Test yourself: 4

EU name: TESTT

(From: ../EUDIR ) (Date: Jan 27 17:59 ../EUDI)

The remainder of this page holds a series of questions from exams from previous years. This year's exam will have a few questions with a similar degree of difficulty (after all, I get reprimanded if you all score 8, 9, or 10 points).

Question 104: A small part of the large protein nexistepas has as sequence: 

 ASSNTFECTVGPITWCVKSASNA
The rest of the sequence contains all thinkable amino acids but no cysteine. It was observed that nexistepas changes its weight a little bit if it stands for many hours at pH 7.2 at room temperature. And the weight change is compatible with the oxidation of one cysteine. Can you help the group that works on nexistepas by predicting which of the two cysteines gets oxidized?

Answer

Question 105: Are the Cysteines likely to be bridged or not in the following sequence? Motivate your answer in just a few words. 

 SNSPDLCELLIKALIRLLAQACAGGSSN

Answer

Question 106: The C-terminal peptide of the protein kannietus from bacillus subtilis has as sequence: 

 GIGSGPDLVAEFMMKAWLQGSS
We mutated the W into an R and got much better binding to a regulatory element.
The following sequence is the C-terminal peptide of the protein kannietus from the related bacillus bacillus thermotaga: 
 SSAAELLRAFAQLLAMGGSASG
Which residue would you mutate in the kannietus from bacillus thermotaga to get the same improved binding to the similar regulatory element in this bacillus? Motivate your answer in less than 20 words.

Answer

Question 107: The slime mould mofope has a very small serine protease with the sequence: 

 GSVEFKITSGGNGPAELLKALIQGSGSVTITWEVHGNGNSALELALQLLKGSGTVEFIDGNGN
Can you find its active site residues? Motivate your answer in less than 20 words.

Answer

Question 108: Use all 20 amino acid types exactly two times in total to design peptides that strongly predict to become respectively:
1) α-helix; 2) β-strand; 3) β-hairpin; and 4) loop.
(So you have on average 10 amino acids per element).

Answer

EU name: TESTT2

(Date: Aug 24 2016 TESTT2 )

Question 109: Which cysteine can be oxidized in this protein fragment: 

NHSADCLMLALLSAACLMIFALLLGTSKKT

Answer

Question 110: A protein from the bacterium pocointellicus strongly triggers the human immune system, but we want to use it in a human-rich environment anyway. Using several techniques, this effect was found to originate from the peptide: 

NHSADCLMLALLSAACLMIFALLLGTSKKT

Can you suggest a mutation that will make the whole protein less antigenic? (Hint: look up the so-called positive-in rule).

Answer

Question 111: Maleimide spinlabels can be attached to proteins via a reaction with a cysteine. In the peptide shown below, only one cysteine could be spinlabeled because the other two seemed bridged to each other. Which cysteine can be spinlabeled in: 

SNGPAELCLKACLCALQALGGKS

Answer

Question 112: Are the cysteines likely to be bridged in: 

SGGVTCTIEIGPVKIECVIRP

Answer

Question 113: Given the sequences ASDFGCHIKLMCNPQRSCTVW, YSDYGCNIKLFCQPQRSCTWW, ATDYPVQIKLMCNPQKSCSMW, YTDFGCHVKLLVQPNRSVTVW, and TDFGVHVKLMCNPQKSCSFW the question is which of the cysteines are bridged?

Answer

EU name: EXINT4

 (Date: Aug 24 2016 EXINT4 )

This page contains a randomly selected series of exam questions that we have used in the past in real exams, and that you should be able to answer by now.

You find all these questions again in the ′Test-exams′ section, and in that section, you often also find the answers.

Exam questions used in the past:

  1. Look at the sequence SSNPDLCLQACAKGGSGALEACIALCARLGSSN
    How many cysteines do you count in it?
    Which pairs of cysteines form bridges?
  2. These two sequence predict to have the same secondary structure.
    Which is that secondary structure?
    And which of the two are you most certain of that it will actually adopt that secondary structure in solution and why?
    A) SGWEITVEGPKITFKV B) VKFKIENNTFKIEINT
  3. Three of the following, aligned, sequences bind Calcium. Which three, and why do you think that? 
     SFTDALKNMKPYESSFTRIVN
    
 SYTDALKNVKPYESSFTRVVN
    
 SFTASLKNLKPYCSSFTRVIG
    
 SFTDALKLIVPYESSFTDVIH
    
 SWTAVLKLMVPYLSSFTDILR
  4. Which cysteine can be oxidized in this protein fragment (an why?): NHSADCLMLALLSAACLMIFALLLGTSKKT
  5. Align CWEALALLAELALAAMKGSTPNGS with CWEALALLLEALMRGTTPNGG
  6. Whatever I try, I can only bind the small organic molecule cystinofilus to one of the cysteines in SNGPAELCLKACLCALQALGGKS. Which one, and why?

These questions are also available as a .doc file from the Excercise Files.