Developmental Bio - Exam 1

Immunolabeling

uses an antibody that specifically recognizes the protein you are looking for. The antibody is attached to a detectable label, allowing researchers to see where the protein is located in the embryonic tissue. 

In situ hybridization

allows researchers to see where a specific mRNA is located within an embryo or tissue, so it preserves spatial information. 

miR-430

helps make sure the old material instructions are turned off at the appropriate time.

Oogenesis

the biological process of formation, development, and maturation of a female gamete (an egg cell or ovum)

Importance of cadherins

cell-cell adhesion: cell-surface adhesion proteins that help neighboring cells (cell-surface adhesion proteins that help neighboring cells stick together.)

Catenin

connects cadherin to cytoskeleton through intracellular tails

Morphogenesis 

Is the process by which cells acquire their shape, organization, and spatial arrangement. (basically... How does the embryo physically become shaped like and organism)  

Involves:

• Cellmovement/migration/shape/division/adhesion

Gastrulation

Cells can move inward, spread, change shape  

What does specification ask

what will this cell become

what does morphogenesis ask

how do cells physically organize into their correct structure

Enhancer

A regulatory DNA sequence that can increase the transcription of a gene (contain binding sites for TFs)

• when, where, and how strongly a gene is expressed

Spatial control of transcription (enhancer) 

• = gene expression being controlled based on WHERE the cells are/tissue type 

• *** Spatial = Space = Where  

Temporal control of transcription (enhancer) 

• = WHEN the gene is expressed 

• *** Temporal = Time = When

Pioneer TFs

Are TFs that can bind their target DNA sequences even when the DNA is located within closed/condensed chromatin (normally when closed chromatin TFs can’t easily access DNA but pioneer TFs help initate the process of opening that chromatin.)  

• for transcription

FoxA1

binds to certain liver-promoting enhancers and opens up the chromatin, allowing other transcription factors access to the promoter 

Oct4, Sox2, Klf4, c-Myc

Yamanaka Pioneer Factors → that give rise to any cell type of the embryo. 

pluripotent

(of an immature cell or stem cell) capable of giving rise to several different cell types

Cellular reprograming

occurs when a differentiated cell is converted back into a more pluripotent, stem cell like state by changing its gene-expression program  

RNA polymerase II transcribes the gene results in what

mRNA

Mediator

• The “communication bridge” between regularity proteins and the machinery that actually transcribes the gene.  

• Helps communicate “This enhancer says the gene should be expressed  

• Necessary because: a TF binding to an enhancer isn’t necessarily enough by itself to initiate transcription  

what is DNA methylation

• addition of a methyl group (–CH₃) to DNA

• gene repression (less accessible, more compact chromatin)

histone methylation targets

lysine and arginine

what does histone methylation depend on

the specific amino acid residue that is modified

what does a nucleosome core contain

1. H2A - Helps form the nucleosome structure and interacts with H2B 

2. H2B - Partners with H2A to help create the outer portion of the histone core   

3. H3 - Helps form the center part of the nucleosome and has a long tail where many modifications occur  

4. H4 - Partners with H3 and helps stabilize the nucleosome 

how many histone molecules in one nucleosome

8

What happens to the RNA polymerase when DNA is methylated

it can’t easily bind

euchromatin

chromatin is open - more accessible - book is open and transcription machinery can access the gene

heterochromatin

chromatin becomes more compact - less accessible - book is closed and can’t easily read the genes

When miRNA binds to an mRNA it can: (2 things)

1. Inhibit translation – the ribosome doesn’t efficiently make the protein  

2. Destabilize/degrade the mRNA – the mRNA is broken down, so less protein can be produced.  

what is miRNA

post-transcriptional gene regulation - function is to degrade unwanted RNA or stall/block translation

Splicing

Introns are removed and exons are joined together  

where is the Poly (A) tail added and what does it do

• added to the 3’ end

• increasing mRNA stability, help with nuclear export, help tranlsation

Alternative splicing  

Different combinations of exons can be included in the final mRNA  

• Gene: Exon 1 – 2 – 3 – 4  

• Once cell might take: 1 – 2 – 3 – 4 

• Another might take: 1 – 2  – 4 

• Big ideas: 

• Same gene, different mRNAs, potentially different proteins  

• Allows one genes to have multiple different protein products 

The 5’ splice site: 

Marks the start of the intron

If destroyed = the spliceosome may fail to properly remove the intron, potentially causing abnormal splicing and abnormal mRNA  

The 3’ splice site: 

Marks the end of the intron 

If mutated: Spliceosome has trouble recognizing where the intron ends  

• Abnormal splicing  

• Abnormal mRNA  

• Abnormal protein  

Translation (definition and process)

• production of a protein using information encoded in an mRNA.  

• Process: mRNA -> ribosome -> protein   

Ribosomal selectivity

translation can be selective (A cell doesn't simply translate every mRNA at the same rate.)

Nuclear transfer

an experiment in which the nucleus from one cell is placed into an egg cell whose own nucleus has been removed

• The genes are still largely there and the cell has established a particular pattern of gene expression  

• Importance = it tests whether a differentiated cell’s nucleus still contains the complete genetic information needed to make an entire organism  

• * same genome -> different gene expression -> different cell types  

Dolly

• Produces using somatic cell nuclear transfer (SCNT) 

• Main idea: The nucleus of a differentiated cell retains the genetic information necessary to produce an entire organism  

 Cell dissociation/reaggregation experiment  

The experiment asks: Do cells know what they’re supposed to become on their own, or do they need interactions with neighboring cells  

• Scientists can take embryonic tissue and: 

1) dissociate cells - Separate cells from one another 

2) mix/reaggregate them - Allow them to come back together  

3) observes what happens  -Cells sometimes sort themselves into organizes tissues  

This demonstrates that cells have intrinsic properties that influence: 

• Cell-cell adhesion  

• Cell sorting  

• Tissue organization  

 Quail-chick experiments 

cell linage/cell migration

c-Kit

Is a receptor tyrosine kinase (RTK) that provides signaling roles important in cell survival, proliferation, migration, and differentiation.  

If c-Kit is disrupted

• Fail to survive  

• Fail to migrate properly  

• Fail to proliferate  

• Fail to differentiate properly  

c-Kit cell populations

• melanocytes 

• Hematopoietic cells 

• Germ cells 

• Certain stem/progenitor cells  

Dystrophin 

• Helps connect the cytoskeleton of muscle cells with proteins associated with the cell membrane/extracellular environment  

• This helps stabilize muscle fibers during contraction  

Exon-skipping therapy  

Intentionally alters/deleted splicing to skip a specific exon and restore the reading frame, producing a shorter but potentially partially functional dystrophin

Aberrant splicing

accidental/incorrect splicing caused by mutation → dysfunctional protein 

Genomic imprinting 

• an epigenetic phenomenon in which the expression of a gene depends on whether the gene was inherited from the mother or the father 

• Normally you inherit one copy of a gene from your mother and one copy from your father and for most genes, both copies can potentially be expressed.  

• With _____ , one parental copy is preferentially silenced.  

Genomic imprinting: why?

Leaves an epigenetic mark → alters chromatin/gene expression → gene silenced or activated

To understand complex gene regulation, embryonic development, and inherited diseases

Somatic cell reprogramming

Is the process of taking a differentiated somatic cell and resetting its gene-expression/epigenetic state toward a more embryonic or pluripotent state  

Induced Pluripotent Stem Cells (iPSCs) 

• Differentiated cells can also be reprogramed by introducing specific TFs  

• The classic = Yamanaka factors = Oct4, Sox2, Klf4, c-Myc 

• Together they can push a differentiated cell toward a pluripotent state 

Big idea: Differentiated ≠ genetically irreversible  

• A cell can potentially have its developmental program reset 

Totipotent

Can give rise to all embryonic cell types + extraembryonic tissues needed to produce an entire organism  

Pluripotent

Can give rise to essentially all embryonic cell types, but cannot by itself produce an entire organism because it lacks full extraembryonic developmental potential.  

Multipotent: 

More restrictive – can produce several related cell types within a particular lineage.  

Homologous structures

Is a structure found in different organisms that reflects common evolutionary ancestry, even if the structures now preform different functions

ex: Human arm, bat wing, whale flipper – look different and preform different functions but they share a similar skeletal organization because they were inherited from a common ancestral structure and modified through evolution.  

Phylotypic stage

Is a developmental state during which embryos of related species within a major evolutionary group tend to show greater morphological similarity to one another 

Transcriptome conservation: 

Is the collection of RNA transcripts expressed by a cell, tissue, or organism at a particular time. 

• Compare transcriptomes across species during development  

• Find that some stages have similar patterns of gene expression among related organisms. 

Christain Heinrich Pander 

An early embryologist who studied chick embryos  

• Helped establish the idea that embryos develop through the formation and organization of germ layers.  

He described the early embryonic layers that eventually became the conceptual foundation for

• Ectoderm 

• Mesoderm 

• Endoderm  

• Work contributed to the developing idea that the embryo is organizes into layers that give rise to different tissues  

Karl Ernst von Baer

Observations about comparative embryology. Scientists can identify: 

• Conserved developmental process  

• Shared structures  

• Evolutionary relationships  

• Differences in developmental timing   

Von Baer’s laws: 

1. General features appear before specialized features 

2. Development proceeds from more general to more specific  

• An embryo doesn’t start out looking like a miniature adult  

• General body plan -> increasingly specializes structures.  

3. Embryos of different species do NOT simply pass through the adult form of other species  

• Aka an embryo doesn’t literally evolve through the adult forms of its ancestors.  

Polycom group proteins

A developmental gene must remain stably repressed through many cell divisions. Which group of proteins can help maintain this state.