My rudimentary understanding is...

  1. a gene gets transcribed to mRNA
  2. that mRNA is sent off to the ribosome
  3. that ribosome pumps out whatever proteins are coded by that gene
  4. each protein floats around in the cell until it encounters an enzyme that it fits into, and along with other molecules that may have floated into the same enzyme a chemical reaction occurs and one or more products are formed.

I'm assuming "products" are either new protein molecules or maybe the amino acids that made up the original input proteins. What I don't understand is what the overall end result of these reactions are. So there's a reaction, but what does that mean? How does that reaction, lets say, result in some physical attribute of the organism?

Any examples would be helpful.

  • $\begingroup$ Your question is a bit broad. Even though someone answered your question to your satisfaction, your question itself seems to ask for the entire molecular biology behind life. Can you please rephrase your question to make it precise while keeping the current answer relevant to it? $\endgroup$ – WYSIWYG Feb 6 '19 at 13:47
  • $\begingroup$ @Mowgli has been kind enough to answer this question, but it shows a basic lack of knowledge about proteins and enzymes that any answer here would not be able to remedy. You need to read about proteins in a standard text book of biochemistry or molecular biology, written and illustrated in a professional manner. There are some old editions (all you need) of very reputable books online at NCBI Bookshelf, where you can search for these terms. Alberts et al. might be suitable. $\endgroup$ – David Feb 6 '19 at 14:04

At a high level, points 1 to 3 are reasonably correct, but 4 is only a special case.

Say we're at end of point 3. You get a protein. Some proteins are enzymes (the majority of enzymes are proteins), others are not. Example of proteins that are not enzymes would be, for example, hemoglobin, which is "just" a (very high-tech) carrier.

Now, each enzyme catalyzes (at a very high level) one reaction, which may or may not involve other proteins:

  • Reactions without protein other than the enzyme: for example, the cleavage of sucrose into glucose and galactose (two small sugars) performed by an enzyme called sucrase. Such reactions can assemble, cut and modify small molecules or large organic molecules that are not proteins (for example, starch, which is a large polymer of sugar, or even DNA itself)
  • Reactions mediated by enzymes, that act on non-enzyme proteins: for example, your digestive enzymes can cut proteins from food into building blocks (amino acids) that your body can use to build its own proteins. Similarly, some proteins can ligate proteins together, or add things on them (the proteins on the surface of cells are commonly modified with small sugar chains that control their activity).
  • Enzymes that catalyze reactions that involve other enzymes: since enzymes are proteins, they can be the target of other enzymes. A very well described example is the cascade of enzymes called kinases. When a cell is stimulated by a hormone, a kinase gets activated by addition of a small phosphate group. Once it is activated, the kinase phosphorylates (i.e. it adds a phosphate group on) another type of kinase, which phosphorylates yet another type of kinase etc; that's a way to amplify small signals.

So the overall result of an enzymatic reaction, regardless of whether it acts on other proteins or not, is usually either

  • The conversion of a molecule into some other molecule (1 to 1)
  • The assembly of several molecules into a larger, new molecule (N to 1)
  • The separation of a large molecule into smaller fragments (1 to N)
  • The transfer of a fragment of molecule on another molecule (N to N)

Examples of these four types of processes when enzymes act on other proteins:

  • 1 to 1: a "protein disulfide isomerase" can rearrange the topology of the so-called disulfide bridges, that connect cysteine amino acids together in the target protein. This allows a misfolded, non-functional protein to turn into a functional molecular machine.
  • 2 to 1: a "ubiquitin ligase" can covalently attach small proteins (ubiquitin) to old, broken proteins and target them for recycling, thereby preventing the accumulation of dysfunctional proteins in the cell.
  • 1 to 2: a "protease" can cut another protein into two smaller proteins
  • 2 to 2: a "protein kinase" removes the phosphate from a small molecule called ATP, and sticks it on another protein
  • $\begingroup$ Thank you for the thorough answer. Are the physical attributes of an organism the result of enzymes manipulating molecules? So for example, is some enzyme responsible for glueing molecules together to pump out hair? nails? etc.. I'm trying to relate what's happening to some higher level biological process. $\endgroup$ – offbynull Feb 6 '19 at 0:21
  • $\begingroup$ @offbynull physical attributes or phenotypes are governed by a lot of molecules and all of them have been formed because of the action some enzyme or the other (for e.g. RNA polymerase is needed for the expression of all the genes). So your statement is correct but is gross oversimplification of the biology. $\endgroup$ – WYSIWYG Feb 6 '19 at 5:51

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