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Its taken from a practice paper. Sorry for the low quality

Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å

Please read: The reason I didn't submit my attempt is that, I thought because there isn't an exact and precise depiction of the protien molecule and also the question is vague so I hesitated. I counted the number of turns ie 7 but still there was a lingering doubt "what if I am wrong, I would make a fool of myself."

What I know:

  1. Protiens basically bunch of amino acids bound by polypeptide bond.
  2. Primary structure is the sequence of the amino acids.
  3. The secondary structure us due to the Hydrogen Bonding between the Oxygen atoms having partial -ve charge and Hydrogen atom attached to the Nitrogen, within the backbone only. eg: alpha-helixes, beta-sheets, Turns, Loops
  4. Tertiary Structure is due to the interaction between the different R groups in the amino acids. Like the disulphide bonds, hydrophobic interactions, H-bonds, Vanderwaal forces.
  5. Quaternary Structure is due to the overall 3D structure which is result of the aggregation of the polypeptide subunits.

Please go easy on me, its my first time posting here and I am still a 1st year in college and 2nd Sem is gonna start next week.

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    $\begingroup$ Please finish the Tour to find out how this site works. Your question is incomprehensible without reference to external sites, which is quite unacceptable. It would also appear to be a homework question which, should you edit it so it is comprehensible by itself, requires you to show your attempt to solve it. $\endgroup$ – David Mar 3 at 20:07
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    $\begingroup$ Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please edit your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Unresearched questions may be subject to down-voting and closure. Please see our homework policy for more information. $\endgroup$ – MattDMo Mar 3 at 20:31
  • $\begingroup$ @David Sorry, I should have included it in here too. It's my first time posting here. $\endgroup$ – Anirudh Kanaparthy Mar 4 at 15:26
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The question begins by telling you that only the alpha helices are embedded in the membrane. This means that if you can calculate how long the alpha helices are, you can work out the thickness of the membrane it is embedded in.

Alpha helices look like spirals (similar to fusilli pasta shapes). These are highlighted in figure A) below.

The question also tells you that each turn of the alpha helix is 5.4 angstroms. One turn if shown in figure B) below.

Looking at the picture, it seems that each helix is about 7 turns long. As each turn is 5.4 A, the length of the helices must be approximately 7 * 5.4 A which is 37.8 A.

Therefore, using the information that the membrane must be about as thick as the helices in the transmembrane proteins are long, you can deduce that the membrane must be up to 37.8 A thick, however the membrane may not actually be this thick as the question from the paper doesn't specify how much of the alpha helices are embedded in the membrane (60%, 80%, 100%?). I guess the assumption is that the entire alpha helix section of the transmembrane protein is fully embedded within the membrane.

Annotated version of the figure from the question.

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  • $\begingroup$ Are the alpha helices always straight within a membrane, or could they be bent? $\endgroup$ – jakebeal Mar 3 at 17:18
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    $\begingroup$ From what I understand, alpha helices tend to be straight due to the strong hydrogen bonding which takes place throughout the structure, so it would be unusual for kinks to appear. However, there are structures called helix-turn-helix (common in DNA binding proteins) which form an alpha helix with a kink in it. There’s some good information on this here: sciencedirect.com/topics/… and here: sciencedirect.com/science/article/pii/S0005273618300518 $\endgroup$ – Brad0440 Mar 3 at 19:39
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    $\begingroup$ Please do not answer questions that do not respect the model of this site. $\endgroup$ – David Mar 3 at 20:08
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    $\begingroup$ From How do I write a good answer? in the help center, Answer well-asked questions. Not all questions can or should be answered here. $\endgroup$ – MattDMo Mar 3 at 20:30
  • $\begingroup$ Thanks a lot for the answer. And yeah, the question asked is very vague. I had problems because of this vagueness. $\endgroup$ – Anirudh Kanaparthy Mar 4 at 16:01

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