Questions about amino acids/ proteins

[MrSandman]

I'm taking BIO 121 right now and I'm just skiming through my book and notice this:

 

NH2=amino

 

R=20 different things

 

COHO=Carboxyl

 

Now, when I look at a table of the "R" groups bonded to the protein. It shows the Amino group as being +NH3. In the polar and charged groups this makes sense, shows that something in the R group is -. Meaning the Electron just moved. However this doesn't make since in the acidic state, because it has to give off electrons. I'm a little confussed, so enlighten me.

[ecoli]

In biological conditions, meaning roughly neutral pH, the NH2 group will be protonated, thus having an extra hydrogen (and a plus charge). The carboxyllic acid group will be deprotonated with a negative charge.

[pioneer]

An amino group and a carboxyl group are common to all amino acids. These two groups react, between two different animo acids, to form the peptide linkage. With two animo acids stuck together, we still have an animo on one side and the carboxyl on the opposite side of the two. These are also reactive with other animo acids. The result are long polymer molecules; proteins. The animo acids link like the cars of a protein train.

 

The R- groups are the 20 different types of side chains that stick out of side of each amino acid. Some of these are short, some are long, some have negative charge, some have postive charge, others are organic with no charge, other are organic with resonance structures.

 

When the protein train forms, it is like a long string, with all different sized -R strings sticking out sideways, close to each peptide bond. Near the peptide bond, there is also hydrogen bonding hydrogen. These will turn the long protein string into a helix. While all the -R side strings, using their own weak secondary bonding forces, also try to attract. The final shape, depends on the -R groups. Some proteins look like long helixes, while some end up looking like very large, odd, 3-D shapes.

 

In cells, the protein chains are made from RNA templates. As the protein train comes off the template, is sort of like a long string of tickets that one may try to win at an arcade. As the first tickets come out, they start to get their helix twist, at the same time, the R- groups pull and tug for their shape affect. This sort of starts a snowball affect, that the rest of the protein train further builds upon. When these snowballs are released, they rest a spell, so their structures can fine tune. The rest is sort of like an oven, where they are subjected to H-potential. When fully baked, the cell transports them to their proper place, all shiny and new.

[MrSandman]

In biological conditions, meaning roughly neutral pH, the NH2 group will be protonated, thus having an extra hydrogen (and a plus charge). The carboxyllic acid group will be deprotonated with a negative charge.

 

I don't agree it isn't necessarily Protonated. It loses an electron or gains It doesn't gain or loses a proton. You must be mistaken.

 

However, I agree with your ph comment to some extent.

 

Reply to Pioneer

 

That makes sense, are you a professor? However, are you saying that they the NH2 group never actually appears naturally, but is the basic building block for the proteins. The reason why in some cases the electron moves from one place to another is because of the Cytochromes (which is another protein). Anyways the NH2 group only is made if you take away the R-group. So without the R group it isn't a protein. I thought that was sort of interesting.

[immortal]

Amino acids are zwitterions i.e. they will have both positive charge as well as negative charge. For example ,Alanine

 

 

 

 

In the case of peptides,

 

 

I don't see anywhere the molecule losing or gaining an electron, However the electrons of bonded nitrogen are shared between two C-atoms and one H-atoms and has two lone pair of electrons. The amine group is protonated and the carboxyl group is deprotonated.

Cytochromes have Fe+++ and Fe++ ions which alternately get reduced and oxidised and there by transfering electrons. It is one of the member of electron transport chain.

 

 

 

Amino acids are zwitterions i.e. they will have both positive charge as well as negative charge. For example ,Alanine

 

 

 

 

In the case of peptides,

 

 

I don't see anywhere the molecule losing or gaining an electron, However the electrons of bonded nitrogen are shared between two C-atoms and one H-atoms and has two lone pair of electrons. The amine group is protonated and the carboxyl group is deprotonated.

 

 

[CharonY]

Of all the answers Ecoli is the only one really hitting the spot.

BTW, the OP is a bit unclear which amino group is supposed to be protonated: the one in the backbone, involved in peptide bonds, or that in the residues of a few amino acids (e.g. lysine, asparagine).

Specifically this bit is misleading:

Now, when I look at a table of the "R" groups bonded to the protein.

In a protein the amino group would form a peptide bound and thus will not be free for protonation anymore.

 

Regardless on the details, under physiological conditions peptides are always in aqueous conditions. Thus they are surrounded by a given concentration of H+ or OH- ions, depending on the pH of the solution. Actually MrSandman already demonstrated that the charge is a protonation event (and not a loss of electron charge):

 

It shows the Amino group as being +NH3

See? NH2 -> NH3+ (addition of H+, or proton).

 

 

Anyways the NH2 group only is made if you take away the R-group. So without the R group it isn't a protein.

Unfortunately here is another serious misconception what amino acids are. Maybe you should check on Wikipedia (did I really say that). The backbone of all amino acids is (+)H3N-CHR-COO(-). The "R" is just for residues as the various amino acids simply have different residues. The simplest amino acid is glycine in which R is simply a hydrogen. Now, if amino acids form proteins it is realized by above mentioned peptide bonds under loss of a water molecule: (+)H3N-CHR-CONH-CHR-COO(-)

Note that the bonds are not depicted properly here in this text form, but you'll find information about that basically everywhere (how about textbooks )

[MrSandman]

Amino acids are zwitterions i.e. they will have both positive charge as well as negative charge. For example ,Alanine

 

 

 

 

In the case of peptides,

 

 

I don't see anywhere the molecule losing or gaining an electron, However the electrons of bonded nitrogen are shared between two C-atoms and one H-atoms and has two lone pair of electrons. The amine group is protonated and the carboxyl group is deprotonated.

Cytochromes have Fe+++ and Fe++ ions which alternately get reduced and oxidised and there by transfering electrons. It is one of the member of electron transport chain.

 

 

 

Amino acids are zwitterions i.e. they will have both positive charge as well as negative charge. For example ,Alanine

 

 

 

 

In the case of peptides,

 

 

I don't see anywhere the molecule losing or gaining an electron, However the electrons of bonded nitrogen are shared between two C-atoms and one H-atoms and has two lone pair of electrons. The amine group is protonated and the carboxyl group is deprotonated.

 

 

 

 

I do look harder I'll reply later got to get to class.

[MrSandman]

well it could be at the NH3 and the Oxygen, but you're right I talked to my professor it is protonated.

 

How do you get subscripts?

[John Cuthber]

"I talked to my professor "

It might have been more helpful and more polite to do that before posting.

[MrSandman]

Well it seemed easy to think of a transfer of elections then the addition of protons. Who cares that much about politeness? It's a cruel world. People say things, but don't mean it. That's another ethical issue, so please keep it away from science. I couldn't understand it until my professor explained it. Now, stop being a mother of ethics.

[John Cuthber]

OK if you want the science side of things; it's poor science to pontificate about things when you are an ignoramus.

And, BTW, as for "Who cares that much about politeness? ", I think you will find that many of us do.

Have you read this?

http://www.scienceforums.net/forum/announcement.php?f=51&a=14

[MrSandman]

I'm sorry. I should have not have been so blunt. However, beating around the bush isn't my method. You don't believe what someone says you say something that refutes it. Then you get the poster angry and they reply quicker. It was my method to get him to support his answer. Without me asking about every single point. Politeness as in being rude is perfectly abhorrent, but openly refuting what someone says isn't. Just get the conversation going faster.

 

I would also like it if we can keep with amino acids. You have anything to add about them please post. However, I will want you to support what you tell me.

[John Cuthber]

OK first point.

"you get the poster angry and they reply quicker. It was my method to get him to support his answer."

He didn't ; your idea failed.

Secondly.

"but openly refuting what someone says isn't."

You need to look up what refuting means. If you had genuinely provided evidence refuting his point then this would be fair comment. Simply saying he's wrong isn't the same thing, and it makes you sound like a 2 year old.

 

Thirdly

"However, I will want you to support what you tell me."

Surely you are joking? You didn't offer any suport for your wrong headed idea. On the other hand you were prepared to accept the word of your prof.

Perhaps you should learn that some of the people how post here are respected scientists. At the very least you ought to accept that, given his post count, ecoli is quite likely to be right. People don't generally get by here for that long unless they know what they are on about.

[MrSandman]

Ummmm, did you read my post or not? However, since you want to stay on this subject.

 

Let me ask you a question. If someone says "your wrong" don't you want to prove otherwise? I know I do. I don't know much about the subject I'm just hypothesizing. That's is why I made the thread in the first place. Maybe It would be better that I state that you are WRONG unless you give me substancial proof that it is RIGHT. It helps me learn and the people who post, and that is what the forum is about. I'm not just going to accept something tells me. I would be a fool if I did.

 

Now, please keep with the topic.

[Cap'n Refsmmat]

Regardless of much you think MrSandman deserves them, please save your comments for a more appropriate place.

[MrSandman]

Well put... I don't need this thread anymore. Can you delete it?

[Cap'n Refsmmat]

We generally save threads so that people who search the forums can find answers to their questions. If the thread derails again, I can close it.

[MrSandman]

Okay, thanx.