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174 Cards in this Set
- Front
- Back
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What is a routine procedure and has enabled many previously infertile couples to have ababy. Its variants include artificial insemination by donor (AID), egg donation, and storage of fertilized eggs by freezing called?
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in vitro
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What is after the general body plan is formed, while individual organs are being laid down called?
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organogenesis
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What is separating and identifying all the proteins in a particular tissue sample?
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proteomics
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What is the structure of organisms that changes with time called?
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morphology
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What is asexual reproduction?
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forms buds associated with regeneration.
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What are regulatory molecules deposited in particular positions within the fertilized egg called-these molecules help with determining different parts such as head, tails etc.
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determinants
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How do different parts of an organism arise at the correct time and place?
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regional specification
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What deals with how pattern appears in a previously similar population of cells and occurs in early development?-programs different parts such as ahead, trunk and tail.
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regional specification
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How do cells become physically distinct cell types, like muscle cells and neurons? different sorts of cells arise.
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differentiation
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What involves intercellular signaling, leading to the activation of different combinations of regulatory genes in each region?
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embryonic induction
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How do cells migrate, stick together or come apart, or die to produce tissues and organs?
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morphogenesis
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What refers to the cell and tissue movements that give the developing organ or organism its shape in 3D?
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morphogenesis
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How do cells start and stop dividing?
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growth
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What refers to increase of size and the control of proportion between body parts?
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growth- least well understood aspect in terms of molecular mechanisms
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How do these processes change over time?
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evolution
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What is a stage where most early embryos pass through which they consist of a featureless ball or sheet of cells?
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blastula or blastoderm.
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What is any animal the sperm and eggs and their precursor cells?
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germ line
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What are all other cell types- that aren’t from the sperm and eggs?
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somatic cells
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What would you use to – be able to distinguish an animal arising from the donor nucleus from one arising from the original egg nucleus?
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genetic marker
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What is this called :can take a single nucleus from a somatic cell and can create a whole animal?
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cloning
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What is a oocyte?
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egg
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What is the whole chromosome set is doubled or quadrupled, can occur in some mammalian tissues, such as the liver?
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polyploidy
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What do you call where DNA replication occurs repeatedly without chromosomal division, leading to giant chromosomes, occurs in some tissues in Drosophila?
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polyteny
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What is is the theory that all organisms were created at the same time, and that succeeding generations grow from homunculi, animalcules, or other fully-formed but miniature versions of themselves that have existed since the beginning of creation?
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preformation
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What is based on the idea that the unfolding development of an organism, and in particular the development of a plant or animal from an egg or spore through a sequence of steps in which cells differentiate and organs form;
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epigenesis
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Who observed blood vessels in chick, embryonic kidney and suggested vis essentialis "essential force" that directs development?
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Wolff
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What is when the sperm fuses with the egg there is a fairly rapid change in egg structure that excludes the fusion of any further sperm?
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polyspermy
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What is is a molecule of RNA encoding a chemical "blueprint" for a protein product?
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mRNA
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What control of transcription by proteins that interact with regulatory sequences of DNA?
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transcription factors
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What is the region of a gene is a region just upstream from the transcription start site to which the RNA polymerase binds?
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promoter region
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Regulatory sites at a distance from the gene are called?
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enahncers
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What are the chief protein components of chromatin?
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histones
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What is a metabolic pathway connecting a cell surface receptor to its intracellular effector - involves a sequence of protein phosphrylation events and movement of activated transcription factors into the nucleus where they can regulate gene activity?
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signal transduction pathway
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What is - an inducing factor that can evoke more than one response at different concentrations?
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morphagen
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What are two repressor complexes recruited by transcription factors?
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DNA methylation enzymes or hiostone deacetylation enzymes
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What affects would negative regulation of g-protein receptors have?
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can affect metabolism or gene expression- ex. blood vessel formation in mice
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What do mutations in the RTK (receptor tyrosine kinase) pathway cause?
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mutations that cause Ras to be over-active are common in tumors
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What happens if TGF betas are inhibitory?
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they inhibit cell division and promote the secretion of extracellular matrix materials.
involved with skeleton development, and specficiation in the early body plan. it controls body size |
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What are the 7 major signaling pathways?
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notch, Wnt, hedgehog, transforming growth factor (TGF-beta), receptor tyrosine knase
Jak/Stat and nuclear hormone receptor |
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What is the function of the nuclear hormone receptors?
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regulate gene expression
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What kind of development consists of the zygote containing all necessary determinants for differentiations and cell division partitions determinants until all cells contain only a single determinant type?
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mosaic development
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What development consists of embryonic cells responding to their surroundings that can change their fate?
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regulative development
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What are sequence logos?
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The sequence logo will show how well residues are conserved at each position: the fewer the number of residues, the higher the letters will be, because the better the conservation is at that position.can be used to represent conserved DNA binding sites, where transcription factors bind.
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What is a way of representing the results of a multiple sequence alignment, where related sequences are compared to each other, and similar functional sequence motifs are found; shows which residues are conserved (are always the same), and which residues are variable?
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consensus sequence
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What is the difference between a consensus sequence and a sequence logo?
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sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
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What is the consensus sequence?
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For multiple sequences the last row in each column
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What is a signaling cascade?
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cascade of kinases that activate eachother downt he chain, finalizing in the activatiion of a transcription factor
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What do cell signaling molecules effect?
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metabolism, gene expression and cell permeability
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What do ion channel pathways effect?
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ions flowing in or out, Ca 2+ in fertilization
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Where do nuclear hormone receptor ligands bind?
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in cytoplasm
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Describe the G-protein receptor pathway?
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receptor is 7-ass membrane protein, binds to trimeric G-protein, ligand binds in cytoplasm, G-protein releases GDP and binds GTP and releases from receptor, activates other enzymes, ex. adenylyl cyclase, can effect metabolism or gene expression
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Describe the enzyme-linked receptors and their affects on development?
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most common and impot. in development, ligand binds cell-surface receptor, modifeis target protein, direct effect on gene expression, work through a cascade
ex. bone morphogenetic proteins (BMP's) |
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What an ex. of enzyme-linked receptors and where does the ligand bind to them?
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on cell-surface, bone morphogenetic proteins (BMP's)
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What can G-protein receptors affect during development?
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metabolism or gene expression
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Describe the notch pathway?
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ligand (Delta) and receptor (notch) bind in cytoplasm, can't diffuse long distances therefore pass from neighbor to neighbro
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What does the notch system pathway do when the transcriptor factor is activated?
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suppressor of hairless, impt. in neurogeneiss, somitogenesi and imaginal disc devleopment
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Which pathway is impt, in kidney development, Drosophila segmentation and drosoventral patterning in Xenopus?
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Wnt family
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What happens when Wnt pathway is inactive? how iti s activated?
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Gsk3 is targeted for destruction and target genes are inactive; inhibiting an inhibitor
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What happens when Wnt pathway is active?
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dishelved protein inactivated GSK3 and target genes activated
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What is Wnt impt in?
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regulating cell growth and activating mutations that are linked to colon cancer.
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What does notch pathway do?
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suppressor of hairless, generates peptide that leads to alzheimers disease
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What does TGF beta pathway do?
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controls body size
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What does RTK pathway do?
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mutations that causes RAs to be over-active are common in tumor, can lead to excess growth
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What does hedgehog do that is impt>
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activates mutations linked to basal cell carcinoma, impt, in skeletal development, and dorsoventral patterning of neural tube and anteroposterior patterning of limbs
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Which two pathways are activated by inhibiting an inhibitor?
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Wnt pathway and hedgehog pathway
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What happens when Hedgehog is present? absent?
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patched inactive, smoothened active, Gli activates target genes;
patched active, smoothened inactive, Gli represses target genes |
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What is the sperma nd egg pronuclei fuse to form a single nucelus and the egg is fertilized called?
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zygote
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What are early cell divisions called?
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cleavages- no growth between successive divisions
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What are the products of cleavages called?
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blastomeres
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What controls the different type of cleavage groups different animals have?
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the amount of yolk in the egg
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What are the three tissue layers formed during gastrulation?
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ectoderm, mesoderm and endoderm
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What is the course of development which a typical embryo follows ins tandard laboratory conditions when it is free from experimental disturbance?
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normal development
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What is the micrscope section taken across the long axis of the animal?
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transverse section
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What sections are parallel to transverse sections?
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longitudinal
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What does the rate of development depend on for free-living embryos?
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temperature
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What is a diagram that shows what will become of reach region of the embryo in the course of normal development? ex. where it will move, how it will change shape, what structures it will turn into?
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fate map
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What does precision of a fate map depend on?
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how much random cell mixing occurs in development
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What are genetic mosaics?
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organisms consisting of cells of different genotypes
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What can a clonal analysis prove?
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lack of commitment but not presence of commitment
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What is a combination of transcription factors present in the cell and so it can be visualized directly by observing the expresion of relevant genes using in situ hybridization?
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commitment
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What is a cell or tissue explant that becomes a particular structure if it will develop autonomously into that structure after ioslation from the embryo?
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specification
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What is a region of tissue will also develop autonomously in isolation but differs in that its commitment is irreversible with respect to the range of environments present in the embryo?
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determination
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What is used to mean the range of possible cell types or structures into which a particular cell population can develop?
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potency
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What is the ability to adopt any cell fate called? and the ability to adopty many cell fate called? where is it located on the hierarchy ?
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toti-potent
pluripotent at the top |
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What is a substance or substances located inn part of an egg or blastomere that guarantees the assumption of a particular state or commitment by the cells which inhiert it during cleavage?
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a determinant
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What are determinants (not their function?
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sometimes mRNA's that are localized to a party of the cell in association with the cytoskeleton or they may be proteins
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How can we analyze specification and determination of cells?
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transplantation ex. grafting, move it- isolate for specification, move for determination
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What restricts determination?
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potency (cell tyep ranges possible)
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What does most regional specification in development arise from?
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inducing factors- the operation of extracellular signals
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What does competence require? and what is it?
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the ability to respond to an inductive signal takes the presence of specific receptors but also a functioning signal transduction pathway coupled to the regulation of transcription factors
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What is an interaction of responding tissue that has a choice before it (either mesoderm or ectoderm) in normal development results in an increase in complexity of the embryo?
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instructive induction
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What is one factor that is on e of the two different types of instructive induction that invokes different responses to different concentration gradients with more than one positive outcome?
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morphagen
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What is the possibility that the signaling centers lie in one cell sheet and the responding cells in another and when brought together appropriate structres are induced as a result of a single threshhold response in those parts of the responding tissue immediately adjacent to signaling centers?
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appositional induction
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What can disrupt morphagen gradients?
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treat animal with chemical (blocks the morphagen gradient) and animal can lose head, tail or brain, etc, blocks development effects ex. retinoic acid to frog embryos causes loss of posterior structures
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What are the two types of inductions?
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instructive and permissive
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What is the inductive interaction which the signal is necessary for the succesful differentation of the responding tissue but cannot influence the developmental pathway selected? impt in late development
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permissive induction
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What is the different between permissive and instructive induction?
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instructive inductions lead to subdivision of the competent tissue while permissive inductions do not.
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What is fate?q
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what a particular cell or tissue will become
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What is differentiation?
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– a cell or tissue is differentiated if it has all
the physical characteristics of a specific cell type |
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How do you identify cell fates?
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introduce label into one or few cells, allow development to proceed, identify structures the dye is found in at later stages, repeat by introducing label in diff. location
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What are the steps of experimental embryology?
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observe and label cell fates, transplant and determien specification state and inductive properties, block with with chemicals to determine characterization of impt. molecules or pathways
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What are model organisms? what are the examples?
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small number of organisms that are studied to understand how that animal and all naimals develop; Xenopus, zebrafish, fruit fly chick, frog, and nematode C. elegans
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What does access refer to for model organisms?
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refers to how easy it is to get at embryos at all stages of development.
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In terms of access which oranisms are most favorable?
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those that are free-living, with external fertilization
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Which model organism is the least good in terms of access?
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mice
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Which model organisms are the most expensive? and the cheapest?
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mouse, chepaest- C. elegans and chicks
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What is microsurgical manipulation?
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requirement for embryonic experimentation removing a single cell, small piece of tissue, grafting an explant to another position ina second embryo, injecting individual cells with substances
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Which model organisms are favored in microsurgical manipulation?
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chicks and Xenopus
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Which model organisms are favored in genetics?
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mice, C. elegans and Drosophil
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Which model organism was the first sequenced genome?
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C. elegans
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What genetic approach starts witha screen for mutations that confer a particular phenotype and then identify molecular identify of a gene called?
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forward genetics
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What genetic approach starts with molecularly identified gene and determines effects of gene disruption called?
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reverse genetics
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How can you approach forward genetics?
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induce mutations and look for mutations that produce animals with particular phenotypes
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How can you approach reverse genetics?
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start with DNA sequence then disrupt function of gene and see what the phenotype is
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What is loss of function?
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the most common type of mutation meaning that the protein produce of the mutant gnee is less active than the wild type
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What is a null mutation?
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complete loss of function from a mutation
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What is gain-of-function?
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can be given a completely new function or increase in normal fuunction
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What are genes often named for?
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their mutant phenotype
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How many generations of fish do you need before idnetifying mutations on genetic screens?
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3 generations
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Describe the genetic screen for tubingen for zebrafish mutants?
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found mutations all at one shot- defects in tail both are much shorter-
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Why are genetic screens impt?
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gives us mutations that effect normal development and the processes affected by the mutations.
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Describe genetic mapping.
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if you have a mutant animal you can put the wildtype back into the DNA it will correct the defect.
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What is positional cloning?
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mutation is mapped to very high resolution using microsatellite polymorphisms or restriction fragment length polymorphisms-mutant + DNA sequence that rescues that mutant shows that molecular and genetic identity are shared
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What is a gene regarded as cloned when the complete coding sequence is incorporated into a bacterial plasmid, or other cloning vector, so that is can be amplified and purified in a quanitity suitable for use in any of the types of investigation called?
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reverse genetics
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How can polymorphisms scattered through the genome's position be known?
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if the genome has been sequenced
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What do you base the order of pathways for mutants with the same phenotype?
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on their rescue experiment
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What do you base the order of pathways for mutants with different phenotypes?
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epistasis
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What is genetic mosaic analysis?
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generate mutant cells inside a field of wild-type cells and determine whether mutant cells dsiplay mutant phenotype or wildtype phenotype
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What is it called if genotype and phenotype of mutant cells is abnormal because it affects the region in which the gene is normally active?
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autonomous
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What is it called when a cell mutant shows the abnormal phenotype because it is affecting the structure outside the domain of action of the gene?
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nonautonomous
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What does nonautonomous mutations affect?
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an inductive signaling step
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What is it called when you have a gene and specifically remove gene from the genome of animal to see the effect?
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knockout, targeted deletion
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What is the direct replacement of a gene by a modified version made in vitro called?
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homologous recombination
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How do we eliminate gene function by targeted delection?
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target vector-mark gene= antibiotic resisntance marker disrupts gene function- put on embryonic stem cells, homologous recombination works- then cells with be neor and ganciclovir, if inserts elsewhere, cells will be neoR but willl die on ganciclovir
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How many generations do we need to do for targeted deletion to check and see phenotype?
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3 generations
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If targeting deletion is dead really early what system can allow gene deletion in specific tissues?
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Cre-lox system
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What is a DNA sequence that Cre enzyme recognizes and chops around and what happens after the mouse is carrying the floxed gene?
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loxP sites- floxed gene will be deleted only in desired tissue
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How can we elminate gene function by RNAi?
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RNA interference-introduce double stranded RNA into organism, dsRNA is digested into small fragments, small RNA fragments trigger enzymatic digestions of RNA for gene or itnerest that has the same sequences as fragments, assess phenotype
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Waht is the RNAi doing to eliminate gene function?
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tricking the cell into digesting some of its own RNA- can be a quick way to identify loss of a gene
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Describe how e can do reverse genetic screens with RNAi.
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produce library of dsRNA for all genes, look for phenotypes of interest in animals, immmediately determine molecular identiy fo gene that generated phenotype
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What are some of the primary differences between forward and reverse genetics?
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foward genetics- alters gene function by mutation and reverse by RNAi, phenotype for forward is heritable and non-heritable for reverse genetics. Reverse gneetics is quicker
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What is misexpression?
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molecular version of moving-switching genes on times they are not usually active to determine if gene activity is sufficient to generate a particular structure
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What is the difference between knocking out and misexpression?
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misexpression-molecular and tells whether the gnee is sufficient
knocking out tells whether the genes are necessary |
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What are the molecular tools in developmental biology? give examples.
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1st-find it-detecting expression
1. in situ hybridization 2. immunostaining 3. reporter genes 4. microarrays |
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What are the experimental embryology approaches to developmental biolgoy for genetics?
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forward genetic screens, mapping and cloning, ordering genetic pathways, reverse genetics, misexpression genetics
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What is in situ hybridization?
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used to detect RNA, fix specimen, preserve with formaldehyde-specimens can be whole-mount or sections, synthesize complementary RNA moelcule to mRNA of interest, probe is recognized by antibody b/c of chemical addition, antibody is hooked to an enzyme and substrates form colored precipitate.
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What does in situ hybridization reveal?
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mRNA abundance and position during development- can tell when and where gene is switched on using this technique
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What is the method of immunostaining?
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used to detect proteins and not RNA molecules, anitbodies only bind proteins of interest, have to make antibodies that will recognize protein of interest-take a bunch of tubulin proteins, crankz out antibodies b/c it thinks its under attack and takes blood with antibodies-purifies it-now have primary anitbody and use secondary antibody
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What is a method for detecting the presence of specific protein moeclules called?
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immunohistochemistry or immunofluoresence
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What is a primary antibody?
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for each protein you want to detect must have an antibody
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What is a secondary antibody?
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specifically recognizes a region of the primary antibody and is either hooked to an enzyme or to a fluorescenct molecule
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What is a type of fluorescent microscope?
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confocal
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What can be used to demonstrate co-expression of developmental genes? and how?
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antibody staining- use 2 diff. primary antibodies and 2 diff. secondary antibodies at once-can determine whether they are int he same cell at the same time
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What are reporter genes?
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easy to see-used to report status of other genes- fused to protein of interest or used to assess function of cis-regulatory elementts
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What is the epitope tag?
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a small protein sequence for which an antibody is available, inserted into protein of interest
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What are microarrays?
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molecular method to assess gene expression- doesn't give spatial info, lets you look at thousands of genes rather than 1 by 1- mRNA is located from tissue of interested, labelled with fluroscent marker, hybridized to microarray, binds to complementary sequences, intensity of fluroscence represents the amount of mRNA in original tissue sample-compare two tissues to determine genes expressed
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Which molecular methods give spatial info and level of expression?
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in situ and anti body staining
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What did the genetic screen for mutations affecting anterior and posterior patterns find in Drosophila?
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Nusslein-Volhard and Wieschause, 40,000 mutations, identified 15 gnees, came up with 3 distinct groups of genes
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What type of genes affected whole chunks of the larvae that were missing ?
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gap genes
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What is the specification of structures along the anteroposterior axis conrolled by and what are they turned on by?
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turned on by bicoid and nanos, controlled by maternal systems
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What three maternal systems establish initial polarity in Drosophila?
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anterior system (bicoid), posterior system (nanos) and terminal system (torso)-no mouth parts have all segments in the middle
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What is the first morphagen gradient of the anteroposterior system?
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bicoid- disrupts the microtubular transport, after fertilization RNA will translate protein, diffuses through embryo, then set up stable gradient, in situ hybridization-mRNA, protein immunostaining
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What happens when transplanting cytoplasm in bicoid mutant takes place?
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get more anterior development, cocentration depend on the bicoid mutant development
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What happens when increased dosages of bicoid occurs to hunchback expression and threshold?
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it is transcription facto that swtichs one hunchback expression, more bicoid, threshold of activation extends further along egg, hunchback expands
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Describe the function of nanos in anteroposterior system of Drosophila.
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binding protein controls gene expression by binding to RNA molecules and preventing them from translating. Maternal hunchback uniformly distributed throughout egg-nanos prevents from being translated.
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What does bicoid do to caudal mRNAs?
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inhibits maternal caudal-prevents translation
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Where is torso distributed and what is it?
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receptor tyrosine kindase, uniformly distributed throughout surface of eggs and signal comes from end of eggs, cleaves trunk (ligand for torso) allowing it to be released triggers gap genes
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What are the first zygotic genes that are activated and what are they?
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transcription factors called gap genes, anterior and posterior maternal systems controls which gap genes will be expressed where, cross-talk with one another
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What are drosophila embryos divided into?
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14 parasegments, true segments are offset from parasegments by half a segment
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What do pair rules genes do?
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when fitz gene is lost fitz mutations causes defects in every other segment, lose entire segments, even-skipped expressed in odd parasegments, fushi tarazu is expressed in even parasemengets
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What genes establish positional information for pair-rule expression?
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maternal and gap genes
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What are pair-rule genes?
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function as a layer in the developmental hierarchy between the gap genes and the segment polarity genes.
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What are even-skipped stripes made by pair rule genes?
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the even numbered segments are reduced or lost in the orignal mutant
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What are heterochronic genes?
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is a shift in the relative timing of two developmental processes- mutations in these genes affect developmental timing.
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