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What catalyzes the formation of a new peptide bond? Ribosome How many stop codons? 3 What is start codon? Methionine-AUG What ar e the termination codons? UAA,UAG, UGA Define the Open reading frame series of codons without stop codons, What do long open reading frames indicate? usually indicate a gene How is the genetic code degenerate? 61 codons encode 21 AA codon a sequence of 3 nucleotides that codes for an AA nonsense mutation change an AA to a stop codon T/F: nonsense mutations almost always alter protein function True What does PTC124 do? suppresses nonsense mutations, allows normal protein expression. prevents translation termination at aberrant stop codons (nonsense mutations) How are AA activated for translation? by being covalently linked to tRNAs How is the genetic code considered degenerate? 61 codons encode 21 AA How do anticodons base pair with codons? Antiparallel (Anticodon 3' with codon 5') T/F: there are MORE tRNAs then codons False, there are LESS due to wobble Where do wobbles occur? 1st postion of anticodon, 3rd position of codon describe wobble base pairing 5' position of anticodon tolerates non standard base pairing. Some anticodons have Inosine What can inosine bind to? A, U, C What is selenocysteine? one of the uncommon AA, required for a few enzymes, What type of mutation is predominant in dicer mutations? nonsense mutations T/F: an insertion coupled with a deletion is less deleterious than either would be individually True What is a nonsense suppressor? a mutation in tRNA anticodon that makes it complementary to a stop codon What is a frameshift suppressor? a mutation in tRNA that gives the anticodon 4 residues. can restore a frame shift mutation What are the 5 stages of protein synthesis? 1. activation of AA (tRNA loading) 2. initiation 3. elongation 4. termination and release 5. folding and post translational processing What is translational frame shifting? used by retroviruses, changes the reading frame to get different protein expression (retroviruses get 2 proteins instead of the normal 1) What are the two sources of specificity in formation of aminoacyl tRNA snthetases? 1. multiple sites on tRNA recognized by synthetases 2. charging reaction is specific-binding and activation of AA to tRNA( most tRNA synthetases have editing activity-hydrolases that hydrolyze f wrong) T/F: ribosomes contain RNA and protein components True What are the 3 sites for tRNAs in ribosomes? E-Exit site, P-Peptidly, A-Aminoacyl T/F: ribosomes have three sites for tRNAs and a channel for the mRNA True What enzyme is active in ribosome that catalyzes the formation of peptide bonds? peptidyl transferase T/F: there are initiation factors needed to initiate translation True What are the general steps for initiation of translation? Protein synthesis initiates at AUG codons, Initiator Factors bind to small subunit of ribosome (requires GTP hydrolysis), small subunit binds the 5' cap, mRNA binds to smal subunit, small subunit tracks along mRNA to first AUG, IFs dissociate, large subunit binds, aminoacyl-tRNA binds to A site and first peptide bond forms A site function? incoming aminoacyl tRNA P site function accomadates growing peptide E sidte holds empty tRNA as it exits T/F: the prokaryotic mRNAs contain several open reading frames True what is it called when you have several genes on one mRNA polycistronic message What is a hallmark of translation GTP hydrolysis How much energy is consumed per new peptide bond and where is it consumed? 4 high energy bonds (charging tRNA cleaves ATP to AMP and 2 Phosphates) Translation Cycle takes 2 GTP to get amino acyl tRNAonto A site What is ricin toxic enzyme from castor bean that irreversibly inhibits ribosomes, very lethal Where does the accuracy of translation come from? Multiple Steps it takes for A site to bind amino acyl tRNA What are release factors? Factors that bind to the a site of the ribosome causing water to be added to the protein and hydrolyze it. Look like tRNA what does erythromycin do? inhibits ribosomal translation on bacteria T/F: many antibiotics inhibit protein or RNA synthesis True What differences in initiation of prokaryotes allow them to have a polycistronic message in mRNA but eukaryotes can't? because the prokaryotic ribosome is able to initate translation by interacting with any ribosome binding site (RBS or shine- Dalargno sequence). Eukaryotic ribosome binds 5'cap What is ferritin? stores iron What is transferrin receptor helps cells take up iron What regulates ferritin protein expression? At low levels of iron, aconitase binds to the 5' end of ferritin, which blocks translation. At high levels of iron, aconitase binds iron, not ferritin, which increases expression What regulates expression of transferrin receptor? aconitase binds to 3' end of transferrin receptor, stabilizing the mRNA, and increasing expression during times of low iron. At high iron, aconitase does not bind to trnasferrin receptor, destablilizing it What is the nonsense mediated mRNA decay pathway? acts on transcripts right after splicing to degrade RNAs that contain nonseense mutations In the nonsense mediated mRNA decay pathway, where does it have problem degrading nonsense mutations? In the last exon-3' region with the nonsense mediated mRNA decay pathway in mind, which would you expect to cause more severe problems: nonsense mutation in the 3' or 5' region and why. Mutations in the 3' region-this defective protein will not be effectively degraded T/F: location of nonsense mutation affects mRNA stability and mutant protein expresion levels True Where do you commonly see alternate meanings for specific codons mitochondria RNA editing modification of RNA after synthesis, modification of bases to change meaning of message Where do you see RNA editing in humans? the apoB protein of LDL. Has a longer liver form, and a shorter intestinal form. both of which come from the same RNA. In the intestinal form, there is a cytosinse converted to a uracil, resulting in a premature stop codon where is cytosine deaminase important in creating the short apoB transcript in the intestine, by deaminating the cytosine to the uracil T/F: proteins are folded as they are being synthesized true molecular chaperones do what help proteins fold T/F: molecular chaperones don't need energy to fold proteins False, they require lots of ATP what do hsp70 like chaperones do? bind to protein as it is being translating to slow initial folding so that it folds corectly what do hsp60 like chaperones do bind to incorrectly folded proteins and provide a favorable environment for refolding What is function of proteosome degrade proteins what is signal for protein degradation? Poly ubiquitin tail describe ubiquitin highl conserved protein that is a signal for protein degradation describe ubiquitination of proteins ubiquitin is activated by e1, transfered to e2/e2 (ubiquitin ligase complex), recognizes proteins and covalently links ubiquitin to the epsilon n terminal of LYSINE Peptide signal signifies what directs secretion of a protein signal sequence N terminus sequence that has at least one basic residue and a number of hydrophobic residues that are signal for secretion, cleaved after secretion