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IBO 2003 questions- please help me out

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IBO 2003 questions- please help me out

Postby tittu » Mon May 12, 2008 2:34 pm

I could not solve these questions.
Can you please help me?

A: List the following proteins in the order of decreasing evolutionary conservativeness of their primary structure:
1. Somatotropin.
2. Catalytic subunit of a DNA – polymerase.
3. Histone H1.
4. Prolamines (storage proteins of cereals).
(A hint will do - how will i go about it?)

B: Nucleoside phosphates can be interphosphorylated enzymatically. Which one of the following reactions is impossible?
А. ADP + ADP = AMP + ATP.
В. AMP + GTP = ADP + GDP.
С. ATP + GDP = ADP + GTP.
D. ATP + UMP = ADP + UDP.
E. ADP + AMP = ATP + adenosine.
(I think it might be option A, because disproportionation among ADP sounds improbable)

Also, anyone got the solutions/ answer keys for IBO papers?
Last edited by tittu on Mon May 12, 2008 2:55 pm, edited 2 times in total.
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Re: IBO 2003 questions- please help me out

Postby tittu » Mon May 12, 2008 2:41 pm

C:
The lactose operon of E.coli consists of three genes:
lacZ encodes β-galactosidase,
lacY encodes galactosidepermease which carries out lactose transport to the cell,
lacA encodes galactoside-transacetylase.
Lac operon is under the control of LacI (repressor), which is inactive in the presence of lactose (inductor). There is a wide diversity of the chemical lactose analogs, for example: Orthonitrophenyl-β-D-galactoside (ONPG) – is a substrate for β-galactosidase but not an inductor. The product of this reaction orthonitrophenol is toxic for a cell. Isopropyl-β-D-thiogalactoside (IPTG) - is an inductor but not a substrate for β-galactosidase. Phenyl-β-D-galactoside (PG) - is a substrate for β-galactosidase but not an inducer. The products of its hydrolysis are nontoxic for a cell.

Which cells will grow in the medium with PG as the only source of carbon and energy?
А. lacI −.
B. lacZ −.
C. lacy −.
D. lacZ − lacy −.
E. lacI − lacZ −.

Will these cells grow in the medium with ONPG?
A. Yes.
B. No.

Galactose is a toxic compound for the cells which have galE– mutation.
Which cells with this mutation will grow in the IPTG+PG medium (with arabinose as an additional source of carbon and energy available)?
А. lacI −.
B. lacZ −.
C. lacA −.
D. lacI − lacA −.

My choices are options A and B for the first two. Am I on the right track?
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Re: IBO 2003 questions- please help me out

Postby blcr11 » Mon May 12, 2008 5:54 pm

To answer the first question quantitatively you need to compare the rates at which mutations are accepted for these proteins over their evolutionary histories. I don’t know of any good place to send you for that information. So if your instructor or your textbook hasn’t compiled it for you I don’t know exactly what you’re supposed to do. You can make some educated guesses based on the functions of the proteins in question. The more crucial the function to a wide variety of organisms, the more likely it is to be highly conserved. Somatotropin is the formal name for growth hormone. It is a peptide hormone made in the pituitary gland. DNA polymerase comes in a variety of flavors, but the major eukaryotic DNA polymerase is involved with replication of genomic DNA. Viruses, bacteria, and plants all have DNA polymerases with distinct properties. Histones are important for packing chromosomal DNA into nucleosomes and may be important regulators of cytosine methylation. The function of seed storage proteins is to act as a deterrant to dehydration prior to germination, and after germination, to act as a source of amino acids for protein synthesis until the sprout can supply its own nutrients.

Not sure about part B. My guess is E. AMP goes to Adenosine + Pi in the catabolism of purines. It is essentially the hydrolysis of AMP and most certainly doesn’t generate a high-energy source like ATP. All the other reactions are possible via nucleotide and dinucleotide kinases. These kinase reactions are reversible.
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Postby MrMistery » Tue May 13, 2008 6:16 pm

A.
2. Catalytic subunit of DNA polymerase(very important, it's the subunit that actually does the work, so maintaining its structure is important).
3. Histone H1(although not known what it actually does, it's present in all EK with small variations in structure, so I bet it's important.
1. Somatotropin(only present in higher vertebrates, but it's structure is very important as it is a hormone, it needs to fit in the receptor)
4. Prolamines(they just store stuff, doesn't really matter what they look like).

B. Agreed with blcr11

C.
Which cells will grow in the medium with PG as the only source of carbon and energy?
А. lacI −.
B. lacZ −.
C. lacy −.
D. lacZ − lacy −.
E. lacI − lacZ −.
The answer is A: PG is not an inductor, so it will not be able to inactivate the repressor. Therefore, only a bacterium that lacks a repressor can live in such a medium. E is obviously wrong, as it needs to have the enzyme to break down the stuff.

Will these cells grow in the medium with ONPG?
A. Yes.
B. No.
The answer is B. They will break down the stuff, unleash it's toxic metabolites upon the cell => DOOM.

Galactose is a toxic compound for the cells which have galE– mutation.
Which cells with this mutation will grow in the IPTG+PG medium (with arabinose as an additional source of carbon and energy available)?
А. lacI −.
B. lacZ −.
C. lacA −.
D. lacI − lacA −.

I have no idea what transacetylase does, but B is correct anyway. You have both an inducer and a substrate for the enzyme, but no enzyme, and therefore no galactose present. Ergo the cell lives.

Cheers.
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Re: IBO 2003 questions- please help me out

Postby blcr11 » Tue May 13, 2008 10:29 pm

I hadn’t meant to suggest that the order I listed the protein functions was the order I thought was most to least conserved. I just followed the order in the question. My private guess had been 1. Histone, 2. DNA Polymerase subunit, 3. Somatotropin, 4. Prolamine. My intuitive argument was that Histones are small and perform a specific, but absolutely crucial function for everything that has distinct chromosomes. There aren’t very many places on a histone that can accept mutations. Almost the entire molecule is either binding to DNA or interacting with another histone or other protein. Both DNA polymerase and somatotropin are proteins; polymerase is an enzyme, somatotropin is a growth factor. The 3D-structure needs to be maintained for both, but there are crucial residues that are either active-site or binding-site residues, and these are surrounded by residues that are needed “only” to ensure proper folding—and there are more pure structural residues than there are critical ones. Not that proper folding is a trivial thing, but there are many ways for a protein to attain the same overall fold, while only a few of those sequences would properly align the catalytic- or receptor-binding residues. I guessed that DNA polymerase is the more critical of the two so my order places a DNA polymerase subunit as more conserved than somatoropin, but without data I think it’s a tossup. I don’t think there’s any argument about where the seed storage protein belongs—namely, least conserved of all.

I don’t have any good source that shows the mutations of these proteins over evolutionary time. As a rough check I went to the Expasy proteomics site and did a quick BLAST on each of the first three proteins and looked at just the %identity for proteins that were, as best as I could find, equally distant from a human protein. Here’s what I found.:

Histone H1 (Human) is 72% identical to Xenopus (frog) H1 and 54% identical to Sea Urchin H1
DNA Polymerase A (Human) is 67% identical to Xenopus Polym A and 37% identical to Arabadopsis (a plant)—I didn’t see a sea urchin entry, but there were a lot of polymerases, so I could have missed it.
Somatotropin (Human) is 41% identical to RANA (another frog) and 32% identical to carp; I think somatotropin is likely only to be found in vertebrates.
Prolamine—I didn’t check.

So my best guess is 1. Histone, 2. DNA Polymerase, 3. Somatotropin, 4. plant seed storage protein, though you might be able to argue about the order of 2 and 3. Nor would I consider my argument definitive.
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Postby tittu » Wed May 14, 2008 3:14 am

I found a tool at Expasy http://www.expasy.org/tools/ called ConSurf http://consurf.tau.ac.il/ whose job was "Projection of evolutionary conservation scores of residues on protein structures "
running polymerase and histone H1 (the DNA linker in nucleosome model outside octamer), , i got the following degree of conservancy scores:
..polymerase,
(1. 56 Variable) [2. 25] [3. 22 ] [4. 33 ] [5. 49] [ 6. 48] [7. 50] [8. 55] [9. 28 Conserved]
...H1
[1. 11 Variable ] [2. 3][ 3. 0] [4. 0] [ 5. 2] [ 6. 7 ] [ 7. 15] [ 8. 6 ] [9. 9 Conserved ]
the numbers denote no of amino acids of each conservancy grade, 1 variable to 9 conserved.
the other two didnt run, because, they didnt have the pdb file (1bst) for somatotropin and prolamine had 4 BLAST homologue site, while it needed 5 to calculate.
A weighted mead comparison of this would tell the answer, but you dont get to use expasy tools at IBO, do you? :) there must be an "easier" logic :(
the results sites are at,
http://consurf.tau.ac.il/fgij/fg.htm?mo ... 0_pipe.pdb
http://consurf.tau.ac.il/fgij/fg.htm?mo ... 6_pipe.pdb
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Re: IBO 2003 questions- please help me out

Postby blcr11 » Wed May 14, 2008 1:58 pm

So for close homologues there isn't a huge difference in % conserved residues for polymerase vs H1. There seems to be a slight tendency toward fewer category 1 and more category 9 residues for H1, but I don't know if those numbers are significant or not, and the mid-range type percentages look virtually identical to me. I haven't used ConSurf that much. I'm not used to its output. I guess you'll have to decide what your criterion for conservation is going to be and then make your best argument.
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Postby blcr11 » Wed May 14, 2008 2:05 pm

There's also a significant chunk of the H1 molecule that ConSurf is not analyzing (just visually I'd guess that 30-50% of the residues have no conservation analysis), so I don't know you're getting the full picture for H1.
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Postby MrMistery » Wed May 14, 2008 7:21 pm

OK, guys, you are way overthinking. In the olympiad, you have about half a minute to think about a question. Now, obviously you are not supposed to know how each of them evolved and you are NOT supposed to do any research. You ARE supposed to reason through the question, and then guess. Actually, there are a lot of questions where you're supposed to guess. Some are even formulated like "What is probably the way...?"
So it's between catalytic subunit and H1.
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Re: IBO 2003 questions- please help me out

Postby tittu » Tue May 27, 2008 2:36 pm

I just saw this, regarding question B, ADP+ADP=ATP+AMP really happens in muscles, catalyzed by adenylyl kinase.
Talk about eating words...... :oops: Probably blcr11 is correct.
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