Coding 3 & 4 Flashcards
How is the genome in each somatic cell related?
The genome in each somatic cell made from the same fertilized egg are identical
What happens to unexpressed genes?
Nothing they are not mutated, destroyed, or expressed
What are the 4 levels of regulation?
- Transcription makes pre-mRNA
- Pre-mRNA processing to mature mRNA
- Mature mRNA leaves the nucleus to be translated
- Protein processing post-translation
How was genomic equivalence determined?
Through Dolly
What can be concluded from different areas puffing at a time to produce RNA?
That RNA was being produced in different areas
What is SCNT?
Somatic cell nuclear transfer is a method that was used to determine the reprogramming of a nucleus into a whole organism to determine genomic equivalence
What is genomic equivalence?
When one differentiated cell becomes another differentiated cell
What were the steps to making Dolly?
- From the oocyte donor the egg was removed
- The DNA was extracted from the donated oocyte
- The DNA from the mammary gland of the donor was taken and put into the enucleated oocyte
- The oocyte now with a nucleus was put in a serrogate to grow
- Dolly was born
- Dolly then became a sexually mature adult and gave birth normally
What is the function of transcription factors?
To stabalize RNA polymerase II
What is a cis-regulatory element?
When the transcription factor binds to a region on the same chromosome
What are CREs that promote transcription?
Enhancers
What are CREs that repress transcription?
Repressors
What is the Poly-A tail?
This is a tail of adenosines that are added to the 3’ end and is used to prevent degradation
What is a chromatin?
A region of DNA with its associating histones
What are nucleosomes?
A molecule with 8 histones 2x(H2A, H2B, H3, H4) with DNA wrapped around it
What is heterochromatin?
When the DNA is wrapped around the histones very tightly
What is the euchromatin?
When the DNA is wrapped around the histones very losely
What are exons?
These are the coding regions of the DNA that can be translated or transcribed
What are introns?
These are the noncoding regions of DNA that is not transcribed or translated
What is the 5’ Cap?
This is a 5’ modification that protects the mRNA from exonucleases
What are CpG islands?
This is a region that exists before the promoter where the basal transcription factors bind and recruit RNA pol II
How do enhancers promote transcription?
Enhancers promote activation by binding to transcription factors and bending the DNA to bridge the synthesis of mRNA
What is epigenetics?
This is modifying gene expression
What does methylation do?
Methylation increases packing and leads to heterochromatin by methyltransferase
What does unmethylation do?
Demethylation decreases packing and leads to euchromatin by demethyltransferase
What does acetylation do?
Histone acetyltransferase adds acetyl groups which counters the negative charge of the DNA and that leads to euchromatin
What does deacetylation do?
Histone deacetyltransferae removes acetyl groups and leads to heterochromatin
Which lysines are associated with activation due to methylation?
4, 38, 70
Which lysines are associated with repression due to methylation?
9 and 27
What does MeCP2 do?
MeCP2 recognizes methylated cytosine in DNA which recruits methyl transferase Dnmt3 to increase packing or histone deacetylase to increase packing
What is a DNA binding domain?
These often classify major transription families and the DNA binding domain recognizes a particular DNA sequence in the enhancer
What is a trans-activating domain?
Trans activating domain can activate or suppress the gene transcription
What is a protein-protein interaction domain?
This allows transcription factors to be modulated by transcriptional co-regulators
How is a hemoglobin produced?
The beta globin gene is expressed the pre-mRNA containing exons and introns cap, and tail are processed and the beta globin protein is inactive until its modified with an alpha globin and heme to form an active hemoglobin
What is a basal transcription factor?
These transcription factors bind to the promoter where RNA pol II is initated instead of an enhancer
What is an enhancer?
It is a noncoding DNA sequence that binds transcription factors and activates transcription of a specific gene in cis
What determine the type of enhancer?
The tissue
What is the mediator?
It stabalizes the RNA pol II at the promoter
What is the PAX6 gene?
The protein secreted from it is necessary for the pancreas, the lens, and the neural tube
What are the PAX6 transcription factors?
Pbx1 and Meis
Does histone modification impact DNA in the same way?
Yes the modification are very much the same
What is intron-exon splicing?
Removing the non-coding intron regions using spliceosomes which recognizes the 5’ GU and 3’AG
What is homophilic binding?
When the receptor of one cell binds to the same receptor of another cell
What is heterophilic binding?
When receptor of one cell binds to a different receptor of another cell
How do embryonic cells demonstrate differential affinity?
If you were to aggregate mesoderm, ectoderm, and endoderm cells the cells would sort themselves based on adhesion strength
What are cadherins?
These are calcium dependent transmembrane proteins that are crucial for cell segregation
How do epithelial cells sort themselves?
Epithelial cells sort by the types of cadherin protein in their cell membrane
How does EMT occur in relation to E-cadherins?
Lower E-cadherin expression or repress it which can lead to EMT
What happens when there is EMT? (SLUG/SNAIL)
During EMT SLUG and SNAIL represses transcription genes in the epithelial phenotype which leads to the formation of mesenchymal cells
What is the adhesive recognition site?
EC1
What are the calcium binding sites?
EC2, EC3, EC4, and EC5
What happens when antibodies bind?
The cells can disaggregate when antibodies bind and render inactive cadherins useless
What are the functions of cadherins?
- Adhere cells together
- Cadherins link to the cytoskeleton to form tubes and sheets
- Cadherins initiate and transduce signals to lead to changes in gene expression
What are protocadherins?
These are a special type of cadherins that bind to actin cytoskeleton through catenins
What are proteoglycans?
These are large extracellular proteins with glycosaminoglycan polysaccharide side chains that send signals to paracrine factors to cells
What are fibronectins?
These are large glycoprotein dimers that function as an adhesive molecule linking cells to each other and to other substrates
What is the basal lamina?
A close knitted sheet of epithelial tissue and it is made up of laminin which is a type IV collagen
What is the function of laminin?
- ECM assembly
- Cell adhesion and growth
- Changing cell shape
- Encouraging cell migration
What is integrin?
It is a large fibronectin receptor that binds to the intracellular cytoskeletal material and the extracellular R-G-D
How do paracrine factors contribute to EMT?
The signals from the paracrine factors lead to the down regulation of cadherins which converts the epithelium to mesenchymal cells
What is induction?
The process where intracellular interactions and signaling organizes, migrates, and differentiates the cell
What are inducers?
Tissues that send signals and change the behavior of other tissues
Where can eye morphogenesis occur?
The competent head ectoderm
What is competence?
The ability to respond to an inducer
How does the lens form?
- Inducers cause the synthesis of Otx2 transcription factor in the head ectoderm during the late gastrula stage
- Neural fold rises the anterior neural plate induces PAX6 gene expression to make the lens
- During the neurula stage PAX6 responds to the optic vesicle
- Optic vesicle secretes Fgf8 and BMP4
What is Fgf8?
Induces expression of the SOX2/3 transcription factor genes
What is BMP4?
Induces expression of the L-Maf transcription factor genes
What does the cell need to be competent?
To respond to FGF8 and BMP4 signals the ectoderm must express the receptors for these proteins as well as PAX6
What is the JAK-STAT pathway for?
It is seen in bone development and in chondracyte or muscle formation
What is achondroplasia?
Dwarfism
What is atophoric displasia?
A gain of function mutation of FGFR3 which leads to the ribs crushing a baby
What happens when hedgehog is absent?
- HH binds to patch
- Smoothened is inactive and degrades
- Gli is tethered to the microtubule
- FuSU and PKA cleaves the gli cell where it acts as a repressor
What happens when hedgehog is present?
- A strong HH-patched interaction occur
- Patched confronts and activates smoothened
- Patched is degraded
- Smoothened releases Gli from microtubules by phosphorylation
- Gli cells act as transcription activators for the gene
What are the 3 key components of the developmental toolbox?
- Transcription factors
- Secreted signalling
- Cell surface receptor proteins
What pathway can also be activated by Fgf?
It can act as a ligand and activate the RTK pathway
Where does the Fgf interfere with the JAK-STAT pathway?
Between the Ras and MAP kinase pathway
What happens when Wnt is absent?
- Beta catenin interacts with GSK3
2.Beta catenin is a transcription factor - Frizzled inactivates disheveled to activate GSK3
- This allows Beta catenin to remain bound to APC proteins and it is not freed by the Wnt signal
What happens when Wnt is present?
- Wnt binds to the receptor frizzled along with LRP5/6 and Lgr
2.Beta catenin is a transcription factor - Frizzled activates disheveled to inhibit GSK3
- This allows Beta catenin to remain bound to APC proteins and it is freed by the Wnt signal
What is the planar cell polarity pathway?
When activating disheveled some activation leads to Rho GTPases such as Rac and Rhoa which coordinate changes in cytoskeleton organization through JNK
What are the types of the TGF-B superfamilies?
- BMP4s
- Nodal
- Activin
What is the SMAD pathway?
- The ligand binds to the receptor which dimerizes
- SMAD 2/3 or 1/5 is phosphorylated
- This leads to SMAD 4 synthesis
- The activation or repression of the gene
What is the notch activity?
- Ligand delta binds to the notch receptor
- Protease then cleaves the jagged end of the notch
- The jagged end then acts as a transcription factor
What is added to the cloning process of HH and ZZ to ensure that the genes are turned “on” for expression?
Kdm4d it ensures demethylation of H3Lys 9
When is the promoter activated?
When Gata1 transcription factors bind and recruit other transcription factors like Ldb1
