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
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
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.
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.
5
Q
Why is the DNA repair phenotype important?
A
Without it, DNA cannot be repaired; often cancer-prone
6
Q
Define silencer.
A
Blocks gene transcription
Therefore the protein is not transcribed
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.
8
Q
What is ectopic expression?
A
Gene is active in locations in which it does not normally function
9
Q
Define mesenchyme.
A
tissue compose of mesenchymal cells that are unconnected or loosely connected cells
CAN MOVE
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
11
Q
CRISPR/Cas 9 Process: What are two main applications of CRISPR/Cas9?
A
- Gene knockout – Using NHEJ to disrupt a gene.
- Gene knock-in – Using HR with donor DNA to insert a gene.
12
Q
What is Self-renewal?
A
The ability of a cell to divide and produce a replica of itself.
13
Q
Define Cis-regulatory element (AKA genome equivalence).
A
Regulatory elements residing on the same stretch of DNA as the gene they regulate
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
15
Q
What is an inducer?
A
Tissue that produces a signal that causes change
16
Q
What is embryogenesis?
A
stages from fertilization trhough hatching
formation of embryo
17
Q
Homogametic vs Heterogametic
A
Homo: identical sex chromosomes
Hetero: Diff sex chromosomes
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.
19
Q
Stem Cells: Unipotent
A
Give rise to one type of cell
EX: Spermatogonia –> sperm cells
20
Q
What does it mean by allelic series?
A
the variable degree of severity from complete loss of function (Null) –> a wild type
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
22
Q
Genome vs Allele
A
Genome: complete DNA seq
Allele: Diff version of a gene
23
Q
What is syncytial specification?
A
Specification of nuclei within a multi-nucleated single cells
24
Q
Medial - lateral
A
Middle - sides
25
CRISPR/Cas 9 Process: What is an insertion or deletion?
Small **mutations are caused by NHEJ,** where extra bases are added (insertion) or removed (deletion), often leading to gene disruption.
26
Explain the role of Macho.
Macho mRNA regulates muscle development in tunicates.
If removed --> no muscle cells
If more added --> more muscle cells
27
Define lineage tracing
Tracking development of cell maturation to form a fate map.
28
Population asymmetry stem cell
cell can divide symmetrically to form 2 stem cells OR 2 committed cells
29
CRISPR/Cas 9 Process: What is donor DNA?
**Synthetic DNA template** used in **homologous recombination (HR)** to precisely insert or modify a gene
30
Define enhancer.
**Activate gene transcription**
| RNA Polymerase then transcribes gene
31
Define cell fate map.
diagram that shows what will become of each region of the embryo
32
Autosomes
chromosomes that are not sex chromosomes
33
List and describe 3 types of cell division.
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)
34
What occurs during fertilization?
Formation of diploid zygote
35
Competence in early vs later stages
**Early**: Compensation, grafting holds
**Late**: Not competent bc tissue already specified and determined
36
What happens if Wnt is absent?
B-catenin is degraded; no gene expression
37
3 Step process to build multicellular organisms?
1. Cell division
2. Morphogenesis
3. Differentiation
38
Define epithelial mesenchymal transition (EMT).
Series of events where the **cells of an epithelial sheet** are **transformed into migratory mesenchymal cells**.
Caused by the digestion of paracrine factors
39
Somatic cells
Everything BUT germ cells
40
Animal life cycle stages (5)
1. Gametogenesis
2. Fertilization
3. Cleavage
4. Gastrulation
5. Organogenesis
41
Stem Cells: Totipotent + Example
form all structures of an organism
("Capable of all")
EX: Neoblasts in planarians
42
Dorsal- ventral
Top - bottom
43
Explain conditional specification in term of potency.
As a cell's commitment increases, the potency decreases (what it could become)
44
If the stem cell has the cytoplasmic determinants, then...
have ability to self-renew into stem cells
45
Example of conditional specification: induction and competence.
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.
46
What is a Knockdown mutation?
Reducing the expression of a gene, but not completely eliminating it.
47
Define gene regulatory network.
Pattern generated by the **interactions among transcription factors and enhancers** that help **define** the course of **development**.
48
What is a knock-in mutation?
Inserting a desired modification at a particular location.
49
Wnt Signaling Pathway Steps (6 steps, 5 arrows)
**Wnt**
↓ *(binds)*
**Frizzled**
↓*(Recruits)*
**Dishevelled (Dsh)**
┴ *(Recruits)*
**GSK3**
┴ *(Phosphorylates, target for degration)*
**B-catenin**
↓ *(To nucleus)*
**Activates transcription w/ TCF/Lef**
50
Define morphogen gradient in terms of Bicoid and Caudal concentrations.
**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)
51
Example of syncytial specification
Drosophila (AKA fruit fly)
52
CRISPR/Cas 9 Process: What is homologous recombination (HR)?
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
53
Notch Signaling Pathway Steps (4 steps; 2 arrows)
**Delta/Jagged**
↓ *(Binds w/ Notch & causes conformational change, leads to Notch's cytoplasmic cleavage)*
**Notch**
↓
**Notch intracellular domain**
↓ *(go to nucleus)*
**Activates transcription**
54
Why is Haploinsufficiency Considered Dominant?
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.
55
What is conditional specification?
Specification depends on the conditions
56
Define Determination
Cell fate is secured and cannot be changed
57
Explain what induced pluripotent stem cells (iPSCs) are.
Adult cells that have been **converted to cells with the pluripotency** of embryonic stem cells.
- Can be in all three germ layers
58
The recessive mutant allele is compensated by the wild-type allele. Why?
**Wild type is the dominant allele** and can produce enough of the necessary protein to maintain normal function
59
What is haploinsufficiency?
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
What is a Blastula?
Early-stage embryo of **sphere of cells surrounding** an inner fluid-filled cavity, the **blastocoel.**
61
Explain how induced pluripotent stem cells (iPSCs) are generated
Activation of **Yamanaka transcription factors** to **reprogram** cells into iPSCs.
1. Oct4
2. c-Myc
3. Sox2
3. Klf4
62
What is a Knock-out mutation?
completely removing or inactivating a gene
63
Give an example of the epithelial mesenchymal transition (EMT).
vertebrate embryos during the **formation of the mesoderm** by mesenchymal cells delaminating from the epiblast
64
Explain conditional specification in term of plasticity.
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
TGF-beta Signaling Pathway Steps (5 steps; 4 arrows)
**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
What are sex-linked mutations?
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
What is induction?
tissue organization via intercellular interactions
68
What is a gain of function mutation?
An overexpression of a gene OR loss of regulation of activity (always active)
69
What is the wild-type allele? What about the mutant allele?
the "normal functioning" allele; the defective allele
70
Single celled asymmetry stem cell
dividing stem cell can produce another stem cells while also producing a cell committed to undergoing differentiation
ONE OF EACH
71
Define double negative gate.
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
Define specification.
Cell is thinking about fate
73
What is the notochord?
Stiff rod that gives structure
74
What is a Loss of function?
protein product of the mutant gene is less active than the wild type
75
What is differentiation?
Process during which a **cell develops distinct functional properties**
76
Define invariant/fixed lineage development. Example.
Cells of an embryo give **rise to the same number and type of cells in every embryo** of that species
Ex: Roundworm
77
Ectoderm Types of cell differentiation (3)
1. Skin epidermal
2. Neurons
3. Skin pigment
78
Explain Cre recombination (OVERVIEW)
- **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
What is Juxtacrine signaling?
Signaling between cells that are in **direct contact with one another** via **homophillic or heterophilic binding**
Homo: same proteins
Hetero: diff proteins
80
What is a responder? Connect it with competence.
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
What are morpholinos (MO)?
Short oligonucleotide complementary to mRNA translation start site (Inhibit translation) or splicing site (inhibit splicing)
NOTE: BLOCK TRANSLATION
82
Name the three germ layers in order from outermost to innermost.
1. Ectoderm (outer)
2. Mesoderm (middle)
3. Endoderm (inner)
83
What happens if Notch is absent?
Leads to the repression of gene transcription
84
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.
D. There must be an inducer that produces signals and a responder that acts upon receiving the signal.
85
Define commitment.
moment when the developmental fate has become restricted
86
Dominant mutant allele is not compensated by the wild-type allele. Why?
Mutation overrides or interferes with the function of the wild-type copy
87
What is the stem cell niche?
The environment that maintains stem cells (ex: cytoplasmic determinants, paracrine signaling, notch signaling, endocrine signaling
88
Differentiation Process Steps (4)
1. Undifferentiated cell
2. Commitment (Specification & determination)
3. Differentiation
4. Specialized cell
89
What are precursor stem cells?
Term to denote any ancestral stem/progenitor type cells of a....
.... particular lineage (e.g., neuronal precursors; blood cell precursors)
90
What is Morphogen?
**Diffusible molecule** that **acts** directly **on other cells to alter their fate** AND induces different cell fates at **different concentrations.**
91
Anterior (rostral) - posterior (caudal)
front - back
92
What occurs during cleavage?
Zygote cytoplasm divides until it forms a blastula.
DOES NOT INCREASE MASS
93
What is mechanical stress?
Applying physical force or pressure to trigger specific cellular responses
94
Homozygote vs Heterozygote
**Homozygote**: 2 identical alleles
**Heterozygote**: 2 diff alleles (dominant will give phenotype)
95
What does RNAi do?
Causes mRNA degradation
96
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.
Its fate has not yet been determined at the time of transplant.
97
What are the three types of Loss-of-function mutations?
1. Dominant negative
2. Haploinsufficiency
3. Null
98
What occurs during organogenesis?
Rearrangement of the three germ layers to produce tissues and organs.
99
What is conditional deletion?
The targeted removal of a specific gene or genetic sequence under certain condition
100
The TGF-beta signaling pathway is similar to the ....
BMP signaling pathway
101
What is pracrine signaling?
one cell secretes a signaling protein (ligand) into the environment
102
Cre recombination: Excision analogy
Cut
103
Explain conditional specification in term of compensation.
If cells are removed from the embryo, the remaining cells can compensate for the missing part.
104
What is autonomous specification?
Fate determined by cytoplasmic determinants in the egg
(transcription factors that tell the cell what to become)
105
CRISPR/Cas 9 Process: What is a double-stranded break (DSB)?
A cut in both strands of the DNA helix, made by Cas9, which triggers the cell’s DNA repair mechanisms
106
What is a transgene?
A gene that has been introduced into an org by transgenesis
107
List the four levels of gene expression regulation.
**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
What is the Maternal to Zygotic transition?
Control of gene expression shifts from **stored maternal mRNAs** within the to being controlled by **new transcription from the zygotic** genome
109
What occurs during gametogenesis?
Formation of germ cells
110
How does binding to ECM influence the morphogen gradient?
Slows it down; forms an exponential gradient
ex: Fgf8
111
Phenotype vs Genotype
**Phenotype**: Observable trait
**Genotype**: Gene seq for trait
112
Mesoderm Types of cell differentiation (5)
1. Notochord
2. Bone
3. Kidney cells
4. RBC
5. Facial muscle head
113
What are "lose it" experiments? They are also known as.... (2)
Whether the **thing lost is necessary for a given process**
Known as necessity/ loss-of-function (via knock-out)
114
Explain the signal transduction cascade.
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
CRISPR/Cas9 analogy
Cntrl F + delete
116
CRISPR/Cas 9 Process: What is Cas9?
DNA-cutting enzyme (endonuclease) that creates double-stranded breaks at a specific target site in DNA
117
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.
D. Genes can be regulated at multiple levels.
118
Explain the CRISPR/Cas 9 overall system.
**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
What are "move it" experiments? They are also known as.... (2)
Tell you whether that **thing is sufficient for that process.**
Known as sufficient/gain-of-function (via overexpression)
120
Explain the Waddington landscape.
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
CRISPR/Cas 9 Process: What is exogenous DNA?
**Foreign DNA** introduced into a cell, often used in gene editing to replace or insert new genetic material.
122
What are constitutive genes?
Gene products that are active all the time
123
Define cell fate.
future type of a cell
124
What is Morphogenesis?
Cell and tissue **movements that give** the developing organ/ organism **its 3D shape**
125
Does phenotype indicate genotype? Provide an example.
No, heterozygous alleles (you get the dominant phenotype but genetically, it could be AA or Aa)
126
Loss of function: Dominant Negative
mutant form of the gene product itself has no function, but it interferes with the function of the wild-type form.
127
CRISPR/Cas 9 Process: What is non-homologous end joining (NHEJ)?
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
What are the two types of Gain-of-function mutations?
1. Constitutive
2. Ectopic expression
129
What is a zygote?
Fertilized egg
130
What are germ cells?
Cells of the three germ layers
131
Germ cells
cells that will form gametes
132
Which stage of embryogenesis involves the most substantial rearrangement of cells, giving rise to three embryonic tissue layers?
Gastrulation
Neurulation
Cleavage
Organogenesis
Gastrulation
133
Sex chromosomes
chromosomes that differ between both sexes
134
What is a null mutation/allele?
A complete loss of function AKA KNOCK-OUT
135
What occurs during gastrulation?
**Movement** of the embryo **blastomeres** resulting in the **positioning of the three germ layers**
136
Endoderm Types of cell differentiation (3)
1. Digestive
2. Pharynx
3. Resp.
137
Give an example of autonomous specification.
Tunicates embryo
138
What are "find it" experiments? They are also known as....
**Association between one thing** (tissue, cell, gene) **and another** (organ, process, enzyme)
Known as localization experiments (via staining)
139
CRISPR/Cas 9 Process: What is guide RNA (gRNA)?
Synthetic RNA sequence that **directs Cas9 to the correct DNA target by base-pairing** with the complementary DNA sequence.
140
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. Morphogens are not always water-soluble.
141
Hedgehog Signaling Pathway Steps (5 steps; 4 arrows)
**Hedgehog**
┴ *(binds)*
**Patched**
┴ *(Recruits)*
**Smoothened**
↓ *(Prevent cleavage)*
**Gli**
↓ *(To nucleus)*
**Regulates transcription:**
1. Cleaved = gene repression
2. Full length = active gene expression
142
Define epithelium.
tissue compose of **tightly linked** epithelial cells **to form a sheet**
