Foundations of Biology 2 Course Notes
Foundations of Biology 2 Course Notes BIOSC 0160
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Chapter 8 Study Guide Vocabulary 81 Metabolic Pathway a series of chemical reactions that either builds a complex molecule anabolic pathway or breaks down a complex molecule catabolic pathway Catabolic Pathways a metabolic pathway that releases energy by breaking down complex molecules to simpler compounds Anabolic Pathways a metabolic pathway that synthesizes a complex molecule form simpler compounds Bioenergetics the ow of energy through an animal taking into account the energy stored in the food it consumes the energy used for basic functions activity growth reproduction and regulation and the energy lost to the environment as heat or in waste Energy the capacity to cause change do workto move matter against an opposing force Kinetic Energy the energy of motion which is directly related to the speed of that motionmoving matter does work by imparting motion to other matter HeatThermal Energy the total amount of kinetic energy due to molecular motion in a body of matterheat is energy in its most random form Potential Energy the energy stored by matter as a result of its location or spatial arrangement Chemical Energy energy stored in the chemical bonds of molecules a form of potential energy Thermodynamics the study of energy transformations that occur in a collection of matter closed open systems organisms are open systems First law of Thermodynamics the principle of conservation of energyenergy can be transferred and transformed but it can t be created nor destroyed Entropy a quantitative measure of disorder or randomness symbolized by 5 Second Law of Thermodynamics the principle whereby every energy transfer of transformation increases the entropy of the universeordered forms of energy are at least partly converted to heat and in spontaneous reactions the free energy of the system also decreases 82 Free energy the portion of a system s energy that can perform work when temperature ad pressure are uniform throughout the systemthe change in free energy of a system is calculated by the equation AG AH TAS where T is absolute temperature AG change in free energycan only be negative when there is a loss of free energyunstable higher G stable lower G NEGATIVEspontaneous POSITIVE or Ononspontaneous AH change in enthalpy equivalent to total energy AS change in entropy T temperature Kelvin Exergonic Reaction a spontaneous chemical reaction in which there is a net release of free energy AG is negative Endergonic Reaction a nonspontaneous chemical reaction in which free energy is absorbed from the surroundings AG is positive 84 Catalyst a chemical agent that changes the rate of a reaction without being consumed by the reaction Enzyme a protein serving as a catalyst a chemical agent that changes the rate of a reaction without being consumed by the reaction Free Energy of Activation the amount of energy that reactants must absorb before a chemical reaction will start also called activation energy Substrate the reactant on which an enzyme works EnzymeSubstrate Complex a temporary complex formed when an enzyme binds to its substrate molecules Active Site the specific portion of an enzyme that attached to the substrate by means of weak chemical bonds Induced Fit that change in shape of the active site of an enzyme so that it binds more snugly to the substrate induced by entry of the substrate Cofactors any nonprotein molecule of ion that is required for the proper functioning of an enzymethese can be permanently bound to the active site or may bind loosely with the substrate during catalysis Coenzyme an organic molecule serving as a cofactormost vitamins function as coenzymes in important metabolic reactions Competitive Inhibitors a substance that reduced the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics Noncompetitive Inhibitors a substance that reduced the activity of an enzyme by binding to a location remote from the active site changing its conformation so that it no longer binds to the substrate 85 Allosteric Regulation the binding of a molecule to a protein that affects the function of the protein at a different site Cooperativity an interaction of the constituent subunits of a protein whereby a conformational change in one subunit is transmitted to all the others Feedback Inhibition a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway Chapter 14 DNA and the Gene Synthesis and Repair 1 What are genes made of a Originally thought to be proteins i Most obvious choice 1 Complex 2 Variable 3 Big 4 DNA only has four nucleotides b How did we figure it out i Hershey Chase experiment 1 T2 virus bacteriophage only infect bacterial cells Ecoli Head contains the genetic information Virus injects its genes into the cell Capsid protein coat is left behind attached to the exterior of the cell 2 Virus was grown in the presence of a radioactive isotope 32F DNA 355 proteins ii Hershey Chase Hypothesis 1 If genes consist of DNA then radioactive DNA would be found inside the cells while radioactive proteins would be found only in the ghosts outside the cells 2 Centrifuge results Radioactive DNA in the pellet radioactive protein is in the solution 11 DNA Primary Structure a Deoxyribonucleotide alignment of nucleotide monomers i Phosphate group on 5 C ii Sugar deoxyribose iii Nitrogenous base on 1 C 1 Adenine 2 Thymine 3 Cytosine 4 Guanine iv Nucleotides joined on 3 C by phosphodiester bonds sugar phosphate backbone 111 DNA Secondary Structure a Antiparallel nature based on directionality 5 3 and 3 5 b Complimentary base pairing 1 ThymineCytosine pyrimidines single ring 2 Adenine Guanine purines double ring 3 Hydrogen bonding CG 3 gt AT 2 H bonds must be broken for replication c Double helix helps save space stabilizes the structure IV How does DNA Replicate a Watson and Crick suggested that the existing strands of DNA served as a template pattern for the productions of new strands with bases being added to the new strands according to complimentary base pairing 1 Semiconservative replication i First replication conserves 12 of the original parent cell ii Once it s split once it s always split 2 Conservative replication i Parental DNA always remains intact together 3 Dispersive replication i Pieces of the parent cell are dispersed throughout the resulting DNA b MeselsonStahl Experiment 1 Grew Ecoli in the presence of heavy Nitrogen M in solution it will settle to the bottom to label the bacterial DNA i Generation 0 ii One thick band gives relative idea of amount of DNA 2 After several generations switched bacteria back to normal 14N media less dense than heavy Nitrogen i Generation 1 ii 15N is already incorporated into the DNA ladder no more is added it is not free or oating ii Generation 2 is simply letting the DNA replicate for 20 more mins this provides the definitive answer 3 Separated DNA by densities i Three quotbandsquot 14N 15N and hybrid intermediate ii Old strands 15N iii New strands 14N iv Semiconservative replication evidence one hybrid band and one 14N band equal thickness v Conservative replication evidence one 15N band and one 14N thicker 14N band vi Dispersive replication evidence one hybrid band 4 Results i Generation 0 15N ii Generation 1 Hybrid iii Generation 2 14N and hybrid semiconservative replication V What are the differences in replication between eukaryotes and prokaryotes a Prokaryote 1 Bacterial chromosomes have a single origin of replication replication proceeds in both directions CIRCULAR b Eukaryote 1 Chromosomes are LINEAR 2 Have multiple origins of replication quotbubblesquot VI Replication forks a Enzymes all present in the nucleus 1 Helicase9 unwinds the double helix breaks hydrogen bonds works in between on both strands 2 Primase9 RNA polymerase makes stretches of DNA makes a polymer not stable enough to stay on stretch of DNA adds a few primers then falls off capable of de novo synthesis with the RNA primer 3 T0p0isomerase9 Gyrase enzyme active before helicase nick it and repair it prevents strand from overcoiling it clips bonds the backbone of the DNA unwinds and straightens strand 4 DNA Polymerase9 I II 111 must have a free 3 hydroxyl group Critical characteristic can only work in ONE direction Adds dNTPs free DNA nucleotides with 3 phosphates attached to the 3 end DNA polymerization is exergonic spontaneous two phosphate groups and a water is released ENERGY Has sliding clamp to stabilize DNA polymerase III has an intrinsic proofreading ability DNA polymerase I proofreading enzyme 5 Singlestrand binding proteins9 hold strand open so DNA can t go back together once all of the enzymes go through it leaves so the strands can come back together b DNA grows bidirectionally 5 3 new and leading strand 3 5 old strand but replicates in one direction 1 The lagging strand synthesis Requires the primase so that there is now a free hydroxyl group to add new nucleotides Synthesized discontinuously Moves AWAY from the replication fork STEPS 1 Primase synthesizes a short RNA primer 515 nucleotides PRIMER ADDED 2 DNA polymerase III adds bases to free 3 end of the RNA primer can only move 5 9 3 moving away from the replication fork FIRST FRAGMENT SYNTHESIZED 3 Synthesized as short discontinuous fragments Okazaki fragments SECOND FRAGMENT SYNTHESIZED 4 DNA polymerase I replaces the RNA primer at the beginning of each Okazaki fragment with DNA nucleotides editor PRIMER REPLACED 5 DNA ligase joins the Okazaki fragments GAP CLOSED 2 The leading strand synthesis Free 3 OH group is required Only requires one primer DNA polymerase III stabilized by sliding clamp which is a series of proteins uses free 3 OH group Always synthesized continuously Moves TOWARD the replication fork Replisome Enzymes responsible for DNA synthesis around the replication fork all of the enzymes working together in DNA joined together in one large complex oined into one large multienzyme machine Q Which of the following represents the correct order of events as they occur in the process of DNA replications A Helicase opens the helix DNA polymerase III elongates primer and synthesizes leading and lagging strands DNA ligase links fragments of DNA Telomeres Regions at the ends of linear chromosomes Do not contain genes Short stretches of repeating bases Sections of the DNA that repeat nucleotides over and over Do not code for any sort of protein not a gene a As replication fork reaches the end of a linear chromosome no way to replace the RNA primer b When primer is removed single stranded DNA is left at end of each new chromosome Telomere on lagging strand gets a little bit shorter truncated after each replication eventually nucleotides will be pulled out from the coding region which leads to defective proteins Problems 1 RNA primer is removed by DNA polymerase I 2 Leaves section of ssDNA on the lagging strand 3 Remaining ssDNA is eventually degraded 4 Chromosome is shortened Telomerase to the rescue Adds repeating bases to the end of the lagging strand Carries an RNA template with it embedded Prevents lagging strand from getting shorter with each replication Goal is to extend the length of the telomere enough so that when it gets shortened it does not go into the coding region Somatic cells Normally lack telomerase Chromosome progressively shortens as individual ages Limits active growing time Telomerase is most active in reproductive organs egg and sperm Limits the growing time for every cell The length of the telomere dictates how many times a cell can divide a the longer the telomere9 the longer the cell life and vice versa VII What if a mistake is made Mistakes rarely happen a Error rate of less than one mistake per billion bases However if mistakes happen repair enzymes are available 1 Proofreading a DNA polymerase can proofread its work b DNA polymerase III checks match between paired bases and corrects errors pauses and removes the mismatched bases Epsilon subunit acts as an exonuclease it can remove a nucleotide as well as add a nucleotide VIII What if the mistake isn t caught Mismatch repair enzymes 1 Recognize the mismatched pair 2 Remove a section of the newly synthesized strand that contains the incorrect base 3 Fills in the correct base Vllll Damaged DNA Tanning beds sun radiation UV light vAv Thymine dimers iv a 2 thymines binding together Nucleotide excision repair system a Recognizes damaged DNA b Removes ssDNA in damaged area does not remove both sides because the compliment strand is the template occurs after replication occurs no primer needed because there is a free 3 hydroxyl What if the mutation is not repaired a Uncontrolled cell growth cancer formation Chapter 15 How Genes Work 1 Central Dogma accepted norm of Molecular Biology 1 Information ows from DNA 9 RNA 9 protein Goal is to get a functional protein at the end 2 DNA is transcribed To messenger RNA By RNA polymerase a Transcription process by which information in DNA is copied to RNA 3 mRNA is then translated to protein b Translation process where the order of nucleotide bases is converted to the order of amino acids 4 According to the central dogma Genotype is determined by the sequence of bases in its DNA what s encoded for in the DNA Phenolype is a product of the proteins it produces Phenotype DOES NOT always re ect genotype sometimes due to mistakes in sequence a single nucleotide change can have a HUGE impact on phenotype i DNA polymerase IIII could have not caught the mistake ii Could have been altered after the DNA was replicated II The Genetic Code 1 How does the sequence of bases in a strand of mRNA code for the amino acids in a protein There are 4 RNA bases U A G C and they must specify 20 amino acids A three base code CODON could specify a maximum of 4x4x4 64 amino acids 2 How long is a word in the genetic code a The triplet code is redundant Some amino acids are specified by more than one triplet code bCodon Group of three bases Specifies a particular amino acid c The reading frame sequence of codons is critical to protein production The third nucleotide base is not nearly as important as the starting two nucleotides d START CODON AUG 9 does code for an amino acid e STOP CODON UGAUAAUAG 9 do not code for amino acids 3 Important properties ofthe code i It is redundant All amino acids except two are encoded by more than one codon ii It is unambiguous One codon never codes for more than one amino acid iii It is nearly universal With a few minor exceptions all codons specify the same amino acids in all organisms iv It is conservative The first two bases are usually identical when multiple codons specify the same amino acids 111 Mutations Any permanent change in an organism s DNA a change in genotype May or may not lead to a change in phenotype 1 Types of Mutations a Point mutations single base substitution 9 result from a single base change i Missesne mutation Example Sickle Cell Anemia New base alters the codon resulting in a different amino acid 3 GAC GTC TGA 5 normal DNA 5 CUG CAG ACU 3 normal RNA leucine glutamine threonine normal 5 CUG CGG ACU 3 mutated RNA leucine arginine threonine mutated ii Nonsense mutation Example Cystic Fibrosis and Hemophilia New base changes a codon into a stop codon 3 GAC GTC TGA 5 normal DNA 5 CUG CAG ACU 3 normal RNA leucine glutamine threonine normal 5 CUG UAG ACU 3 mutated RNA leucine STOP mutated iii Silent mutation New base causes no change in the final protein 3 GAC GTC TGA 5 normal DNA 5 CUG CAG ACU 3 normal RNA leucine glutamine threonine normal 5 CUG CAA ACU 3 mutated RNA leucine glutamine threonine same iv Insertions and Deletions Frameshift mutation Example Hun tington s Disease Extra base pairs added or deleted from the gene Insertions and deletions of one or two bases cause frame shifts Insertions and deletions of 3 bases may be less serious 3 GAC GTC TGA AAA TCA CCT 5 normal DNA 5 CUG CAG ACU UUU AGU GGA 3 normal RNA leucine glutamine threonine phenylalanine serine glycine 5 CUG AGA CUU UUA GUG GA 3 mutated RNA Leucine Arginine Leucine Leucine Valine mutated b Chromosome level mutations 9 may involve changes in chromosomes Generally occur during crossing over stage of meiosis May involve changes in chromosome number c Polyploidy 9 increase in number of each type of chromosome d Aneuploidy 9 addition or deletion of a chromosome e Inversions 9 Sections of chromosomes break and rotate before rejoining f Translocations 9 broke section of one chromosome become attached to another 2 Effects of mutations a Mutations fall into one of three categories 1 Beneficial mutations increase the fitness of the organism 2 Neutral mutations do not affect an organism s fitness Silent mutations are usually neutral 3 Deleterious mutations decrease the fitness of the organism Most mutations are neutral or slightly deleterious Chapter 16 Transcription and Translation I Transcription Synthesis of an mRNA from instructions stored in the DNA RNA polymerase performs this synthesis Only one strand of DNA is transcribed the template strand The other DNA strand is called the nontemplate strand coding strand 9 because it matches the RNA the same code the protein will be using 11 RNA Polymerase RNA polymerase performs template directed synthesis in the 5 to 3 direction RNA polymerases do NOT require a primer to begin transcription de novo synthesis Terminology a Upstream DNA DNA in the OPPOSITE direction RNA polymerase is running b Downstream DNA DNA in the SAME direction RNA polymerase is running 111 Bacterial and Eukaryotic Differences Bacteria do not have nuclei i DNA is not segregated from ribosomes ii This allows translation to begin while transcription is still in process iii Transcription and translation are tightly coupled iv Polyribosome multiple ribosomes can attached to the mRNA Eukaryotes have a nucleus i Transcription is in the nucleus ii Translation is in the cytoplasm In prokaryotes mRNA can be immediately translated without more processing In eukaryotes RNA transcripts must be modified through RNA processing prior to translation IV What is the bacterial promoter Bacterial promoters in the DNA upstream of the start site where transcription begins i 4050 base pairs ii 2 key regions a 10 box10 bases upstream from the transcription start site 1 site first nucleotide that will be transcribed b TATAAT weaker hydrogen bonding easier to open c 35 box35 bases upstream from the 1 site dTTGACA V Initiation in Bacteria 1 Initiation Sigma a protein subunit must bind to RNA polymerase Sigma and RNA polymerase form a holoenzyme 9 binds to the promoter region to begin transcription Sigma guides RNA polymerase to the promoter on the DNA template strand Sigma is similar to the sliding clamp in DNA replication Sigma portion of the holoenzyme binds to the 35 and 10 boxes Bacteria have several types of sigma proteins i Each type allows RNA polymerase to bind to a different type of promoter Sigma opens the DNA double helix Template DNA is threaded through RNA polymerase active site Incoming nucleotide pairs with complementary base on DNA template Sigma dissociates from core enzyme once initiation is completed Other players in initiation i Zipper keeps the DNA helix open takes place of SSBPs ii Rudder keeps DNA on track through RNA polymerase 2 Elongation 3 Termination VI What is the eukaryotic promoter Eukaryotic promoters i Most include a TATA box a 30 base pairs upstream of the transcription start site b TATAAA c Defines the direction of transcription d Defines the DNA strand to be read VII Initiation in Eukaryotes RNA polymerase does NOT bind directly to the promoter Basal transcription factors bind to the DNA promoter initiating transcription Transcription factors RNA polymerase II Transcription Initiation Complex Strand that s opposite the TATA box is used for the template strand VIII Termination Transcription ends with a termination phase In bacteria i Polymerase stops transcription at the end of the terminator ii Termination signal codes for a hairpin structure which causes the RNA polymerase to fall off the RNA transcript In eukaryotes i RNA polymerase continues transcription after premRNA is cleaved from the growing RNA chain ii Polymerase eventually falls off the DNA VIIII RNA processing in eukaryotes 5 cap serves as a recognition site for the translational machinery The polyAtail extends the life of the mRNA by protecting it from degradation Polyadenylation signal add a tail of adenines onquot Most eukaryotic genes have stretches of noncoding regions between coding regions a Introns noncoding regions b Exons coding regions RNA splicing removes introns and joins exons X Splicing Small nuclear ribonucleoproteins snRNPs form a complex called a spliceosome Spliceosome catalyzes the splicing reaction snRNPs cut the introns and paste the exons XI Function of Introns Some genes encode more than one kind of polypeptide Depends on which segments are read as exons Alternative RNA splicing Number of proteins produced is MUCH greater than the number of genes XII Translation Synthesis of a polypeptide Occurs under direction of mRNA CHANGE in LANGUAGE Site of translation ribosome in both prokaryotes and eukaryotes XIII tRNA Single RNA strand that is approx 80 nucleotides long Flattened looks like a cloverleaf a In 3 dimension L shaped due to H bonds Each tRNA carries a specific amino acid on one end and an anticodon on the other Accurate translation requires two steps 1 A correct match between a tRNA and an amino acid done by the enzyme aminoacyltRNA synthetase charging 2 A correct match between the tRNA anticodon and an mRNA codon XIV How many tRNAs are there 61 different codons 40 different tRNAs Wobble Hypothesis explains this i The anticodon of tRNAs can still bind successfully to ta codon whose third position requires a non standard base pairing One tRNA can base pair with more than one type of codon XV Aminoacyl tRNA synthetase For each of the 20 amino acids there is a different aminoacyl tRNA synthetase 9 very big enzyme tRNA covalently linked to its corresponding amino acid is called an aminoacyl tRNA XVI Ribosomes Facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis The two ribosomal subunits large and small are made of proteins and ribosomal RNA rRNA a Small subunit holds mRNA in place b Large subunit is where peptide bond forms bonding between amino acids specific to proteins A ribosome has three binding sites for the tRNA 1 The Peptide site holds the tRNA that carries the growing polypeptide chain 2 The Acceptor site holds the tRNA that carries the next amino acid to be added to the chain 3 The Exit site is where discharged tRNAs leave the ribosome XVII Building a polypeptide The three stages of translation 1 Initiation 2 Elongation 3 Termination All three stages require protein factors that aid in the translation process XVIII Ribosome Association and Initiation of Translation Initiation brings together mRNA a tRNA with the first amino acid and the two ribosomal subunits Small ribosomal subunit binds with mRNA and a special initiator tRNA first Then the small subunit moves along the mRNA until it reaches the start codon AUG Proteins called initiation factors bring in the large subunit that completes the translation initiation complex In bacteria start codon is preceded by ribosome binding site Shine Dalgarno sequence a Complementary to a section of rRNA in small ribosomal subunit Elongation of the Polypeptide Chain During elongation amino acids are added one by one to the preceding amino acid Each addition involves proteins called elongation factors and occurs in three steps 1 Codon recognition arrival of aminoacyl tRNA 2 Peptide bond formation 3 Translocation Termination of translation Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome The A site accepts a protein called a release factor Release factor causes the addition of a water molecule instead of an amino acid This reaction releases the polypeptide and the translation assembly then comes apart Let s tie up the loose ends Polyribosomes Completing the protein a Often modifications are needed after translation b Completed proteins are targeted to specific sites in the cell Protein Modification posttranslational modification a Polypeptide chain spontaneously coils and folds into 3D shape i Molecular chaperones speed protein folding b Some are activated by enzymes that cleave them c Phosphate groups can be added active vs inactive d Some must come together to form a larger molecule Comparing gene expression in bacteria archaea and eukarya a Bacteria and eukarya differ in their RNA polymerases termination of transcription and ribosomes archaea tend to resemble eukarya in these respects b Bacteria can simultaneously transcribe and translate the same gene c In eukarya transcription and translation are separated by nuclear envelope d In archaea transcription and translation are likely coupled Chapter 17 Control of Gene Expression in Bacteria 1 Control of Gene Expression Can be controlled at 3 levels 1 Transcription 2 Translation 3 Posttranslation Allows for response to environment Can be negative or positive All of our cells have the same DNA and genes but different genes are activated in different environments Gene expression is getting to a functional protein 11 Gene Expression Occurs when a gene product is actively being synthesized and used in a cell A cell does not express all of its genes all of the time a Very selective process 111 Sugar Like many other organisms E coli like sugar a Glucose does not need to be modified at all MONOMER b Goes straight to glycolysis Gene control allows E coli to switch its use of sugars Bacterium want to be Bacteria a little to a lot9 goal is to make many copies of itself bring in nutrients in order to make copies Bacteria cannot anticipate the future a React fast b Adapt synthesis of new proteins c Endure d Hedge e Die NOT an option IV Expansion of the Central Dogma Information ow occurs in three steps represented by arrows DNA 9 RNA 9 protein 9 activated protein 1 Transcriptional control a Occurs when the cell does not produce mRNA for specific enzymes i Cell avoids production by preventing RNA polymerase from binding to a promoter DNA RNA 9 protein 9 activated protein 2 Translational control a Prevents translation of an mRNA molecule that has already been transcribed i Regulatory molecules speed up mRNA degradation ii Translation initiation is altered iii Translational proteins can be affected DNA 9 mRNprotein 9 activated protein 3 Posttranslational control a Cell fails to activate a manufactured a tein DNA 9 mRNA 9 protei activated protein Which is best Transcriptional control is slow but efficient Translational control allows a cell to quickly change which proteins are produced Posttranslational control provides the most rapid response but is energetically expensive protein is already there V Metabolizing lactose E coli prefers to use glucose as a carbon source a Only uses lactose when glucose is depleted Lactose a Disaccharide glucose galactose b Joined by a B galactoside linkage c Bgalactosidase E coli produces B galactosidase when lactose is present Does E coli produce B galactosidase when both glucose and lactose are present NO a Conclusion Glucose prevents gene expression of the gene for B galactosidase The presence of lactose without glucose stimulates expression of that gene VI Operons The Basic Concept A cluster of functionally related a Under coordinated control by a single onoff switch The regulatory quotswitch a Segment of DNA called an operator usually positioned within the promoter An operon a Entire stretch of DNA that include the operator the promoter and the genes that they control The operon can be switched off by a protein repressor a Prevents gene transcription by binding to the operator and blocking RNA polymerase b Product of a separate regulatory gene c Can be in an active or inactive form depending on the presence of other molecules d Corepresor is a molecule that cooperates with a repressor protein to switch an operon off VII Repressible and Inducible Operons Two Types of Negative Gene Regulation A repressible operon is one that is usually ON binding of a repressor to the operator shuts off transcription An inducible operon is one that is usually OFF a molecule called an inducer inactivates the repressor and turns on transcription The ac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose By itself the lac repressor is active and switches the lac operon off A molecule called an inducer inactivates the repressor to turn the lac operon on In its normal state the lac operon is OFF VIII What do bacteria need to metabolize lactose Functional Bgalactosidase lacZ Functional galactoside permease lacY Transacetylase lacA lacI repressor9 NOT part ofthe operon a Has is own promoter own region b Upstream of the promoter operator site for the operon IX Genes lacZ lacY and lacA code for proteins operon lacO codes for the operator lacI serves a regulatory function repressor protein a In the absence of lactose lacI shuts down expression of lacZ and lacY E coli mutate a lot because their proofreading system aren t as accurate as eukaryotic cells 9 mutations may be beneficial for them X Mutants IacZ mutants lack functional Bgalactosidase a means mutated not functional b means functional IacY mutants lack galactoside permease IacI mutants constitutive mutants a Produce Bgalactosidase and galactoside permease even when lactose is absent Iac0 mutants constitutive mutants 9 repressor can t bind to it will always be on XI Jacob and Monod Late 1950s ournal of molecular Biology Won Nobel Prize Found mutations in genes encoding proteins that regulate Bgalactosidase gene transcription E coli cells Experiment a Isolated and analyzed E coli mutants that could metabolize lactose i Generate large numbers ii Screen b Xgal used to detect Bgal activity BLUE c IPTG in place of lactose is a nonmetabolized inducer of transcription of the Bgal gene of the lac operon d Glycerol is the carbon and energy source Looking for a mutation White colonies repress Bgal gene transcription when there is no inducer E coli with mutations in the regulatory gene transcribe the Bgal gene with there is no inducer and the colony is BLUE Genotype Phenotype IacZ Lac 9 unable to ferment lactose white in the presence of Xgal IacY1 Lac 9 unable to ferment lactose in whole cells Unable to take up lactose and so unable to convert lactose uninducible IacOC Lac 9 ferments lactose all the time even in absence of inducer Operator that is not recognized by repressor Called Constitutive IacIC Lac 9 ferments lactose all the time even in absence of inducer Repressor that doesn t bind operator Called constitutive IacIS Lac 9 unable to ferment lactose Repressor doesn t bind lactose Operator always blocked Negative regulation9 when negative regulator operator or repressor is broken by a mutation the process always constitutively happens even when the inducer is absent XII Glucose Inhibits Bgalactosidase induction How a POSITIVE control of the lac operon cAMP and CRP a CRP CAMP receptor protein regulator bCRP and cAMP bind i Together they bind to DNA and ACTIVATE transcription ii Must have BOTH to bind to DNA consensus sequence weak they allow RNA polymerase to bind to DNA more efficiently c Glucose inhibits cAMP synthesis i cAMP measures glucose in cells glucose sensor ii Glucose high cAMP low iii Glucose low cAMP high XIII Summary Glucose is the normal energy and carbon source Cell has backupquot system to use lactose Even if lactose is present cell won t make IacZ if glucose is present Even if no glucose is present operon isn t induced until lactose appears Lactose inhibits inhibition of ac expression lactose can start the system Chapter 18 Control of Gene Expression in Eukaryotes Consensus sequence of TATA box 1030 bases upstreamnuclear membrane Make sure you know the difference between what belongs in a eukaryote and and prokaryote 1 Why regulate genes Bacteria regulate genes to respond to changes in their environment Unicellular eukaryotes Saccharomyces cerevisiae must deal with rapid temperature and humidity changes Multicellular eukaryotes have multiple challenges a Must generate trillions of cells each with a unique structure and function 11 Multicellular Eukaryotes Like prokaryotes eukaryotes respond to their environment Unlike prokaryotes multicellular eukaryotes express different genes in response to changes in the internal environment DNA is the same in EVERY cell in the body 111 Differential Gene Expression Creates cell types Arranges them into tissues Coordinates activities IV Overview of Gene Regulation Like prokaryotes eukaryotes can control gene expression at the levels of transcription translation and posttranslation 3 additional levels are unique to eukaryotes 1 Chromatin remodeling 2 RNA processing 3 Regulation of mRNA like span or stability cap and tail V Chromatin Remodeling 6 billion base pairs 2 65 feet of DNA In eukaryotes DNA is wrapped around histone proteins to create chromatin generally prokaryotes do NOT have histone proteins some do a RNA polymerase cannot access the DNA when it is supercoiled within the nucleus b Histone proteins are charged DNA is charged c Promoters become hidden transcription cannot occur must be unwrapped to begin transcription DNA near the promoter must be released before transcription can begin Structure a Chromatin has a regular structure b Beads nucleosomes i 8 histone proteins ii 146 base pairs textbook says 1479 20 base pairs extend between nucleosomes VI Nucleosome Formation DNA is negatively charged phosphate groups Histones are positively charged glycine and arginine a If the positive charge did not exist it would not be condensed DNA wraps around 8 histone proteins a 4 sets of 2 i 2 H2A s ii 2 H2B s iii 2 H3 s iv 2H4 s Linker stretch of DNA approx 20 nucleotides between nucleosomes H1 histone holds everything together found on the outside H1 proteins have an affinity for one another drawn to and attached to one another a 30 nm fiber several of the nucleosomes drawn together with the H1 molecule as their core H1 protein is external to the histone OCTAMER VII Chromatin Structure is altered in active Genes Chromatin must be relaxed for RNA polymerase to bind to the promoter Experiment a DNAse cuts DNA at random locations b Cannot cut DNA that is wound tightly c Weintraub and Groudine i Compared chromatin structure of genes in blood cells of chickens ii Betaglobin high transcription9 highly transcribed in blood promoter regions are needed to transcribe iii Ovalbumin no transcription9 not transcribed in blood will stay tightly wound because promoter regions are not needed iv What did the DNAse cut Experiment a Mutant yeast cells b Genes that are normally never transcribed are transcribed at high levels they LACK HIS TONE PROTEINS c Lack of histone proteins prevented assembly of normal chromatin Conclusions 1 Normal default state of eukaryotic genes OFF 2 NEGATIVE CONTROL 3 A form of positive control must be at work somewhere to open the promoter regions VIII Chromatin Remodeling Chromatin remodeling complexes a Move eject or restructure nucleosome complex b Use ATP ATPase c Multiprotein molecule interacts directly with the DNA d Interaction on surface of nucleosome e Allows DNA to pull away from histone octamer for transcription Acetylation and methylation 1 Methylation i CH3 ii Occurs on cytosine residues iii DNA methyltransferase adds methyl group iv Demethylase removes methyl group v Methylated Cs bind to Gs as normal vi Extra methyl groups near promoter attract protein involved in repression of gene transcription vii Methylated genes tend to be inactive viii If DNA is HIGHLY methylated those genes tend to be INACTIVE Epigenetic Regulation changes in gene expression that occur without changes in the DNA affiliation with cancers 2 Acetylation i Each histone protein has a quottailquot of approx 20 amino acids that stick out Positively charged amino acids particularly lysine ii Usually associated with positive control CH3COOH Histone acetyl transferase HATs a Acetylate charged lysine residues in histones b When acetylated positive charge is reduced c DNA opens Histone deacteylases HDACs a Remove acetyl group so chromatin recondenses HATs are ON switches relaxes DNA HDACs are OFF switches tightens DNA IX Can we inherit chromatin modifications Histone code a Patterns of chemical modifications of histones contain information similar to the genetic code b Histones in uence whether or not a gene is expressed c EPIGENETIC inheritance i Patterns of inheritance not due to differences in DNA sequence not a mutation in the DNA code itself but a mutation in the DNA expression X Transcriptional Regulation Eukaryotic Promoter a Most are located close to the point where RNA polymerase begins transcription b 3 conserved sequences have 2 of the 3 3 different eukaryotic promoters c Most common TATA box After exposed by chromatin remodeling first step in transcription is interaction with TATA binding protein TBP a This does NOT guarantee expression what does XI How do you get expression Regulatory sequences a Similar to prokaryotic CAP binding site b Sections of DNA that control activity of genes c When regulatory proteins bind gene activity changes How do we know this a S cerevisiae i Metabolize galactose ii When galactose is absent enzymes to metabolize it are made in low levels iii When galactose is present transcription of these enzymes increase 1000 fold b Mutations mutant cells fail to produce any of the enzymes required for galactose metabolism i Three hypotheses 1 The five genes are regulated together even though they are on different chromosomes 2 Normal cells have a CAPlike regulatory protein that exerts positive control over the five genes 3 The mutant cells have a lossoffunction mutation that completely disables the regulatory protein XII What regulates the enzyme production Regulatory proteins a Binds to DNA located just upstream from the promoter for the 5 genes b These are called promoterproximal elements piece of DNA unique to gene c Promoters are pretty generic proximal elements are unique XIII Promoter proximal elements Promoter has sequences common to most genes Proximal elements have sequences unique to specific genes a Allow eukaryotes to express certain genes but not others b POSITIVE CONTROL Not exactly like prokaryotes a Tonegawa and colleagues i Discovered the intron rather than the exon contains a regulatory sequence required for transcription XIV Tonegawa s experiment PremRNA in the nucleus Started with a human antibody producing gene intron anked by 2 exons Used enzymes to remove pieces of the intron from different samples of the gene Used enzymes to ligate remaining sections of the gene back together missing part of the intron Insert gene into mouse cells The intron contains regulatory sequences that is required for transcription regulatory sequences in DNA may be located far from the promoter DOWNSTREAM in the case of an intron Conclusion a Intron contains a regulatory sequence required for transcription to occur Remarkable a The regulatory sequence was thousands of base pairs away from the promoter b The regulatory sequence was downstream of the promoter rather than upstream c Regulatory elements far from the promoter are called enhancers XV Enhancers Can be more than 100000 base pairs away from the promoter In all eukaryotes Can be in introns or untranscribed regions on either the 5 or 3 side of the gene Work even if ipped 3 to 5 9 do NOT exhibit directionality Work even if moved to a new location on the same chromosome Have NOT been found in exons XVI Enhancers and Silencers Enhancers function using positive control a When regulatory proteins bind to enhancers transcription begins SiIencers function using negative control a Repress gene expression b When regulatory proteins bind to silencers transcription ends NEW definition of a gene 9 DNA that codes for a functional polypeptide or RNA molecule AND the regulatory sequences required for expression ummary K Different cell types express different genes because they have different histone modifications and contain different regulatory proteins Regulatory proteins are produced in response to signals form other cells in early development Differential gene expression is a result of the production or activation of specific regulatory proteins a ON when specific regulatory proteins bind to enhancers and promoter proximal elements b OFF when specific regulatory proteins bind to silencers or chromatin remains condensed J XVII Transcription Initiation Initiation Complex two classes of regulatory proteins 1 Regulatory transcription factors i Bind to enhancers silencers and promoter proximal elements ii Responsible for expression of particular genes in particular cell types at particular sages of development 2 Basal transcription factors i Interact with the promoter ii Not restricted to particular cell types iii Required for transcription but DO NOT regulate gene expression Mediator complex a Protein complex that does NOT bind to DNA b Creates physical link between regulatory transcription factors and basal transcription factors Why don t eukaryotes need a repressor protein like prokaryotes 9 The DNA is wrapped up the promoters are hidden Put it all together 1 Regulatory transcription factors bind to DNA and recruit chromatin remodeling complexes HATs 2 Chromatin is opened up exposing the promoter region 3 Regulatory transcription factors bind to exposed enhancers or promoter proximal elements 4 Basal transcription factors bind to the promoter 5 Mediator complexes connect the two and DNA loops 6 RNA polymerase II is recruited to the site forming a basal transcription complex 7 TRANSCRIPTION CAN BEGIN XVIII Post Transcriptional Control Alternative splicing a During splicing changes in gene expression are possible because selected exons may be removed b Same primary RNA transcript can yield more than one kind of mature mRNA i T ropomyosin 1 Expressed in smooth and skeletal muscle cells 2 14 exons in the primary transcript premRNA 3 Alternative splicing is the difference between voluntary and involuntary control in your muscles c Controlled by proteins that bind to RNAs in the nucleus and interact with spliceosomes d Proteins are produced during development mRNA stability a Lifespan of mRNA in the cell can vary b Casein milk protein i Normally mRNA persist for just an hour ii When female is lactating mRNA lasts 30x longer c Stability of the mRNA is increased by an increased polyAtail length on 3 end added in the nucleus part of premRNA processing RNA interference a mRNA lifespan can be controlled by tiny single stranded RNA molecules that bind complementary mRNA b Once a double stranded RNA proteins degrade mRNA every mRNA is being constantly actively degrade finite lifespan how long the lifespan is can be regulated c Similar to antisense oligonucleotide therapy d Regulatory element encoded for in the DNA RNA Interference Steps 1 RNA polymerase transcribes DNA sequences that code for small RNA molecule that forms a hairpin loop due to complementary bases 2 RNA is trimmed by enzymes in the nucleus and then exported to the cytoplasm 3 Transported out of the nucleus into the cytoplasm where RNA is cut into 22 basepairs 4 RNA is taken up by RNA induced silencing complex RISC RNA now called miRNA microRNA or siRNA small interfering RNA 5 Once part of RISC miRNA binds to complementary mRNA 3 options i Doesn t bind ii Binds to something loosely iii Binds to something tightly quotkiss of deathquot mRNA is degraded 6 If it matches mRNA enzymes in RISC destroy mRNA TRANSLATIONAL CONTROL XIV Translational Control Modification of cap and or tail Translation may stop in response to temperature that s why we have a fever in order to prohibit bacterialviral protein production Phosphorylation of ribosome XV Posttranslational Control LEAST energy efficient but very quick Protein folding Modification by enzymes Phosphorylation activating or deactivating Targeted destruction of proteins a Ubiquitin tags added to protein b Recognized by proteasome and cut into short segments XVI Prokaryotes vs Eukaryotes 4 primary differences 1 Packaging9 chromatin structure provides mechanism of negative control in eukaryotes not found in bacteria 2 Alternative splicing9 not found in bacteria just have DNA translated to RNA 3 Complexity9 Transcriptional control much more complex in eukaryotes than bacteria 4 Coordinated expression9 operons in bacteria not in eukaryotes Chapter 24 Evolution by Natural Selection I What Evolution is A wellsupported theory a Inferred factquot A process Currently happening Change over time Active at the population level 1 What Evolution is NOT Does not include the origin of life A mechanism Active at the individual level The idea that people came from monkeys A chain more like a branching tree Necessarily in con ict with individuals of faith III Lamark Proposed species are not static but change through time BUT based on a chain a Simple organism became a more complex organism b Progressive always producing a better species Phenotype changes as individuals develop in response to environmental changes IV Darwin s Differences Claimed that variation among individuals in the population was the key to understanding the nature of species Population thinking Theory of natural selection a Overturned the idea that species are static typological thinking b Replaced typological thinking with population thinking c Scientific proposed a mechanism that could account for change through time and make testable predictions V Descent with Modification Species that lived are past ancestors of species existing today Species and their descendants change through time VI Natural Selection 1 Species change through time 2 Species are relate by a common ancestry VII Homology Study of likeness a Genetic homology similarities in the DNA sequences b Developmental homology embryonic development similarities c Structural homology adult morphology similarities in the adult state Genetic homologies cause developmental homologies that lead to structural homologies VIII Darwin s 4 Postulates 1 Individual organisms make up a population and they vary in traits 2 Some trait differences are inheritable and passed on genetically 3 In each generation more offspring are produced than can possibly survive 4 Individuals that survive best have heritable traits that make them more likely to survive and reproduce Evolution by natural selection occurs when heritable variations lead to differential reproductive success IX Misconceptions Lamarckian vs Darwinian view Acclimation is not adaptation a Not passed to offspring Not goal directed a Adaptations do not occur because individuals want them Not progressive a Organisms don t get better over time No such thing as higher or lower Organisms do not act for the good of the species X Natural selection at Work Resistance to Antibiotics M tuberculosis a Mycobacterium tuberculosis causes tuberculosis TB a disease that was once as great a public health issue as cancer is now b Sanitation nutrition and antibiotics such as rifampin greatly reduced deaths due to TB in industrialized nations between 1950 and about1990 c However in the late 1980s rate of TB started to surge due to the evolution of drugresistant strains i In 1993 the World Health Organization declared TB a global health emergency d DNA from rifampinresistant bacteria was found to have a single point mutation in a gene called rpoB TCG to TTG e Rifampin works by interfering with RNA polymerase and transcription but the mutation prevents rifampin from binding f Under normal conditions mutant forms of RNA polymerase do not work as well as the normal form i However during antibiotic therapy cells with normal RNA polymerase grow more slowly or die while those with mutant RNA polymerase proliferate XI Testing Darwin s Postulates Variati0n existed in the population a Due to mutation both resistant and nonresistant strands of TB were present prior to administration of the drug The variation was heritable a The variation in the phenotypes of the two strains was due to variation in their genotypes There was variation in reproductive success a Only a tiny fraction of M tuberculosis cells survived the first round of antibiotics long enough to reproduce Selecti0n occurred a The cells with the drugresistant allele had higher reproductive success XII Evolution Change over time Changes in allele frequencies in a population over time Based on Darwin s 4 postulates XIII Essence of Evolution by natural Selection Evolution of natural selection occurs wen heritable variation leads to differential reproductive success XIV Biological Fitness Ability of an individual to produce surviving offspring Relative to that ability in other individuals in the population Fitness is a measurable quantity Individuals in a particular population XV Adaptation Heritable trait that increase the fitness of an individual in a particular environment relative to individuals lacking that trait Adaptation increases fitness a Heritable traits increase the ability of an individual to produce surviving offspring XVI Acclimation Not a genetic change Summary Evolution by natural selection occurs when heritable variation in traits leads to differential reproductive success If individuals with certain alleles produce the most offspring in a population then those alleles increase in frequency over time XVII Fitness Trade Offs Compromise between traits in terms of how those traits perform in the environment Adaptation is always a compromise XVIII Common Misconceptions Individuals do NOT change when they are selected they simply produce more offspring than other individuals do Acclimation is NOT adaptation a Acclimation are changes in phenotype that occurred in response to changes in the environment b Phenotypic changes due to acclimation are NOT passed on to offspring because alleles have not changed Evolution is not goal directed a Not what organisms quotwantquot or quotneedquot Evolution is not progressive a Not getting better over time No higher and lower organisms Organisms do not act for the good of the species no altruism Chapter 2 5 Evolutionary Processes 1 Natural Selection is not the only way There are actually 4 mechanisms that shift allele frequencies in populations 1 Natural selection increases the frequency of those alleles that contribute to reproductive success in a particular environment 2 Genetic drift causes allele frequencies to change randomly 3 Gene ow occurs when individuals leave one population join another and breed must be capable of interbreeding 4 Mutation modifies allele frequencies by continually introducing new alleles 11 Important Assumptions of the HardyWeinberg Model For a population to conform to the HardyWeinberg principle none of the four mechanisms of evolution can be acting on the population In addition the model assumes that mating is random with respect to the gene in question a Thus here are the five assumptions that must be met 1 No natural selection 2 No genetic drift or random allele frequency 3 No gene ow 4 No mutation 5 Random mating III HardyWeinberg Principle Analysis of the frequencies of alleles when many individuals in a population mate and produce offspring What happens to the entire population when ALL of the individuals and ALL of the genotypes breed a Ignores biological fitness IV Basic Principles All the gametes produced in each generation go into a single group called the gene pool These gametes combine at random to form offspring Their calculations predict the genotypes of the offspring that the population would produce as well as the frequency of each genotype V Deriving the HardyWeinberg Principle They started with the simplest situation a gene with two alleles A1 and A2 The frequency of A1 is represented by p and the frequency of A2 is represented by q a Because there are only two alleles p q 1 In this situation three genotypes are possible A1A1 A1A2 A2A2 a The model predicts the following genotype frequencies 1 The frequency of the A1A1 genotype is p2 i HOMOZYGOUS DOMINANT 2 The frequency of the AzAz genotype is q2 i HOMOZYGOUS RECESSIVE 3 The frequency of the A1A2 genotype is 2pq i HETEROZYGOUS Because all individuals in the new generation must have one of the three genotypes the sum of the three genotype frequencies must equal 1 100 of the population p2 2pq q2 1 a This is the HardyWeinberg equation When allele frequencies are calculated for this new generation the frequency of A1 is still p and the frequency of A2 is still q VI The HardyWeinberg Principle Makes two fundamental claims 1 If the frequencies of alleles A1 and A2 in a population are given by p and q then the frequencies of genotypes A1A1 A1A2 and A2A2 will be given by p2 2pq and q2 for generation after generation 2 When alleles are transmitted via meiosis and random combination of gametes their frequencies do not change over time for evolution to occur some other factor or factors must come into play REMEMBER p frequency of the dominant allele in the population q frequency of the recessive allele in the population p2 percentage of homozygous dominant individuals genotype q2 percentage of homozygous recessive individuals genotype 2pq percentage of heterozygous individuals genotype 2 alleles in a genotype 4 Mechanisms that Shift Allele Frequencies over Time 1 Natural Selection Occurs when individuals with certain phenotypes produce more offspring than individuals with other phenotypes Only acts on phenotype NOT random Directed by the environment Results in adaptation change in the genotype 3 different ways natural selection can occur 1 Directional selection9 average phenotype of the populations changed in one direction changes the average value of a trait a TB example b If it continues over time i Favored alleles will approach a frequency of 10 fixed ii Disadvantageous alleles will approach a frequency of 00 lost iii Purifying selectionquot 2 Stabilizing selection reduces the amount of variation in a trait a NO change in the average value of a trait over time b Genetic variation in the population is reduced c Human baby example 3 Disruptive selection eliminated phenotypes near the average favors extreme phenotypes a Increases the amount of variation in a trait b Genetic variation in the population is maintained c Salmon example Can lead to the formation of a new species 2 Genetic Drift Undirected and random Any change in allele frequencies in a population due to chance sampling errorblind luck Occurs in every population in every generation Causes allele frequencies to drift up and down randomly overtime Key points about genetic drift a Over time can lead to the random loss or fixation of alleles b When random loss or fixation occurs genetic variation in the population declines c More pronounced in small populations than in large ones generally in large populations there is enough diversity to balance that out Genetic drift is of great concern to conservation biologists because the small populations Two examples are the founder effect and bottlenecks 1 Founder event occurs when a group starts a new population in a new area 2 Founder e ect especially in small groups allele frequencies probably differ from the source population this change in allele frequency is called this a Martha s Vineyard example 3 Population bottleneck a sudden decrease in population size a Commonly caused by disease outbreaks and natural catastrophes 4 Genetic bottlenecks stem from population bottlenecks a sudden reduction in the number of alleles in a population a Drift occurs during genetic bottlenecks and causes a change in allele frequency 3 Gene Flow Movement of alleles from one population to another Occurs whenever a Individuals leave one population join another and breed Equalizes gene frequencies between the source and recipient populations Homogenizes populations Random with respect to fitness Arrival or departure of alleles can increase or decrease average fitness Most forms of selection favor certain alleles and lead to decrease in overall genetic variation so what restores genetic diversity 4 Mutations Mutation restores genetic diversity by creating new alleles Random with respect to the fitness of the affected allele Most mutations result in deleterious alleles A mutation that produces a beneficial allele should increase in frequency in a population due to natural selection TakeHome Messagesquot Mutation plays an important role in evolution 1 Mutation is the ultimate source of genetic variation ONLY mutation creates new alleles 2 Without mutation evolution would eventually stop 3 Mutation alone is usually inconsequential in changing allele frequencies at a particular gene Each of the four evolutionary forces has different consequences for allele frequencies VII Nonrandom mating In nature mating may not be random with respect to any particular gene in question Two mechanisms that violate the HardyWeinberg assumption of random mating are inbreeding and sexual selection VIII Inbreeding Mating between relatives Increases frequencies of homozygotes and reduces the frequency of heterozygotes in each generation Does not cause evolution because allele frequencies do not change in the population as a whole Inbreeding and other forms of nonrandom mating change genotype frequencies not allele frequencies Inbreeding depression a decline in average fitness that takes place when homozygosity increases and heterozygostiy decreases in a population a Results from two processes i Many recessive alleles represent lossoffunction mutations ii Many genes especially those involved in fighting disease are under intense selectin for heterozygote advantage iii If an individual is homozygous at these genes then fitness declines Even though it does not cause evolution directly because it does not change allele frequencies inbreeding can speed the rate of evolutionary change Increase the rate at which purifying selection eliminates recessive deleterious alleles from a population IX Sexual selection Occurs when individuals within a population differ in their ability to attract mates Favors individuals with heritable traits that enhance their ability to obtain mates Special form of natural selection The fundamental asymmetry of sex a Females usually invest more in their offspring than males do b Two broad types of sexual selection female choice and malemale competition c Sexual selection should act more strongly on males than on females Female choice for good allelesquot a Females may choose mates on the basis of physical characteristics that signal male genetic quality b For example research has shown that female zebra finches preferred males with more colorful beaks and feathers indicating better health Female choice for paternal care a In many species females prefer to mate with males that care for young or that provide the resources required to produce eggs b Brown kiwi females make an enormous initial investment in their offspring i Their eggs routinely represent over 15 of the mother s total body weight ii Mate with males that take over all of the incubation and other care of the offspring MaleMale Competition a Sexual selection is intense in elephant seals and is driven by male male competition b Male elephant seals establish territories areas that they defend and can use exclusively c Evidence for intense sexual selection in males is indicated by the fact that variation in reproductive success is high in males whereas females have lower variation in reproductive success i Males with larger territories father more offspring and their alleles rapidly increase in the population What are the consequences of sexual selection a Sexually selected traits often differ sharply between the sexes b Sexual dimorphism refers to any trait that differs between males and females of the same species c Sexual selection violates the assumptions of the HardyWeinberg principle by causing certain alleles to increase or decrease in frequency and resulting in evolutionary change Chapter 26 Speciation I Speciation Changes between populations Darwin talked about changes within populations 0n the origin of Species Occurs when populations of the same species become genetically isolated a Lack of gene ow b Diverge from each other i Natural selection ii Genetic drift iii Mutation Splitting eventquot Results from BOTH a Genetic isolation lack of gene ow b Genetic divergence mutation natural selection genetic drift II Species An evolutionarily independent population Three approaches to consider 1 Biological Species Concept strong theory difficult to apply a Considers population to be evolutionarily independent if they are reproductively isolated from each other i DO NOT interbreed ii Fail to produce viable fertile offspring iii No gene ow between the populations b Disadvantages i Can t be evaluated in fossils ii Can t be evaluated in species that reproduce asexually iii Only applied to populations that overlap geographically c Mechanisms that stop gene ow i Prezygotic isolation species are prevented from mating 1 Temporal 2 Habitat 3 Behavioral 4 Gametic Barrier 5 Mechanical ii Postzygotic isolation species mate but hybrid offspring have low fitness and do not survive or produce offspring sterile 1 Hybrid viability 2 Hybrid sterility d Based on ability to interbreed NOT based on similarity of appearance e Appearance isn t everything a Western meadowlark and Eastern meadowlark i Look almost identical do not interbreed not same species 2 Morphospecies Concept a Identify evolutionarily independent lineages by different morphological features b Widely applied c Disadvantages i Cannot identify species that differ in nonmorphological traits cryptic species ii Features used to distinguish species can be subjective and controversial d Groups of individuals that are morphologically similar are considered to be a species e Assumption that similar morphology indicated relatedness f Can be preserved in dead individuals g Enables us to name species that are instinct h Can be used regardless of reproduction strategy 3 Phylogenetic Species Concept a Based on reconstructing the evolutionary history of populations b Phylogenetic trees i Ancestral population plus all of its descendants is called a monophyletic group or clade single clipquot ii Identified by synapomorphies Homologous traits inherited form a common ancestor unique to certain populations c Being used more and more frequently d Species is defined as the smallest monophyletic group on the tree e Advantages i Can be applied to any population ii Logical because different species have synapomorphies only if they evolve independently what about convergent evolution f Disadvantages i Phylogenies are only available for a small subset of populations ii May lead to many more species than either of the other concepts g No need for living individuals h Measures similarity of sequence of DNA i Large numbers of individuals can be evaluated j What constitutes a big enoughquot difference Still debated In reality all three species concepts are used to identify species Example Olinguito or Olingo a Sometimes things that look very similar are NOT of the same species 111 Subspecies Finer levels of distinction than species a Have own identifying traits b Therefore they should be able to mate and produce offspring c Always differ in morphology Populations that live in discrete geographic areas a Have own identifying traits b Not distinct enough to be considered separate species Examples a Dusky Seaside Sparrow i Live along Atlantic and Gulf coasts ii Physically isolated from one another iii Based on biological species and morphospecies concepts considered separate species iv One species was nearing extinction FALSE Phylogenetic analysis of gene sequences revealed only two distinct species Dusky sparrow was genetically indistinguishable from other Atlantic Coast sparrows Con icts of Species Concepts different approaches led to different answers IV Allopatric Speciation Fancy name for speciation by geographic isolationquot Populations living indifferent places Separateness will eventually lead to distinctness Geographical barriers include mountains rives oceans rivers a Barrier may develop slowly over time Grand Canyon Speciation that beings with physical isolation a Dispersal basically the Founder Effect i Smaller population much more sensitive to genetic drift ii Two populations become separate no gene ownatural selection occurs mutations may become different species b Vicariance some sort of chance separation i Land Before Time example ii Two populations become separate no gene ownatural selection occurs mutations may become different species Might become separate species but they do NOT have to become separate spec1es V Sympatric Speciation Species that live in the same geographic regions close enough to mate There is no gene ow between them Populations may be isolated by preferences for different habitats Often have a different niche a Example i Living in a dorm ii Apple maggot ies Originally laid eggs on hawthorns Now can also lay eggs on domestic apples Females will generally lay eggs on only the type of fruit they grew up in Males tend to look for mates on the type of fruit they grew up in Hawthorn ies generally end up mating with other hawthorn ies Apple ies generally end up mating with other apple ies Gene ow between the two populations reduced VI Definitions PonpIoidy a Having more then two sets of chromosomes i Often causes speciation in plants Tetraploidy a Produce diploid gametes rather than haploid gametes Tetraploid and diploid individuals rarely produce fertile offspring As a result tetraploid and diploid populations are reproductively isolated Mutations do not lead to evolution UNLESS When mutations reduce gene ow between mutant and wild type individuals mutations can result in divergence and speciation VII Reunited What happens when isolated populations of related species meet again a If they have diverged genetically i Divergence affects when where or how individuals mate Prezygotic isolation exists Mating is rare Gene ow is minimal Populations continue to diverge b If the have NOT diverged genetically or the divergence doesn t prevent mating Interbreeding may occur Gene ow occurs Distinctions between the two populations may be erased Chapter 44 Gas Exchange and Circulation 1 Circulation Open circulatory system a Hemolymph uid connective tissue b Pumped actively through body by a heart c Not confined exclusively to vessels d No pressure present lake analogy Closed circulatory system a Blood ows in a continuous circuit through the body b Pressure generated by heart c Confined exclusively to vessels d Found in vertebrates and other active lineages e Annelids worm squid octopuses cephalopods lowest level of organisms with closed circulatory system 11 Anatomy of the Heart Cardiovascular system has two components 1 Heart 2 Blood vessels Two functional systems 1 Pulmonary circuit pumps blood to the lungs deoxygenated BLUE a RIGHT side of the heart 2 Systemic circuit pumps blood to the rest of the body oxygenated RED a LEFT side of the heart Copyright The McGrawHill Companies Inc Permission required for reproduction or display head and CO2 arms 02 carotid artery also subclavian artery to arms jugular vein also subclavian vein from arms pulmonary pulmonary artery vein supenor vena cava aorta inferior vena cava hepatic vein w l intestinal arteries hepa c portal vein renal artery renal vein iliac vein iliac artery Heart functions a Keeps the 02 poor blood separate from 02 rich blood i If this did not happen then the 02 from the 02 rich blood would diffuse due to a concentration gradient b Keeps the blood owing in one direction c Creates blood pressure d Regulates the blood supply Superior Aorta vena cava Parietal pleura cut Pulmonary Left lung trunk Pericardium cut Apex of Diaphragm heart c c Heart sits slightly to the left The wall and coverings of the heart a Endocardium i Inner layer of heart ii Composed of simple squamous epithelium b Myocardium i Thickest part of the heart wall ii Made of cardiac muscle smooth striated c Pericardium i Twolayered serous membrane that encloses the heart ii Visceral pericardium epicardium forms the outer surface of the heart d Pericardial uid i Secreted by epicardium and parietal pericardium Ziploc baggy ii Reduces friction as the heart beats Copyright c The McGrewHill Companies Inc Permission required for reproduction or display pericardial cavity parietal pericardium fibrous pericardium coronary myocardium blood vessel epicardium visceral pericardium Layers of the heart a Protect the heart b Hold the heart in its place c Prevent the heart from overfilling Humans and other vertebrates have a closed circulatory system often call the cardiovascular system a Blood circulates to and from the heart through an extensive network of vessels The three main types of blood vessels are 1 Arteries a Tough thick walled vessels b Carry blood away from the heart to organs throughout the body c Under high pressure d Branch into arterioles e Carry blood to capillaries 2 Capillaries a Microscopic vessels with very thin porous walls b Walls are just one cell thick c Allows for gas and other molecule exchange d Networks of capillaries called capillary beds infiltrate each tissue and are the sites of chemical exchange between the blood and interstitial uid e Capillaries then converge into venules small veins i They converge into veins and return blood from capillaries to the heart 3 Veins a Vessels that return blood to the heart b Under low pressure With each type blood only ows in ONE direction K 2 K A Vein Artery Mediumsized Mediumsized Fibrous tissue Muscle tissue Elastic tissue Endothelium Arteries and veins are distinguished by the direction in which they carry the blood not by the oxygen content of the blood a Arteries carry blood from the heart toward capillaries AWAY from the heart b Veins return blood TO the heart from the capillaries c One exception is portal veinscarry blood between pairs of capillary beds d Capillaries are where gas exchange occurs Human hearts contain four chambers Blood enters through an atrium and is pumped out through a ventricle Amphibian reptiles and mammals have double circulation Oxygen poor and oxygen rich blood are pumped separately from the right and left sides of the heart a RIGHT side of the heart delivers oxygen poor blood to lungs pulmonary circuit b Oxygen rich blood enters the left side of the heart this blood is pumped to organs and tissues systematic circuit Within each type of vessel blood only ows in one direction Visceral means it s directly attached to an organ Anatomical position is OPPOSITE of pictures 111 Lungs Left lung is a little bit smaller than the right lung a Cardiac notche Left lung 2 nodes Right lung 3 nodes IV Closer Look at the Anatomy of the Heart Pulmonary artery Left atrium Semilunar valve Atrioventricular Atrioventricula Q valve valve Right Left ventricle ventricle Atria The Receiving Chambers Vessels entering right atrium a Superior vena cava b Inferior vena cava c Coronary sinus d Right atrium receives oxygen poor blood Vessels entering left atrium a Right and left pulmonary veins b Receives oxygen rich blood Ventricles The Discharging Chambers Vessel leaving the right ventricle a Pulmonary trunk Vessel leaving the left ventricle a Aorta b Left ventricle forms the apex of the heart Anatomy of the Heart Chambers of the heart 1 Right atrium a Receives oxygen poor blood b Vessels that empty into right atrium i Superior vena cava ii Inferior vena cava iii Coronary sinus 2 Right ventricle a Blood leaves right ventricle through pulmonary trunk 3 Left Atrium a Receives oxygen rich blood b Blood enters atrium through 4 pulmonary veins c Blood leaves left atrium through an AV valve bicuspid or mitral 4 Left Ventricle a Forms apex of the heart b Blood leaves the left ventricle through the aortic semilunar valve and enters the aorta Atria and Ventricles Summary 1 Atria a Thin walled b Receives blood 2 Ventricles a Thick wall b Pumps blood PROCESS PULMONARY CIRCULATION SYSTEMIC CIRCULATION 4 Blood returns to left atrium from lungs 1 Blood returns to heart from body enters right atrium 5 Blood enters left 2 Blood enters superior Aorta ventricle right ventricle vena cava 6 mood is pumped from left ventricle to body P I 3 Blood is pumped v lirrgonary from right ventricle to lun s 3 Pu39mona 9 W 1 Blood returns to heart from body 4 Blood returns to left Right I enters right atrium atrium from lungs Pulmonary valve atrium Left atrium Right atrioventricular AV valve Left atrioventricular AV valve Left ventricle Right Inferior ventricle vena cava 2011 Pearson Education Inc Four valves prevent back ow of blood in the heart and keep blood moving in the right direction The atrioventricular AV valves separate each atrium and ventricle a Tricuspid separates right atrium and right ventricle b Bicuspid mitral 9 separates left atrium and left ventricle The semilunar valves control blood ow to the aorta and the pulmonary artery a Pulmonary semilunar valve b Aortic semilunar valve Operation of heart valves a AV valves i Normally open ii When ventricle contracts AV valves shut b Semilunar valves i Normally closed ii Contraction of ventricles forces valves open V The Cardiac Cycle Systole a Contraction pumping of atria and ventricles Diastole a Relaxation filling phase One complete systole and diastole is a cardiac cycle Cardiac cycle A f l Ventricular diastole VentriCUIar Syst0e 12 quotquotquotquotquotquot quotS39y tb39l39i39 b39l39 b39d39b i ui quotquotquotquotquotquotquotquotquotquotquotquotquotquotquot A 100 E 80 h E DIaStOllC blood pressure E 60 e Aortic pressure g 40 I Ventricular pressure 2 20 I Atrial pressure 0 l I I 0 02 04 g g 06 Av T39me Sewnds AV Aortic Aortic valves valves valve valve open close opens closes 2011 Pearson Education Inc Heart Sounds 1 First sound lub a Heard when ventricles begin to contract b AV valves close c Lasts longer and has a lower pitch 2 Second sound dup a When semilunar ventricles relax b Semilunar valves close 3 Heart murmurs a Due to ineffective leaky valves b Valves do not close properly c Allows blood to back ow into atria or ventricles after valves have closed VI Physiology of Circulation Blood pressure a Usually measured in brachial artery b The blood pressure cuff is in ated until no blood ows through the artery c Korotko r sounds i Produced when the pressure in the cuff is released and blood begins to hit the arterial walls ii Systolic pressure iii When sounds end diastolic pressure is recorded a Normal blood pressure 12080 i Higher number systolic pressure Recorded when left ventricle contracts ii Lower number diastolic pressure Recorded when the left ventricle relaxes b Hypertension high blood pressure i Systolic pressure 140 lt ii Diastolic pressure 90 lt VII Physiology of the heart Conduction System of the Heart a Initiates and stimulates contraction of the atria and ventricles b is instrinsic does NOT require nervous stimulation c Coordinates contraction of atria and ventricles Nodal Tissue a Has muscular and nervous characteristics b SA sinoatrial node upper posterior wall of the right atrium i Initiates the heartbeat ii Sends out an excitation impulse every 085 seconds iii Pacemaker of the heart b AV atrioventricular node base of the right atrium i Impulse is delayed ii Signals the ventricles to contract c Atrioventricular bundle AV bundle d Purkinje fibers Copyright The McGrawHill Companies Inc Permission required for reproduction or display Stimulus originates in the SA node and travels across the walls of the atria causrng them to contract SA node Stimulus arrives at the AV node and travels along the AV bundle AV node AV bundle branches of Stimulus descends to the apex of the heart Av through the bundle branches bundle After stimulus reaches the Purkinje fibers the ventricles contract Purkinje fibers VIII Electrical Activation of the Heart Key events in the heart s electrical activation include 1 The SA node originates a signal 2 The signal from the SA node is propagated over the atria which contract simultaneously and fill the ventricles 3 The signal is conducted to the AV node which relays the signal to the ventricles after they fill completely with blood 4 The electrical impulse is rapidly transmitted through both ventricles causing them to contract as the atria relax 5 The final electrical event occurs as the ventricles relax and their cells recover IX Intercalated Discs Specialized structures that join cardiac muscle cells to neighboring cells Contain numerous gap junctions E1ectrical signals can pass directly form one cardiac muscle to the next X EKG ECG P wave depolarization of the atria QRS complex depolarization of the ventricles ST segment time between ventricle depolarization and repolarization T wave ventricle repolarization PROCESS ELECTRICAL ACTIVATION OF THE HEART WU T gt IE kl kl I a 1 Signal originates 2 Signal spreads over 3 Signa deays 4 Signal spreads down 5 Ventricles relax at SA node atria atria contract at Av node conducting fibers to bottom of ventricles ventricles contract 0 Electrical activity millivolts P c 0 01 012 03 04 05 Time seconds t D 2011 Pearson Education Inc XI Respiratory System Major function is gas exchange Works with cardiovascular system to accomplish 1 Breathing 2 External respiration 3 Internal respiration 4 Transport of gases XII Lungs Paired coneshaped organs Each lobe is divided onto lobules Each lobule has a bronchiole that serves many alveoli Pleurae a Double layered membrane i The visceral pleura adheres to the surface of the lung ii The parietal pleura lines the inside of the thoracic cavity b Produces a lubricating serous uid Trachea Superior lobe of left lung Left main primary bronchus Lobar Superior lobe of right lung secondary bronchus Segmental Middle lobe tertiary of right lung bronchus Inferior lobe of left lung Inferior lobe of right lung XIII Alveoli Alveolar sacs are made up of epithelium surrounded by blood capillaries Site of gas exchange Alveoli must stay open to receive inhaled air a Surfactant lowers the surface tension of water linig the alveoli preventing them from collapsing completely b Respiratory distress syndrome occurs in premature infants who lack surfactant a Airways into the b Alveoli c The alveolar gas human lungs exchange surface Smallest bronchiole Air A ueous film oxygen 1 g f t Oxygenrich oxygen q V quotI blOOd out E 39 h poor v I plt elum blood in 21 39 a of alveolus t gem 399 Q A Wall of capillary Bronchioles Alveolus Capillaries 2011 Pearson Education Inc XIV Ventilation Manner in which air enters and exits the lungs Humans pull air into the lungs via negative pressure ventilation Consider a Lungs lie within sealed thoracic cavity b Lungs adhere to the thoracic cavity via pleurae c Column of air from pharynx to alveoli XV Mechanics of Breathing Pulmonary ventilation consists of two repetitive phases 1 Inspiration gases ow into the lungs 2 Expiration gases exit the lungs Respiratory cycle one complete inspiration and expiration a Quiet respiration while at rest effortless automatic b Forced respiration deep rapid breathing such as during exercise Flow of air in and out of lung depends on a pressure difference between air pressure within lungs and outside body Breathing muscles change lung volumes and create differences in pressure relative to the atmosphere XVI Respiratory Muscles Diaphragm a Prime mover of respiration b Contraction attens diaphragm and enlarging thoracic cavity and pulling air into lungs c Relaxation allows diaphragm to bulge upward again compressing the lungs and expelling air d Accounts for twothirds of air ow Internal and external intercostal muscles a Between ribs b Prevents rib cage from caving inward when diaphragm descends c Contribute to enlargement and contraction of thoracic cage a Lungs expand and contract in response to changes in pressure inside the chest cavity v caresslame 1 ess 8 t e gati e XVII Inspiration Active phase of ventilation Diaphragm contracts and attens External intercostal muscles contract and the rib cage moves upward and outward Thoracic cavity volume increase causing the lungs to increase in volume Air pressure within the alveoli intrapulmonary pressure decreases Air ows form an area of higher pressure atmospheric pressure to an area of lower pressure within the lungs XVIII Expiration Usually the passive phase of ventilation The diaphragm relaxes and resumes its dome shape The intercostal muscles relax and the rib cage moves down and in The volume of the thoracic cavity decreases and the lungs recoil Lung volume decreases and the intrapulmonary pressure increases Since intrapulmonary pressure is now greater than atmospheric pressure air will ow out of the lungs Inspiration Copyright The McGrawHill Companies Inc Permission required for reproduction or display trachea Rib cage moves up and out External intercostal muscles pull the ribs outward lungs Diaphragm contracts and moves down When pressure inlungs decreases air comes rushing in a Inspiration Expiration Copyright The McGrawHill Companies Inc Permission required for reproduction or display Rib cage moves down and in Internal intercostal muscles pull the ribs inward during forced expiration Diaphragm relaxes and moves up When pressure inlungs increases air is pushed out b Expiration b Ventilatory forces can be modeled by a balloon in a jar Pressure Pressure more leSS negative negative When the When the a diaphragm diaphragm A is pulled is released 1quotquot down the the balloon balloon inflates 39 deflates 2011 Pearson Education Inc Chapter 49 Immunity I Three Interesting Observations 1 Wounds usually heal even is they become infected 2 Most people who contract a bacterial or viral illness eventually recover without medication 3 People who acquire bacterial or viral infections and recover frequently do not contract the same disease again immunity a Smallpox people would snort sprinkle smallpox particles into their body and would gain resistance to the virus II Introduction Immunology9 scientific study of how the immune system functions in the body to prevent or destroy foreign material Two types of immunity 1 Innate nonspecific immune response a Immediate response 2 Acquired adaptedrequiredspecific III Host Immune Defenses Blood consists of 3 major components 1 Serum the uid portion ofthe blood a Minerals b Salts c Proteins etc 2 Plasma serum that contain clotting agents a Fibrinogen b Prothrombin 3 Cells a Blood platelets no nucleus bloodclotting function i Not technically a cell b Erythrocytes red blood cells c Leukocytes immune cells IV Cells of the Immune System Always found in normal blood a Numbers increase during infection Some cells play dual roles in both innate and adaptive immunity Blood cell formation called hematopoiesis a Blood cells including immune cells originate from hematopoietic stem cells this is a restricted stem cell it can ONLY become blood cells in bone marrow Proliferate to make more of a Cells have the ability to replicate Di feren tiate Granulocytes a Contain prominent cytoplasmic granules filled with biologically active chemicals b Divided into three types based on their staining properties 1 Neutrophils 5565 Most abundant and important in innate response Sometimes called polymorphonuclear neutrophilic leukocytes PMNs Highly efficient at phagocytizing and destroying bacteria Granules contain antimicrobial substances and degradative enzymes Numbers increase during most acute bacterial infections Few in tissues except during in ammation usually found in the blood Short lifespan only about one or two days so continually replenished from the bone marrow I b Neutrophils ingest and kill pathogens Multilobed nucleus Granules contain pathogenkilling molecules 3 o 0 f c I s 1 Ig m 9 a u 2 Basophils 04 Involved in allergic reaction and in ammation Granules stain blue contain histamine Found in circulation Mast cells are similar to basophils but found in tissues 3 Eosinophils 24 Important in expelling parasitic worms Active in allergic reactions Few are found in the blood because they enter local secretions Few found in tissues except in certain allergies Granules have antimicrobial substances and histamines Some have phagocytic activity l a Mast cells secrete signals that increase blood flow Granules contain Nucleus signaling molecules Anything involved in immunity are white blood cells Monocytes 38 a Circulate in blood b Differentiate into macrophage or dendritic cells when they migrate into cells c Two week life span Macrophages a Differentiate from monocytes i Present in virtually all tissues ii Abundant in live spleen lymph nodes lungs and peritoneal cavity iii Named based on the tissues in which they are found b May live for several months c Effective phagocytes I c Macrophages recruit other cells and ingest and kill pathogens Pseudopodia Lysosomes 1 1 engulf digest bacteria bacteria gmquot Dendritic cells a Branched cells involved in adaptive immunity b Found in the skin Langerhans cells and in the tissues c Function as scout in tissues i Engulf material in tissue and bring it to cells of adaptive immunity Lymphocytes a Involved in adaptive immunity b Two major groups i B lymphocytes ii T lymphocytes c Natural killer i Lacks specificity of B and T cells ii Destroy Virusinfected and abnormal cells Primary lymphoid tissues a Thymus behind the breast bone b Bone marrow c Sites where immune cells form or mature Secondary lymphoid tissues a Sites where mature immune cells interact with pathogens i Spleen ii Lymph nodes neck armpits groin iii Intestine iV Appendix V TonsilsAdenoids Components of the immune system Lymphocyte origin Bone marrow Lymphocyte maturation Bone marrow B cells Thymus T cells Lymphocyte activation Spleen Lymph nodes Lymphocyte transport Lymphatic ducts Blood vessels 6 2011 Pearson Education Inc V Innate immunity nonspecific resistance Geneticallyencoded to recognize a Common pathogenic features b Foreign substance Early warning system Responds within hours after infection can respond within minutes Tries to eliminate or hold an infection in check while communicating with the body that something is wrong VI Cell Communication In order for immune system to respond cells must communicate with environment with the environment and with each other a Cytokines are the voice i Small protein chemical signals sent by many immune cells ii Produced by macrophages lymphocytes mast cells and dendritic cells VII Acquired Immunity specific resistance We don t want it on unless we need it on Involves production of a Lymphocytes b Antibodies Only exists in vertebrates Relatively slow compared to the innate response KEY it has memory VIII Innate Defenses First line defenses are barriers that shield interior of body from external surroundings 1 Anatomical mechanical barriers a Provide physical separation b First line of defense SKIN i Most visible barrier ii Most difficult carrier to penetrate iii Epidermis is constantly being sloughed off taking microbes with it iv Poor source of nutrition for invading microbes low water content v High salt vi Slightly acidic c MUCOUS MEMBRANE MUCOSA i Lines digestive tract respiratory tract and genitourinary tract Constantly bathed with mucus ii Mechanisms to propel microorganisms to areas where they can be eliminated Peristalsis in the GI tract Cilia in the respiratory tract Urine in the urinary tract 2 Chemical barriers a Membranes bathed in antimicrobial secretions b Examples i Low pHvaginal tract urinary tract stomach ii Sweat high in salt iii Lactoferrin Hides free iron iv Lysozyme Degrade peptidoglycan bacterial cell walls Found in tears saliva blood and phagocytes V Peroxidase Found in saliva milk body tissues and phagocytes Breaks down hydrogen peroxide to produce reactive oxygen 3 Microbiological barriers a Normal ora9 sterile environment womb b Not technically part of the immune system c Protects through the competitive exclusion i Covers binding sites ii Competes for nutrients iii Produce compounds toxic to other bacteria d Disrupting normal ora taking antibiotics can predispose a person to various infections Eyes Blinking wipes tears across the eye Tears contain the antibacterial enzyme lysozyme Ears Hairs and earwax trap pathogens in the passageway of the external ear Airways lining of trachea Most pathogens are trapped in mucus before they can reach the lungs Beating cilia sweep pathogens up and out of the airway ll Nose The nasal passages are lined with mucus secretions and hairs that trap pathogens Digestive tract Pathogens are trapped in saliva and mucus then swallowed Most are destroyed by the Mucussecreting Ciliated low pH of the stomach cells cells 2011 Pearson Education Inc 2011 Pearson Education Inc Portal of entry for pathogens aEyes b Ears c Nose d Digestive tract e Genital tract IX In ammation Occurs in response to tissue damage Role is to contain a site of damage localize the response and resort tissue function 4 cardinal signs 1 Heat 2 Pain 3 Redness 4 Swelling X The In ammatory Response A multistep innate immune response in mammals occurs at the site of an injury Steps ofthe process 1 When skin breaks pathogens enter a wound 2 Platelets release bloodclotting proteins at the wound site 3 Wounded tissues and macrophages at the wound site secrete chemokines signaling molecule that recruit immune cells by forming a gradient to mark the path to the site 4 Mast cells release chemical messengers that constrict blood vessel near the wound reducing blood ow and thus blood loss Mast cells also secrete histamine and other signaling molecules which dilate blood vessels slightly farther away from the wound making them more permeable 5 Neutrophils and macrophages remove pathogens by phagocytosis the engulfing and digesting of foreign particles 6 Macrophages secrete cytokines chemicals that attract other immune system cells to the site and activate cells involved in tissue repair They also induce fever elevated body temperature that aids in healing In ammatory response continues until the foreign material is eliminated and the wound is repaired PROCESS THE INFLAMMATORY RESPONSE PROCESS THE INFLAMMATORY RESPONSE 4 Mast cells release factors that constrict blood vessels at wound and dilate vessels nearby I 1 Pathogens enter wound 5 Neutrophils arrive and begin phagocytizing pathogens 2 Platelets release bloodclotting proteins 6 Leukocytes arrive and mature into macrophages 3 Injured tissues and macrophages release chemokines to recruit help Induce fever increase leukocyte production 39K l39 lilifygii 2011 Pearson Education Inc 2011 Pearson Education Inc SUMMARY TABLE 491 The Innate Immune System a Key Cells Name Primary Function Mast cells Release signals that increase blood flow to wound site Neutrophils Kill invading cells via phagocytosis Macrophages Release cytokines that recruit other cells to wound site kill invading cells via phagocytosis b Key Signaling Molecules Name Produced By Received By Message Function Histamine Mast cells Blood vessels High concentration next to wound constricts blood vessels low concentration fartherfrom wound dilates blood vessels Chemokines Injured tissues and Neutrophils and macrophages Mark path to wound promote dilation and increased macrophages in tissues permeability of blood vessels Cytokines other Macrophages Leukocytes Mark path to wound than ChemOkmes Bone marrow Increase production ofmacrophages and neutrophils CNS Induce fever by increasing set point for control of body temperature Local tissues Stimulate cells involved in wound repair Note that chemokines are a subset ofcytokines 2011 Pearson Education lnc XI Overview of the Acquired Immune Response Acquired immunitydefense against a tremendous variety of potential pathogens based on 4 attributes 1 Specificity a Antigens antibody generators i Anything that provokes an immune response ii Can be toxins viruses cells or large complex molecules b Immune deficiency is the loss of the body s ability to respond to antigens 2 Tolerance of self a Molecules produced by an individual do not act as antigen b Distinguishes between self and nonself c Minimal selfdamage 3 Diversity a Adaptive response recognizes an almost limitless array of antigens 4 Immunological Memory a The ability to remember past pathogen exposures b Second exposure to the previously encountered pathogen produces a rapid and potent response XII Strategy of Adaptive Immune Response First response to particular antigen called primary response a May take a week or more to develop Immune system remembers pathogen on subsequent exposure a Termed secondary response ll Initial exposure to antigen Second exposure to antigen Secondary g immune 3 response L 4 5 Response 0 is larger o 0 gt1 396 a Primary immune 5 response lt V Response 39 is faster gt gt Time Time Adaptive immunity divided into 1 Humoral immunity a Eliminates extracellular pathogens 2 Cellular immunity a Eliminates intracellular pathogens XIII Acquired Immunity An Overview B cells and T cells have receptor proteins that can bind to foreign molecules Each individual lymphocyte is specialized to recognize a specific type of molecule All antigen receptors on a single lymphocyte recognize the same epitope or antigenic determinant on an antigen B cells give rise to plasma cells which secrete proteins called antibodies or immunoglobulins Humgfmagzggbrgga ggiaml Cellmediated Immune response K0 gt Stimulates Engulfed by q Gives rise to Antigen presentlng cell Cytotoxic 0 O u Memory helper T cell 1 Plasma Memory Memo Active cytotoxic cons cytotoxic T cells cm 99 V Secreted amp quot am39m39es Defend against Defend against intracellular 7 4 extracellular pathogens pathogens and cancer B cell 2 iv INNATE IMMUNITY Barrier defenses Skin Recognitlon of traits Mucous membranes shared by broad ranges Secretions of pathogens using a small set of receptors lntemal defenses Rapid response Phagocytic cells Antimicrobial proteins Inflammatory response Natural killer cells Humoral response Antibodies defend against Infection In body fluids Cellmediated response Cytotoxic lymphocytes defend against infection In body cells Antigen Antigen binding binding site site Disul de Variable regions Constant regions Transmembrane region Plasma membrane B cell iiii e39lm i ei rhrl Antigen receptor Antibody t 7 a E a B cell antigen receptors and antibodies Antig Antibody c Antibody A Antibody B e Antigen b Antigen receptor speci city TABLE 492 Five Classes of lmmunoglobulins Structure Name secreted form Function lgG Monomer The most abundant type of secreted I antibody Circulates in blood and Y interstitial fluid Protects against bacteria viruses and toxins lgD Monomer Present on membranes of immature B Y cells rarely secreted Serves as BCR lgE Monomer Secreted in minute amounts Involved l in response to parasitic worms Also Y responsible for hypersensitive reaction that produces allergies lgA Dimer Most common antibody in breast milk I tears saliva and the mucus lining the H respiratory and digestive tracts Prevents bacteria and viruses from attaching to mucous membranes helps immunize breastfed newborns lgM Pentamer First type of secreted antibody to appear during an infection Binds I many antigens at once effective at f clumping viruses and bacteria so l I that they can be killed 2011 Pearson Education Inc IMPORTANT FOR EXAM Respiration know what happens at each muscles volume pressure Ignore gene rearrangement Humoral immune system extracellular B cells in the blood T cells involved in cell mediated immune response thingsquot in the cell Phagocytic cells Neutrophils Dendritic cells Macrophages MHC I internal check on all types of nucleated cells MHC II antigen presenting cells dendritic cells B cells macrophages Helper t cells cd4 T cells release a LOT of cytokines give a lot of instruction orchestrate Cytotoxic t cells cd8 T cells KILL B cells never kill cells they make antibodies do not kill they BIND attach proliferate differentiate plasma and memory cells Plasma cells make antibodies have nuclei and filled with rough ER Memory cells don t know where they go respond quickly Copyright The McGraw Hill Companies Inc Permission required for reproduction or display A Hematopoietic stem cell in bone marrow Myeloid progenitor t Lymphoid progenitor Natural killer NK cells Erythroblast Megakaryoblast Putative Myeloblast Monoblast Lymphoblasts mast cell i precursor White blood cells leukocytes Megakaryocyte l l i ii i Granulocytes Agranulocytes V f 4 T l N B u w C J a v 2 8 8 52 2 gt22 Monocytes Lymphocytes I 3933 o 392 2 g g Blood phagocytes that Primary cells involved in 8 53 g 8 D g 9 rapidly leave the circulation specific immune reactions 5 U c a lt6 E 395 g m a mature into macrophages to foreign matter O 8 393 398 g 79 E E g 9 and dendritic cells 82 5 2 53 58 quot9 8 m m E E E 2 gig g E 392 E 3 93 E Perform a number of specific 2 C l HS 8 3 3 32 09 9 435 g 89 E cellular immune responses 3 Q E g E 3 0C 3 3 g E 02 35 such as assisting B cells and g 8 g g g g g g 5 g l1 g Ilo E 5 killing foreign cells cell w 39 mediated immunity Macrophages Bcequots Largest phagocytes that Differentiate into plasma cells and form antibodies humoral ingest and kill foreign cells immunity strategic partrcrpants in certain specific immune Mast cells reaCtionS Specialized tissue cells similar to basophils that DeNdritic ce39ls trigger iocai in ammatory Relatives of macrophages that reactions and are responsible reSide throughout the ti SueS for many allergic symptoms responSIb39e for processmg foreign matter and presenting it to lymphocytes Chapter 50 Introduction to Ecology DEFINITIONS 1 Introduction Ecology9 study of how organisms interact with their environment a Primary goal understand the distribution and abundance or organisms II Hierarchy Biosphere global sum of all ecosystems Biome world s major communities classified according to predominant vegetation and characterized by adaptations of organisms to that particular environment a Aquatic b Desert c Forest d Grassland e Tundra Ecosystem9 living organisms biotic in conjunction with the nonliving components abiotic of the environment Community Group of interacting living organisms sharing a populated environment Population9 all the organisms that belong to the same species and live in the same geographical area Species group of organisms capable of interbreeding and producing fertile offspring III Areas of Ecological Study 4 levels 1 Organisms 2 Populations 3 Communities 4 Ecosystems 1 Organismal Ecology How do individuals interact with each other and their physical environmentquot Explores morphological physical and behavioral adaptations that allow individual organisms to live successfully in a particular area Includes adaptations organisms possess and the impact those adaptations have on the ability of an organism to survive Questions a How do these individuals interact with their physical surroundings i With other organisms in and around the stream b How do they cope with transition from living in salt water to living in freshwater c Which females get the best nesting sites and lay the most eggs d Which males are most successful in fertilizing eggs a Organismal ecology How do individuals interact with each other and their physical environment Salmon migrate from saltwater to freshwater environments to breed 2011 Pearson Education Inc 2 Populations How and why does population size change over timequot A population is a group of individuals of the same species that live in the same area at the same time Focuses on how the numbers of individuals in a population change over time Very mathematically based use mathematical models to predict the future of salmon populations Models can asses impact of proposed dams changes in weather patterns altered harvest levels specific types of protection efforts Population Density individuals per unit area or volume a MarkRecapture Patterns of Dispersion a Clumped uniform random Population Growth Models a Bacterial growth curve vs elephant reproduction b 2 every 20 minutes vs 6 young per 100 years b Population ecology How and why does population size change over time u Q 39 oi ampi a r u 39 u 3 quot Each female salmon produces thousands of eggs Only a few will survive to adulthood On average only two will return to the stream of their birth to breed 2011 Pearson Education Inc 3 Communities How do species interact and what are the consequencesquot Study of the nature and consequences of the interactions between species and the consequences of those actions Concentrations on predatism paratism competition Explores how species respond to fires oods or other disturbances r 1 Salmon eat smaller fish 2 Salmon are hunted by orcas sea lions humans and other mammals in the sea 3 When they return to freshwater to breed they are preyed on by bears and bald eagles K 4 In both environments salmon are subject to parasitism and disease I How do species interact and what are the consequences Salmon are prey as well as predators 2011 Pearson Education Inc 4 Ecosystems How do energy and nutrients cycle through the environmentquot Study of how nutrients and energy move among and between organisms and the surrounding atmosphere and soil or water Assess impact of pollution and increased temperature on the distribution and abundance of species Salmon link marine and freshwater environments Harvest nutrients in the ocean and then when they migrate die and decompose transport those to streams Salmon transport chemical energy and nutrients from one habitat to another d Ecosystem ecology How do energy and nutrients cycle through the environment Salmon die and then decompose releasing nutrients that are used by bacteria archaea plants protists young salmon and other organisms 2011 Pearson Education Inc IV Conservation Biology 4 levels are synthesized and applied in conservation biology Study preserve and restore threatened populations communities and ecosystems Prescribe remedies for environments so they produce a diversity of species pure water and productive soils Organisms have a restricted set of physical conditions in which they can survive and thrive Abiotic physical temperature precipitation sunlight wind Biotic living members of the same or different species V Abiotic Conditions Temperature a In uential role on metabolism b Most organisms operate optimally between 32 F and 122 F c Some species however are adapted to extreme temperatures i Also contributes to erosion and creation of soil Water precipitation a Ability to conserve water or get rid of excess water are important adaptations b Chemical balance of living tissues is a challenge in terrestrial and freshwater environments c Important in erosion and creation of soils Sunlight a Intensity varies with location and time of year b Daily duration varies with location and time of year c Competition for d Light is a selective factor in many environments e Animals and plants react to light dark cycles with behavioral changes Wind a Groups that live on nutrient poor substrates depend on wind to blow in nutrients b Plants depend on wind to disperse sperm and seeds c In uences rate of water loss by plants desiccation d Important in evaporative cooling affecting internal temperature e Contributes to erosion Rocks soil a Topography creates habitat b Mineral content of rock affects ora c pH of rock soil affects ora d Affects any water that come in contact with it Maj or environmental disturbances a Fire Hurricanes Tornadoes Volcanoes Comets VI More on Organismal Ecology Ability to survive extremes of environment determine survival and reproduction This includes being able to control internal environment Regulat0rs organisms that use metabolic means to regulate their internal environment a Thermoregulation temperature control birds and mammals b Osmoregulation salt balance fish C0nf0rmers internal conditions are controlled primarily by the environment a Thermoregulation insects b Osmoregulation echinoderms starfish sea urchins lack excretory system VII Definitions Ect0therm9 obtains heat from the environment conformer End0therm9 obtains heat from metabolic reactions regulator P0ikilotherm9 temperature regulated by environment conformer H0meotherm9 temperature regulated by internal mechanisms regulator VIII Aquatic Ecosystems Marine vs Freshwater a Nutrient availability i Often nitrogen and phosphorous are in short supply ii When water is moving nutrients tend to be washed away iii If water is still nutrients tend to fall to the bottom b Water depth i Light water absorbs and scatters light ii Light intensity decreases wavelengths available decrease iii Major in uence on productivity amount of carbon fixed by photosynthesis a Only certain wavelengths of light are available 03 Intens39ty 0f 9quot deCI39quotes W39th water depth under water E 3 20 In green algae gt 1390 g E photosynthesis 1 E s driven meet 08 9 Light penetrates 3M5 3 fth39fht m ef fcnently by c ar er In res wa er 3 5 wavmengths of 1 06 0 than in seawater quot5 E 10 about 425 nm 5 o g g and 680 nm 3 04 o 55 395 2 o r c E 5 395 02 Pure seawater Pure freshwater 3 3 o o 33 CC 9 o 0 TB 0 0 I 9 I I I I 400 500 600 700 0 20 40 60 80 100 120 Wavelength nm m Depth m c Water movement i Water ow creates a physical challenge IX Marine Environment The Ocean a Continuous body of salt water b Pelagic water environment and Benthic bottom interface i Pelagic zone 1 Intertidal zone Rocky sandy muddy beach exposed to air at low tide covered in water at high tide 2 Neritic zone Extends from intertidal zone to depths of about ZOOm outermost edge is continental shelf 3 Oceanic zone Open ocean deep region beyond the continental shelf a Epipelagic photic zone b Mesopelagic aphotic zone c Bathypelagic aphotic zone d Abyssopelagic aphotic zone Intertidal zone Nentlc zone Oceanic 2 Sea level I x one 200 m 39 r 39 MM v 39 w M 1 l Photlc zone Continental shelf Aphotic zone Ocean Upswelling a Nutrients in sunlight surface waters are lost to depths b Currents bring deep cold water to the surface of ocean PROCESS OCEAN UPWELLING 1 Winds blow 2 Surface water 3 Upwelling As Along the coast of moves As the Earth surface water leaves Peru the prevailing rotates the moving it is replaced by winds blow north surface water is nutrientladen water moving water at forced offshore welling up from the the surface bottom c Effects of upswelling i Biodiversity and productivity Deep water brought up is often rich in nutrients leading to seaweed and plankton growth ii Animal movement iii Coastal climate Sea fog Water movement in the ocean is different depending on the depth a Intertidal zone tides and wave action are major in uences b Neritic zone currents that bring up nutrient rich water c Throughout the ocean large scale currents in response to winds and Earth s rotation d Nutrient availability is dictated by water movement Each ocean zone has distinct species adapted to the physical conditions present a Intertidal zone organisms must be able to withstand physical pounding from waves desiccation and high temps from low tide high productivity in intertidal region i Splash zone usually dry Periwinkle snails fingernail limpets buckshot barnacles ii High intertidal larger barnacles and mussels iii Mid intertidal anemones sea stars prey here and in high intertidal zone after high tide iv Low intertidal sea stars anemones sea urchins b Neritic zone world s major fisheries i Dolphins all kinds of fish turtles ii In tropics neritic zone hosts coral reefs iii Productivity is high here as well c Oceanic zone desert of the ocean i Sunlight in the photic zone but no nutrients Plankton jellyfish ii Aphotic zones are extremely unproductive Squid chambered nautilis giant squid bioluminescent jelly fish iii Organisms that live here do so because of raining dead bodies X Freshwater Environment 1 Lakes and Ponds a Ponds are small b Lakes are large enough that the water in them can be mixed by wind and wave action c Most natural lakes and ponds occur at high latitudes d In the tropics most lakes are old river channels e Most lakes and ponds are man made 5 Zones of water depth 1 Littoral seashore zone shallow waters along the shore where owering plants are rooted 2 Limnetic lake zone offshore and has water that receives enough light to support photosynthesis 3 Benthic depth zone bottom or substrate 4 Photic zone regions that receive light 5 Aphotic zone regions that don t receive light IPho c zone Apho c zone 2011 Pearson Education Inc Water movement is driven by wind and changes in temperature a Littoral amp limnetic zones are much warmer and better oxygenated b Benthic zone is relatively nutrient rich because of dead stuff Critters a Cyanobacteria algae and other microscopic organisms plankton live in the photic zone b Fish and small crustaceans eat them c Animals that consume dead organic matter detritus are found in the benthic zone PROCESS LAKE TURNOVER High 02 concentration V J 2amp2 we 1 Winter stratification 2 Spring turnover 3 Summer stratification 4 Fall turnover L 2011 Pearson Education Inc 2 Wetlands a Shallow water habitats b Soil is saturated with water at least part of the year c Indicator plants d Emergent plants grow above the surface of the water e 3 types 1 Bogs i Low or nonexistent water ow ii Acidic iii Nonproductive a Bogs are stagnant and acidic 2 Marshes i Slow but steady ow of water ii Relatively nutrient rich iii Highly productive iv NONWOODY PLANTS b Marshes have nonwoody plants 439 nimammyvm w lim gi 2011 Pearson Education Inc 3 Swamps i Slow but steady ow of water ii Relatively nutrient rich iii Highly productive iv WOODY PLANTS c Swamps have trees and shrubs gnawmm 2011 Pearson Education Inc 3 Streams a Move constantly in one direction b Creeks are small stream rivers are large c Most are shallow enough for sunlight to reach bottom d Origination cold narrow fast few organisms e End warmer wider slower more organisms V quot 4 fly lquot 1quot Near sour e f quot4quotquot water is fast 39 cold nutrient poor high in 02 Later water slows down becomes warmer more nutrient rich 39 lower in 3902 2011 Pearson Educalion Inc 4 Estuary a Forms where river meets ocean and mixes freshwater and saltwater b Salinity varies with changes in river ows and distance to ocean c Species that live in estuaries must deal with variations in salinity d Very productive environments XI Biomes Maj or groupings of plant and animal communities defined by a dominant vegetation type Each biome is associated with distinctive abiotic conditions Biome usually depends on climate prevailing long term weather conditions Weather is shortterm atmospheric conditions Climate and weather consist of temperature moisture sunlight and wind Cl Arctic tundra Temperate forest Subtropical desert Boreal forest Temperate grassland Tropical wet forest Tropical dry forest Tropical coniferous forest Tropical grassland Mangrove Mediterranean forest Flooded grassland Montane grassland Temperate coniferous forest Equator 308 2011 Pearson Education Inc Terrestria1 Ecosystems a Biome governed by i Average annual temp and precipitation ii Annual variation in temperature and precipitation b Temperature and moisture in uence net primary productivity NPP i Represents organic matter available as food for other organisms XII Terrestrial Biomes 1 Tropical Wet Forests a Rain forest b Equatorial regions c Temp and rainfall are high d Variation in temp is very low e Year round favorable growing conditions f High productivity a g 30 Average In 5 A 20 HIGH 5 h o h o o 3 av 10 Variation lt E VERY LOW o 1 O Freezing 50 g 40 o Annual total 3 g E 3 VERY HIGH 3 93 2 8 20 Variation 3 HIGH 10 0 JFMAMJJASOND Month g Very diverse species of plants h Tree canopy uppermost layers of branches intermingled with vines epiphytes plants that grow entirely on other plants shrubs and herbs 2 Subtropical Deserts a 30 N and 30 S latitudes b High average annual temperatures c Moderate variation in temperature d Low precipitation e Scarcity of water means conditions are rarely favorable for photosynthesis f Productivity is low g Plants are widely spaced h Species adapt to extreme temperature and aridity by i Growing at a low rate year round ii Breaking dormancy and growing rapidly in response to any rainfall 40 q g 30 m a A Average g 3 g 20 HIGH gt a lt E 10 Variation quotquot MODERATE 0 c 20 Freezmg a 3 Annual total 3 g E VERY LOW 3 o 10 E 8quot Varlatlon L LOW 939 OW J FMAMJJASOND Month 3 Temperate grasslands a Temperate i Moderate temperatures relative to tropics and polar regions ii long warm summers short cold winters b Temperate grasslands i Low precipitation ii Temperature variation dictates well defined growing season iii Plant growth possible only in spring summer and fall months when water and warmth are adequate iv Grasses are dominant life form here Conditions are too dry for trees Encroaching trees are burned by fires V Productivity is moderate Lower than forest communities but soils are fertile 30 o L 0 3 g E a 20 Average 3 a 2 MODERATE 2 239 10 0 Variation quotquot MODERATE 0 Freezing 20 a 3 Annual total 01 u A LOW 9 E E 10 g 395 V Variation lt 2 MODERATE 9 0 JFMAMJJASOND Month 4 Temperate Forests a Temperate areas with relatively high precipitation become temperate forests b Experience a freeze where plant growth stops c Compared with grassland climates precipitation is moderately high and constant d Dominated by deciduous trees e Productivity lower than tropical forests but higher than deserts and grasslands 30 o g 20 Average m A MODERATE E E o 3 ga 10 Variation 1 E MODERATE 3 0 Freezing a 2 20 Annual total 3 E E MODERATE L g 393 Variation 2 LOW a JFMAMJJASOND Month 5 Boreal Forest a Taiga forms on subarctic lands just south of the Arctic Circle b Climate very cold winters and short cool summers c Extreme temperature variation d low annual precipitation but temperatures are so cold that evaporation is minimal e Usually enough moisture to support tree growth f Dominated by highly cold tolerant conifers g Productivity is low h Exceptionally low species diversity 20 10 Average 2 Low 0 3 o m Lu 9 a Freezmg Varlatlon g g 0 VERY HIGH lt E 10 a 40 20 30 c 20 a 3 Annual total 3 E LOW 3 9 o 10 gt quota V Varlatlon lt 95 LOW JFMAMJJASOND Month 2011 Pearson Education Inc 6 Arctic Tundra a Found throughout the arctic regions where land is not covered in ice b Low temps with high variation c Low annual precipitation d Growing season is 68 weeks at most temperatures are below freezing the rest of the year e Most tundra soils are in the perennially frozen state known as permafrost f Dominated by small woody shrubs lichens and herbaceous plants g Low species plant diversity h Low productivity i Animal diversity is low 10 q o g E Freezing Average 9 g a VERY LOW a 0 9710quot 5 9 Variation 5 HIGH 4 20 30 20 a g Annual total a 3 E VERY Low 331 0 1 quot gt 0 V Variatlon lt g Low JFMAMJJASOND Month XIII Why are the tropics wet Areas along the equator receive the most moisture Locations at about 30 N and 30 S latitudes are among the driest on Earth Major cycle in global air circulation Hadley cells is responsible for this a Air heated by the strong sunlight along equator expands and rises b Warm air can hold a great deal of moisture because warm water molecules tend to stay in vapor form instead of condensing into droplets c As air rises it radiates heat and beings to cool d Air expands into larger volume of upper atmosphere which lowers its density and temp a phenomenon known as adiabatic cooling e As it cools its ability to hold water declines water condenses and high levels of precipitation occur along the equator f As more air is heated along equator the cooler air above Earth s surface is pushed poleward g As the air mass cools its density increases and it beings to sink b As it sinks it absorbs more and more solar radiation form Earth s surface and begins to warm gaining water holding capacity i This results in very little precipitation at 30 N and 30 S latitudes Three such circulation cells in both Northern and Southern hemispheres b and at hi her latitudes a Circulation cells exist at the equator l 9 There are three circulation cells in the Northern Hemisphere Warm air rises and cools dropping rain V Cooled air is pushed poleward There are also three circulation cells in the Southern Hemisphere draw them in Dense dry air descends warms and absorbs moisture XIV Why are the tropics warm and the poles cold Areas of the world are warm if they receive a large amount of sunlight per unit area they are cold if they receive a small amount of sunlight per unit area Earth s spherical shape dictates that regions at or near the equator receive more sunlight per unit area than regions closer to the poles a This is due to the angle at which solar radiation hits the Earth Small amount of North pole sunlight per unIt area w angle of coming sunlight ederate angle of oming sunlight light directly 2 erhead Equator N Large amount of quot sunlight per unit area 2011 Pearson Education Inc XV What causes seasonality Seasons a Regular annual uctuations in temperature precipitation or both b Due to Earth s tilt of 235 on its axis une a Northern hemisphere tilted toward the sun so it faces the sun most directly December a Southern hemisphere tilted toward the sun so it receives the most solar radiation per unit area Therefore summer is in June in Northern Hemisphere and December is summer in the Southern Hemisphere March and September equator faces sun most directly so tropics receive the most solar radiation If Earth was not tilted on an axis no seasons would occur March 20 Equator faces Sun directly I December 21 Southern Hemisphere faces Sun at most direct angle June 21 Northern Hemisphere faces Sun at most direct angle If Earth did not tilt on its axis there would be no seasons 2011 Pearson Education Inc September 22 Equator faces Sun directly XVI Physical Features Contributing to Climate Broad patterns of climate are directed by Hadley cells and global heating patterns Regional effects are also important a Mountain ranges b Proximity to an ocean Mountain ranges produce extremes in precipitation a Rain shadow effect winds from ocean cool and drop precipitation on one side of a mountain range and not on the other side creating deserts Air rises over mountains and cools rain falls East Dry air creates desert conditions West Moistureladen air blows onshore from Pacific Ocean 39 A n J Iy iii atfw I I Cascade Mountains This area is in a rain shadow 2011 Pearson Education Inc Chapter 51 Behavioral Ecology I Introduction Behavior is an action a A response to a stimulus Ecology is the study of how organisms interact with their physical and biological environments Behavioral ecology is the study of how organisms respond to particular stimuli from those environments 11 Behavioral Ecology Behavioral ecologists ask questions and test hypotheses at two fundamental levels 1 Proximal 2 Ultimate Behavioral ecologists start by observing what animals do in response to specific problems or situations Then they use experimental approaches to probe proximate and ultimate causes of behavior a Proximate mechanistic explains HOW actions occur b Ultimate evolutionary explains WHY actions occur III Proximate and Ultimate Causation Spiny lobsters are able to find their way back to one of their dens after a night of hunting a Proximate research indicates they use special receptors in their brains to detect Earth s magnetic fields b Ultimate ability to navigate allows them to search for food over a wide area under cover of darkness then return home before predators find them IV Strategies and Decision Making Often animals respond to a change in their environment in highly predictable ways Fixed action patterns are highly in exible stereotypical behavior patterns a Examples of innate behavior behavior inherited and that shows little variation based on learning or the individual s condition b Bird example c Fish responding to color Innate behavior is relatively rare Most behavior shows changes in response to learning and changing environmental conditions Animals take in information from the environment and based on that information make decisions about what to do a This is condition dependent behavior opposite of an innate pattern i A cost benefit analysis can be used Animals appear to weigh the costs and benefits of responding to a particular situation Costs and benefits are measured in terms of impact on their ability to produce offspring V Question What should I eat Seeking food is foraging Most animals have a wide range of foods they can eat Example a Fruit y larvae exhibit one of two behaviors during feeding i Rover move after feeding in a particular location ii Sitter stay in one location to feed b Experiments determined the behavior is inherited via the foraging for gene c Rovers and sitters behave differently because they have different alleles for the for gene Sitters Fruit fly larvae Rovers eering of revere ffepring er eittere be revere tend to be sitters VI Optimal Foraging Biologists usually assume that individuals make decisions that maximize the amount of usable energy they take in given the costs of finding and ingesting their food and the risk of being eaten while they are at it This is optimal foraging a Depends on distance between their nesting area and feeding territory White footed beeeater a Dig tunnels in riverbanks and raise their young inside b To feed young must leave colony capture insects and bring prey back to nest c Some forage close to home others go hundreds of meters away d Decisions to maximize the energy they deliver to their offspring given the cost of finding food e Behavior is highly exible and condition dependent b Foraging behavior depends on distance traveled 250 M O O l L 01 O 100 carried to colony mg 0 Average mass of insects 01 O l 0 I 0 100 200 300 400 500 600 Distance of foraging territory from colony m 2011 Pearson Education Inc VII Who should I mate with What role do hormonal mechanisms have on sexual activity Why does variation in mate choices affect fitness Anolis carolinenis lizard a Live in the woodlands of southeastern US b Spend winter under a log or rock c Males emerge in January and establish breeding territories 1 Females become active in February e Breeding season beings in April f Females lay eggs every 1014 days in May g By the end of breeding season eggs produced by female will total twice her body mass i When breeding season beings male gonads enlargeBEFORE female gonads enlarge ii In both sexes gonads shrink during fall and winter iii QUESTION What causes these seasonal changes in behavior Sex hormones testosterone in males and estradiol in females are proximate cause of dramatic seasonal changes in behavior b Changes in sexual organs through the year A Relative size of testes Relative size of eggproducing structures Size of sexual organs Breeding season N l D l J F 1 MI A l Ml J l J l A S l o 1 Month h Critical for all Anolis individuals to start their sexual activity at the same time i What conditions trigger the production of sex hormones early in the spring VIII Anolis Lizard Experiment Hypothesis a Social interactions among individuals are responsible for synchronizing sexual behavior b 5 groups 1 Single isolated female 2 Group of females 3 Single female with single male 4 Single female with group of castrated males 5 Single female with group of uncastrated males 10039 Female paired A A with male Female with group 0f males Allfemale group Female alone oo 0 I O O I Female with group of castrated males Percentage of females WIth mature follicles A o I 20 Females in 39 natural winter habitat 0 39 F ii i T 0 1 2 3 4 5 6 Weeks 2011 P eeee on Education Inc Results a Experiments show two types of stimulation are necessary to produce hormonal changes i Females need to experience springlike light and temperatures ii Females needs to have exposure to breeding mates b Data supports the hypothesis that two types of stimulation are necessary What about breeding males triggers earlier estradiol release a Males induce estradiol release in females by exhibiting a specific mating signal i Extend brightly covered patch of skin called the dewlap ii Experiment with intact dewlap and surgically removed dewlap Females with dewlapless males produced eggs slowly same as castrated males VIII Where should I live Should juveniles disperse from the area where they were raised How large of a territory should be defended against competitors How do habitat density and quality affect fitness IX Migration Migration is the long distance movement of a population associated with change of seasons Pr0ximate question How do animals know where to go UItimate question Why is it worth the cost in time energy and risk of predation or accident Three categories of navigation a Piloting use of familiar landmarks i Offspring follow their parents and memorize the route ii Homing pigeons can find their way home even when released in strange terrain iii BUT when they have on foggy glasses they only return to a mile or so of their homethey can t find their home b Compass orientation movement oriented in a specific direction i Use the sun during the day and the stars at night Sun is difficult because it moves in the sky so animals also use their circadian clock to tell them where the sun should be located If sun and start aren t available birds use earth s magnetic field c True navigation ability to locate a specific place on Earth s surface X Why move with a change of season Individuals that migrate have higher reproductive success than individuals that do not migrate Increased access to food is a benefit of migration a However there is high cost in time energy and predation risk b At the proximate level explaining migratory movements is often extremely difficult XI How should I communicate Communication is a process in which a signal from one individual modifies the behavior of another individual Communication is a social processsignal must be sent AND received and acted on Honeybee language a Highly social b Workers care of young maintain hive and obtain food c Successful food finders must communicate the location of food to other individuals d At the ultimate level this communication is easily understood e At the proximate level this is more difficult How do bees communicate f Dance hypothesis i Round dance and waggle dance ii Both dances communicate information about the food source iii Both are the same behavior round dances can have a waggle phase Orientation of waggle varies Direction of waggle correlates with direction of food Length of waggle is proportional to distance to food iv Dance also involves sounds and scents a The round dance b The waggle dance x l 5 V 397 lquot ll 9 m I A L Other bee workers follow the progress of the dance by touching the displaying 4 individual a Straight runs down the wall of the hive indicate b Straight runs to the right indicate that food is that food is opposite the direction of the Sun 90 to the right of the Sun Sideways 7 is a waggle dance 39 on honeycomb Downward waggle dance 7 r quot on honeycomb I y 2 Lt i Beehive 3f Tz Food source at right angle lt to Sun l gfl Food source quot away from Sun 9 2011 Pearson Education Inc
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