,Contents
Chapter 1 — Introduction to Molecular Regulation and Signaling .. 3
Chapter 2 – Gametogenesis ................................................................ 12
Chapter 3 – First Week of Development ........................................... 20
Chapter 4 – Second Week of Development: Bilaminar Germ Disc . 27
Chapter 5 – Third Week of Development: Trilaminar Germ Disc . 34
Chapter 6 – The Embryonic Period (Third to Eighth Weeks) ......... 41
Chapter 7 – The Gut Tube and the Body Cavities ............................ 48
Chapter 8 – Third Month to Birth: The Fetus and Placenta ........... 55
Chapter 9 – Birth Defects and Prenatal Diagnosis ........................... 62
Chapter 10 – The Axial Skeleton ....................................................... 69
Chapter 11 – Muscular System .......................................................... 76
Chapter 12 – Limbs ............................................................................ 83
Chapter 13 – Cardiovascular System ................................................ 89
Chapter 14 – Respiratory System ...................................................... 96
Chapter 15 – Digestive System ......................................................... 103
Chapter 16 – Urogenital System ...................................................... 110
Chapter 17 – Head and Neck ........................................................... 117
Chapter 18 – Central Nervous System ............................................ 123
Chapter 19 – Ear ............................................................................... 129
Chapter 20 – Eye ............................................................................... 135
Chapter 21 – Integumentary System ............................................... 141
,Chapter 1 — Introduction to Molecular
Regulation and Signaling
Introduction to Molecular Regulation & Signaling
20 Multiple-choice questions (A–D).
Each question is aligned with the chapter theme (gene expression, transcription
factors, signaling pathways, morphogens, cell migration/adhesion, and molecular
basis of malformations).
Answer format: Answer: X.
Below each question: a deep rationale and 3–6 key words.
Q1. Homeobox (HOX) genes encode transcription factors that contain which
conserved structural motif responsible for DNA binding and specifying positional
identity?
A. C2H2 zinc finger
B. Homeodomain (helix–turn–helix–like)
C. Basic leucine zipper (bZIP)
D. Basic helix–loop–helix (bHLH)
Answer: B
Deep rationale: HOX proteins contain a ~60 amino-acid homeodomain that
adopts a helix–turn–helix–like fold enabling sequence-specific binding to
regulatory DNA elements (enhancers/promoters). This DNA-binding property
allows HOX proteins to regulate downstream genes that define
segmental/positional identity during embryogenesis. Loss or misexpression of
HOX genes produces homeotic transformations because positional identity
programs are changed.
Key words: HOX, homeodomain, positional identity, transcription factor
Q2. Which intracellular effector is stabilized and translocates to the nucleus to
activate target genes in the canonical Wnt signaling pathway?
A. SMAD4
,B. β-catenin
C. Gli3
D. Notch intracellular domain (NICD)
Answer: B
Deep rationale: In canonical Wnt signaling, Wnt ligand binding to
Frizzled/LRP5/6 inhibits the β-catenin destruction complex (APC/Axin/GSK3β),
stabilizing cytosolic β-catenin. Stabilized β-catenin accumulates, enters the
nucleus, and associates with TCF/LEF transcription factors to activate Wnt target
genes that regulate proliferation and fate decisions. SMADs, GLI, and NICD are
effectors of other pathways (TGF-β/BMP, Hedgehog, Notch respectively).
Key words: Wnt, β-catenin, TCF/LEF, destruction complex
Q3. Loss-of-function mutations in which molecule of the Sonic hedgehog (SHH)
signaling pathway are classically associated with midline defects such as
holoprosencephaly?
A. Patched1 (PTCH1) — gain-of-function
B. SHH — loss-of-function
C. Smoothened (SMO) — constitutive activation
D. Gli1 — overexpression
Answer: B
Deep rationale: SHH is a secreted morphogen essential for midline patterning of
the forebrain and face. Loss-of-function mutations in SHH reduce the morphogen
gradient required for proper separation and patterning of the cerebral hemispheres,
producing holoprosencephaly. PTCH1, SMO, and GLI perturbations can alter
signaling but classical holoprosencephaly is typically linked to reduced SHH
activity.
Key words: SHH, holoprosencephaly, midline patterning, morphogen
Q4. The apical ectodermal ridge (AER) of the limb bud is a critical signaling
center. Experimental removal of the AER during early limb development most
likely causes:
A. Truncation of limb along the proximal–distal axis (loss of distal structures)
B. Failure of anterior–posterior patterning (mirror-image duplication)
C. Complete loss of dorsal–ventral polarity only
D. Isolated loss of cartilage condensation without muscular defects
Answer: A
,Deep rationale: The AER secretes FGFs (notably FGF8) that maintain underlying
mesenchyme in a proliferative “progress zone” necessary for proximal–distal
outgrowth. Early removal of the AER halts progress zone signaling, resulting in
loss of distal limb structures (e.g., missing radius/ulna or digits). Anterior–
posterior patterning is governed primarily by the zone of polarizing activity (SHH).
Key words: AER, FGF, proximal–distal, progress zone
Q5. During neural induction, inhibition of which family of signals is required for
ectoderm to adopt a neural fate rather than epidermal fate?
A. Wnt family
B. Bone morphogenetic proteins (BMPs)
C. Fibroblast growth factors (FGFs)
D. Notch ligands
Answer: B
Deep rationale: BMP signaling promotes epidermal fate in the ectoderm. Neural
induction requires antagonism of BMPs by secreted inhibitors (e.g., Noggin,
Chordin, Follistatin) produced by the organizer. BMP inhibition allows ectodermal
cells to adopt neural plate identity. Wnt and FGF modulate anterior–posterior
patterning and posteriorization, while Notch has distinct roles in lateral inhibition
and cell fate.
Key words: BMP, Noggin, neural induction, organizer
Q6. Mutations in JAG1, a ligand for the Notch receptor, most commonly cause
which clinical syndrome associated with bile duct paucity and congenital heart
defects?
A. Williams syndrome
B. Alagille syndrome
C. Noonan syndrome
D. Cornelia de Lange syndrome
Answer: B
Deep rationale: JAG1 encodes a Notch ligand; heterozygous mutations in JAG1
(and occasionally NOTCH2) underlie Alagille syndrome, which features
intrahepatic bile duct paucity, cholestasis, pulmonary artery stenosis, and
characteristic facial features. Notch signaling is critical for cell fate decisions in
multiple embryonic tissues including liver and heart.
Key words: Notch, JAG1, Alagille, bile duct paucity
, Q7. A defining property of a developmental morphogen is that a single diffusible
molecule can elicit distinct cell fates at different concentrations. Which
experimental outcome would best support that a secreted factor functions as a
morphogen?
A. Implanting a localized source of the factor causes concentric rings of different
cell fates in surrounding tissue in a concentration-dependent manner
B. The factor acts only when combined with a second unrelated factor; neither
alone has effect
C. Cells adopt fate according to lineage irrespective of distance from the source
D. The factor uniformly induces the same fate throughout the tissue at any dose
Answer: A
Deep rationale: The morphogen model predicts that positional information is
provided by a graded distribution of a signaling molecule; different threshold
concentrations specify different cell fates. Creating an ectopic source that produces
spatially distinct fates with distance (concentration) dependence is classic evidence
for morphogen activity (e.g., SHH in limb digit patterning, Bicoid in Drosophila).
Key words: morphogen, gradient, threshold, positional information
Q8. Which enzyme is primarily responsible for adding methyl groups to CpG
dinucleotides in DNA, a mechanism commonly used to stably repress gene
expression during differentiation?
A. DNA methyltransferase (DNMT)
B. TET family dioxygenases
C. Histone acetyltransferase (HAT)
D. Histone deacetylase (HDAC)
Answer: A
Deep rationale: DNA methyltransferases (DNMTs) catalyze the transfer of methyl
groups to the 5-position of cytosines within CpG dinucleotides, generating 5-
methylcytosine. Promoter CpG methylation typically blocks transcription factor
binding and recruits methyl-CpG–binding proteins that silence genes—an
important mechanism for lineage-specific gene repression during development.
TET enzymes oxidize 5mC (demethylation), HATs/HDACs modify histones rather
than DNA.
Key words: DNMT, CpG methylation, epigenetics, gene silencing
Chapter 1 — Introduction to Molecular Regulation and Signaling .. 3
Chapter 2 – Gametogenesis ................................................................ 12
Chapter 3 – First Week of Development ........................................... 20
Chapter 4 – Second Week of Development: Bilaminar Germ Disc . 27
Chapter 5 – Third Week of Development: Trilaminar Germ Disc . 34
Chapter 6 – The Embryonic Period (Third to Eighth Weeks) ......... 41
Chapter 7 – The Gut Tube and the Body Cavities ............................ 48
Chapter 8 – Third Month to Birth: The Fetus and Placenta ........... 55
Chapter 9 – Birth Defects and Prenatal Diagnosis ........................... 62
Chapter 10 – The Axial Skeleton ....................................................... 69
Chapter 11 – Muscular System .......................................................... 76
Chapter 12 – Limbs ............................................................................ 83
Chapter 13 – Cardiovascular System ................................................ 89
Chapter 14 – Respiratory System ...................................................... 96
Chapter 15 – Digestive System ......................................................... 103
Chapter 16 – Urogenital System ...................................................... 110
Chapter 17 – Head and Neck ........................................................... 117
Chapter 18 – Central Nervous System ............................................ 123
Chapter 19 – Ear ............................................................................... 129
Chapter 20 – Eye ............................................................................... 135
Chapter 21 – Integumentary System ............................................... 141
,Chapter 1 — Introduction to Molecular
Regulation and Signaling
Introduction to Molecular Regulation & Signaling
20 Multiple-choice questions (A–D).
Each question is aligned with the chapter theme (gene expression, transcription
factors, signaling pathways, morphogens, cell migration/adhesion, and molecular
basis of malformations).
Answer format: Answer: X.
Below each question: a deep rationale and 3–6 key words.
Q1. Homeobox (HOX) genes encode transcription factors that contain which
conserved structural motif responsible for DNA binding and specifying positional
identity?
A. C2H2 zinc finger
B. Homeodomain (helix–turn–helix–like)
C. Basic leucine zipper (bZIP)
D. Basic helix–loop–helix (bHLH)
Answer: B
Deep rationale: HOX proteins contain a ~60 amino-acid homeodomain that
adopts a helix–turn–helix–like fold enabling sequence-specific binding to
regulatory DNA elements (enhancers/promoters). This DNA-binding property
allows HOX proteins to regulate downstream genes that define
segmental/positional identity during embryogenesis. Loss or misexpression of
HOX genes produces homeotic transformations because positional identity
programs are changed.
Key words: HOX, homeodomain, positional identity, transcription factor
Q2. Which intracellular effector is stabilized and translocates to the nucleus to
activate target genes in the canonical Wnt signaling pathway?
A. SMAD4
,B. β-catenin
C. Gli3
D. Notch intracellular domain (NICD)
Answer: B
Deep rationale: In canonical Wnt signaling, Wnt ligand binding to
Frizzled/LRP5/6 inhibits the β-catenin destruction complex (APC/Axin/GSK3β),
stabilizing cytosolic β-catenin. Stabilized β-catenin accumulates, enters the
nucleus, and associates with TCF/LEF transcription factors to activate Wnt target
genes that regulate proliferation and fate decisions. SMADs, GLI, and NICD are
effectors of other pathways (TGF-β/BMP, Hedgehog, Notch respectively).
Key words: Wnt, β-catenin, TCF/LEF, destruction complex
Q3. Loss-of-function mutations in which molecule of the Sonic hedgehog (SHH)
signaling pathway are classically associated with midline defects such as
holoprosencephaly?
A. Patched1 (PTCH1) — gain-of-function
B. SHH — loss-of-function
C. Smoothened (SMO) — constitutive activation
D. Gli1 — overexpression
Answer: B
Deep rationale: SHH is a secreted morphogen essential for midline patterning of
the forebrain and face. Loss-of-function mutations in SHH reduce the morphogen
gradient required for proper separation and patterning of the cerebral hemispheres,
producing holoprosencephaly. PTCH1, SMO, and GLI perturbations can alter
signaling but classical holoprosencephaly is typically linked to reduced SHH
activity.
Key words: SHH, holoprosencephaly, midline patterning, morphogen
Q4. The apical ectodermal ridge (AER) of the limb bud is a critical signaling
center. Experimental removal of the AER during early limb development most
likely causes:
A. Truncation of limb along the proximal–distal axis (loss of distal structures)
B. Failure of anterior–posterior patterning (mirror-image duplication)
C. Complete loss of dorsal–ventral polarity only
D. Isolated loss of cartilage condensation without muscular defects
Answer: A
,Deep rationale: The AER secretes FGFs (notably FGF8) that maintain underlying
mesenchyme in a proliferative “progress zone” necessary for proximal–distal
outgrowth. Early removal of the AER halts progress zone signaling, resulting in
loss of distal limb structures (e.g., missing radius/ulna or digits). Anterior–
posterior patterning is governed primarily by the zone of polarizing activity (SHH).
Key words: AER, FGF, proximal–distal, progress zone
Q5. During neural induction, inhibition of which family of signals is required for
ectoderm to adopt a neural fate rather than epidermal fate?
A. Wnt family
B. Bone morphogenetic proteins (BMPs)
C. Fibroblast growth factors (FGFs)
D. Notch ligands
Answer: B
Deep rationale: BMP signaling promotes epidermal fate in the ectoderm. Neural
induction requires antagonism of BMPs by secreted inhibitors (e.g., Noggin,
Chordin, Follistatin) produced by the organizer. BMP inhibition allows ectodermal
cells to adopt neural plate identity. Wnt and FGF modulate anterior–posterior
patterning and posteriorization, while Notch has distinct roles in lateral inhibition
and cell fate.
Key words: BMP, Noggin, neural induction, organizer
Q6. Mutations in JAG1, a ligand for the Notch receptor, most commonly cause
which clinical syndrome associated with bile duct paucity and congenital heart
defects?
A. Williams syndrome
B. Alagille syndrome
C. Noonan syndrome
D. Cornelia de Lange syndrome
Answer: B
Deep rationale: JAG1 encodes a Notch ligand; heterozygous mutations in JAG1
(and occasionally NOTCH2) underlie Alagille syndrome, which features
intrahepatic bile duct paucity, cholestasis, pulmonary artery stenosis, and
characteristic facial features. Notch signaling is critical for cell fate decisions in
multiple embryonic tissues including liver and heart.
Key words: Notch, JAG1, Alagille, bile duct paucity
, Q7. A defining property of a developmental morphogen is that a single diffusible
molecule can elicit distinct cell fates at different concentrations. Which
experimental outcome would best support that a secreted factor functions as a
morphogen?
A. Implanting a localized source of the factor causes concentric rings of different
cell fates in surrounding tissue in a concentration-dependent manner
B. The factor acts only when combined with a second unrelated factor; neither
alone has effect
C. Cells adopt fate according to lineage irrespective of distance from the source
D. The factor uniformly induces the same fate throughout the tissue at any dose
Answer: A
Deep rationale: The morphogen model predicts that positional information is
provided by a graded distribution of a signaling molecule; different threshold
concentrations specify different cell fates. Creating an ectopic source that produces
spatially distinct fates with distance (concentration) dependence is classic evidence
for morphogen activity (e.g., SHH in limb digit patterning, Bicoid in Drosophila).
Key words: morphogen, gradient, threshold, positional information
Q8. Which enzyme is primarily responsible for adding methyl groups to CpG
dinucleotides in DNA, a mechanism commonly used to stably repress gene
expression during differentiation?
A. DNA methyltransferase (DNMT)
B. TET family dioxygenases
C. Histone acetyltransferase (HAT)
D. Histone deacetylase (HDAC)
Answer: A
Deep rationale: DNA methyltransferases (DNMTs) catalyze the transfer of methyl
groups to the 5-position of cytosines within CpG dinucleotides, generating 5-
methylcytosine. Promoter CpG methylation typically blocks transcription factor
binding and recruits methyl-CpG–binding proteins that silence genes—an
important mechanism for lineage-specific gene repression during development.
TET enzymes oxidize 5mC (demethylation), HATs/HDACs modify histones rather
than DNA.
Key words: DNMT, CpG methylation, epigenetics, gene silencing
