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The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do you account for the presence of more variation among of proteins than there are in genes?

The simple answer would be "there are more proteins than genes", but I'm more interested in why. Is it sufficient to say that during gene expression a single gene codes for multiple proteins (Alternative Splicing) and ribosomes translating mRNA to polypeptide chains (Posttranslational modification)? Could someone expand more on this?

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There are several concepts to understand:

  1. Alternative splicing
    • From one gene, several proteins can be constructed depending on which introns are spliced.
  2. Tissue-specific genetic expression
    • Genes are differentially expressed (and differentially spliced) depending on the tissue.
  3. Post-transcriptional modifications
    • Those are modifications that are made directly on the proteins (in opposition with alternative splicing which are modifications made on the RNA)
  4. Structure of the proteins
    • Proteins may fold (to what we call primary, secondary, tertiary and quaternary structures) differently in different environment.

Therefore there is variance in proteome between cells although there is no variance in genome between cells (except mutations and red blood cells). Moreover, one gene sequence can give rise to many different proteins due to the processes of alternative splicing and PMT.

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  • $\begingroup$ On a similar note: What is meant by the 'complexity' of the proteome? Why is it described "the proteome has at least two levels of complexity lacking in the genome"? $\endgroup$
    – Cloud
    Commented Dec 12, 2013 at 1:27
  • $\begingroup$ The word complexity is used with many different meanings. Here is another post that maybe interest you. Or the Wiki article I don't quite know what can be meant with this sentence: "the proteome has at least two [...]". I guess that indeed it is closely related to your question. I would suggest you to post it as another question and give a link to your article and maybe a small summary of the context in which this sentence come from. $\endgroup$
    – Remi.b
    Commented Dec 12, 2013 at 1:41
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    $\begingroup$ This is according to the Wiki page regarding the proteome. Perhaps the following sentences will help: "The proteome has at least two levels of complexity lacking in the genome. While the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins." $\endgroup$
    – Cloud
    Commented Dec 12, 2013 at 1:47
  • $\begingroup$ aha. Here is the link to the wiki page for others. Ok, so I missed this point in my answer. The proteom is indeed greater than the genome due to alternative splicing and PTM. Let me try to improve my answer (but I am slowly affraid to go into details that I might not know very well..) $\endgroup$
    – Remi.b
    Commented Dec 12, 2013 at 1:56
  • $\begingroup$ @Cloud I think, by saying two levels of complexity , it means that proteins are not mere chains of amino acids they also have to have specific structure and interaction with other molecules. $\endgroup$
    – biogirl
    Commented Dec 12, 2013 at 6:51
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To comment on the "why" question: I would say that its a relatively simple way to get a high number of proteins with more or less slight differentiations. This can include exons which are only present in special environments or cell types and so on. It saves a lot of energy for keeping all the information about every single transcript (the BNC2 gene for example can produce up to 90.000 different mRNA transcripts coding for up to 2000 different proteins of unknown function, see here) and makes the genome a lot less complex, despite the fact that we now need an also complex regulation.

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  • $\begingroup$ 90 or 90,000 mRNA Transcripts? $\endgroup$
    – Failed Scientist
    Commented Feb 7, 2016 at 0:23
  • $\begingroup$ @TalhaIrfan If you look at the linked paper, you would see that the number 90.000 is true. I think that this is a theoretical number and less transcripts are made, but it shows the possibilities. $\endgroup$
    – Chris ♦
    Commented Feb 7, 2016 at 10:32

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