5
Transcription, RNA Processing,
and Translation
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Fig. 1. DNA-dependent synthesis of RNA. In this example, a cytidine triphosphate (rCTP) precursor
is added to the 3' end of an elongating RNA chain by forming a phosphodiester bond
between the 5' phosphate of the rCTP precursor and the 3' OH of the previously added nucleotide.
The nucleotide sequence of the nascent RNA is specified by the complementary nucleotide
sequence of the DNA template strand according to Watson-Crick base pairing. The circled C residue indicates the position of the newly added nucleotide.
Fig. 2. Schematic of the transcription elongation complex.
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Fig. 3. Model for sequential assembly of the general transcription factors (GTFs) and pol II into the
pre-initiation complex (PIC). The right angled arrow indicates the position and direction of transcription initiation.
Fig. 4. Capping and polyadenylation. (A) The 5' mRNA cap structure. (B) 3' polyadenylation of mRNA.
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Fig. 5. Schematic of RNA splicing. (A) Location of conserved elements involved in RNA splicing.
(B) Sequence of reactions in RNA splicing. (C) Alternative RNA splicing; a gene with three transcribed exons produces two different mRNAs via alternative splicing pathways.
Fig. 6. The genetic code, as used by most organisms. The first base of the codon (5' end) is shown in
the first column, and the second base is shown in the top row. AUG (and sometimes GUG and UUG)
usually serves as the initiation codon, when it occurs at the beginning of the open reading frame. The
three termination codons (end) are recognized by termination factors.
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Fig. 7. Transfer RNA structure. Shown here is the secondary structure of phenylalanyl-tRNA (PhetRNA), in the familiar cloverleaf diagram characteristic of most tRNAs. The anticodon, 5'GAA, is
complementary to one of the two codons for Phe (5'UUC) in Fig. 6. D, dihydrouridine; Ψ,
pseudouridine; T, ribothymidine.
Fig. 8. Elongation factors EF-Tu and EF-G. (A) EF-Tu (lighter gray) is shown as a ternary complex with
bound amino acyl-tRNA and GTP. (B) EF-G resembles the complex of the protein EF-Tu and amino
acyl-tRNA. This is an example of macromolecular mimicry where similar binding sites accommodate
the different species.
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Fig. 9. Secondary structure of E. coli 16S rRNA. Several non-canonical base pairs are evident in the
molecule, including A-G, G-G, U-G and U-U base pairs. The 16S RNA folds into a compact structure
which defines the overall shape of the 30S subunit (see Fig. 10).
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Fig. 10. Structure of the small and large subunits of the bacterial ribosome. (A) Interfacial aspect of
the 30S subunit, showing the 16S RNA backbone (thin dark tracing) and associated proteins (alternatively shaded). A section of bound mRNA (thick bright backbone) includes the Shine-Dalgarno
region (5' helical structure on the right), the initiation codon and an adjacent Phe codon. The
anticodon of the initiator tRNA, fMet-tRNA (thick dark backbone) is base paired with the initiation
codon in the P site. (B) Same as (A) with the addition of Phe-tRNA at the adjacent codon in the A
site. (C) Peptidyl transferase catalyzed transfer of the fMet to the Phe-tRNA, resulting in a dipeptidyltRNA in the A site. (D) Post translocation state of the ribosomal small subunit. Through the action
of EF-G with bound GTP, the uncharged initiator tRNA, fMet-Phe-tRNA and the mRNA are moved,
in register, into the E and P sites. (E) Entry of the third amino acyl-tRNA into the A site, in advance
of the ejection of the E site tRNA and peptide transfer (peptidyl transferase reaction). (F) Interfacial
aspect of the 50S subunit, showing the 5S and 23S RNA (thick backbone) and associated proteins
(variously shaded). The peptidyl transferase activity lies deep within a cleft in the 23S RNA, an area
entirely devoid of protein. The coordinates for the 30S subunit, mRNA fragment, A, P, and E site
tRNAs are available at the RCSB data base with PDB accession numbers 1GIX and 1JGO.
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