Exam Tip: If a question asks why RNA is more chemically reactive than DNA, remember the extra $-OH$ group on the ribose sugar!
Transcription: Copying the Blueprint
Transcription is the process of synthesizing an RNA molecule from a DNA template. This process is catalyzed by the enzyme RNA polymerase, which unwinds the DNA helix and adds nucleotides one by one to the growing RNA chain. The resulting RNA molecule is called a transcript.
In bacteria (prokaryotes), transcription is relatively straightforward. The RNA polymerase uses a subunit called the sigma factor to recognize a specific DNA sequence known as the promoter. Once transcription begins, the sigma factor is released, and the enzyme continues until it hits a terminator sequence.
In eukaryotic cells, the process is much more complex. Eukaryotic cells utilize three different types of RNA polymerase, and they require a large assembly of general transcription factors to initiate the process. For example, RNA polymerase II (which transcribes mRNA) relies on the TATA box sequence, which is recognized by the TATA-binding protein (TBP) to help orient the transcription machinery.
RNA Processing in Eukaryotes
Unlike prokaryotic mRNA, which is often ready for use immediately, eukaryotic transcripts undergo significant modification in the nucleus before they can be exported to the cytoplasm:
- Capping: A 7-methyl guanine (m7G) cap is added to the 5' end.
- Polyadenylation: A "poly-A tail" of repeated adenine nucleotides is added to the 3' end.
- RNA Splicing: Most eukaryotic genes are composed of coding regions called exons interspersed with noncoding regions called introns. During splicing, a complex called the spliceosome (made of snRNPs) removes the introns and joins the exons together into a continuous coding sequence.
Translation: Building the Protein
Once the mature mRNA reaches the cytoplasm, the cell begins translation—the process of turning the nucleotide sequence into an amino acid sequence. This relies on the genetic code, where groups of three nucleotides called codons specify particular amino acids.
Translation requires two essential "adaptors":
- tRNA (transfer RNA): These molecules have an anticodon that base-pairs with the mRNA codon and carries the corresponding amino acid.
- Aminoacyl-tRNA synthetase: This enzyme "charges" the tRNA by correctly attaching the specific amino acid to it.
The actual assembly occurs on the ribosome, a massive complex of RNA and proteins. The ribosome has three distinct binding sites for tRNA: the A-site (aminoacyl), the P-site (peptidyl), and the E-site (exit).
The Translation Cycle
The process follows a repeating four-step cycle:
- Binding: A charged tRNA enters the vacant A-site by matching its anticodon to the mRNA codon.
- Peptide Bond Formation: The growing polypeptide chain is transferred from the tRNA in the P-site to the amino acid on the tRNA in the A-site.
- Translocation: The ribosome shifts forward by three nucleotides, moving the tRNAs from the A and P sites to the P and E sites.
- Resetting: The empty tRNA exits through the E-site, leaving the A-site open for the next cycle.
Translation ends when the ribosome encounters a stop codon (UAA, UAG, or UGA). Since no tRNA matches these codons, release factors bind to the A-site, causing the ribosome to release the completed protein and dissociate.
Regulation and Post-Translational Control
The concentration of a protein in a cell is not just determined by how fast it is made, but also by how it is regulated after synthesis. Some proteins require post-translational modifications, such as phosphorylation or glycosylation, to become fully functional. Conversely, cells must also remove proteins that are misfolded or no longer needed. In eukaryotes, this is often handled by the Ubiquitin-Proteasome Pathway (UPP), where proteins are tagged with ubiquitin and subsequently degraded by the proteasome.
