involves bronectin integrins and micro laments of the cytoskeleton 2 changes in skeleton may trigger chemical signaling pathways inside the cell 3 leading to changes in a set of proteins being made by the cell 4 changing the cells In Intercellular Junction Plasmodesmata cell walls are perforated with channels called plasmodesmata cytosol passes through plasmodesmata and connects chemical environments of adjacent cells these connections unify most of the plant into one living continuum plasma membranes of adjacent cells line the channel of each plasmodesmata and are continuous macromolecules transported to neighboring cells seem to reach the plasmodesmata by moving along bers of the cytoskeleton Animal Junctions l tight plasma membranes of neighboring cells tightly pressed against each other bound together by speci c proteins form continuous water tight seals around the bells prevent leaks of extracellular uid across a layer of epithelial cells ex39 tight junctions between skin cells make us water tight by preventing leakage between cells in our sweat glands 2 desmosomes primary role is to bind animal cells together aka anchoring junctions increase rigidity fasten cells together like sheets protecting against pulling forces intermediate laments made of sturdy keratin proteins anchor desmosomes in the cytoplasm attach muscle cells to each other in a muscle 3 gap aka communicating junctions provide cytoplasmic channels from one cell to an adjacent cells consist of a membrane proteins that surround a pore through which ions sugars and amino acids and other small molecules may pass ex39 hormone that stimulates one cell often signals adjacent cells through gap junctions most similar to the plasmodesmata necessary for communication between cells in many types of tissues coordinate activities of adjacent animal cells ex39 heart muscle bc it requires rapid signaling and animal embryos if it were not for plasmodesmata the cell walls would essentially imprison the plant s cells making intercellular communication and the distribution of nutrients nearly impossible peptid0glycan polymer that consists of sugars and amino acids forming a mesh like layer outside the plasma membrane of bacteria forming a cell wall end0symbi0nt any organism that lives within the body of cells of another organism it is generally agreed that certain organelles mito and chloro originated as bacterial endosymbionts 7 Membrane Structure and F11 Fluid Mosaic lipids and proteins are staple ingredients of membranes phospholipids are amphipathic are the most abundant lipid in the membrane uid mosaic model uid structure with a mosaic of various proteins embedded in or attached to a double layer of phospholipids cholesterol makes the membrane less uid by restraining phospholipid movement 39 39is 391 Ja r buffer it hinders close backing of phospholipids and lowers T required for a membrane to solidify resists change in membrane uidity that can be caused by changes in T membranes have to be uid to work properly unsaturated phospholipids increase uidity because they have kinks they also move laterally and ip op Membrane Proteins membrane is a collage of diff proteins embedded in the uid matric of the lipid bilayer phospholipids from the main fabric of the membrane but proteins determine most of the membrane fn molecular a1rangement maximizes contact of hydrophilic regions of proteins and phospholipids with H20 in the cytosol and extracellular uids provides hydrophobic parts with an aqueous environment 2 major populations of proteins 1 integral penetrate the hydrophobic core of the lipid bilayer many are trans membrane proteins that span the membrane some extend only part of the way hydrophobic region of an integral protein consists of one or more stretches of amino acids typically coiled in helices 2 peripheral not embedded in the lipid bilayer they are appendages loosely bound to the surface of the membrane often exposed to parts of integral proteins on the cytoplasmic side of the plasma membrane some proteins are attached to the cytoskeleton on the extracellular side certain membrane proteins are attached to the bers of the ECM these attachments combine to give animal cells a stronger framework than the plasma membrane alone can provide fns of membrane proteins 1 transpOIt proteins that span the membrane may provide a hydrophilic channel across the membrane that is selective to a specific solute other proteins shuttle a substance from one side to the other by changing shape 2 enzymatic activity 3 signaling a membrane protein may have a binding site with specific shape that ts a chemical messenger such as a hormone the external messenger signaling molecule may cause a shape change in the protein that relays the message to the inside of the cell usually by binding to a cytoplasmic protein 4 cell cell recognition some glycoproteins serve as ID tags that are speci cally recognized by membrane proteins of other cells 5 intercellular joining membrane proteins of adjacent cells may hook together in various types of junctions such as gap or tight junctions 6 attachment to cytoskeleton and ECM this helps maintain cell shape and stabilizes location of certain membrane proteins proteins that can bind to ECM 39 39 can 139 quot 39 and intracellular changes Carbs in CellCell ability to distinguish one type of neighboring cell from another is crucial eX for sorting cells into tissues and organs cells recognize other cells by binding to surface molecules often to carbs on the membrane membrane carbs are usually short branched chains with fewer than 15 sugar units some are covalently bonded to lipids forming glycolipids glyco indicates presence ofa carb most are bonded to proteins and therefore use glycoproteins the 4 human blood types refer to the variation in the carbs on the surface of red blood cells Sides of Membranes membranes have distinct inside and outside faces the two lipid layers might differ in lipid composition each protein has a directional orientation in the membrane when a vesicle fuses with the plasma membrane the outside layer of the vesicle becomes continuous with the cytoplasmic inner layer of the plasma membrane therefore molecules that start out on the inside face of the ER end up on the outside face of the plasma membrane synthesis of membrane components and their orientation on the resulting membrane 1 synthesis of membrane proteins and lipids in the ER carbs are added to proteins and lipids in the ER carbs are added to proteins making them glycoproteins then the carb portion can be modified 2 within the golgi glycoproteins undergo more carb modification and lipids acquire carbs becoming glycolipids 3 transmembrane proteins membrane glycolipids and secretory proteins are transported in vesicles to the plasma membrane 4 in the plasma membrane vesicles fuse with the membrane releasing secretory proteins from the cell vesicle fusion puts the carbs of membrane glycoproteins and glycolipids on the outside of the plasma membrane asymmetrical arrangement ofproteins lipids and their associated carbs in the A l I I I n and the golgi Selective Permeability essential fn ofthe cells existence is to regulate transport across cellular boundaries steady tra ic in both directions factor quotquot puialil of lipids can dissolve in the bilayer and move down their concentration gradient ex of diffusion 39 39 mu c down its concentration gradient Lipid Bilayer hydrocarbons C01 02 and other nonpolar molecules are hydrophobic and can therefore dissolve in the lipid bilayer ofthe membrane can cross easily without aid L J L39 f 39 r fions and polar molecules purar 4 an pa low quot even H20 crosses slowly through the bil er a charged atom or molecule and its hydration shell have issues crossing the hydrophobic part Transport Proteins r 39 39 r IIIUICLulC these hydrophilic sub stances avoid contact with the bilayer they pass through transport proteins that span the m rane channel protei type oftransport protein that 1s by having a hydrophilic channel that some molecules or ions use as a tunnel through the membrane provide continuous path across a membrane allow water molecules and small ions to ow quickly across the membrane aquaporins type of channel protein without aquapor39 s only a small fraction of H20 molecules could di use through the ea of a membrane in a given secon channel protein brings a large increase in rate y channel transported pmzem V p solute carrier protein type of 39 shape such that they can be shuttled across the membrane undergo a change in shape to transport solutes across the membrane transport primarily small polar organic molecules a transport protein is specific to the substance it moves 4 it 39 tnnsporled Protein a so me both channels and carriers are integral membrane proteins transport solutes down a concentration of electrochemical gradient protect polar or charged solutes from coming into contact with the hydrophobic interior of the lipid bilayer provide a hydrophilic path across the membrane involved in facilitated dif ision Passive Transport passive transport is dif ision of a substance across a membrane With no energy investment molecules have a type of energy called thermal motion heat diffusion movement of molecules of any substance so that they spread out evenly into the available space movement of particles down their concentration gradient result of thermal motion in the absence of other forces a substance Will diffuse from Where it is more concentrated to Where it is less concentrated or to Where it is less concentrate concentration gradient region along Which the density ofa chemical substance decreases diffusion is a spontaneous process requires no energy inpu each substance dif ises down its own concentration gradient it is unaffected by concentration differences of other substances diffusion of a substance across a biological membrane is called passive transport because they cell does not have to expend energy for it to happen concentration gradient represents potential energy Osmosis and H20 Balance in Cells Wo Walls usmo 39 diffusion oszO along a selectively permeable membrane passive transport of Water tonicity ability of a soln to loose or gain HzO depends on concentration of solutes that can t cross themembrane relative to in the cell if there is a higher concentration of nonpenetrating solutes in surrounding soln HZO Will tend to leave the cell ifthere is a higher concentration ofnonpenetrating solutes in the cell HZO Will come in to the cell E m nonpenetrating refers to Whether or not they can cross the membrane if a cell doesn t have a Wall like an animal cell there is no net movement oszO across the plasma membrane water ows across the membrane but at the same rate in both directions in an isotonic environment volume is stab e hypertonic hypertonic soln has a solute concentration higher thanthe cell cell looses HZO to environment shrivels and dies hypotonic lesser solute concentration than the other solution at 39 ow into the cell causing it to swell and possibly burst animals and other organisms without cell walls that live in hyper or hypo tonic solutions will have special adaptations for osmoregulation control of water balance zO Balance in Cells w Walls turgid very rm healthy state for most plant cells if a plants cells and surrounding are isotonic there s no reason for water cells become accid when placed in a hypertonic soln the cell loses HZO to its surroundings an 39 as the cell shiives its plasma membrane pulls away from the w called plasmolysis causes the plant to wilt and can lead to death Osmosis water movement across membrane lk flow viz integral pmlem AQUEDUYEquot r a water dl uslan a AM 2 hydraphillc rye hydru E pnomc quot39139 L 4 cell wall Slde i W phosphollpld bllayer if 3 3 gt5 cylnsolic side A Facilitated Diffusion phenomenon of polar molecules and ions that are impeded by the lipid bilayer diffusing passively with help om transport proteins most transport proteins are speci c and will selectively choose what to transport recall 2 types of transport proteins 1 channel provide corridors that allow a speci c molecule or ion to cross a membrane hydrophilic passage provided by these proteins allow HZO molecules or ions to ow quickly ex39 ion channels pore formingproteins that help establish a small voltage gradient across the plasma membrane by allowinglow ofions down their electrochemical gradient many are gated and respond to electrical or chemical stimulus if chemical the stimulus is something other than the thing being spo d 2 carrier undergo a slight change in shape refers to when its openclosed binding site across the membrane shape changes can be triggered by binding and release of transport proteins despite the help of transport proteins facilitated diffusion is still considered passive because the solute is moving down its concentration gradient does not alter the direction of transpo provides ef cient passage through the membrane dissolved 02 diffuses into a cell across the plasma membrane as long as cell respimtion consumes 02 as it enters diffusion into the cell continues because the concentmtion gradient favors movement in that direction ex What Would increase the rate of sucrose transport into the cell decreasing extracellular pH Active Transport o push a solute across amembrane against its gradient the cell expends energy Work is rq transport proteins that move solutes against mther than With a concentration gradient are all carrier proteins makes sense because then channel proteins are open they only allow solutes to ow down their concentration gmdient instead of picking them up and transporting them against their gmdient active transport allows a cell to maintain internal concentrations of small solutes different from centrations in its environment ex39 relative to rurrpoundingr an animal cell has a higher concentration ofK and lower Na p m membrane maintains this like other types of Work in a cell ATP supplies the energy for most active tmnsport one Way it does is by transferring its terminal phosphate group directly to the tmnsport protein 39 uces the protein to change its shape such that a solute bound to the protein can move across the membrane the NaK pump Works this Way exchanges Na r for ICr across the plasma membrane Actlre trallsoun bv the Sudlllmrpulasslllm pthhptellerhs thls cycle 0 Three lte leths hunt the eltesel bllltl tn the Dump 0 The elhmrlg etlta stlmttletes the phesheryletleh elthe pllmp prutElll DVATP o mltsldE the sell 0 The release etthe lta leths permlts t39r ru K rehs trem uutslde the sell te bllld lo the sump arm the phesohate grmlp ls released n 0 Electrochemical Gradient all cells have voltages across their plasma membrane voltage is electrical potential energy a separation of opposite charges cytoplasm is negative relative to extracellular uid because of the unequal distribution of anions and cations on opposite sides of the membrane membmne potential voltage across a membrane acts like a battery because inside the cell is negative membrane potential favors passive transport of cations into the cell and anions ou so 2 forces drive diffusion of ions across a membrane 1 chemical ion concentration gra em 2 electrical effect of membrane potential on the ion movement electrochemical gradient combination of forces acting on an ion passive transport is de nes as an anion dif lsing down its concentration gradient electrogenic pump transport protein that generates voltage across a membrane NaK is the major electrogenic pump of cells proton pump is the main electrogenic pump of plant actively pumps H4 charge out of the cell and by doing so generates voltage across the membrane which can be used for cellular work important use of proton gradient in a cell is for ATP synthesis during cell respiration autsidecall iv 3 r lNa l hlgh excess n my rw somumrrmlasslum Dumu lNE39l DW excess rm high charge insidz ell Cotransport mechanism that indirectly drives active transport of several other solutes by using a single ATP powered pump that transports a speci c solute another transport protein the cotransporter separate from the pump couples downhill with uphill diffusion against gradient work can be done by a substance that has been pumped across a membrane as it moves back across the membrane main ideaex athletes consume solute rich sports drinks because of speci c transport proteins involved glucose and sodium ions from salt must be present Na and glucose move into the cell through a cotransporter protein Na moves down its concentration gradient created by the NaK balance and glucose moves against its concentration gradient eX concentration of Na in a resting nerve cell is lower inside the cell than outside the cell when the cell is stimulated gated channels that facilitate Na diffusion open and Na ions fall down their concentration gradient driven b 39 omdi ent and attmr ti on of L i to the negative side of the membrane eX in a plant one transport protein couples the return of H with the transport of sucrose into the cell allows sucrose in against its concentration gradient but only if sucrose travels with a H ion this is how plants deliver sugar out to the roots 8 utside cell Na hlgil glucosescam iglumsel law wtranspal er Ly glmse LNa moves am itseiecuomemlcaigradlem ua llnw W I gt z mucosa mums against ltsconmntratlon gradient inside call Summary Type of molecule Hydrophobic or ble to cross Transport prolein hydrophilic lipid bilayer required a lluvmlm mclmllas I a ham can 05 EM no tlanspnl 39 p V pl nteln l39equlled 39uxal rp have dif cll tv 39 transport pl arein F Ol i IT ifilflliF 5 hyal39oah cvc55gtng 5 required m quot hydmwobl pa39t Class ef ciently have difflcu ty l39ansnol39t pl nrein mar33h I c 3905 ng e is we ta hydropch paquott cross ef ciently water oxygen lipids and C02 can cross the lipid bilayer of a membrane directly without a transport protein or other mechanism Cell Membrane Protein Types The Wt have slrmlar articulated Daripheral protein mavemams me n l n Fluid Mnsalc ulrgosaeehandes l cell wall Side phosphohpld g bllsyer osnlic sme New pmlem penanml Drutem Bulk Transport Exoc osrs process during which the cell secretes biological molecules by fusion of vesicles with the plasma membrane increases surface area of plasma membrane requires fusion of vesicles with plasma membrane a transport vesicle that has budded from the golgi moves along the microtubules of the cytoskeleton to the plasma membrane when the vesicles and membrane come into contact lipid molecules come into contact lipid molecules of 2 bilayers rearrange themselves so that the membranes fus contents of the vesicle membrane then become part of the plasma membrane many secretory cells use exocytosis to export products e 39 anereas nerve cell to release neurotransmitters when plant cells make walls exocytosis supplies proteins and carbs from golgi to outside the cell Endoc osis process by which a cell takes in biological molecules and particulates by forming new vesicles om the plasma membrane small area of the plasma membrane sinks in to form a pocket as the pocket deepens it pinches in and forms a vesicle containing material that had been outside the cell decreases the surface area of plasma membrane 1 phagocytosis cell engulfs a particle by wrapping a pseudopod around it within the membrane enclosed sac large enough to be classi ed as a vacuo e particle is digested alter the vacuole fuses with a lysosome containing hydrolytic enzymes 2 pinocytosis cell gulps droplets of extracellular uid into tiny vesicles a cell doesn t need the uid it needs the stqu dissolved init nonspeci c in what it trans orts 3 receptor mediated enables a cell to acquire large quanti es of speci c substances ex we use this to take in cholesterol there are proteins in the membrane that have speci c receptor sites exposed to extracellular uid they are typically clustered in regions of the membrane called coated pits which are lined on the cytoplasm side with a fuzzy layer of coat proteins espeer e snbstanees1rgands bmdto reeeptdrs rcoated prt forms a yesrete epntarmng ugand molecules membrane bytne same yesrele rm both processes endoexo ee11u1ar energy rs requrred and the transported substanees neyer pnysreany cross the membrane ennryrnsn at am enndrmsrg I m mm m s um I L l gt n H eyesreles also serye m rejuvenatingremodeling the membrane Metahnusrn rm zhn m totalrty of an organrsms ehemreal reaeuons enyrronment ofthe eeu Ch Ivar t 50l re M or t a H x AG 7756 kmUmul 172 0 anml organrzadon sequence ofsteps that result m a eertam produet reach step of arxn pathway rs eata1yzed by a speer e enzyme e hamsms thatregulate enzymes ba1anee metabolre supply and demand emetabolrsm as awhole regulates the matena1 and energy resources ofthe eeu to srmp1er compounds results in lower energy pdts like C02 and H20 have less chemical energy than the food they came from did depletion of chemical energy is accounted for by the heat generated by metabolism chemical energy refers to the potential energy available for release in a chemical reaction ex39 cellular respiration anabolic pathway consume energy to build complicated molecules from simple ones using energy derived from catabolic pathways ex39 synthesis of a protein from an amino acid bi0energetics how energy ows through living organisms Thermodynamics study of energy transformations that occur in a collection of matter for a process to occur spontaneously it must increase the entropy of the universe energy transfer or transformation increases the entropy of the universe sp0ntane0us process that can occur without an input of energy for a nonspontaneous process to occur energy must be added to the system cells cannot store heat they rapidly loose it to their surroundings Biology and Disorder we take in ordered molecules and break them down into disordered pieces entropy of a system can decrease as long as the total entropy of the universe increases Free Energy recall that the universe system surroundings free energy portion of a systems energy that can perform work when T and P are uniform throughout the system AGAHTAS once we know AG we can predict whether or not a process is spontaneous only processes with AG are spontaneous sign and magnitude of AG tell us nothing about the rate of rxn something with high G has a high work capacity eX gravity things tend to move from a higher altitude to a lower one because they re more stable at a lower place for a system at constant VampT total G can only decrease during a spontaneous change total amount of work that can be extracted is limited by this A in G a system will proceed in the direction its spontaneous until its G is lowered the equilibrium position represents the lowest G value available to the rxn system for a process to occur spontaneously the system has to 1 release enthalpy OR 2 give up order TAS increases spontaneous process decreases the systems free energy some spontaneous processes can be taken advantage of to perform work important in metabolism where a major objective is determining which rxns can provide energy for cellular work ex from the free energy formula it is clear that a decrease in the systems total energy will increase the probability of spontaneous change an increase in entropy increases the probability of a spontaneous change increased temperature means increased possibility of a spontaneous change AG Stability and E9 another way to remember that AG is required for spontaneity is AGG nal G initial AG can only be negative if there is a loss of energy going for initial 9 nal at that state it is less likely to change it has to be more stable than it was before free energy is kind of a measure of instability quantitatively showing a tendency to change to a more stable state unless something intervenes a system will try to move toward a greater stability another term for maximum stability is equilibrium as a rxn proceeds toward equilibrium free energy of pdts and rxts decreases free energy increases when a rxn is pushed away from equilibrium somehow ex39 removing product for a system at equilibrium G is at its lowest possible value when energy is coupled AG changes throughout the rxn and then becomes constant any change from the equilibrium position will have a pos AG and is therefore nonspontaneous a system at equilibrium cannot spontaneously change so it can t do work a process is spontaneous and can perform work ONLY when it is moving toward equilibrium Metabolism based on AG values rxns can be classified as exergonic or endergonic exergonics proceed with a net release of energy ne g AG spontaneous magnitude of AG for an exergonic rxn represents the amount of work the rxn can perform greater decrease in G greater net amount of work that can be done endergonics absorb G from surroundings pos AG nonspontaneous the magnitude of AG here represents the amount of energy input necessary to drive the rxn if aprocess is endergonic its reverse is exergonic metabolism as a whole is never at equilibrium a cell is not in equilibrium if it was it would be dead consistent ow of matetial inout keeps metabolic processes from reaching equilibrium cell continues to work throughout its life a catabolic pathway in a cell releases energy in a series of rxns so some of the reversible rxns are constantly pulled to one direction kept out of equilibrium key is that the pdt doesn t accumulate it becomes a rxt in the next step then waste is finally expelled from the cell heat from environment is necessary for substrates to get over the Ea bairier ATP and Coupling a cell does 3 types of work 1 chemical pushing endergonic rxns ex39 synthesis of polymers from monomers 2 transpon pumping substances across membranes against direction of spontaneous movement 3 mechanical ex39 beating cilia contracting muscle cells movement of chromosomes during cell respiration energy coupling use of an exergonic process to drive an endergonic one key to coupling is the phosphorylated intermediate which itself is less stable than the substance was before ATP contains sugar ribose adenosine nitrogenous base and a chain of 3 phosphate groups plays a major role in energy coupling and is also one of the nucleotide triphosphates used to make RNA bonds between phosphate groups can be broken by hydrolysis if the terminal phosphate bond is broken an inorganic phosphate HOPO3239 or Pi leaves ATP ATP becomes ADP exergonic because the hydrolysis releases energy phosphate bonds of ATP are also known as high energy phosphate bonds they aren t usually super strong they just have high energy relative to the products ADP and Pi release of energy comes from a change in chemical state going to a lower energy not from the phosphate bonds the hydrolysis releases so much energy because all 3 phosphate groups are negatively charged like charges together mutual repulsion contributes to instability in that region ex39 compressed spring in a cell most of the hydroxyl groups of phosphate are ionized Performing Work cell proteins harness the energy generated to do the 3 types of cell work if the AG of an endergonic is less than the amount released by ATP hydrolysis the two rxns can be coupled and still be exergonic overall usually involves transfer of a phosphate group from ATP to another molecule recipient of the phosphate is said to be phosphorylated key to coupling exerende is the formation of the phosphorylated intermediate which is less stable than the original molecule transport and mechanical work in the cell are nearly always powered by hydrolysis of ATP ATP hydrolysis leads to a change in the proteins shape and often its ability so bind to another molecule this sometimes happens with motor proteins cycle 1 ATP is bound noncovalently to the motor protein changing the shape and ability to bind 2 ATP is hydrolyzed releasing ADP and Pi 3 another molecule can bind bc of the above step at each stage of the process the motor protein changes its shape and ability to bind to the cytoskeleton resulting in a movement of the protein along the cytoskeletal track Regeneration of ATP ATP is a renewable resource that can be regenerated by addition of phosphate to ADP energy required to phosphorylate ADP comes from exergonic breakdown rxns catabolism in the cell shuttling of inorganic phosphate and energy is called the ATP cycle energy passing from catabolic to anabolic pathways regeneration of ATP from ADP and Pi is endergonic catabolic exergonic pathways provide the energy for this endergonic process ATP cycle provides energy during transfer from catabolic to anabolic pathways chemical potential energy temporarily stored in ATP drives most cellular work Activation Energy Ea catalyst chemical agent that speeds up the rxn without being consumed every chemical rxn involves bond breaking and bond forming ex39 hydrolysis of sucrose bonds between glucose and fructose and 1 H 20 break and then two new bonds are formed changing a molecule involves changing it into a very unstable state before the rxn can proceed to reach this state rXt molecules must absorb energy from surroundings when the new bonds of pdt form energy is released as heat and molecules return to stable shapes with lower energy than it had at a contorted state Ea initial investment of energy for starting a rxn energy required to contort the molecules to they can break during the activation the uphill portion the free energy of the rXt molecules is increasing at the summit rth are unstable in a transition state bond forming phase is the downhill portion of the curve involves a loss of free energy by the molecules Ea is usually supplied as heat that rXt molecules absorb from surroundings bonds break only with rXt molecules have absorbed enough energy to become unstable meaning to enter atransition state heat speeds up molecule movement collisions between them and force they collide with as the atoms settle energy is released into the surroundings if it s exergonic the formation of new bonds releases more energy than was input to break the bond Ea barrier determines rate of rxn Enz mes and E2 ba1riers for selected rxns have to be overcome for the cell to live heat would speed up a rxn but that would be bad for some biological systems high energy denatures proteins then cells rheat speeds up all nrns not just tlne ones that needrt rorganlsms use eatalysrs an enzyme eatalyzes anrn bylowenng rts Ezbamer renables tlne nrt moleeules to take m enough energy to reach transrtron state enzymes do not changeAG etlney ean39t make an endergom change to exergom enzymes only speed up reaeuons that would oeeur anyway on m the eell at any ume go Sgecl cl rsuhstrzte nrt an e yme aets on enzyme blnds to a substate formlng an enzyme substrate complex 7 mzvmersubskate mzyme r substrate quot complex pdt SMLASE 5 rant same r mew e slum H u e Elmm t Example u t rm Lx l l nu espeer erty ofan enzyme results from rts shape 7 luen ls a consequence oflts ammo aerd sequence ronly arestnetedregron of an enzyme moleeule aetually b ractlve lnds to tlne substrate srte ls formed by afew othe ammo aclds ofth enzyme srte flts snugly around tlne substanee m uee r rbnngs chemlcal groups of aeuye srte rnto posmons tlnat ean enhance abrlrtyto eatalyze chemlcal nrns Catalysrs 7mm My weak Wm r h w Mk W R F substrate to pdt tlnen tlne pdt departs from tlne aetrye srte rthe enzyme ls tnen free to take anotlner substrate moleeule rnto rts aeuye srte rmostmetabollc nrns are reverslble produet for Xn wrtln tlne next enzyme eeontrnues unul tlne nal pdtrs made rwhlch depends on relauye eoneentrauon ofxxt and pdt enet effectls always m dlrecuon of equlllbnum enzymes use diff mechanisms to lower Ea l inran that have 2 or more rth active site provides a template so substrates can come together in the proper orientation for rxn to occur between them 2 as the active site holds onto the bound substance the enzyme may stretch the substrate toward their transition state form distorting the substrate helps it approach its transition state reduces G rqd to reach the transition state 3 may provide a microenvironment that is more conducive to a speci c rxn than the soln itself would be without the enzyme 4 direct participation of the active site in the rxn rate a given amount of enzyme converts substrate to pdt is partially dependent on the initial concentration of the substance more substrate molecules available more frequently they can access active sites a saturated enzyme is one with all the active sites occupied by substrate molecules when saturated only way to increase activity is to add enzyme saturated refers to the concentration of substrate at which all active sites are engaged Conditions and Enzme Activity Temperature and Pressure some enzymes work better under certain conditions than others do optimal conditions favor the most active shape of the molecule up to a point activity increases with temperature because molecules collide with active site more frequently but above a certain point activity drops sharply thermal agitation disrupts H bonds ionic bonds and any other interactions stabilizing shape of the enzyme protein molecule eventually denatures at the optimal temp the greatest number of molecular collisions and fastest conversion from rXt to pdt occurs there is also an optimal pH for enzymes its usually 68 Cofactors lots of enzymes require non protein helpers for activity called cofactors may be bound tightly to the enzyme or may bind loosely and reversibly along with the substrate some are inorganic Zn Fe Cu ions c0enzyme enzyme cofactor ex39 most vitamins act as coenzymes of raw material to make coenzymes Inhibitors if an inhibitor attaches to an enzyme by covalent bonds its usually irreversible however many bind to the enzyme by weak interactions so inhibition is reversible c0mpetitive inhibitors resemble the normal substrate and compete for active site reduces productivity by blocking substrate from entering active sites can be overcome by increasing concentration of substrate so as active sites become available there s a higher probability that a substrate molecule and not an inhibitor will get in n0nc0mpetitive inhibitor bind to another part of the enzyme indirectly toxins and poisons are examples of irreversible inhibitors Regulation molecules that regulate enzyme activity behave like reversible noncompetitive inhibitors change shape and fn of the active site by binding somewhere else on the molecule by non covalent interactions aloste139ic describes case where protein fn at one active site is affected by regulatory molecules to a separate site bonds somewhere besides the active site may inhibit or stimulate activity are more speci c than regulators that bind at the active site most allosterically regulated enzymes are made from two or more subunits each composed of a polypeptide chain and has its own active site entire complex oscillates between 2 diff shapes one active and one inactive binding of an activator to a regulatory site stabilizes shape with functional active sites binding of an inhibitor stabilizes an inactive form of the enzyme subunits of allosteric enzymes fit together such that a change in one is transmitted to all others single activator binding to one regulatory site affects the active sites of all subunits feedback inhibition metabolic pathway is switched off by inhibitory binding of an end pdt to an enzyme that acts early in the pathway ex39 when ATP allosterically inhibits an enzyme in itsATP generating pathway prevents cell from wasting chemical resources by making more than is necessary Feedback mtnlimon mm 7 ii Location teamoien me in 39 quot 39 L39 439 facilitates asequence oflxns p mm 1 enzyme is substrate for adjacent enzyme keeps going until end pdt is released 39 quot 39 int e e 39 39 others are in soln with speci c membrane enclosed eukaryotic organelles has its own internal chemical enVlronment 9 Cell Regnlrauon Auch To 4 H n 7 rm H Hunk Phnmulo 113w H OH UH A Figure 5 The 5mmquot of adeunslne niphasphate AWL men mm ly mlvlnmwmlln39vsv nxmslll Un39rml n l e39 transfer plays a major role inbreaking down complex molecules We F2 NADH v 4 1 2 mm a 4 l Krebs vs MADE Ia cycle l runny qh Total net ATP yleld 35 CatabolicATP organic components possess potential energy as a result of their armngement of atoms compounds that can p 39cipate in exergonic rxns can act as fuels With help from enzymes the cell degrades complex org molecules rich in potential energy into simpler molecules With less ener some energy used to do chemical storage can be used to do Work the rest is expelled as heat fermentation catabolic process partial degradation of sugar Without the use of 02 aerobic 02 consumed as a reactant along with organic fuel anerobic harvests energy Without use of 02 glucose is the lel that cells use most o en its breakdown is exergoni Mempvane l ATP Theoretical Yield Anaerobic Aerobic In mnochandvla a c39buquot amlm lusgw wan mm e39rrpnmm Mitochondvion Cytosol catabolic processes do not directlymove agella pump solutes across membranes polymerize monomers or do other cellular Work 1t ts 1tnkeo1 to wotk by ATP rte keep Workmg a eeu has to tegenetate tts supply of ATP torn ADP and P Redox Xe39 Y gt x Ye exe ts the e39 donor the teduetng agent 31 ts the e39 aeeeptot the oxtdtztng agent not all redox txns tnyotye eonnptete e39ttansfet rsmce 02 ts so e1eettonegattye tt39s one ofthe nnost potent oxtdtztng agents t c t t synthestze ATP roxxdanon gatn of oxygen 1oss ofhyobogen ot1oss ofer Eduction loss of oxygen gatn ofhyobogen otgatn ofer Redox an otg Fuel etn ee11 tespttatton g1ueose ts oxtdtzed and 0 ts reduced 39 oose potentta1 enetgy along the way 39 whose enetgy ean be te1easeo1 as they fall down an enetgy gtadtent when transfenedto o etn tespttatton oxtdataon ofglucose txansfets erto a1owet enetgy state freeing enet y then ayat1ab1e forATP synthests egtueose and othet otg fuels are broken down tn steps reach step ts eata1yzeo1 by an enzyme at key steps e39ate smpped torn g1ueose 7H atonns aren39tttansfene atteettyto o rusually passed fttst to an er Earner a eoenzynne eaned NAD NAD39 ts an e39 eee tot and fns as an oxtdtztng agent tn tespttataon renzymes eaned dehydrogenases tennoye apatt ofH atonns torn the substxate ethetefote oxtdtztng tt nut tuntwtt tnt t tlr ltNtD Lquot0NHH renzyme dehyets 2e wtth 1 ptoton to tts eoenzytneNAD rotherproton ts released as H to sunoundmg so1n H shows was teeetyed NAD39 ts the nnost yetsattte e39 aeeeptot tn tespttatton re 1oose ahnostno potentaa1 enetgy when ttansfened tom g1ueose to NAD aspiration uses e39 txanspott ehatn breaks the fall ofe39to o n seyeta1 enetgy te1eastng steps e r m a re m TADH to the top at the bottom ot1owet enetgy state 02 gets the e39 along wtth H39 nue1et fonntng H20 7339 txansfet torn NADHto 02 ts exetgonte re the ehatn torn one eatnet to the next tn abuneh ofredox txns aeeeptot yety e1eettonegattye reach eametts nnote e1eetxonegattye than the one before tt anathetefote eapab1e of oxtdtztngtt e39 removed from glucose by NAD fall down the energy gradient in the e39 transport chain to a much more stable location Nimvnnmvdo Nummamide Uh Wm i 2 citric acid cycle CAC 3 oxidative phosphorylation 1 ttwo ste s are catabolic and breakdown glucose and other org iels glycolysis happens in the cytos it begins the degradation by breaking down glucose into two molecules of pyruvate 39 39 f ks CAC happens in the mito matrix of euks in cytosol 0 pro of p u at m co2 so the C02 produced represents pieces of oxidized org molecules some steps of 39 aremm u e from forms NADH oxidative phosphorylation 3m stage the e39 transport chain accepts e39 from breakdown of pdt from the rst 2 sta es passes these e39 from one molecule to another at the end e39are combined with Oz and PF to form HZO energy released in each step is stored in the mito in a form used to make ATP name of this process is from it being powered by redox rxns in euks the inner membrane of the mito is the site of e39 transport and other processes that together make up oxidative phosphorylation in proks its in the plasma membrane oxidative phosphorylation makes 90 of ATP generated by respiration small amount also made directly by glycolysis and CAC by substrate level phosphorylation w en an enzym an e phosphate group from a substrate to ADP instead of adding an inorganic phosphate to ADP Glycol is means sugar splitting split into 2three carbon sugars which are then oxidized and rearrangedto form 2 pyruvates glycolysis can be divided into 1 en 39 ment rgy payoff net energy yield from glycolysis per glucose molecule is 2 ATP NADH 4 go in it takes 2 ATP tornake 4 in the end all carbon on39ginally present is accounted for in 2 pyruvates no co2 is released in glycolysis occurs whether if02 is present chemical energy stored in pyruvate andNADH can be extracted by CAC and oxidative phosphorylation among the pro ucts pyruvate ATP andNADH contain energy that can be used by other biological rxns e e u r c r respiration a r rd c t CAC under aerobic and anerobic conditions dummy 1 toquot ATP starts the process ofglucose oxidation Energy lnvnslmnnl phasu v Emmy psych pm 39 smm j r r su 39 u ui gti Hutuhm my A w rem 2m urn nub V 1o w t Citric Acid Cycle CA c glycolysis releases less than v ofthe chemical energy stored in glucose rnost is still in pyruvate major energy accomplishment of the CAC is the formation of NADH and FADH2 if molecular 02 is present pyruvate enters the mito and enzymes of the CAC complete oxidation after entering the mito by active transport pyruvate is converted to acetyl CoA junction between glycolysis and CAC accomplished by multienzymecomplez 3 rxns to form Acetyl CoA l pyruvates carboxyl C0039 grp that has already been oxidized and therefore has little chemical energy is removes and given off as a molecule of C02 this is the first step where C02 is released in cellular respiration 2 a two carbon fragment remaining is oxidized forming acetate an enzyme transfers the extracted e39 to NAD storing energy as NADH 3 CoA sulfur containing derived from B vitamin is attached to the acetate by an unstable high energy bond pdt is then ready to go into the CAC for further oxidation cycle generates 1 ATP per turn by substrate level phosphorylation most of the chemical energy is transferred to NAD reduced coenzymes NADH and FADH2 move e39 to the e39 transport chain in each turn of the cycle 2 CS go into sort of a reduced form of an acetyl group 2 different C s leave completely oxidized as C02 acetyl group joins the cycle by combining with oxaloacetate to form citrate next 7 steps decompose citrate back into oxaloacetate to form citrate for each acetyl group entering 3 NAD are reduced to NADH in steps 3 4 and 5 ATP is formed directly in step 5 by substrate level phosphorylation output from step 5 is the only ATP directly generated by the CAC most of the ATP is from oxidative phosphorylation when the NADH and FADH2 produced by CAC relay e39 extracted by food to the e39 transport chain they supply necessary energy for phosphorylation of ADP to ATP after the completion of the CAC most of the usable energy from the original glucose is in the form of NADH ex what part of catabolism of glucose requires molecular 02 and produces C02 combination of the CAC and the e transport chain e Transport Chain makes no ATP directly eases fall of e39 from food to 02 breaks a large G drop into a series of smaller steps that release energy in smaller amounts chain is a collection of molecules embedded in the inner membrane of the mito proteins of the e transport chain are in the inner mito membrane folding to form cristae increases surface area which is more space for 1000 s of copies of the chain in each mito most components are proteins exist in multiprotein complexes ed IIV ughuy bound to the muluprotern complexes alon e39 earners a1temate between redueed and oxxdued forms as they aeeeptdonate e39 r h A A u n ethen rt returns to oxxdued form as rtpassed e39to rts downhru more e1eetroneg ee39r m on m tu by NAD to the 1 mo1eeu1e ofthe cham In complex I rwhxch rs a avoprotern nergnbor NADH then the avoprotern returns to rts oxxdued form as rtpasses e39to aFerS protern rthe Fees protern then passes e39 to ubrqurnone m tr m mm 39 etherr prostheue group rs eaned a heme rhas aFe that aeeeptsdonates e39 ee39trans cham has several types ofeytoehromes reach a our protern wrth shghdy our e39 earryrng heme group etast eytoehrome m the cham passes e39to o reach 2 atom so preks up aparr oforom the aqueous so1n formrng H20 rwhen er ow along the ertransport cham othe mrto the pH ofthe matnn rnereases chemrosmosrs rATI populates mnermembrane ofthe mrto 6 77 ATP H10 ADPEH AW 110 gtADP T AG 77 s healnun 7305 hImul a Mg mm n on Ma rte u ADV rworks hke an ron pump m reverse TD synthase uses energy ofan emstrng ron gradmntto power ATP sunthesrs renergy stored as H gradnent aeross membrane to dnve ee11u1ar work rATP synthase rs amu1tr subumt complex wrth 4 mam parts each made of multipolypeptides protons move one by one to binding sites on one of the parts causing it to spin so it catalyzes ATP production from ADP and inorganic phosphate ow of protons acts as a stream that turns a water wheel establishing H gradient is a major fn in the e39 transport chain the chain is an energy converter that uses the exergonic ow of e from NADH to F ADHz to pump H across the membrane from the mito matrix to intermembrane space ATP synthases are the only sites that provide a route through the membrane for H Oxidative Phosphoglation passage of H through ATP synthase uses exergonic ow of H to drive phosphorylation of ADP energy stored in a H gradient across a membrane couples redox rxns of e39 transport chemiosmosis to ATP synthesis at certain steps e39 transfers cause H to be taken up and released into the surrounding soln in euks e39 carriers are arranged in the membrane such that Hl is accepted from the mito matrix and deposited into the intermembrane space pr0t0n motive force H gradient resultant chemiosmosis is an energy coupling mechanism that uses energy stored in an H gradient to drive cellular work chloroplasts also use chemiosmosis to generate ATP Respiration wo Oxygen estimate of ATP yielded from aerobic respiration depends on supply of 02 to the cell 2 methods of oxidating organic fuel and generate ATP without 02 l anerobic respiration 2 fermentation distinction is by whether or not e39transport chain is present fermentation is a way of harvesting chemical energy without oxygen or e39 transport chain without cellular respiration its an expansion of glycolysis allows generation of ATP by substratie level phosphorylation requires supply of NAD to accept e39 under aerobic conditions NAD is recycled from NADH by transfer of e39 transport chain aerobic alternative is to transfer e39 from the NADH to pyruvate end product of glycolysis Fermentation regenerated NAD by transferring e39 from NADH to pyruvate NAD can then be reused to oxidize sugar by glycolysis yields 2 molecules of ATP by substrate level phosphorylation types of fermentation differ by end products formed from pyruvate alc0hol fermentation pyruvate converted to ethanol lactic acid fermentation pyruvate reduced directly by NADH to form lactate as an end product no release of C02 human muscle cells make ATP by lactic acid fermentation when oxygen is scarce Fermentation V Aerobic Resp both use glycolysis to oxidize glucose and other organic fuels to pyruvate net release of 2 ATP by substrate level phosphorylate NAD is the oxidizing agent in both accepts e39 from food during glycolysis key diff mechanism for oxidizing NADH back to NAD a process rqd to sustain glycolysis in fermentation final e39 acceptor is an organic molecule like pyruvate or acetaldehyde in aerobic nal e39 acceptor from NADH is oxygen cell respiration harvests more energy than fermentation can 0bligate anerobes cannot survive in presence of oxygen carry out only fermentation or anerobic facultative can make enough ATP to survive by fermentation or anerobic respiration Versatility of Catabolism glycolysis can accept a large range of carbs for catabolism in digestion starch is hydrolyzed to glucose which can then be broken down by glycolysis and CAC glycogen what we store in the liver and muscle can be hydrolyzed to glucose between meals proteins can be used as fuel f1rst must be broken down into amino acids amino acids present in excess are converted by enzymes to intermediates of glycolysis and CAC amino groups removed deamination beta oxidation breaking down of fatty acids to 2 C fragmens that enter the CAC as acetyl CoA NADH and FADHZ are also generated by B oxidation they can enter e39 transport chain leads to more ATP production fats are very good fuels because of their chemical structure higher energy level e39 compared to e39 in carbs Biosynthesis Anabolic food isn t just energy it provides C skeletons that cells need to make other necessary molecules compounds formed as intermediates of glycolysis and CAC can be diverted into anabolic path as precoursors the cell can use to synthesize the molecule it requires these pathways consume ATP Regulation by Feedback most common mechanism for feedback control is feedback inhibition end pdt of an anabolic pathway inhibits enzyme that catalyzes an early step of the pathway cell also used catabolism if its working hard and ATP drops respiration speeds up if there s a lot of ATP resp slows down control is based mainly on regulating activity of enzymes at strategic points in the catabolic path if ATP is already prevalent acetyl CoA serves as the basis for fatty acid synthesis atty 39 s are our bodies long term stomge 0r acetyl CoA enters the CAC Three fates of pyruvate produced by glycolysis Anaeroblc Anaerobic Aeroble oxlua on lame acl fermentation aleohollc rename K x07 Pymvalc Pyruvale Os 07 Pymvale i f u o c 0 CH m at COA39SH k co NA i E NM 002 2 3 x H NADH HJ I Acelaldehyue Mgr cu A NAB 1 Acc yLCoA o o C0 C Lamale I HOiC 7 H H CH3 n awn CH3 CH3 39 Etham cm acid cyc e and H7070 Oxmaxwe pnuznhoryiauon CH3 s Wm Dndnlv pllosplxurv39dlm39l etanron ransnon n r in hamm musis my J L m w Cellular respiration the process is exergonic carbon and hydrogen atoms of the sugar are oxidized lose in their sharing of e39 oxygen atoms are reduced gain in their sharing o e39 e39 lose energy as they travel downthe e39 transport chain energy is used to produce ATP Water is formed from oxygen electrons from sugar s carbon and hydrogen atoms lose potential energy oxidation as they are transferred to oxygen the process is endergonic requires light eneIgy carbon and hydrogen atoms from carbon dioxide and Water are reduced gain in their sharing of e39 oxygen atoms of Water are oxidized lose in their sharing of e39 e39 gain energy from light energy as they tmvel up the e39 tmnsport c ain energy is used to produce sugar and ATP oxygen is formed from Water e39 from Water s hydrogen atoms and carbon dioxide s carbon atoms gain potential energy reduction as the are tran Femad toward n ar Photos thesis autotroph producers of the biosphere an organism that produces complex organic compounds ns from simple organic molecules using energy from light or inorganic chemical 1x amost all plants are autotrop most use Water as a reducing agent converts physical energy from sun light into chemical energy in the form of reduced carbon canbe phototrophs or lithotrophs photo use light as an energy source 1itho oxidize inorganic compounds photo and litho use aponion of ATP produced during photosynthesis or oxidation of inorganic compounds to reduce NADP to NADPH to form energy rich organic compounds such as carbs heterotroph consumers of the biosphere unable to make organic material by photosynthesis live on cmpds produced by other organisms decomposers consume remains of dead organisms most fungi and some prokaryotes get iel this Way dependent on photoautotrophs for food and also for 02 l n mm Humelm Chloroplasts chloroplasts are the major site of photosynthesis in most plants color of the leaf is from chlorophyll a green pigment in the chloroplast light energy absorbed by chlorophyll drives synthesis of organic molecules in a chloroplast chloroplasts are found in the mesophyll the tissue in the interior of the leaf COZ enters the leaf Oz exits through stomata pores water absorbed by the roots is delivered to the veins str0ma dense uid within the chloroplast enclosed by an envelope of two membranes stroma is separated from in the thylakoid space interior of the thylakoids by a system of interconnected membranous sacs called thylakoids Thylakaid Light dependant Outer cumgznment reactions take lntemem rane space place here 7 5mm Granum stack of thylakoids Chloroplast Stages two stages are light rxns photo part and the Calvin cycle synthesis part light rxns converts solar energy to chemical energy water is split providing a source of protons H and e39 light absorbed by chlorophyll drives transfer of e39 and H4r from water to an acceptor NADP where they are temporarily stored light rxns use solar power to reduce NADPJr to NADPH by adding a pair of e39 along with an Hir they also generate ATP ph0t0phosph0rylati0n use of chemiosmosis to power addition of phosphate to ADP so light energy is initially converted to chemical energy as two compounds NADPH a source of e39 for reducing that can be passed on to an e39 acceptor reducing it ATP light rxns don t produce sugar thylakoids of the chloroplast are sites of light rxns molecules of NADPJr and ADP pick up e39 and phosphate then NADPH and ATP are released to the stroma where they play an important role in the calvin cycle calvin cycle begins by carbon xation incorporating C02 from the air into organic molecules already present in the chloroplast then the fixed carbon to carbs by the addition of e39 steps of calvin cycle are sometimes called dark or light independent rxns because none of the steps require light directly for most plants this process still occurs in daylight because then light rxns can provide the NADPH and ATP that the cycle needs occurs in the stroma PhotosystemsMechanism ph0t0system units of protein complexes involved in photosynthesis that carry out absorption of light and transfer of energy and e39 found in the thylakoid membranes of plants algae and some bacteria rxn center an enzyme that uses light to reduce molecules inside the photosystem surrounded by light harvesting complexes that aid absorption of light and transfers energy to rxn centers each light harvesting complex consists of various pigment molecules contains a molecule able to accept e39 being reduced called the primary e39 acceptor light harvesting and rxn center complexes are membrane protein complexes thylakoid membrane has photosystem I and photosystem II photosystem II fns first in light rxns contain different pigments each absorbing a different wavelength of light light drives synthesis of ATP and NADPH by energizing the two photosystems in the thylakoid membranes of chloroplasts key to this is linear e ow ow of e39 through the photosystems and other components built into the thylakoid membrane linear e39 ow occurs during the light rxns of photosynthesis cycic e flow usues photosystem I but not photosystem II e39 cycle back from ferredoxin Fd to the cytochrome complex and then continue to PS I no production of NADPH and no release of 02 does generate ATP gt Pigment malemla phmsystem II PS I Phakosystem 1 PS 1 Linear e39 ow Cyclic e39 ow excited e39 from each of the photosystems can be donated to a 1 electron acceptor both photosystems active e39 flow from one e39 carrier to the next a light excites electrons in PS H b e39transferred to the l e39 acceptor c e39 flow down the e39 transport chain at e39transferred to PS l e light excites e39 inPS I f e39 transferred to the 1 e39 acceptor g e39 transferred to NADP e39 and reducing power are stored in NADPH e39 from the splitting of H20 replace the e39 lost from PS 11 and generate 02 as a byproduct e39 are gaining ener the flow of e39 and the splitting of water also creates a Hl gradient across the thylakoid membrane which then is used to synthesize ATP by chem iosmosis This process is known as linear photophosphorylation only photosystem I is active e39 ow from one e39 carrier to the next a light excites electrons in PSI 17 e39 transferred to the l e39 acceptor c e39 ow down the electron transport chain 51 e39 transferred to PS I e39 from the electron transport chain replace electrons lost from PS no H20 split and no 02 generated flow of e39 creates a H gradient across the thylakoid membrane which is used to synthesize ATP by chemiosm osis cyclic photophosphorylation Chemiosmosis mito and chloro both generate ATP by this method an e39 transport chain assembled in the membrane pumps protons across the membrane as e39 are passed through a bunch of carriers that get progressively more electronegative transform redox energy stored as an H gradient across a membrane ATP synthase is also in the membrane it couples diffusion of hydrogen ions down their gradient with phosphorylation of ADP Respiration mito both Photosynthesis chloro e39 come from food by NADH chemical energy from food e39 pumped across the inner mito membrane e39 transport chains move protons across membrane as e39 are moving down the chain ATP synthase is in the same e39 come from H20 or PS I energy is light e39 pumped across the thylakoid space membrane as the e39transport chain diffusion of H is coupled to ATP production many components are very similar in structure Calvin Cycle uses ATP and NADPH to convert C02 to sugar occurs in the chloroplast stroma incorporates C02 into organic molecules by carbon xation and then reduces the xed carbon to carbohydrate carb0n xation no direct light energy required ATP and NADPH from the light reaction NADPH provides the reducing power and ATP provides the chemical energy cycle produces a 3carbon sugar glyceraldehyde3phosphate G3P cycle has 3 phases 1 Input phase C02 is xed by rubisc0enzyme that catalyzes the rst step C02 is incorporated one at atime by attaching to ribulosebiphosphate RuBP pdt is a 6 C intermediate that is unstable and splits in half two moleculesphosphoglycerate per C02 xed 2 Reduction phase ATP is used for phosphorylation NADPH is used for reduction 3 Regeneration of CO2 Acceptor RuBP sugar carbons are shuf ed around to make 3 5carbon sugars RuBP from 5 3carbon sugars spends three ATP RuBP can take C02 again and cycle continues to produce one molecule of glyceraldehyde 3phosphate 3 C02 molecules are xed two molecules of glyceraldehyde 3phosphate are required to make one molecule of glucose mm to llanq p to I unset anon xilmn nun quotand Winn ations environmental conditions that promote photorespiration hot bright dry days in these climates A A I 39 L 39 39 39 39 39 the two most important ofthese adaptations are exhibited by CA and CAM c4 lants when their stomata close on hot days c3 plants produce less sugarbecause the declining level ofCOz starves the calvin cycle as co2 becomes scarce in the leaf rubisco adds 02 to the calvin cycle instead of co2 pdt splits and a 2 c cmpd leaves the chloro r u u u A While producing col produces no ATP consumes ATP r A 4 r the calvin cycle and releases col that would otherwise be xed 02 and more co2 than today 39 39 39 w 39 02 an photorespiration is inevitable to some extent probability thatRuBisCO reacts with oxygen vs col depends on the relative concentrations of the two molecules at the site ofthe reaction g3 c02 is initially xed to the 3 carbon sugar phosphoenolpyvuvate PEP forming a4 carbon compound oxaloacetate rxn catalyzed by PEPcarboxylase which is better at distinguishing between 02 and C02 than ru isco is PEP carboxylase is only in mesophyll cells ofC4 plants rubisco is more concentrated in cells of surrounding leaf veins bundle sheath cells C02 enrichment allows C4 plants to sustain higher rates of photosynthesis than non C4 plants especially at higher temperatures concentration of C02 relative to 02 in bundle sheath cells is higher mesophyll cells of a C4 plant pumpC02 into the bundle sheath keeping the C02 concentration in the bundle sheath cells high enough for rubisco to bind carbon dioxide rather than oxygen reactions with PEP carboxylase and the regeneration ofPEP can be thought of as a C02 concentrating pump powered by ATP rates of photorespiration in C4 plants are lower than in C3 plants ef cient use of C02 allows C4 plants to grow better at higher temperatures and use less water C4 plants operate these two processes in separate cell es CAM plants operate these two pathways at different times of day CAM CAM plants close their stomata during the day and usually only open them at night stomatabeing closed prevents C02 from entering leaves and also prevents water loss C02colected at night through the open stomata stored as organic acids until the day during the day the C02 is released from these organic acids inside the leaf and functions to drive the calvin cycle carbon xation C02 is xed to RuBP Light rections that produce the NADPH and ATP for the reduction of C and the regeneration of RuBP occur all day CAM plants truly have light reactions and dark reactions C4 0 co Mesnnhyll o 0 mmmeu 397 Night cell Orgalvlrduu llllufmllrtamun orgal llc Edd lLaV JOll x llml Bundle m 0 Day sheath x quotl39 a lgallll aids l leleAS 0 lo Lalle rytle Sugar Sugar Spatial separation ol steps Temporal separation ol steps lrl Cl lanls non llxalmn anll m AM 1 am rallmn llxalwl ll l9 Calm Lycle mull ll39l dlllerev ll and ll Calvll39l Lycle urcul ll ille typeset lull Same LEM mlllmmume Photosgthesis Summag lightrxns capture solar energy and use it to make ATP and transfer e39 from water to NADP forming NADPH calvin cycle uses ATP and NADPH to produce sugar from C02 Biology Notes Test 3 Chapter 10 Photosynthesis Conversion oflight energy from the Sun into chemical energy that s stored in sugar and other organic molecules Autotrophs quotSelffeeders sustain themselves without eating anything derived from other living beings Produce their organic molecules from C02 and other inorganic raw materials obtained from the environment The quotProducersquot Ultimate sources of organic compounds for all non autotrophic organisms Almost all plants are autotrophs only require water minerals and C02 Plants are photoautotrophs organisms that use light as a source of energy to synthesize organic substances Occurs in algae certain other protists and some prokaryotes Heterotrophs Obtain their organic material by the second major mode of nutrition live on compounds produced by other organisms The quotConsumersquot Animal feeds on plantother animal The quotDecomposersquot Consume remains ofdead organisms by decomposing and feeding on organic litter Most fungi and many types ofprokaryotes Almost all heterotrophs are completely dependent on photoautotrophs for food andor oxygen byproduct ofphotosynthesis Chloroplasts Found mainly in the cells of the mesophyll the tissue in the interior of the leaf C02 enters the leaf and oxygen exits the leaf by way of the stomata microscopic pores Water is absorbed and sugar is exported through veins Chloroplast has envelope of two membranes surrounding a dense uid called stroma Suspended within stroma is a third membrane system made up of sacs called thylakoids which separates the stroma from the thylakoid space inside these sacs Thylakoid sacs are stacked in columns called grana or a granum Chlorophyll green pigment resides in thylakoid membranes The light energy absorbed by chlorophyll drives the synthesis of organic molecules of chloroplast Photosynthesis occurs as redox reaction Carbon dioxide is reduced to glucose water is oxidized to oxygen Endergonic reaction Requires energy provided by light Two steps of Photosynthesis Light Reaction quotPhotoquot Occurs in TllYLAKOIDS Convert solar energy to chemical energy Water is split providing source of electrons and protons hydrogen ions H and giving off 02 as byproduct NADP acts as acceptor ofH which becomes NADPH reduction process Also generate ATP using chemiosmosis to power the addition of a phosphate group to ADP called photophosphorylation Dark Reaction Calvin Cycle quotSynthesisquot Occurs in STROMA Carbon fixation incorporation of C02 from air into organic molecules Fixed carbon is reduced to carbohydrate by electron addition Visible light The light that can be detected as various colors by the human eye and is the light energy that drives photosynthesis Wavelength 380 nm to 750 nm Photons Discrete particles not tangible that act like objects in that each of them has a fixed quantity of energy Inversely related to wavelength of light the shorter the wavelength the greater the energy of each photon Photosynthetic Pigments Light Receptors Light can be re ected transmitted or absorbed Pigments Substances that absorb visible light Different pigments absorb light of different wavelengths Spectrophotometer Instrument used to measure the ability ofa pigment to absorb various wavelengths oflight Absorption spectrum A graph plotting a pigment s light absorption vs wavelength Chlorophyll A Participates directly in light reaction Bluegreen Chlorophyll B Accessory pigment Olive green Carotenoids A group of accessory pigments Yelloworange Photoprotection These compounds absorb and dissipate excessive light energy that damages chlorophyll or interacts with oxygen forming reactive oxidative molecules that are dangerous to the cell Action spectrum Profiles the relative effectiveness of different wavelengths of radiation in driving the process Prepared by illuminating chloroplasts with lights of diff colors and plotting wavelength against some measure of photosynthetic rate Excitation of Chlorophyll by Light Electron starts offin its normal orbital pigment molecule is in ground state A molecule absorbs a photon of light which boosts the electron to an orbital of higher energy and the pigment molecule to its excited state The only photons absorbed are those whose energy is equal to the energy difference between ground and excited states Varies among molecules A particular compound absorbs only photons with specific wavelength ie each pigment has unique absorption spectrum Electron in excited state is unstable so excited electrons drop back down to ground state and release their excess energy as heat Photosystem Composed ofa reactioncenter complex surrounded by several lightharvesting complexes LightHarvesting Complex Consists of various pigment molecules Chlorophyll A Chlorophyll B and Carotenoids bound to proteins When a pigment molecule absorbs a photon the energy is transferred to pigment molecule to pigment molecule within a light harvesting complex until passed into the reactioncenter complex ReactionCenter Complex Organized association ofproteins holding a special pair of Chlorophyll A molecules Contains a molecule capable of accepting electrons and becoming reduced called the primary electron acceptor The solarpowered transfer of an electron from the reactioncenter Chlorophyll A pair to the primary electron acceptor is the first step of the light reactions The thylakoid membrane has two types ofphotosystems that contribute to the light reactions Photosystem 11 PS 11 Photosystem 11 functions first in light reactions P680 because pigment absorbs light at wavelength of 680 nm Photosystem I PS I P700 because pigment absorbs light at wavelength of 700 nm Linear Electron Flow Flow of electrons through the photosystems and other molecular components built into the thylakoid membrane Cyclic Electron Flow When photoexcited electrons take an alternative path that only uses photosystem I No production of NADPH or release of oxygen but ATP is produced Occurs in some bacteria and prokaryotes Chemiosmosis in Chloroplasts Light energy gt Chemical energy in ATP ATP is generated by electron transport chain assembled in membrane which pumps protons across the membrane as electrons are passed through a series of carriers that are progressively more electronegative Photophosphorylation in chloroplasts Phosphorylation in mitochondria Water is the source of electrons in chloroplasts Do not need molecules from food photosystems capture light energy The thylakoid membrane of the chloroplast pumps protons from the stroma into the thylakoid space In the chloroplast ATP is synthesized as the H ions diffuse from the thylakoid space back to the stroma though ATP synthase complexes ATP forms in the STROMA where it s used to drive sugar synthesis during Calvin Cycle NADPH and ATP are produced on the side of the thylakoid membrane facing the stroma where the Calvin cycle occurs Summary of Light Reactions Electron ow pushes electrons from water to NADPH Low to high PE state Electron current also generates ATP Oxygen is a byproduct Thylakoid membrane converts light energy to chemical energy The Calvin Cycle Anabolic builds carbohydrates from smaller molecules and consumes energy Carbon enters Calvin Cycle in form of C02 and leaves in the form of sugar ATP is used as energy source and NADPH is used as reducing power for adding highenergy to make the sugar The 3carbon sugar produced is Glyceraldehyde 3PhosphateG3P The cycle occurs 3 times fixing 3 molecules of C02 Carbon fixation 3 phases 1 Carbon Fixation C02 is incorporated one at a time by attaching to 5carbon sugar RuBP The enzyme that catalyzes this step is rubisco most abundant protein in chloroplastsEarth The product is a 6carbon intermediate that s unstable so immediately splits in half forming two molecules of 3phosphoglycerate 2 Reduction Each molecule of3phosphoglycerate receives additional phosphate group from ATP becoming 13 bisphosphoglycerate NADPH donates pair of electrons to reduce 13 bisphosphoglycerate which also loses phosphate group to G3P For every 3 C02 molecules there are 6 G3P formed but only one molecule is counted as net gain One molecule of G3P eXits the cycle to be used by plant cell while the other five are used to regenerate 3 RuBP 3 Regeneration of C02 acceptor RuBP The carbon skeletons of5 G3 are rearranged into 3 RuBP In order to do this 3 molecules of ATP are used RuBP is now prepared to receive C02 again Net synthesis of1 G3P molecule 9 ATP and 6 NADPH Light reactions regenerate ATP and NADPH The G3P spun off from cycle becomes starting material for metabolic pathways that synthesize other organic compounds including glucose and other carbs Chapter 16 DNA replication The process by which a DNA molecule is copied and how cells repair their DNA Griffith s phenomenon Transformation The change in genotype and phenotype due to the assimilation of external DNA by a cell Avery s Experiment 3 Main Candidates DNA RNA and protein Found out DNA was the transforming agent Evidence that Viral DNA can program cells Bacteriophages or phages Viruses that infect bacteria Virus Can be DNA or RNA enclosed by a protective coat which is often simply protein To produce more viruses a virus must infect a cell and take over its metabolic machinery Hershey and Chase Experiment Showed that DNA is the genetic material ofa phage known as T2 which infect E coli a bacterium that lives in the intestines of mammals T2 composed of DNA and protein could turn an E coli cell into a T2 producing factory that released many copies when the cell ruptured Found that the phage DNA entered the host cells but the phage protein did not therefore concluding that DNA holds genetic info The Structural Model ofDNA Early 1950s arrangement of covalent bonds in nucleic acid polymer established Watson and Crick Used Xray crystallography Double helix The presence of two strands Sugarphosphate backbones on the outside of the DNA molecule hydrophobic nitrogenous bases on the inside of the DNA molecule The two sugarphosphate backbones are antiparallel subunits run in opposite directions Adenine paired with thymine Cytosine paired with guanine Adenine and guanine purinestwo organic rings Cytosine and thymine pyrimidines one organic ring Adenine equals the amount of thymine Cytosine equals the amount of guanine Base Pairing to a Template Strand Conservative model The two parental strands reassociate after acting as templates for new strands thus restoring the parental double heliX Semiconservative model The two parental strands somehow come back together after the process parental molecule is conserved Dispersive model All four strands of DNA following replication have a miXture of old and new DNA Meselson and Stahl Devised an experiment that supported the semiconservative model of DNA replication as predicted by Watson and Crick and is widely accepted now DNA Replication A Closer Look Each ofyour cells has 46 DNA molecules in its nucleus About 6 billion nucleotide pairs total Origins of replication Short stretches of DNA having a specific sequence of nucleotides where replication begins Proteins that initiate DNA replication separate the two strands and open up a replication quotbubblequot Replication proceeds in both directions until entire molecule is copied At the end of a replication bubble is replication fork Yshaped region where the parental strands of DNA are being unwound Several kinds ofproteins participate in the unwinding Helicase Enzymes that untwist the double heliX at the replication forks separating the two parental strands and making them available as template strands SingleStrand Binding Proteins Bind to the unpaired DNA strands keeping them from repairing Topoisomerase Relieves the strain ahead of the replication fork by breaking swiveling and rejoining DNA strands The enzymes that synthesize DNA cannot initiate the synthesis ofa polynucleotide they can only add nucleotides to the end of an already existing chain that is basepaired with the template strand The initial nucleotide chain that is produced during DNA synthesis is a short stretch of RNA not DNA Primer The RNA chain Primase The enzyme that synthesizes the RNA chain by starting a complementary RNA chain from a single RNA nucleotide adding RNA nucleotides one at a time using the parental DNA strand as template The completed primer 510 nucleotides long is basepaired to the template strand The new DNA strand will start from the 3 end of the RNA primer Synthesizing a New DNA Strand DNA Polymerases Catalyze the synthesis ofnew DNA by adding nucleotides to a preexisting chain Eukaryotes have at least 11 different DNA polymerases Most require a primer and DNA template strand along which DNA nucleotides line up Each nucleotide added to a growing DNA strand comes from a nucleoside triphosphate which is nucleoside sugar and base with three phosphate groups EX dATP supplies adenine Antiparallel Arrangement DNA polymerases can add nucleotides only to the free 3 end ofa primer or growing DNA strand Thus a new DNA strand can elongate in 5 to 3 direction Leading strand Requires only one primer for synthesis Lagging strand When DNA polymerase must work along the template strand in the direction away from the replication fork Synthesized as a series of segments Okazaki fragments segments of the lagging strand 100200 nucleotides long in eukaryotes DNA ligase An enzyme thatjoins the sugarphosphate backbones of all the Okazaki fragments into a continuous DNA strand Proofreading and Repairing DNA Mismatch repair Enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors A common mechanism involves a segment of the strand containing the damage being cut out excised by a DNAcutting enzyme a nuclease and the resulting gap is then filled with nucleotides using the undamaged strand as a template DNA Polymerase and DNA ligase enzymes involved in filing the gap Nucleotide Excision Repair DNA repair system When a mismatched nucleotide pair is replicated the subsequence change is permanent in the daughter molecule that has the incorrect nucleotide as a well as in any subsequent copies Mutation Replicating the Ends of DNA Molecules Repeated rounds of replication produce shorter and shorter DNA molecules with uneven quotstaggeredquot ends Telomeres Special nucleotide sequences in eukaryotes that do not contain genes instead the DNA consists of multiple repetitions of one short nucleotide sequence EX A human telomere TTAGGG is repeated 1001000x Acts a kind ofbuffer zone to protect organism s genes Specific associated proteins prevent the staggered ends of the daughter molecule from activating the cell s systems for monitoring DNA damage Telomerase Enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells thus restoring their original length and compensating for the shortening that occurs during DNA replication Not active in human somatic cells but its activity in germ cells results in telomeres of maximum length in the zygote Chromosome DNA molecule packaged together with proteins Nucleoid The dense region of DNA in a bacterium not bounded by membrane Chromatin complex of DNA and protein that fits into the nucleus through an elaborate multilevel system of packing The chromatin of each chromosome occupies a specific restricted area within the interphase nucleus and the chromatin fibers of different chromosomes do not become entangled Not condensed but still high order organization Heterochromatin Type of interphase chromatin that s in a highly condensed state and visible as irregular clumps with a light microscope Largely inaccessible to the machinery in the cell responsible for transcribing the genetic info coded in the DNA Euchromatin Less compacted more dispersed type of chromatin Accessible to this machinery so the genes can be transcribed Chapter 17 Gene expression The process by which DNA directs the synthesis ofproteins or in some cases just RNAs Proteins are the link between genotype and phenotype Two Stages 1 Transcription 2 Translation Background on GenesProteins Beadle and Tatum 0ne geneone enzyme hypothesis The function of a gene is to dictate the production ofa specific enzyme Won the Nobel Prize Restated as one geneone polypeptide hypothesis Basic Principles of Transcription and Translation Genes provide the instructions for making a specific protein but do not build proteins directly RNA is the bridge between DNA and protein synthesis Two different chemical languages Crick dubbed this concept Transcription The synthesis of RNA using info in the DNA The info between DNA and RNA is quotrewrittenquot or quottranscribedquot from DNA to RNA Occurs in the nucleus For a proteincoding gene the resulting RNA molecule is messenger RNA mRNA because it carries a genetic message from the DNA to the proteinsynthesizing machinery of the cell Translation The synthesis of a polypeptide protein using the information in the mRNA Occurs in cytoplasm ribosomes Change in quotlanguagequot Cell must translate mRNA into amino acid sequence of polypeptide Ribosomes Sites of translation complex particles that facilitate the orderly linking of amino acids into polypeptide chains Occur in ALL organisms prokaryotic and eukaryotic Prokaryotes not membranebound have a lack of compartmentalization which allows translation of mRNA to begin while transcription is still in progress Eukaryotes have nuclear envelope to separate the two stages Primary transcript The initial RNA transcript from any gene including those specifying RNA that is not translated into protein Codons Triplets ofNucleotides Smallest units of uniform length that can code for all the amino acids Triplet code The genetic instructions for a polypeptide chain are written in DNA as a series ofnonoverlapping threenucleotide words Template strand The pattern or template for the sequence of nucleotides in a RNA transcript For any given gene the same strand is used as the template every time the gene is transcribed An mRNA molecule is complementary rather than identical to its DNA template because RNA nucleotides are assembled by the basepairing rules Synthesized in the antiparallel direction EX 3 ACC5 transcripts 5 UGG3 Codons The mRNA nucleotide triplets written usually 5 3 EX 5 UGG3 codes for Tryptophan Trp The nontemplate DNA strand is sometimes called quotcoding strand During translation codons are read by translation machinery in 5 3 direction Must be 3X the of nucleotides to make the of amino acids Cracking the Code Nirenberg Synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base Could only contain one codon in repetition quotUUUquot Discovered the specific amino acid for this codon as well as for AAA GGG and CCC Start Codon AUG Also specifies an amino acid Stop Codons UAA UAG and UGA Reading Frame The ability to extract the intended message from a written language depending on the reading of the symbols in the correct groupings Molecular Components of Transcription RNA Polymerase Pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand thus elongating the RNA polynucleotide 5 3 direction Don t require a primer Promoter The DNA sequence where RNA polymerase attaches and initiates transcription Upstream Terminator In bacteria The sequence that signals the end of transcription Downstream Transcription unit The stretch of DNA that is transcribed into an RNA molecule Bacteria have a single type of RNA polymerase eukaryotes have at least three types of RNA polymerase Synthesis of an RNA Transcript Start point The nucleotide where RNA synthesis actually begins In bacteria the RNA polymerase specifically recognizes and binds to the promoter In eukaryotes a collection of proteins called transcription factors mediate the binding of RNA polymerase and initiation of transcription Transcription initiation complex The whole complex of transcription factors and RNA polymerase II bound to the promoter TATA box Crucial promoter DNA sequence The interaction of eukaryotic RNA polymerase II and transcription factors is an example of the importance of proteinprotein interactions in controlling eukaryotic transcription Elongation of the RNA strand RNA polymerase adds nucleotides to the 3 end of the RNA molecule Transcription occurs at rate of 40 nucleotides per second in eukaryotes A single gene can be transcribed simultaneously by several RNA polymerases Termination of Transcription Termination differs between bacteria and eukaryotes In bacteria transcription proceeds through the terminator sequence in the DNA In eukaryotes RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence then about 1035 nucleotides later proteins associated with the growing RNA transcript cut it free from the polymerase releasing the premRNA Eukaryotic cells modify RNA after transcription RNA processing Both ends of the primary transcript premRNA are altered The 5 end of premRNAis synthesized first receiving 5 cap modified form of guanine G nucleotide added onto the 5 end after transcription of the first 2040 nucleotides At the 3 end an enzyme adds 50250 more adenine A nucleotides forming a polyA tail The 5 cap and polyA tail functions 1 Facilitate export of mature mRNA from nucleus 2 Protect mRNA from degradation by hydrolytic enzymes 3 Help ribosomes attach to the 5 d end omeNA Split Genes and RNA Splicing RNA splicing The removal oflarge portions of the RNA molecule that is initially synthesized quotCut and paste job Introns The noncoding segments of nucleic acid that lie between coding regions are called intervening sequences Exons The other regions that are eventually expressed by being translated into amino acid sequences EXIT THE NUCLEUS When the mRNA molecule enters the cytoplasm the introns are cut out and the exons are joining together Spliceosome The large assembly of several different snRNPs joined with additional proteinswhich conducts RNA splicing Ribozymes RNA molecules that function as enzymes These are the basis of the idea of selfsplicing Alternative RNA splicing The idea that many genes are known to give rise to two or more different polypeptides depending on which segments are treated as exons during RNA processing The of different protein products an organism produces can be much greater than its of genes Proteins often have a modular architecture consisting of discrete structural and functional regions called domains Translation Transfer RNA tRNAThe translator which transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome A tRNA molecule arrives at a ribosome with a specific amino acid at one end and at the other end a nucleotide triplet called an anticodon which basepairs with a complementary codon on mRNA EX Consider the mRNA codon GGC which translates into amino acid glycine The tRNA that basepairs with this codon by hydrogen bonding has CCG as its anticodon and carries glycine at its other end The tRNA molecule reads the mRNA codon and interprets it into an amino acid Transcribed from DNA templates made in the nucleus Single RNA strand only 80 nucleotides long AminoacyltRNA Synthetases Related enzymes that make sure the correct matching up of tRNA and amino acid is carried out Wobble The exible base pairing at this codon position EX A tRNA with the anticodon 3 UCU5 can base pair with either the mRNA codon 5 AGA3 or 5 AGG3 Ribosomes Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis A ribosome consists ofa large subunit and a small subunit each made up of proteins and one or more ribosomal RNAs rRNAs In eukaryotes these subunits are made in the nucleolus The rRNA is the most abundant type of cellular RNA Ribosomes contain a binding site for mRNA then three binding sites for tRNA P site PeptidyltRNA binding site holds the tRNA carrying the growing polypeptide chain A site AminoaccyltRNA binding site holds the tRNA carrying the neXt amino acid to be added to the chain E site Exit site where the discharged tRNAs leave the ribosome Building a Polypeptide Initiation Nterminus Brings together mRNA a tRNA bearing the first amino acid of the polypeptide and two subunits ofa ribosome A small ribosomal subunit binds to both mRNA and a specific initiator tRNA called the translation initiation complex This process requires initiation factors proteins The mRNA moves down the chain till it reaches the start codon The start codon signals the start of translation Elongation Amino acids are added one by one to the previous amino acid at the Cterminus of the previous chain This requires several proteins called elongation factors and occurs in a threestep cycle The mRNA and ribosome move relative to each other Termination Cterminus The mRNA reaches the stop codon in the A site of the ribosome Release factor Binds directly to the stop codon in the A site Causes the addition ofa water molecule instead of an amino acid to the polypeptide chain This reaction breaks the bond between the completed polypeptide and tRNA in the P site releasing the polypeptide through the eXit tunnel of the ribosome s large subunit Polyribosomes Multiple ribosomes translate an mRNA at the same time Polyribosomes Strings of ribosomes Found in bacterial and eukaryotic cells enable a cell to make many copies ofa polypeptide very quickly Mutations Mutations Permanent changes that are responsible for huge diversity of genes found among organisms Point mutations Change a single nucleotide pair of a gene Nucleotidepair substitution The replacement of one nucleotide and its partner with another pair of nucleotides Silent mutation Mutation with no observable effect on the phenotype Results in same amino acid EX If 3 CCG5 on template strand mutated to 3 CCA5 then the mRNA codon that used to be GGC would become GGU which is still glycine Missense mutation Substitutions that change one amino acid to another one Nonsense mutation Causes the translation to be terminated prematurely by changing a codon for an amino acid into a stop codon thus resulting in a shorter than normal polypeptide Insertions and Deletions The additions or losses of nucleotide pairs in a gene Frameshift mutation Occurs whenever the numb er of nucleotides inserted or deleted is not a multiple of 3 Can be okay ifnear the end of the gene Mutagens Mutagens The physical and chemical agents that interact with DNA and cause mutations EX Xrays UV light Chapter 20 Recombinant DNA DNA molecules formed when segments of DNA from two different sources often different species are combined in vitro test tube Biotechnology The manipulation of organisms or their components to make useful products Includes selective breeding of farm animals and using microorganisms to produce wine and cheese Genetic engineering The direct manipulation of genes for practical purposes DNA Cloning Preparing welldefined segments of DNA in multiple identical copies Common approach of DNA cloning uses bacteria specifically E coli Plasmids Small circular DNA molecules that replicate separately from the bacterial chromosome Obtain a plasmid and then insert DNA quotforeignquot DNA The resulting plasmid is now a recombinant DNA molecule Then the plasmid is returned to a bacterial cell producing a recombinant bacterium This single cell reproduces to form a clone of cells population of genetically identical cells Gene cloning The production of multiple copies ofa single gene Two Basic Purposes 1 To make many copies of or amplify a particular gene 2 To produce a protein product Using Restriction Enzymes to Make Recombinant DNA Restriction enzymes Enzymes that cut DNA molecules at a limited number of specific locations Protect the bacterial cell by cutting up foreign DNA from other organisms or phages Each is very specific recognizing a particular short DNA sequence or restriction site and cutting both DNA strands at precise points within this restriction site Most restriction sites are symmetrical and the sequence of nucleotides is the same on both strands when read in 5 3 direction Restriction enzymes usually contain 48 nucleotides MANY cuts All copies of a particular DNA molecule always yield the same set of restriction fragments when exposed to the same set of restriction enzyme The most useful restriction enzymes cleave the sugarphosphate backbones in the two DNA strands in a staggered manner Sticky ends The resulting doublestranded restriction fragment with at least one singlestranded end Sticky ends form hydrogenbonded base pairs with complementary sticky ends on any other DNA molecules cut with the same enzyme DNA ligase makes this process permanent Cloning a Eukaryotic Gene in a Bacterial Plasmid Cloning vector The original plasmid the DNA molecule that can carry foreign DNA into a host cell and replicate there Bacterial plasmids are used for various reasons 1 Readily obtained from commercial suppliers 2 Manipulated to form recombinant plasmids by insertion of foreign DNA in vitro 3 Introduced into bacterial cells Storing Cloned Genes in DNA Libraries The cloning procedure which starts with a mixture of fragments from the entire genome of an organism is called a quotshotgunquot approach no single gene is targeted for cloning Genomic library The complete set ofplasmidcontaining cell clones each carrying copies ofa particular segment from the initial genome Bacterial Artificial Chromosome BAC A type of vector used in library construction Can carry an insert of100300 kb ofbase pairs advantage Eukaryotic Cloning and Expression Systems Yeast singlecelled fungi Two Advantages 1 As easy to grow as bacteria 2 Have plasmids Scientists have constructed recombinant plasmids that combine yeast and bacterial DNA and can replicate in either type of cell Eukaryotic host cells are used for expressing a cloned eukaryotic gene Eukaryotic proteins will not function unless modified after translation by either adding a carbohydrate or lipid Bacterial cells cannot undergo such modifications Electroporation Brief electrical pulse applied to a solution containing cells that creates temporary holes in their plasma membranes through which DNA can enter Amplifying DNA in Vitro The Polymerase Chain Reaction PCR Polymerase chain reaction PCR Quick selective process to clone or amplify DNA One or many DNA molecules can be quickly amplified in a test tube PCR procedure includes a threestep cycle which brings about a chain reaction 1 During each cycle the reaction mixture is heated to denature separate the DNA strands 2 Then the reaction mixture is cooled to allow hydrogen bonding annealing of short singlestranded DNA primers complementary to sequences on opposite strands of each end at the target sequence 3 Finally a heatstable DNA polymerase extends the primers in the 5 3 direction PCR uses an unusual heatstable DNA polymerase called Taq polymerase Isolated from a bacteria that lives in hot springs The primers can only hydrogen bond to sequences at opposite ends of the target segment at least 15 nucleotides long With each successive cycle the number of target segment molecules of the correct length doubles so the number of molecules equals 2quotn where n is the number of cycles Occasional errors during PCR replication impose limits on the number of good copies that can be made Gel Electrophoresis Gel electrophoresis The technique that uses a gel made ofa polymer such as the polysaccharide agarose Separates nucleic acids or proteins on the basis of size electrical charge and other physical properties Human Gene Therapy Gene therapy Introducing genes into an af icted individual for therapeutic purposes hold great potential for treating the relatively small number of disorders traceable to a single defective gene For gene therapy to be permanent the cells that receive the normal allele must be the ones that multiply continuously Protein Production in Cell Cultures The first pharmaceutical products quotmanufacturedquot by producing large amounts of proteins that are usually present in small amounts were human insulin and human growth hormone HGH Protein Production by quotPharmquot Animals Whole animals can be used to produce large quantities ofprotein products Transgenic animal When the gene from an animal of one genotype is introduced into the genome of another individual often of different species 1 They first remove the eggs from a female of the recipient species and fertilize them in vitro 2 They cloned the desired gene from the donor organism 3 They then inject the cloned DNA directly into the nuclei of the fertilized eggs 4 Some of the cells integrate the foreign DNA transgene into their genomes and are able to express the foreign gene 5 The engineered embryos are then implanted in a surrogate mother Forensic Evidence and Genetic Profiles Genetic profile Unique set of genetic markers quotDNA fingerprint Short tandem repeats STRS Variations in length of genetic markers tandemly repeated units of two to fivebase sequences in specific regions of the genome The of repeats is highly variable fro person to person polymorphic PCR is used to amplify particular STRs using sets of primers that are labeled with differentcolored uorescent tags the length of the region and thus the of repeats can be determined by electrophoresis PCR is used when DNA is in poor condition or in small amounts The Innocence Project uses STR analysis to revisit old cases Agricultural Applications Ti plasmid The most commonly used vector for introducing new genes into plant cells is this plasmid which comes from soil bacterium Integrates a segment ofits DNA T DNA into the chromosomal DNA ofits host plant cells Chapter 12 Cell division The continuity of life based on the reproduction of cells Cell cycle The life of a cell from the time it is first formed from a dividing parent cell until its own division into two daughter cells Cellular Organization of the Genetic Material Genome The cell s endowment ofDNA its genetic information Before the cell can divide to form genetically identical daughter cells all of this DNA must be replicated and then the two copies must be separated Chromosome very long linear DNA molecule associated with many proteins Chromatin The entire complex of DNA and proteins that is the building material of chromosomes Somatic cells All body cells except the reproductive cells Contain 46 chromosomes made up of two sets of 23 one set inherited from each parent Reproductive cells or gametes Sperm and eggs Have half as many chromosomes as human somatic cells or one set of 23 chromosomes in humans Distribution of Chromosomes During Eukaryotic Cell Division Chromosomes are usually in the form ofa long thin chromatin fiber but after DNA replication the chromosomes condense as the chromatin fiber becomes densely coiled and folded Sister chromatids Joined copies of the original chromosome Each duplicated chromosome has two sister chromatids Originally attached along their lengths by protein complexes called cohesionsin an attachment called sister chromatid cohesion Centromere A region containing DNA sequences where the chromatid is attached most closely to its sister chromatid Each sister chromatid has a centromere This attachment is mediated by proteins bound to the centromeric DNA giving the chromosome a narrow quotwaistquot Mitosis The division of genetic material in the nucleus Cytokinesis The division of the cytoplasm Meiosis in humans occurs only in the gonads ovaries or testes Phases of the Cell Cycle Mitotic M phase Includes both mitosis and cytokinesis Shortest part of the cell cycle Mitotic cell division alternates with much longer stage called interphase which often accounts for about 90 of the cycle The cell that s about to divide grows and copies its chromosomes in preparation for cell division Interphase is divided into subphases 1 61 Phase quotFirst gap The phase when the cell grows 2 S Phase quotSynthesisquot The only phase that chromosomes are duplicated in 3 62 Phase quotSecond gap The phase when the cell grows more in preparation for cell division Mitosis is broken down into five stages Prophase Prometaphase Metaphase Anaphase and Telophase The Mitotic Spindle A Closer Look Mitotic spindle The structure that consists of fibers made of microtubules and associated proteins Forms in the cytoplasm during prophase At the same time the other microtubules of the cytoskeleton partially disassemble Centrosome The subcellular region containing material that functions throughout the cell cycle to organize the cell s microtubules This is the where the assembly of spindle microtubules starts A pair of centrioles is located at the center of the centrosome but they are not essential for cell division The single centrosome duplicates during interphase forming two centrosomes The two centrosomes move apart during prophase and prometaphase as spindle microtubules grow out from them By the end of prometaphase the two centrosomes are at each pole of the spindle opposite ends of the cell Aster A radial array of short microtubules extends from each centrosome The mitotic spindle includes the centrosomes the spindle microtubules and the asters Kinetochore A structure ofproteins associated with specific sections of chromosomal DNA at each centromere Each of the two sister chromatids has a kinetochore They face in opposite directions During prometaphase some of the spindle microtubules attach to the kinetochores The mitotic spindle is complete by metaphase Anaphase initiates the enzyme separase to cut the cohesions holding together the sister chromatids of each chromosome which moves them towards opposite ends of the cell The nuclei reform during telophase Cytokinesis generally begins during anaphase or telophase and the spindle eventually disassembles Cytokinesis A Closer Look Cleavage The process that cytokinesis occurs by in animal cells Cleavage furrow A shallow groove in the cell surface near the old metaphase plate The first sign of cleavage On the cytoplasmic side of the furrow is a contractile ring of actin microfilaments associated with the protein myosin The cleavage furrow deepens until the parent cell is pinched into two completely separate cells each with its own nucleus and share or cytosol organelles and other subcellular structures Binary Fission in Bacteria Prokaryotes undergo the type of reproduction in which its cell grows to roughly double its size and then divides to form two cells Binary fission Refers to the process above and the asexual reproduction of singlecelled eukaryotes such as amoeba Chapter 18 Operons The Basic Concept Promoter The site where RNA Polymerase binds to DNA and begins transcription A single promoter serves all five genes that code for the subunits of the enzymes which together constitute a transcription unit Thus transcription produces one long mRNA molecule coding for five polypeptides making up the enzymes in the tryptophan pathway The cell can translate this mRNA into five separate polypeptides with the start and stop codons A single quotonoff switch controls the whole cluster of functionally related genes the genes are coordinately controlled Operator A segment of DNA composing the switch Controls the access of RNA Polymerase to the genes It s positioned within the promoter or sometimes between the promoter and the enzymecoding genes Operon The operator the promoter and the genes they control the entire stretch of DNA required for enzyme production for the tryptophan pathway EX The trp operon Repressor The off switch to the operon The repressor binds to the operator and blocks the attachment of RNA Polymerase to the promoter preventing transcription of genes The binding of repressors to operators is reversible Only if tryptophan binds to the trp repressor at an allosteric site does the repressor protein change to the active form that can attach to the operator turning the operon off Regulatory gene Has its own promoter and produces the trp repressor Corepressor A small molecule that cooperates with a repressor protein to switch an operon off This is how tryptophan functions in this system If the tryptophan level drops then the transcription of the operon s genes resumes Indirectly related Repressible and Inducible Operons Two Types ofNegative Gene Regulation The trp operon is a repressible operon because its transcription can be repressed when a specific small molecule tryptophan binds allosterically to a regulatory protein trp absent The lac operon is an inducible operon because it can be induced when a specific small molecule interacts with a regulatory protein lac present glucose absent The lac repressor is active by itself binding to the operator and switching the lac operon off Inducer A specific small molecule that inactivates the lac repressor Carbon carbon being tetravalent is one of the things that make such large complex molecules possible geometric isomers same covalent partnerships but differ in spatial arrangements a molecule with one CC double bond has 2 geometric isomers cis same side trans opposite sides enantiomers isomers that are mirror images of each other seven chemical groups that are the most important in biological processes are hydroxyl carbonyl carboxyl amino sulfhydryl phosphate and methyl of the functional groups most important to life they all have in common they are hydrophilic and increase solubility in H20 carbonyl in aldehydes and ketones make 2 groups of sugar aldose and ketose carboxyl in cells with a 139 charge called a carboxylate ion likely to ionize when a base is added to soln amino acts as a base charge with 1 in a cell sulfhydryl 2 of these react to form a covalent bond crosslinking which helps stabilize protein structure in hair proteins phosphate brings negative charge 239if at the end of a molecule l39if in a chain of phosphates can react with H2O to release energy plays a large role in energy transfer comes from the release of energy when it s removed from the carbon skeleton with H20 cells can harvest this to perform many fns has the most ionized forms of all the groups ATP is said to store energy but it stores the potential to react with water which releases energy chemical groups SH is characteristic of thiols alcohols are highly polar and may act as a weak acid hydroxyl groups ionize more readily when bonded to CO than when bonded to CH2 biological buffer system H20 C023 HZCO3S Hl HCO339 Monomer macromolecules carbs proteins nucleic acids another large biomolecule not a macromolecule is a lipid nucleic acids carbs and proteins are polymers linked by covalent bonds monomers are connected by condensation also called dehydration rxn loss of H20 molecule one m lecule provides hydroxyl and one provides a H dehydration is facilitated by en mes mes specialized macromolecules that speed up chemical rxns in cells polymers are broken apart by hydrolysis the reverse of dehydration H and OH anach to different monomers ex of hydrolysis digestion monomers released into the body absorbed into the bloodstream so they can be sent to body cells cells then use dehydration rxns to assemble monomers into different polymers that erform speci c actions in a ce 1 difference between human siblings are shovm mostly in polymers I 1 mal are or ere chH chH 0H OH chH chH o 0 0H OH H0 0 0H 0H H20 0H Carbohydrates structural support and energy storage includes sugars and polymers of sugars imule 39 quot then glucose is the most common monosaccharide trademark identifying chemical property of a sugar carbonyl group and multiple hydroxyl hydmlysis dehydratinn synthesis groups asymmetric carbon attached to 4 different atoms or groups of atoms monosaccharides are nutrients for cel s especially glucose in cell respiration cells get energy in a bunch of rxns starting with glucose molecules carbon skeletons are material for synthesis of other kinds of small organic molecules like amino acid and fany acids if sugar molecules are not used that way they are usually made into disaccharides or polysaccharides 2 monosaccs are joinedby a covalent bond in a dehydmtion rxn maltose glucose glucose has a 14 link e most prevalent disshac sucrose glucose fructose plants move carbs from leaves to roots and other nonphotosynthetic organs in the form of sucrose lactose glucose galactose cuzou cuzou anion cHiok F0 candensanon 0T T i 0H cl on 0H 1 on OH 035 on on I Id ng Yeas c 0quot mm an OR Glucose mucosa maltose water polysaccs are macromolecules polymers W hundreds or thousands of monomers joined by glycosidic links some polysaccs serve as sto e hydrolyzed as needed provides sugar to cells some are building material that protect the cell or the Whole organism function and look of a polysacc is determined by positions of its ycosidic links both plants and animals store sugar W storage polysaccs plants produce starch to store carbs store glucose in starch to be available starch represents stored energy is taken by hydrolysis breaking the bonds between glucose monomers simplest form of starch amylose unbranched most animals including humans have enzymes that hydrolyze plant starch es glucose an available nutrient for cells amylopectin is a more complex starch branched polymer W 16 links animals store glycogen polysacc polymer of glucose similar to amylopectin more extensively branched humans and other vertebrates store glycogen mainly in liver and muscle cells not sustaining long term organisms use polysaccs for structure cellulose major part of the tough Wall in plant cell Walls most abundant compound on earth also apolymer ofglucose f1ber refrned carbs produce more rapid rise in blood sugar levels loW in ber vitamins and mine in starch glucose monomers are Litlinked cellulose has links different links give them distinct shapes estareh helur mostly t eorl rcellulose stratghtneyerbranehed hydroxyl groups ean H bonol wrth other hydroxyls on the moleeule next to rt parallel to rt parallel eellulose moleeules are goupedmto mlcroflbnls eons get ego e r u m tn urneuttutrtrrmttemm about 80 eellulose moleeules assoelate to form amlcroflbnl rmlcroflbnls are the man struetural u tof aplant eell wall er Hbonols between c atoms 3 and 6 rs an unbranched glueose monomer rstmch ls dlgested by enzymes through hydrolysls hydrolyze ltsu lmks rfew organlsms haye enz another struetural polysaee rexoske rslm ar ymes that ean dlgest B llnks ehrtan letons to eellulose but aglueose monomer ofchmn has an appendage w N Lipids do not lnclude true po mers ly rgenerall notblg enou h to be consldered maeromoleeules rcompounds classlfled as llplds are so beeause they don39t mur well wth H20 some function for energy storage lg fat stores more than twice the energy in lg carb biologically important lipids fats phospholipids and steroids Fats not polymers but are large and assembled from some smaller molecules by dehydration rxns fat composed of 2 kinds of smaller molecules glycerol and fatty acids fatty acid long C skeleton usually 1618 C s to make a fat 3 fatty acid molecules join to glycerol by ester linkage bond between hydroxyl and carboxyl resulting fat is called a trigylcerol 3 fatty acids linked to a glycerol molecule fat made from saturated fatty acids is a saturated fat saturating or hydrogenating something makes it less uid 0 HOW transOleic acid HO cisOleic acid cis is most prevalent is What cause the kink transfats contribute more than saturated ones to atherosclerosis fat is a compound resovior of fuel and also cushion organs Whales have such think layers to protect them in icy water long term reserves adipose cells water condensation fatty acids glycerol fat hydrolysis water Synthests oH o m1 g 0 Hydrolysis l 1 C39H Cths ill c Oll H30 CH9 3 any acads i gaycemi Phospholipids cells would not exist if not for this type of lipid makes up cell membranes phospholipids have in common ester linkage most important function is preventing leakage from cells to move through the body fats need the help of phospholipids synthesis of phospholipids uses fatty acids some tails have double bonds the most amphipathic type of lipid have a charged end and a noncharged end assemble with molecules pointing outwards toward H2O when placed in H2O only has 2 fatty acids attached to glycerol 3rd hydroxyl in glycerol is joined to a phosphate group phosphate group contributes to charge additional small molecules usually charged or polar can be linked to phosphate groups to form phospholipids Choline u n a z quotquotquotquotquotquotquotquotquot A 2 E Phosphate a e u gt I 395 u Fatty aclds g Hydraphilic g head I Hydrophobic tails Ster01ds many hormones are steroids steroids lipids with C skeleton made of 4 fused rings steroids differ by chemical groups attached to the ensemble of rings cholesterol is a common component of animal cell membranes also a precursor for other steroids cannot be hydrolyzed for vertebrates cholesterol is synthesized in the liver the negative impact of sat and unsat fats come from the effect they have on cholesterol levels Proteins more than 50 ofdry mass of cells some speed up chemical reactions some play arole in structural support storage transport communication movement and defense against foreign substances complete proteins contain all 8 essential amino acids most enzymes are proteins gulate metabolism by acting as cat s s p im re aly t su er portant because they are not consumed in the reaction Ammo n n s u n s u u mamava and gslb LplsusELVLKuln1 l w l M nydmoenunndsbstmn nbeur aminnlddxndl tmnl as n imitunsinoalr v u Min Protein polymers of amino acids proteins are directly involved in breaking food polymers into smaller molecules defending cell against viruses c anging the shape of the cell protein consists of one or more polypeptides each folded and coiled into speci c 3D structure Amino Acid Monomer amino acid organic molecules with carboxyl and amino grou s there s an asymmetric connected to 4 diff things carbon in the center called the or carbon only ionized forms exist in the cell in the pH of a cell acidic amino acids have side chains that are generally negative because of the carboxyl with is generally ionized at cell pH basic amino acids are usually pos at cell pH charged side chains make them hydrophilic nonpolar R side chains contain alkyl or aromatic groups polar R has thiol hydroxyl or amide acidic R has carboxylate basic Rhas derivatives of ammonia Amino Acid Monomer j oined by dehydration rxn results in a covalent bond called a peptide bond one end has an amino group other end has a ee carboxyl chain has an amino end N terminus and a carboxyl end Cterminus repeated sequence is called polypeptide backbone functional protein is not a polypeptide it is l or more polypeptides twisted folded and coiled with a sequence having 127 amino acids there are 20127 ways to make a chain that long when a cell makes a polypeptide the chain folds to assume a functional structure for the protein driven and reinforced by formation of a variety of bonds between parts of the chain which depends on the arrangement of amino aci some proteins appear spherical globular acquire compact spherical shapes when 2 structures are folded over each other some proteins are long and brous brous found in cells and tissues function of a protein is completely dependent on the molecular order Protein Structure particular sequence of amino acids not random inherited by genetic information R H r 0 0 N c c N c c H I l v H20 when proteins are hydrolyzed it disrupts the primary structure because it messes with the covalent bond that s holding amino acids together a change in primary can alter forces that determine structure this happens in digestion Seconda proteins have sequences repeatedly coiled or folded these coils or folds are referred to as 2 structure secondary is the result of H bonds between repeating constituents of the peptide backbone not the side chain 0 and N atoms form H bonds off the side chain alone they are weak but all together they support the protein shape one type of structure is the or helix H bonding in every 43911 amino acid this depends on the regular occurance of CO and NH some proteins have stretches of or helix separated by nonhelical regions some have helix over most of their length B pleated sheet is 2 or more regions connected by H bonds between 2 parallel polypeptide backbones Tertiary overall shape of a polypeptide resulting from interactions between R groups in contrast to 2 which has interactions between side chains hydrophobic interaction amino acid with nonpolar R groups usually end up in clusters at the center of the protein out of contact with H20 caused by action of H20 molecules exclude nonpolars as they form H bonds with each other and with hydrophilic parts once they re together Van der Waals hold them together cumulative effect further reinforcement comes from disulfide bridges 2 cystene monomers SH groups brought together by folding of protein SS strongest stabilizing feature but cells don t rely much on them because they make the protein rigid and many proteins need to change shape as they work Quatemary proteins that have 2 or more polypeptide chains into one functional macromolecule overall protein structure results from aggregation of polypeptide units ex collagen fibrous helical sub units into a triple helix that give the fibers lots of strength found in connective tissue blood vessels skin tendons ligaments cornea and cartilage Polypeptide mam 7 Hemoglobin Molecule muesnanaeu collagen i iron gem mam L acham quot chain nu Callagan mm V red blood cell Timon Hm Chmquot a chain hlical shape DI the H 91 nm polypeplide molecule eX hemoglobin globular 4 polypeptide units on and 2B both on and B sub units consist of a helical 2 structure each unit has a non polypeptide component called a heme which has a Pb atom that binds to O Si ificance sickle cell disease is caused by the substitution of one amino acid primary structure polypeptide chain of some amino acid sequence can arrange itself into a 3D form ed and maintained by 2 and 3 structure protein folding normally occurs as the protein is being synthesized if you were to replace every lysine with serine the protein folding would be less sensitive to pH because you re going from an amino group to CHZOH structure also in uenced by the conditions around it ipr salt concentration temperature or other stu changes enough the protein can unrave which is a process called denaturation mean the protein is now biologically inactive can happen with the protein goes from an aqueous environment to an organic solvent basically stu quot disrupts the H bonds ionic bonds or disul de bridges heat can agitate it so much so that the interactions stabilizing the structure are broken proteins in the blood denature at high body temps if a protein is not very sensitive to pH it probably has many side chains with CHZOH agem pH temp mm nrznglh xnlublhry A E E 39i hmlcglcnl lt f mm j v lmc upquot 5 I to a v A f V C LJ x i in 39 uclmty 39 I Nurmal pruleln fenmuramg Denatured pmleln some proteins go through many intermediates before reaching a stablmeishape quotgums rflnal shape reyeals hothmg about the proeess rchaperomns ehaperohe protems help the foldlng of other protems a protem that has folded properly rmlsfoldmg ls respondslble for Alzhelmers and Parklnsons x ray erystallography ls usedto determme the 3D strueture of3D protems rothertechmques are N39MR speetrography and blolnfor matlcs Nucleic Acids rgene umt ofmhehtahee eohslsts ofDNA rwhlch ls a polymer of huelere aclds geheratloh to another rDNA provldes dlrect or for lts own repheah on DNA dreets A s h esls E gt S p 3 g E sls reach ehromosome as one long DNA moleeule rusually w several hundred genes nN gehetle progams moleeular hardwarequot stuff for llfe functions ls mostly protems reach gene along aDNAmoleeule eoordmates syhthesrs of mRNA rmRNA mteraets w eell syhtheslzmg maehmery to dreet the formation of a polypeph de rwhlch folds mto all of part of a protem DNA gt RNA gt protem 7mm 4 4 huelele aclds are maeromoleeules rexlst as polymers polyhueleotrdes Nuclenu39des Phusphale gmup DEDXyHbDSE Ease Nucleotides consist of3 parts nitrogenous base 5 c sugar and phosphate group area ofthe unit without a phosphate group is a nucleosi e 2 families ofnitrogenous bases are pyrmidines and purines I I I Luv Jan pyrmidines have a 5 member ring ofC andN atoms NtakesH from soln which is why its called a nitrogenous base members ofthis family are cytosine c thymine T and uracil U punnes have alargero mem er ring sedto as member ring adenine A and guanine G adenine guanine and cytosine are in both types ofnucleic acids DNA exclusively has deoxyiibose andthymine Both DNA and RNA have phosphate guanine and adenine RNA exclusively has uracil and nbose in RNA the sugar connectedto the N base is nbose the 2 0 on nbose makes RNA more vulnerable to breakdown ensure that conect levels of protein are maintained in the cell for DNA the sugar connected to the N base is deoxyri ose the two diffel by one 0 atom DNA is much longer than RNA which is made by copying short segments ofDNA atoms in sugar have lt after them phosphate group attaches to the 5 c in the sugar called a nucleoside phosphate or a nucleotide nucleotides I t t quot on 3 C directionalityis rom 5 a 3 along the sugar phosphate backbone there are appendages consisting ofN bases a A u linear order of the bases 1 0 speci es amino acid sequence Which speci es a proteins 3D structure and inction RNA molecules have a single polynucleotide chain cellular DNA molecules have 2 polynucleotides double helix 5 9 3 directional arrangement referred to as antiparallel sugar phosphate backbone is on the outside of the helix N bases paired on the interior 2 l 39 paired bases and Van der Waals interactions between stacked bases each gene is a particular segment ofthe molecule the fact that A only goes With T and C goes With G gives it the property of being able to make an exact copy 0 itse f linear sequences of nucleotides in DNA molecules determine the amino acid sequence of proteins 5 ram llenl ldlel HlS z ilr r u I und lsl mr rnme 1 euoreue D D u Nieuee eou e quotyeeueLeu H R munumevammu ecu 2 COMPLEX CARBOHYDRATES emu r g r U D r r r r r e lured e e r r DH H phusphumes v band H W H The Cell rbemg able to reproduce uselfrs akey ddfference between Me and nonlee 8115 can msh the reprodueuor cycle before they actually dmde rprotem kmases are used to regulate what otherprotems do rorganelles membranerenclosed eompmmems rseen with e39 rrueroseopes mmcuaxnm Nmnnlmt mumlm mu alumni mu m quottonalLAST Size l mhni Hairpin Ilnimi Nuclear envelop snr Presch mi cnrenmsomns Smyemlrmlanwhh Muldplul linunwound singlemiiruhnwht no noslsesomes on nuslsasmwss no nnriuemmes Gnlgl apparatus Ahxnn Fmem AhslnL Endnphsmlcruimlum Absent Vrmcm bse lyxosnmes peroxlsnmu Miter n n Praznf Chlnmphy I Nos in hlmplasu h shterapians bosomes Keladve ysma Relatively urge RInivuy mull em Present Ahsan Mluotuhulesdntermedlau Abs llmenrsml m lamenks flagella Lack mizmwhn u Cunhin mlmmhules EukarxowProkarxote bactaquotia and archea are prokaryote protism fungi animals and plants are euk ote all cells have a selective balrier called a plasma membrane cytosol melosed in the ma39nbrane seni uidjellylike stuff all cells contain chromosomes which carry gmes in the form ofDNA all cells have ribosomes anaju 39 39 eukaryote most DNA in the nucleus which is bound by a double membrane prokaryote DNA conceitrated but not ma39nbmne melosed in a nucleoid i aim called cytoplasm Cyt0plasm also refas 39 39 39 organelles suspmded in cytosol wcytoplasm 39 39 is one way r eukary es aremuch larger cell size limits cellular metabolism e are uppaquot and Iowaquot limits 39 39 39 39 nquimts andwaste Eukggyote i L i u r 394 39 39 mun bc mzymes are built into the membranes divaquotse proteins are embedded in the lipid bilayaquot mzn39nes in mitochondria ma39nbmne function in cellular respiration Animal Vs plant animals have lysosomes cmtrosomes with cmtrioles and agella although agella are sometimes presmt in plant spam plant cells have chloroplasts central vacuoles cell walls and plasmodesmata Nucleus and Ribosomes nucleus houses most of the cells DNA ribosomes use info from DNA to make proteins nucleus has most of the genes some are in mitochondria and chloroplasts nuclear envelope separates nuclear contents from the cytoplasm double lipid bilayer encloses genetic material in eukaryotic cells perforated by pores complex lines each pore and regulates entryexit of most proteins and RNAs but also large complexes of macromolecules each membrane of the nuclear envelope has a lipid bilayer outer is continuous with the RER and has ribos attached inner has several inner nuclear membrane proteins membranes are connected at pore sites nuclear side of the envelope except at the pores is lined by the nuclear lamina netlike arrangement of protein laments maintains shape of nucleus by supporting nuclear envelope evidence also suggests a nuclear matrix framework of bers entending throughout the interior in the nucleus DNA is organized into chromosomes carry genetic info each chromosome is made up of chromatin complex of proteins and DNA nucleolus structure within the nondividing nucleus adjoins part of the chromatin in the nucleolus ribosomal RNA rRNA is synthesized proteins taken in from the cytoplasm are put together with rRNA into large and small ribosomal subunits which exist in the nucleus through the nuclear pores to the cytoplasm when it gets back to the cytoplasm a large and small unit can assemble into a ribosome there can be 2 or more nucleoli it depends Ribosomes complexes of rRNA that carry out protein synthesis cells active in protein synthesis also have prominent nucleoli ribosomes build proteins in 2 cytoplasm locations at any time free ribosomes are suspended in the cytosol bound ribosomes are attached to the outside of the ER or nuclear envelope bound and free ribos are almost identical they can alternate between the 2 roles most proteins made by free ribos function within the cytosol ex enzymes that catalyze the rst steps in sugar breakdown bound membranes generally make proteins for insertion into membrane for packaging with certain organelles ex with lysosomes or for export secretion cells that specialize in secretion like in the pancreas which secrete digestive enzymes have high proportions of bound ribos Endomembrane System membranes of this system are related either by physical continuity or by transfer of membrane segments as vesicles sacs made of membrane segment thickness molecular composition and types of rxns in a given membrane vary and can be modi ed several times endo system nuclear envelope golgi apparatus lysosomes various kinds of vacuoles and plasma membrane plasma membrane isn t really in the right place but is similar enough to be included Endoplasmic Reticulum extensive network or membranes accounts for hald the total membrane in eukaryotic cells has a network of membraneous tubules and sacs called cistemae resovior for liquid ER membrane seperates the inside area the ER lumen cavity or cistemal space from the cytosol ER membrane is continuous with the nuclear envelope so space between 2 membranes of the envelope is continuous with the lumen of the ER 2 distinct but connected regions smooth and rough Smooth Endoplasmic Reticulum outer surface lacks ribosomes functions in many metabolic processes such as synthesis of lipids metabolism of carbs and detox of drugspoisons enzymes of the smooth ER are important in synthesis of lipids including oils phospholipids and steroids enzymes involved in detox are typically in the liver involves adding OH groups to drug molecules to make it more soluble so the body can ush it out of the system also stores Ca2 ions in muscle cells special smooth ER pushes calcium ions from the cytosol to the ER lumen respondsible for the process stimulation 9 contraction of a muscle cell Rougl1 Endoplasmic Reticulum many types of cells secrete proteins by ribos attached to the rough ER as a polypeptide chain goes from a bound ribo its threaded into the ER lumen through a pore formed by a protein complex in the ER membrance as the protein enters the ER lumen it folds into its proper shape glycoproteins proteins with carbohydrates covalently bonded to them secretory protein after secretory proteins are formed ER membrane keeps them separate from proteins produced by free ribosomes depart from ER wrapped in membranes of vesicles bud like bubbles from a different region called the transitional ER transport vesicles go from one part of the cell to another rough ER is also a membrane factory grows in one place by adding membrane proteins and phospholipids to its own membrane polypeptides that are going to be membrane proteins come from ribosomes are inserted into the ER membrane and anchored by hydrophobic portions rough ER can also make its own phospholipids enzymes built into the ER membrane put together phospholipids from precursors in cytosol ER membrane is transferred in the form of transport vesicles to other components to the endo system Golgi Apparatus after leaving the ER many transport vesicles go to the golgi center of manufacturing sorting and shipping products of the ER like proteins are modified stored and sent to other locations golgi is very extensive in cells specialized for secretion consists of at membranous sacs cistemae cell may have hundreds of them Membrane of the cistemae in a stack separates internal space from cytosol vesicles near the golgi are used in the transfer of stuff between parts of the golgi and other functions a stack has structural polarity 2 poles are the cis face and trans face cis is usually near the ER trans vesicles move stuff between the golgi and ER vesicle buds from the ER and adds its membrane and contents of its lumen to cis face by fusing with the golgi trans face gives rise to vesicles pinch off and travel products of ER are modified in their transit from the cis to trans region golgi finishes stuff but also makes macromolecules many secreted polysaccs are golgi products including pectins nonproteingolgi products depart from the trans face inside transport vesicles that eventually fuse with the plasma membrane golgi manufactures and refines in stages with different cistemae containing unique groups of enzymes cistemal maturation model suggests the cistemae of the golgi progress forward from the cis to the trans face of the golgi carry and modify cargo as they move before a golgi stack releases product from the trans face it sorts and targets them molecular ID tags like phosphate groups added to golgi products are like ZIP codes Lysosomes membranes sac of hydrolytic enzymes an animal uses to digest macromolecules enzymes work best in acidic environments of lysosomes if a lysosome breaks open the enzymes aren t very active because cytosol has a neutral P excessive leaks can destroy the cell hydrolytic enzymes and lysosomal membrane are made by the rough ER and transported to the golgi some proteins come by budding from the trans face of the golgi
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