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Developmental Biology > Principles of Development > Flashcards

Principles of Development Flashcards

Exam 1

1
Q

Stem Cells: Multipotent + Example

A

Generate different cell types with restricted specificity for the tissue in which they reside.

EX: Mesenchymal stem cells –> other mesenchymal cells

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2
Q

BMP Signaling Pathway Steps (6 steps; 5 arrows)

A

BMP |—- (binds) Chordin, Noggin
↓ (binds)
Type 2 and 1 receptor
↓ (phosphorylation)
Smad 1/5
↓ (Dimerization & recruit)
2 Smad 1/5 + Smad 4
↓ (Go to nucleus)
Regulate transcription

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3
Q

What is CRISPR/Cas9?

A

A gene-editing tool that allows scientists to precisely cut and modify DNA using a guide RNA and the Cas9 enzyme.

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4
Q

Explain the effect of antisense reagent for loss of function.

A

Antisense reagents (morpholino and RNAi) work by binding to complementary mRNA sequences to prevent protein production. AKA LOSS OF FUNCTION

  • Morpholinos block translation.
  • While RNAi leads to mRNA degradation.
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5
Q

Why is the DNA repair phenotype important?

A

Without it, DNA cannot be repaired; often cancer-prone

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6
Q

Define silencer.

A

Blocks gene transcription

Therefore the protein is not transcribed

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7
Q

Explain how differential gene expression underlines differentiation.

A

By expressing different genes, cells produce different proteins that lead to the differentiation of different cell types.

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8
Q

What is ectopic expression?

A

Gene is active in locations in which it does not normally function

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9
Q

Define mesenchyme.

A

tissue compose of mesenchymal cells that are unconnected or loosely connected cells

CAN MOVE

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10
Q

What are progenitors?

A

Relatively undifferentiated cells that have the capacity to divide a few times before differentiating

NOT CAPABLE OF UNLIMITED SELF-RENEWAL

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11
Q

CRISPR/Cas 9 Process: What are two main applications of CRISPR/Cas9?

A
  1. Gene knockout – Using NHEJ to disrupt a gene.
  2. Gene knock-in – Using HR with donor DNA to insert a gene.
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12
Q

What is Self-renewal?

A

The ability of a cell to divide and produce a replica of itself.

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13
Q

Define Cis-regulatory element (AKA genome equivalence).

A

Regulatory elements residing on the same stretch of DNA as the gene they regulate

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14
Q

Stem Cells: Pluripotent + Example

A

Ability to give rise to cells that develop into the germ layers
(“Capable of many things”)

EX: Inner cell mass of mammals

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15
Q

What is an inducer?

A

Tissue that produces a signal that causes change

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16
Q

What is embryogenesis?

A

stages from fertilization trhough hatching

formation of embryo

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17
Q

Homogametic vs Heterogametic

A

Homo: identical sex chromosomes

Hetero: Diff sex chromosomes

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18
Q

What is stem cell asymmetry?

A. A common pattern in which stem cells in which the cell contents are asymmetrically distributed in the cytoplasm.

B. The division of a stem cell into two daughter cells, each destined to differentiate into a different mature cell type.

C. A common pattern in which stem cells divide at irregular, unpredictable times in response to chemical signals.

D. The division of a stem cell into two different daughter cells: a stem cell and a cell that is destined to differentiate.

A

D. The division of a stem cell into two different daughter cells: a stem cell and a cell that is destined to differentiate.

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19
Q

Stem Cells: Unipotent

A

Give rise to one type of cell

EX: Spermatogonia –> sperm cells

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20
Q

What does it mean by allelic series?

A

the variable degree of severity from complete loss of function (Null) –> a wild type

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21
Q

FGF and RTK Signaling Pathway Steps (9 steps; 7 arrows)

A

FGF
↓ (binds)
Tyrosine Kinase Receptor
↓(Dimerization, phosphorylation, recruit/activate)
GAP / GEF
┴ (GTP to GDP = inhibit) / ↓**(GDP to GTP = activates)*
RAS
↓ (recruits)
Raf
↓ (Phosphorylates)
MEK
↓ (Phosphorylates)
ERK
↓ (To nucleus and phosphorylates)
Ets fam transcription factors
↓
Regulate transcription

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22
Q

Genome vs Allele

A

Genome: complete DNA seq

Allele: Diff version of a gene

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23
Q

What is syncytial specification?

A

Specification of nuclei within a multi-nucleated single cells

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24
Q

Medial - lateral

A

Middle - sides

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25
Q

CRISPR/Cas 9 Process: What is an insertion or deletion?

A

Small mutations are caused by NHEJ, where extra bases are added (insertion) or removed (deletion), often leading to gene disruption.

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26
Q

Explain the role of Macho.

A

Macho mRNA regulates muscle development in tunicates.

If removed –> no muscle cells
If more added –> more muscle cells

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27
Q

Define lineage tracing

A

Tracking development of cell maturation to form a fate map.

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28
Q

Population asymmetry stem cell

A

cell can divide symmetrically to form 2 stem cells OR 2 committed cells

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29
Q

CRISPR/Cas 9 Process: What is donor DNA?

A

Synthetic DNA template used in homologous recombination (HR) to precisely insert or modify a gene

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30
Q

Define enhancer.

A

Activate gene transcription

RNA Polymerase then transcribes gene

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31
Q

Define cell fate map.

A

diagram that shows what will become of each region of the embryo

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32
Q

Autosomes

A

chromosomes that are not sex chromosomes

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33
Q

List and describe 3 types of cell division.

A
  1. Cleavage (no growth-G1/G2, but ↑of cells)
  2. Symmetrical (Exponential growth w same daughter cells)
  3. Asymmetrical (Diff sized daughter cells, one stem cell and one committed cell)
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34
Q

What occurs during fertilization?

A

Formation of diploid zygote

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35
Q

Competence in early vs later stages

A

Early: Compensation, grafting holds

Late: Not competent bc tissue already specified and determined

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36
Q

What happens if Wnt is absent?

A

B-catenin is degraded; no gene expression

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37
Q

3 Step process to build multicellular organisms?

A
  1. Cell division
  2. Morphogenesis
  3. Differentiation
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38
Q

Define epithelial mesenchymal transition (EMT).

A

Series of events where the cells of an epithelial sheet are transformed into migratory mesenchymal cells.

Caused by the digestion of paracrine factors

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39
Q

Somatic cells

A

Everything BUT germ cells

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40
Q

Animal life cycle stages (5)

A
  1. Gametogenesis
  2. Fertilization
  3. Cleavage
  4. Gastrulation
  5. Organogenesis
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41
Q

Stem Cells: Totipotent + Example

A

form all structures of an organism
(“Capable of all”)

EX: Neoblasts in planarians

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42
Q

Dorsal- ventral

A

Top - bottom

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43
Q

Explain conditional specification in term of potency.

A

As a cell’s commitment increases, the potency decreases (what it could become)

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44
Q

If the stem cell has the cytoplasmic determinants, then…

A

have ability to self-renew into stem cells

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45
Q

Example of conditional specification: induction and competence.

A

Optical vesicle in frog. Can form a third eye bc head is competent. Cannot form an eye in trunk bc trunk ectoderm is not competent.

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46
Q

What is a Knockdown mutation?

A

Reducing the expression of a gene, but not completely eliminating it.

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47
Q

Define gene regulatory network.

A

Pattern generated by the interactions among transcription factors and enhancers that help define the course of development.

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48
Q

What is a knock-in mutation?

A

Inserting a desired modification at a particular location.

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49
Q

Wnt Signaling Pathway Steps (6 steps, 5 arrows)

A

Wnt
↓ (binds)
Frizzled
↓(Recruits)
Dishevelled (Dsh)
┴ (Recruits)
GSK3
┴ (Phosphorylates, target for degration)
B-catenin
↓ (To nucleus)
Activates transcription w/ TCF/Lef

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50
Q

Define morphogen gradient in terms of Bicoid and Caudal concentrations.

A

Bicoid: Highest anteriorly and diminish posteriorly. Denotes head and slight thorax.

Caudal: Highest posteriorly and diminish anteriorly. Denotes Tail and slight abdomen.

Concentrations of these two proteins specify which segment of fruit fly forms.

DIFFUSION (source –> sink)

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51
Q

Example of syncytial specification

A

Drosophila (AKA fruit fly)

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52
Q

CRISPR/Cas 9 Process: What is homologous recombination (HR)?

A

DNA repair method that uses a donor DNA template to insert or replace a sequence at the target site

genetic information is exchanged to replace sequence

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53
Q

Notch Signaling Pathway Steps (4 steps; 2 arrows)

A

Delta/Jagged
↓ (Binds w/ Notch & causes conformational change, leads to Notch’s cytoplasmic cleavage)
Notch
↓
Notch intracellular domain
↓ (go to nucleus)
Activates transcription

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54
Q

Why is Haploinsufficiency Considered Dominant?

A

the single working gene copy can’t produce enough protein to maintain normal function.

Hence, the trait or disorder shows up even if only one mutant allele is present, making it dominant.

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55
Q

What is conditional specification?

A

Specification depends on the conditions

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56
Q

Define Determination

A

Cell fate is secured and cannot be changed

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57
Q

Explain what induced pluripotent stem cells (iPSCs) are.

A

Adult cells that have been converted to cells with the pluripotency of embryonic stem cells.

  • Can be in all three germ layers
58
Q

The recessive mutant allele is compensated by the wild-type allele. Why?

A

Wild type is the dominant allele and can produce enough of the necessary protein to maintain normal function

59
Q

What is haploinsufficiency?

A

occurs when one copy of a gene is not enough to maintain normal function, leading to an abnormal phenotype (even if the other copy is the wild-type).

60
Q

What is a Blastula?

A

Early-stage embryo of sphere of cells surrounding an inner fluid-filled cavity, the blastocoel.

61
Q

Explain how induced pluripotent stem cells (iPSCs) are generated

A

Activation of Yamanaka transcription factors to reprogram cells into iPSCs.

  1. Oct4
  2. c-Myc
  3. Sox2
  4. Klf4
62
Q

What is a Knock-out mutation?

A

completely removing or inactivating a gene

63
Q

Give an example of the epithelial mesenchymal transition (EMT).

A

vertebrate embryos during the formation of the mesoderm by mesenchymal cells delami­nating from the epiblast

64
Q

Explain conditional specification in term of plasticity.

A

cell changes fate due to neighboring interactions, showing that it was not yet determined and could adapt

EX; muscle cell specified but changes to neuron bc not yet determined

65
Q

TGF-beta Signaling Pathway Steps (5 steps; 4 arrows)

A

Nodal & TGF-beta
↓ (binds)
Type 2 and 1 receptor
↓ (phosphorylation)
Smad 2/3
↓ (Dimerization & recruit)
2 Smad 2/3 + Smad 4
↓ (Go to nucleus)
Regulate transcription

66
Q

What are sex-linked mutations?

A

Mutations on the sex chromosomes

  • Heterogametic sex (XY) → No backup X → Recessive mutation is expressed (more affected).
  • Homogametic sex (XX) → One normal X can compensate → Recessive mutation is masked (carriers, but not affected).
67
Q

What is induction?

A

tissue organization via intercellular interactions

68
Q

What is a gain of function mutation?

A

An overexpression of a gene OR loss of regulation of activity (always active)

69
Q

What is the wild-type allele? What about the mutant allele?

A

the “normal functioning” allele; the defective allele

70
Q

Single celled asymmetry stem cell

A

dividing stem cell can produce another stem cells while also producing a cell committed to undergoing differentiation

ONE OF EACH

71
Q

Define double negative gate.

A

silencing 2 genes by silencing one and that one has a sequence that would normally cause a gene expression

Ex: silencing gene A inhibits Gene B that normally activates gene C

72
Q

Define specification.

A

Cell is thinking about fate

73
Q

What is the notochord?

A

Stiff rod that gives structure

74
Q

What is a Loss of function?

A

protein product of the mutant gene is less active than the wild type

75
Q

What is differentiation?

A

Process during which a cell develops distinct functional properties

76
Q

Define invariant/fixed lineage development. Example.

A

Cells of an embryo give rise to the same number and type of cells in every embryo of that species

Ex: Roundworm

77
Q

Ectoderm Types of cell differentiation (3)

A
  1. Skin epidermal
  2. Neurons
  3. Skin pigment
78
Q

Explain Cre recombination (OVERVIEW)

A
  • Cre recombinase recognizes loxP sites and catalyzes recombination events at those sites.
  • Excision is the process by which Cre removes DNA between two loxP sites.
  • Conditional deletion allows scientists to delete genes in specific tissues, at specific times, or under certain conditions.
79
Q

What is Juxtacrine signaling?

A

Signaling between cells that are in direct contact with one another via homophillic or heterophilic binding

Homo: same proteins
Hetero: diff proteins

80
Q

What is a responder? Connect it with competence.

A

the tissue being induced; Cells of the responding tissue must have receptors for the inducing molecules and be competent to respond to the inducer.

81
Q

What are morpholinos (MO)?

A

Short oligonucleotide complementary to mRNA translation start site (Inhibit translation) or splicing site (inhibit splicing)

NOTE: BLOCK TRANSLATION

82
Q

Name the three germ layers in order from outermost to innermost.

A
  1. Ectoderm (outer)
  2. Mesoderm (middle)
  3. Endoderm (inner)
83
Q

What happens if Notch is absent?

A

Leads to the repression of gene transcription

84
Q

What component or components must be present for induction to occur?

A. There must be at least two different types of tissue present.

B. There must be cells present that can produce endocrine signals and sufficient blood supply to transport the signals.

C. There must be a basal lamina with associated epithelial cells.

D. There must be an inducer that produces signals and a responder that acts upon receiving the signal.

A

D. There must be an inducer that produces signals and a responder that acts upon receiving the signal.

85
Q

Define commitment.

A

moment when the developmental fate has become restricted

86
Q

Dominant mutant allele is not compensated by the wild-type allele. Why?

A

Mutation overrides or interferes with the function of the wild-type copy

87
Q

What is the stem cell niche?

A

The environment that maintains stem cells (ex: cytoplasmic determinants, paracrine signaling, notch signaling, endocrine signaling

88
Q

Differentiation Process Steps (4)

A
  1. Undifferentiated cell
  2. Commitment (Specification & determination)
  3. Differentiation
  4. Specialized cell
89
Q

What are precursor stem cells?

A

Term to denote any ancestral stem/progenitor type cells of a….

…. particular lineage (e.g., neuronal precursors; blood cell precursors)

90
Q

What is Morphogen?

A

Diffusible molecule that acts directly on other cells to alter their fate AND induces different cell fates at different concentrations.

91
Q

Anterior (rostral) - posterior (caudal)

A

front - back

92
Q

What occurs during cleavage?

A

Zygote cytoplasm divides until it forms a blastula.

DOES NOT INCREASE MASS

93
Q

What is mechanical stress?

A

Applying physical force or pressure to trigger specific cellular responses

94
Q

Homozygote vs Heterozygote

A

Homozygote: 2 identical alleles

Heterozygote: 2 diff alleles (dominant will give phenotype)

95
Q

What does RNAi do?

A

Causes mRNA degradation

96
Q

If you transplant a cell from the dorsal surface of a gastrula (an embryo undergoing gastrulation) to its ventral surface and the embryo develops normal dorsal and ventral structures, then which term best describes the tissue that was removed for transplant?

It is fully differentiated at the time of transplant.
It is fully determined at the time of transplant.
It is still identical to the other embryonic cells at the time of transplant.
Its fate has not yet been determined at the time of transplant.

A

Its fate has not yet been determined at the time of transplant.

97
Q

What are the three types of Loss-of-function mutations?

A
  1. Dominant negative
  2. Haploinsufficiency
  3. Null
98
Q

What occurs during organogenesis?

A

Rearrangement of the three germ layers to produce tissues and organs.

99
Q

What is conditional deletion?

A

The targeted removal of a specific gene or genetic sequence under certain condition

100
Q

The TGF-beta signaling pathway is similar to the ….

A

BMP signaling pathway

101
Q

What is pracrine signaling?

A

one cell secretes a signaling protein (ligand) into the environment

102
Q

Cre recombination: Excision analogy

A

Cut

103
Q

Explain conditional specification in term of compensation.

A

If cells are removed from the embryo, the remaining cells can compensate for the missing part.

104
Q

What is autonomous specification?

A

Fate determined by cytoplasmic determinants in the egg

(transcription factors that tell the cell what to become)

105
Q

CRISPR/Cas 9 Process: What is a double-stranded break (DSB)?

A

A cut in both strands of the DNA helix, made by Cas9, which triggers the cell’s DNA repair mechanisms

106
Q

What is a transgene?

A

A gene that has been introduced into an org by transgenesis

107
Q

List the four levels of gene expression regulation.

A

L1: Transcription control – Determines which genes are transcribed.

L2: RNA processing – Regulates which pre-mRNAs become mRNAs.

L3: Translation control – Determines which mRNAs are translated.

L4: Protein modification – Regulates protein stability and function.

108
Q

What is the Maternal to Zygotic transition?

A

Control of gene expression shifts from stored maternal mRNAs within the to being controlled by new transcription from the zygotic genome

109
Q

What occurs during gametogenesis?

A

Formation of germ cells

110
Q

How does binding to ECM influence the morphogen gradient?

A

Slows it down; forms an exponential gradient

ex: Fgf8

111
Q

Phenotype vs Genotype

A

Phenotype: Observable trait

Genotype: Gene seq for trait

112
Q

Mesoderm Types of cell differentiation (5)

A
  1. Notochord
  2. Bone
  3. Kidney cells
  4. RBC
  5. Facial muscle head
113
Q

What are “lose it” experiments? They are also known as…. (2)

A

Whether the thing lost is necessary for a given process

Known as necessity/ loss-of-function (via knock-out)

114
Q

Explain the signal transduction cascade.

A
  1. Ligand binds to receptor
  2. Binding causes a change in receptor conformation
  3. Cytoplasmic signaling cascade
  4. Effectors: Cytoplasmic (cytoskeletal) or nuclear (transcription factors)
  5. Response (morphogenesis or changes in gene expression
  6. Negative feedback loop to signal termination
115
Q

CRISPR/Cas9 analogy

A

Cntrl F + delete

116
Q

CRISPR/Cas 9 Process: What is Cas9?

A

DNA-cutting enzyme (endonuclease) that creates double-stranded breaks at a specific target site in DNA

117
Q

Which statement is true about the regulation of gene expression?

A. Expression of each gene is regulated at a single level, such as differential gene transcription.

B. Gene expression can only be regulated before proteins are produced.

C. Most gene expression is determined by which genes are present in a particular cell type.

D. Genes can be regulated at multiple levels.

A

D. Genes can be regulated at multiple levels.

118
Q

Explain the CRISPR/Cas 9 overall system.

A

CRISPR/Cas9 uses Cas9 (endonuclease) guided by guide RNA to create a double-stranded break (DSB) in DNA. The break is repaired either by non-homologous end joining (NHEJ), which often introduces insertions or deletions (indels), or by homologous recombination (HR), which allows precise editing using an exogenous homologous DNA sequence (donor DNA). Scientists can also insert exogenous DNA to introduce new traits or correct mutations.

119
Q

What are “move it” experiments? They are also known as…. (2)

A

Tell you whether that thing is sufficient for that process.

Known as sufficient/gain-of-function (via overexpression)

120
Q

Explain the Waddington landscape.

A

A metaphor for cell differentiation, where a ball rolls down a hilly terrain, with valleys representing stable cell fates and ridges as barriers, illustrating lineage commitment.

121
Q

CRISPR/Cas 9 Process: What is exogenous DNA?

A

Foreign DNA introduced into a cell, often used in gene editing to replace or insert new genetic material.

122
Q

What are constitutive genes?

A

Gene products that are active all the time

123
Q

Define cell fate.

A

future type of a cell

124
Q

What is Morphogenesis?

A

Cell and tissue movements that give the developing organ/ organism its 3D shape

125
Q

Does phenotype indicate genotype? Provide an example.

A

No, heterozygous alleles (you get the dominant phenotype but genetically, it could be AA or Aa)

126
Q

Loss of function: Dominant Negative

A

mutant form of the gene product itself has no function, but it interferes with the function of the wild-type form.

127
Q

CRISPR/Cas 9 Process: What is non-homologous end joining (NHEJ)?

A

DNA repair process that joins broken ends, often leading to insertions or deletions that can disrupt a gene.

ligates broken DNA ends together without sequence matching

128
Q

What are the two types of Gain-of-function mutations?

A
  1. Constitutive
  2. Ectopic expression
129
Q

What is a zygote?

A

Fertilized egg

130
Q

What are germ cells?

A

Cells of the three germ layers

131
Q

Germ cells

A

cells that will form gametes

132
Q

Which stage of embryogenesis involves the most substantial rearrangement of cells, giving rise to three embryonic tissue layers?

Gastrulation
Neurulation
Cleavage
Organogenesis

A

Gastrulation

133
Q

Sex chromosomes

A

chromosomes that differ between both sexes

134
Q

What is a null mutation/allele?

A

A complete loss of function AKA KNOCK-OUT

135
Q

What occurs during gastrulation?

A

Movement of the embryo blastomeres resulting in the positioning of the three germ layers

136
Q

Endoderm Types of cell differentiation (3)

A
  1. Digestive
  2. Pharynx
  3. Resp.
137
Q

Give an example of autonomous specification.

A

Tunicates embryo

138
Q

What are “find it” experiments? They are also known as….

A

Association between one thing (tissue, cell, gene) and another (organ, process, enzyme)

Known as localization experiments (via staining)

139
Q

CRISPR/Cas 9 Process: What is guide RNA (gRNA)?

A

Synthetic RNA sequence that directs Cas9 to the correct DNA target by base-pairing with the complementary DNA sequence.

140
Q

What is one obstacle to the use of simple diffusion to transport morphogens to the locations where they are needed?

A. Morphogens are not always water-soluble.

B. Morphogens are generally very large.

C. Morphogens are anchored to the cytoskeleton.

D. Morphogens are usually sequestered (hidden away) within organelles.

A

A. Morphogens are not always water-soluble.

141
Q

Hedgehog Signaling Pathway Steps (5 steps; 4 arrows)

A

Hedgehog
┴ (binds)
Patched
┴ (Recruits)
Smoothened
↓ (Prevent cleavage)
Gli
↓ (To nucleus)
Regulates transcription:
1. Cleaved = gene repression
2. Full length = active gene expression

142
Q

Define epithelium.

A

tissue compose of tightly linked epithelial cells to form a sheet

Developmental Biology (2 decks)

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