Ribosome sites involved

Of the fonr possible optical isomers of chloramphenicol, only the o-threo form is active. This antibiotic selectively inhibits protein synthesis in bacterial ribosomes by binding to the 50S subunit in the region of the A site involving the 23 S rRNA. The normal binding of the aminoacyl-tRNA in the A site is affected by chloramphenicol in such a... 

Formation of the first peptide linkage. The formylmethionine group is transferred from its tRNA at the P site to the amino group of the second aminoacyl-tRNA at the A site of the ribosome. This involves nucleophilic attack by the amino group of the second amino acid on the carboxyl carbon of the methionine. The resulting bond formation attaches both amino acids to the tRNA at the A site. 

Three tRNA binding sites on the 70S ribosome are involved in the process of elongation. Figure 27.22 shows a single round of this cycle, which is repeated until a signal for termination is encountered. The cycle goes as follows ... 

The location of binding of EF-Tu on ribosomes has been established directly by cryo-EM. It binds both to the L7/L12 stalk and to the body of the 505 ribosomal subunit. The other end of the P site is at the pepti-dyltransferase locus and has been photochemically labeled by azide derivatives of aminoacyl groups bound to a tRNA. The labeling is primarily in the 505 subunit of E. coli ribosomes and involves the central loop of domain V (residues 2043 - 2625) of the 235 RNA. Residues U2584 and U2585 are major sites of crosslinking (see Fig. 29-14). The presence of nearby sites of mutation leading to resistance to chloramphenicol or erythromycin (Box 29-B) served to confirm the central loop as part of the peptidyltrans-ferase. Domain II of 235 RNA is also involved, and there is evidence that the unique sequence UGG at positions 807-809 may also interact with the CCA end of tRNA in the P site. ... 

Sites Studied. Interactions of tRNA with the ribosome can be broadly classified into two types, (a) Interactions with the peptidyltransferase center of the 50 S ribosomal subunit involving the 3 terminus of peptidyl-or aminoacyl-tRNA occupying, respectively, the donor (peptidyl) or acceptor (aminoacyl) site of the catalytic center, (b) Interactions likely to involve internal parts of the tRNA molecule and designed to align and stabilize the binding of cognate tRNAs to the ribosome. 

Affinity labeling probes for mapping of ribosomal components involved in interactions of the first type were constructed by introducing suitable substituents at the free terminal amino group of aminoacyl or peptidyl tRNA. To study the second class interactions, sites within the tRNA molecule must be rendered capable of reacting with potential binding sites on the ribosome. Most studies to date have centered on the elucidation of ribosomal components involved in peptidyl transfer. Attempts at unraveling components involved in the second class of interactions are still very few. 

Fig. 2.1. Peptide bond formation in the biological system. The entire process takes place on the ribosome and involves two binding sites, the P (peptidyl) and A (aminoacyl) sites. The reaction is catalyzed by the enzyme peptidyl transferase. It is the message carried by mRNA (which in turn is dictated by the genetic material DNA) which determines by specific interactions as to which aminoacyl-tRNA will bind at the P and...

Polyribosomes diXQ associations between mRNA and a variable number of ribosomes. The ribosomes are strung on the mRNA like beads on a thread. Often only half a dozen ribosomes are involved. Electron optical micrographs of polyribosomes often reveal a helical structure. Polyribosomes are the sites of polypeptide synthesis. At least in the living organism it is likely that polypeptide synthesis proceeds primarily on such polyribosomes and more rarely on single ribosomes. 

The process of RNA synthesis in bacteria—depicted in Figure 37-3—involves first the binding of the RNA holopolymerase molecule to the template at the promoter site to form a PIC. Binding is followed by a conformational change of the RNAP, and the first nucleotide (almost always a purine) then associates with the initiation site on the 3 subunit of the enzyme. In the presence of the appropriate nucleotide, the RNAP catalyzes the formation of a phosphodiester bond, and the nascent chain is now attached to the polymerization site on the P subunit of RNAP. (The analogy to the A and P sites on the ribosome should be noted see Figure... 

The regions of the tRNA molecule teferred to in Chapter 35 (and illustrated in Figure 35-11) now become important. The thymidine-pseudouridine-cyti-dine (T PC) arm is involved in binding of the amino-acyl-tRNA to the ribosomal surface at the site of protein synthesis. The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase. The acceptor arm, located at the 3 -hydroxyl adenosyl terminal, is the site of attachment of the specific amino acid. 

The binding of the 60S ribosomal subunit to the 48S initiation complex involves hydtolysis of the GTP bound to elF-2 by elF-5. This teaction tesults in telease of the initiation factots bound to the 48S initiation complex (these factots then ate tecycled) and the tapid association of the 40S and 60S subunits to fotm the 80S ribosome. At this point, the met-tRNA is on the P site of the ribosome, ready for the elongation cycle to commence. 

Elongation is a cycUc process on the ribosome in which one amino acid at a time is added to the nascent peptide chain. The peptide sequence is determined by the order of the codons in the mRNA. Elongation involves several steps catalyzed by proteins called elongation factors (EFs). These steps are (1) binding of aminoacyl-tRNA to the A site, (2) peptide bond formation, and (3) translocation. 

The answer is d. (Hardman, pp 1105-1108.) The bactericidal activity of streptomycin and other aminoglycosides involves a direct action on the 305 ribosomal subunit, the site at which these agents both inhibit protein... 

Fig. 4.1. Fundamentals of the ubiquitin system. Adapted from Ref [5]. Figure 4.1 shows the fundamentals of the ubiquitin system. (1) Ubiquitin is synthesized in linear chains or as the N-terminal fusion with small ribosomal subunits that are cleaved by de-ubiquitylating enzymes to form the active protein. Ubiquitin is then activated in an ATP-dependent manner by El where a thiolester linkage is formed. It is then transthiolated to the active-site cysteine of an E2. E2s interact with E3s and with substrates and mediate either the indirect (in the case of HECT E3s) or direct transfer of ubiquitin to substrate. A number of factors can affect this process. We know that interactions with Hsp70 can facilitate ubiquitylation in specific instances and competition for lysines on substrates with the processes of acetylation and sumoylation may be inhibitory in certain instances. (2) For efficient proteasomal targeting to occur chains of ubiquitin linked internally through K48 must be formed. This appears to involve multiple...

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