1) Please describe briefly the main principles of the mechanism of action of the glucocortoid (cortisol) receptor and a receptor tyrosine kinase RTK, such as EGF or PDGF receptors. (2 points)
2) Describe the mechanism by which proto-oncogenes can be converted into oncogenes. (2 points)
3) The EGFR is frequently mutated in human tumors. Would you consider the EGFR as protooncogene or tumor suppressor gene product? Please explain briefly why. (1 point)
1) the ligand cortisol diffuses into the cell and binds to the glucocortoid receptor in the cytoplasm dissociating HSPs and releasing it to be tranlocated to the nucleus where it dimerizes at its DNA binding site (it can act both as activator and repressor) —> effects of glucocorticoids is their anti-inflammatory action, achieved by suppressing the expression of pro-inflammatory genes
a receptor tyrosine kinase binds its ligand with an extracellular domain that causes the RTK to dimerize, that enables autophosphorylation of the intracellular domain of the RTK with the special phosphorylation identity it activates various downstream signaling pathways (Ras raf mek erk)
2) the conversion can be cause by alteration in the DNA sequence of the proto-oncogene causing a gain of function mutation and e.g. perma activating it
possible ways to cause this by mutations, transposons (other mobile genetic elements), but also by splicing errors or alternative splicing and by errors in chromosomal recombination (Bcr-Abl) a different source can also be oncoviruses
3) I would consider it a proto-oncogene because onyl a gain of function (hyperactivity) would cause permanent signaling that pathway enables cell proliferation, survival, differentiation, and migration, a tumor suppressor is defined by a loss of function mutation which in this case would not empower a tumor to lose this pathway
Neubüser The basal lamina:
a) Name at least two core components of the basal lamina and explain their function. (2 points)
b) Schematically draw the structure of a hemidesmosome and label its components. (2 points)
c) What is the function of a hemidesmosome? (1 point)
a) collagen (VII / IV / XVII)—> gives mechanical stability and connection to tissue under the basal lamina / builing filaments of the basal lamina and giving stability / connection the the intermediate filaments inside epithelial cells together with —>
integrin —> transmembrane protein to connect cell to basal lamina component which is —> laminin
other are nidogen and perlecan (interconnecting basal components)
b)
basal lamina with collagen and laminin connected with integrins which are transmembrane and in the cell connected to intermediate filaments via plectin paralell collagen XVII also connects cell with basel lamina and in the cell BP230 connects it to IF
c)
connecting the intermediate ilaments of a cell to the basal lamina and thereby gaining strong adhesion of the epithelial cell to the tissue below, is gives mechanical strengh and protects the skin from just ripping away
Baumeister (skipped the fucking long preamble) […] mRNA vaccines from Biontech/Pfizer against Sars-CoV-2 […]
A) Design RNA probe […] Which additional features does your/any synthetic RNA need to have in order to survive and be translated in human cells? (2 points)
B) Develop an idea how synthetic RNA can enter human cells. (Hint: […] vaccines delivered into bloodstream […]) (1 point)
C) In which cellular compartment will the RNA be translated in order to produce Spike protein? Spike protein has to leave the cells to generate immune response. Which feature allows the newly generated protein to be transported into an extracellular environment? (1 point)
D) […] Vaccine has to be stored at -80°C. Why is this necessary? Why are other vaccines, containing proteins etc, not stored in such low temperatures? (1 point)
A)
A RNA probe definity needs a poly adenylated 3´-tail without it it would be degraded in the cytoplasm, it also needs a 5´cap structure that that enables translation initiation factors to guide it to ribosome and to even be translated
additionaly you need to make sure in the sequence are no splicing sites (consensus sequences) and you have a nuclear export signal ! but only if you RNA probe is even produced by the organism itself (splicing of cause in nucleus)if you insert it differently you need to make sure it reaches its target in the cytoplasm through the organism and it needs to be transported across the membrane
other then that the RNA probe should not have a sequence that forms confomational structures that inhibit its translation
B)
it could be encapsuled in a protein coat that can be altered so it has a translocalization signal into the cytoplasm even of specific target cells
C)
the translated sequence will have a ER specific translocation signal that is detected by a signal binding partical from the ER and co-transcriptionally it will together with the ribosome be translocated to the ER membrane where it will be transported intop the ER lumen to be further transported (if it does not have a ER retention signal) to the golgi in vesicals again with special location signals and then secreted out of the cell
D)
possibly to really stop any interactions between the nucleotides at minus 80 ° there is very low possibility of diffusion and thereby interactions of basepairs, also so conformational changes
for other vaccines this is not necessary becuase they dont interact with each other so easily and of cause to save money because freezing is energy consuming and if its not needed dont waste it
Baumeister
A) What are the (individual) names of the proteins that build up eight units of a nucleosome? (2 points)
B) Nucleosomes bind DNA sequence-independently but still allows binding of transcription factors […]. How do nucleosomes achieve this kind of binding? (2 points)
C) Describe an experiment how to demonstrate that N-terminal ends of nucleosome protein subunits are not required for DNA binding but for chromatin dynamics. (1 point)
A) H2A, H2A, H2B, H2B, H3, H3, H4, H4
B) Histones (the core proteins of nucleosomes) have tails (AA sequence) that have many post-translational modifications like methylation, acetylation or phosphorylation. Depending on the modifications the chromatin remodeling complex can be recuited to form Euchromatin —> open the packaging enabling the DNA to be transcribed (linked to acetylation) or to form heterochromatin —> tightly pack the DNA nucleosomes together making it very unlikely for a protein to bind (liked to methylation)
C) ablation (or transfer) of the N-terminal sequence and analyze how it changes the chromatin dynamics and whether it still binds (unspecificly) to DNA to package it or if that trait is lost
another possibility maybe silencing / inhibition of the sequence
Baumeister Epistasis Analysis […] Vulvaless (Vul) and Multivulva (Muv) in C. elegans […] genes encoding Vul are vul-1, vul-2, vul-3 and genes encoding Muv are muv-1 and muv-2.
muv-1 muv-2
vul-1 Vul Muv
vul-2 Muv Muv
vul-3 Vul Muv
A) Analyze phenotypic results shown in this table and order the genes with respect to one another in a regulatory cascade. (4 points)
B) […] vul-1 and vul-3 have the same phenotype, what is a consequence of this result? Do you know a genetic trick how you could determine the order of vul-1 and vul-3 with respect to each other? (1 point)
the phenotypes of the experiment give information which genes are dominant (or further downstream) to the others the order of the regulatory cascade would be
vul-1 —> muv-1 —> vul-1 and vul-3 —> muv-2
B) a new phenotype is needed to distinguish between the two genes, we need to try to cause a gain / loss of function mutation in the genes so they cause a new phenmotype e.g. multi vulva then we cross them like in the first experiment and see which phenotype dominates that one would be more downstream in the cascade
Driever (5 points)
A) Please explain briefly four different mechanisms for generation of patterns in a biological system.
B) What does the following statement mean: “Morphogen gradients are scalable”?
C) How can morphogen gradients be generated starting from morphogen encoding mRNA initially being expressed equally in all cells of embryonic field?
lateral inhibition (through receptor - ligand interaction on cell surfaces a pattern of one activated cell and all inhibited cells around it can form —> Notch / Delta)
morphogenic gradients (simply the diffusion of a signal molecule forming a decreasing gradient, can also be formed by a reverse gradient e.g. inhibitor)
induction cascades (gradients overlap and induce a new gradient in the overlapping area, from there again a new signal can reach into the other two gradients and induce 2 new ones)
reaction diffusion systems (slef activating activator also activates inhibitor of its own signal)
oscillating systems (on 3 tiers waves of signals synchronize and can form sequencial patterns)
asymmetric cell division
a gradient can expand propotionally with the tissue size (growth) but it might need adjustment of stability, diffusion and transport rate
the mRNA can be activly transported along cytoskeleton or diffuse and then be locally anchored or locally protected and then translate into the gradient forming protein
A) Please explain the principle mechanism of canonical WNT/β-catenin signalling in presence and absence of WNT ligand.
B) Please give two examples of developmental processes controlled by WNT signalling
WNT as a ligand activates the frizzeled receptor by binding -_> then activate dishevelled which inhibits the ß-catenin destruction complex —> accumulation of ß-catenin and translocation to the nucleus where it can act as TF
Absence of WNT means the ß-catenin destruction complex is active and destroys the ß-catenin
A-P axis formation in Drosophila
D-V axis formation in xenopus where WNT signaling is essential for the formation of the Niewcoop center
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