[Borek]

jsmith613: please don't add [quоte] tag to your posts.

[cliverlong]

is it that the ends of the monomers contain the SAME atoms (OH-OH) and (H2N-NH2).

Almost !

Remember, the amide link is formed from the reaction of COOH with NH₂ (or COCl with NH₂).
If we use R₁ and R₂ to denote pretty much any combination of atoms, but for simplicity sake chains or rings of CH, such as ethyl or phenyl

We have the reaction of di-carboxylic HOOC-R₁-COOH with diamine H₂N-R₂-NH₂ to form the chain. look at the structure of the chemicals in the wikipedia articles to confirm that.

I still dont know what is special about the number of functional groups, please enlighten me. But with the position, they are ends are a reflection of the other (basically the opposite way round with the same atoms)

All (pretty much all) that is important is the existence of 2 COOH on one monomer and 2 NH₂ on the other monomer - leading to the chain

... -CONH-R₂-HNCO-R₁-CONH-R₂-NHCO-R₁-CONH-...

I have written CONH and HNCO to try and show which of the C and the N in the link is bonded to either R₁ or R₂.

Can you see that? Can you see without every monomer having two functional groups you will not get chains? Can you draw it "structurally" to more clearly see the bonds between the various atoms?

Now, can you go back to the amino acids I listed (any two will do), describe what two functional groups are on every amino acid and what that means for the bonding between amino acids?

[jsmith613]

Now, can you go back to the amino acids I listed (any two will do), describe what two functional groups are on every amino acid and what that means for the bonding between amino acids?

on every amino acid, there is the functional group NH2-H2N. This means they can bond with any Carboxyl acid to form an amide link

[UG]

Note that he said "describe what two functional groups are on every amino acid"

[cliverlong]

Note that he said "describe what two functional groups are on every amino acid"

jsmith

Google and wikipedia are (usually) your friends

http://en.wikipedia.org/wiki/Amino_acid

[jsmith613]

Note that he said "describe what two functional groups are on every amino acid"

jsmith

Google and wikipedia are (usually) your friends

http://en.wikipedia.org/wiki/Amino_acid

an amino acid is something containing both A Carboxyl acid and an amine. That means ANY two amino acids can join to form the amide link. In the case of Alanine and Lysine the left end of Alanine is carboxyl acid and the right end of Lysine is the amine. This means that the two molecules can join together and elimiante a water molecule in the process

[cliverlong]

an amino acid is something containing both A Carboxyl acid and an amine. That means ANY two amino acids can join to form the amide link. In the case of Alanine and Lysine the left end of Alanine is carboxyl acid and the right end of Lysine is the amine. This means that the two molecules can join together and elimiante a water molecule in the process

OK. Take the next step. What is left on the ends of the monomers that has not reacted?  What implication is there for the formation of chains of monomers?

What is different between the chains that can be formed from amino acids and those formed from dicarboxylic acids and diamines?

Clive

[jsmith613]

OK. Take the next step. What is left on the ends of the monomers that has not reacted?  What implication is there for the formation of chains of monomers?

on the ends of the monomers we are left an amine (on one of the amino acids) and a carboxyl acid (on the other). This basically means that the end of the amino acids will keep on joining on to another acid if available

What is different between the chains that can be formed from amino acids and those formed from dicarboxylic acids and diamines?

there is not much difference. on both amino acids and carboxyl acids / amines the the ends the ends of the molecules can still join on to other monomers if they are available.

By the way clive: I am not going to have internet connection for the next week (until next thursday/friday at the latest) and will not be able to look at any reply until then. I would love to continue this interesting conversation as soon as possible, but due to the circumstances beyond my control I will not be able to reply. I really do appreciate your help and look forward to continuing this conversation as soon as I get back internet connection.

many thanks jsmith

[jsmith613]

By the way clive: I am not going to have internet connection for the next week (until next thursday/friday at the latest) and will not be able to look at any reply until then. I would love to continue this interesting conversation as soon as possible, but due to the circumstances beyond my control I will not be able to reply. I really do appreciate your help and look forward to continuing this conversation as soon as I get back internet connection.

I have got connection back, i do hope we can carry on talking

[cliverlong]

Attached is a diagram of how the amide bond is formed and the structure of a small section of a polyamide.

Can you draw the structure of a small section of polypeptide or protein?

Clive

[jsmith613]

Can you draw the structure of a small section of polypeptide or protein?

Clive

A polypeptide is formed when the carboxyl acid of one molecule reacts with the amine of another molecule. This linkage is know as the peptide link / bond.

I am doing the structure in MS Paint because I have no readily available scanner.
http://s359.photobucket.com/albums/oo40/jsmith613/?action=view&current=PolyPeptide.jpg

[jsmith613]

a) Can you find the structural formulae for the monomers pentamethylene diamine and sebacic acid? What is it about these two monomers that allow long chains to be formed rather than just one amide link?

Look for the structure of two amino acids, say lycine and alanine (any two will do). How do they bond to form a polypeptide such as ...lycine-alanine-lycine-alanine-lycine-alanine.... ?

b) What is the similarity and difference in the bonding between the monomers in nylon (polyamide) versus a polypeptide?

Clive

for a) are you looking for the fact that both monomers after loosing an H+ and OH- become charged and hence want to join together with another molecule. The ends of one join on to the beginning of the next molecule
for b) i am not quite sure of the differences, please can you tell me some

John

As well as what we are still doing now, is it possible to get back to this as I am not sure that you answered it. Many thanks

[cliverlong]

OK.

I keep on trying to push you towards drawing several monomers in a chain and then get you to look at the relationship of the carboxyl and amine groups to the "backbone" - whereas you keep on focussing on a single bond.

Look at the diagram I have drawn above for the polyamide.

I summarise it (crudely) as

...NHOC-R₁-CONH-R₂-NHOC-R₁-CONH-R₂-NHOC-R₁-CONH-R₂-...

I write "crudely" because it is tricky to show what is bonded to what when writing the atoms on a single line.

Now .

if you use various amino acids not just one type of dicarboxylic acid and one type of diamine, if I start you off with:

...NHOC-R₁-NHOC-R₂-NHOC-R₃-NHOC-...

Look hard at both chains, draw out the second one with more "structure".

Look carefully at the orientation of the bonds in the polypeptide compared against the polyamide. What do you see?

Look carefully at the backbone parts of the molecule: R₁, R₂, ... What do you see? What does this mean about the monomers that make up a polypeptide and how is that different from the monomers that make up a polyamide?

Clive

[jsmith613]

Look hard at both chains, draw out the second one with more "structure".

a) Look carefully at the orientation of the bonds in the polypeptide compared against the polyamide. What do you see?

b) Look carefully at the backbone parts of the molecule: R1, R2, ... What do you see?
c) What does this mean about the monomers that make up a polypeptide and how is that different from the monomers that make up a polyamide?

a) from what I can see, in polypeptide the R1, R2 ... are below the carbon atom (Not part of COOH) rather than being next to it (i think this is what you are looking for)
Here is a chain of polypeptide done by me: http://s359.photobucket.com/albums/oo40/jsmith613/?action=view&current=PolyPeptide2.jpg

b) with the backbone parts of the molecule in polypeptides, the R1, R2 etc ,are not the 'diving link' between the CONH, NHOC anymore. Rather it is a Carbon atom with a Hydrogen atom and the R1 / R2 linked to it.

c) I think the answer you want is that it is possible to use just ONE type of monomer (amino acid) in a polypeptide but in a polyamide there MUST be 2 monomers.

[sjb]

Look hard at both chains, draw out the second one with more "structure".

a) Look carefully at the orientation of the bonds in the polypeptide compared against the polyamide. What do you see?

b) Look carefully at the backbone parts of the molecule: R1, R2, ... What do you see?
c) What does this mean about the monomers that make up a polypeptide and how is that different from the monomers that make up a polyamide?

a) from what I can see, in polypeptide the R1, R2 ... are below the carbon atom (Not part of COOH) rather than being next to it (i think this is what you are looking for)

That I think is a limitation of the ASCII (text) representation.

Here is a chain of polypeptide done by me: http://s359.photobucket.com/albums/oo40/jsmith613/?action=view&current=PolyPeptide2.jpg

b) with the backbone parts of the molecule in polypeptides, the R1, R2 etc ,are not the 'diving link' between the CONH, NHOC anymore. Rather it is a Carbon atom with a Hydrogen atom and the R1 / R2 linked to it.

c) I think the answer you want is that it is possible to use just ONE type of monomer (amino acid) in a polypeptide but in a polyamide there MUST be 2 monomers.

But *why* can you get away with one type of monomer for polypeptides, as opposed to nylons?