Exam 1 Study Guide - Developmental Biology | ZOL 320, Exams of Developmental biology

Download Exam 1 Study Guide - Developmental Biology | ZOL 320 and more Exams Developmental biology in PDF only on Docsity! EXAM 1 STUDY GUIDE Introductory Ideas into Developmental Biology Developmental biology: the study of how organisms develop, from egg to adult. Not just embryos; any event with a relatively permanent progressive change from one stage or cell type to another. Ex: embryology, growth, sexual maturity, metamorphosis, regeneration (regrowing body parts), aging Embryology: the study of embryonic development Life cycle: from fertilization to adult  death Ontogeny: the development of an organism in its life cycle starting from a single gamete cell (an egg for instance) to an adult. Ontogeny is driven by factors that affect an individual over the course of one life cycle – genetic makeup, environmental variables, etc. In short: ontogeny is change in individual life cyle Phylogeny: the historical development of a species over evolutionary history. Phylogeny is driven by both the ontogenetic changes within individuals as well as environmental variables that affect ontogeny, genetic reshuffling between generations, and so on. Phylogeny depends on ontogeny! In short: phylogeny is evolutionary change Sexual reproduction: reproduction involving a sperm meeting an egg. Adv: increased generation of variation, useful for adapting to new environments. Asexual reproduction: reproduction from groups of cells (budding). Adv: no need for sexes, time of development is shorter, less energy needed to develop, little variation. Dis: inheritable variation is low, lack of cooperation among cells, rogue cells Germ line cells: only cells that give rise to cells that can undergo meiosis. Directly give rise to the offspring; variation in genotype Meiosis: A single cell divides into four cells, each of which contains half the number of chromosomes of the original cell. Morphogenesis: organization of cells (which are different) into more complex, organized tissues and structures. Generation of form through cell movements. Ordered form rather than random growth. Growth, differentiation, and morphogenesis all occur within the life cycle of an individual. Growth: biosynthesis of substances in the cell, such as an increase in cell mass, tissue mass, organ and organismal mass Differentiation: division of labor among cell types Genetic recombination: the production of new combinations of alleles, encoding a novel set of genetic information Cambrian explosion: the relatively rapid appearance of most major animal phyla (around 542 mya). Accompanied by major diversification of other organisms. Before the Cambrian explosion, most organisms were simple, composed of individual cells occasionally organized into colonies. Allometric growth: Disproportionate growth; e.g. fiddler crab claw Epigenesis: all of the cells have the same DNA but express different genes. New structures arise from components that are not already there; the common inherited genome of all cells in an individual is expressed differently in different cells Biogenetic law: von Baer’s law – early stages that are similar in embryos Phylotypic stage: stage that develops characteristics which define that particular phylum phylogically; e.g. notochord, dorsal hollow nerve tubes, and pharyngeal arches, which are phylotypic of Chordata Teratology: study of non-genetic effects on development (e.g. Cyclops lamb; mother ate plant that caused birth defects). Disruption of Sonic hedgehog gene disrupts morphogenesis Evo/devo: Relatively new discipline; examines the connection of the two types of development: (1) how development evolved and (2) how development affects evolution Generation time: time elapsed between the fertilization of an egg and the time that individual becomes sexually mature Gamete: has half the normal number of chromosomes; unites with a cell of the opposite sex during sexual reproduction August Weismann: germ plasm theory; states that the only cells that directly give rise to the offspring are from the germ line, not the somatic cell lines Somatic cells (soma): Body cells; all somatic cells have the same DNA chromosome reassortment paragenetic information Parthenogenesis: Asexual development from an unfertilized egg; diploidy restored by not reducing chromosome number (or fusion of oocyte to a polar body); occurs when species are kept isolated; occurs naturally in some insects and whiptail lizards Pattern formation: changes in growth patterns (such as size, duration, timing) can have huge effects on the development of an organism without changing the basic units that make up an organ or system. Ex: homologies within vertebrate forelimbs, such as between people, bats, birds, and whales – same basic parts but with a very different outcome) Preformation: Preformation means that structure in question is already made in whole or part in the existing structure, or cell and that during development there is an unfolding and growth of this pre-made structure. Stuff is building on top of already-existing stuff. Recapitulation: going through successive stages during the embryonic period of an animal’s life that duplicate the evolutionary stages the species experienced. Ernst Haeckel: Ontogeny recapitulates phylogeny. “Higher” animals he thought look like and therefore are the adult form of “lower” animals at some point in development. At early stages the similarities between related species can be observed. E.g. gill slits in early human embryos. K.E. von Baer: embryologist who made detailed comparisons of vertebrate embryos and emphasized key conclusions that are now referred to as von Baer’s laws. He found that among vertebrates, the early stages show the more general features common to many species which later rise to more specialized features that are specific to a certain species (e.g. gills in some but ear bones in others). Label fell off of a jar and he couldn’t ID the organism; shows that there is a lot of similarity in the early stages of development. The stages in early vertebrate development are: zygote, blastula, gastrula, neurula, followed by organogenesis (formation of organs). Germ cells giving rise to the gametes are always set aside early from the somatic cells. Frog oocyte – lots of stored mRNA, not translated, long-lived 1. What is the relationship between ontogeny and phylogeny? Phylogeny is the development over time of a species, genus, etc. as contrasted with the development of an individual ontogeny. Ontogeny is the development in the individual life cycle and is one part of a longer phylogenetic development in a species. The two are related cytoskeleton (which includes actin and microtubules which affect the shape of the cell and whether it’s going to grow or divide – involved in movement; maybe the signal goes back into the nucleus to change which genes are going to be turned on/off) transcription factors (which are proteins, which affect which genes are turned on/off) The genes are affected by what transcription factors are present extracellular matrix (stuff outside the cell) Epithelial cell: cell arranged into a sheet layer; from one cell to multiple cells in depth; immotile; in tight contact with one another; make up skin and all sorts of organs Mesenchymal cell: cell that is sometimes motile with a varying shapes, lacking in strong connections to neighboring cells; more loosely attached and spread-out. Phospholipid: found in double-layered cell membranes; all membranes are made up of phospholipids Self-assembly: phospholipids in water can spontaneously self-assembly to form a higher structure; forms on its own Plasma membrane: reception of paracrine cell signals (one cell makes it, another cell bonds to it), and is received and diffuses out by other cells); adhesion of the cell to the ECM or to other cells; occasional fusion of the plasma membrane (cells normally don’t want to fuse; example is sperm + egg fusion); connection of the cytoplasm to neighboring cells through gap junctions that allow the cells to exchange info through the plasma membrane Signal transduction: Polypeptide growth factors: Intracellular signaling: either by contact-dependent (non-diffusible; cells have to be in contact with each other) or paracrine interactions (diffusible; random motion, random diffusion, and some of the ligands by random motion can contact the receptors of neighboring cells. One cell makes it, another cell binds to it.) Hyperplasia: continuous cell formation/rapid growth; in cell reproduction, all lineages start with a period of hyperplasia In mammals after embryonic hyperplasia, cells may be retained with (1) unlimited cell division capacity (e.g. skin, intestines, blood cells); stem cells, (2) limited capacity (e.g. liver, pancreas) where the differentiated cells divide again, and (3) loss of capacity (e.g. CNS neurons) Stem cells: dividing but relatively undifferentiated cells that later give rise to one cell that does differentiate and another continuing as a stem cell Blasts vs cytes: embryonic diving cells are often “-blasts,” whereas differentiated cells are often “-cytes” Germinative region: the region in a specific area of the body in which does not overlap with the region containing mature cells; contains stem cells; unlimited cell division capacity Compensatory hyperplasia: an organ or tissue that has been damaged will grow back to replace lost tissue and function Cell differentiation: a result of differential gene expression to create dissimilar cells (the genome of somatic cells except for immune cells does not change). Differentiation is gradual, often at the end of hyperplasia (but not always) Apoptosis: a form of cell death necessary to make way for new cells and remove cells whose DNA has been damaged Prospective fate: what a cell can become Determination: process through which a cell’s fate is fixed; occurs before obvious differentiation; whether or not this has already occurred can be tested by transplantation, through which cells are moved to a new location and observed to grow according to the old location (already determined) or the new location (had not been determined before transplantation) Cytoskeleton: 3 major cytoskeletal networks are microtubules (tubulin), microfilaments (actin), and intermediate filaments (vimentin); others are cytokeratins Microtubules: play a role in causing a cell to have a particular shape; made at one end and disassembled at the other; originate from the microtubule organizing center (MTOC). Some will “hit” the centromeres of mitotic chromosomes; also, make up a large portion of the flagellum proteins (spiral motion); All eukaryotic cells contain microtubules that vary in arrangement under different conditions. IN SHORT, microtubules… help form the mitotic spindle (line up and form long structures) keep an elongated cell in that shape help create cell polarity (microtubules go everywhere and don’t have much organization in a non- polarized cell) Alpha and beta tubulin: dimers of this make up the rods of microtubules Exploratory behavior: shown by microtubules Centriole (MTOC): where microtubules form Spindle: made of microtubules; pull chromatids apart towards opposite poles during mitosis Asters: microtubule organizing center (or centriole); made up microtubules; contact the plasma membrane and radiate out from the cytoplasm, but don’t contact the chromosome. Microfilaments: adopt different shapes within the cell. Made with actin, and, with myosin, play a role in movement. Actin: what microfilaments are made of; with myosin they play a role in the cell’s movement. Cytochalasin: inhibits microfilaments! Filaments form from an active molecule sticking on to another active molecule – all rod-shaped than a big glob; if you add this drug to dividing cells, the cell will not divide, because you’ve inhibited that “band” of microfilaments from pinching off the cell. Colchicine: a drug that prevents the polymerization of microtubules (meaning they can’t extend anymore). Blocks the mitosis, so you see many more chromosomes spread  makes it a lot easier to karyotype the chromosomes and check the genetics/sex of the embryo. MTs are in a constant state of polymerization and degrading – if you prevent the polymerization, there is only degrading. Intermediate filaments: the third kind of cytoskeleton network in a cell. Intermediate in size; used by the cell the make it very tough – they’re strong. Lots of it around. Throughout the cytoplasm, on the inner surface of the nuclear envelope. Connections between adjacent cells gives the sheets of cells strength and stability, like in skin. Microtubules are pretty big, microfilaments are pretty small, and intermediate filaments (vementin) are intermediate in size Cytokeratins: cells have a lot of it; 80% are proteins; thin but tough Cytokinesis: separation of two daughter cells; the pinching off of two newly-formed cells Cell migration: neuralcrest and primordial germ cells must migrate during embryogenesis. Yolk sac has cells set aside from later on – the cells need to take a long route later to the gonads, which haven’t formed yet. Molecules and structures of cell adhesion – cells need to stick together! Tight junctions: made of occludin proteins; also seal off compartments to prevent stuff from leaking out Desmosomes of cadherins: anchor epithelial cells together to form lateral connection (cadherins make up the desmosomes; are involved in cell type specific adhesion) Free cadherins: not found in desmosomes (cadherins are adhesive molecules that require calcium and cells used for making up cell-type specific adhesions in morphogenesis) kinetochore of the chromosome, make a stable connection and thereby be used to pull the chromosome in anaphase to the pole. 9. How is the role of intermediate filaments different from other parts of the cytoskeleton? Intermediate filaments are more stable than MTs or MFs and play a differentiation role by filling up a cell and making it tough. For instance keratinocytes in the skin fill up with cytokeratins, one type of intermediate filament. 10. Give an example with drawings or descriptions or both of how an epithelial cell is anchored to the extracellular matrix (ECM). Cells can anchor to basal lamina via their integrin protein in the plasma membrane connecting to the RGD peptide of fibronectin. Fibronectin in turn binds to other molecules (laminin, collagen type IV and proteoglycans. Epithelial cells might also be anchored on their sides away from the basal lamina with the very strong desmosomes made of cadherins. Tight junctions made of occludin play a role in making a seal along a line of cells and contribute some to anchorage. 11. What is the evidence that gap junctions connect cells? What do gap junctions do? 11. Small molecules less than 1000 daltons such as Lucifer yellow can be injected in one cell and observed to cross into the cytoplasm of neighboring cells if gap junctions connect them. By this method it can be shown that cells are connected with gap junctions. 12. Describe how you would determine that a particular protein was present in only some cells of the frog gastrula. Indirect immunofluorescence can be used to show that a protein is present in certain cells in a sectioned tissue. An antibody to the protein is added to the section and a second antibody to the first antibody is added. The location is visualized by observing fluorescence from fluorescein which is coupled to the second antibody. Genes and Development Epigenesis: embryonic development by gradual change Gene expression: all cells have the same DNA; there are five possible control steps in gene expression that determine which genes are expressed, how much, when, and in what cells: Regulatory DNA sequences: around the gene (promotor, enhancer, and silencer – these are sequences) Chromatin remodeling: rearranging the histones in chromatin Transcription: making RNA from the gene sequence. Exons – sequence gets into mRNA and then into the polypeptide sequence. Interested in the regulatory sequences that control transcription – whether it’s going to be transcribed or not. RNA polymerase doesn’t know where to go to code for the protein RNA processing: mainly splicing Translation: protein synthesis and mRNA stability Protein modifications for activation or inactivation Regulatory transcription factors: Recruit RNA polymerase II. Expressed in a cell for RNA transcription For RNA transcription, there are three main elements: histone proteins that coat DNA (DNA is never naked) which are positively-charged; DNA is negatively-charged with its sugars and phosphate backbone; DNA regulatory sequences around the gene, and transcription factor. Nucleosome: DNA is normally surrounded by basic histone proteins (making chromatin) and assembled into nucleosomes; nucleosomes are units of 180bp of DNA wound around a histone core. Compaction in the nucleosome inhibits transcription. X- chromosome inactivation: one of the x chromosomes in a female is inactivated on a random basis in early development. Barr body: Dense, dark material in an X chromosome (only found in females) Chromatin remodeling: DNA wound tightly around histones, which makes the nucleus of the cell. Genes are in a dormant state and must be modified. You want chromatin to relax its grip on DNA. Chromatin is very condensed; has to be remodeled during spermatogenesis and oogenesis. DNA in a cell’s life is completely condensed in metaphase, during the cell cycle. Transcriptional control: what transcription factors you have and whether or not they bind, and if they bind to promotors, enhancers, or silencers. Promoter: upstream of the coding sequence for the protein on DNA. Transcription factor binds to the promotor to copy RNA. Enhancer: short region of the DNA that can be bound with proteins to enhance transcription levels of the genes Basal transcription complex: repressor (stops genes), activator (turns on genes), RNA polymerase takes DNA. Promotor, assembly of RNA, transcription factors (basal transcription complex). Necessary for all; not special for one gene or cell Post-transcriptional control: after transcription. RNA splicing, processing, then getting mRNA which gets into the cytoplasm. Alternative splicing: of the exon transcribed sequences; multiple forms of fibronectin for instance mRNA stability: short-lived mRNA for growth regulatory proteins Translational control: Translation is protein synthesis through the use of mRNA; transcription is RNA synthesis. Translational control – whether you’re going to translate the mRNA or not, and for how long will the mRNA last in the cell? You make a lot of DNA and have to have histones to coat it. Stockpile a bunch of histone mRNAs, keep them around, don’t translation, after translation signal inside the cell they all get translated at once. Translation needs to keep up with rapid DNA replication. Post-translational control: Proteins are already there; need to determine whether or not to activate it now, or store it in a non-functional state and activate it later Masked mRNA: long-lived mRNA in an oocyte In situ hybridization (ISH): compare cellular distribution of gene expression (which cells make the mRNA?) Northern blot: a way to compare expression between tissues (how much and which tissues make the mRNA?) 1 What are five steps at which gene expression can be controlled? The five steps are (1) chromatin remodeling in which the nucleosomal structure is modified; (2) transcriptional control in which the gene is transcribed or not; (3) processing control in which the primary RNA transcript is assembled using the transcribed exon sequences; (4) translational control in which the mRNA now in the cytoplasm is used for protein synthesis or not and (5) post-translational control in which the protein may be activated or deactivated. 2. Describe three regulatory parts of transcriptional control of gene expression and how they interact. The three regulatory parts are the (1) chromatin made of histones and DNA in a nucleosome (2) DNA regulatory sequences like promoters, enhancers and silencers and (3) the class of proteins called transcription factors. To make a transcript first the nucleosome arrangement around the DNA regulatory sequences must be opened up to make it less compact and therefore accessible to the regulatory transcription factors which bind to specific short sequences in the regulatory DNA sequence. Sometimes the nucleosomes slide away from the regulatory DNA sequence but in either case now the basal and regulatory transcription factors can start to assemble the transcription complex which includes RNA polymerase II. Enhancers and silencers work by binding their cognate regulatory transcription factor for which they have a DNA sequence for recognition and then the DNA and protein loop back to contact the transcription complex forming at the promoter just ahead of the coding sequence of the gene to be transcribed. 3. What happens in X chromosome inactivation? Give its purpose; tell when it happens and what happens. Female mammals have two X chromosomes but only need one for proper development. X chromosome inactivation occurs early when cells are dividing to prevent twice as much gene expression from the X chromosome genes as is necessary. Apparently even two times as much gene expression can lead to developmental defects. So the mechanism of X chromosome inactivation involves a random choice of making either the paternally derived or the maternally derived X chromosome in each cell transcriptionally inactive. Basically one whole X chromosome become heterochromatin and can be seen in the nucleus as a darkly staining mass called a Barr body. 4. In phylogenetic development how can regulatory gene sequences be changed to create new phenotypes? The movement of regulatory DNA sequences by mutational changes in which breaks in the DNA insert a regulatory sequence or delete a sequence is very important for phylogenetic development. In this way a new gene can come under the control of a transcription factor just by now having the cognate DNA regulatory sequence to which it binds moved close to the promoter. Because the transcription factors are the master regulatory molecules determining which genes are or are not expressed changes in growth, differentiation and morphogenesis can be made simply by moving the DNA regulatory sequences. 5. What forms of gene expression control are used a lot in frog oocytes before and soon after fertilization? Frog oocytes must get going in development soon after fertilization. At this time they require tremendous quantities of new proteins because their cell division rate is the fastest it will ever be in the life cycle. To cope with this problem the oocyte during the three years in its making stockpiles histone mRNAs so that at fertilization it can use them to quickly make a lot of histone for nucleosomes. mRNAs of this type which are made but not translated later are called Protostomes (arthropods, annelids, nematodes, molluscs and other invertebrates) versus deuterostomes (echinoderms and chordates and a few minor phyla). Bilateral symmetry found in all except the diploblasts. 7. Name examples of synapomorphies of chordates. The theoretical pharyngula stage shows the phylotypic characteristics of notochord, dorsal hollow nerve tube, the pharyngeal arches, (plus post-anal tail). 8. What are advantages and disadvantages to having indirect development versus direct development? Advantages include greater time for growth and overall development in certain environments, having a body plan that allows adaptation to an ecological environment that does not compete with the adult or avoids predation found in the adult environment, and dispersal especially for many marine invertebrate larvae. Disadvantages include the complications of having to make two body plans (larval and adult),and the metamorphosis from larva to adult, sometimes the delay in development makes the larvae more susceptible to predation. 9. Give an example of heterochrony and how it could be used to evolve a new type of species? Neoteny as in the axolotl is a change in timing such that the larval tadpole stage becomes sexually mature and never undergoes metamorphosis into a terrestrial adult salamander. The axolotl (and other species like it) now can now permanently exploit the fresh water rivers and ponds. 10. What is the evidence that cell distances, not numbers are counted in development? There is some evidence that pentaploid salamander embryos with much larger cells than the diploid embryo, develop to form normally sized and proportioned tadpoles. Even though the structures are made of fewer cells development occurred normally. 11. How many more cell types are required in the transition from sponges and cnidarians to arthropods and then to chordates? From the diploblast phyla with about 10 cell types there is a five fold increase to the triploblast invertebrate phyla including arthropods with about 55 cells types but only about a two fold increase to the chordates with about 120 cell types. 12. Describe a theoretical model to show how cells determine where they are in space. If there is a morphogen given off from one area and it diffuses out from that area cells in the surroundings will experience different levels of the morphogen; the morphogen conveys positional information to the cells. The cells interpret the concentration of morphogen that they sense in determining their positional value which leads them to make decisions on what genes they will, or will not, express and how they will differentiate. 13. In spite of vastly different body plans some genes involved in patterning are shared between insects and vertebrates. What are these and were do they act? Along the dorsal ventral and anterior posterior axes there are related homologous genes and proteins that play a role in positional information or positional value. For the D-V axis there are homologous paracrine diffusible proteins acting as morphogens carrying positional information. Dpp (dectapentaplegic) conveys dorsal information to flies but its homolog BMP (bone morphogenetic protein) of vertebrates conveys ventral information to chordates. Sog (short gastrulation) of flies conveys ventral information in flies and is homologous the chordin protein conveying dorsal side information of vertebrates. For the A-P axis both insects and vertebrates use homologous homeotic genes (Hox genes) and their proteins to allow cells to determine how they will determine positional value along the axis. There is no inversion along this axis between insects and vertebrates.