Test 1 Flashcards
Stages of development
- Fertilization
- Cleavage
- Gastrulaton
- Organogenesis
- Larval stages
- Maturity
- Gametogenesis
Morula
Solid ball of cells
Blastula
Hollow ball of cells
Blastomere
1 cell within the blastula
Fertilization
Union of male and female gametes to form the diploid zygote
Cleavage
Synchronized mitotic cell divisions of a fertilized egg that results in formation of blastomeres and changes the single celled zygote into a multicellular embryo
What happens to the embryo size during cleavage
Embryo size stays the same, cell size gets smaller and smaller
Gastrulation
Big cell movements. Transformation of the blastula to the gastrula and development of germ layers
Axis development
Developing a left/right, anterior/posterior, dorsal ventral, and proximal distal axis
What governs the different types of cleavage
The amount of yolk determines the cleavage patterns
Where does division occur if there is a lot of yolk
Division only at the top
Invagination
Infolding of a sheet (epithelium) of cells, much like the indention of a soft rubber ball when its poked
Involution
Inward movement of an expanding outer layer so that it spreads over the internal surface of the remaining external cells
Ingression
Migration of individual cells from the surface into the embryos interior (move away from neighbors, loss of cadhesion)
Delamination
Splitting one cellular sheet into two or more parallel sheets
Epiboly
Movement of the epithelial sheets spreading as a unit to enclose deeper layers of the embryo
Germ layers
Ectoderm, mesoderm, endoderm
Ectoderm
Skin and CNS
Mesoderm
Bones and muscle
Endoderm
Organs (respiratory and digestive tract)
Methods of tracking cells
- Fate maps
- Direct observations of living embryos
- Dye markings
- Genetic labeling
- Transgenic DNA chimeras
Epithelial cells
Have tight connections to neighboring cells (do not move–> only move in epiboly but do not leave neighbors)
Mesenchymal cells
Are loose or unconnected to one another and can move
Fate maps and methods
Following a cell through development using dyes to see what each cell would turn into
- Dye marking
- Flourescent dye
- Chimera
Dye marking
Method of creating a fate map. Most cells are colorless, dyes stain cells but dont kill them
Chimera
Tissue from the embryo of one animal is removed and replaced by another using a graft (tissue a different color or labelled)
Transgenic DNA chimeras
Donor embryo is infected with a virus with a gene to express GFP. Infected cells glow green in UV light. Glowing cells transplanted into a host embryo and track movement
Why is evolutionary embryology important
Embryos pass through the same developmental stages as their ancestors
Homologous
Similaity based on a common ancestor
Analgous
Perform similar function but do not have a common ancestor
Causes of abnormalities
Generic mutation
Environmental cause
Multifctorial
Types of genetic mutations
- Gene mutations
- Chromosomal aneupolidy
- Translocations
Environmental causes of mutations
- Teratogen - chemicals, viruses, radiation, hyperthermia
Multifactoral causes
Combination, we are not sure
Differentiation
Development of cellular specialization
What step comes before differentitation
Commitment
Parts of comitment
- Specification
2. Determination
Specification
Capable of differentiating autonomously when placed in a neutral environment, not in non neutral environment (reversible)
Determination
Capable of differentiatin autonomously even when placed into another embryonic region (irreversible)
Where do the factors come from that create specification
- Cell has components within it that causes it to become that cell type
- Neighboring cells influence cells to be specified
Autonomous specification
Removed blastomere will produce the same cells it would if it were still part of the embryo. The embryo will lack the cells taken
Morphogenic determinants
Molecules of transcription factors that will influence gene expression that directs a cell into a particular path of development. The cell knows very early what it will become
Where does the cell get morphogenic determinants
From mother
Conditional specifiation
Each cell origially has ability to make many different cell types. Interactions with other cells restricts the fate of one or both participants. Fate of cell depends upon the conditions in which the cell finds itself
- Cells retain identity but grow according to the cells around them (flag)
What are cell comittment and differentiation programmed by
morphogen gradients
Differential gene expression
Process by which cells become different from one another based upon the unique combination of genes that are active or expressed
What does expression of different genes cause the production of
Proteins that lead to the differentiation of different cell types
Three postulates of differential gene expression
- Every somatic cell nucleus of an organism contains the complete genome established in the fertilized egg (DNA of all differentiated cells is identical)
- Unused genes in differentiated cells are neither destroyed nor mutated. They retain potential for being expressed
- Only a small percentage of the genome is expressed in each cell and a portion of the RNA synthesized in each cell is specific for that cell type
Regulaiton of gene expression
- Differential gene expression: regulates which nuclear genes are transcipred into nuclear RNA
- Selective nuclear RNA processing: regulates which of the transcribed RNAs are able to enter the cytoplasm and become mRNA
- Selective messanger RNA translation: regulated which of the mRNAs in the cytoplasm are changed into proteins
- Differential protein modification: regulates which proteins are allowed to remain or function in the cell
The genome across all cells is the same but ______ is not
the expression of the same mRNA across all cells
Explanation behind cloning
If each cells nucelus is identical to the zygote nucleus then each cells nucelus should be capable of developing an entire organism
Chromatin
DNA and protein complex found in eukaryotic genes (DNA and histones condensed –> no access to genes)
DNA histone complex
Called nucleosome
DNA wound around histones
Histones
Protein component made up of an octamer of histone proteins
Nucleosome
The histone plus about 147 bp of DNA that wraps around it in two loops with many contact points
Heterochromin
Tightly packed DNA around histones
Euchromatin
Loosely packed DNA around histones
What is gene expression dependent upon
How tightly packed a given region of chromatin may be (regulating if genes are accesible for transcription)
What two groups modify the H3 and H4 tails
- Methyl (CH3)
- Acetyl (COCH3)
Histone acetylation
Loosens histones and promotes transcription
What causes histone acetylation
Histone Acetyltransferases
Histone methylation
Tightens histones and promotes transcriptional repression
What causes histone methylation
Histone methyltransferases
What could methylation also do to the histone
It can activate transcription depending on the amino acid being methylated and the presence of acetyl or methyl groups in the vicinity
Exons
Regions of the DNA that code for parts of the protein
Introns
Regions of the DNA that have nothing to do with the protein sequence
Parts of a gene `
- Exon
- Intron
- Promotor
- Transcription initiation site
- 5’ untranslated region
- Translation initiation site
- Translation termination codon
- 3’ untranslated region (3’ UTR)
- Transcription termination sequnece
Promotor region
Where RNA polymerase II binds to intiate transcription. Same have the sequence TATA (tata box) which binds to TBP and helps anchor RNA polymerase II to the promotor . Where proteins are prepared for transcription to occur
Where is the promotor region located
In front of the gene
Transcription initiation site
The DNA sequence that will code for the addition of the 5’ cap after the RNA is transcribed
What does the cap sequence begin
It begins the first exon
5’ untranslated region
Determines the rate at which translation is initiated
Translation initiation site
ATG (AUG in RNA). This codon is found after the translation initiation site (distance varies). ATG translation start sequence is the same in every gene
Translation termination codon
TAA (UAA in mRNA). When ribosome enters this codon, the ribosome dissociates and protein is released. Can be TAG or TGA in other genes
3’ untranslated region
Transcribed but not translated into protein. Has the sequence for polyadenylation (addition of tail)
Roles of polyA tail `
- confers stability on mRNA
- Allows mRNA to exit nucleus
- Permits the mRNA to be translated into protein
Transcription termination sequence
Transcription continues beyond the AATAAA site for about 1000 nucleotides before being terminated (end portion of mRNA)
Cis regulatory elements
The on, off and dimmer switches of a gene
Cis
Located on the same chromosome
Cis regulatory elements of DNA
Promotors
Enhancers - like promotors
Silencers - prevent transcription
Cis regulatory elements of proteins
Transcription factors
Promotor
Sites where RNA polymerase binds to initiate transcription. Promotors usually have a 1000 bp site of repeating CG
CpG islands
Repeating CG
Enhancers
Control the rate and efficiency of transcription from a specific promotor, recruit and stabilize RNA polymerase
Silencers
Prevent promotor use and inhibit gene transcription
Basal transcription factors
Bind to CpG islands. They also recruit RNA polymerase and orient it
What will other transcription factors do
Bind to enhancers activating genes
What is the job of transcription factors
- Recruit enzymes to break up the nucleosomes in the area (histone acetyl transferases to make it accesible for RNA polymerase)
- Loop the chromatin so that the enhancer with all its tanscription factors will be brought closer to the promotor (creates a bridge)
Differential RNA processing
Splicing of the mRNA precursors into messages that specify different proteins by using different combinations of potential exons
Splicing isoforms
Different proteins encoded by the same gene
Alternative nRNA splicing
Producing a wide variety of proteins from the same gene, and most vertebrate make nRNAs that are alternatively spliced
How does the cell know where an exon ends and intron begins
Consensus sequences
Consensus sequences
found at the 5’ and 3’ end of an intron. These sequences are splice sites of an intron
What splices nRNA at consensus sequences
Spliceosomes
Spliceosomes
Small nRNA that bind to splice sites
Splicing factors
Made up of proteins that bind to the splice sites or to areas adjacent to them
How does alternative splicing occur
Specific splicing factors are produced. Each cell type produces a different set so an exon can be included in one and omitted in another
Control of gene expression at the level of translation
- Differential mRNA longevity
- Stored oocyte mRNAs selective inhibition of mRNA translation
- Ribosomal activation of mRNA translation
- microRNAs: specific regulation of mRNAs translation and transcription
Differential mRNA longevity
- not all mRNA lasts for the same amount of time after transcription
- mRNA is easily destroyed in the cell
- the longer mRNA lasts, the more protein can be translated from it
Stored oocyte mRNAs selective inhibition of mRNA transation
Oocyte makes and stores mRNA prior to meiosis to be used after fertilization
What are stored mRNAs called
Maternal contributions
Why are maternal contributions benefitial
The zygote does not need to have any trascription or traslation and can go right into cleavage after fertilization using up the mRNA and proteins deposited by its mother
What will not occur is maternal contributions are used up
Gastrulation
What keeps maternal contributions in a dormant state
There has to be an inhibitor. Maskin (protein) forms repressive loop structures by bringing 5’ and 3’ ends together in oocytes
What removes the inhibition sequence
Progesterone
What stimulates progesterone release and what does it lead to
Ovulation Stimulates progesterone release which triggers translation of the mRNA
Morphogenesis
Construction of different shapes and organs. Cells must be differentiated
What causes changes
Protein-protein interactions
What mediated cell communication and where do they come from
Informational molecules secreted or positioned in the cells membrane
Juxtacrine signaling
Contact dependent. A cell is communicating to a neighboring cell (must touch)
Paracrine signaling
Neighboring cells. A cell is communicating to cells surrounding it and further away
Ligand
A protein secerted from a cell designed to communicate with another cell
Receptor
Proteins within a membrane designed to bind to signaling proteins or a ligand
Homophilic binding
A receptor in the membrane of one cell that binds to the same type of receptor in another cell
Heterophilic binding
Occurs between two different receptor types
What does binding of a receptor to a ligand do
- Changes the extracellular receptor shape (dimerize)
- Changes the intracellular receptor shape (phosphorylate)
- Causes a cascade of events within the cell
Differential cell affinity
Experient: embryos mixed but went back to normal
- cells must have already recieved signal to know where theyre supposed to be
Term for cells knowing where to go back to when mixed
Selective affinity
How do cells sort themselves
- Cells with greater cohesion migrate centrally compared to those with less surface tension (more contact possible = move inward)
“Glue” on the cell surface that connects them to other cells
Cadherin
Cadherins
Calcium dependent adhesion molecules. Transmembrane proteins that interact with cadherins on other cells
What anchors the cadherins inside the cell
Catenins
Where is cadherin located
Transmembrane
How does one cell leave another cell
Change its plasma membrane to no longer have cadherin on it. Will detach from other cell
Quantity and cohesion
The more cadhesion, the more surface tension
Linear relationship
What can cadhesion expression affect
The timing of developmental events
Signal transduction cascades
- Fibroblast growth factors and RTK
- Hedgehog
- Wnt
- TGF-B superfamily
Basic blueprint of a signal transduction
- A signal
- A receptor for that signal
- Mechanism to translate or transport the signal
- Mechanism to translate the signal to a stimulation or repression of gene expression
What is it called when receptors come together after ligand binding
Dimerized
What causes the cascade inside the cell in RTK
phosphorylation
What type of molecules phosphorylates
Kinase
End goal of RTK
Stimulation or repression of gene expression
What activates a protein
Phosphorylation
RTK pathway
- Ligand
- RTK
- GEF
- RAS
- RAF
- MEK
- ERK
- Transcription factor
- Transcription
What dephosphorylates RAS to stop transcription
GAP
What happens if RAS is stuck turned on
Uncontrolled growth (cancer)
No Wnt pathway
Beta catenin is destroyed
Wnt bound pathway
B catenin binds in the nucelus and turns on gene transcription
TGF-B superfamily pathway
- TGF-B ligand
- Receptor II
- Receptor I
- Smad activation
- Smad dimerization
- New transcription
Acetylation of tails along with addition of 3 methyl groups causes
Actively transcribed chromatin
Lack of acetylation with methylation of lysine in 9th position of H3 is associated with
Highly repressed chromatin
