Biochemistry & Molecular Biology Amino Acid question

[simpak]

You just need to draw a possible plot so you don't have to worry about where the values are from 0-3 as long as they're above the x axis for hydrophobic and below the x axis for hydrophilic.
I was gonna post mine here but then El2012 PM'd me so I can post it here for you if you like!

Here: http://imgur.com/64WX8GO

[Starlight]

You just need to draw a possible plot so you don't have to worry about where the values are from 0-3 as long as they're above the x axis for hydrophobic and below the x axis for hydrophilic.
I was gonna post mine here but then El2012 PM'd me so I can post it here for you if you like!

Here: http://imgur.com/64WX8GO

Thanks for posting!

[simpak]

Did you get my PM!  Or did it not work 3:

[Starlight]

Did you get my PM!  Or did it not work 3:

Ah yes forgot to reply thanks for responding to that too! But I guess I was a little confused with the hydrophilic regions? I thought there was only 3 but i'll check it again later

I think it's a different protein to the 2010 one, the one I drew looked like a parabola sort of thing (from the 2012 paper) but the one in the 2010 has the alpha helical arrangement

[Turtle]

Thanks Mavis, I appreciate it! 

[Turtle]

I am sorry for the blurry image, but you can just make out what I am asking.

I am drawing 2 glucoses linked together by a beta 1,4 glycosidic bond.

I am wondering drawing which set is correct?

I thought this was the case because in both beta and alpha glucose, the 4C' -OH both point down, and the only thing that differs is the C1' -OH.

Therefore, I thought the 1st drawing was correct, but our notes only have the 2nd drawing. I do not understand how the 2nd drawing can be correct.

[simpak]

Ah yes forgot to reply thanks for responding to that too! But I guess I was a little confused with the hydrophilic regions? I thought there was only 3 but i'll check it again later

I think it's a different protein to the 2010 one, the one I drew looked like a parabola sort of thing (from the 2012 paper) but the one in the 2010 has the alpha helical arrangement

I only looked at it briefly but I think it's the same protein but a different representation ie every TM domain will usually be an alpha helical conformation anyway, and if you have an N and C terminus outside of the membrane and three internal hydrophobic domains you must have two other regions outside of the membrane to link them together, so four in total.

I am sorry for the blurry image, but you can just make out what I am asking.

I am drawing 2 glucoses linked together by a beta 1,4 glycosidic bond.

I am wondering drawing which set is correct?

I thought this was the case because in both beta and alpha glucose, the 4C' -OH both point down, and the only thing that differs is the C1' -OH.

Therefore, I thought the 1st drawing was correct, but our notes only have the 2nd drawing. I do not understand how the 2nd drawing can be correct.

Turtle, which slide is the one you're referring to with the incorrect picture?  The second drawing you've give is one of lactose (galactose and glucose) rather than two glucose monomers, maybe you looked at that one by accident?  I definitely agree that the one you've drawn first is right

[Turtle]

Turtle, which slide is the one you're referring to with the incorrect picture?  The second drawing you've give is one of lactose (galactose and glucose) rather than two glucose monomers, maybe you looked at that one by accident?  I definitely agree that the one you've drawn first is right

Oh, now I get it. So Galactose can have a C4' -OH pointing up, unlike glucose?

[simpak]

Oh, now I get it. So Galactose can have a C4' -OH pointing up, unlike glucose?

Yup, galactose should be a glucose C4 epimer I think so it has the C4 OH in the L configuration rather than the D!  Just remember that D points down and glucose is all D except 3 and then in Fischer projections L is on the left and D is on the right!

[Starlight]

Hey does anyone know much about trypsin (was the question underneath the hydropathy plot of 2010 paper_

Intact cells which express M are treated with trypsin. State how many fragments of the digested protein M remain associated with the membrane

Is it just 3?

[simpak]

Two; the trypsin can't get through the cell membrane so it only cuts domains on the outer side.
So two internal regions would remain connected on the underside!

Omg I don't have the paper printed out so I keep trying to visualise that protein every time we discuss it, I hope I'm even telling you the right thing.  The concept is totes there though >.>

[Turtle]

Do you guys know why the C1 -OH sticks upwards on N-actylglucosamine.
I know the C1 -OH sticks downwards in Glucose, so why would it be flipped in this case?
Here is a picture to show what I mean:
http://www.cryst.bbk.ac.uk/PPS95/course/10_interactions/NAMNAG_t.gif

[Starlight]

@ Turtle, haven't covered carbohydrates yet sorry!

Just wondering with the amino acids stuff Section III 2009 paper question (ii) "Give a residue to substitute for x, justify your choice"

What kind of answer are they expecting from us?

Similarly does anyone know about (e) i and (e) ii?

[simpak]

X is in contact with an aliphatic chain so you'd expect it to be hydrophobic (eg X = valine).
Y: probably choose a salt bridge as interaction (or H bond) and then you expect Y to be negatively charged eg glutamate COO-
Hope this helped?

[Starlight]

X is in contact with an aliphatic chain so you'd expect it to be hydrophobic (eg X = valine).
Y: probably choose a salt bridge as interaction (or H bond) and then you expect Y to be negatively charged eg glutamate COO-
Hope this helped?

thanks it did!

also with b oxidation etc. we just need to know the names of the steps like oxidation. blah blah (i haven't revised it yet). Like no chemical structures as for glycolysis?