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It is believed that the rst loop on the 3 side (the T- or T- -C-loop) is involved in making the transfer RNA recognizable to the ribosome. The ribosome must hold each transfer RNA in the proper orientation to check the complementarity of the anticodon of the transfer RNA and the codon of the messenger RNA. The center loop of transfer RNA is the anticodon loop. The aminoacyl-tRNA synthetases seem to recognize many points all over the transfer RNA molecule (see chapter 11). The amino acid is attached to the ACC sequence on the 3 end of the transfer RNA. The ribosome-binding
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loop on all transfer RNAs has the T- -C-G sequence. The anticodon on all is bounded by uracil on the 5 side and a purine on the 3 side.Thus, there is a good deal of general similarity among all the transfer RNAs, consistent with the fact that they all enter protein synthesis in the same way. The actual shape of the functional transfer RNA in the cell is not an open cloverleaf, as shown in gure 10.17; rather, the whole molecule exhibits helical twisting due to pairing of complementary regions ( g. 10.19). Earlier we considered a rough de nition of a gene as a length of DNA that codes for one protein. But we have just encountered an inconsistency genes code for both transfer RNAs and ribosomal RNAs, yet neither is eventu-
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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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10. Gene Expression: Transcription
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The McGraw Hill Companies, 2001
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Transfer RNA
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O H N C H N C C C N C N Ribose Inosine (I) O H N C O N Ribose Ribothymidine (T) Figure 10.18 C C C H O CH3 H N C H C H CH3 N
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O C C C N N C N Ribose 1-Methylinosine (MI) O C N C C Ribose Pseudouridine ( ) H O H H N C H H N H C CH3 N
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O C C C N N C N Ribose H
1-Methylguanosine (MG) O H C C C N OH Ribose Dihydrouridine (D) OH H
Structures of the modi ed bases found in alanine transfer RNA of yeast. The various modi cations of normal bases are shown in red.
T-stem T-loop 64 54 4 1
Acceptor stem 76 72 60 50 15 7 12 69 3 Acceptor end
56 D-loop 20
Variable loop
D-stem 44 26
Anticodon stem Anticodon loop (a) Figure 10.19 32
Anticodon
Structure of yeast phenylalanine transfer RNA. (a) A diagram showing coiling of the sugar-phosphate backbone. (b) A molecular model with bases in yellow and backbone in blue. The two parts of the gure (a and b) are in the same orientation.
([b] Courtesy of Alexander Rich.)
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
10. Gene Expression: Transcription
The McGraw Hill Companies, 2001
Ten
Gene Expression: Transcription
ally translated into a protein.Their transcripts function as nal products without ever being translated. Thus, transfer RNA and ribosomal RNA are the major exceptions to the general rule that a gene codes for a protein.
EUKARYOTIC DNA TRANSCRIPTION
The Nucleolus in Eukaryotes
Eukaryotes have four segments of ribosomal RNA in the ribosome, compared with three in prokaryotes. The smaller ribosomal subunit has an 18S piece of RNA, and the larger subunit has 5S, 5.8S, and 28S segments. All but the 5S ribosomal RNA section are transcribed as part of the same piece of RNA. However, eukaryotic cells have many copies of these ribosomal RNA genes, depending on the species. For example, the fruit y, Drosophila melanogaster, has about 130 copies of the DNA region that the larger segments of ribosomal RNA are transcribed from. These regions occur in tandem on the sex (X and Y) chromosomes and are known collectively as the nucleolar organizer (see chapter 3).The smallest ribosomal RNA subunit is also produced from a duplicated gene, but at a different point in the genome. For example, in D. melanogaster, the 5S subunit is produced on chromosome 2. Eukaryotes unlike prokaryotes, which have only one RNA polymerase have three RNA polymerases. Eukaryotic RNA polymerase I (or polymerase A) transcribes only the nucleolar organizer DNA. RNA polymerase II (or polymerase B) transcribes most genes. RNA polymerase III (or polymerase C) transcribes small genes, primarily the 5S ribosomal RNA gene and transfer RNA genes (table 10.3). In addition, mitochondria, chloroplasts, and some phages have other RNA polymerases.
Figure 10.20 Transcription in the nucleolus of the newt, Triturus. Tandem repeats of the large ribosomal RNA genes are being transcribed. The polarity of the process (progressing from small to large transcripts), as well as the spacer DNA (thin lines between transcribing areas), is clearly visible. Magni cation 18,000 . ( O. L. Miller, B. R. Beatty, D. W. Fawcett/Visuals Unlimited.)
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