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CMMB 403 > Midterm > Flashcards

Midterm Flashcards

1
Q

MeCP2

A

the protein which this gene codes for binds methylated cytosine residues. It recruits histone deacetylases (which remove acetyl groups from the histones) or methyl transferases (which add methyl groups to histones)
BOTH repressing gene expression!

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2
Q

histone acetyltransferases

A

HATs - These add acetyl groups onto histones. This PROMOTES GENE EXPRESSION because the positive charge on the lysine residue is neutralized by the acetyl group and thus does not bind tightly to the negatively charged DNA - loosens the DNA

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3
Q

histone methyltransferases

A

Transfer methyl groups onto histones

- this usually represses gene expression

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4
Q

histone deacetylases

A

Remove acetyl groups from histones

This represses gene expression.

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5
Q

Rett Syndrome

A

Debilitating neurological disorder in females. Mutation of the MeCP2 gene which lies on the X chromosome.
The gene is haploinsufficient. So men who have mutated MeCP2 gene will die before being born.

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6
Q

Where is the Pax6 gene expressed?

A

lens, cornea, retina, in the neural tube, and in the pancreas

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7
Q

Blastomere

A

The cell of any cleavage stage embryo

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8
Q

neurula

A

Name from an embryo that has a neural tube forming (we won’t use this term for mammals)

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9
Q

meroblastic cleavage

A

when the entire egg is NOT cleaved into cells (ie. some is cleaved into something else)

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10
Q

holoblastic cleavage

A

the entire egg is cleaved into cells (so the entire egg becomes part of the embryo - minus any extracellular material)

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11
Q

What does specification mean?

A

When a cell is committed to a given fate, but this commitment can still be reversed. In this stage, a cell will differentiate along a certain path (unless the signaling or environment changes).

  • In this stage, a cell can differentiate autonomously (by itself) into a specific cell type in a neutral environment
  • This is the only stage of commitment where the fate of the cell can be changed
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12
Q

What does determination mean?

A

The stage of cell commitment where its given fate is irreversible. Changing the environment will no longer have an effect on what the cell differentiates into.
- When a cell can differentiate autonomously AND its fate cannot be reversed from signals.

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13
Q

What does differentiation mean?

A

Development into a specialized cell type. At this stage, the cell is overtly of a certain type at a biochemical and functional level
- See literal changes to the cell function here

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14
Q

Autonomous specification

A

Blastomeres acquire determination factors from the egg cytoplasm

  • They have some factor within the cytoplasm that specifies them towards a certain fate.
  • A mode of cell commitment in which the blastomere inherits a determinant, usually a set of TF’s from the egg cytoplasm, which regulate gene expression to direct the cell into a particular path of development
  • tunicates
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15
Q

Conditional Specification

A

Embryonic cells are specified by external signals from their neighbouring cells.

ex. Removing cell from 4 cell embryo - each piece will develop fine because they are conditionally specified and thus their fate hasn’t been internally determined yet.
- The ability of cells to achieve their respective fates by interactions with other cells. (paracrine factors)

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16
Q

What type of tissue is the notochord derived from?

A

The mesoderm. The notochord later develops into the vertebral column.

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17
Q

Epithelial to mesenchymal transition (EMT)

A

Transition of cells from an epithelial sheet to individualized migratory cells. This is important in developmental processes and cancer.

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18
Q

Invagination

A

Type of cell movement during gastrulation (formation of 3 germ layers)

  • In folding of sheet of epithelium of cells. Indentation of a ball. Cells are entering inside the embryo without contacting the outside layer
  • Neural tube originally forms from this process
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19
Q

Involution

A

Inward movement of an expanding outer layer so that it spreads over the internal surface of the remaining external cells. Outer layer becomes inner layer - outer and inner in contact.
migration of sheet of cells

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20
Q

Ingression

A

Migration of individual cells from the surface of the embryo’s interior. Individual cells become mesenchymal (separate from one another) + migrate independently. These cells will become meso- and endoderm in mammals

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21
Q

delamination

A

splitting of one cellular sheet into two more or less parallel sheets. End result is formation of a new additional epithelial sheet of cells.

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22
Q

epiboly

A

movement of epithelial sheets (usually ectodermal) spreading as a unit to close deeper layers of the embryo. Can occur by cells dividing, cells changing their shape, or by several layers of cells intercalating into fewer layers.

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23
Q

What tissues are derived from the ectoderm?

A

Epidermal (skin) cells, nervous system, neural crest, pigment cells

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24
Q

What tissues are derived from the mesoderm?

A

Connective tissue, notochord, red blood cells, bone and muscles
kidneys, gonads

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25
Q

What tissues are derived from the endoderm?

A

Digestive tube (gut), stomach cells, pharynx, thyroid, lungs, inner linings

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26
Q

What is syncytial specification?

A
  • Predominates in most insect classes
  • Specification of body regions by interactions between cytoplasmic regions prior to cellularization of the blastoderm
  • Variable cleavage produces no rigid cell fates for particular nuclei
  • After cellularization, both autonomous and conditional specification are seen
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27
Q

Syncytium

A

A cytoplasm containing multiple nuclei. Cell membranes haven’t formed around nuclei

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28
Q

Morphogen

A

A long range signaling molecule that forms a concentration gradient in the specification/determination of the cell depends on the concentration of the molecule
Nuclear genes are differentially activated by the differing ratios of morphogens present in the given location
ie. bicoid, nanos, caudal
- A morphogen influences the fates of other cells, as it diffuses

In a syncytium, a TF can act as the morphogen because it never leaves the cytoplasm. In mammals, TF can’t leave cells and thus cannot act as morphogens or signaling molecules.

To function as a morphogen, a protein must be able to diffuse to form a concentration gradient.

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29
Q

Determinant

A

Influences cell fate in the cell which it is found or produced

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30
Q

What are features of all early vertebrate embryos?

A

Primitive kidneys, gill arches, notochord, a spinal cord, and a neural tube flanked by somites.
- Gene expression is most similar among different types of vertebrate embryos when these similar features are observable.

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31
Q

What is a chimeric embryo?

A

An embryo made from tissues of more than one genetic source

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32
Q

Homologous structures

A

Organs or body parts whose underlying similarity arises from their bodies being derived from a common ancestral structure.
ex. wing of bird and arm of human

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33
Q

Analogous structure

A

Similarity in organs or body part comes from their performing a similar function rather than their arising from a common ancestor

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34
Q

histone acetylation

A

Addition of negatively charged group histones - neutralizes the positive charge of lysine
PROMOTES TRANSCRIPTION

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35
Q

histone methylation

A

Can either repress or activate gene expression depending on the amino acid targeted.
- Usually represses transcription.

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36
Q

Which part of the cell cycle should the differentiated donor cell be in SCNT?

A

G1 - so that the cell is NOT dividing.

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37
Q

What phase should the oocyte donor be enucleated?

A

The enucleation (removal of meiotic spindle with the chromosomes) should occur at metaphase ll.

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38
Q

What was the secret to success in the cloning of monkeys?

A

an mRNA called Kdm4d was injected into the enucleated egg fused with monkey fetal fibroblasts. This mRNA is translated to form a H3L9 trimethyl demethylase. The trimethyl groups block gene expression… so once the methyl groups are removed - gene expression is then activated!
- Secret: an enzyme that demethylates histone 3 at lysine 9

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39
Q

Do methyl groups on histones normally repress or activate gene expression?

A

Normally repress - condense the chromatin

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40
Q

Do acetyl groups on histones normally repress or activate gene expression?

A

Acetyl groups loosen nucleosome packing - activate gene expression.

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41
Q

Which methylations of lysine residues on histone 3 result in gene repression and which result in gene activation?

A

Methylated Lysine:
- 4, 38, 79 - gene activation
- 9, 27 - gene repression
Ex. methylated H3L9 - represses gene expression.

42
Q

What happens when H3L9 is methylated?

A

HP1 protein binds methylated H3L9 - associated with silent, heterochromatin (condensed)
- Blocks important TF’s from binding to activate gene expression

43
Q

What happens if lysines on H3 are acetylated?

A

Gene activation!

44
Q

What is an enhancer?

A

A noncoding DNA sequence that binds TFs and activates transcription of a specific gene in cys.
Separate, discrete enhancers often control the expression of a developmental gene in different tissues
Enhancers are often tissue specific - they assist in activating transcription in only particular tissues.
Because enhancers are DNA sequences, they are present in all cells, however they are differentially activated depending on the TFs present in the cell at that given time.
When specific TFs bind to the specific enhancer, a mediator protein is recruited that links the promoter to the enhancer to activate transcription of a given gene.

45
Q

What is Pax6?

A

Pax 6 is a gene that codes for a TF. It is required for the formation of the eyes, pancreas, and neural tube.

  • Enhancer modularity: there are different enhancers in front of the gene coding for Pax6. This allows for Pax6 to be produced in some tissues, but not others at the same time.
  • EX. there is a pancreas specific TF that binds to the pancreas enhancer to activate Pax6 expression in the pancreas.
46
Q

What does the neural tube become?

A

The spinal cord and the brain

47
Q

Where is DNA methylated and what is the result?

A

On the 5th position of a cytosine molecule. This tends to silence gene transcription via the recruitment of proteins.
DNA methylation only occurs in the promoter regions of genes.
DNA methylation at a given promoter can switch on and off throughout development.

48
Q

genital ridge

A

the ventral thickening of the epithelium and underlying mesenchyme of the mesonephros that is a precursor of the gonads

49
Q

What signaling is involved in attracting primordial germ cells to the genital ridge?

A

Secretion of CXCL12/SDF1 from the genital ridge cells
Release of Steel/Stem Cell factor from cells surrounding the PGC
- Need BOTH of these signals

50
Q

What receptor does CXCL12/SDF1 ligand bind to?

A

CXCR4, a GPCR

- this receptor is present on primordial germ cells cell membranes and HSC’s cell membranes

51
Q

What receptor does Steel/Stem cell factor bind to?

A

C-kit, a receptor tyrosine kinase on the surface of primordial germ cells

52
Q

Rett Syndrome

A

A severe debilitating neurological disorder affecting girls.
- Caused by mutations to the MeCP2 gene, a gene on the X chromosome. This mutation is haploinsufficient and thus boys with

53
Q

Dnmt3

A

de novo methyltransferase recruited by MeCp2

  • methylates a cytosine on one strand of DNA (on the promoter)
  • methylation of DNA represses gene expression
54
Q

Dnmt1

A

perpetuating methyltransferase - recognizes methylated cytosines on one strand of promoter region of DNA - methylates the CG pair on the other strand - which further represses the promoter and thus gene expression.
- allows DNA methylation patterns to be maintained after DNA replication (during cell division) occurs.

55
Q

Dscam gene

A

In Drosophila - can be alternatively spliced into 38000 different proteins – creates more proteins than there are genes in the body. This creates slightly different cell adhesion molecules and prevent inappropriate interaction of neurons.
- Want to ensure the neurons are interacting only when they are supposed to do so.

56
Q

E-cadherin

A

Embryonic cadherin. When the repression of this gene is repressed, cells undergo EMT and become mesenchymal, individual cells.

57
Q

What type of signaling do cadherins mediate?

A

juxtacrine signaling

58
Q

Juxtacrine signalling

A
  • cell signaling where cells are next to each other
  • ex: cadherins
  • can be homophilic or heterophilic binding
59
Q

paracrine signalling

A

long range signaling where one cell secretes a signaling protein (ligand) into the environment and across the distance of many cells. Only those cells expressing that ligand’s receptor are able to respond to the signal

  • cells can react through chemical reactions or changes to gene expression
  • Does NOT require the blood stream (this is endocrine)
60
Q

Cadherins

A
  • calcium dependent adhesion proteins
  • Has intracellular, transmembrane, and extracellular (binding) domain
  • needs to have calcium bound to the extracellular domains for proper mediation of interaction
  • NORMALLY cadherins bind to the same cadherins but there are some exceptions
  • mediates cells sticking together, like in an epithelium for example.
61
Q

epiblast

A

(also known as the primitive ectoderm) is one of two distinct layers arising from the inner cell mass in the mammalian blastocyst

62
Q

hypoblast

A

the hypoblast, is one of two distinct layers arising from the inner cell mass in the mammalian blastocyst
-hypoblast gives rise to the yolk sac, which in turn gives rise to the chorion
primitive endoderm

63
Q

N-cadherin

A

Neural cadherin
- All ectodermal cells originally express embryonic cadherin, however some cells begin to express N-cadherin and this mediates formation of the neural tube.

64
Q

Induction

A

the process by which one cell population influences the development of neighbouring cells via close range interactions.
ex. The optic vesicle (outpocket of neural tube) induces surface ectoderm cells to form the lens.

65
Q

Competence

A

For a cell or cell population to be induced to form a structure, they must be competent to do so. Ex. they must express the appropriate receptor that the inducing ligand can bind to.

66
Q

What gene must be expressed in both the surface ectoderm cells and the optic vesicle for lens formation to occur?

A

Pax6

67
Q

What paracrine factors are secreted by the cells of the optic vesicle to induce lens formation in the surface ectoderm cells?

A

FGF8 and BMP4. The surface ectoderm cells MUST express the receptors for these ligands. & Pax6

  • BMP4 - induces expression of the Sox2/3 TF genes
  • FGF8 induces expression of the L-Maf TF
68
Q

What does the BMP4 ligand do in lens formation?

A

Secreted by optic vesicle, receptor on surface ectoderm cells.
- Surface ectoderm cells respond by expressing Sox2/3 transcription factor genes
Sox2 then binds to an enhancer (turns on) for delta crystallin gene (structural component of the lens)
Sox2 cooperates with Pax6 to activate this gene.

69
Q

What does the FGF8 ligand do in lens formation?

A

Ligand is secreted by optic vesicle cells. Receptor is expressed by surface ectoderm cells.

  • The ligand induces expression of the L-Maf transcription factor gene
  • FGF8 expression domains also include regions of the brain (patterning) and limbs
70
Q

Pax6

A

Gene that is necessary for the formation of eyes.

  • Expressed by both cells of the optic vesicle and the surface ectoderm cells during lens formation.
  • Pax6 TF is required for the expression of the delta crystallin gene
  • Pax6 is only ‘required’ to be WT in the surface ectoderm cells for lens formation.
  • haploinsufficient
71
Q

What are the 4 most prominent families of paracrine factors?

A

These paracrine factors are the INDUCERS

  1. The fibroblast growth factors (FGFs) and other RTK ligands (receptor tyrosine kinase)
  2. Hedgehog proteins
  3. Wnt proteins
  4. TGF-beta superfamily proteins
    a. BMPs (Bone morphogenic proteins)
    b. Nodal-like proteins
72
Q

TGF-beta superfamily proteins

A

Includes 2 subdivisions

  1. BMPs (bone morphogenic proteins). These are upstream of Smad 1,5
  2. Activin, Nodal, TGF- beta family proteins (Nodal-like). These are upstream of Smad 2,3
73
Q

What pathway(s) do FGF ligands activate?

A
  • Receptor Tyrosine Kinase (RTK)

- Jak Stat Pathway

74
Q

RTK pathway

A
  1. FGF ligand binds 2. Stimulates receptor dimerization and their autophosphorylation of eachother in cytoplasmic domain 3. Recruits Adaptor proteins 4. GEF is activated and mediates the exchange of Ras-GDP to Ras-GTP, thereby activating it (Ras is a G protein) 5. Ras-GTP activates Raf (a protein kinase C) 6. Raf activates a series of MAP kinases, first of which is Mek and than eventually Erk 7. Phosphorylated (activated) Erk translocates into the nucleus and alters gene expression by activating a transcription factor
75
Q

Jak Stat Pathway

A

Can also be activated by FGF ligands
Tyrosine Kinase Pathway.
1. Ligand binds and causes receptors to dimerize 2. This dimerization brings together Jak 2 proteins (which are associated with the cytoplasmic domains of the receptors) - Jak 2’s auto phopshorylate eachother and the receptors 3. Phosphorylated receptors can then phosphorylate Stat5 on tyrosine residues. 4. Stat5-P’s dimerize 5. The complex can then translocate into the nucleus and alter gene expression by binding to promoter regions

76
Q

Thanatophoric Dysplasia

A

Causes by a mutation in the Fgfr3 receptor (STAT pathway)

  • Mutation causes the receptor to be constantly active and activate a gene involved in premature termination of chondrocyte division - Very short bones result
  • lethal
  • haploinsufficient
  • RECEPTOR SIGNALS IN ABSENCE OF LIGAND
77
Q

Achrondoplasia

A
  • Heterozygous gain-of-function mutation in the gene coding for the Fgfr3 receptor
  • Gly380Arg mutation in transmembrane domain
  • human dwarfism
  • gain of function mutation results in the constant activation of this receptor - leads to reduction in chrondrocyte division - bone growth is attenuated
  • RECEPTOR SIGNALS IN ABSENCE OF LIGAND
78
Q

Hedgehog Signaling Pathway

A
  1. Hedgehog ligand bound 2. Patch does not inhibit Smoothened 3. Active smoothened then inactivates PKA 4. Inactive PKA cannot phosphorylate Ci/Gli proteins 5. Ci/Gli remain intact and can ACTIVATE transcription

NO LIGAND BOUND
1. Patch INHIBITS smoothened protein 2. Inactive smoothened allows PKA phosphorylate Ci/Gli with Slimb 3. Phosphylated Ci/Gli gets cleaved 4. REPRESSES TRANSCRIPTION

79
Q

What is the receptor for sonic hedgehog ligand?

A

Patched

When sonic hedgehog ligand is bound, gene transcription is activated because Ci/Gli does not get cleaved

80
Q

What is the primary cilium?

A

Organelle in the vertebrate sonic hedgehog pathway.
Receives signal from the hedgehog ligand
When hedgehog ligand is bound, the smoothened transmembrane protein ends up in the primary cilium (antenna-like projection) - hedgehog causes relief of inhibition of smoothened by patched - active smoothened inhibits PKA so Gli cannot be phosphorylated and cleaved - Gli activates transcription.

81
Q

What roles does sonic hedgehog play in the body?

A
  • Shh is released from the notocord and induces somites to become floor plate and sclerotome (sclerotome becomes vertebrae)
  • separating eyes into two units
    cyclopedia results without it…
    -acts a morphogen in the limb buds
    -w/o hedgehog, you get cerebral hemisphere fusion
82
Q

Wnt4

A

Need this ligand to get kidney formation and for female sex determination
- No Wnt - ovary starts producing testosterone

83
Q

What is the receptor for Wnt ligands?

A

Frizzled

84
Q

Canonical Wnt Pathway

A

Wnt ligand present
1. Ligand binds to Frizzled and associated LRP5/6 receptors. 2. Disheveled protein is recruited and activated 3. Active disheveled recruits GSK3 and Axin - prevents them from associating with the APC and complexing with B-catenin (phosphorylating it and thus targeting it for destruction from the proteosome) 4. Intact B -catenin and go into the nucleus, associate with other TFs and by doing so, activate gene expression

NO LIGAND PRESENT
1. Frizzled and LRP5/6 transmembrane receptors do not associate without Wnt ligand bound 2. Disheveled is not activated and does not recruit any proteins 3. Thus, Axin and GSK3 are free to associate with the APC, phosphorylate B-catenin and thereby target it for destruction by the proteosome. 4. Gene expression is OFF if B catenin is not present in the nucleus

85
Q

B-catenin

A

A transcription factor that does not bind DNA. It binds other proteins.

86
Q

What proteins are involved in the RTK pathway?

A

Ligand: FGF ligands

Receptor tyrosine kinase, Adaptor proteins, GEF (guanine nucleuotide exchange factor), Ras, Raf, Mek, Erk

87
Q

What proteins are present in the Jak-STAT pathway?

A

FGF ligands bind receptor
Jak2 (w/the kinase activity)
Stat5

88
Q

What proteins are present in the Canonical Wnt pathway?

A

Frizzled Receptor, LRP5/6 receptor, Disheveled, APC, Axin, GSK3, B-catenin

89
Q

What proteins are present in the hedgehog signaling pathway?

A

Ligand: Hedgehog

Patched (receptor), Smoothened, PKA, Slimb, Ci/Gli

90
Q

Wnt signaling easy

A

Wnt ligand bound –> B-catenin remains intact - promotes gene expression
No Wnt ligand bound - B-catenin is targeted for destruction by the proteosome - no gene expression.

91
Q

Condition where you get too many polyps in your colon

A
  • predisposes you for colon cancer
  • APC protein is named after this condition
  • APC protein is involved in the destruction complex of B-catenin when no ligand is bound to Frizzled.
  • result is too much B-catenin present when there is no ligand bound - causes polyps to form in the colon
92
Q

Where can B-catenin be located within a cell?

A

attached to cadherins, in the cytoplasm, and in the nucleus

93
Q

Planar Cell polarity Pathway

A

Wnt ligand present
1. Wnt binds Frizzled receptor - associates with LRP receptor 2. Disheveled protein is activated 3. Disheveled activates RhoGTPases which act on the cell cytoskeleton –> changes cells shape/behaviour. JNK kinases can associate with Rho GTPases to alter gene expression in the nucleus

94
Q

TGF- β Superfamily Pathway

A

Involves both BMP ligands and Nodal-related ligands (TGF-β family, Activin, Nodal)
1. Ligand binds receptor ( one is a Ser-Thr Kinase receptor) 2. This causes a dimerization with another receptor (Receptor 1 and 2) and Receptor 2 phosphorylates Receptor 1 3. These then phosphorylate the Smad TFs 4. Phosphorylated Smads (activated) enter the nucleus and alter gene transcription.

95
Q

Nodal-related ligand activation of TGF-β super family pathway

A

ligand binds - receptors dimerize - Ser-Thr kinase involved
Smad 2,3 is phosphorylated by the heterodimer receptor
Phosphorylated Smad2,3 then phosphorylates Smad4
Smad 4 - P translocates into the nucleus and alters gene expression

96
Q

BMP ligand activation of TGF-β superfamily pathway

A

BMP ligand binds receptor - receptors dimerize (heterodimer) - SerThr kinase activity of Receptor 2 is activated - Phosphorylated receptor can phosphorylate Smad1, 5 which then phosphorylate Smad4 - Smad4-P can translocate into the nucleus and alter gene expression

97
Q

Notch Pathway

A

Notch signaling is important for the formation of somites. Segmentation of the vertebrate embryo
LIGAND PRESENT
1. Adjacent cell is expressing Delta ligand and this binds to Notch receptor 2. stimulates a protease in the cytoplasm to cleave cytoplasmic domain of Notch receptor
3. Domain of Notch receptor translocates into the cytoplasm and activates gene transcription (ACTS AS A TF)

NO DELTA LIGAND expressed in adjacent cell 1. No ligand present means Notch receptor is not stimulated 2. Cytoplasmic domain remains bound to Notch receptor 3. Transcription is not activated.

98
Q

What happens when DLL3 is mutated?

A

DLL3 is a notch ligand. Result of mutation is a jumbled spinal column

99
Q

Oct4

A

This gene being expressed is a marker for pluripotency. Cells of the inner cell mass are pluripotent and thus express Oct4

100
Q

Primordial Germ cells

A

bipotential - whether they develop into sperm or eggs depends on the hormones released in the genital ridge.

  • maintain their pluripotency (Oct4 expression) for a while
  • Don’t arrive at the genital ridge until ~6 weeks in humans
  • aka embryonic germ cells - can become cultured pluripotent stem cells
101
Q

Embryonic stem cells

A

Cells of the inner cell mass that express Oct4

They can be cultured as ESC (embryonic stem cells)

102
Q

Induced Pluripotent stem cells

A

CMMB 403 (7 decks)

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