MRNA alignments

After attachment of amino acids to tRNA, the amino acids are assembled beginning with the amino terminus and proceeding in the direction of the carboxy terminus. The ribosome is the machinery that translates the mRNA into protein. The ribosome is a very complex protein that contains ribosomal RNA as a functional and structural component. The ribosome assembles around the mRNA, and the cap and other signals allow alignment of the mRNA into the correct position. The initial assembly of the mRNA into the ribosome requires association of the small ribosomal subunit with an initiator tRNA (Met or fMet). Small is a misstatement, because the small ribosomal subunit is a large, complex assembly of numerous smaller proteins—it s just smaller than the... 

Incompletely spliced primary messenger, as well as unprocessed genomic material, may be present as impurities in a mRNA preparation and may obscure the alignment of autologous ESTs necessary for finding variants. 

We performed a benchmark analysis on a set of genes for which the full mRNA and/or the pertinent protein sequence was documented in the literature. Instead of clustering ESTs without any template, we aligned them by a BLAST search (Altshul et al., 1997) to this set of master mRNA sequences and looked in these alignments for variant letters. We applied a set of filters as follows ... 

ESTs that aligned to >1 mRNA of the panel were excluded. 

ESTs were aligned against the set of about 9,000 human mRNA sequences. Candidate cSNPs were extracted and subjected to various algorithmic quality filters, as described in the text. 

Our EST studies cover about 9000 mRNAs. About 6.3 million positions were aligned to more than one EST. There were about 9200 reliably... 

A charged tRNA binds in the A site. The particular aminoacyl-tRNA is determined by the mRNA codon aligned with the A site. 

On each of the tRNA molecules, one of the single-stranded loops contains a trinucleotide sequence that is complementary to the triplet codon sequence used in the genetic code to specify a particular amino acid. This loop on the tRNA is known as the anticodon loop, and it is used to match the tRNA with a complementary codon on the mRNA. In this way the amino acids carried by the tRNA molecules can be aligned in the proper sequence for polymerization into a functional protein. 

All ribosomes have two subunits, and each subunit contains several protein chains and one or more chains of RNA (ribosomal RNA, or rRNA). In the ribosome from E. coli, the smaller of the two subunits is known as the 30S subunit and the larger is referred to as the 50S subunit. (The unit S stands for Svedberg, a measure of how rapidly a particle sediments in a centrifuge.) The two subunits combine to form the active 70S ribosomal assembly. The special RNA molecules that are a part of the ribosome are quite distinct from messenger or transfer RNA molecules, and they play important roles in forming the overall ribosomal quaternary structure and in aligning mRNA and tRNA molecules during protein biosynthesis. 

Table 6.1 shows the relationship between the codon sequence in mRNA and its corresponding amino acid in the new protein. Because there are 64 (43) different anticodon combinations and only 20 encoded amino acids, some different anticodon sequences encode for the same amino acid. Generally, all the anticodons matching a given amino acid will have the same first two nucleotides. Exceptions are arginine, serine, and isoleucine. For example, the codon for proline will always start with CC, but the arginine codon may start with either AG or CG. The 3 end of the tRNA anticodon pairs with the 5 end of the mRNA codon. In other words, the codon and anticodon align and bind in an antiparallel fashion. 

Figure 9.9. Sequence alignment with BioEdit. The sequences of DNA encoding preprosomatostatin mRNA are aligned to identify the consensus sequence.

The first step of RNA translation begins with the initiation of polypeptide synthesis (Fig. 17-10). GTP is bound into the 30S initiation complex and is subsequently hydrolyzed and released upon binding to the 50S subunit. The fMet-tRNA eI occupies what is known as the peptidyl (P) site of the ribosome (Fig. 17-9) another site (A), capable of accommodating an aminoacyl-tRNA, is empty at this stage. It is aligned with the next codon (shown as xxx in Fig. 17-10) in the mRNA. 

The ribosome is the enzyme that catalyzes peptide bond formation. The bacterial ribosome is a large 2500 kDa ribonucleic acid/protein complex comprised of a large subunit (LSU or SOS subunit) and a small subunit (SSU or 30S subunit) (Fig. 4.1). The small ribosomal subunit binds to messenger RNA (mRNA) and reads the genetic code by aligning its base triplet codons with anticodons of transfer RNA molecules (tRNA). The large ribosomal subunit binds to opposite ends of tRNA molecules and catalyzes peptide bond formation. 

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