Relationship (If Any) Of Codon Start/Stop And Gene Base Pair Position

Question

[James Hardwick]

I'm a bit of a Bio noob doing some software engineering in the bio domain. I've been gradually figuring things out on my own but occasionally stumble across what are probably simple concepts that trip me up.

I'm curious if there is any relationship between a codon start/stop and a gene's base pair position (position on the chromosome). Are they the same thing? Does the codon start/stop only represent the bounds of the peptide? Are neither of these anywhere close to correct? Can someone explain these subtleties?

Answer 1

[Swbarnes2]

People generally count the "gene" as starting where the transcript starts and stops. (Though obviously sequences upstream and downstream of this can be important in controlling transcription) But the transcript is longer than the coding region, as there is often untranslated region (UTR) upstream of the start codon, and downstream of the stop codon.

So you can't predict from the gene coordinates where the coding starts.

[James Hardwick]

So then correct me if I'm interpreting this wrong, the codon indicates the start/stop of the polypeptide within a given transcript?

[Swbarnes2]

A codon is a 3-base sequence that associates with an amino acid, (because it is the template that allows a particular tRNA carrying the complementary anti-codon and a particular amino acid to bind to it and add that amino acid to the growing peptide chain) or a stop. The start codon is the first 3-base sequence that is translated. The only way to know where the start codon is in a gene is to look up what the protein sequences is, and deduce where translation must start in order to get that sequence.

[James Hardwick]

Ok, but referring back to your original answer, the start/stop codons essentially mark the division between UTR and translated regions of a transcript?

[Swbarnes2]

Of a processed transcript (introns taken out), yes

Answer 2

[Larry_Parnell]

Another way to think of is is human chromosome 1 of some 230 million base pairs in length encoding some 3300 genes. Everyone one of those genes has a position #1 for the beginning of its transcript, as swbarnes2 writes (+1), but all of those genes have a unique start position with respect to the coordinate position along chromosome 1.

For protein-coding genes the mRNA is longer than the portion that codes for or is translated into protein. (This is not always true - there are cases where the untranslated regions are not known or not defined.) Thus, for gene NADK, involved in success of smoking cessation, it is 27239 bp along chromosome 1; the mRNA of isoform 1 (of 3) is 3244 nt in length and encodes a protein of 446 amino acids. In this mRNA, the protein translation begins at position 223 and terminates at position 1563 for a total "protein-encoding" length of 1341 (= 446 a.a. + termination codon).

For another mRNA, these values will naturally be different - start and stop will be at different positions.