Protein biosynthesis

Cells constantly make new proteins to replace those lost through breakdown or export. This process, called protein biosynthesis or protein synthesis, is essential for life. Proteins serve as enzymes, structural components, and hormones. While the basic steps are similar in prokaryotes and eukaryotes, there are key differences.

Protein synthesis happens in two main stages: transcription and translation. In transcription, a gene—a DNA segment coding for a protein—is copied into messenger RNA (mRNA). Enzymes called RNA polymerases carry out this conversion inside the nucleus. In eukaryotes, the initial copy is a premature form (pre-mRNA) that must undergo post-transcriptional modifications to become mature mRNA. This mature mRNA then exits the nucleus through nuclear pores into the cytoplasm. During translation, ribosomes read the mRNA sequence and use it to determine the order of amino acids. The ribosomes catalyze the formation of covalent peptide bonds between these amino acids, building a polypeptide chain.

After translation, the polypeptide chain must fold into a functional shape. For example, an enzyme needs a correctly folded active site to work. Folding begins with the formation of smaller secondary structures, which then arrange into the overall three-dimensional tertiary structure. Once folded, the protein may undergo further maturation through post-translational modifications. These changes can affect the protein’s function, its location within the cell (such as the cytoplasm or nucleus), and its ability to interact with other proteins.

Errors in protein biosynthesis often underlie disease. DNA mutations alter the mRNA sequence, which in turn changes the amino acid sequence of the polypeptide. A mutation might introduce a premature stop signal, shortening the chain, or it might swap one amino acid for another. Such changes can impair the protein’s function or its ability to fold correctly. Misfolded proteins tend to form dense clumps, which are linked to neurological disorders like Alzheimer’s and Parkinson’s disease.

**Transcription**

Transcription takes place in the nucleus, using DNA as a template to produce mRNA. In eukaryotes, the initial product is pre-mRNA, which undergoes post-transcriptional modifications inside the nucleus to become mature mRNA. In prokaryotes, no such modifications are needed; transcription directly yields mature mRNA.

First, an enzyme called helicase acts on the DNA molecule. DNA has an antiparallel double helix, with two complementary strands held together by hydrogen bonds between base pairs. Helicase breaks these bonds, unwinding a region of DNA (corresponding to a gene) and exposing the bases. Only one of the two strands serves as the template for pre-mRNA synthesis; this is the template strand. The other strand, complementary to the template, is called the coding strand.

DNA and RNA have directionality, meaning each molecule has two distinct ends. This arises from the asymmetric structure of nucleotides: a phosphate group on one side of the pentose sugar and a base on the other. The five carbons in the sugar are numbered 1' to 5'. Phosphodiester bonds link the 3' carbon of one nucleotide to the 5' carbon of the next. Thus, the coding strand runs 5' to 3', while the complementary template strand runs 3' to 5'.

RNA polymerase binds to the exposed template strand and reads it in the 3' to 5' direction. As it moves, it synthesizes a single strand of pre-mRNA in the 5' to 3' direction, catalyzing the formation of phosphodiester bonds between free nucleotides that base-pair with the template. Behind the moving polymerase, the two DNA strands rejoin, so only about 12 base pairs are exposed at any time. RNA polymerase builds pre-mRNA at about 20 nucleotides per second, allowing thousands of copies from the same gene in an hour. Despite this speed, the enzyme has a proofreading mechanism: it can remove incorrect nucleotides (those not complementary to the template) via an excision reaction. When RNA polymerase reaches a specific DNA sequence that signals termination, it detaches, and pre-mRNA synthesis is complete.

The resulting pre-mRNA is complementary to the template DNA strand and identical in sequence to the coding DNA strand, except for one key difference: RNA uses uracil instead of thymine.