Ribosome Structure and Function in Translation 17.5

A peptide bond forms between the amino acid held by the aminoacyl tRNA in the A site and the growing polypeptide, which was held by a tRNA in the

P site.

Figure 17.13 shows two views of how the molecules required for translation fit together. Note that the ribosome can accommodate three tRNAs bound to codons in mRNA

The tRNA on the right in the figure (colored red) carries an amino acid. The site in the ribosome that holds this tRNA is the A site—"A" for acceptor, or aminoacyl. The tRNA that is in the middle (green) holds the growing polypeptide chain and occupies the P (for peptidyl) site inside the ribosome. (Also think of "P" for peptide-bond formation.) The left-hand (blue) tRNA no longer has an amino acid attached and is about to leave the ribosome. It occupies the ribosome's E site—"E" for exit.

The ribosome moves relative to the mRNA by one codon, and all three tRNAs are shifted one position within the ribosome. The tRNA in the E site exits; the tRNA in the P site moves to the E site; the tRNA in the A site switches to the P site; the A site is now empty and ready to accept another

aminoacyl tRNA.

The translation of each codon in mRNA into the next amino acid in a polypeptide chain begins when the anticodon of an aminoacyl tRNA binds to the

codon

The interactions between the small subunit, the message, and the tRNA are mediated by proteins called

initiation factors (see Figure 17.14, step 1)

Initiation in eukaryotes differs in a number of ways. For example, many more initiation factors are needed, the ribosome first associates with the cap at the 5′ end of the mRNA, and the initiator tRNA carries a normal

methionine.

Polypeptide Folding A fundamental principle of biology is that a protein's function depends on its shape, and in turn, a protein's shape depends on how it folds (Chapter 3). Folding is determined by the amino acid sequence of a polypeptide chain. Although folding can occur spontaneously, it is frequently guided and accelerated by proteins called

molecular chaperones.

ribosomes can separate into two parts, called the large subunit and small subunit. Each ribosome subunit consists of a complex of rRNA molecules and proteins. During translation, the small subunit holds the mRNA and the large subunit is where

peptide bonds are formed.

Translation of a codon is complete when a peptide bond forms between the amino acid originally carried by the tRNA and the growing .

polypeptide

Chemical Modifications An earlier chapter described how eukaryotic proteins are often extensively modified after they are synthesized. For example, in the organelles called the rough endoplasmic reticulum and the Golgi apparatus, small chemical groups may be added to proteins—often sugars (in the process of glycosylation; Ch. 7, Section 7.5) or lipid groups that are critical for normal functioning or to target them to specific locations. Another common post-translational modification is the addition of a phosphate group (in the process of phosphorylation) by enzymes called protein kinases. Adding a phosphate group—and removing it later—often dramatically affects the protein's activity

Figure 17.17 reviews how gene expression works in a eukaryotic cell. Take a close look to see how all these steps fit together. The take-home message is that gene expression is a multistep process that begins with transcription. What's critical to remember is that the RNAs and proteins produced during gene expression give the cell and organism its characteristics. These molecules truly are the basis of life.

Protein synthesis starts at the amino end (N-terminus) of a polypeptide and proceeds to the

carboxy end (C-terminus

Then the ribosome separates from the

mRNA, and the two ribosomal subunits dissociate (step 3).

Step 3 shows translocation, the process in which the ribosome moves one codon down the mRNA once a new

peptide bond is formed. In reality, it is often the mRNA that is ratcheted through a stationary ribosome, but the important point is that translocation involves the codon-by-codon movement of the mRNA relative to the ribosome

When both the P and A sites are occupied by tRNAs, the amino acids on the tRNAs are in the ribosome's active site. This is where

peptide-bond formation—the essence of protein synthesis—occurs. Peptide-bond formation is one of the most important reactions that takes place in cells because manufacturing proteins is central to all cell processes.

Release factors fit tightly into the A site because they have the size and shape of an aminoacyl tRNA coming into the ribosome. Once in the A site, the release factor triggers the hydrolysis of the bond that links the tRNA in the P site to the

polypeptide chain. This reaction frees the polypeptide.

Terminating Translation genetic code includes three stop codons: UAA, UAG, and UGA (Ch. 16, Section 16.3). Instead of tRNAs working to terminate translation, translation is brought to an end when the translocating ribosome reaches one of the stop codons and a protein called a

release factor recognizes the stop codon and fills the A site (Figure 17.16, step 1). Stop codons are found in the 3′ region of an mRNA, but never at the very end of an mRNA.

1. An aminoacyl tRNA diffuses into the A site; if its anticodon matches a codon in mRNA, it stays in the

ribosome

With the help of other proteins, the newly synthesized polypeptide and uncharged tRNAs are released from the

ribosome (step 2).

Translocation requires a type of protein called an elongation factor. (Other elongation factors that are involved in steps beside translocation are not shown in Figure 17.15.) Translocation requires energy, and this energy is obtained as one of the elongation factors binds to the

ribosome and breaks down the energy-rich molecule GTP.

in bacteria. Translation begins when a section of rRNA in a small ribosomal subunit binds to a complementary sequence on an mRNA. This mRNA region is called the

ribosome binding site, or Shine-Dalgarno sequence, after the biologists who discovered it. This site is about six nucleotides upstream from the start codon.

Initiation factors help in preparing the ribosome for translation and in binding the first aminoacyl tRNA to the

ribosome. In bacteria this is a specialized tRNA, called the initiator tRNA, that bears a modified form of methionine— N-formylmethionine (abbreviated f-Met; step 2)

Initiation is complete when the large subunit joins the complex (step 3). At this point, the initiator tRNA occupies the P site of the assembled

ribosome. This is the only time a tRNA carrying a single amino acid occupies the P site.

Initiating Translation To translate an mRNA, a ribosome must begin at the first codon in a message, translate the mRNA up to the message's termination codon, and then

stop

translation initiation is to recall that a start codon (usually AUG) is found near, but never at, the

5′ end of mRNAs, and that it codes for the amino acid methionine

Elongation: Extending the Polypeptide At the start of elongation, the E and A sites in the ribosome are empty of tRNAs. As a result, an mRNA codon is exposed in the A site. As step 1 in Figure 17.15 illustrates, the elongation phase begins when an aminoacyl tRNA binds to the codon in the

A site by complementary base pairing between the anticodon and codon.

Translocation does several things: Because the anticodons of tRNA remain bound to the codons in mRNA, movement of the ribosome brings the uncharged tRNA into the E site and the tRNA containing the growing polypeptide into the P site. Translocation of the ribosome also exposes a new codon in the

A site, which is now open and free to accept a new charged tRNA. The tRNA that transferred the polypeptide to the amino acid of the tRNA in the A site now finds itself in the E site and is ejected from the ribosome.

Moving Down the mRNA What happens after a peptide bond forms? Step 2 in Figure 17.15 shows that peptide-bond formation involves the transfer of the amino acid linked to the tRNA in the P site to the amino acid held by the tRNA in the

A site.