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Offline crays

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Protein molecule
« on: May 22, 2008, 09:33:51 AM »
Hi guys, I got a question here. I tried asking my teacher but she can't answer it so i decided to ask for help here. Its about the protein molecules. As my book writes, Protein can be polar, non polar, acidic and basic. But why can non polar molecule, for example Glycine to have H+ and O- ? They're non polar right? Wouldn't that make them acidic ?

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Re: Protein molecule
« Reply #1 on: May 22, 2008, 09:55:46 AM »
But why can non polar molecule, for example Glycine to have H+ and O- ? They're non polar right? Wouldn't that make them acidic ?

Please elaborate. It doesn't make sense.
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Offline cliverlong

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Re: Protein molecule
« Reply #2 on: May 22, 2008, 02:56:30 PM »
You have mixed up a lot of concepts here.

I suggest you understand first what an amino acid is (of which glycine is one)

Then you understand how amino acids bond to form proteins. (there is a key chemical bond in this - search google or wiki or your textbook and find out).

Then you rephrase your question.

The above about amino acids and proteins is necessary understanding in this area.

Can you post a two-line definition of amino acids and proteins on this thread then look back at your question and see if it makes sense?


Clive

Offline crays

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Re: Protein molecule
« Reply #3 on: May 23, 2008, 02:54:42 AM »
Sorry for my bad English. I guess a picture would help me a little here.
My book's example of glycine is as so. Me and my classmate were both confused why there is a H+ and O- since Glycine is a non polar protein. My teacher could not explain as well.

Offline cliverlong

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Re: Protein molecule
« Reply #4 on: May 23, 2008, 03:29:34 AM »
Aha!

I think I have a better idea of what you mean. Diagrams are good in Chemistry.

My thinking is this (it may be wrong)

Given the glycine molecule has formula

H2NCH2COOH and the carbon backbone you have given . Glycine is an amino acid NOT a protein you keep on mixing up the two concepts. Read up on the relationship between amino acids and proteins. Do this. The groups are key to this.

See the molecule image below (1) from wikipedia, which has an amine group (NH2) at one end and carboxylic acid group (COOH) at the other end

The NH2 can attach a H+ ion. Therefore glycine can act as a base.

The COOH can release a H+ ion. Therefore glycine can act as an acid. Read up about COOH and you will see you don't consider O- on its own. The COO- is considered more a single entity.

This gives your version of glycine.

Because of this behaviour, glycine is soluble in water.

I have copied the generic diagram(2) from http://www.chemguide.co.uk/organicprops/aminoacids/background.html

Note the structure where NH2 and COOH are close to each other, not at opposite ends of the molecule. I guess this has biological significance. Read the comment in chemguide on zwitterions. Glycine is the simplest amino acid and is the only one where NH2 and COOH are at opposite ends of the molecule ONLY because the central carbon chain has one carbon. This is not typical.

Given the above, where does that get you?


Clive
« Last Edit: May 23, 2008, 03:39:46 AM by cliverlong »

Offline crays

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Re: Protein molecule
« Reply #5 on: May 23, 2008, 04:41:17 AM »
Thank you for your reply, Its helpful. Sorry that i mixed up protein and amino acid. Just to make sure, so it means that, even in a solid state, the amino acid are all linked up together by an ionic bond ? and the H3N+ is actually an ionic bonding to another amino acid? But so far as i know, Nitrogen can only have 3 valance electron right? How can it have 3 hydrogen and a carbon bonded to it?

Offline Sev

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Re: Protein molecule
« Reply #6 on: May 23, 2008, 05:09:55 AM »
Quote
...the amino acid are all linked up together by an ionic bond ? and the H3N+ is actually an ionic bonding to another amino acid?

The aa's are linked by covalent bonds - called amide (or peptide) bonds.

Offline crays

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Re: Protein molecule
« Reply #7 on: May 23, 2008, 05:22:48 AM »
so the H3N+ (the extra H) is actually a peptide bond?

Offline Astrokel

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Re: Protein molecule
« Reply #8 on: May 23, 2008, 06:28:59 AM »
No!

When many amino acids come together they form protein.

The amino acids in protein are connected through petide/amide bond -CONH-

The polarity of amino acids are usually determine by its side group.

In glycine, the side group is -H, and the H atom is non polar.

An example of polar amino acid is serine, due to the presence of -CH2OH side group
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Offline cliverlong

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Re: Protein molecule
« Reply #9 on: May 23, 2008, 07:21:34 AM »
Thank you for your reply, Its helpful. Sorry that i mixed up protein and amino acid. Just to make sure, so it means that, even in a solid state, the amino acid are all linked up together by an ionic bond ? and the H3N+ is actually an ionic bonding to another amino acid? But so far as i know, Nitrogen can only have 3 valance electron right? How can it have 3 hydrogen and a carbon bonded to it?
Hi

I was trying to push you towards reading up on amino acids and proteins so you discovered the peptide link yourself. But the answer is in the other posts.

As a side comment, going back to the ionized form of glycine (and I don't think this is anywhere as important as the peptide link) there is ionic  / electrostatic attraction in pure glycine. This has nothing to do with the peptide links in proteins

From the link I gave you to chemguide ...

.

This is called a zwitterion.

This is the form that amino acids exist in even in the solid state. Instead of the weaker hydrogen bonds and other intermolecular forces that you might have expected, you actually have much stronger ionic attractions between one ion and its neighbours.

These ionic attractions take more energy to break and so the amino acids have high melting points for the size of the molecules.

..

Read Jim Clarke's chem guide on amino acids and proteins and understand ...


Clive

Offline cliverlong

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Re: Protein molecule
« Reply #10 on: May 23, 2008, 08:32:26 AM »
<< snip >>
But so far as i know, Nitrogen can only have 3 valance electron right? How can it have 3 hydrogen and a carbon bonded to it?

Aha !  The tyranny of the full outer shell ( I have written on this concept before)

As is often the case, Jim Clarke's chemguide is clear on this

Read the entry

http://www.chemguide.co.uk/atoms/bonding/dative.html#top

(all of it)

The section

The reaction between ammonia and hydrogen chloride

is particularly relevant to the (good) question you have raised - which is entirely a logical thing to write - if incorrect.

The question is really about how does the N bond a H+ when the simple model says N in glycine cannot form any more bonds.

After reading the entry, can you answer your own question and post back on this forum?


Clive

Offline crays

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Re: Protein molecule
« Reply #11 on: May 23, 2008, 09:36:30 AM »
Oh sorry clive, i was just simply searching for the answer x(. Anyway, thanks for the link. I kinda get what it is now already. But again just to make sure, its the whole hydrogen nucleus that is transfered but the electron is left behind right?

Offline cliverlong

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Re: Protein molecule
« Reply #12 on: May 23, 2008, 10:08:22 AM »
Oh sorry clive, i was just simply searching for the answer x(. Anyway, thanks for the link. I kinda get what it is now already. But again just to make sure, its the whole hydrogen nucleus that is transfered but the electron is left behind right?
My understanding of the dative bond is nothing gets "left behind". The two species "munge" (that's a technical term  ;)  ) together ( NH2 and COOH in the amino acid zwitterion ) and share the electrons.

Does that make sense?

I just read about polyamides.

Can you find out the similarities and differences between

1) Polypeptides or proteins

versus

2) Polyamides

I never thought of the polyamide configuration before. You learn something new .


Clive

Offline crays

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Re: Protein molecule
« Reply #13 on: May 23, 2008, 10:36:44 AM »
Thank you for your help. But refering back to my question why does it have an H+ on the amino group and a H taken away from the COOH group. is it because of the amino acid is linking each another ? so the NH2-C-COO(H)NH2-C-COOH the H is linked that way ?

Offline Astrokel

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Re: Protein molecule
« Reply #14 on: May 23, 2008, 11:48:51 AM »
Thank you for your help. But refering back to my question why does it have an H+ on the amino group and a H taken away from the COOH group. is it because of the amino acid is linking each another ? so the NH2-C-COO(H)NH2-C-COOH the H is linked that way ?

Amino acids can undergo internal acid-base reaction forming dipolar ions known as the zwitterions in the solid state and at the isoelectric point.

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