MCAT Biochemistry Review
Chapter 7: RNA and the Genetic Code
Once the mRNA transcript is created and processed, it can exit the nucleus through nuclear pores. Once in the cytoplasm, mRNA finds a ribosome to begin the process of translation—converting the mRNA transcript into a functional protein. Translation is a complex process that requires mRNA, tRNA, ribosomes, amino acids, and energy in the form of GTP.
Terminology and 5′ → 3′
· DNA → DNA = replication: new DNA synthesized in 5′ → 3′ direction
· DNA → RNA = transcription: new RNA synthesized in 5′ → 3′ direction (template is read 3′ → 5′)
· RNA → protein = translation: mRNA read in 5′ → 3′ direction
As mentioned earlier, the anticodon of the tRNA binds to the codon on the mature mRNA in the ribosome. The ribosome is composed of proteins and rRNA. In both prokaryotes and eukaryotes, there are large and small subunits; the subunits only bind together during protein synthesis. The structure of the ribosome dictates its main function, which is to bring the mRNA message together with the charged aminoacyl-tRNA complex to generate the protein. There are three binding sites in the ribosome for tRNA: the A site (aminoacyl), P site (peptidyl), and E site (exit). These are described further in the section on translation below.
Eukaryotic ribosomes contain four strands of rRNA, designated the 28S, 18S, 5.8S, and the 5S rRNAs; the “S” values indicate the size of the strand. The genes for some of the rRNAs (28S, 18S, and 5.8S rRNAs) used to construct the ribosome are found in the nucleolus. RNA polymerase I transcribes the 28S, 18S, and 5.8S rRNAs as a single unit within the nucleolus, which results in a 45S ribosomal precursor RNA. This 45S pre-rRNA is processed to become the 18S rRNA of the 40S (small) ribosomal subunit and to the 28S and 5.8S rRNAs of the 60S (large) ribosomal subunit. RNA polymerase III transcribes the 5S rRNA, which is also found in the 60S ribosomal subunit; this process takes place outside of the nucleolus. The ribosomal subunits created are the 60S and 40S subunits; these subunits join during protein synthesis to form the whole 80S ribosome.
Figure 7.11. The Composition of Prokaryotic and Eukaryotic Ribosomes
In comparison with eukaryotes, prokaryotes have 50S and 30S large and small subunits, which assemble to create the complete 70S ribosome. Note that the “S” value is determined experimentally by studying the behavior of particles in a ultracentrifuge; thus, the numbers of each subunit and each rRNA are not additive because they are based on size and shape, not size alone. The structure of eukaryotic and prokaryotic ribosomes are shown in Figure 7.11.
The fact that prokaryotic and eukaryotic ribosomes have slightly different structure is no small fact. This difference allows us to target antibiotics, like macrolides (azithromycin, erythromycin), tetracyclines (doxycycline), vancomycin, and others to bacterial cells with fewer side effects to humans.
MECHANISM OF TRANSLATION
Translation occurs in the cytoplasm in prokaryotes and eukaryotes. In prokaryotes, the ribosomes start translating before the mRNA is complete; in eukaryotes, however, transcription and translation occur at separate times and in separate locations within the cell. The process of translation occurs in three stages, as shown in Figure 7.12: initiation, elongation, and termination. Specialized factors for initiation (initiation factors, IF), elongation (elongation factors, EF), and termination (release factors, RF), as well as GTP are required for each step.
Figure 7.12. Steps in Translation
The small ribosomal subunit binds to the mRNA. In prokaryotes, the small subunit binds to the Shine–Dalgarno sequence in the 5′ untranslated region of the mRNA. In eukaryotes, the small subunit binds to the 5′ cap structure. The charged initiator tRNA binds to the AUG start codonthrough base-pairing with its anticodon within the P site of the ribosome. The initial amino acid in prokaryotes is N-formylmethionine (fMet); in eukaryotes, it's methionine.
The large subunit then binds to the small subunit, forming the completed initiation complex. This is assisted by initiation factors (IFs) that are not permanently associated with the ribosome.
Order of Sites in the Ribosome During Translation: APE.
Elongation is a three-step cycle that is repeated for each amino acid added to the protein after the initiator methionine. During elongation, the ribosome moves in the 5′ to 3′ direction along the mRNA, synthesizing the protein from its amino (N) to carboxyl (C) terminus. The ribosome contains three very important binding sites:
· The A site holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the A site.
· The P site holds the tRNA that carries the growing polypeptide chain. It is also where the first amino acid (methionine) binds because it is starting the polypeptide chain. A peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site. This requires peptidyl transferase, an enzyme that is part of the large subunit. GTP is used for energy during the formation of this bond.
· The E site (not shown in Figure 7.12) is where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome. As the now-uncharged tRNA enters the E site, it quickly unbinds with the mRNA and is ready to be recharged.
Elongation factors (EFs) assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used.
Some eukaryotic proteins contain signal sequences, which designate a particular destination for the protein, as shown in Figure 7.13. For peptides that will be secreted, such as hormones and digestive enzymes, a signal sequence directs the ribosome to move to the endoplasmic reticulum (ER), so that the protein can be translated directly into the lumen of the rough ER. From there, the protein can be sent to the Golgi apparatus and be secreted from a vesicle via exocytosis. Other signal sequences direct proteins to the nucleus, lysosomes, or cell membrane.
Figure 7.13. Synthesis of Secretory, Membrane, and Lysosomal Proteins
When any of the three stop codons moves into the A site, a protein called release factor (RF) binds to the termination codon, causing a water molecule to be added to the polypeptide chain. The addition of this water molecule allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from the final tRNA. The polypeptide chain will then be released from the tRNA in the P site, and the two ribosomal subunits will dissociate.
The nascent polypeptide chain is subject to posttranslational modifications before it will become a functioning protein, similar to how hnRNA is modified prior to being released from the nucleus. One essential step for the final synthesis of the protein is proper folding. There is a specialized class of proteins called chaperones, the main function of which is to assist in the protein-folding process.
Many proteins are also modified by cleavage events. A common example of this is insulin, which needs to be cleaved from a larger, inactive peptide to achieve its active form. In peptides with signal sequences, the signal sequence must be cleaved if the protein is to enter the organelle and accomplish its function.
In peptides with quaternary structure, subunits come together to form the functional protein. A classic example is hemoglobin, which is composed of two alpha chains and two beta chains.
Other biomolecules may be added to the peptide via the following processes:
· Phosphorylation: addition of phosphates by protein kinases to activate or deactivate proteins
· Carboxylation: addition of carboxylic acid groups, usually to serve as calcium-binding sites
· Glycosylation: addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination
· Prenylation: addition of lipid groups to certain membrane-bound enzymes
Posttranslational modifications are often important for proper protein functioning. For example, several clotting factors, including prothrombin, require posttranslational carboxylation of some of their glutamic acid residues in order to function properly. Vitamin K is required as a cofactor for these reactions; thus, vitamin K deficiency may result in a bleeding disorder.
MCAT Concept Check 7.3:
Before you move on, assess your understanding of the material with these questions.
1. What are the three steps of translation?
2. What are the roles of each site in the ribosome?
· A site:
· P site:
· E site:
3. What are the major posttranslational modifications that occur in proteins?