protein's secondary structure

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DrAdrenaline
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#1
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In a protein's secondary structure,
why does some polypeptides coil to form alpha helix while others coil to form beta pleated sheet?

anyone know? Thanks
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Hal.A
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#2
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Formation of hydrogen bonds at different places a long the polypeptide, that's why the sequence of amino acids coded for by the mRNA effects the shape, that's all you need to know at this level
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DrAdrenaline
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#3
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(Original post by Hal.A)
Formation of hydrogen bonds at different places a long the polypeptide, that's why the sequence of amino acids coded for by the mRNA effects the shape, that's all you need to know at this level
yes, but that wasn't the answer i was looking for. maybe i wasn't clear in my question sorry.

what i meant to ask was, if you join the amino acids together it should form a straight chain of polypeptide but it doesn't. it actually coils to form alpha helix or a beta sheet. why is this?

ps. hydrogen bond can only form once the polypeptides has coiled and are parallel to each other.
H-bond is only there to hold the coiled structure together.

please do correct me if i am wrong.
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Icecream1
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#4
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(Original post by swopnil)
yes, but that wasn't the answer i was looking for. maybe i wasn't clear in my question sorry.

what i meant to ask was, if you join the amino acids together it should form a straight chain of polypeptide but it doesn't. it actually coils to form alpha helix or a beta sheet. why is this?

ps. hydrogen bond can only form once the polypeptides has coiled and are parallel to each other.
H-bond is only there to hold the coiled structure together.
It is due to the inter molecular forces that cause the different side groups to interact and form different bonds, causing different shapes. for example, It depends on the side groups, sulphur in cysteine binds to other sulphur to form a strong disulphide bond.

hope that helps.
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DrAdrenaline
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#5
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(Original post by Icecream1)
It is due to the inter molecular forces that cause the different side groups to interact and form different bonds, causing different shapes. for example, It depends on the side groups, sulphur in cysteine binds to other sulphur to form a strong disulphide bond.

hope that helps.
yes, you're right. but that's its tertiary structure. i thought R group wasn't involved in secondary structure anyway.

if you mean those forces between R group of different polypeptide then that's its quaternary structure that leads to more folding indeed as you said,.
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Icecream1
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#6
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(Original post by swopnil)
yes, you're right. but that's its tertiary structure. i thought R group wasn't involved in secondary structure anyway.

if you mean those forces between R group of different polypeptide then that's its quaternary structure that leads to more folding indeed as you said,.

ImageImage

Intermolecular forces, causing the shapes to form. The ratios of different amino acids will influence its secondary shape, they lead to a particular shape.

http://www.chembio.uoguelph.ca/educm...6/456lec01.htm
"Amino acid preferences for different secondary structure:

Alpha helix may be considered the default state for secondary structure. Although the potential energy is not as low as for beta sheet, H-bond formation is intra-strand, so there is an entropic advantage over beta sheet, where H-bonds must form from strand to strand, with strand segments that may be quite distant in the polypeptide sequence.
The main criterion for alpha helix preference is that the amino acid side chain should cover and protect the backbone H-bonds in the core of the helix."
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DrAdrenaline
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#7
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(Original post by Icecream1)
ImageImage

Intermolecular forces, causing the shapes to form. The ratios of different amino acids will influence its secondary shape, they lead to a particular shape.

http://www.chembio.uoguelph.ca/educm...6/456lec01.htm
"Amino acid preferences for different secondary structure:

Alpha helix may be considered the default state for secondary structure. Although the potential energy is not as low as for beta sheet, H-bond formation is intra-strand, so there is an entropic advantage over beta sheet, where H-bonds must form from strand to strand, with strand segments that may be quite distant in the polypeptide sequence.
The main criterion for alpha helix preference is that the amino acid side chain should cover and protect the backbone H-bonds in the core of the helix."
wow, that was so helpful. i understand it now. Thanks for your effort on finding these links.

reps
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Icecream1
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#8
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#8
(Original post by swopnil)
wow, that was so helpful. i understand it now. Thanks for your effort on finding these links.

reps
np enjoy!
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kanra
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#9
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#9
Partly due to steric restrictions and amino acid sequence. So the bond between the carbon in the centre of the amino acid is bonded to a nitrogen and a carbonyl-carbon. These bonds can only be twisted to certain degrees, otherwise you start to get groups on the amino acid clashing with other groups. You get different restrictions for different amino acids.

Also, consider proteins inside the cell that help other proteins fold (chaperones). A particular protein sequence could potentially become an alpha helix, or a beta sheet, or even a random coil - but chaperones will interact with a newly synthesised protein and help it to fold into one specific secondary (and tertiary) structure.
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