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by: Renee Lehner


Renee Lehner
GPA 3.73


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This 16 page Class Notes was uploaded by Renee Lehner on Wednesday September 9, 2015. The Class Notes belongs to BIOL 200 at University of Washington taught by Ruohola-Baker in Fall. Since its upload, it has received 7 views. For similar materials see /class/192317/biol-200-university-of-washington in Biology at University of Washington.


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Date Created: 09/09/15
1 Eukaryotic gene Regulation 11 7039 All cells have the same genes the way their gene expression is controlled is what makes cells different High level of regulation is needed to generate multicellular organisms Signaling molecules alter gene expression in cells i Cells talk to each other cell signaling ii Leads to patterning pattern formation 1 le limb bud a Cell differentiation division death iii lnduce differential expression of genes at multiple levels DNAgtRNAgtPROTEN Gene regulation Mechanisms i Chromatin remodeling Chromatin DNA histonesprotein DNA near promoter must be released from tight interactions with proteins before transcription can begin 1 RNA polymerase cannot access closed chromatin 2 Alteration of nucleosomes so proteins can gain access to the gene a Nucleosomes repeating beadlike structures in chromatin negatively charged DNA wrapped twice around eight positively charged histone proteins i Side chains have charges phosphodiester bonds give DNA a negative charge ii Hlprotein attached to linker DNA Maintains structure of nucleosome 30 nm fiber b Enzymes catalyze covalent modifications on histone tails 39 Acetylation activation of genesand methylation activation or inactivation also phosphorylation Histone acetyl transferasesHATs decondenses chromatin by adding negatively charged acetyl groups Histone deacetylasesHDACs condenses chromatin by removing acetyl groups from histones 3 Chromatin modifications can be inherited a Histone tail code hypothesis histone modifications influence whether gene is expressed or not b Daughter cells inherit the pattern of histone modification i quotepigenetic inheritance patterns of inheritance that are not due to differences in gene sequence ii Transcription assembly of the core transcription complex 1 Eukaryotic DNA is tightly packed with proteins histones into structures that must be opened before transcription can occur 2 ln eukaryotes transcription is triggered by regulatory proteins that bind to promoter and sequences close to and far from promoter a TATAbinding protein TBP binds to a TATAbox specificity for binding given by amino acid side chains and bases Promoter has sequence that is common to most genes Promoter proximal element has sequence that is unique to this gene 3 Enhancers intron contains regulatory sequence necessary for transcription to occur far from promoter downstream PO a all eukaryotes have enhancers b some have more than one and they can work if normal orientation is flipped or if they re moved to a new location on same chromosome c DNA binding sites for transcription factors 4 Transcription initiation a Regulatory transcription factors bind to DNA and recruit chromatinremodeling complexes HATs b Chromatin remodeling results in loosening of the chromatin structure exposing the promoter region c Additional regulatory transcription factors bind to enhancers Mitotic prophase Chromosome condensation ASE ENZYME and promoterproximal elements they also interact with basal transcription factors that bind to the promoter d All of the basal transcription factors form the basal transcription complex which recruits RNA polymerase so that transcription can begin iii mRNA processing splicing introns from mRNA 1 Alternative splicing of mRNAs leads to production of different proteins a lntrons are spliced out of primary RNA transcripts while it is still in nucleus b During splicing changes in gene expression are possible because selected exons may be removed from the primary transcript along with the introns c Regulated by proteins that bind to the mRNAs in nucleus and interact with the spliceosomes d Over 90 of human sequences for primary mRNA trncripts undergo alternative splicing iv mRNA stability rate of mRNA degradation 1 stability of mRNAs in cytoplasm is highly variable 2 Lifespan of mRNA controlled by RNA interference a Specific mRNAs are targeted by microRNAs miRNAs Tiny singlestranded RNA molecules hairpins b After binding to proteins called RISC protein complex miRNAs bind to complementary sequences in mRNA becomes dbl stranded c Specific proteins degrade mRNA prevent it from being translated into a polypeptide enzyme cuts out dbl stranded section d 2023 of animal and plant genes are regulated by miRNAs v Translation vi Posttranslational Modifications activation of protein by phosphorylation etc rate at which protein is degraded R l d Feb 9 2011 1 MicroRNAs 2030 bp long a PAZ cup ruler helix RNaselllb RNasellla b Endogenous dsRNAs completely bind to target mRNA Silence transposons Retrotransposon mobile genetic elements which can amplify themselves selfish and change the maount of DNA ina genome 1 Mechanism a Copy themselves to RNA b Forms DNA via a reverse transcriptase that may be encoded by the retrotransposon c Integrates back into genome 2 Can induce stable mutations by inserting near or within a gene EndosiRNAs protect us against retrotransposon activity by inhibiting the amplification of retrotransposons and reducing the retrotransposon RNA stability 2 How is Translation controlled a Many miRNAs interfere directly with translation b Mechanisms that do not involemiRNAs are responsible for controlling the timing or rate of translation i le regulatory proteins may bind to mRNAs or ribosomes to regulate translation c In addition in response to viral infection translation can be slowed or stopped by phosphorylation of a certain ribosomal protein 3 PostTranslational Control a Mechanisms for posttranslational regulation allow the cell to respond to new conditions rapidly by activatin or inactivating existing proteins b Regulatory mechanisms occurring late in the flow of information from DNA to RNA to protein involve a tradeoff between speed and resource use c Mechanisms Chaperone proteins can regulate protein folding Enzymes may modify proteins by adding carbohydrate groups or cleaving off certain amino acids Proteins may be activated or deactivated by phosphorylation Targeted protein destruction 1 Ubiquitin tags are added to proteins ie cyclins and are recognized by a multimolecular machine called a proteasome which cuts the protein into short segments 239 E a Packaging chromatin structure provides a mechanism of negative control in eukaryotes that does not exist in bacteria b Alternative Splicing Primary transcripts in eukaryotes must be spliced does not occur in bacteria c Complexity Transcriptional control in much more complex in eukaryotes than in bacteria d Coordinated Expression ln bacteria genes may be organized into operons such operons are rare in eukaryotes e The need for each cell type to have a unique pattern of gene expression may explain why control of gene expression is so much more complex in multicellular eukaryotes than in bacteria Chapter 19 pgs 338347 table 1912 1 Genetic engineering manipulation of DNA sequences in organisms Recombinant DNA technology techniques used to engineer genes a b Key concepts i Enzymes that cut DNA at specific locations restriction enzymes and other enzymes that piece DNA segments nack together ligase allow biologists to move genes from one place to another ii Biologists can obtain identical copies of a gene by 1 5 Inserting it modified plasmid into a bacterial cell that copies the gene each time the cell divides by conducting a polymerase chain reaction PCR The sequence of bases in a gene can be determined by dideoxy sequencing Example Pituitary Dwarfism i Results from the lack of production of growth hormone encoded by the GH1 gene ii Pituitary dwarfism type 1 is an autosomal recessive trait affected individuals have two copies of the defective allele iii Humans affected by pituitary dwarfism grow slowly reach a max adult height of about4 ft 1 Growth hormone therapy helps but only if growth hormone comes from humans this practice was banned in 1980 due to possible contamination with prions misfolded proteins neurodegenerative disorders Develop a recombinant DNA strategy for producing HGH cloning human gene having bacterial cells produce hormone iv What was needed to produce GH1 in bacteria 1 2 3 4 mRNA isolated from human pituitary cells so that there aren t introns Reverse transcriptase to synthesize DNA from the pituitary mRNA into complementary DNA cDNA a Reverse transcriptase makes dblstarndechNA OR b DNA polymerase makes dblstranded cDNA DNA cloning copy the cDNAs a Restriction endonucleases bacterial enzymes that cut DNA at specific base sequences called recognition sites b The first step in cloning genes into plasmids is to cut the plasmid and the cDNA with the same restriction endonuclease i Restriction endonucleases often make staggered cuts in the DNA resulting in sticky ends complementary singlestranded ends palindromes c Add the cDNA plasmid and ligase the sticky ends of the plasmids and cDNAs will bind by complementary base pairing Ligase then seals the recombinant pieces of DNA together i The gene is inserted into the plasmid ii Sticky ends get ligated based on their DNA sequence not which enzyme cut them d Transform and amplify the vector and insert in bacteria Determine which cDNA encoded the growth hormone protein a A cDNA library is a collection of bacterial cells each containing a vector with one cDNA i Isolate mRNAs Synthesize cDNA Make cDNA doublestranded iv Make recombinant plasmid Transformation b DNA probe a singlestranded fragment of a known gene that binds a complementary sequence in the sample of DNA being analyzed i Make labeled probe ii Expose probe to DNA iii Isolated labeled DNA v The transformed E coli cells produced HGH that could be isolated and purified in large quantities 2 Key discoveries that made genetic engineering possible a The ability to cut DNA at specific sites and join different fragments together b PCR Polymerase Chain reaction c Ability to transform different organisms with foreign recombinant DNA Feb 112011 1 What is PCR Polymerase Chain Reaction In vitro DNA synthesis ii Specific section of DNA is replicated using primers iii Produces millions of copies of the desired section of DNA b Requirements of PCR a Info on DNA sequence surrounding gene is available PCR requires primers that match sequences on either side of the gene b One primer is complementary to a sequence on one strand upstream of target DNA other primer is complementary to sequence on other strand downstream of target c Primers will bind to singlestranded target DNA c Steps of PCR i A reaction mix containing dNTPs a DNA template copies of the two primers What are the and Taq polymerase Deanturation heating the mixture to 95C seperates the two strands of DNA differences between breaks hydrogen bonds between bases primers used in in iii Primer Annealing cooling the mixture allows the primers to bond anneal to Vim replication and complementary sections of singlestranded target DNA in in vitro PCR iv Extension heating mixture to 72C causes Taq polymerase to synthesize complementary DNA strand from the dNTPS starting at the primer lt Repeat steps 24 are repeated to yield the necessary number of copies of the gene d PCR is used in research clinical studies and forensics paternity testing ancestral testing disease analysis SNP 39 Convicted of a felony in Washington swab cheek cells for PCR EthicsPCR as long as someone has our identifiable DNA sample he or she will be able to learn things about us that we may not know may not want to know and certainly don t want others to know 1 Genetic Information Nondiscrimination Act 2008 2 Sequencing how to tell the right gene got amplified a Dideoxy Sequencing Sanger method for determining DNA sequence 2 Based on an in vitro DNA synthesis reaction DNA polymerase Template primerdNTPs Carried out by adding ddNTPs and dNTPs to the synthesis rxns ddNTPs are identical to dNTPs except that they lack 3 hydroxyl group 1 DNA polymerization stops once ddNTP is added to a growing strand 2 Use one kind of ddNTPrxn 3 Run produced fragments on a gel separation based on size a Differentlength strands can be lined up by size to determine DNA sequence 4 Largest fragments 3 ends smaller fragments 5 ends The current technique uses fluorescent markers to each ddNTP to simplify the DNA sequencing 1 Allows DNA to be sequences with one dideoxy reaction instead of four b Pyrosequencing quotnext generation sequencing iv Possible to compare sequences from individuals of a particular species much faster and cheaper than dideoxy method Pyrosequencing the pyrophosphate that is released after a DNA polymerase adds a dNTP to a growing DNA strand is detected These pyrophosphates drive a set of other reactions that result in luminescence which can be detected Addition of one dNTP at a time release of pyrophosphate PPi 2 PPi is converted to ATP 3 ATP activates the conversion of luciferin into oxyluciferin which generates visible light measured peak height indicates how many nucleotides are found at that point in the DNA 4 Unincorporated nucleotides are degraded 5 Cycle is repeated with the next nucleotide The Human Genome Project 1 Shotgun sequencing a Cut DNA at random locations into fragments of 160 kb Clone fragments using BACs Cut clones into 1kb fragments Clone smaller fragments using plasmids Sequence each fragment Assemble all 1kb fragments g Assemble 160kb fragments Pyrosequencing is cheap and fast It takes place on a single DNA fragment rather than multiple copies of the same fragment 1 Only works with fragments that are too small to be pieced back together a If the entire genome of the organism is known pyrosequencing produces the sequence of an individual for comparison to the quotmaster genome i ldentify genes monlty c Annotation finding the locations of genes in genomic sequence bioinformatics Prokaryote genomes the locations of genes are identified by searching for promoter and translation startstop sites largest Open reading frame Eukaryotic genomes genes are identified by searching for sequences that match those in a cDNA library of expressed genes and by using llgene finder computer programs 1 Using reverse transcriptase to produce a cDNA version of each mRNA 2 Sequence a portion of the resulting molecule to produce an expressed sequence tag EST represent proteincoding genes 3 Comparative Genomics a In bacteria there is a general correlation between the size of the genome and the metabolic capabilities of the organism Lateral gene transfer a significant portion of the genome appears to have been acquired from other often distantly related species This results because genes are carried on plasmids 1 Also occurs through transformation taking up DNA fragments from the environment 2 Thus mutation and genetic recombination within species are not the only sources of genetic variation in bacteria and archaea Environmental sequencing metagenomics practice of cataloging all of the genes present in a community of bacteria and archaea 1 The subject of these studies is genes not organisms b Organisms with complex morphology and behavior do not appear to have large numbers of genes lt lt Alternativesplicing hypothesis certain multicellular eukaryote do not need large numbers of genes because alternative splicing creates different proteins from the same gene Gene families are thought to arise by gene duplication and may be the most important way of generating new genes in eukaryotes Exons comprise a small percentage of the genome 5 Repeated sequences make up the majority of DNA 1 Most repeated sequences are derived from transposable elements 2 Simple sequence repeats are the basis for DNA fingerprinting since they are hypervariable and vary among individuals much more than any other type of sequence Short tandem repeats STRs used in forensics a Homologs pair up repeats misalign crossing over and recombination occur and produce unique products i Chromosomes produced by unequal crossover contain different numbers of repeats DNA fingerprinting any technique for identifying individuals on the basis of unique features of their genomes 1 Because microsatellite and minisatellite loci vary so much among individuals they are now the markers of choice for DNA fingerprinting a They can be amplified by PCR SNP Single Nucleotide Polymorphism variation in the DNA sequence of the population IE two alleles AGACCTTA AGACT39I39I39A 1 SNPS are inherited the do not change much from generation to generation 2 They are good markers they help find genes associated with diseases Huntington s 3 HapMap haplotype map that describes the common patterns in genetic variation linked gene variation inherited together c Chimpanzee vs Human 2004 HumanChimp12 difference i Human uniqueness lies in our ability to reason about things we can t observe especially the content of others minds and to employ this skill in the collaborative enterprise we call civilization d microRNAs over 1000 predicted miRNAs found through the genome project i RNAbased mechanism of gene silencing ii lmperfect basepairing to 3 UTR of mRNAs e Changed the way we build evolutionary trees sequence difference is translated into distance between species Primates are more closely related to rodents than to carnivores or artiodactyls 4 Functional Genomics the study of how the products of all the genes interact in the organism a DNA microarrays show changes in gene expression b Proteomics use a protein microarray or massspeck to identify proteinprotein interactions c Gene knockouts and phenotypic analysis in model organisms d Bioinformatics e Large scale sequencing tumors patients individualized medicine f Make a mutant model organism phenotype i How does a protein function in one organism relate to the function in another organism How similar are the genes from on organism to another Homologues Functional similarity sequence comparisonblast 1 Eyeless gene found in fruitfly a Human aniridia b Mouse Pax6 i Introduced mouse eye to fruitfly additional FLY eyes sprouted at the site of gene expression Feb 15 2011 Exam on Eukaryotic Gene expression SequencingPCR Genomics Deveopment Lab PCRChick Development Chapter 21 Principles of Development 1 When development begins early cellcell signals trigger a cascade of effects that cause increasing specialization as development proceeds 2 There are 5 essential cellular processes that lead to an individual organism s development a Cell Division proliferation b Programmed cell death apoptosis a carefully regulated aspect of normal development i Abnormal apoptosis either too much or too little cell death can lead to disease or deformation IE Webbing between toes brain malformations Cell movement and differential expansion Cell differentiation 0 Cellcell interactions signals between cells trigger differential gene expression The fate of a cell depends on timing the current stage of development of the organism and its spatial location where it is in the body of the organism Spatial location in early development is determined by three major body axes Anteriorposterior toward headtoward tail 2 Ventraldorsal toward bellytoward back 3 Leftright either side a Three body axes observed in humans and other animals are initially established in embryos Cellcell signals tell cells where they are in time and space This information activates transcription factors that turn specific genes on or off resulting in differentiation 3 Master Regulators set up the major body axes a Pattern formation series of events that determine the spatial organization of an embryo b Certain early signals act as master regulators setting up the major body axes of the embryo i These master regulators activate a network of genes that sends signals with more specific information about the spatial location of cells c As development proceeds a series of signals arrive and activate genes that specify finer and finer control over what a cell becomes 4 Logic in Development a Logic is not yet understood in human embryonic development however we have a reasonable understanding of the logic in model organisms Chapter 21 Principles of Development Nobel Prize in Physiology or Medicine 1995 Edward Lewis Christiane NuusleinVolhard and Eric Wieschaus for discoveries concering quotthe genetic control of early embryonic development gtgt ldea Find the critical genes by mutant analysis 1 The bicoid Gene twotailed gene responsible for replacement of anterior end structures with posterior end structures a NuusleinVolhard and Wieschaus suspected that bicoid gene product provides positional information coded for a signal that tells cells where they are located along the anteriorposterior body axis i In situ hybridization 1 Obtained probe labeled probe added probe to specimen removed excess probe observed location of probe Bicoid mRNA is located in the anterior end of the egg i Bicoidproduct protein is made from mRNA in the anterior end and diffuses away from that end of the embryo 1 This produces a steep concentration gradient from the anterior to the 57 posterior end How does Bicoid work 39 Bicoid protein is a regulatory transcription factor shown to act as a mastor regulator within fruit fly embryos The concentration gradient formed by bicoid protein provides cells with information about their position along the anteriorposterior axis 0 e f iii Bicoid also turns on genes responsible for forming anterior structures The absence of bicoid contributes to the formation of posterior structures Maternal determinant Bicoid genes expressed during oogenesis by the mother Act upon or within the maturing oocyte i Regulatory transcription factor ii Affects cell fate in a concentration dependent manner localized in a gradient iii Regulates transcription of llsegmentation genes Segmentation genes i Marking relatively large regions of the developing embryonic body 1 Gap genes define the general position of head thorax and abdominal regions early in development organize cells into groups of segments along AP axis 2 Pairrule genes establish the edges of individual segments later in development organize cells into individual segments 3 Segment polarity genes define boundaries within individual segments still later establish AP gradient within each segment ii Segmentation genes regulate each other iii Expressed after fertilization Mutations in these genes alter the number or polarity of segments Three groups of segmentation genes act sequentially to define increasingly smaller regions of the embryo Homeotic Hox genes i Control the identity of a segment but do not affect the number polarity or size of segments Mutations in these genes cause one body part to develop the phenotype of another part ii Function in development 1 Mutant phenotype a structure found in one place in the body is substituted for the normal structure usually found at another location 2 Function control segment identity iii Molecular function 1 Homeotic genes gtgthomeodomain proteins a Transcription factors contain a conserved 6O aminoacid domain homeodomain b Homeodomain binds to DNA iv Hox gene clusters the order in the genome corresponds to expression and function along the AP axis spatial colinearity 1 Hox gene order in the genome strictly corresponds to their expression domains and function along the body of the embryo AP v Hox genes are conserved from flies to mice to man they define the position of cells along the AP axis in most animals spatial colinearity is conserved between specnes 2 Regulatory Cascade each gene defines a level in the cascade from undifferentiated cells to differentiated cells a rnonlt7 Master regulator establishes AP gradient of embryo Gap genes organize cells into groups of segments along AP axis Pairrule genes Organize cells into individual segments Segment polarity genes establish AP gradient within each segment Homeotic genes trigger development of structures Effector genes change proliferation death movement and differentiation of cells 3 Overall Function of Regulatory Genes a Regulatory genes act in a sequence triggering gene cascades that provide progressively detailed information about where cells are located in time and space i Cells receive unique positional information because the identity and concentration of signals and transcription factors vary along the three major body axes 4 Developmental pathways and Evolutionary Change a Once biologists began working out regulatory signals and cascades they realized that the genetic changes altering these developmental processes must be the foundation of evolutionary change b EvoDevo changes in regulation of where certain homeotic genes are expressed lead to evolutionary losses of limbs etc Ch 22 An Introduction to Animal Development 1 Key concepts a Fertilization begins with specific interactions between proteins on the plasma membranes of sperm and egg b The earliest cell divisions divide the fertilized egg into a mass of cells whose individual fates depend on key regulatory molecules they contain and the signals they receive c Early in development cells undergo massive coordinated movements to form distinct tissue layers Each layer gives rise to a different set of tissues and organs in the adult d As development proceeds specialized organs and other structures form through the interacting effects of cellcell signals cell proliferation cell movements and differentiation Differentiation is complete when cells express tissuespecific proteins e Single cell gtgt multicellular individual 2 Gametes are haploid reproductive cells Male gametes are called sperm female gametes are called eggs 3 Development proceeds in ordered phases a Gametogenesis formation of gametes in the reproductive organs of adult organisms i Both sperm and egg contribute chromosomes haploid genome containing one allele of each gene to the offspring ii Eggs contribute much more and are much larger than sperm b Fertilization occurs when a haploid sperm and egg cells fuse forming a diploid zygote i Sperm Structure and Function Head contains nucleus and enzymefilled acrosome which allows the sperm to penetrate the egg s barriers 2 Neck encloses a centriole which will fuse with a second centriole contributed by the egg to form the centrosome 3 Midpiece packed with mitochondria which produce ATP necessary for movement 4 Tail has flagellum that act as a propeller ii Egg structure and function 1 Egg cells are relatively large and nonmotile 2 Size is largely due to nutrient storage required for early embryonic development 3 Quantity of nutrients varies across species a Mammalian egg is relatively small only has to supply nutrients for early development as embryos start to obtain nutrition through the placenta shortly following fertilization b Egglaying species produce larger eggs yolk is embryo s sole source of nutrition prior to hatching 4 Eggs of many species contain cytoplasmic determinants that control the early events of development 5 Many eggs also contain cortical granules small enzymefilled vesicles that are activated during fertilization 6 The vitelline envelope a fibrous matlike sheet of glycoproteins surrounds the egg a Mammals have an unusually thick vitelline envelope called the zonapellucida 7 Some species have a jelly layer a thick gelatinous matrix around the vitelline envelope for further protection iii Gametes from the same Species Recognize Each Other 1 Bindin is a protein on the head of sea urchin sperm that binds to the surface of sea urchin eggs a Bindin acts as a quotkeyquot such that a sperm binds only to eggs of the same species 2 Fertilizin is a compound on the surface of sea urchin egg cells acts as the quotlockquot to bindin s quotkeyquot a Each species has its own version of fertilizing and bindin making the lockandkey interaction both necessary for fertilization and species specific 3 Speciesspecific bindin molecules on sperm interact with species specific receptors on the surface of the egg This interaction is required for the plasma membranes of sperm and egg to fuse iv Many conditions must be met before a zygote can form 1 Gametes must be in same place at same time a Egg is viable for about a day sperm is viable for about 5 days b 10 of couples have fertility problems 2 Gametes must recognize and bind to each other enzymes from the sperm s acrosome digest through the egg s jelly layer and vitelline envelope 3 Gametes must fuse together plasma membranes of sperm and egg fuse when the sperm head contacts the surface of the egg cell 4 Fusion must trigger the onset of development v Fertilization is complete when sperm nucleus mitochondria and centriole enter the egg and the sperm and egg nuclei fuse to form the zygote nucleus vi Why does only on sperm enter the egg Animals employ different mechanism to avoid polyspermyfertilization by more than one sperm 1 Sea urchins fertilization stimulates creation of a physical barrier Ca2 based signal is rapidly induced and propagated throughout the egg resulting in the formation of a fertilization envelope which keeps away additional sperm 2 Mammals cortical granules release enzymes that modify egg cell receptors preventing binding by additional sperm 0 vii In vitro Fertilization Nobel Prize 2010 1 Oocyte Hormone induced maturation and collection a Egg cell isolated from human ovary 2 Sperm washed separated from seminal fluid a Egg and human semen incubated together gtgt fertilization i Embryo surgically implanted to mother s uterus 3 Can be used to treat infertility and to decrease the risk of HIV transmission 4 Twins are frequent 5 23 of all newborns are conceived with the help of NF Cleavage the set of rapid cell divisions that take place in animal zygotes immediately after fertilization The first step in embryogenesis process that makes a singlecelled zygote into a multicellular embryo Partitions the egg cytoplasm without any additional growth of the zygote Cells created by cleavage divisions are called blastomeres iv When cleavage is complete the embryo consists of a mass of blastomere cells called a blastula v What role to Cytoplasmic Determinants play Cytoplasmic determinants are found in specific locations within the egg sytoplasm so they end up in specific populations of blastomeres 2 By dividing the egg cytoplasm to precisely distribute cytoplasmic determinants to certain cells cleavage initiates the stepbystep process that in combination with signals received from other cells results in the differentiation of cells vi Cleavage in Mammals 1 Occurs in mammalian oviductfalopian tube which connects the ovary where the egg matures to the uterus where the embryo develops 2 Cleavage results in a blastocyst a specialized blastula consisting of two populations of cells a The external thinwalled hollow trophoblastsurrounds the inner cell mass ICM After blastocyst embeds in the uterine wall a mixture of trophoblast and maternal cells form the placenta an organ which provides nourishment and waste removal for the developing embryo implantation c The ICM contains the cells that undergo gastrulation and develop into the embryo 57 Gastrulation extensive and highly organized cell movements that radically rearrange the embryonic cells into a structure called the gastrula i Results in the formation of embryonic tissue layers 1 Tissue integrated set of cells that function as a unit i Most early embryos have three primary tissue layers called germ layers because they give rise to adult tissue and organs 1 Ectoderm forms outer covering of the adult body epidermis and the nervous system brain cornea and lens of eye epithelial lining of mouth and rectum 2 Mesoderm gives rise to muscle most internal organs and connective tissues such as bone and cartilage circulatory system lymphatic system excretory system reproductive system dermis of skin lining of body cavity 3 Endoderm produces the lining of the digestive tract or gut along with some of the associated organs respiratory tract reproductive tract urinary tract liver pancreas thyroid parathyroids thymus iii In frog embryos 1 Frog blastula contains a fluidfilled space called the blastocoel 2 Gastrulation begins with the formation of an opening called a blastopore 3 Cells from the periphery move inward through the blastopore forming a tubelike structure that will become the gut iv Completion of Gastrulation 1 Embryonic tissue layers are established 2 The major body axes become visible 3 At the end of gastrulation the three embryonic tissues are arranged in layers the gut has formed and the major body axes have become visible 4 Human and Chick embryos Gastrulation along the primitive streak results in the germ layer formation Neurulation lateral surfaces of the neural tube meet and fuse to form a tube midway in the future tube day 2122 Anterior and posterior neural pores ultimately close off i Failure of this process results in neural tube defects spina bifida etc ii thick vitelline envelope called the zonapellucida Organogenesis cells proliferate and become differentiated meaning that they become a specialized cell type i Differentiated cells have a distinctive structure and function because they express a distinctive suite of genes Organizing the Mesoderm into Somites 1 Early in organogenesis rodlike notochord appears in the dorsal mesoderm a Structure is unique to the animal group called chordates which includes humans and other vertebrates b Functions as a key organizing element c In many chordates the notochord cells undergo apoptosis 2 Signals from notochord trigger reorganization of dorsal ectodermal cells leading to neural tube formation a Notochord forms notochord signals ectoderm to fold neural tube is complete 3 Neural tube is precursor to the brain and spinal cord iii Somite formation once neural tube forms mesodermal cells become organized into blocks of tissues somites which form on both sides of the neural tube down the length of the body 1 Cells in the somite are differentiated for function based on their location within the somite 2 What controls identity of the somites along AP axis a HOX G EN ES iv Somite Maturation and Determination 1 Somite cells form a variety of structures but are initially not determined meaning they can become any of the somitederived elements of the body a Closest to neural tubemuscles of back b Furthest from neural tubemuscle in limbs c Bottom of somitecells that build bone vertebra d Top of somiteconnective tissue of skin 2 Somites contain the precursors of the vertebrae the ribs the skeletal muscles of the body wall and limbs and the dermis of the back 3 As the somite matures cells become determined differentiate into a specific cell type based on their location within the somite a In the process of determination somite cells differentiate in response to signals from nearby tissues b Signal are sent from the notochord neural tube and nearby ectoderm and mesoderm v Differentiation of Muscle Cells Myoblast a cell that is determined to become a muscle cell but has not begun producing musclespecific proteins 2 Researchers found that MyoD was the protein that causes muscle cell differentiation 3 MyoD is a regulatory transcription factor that binds to enhancers upstream of musclespecific genes vi Overview of Cell Differentiation 1 Differentiation is a step bystep process that is complete when cells begin producing cellspecific proteins 2 Steps of differentiation in a muscle cell a Fertilization triggers cleavage resulting in a blastocyst b Blastocyst cell signals trigger gene cascades resulting in positional changes during gastrulation c During organogenesis notochord signals specific somite cells to begin MyoD production targeting these cells as belonging to specific muscles d These muscle cells begin expressing musclespecific proteins vii Do signals from nearby tissues induce development of somite cells into specific tissue types YES determined by in vitro cell culture assays for factors influencing somite myogenesis 1 Isolated somite cultures plus or minus putative inducing tissues a lncubate somite with nothing else b lncubate somite with neural tubeNC 2 Look at phenotypes a Morphological phenotype crossstriated multinucleated muscle fibers 3 Musclespecific proteins a Thin filaments actin b Thick filament myosin 4 Without neural tube no differentiated muscle cells viii What signals are produced by the neural tube and notochord that might induce back muscle formation Wnts and SHH The key myogenic regulatory genes that Wnts and SHH activate are 1 Isolate mRNAs from myoblasts 2 Use reverse transcriptase to convert mRNAs to cDNAs 3 Attach llgeneral purpose I promoters to cDNAs to create a cDNA library 4 Introduce cDNAs to fibroblasts nonmuscle cell type that grows well inculture 5 Assay for the presence of musclelike cells 6 Recover cDNA responsible for muscle conversion Named MyoD myogenic determination factor ix MyoD is expressed in somites 22211 EXAM FRIDAY Pgs to read 319332 338347 th 191192 359372 375376 379385 388399 To study student made problems problem sets practice exam EmbryologyFetal Development Main Divisions a Weeks 13 Fertilization Implantation Gastrulation b Weeks 38 Embryo c Weeks 938 birth Fetus 22311


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