Notes in BIOL300 Final

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Published	12/17/2024	What is signal transduction
Published	12/17/2024	What are the main steps of signal transduction?
Published	12/17/2024	What are the two response speeds associated with signal transduction and what molecules are they typically mediated by?
Published	12/17/2024	What are the four ranges of signaling? Give a short description for each
Published	12/17/2024	What are G protein-coupled receptors?
Published	12/17/2024	Describe the protein structure of G proteins
Published	12/17/2024	Why is G protein-linked receptor mediated signal transduction so fast?
Published	12/17/2024	What occurs to the GPCR upon ligand binding? What effect does this have on the associated G protein?
Published	12/17/2024	What single amino acid mutation leads to a G protein being virtually non-functional and why?
Published	12/17/2024	What is a GTP analog?
Published	12/17/2024	What are the two important classes of G protein?
Published	12/17/2024	How was the location of binding of G protein to GPCR initially discovered
Published	12/17/2024	What hormone mediate the flight-or-flight response? What effector protein is modulated by the GPCR that binds to that hormone?
Published	12/17/2024	What is cAMP? What protein is it secreted by and what does it activate?
Published	12/17/2024	What responses does the activation of PKA lead to?
Published	12/17/2024	How is cAMP recycled and why?
Published	12/17/2024	How does PKA stimulate glycogen breakdown?
Published	12/17/2024	What is signal amplification? Give an example with epinephrine
Published	12/17/2024	Why do pharmaceutical drugs then to target signal transduction at the ligand or hormone level?
Published	12/17/2024	How is signal response terminated by default?
Published	12/17/2024	Describe desensitization/adaptation of GPCRs
Published	12/17/2024	What organ is usually mutated to study to study RTKs and their downstream effects? Why this organ specifically?
Published	12/17/2024	What does the RAF constitutively active mutant do?
Published	12/17/2024	Say A and B, genes in the same pathway. If a recessive mutation of A supresses the effect CA mutating B, where in the pathway is A likely located rela…
Published	12/17/2024	T/F: RNA splicing always happens after polyadenylation
Published	12/17/2024	Describe the process of 5' capping of mRNA
Published	12/17/2024	Why are most RNA transcribed by RNA pol II 5' capped?
Published	12/17/2024	Is transcription terminated immediately at the polyA signal or is some RNA transcribed past the signal transcribed?
Published	12/17/2024	How can you detect is DNA gets transcribed, even at low abundance? How was this technique used to determined where RNA transcripted is terminated…
Published	12/17/2024	Describe the process of cleave of polyadenylation of mRNA. Name proteins involved.
Published	12/17/2024	Why does the cleave factor wait before cleaving off RNA at the polyA site
Published	12/17/2024	Describe the two stages of polyadenylation.
Published	12/17/2024	Where on the DNA sequence does transcription terminate?
Published	12/17/2024	How is RNA pol II removed from the DNA strand during transcription termination?
Published	12/17/2024	Describe the "torpedo model" of transcription termination
Published	12/17/2024	How was RNA splicing discovered? Described the experiment involving the adenovirus hexon gene.
Published	12/17/2024	What sequence of unspliced RNA is usually genetically conserved?
Published	12/17/2024	Why is RNA more unstable than DNA?
Published	12/17/2024	Describe the two transesterification reactions required in RNA splicing
Published	12/17/2024	T/F: The RNA splicing machinery is necessary for the RNA transesterification reactions needed for splicing
Published	12/17/2024	What is the role of snRNAs U1 and U2 in canonical splicing?
Published	12/17/2024	What is U2AF?
Published	12/17/2024	Describe how the Brr2 helicase promotes the first transesterification reaction
Published	12/17/2024	How is transcription in the opposite direction quickly terminated?
Published	12/17/2024	There may be cases where the polyA sequence is present in the DNA sequence in the right orientation (just by random chance), but is upstream of where …
Published	12/17/2024	How is the exon-intron junction specified? What complex is responsible for this process?
Published	12/17/2024	What are SR proteins?
Published	12/17/2024	What is alternative splicing?
Published	12/17/2024	What proteins usually bind exonic/intronic enhancers?
Published	12/17/2024	What proteins usually bind exonic/intronic silencers?
Published	12/17/2024	How does Sxl (sex lethal) regulate the splicing of genes sxl and tra, contributing to sex determination in Drosophila?
Published	12/17/2024	How is the splicing of RNA for the TF dsx regulated for sex determination in Drosophila?
Published	12/17/2024	What is a protein isoform?
Published	12/17/2024	What are the major forms of alternative splicing?
Published	12/17/2024	Why is mutually exclusive exons different from other forms of alternative splicing?
Published	12/17/2024	What are the 3 classes of mutations that affect RNA splicing?
Published	12/17/2024	What are microexons and why is splicing of these RNA transcripts particular?
Published	12/17/2024	How is SMN2 manipulated in RNA splicing therapy to treat spinal muscular atrophy?
Published	12/17/2024	Why is a minimum intron distance necessary for splicing?
Published	12/17/2024	Describe steric interference in RNA splicing
Published	12/17/2024	T/F: steric interference can happen with introns longer than the minimum distance
Published	12/17/2024	How are some introns non typical in their splicing sites?
Published	12/17/2024	Why are non-typical introns relevant for mutually exclusive exon splicing, specifically in spliceosomal incompatibility?
Published	12/17/2024	Why is nonsense mediated decay relevant for mutually exclusive splicing?
Published	12/17/2024	What is DSCAM and why is it relevant for neuron formation?
Published	12/17/2024	Why do none of the common method for exon mutual exclusivity explain DSCAM?
Published	12/17/2024	How are the 4 exons of DSCAM chosen during splicing?
Published	12/17/2024	What is RNA editing?
Published	12/17/2024	Describe the effect of RNA editing in non-coding regions versus coding regions
Published	12/17/2024	What RNA editing function does the APOBEC family have?
Published	12/17/2024	What RNA editing function does ADAR have, and what effect does this editing have on the structure of RNA?
Published	12/17/2024	How does the APOBEC1 enzyme control protein expression of the ApoB proteins, namely to produce isoforms ApoB-100 and ApoB-48?
Published	12/17/2024	What differentiates APOBEC1 from other cytidine deaminases in the APOBEC family?
Published	12/17/2024	T/F Deaminase APOBEC1 has an RNA binding domain
Published	12/17/2024	How did researchers conclude that APOBEC1 affect more than just the ApoB protein? What sequence was determined to characterize the RNA that APOBEC1 ac…
Published	12/17/2024	What form of RNA does the ADAR family act on? How does this form typically arise?
Published	12/17/2024	Which snRNP can act on introns with non-typical splicing sites?
Published	12/17/2024	How does ADAR2 regulate its own expression?
Published	12/17/2024	What are the major RNA targets of the ADAR family? Justify this based on the structure of the target.
Published	12/17/2024	How does the RNA modification by ADAR1 modification prevent innate immune response to some transcripts?
Published	12/17/2024	How does RNA modification of ADAR2 affect glutamate receptors expressed in the brain?
Published	12/17/2024	How does RNA editing by the ADAR family affect serotonine receptors?
Published	12/17/2024	What evidence is there that A-to-I RNA editing promotes cancer development? Give two (related) points of evidence
Published	12/17/2024	What differentiates cowpox from smallpox? Why was this relevant for the development of the first smallpox vaccine?
Published	12/17/2024	What characterizes next-generation vaccines? What is their main advantage?
Published	12/17/2024	What are the 4 common plateforms through which they are introduced to cells?
Published	12/17/2024	Describe the viral vector vacine
Published	12/17/2024	Why are viral vector vaccines typically non-replicating?
Published	12/17/2024	What is the main advantage of nucleic acid vaccines (RNA/DNA) versus viral vectors?
Published	12/17/2024	Describe DNA vaccines. Why are they much rarer than RNA vaccines?
Published	12/17/2024	Describe mRNA vaccines and 2 disadvantages associated with them.
Published	12/17/2024	What is one disadvatange of nucleic acid vaccines?
Published	12/17/2024	What can DNA vaccines be modified to avoid illiciting an immune response?
Published	12/17/2024	When developing mRNA vaccines, researchers found that the 2-thiouridine nucleoside modification was less immunogenic than the pseudouridine modificati…
Published	12/17/2024	Describe how proteins enter the nucleus via brownian diffusion. Explain why it is not an efficient mechanism
Published	12/17/2024	Give an example of a cis-acting localization factor
Published	12/17/2024	What is a GTPase?
Published	12/17/2024	What is the function of the GAP (GTPase binding protein)?
Published	12/17/2024	What is the function of GEF (Guanine exchange protein)?
Published	12/17/2024	Why does the supply of GTP typically never run out?
Published	12/17/2024	Describe the constitutively active mutant of GTPase
Published	12/17/2024	Describe the dominant negative mutant of GTPase
Published	12/17/2024	Describe the nuclear import process by RAN GTPase.
Published	12/17/2024	Where are the GEF and GAP proteins usually located and why? How is this relevant for nuclear import?
Published	12/17/2024	How does RAN-GTPase return to the nucleus after nuclear import?
Published	12/17/2024	Describe the kinetics studies that concluded that more than just the RAN-GTPase model of import involving NLS is not sufficient to explain how protein…
Published	12/17/2024	How was nuclear export and NES experimentally discovered? (human hamster hybrid)
Published	12/17/2024	Describe the nuclear export process.
Published	12/17/2024	What are messenger ribonucleic particles?
Published	12/17/2024	Ribosomes located in the cytoplasm line up at the nuclear membrane to receive and start translation of mRNPs. What does this indicate about the orient…
Published	12/17/2024	Described how messenger ribonucleoparticles are transported out of the nucleus via the NXF1 and NXT1 proteins.
Published	12/17/2024	T/F: the nuclear side of the membrane is essentially the same as the cytosolic side
Published	12/17/2024	What protein form a mesh network over the nuclear pores?
Published	12/17/2024	Describe how FG proteins form a mesh network, and how transport proteins are able to pass through them.
Published	12/17/2024	Name 3 types of transport proteins between the nucleus and cytoplasm
Published	12/17/2024	What are the 2 factors that accelerate nuclear transport?
Published	12/17/2024	Name 4 mechanisms quality control mechanism for nuclear transport
Published	12/17/2024	Describe quality control necessary for mRNA transport.
Published	12/17/2024	Why is polyA tail recognition plays an important role in quality control of mRNA transport?
Published	12/17/2024	Explain how poorly spliced RNA is blocked from exiting the nucleus.
Published	12/17/2024	How does the RNA transcript of the HIV virus get exported out of the nucleus?
Published	12/17/2024	What is mRNA localization and why does it occur?
Published	12/17/2024	What are 3 different method of mRNA localization?
Published	12/17/2024	Give and describe two applications of mRNA localization
Published	12/17/2024	What is the exon junction complex?
Published	12/17/2024	Describe the structure of the exon-exon complex.
Published	12/17/2024	If eIF4AIII binds to the sugar backbone of RNA in a non-specific manner, how does it ensure to only bind at the exon-exon junction?
Published	12/17/2024	How is the EJC removed from mRNA?
Published	12/17/2024	What is the oskar gene?
Published	12/17/2024	Why is the mutant oskar gene not rescuable by cDNA with only coding genes?
Published	12/17/2024	How can one determine the introns necessary for mRNA localization of a given gene?
Published	12/17/2024	Why is the stop codon located very close to the exon-exon junction of the last exon?
Published	12/17/2024	Describe the process of nonsense mediated decay
Published	12/17/2024	Describe how NMD can be used as a regulatory mechanism.
Published	12/17/2024	What is global regulation in eggs cells, and why is it necessary?
Published	12/17/2024	What is eIF4?
Published	12/17/2024	Describe the process of global downregulation
Published	12/17/2024	Why would it make sense that the 5' cap protein would bind to the polyA tail to make circular mRNA. How was this disproven experimentally.
Published	12/17/2024	Describe local regulation using the ferritin regulation as an example.
Published	12/17/2024	Describe cap independent translation via IRES.
Published	12/17/2024	Explain how a virus can make use of the cap independent translation to spread via a cell.
Published	12/17/2024	Why is food supply dependent global regulation important?
Published	12/17/2024	What protein is reponsible for food supply dependent global regulation of translation?
Published	12/17/2024	How does mTOR kinase activate transcription (5)?
Published	12/17/2024	What proteins deactivate mTOR kinase?
Published	12/17/2024	How does TSC1/TSC2 sense the nutrional status of the body (3)?
Published	12/17/2024	Why does the mTOR heterozygous mouse mutant live longer?
Published	12/17/2024	Describe how the 4E binding protein inhibits translation
Published	12/17/2024	Describe how mTOR kinase inhibits the 4E binding protein
Published	12/17/2024	How does the unfolded protein response arise?
Published	12/17/2024	Describe the unfolded protein response. Give both the short-term and long-term responses
Published	12/17/2024	What sensor protein is used for the unfolded protein response?
Published	12/17/2024	How does BiP sense unfolded proteins?
Published	12/17/2024	Describe the long-term unfolded protein response
Published	12/17/2024	Describe the short term unfolded protein response
Published	12/17/2024	How does the activated PERK kinase inhibit translation?
Published	12/17/2024	How is diabetes related to UPR?
Published	12/17/2024	What are micro RNA?
Published	12/17/2024	What is reverse genetics?
Published	12/17/2024	How do we know that the unc22 miRNA repression is a cytoplasmic mechanism?
Published	12/17/2024	What does a high stochiometric ratio of mRNA and unc22 dsRNA that regulates it tell you?
Published	12/17/2024	Describe how miRNA can be taken up by the RISC complex to regulate mRNA.
Published	12/17/2024	What happens if the miRNA in the RISC complex has a perfect base pairing with the target mRNA
Published	12/17/2024	What happens if the miRNA in the RISC complex has a imperfect base pairing with the target mRNA
Published	12/17/2024	How are miRNA exported from the nucleus?
Published	12/17/2024	How is the turnip crinkle virus affect the Dicer mechanism in turnips?
Published	12/17/2024	What is the mid-blastula transition?
Published	12/17/2024	What happens to maternal mRNA after the mid-bastula transition?
Published	12/17/2024	Why are DNA vaccines much rarer than RNA vaccines?
Published	12/18/2024	What are GPCRs?
Published	12/18/2024	Describe how mass spectrometry can determine the residue composition of a protein
Published	12/18/2024	After determining the peptide composition of a protein using mass spectrometry, how can the protein sequence be estimated?
Published	12/18/2024	How can one confirm the protein sequence of a ligand after estimating it using bioinformatics?
Published	12/18/2024	Once a ligand has been sequenced and isolated, how can one isolate the corresponding receptor?
Published	12/18/2024	T/F: Receptor-Ligand binding is reversible
Published	12/18/2024	If the receptor-ligand binding is very tight, what does that say about the "on" and "off" rates of the binding reactions?
Published	12/18/2024	Give the chemical equilibrium formula for ligand-receptor binding
Published	12/18/2024	In what situation does \([L] = k_D\) in a ligand-receptor binding reaction?
Published	12/18/2024	Describe this graph. What do each of the 3 curves signify, and how were they found? What specific values can we read off this graph?
Published	12/18/2024	Why is it that 50% of receptor binding, the pathway is most active?
Published	12/18/2024	Why is the \(k_D\) for endocrine signaling typically low?
Published	12/18/2024	What are signaling proteins?
Published	12/18/2024	What are the 2 types of molecular switches signaling proteins can act as?
Published	12/18/2024	What are the 3 amino acids that can get phosphorylated in eukaryotes? Which two of them are typically associated?
Published	12/18/2024	In the kinase signaling mechanism, which class of proteins typically inactivates the substrate protein?
Published	12/18/2024	Why are there more kinases proteins than phosphatases?
Published	12/18/2024	What are 2 mutations that can be done to study the specific residues on a protein substrate that are phosphorylated by a given kinase?
Published	12/18/2024	T/F: in kinase signaling, the phosphate group itself is necessary to carry the signal on the substrate protein
Published	12/18/2024	How is the signal typically terminated?
Published	12/18/2024	How do endosomes terminate signaling?
Published	12/18/2024	Describe the complementation test. How can this be used to determine if two genes are in the same pathway?
Published	12/18/2024	Describe deletion analysis. How can this be used to determine if a given mutation is null or missense?
Published	12/18/2024	What is one pitfall of using the complementation test with a deletion?
Published	12/18/2024	How can a double mutant test be used to determine the signal pathway
Published	12/18/2024	Why do both mutations in the double mutant experiment have to be null mutations?
Published	12/18/2024	What are the 2 main categories of mutations? Give the 2 subcategories for each as well
Published	12/18/2024	Describe the GPCR signaling mechanism
Published	12/18/2024	How is AMP and cAMP produced?
Published	12/18/2024	How does gene transcription get activated downtream by GPCRs?
Published	12/18/2024	What is unusual about GPCRs that regulate ion channels?
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