Proteins

[Stick]

A particular small polypeptide contains nine amino acids. The polypeptide has been fragmented in various experiments by breaking particular peptide bonds. The fragments obtained were:

ser-cys-his-pro-arg-cys
pro-arg-cys
X-gly-met-cys
his-pro-arg-cys
X-gly-met-cys-ser-cys

X is known to be the first amino acid in the polypeptide. What is the primary structure of the polypeptide?

I've never come across this type of question before. Am I right in thinking it's cys-gly-met-cys-ser-cys-his-pro-arg? (I'm sort of assuming a ring is formed.) If not, can someone explain how this problem is solved? Thanks.

[pi]

LOL, what a coincidence, I wrote a question like this for the AN guide haha

The sequence is:

X-gly-met-cys-ser-cys-his-pro-arg-cys

Just find the smallest sequence to be formed

Given the wording of the question, specifying 9 amino acids, you'd let X = cys and it would be circular. Although irl not many peptides are like that

[Stick]

So I was right? Yay! :3

Also, I got stuck on this one:

A piece of RNA has the sequence:
U-A-C-G-A-U-U-C-G-A-A-C-A-U-G

a) Are you able to determine the kind of RNA this molecule is without any further information?
b) If you were told this piece of RNA carries the code for five amino acids, would you change your answer to part (a)? If so, what would your explanation be?

Would I be correct for thinking this?

a) Cannot be determined.
b) Given the wording in that sentence, this is messenger RNA.

[Russ]

You didn't provide an explanation in b)

[Stick]

Yes, I know, but I didn't want to give an explanation if it was completely wrong. Do I take it that it is messenger RNA?

[paulsterio]

Yes, it is mRNA, now have a go at explaining

[Stick]

Thanks.

[teletubbies_95]

great questions!
the first one took me liek 10 minutes to work out.

[shinny]

For the first question, my impression is that it's methionine given that that's the start codon by definition. A protein in their primary structure must start with methionine, with this later cleaved off in post-transcriptional modification as required. The 'circular' protein explanation doesn't make much sense given that we're dealing with a primary structure here and these are by definition linear. Pretty sure this question's from the Nature of Biology book and I remember answering this back then, so it's by no means some random fact I've picked up from uni.

[Stick]

Yes, it's from Nature of Biology 4th Edition. The thing is, your reasoning isn't really discussed in the theory pages just yet, so I think it was more of a case of getting the students to think in a general sense.

[shinny]

Hmm, just realised that they said 9 amino acids and if you solve using my reasoning, that chain's actually made of 10. I'm still not convinced by the circular protein reasoning however. Doesn't really make much sense to talk about a primary structure being circular. Even a protein which is eventually circular in a tertiary sense must have a linear primary structure as that's dictated by the specific codons in the DNA itself. Maybe the 9 was a typo?

[pi]

Maybe the 9 was a typo?

I think this is the most likely problem. As I said in my post, I doubt many peptides chains would be circular and only 9 amino acids in length.

I'm with shinny on this one, bit of a dodgy question.

[paulsterio]

I agree with Shinny on this one, I don't think that the primary structure of a protein can be circular.

[Stick]

I just double checked and nine is in the book. :S Students wouldn't know the start codon is methionine though, and there would be no other way to solve for X.

A very interesting problem indeed!

[curry_bro]

dont worry. i dont think vcaa would ever ask u a question like this. its very dodgy tbh. no question on the exam is ever ambiguous to this degree, and none require such an abstract approach to figure out. If its any consolation, i couldnt work out this question till a month after the unit 3 exam haha