Gene Expression Fundamentals: Transcription, RNA Processing, and Translation

Transcription: From DNA to RNA

Steps of Transcription

Initiation

• Transcription begins when transcription factors bind to a specific nucleotide sequence of DNA known as the promoter region or the "TATAA box."
• These transcription factors signal RNA polymerase II to attach to the DNA at the promoter.

Elongation

• Once attached to the DNA, RNA polymerase synthesizes a single-stranded RNA molecule in a 5’ → 3’ direction.
• RNA nucleotides are added to the growing polymer, which are complementary to the DNA template.

Termination

• Eventually, RNA polymerase will reach a termination sequence in the DNA.
• This causes RNA polymerase to release the newly synthesized mRNA and to dislodge from the DNA.

Note: The template strand is also known as the antisense strand, and the non-template strand is known as the sense strand.

RNA Modification: Processing the Transcript

• Alternative Splicing: A regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.
• Introns: The non-coding regions of RNA that are removed during processing.
• Exons: The coding regions of RNA that are retained and expressed.
• Proteins known as small nuclear ribonucleoproteins (snRNPs) help in splicing out introns.
• Several snRNPs that recognize the splice site sequence form a complex called the spliceosome.
• This then allows exons to join and form a protein, which then folds into its appropriate shape (primary, secondary, tertiary, or quaternary).
• RNA Processing (Capping and Tailing): To protect mRNA from enzymes in the cytoplasm, a 5’ GTP cap and a 3’ poly-A tail are attached before the RNA leaves the nucleus.

Translation: Synthesizing Proteins

Steps of Translation

Initiation

• mRNA moves to the ribosome from the nucleus through the nuclear pore as the small ribosomal subunit binds to the mRNA at the start codon AUG (which codes for methionine, MET).
• tRNA with a complementary anticodon binds to the mRNA.
• A functional ribosome is formed once the large ribosomal subunit binds.

Elongation

• Codon Recognition: An mRNA codon in the A site, along with the tRNA with a complementary anticodon, hydrogen bonds to the codon in the A site, bringing the appropriate amino acid to the ribosome.
• Bond Formation: Peptide bonds form between amino acids in the A site and the amino acids in the P site. These bonds are created through condensation by the large ribosomal subunit as new amino acids are added in a 5’ → 3’ direction.
• Translocation: The ribosome moves towards the 3’ end, resulting in a binding site shift (A → P → E). The E site leads to the ejection of tRNA.

Termination

• Adding amino acids to the polypeptide chain continues until there is a STOP codon on the RNA (UAA, UGA, or UAG).
• A "release factor" binds to the stop codon and releases the amino acid chain.
• The ribosome dissociates into its two subunits, and the amino acid chain is released and can now fold into its secondary, tertiary, and/or quaternary structure to become a functional protein.