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25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;}div.WordSection1 {page:WordSection1;}–            Thecentral dogma of modern biochemistry is based on the coded informationcontained within deoxyribonucleic acid (DNA). Double-stranded DNA is converted to single-stranded RNA.  RNA is then converted to a linear strand ofamino acids, which subsequently fold into three-dimensional proteins.  These proteins act as structural componentsof cells within the body or as functional biochemical machines.  The building of cellular proteins from theencoded instructions within DNA occurs in two steps:  transcription and translation.

  During transcription, the four nucleotides ofDNA (adenine, cytosine, guanine, and thymine) are rewritten in the form of theportable messenger ribonucleic acid (mRNA), which is composed of adenine,cytosine, guanine, and uracil.  Thetranslation process decrypts this transcribed mRNA code into a linear string ofamino acids.  This procedure isaccomplished by matching transfer RNAs (tRNAs) and their associated amino acidto the sequence of mRNA nucleotides. After the protein has completed translation, it undergoes manystructural changes to fold into its native conformation.

  The protein is now ready to play itsfunctional role in the life of the organism. To thoroughlyanalyze the translation process, we would first begin by examining theinterrelationship between nucleic acid sequences and polypeptide sequences, thegenetic code.  Next, we consider the structuresand properties of tRNAs, the amino acid carriers that mediate the translationprocess.  Following this, we consider thestructure and functions of ribosomes, the intricate molecular mechanisms thatcatalyze peptide bond formation between the mRNA-specified amino acids.  Finally, we investigate how cells degradeproteins, a process that must balance protein synthesis.To decipher thegenetic code, researchers needed to figure out how sequences of nucleotides ina DNA or RNA molecule could encode the sequence of amino acids in apolypeptide.

  Cells interpret mRNAs byreading their nucleotides in groups of three, called codons.   Of 64 codons,there are 61 that are each read to specify a certain amino acid.  The use of repeating tetranucleotidesindicated the reading direction of the code in that mRNAs are read in the 5′ to3′ direction.   There are three codons thatdo not specify amino acids.  Thesecodons, UAG, UAA, and UGA are chain termination signals known as stopcodons.

  The codons AUG, and lessfrequently GUG, form part of the chain initiation sequence known as startcodons.  These codons however, alsospecify the amino acid residues Met and Val. The tripletcharacter of the genetic code was established through the use of chemicalmutagens, substances that chemically induce mutations.  There are two major classes of mutations:Point mutations, and insertion/deletion mutations.  Point mutations are changes within a gene inwhich one base pair replaces another. These mutations are caused by either base analogs that mispair duringDNA replication or by substances that react with bases to form products thatmispair.  During insertion/deletionmutations, one or more nucleotide pairs are inserted or deleted from DNA.  The insertion or deletion of a nucleotideshifts the frame (grouping) in which succeeding nucleotides are read as codons.

  Insertions or deletions of nucleotides aretherefore also known as frameshift mutations. These mutations arise from the association of DNA with intercalatingagents that distort the DNA structure. The analysis of a series of frameshiftmutations that suppress one another established that the genetic code is an unpunctuatedtriplet code. The genetic codecould be determined by simply comparing the base sequence of an mRNA with theamino acid sequence of the polypeptide it specifies.  However, in the 1960s, techniques forisolating and sequencing mRNAs had not yet been developed.  Therefore, the elucidation of the geneticcode proved to be a difficult task.       In a cell-free protein synthesizing system,poly (U) directs the synthesis of poly (Phe), thereby demonstrating that UUU isthe codon specifying Phe.

  This wasestablished in 1961 by Marshall Nirenberg and Heinrich Matthaei, and served asa major breakthrough in deciphering the genetic code.  The genetic code was elucidated through theuse of polynucleotides of known composition but random sequence, by the abilityof defined triplets to promote the ribosomal binding of tRNAs bearing specific aminoacids, and through the use of synthetic mRNAs of known alternating sequences.  The latter investigations have alsodemonstrated that the 5′ end of mRNA corresponds to the N terminus of thepolypeptide it specifies and have established the sequences of the Stop codons.

Degenerate codons differ mostly in the identities of their third base. Smallsingle-stranded DNA phages such as _X174 contain overlapping genes in differentreading frames.  The genetic code used bymitochondria differs in several codons from the “standard” genetic code.Therefore, the “standard” genetic code, although very widely utilized, is notuniversal. Transfer RNAs consistof 54 to 100 nucleotides that can be arranged in thecloverleaf secondarystructure.  It is possible for up to 10%of a tRNA’s bases to be modified.

  YeasttRNAPhe forms a narrow, L-shaped, three-dimensional structure that resemblesthat of other tRNAs. Most of the bases are involved in stacking andbase pairing associations includingnine tertiary interactions that appear to be essential for maintaining themolecule’s native conformation.  Aminoacids are appended to their cognate tRNAs in a two-stage reaction catalyzed bythe corresponding aminoacyl–tRNA synthetase (aaRS).  There are two classes ofaaRSs, each containing 10 members.Class I aaRSs have two conserved sequence motifs that occur in the Rossmannfold common to the catalytic domain of these enzymes. Class II aaRSs have threeconserved sequence motifs that occur in the7-stranded antiparallel  sheet–containing fold that forms the core oftheir catalytic domains.

 In binding onlytheir cognate tRNAs, aaRSs recognize only an idiosyncratic but limited number ofbases (identity elements) that are, most often, located atthe anticodon and in the acceptorstem. The great accuracy of tRNA charging arises from the proofreading of thebound amino acid by certain aminoacyl–tRNA synthetases via a double-sievemechanism and at the expense of ATP hydrolysis.Many organisms and organelles lacka GlnRS and instead synthesize Gln–tRNAGln by the GluRS-catalyzed charging of tRNAGlnwith glutamate followed by its transamidation using glutamine as the amidogroup source in a reaction mediatedby Glu–tRNAGln amidotransferase(Glu-AdT).

 Ribosomes select tRNAs solelyon the basis of their anticodons. A single tRNA, through wobble pairing, readssets of degenerate codons.  The UGA codon,which is normally the opal Stop codon may, depending on its context in mRNA,specify a selenoCys (Sec) residue, which is carried by a specific tRNA (tRNASec),thereby forming a selenoprotein. Nonsense mutations may be suppressed by tRNAswhose anticodons have mutated to recognize a Stop codon. 

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