Exam 2 Flashcards
What is are the functions of the 5’ cap?
protect mRNA from degradation
assists ribosome binding in translation
Describe the translation initiation complex.
Poly A tail binds poly A binding protein (PABP) which interacts with translation initiation factor eIF4G. eIF4G interacts with 5’ cap binding protein eIF4E which forms a loop by bringing the 5’ and 3’ ends together.
What enzyme cleaves decapped mRNA? And in what direction?
XRN1 in 5’ to 3’ direction
Where does XRN1 come from? Where does it bind (5/3)?
The removal of a polyA tail and subsequential interaction with decapping proteins, binds 5’ side.
What is CPE?
Cytoplasmic Polyadenylation Element
Poly A tail in absence of sperm
Not able to bind PABP as Poly A tail is shorter (not elongated)
Describe the translation complex before fertilization.
CPEB bind CPE contained in maternal mRNA. CPEB interacts with maskin which interacts with the cap binding protein eIF4E. Maskin inhibits interaction eIF4e with eIF4G and 40s recruitment does not occur.
What is the cap binding protein?
eIF4E
What links PABP and eIF4E
eIF4G
Describe what happens to the initiation complex following fertilization.
Signals from fertilization stimulate phosphorylation of CPEB allowing for elongation of the poly A tail and the PABP is allowed to interact eIF4G and 5’ initiation factor eIF4E which displaces maskin, initiating translation
In what region of DNA initiates translation in oocyte?
3’ UTR
What is ribosomal heterogeneity?
ribosomes have some structural differences that allow for specialization of their function. These differences essentially mean that ribosomes are able to select what mRNA is translated
What is epigenetics?
Molecular mechanisms that allow the environment to alter how genes behave without changing the information they contain
What are some major non-coding mRNAs?
miRNA, siRNA, piRNA, lncRNA
What is the function of non-coding RNA?
To protect from mutation
What is the RNA induced silencing complex (RISC), and name at least three components?
The RISC targets mRNA with complementary sequences to the guide RNA. It binds si and mi RNA which mediate repression of RNA. Three components: si and mi RNA along with argonaute protein
What happens when imperfect base pairing occurs between small RNA and target gene?
repression of translation or deadenylation and degradation in P-body
What happens when perfect base pairing occurs between small RNA and target gene?
Ago is endonucleolytic to target mRNA
Describe the synthesis of siRNA
anti-sense mRNA (ds) (anti sense to target gene) which is cleaved and shortened by dicer to produce short nt sequence for RISC
Describe synthesis of miRNA
miRNA gene forms pri-miRNA which has multiple hairpins, drosha cleaves one hairpin at end and exits nucleus to be cleaved into short dsRNA by dicer that will bind to RISC
Which strand of miRNA/siRNA recognizes DNA to be silenced
guide strand, passenger strand is discarded
What effect does the RISC have on translation?
-mRNA target cleavage
-Translational repression
mRNA deadenylation
What is the use of shRNA
Since introduction of RNA-RNA duplexes to cytoplasm results in protein synthesis inhibition, shRNA has a hairpin loop effective for cleavage by dicer to effectively silence genes
What is the role of miRNA430 in transition from mother to zygote
Rids zygote of mRNA no longer needed
Name three possible locations of mRNA
diffusion and local anchoring
localized protection with deadenylation in cytoplasm
active transport along cytoskeleton via microtubule mol.
Describe a gene regulatory network
controlled by signaling ligands (hormones used in cell to cell communication) and are able to control cell differentiation
Do (housekeeping genes/transcription factors) have a longer half-time?
House-keeping genes bc produce enzymes used for creation of energy or other essential processes.
What is the fn of the poly-A tail?
prevent mRNA degradation
aids in the export of mature mRNA to the cytoplasm
binds proteins involved in initiating translation
What is the function of shRNA
provide a single stranded 3’ end to anchor the PAZ domain of dicer which brings about silencing
What conveys a message from outside the cell to influence cell differentiation?
Extrinsic factors
Give an example of an extrinsic factor
Constitutive production of ecdysone. However, cells only respond once receptor begins to be produced
What is local cell signaling called?
juxtacrine signaling
If local cell signaling is between two of the same recepotrs, what is it called?
homophillic binding
If local cell signaling is between two different proteins it is called…
heterophilic binding
Signaling between distant cells is called
paracrine signaling
Proteins that are secreted from a cell and designed to communicate a response in another cell
ligands
Which type of signaling is transmembrane
juxtacrine
Which type of signaling is ligand-receptor
paracrine
Cells found centrally have
greater surface cohesion (attachments to one another)
Which cells will have the greatest surface tension
The ones found inside the gastrula
What are the glue-like proteins responsible for creating the adhesion gradient?
Cadherins
Where can P cadherin be found?
placenta for adhesions to uterus
Where is E cadherin found
Early embryo for migration and epiboly of the epiblast in zebrafish
Where is N-cadherin found
throughout developing cells of the nervous system
Where is R-cadherin found?
retina formation
What is the function of protocadherins and what makes them structurally different? What is its function?
lacks the attachment to the actin cytoskeleton through catenin, keeping migrating epithelial cells together, and expressing dissimilar protocadherins is an important way of separating tissues
What causes epiboly in the early embryo zebrafish?
E cadherin is expressed at higher levels in more superficial layers
E/M: regular columnar morphology
Epithelial cells
E/M: loss of apico-basal polarity
Mesenchymal
E/M: high degree of cell adhesion
epithelial
E/M: irregular rounded or elongate morphology
E
E/M: cell-cell junctions
E
E/M: highly motile
M
E/M: underlying basement membrane composed of basal lamina and reticular lamina
epithelial
E/M: front back polarity
M
E/M specialized apical membrane
E
E/M: static
E
E/M: dynamic adhesions
M
E/M: lamellipodia and filopodia
M
The ability to control cell differentiation and are controlled by cell signaling
Gene regulatory networks
These genes have a longer half-life, enzymes used for creation of energy or other essential processes that need to be conducted by the cell
House-keeping genes
These have a shorter mRNA half-life
transcription factors
This post-transcriptional modification prevents mRNA degradation and assists in ribosome binding during translation
5’ guanosine cap
This post-transcriptional modification helps to prevent mRNA degradation, aids in export of mature mRNA into cytoplasm and is involved in binding protein involved in translation.
3’ poly A tail
Part of the mRNA that are removed in the nucleus prior to cytoplasmic export
introns
Longer poly A tail confers
longer mRNA half life
Controlling mRNA controls…
the amount of protein produced by a cell
Initiation of translation is controlled by
interactions between the 5’ cap and 3’ poly A tail
What are transpsons?
known as “jumping genes” since they can insert into other parts of the genome. An important source of mutation that helps with adaptation to environmental stressors
