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Transfer RNA (tRNA) carries individual amino acids into the ribosome for assembly into the growing polypeptide chain. The tRNA molecules contain 70 to 80 nucleotides and fold into a characteristic cloverleaf structure. Specialized tRNAs exist for each of the 20 amino acids needed for protein synthesis, and in many cases more than one tRNA for…

Ribosomal RNA (rRNA) molecules are the structural components of the ribosome. The rRNAs form extensive secondary structures and play an active role in recognizing conserved portions of mRNAs and tRNAs. They also assist with the catalysis of protein synthesis. In the prokaryote E. coli, seven copies of the rRNA genes synthesize about 15,000 ribosomes per cell. In eukaryotes…

Messenger RNA (mRNA) Messenger RNA (mRNA) delivers the information encoded in one or more genes from the DNA to the ribosome, a specialized structure, or organelle, where that information is decoded into a protein. In prokaryotes, mRNAs contain an exact transcribed copy of the original DNA sequence with a terminal 5′-triphosphate group and a 3′-hydroxyl residue. In…

Whereas DNA provides the genetic information for the cell and is inherently quite stable, RNA has many roles and is much more reactive chemically. RNA is sensitive to oxidizing agents such as periodate that lead to opening of the 3′-terminal ribose ring. The 2′-hydroxyl group on the ribose ring is a major cause of instability…

RNA is a single-stranded nucleic acid polymer of the four nucleotides A, C, G, and U joined through a backbone of alternating phosphate and ribose sugar residues. It is the first intermediate in converting the information from DNA into proteins essential for the working of a cell. Some RNAs also serve direct roles in cellular metabolism. RNA is made by copying the base sequence…

Methods to determine the sequences of bases in DNA were pioneered in the 1970s by Frederick Sanger and Walter Gilbert, whose efforts won them a Nobel Prize in 1980. The Gilbert-Maxam method relies on the different chemical reactivities of the bases, while the Sanger method is based on enzymatic synthesis of DNA in vitro. Both methods measure the distance from…

Circular DNA molecules such as those found in plasmids or bacterial chromosomes can adopt many different topologies. One is active supercoiling, which involves the cleavage of one DNA strand, its winding one or more turns around the complementary strand, and then the resealing of the molecule. Each complete rotation leads to the introduction of one supercoiled turn…

Chemical modification of DNA can lead to mutations in the genetic material. Anions such as bisulfite can deaminate cytosine to form uracil, changing the genetic message by causing C-to-T transitions. Exposure to acid causes the loss of purine residues, though specific enzymes exist in cells to repair these lesions. Exposure to UV light can cause adjacent pyrimidines to dimerize, while oxidative damage…

Nucleases are enzymes that hydrolytically cleave the phosphodiester backbone of DNA. Endonucleases cleave in the middle of chains, while exonucleases operate selectively by degrading from the end of the chain. Nucleases that act on both single- and double-stranded DNA are known. Restriction endonucleases are a special class that recognize and cleave specific sequences in DNA. Type II restriction endonucleases always…

Three types of natural methylation have been reported in DNA. Cytosine can be modified either on the ring to form 5-methylcytosine or on the exocyclic amino group to form N4-methylcytosine. Adenine may be modified to form N6-methyladenine. N4-methylcytosine and N6-methyladenine are found only in bacteria and archaea, whereas 5-methylcytosine is widely distributed. Special enzymes called DNA methyltransferases are responsible…