Re: What are ribosomes made out of and how do they make proteins?

Ribosomes are large complexes of multiple proteins and ribosomal ribonucleic acids (rRNA's). Each ribosome is composed of two parts: a smaller 40S (S is for Svedberg, a coefficient of sedimentation that roughly approximates size.) subunit composed of the 18S rRNA and 33 proteins; and a larger 60S subunit composed of the 28S, 5S, and 5.8S rRNA's and 49 proteins. For decades, the many enzymatic functions of the ribosome were assigned to the various protein components, with the rRNA molecules acting as scaffolds; however, molecular studies of the last ten years have shown that it is the rRNA molecules themselves that carry out the reactions, and the proteins that simply stabilize the complex. This was summarized recently by Tom Cech in Science magazine.

Ribosomes are common to all life, because of their central role in converting stored genetic information into functional proteins. Without going into the overwhelming details of initiation and elongation factors, and ribosomal assembly and positioning, I'll try to describe protein synthesis. (If this is too complicated, there is a more basic description in the archive.)

Setting the Table

For protein synthesis to occur, several components have to be made and available for the ribosome to use. First, the various RNA polymerases have to transcribe the tRNA's and rRNA's that run the synthesis, as well as the mRNA messages that contain the codes for constructing the proteins. As the rRNA's assemble with their proteins to form the ribosomes, each tRNA binds to a special enzyme called an aminoacyl-tRNA synthetase that reads the tRNA's anti codon and attaches the correct amino acid to its end. It is the specificity of the different aminoacyl-tRNA synthetases that determines the genetic code. So, before protein synthesis can occur, the cell needs functional ribosomes, properly aminoacylated tRNA's, and mRNA containing the proper codes.

Building the Proteins

When the large and small subunits of the ribosome come in contact with a molecule of mRNA, they join just up from the coding region to form a functional ribosome. The ribosome then moves down the mRNA until it finds the base-triplet AUG (adenine-uracil-guanine). At this point, it recruits a tRNA with the corresponding anticodon, CAU (like DNA, RNA strands run in opposite directions), which is already "charged" with the amino acid, methionine (Met, M). The ribosome then "ratchets" down to the next three base codon, which is recognized by a charged tRNA with the corresponding anticodon. With a charged tRNA in each of its binding sites, the ribosome then proceeds to disconnect the methionine from its tRNA and attach it to the amino acid on the next tRNA. The ribosome ratchets down another three bases, and carries out the same reaction, this time removing the two connected amino acids from the upstream tRNA and attaching them to the amino acid on the downstream tRNA, to generate an string of three amino acids. This process repeats as many times as there are codons in the message, assembling a long strand of amino acids ordered according to the order of codons the ribosome encounters. Eventually, the ribosome ratchets over to a codon, for which there is no corresponding tRNA. At this point, the ribosome stops moving (hence these are called "stop" codons) and performs half of the amino acid transfer reaction, releasing the amino acid strand - the bond formed between adjacent amino acids is called a "peptide" linkage, so the new amino acid strand is referred to as a "polypeptide". After release from the ribosome, the polypeptide can be modified or simply folded to form a functional protein.

As mentioned above, all of the important activities of the ribosome - mRNA recognition and binding, tRNA binding, mRNA/tRNA translocation, and amino acid transfer - are carried out by the various rRNA molecules. Like proteins, the three-dimensional shapes and interactions within each rRNA give them their activities, and allow them to perform the necessary reactions.