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DEVELOPMENTAL BIOLOGY > Midterm 1 (Ch 1, 2, 3) > Flashcards

Midterm 1 (Ch 1, 2, 3) Flashcards

1
Q

what are the reasons you are you?

A
  • differentiation: one cell into 110 different cell types in humans
  • pattern formation: body parts in certain locations
  • morphogenesis: organization into ordered form
  • growth: cells know when to start and stop growing
  • reproduction: germ cells set aside very early in dev
  • regeneration: copy and regeneration (ex. skin cells (daily) liver ( yearly, with stem cell help)
  • environmental integration: ex-temperature affecting gender
  • evolution: all from the same tree of life but so diverse (DNA/proteins change over time)
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2
Q

what occurs in meiosis I?

A
  • homologous chromosomes are separated (reductional division 2n - n)
  • interphase (DNA replicates
  • early prophase I (DNA condenses
  • mid prophase I (mitotic spindles form)
  • late prophase I (nuclear envelope is broken down, chromosomes align in pairs and crossing over can occur allowing swapping of info on chromosomes)
  • metaphase (mitotic spindle attaches to chromosome pairs to separate them)
  • anaphase (chromosomes pulled to opposite poles)
  • telophase (cell is pinched into two separate cells each with own chromosome)
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3
Q

what occurs in meiosis II?

A
  • sister chromatids are separated
  • metaphase II (chromosomes line up in centre of cell)
  • anaphase II (chromosomes are pulled apart by centromeres being split)
  • telophase II (for new cells each have one copy of each chromosome (maternal and paternal))
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4
Q

what are the steps of the cycle of life?

A
  1. fertilization (meiosis (egg and sperm) n - 2n
  2. cleavage (one egg makes many cells)
  3. gastrulation (3 germ layers form: endoderm, ectoderm, and mesoderm)
  4. organogenesis: cells become what they’re final role is)
  5. metamorphosis/maturity (becomes sexually mature)
  6. gametogenesis (sex organs formed)
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5
Q

how is frog reproduction dependant on environmental influences?

A
  • they wait for signals to know that there’s been a change in photoperiod and temperature (no longer winter)
  • this triggers pituitary glands and frogs get their eggs/spren prepared (females release clutch of eggs and male’s sperm fertilizes them)
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6
Q

why is the blastocoel in the blastula important (early development)?

A

it allows cells to migrate into the middle through the blastopore

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7
Q

what do the two hemispheres of the egg look like?

A
  • animal hemisphere: darker pigment contains blastocoel (smaller cells b/c they can divide faster)
  • vegetal hemisphere: white, yolky, thicker/dense (more difficult to divide)
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8
Q

what happens immediately after an egg has been fertilized?

A
  • the outside of the egg goes through a 30 degree cordial rotation
  • allows vegetal and animal to mesh together in one area
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9
Q

where does gastrulation begin in xenopus (germ layer formation)?

A

-180 degrees from where sperm entered the egg

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10
Q

in xenopus, how many cells are made in the first 48 hours after fertilization?

A

-around 37,000 cells

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11
Q

why is the egg so large?

A

-it doesn’t change in size during cleavage

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12
Q

what is the endoderm germ layer a precursor for?

A
  • gut and respiratory system

- first is archenteron

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13
Q

what is the ectoderm a precursor for?

A
  • epidermis, brain, and nerves

- first becomes neural folds/ neural tube

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14
Q

what is the mesoderm a precursor for?

A
  • connective tissue, muscle, dermis, blood, heart, skeleton, gonads, and kidneys
  • first becomes blood vessels, somite, notochord
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15
Q

what is spina bifida and what are the types?

A

-birth defect that happens when a baby’s backbone does not form normally
Occulta: gap in spinal processes but spinal cord is unaffected
Meningocele: gap in spinal processes and meninges and cerebrospinal fluid comes through
Myelomeningocele: cerebrospinal fluid, meninges and neural tissue is out of place

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16
Q

how can you identify the dorsal end on invertebrates in early dev?

A

-locate neural folds that form CNS

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17
Q

what is the fertilized egg called after gastrolation?

A
  • a neurula
  • mesoderm: notochord, somite, and blood vessels
  • ectoderm: neural tube and epidermis
  • endoderm: contains archenteron
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18
Q

how can spina bifida be prevented?

A

folic acid: synthetic from of falcate that helps RBC’s and other cells male sure they have enough DNA and RNA and that everything is working properly

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19
Q

what affects how a cell will differentiate?

A

the environment they’re in, what other cell types are around them and their general location

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20
Q

what can somites become?

A
  • though they are mesoderm, they can become vertebrae, ribs, and muscles of the back
  • they are located along the spine in pairs in dev
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21
Q

what initiates xenopus metamorphosis?

A

-hormones from tadpole thyroid gland

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22
Q

what happens during xenopus metamorphosis?

A
  • organs get modified
  • hind and forelimbs differentiate
  • tail recedes
  • cartillaginous skull becomes bone
  • teeth change shape
  • fly-catching tongue muscle developes
  • intestine shortens (herbivore to carnivore)
  • gills turn into lungs
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23
Q

what are the two major parameters of determining cleavage pattern?

A
  1. amount and distribution of yolk protein in cytoplasm

2. factors in egg cytoplasm that influence angle of mitotic spindle and timing of its formation

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24
Q

what are the two types of cleavage?

A
  • meroblastic: incomplete

- holoblastic: complete

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25
Q

what are the two types of mesoblastic cleavage?

A
  1. centrolecithal: yolk is in the centre of the egg (usually insects)
    - syncytial embryo formed where nuclei are replicated but don’t have their own membranes (form membranes after moving to outside of embryo)
  2. telolecithal: dense yolk through most of cell (usually fish, reptiles, birds)
    - discoidal cleavage where dev happens on top of yolk (divisions only in animal pole)
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26
Q

what are the two types of holoblastic cleavage?

A
  1. bilateral: evenly dispersed sparse yolk (tunicates)
  2. mesolecithial: moderate vegetal yolk disposition (amphibians)
  3. rotational evenly dispersed sparse yolk (mammal)
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27
Q

what is the definition of gastrulation?

A

movement of blastomeres of embryo relative to one another resulting in formation of three germ layers
-sets up cells for rest of dev

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28
Q

there are many types of cell movement during gastrulation, what are they?

A
  • invagination: infolding of a sheet of cells (ex. sea urchin endoderm)
  • involution: inward movement of expanding outer layer so it spreads over surface of other cells (amphibian mesoderm)
  • ingression: migration of indiv. cells from the surface into embryo interior which becomes mesenchymal and migrates individually (ex. sea urchin mesoderm)
  • delamination: splitting one cellular sheet into two or less parallel sheets resulting in formations of new epithelial sheet of cells (ex. hypoblast formation in birds/mammals)
  • epiboly: movement of epithelial sheets spreading as one unit to enclose deep layers of embryo (ex. ectoderm formation in sea urchins, truncates, and amphibians)
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29
Q

who discovered the three germ layers?

A

christian pander

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30
Q

what can fate maps help us understand about morphogenesis and dev. in general?

A
  1. direction and number of cell divisions
  2. cell shape changes
  3. cell migration
  4. cell growth
  5. cell death
  6. changes in composition of cell membrane or secreted products
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31
Q

who made one of the first fate maps and what was it of?

A
  • Edwin Conklin
  • tunicate fate map
  • helped find out endoderm (yellow) became muscles in larva of tunicates
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32
Q

how can we determine a cell fate?

A
  • vital dye staining: tracks individual cells in a embryo

- we used to use agar chips with dye (1929) but now we can use green fluorescent dyes to inject into embryos

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33
Q

what is an epithelial cell?

A

-tightly connected cells in sheets or tubes

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34
Q

what is a mesenchymal cell?

A

-independent or loosely associated cells that operate as independent units

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35
Q

what is the epithelial to mesenchymal transition (EMT)?

A

an epithelial cell loses cell polarity and cell-cell interactions and gains migratory and invasive properties to become mesenchymal

  • good during dev- ingestion to form mesoderm
  • bad during adulthood- could allow cancerous cells to migrate

note: MET happens too

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36
Q

what is the 1980’s example of chimeric graft experiments?

A

-cells from quail embryo were added to exact same spot on chick embryo (these cells will undergo EMT)
results:
-from small neural tube section: chick was white with a black mid region
-from overlying neural crest cells: chick was all white with a black head
-from larger section of neural tube: chicks were mostly black
conclusion:
neural crest cells become melanocytes by migration (EMT and back to E)

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37
Q

what is piebaldish condition?

A
  • condition where KIT gene causes of different phenotype
  • KIT is responsible for making tyrosine kinase that’s important for signalling and melanocyte dev.
  • a mutation in it creates patches of skin and hair without melanocytes
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38
Q

other than becoming melanocytes, what other important things to neural crest cells do?

A
  • make gut neutrons (discovered by fate mapping with GFP)

- dev. into pharyngewal arch cells in vertebrate heads (Heinrich Rathke- 1820’s)

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39
Q

how are some groups of organisms discovered to have relationships?

A

-common embryonic or larval forms (shoes relatedness to other animals)

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40
Q

what are von Baer’s laws of vertebrate embryology?

A
  1. general features of a large group of animals appear earlier in dev. than do the specialized features of a small group (all vertebrates similar from start until differentiation)
  2. less general characters develops from the more general, until finally the most specialized appear
  3. the embryo of a given species, instead of passing through the adult stages of lower animals, departs more and more from them
  4. therefore, the early embryo of a higher animal is never like a lower animal but only like its early embryo
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41
Q

what do all invertebrates initially have in common?

A
  • gill arches
  • notochord
  • spinal cord
  • primitive kidneys
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42
Q

what is the phylotypic stage?

A

-all vertebrate embryos look most similar (after this they specialize)

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43
Q

what are the common homologous structure shared by a human arm, a seal limb, a bird wing, and a bat wing?

A
  • hand/wrist/fingers
  • radius
  • ulna
  • humorous
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44
Q

what is an analogous structure?

A
  • trait not gained from common ancestor, instead was gained down the line
    ex. bird wing and bat wing:
  • common ancestor did not have flying trait
  • lineage derived to bats (mammals) and birds (avian) and the flying ability developed separately
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45
Q

what happens in a mouse embryo that does doesn’t in a bat to allow it to have wings?

A
  • day 14: mouse loses cells between digits to develope fingers (apoptosis of these cells)
  • bats cells between digits don’t undergo apoptosis
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46
Q

why do daschounds have short legs?

A

-extra copy of Fgf4 tells cartilage precursor cells to start differentiating and stop growing

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47
Q

how could you selectively breed a daschound to have long hair?

A

-mutated Fgf5 that doesn’t tell cells to stop growth of hair

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48
Q

what are choanoflagellates?

A
  • thought to be common ancestor of all animals
  • have loosely associated cells
  • made of rosettless (protein that is leptin-like and is important for signalling and adhesion- can up regulate cadherins of other moleculrs to hold cells together)
  • collonial theory is that this is how multicellular organisms evolved-tighter and tighter associations of molecules)
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49
Q

what are malformations?

A

-abnormalities caused by genetic events

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50
Q

what is a syndrome?

A

-two or more abnormalities occurring together

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51
Q

what is a teratogen?

A
  • exogenous agents that produce developmental abnormalities (teratogenesis)
    ex. thalidomide (causes degrading of transcription factors by binding to specific enzyme complex, babies were born with extreme limb abnormalities
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52
Q

how can malformations help us study development?

A

-helps us study that genes are supposed to be doing by seeing what they aren’t doing

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53
Q

a zygote is totipotent, what does this mean?

A

-can produce an entire organism (no specific cells)

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54
Q

a blastula is pluripotent, what does this mean?

A

-any cell could be any type of cell in the body but couldn’t become placenta

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55
Q

a gastrula is multipoint, what does this mean?

A
  • can differentiate into specific types of cells

(ex. ectoderm that could become skin or neutron of brain)

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56
Q

what does it mean when a cell is unipotent?

A

-differentiated as one cell, can’t go back and become anything else

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57
Q

what is cell differentiation?

A

process by which a cell acquires structural and functional properties unique to a given cell type (can have different gene expression depending on cell)

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58
Q

what is a differentiated cell?

A

-a cell that can’t divide and developed specialized structural elements and distinct functionals properties (it expresses specific set of genes)

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59
Q

what is commitment during dev?

A

-a cell that has become programmatically restricted even though it is not yet displaying overt changes in cellular biochem and function

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60
Q

what are the steps a cell takes to become differentiated?

A
  1. unspecified
  2. specification (can be changed if environment supports a diff cell type)
  3. determination (won’t switch to a diff type, no going back)
  4. differentiation
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61
Q

what are the three types of specification?

A
  1. autonomous: transcription factors localized in cytoplasm and are inherited by cells containing that cytoplasm
  2. conditional: cells influenced by neighbours, paracrine factors from one cell are received by another cell and activate TF’s in that cell (doesn’t reach far away about 20 cells)
  3. syncytial: TF’s form gradients within a large cell that contains many nuclei, nuclei express gene depending on ratios of these TF’s (happens in Drosophila)
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62
Q

what is the gene that regulates muscle cells in tunicates (forms the yellow crescent early in development that turns into muscle)

A

-macho gene

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63
Q

what is the basic strategy in dev bio for showing that a particular entity regulates a particular trait?

A
  1. find it (ex. macho mRNA is found in the right places in the cytoplasm for forming muscles)
  2. lose it (ex. degrading macho mRNA (with antisense mRNA’s) blocks the production of muscle cells)
  3. move it (ex. expressing macho mRNA in other cells converts them into muscle-forming cells)
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64
Q

what does what a cell becomes depend on its position in the embryo?

A
  • fate is determined by interactions with neighbouring cells

- physical property in cell environment at specific spots (mechanical stress)

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65
Q

what was Roux’s attempt to demonstrate autonomous specification in frogs?

A
  • used a hot needle to kill one cell in the 2 cell stage of dev
  • in the neurula stage, only half an embryo was formed
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66
Q

what was Driesch’s demonstration of conditional specification in sea urchins?

A
  • took a fertilized cell stage and separated the 4 into 4 single cells
  • they each went on to become full plates larva
67
Q

what did Driesch conclude from his experiment on the sea urchin embryo?

A
  1. prospective potency of an isolated blastomere is great than blastomeres actual prospective fate
  2. cell interation is critical for normal dev. and if each blastomere can form all embryonic cells when isolated, community of cells must prevent it from doing so
  3. fate of nucleus depended solely on its location in embryo
68
Q

a drosophila has a syncytial blastoderm, what is this like?

A
  • combination of conditional and autonomous
  • early on its mostly autonomous because TFs across developing embryo are present producing anterior and posterior axis of blastoderm
  • dipolid egg goes through cleavage but down go through cytokinesis (syncytium forms)
  • at cycle 10 of cleavage nuclear migration occurs
  • at cycle 13, global wave of nuclear divisions occurs and nucei use centrosomes to space out so they get enough TFs and other morphogens
  • at cycle 14 nuclei become individual cells and whole cell can now divide
  • TFS get trapped in cells when they get indiv membranes and that decides cell fate
69
Q

what is a morphogen?

A

a diffusible biochemical molecule that can determine fate of a cell by their concentrations

  • ex. high expression of bicoid (head) at anterior end and high expression of caudal
    (tail) at posterior end
70
Q

how do you make a developmental landscape of cell fate maturation?

A
  • get embryos of different stages
  • dissociate cells of embryos into single cells
  • run single cells with RNA released and reverse transcribe into cDNA
  • sequence ds cDNA
  • look at gene expression of RNA in space
  • 4 hours post fertilization: 4277 cells, cleavage has occurred (most epiblast)
  • 8 hpf: finished gastrulation (germ layers present)
  • 10+: organogenesis and neurulation
  • cells in space are organized and colour coded
71
Q

what do enhancers do?

A

-help the genes be expressed at the right place and time

72
Q

what elements are involved in the proximal region at transcription?

A
  • RNA pol II
  • general TF’s
  • other proteins
73
Q

what does a transcription factor do ?

A

-help guide the ay for specific cell types to become the right cell at the right time

74
Q

what is the hemoglobin of embryos made up of? what about when placenta forms? birth?

A

-2 zeta and 2 epsilon globin
proteins
-when placenta forms baby gets oxygen from maternal blood stream, baby has 2 alpha and 2 gamma
-once baby is about to be born, it has adult version 2 alpha and 2 beta

75
Q

what regions controls this change in the globins of the blood during embryonic dev?

A

-locus control region controls the expression of different types of globin

76
Q

what is genomic equivalence?

A

-each somatic cell nucleus has the same chromosomes or set of chromosomes

77
Q

what is differential gene expression?

A
  • DNA of all differentiated cells are identical
  • the unused genes are not destroyed or mutated
  • only a small amount of the genome is expressed for each cell
78
Q

what is the evidence of genomic equivalence?

A
  • giemsa dyes: different types of cells were dyed and they all had the same banding patterns
  • nucleic acid hybridization: probing for specific genes in DNA
79
Q

polytene chromosomes occur in drosophila, what are they?

A
  • chromosomes that replicated many times but stuck together

- the banding of the DNA doesn’t change but puffs are present on chromosomes where they is lots of active transcription

80
Q

how was the sheep cloning experiment carried out to make Dolly?

A
  1. eggs (n) were removed from a Scottish Blackface sheep and udder cells (2n) were removed from a Finn-Dorset
  2. eggs were enucleated and udder cells (was determined) were transferred into them
  3. they were fused together
  4. the embryo was cultured for 7 days and a blastocyst formed
  5. the egg was placed back into the surrogate mother
  6. mother gave birth to a Finn-Dorset (Dolly)

-experiment showed that genome of one cell had the ability to make an entire organism

81
Q

in what ways can gene expression be regulated?

A
  1. transcription
  2. RNA processing
  3. transport out of nucleus
  4. translation
  5. protein modification
82
Q

what is chromatin?

A

-complex of DNA and protein in which eukaryotic genes are contained

83
Q

what is a nucleosome?

A

-basic unit of chromatin structure composed of an octamer of histone proteins: 2(H2A, H2B, H3, and H4)

84
Q

what is histone?

A

-positively charged proteins that are the major protein component of chromatin

85
Q

what is the difference between heterochromatin and euchromatin?

A
  • hetero: condensed (no gene expression)

- eu: open (chance gene will be expressed)

86
Q

how are histones associated with DNA?

A
  • 147 bp are lopped twice around each histone octamer

- 60-80 bp of DNA link the nucleosomes

87
Q

what is the function of the H1 histone?

A

holds DNA in place, not part of the octomers

88
Q

how many points of contact is there between DNA and histones in one nucleosomes?

A

14

89
Q

what are the histone tails?

A

part of the protein that sticks out and can be modifed to make the nucleosome condensed or uncondensed

90
Q

what does it mean when the histone tails are mostly methylated?

A

-nucleosome is condensed (condensed chromatin)

91
Q

what does it mean when the histone tails are largely acetylated?

A

uncondensed (nucleosome, chromatin)

92
Q

what amino acid of histone can be acetylated?

A

lysine

93
Q

why are nucleosomes (and residue a.a.’s) and DNA loosely associated?

A

-nucleosome is positively charged, DNA is negatively

94
Q

why does the chromatin become decondensed when histone is acetylated?

A
  • lysine no longer has positive charge so DNA and nucleosomes compel
  • proteins are recruited to keep things open
95
Q

why does the chromatin become condensed when histone is methylated?

A
  • positive charge of nucleosome stays

- proteins are recruited to condense the chromatin

96
Q

what do general TF’s do?

A

-help recruit and activate RNA pol at every promoter

97
Q

what TF’s are at the TATA box promoter?

A

-basal TF (TATA-box binding protein saddles DNA to recruit RNA pol II)

98
Q

what is the mediator complex?

A

-large multimeric complex of about 30 protein subunits that in many genes is link that connects RNA pol II to enhancer sequence (forming pre-initiation complex)

99
Q

what stabilizes the mediator complex?

A

-cohesin (promoter, enhancer, and mediator connection)

100
Q

what does the mediator complex interact with?

A
  • general TFs
  • TF’s
  • chromatin remodelling complexes
  • histone modifers
101
Q

what do enhancers do?

A
  • signal where and when a promoter can be used and how much gene product to make by binding to TFs
  • controls efficiently and rate of transcription from specific promoter
102
Q

how to TFs help regulate gene expression at enhancers?

A
  1. recuit enzymes (Histone Acetyl Transferase, Histone Deacetlylase, Histone Methyl Transferase, Histone Demethylase)
  2. form bridges, lopping chromatin such that TFs on enhancers can be brought in vicinity of promoter
103
Q

why does a bridge form between the enhancer and promoter region of DNA?

A
  • links the two by protein on enhancer binding to other TFs

- allows transcription of genes to begin and for gene to be tightly regulated

104
Q

what is an alternative option for enhancer and promoter to be connected instead of using the bridge?

A
  • use of mediator
  • at enhancer site, TFs bind with mediator and bring enhancer close to transcription site
  • this way to connect enhancer and promoter can be useful when two enhancer sites use same promoter region (take turns using mediator to connect to promoter and mRNA gets expressed)
105
Q

what does Pax6 do?

A
  • master regulator that helps turn on a lot of genes downstream
  • has many enhancer sites in diff parts of the body so correct TFs are important
106
Q

what are two ways to dye genes to see when they are expressed?

A
  • GFP

- B-gal

107
Q

what is silencer repressing gene transcription?

A
  • makes sure genes aren’t turned on at wrong time and place
  • uses Neural Restictive Silencer Element (NRSE) that binds to neural restrictive silencer factor (NRSF) found in every cell that’s not a mature neutron
108
Q

what features do TFs have?

A
  • DNA-binding domain: to recognize enhancer region
  • protein-protein binding domain: allows a protein to recognize another protein and form a dimer
  • trans-acting domain: carboxy termini recruits other TFs to same site
109
Q

cells must have on/off memory, what is this?

A

-way for cell to remember specific gene expression signature after transcription regulators disappear and as cell replicates

110
Q

what two proteins maintain on/off memory?

A
  1. trithorax group proteins

2. poly comb group proteins

111
Q

where were the TrxG and PcG first discovered?

A

in drosophila (when absent, the anterior to posterior axis was messed up)

112
Q

what do the trithorax proteins do?

A
  • maintain gene expression (on)

- H3K4 for example activates marks on nucleosome or chromatin remodelling

113
Q

what do the polycomb proteins do?

A
  • silence gene expression (off)
  • PCR1 is maintenance
  • PCR2 is HMT activity (H3K27 and H3K9 help shut down regions)
114
Q

what are pioneer TFs?

A
  • can penerate repressed chromatin to open up compact chromatin
  • ex. FoxA1 and Pax7
115
Q

what are silencer TFs?

A

-DNA recognize elements that actively repress transcription of a particular gene (NRSE)

116
Q

what do insulator do?

A
  • sequences that limit range in which an enhancer can activate gene expression
  • ex. if a PcG and a TrxG are too close, insulator puts a wall up between them called a CTCF boundary (increased CTCF, cohesion, H2A.Z and H3K4)
117
Q

what happened in 2006 that was a break through for understanding chromatin?

A
  • 4 pioneer TF were expressed (Yaminaka proteins) using mouse fibroblast cell infected by a virus
  • some of the cells that went back to an induced pluripotent stem cell (iPSC)
  • this means that fibroblastic cells could be taken, reverted to stem cells, then into any type of cell by yaminaka factors
118
Q

what nucleotides can be methylated in chromatin?

A

-any C followed by a G can be methylated (5’ to 3’)

119
Q

what are CpG islands?

A
  • regions with high frequency of CpG sites
  • at least 200 bp
  • GC % over 50
  • observed to expected CpG ratio grater than 60%
120
Q

what is a high CpG content promoter?

A
  • much greater than 50% GC and 60% o-e CpG
  • usually found in dev control genes and house keeping genes that need to be on (70% of genes are high CpG content)
  • default is on and must be actively repressed (poly comb groups recruited for this)
121
Q

what is a low CpG content promoter?

A
  • genes expressed in mature cells (ex. TATA box promoters)
  • default is off and must be actively turned on
  • more regulated and controlled - helps differentiate between cell types later on
122
Q

how is chromatin regulated in HCPs?

A

early in dev:

  • rich in general TF which protect CGI from methylation
  • CpG rich region promotes H3K4me3 which promotes active genet transcription
  • GC rich regions promote H3K27me3 that promotes the poised state of genes - could be turned on later
123
Q

how is chromatin regulated in LCPs?

A

early in dev:

  • default is off
  • CpGs present have methyl groups and few histone modifications
  • TFs come in if genes need to be turned on
  • under tight regulation
  • differientially expressed with enhancers
124
Q

when a CpG is methylated, what does the gene do?

A
  • is inactive and not transcribing

- happens at promoters and enhancers

125
Q

what does methyl CpG binding protein 2 do?

A

-uses its binding pocket to recognize methyl groups on cysteine and recruits proteins like histone deacetylase (removes acetyl groups (active markers)) and histone methyltransferase (adds methyl groups to histone tail to mark for inactive)

126
Q

how is gene expression inhibited by DNA methylation?

A
  1. blocks binding of TF’s to enhancers and promoters

2. methylated cytosine recruits binding of proteins that facilitate methylation (H3K27me3) or deaceltylation (MeCP2)

127
Q

what are the two proteins responsible for adding methyl groups?

A

dnmt3: shut off gene expression in an area (de novo)
dnmt1: maintains methylation as cell copies

128
Q

how does the methylation affect embryos globin?

A
  • epison globin is transcribed and promoter is unmethylated (gamma is methylated (off)) in first 6 weeks
  • at 12 weeks, gamma is unmethylated and Epison promoter is methylated (by HDAT, HMTK27me, PRC2-1, dnmt1 and dnmt3)
129
Q

how do you turn a gene from off to on?

A

-remove methyl groups from DNA and add acetyl groups to histones

130
Q

what are the features of active chromatin?

A
  • no DNA methylation
  • acetylated histones
  • H3K4me3
  • RNA pol II and GTF bound to promoter
  • TrxG (if gene needs to remain active)
131
Q

what are the featured of repressed chromatin?

A
  • DNA methylation
  • little to no acetylation
  • H3K27me3 or H3K9me3
  • no TFs
  • PcG (if needs to remain repressed)
132
Q

what are the features of poised-bivalent state?

A
  • low to no DNA methylation
  • both H3K4me3 and h3K27me3 (HCP)
  • H3k4me2 (LCP)
  • many have RNA pol II bound and poised but not actively transcribing
133
Q

what are the specific imprinted marks on a genome?

A
  • methylation specific pattern (can be found on sperm and egg)
  • expressed in a parent-of-origin manner where cis-acting DNA methylation at imprinting control regions
134
Q

lgf2 is imprinted in the genome and is different for egg and sperm, how?

A

EGG:
-CTCF insulator proteins and bound to DMR (differentially methylated region)
-no methlyation
-wall prevents TFs from activating lgF2 but can activate H19 in front of the wall
SPERM:
-DMR is methylated, CTCF can’t bind
-TFs can transcribe lgf2

135
Q

what modifications get done post-transcription to control gene expression?

A
  1. differiential RNA processing/splicing (gene can be turned on but maybe spliced differently to express diff things)
  2. translational control (gene may be transcribed but not translated)
  3. cytoplasmic location (sequestering in diff locations in cell until needed)
  4. post translational mods (not active until something is added
136
Q

what is the job of the splicosome?

A

-recog where introns/exon boundaries are and where or not it should skip exons as well or keep them in

137
Q

what is a splicing enhancer?

A

a sequence that promotes recognition and use of splice site (exon is kept in and used)
-there are exonic and intronic ones, both recruit splicosome

138
Q

what is a splicing silencer?

A

sequence that reduces recognition and use of splicing site (exotic and intronic ones that both block splicosome)

139
Q

what are ways you can control translation?

A
  1. protect the mRNA for later use (increase its half life by making it more stable)
  2. storing the mRNA (protects it until needed?
  3. ribosomal selectivity (pick the mRNAs they want translation)
  4. micro RNAs (regulate mRNAs by block them from translation, gets rid of mRNAs that aren’t needed anymore)
140
Q

iron levels in the blood are regulated by post-translational control, how?

A
  • the level of iron in the blood dictates which of the two genes of iron response element are translated
  • high levels: iron-response element binding protein is inactivated, ferritin is translated which helps sequester iron
  • low levels: IRE-BP is activated and bind in the 5’uTR to block ferritin, IRE-BP binds to 3’uTR of transferritin (transfer iron to cells) to stabilize it so it can be translated
141
Q

what does the maternal stored mRNA that gets past down to the embryo have that will be needed for cleavage?

A

-histone, actin, tubulin, cyclins (cell div), and proteins to dictate cell fate

142
Q

how is the maternal mRNA stored and when does it get triggered to be used by the embryo?

A
  • mRNA is circularized (uses maskin, cap with cap BPs, and CPEB link from 5’ to 3’)
  • triggered by fertalization
143
Q

what is ribosomal heterogeneity?

A

in different tissues the ribosome will have a different composition and mRNA preference

144
Q

what is an example of ribosomal heterogeneity with ribs?

A
  • in the wild type: translation of Hox mRNAs are recognized by a specific ribosome with RPL38
  • in mutant: the right RNA is not expressed in the tissue so there’s less expression of Hox mRNAs which results in an extra set of ribs
145
Q

what are microRNAs?

A
  • regulate about 50% of protein-coding genes (about 1000 of them)
  • transcribed from the genome but not translated
  • made from long precursors but then cut into 22 nt long
146
Q

how do microRNA regulate translation?

A
  1. binding can block initiation or termination of Tl
  2. can recruit endonuclease that digest mRNA (3’ end) or decap the mRNA (useful in dev so zygotic miRNA can turn of maternal RNA and start using its own)
147
Q

how are siRNAs different from miRNAs?

A
  • si has specific target that is a perfect match and degrades
  • mi can bind to many RNA
148
Q

what is the function of the cytoskeleton?

A

-cell shape and support

149
Q

what is the function of actin filaments and microfilaments?

A

-tracks for myosin motors

150
Q

what is the function of intermediate filaments?

A

-mechanical support for plasma membrane

151
Q

what is the function of microtubules?

A

-tracks for kinesins and dyneins?

152
Q

how can anchoring help localize mRNAs in cytoplasm so the right genes are expressed in the right area?

A
  • anchor proteins localize specific mRNA to one area of the cell and the free mRNAs can diffuse away but as they get further from where they are anchored, there is much less of them
    ex. Oskar anchor localizes nanos RNA to the anterior end of the cell and helps translate it
153
Q

what is localized protection?

A

-protector protein complex bind to correct mRNA to protect it from being degraded by complexes like deadenylase complex

154
Q

what techniques can you use to find specific genes for “find it, lose it, move it”?

A
  • in situ hybridization
  • chromatin immunopreciption
  • deep sequencing: RNA-seq
155
Q

what techniques can you use to lose or move specific genes to help discover function?

A
  • CRISPR-Cas9
  • GAL4-UAS
  • Cre-Lox
156
Q

what is an example of the use of in situ hybridization in preserved cells?

A
  • to find the odd-skipped gene expression, antisense RNA that’s complementary to odd-skipped gene is added that contains DIG-conjugated probe on Uracils (and alkaline phosphatase and NBT/BCIP)
  • so when the antisense binds to the RNA of the perserved cell it turns blue
157
Q

what is an example of in situ in live cells?

A

-cells expressing GFP under the same conditions the normal gene is expressed

158
Q

how does ChIp-Seq work?

A
  • locates the site of the TF binding to DNA or identify modified nucleosomes by using an antibody specific to TF or modifier histone being studied
  • crosslimk to get proteins, attached DNA gets stuck there, antibody is added, precipitation and purification, sequence genome or do PCR
159
Q

how does deep sequencing work?

A

-sequencing what RNA transcripts are being produced at a certain time and place by collecting RNA, making cDNA, sequencing it to find what transcripts are on

160
Q

what is the function of Cas9?

A

-cuts DNA

161
Q

what is gRNA?

A

-guide RNA used to recognizer specific target gene when preforming CRISPR (gets added to cell often as a vector)

162
Q

how do Cre-Lox and GAL4-UAS work?

A
  • Cre-Lox: cutting out needed exons

- GAL4: having different genes be expressed at wrong place

163
Q

what did Jeffrey Hall, Rosbach, and Michael Young discover?

A
  • circadian rhythm: transcriptional regulation

- “molecular clock” first discovered in Drosophila

DEVELOPMENTAL BIOLOGY (2 decks)

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