Timeline for Protein - one polypeptide molecule or a collection of molecules?
Current License: CC BY-SA 4.0
12 events
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| Jun 30, 2018 at 15:25 | comment | added | Byron1948 | Thank you for the clarification. I have, as you suggested, turned to the Oxford Chemical Dictionary in order to better understand precise definitions of these terms. And, although some answers come across as pedantic and condescending, I have no intention of violating the "be nice" ethos. Most of the time I find StackExchange to be a very helpful resource. | |
| Jun 30, 2018 at 13:19 | comment | added | David | @Byron1948 — A Polypeptide chain has two ends (also referred to as termini): an amino end (with a NH3+) and a carboxyl end (with a COO–). Neither of these is portrayed in the left side of the diagram (all COs and NHs) and, indeed they are never parts of beta-sheets as they are chemically different and not part of peptide bonds. Nor, in globular proteins are they generally even near beta-sheets, as the right hand part of the diagram illustrates. And btw., although I am sure it was not intentional, the phrasing of your comment is close to violating the list's "be nice" ethos. | |
| Jun 30, 2018 at 12:06 | comment | added | Byron1948 | So, dotted lines aren't hydrogen bonds then. Guess I was misinformed. | |
| Jun 29, 2018 at 8:48 | comment | added | David | @Byron1948 — Your question related to text book diagrams of beta-sheets of proteins, leading to the statement: "But a beta-pleated secondary structure would have to be two or more chains (molecules) connected by hydrogen bonds. No?" My answer was "No" — the diagram (unless it stated it was silk fibroin) represented hydrogen bonds between parts of a single polypeptide chain (and not at the ends, as you state). If you want to discuss the meaning of the term "molecule" start with Chemistry SE. Ask separately about protein molecules here when you are more familiar with different proteins. | |
| Jun 28, 2018 at 22:15 | comment | added | Byron1948 | Thanks Dan. No, I don't think I have a clear answer yet. The illustration on the left of David's first comment show hydrogen bonds a the ends of the polypeptide chains (the dotted lines). I'm looking for a definition of molecule in terms of bonding. If the definition is "multiple atoms bonded together", then fine. Technically all water in a drop is one molecule due to hydrogen bonds. But this doesn't sound like a reasonable definition to me. What am I missing? | |
| Jun 27, 2018 at 19:53 | comment | added | De Novo | @Byron1948 your question is a natural one for someone approaching protein structure after some chemistry. Has David answered your question? Do you see that the atoms in the $\beta$-pleated sheet are in fact all connected by covalent bonds (in addition to hydrogen bonds); that the molecule is just long and flexible enough that more than one type of interaction can be involved? | |
| Jun 27, 2018 at 18:11 | history | edited | David | CC BY-SA 4.0 |
Added a rider explaining why diagrams of beta-sheets are the way they are.
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| Jun 27, 2018 at 18:07 | comment | added | David | My answer assumed that you were taking an introductory course which included something about proteins, and this was likely to be dealing predominantly with globular proteins. If there is any aspect of it that is unclear or which you dispute, please tell me. As regards the meaning of the word molecule in relation to proteins in general, this is another question and concerns mainly higher order structures. If this really interests you, please ask it as a separate question. However, of one thing there is no doubt: the polypeptide chain translated from a mRNA encoded by a gene, is a molecule. | |
| Jun 27, 2018 at 16:23 | comment | added | Byron1948 | Well David, as it happens, my question is a result of taking Bio 111 in college right now. Our Pearson textbook doesn't show the ends of the polypeptide chains in the illustration of secondary structures. The illustration on the left in your answer would have provided great insight but doesn't explain the fact that proteins are called "molecules" in other parts of the text. The consensus I'm receiving is that there is no clear consensus on the definition of "molecule" with respect to bonding. Everyone does agree that hydrogen bonds between water molecules do not make all of them one molecule. | |
| Jun 25, 2018 at 20:01 | history | edited | David | CC BY-SA 4.0 |
fixed typo
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| Jun 25, 2018 at 8:51 | history | edited | David | CC BY-SA 4.0 |
Corrected typo, clarified a little, consolidated diagrams to make more compact.
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| Jun 24, 2018 at 22:40 | history | answered | David | CC BY-SA 4.0 |