RNA differs from DNA in having a 2' hydroxy group on the ribose. Other differences:

• Uracil replaces the thymine (methyluracil) found in DNA

• RNA is single-stranded

A few RNA molecules adopt a helical conformation, such as Poly A, below, gaining some stabilization by partial stacking of the bases:

Synthetic Polyadenosine (PolyA)

In general, however, RNA (like proteins) has three levels of structure:

• Primary - the sequence of bases

• Secondary - helical or partially helical regions formed by base pairing

• Tertiary - structure formed by stacking the helical regions upon one another

The rat ribosomal RNA below illustrates the first two types of structure.

Rat Ribosomal RNA (430d)

Four major classes of RNA are found in living cells:

• Ribosomal RNA (rRNA): is an integral part of cellular ribosomes, the complexes of protein and RNA that function as protein synthesis factories; about 80% of all RNA

• Messenger RNA (mRNA): is the carrier of the genetic code from nuclear DNA to the ribosomes; about 3% of RNA

• Transfer RNA (tRNA): ferries individual amino acid molecules to the ribosomes for incorporation into protein; about 15% of RNA

• Miscellaneous Small RNA: serves a variety of functions, including some enzyme-like catalysis; many are involved in processing RNA after it is formed; the remaining 2% of RNA
  • Recent evidence suggests that some of these small RNAs may serve as switches, turning genes on and off

  • Others, called RNAi, silence genes by tagging their mRNA for destruction

Not many crystal or nmr structures are available for RNA, except transfer RNA and some introns.

• In part this follows from the "stickiness" of single-stranded nucleic acids; they tend to complex quite strongly with proteins and other nucleic acids, and thus are hard to isolate.

• We will see examples of tRNA and ribosomes later.

The first structure is a segment of mRNA complexed to one protein from the ribosome (a complex of protein and RNA) on which it was being used to manufacture protein (more about this later).

Messenger RNA and Ribosomal Protein (1cn8)

• The two nucleosides colored in orange are the 3' and 5' ends of the mRNA; clearly the chain is folded back on itself, making a hairpin as in the cartoon shown earlier

• At the bottom of the loop, the pairing of bases is evident

We will look at a complete ribosome shortly.

Because tRNAs are small, and don't spend all their time complexed to proteins, several good tRNA structures are available. The one we'll play with here is a yeast phenylalanine tRNA.

The basic secondary structure of a tRNA is a cloverleaf:

• The arms are formed by Watson-Crick hydrogen bonding between base pairs

• The region where the 3' and 5' ends are paired is the site of amino acid attachment; the nucleotides at the 3' end are always CCA

• The amino acid is esterified to the 2' or 3' OH of the terminal A

• Other nucleotides that are conserved are indicated in gray

• The loop at the bottom is where the tRNA binds to the mRNA; this area tends to be particularly rich in modified nucleotides such as pseudouridine, inosine, and bases having their 2' OH methylated

• The D arm is named for the presence of the modified base dihydrouridine; the TYC arm for the presence of pseudouracil

• The variable arm is so named because it varies in length; it also is sometimes called the extra arm

The molecule adopts a tertiary structure resembling an L shape, obtained by folding the TYC arm back over the D and variable arms; base pairing then occurs in a non-Watson-Crick manner between the arms:

Yeast tRNAphe
Color Code: Violet = Acceptor arm Blue = mRNA binding arm Yellow = Variable (extra) arm Red = D arm Green = TYC arm
tRNA in a Jmol Window

tRNA tends to have numerous modified bases (methylated, etc.), base triplets, and non-Watson-Crick base pairing.

Base Triplets in Yeast tRNA (1tra)

tRNA in mitochondria and chloroplasts is somewhat smaller than that from bacteria and the cytosol of eukaryotes, but is otherwise similar. At least 32 tRNAs are required to recognize all of the codes for the amino acids; some cells make use of even more.

• Protein synthesis is the slowest of the three processes, in part because tRNA-bound amino acids must be assembled from throughout the cytosol

• A proofreading component of the ribosome checks to see that the right tRNA is in place, and dissociates it from the ribosome if it is incorrect

• No check is made for amino acid attached to the tRNA; attach an incorrect amino acid, it will be efficiently incorporated into the protein