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429 Cards in this Set
- Front
- Back
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What are the three binding sites on tRNA?
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A-site, P-site, E-site
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What type of mRNA can code for multiple proteins on one strand?
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Prokaryotic mRNA
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What is the name for the ambiguous third letter in the codon sequence?
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Wobble position
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Is prokaryotic or eukaryotic transcription more effecient?
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Prokaryotic transcription
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What is the start codon in translation?
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AUG
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What are ribosomes composed of?
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2/3 rRNA and 1/3 proteins
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What is it called when multiple ribosomes attach to one mRNA strand at the same time?
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A polyribosome
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What organelle has its own DNA?
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Mitochondria
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Where should proteins destined for membrane location or secretion be directed?
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Endoplasmic reticulum
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What is te multiprotein comples that degrades incorrectly folded proteins?
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Proteasome
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Diseases such as Huntington's disease, Alzheimer's disease, and prion disease are caused by what?
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Protein aggregates
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What is the purpose of chaperone proteins?
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Help fold proteins
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What is the less condensed, sometimes transcriptionally active form of chromatin called?
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Euchromatin
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What is the more codensed, transcriptionally inactive form of chromatin called?
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Heterochromatin
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What makes DNA and histones bind so tightly that transcription cannot occur?
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Histone deacetylase (HDAC)
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What makes DNA and histones loose so that transcription can occur?
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Histone acetyltransferase (HAT)
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What is the antibiotic that blocks the forward pathway from the endoplasmic reticulum to the golgi apparatus?
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Brefeldin A
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What protein forms a shell around vesicles?
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Clathrin
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The hydrolytic enzymes in what organelle only function at an acidic pH of 5?
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Lysosome
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What type of channels can open in response to voltage,ligand binding, or mechanical events?
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Ion channel linked receptors
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How many amino acids per second does a prokaryotic ribosome add to a polypeptide?
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20 amino acids/second
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What is the name of the RNA sequence that the 16S rRNA in prokaryotic ribosomes recognizes during translation initiation?
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Shine-Dalgarno sequence
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What is the role of IF2 during initiation of prokaryotic protein synthesis?
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It transfers fMet-tRNA to the P position of the ribosome
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What elongation factor catalyzes peptide translocation in prokaryotes?
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EF-G
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Which component of a ribosome is responsible for its enzymatic functon during protein synthesis?
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rRNA
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During eukaryotic translation initiation, the initiator tRNA moves along rRNA searching for the first start codon, but it may miss the first or second start codon. What is the phenomenon called?
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Leaky scanning
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Where in the cell is the N-linked precursor oligosaccharide added to most proteins?
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Endoplasmic reticulum lumen
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What is the name of the human disease caused by eating meat contaminated with prion proteins?
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Creuzfeldt-Jacob disease
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What are the three steps of ubiquitin dependent protein degradation?
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Activation, conjugation, ligation
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What is the post translational modification that causes DNA to be less tightly bound to histones in euchromatin?
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Acetylation
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O-linked glycosylations occur on which amino acid residues?
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Serine and threonine
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What is the name of the drug that disrupts microtubules on the Golgi body's return pathway?
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Nocodazole
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What is the name of the protein that pinches the clathrin coated vesicle from the membrane during exoctyosis?
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Dynamin
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Why is the lysosome controlled tightly by pH?
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It is a safety factor to prevent its contents from destroying the cell
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What is the difference between a constitutive secretory pathway and a regulated secretory pathway?
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Constitutive pathways occur all the time, whereas regulated pathways occur in response to a stimulus from environment
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What subunit of heterotimeric G protein coupled receptor binds guanine nucleotides?
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Alpha
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What is a hallmark feature of receptor tyrosine kinases?
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Receptor dimerization
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How do tRNA synthetases ensure the correct amino acid is bound to tRNA?
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The correct amino acid has the highest affinity for the active site pocket of the synthetase, and there is an additional editing pocket where incorrect amino acids are removed
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What enzyme catalyzes peptide bond formation?
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Peptidyl transferase
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What type of RNA locates where to cleave 45S precursor rRNA in eukaryotes?
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snoRNA
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What are the four major PTM's?
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Phosphorylation,Acetylation, Ubiquitination, Glycosylation
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What is the major function of phosphorylation?
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Cell signaling and protein regulation
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What is the major function of acetylation?
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Histones and gene regulation
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What is the major function of ubiquitination?
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Protein degradation
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What is the major function of glycosylation?
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Protein targeting and cell adhesion
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How does glucose interact with hexokinase and what is the result of that interaction?
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Glucose enters and binds to hexokinase causng a conformational change in the two lobes. This conformational change allows hexokinase to add a phosphate to the glucose from an ATP molecule
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What does an allosteric effect mean?
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A change in one part of the protein causes there to be a change in another part of the protein
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What is the allosteric effect that takes place in the example above (number 50) of glucose binding to hexokinase?
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When glucose is bound to hexokinase the part of hexokinase that binds ATP has ~50 times greater affinity for ATP than it does when glucose is not bound to hexokinase
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What are the 3 amino acids that get phosphorylated in mammalian cells?
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Serine, Tyrosine, and Threonine
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Why are they the only three that are phosphorylated?
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They have hydroxyl groups on their side chains and therefore have the capability to bind the phosphate group
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How does phosphorylation cause a conformational change in a protein?
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The negatively charged phosphate interacts with the positively charged side chains of amino acids
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What is the effect of conformational changes on a protein? Why?
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Conformational changes effect the function of the protein because there is a direct relationship between the structure and the function of a protein
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What are the 3 common domains of protein kinases?
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N-terminus, C-terminus and the activation loop
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In which one of the domains in question 57 does ATP bind?
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The N-terminus
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Which one of the domains in question 57 gets a negatively charged phosphate group bound to it?
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The activation loop
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To which one of the domains in question 57 does the substrate bind?
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The C-terminus
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Which proteins can remove a phosphate group?
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Protein phosphatases
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Does the additon of a phosphate group always mean that the protein is "turned on"?
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No. Sometimes removal of the phosphate group activates the protein.
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What three criteria must be met in cyclin dependent kinases in order to activate the kinase?
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A phosphate must be removed, a phosphate must be added, and cyclin must be bound to the kinase
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What is the name of the drug that inhibits cyclin dependent kinases and what is the mechanism of action?
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Flavopiridol. It competes for the ATP binding site in the kinase.
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What are the two subunits of prokaryotic ribosome?
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50S and 30S
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What are the two subunits of eukaryotic ribosome?
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60S and 40S
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What are the major types of receptors?
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Ion channel linked, G-protein coupled & Enzyme linked
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What type of ion channel depolarizes membrane?
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Excitatory
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What type of ion channel hyperpolarizes membrane?
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Inhibitory
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Name the signaling molecules in Phospholipase activation of Protein Kinase C (PKC)
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Inositol 1,4,5-triphosphate (IP3) and Diacylglycerol (DAG)
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Name the three ubiquitin conjugating regulatory enzymes and their functions
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E1 enzyme: forms thioester linkage; E2 enzyme: couples to Ub; E3 enzyme: conjugates protein to Ub
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What is the peptide sequence that retains ER proteins?
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KDEL in C-terminus
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What is the peptide sequence that import proteins into the nucleus?
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PPKKKRKV
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What is the peptide sequence that export proteins out of the nucleus?
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ALQKKLEELEL
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What is the default pathway in protein sorting?
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ER > Golgi > Cell Surface
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Name the enzyme that catalyzes glycosylation
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Glycosyl transferase
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What is the spatial organization of Golgi?
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Cis (closest to ER), Stacks & Trans
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Name the drugs that block return pathway of Golgi protein transport
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Nocodazole
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Name the vesicle coat proteins
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Clathrin, COP I & COP II
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Which coat protein is found in vesicle trafficking between Golgi and plasma membrane?
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Clathrin
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Name two types of exocytosis pathways
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Regulated and Constitutive
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Name the three pathways to protein degradation in lysosomes
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Phagocytosis; Endocytosis; Autophagy
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How are protein targeted to lysosome?
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Addition of Mannose 6-phosphate
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Which exocytosis pathway require external signal like hormones, neurotransmitters or digestive enzymes?
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Regulated secretory pathway
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What are chaperone proteins?
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Hsp60 and Hsp70
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Which proteins lead to cellular indegestion which can get rid of misfolded proteins?
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Aggresomes and Russell Bodies
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which proteins does proteasome get rid of?
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recognize the ubiquitin and degrade those ubiquitinated proteins
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What is an example of proteasome inhibitor?
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Bortezomib (Velcade)
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How does Velcade work?
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It binds to catalytic site of the proteasome
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Where does N-linked glycosylation occur?
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It occurs in asparagine
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Where does O-linked glycosylation occur?
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It Occur on hydroxyl group of serine and threonine
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What is mucin?
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Mucin is glycosylated membrane protein, involved in cell recognition and possibly intracellular signaling
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What is an example of sulfated proteoglycan?
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heparin sulfate which is important in blood coagulation
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what is ERSDs, Endoplasmic reticulum storage diseases?
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improperly folded proteins that are retained in endoplasmic reticulum which can’t be degraded from the proteomic system
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What is congenital hypothyroid goiter?
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Defective thyroglobulin synthesis or secretion due to post-translation defects
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What are the functions of cis part of the golgi?
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Sorting and phosphorylation of oligosaccarides on lysosomal proteins
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what are the functions of stacks part of the golgi?
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removing and additions of sugar molecules
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what are the functions of trans part of the golgi?
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sulfation of tyrosines and carbohydrates and sorting into various vesicles to be transported out of the golgi
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What is SNARE and SNAP?
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SNAP Receptor and soluble NSF attachment protein which both direct specific vesicles from one place to another.
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Where is V-SNARE found at?
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Found on the vesicles of the donor compartment
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Where is T-SNARE found at?
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Found on the vesicles of the destination compartment
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What is Rab protein?
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GTPases that provides specificity facilitated by hydrolysis of GTP for targeting vesicles
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What is one example of lysosomal enzyme deficiency?
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Tay-Sach which has Hexosaminidase A enzyme deficiency
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What is general mechanism of phagocytosis?
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It's processed into a phagosome and passed onto lysosome.
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What is an inosine and what is its role?
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A deaminated guanine that is a possible anti-codon base and can bind to codon base
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What is peptidyl transferase and what is its role?
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A ribozyme that functions through the large ribosomal subunit to catalyze peptide bonds between amino acids
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Translation terminates when
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Release factor binds to the A site and other factors help detach mRNA and dissemble ribosome
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EF-Tu in prokaryotes is similar to eEF1 in eukaryotes, what are their functions?
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Both recognize and send the correct tRNA into the A site
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EF-G in prokaryotes is similar to eEF2 in eukaryotes, what are their functions?
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Both translocate (move) tRNA along the sites of ribosome complex
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How does cycloheximide inhibit protein synthesis?
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Inhibits the peptidyl transferase activity of 60s subunit (eukaryotes)
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How does mRNA get to anchor proteins?
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Transport on cytoskeleton, random diffusion and trapping, or degradation
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How is 3’UTR important in cytoplasmic localization?
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Contains a “zip code” to signal where mRNA is to be sent
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What stressful events decrease protein synthesis in eukaryotes?
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Scarcity of growth factors or nutrients, viral infections, increase in temperatures, and hypoxia (low oxygen)
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How is guanine exchange factor deactivated?
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Under stressful conditions, the protein is phosphorylated
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What is mTOR?
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Mammalian target of rapamycin, it is a protein kinase that phosphorylates 4E-BP to initiate translation
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Protein glycosylation involves linkage of sugar with what amino acid?
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Asparagine
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Tagging a misfolded/misassembled protein with what molecule signals the protein for degradation
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Ubiquitin
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Signal that targets specific proteins for the lysosome
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Mannose-6-phosphate
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Ion channel receptors are targets for what group of drugs
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Psychoactive drugs
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Glycogen breakdown is mediated by what type of receptor?
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G-coupled protein receptors
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Receptor tyrosine kinases are activated by
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Receptor dimerization, autophosphorylation, and recruitment of signal proteins
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Agonist removal, receptor uncoupling, receptor endocytosis, and receptor-down regulation are types of
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Termination of receptor activity
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Protein involved in the cleavage of newly formed vesicles from ER
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Dynamin
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The deletion of this amino acid is common in 70% of cystic fibrosis patients
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Phenylalanine
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What does proteasome composed of?
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minimum of 10 polypeptides, ATP hydrolysis, and covalently attches to ubiquitin
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What regulates half-life of proteins?
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proteasome
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How many amino acids does ubituitin have?
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76 amino acids
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What treatment does Bortezomib (Velcade) provide?
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Bortezomib is used to treat myeloma and lymphoma
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Name several diseases related to aggresomes and Russell bodies
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liver, cystic fibrosis, neurodegeneration
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Where does acetylation occur?
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acetylation occurs on lysine residues of histones
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What are components of nucleosome?
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histone octamer, 2-turns of DNA, and linker DNA
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Describe the process of acetylation and transcription of active chromosome?
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The process occur at H3 and H4, along with phosphorylation, the charge of N-terminal region is altered, separating histone and DNA, and transcription factors can access the DNA.
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During the process of chemical acetylation, what intermediate compound is a mutagen that target DNA, lipids, and proteins?
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Acetaldehyde
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What enzyme activate mutation during chemical acetylation process?
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alcohol dehydrogenase
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What enzyme inactivate mutation during chemical acetylation process?
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aldehyde dehydrogenase
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What are enzymes involved in glycosylation?
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Glycosylatransferase and glycosidase
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Where does glycosylaton take place?
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Glycosylation take place in endoplasmic reticulum and Golgi complex
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Where does sulfation occur on proteoglycan?
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on sugar residues and tyrosine residues
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Defects in sulfation can cause
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skeletal deformities
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What diseases are related to defects in cytoskeletal proteins participating in membrane transport?
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Griscelli's syndrome, Elejalde's syndrome
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Occulocerebrorenal syndrome is caused by
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lipid disorders affecting transportation of vesicles
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What is proopiomelanocortin?
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precursor protein containing 265 amino acids that is processed by the Golgi to form ACTH, MSH, endorphins, and other small peptides
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What disease is caused by a mutation in LDL receptor encoding gene?
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atherosclerosis
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What are the fates of endocytosed receptor?
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recycling, degradation, transcytosis
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Where is the site of protein translation?
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Ribosomes
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How many tRNA binding sites do ribosomes have?
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3
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What are the 3 tRNA binding sites of the ribosomes
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A site, P site, E site
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What is the elongation factors in eukaryotes?
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eEF1, eEF2
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What is the elongation factors in prokaryotes?
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EF1A (EF-Tu), EF1B (EF-Ts), EF2 (EF-G)
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What is the role of the 19S cap in the proteasome?
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The 19S cap’s role is the recognition and unfolding of misfolded proteins.
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What is the role of the 20S cylinder in the proteasome?
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The 20S cylinder’s role is the digestion of proteins.
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Do the eukaryotes or prokaryotes have their mRNA capped at the 5’ end?
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Eukaryotes
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What are Huntington’s, Alzheimer’s, and Prion Diseases caused by?
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Protein aggregations
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What are the 2 forms of chromatin?
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Euchromatin and Heterochromatin
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Where are proteins processed?
|
Golgi apparatus
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What type of transport occurs between the cytosol and nucleus?
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Gated transport
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Does Brefeldin A block the forward or return pathway?
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Forward pathway
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Does Nocodazole block the forward or return pathway?
|
Return pathway
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What is the required pH for the lysosome to function?
|
5
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What type of secretory pathways do neurotransmitters, digestive enzymes and hormones fall under?
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Regulated
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What type of secretory pathways do extracellular matrix proteins such as glycoproteins and proteoglycans fall under?
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Constitutive
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Which is closer to the ER, the cis or trans part of the Golgi apparatus?
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Cis
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What type of post-translational modifications mainly deals with cell signaling and protein regulation?
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Phosphorylation
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What type of post-translational modifications mainly deals with histones and gene regulation?
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Acetylation
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What constitutes ~20% of a cell's dry mass?
|
Proteins
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What special sequence of the mRNA do prokaryotic ribosomes recognize?
|
Shine Dalgarno sequence
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Do some amino acids have more than one tRNA?
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Yes
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During protein synthesis in prokaryotes, what is the function of IF1?
|
IF1 interacts with the A site, prevents the free access of fMet-tRNA, and prevents binding of the 50S subunit.
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During protein synthesis in prokaryotes, what is the role of IF2?
|
IF2 transfers the fMet-tRNAf to the P position in the ribosome.
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What is peptide bond formation catalyzed by?
|
Peptidyl transferase
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What molecule locates the sites of chemical modification?
|
snoRNA
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What are the release factors in eukaryotes?
|
eRF1 and eRF3.
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In which organisms is translation coupled to transcription?
|
Bacteria
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In which organisms is their mRNA capped?
|
Eukaryotes
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Are all mRNA polyadenylated at the 3' end?
|
No, only in eukaryotes.
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Where does translation occur in eukaryotes?
|
Cytoplasm
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Which antibiotic causes premature chain termination by acting as an analog of aminoacyl-tRNA?
|
Puromycin
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What is the primary cause of antibiotic resistance?
|
Mutation, through "horizontal gene transfer."
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How many human proteins are there known to be?
|
1 million
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What is a function of the golgi involving protein sorting and trafficking?
|
Glycosylation
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What is a purpose of glycosylation in the golgi?
|
Protein folding, target, recognition, signaling, or protection of the cell surface.
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What is a drug that blocks golgi protein transport pathways?
|
Brefeldin A or Nocodazole.
|
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Where is proopiomelanocortin synthesized?
|
Anterior pituitary
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What does MSH do?
|
MSH stimulates the production of melanin.
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What is an enzyme that hydrolyzes lipids and generates signaling molecules?
|
Phospholipase C
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|
What are three fates of endocytosed receptor?
|
Recycling, degradation, and transcytosis
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What is a function of statin?
|
It inhibits de novo synthesis of cholesterol.
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What allows exposure of DNA binding site and Hsp90 release?
|
Steroid
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What does PEPCK stand for?
|
phosphoenol pyruvate carboxykinase
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What is the early response of steroid hormones?
|
Induction of a select number of genes (primary response).
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What are two symptoms of AME (Apparent Mineralocorticoid Excess)?
|
"Hypertension and suppression of renin-angiotensin-aldosterone system (suggests aldosterone hypersecretion).
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What causes AME (Apparent Mineralocorticoid Excess)?
|
It can be caused by licorice ingestion.
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Name three examples of post-translational modifications.
|
Phosphorylation, acetylation, and ubiquitylation.
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What are three structural features of protein kinases?
|
ATP binding domain (N-terminus), activation loop, and substrate binding regions (C-terminus).
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Is phosphorylation reversible or not?
|
It is reversible.
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What does CDK stand for?
|
Cyclin-Dependent protein Kinase
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What is a potent inhibitor that competes with ATP binding site?
|
Flavopiridol
|
|
|
List three ways to regulate CDK (Cyclin-Dependent protein Kinase) activity.
|
Cyclin synthesis and binding, CDK phosphorylation, and CDK dephosphorylation.
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|
List three diseases related to protein aggregation.
|
"Huntingtons, Alzheimers, and Prion Diseases
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What are two characteristics of heterochromatin?
|
It is highly condensed and transcriptionally inactive.
|
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Name two enzymes that regulate immune response by controlling hematopoiesis, apoptosis, and protein trafficking.
|
Glycosyltransferase and glycosidase enzymes
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|
|
What is a function of o-linked glycosylations?
|
proteoglycan synthesis for extracellular matrix, plasma membrane, and mucus components lining epithelia.
|
|
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Are proteoglycans heavily sulfated or not?
|
Proteoglycans are heavily sulfated.
|
|
|
What is an example of sulfated proteoglycan?
|
Heparin sulfate
|
|
|
What are the 2 functions of the ER signal sequence of a soluable protein?
|
1) to direct the protein to the ER 2) to keep the pore of the translocator open
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What is Co-Translatopnal Folding?
|
The Protein is folded as it is in the process of being translated
|
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|
What effct does a Prion Protein have on other proteins of the same type?
|
It casues other proteins of the same type to misfold
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What kind of bond does an E1 Enzyme create during Ubiquitin-dependant protein degredation?
|
Thioester Linkage
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What does HAT stand for?
|
Histone acetyltransferase
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|
What peptide sequences seems to mean "Retain in the ER"?
|
...KDEL...
|
|
|
What are the 3 major types of Receptors?
|
1) Ion Channel Linked 2) G-protein Coupled 3) Enzyme Linked
|
|
|
What Neurotransmitters are associated with an EXCITATORY action?
|
1) Ach 2) Glutamte 3) Seratonin
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|
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What Neurotransmitters are associated with an INHIBITORY action?
|
1) GABA 2) Glycine
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|
What 3 things can happen to a endocytosed receptor?
|
1) degraded 2) Transcytosis [Moved (ex. Apical --> basal)] 3) recycled (returns to the plasma membrane later)
|
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|
Name 1 negatively charged ions associated with the polarity of a cell
|
Cl-
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Name 3 positively charged ions associated with the polarity of a cell
|
Na+, K+, Ca2+
|
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|
What disease states can drugs that target ion channel receptors be used to treat?
|
insomnia, anxiety, depression, and schizophrenia.
|
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|
What are 4 ways that receptor activity can be terminated?
|
Agonist removal (degradation), Receptor uncoupling (G-protein uncoupling), Receptor endocytosis, Receptor down-regulation (decreased synthesis).
|
|
|
What does classes 1 & 2 of LDL receptor mutations affect?
|
Class 1 and 2 affect receptor synthesis at ER and transport through Golgi complex.
|
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|
What does class 3 of LDL recetor mutations affect?
|
Class 3 affects LDL binding
|
|
|
What does classes 4 & 5 of LDL receptor mutations affect?
|
Class 4 and 5 affect receptor endocytosis and recycling.
|
|
|
What is a "hole" the nuclear envelop called?
|
Nuclear Pore Complex
|
|
|
What is the default pathway of a plasma protein reaching the surface of the cell?
|
ER --> Golgi body --> Cell Surface
|
|
|
What is proopiomelanocortin proteolyzed into?
|
ACTH, MSH, Endorphins, other small peptides
|
|
|
What is the name of the space between a neuron and a mucle cell?
|
synapse
|
|
|
What neurotransmitter acts on heart muscles to decrease contractions in heart tissue?
|
Acetylcholine (Ach)
|
|
|
In a signaling cascade what is the full name of the MAP enzyme?
|
Mitogen activated protein
|
|
|
What are the 4 protein binding domains that mediate molecular interactions in signaling pathways?
|
1. SH2 (Src homology-2) 2. PTB (phosphotyrosine binding) 3. PH (pleckstrin homology) 4. SH3 (Src homology-3)
|
|
|
Cocaine stimulates which neurotransmitter that is strongly associated with the reward system in the brain?
|
dopamine
|
|
|
Which protein is important for immunosuppression and is involved in the rejection of organ transplants?
|
Nuclear factor of activated T-cells (NFAT)
|
|
|
What directly connects the cytoplasm of two cells and allows various molecules and ions to pass freely between the cells?
|
gap junction
|
|
|
What is the function of phospholipase C (PLC)?
|
hydrolyzes lipids and generates signaling molecules
|
|
|
What are the three fates of an endocytosed receptor?
|
1. recycling 2. degradation 3. transcytosis
|
|
|
Do statins increase or decrease LDL receptor levels in the liver?
|
increase
|
|
|
What is the signaling peptide that keeps a protein in the ER and is only found in the ER?
|
KDEL
|
|
|
What is the function of Brefeldin A in the protein transport pathway?
|
Brefeldin A is an antibiotic produced by a fungus that blocks the Golgi protein transport pathway.
|
|
|
Which monomeric G protein hydrolyzes GTP to facilitate specificity?
|
Rab protein
|
|
|
What is the name of the protein kinase that is the mammalian target of rapamycin?
|
mTOR
|
|
|
What is the name of the particle that has a flexible binding pocket and contains 6 subunits of proteins and a small piece of mRNA?
|
signal recognition particle (SRP)
|
|
|
What do misfolded proteins in the ER activate to ensure that the protein's folding capacity is not overwhelmed?
|
unfolded protein response (UPR)
|
|
|
The "mad cow disease" is caused by which misfolded protein?
|
prion protein (PrP)
|
|
|
What are the names of the three tRNA binding sites in ribosomes?
|
A: aminoacyl-tRNA P: peptidyl-tRNA E: exit
|
|
|
A peptide bond formation is catalyzed by which enzyme?
|
peptidyl transferase
|
|
|
What kind of RNAs locate the sites of modification and signals where to cut precursor mRNA?
|
snoRNA
|
|
|
What function do PTM’s have?
|
They regulate protein structures, folding, assembly in the multi-protein complexes, enzymatic activities and expression levels
|
|
|
What enzyme mediates phosphorylation?
|
Protein kinase
|
|
|
What are the three common structural features of protein kinase?
|
ATP binding domain, activation loop, substrate binding region
|
|
|
Where is the ATP binding domain found on the protein kinase?
|
N-terminus
|
|
|
Where is the substrate binding region found on the protein kinase?
|
C-terminus
|
|
|
What do phosphatases do?
|
They remove phosphates from the substrate
|
|
|
What is the purpose of chaperone proteins?
|
They help facilitate proper protein folding and assembly
|
|
|
What are the two chaperone proteins talked about in class?
|
Hsp60 and Hsp70
|
|
|
Which cell structure will degrade an incorrectly folded protein?
|
The proteosome
|
|
|
What is cystic fibrosis?
|
It is a disorder in which thick mucus secretions lead to chronic obstructive lung disease and infection.
|
|
|
What single amino acid deletion is common in CF patients?
|
F508
|
|
|
Which type of chromatin is less condensed?
|
Euchromatin
|
|
|
Where does glycosylation occur?
|
In the endoplasmic reticulum and the golgi complex
|
|
|
What enzyme catalyzes O-linked glycosylations?
|
Glycosyl transferase
|
|
|
If sulfation defects are present, what could this lead to?
|
Skeletal deformities
|
|
|
What two drugs block the golgi protein transport pathways?
|
Brefeldin A and Nocodazole
|
|
|
Which organelle is involved in the processing of propiomelanocortin?
|
The golgi complex
|
|
|
What does SNAP stand for?
|
Soluble NSF-attachment protein
|
|
|
What disease has mutated dynamin proteins, which are normally used for vesicle budding?
|
Charcot-Marie-Tooth
|
|
|
What is the pathway dependent on phosphorylation?
|
Mitogen activated protein (MAP) kinase pathway
|
|
|
What does protein synthesis need to occur?
|
Amino acids, mRNA, tRNA, ribosomes, and accessory protiens are needed
|
|
|
What are the three tRNA binding sites on a ribosome called?
|
The A (aminoacyl-tRNA) site, the P (peptidyl-tRNA) site and the E (exit site)
|
|
|
How many proteins does a eukaryotic mRNA code for?
|
It codes for one (1) protein only. Prokaryotic mRNA's can code for multiple proteins.
|
|
|
What are ribozymes?
|
Ribozymes are rRNA molecules that show enzmatic activity. They help with RNA-splicing reactions and peptidyl transferase reactions.
|
|
|
What purpose of the 3' Untranslated Region (UTR) serve?
|
The UTR is very important for cytoplasmic localization.
|
|
|
How are single-pass transmembrane proteins integrated into the ER membrane?
|
They possess a start-transfer sequence which lets them pass through the protein translocator and a stop-transfer sequence that keeps in in the membrane.
|
|
|
What protein complex degrades misfolded proteins?
|
The proteasome
|
|
|
What are some major diseases caused by protein aggregates?
|
This group of diseases includes Huntington's disease, Alzheimer's disease, and prion disease.
|
|
|
What levels of protein structure do postranslational modifications affect?
|
They affect all of the different levels of protein structure: primary, secondary, tertiary, and quaternary.
|
|
|
What are allosteric effects?
|
Allosteric effects occur when a molecule can change an enzyme's activity by binding a site that is NOT the active site.
|
|
|
What effect does ubiquilylating a protein have?
|
It marks that protein to be degraded.
|
|
|
How do HSP proteins help in protein folding?
|
HSP70 proteins help proteins with their initial folding and HSP60 proteins help proteins refold in the HSP60-like protein complex
|
|
|
Which organelles are involved in protein sorting and trafficking?
|
The active organelles include the nucleus, the rough ER, the Golgi apparatus, lysosomes, endosomes, and secretory vessels
|
|
|
How does vesicular transport occur?
|
The donor compartment buds off a vesicle with desired contents and that vesicle then fuses with the target compartment.
|
|
|
Why are lysosomes acidic relative to the cytoplasm?
|
This is a safety feature in case the lysosome ruptures. The hydrolytic enzymes in the compartment will not damage the rest of the cell.
|
|
|
What clinical relevance is there to clatharin coated endocytosis?
|
Clatharin coated endocytosis imports cholesterol and is relevant to atheroschlerosis.
|
|
|
What are the three major kinds of receptors?
|
They are ion-channel linked, G-protein coupled, and enzyme linked receptors.
|
|
|
Ion-channel receptors can be targeted to treat which disorders?
|
They can be used to treat insomnia, anxiety, depression, and schizophrenia.
|
|
|
What change is caused by class 1 and 2 LDL receptor mutations?
|
Class 1 and 2 mutations affect receptor synthesis at the ER and transport through the Golgi complex
|
|
|
What are the units that compose G-proteins?
|
The alpha, beta, and gamma subunits.
|
|
|
Which two tRNA binding sites extend into the small ribosomal subunit?
|
A-site and P-site
|
|
|
What secondary structure in tRNA recognizes mRNA?
|
Anticodon loop
|
|
|
What high energy bond is formed between an amino acid and the 3' end of tRNA?
|
Ester bond, energy is important for the tranfer of the polypeptide.
|
|
|
What is the significance of the Shine Dalgarno sequence?
|
It is the location where the ribosomes in prokaryotes will be assembled which allows for multiple genes to be translated simultaneously.
|
|
|
What is the difference between EF-Tu and EF-G?
|
EF-tu helps recognize the correct tRNA. EF-G pushes the peptide from A to P position to make A position available again.
|
|
|
What is responsible for the overall structure of the ribosome (A,P, E sites)?
|
rRNA
|
|
|
What is the role of eIF-2 in protein synthesis?
|
EIF2 brings charged initiator tRNA to the small ribosomal subunit with a GTP bound to it.
|
|
|
What are the two functions of the ER signal sequence of a soluble protein?
|
directs the protein to the ER, keeps the pore of translocator open
|
|
|
What are some diseases caused by protein aggregates?
|
Huntinton's disease, Alzheimer's disease, prion disease
|
|
|
What are the three common features of protein kinases?
|
ATP binding domain on N-terminus, activation loop, substrate binding regions on C-terminus
|
|
|
What is the function of Hsp70?
|
recognizes the newly synthesized protein and helps it properly fold
|
|
|
Where does glycosylation occur in the cell?
|
occurs in ER and Golgi complex
|
|
|
In what section will proteins first get into the Golgi?
|
Cis section of the Golgi
|
|
|
How does Brefeldin block Golgi protein transport pathways?
|
Brefeldin blocks vesicles coming from the ER to the Golgi. Blocks the forward pathway.
|
|
|
Where in the Golgi will addition and trimming of sugar molecules take place?
|
Stacks section of the Golgi.
|
|
|
What energy source is needed to transfer phosphates to proteins?
|
ATP
|
|
|
What heat shock protein forms a container where midfolded proteins can enter?
|
Hsp60
|
|
|
In presence of what energy source can misfolded proteins get properly folded in the Hsp protein complex?
|
ATP
|
|
|
What kind of signaled proteins get sent to the proteasome for degredation?
|
ubiquitinated proteins
|
|
|
What gets sent out from the proteasome after proteins are degraded?
|
small peptides and amino acids
|
|
|
What are the three types of signaling proteins that mediate signal transduction?
|
The three types are kinases, phosphatase, GTP binding proteins.
|
|
|
What is paracrine signaling?
|
This is a signaling process in which a molecule is secreted from one cell into the extracellular space. This molecule traverses the extracellular space until it comes upon a target cell where it interacts with receptors to pass along the signal from the original cell.
|
|
|
What is one type of tissue where gap junctions are extensively utilized?
|
Gap junctions are extensively used in cardiac tissue.
|
|
|
What type of response does acetylcholine produce in salivary glands?
|
Acetylcholine induces secretion in the salivary glands.
|
|
|
What are three types of activities that the MAPK pathway is responsible for?
|
The MAPK pathway is responsible for regulation of metabolic pathway, regulation of gene expression, and changes in cytoskeleton.
|
|
|
What is the purpose of phosphorylation of an activated receptor tyrosine kinase?
|
The phosphorylation allows for the creation of a unique recognition motifs for interactions with intracellular signaling proteins.
|
|
|
What is the purpose of scaffolding proteins?
|
These proteins keep intracellular signaling proteins in close proximity to the receptor to allow signaling complexes to quickly form.
|
|
|
What protein feature does the SH2 domain recognize?
|
The SH2 domain recognizes the phosphorylated tyrosine on receptors.
|
|
|
What is the function of the PH domain?
|
The PH domain is responsible for recruitment of intracellular proteins to the inner side of the plasma membrane.
|
|
|
What region of a protein does the SH3 domain interact with?
|
The SH3 domain interacts with proline-rich regions of a protein to facilitate downstream signaling.
|
|
|
What is the central dogma?
|
DNA is transcribed into RNA during transcription. RNA is then translated into protein during translation.
|
|
|
What are the 3 tRNA binding sites?
|
Aminoacyl-tRNA, peptidyl-tRNA and exit site
|
|
|
Which subunit of prokaryote's ribosome is prevented from binding during initation of protein synthesis?
|
50S
|
|
|
Which enzyme catalyzes peptide bond formation?
|
Peptidyl transferase
|
|
|
What is the function of EF-G (translocase) enzyme in protein synthesis?
|
The enzyme transfers the newly formed peptide from A to P position, allowing A-site to be available agan for the next cycle
|
|
|
What is the function of eIF-2 in eukaryotic protein synthesis?
|
eIF-2 is an iniation factor, helping Met-tRNA bind to small ribosomal subunit under the presence of GTP.
|
|
|
In eukaryotes, the polyA tail is shortned by which enzyme?
|
Exonuclease shortens the polyA tail while endonuclease cleaves most of the polyA tail.
|
|
|
Which unit of proteasome can recognize and unfold misfoled protein?
|
19S cap
|
|
|
List common structures of protein kinase
|
ATP-binding domain located at N-terminal, substrate-binding regions located at C-terminal and activation loop
|
|
|
What is the primary function of chaperone proteins such as Hsp60 and Hsp70?
|
Chaperone proteins recognize newly synthesized proteins and help fold them correctly
|
|
|
Where does glycosylation during post-translational modification occur?
|
The process occurs in endoplasic reticulum and golgi
|
|
|
What is the sequence signaling for importing proteins into nucleus?
|
KKKRKV
|
|
|
What is the significance of glycosylation?
|
Glycosylation helps with the process of protein folding, increases specificity for that protein in targeting, signaling or recognition. It also serves as a protection layer for the cell surface.
|
|
|
At which pH will lysosome be functional?
|
Lysosome is functional at pH 5.0
|
|
|
What occurs during excitatory phase at chemical synapse?
|
Ion channels open and membrane is depolarized
|
|
|
What are the steps to activate adenylyl cyclase?
|
Conformational change after hormone binding and interaction with G-protein. GTP/GDP exchange occurs. Then Beta and Gamma subunits are released while alpha subunit interacts with adenylyl cyclase. The alpha subunit hydrolyzes GTP into GDP in order for trimeric G-protein is formed again for the next cycle.
|
|
|
How is LDL receptor endocytosed?
|
LDL receptor will be coated in clathrin, forming clathrin pits.
|
|
|
Which class of LDL receptor mutation affects receptor endocytosis?
|
Class 4 and 5
|
|
|
What is the characteristic of ligands for non-membrane bound receptors?
|
They are small, hydrophobic molecules.
|
|
|
Which enzyme catalyzes the synthesis of eukaryotic tRNAs?
|
RNA polymerase III
|
|
|
How can the anticodons of tRNAs basepair with multiple codons
|
Wobble
|
|
|
What enzyme catalyzes peptide bond formation?
|
Peptidyl transferase
|
|
|
What is the ratio of rRNA to proteins in the ribosome
|
2 to 1
|
|
|
What size subunits form a bacterial ribosome?
|
30S and 50S
|
|
|
What is the primary cause of antibiotic resistance
|
Mutation
|
|
|
What is one of the three mechanisms of mRNA localization?
|
Random Diffusion (or cytoskeletal motors or binding to anchors)
|
|
|
What is a condition during which rate of protein synthesis will decrease?
|
Stress- from viral infection
|
|
|
What organelle organizes proteins to be secreted or membrane associated?
|
Endoplasmic reticulum
|
|
|
What three diseases are caused by protein aggregates?
|
Prion disease, Huntington's disease, and Alzheimer's disease
|
|
|
What is the role of the signal recognition particle?
|
Binds to new peptide to mark it for movement into the endoplasmic reticulum
|
|
|
What type of enzyme reverses phosphorylation?
|
phosphatase
|
|
|
How does Flavoiridol inhbit CDK?
|
Competes with ATP binding site
|
|
|
What chaperone proteins facilitate proper folding and assembly
|
Hsp 60 and Hsp70
|
|
|
What amino acid does acetylation on?
|
Lysine
|
|
|
What is ubiquination
|
Post-translational modification that marks a protein for degradation
|
|
|
What Golgi network interacts with the Endoplasmic Reticulum?
|
Cis
|
|
|
What proteins predominantly aid in intracellular movement toward the plasma membrane?
|
Coatamer protein complex II
|
|
|
What mechanism is used for guiding and targeting vesicles?
|
SNAP and SNARE
|
|
|
What receptor mediates transport to the lysosome?
|
mannose 6-phosphate
|
|
|
What term denotes signal sequences that direct a peptide's own movement?
|
"Zip code"
|
|
|
Procaryotic and eukaryotic mRNAs
|
Procaryotic mRNA has multiple coding regions for different proteins. Eukaryotic mRNAs have one coding region for one specific protien.
|
|
|
Why is the initiation site for translation?
|
Since there can be more than one reading frames, there is a possibility that an important protein will not be transcribed corrected. This is because a wrong initiation site causes a reading frame shift.
|
|
|
Procaryotic protein synthesis is initiated by the...
|
fMet-tRNA, this is different from the Met-tRNAm which only inserts met in internal positions.
|
|
|
The proofreader of the elongation is ...
|
GTPase makes sure that the right amino acid is in the A site.
|
|
|
How is translation terminated?
|
The translation is terminated when the release factor binds to the A site.
|
|
|
Composition of Ribosome
|
2/3 rRNA and 1/3 Protien. The rRNA is responsible for the overall structure of the ribosome and protein synthesis.
|
|
|
The two functions of ER signal sequence.
|
Direct the protien to the ER. Keeps the pore of the translocater open.
|
|
|
Where are incorrectly folded proteins degraded?
|
Proteasome
|
|
|
Examples of diseases caused by protein aggregates
|
Huntington Disease, Alzheimer's Disease, Prion Disease.
|
|
|
Infectious Protien
|
These proteins "infect" other proteins to create an amyloid
|
|
|
Ion Channel
|
Fast acting channel that cause ion influx such as Ca, Na, Cl or K.
|
|
|
Classes of LDL receptor mutations.
|
1 and 2 affect receptor synthesis.
3 affect LDL binding 4 and 5 affect receptor endocytosis and recycling. |
|
|
How does cortisol regulate gene?
|
It binds to intracellular receptor allow it to target the gene and begin the transcription.
|
|
|
Early steroid hormone response.
|
Induces a select number of genes
|
|
|
Ras Activating Protien.
|
Removes the GDP from the inactive Ras protien so that GTP can bind to it.
|
|
|
What are the nearby Amino Acids in the SH2 domain for?
|
They are for specificity because each receptors have different substrate
|
|
|
Examples of MAP functions.
|
Signals, proliferation, inflammation and development.
|
|
|
RAS mutations are associated..
|
cancer and there are cancers that have high number of RAS mutations as pancearicitc cancer
|
|
|
Raf isoforms
|
60% to 70 % of malignant melanoma contain B-raf mutation. Mutation increase catalytic activity.
|
|
|
How MKK1/2 regulated?
|
By phosphorylation and protein-protein interactions.
|
|
|
What time of relationship exists between cardic tissues in mammalian cells?
|
Gap Junctions
|
|
|
What is an example of one mechanism that uses acetylcholine as a signaling response?
|
Exocytosis
|
|
|
What are the three mechanisms of Lithium?
|
It decreases phosphatase activity, decreases G-protein function, and provides protection against neuronal loss.
|
|
|
What are the four protein binding domains?
|
SH2, PTB, PH, and SH3
|
|
|
What happens when cyclic AMP binds during protein kinase A activation?
|
The subunits dissociate.
|
|
|
What does this NES stand for?
|
Nuclear Export Sequence
|
|
|
What is the drug that blocks the process that inhibits immune responses, which helps with reducing the likelihood of a liver transplant rejection?
|
Tacrolimus
|
|
|
What signal transduction pathway leads to the genes that are involved in inflammation turned on?
|
T-Cell Receptor Mediated Signal Transduction and NFAT Regulation.
|
|
|
What are the three cellular responses as a result of MAP Kinase Signaling Pathway?
|
Proliferation, Inflammation and Development.
|
|
|
What is the percentage of malignant melanomas that contains B-Raf?
|
~60-70%
|
|
|
The keys points of phosphorylation of RAF and protein-protein interactions are of what mechanism?
|
MKK1/2 Activation and Regulation
|
|
|
PTEN’s function is as follows?
|
Shutting of the signaling pathway of PI3K/AKT.
|
|
|
The untranslated region is important for what function?
|
Cytoplasmic localization
|
|
|
Which exchange factor brings a charged initiator tRNA to the small ribosomal subunit?
|
eIF-2
|
|
|
Which model shows how a soluble protein is translocated across the ER membrane?
|
Protein Translocator
|
|
|
What is an example of a Prion disease, that occurs when proteins are misfolded by a protein called prion protein?
|
Mad cow disease
|
|
|
What effect is explained when substrates interact with proteins and alter the ability for that protein to interact with other substrate molecules.
|
Allosteric Effects
|
|
|
What are the three common features of protein kinases?
|
An ATP binding domain (N-terminus), Activation loop, and a substrate binding region ( C-terminus).
|
|
|
Which post-translational modification focuses on protein degredation?
|
Ubiquitylation
|
|
|
What is a medication example, of a proteasome inhibitor?
|
Bortezomib (Velcade)
|
|
|
How does CREB affect transcription?
|
recruits CBP and activates transcription
|
|
|
What are the mechanisms of lithium?
|
1) decrease phosphatase activity 2) decrease g-protein function 3) may provid esome protection of neuronal loss
|
|
|
60-70% of malignant melanomas contain what?
|
B-raf mutations
|
|
|
what does ligand induce in JAK/STAT pathways?
|
receptor dimerization
|
|
|
what components does protein kinase A (PKA) have?
|
2 regulatory subunits and 2 catalyitic subunits
|
|
|
where does activated PKA travel to?
|
nucleus
|
|
|
what does MAP stand for?
|
mitogen activated protein
|
|
|
human tumors tend to have activating mutants of what gene?
|
Ras family of GTPases
|
|
|
Where is V599 located
|
in kinase domain; mutation increases Raf catalytics activity and what does it affect?
|
|
|
what is NES regulated by?
|
phosphorylation and protein-protein interactions
|
|
|
who is Janus?
|
roman god of gateways, doorways, and beginnings and endings
|
|
|
what are the steps of JAK/STAT signaling?
|
1) ligand binds, 2) phosphorylation by JAK, 3) STAT binds, 4) STAT phosphorylation and release, 5) nuclear translocation, 6) gene expression
|
|
|
Name three receptor types?
|
ion linked channel, g-protein linked, enzyme linked
|
|
|
what ions typically influx and affect action potentials?
|
Ca+2, Na+, Cl-, K+
|
|
|
which type of ion channel depolarizes membrane?
|
excitatory
|
|
|
which type of ion channel hyperpolarizes membrane?
|
inhibitory
|
|
|
what can psychoatice drugs that target ion channels treat?
|
insomnia, anxiety, depression and schizophrenia
|
|
|
what happens to a receptor once it is enocytosed?
|
recycling, degradation, transcytosis
|
|
|
what do class 3 LDL receptor mutations affect?
|
LDL binding
|
|
|
What is the function of IF3 in the protein synthesis of prokaryotes?
|
Stabilize the 30S subunit and help prevent the binding of the 50S subunit.
|
|
|
What is the function of peptidyl transferase?
|
Catalyze the formation of a peptide bond
|
|
|
Name one antibiotic that only recognizes eukaryotes and cannot be used for clinical treatment.
|
Cycloheximide
|
|
|
What is the primary cause of antibiotic resistance?
|
Mutation often through horizontal gene transfer.
|
|
|
Proteins destined for membrane location or secretion must be directed to the:
|
endoplasmic reticulum
|
|
|
What is the function of Ubiquitin- Conjugating enzymes?
|
Recognize exposed peptide sequence of misfolded proteins
|
|
|
Proopiomelanocortin is proteolyzed into:
|
ACTH, MSH endorphins and other small peptides.
|
|
|
Name the two types of protein localization to the nucleus.
|
1.) Localization of T- Antigen containing its normal nuclear import signal 2.)Localization of T-Antigen containing a mutated nuclear import signal
|
|
|
What is the default pathway for the movement of proteins in the cell?
|
ER >Golgi Apparatus > Cell surface
|
|
|
Important organelle for monitoring the proper folding of a protein:
|
endoplasmic reticulum
|
|
|
What is the Cis Golgi?
|
Region of the Golgi that is closest to the endoplasmic reticulum
|
|
|
Name the antibiotic produced by fungal organisms that blocks the forward pathway.
|
Brefeldin A
|
|
|
Which receptor is referred to as the seven transmembrane spanning receptor?
|
G-protein
|
|
|
What is the first step of the activation of adenylyl cyclase through G-Protein kinase receptors?
|
A hormone engages the G-protein coupled receptor and induces a conformational change that will recruit the alpha, beta and gamma subunits to that receptor.
|
|
|
What is the function of a phospholipase?
|
Hydrolyzes phospholipid components and that hydrolysis is going to create signaling molecules that will affect other types of proteins and cellular functions.
|
|
|
In intracellular signaling, contact-dependent signaling is:
|
when one cell presents a molecule that will interact with the receptor on another cell.
|
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What two signaling molecules will arise from the hydrolysis of inositol phospholipid?
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Diacylglycerol and inositol triphosphate
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What are scaffolding proteins?
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Proteins that bind to multiple signaling molecules.
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By which regulatory molecule is protein kinase A activated?
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Cyclic AMP
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3-tier kinase cascade that describe the MAP kinase signaling pathways:
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Raf, MEK, ERK
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