Biochemistry & Molecular Biology Amino Acid question

[simpak]

Not exactly correct; you're adding more residues in the centre of the chain but those don't have any counter charge (positive or negative) to offer because they are not 'free ends' of the polypeptide and are participating in peptide bonds.  So as you move the ends apart the charge on the molecules at the ends will destabilise; this is what brings the pka values closer together because they become 'weaker' acids and bases since they are less comfortable existing as an ion, the definition of a strong acid being complete ionisation in water.
Although it might seem like as you add more residues in the chain there is more 'space' to distribute the charge, this kind of stabilising effect won't actually happen unless you bring a countercharge close.  So if you have the positive end too far from the negative end (as in the addition of more residues) the pKa values /do/ move closer together but that's because the COO- is increasing (weaker acid, less stable as an ion) and the NH3+ is decreasing (weaker base, less stable as an ion or doesn't hold on to its extra proton as tightly because there is no nearby negative charge pulling that proton towards it).

If you remember that it's the opposite end that stabilises the charge rather than any intervening residues you should be good to go - move the ends further apart and they can't interact so it's less stable.

[Turtle]

Thanks Mavis 

For the 2010 Biochemistry exam. Can anyone tell me if my answer for section IV, table 4 is correct, and help me with table 5.

My table 4 answer is 3. Is this right?

I can't work out how to find the answer to table 5.
I figured Vmax must be 2.
I know I need to find k2, using the equation Vmax=K2 x [Et]
But were are not given the total enzyme concentration, so how can I figured this out?

[simpak]

Yup, Km = 2Mm so 3. is right.

We actually discussed this above!  It says in the question that the figures are per micromol (really subtly) so the total concentration of enzyme is 1micromol but the veloity is micromol/second.
So you end up with 2 x 10^-6 = k2 x 10^-6 ie k2 = 2 as well.
2 per second isn't an answer so you have to convert it to minutes.
2 x 60 seconds = 120 minutes (Option 6).

[Starlight]

Hey (off topic) I was just wondering what lecture you guys are up to at the moment with your studies?

[Turtle]

I still have to do 17,18,19,20,21,22,23. I'm finished the rest, just revising them. I did it in a weird order haha :/

[Starlight]

I still have to do 17,18,19,20,21,22,23. I'm finished the rest, just revising them. I did it in a weird order haha :/

I still have like 15 to go :l

[simpak]

I have like two other frigging exams first D:< ...so kind of neglecting it for now.
I've studied metabolism, proteins, enzyme kinetics...just have to go back through lipids/carbohydrates and all the DNA stuff but I don't find the DNA stuff quite so bad.  And I've done the 2009/2010 exams but not the 2011 one yet gah.
Going to be a rush to the finish-line for Biochem )':

Currently doing immunology, wanting to die.

[Starlight]

Are you guys looking much into a-chymotrypsin, like the reaction mechanism stuff?

I guess i'm wondering whether its' really examinable, there's not much stuff on past papers about the basics of a-chymotrypsin and nothing to do with the reaction mechanisms?

[simpak]

Yeah but she's never taught it before.  I'm going to be really annoyed if she changes the question structure: it's always been the 'choose from the six options' style and I bet she changes it I DON'T LIKE HER.  I gave her the worst comments in the surveys.  Anyway I learnt the reaction mechanism mostly...just like the serine and histidine involvement, and glycine and serine stabilising the O-.  I don't think we need to know it in absolutely perfect detail...I hope not.

[Starlight]

Yeah but she's never taught it before.  I'm going to be really annoyed if she changes the question structure: it's always been the 'choose from the six options' style and I bet she changes it I DON'T LIKE HER.  I gave her the worst comments in the surveys.  Anyway I learnt the reaction mechanism mostly...just like the serine and histidine involvement, and glycine and serine stabilising the O-.  I don't think we need to know it in absolutely perfect detail...I hope not.

Oh ok thanks

[Turtle]

I learnt the entire process almost word for word, but not the structures of the molecules involved.
I did it in case there was question that pops up in extended response, such as...."Explain how alpha-chymotripsin leads to the cleavage of the peptide bond." Not that it will happen, but they are well within their rights to ask such a question, so I don't want to be caught out.

Because it has not been in exams much in previous years, this could mean 1 of 2 things in my opinion:
1) It continues to be this way, and it is not asked about much in this years exam
2) They add in a nice 15 mark extended response question about it

It really takes no time at all to learn it all, I learnt the process in 45 minutes, just then.
I'd take the time to learn it, even if you don't know it perfectly, as Mavis said 

[Starlight]

I learnt the entire process almost word for word, but not the structures of the molecules involved.
I did it in case there was question that pops up in extended response, such as...."Explain how alpha-chymotripsin leads to the cleavage of the peptide bond." Not that it will happen, but they are well within their rights to ask such a question, so I don't want to be caught out.

Because it has not been in exams much in previous years, this could mean 1 of 2 things in my opinion:
1) It continues to be this way, and it is not asked about much in this years exam
2) They add in a nice 15 mark extended response question about it

It really takes no time at all to learn it all, I learnt the process in 45 minutes, just then.
I'd take the time to learn it, even if you don't know it perfectly, as Mavis said 

Yeah I sort of learnt it a bit just before, which ill continue to revise.

Does anyone know how to do the hydropathy plots? I find them so confusing and have no idea how to plot one for those exam type questions. Any ideas?

[simpak]

Plot is: hydropathy index (1-3) v amino acid number.
Should just be with the hydrophobic regions on the positive side of the membrane and hydrophilic on the negative side.
They always ask you to do 300 residues, I just make sure I only have 20 residues in each hydrophobic part (ie 3x20 =60) and then you can kind of divide up the remaining ones (hydrophilic) based on however many times there are extramembraneous domains (i think it's like 5?).  So you could do 240/5 or you could be way more picky and kind of divide it up less evenly but I don't think it matters all that much.  Anyway, plot would be like hydrophilic (say 48 residues) by drawing some kind of arch/squiggly parabolic or fuzzy box looking thing on the negative side, then 20 on the positive side same diff. and etc all the way up to 300 with the important part being you just happen to have three hydrophobic residues for each of the three helices that span 20 amino acids in length on your scale.  I don't actually have the paper in front of me so I hope it's 3 TM domains and not 4 but if it's four FORGIVE ME.
You don't have to worry about why it goes all like crazy fuzzy on either side, it doesn't really matter, I kind of draw a bristly type shape of any form as long as it's all on the same side of the y axis it doesn't matter where it is in relation to 1 to 3, that could be anything because each residue gets a hydrophobic 'rating' from -3 to +3 and you don't know what residues are there so you're just meant to draw what could 'possibly' be a plot.  So the only certainties are like, having three hydrophobic spanning portions (if it is 3) and then having hydrophilic portions (approx 5) in between for each part that comes back out of the membrane.
Hopefully that made some kind of sense argh!  I have to study for my exam tomorrow morning but if it didn't I can upload my drawing of one on the paper tomorrow after my exam?

[Starlight]

Plot is: hydropathy index (1-3) v amino acid number.
Should just be with the hydrophobic regions on the positive side of the membrane and hydrophilic on the negative side.
They always ask you to do 300 residues, I just make sure I only have 20 residues in each hydrophobic part (ie 3x20 =60) and then you can kind of divide up the remaining ones (hydrophilic) based on however many times there are extramembraneous domains (i think it's like 5?).  So you could do 240/5 or you could be way more picky and kind of divide it up less evenly but I don't think it matters all that much.  Anyway, plot would be like hydrophilic (say 48 residues) by drawing some kind of arch/squiggly parabolic or fuzzy box looking thing on the negative side, then 20 on the positive side same diff. and etc all the way up to 300 with the important part being you just happen to have three hydrophobic residues for each of the three helices that span 20 amino acids in length on your scale.  I don't actually have the paper in front of me so I hope it's 3 TM domains and not 4 but if it's four FORGIVE ME.
You don't have to worry about why it goes all like crazy fuzzy on either side, it doesn't really matter, I kind of draw a bristly type shape of any form as long as it's all on the same side of the y axis it doesn't matter where it is in relation to 1 to 3, that could be anything because each residue gets a hydrophobic 'rating' from -3 to +3 and you don't know what residues are there so you're just meant to draw what could 'possibly' be a plot.  So the only certainties are like, having three hydrophobic spanning portions (if it is 3) and then having hydrophilic portions (approx 5) in between for each part that comes back out of the membrane.
Hopefully that made some kind of sense argh!  I have to study for my exam tomorrow morning but if it didn't I can upload my drawing of one on the paper tomorrow after my exam?

Hey thanks for trying to explain it to me!:) I got a bit lost when you started mentioning the extramembranous domains (5?) though, was this a certain past paper you were referring too? That would help so much if you could post a picture But of course make sure to have some time to relax after your exam!

[Turtle]

Hey guys,

Do we need to know how to draw hydropathy plots?

If so, is there a place were I can learn how to draw them, because the lecture notes don't really tell us

They don't say if we get given the hydropathy index? They don't say anything on how to draw them really...