The coding sequence (CDS) is the specific section of a gene or a messenger RNA (mRNA) molecule that holds the instructions for building a protein. It contains the precise molecular information that dictates the construction of the thousands of different proteins a cell needs to operate. This sequence is a continuous stretch of nucleotides, the molecular letters of the genetic code. The cell’s machinery reads the CDS accurately and completely to assemble an amino acid chain and produce a functional protein.
Structure within a Gene
The coding sequence is part of a larger genetic unit called a gene, which is a segment of DNA. In complex organisms, the protein-coding instructions are physically split into multiple segments called exons. These exons are interspersed with non-coding segments known as introns, which do not contribute to the final protein.
When a gene is copied from DNA into a precursor RNA molecule, the transcript contains both the coding exons and the intervening introns. A precise cellular process called RNA splicing then takes place to prepare the message for protein synthesis. During splicing, the non-coding intron sequences are excised, and the separate exon segments are joined together. This processing step results in the mature mRNA molecule, which contains a single, continuous coding sequence ready for translation.
The Process of Protein Creation
The information stored within the coding sequence is realized through a two-step molecular flow that transforms the genetic code into a protein structure. The first step, known as transcription, occurs when the DNA sequence of the gene is copied into a complementary strand of messenger RNA (mRNA). An enzyme called RNA polymerase moves along the DNA template, assembling the mRNA molecule that carries the protein instructions out of the cell nucleus.
Once the mRNA is complete, it travels to the cytoplasm where the second process, translation, begins at the ribosome. The ribosome reads the continuous coding sequence on the mRNA in groups of three nucleotides, called codons. Each codon corresponds to a specific amino acid, which is delivered by a transfer RNA (tRNA) molecule. The ribosome links these individual amino acids together in the order specified by the CDS, forming a long polypeptide chain that folds into a three-dimensional protein.
Start and Stop Signals
The accurate interpretation of the coding sequence depends on precise punctuation marks embedded within the genetic code. Translation must begin at a specific location, signaled by a start codon, typically the sequence AUG on the mRNA. This codon specifies the first amino acid, methionine, and establishes the correct reading frame for the entire sequence.
The reading frame refers to the specific grouping of three nucleotides into non-overlapping codons. If the ribosome begins reading just one nucleotide off the correct start codon, every subsequent triplet will be misread, leading to a non-functional sequence of amino acids. Translation continues until the ribosome encounters one of three specific stop codons—UAA, UAG, or UGA—which signal termination. The polypeptide chain is then released from the ribosome, ending the protein creation process.
Sequence Errors and Human Health
Errors within the coding sequence, known as mutations, can disrupt the instructions for protein synthesis and have consequences for human health. A single alteration to a nucleotide within the CDS is known as a point mutation. If this change results in a different amino acid being incorporated, it can alter the protein’s structure and function.
A classic example is sickle cell anemia, which stems from a single point mutation in the beta-globin gene. The DNA sequence for the sixth codon is changed from GAG to GTG, substituting glutamic acid with valine. This alteration changes the physical properties of the hemoglobin protein, causing red blood cells to deform into a rigid, sickle shape under low oxygen conditions.
More severe alterations include frameshift mutations, which involve the addition or deletion of one or two nucleotides. Because the genetic code is read in three-base increments, adding or removing a non-triplet number of bases shifts the entire reading frame downstream from the mutation site. This results in a completely scrambled sequence of amino acids after the error, yielding a truncated and non-functional protein.