Biochem end of Ch 1 exam

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chibean
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Biochem end of Ch 1 exam

Post by chibean » Sat Mar 07, 2020 1:14 pm

For chapter 1 end of chapter of exam, question #5," Based on the data in Figure 3, which residue on the protein will be found farthest from the cytoplasmic environment? " how do I read the graph and determine the amino acid because it looks like multiple amino acids have the same peaks throughout.
NS_Tutor_Mathias
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Re: Biochem end of Ch 1 exam

Post by NS_Tutor_Mathias » Tue Mar 10, 2020 4:03 pm

Assuming you understood how to determine which AA is which by counting carbons, what is left is just realizing that it doesn't matter that another AA has part of it's sidechain less buried - just look at what is most buried most of the time, particularly at the backbone (N,C and Calpha). That is clearly the set of light circles.
xoapryce
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Re: Biochem end of Ch 1 exam

Post by xoapryce » Thu Apr 09, 2020 11:40 pm

What do you mean exactly by counting carbon to determine with AA it is. I am also having trouble deciphering the burial amount in the graph. I do not understand the axes - especially the x axis fully.
NS_Tutor_Mathias
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Re: Biochem end of Ch 1 exam

Post by NS_Tutor_Mathias » Fri Apr 10, 2020 11:22 pm

There is a convention in chemistry that the carbon adjacent to the carbonyl carbon is called the alpha-carbon. Each additional atom added to THAT alpha carbon gets the next letter in the greek alphabet, so beta, gamma, delta, epsilon etc.

So the x-axis of this graph is talking about the various parts of an amino acid:
N -> terminal nitrogen
C -> carbonyl carbon
O -> carbonyl oxygen
Alpha -> alpha carbon
Beta -> Beta carbon
Gamma -> Gamma substituent (any atom)

And so on.

This means that for each of these lines there is either only one or a very small number of amino acids that it could be represented by the line (the bottom one for instance can only be glycine). That is how we know that the most buried one, going out to only two a beta-carbon and a second atom in the side chain, must be cysteine.

I've attached an image to help you visualize how these positions work. Recall that after the beta-carbon, any atom can be in the designated position.
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NS_Tutor_Mathias
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Re: Biochem end of Ch 1 exam

Post by NS_Tutor_Mathias » Sun Apr 12, 2020 10:10 pm

As a small bonus, here is a cleaner version of the same image (from the newest edition of the EoC materials).
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