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Molecular Genetics
Translation and Protein Synthesis 1
| Question | Answer |
|---|---|
| What are the Svedberg units for the prokaryotic ribosomal large and small subunits? For the assembled ribosome? What are the units for the rRNA molecules integrated into these subunits? | Large = 50S, Small = 30S ; Ribosome = 70S ; Large = 23S rRNA and 5S rRNA, Small = 16S rRNA |
| The "S" designation for the size of the ribosomal subunits stands for what? What is the physical parameter quantified by this unit of measure? | Svedbergs ; sedimentation coefficient |
| How many protein molecules are associated with the rRNA molecules in the formation of the large and small prokaryotic ribosomal subunits? | Large = 31 proteins (note textbook says 34 for E.coli), Small = 21 proteins |
| In ribosomes (in general) are the contact bridges between the large and small subunits mostly composed of RNA or protein molecules? | RNA |
| In ribosomes (in general) are the binding sites for the tRNAs within rRNA or protein molecular structure? | rRNA |
| In prokaryotic ribosomes, how is the mRNA manipulated geometrically so that it can base-pair with both the A and P site tRNAs in the large subunit? | It is bent 45 degrees between the two codons by the ribosome |
| How many protein molecules are associated with the rRNA molecules in the formation of the large and small eukaryotic ribosomal subunits? | Large = 50 proteins, Small = 33 proteins (note: text says 30) |
| What are the Svedberg units for the eukaryotic ribosomal large and small subunits? For the assembled ribosome? What are the units for the rRNA molecules integrated into these subunits? | Large = 60S, Small = 40S ; Ribosome = 80S ; Large = 28S, 5.8S, and 5S rRNA, Small = 18S rRNA |
| What are the names of the prokaryotic ribosomal small subunit substructures (major features), as developed by x-ray crystallography? | Head, beak, shoulder, neck, platform, body, and spur |
| What technique was used to characterize the tertiary rRNA structure of the prokaryotic small ribosomal subunit, and the 3-dimensional incorporation of proteins? | x-ray crystallography |
| What is the name of the enzyme that attaches an amino acid to a tRNA molecule? | aminoacyl tRNA synthetase |
| What are the names of the three ribosomal sites that bind to tRNA? | A = acceptor (or aminoacyl); P = Petidyl; E= Exit |
| What two types of ribosomes are found in the eukaryotic cell, in terms of their location (not including ribosomes within organelles)? | Membrane bound (attached) ribosomes and free ribosomes |
| What is the approximate diameter of the tunnel in the ribosome that serves to transport the growing polypeptide? What is the approximate length? Where is the peptidyl transferase site, at the beginning or the end of the tunnel? | 20 angstroms ; 100 angstroms ; at the beginning |
| What are the two ribosomal base-pair recognition patterns? Which one is more accurate? Which one enables proofreading? What is the disadvantage of the more accurate state? | The ram state and the restrictive state ; the restrictive state is more accurate and enables proofreading ; it is slower and therefore inefficient |
| What are the two roles (functions) played by the prokaryotic 30S ribosomal subunit? These functions were characterized via interference experiments using three drugs. What type of drugs were these? | decoding of the mRNA and translocation along the mRNA ; antibiotics |
| What are the three phases of translation? | Initiation, elongation, and termination |
| What is the name of the ribosome binding site on prokaryotic mRNA? | the Shine-Dalgarno sequence |
| Where would the initiator tRNA molecule be found in the ribosome at the time of completion of initiation? | the P site |
| Which prokaryotic initiation factor prevents reassociation of the small and large ribosomal subunits? | IF3 |
| Which part of the prokaryotic small ribosomal subunit associates with the translation initiation sequence of an mRNA? (Be specific, and give the prominent features also) What is the name of the specific mRNA sequence that binds to this rRNA? | the 3' end of the 16S rRNA, which forms the head and platform area ; the Shine-Dalgarno sequence |
| Which prokaryotic translation initiation factor binds the A site prior to translation, to prevent the binding of non-specific tRNA molecules during the initiation process? | IF1 |
| In which direction does the ribosome move along the mRNA strand? | From 5' to 3' |
| Which prokaryotic initiation factor is bound to GTP molecule prior to translation? Why? How does this impact elongation? | IF2 ; IF2/GTP facilitates binding of Fmet-tRNA to the start codon of the mRNA. GTP is hydrolyzed after the large and small subunits bind and causes IF2 to disassociate. Elongation can begin as new aminoacyl-tRNAs are delivered one by one to the A site. |
| What are the two prokaryotic proteins (not including IF3) that cause the dissociation of the ribosomal large and small subunits? | Ribosomal release factor (RRF) and and an elongation factor (EF-G) |
| What is the name of the complex that forms on the prokaryotic small ribosomal subunit following dissociation of the large and small subunits? | The 30S initiation complex |
| IF3 is capable of binding by itself to the prokaryotic ribosomal subunit to which it binds. What proteins help to stabilize this binding? Can other initiation factors bind by themselves? Explain. | IF1 and IF2 ; IF2 can bind by itself but is stabilized by IF1 and IF3, IF1 cannot bind by itself, it must be assisted by IF2 and IF3 |
| What are the prokaryotic start codons? | AUG, GUG, UUG (only two genes use AUU) |
| Which prokaryotic initiation factor has the start codon AUU and partially regulates its own production through partial prevention of its translation? | IF3 |
| What happens to prokaryotic methionyl-tRNA in order to make it the initiator aminoacyl-tRNA? Can all methionine molecules accept this change? If not, what is the reason for the differential processing of methionyl-tRNAs? | The methionine is formylated, changing it to F-met ; No ; Only methionines that are charged onto special tRNAs (F-met tRNAs) can be formylated, creating two distinct methionyl-aminoacyl-tRNAs, M-met and F-met (initiator) |
| Which prokaryotic initiation factor is the most essential in mediating the binding between the ribosomal small subunit and the mRNA? Who discovered this and when? | IF3 ; Albert Wahba in 1969 |
| What are the components of the prokaryotic 30S ribosomal initiation complex? | mRNA, Fmet-tRNA, 30S ribosomal subunit, GTP, IF1, IF2, IF3 |
| What does the hydrolysis of GTP accomplish in the process of forming the 70S prokaryotic initiation complex? How and why? | It drives the release of IF2, which would otherwise interfere with formation of an active 70S initiation complex. The combination of the 70S ribosome and IF2 constitutes a GTPase |
| What is the name of the transmembrane protein in the endoplasmic reticulum that attaches to the membrane of an organelle and to membrane bound ribosomes? | The translocon |
| Explain how the rRNA structure of the ribosome facilitates the binding of the proteins that make up the ribosome. | Secondary structure creates many stems and loops which have several areas that lack base-pairing. These "bubbles" are the primary sites of protein interaction and binding |
| Name the three prominent features of the prokaryotic large ribosomal subunit (functional subunits) that were discussed in the lecture. | Central protuberance, ridge, and stalk |
| The L7 and L12 E.coli bacterial proteins, together with the large ribosomal subunit, form a GTPase. What is the name of the prominent feature of the large subunit that binds L7 and L12 and creates this enzymatic activity? | The stalk |
| Is the rRNA surface that forms the interface between large and small prokaryotic ribosomal subunits integrated with bound proteins or not? | It is not, it is "naked" rRNA |
| Which molecule in the prokaryotic ribosome contains the peptidyl transferase site? | It is within the 23S rRNA, near the anticodon structures of the A and P site tRNAs |
| Is there an energetic cost when a tRNA attempts to bind to the mRNA codon, if the tRNA is found to not be a match? | Yes, GTP is hydrolyzed to GDP + Pi even when the tRNA doesn't bind because it is found to not be a match |
| Describe the three occurrences of GTP hydrolysis carried out by the prokaryotic ribosome during protein synthesis | GTP is hydrolyzed as IF2 dissociates from the small subunit following the binding of the Fmet-tRNA to the P site anticodon. Also GTP is hydrolyzed each time an aminoacyl tRNA binds to the A site. Also GTP is hydrolyzed in order to facilitate translocation |
| During the formation of the prokaryotic 70S initiation complex (the addition of the 50S subunit), which two initiation factors dissociate from the complex first, upon initial contact of 50S and 30S subunits? | IF1 and IF3 |
| What are the three stop codons? | UAA, UGA, UAG |
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