Bio 160 Midterm Review

This set of flashcards is designed to help students review key concepts and vocabulary related to embryology and developmental biology as outlined in their lecture notes.

Embryo

Name for organisms between fertilization and birth.

Model Organism

A species that multiple scientists agree to study, share information on, and develop tools for, in order to accelerate scientific progress.

Homologous Structures

Structures in different species that share a common evolutionary origin, such as mammalian forelimbs and bat wings, which both have five digits.

Limb Bud

An embryonic structure formed by proliferating mesenchymal cells covered by ectoderm that gives rise to limbs.

Cell Behaviors Used During Development

Processes including cell growth, cell differentiation, cell morphogenesis, movement, adhesion, and division that shape the developing organism.

Cell Differentiation

The process by which unspecialized cells become specialized cells with distinct structures and functions, occurring in stages from a stem cell to a progenitor cell and finally a terminally differentiated cell.

Cell Morphogenesis

The biological process governing how cells generate, change, and organize their shape and structure, transforming single cells into complex, functional tissues and organisms through genetic programs and mechanical forces.

Cell Growth

An increase in the total mass and volume of a cell when biosynthesis exceeds degradation, coordinated with the cell cycle to ensure proper cell size and tissue growth.

Genome Equivalence

The principle that all cells arise from a single cell and contain the same genome, despite differences in cell type.

Experimental Test of Genome Equivalence

Replacing an egg’s nucleus with the nucleus from a differentiated (post-development) cell to determine whether the DNA retains full developmental potential.

Differential Gene Expression

The process by which cells become different from one another based on the unique combination of genes that are active or expressed, producing different proteins.

Evidence for Differential Gene Expression

RNA sequencing results showing different expression patterns of genes in different cell types.

Ectopic Organ Development

The formation or presence of tissues or organs in abnormal anatomical locations due to disordered embryogenesis.

Cause of Ectopic Organ Development

Mis-expression of genes.

Chromatin

The DNA–protein complex in eukaryotic cells that regulates access to genes for transcription.

Cis-Regulatory Elements

Non-coding DNA sequences (promoters, enhancers, silencers) that regulate when and where nearby genes are expressed.

Transcription Factors (Regulators)

Proteins that bind DNA with precise sequence recognition to regulate gene expression.

Coactivators

Proteins that act as transcriptional regulators and help activate transcription without directly binding DNA.

Enhancers

Cis-regulatory DNA elements that determine when, where, and how much a gene is expressed, enabling cell-type-specific expression.

Enhancer Modularity

The property that individual enhancers independently control specific aspects of gene expression.

Reporter Genes

Molecular tools used to track gene expression by producing detectable signals such as fluorescence or luminescence.

Trans-Regulatory Factors

Diffusible gene-encoded molecules, primarily proteins, that regulate the expression of target genes located elsewhere in the genome.

Cis vs. Trans Regulation

Cis acts from the same DNA molecule to regulate nearby genes, while trans acts from a different molecule to regulate gene expression.

Cis-Regulatory Mutations

Mutations in regulatory DNA that can lead to congenital malformations such as aniridia, Pierre Robin sequence, and triphalangeal thumb.

Experimental Embryology

The study of development by observing and physically manipulating embryos before genetics and molecular biology.

Cleavage Stage

The initial phase of embryonic development characterized by rapid mitotic divisions without overall growth.

Blastula

A hollow, spherical embryonic stage formed after cleavage, consisting of a layer of cells surrounding a fluid-filled cavity called the blastocoel.

Gastrulation

An early developmental process where a blastula reorganizes into a multilayered structure called the gastrula.

Spemann–Mangold Organizer Experiment

A landmark experiment demonstrating embryonic induction where specific cells direct the development of others.

Organizer

A specialized region of embryonic tissue that directs the developmental fate of surrounding cells and patterns the body axes.

Fertilization

The event that breaks radial symmetry in the egg and initiates embryonic development.

Anterior (Ventral)

The front side or surface of the body.

Posterior (Dorsal)

Terms referring to the back side of the body, where dorsal is often used for the back of the hands/feet.

Animal Pole

The upper, metabolically active hemisphere of an egg or embryo associated with anterior (head) structures.

Vegetal Pole

The bottom region of an egg or embryo characterized by high yolk concentration, typically associated with posterior (tail) structures.

Sperm Entry

Introduces centrioles and proteins that nucleate microtubules and stimulate cortical rotation.

Gray Crescent

The dorsal region of the embryo formed after cortical rotation that will give rise to the organizer.

Cortical Rotation

A critical process in frog eggs that breaks radial symmetry to establish the dorsal-ventral axis.

Wnt/β-Catenin Signaling

A pathway wherein Wnt signaling stabilizes β-catenin, allowing it to activate specific gene transcription and play a role in establishing the dorsal-ventral axis.

Ectoderm

The outermost primary germ layer in an embryo responsible for developing the nervous system and skin.

Mesoderm

The middle primary germ layer that forms muscles, connective tissues, and the circulatory system.

Endoderm

The innermost primary germ layer that functions as foundational tissue for the digestive and respiratory tracts.

Autonomous Specification

Cell fate determination driven by internal cues that are independent of external signals.

Conditional Specification

Cell fate determination dependent on signals from neighboring cells.

Induction

A developmental concept where one group of cells influences the behavior of adjacent cells.

Mesoderm-Inducing Signals

Secreted signals from the vegetal pole that induce mesoderm formation.

Fate Mapping

Marking a cell and following it through development to determine its eventual fate.

Lineage Tracing

Tracking which cells arise from a specific progenitor cell over time.

Thomas Hunt Morgan

Demonstrated that genes are located on chromosomes using Drosophila, establishing the chromosome theory of inheritance.

Nüsslein-Volhard and Wieschaus

Identified genes controlling embryonic patterning in Drosophila through large-scale mutagenesis screens.

Mutagenesis Screen

A method of inducing random mutations and screening for developmental phenotypes.

Maternal Genes

Genes whose products are deposited in the egg and control early development before zygotic transcription.

Zygotic Genes

Genes transcribed after the mid-blastula transition, controlling later developmental processes.

Complementation Groups

Groups of mutations that, when crossed, can indicate if the mutation is in the same gene.

Bicoid

A transcription factor that directs the specification of anterior structures in a concentration-dependent manner.

Morphogen

A molecule that forms a gradient and induces different cell fates at different concentrations.

Even-Skipped (eve) Enhancers

Specific promoter regions of the eve gene that control distinct transcriptional stripes in the embryo.

To confirm genome equivalence 

Take a nucleus from an old cell with its (post-development) DNA and use it to replace anegg’s (pre development) DNA. It will tell you if the DNA is the same and has equivalence. Main Question: Does it support development?

Yes: development does not change DNA

No: Development does change DNA

What can cause ectopic organ development? 

Mis-expressing genes

Eukaryotic DNA exists as a DNA/protein

complex called

Chromatin

Wnt signaling results in b-catenin induced transcription

Wnt pathway

components like

Dishevelled (Dsh) and

GBP move toward the

future dorsal side. This

movement aligns with

microtubules, leading to

dorsal accumulation of 𝛽-

catenin and inducing the

Spemann organizer. This

localized accumulation

leads to the stabilization

and nuclear localization

of 𝛽-catenin, triggering

dorsal-specific gene

expression (e.g., siamois)

and subsequent dorsal

axis formation.

Significance: This

process ensures the

precise, localized

activation of the Wnt/𝛽-

catenin pathway

necessary for

establishing the dorsal-

ventral axis in amphibian

embryos.

Why is gastrulation triggered?

Mesoderm differentiation during germ layer specification generates cells expressing a migratory program

Which types of proteins could cells use to talk to each other during induction?

• Secreted proteins

• Cell surface ligands that bind cell surface receptors

• Extracellular matrix proteins that bind cell surface receptors

Fate mapping versus cell lineage tracing

Goal: Fate

mapping

identifies where

cells go and what

they become.

Lineage tracing

determines which

cells arose from a

specific

progenitor.

Perspective:

Fate maps are

often prospective

(projecting future

fate). Lineage

tracing is often

retrospective

(reconstructing

history).

Genome Equivalence - What would violate it?

Loss of genes in differentiated cells; different gene expression does NOT violate genome equivalence

Enhancer–Promoter Interaction

Enhancers activate transcription through DNA looping that brings enhancer-bound proteins into contact with promoters.

Cortical Rotation — What if microtubules are disrupted?

Wnt pathway components cannot localize dorsally, the gray crescent does not form, and dorsal–ventral axis fails.

Mesoderm Specification Type

Mesoderm is conditionally specified and requires inductive signals from neighboring cells.

Maternal-Effect Genes — When do they act?

Before the mid-blastula transition, using mRNA and proteins deposited by the mother.

Complementation Test — Failure to Complement Means

The mutations affect the same gene.

Reporter Genes in Fate Mapping

Reporter genes can be used for fate mapping if the label is inherited by descendant cells.

Apical Ectodermal Ridge (AER)

Ectodermal structure that promotes limb outgrowth along the proximal–distal axis by maintaining mesenchymal proliferation

Effect of Removing AER

Distal limb truncation; proximal structures still form; limb identity remains unchanged.

Zone of Polarizing Activity (ZPA)

A mesenchymal signaling center that patterns the anterior–posterior axis of the limb using Sonic hedgehog signaling.

Effect of Removing ZPA

Loss of proper anterior–posterior digit identity.

Effect of Ectopic ZPA

Mirror-image duplication of digits.

Sonic Hedgehog (Shh) in Limb Development

A morphogen secreted by the ZPA that specifies digit identity in a concentration-dependent manner.

Human Limb Defects Linked to Shh Misregulation

Polydactyly, digit malformations, mirror-image duplications.

Limb Identity Is Determined By

Mesoderm, not ectoderm