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I have a book that says:

In humans titin is a chain of 34,350 amino acids, but in mice it is even longer with 35,213 amino acids.

If two polypeptides had different amino acid sequence lengths, how can they be considered the same protein? Or is it because they share in common one or more amino acid sequences - which, if a polypeptide contains, biologists consider it a particular type of protein - that they are both considered the same protein?

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up vote 6 down vote accepted

If they perform the exact same function, they can be considered the same functionally.

Hemoglobin in most humans is the same, down to the amino acid sequence; the hemoglobin in sickle cell anemia, Hemoglobin C, Hemoglobin SC, thalassemia, and others are all different by at least one amino acid, yet they are all hemoglobins, and all do the same job: they carry and release oxygen. Insulin in humans and pigs are not identical (human insulin differs from porcine insulin by a single amino acid - Thr instead of Ala - at the C-terminal residue of the B-chain - but they are both insulin, have an identical function in each animal.

Clearly two proteins of different lengths are not identical. (Did the book claim that they were identical? If it did, it was an error.) If they perform the exact function, they can both be called by the same name and be considered functionally the same protein.

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Human and mouse titin are orthologs, and can be confirmed through an NCBI query for TTN.

Orthologous proteins are not the same, per se. They retain the same function, and basically result from speciation: the common ancestral gene got divided between two species. However, the sequence may potentially differ because obviously the species have diverged.

Homology between the two can be confirmed computationally, through phylogenetic and alignment analyses, but I believe the naming convention Titin for both mouse and Human stems largely from the function of the protein in either organism.

Naming convention and explanations of homology are nicely outlined in this Bio.SE post.

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