Developmental Biology Test 2

• 1. the chromosomes in each cell of an organism’s body are the mitotic descendants of the chromosomes established at fertilization
• A. all somatic cells have same nucleic information
• B. confirmed through cloning

True

• 1. which RNAs enter the '
• GmRNAs
• 2. differential gene transcription
• 3. selective mRNA translation
• A. once selected to be in cytoplasm, which ones are translated
• B. some mRNAs are inactivated,to prevent viruses from invading
• C. ex/exonucleases
• 4. Differential protein modification: which proteins are allowed to remain and/or function in the cell

• 1. dna and proteins
• A. DNA: 
• B. proteins: mostly histones

• 1. def: one unit of histones with dna wrapped twice around it
• A. Octamer of histone proteins (two molecules each of H2A, H2B, H3, and H4)
• B. these histones wrapped with two loops containing ~147 base pairs of DNA
• C. H1 binds 60-80 bp of ‘linker’ DNA between nucleosomes (not apart of octamer)

• 1. Def: nucleosomes fold up and are stacked, forming a helix
• 2. Pro: Inhibits transcription of genes by packing adjacent nucleosomes together into tight arrays
• (Obvi more difficult to transcribe when DNA is packed tightly)

Histone 1

• 1. Histone ‘tails’ are sites of :
• A. acetylation
• B. and methylation,
• 2. Role: which may disrupt
• or stabilize, respectively, the formation
• of nucleosome assemblages
• 3. What chemicals we attach on the tails determines whether the nucleosome unwraps or remains tight

1. largely due to modification of histone tails

• 1. What is going on? Negatively charged acetyl groups attach to lysine groups on H3 and H4.
• 2. these acetyl groups mentioned above are done by acetyl transferases.
• 3. Effect: loosening of histones initiates trancscription

• 1. F(x): 
• A. stabilize nucleosomes
• B. prevent transcription

• 1.F(x): A. activate
• B. repress transcription
• 2. when one or the other is occurring: depends on what a.a. of the histone is methylated, or getting a methyl group attached
• A.

• 1. Exons: coding regions (including leader sequences and 3' UTR sequences)
• 2. Introns: spacers’ that have nothing to do with the amino acid sequence of a protein

• 1. Eukaryotic genes are NOT co-linear (broken up in exons/introns, in which introns aren't really the coding gene)
• A. introns might have some functionality, but do not encode though.

• 1. site for binding RNA polymerase/T.F.s. determines
• A. what dna is read (the rna coding seuence)
• B. the direction of coding
• C. determines transcription start site
• a. usually located near the transcriptions start site and not coded itself

• 1. Def:represents 5’ end of the RNA to receive a ‘cap’ of modified nucleotides 
• A. 3 nucleotides usually
• 2. dubbed: a ‘cap sequence,’

• 1. specific f(x):
• includes a sequence for polyadenylation-> adds a bunch of A’s
• 2. General f(x): part of mRNA that affects stability of the strand and translation of the mRNA

part of the gene sequence of DNA involved in termination of transcription

• 1. another name: nuclear RNA
• 2. What: original transcription product
• 3. this is modified on both ends before leaving the nucleus
• A. A cap of methylated guanosine (guanine + ribose) is placed on 5’ end (necessary for binding mRNA to ribosome)
• B. 3’ terminus is modified by addition of polyA tail (not part of gene sequence)-a. role: protect genome from exonucleases.
• C. As nRNA leaves nucleus, introns are removed and exons spliced together

• 1. DNA:
• A. promoter region
• B. djklfjsdfk

• 1. F(x): where RNA Polymerase binds to initiate transcription
• 2. genetic make up:
• A. CpG island: a cytosine-guanine rich repeat center. ~ 1000 bp long
• 3. what binds to cpg island: basal transcription factor
• A. recruits DNA polymerase
• B. also poistions the DNA polymerase
• 4. another molecule that binds to ___: enhancers!
• A. f(x)#1:recruit and stabilize RNA polymerase 2.
• B. f(x)#2: signal where and when a promoter can be used
• C. f(x)#3: how much gene product to make

1. interaction: bind to TF's.

• 1. f(x):
• A. signal when and where a promoter can be used (on the raw, unmodified DNA)
• B. how much gene product to make
• 2. activated by transcription factors
• A. attaches mostly to cis-linked

• 1. F(x): activate gene
• how they do this?
• A. recruiting enzymes that break up nucleosomes 
• B. stabilize the transcription initiation complex (RNA polymerase and other factors that bind to promoter region) 
• 2. How it works:
• A. Binds to: either enhancer or directly on promoter region of gene
• a. if binds on enhancer, must form a bridge of TF's to connect to the promoter region (so essentially 
• A. TF binds to a cofactor (a non protein complex that catalyzes an enzymatic reaction)->
• a. recruits nucleosome modifying proteins that make DNA accessible to RNA pol II
• B. Can form bridges, looping the chromatin to bring the TF (and cofactors that modify chromatin or stabilize polymerases) near the promoter

• 1. 30 protein subunits that connect RNA pol II to enhancer regions that relay developmental signals)
• A. means this is a bridge between enhancer and promoter since RNA pol II is on promoter
• B. effect: this is pre-initiation complex at promoter
• 2. -> however, connection between mediator and RNA pol II must be broken, in order for initiation to take place:
• A. TEC (Transcription Elongation Complex):
• a. made up of many TF's
• b. 
• 3.

• 1. Transcription Elongation Complex: breaks bond between RNA pol II and mediator
• 2. Transcription Elongation Suppressor: may prevent TEC from interacting w/ RNA pol II.
• (pauses transcription)

Fuse reporter genes (the fluorescent GFP) to suspected enhancer genes....then see what parts of the body were transcripted translated into

• 1. same enhancers in every cell of organism
• 2. differs: combo of TF that enhancers experience
• A. there can be many dif TF that can match with an enhancer
• 3. what happens:
• A. enhancer binds to TF-> either suppress or enhance RNA II to initiate transcription
• 4. different combos of Tf's with enhancers in different cells lead to variety of f(x)'s
• A. gene can have multiple enhancers
• 5. Enhancers activate cis-linked usually.

are soluble molecules whose genes are located elsewhere in the genome, and which bind to the cis-regulatory elements

• 1. 1st enhancer: for pancreas (farthest from promoter)
• 2. 2nd enhancer: surface ectoderm
• 3. 3rd enhancer: neural tube formation
• 4. 4th enhancer:  (in intron) retina expression
• ex/ of enhancer modularity. 
• allows proteins to be expressed in different tissues.
• 5. encodes a TF that works in combination w/ other TF's (in more detail in another card)

–Enhancer in third intron controls time and place of expression

–Pax6 works with Sox2 and L-Maf TFs to activate the gene only in those head cells that will become lens

–This means the cell (1) must be head ectoderm (which expresses Pax6), (2) must be in region of ectoderm capable of forming eyes (L-Maf), and (3) must be in contact with the future retinal cells (which induce Sox2 expression)

Pax6 interacts with Pdx1 (specific for the pancreatic region of endoderm) and Pbx1 for development of endocrine cells

T

• categories: (based off of similar structure)
• 1. have binding site for enhancer as well as other TF (separate binding sites)
• 2. above are called different domains
• A. DNA binding domain: binds to a specific sequence in enhancer
• B. Trans-activating domain: suppressed or activates the transcription of gene by attaching to enhancer or promoter
• C. Protein-protein interaction domain: TF can modify other TF's

combinatorial association of TF's

• 1. Trithorax proteins, when bound to nucleosomes of active genes, keeps the genes active
• 2. Polycomb proteins, when bound to condensed nucleosomes, keeps genes in a repressed state
• 3. A permanent “off” or repressed stage, until these proteins are removed
• 4.Can modify a gene and have it extend over generations
• A. Ex/ if parent experienced time of famine, could pass it down.

• 1. can penetrate repressed chromatin and bind to their enhancer DNA sequences, -> (effect:) opening up chromatin for other TFs
• 2. extra good at penetrating condensed chromatin
• 3.

• 1. DNA regulatory elements that actively repress the transcription of a particular gene (like a negative enhancer)
• A. could be spatially in a particular cell
• B. or could be a temporary thing
• C. some genes are turned on by default, want to turn them off
• 2. EX/ NRSE (neural restrictive silencer element)
• A. prevents activation of an enhancer in all mouse tissue except for neurons
• B. involved in differentiating different cells of nervous system
• C. How it works: the silencer will operate when zinc finger TF binds to it. therefore neurons to do NOT have this TF, since these cells do not have a silencing NRSE 
• D.

neural cells are expressed much more widely

• 1. essentially, different proteins are expressed in different cells
• 2. what happens:
• A. Processed into mRNA by the removal of introns
• B. Translocated from nucleus to cytoplasm
• C. Translated by protein-synthesizing apparatus
• D. And, sometimes, post-translationally modified to become active

• 1. also called "differential mRNA processing"
• 2. purpose: so a single gene can produce an entire family of proteins
• 3. splices from the NUCLEAR RNA not the o.g. DNA
• 4. frequency: happens 10-100 more frequently than changes in gene transcription
• 5. what is spliced out: introns
• 6.

different proteins encoded by the same gene are splicing isoforms

• 1. at 5' and 3' ends of introns
• 2. splice sites recognized by spliceosomes

• 1. splicing factors: how cells identify a splice site
• -> these can vary , therefore an exon in one cell can be an intron in another
• 2. introns: most introns have an identifiable "consensus sequences at 5' and 3' ends . (identified by spliceosomes)
• 3. 4 major types of exon splicing:
• A. cassette exon
• B. mutually exclusive exons
• a.

• 1. Def: a piece of DNA, or cassette, can be used as an exon or intron
• 2. ex/ Type II collagen
• A. makes different kinds of procollagen
• a. chondrocyte percursors and
• b. mature chondrocytes (cartilage cells)
• c. alternative 5' splice site

• 1. Splicing for two separate pieces of RNA to be exons in two separate mRNA strands 
• 2. This means an exon is spliced out (an intron spliced out for one leaving an exon), and that former intron spliced out is an exon in a second possible strand.
• 3. Ex/ such as that used to create the large and small isoforms of the protein Bcl-X

1. the two daughter mRNA's are the same except the 5' splice site is different for one. This means that one mRNA strand has an exon strip that is more shaved off than the other.

• 1. two identical ,separate mRNA's from the nRNA except that one intron is shifted
• 2. ex/ truncated forms of chordin.

• 1. drosophila, a membrane receptor protein that involved in preventing dendrites from binding to one another
• 2. each dendrite has a specific "fingerprint" 
• 3. a lot of variability in options for 3,6,9 
• 4. 115 exons for gene, only 14,000 genes in genome

• 1. nematodes and humans: both contain 20,000 genes
• 2. 92% of human genes form multiple isoforms
• 3. C. elegans rarely makes different isoforms

• 1. Effect: leads to a mutation, or a different PHENOTYPE
• 2. ex# 1/ Dystrophy: a mutation in one splice site of the gene for dystrophin 
• Effect: that exon within that splice site is skipped entirely 
• 3. ex #2/ Myostatin gene: a splice site mutation in the myostatin gene 
• A. myostatin: a negative regulator usually. initiates end of making muscle tissue by telling precursor cells to stop dividing
• B. Effect: a mutation in this delays the signal of saying "stop dividing" -> therefore more precursor cells are made before the myostatin gene ends precursor differentiation
• C. -> bulky, muscular organism

• 1. why this matters: the longer an mRNA lasts, the greater chance the mRNA can produce more proteins
• 2. How "age" of mRNA can increase: 
• A. Length of polyA tail!
• a. longer the tail-> longer the half life
• B. in specific cells at specific times, the mRNA can be selectively stabilized
• a. ex/ prolactin-> in presence of prolactin, the mRNA for casein has a life from 1hr to 24 hours

• 1. ex/ oocyte: stores mRNAs for use during ovulation or fertilization
• A. oocyte mRNA ex's/ during cleavage, when embryo makes enormous amounts of chromatin, cell membranes, and cytoskeletal components

• 1. what: inhibitors that prevent the translation of mRNA
• 2.ex/ in oocyte:
• A. Maskin: protein that acts an inhibitor.
• a. how it works: 
• –binds 5’ and 3’ ends together of mRNA
• in a configuration that prevents formation of a polyA tail, and hence, translation

• 1. Organ formation?
• 2. Separate tissues from various populations of cells?
• 3. Location of organs and how does migration of cells nearly always accurate?
• 4. How is organ growth coordinated?
• 5. How do organs achieve polarity?

• 1. 1850s: mitotic division of all cells that orginated from fertilized egg
• 2. mid 20th century: differences in cell membranes leads in embryonic cells -> organ formation
• 3. late 20th century: membrane components that allow cells to adhere to, migrate over, and induce gene expression in neighboring cells – began to be discovered and described
• 4. Today: pathways and networks are modeled; beginning of understanding of how cells integrate information in nucleus and environment to take their place in the community of cells

• 1. first study: in 1955, Townes and Holtfreter suspended 3 different germ layers (after neural tube was formed) 
• 2. (in normal pH), different layers aggregated
• 3. different sizes/colors of cells allowed them to follow the separation
• 4.  after allowed to re-aggregate, they cells formed same formation as they do in an embryo
• 5. Results:
• A. selective affinity
• B. formation of special structures that mimic actual structures in development such as neural tube
• C. selective affinity shifts during development
• 6.

• 1. Ectoderm on exterior and mesoderm in interior->
• A. means that inner surface of ectoderm has POSITIVE affinity for mesoderm
• B. ectoderm's outer surface has NEGATIVE affinity
• 2. Mesoderm has positive affinities for both ectodermal and endodermal cells-> 
• A. no repelling of mesoderm so gravitates toward center

• 1. Def: cell sorting influenced by thermodynamic principles
• 2. what this means:
• A. depending on what type of cells interacting, cells will either move centrally or peripherally
• B. hierarchy of interactions
• 3. ex/ 

• A. Pigmented retina cells (PRC) migrate internally to neural retina cells, (NRC)
• B. heart cells migrate internally to pigmented retina cells (PRC) —
• C. -> heart cells migrate internally to NRC
• 3. postulated by malcolm steinberg

• 1. differential adhesion hypothesis: sorting due to thermodynamics
• 2. smallest interfacial free energy: rearrangement into most thermodynamic, stable pattern
• A. this argument applies to this ex/ are A-A cell interaction stronger than A-B? will it be random mosaic of cells or associations of same cell types ?
• B. cells with greater cohesion interaction migrate CENTRALLY

• 1. what influences this:
• A. types (essentially quality)
• B. quantity 
• of ADHESION molecules 
• 2. major adhesion molecule-> cadhesions

• 1. def: calcium dependent adhesion molecules
• 2. role: critical for
• A.  establishing intercellular interactions 
• a. ex/ cadherin-catenin structures hold epithelial cells together
• b. ex/ Link and assemble the actin cytoskeleton, providing mechanical forces for forming sheets and tubes
• B. spatial organization of cell types
• C. serve as signaling molecules for cell's gene expression 
• 3. requirements: 
• A. must have Ca2+ in environment
• 4. structure:
• A. transmembrane proteins
• B. base that is attached in cell is called catenin
• C.

• 1. Two parts:
• A. motility
• a. 

• 1.motility: cell first has to be polarized. Has to happen before it moves thru ex. Matrix 
• BOTH have to reorganize actin cytoskeleton
• B. guidance
• a. epithelial: just the most outward cell (rest follow passively)
• 2. BOTH* require reorganization of the actin cytoskeleton

• 1. what :
• A. first stage of cell migration
• signals:
• a. where the cell needs to move
• b. reorganizes the cytoskeleton -> cell has front and back now

• 1. polarization: cell signals for where it needs to move and rearrangement of cytoskeleton
• 2. protrusion of the cell's leading edge: actin filaments polymerize, or forming long parallel bundles that creep out into the direction its moving
• 3. adhesion of cell to extracellular surface
• A. tool used: integrins
• a. where: on cell membrane
• b. what they do: connect ex. matrix w/actin cytoskeleton 
• 4. release of cytoskeleton in the rear, allowing cells to move forward

• 1. def: connections of actin and integrin on cell membrane
• 2. occurs during third phase of cell migration, (adhesion to ex. matrix)

• 1. regulated by cell-to cell signals
• 2. most commonly: 
• A. reciprocal interaction: 
• a. role: direct organ construction in multicellular organs

• 1. Def: a mostly reciprical interaction between 2 or more cells that have different histories and properties.
• 3. roles in induction process:
• A. inducer: tissue that produces signal 
• a. usually send out protein as paracrine factor (signal sent out into ex. matrix and influence only close neighbors)
• B. responder: the cell that receives signal and responds
• requires:
• a. receptor protein (like ears that can hear/absorb the message)
• b. ability to respond to signal (mouth or body to react to oral command)

Ability to respond to a specific inductive signal

• 1. significance: ex/ of induction signaling
• 2. how it works:
• Optic vesicles: 
• Cause: paracrine factors made by optic vesicles
• Effect: Head ectoderm is competent to respond and receive the paracrine factors (made by optic vesicles),
• ->AND head ectoderm has len proteins genes induced to produces lens
• Effect: -> lens secrete paracrine factors to induce optic vesicle to produce retina cells

• Overall: (-> = communication)
• 1. o.v. -> head ectoderm
• 2. head ectoderm: prod. lens
• 3. lens -> o.v.
• 4. o.v.: retina

• However, more to the story:
• former inducers to simplified version above
• 1. anterior ectoderm has already been induced before optic vesicles (still the overall inducer)
• 2. During gastrula: foregut endoderm + cardiac mesoderm -> (signal to) head ectoderm
• a. the foregut endoderm and cardiac mesoderm underlie the lens-forming ectoderm
• E: head ectoderm receives signal and produces TF otx2
• 3. in add'n, anterior neural plate->anterior ectoderm 's pax6 gene is induced
• **significance** pax6 giveshead ectoderm competence to respond to signals delivered by optic vesicle

• Overall: (-> = communication)
• -1: foregut endoderm and cardiac mesoderm-> otx2 tf by head ectoderm
• 1. o.v. -> head ectoderm
• A. p.f.'s fgf8 & bmp4 
• 2. head ectoderm: prod. lens
• A. head ectoderm in response to p.f.'s, ectoderm induces TF 's Sox and L-maf 
• B. -> these TF's induce lens production and crystallin gene
• *also side note anterior neural plate induced ect. to produce pax6 which also works w/ TF above to same goal
• 3. lens -> o.v.
• 4. o.v.: retina
• A. thx to lens' p.f.s, -> o.v. becomes optic cup-> outer layer of o.c. is outerlayer and neural layer

• 1. False!
• 2. ex/ optic vesicle induces the surface ectoderm to become a lens before the optic vesicle has become the retina

• 1. Outer layer: pigmented epithelium
• 2. Inner layer: perspective neural retina
• Now that lens induces the external tissue to be cornea
• E. Fibers fully differentiated

• 1. Instructive interactions:a signal from the inducing cell is necessary for initiating new gene expression in the responding cell (without inducer, responder is not capable of differentiating in that particular way
• ex/ optic vesicle: remove optic vesicle, lens does NOT start forming
• 2. permissive interactions: tissue already specified and just needs an environment allows expression of traits
• A. Ex/ just needs an environmental cue. Some are already induced but can’t do it until an extracellular matrix is formed.

• 1. ex/ epidermis (epithelial), dermis (mesenchymal)
• A. chick embryosL
• First: epidermis secretes proteins-> 
• Second: dermis (m.) forms condensations
• Third: condensed dermis secretes factors->
• Fourth: these signals cause epidermis to form region-specific cutaneous structures (what type of feather or scales)

–Condensed dermal mesenchyme responds by secreting factors that cause the epidermis to form regionally specific cutaneous structures (e.g., broad feathers of wing, narrow feathers of thigh, or scales and claws of feet)

• 1. regional specificity of induction (ex/ epidermis/dermis of chick embryo)
• 2. genetic specificity of induction: 
• Whereas the mesenchyme may instruct the epithelium as to what sets of genes to activate, the responding epithelium can comply with these instructions only so far as its genome permits
• ex/ salamander /tadpole swap of balancers/teeth. 
• A.: swapping of parts had frog like or salamander like parts, but since the genetic code has been swapped, the balancers and teeth aren't as defined as they usually would be.

• 1. soluble vs. insoluble: soluble inducers discovered by placing a filter between cells/tissues, and some mesenchyme/epithelial interactions can still occur
• A. exp. in 1970s
• B. not actual contact between cells when soluble, but necessary for insoluble

• 1. Def: Receptor,membrane protein interactions between adjacent cells
• 2. Requires:
• A. cell to cell contact

• proteins can diffuse over small distances to induce changes in neighboring cells (work in a range of about 15 cell diameters
• A. autocrine interaction: a type of paracrine interaction (the cell secretes a paracrine factor that self stimulates)
• 2. application to animals/organs:
• A. compact toolkit: many of the same proteins are used for various organs
• B. lots of homology of paracrine factors among metazoans: 
• 3. 4 major families:
• A. FGF (firbroblast growth factor) family
• B. Hedghog Family
• C. Wnt  family
• D. TGF-Beta superfamily
• 4. Goal: 
• A. regulation of TF
• B. change/regulation of cytoskeleton (cytoskeleton alteration/interaction can lead to cell migration)
• 5. signal transduction cascades: what p.f.'s cause intracellularly: a pathway of reactions

• 1. receptor: (almost like a hair and its follicle)
• A. extracellular, 
• B. transmembrane
• C. intracellular/cytoplasmic
• A. p.f. induces SHAPE change to receptor when it binds (p.f. is ex/ of a ligand)
• 2. travels through transmembrane region and then changes shape of cytoplasmic region of rec.
• ex/ of inducing cytoplasmic change:
• usually RTK (receptor tyrosine kinase): 
• uses ATP to phosphorylate specific tyrosine residues of particular proteins;

• 1. a type of paracrine factor
• 2. 2 dozen structural members
• 3. can induce two pathways:
• A.Activate RTK.
• a. the receptor tyrosine kinase is now called "fibroblast growth factor receptors" in this situation
• b. Jak-stat pathway

FGFR binds an FGF, the dormant kinase is activated and phosphorylates certain proteins

• The domains activate RAS -> activates GTP,
• GAP only has one transcription , SOS turns on Ras, and GAP turns Ras off.
• * A mutation of RAS, binding area changed, GAP can’t turn it off.
• (rtk patgway of fgf p.f.)

• 1. a pathway involved in the FGF family of p.f.
• 2. ex/s of this:
• A. milk production thru casein gene
• B. limb development
• C. differentiation of blood cells
• D. a. thanatophoric dysplasia 
• 3. Ripple effect of jak-stat pathway: 
• A. Jak proteins of enzymes in the cytoplasmic domain of receptor (stands for Janus-kinase)
• B. bound to receptor, when activated by receptor, Jak phosphorylates STAT family of TF
• C. Phosphorylated (activated) STAT TFs can enter the nucleus and bind to enhancers
• B.

• 1. induce changes in particular cells and distinguish tissue boundaries
• 2. must be complexed w/ cholesterol molecule
• 3. 3 Major groups of Drosophila hedgehog gene:
• A. Sonic hedgehog: the most abundant . 
• a.assures that motor neurons come only from the ventral portion of the neural tube
• b.  that a portion of each somite forms the vertebrae
• c. that feathers form in proper places, that pinkies are  always lateral-most digits
• B. Desert hedgehog: found in sertoli cells of testes
• C. Indian hedgehog: in the gut and cartilage and is important in postnatal bone growth-growth after birth
• 4. Important for (ex's)
• A. vertebrate limb development, neural differentiation, and facial morphogenesis
• B. CYCLOPIA if have two mutant alleles

• 1. NO transducer membrane involved
• 2. Hedgehog binds to "Patched" protein
• A. normal state of patched: normally inhibits smoothen protein.
• B. Smoothen protein role: control Gli protein
• C. Gli protein: when smoothen protein is inhibited, gli is attached to microtubules, and a fraction cleaves off and can travel to nucleus and act as a transcriptional repressor
• 3. when hedgehog  binds to "patched" protein, ->
• b. protein patched changes morphology, -> 
• c. patched no longer able to inhibit smoothen.->
• d. smoothen now active and cleaves Gli from microtubules->
• e. gli itself can no longer be cleaved, and ->
• f. gli cannot travel and become a repressor on the gene->
• g. the gene is EXPRESSED
• 4. Only amino-terminal portion of the protein is functional and secreted

• 1. both jak-stat in fgf pf
• 2. hedgehog pf

• 1. cyclops ex/
• 2. mutations that inactivate hedgehog pathway lead to malformations
• 3. mut. that activate it ectopically can lead to cancers
• 4.

• binds to active N-terminus of Sonic hedgehog,
• which is then able to fuse over a range of a few hundred microns (about 30 cell diameters); without this modification, Shh diffuses too quickly and dissipates into the surrounding space
• (essentially controls /stabilizes protein)
• **hedgehog protein is c

• 1. family of cysteine-rich proteins
• 2. ex/'s of:
• A. wing development in flies,
• B. establishing polarity of insect and vertebrate limbs,
• C. promoting proliferation of stem cells, and 
• D. several steps of the development of the mammalian urogenital system

• 1. β-catenin, or "follicle" part of a cadherin, is degraded normally by proteosomes
• A. How? gsk3 phosphorylates the β-catenin so proteosomes recognize it and degrade it.
• 2. ALso, 
• lef/tcf: binds to deacytelases so that chromatin condenses and cannot be transcribed
• A.**naturally does this, or inhibits. if signal cent through transmembrane receptor, then this will change to not inhibit anymore (an inhibitor inhibits another inhibitor!)
• 2. Separately, WNT contacts a cell->
• 3. receptors dimerize, either frizzled with disheveled or LPR5/6 w/axin and protein->
• 4. GSK3 can't phosphorylate B-catenins->
• 5. Beta catenins build up, -> β-catenin accumulates and enters the nucleus, where it binds to the LEF/TCF TF, displaces the histone deacetylase, and activates transcription
• 6 Non-canonical ways: 
• A. Wnt activates GTPase-> activates kinases-> phosphorylate cytoskeletal proteins-> cell shape altered
• B. receptor protein (Ryk?) activates a phospholipase (PLC)->
• PLC activates compounds that activate Calcium release from E.R.
• -> enzyme can release enzymes, tf's, translation factors

• 1. ex/s: regulating extracellular matrix formation and cell division
• 2. includes: 
• A. TGF-β family
• B. Nodal and activin families
• C. Vg1 family
• D. bone morphogenetic proteins
• a. has 7 cysteines in mature polypeptide
• E. Other proteins, such as glial-derived neurotrophic factor and anti-Mullerian hormone

• *use binding language*
• 1. TGF-B ligands bind to->
• 2. Type 2 receptor->
• 3. receptor binds to type 1 receptor->
• 4. Once in close contact, the type II receptor phosphorylates a serine or threonine on the type I receptor, thereby activating it
• 5. Type 2 rec. phosphorylates a Thr or Ser off of Type 1 rec.
• 6. Type 1 can now phosphorylate SMAD proteins
• 7. bind to smad4 and enter nucleus as TF
• (L, 2,1,2,1,smad4)

• 1. Def: Proteins from the inducing cell’s surface interact w/ receptor proteins of adjacent responding cells w/out diffusing from the producing cell
• 2. Types:
• A. Notch proteins
• a.(which bind to a family of ligands exemplified by the Delta protein)
• B. Ephrin ligands and Ephrin receptors
• a. ephrin on one cell binds with the eph receptor on an adjacent cell, signals are sent to each of the two cells (reciprocal signaling)
• b.

• 1. pathway of juxtacrine interaction
• 2. Notch:Acts like a tethered TF that is attached to the cell membrane
• 3. delta, serrate, or jagged protein activate a neighboring cell w/ notch protein on membrane.
• 4. once interaction occurs-> 
• conformational change of notch->
• cytoplasmic region OF NOTCH cleaved by presenilin-1 protease
• 5. Cleaved proteins enters nucleus and binds to a dormant TF of the CSL family, activating target genes
• **essentially notch/s, j, d protein interaction -> conformational change of notch-> cytoplasmic proteins cleaved by presenilin-1-protease-> cleaved proteins enter nucleus and act as tf's

• 1. also in organ formation such as kidneys and heart
• 2. and extremely important in the nervous system – binding of Delta to Notch in vert. and Drosophila tells the receiving cell not to become neural

• 1. insoluble space in between cells made of macromolecules secreted by cells
• 2. F(x)
• permissive:EM merely serves as a permissive substrate for adherence and migration,
• Active: in others it provides directions for cell movement or the signal for a developmental event

• 1. glycoproteins:
• A. critical for delivery of paracrine factors
• B. small protein, small amount of carbs attached to them
• 2. proteoglycans
• A. LARGE macromolecules!
• B. more than 50% carbohydrates
• 3. Fibronectin:
• A. large glycoprotein dimer
• B. road that leaves cells in final destination

• 1. integrates extracellular and intracellular matrices
• 2. Def: Receptors for EM molecules