MAMMALIAN GENETICS BCH5413 COMPLETE EXAM

30S + 50S - ANSWER What are the 2 subunits of 70S ribosomes? 40S + 60S - ANSWER What are the 2 subunits of 80S ribosomes? The small subunits (30S/40S) decode the mRNA; the large subunits (50S/60S) catalyze the peptide bond formation of the amino acids - ANSWER What are the main functions of the 2 subunits of 70S and 80S ribosomes? rRNA (it base pairs with itself forming the shape of the ribosome) - ANSWER Which part of the ribosome (rRNA or proteins) determines its shape? rRNA (no proteins are found within 18 angstroms of the active site -> rRNA is what directly catalyzes peptide bond formation) - ANSWER Which part of the ribosome (rRNA or proteins) contains the peptidyl transferase activity? Proteins (EF-Tu hydrolyzes GTP) - ANSWER Which part of the ribosome (rRNA or proteins) contains the GTP hydrolysis activity? The small subunit (30S, 40S) - ANSWER Which subunit is the tRNA's anticodon located in? The large subunit (50S, 60S) - ANSWER Which subunit is the tRNA's acceptor stem located in? It helps tRNA enter the ribosome - ANSWER What is the function of EF-Tu? Peptide bond - ANSWER What type of bond joins amino acids during protein synthesis? CCA - ANSWER What is the nucleotide sequence found at the 3' end of all tRNAs? Adenosine (A) - ANSWER Which nucleotide on the tRNA is the target for "charging" with an amino acid? 32 - ANSWER What is the minimum number of tRNAs for bacterial systems? 45 - ANSWER What is the minimum number of tRNAs for eukaryotic systems? The carboxyl group (COOH) and the amino group (NH2) - ANSWER In a peptide bond, what functional groups of the 2 amino acids are involved in the bonding? It recognizes the correct tRNA based on its configuration (binding domains) and its anticodon - ANSWER How does the aminoacyl-tRNA synthetase recognize which tRNA gets its amino acid? An amino acid bound to a tRNA - ANSWER What is aminoacyl-tRNA? (1) The amino acid is attached to AMP (from ATP breakdown), forming aminoacyl-AMP -> (2) The amino acid detaches from AMP and binds to the 3' -OH group on the terminal A of the tRNA, forming aminoacyl-tRNA - ANSWER What is the 2-step process for "charging" the tRNA? The amino acid (its carboxyl group) binds to the 3' -OH group on the terminal A of the tRNA - ANSWER Where does the amino acid get added to the tRNA (specify RNA end and position of binding)? There can be a slight deviation in the 3rd nucleotide of the codon, allowing a tRNA molecule to pair with multiple codons - ANSWER What is the wobble hypothesis? False (it is at the 5' end because it connects with the 3' end of mRNA's 3rd positioned nucleotide in its codon) - ANSWER T/F: the "wobble" nucleotide is at the 3' end of tRNA's anticodon. False (there are slight deviations in the genetic code in some eukaryotic mitochondria and bacteria) - ANSWER T/F: the genetic code is strictly universal. One tRNA can pair with multiple codons through non-Watson/Crick base pairing (G=U) - ANSWER What is the significance of the wobble hypothesis? True (AMP derived from ATP is used to catalyze bond formation between the amino acid and the tRNA) - ANSWER T/F: aminoacylation of tRNAs requires ATP. True (GTP is required for the binding of aminoacyl-tRNA to the A site of the ribosome) - ANSWER T/F: protein synthesis requires GTP. False (one aminoacyl-tRNA can pair with multiple codons, but one codon cannot pair with multiple tRNAs) - ANSWER T/F: wobble allows different aminoacyl-tRNAs to pair with same codon. False (the bond formation between the amino acids and tRNAs is catalyzed by aminoacyl-tRNA SYNTHETASE) - ANSWER T/F: ligase enzyme joins the amino acids to the respective tRNAs. False (it requires ATP) - ANSWER T/F: aminoacylation of tRNAs requires GTP. False (fmet-tRNA is in prokaryotes; met-tRNA is in eukaryotes) - ANSWER T/F: fmet-tRNA is the initiator tRNA in eukaryotes. Prokaryotes: a ribosome binding site in front of the operon; eukaryotes: the 5' cap - ANSWER Where does the ribosome bind to the mRNA in prokaryotes vs. eukaryotes? True (but multiple proteins can be produced from a singular mRNA in prokaryotes) - ANSWER T/F: there is generally only 1 protein produced per mRNA in eukaryotes. ATP - ANSWER What is required in order for the mRNA to be "unwound" during translation in eukaryotes? False (it only regulates translation in eukaryotes) - ANSWER T/F: phosphorylation regulates translation in both prokaryotes and eukaryotes. It binds to the A site in the 30S ribosome, preventing fmet-tRNA from binding - ANSWER What is the function of IF1? It binds fmet-tRNA and GTP, bringing the complex to the P site for GTP hydrolysis - ANSWER What is the function of IF2? IF2 - ANSWER Which IF is able to bind GTP (in bacteria)? It keeps the 30S and 50S subunits separate - ANSWER What is the function of IF3? The 30S subunit - ANSWER Which ribosomal subunit binds to the ribosomal binding site (rbs) in prokaryotes? After (the 50S subunit must also be present for GTP hydrolysis to occur) - ANSWER Does GTP hydrolysis occur BEFORE or AFTER the 70S subunit is formed? (1) IF3 dissociates from the 30S subunit -> (2) the 50S subunit binds forming the 70S complex -> (3) GTP hydrolysis occurs, releasing IF2 and allowing polypeptide formation to begin - ANSWER What are the 3 steps in formation of the 70S complex? To release IF2 from the complex, allowing formation of the polypeptide chain - ANSWER What is the function of GTP hydrolysis in the formation of the 70S complex? Segments of mRNA in front of operons (in prokaryotes) that specific sections of rRNA complementary base pair to - ANSWER What are ribosomal binding sites (rbs)? The amino group does a nucleophilic attack on the adjacent amino acid's carboxyl group - ANSWER During peptide bond formation, which functional group attacks which? Which type of "attack" occurs? (1) The aminoacyl-tRNA binds to the A site by matching its anticodon to the correct codon -> (2) a peptide bond forms between adjacent amino acids -> (3) EGF-G causes translocation of the tRNA from the A site to the P site - ANSWER What are the 3 main steps of elongation? It is needed during both step 1 and 3 of elongation - ANSWER When is GTP needed during elongation? It is needed to align the aminoacyl-tRNA to the A site (step 1) and to translocate the tRNA from the A site to the P site (step 3) - ANSWER Why is GTP needed during elongation? The ribosome reaches a stop codon in the mRNA and release factors + GTP enter the A site -> GTP hydrolysis occurs -> the ribosome subunits dissociate and the polypeptide is released - ANSWER How does translation stop? GTP hydrolysis (in the A site) - ANSWER What reaction causes the polypeptide to be released from the ribosome? The order that the nucleotides in mRNA is read by the ribosome (frameshifts of 1 nucleotide can cause a completely different amino acid sequence to be translated) - ANSWER What is indexing? A primer + reverse transcriptase allows elongation until the P site is reached; wherever the new strand ends are the nucleotides that make up the codon in the P site - ANSWER How does toe-printing allow researchers to determine the codon that is in the P site? All 3 initiation factors - ANSWER Toe-printing experiments show that in order to ratchet to the correct reading frame, indexing requires: 1-3 minutes (very short!) - ANSWER What is the lifetime of bacterial mRNA? The mRNA (it is the ribosomal binding site that the rRNA binds to) - ANSWER Is the Shine-Dalgarno sequence located in the rRNA or the mRNA? Linear mRNA is easily translated (if 1 cistron is in a hairpin structure it will not be translated as often as cistrons that are linear) - ANSWER How does the secondary structure of mRNA affect translation from a polycistronic message? False (eukaryotic mRNA is a polysome, meaning that multiple ribosome can translate it at once) - ANSWER T/F: only 1 ribosome can translate a eukaryotic mRNA at a time. The polyA binding proteins (PABPs) on the mRNA's 3' end interact with the initiation factors bound to the mRNA's 5' cap - ANSWER How do eukaryotic mRNAs become circular in the cytoplasm? Ribosome that finish translation are able to be "recycled" for re-initiation of translation, causing translation to be fast (ribosomes always available) - ANSWER Why is it important for translation that eukaryotic mRNAs become circular in the cytoplasm? eIf4e - ANSWER Which initiation factor is required to allow binding between the 40S subunit and the 5' mRNA cap? False (mRNA-rRNA binding only occurs in prokaryotes) - ANSWER T/F: binding occurs between mRNA and rRNA (in initiation) in both prokaryotes and eukaryotes. False (eukaryotes have many more initiation factors, allowing for more control of translation) - ANSWER T/F: prokaryotes have more initiation factors involved in translation than eukaryotes. Prokaryotes: EF-Tu binds the tRNA to the A site + EGF-G causes translocation of the tRNA to the P site; eukaryotes: eEF1-alpha binds the tRNA to the A site + eEF2-G causes translocation of the tRNA to the P site - ANSWER Differentiate between the prokaryotic vs. eukaryotic proteins used for elongation. Kozak sequence (contains AUG in frame with other necessary-positioned Gs) - ANSWER When the 40S subunit is "scanning" the mRNA, it starts translation at the: Transcription is slow (mRNA processing + moving out of the nucleus), so being able to regulate translation as well helps increase speed of protein synthesis - ANSWER What is the advantage in regulating translation AND transcription in eukaryotes? Maskin binds to eIF4e, preventing the binding of eIF4g (inhibits translation) - ANSWER How does Maskin normally block translation? The phosphorylation of CPEB - ANSWER What causes Maskin to