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Please explain this diagram


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histidine.gif

 

 

I have researched each compound.

 

NH3 is stable.

CH is unstable The Carbon atom wants 3 more electrons in its 2nd shell.

CO2 is stable.

CH2 is unstable. The Carbon atom wants 2 more electrons in its 2nd shell.

N is unstable. It needs 3 more electrons in its 2nd shell.

NH is unstable. It needs 2 more electron in its 2nd shell.

 

 

 

So how does it all fit together?

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the lines in the diagram each represent two shared electrons in a covalent bond. If you look at the CH2 unit, for instance, you'll see there is one pair of electrons for each bond. there are two bonds between the carbon and hydrogens (not shown as lines) and two between the carbon and its neighbouring carbons. Notice that two of the carbons arent shown at all. This is quite common in diagrams of organic molecules. You can tell where the carbons ae because they're at the corners and ends of lines.

 

Anyway to explain it in terms of the octet rule, the carbon in the CH2 unit has four bonds, each of which is a pair of electrons, making a complete octet (8 electrons in the second shell)

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I know this is homework... and I know I'm not supposed to give the entire answer.

 

But I also know that you will get much more than this one exercise... so I'll just show how it all fits together, then you can do all the other exercises yourself.

 

In the picture below, the two formula's are the same! On the left is the "easy" way which is popular because it takes less time to write. The right is the "complete" version. Note that each carbon atom has 4 lines attached to it (4 bonds, sometimes it's a double bond, noted with a =).

 

Note also that the neutral nitrogen has 3 bonds. The neutral oxygen has 2 bonds. The nitrogen with 4 bonds has a +, because the nitrogen itself lost an electron. That also means that it can have not 3, but 4 bonds.

 

The oxygen got an electron (probably from the nitrogen) and it can now no longer have 2 bonds, but only 1.

formula explanation.JPG

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I know this is homework... and I know I'm not supposed to give the entire answer.

 

But I also know that you will get much more than this one exercise... so I'll just show how it all fits together, then you can do all the other exercises yourself.

 

In the picture below, the two formula's are the same! On the left is the "easy" way which is popular because it takes less time to write. The right is the "complete" version. Note that each carbon atom has 4 lines attached to it (4 bonds, sometimes it's a double bond, noted with a =).

 

Note also that the neutral nitrogen has 3 bonds. The neutral oxygen has 2 bonds. The nitrogen with 4 bonds has a +, because the nitrogen itself lost an electron. That also means that it can have not 3, but 4 bonds.

 

The oxygen got an electron (probably from the nitrogen) and it can now no longer have 2 bonds, but only 1.

 

 

Ok. Wow. 1st. I am 15. I'm not in a chemistry class. So this isn't cheating on any homework. Just, my dream is to be an astrobiologist when I grow up. So i need to understand amino acids completely.

 

I'm sure I will have alot of questions. This is alot of information though, so I will have to go through it a couple times.

 

Thank you both very much for your answers though. :)

 

If the hydrocarbon "CH" has 6 electrons and 1 electron.. so thats 5 in its 2nd shell... It shares one with the ammonia... which makes the ammonia unstabe? And it shares one with the carbon dioxide.. which makes it unstable... and shares one with the hydrocarbon to its left... this adds up to 8 electrons.. which makes it stable... but what happens to the ammonia "NH3", and the "CO2" which was already stable.. and now isnt....

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Perhaps you undertstood it, but your last reply suggests that you possibly misunderstood. So... I'll take a step back.

 

First thing you must know is the difference between atoms (examples are: carbon, hydrogen, oxygen) and molecules (examples are ammonia, L-histidine, and all the hydrocarbons (like methane, ethane, propane)).

 

(If you don't know this yet, you will know it once you start physics/chemistry classes).

 

To be able to draw up any molecule, you need the octet-rule.

 

Then you need to figure out how many electrons an atom has. For that, you should take a look at the periodic table. It's a very important piece of information... but if you're interested in amino acids, you only need 5 atoms:

 

Carbon: has 4 electrons in the outer shell, but wants 8

Nitrogen: has 5 electrons in the outer shell, but wants 8

Oxygen: has 6 electrons in the outer shell, but wants 8

Hydrogen: has 1 electrons in the outer shell, but wants 2

Sulphur: doesn't always care so much about the octet rule. For simplicity, you can leave this one out of today's lesson - it's also not present in histidine.

 

So, in the case of ammonia (NH3, 1 nitrogen atom, 3 hydrogen atoms): the nitrogen has 5 atoms, and would like 3 more. The hydrogen all have 1. The nitrogen shares 1 electron with each individual hydrogen: all hydrogens then get 2. The hydrogens in turn also share their electron: so that the nitrogen gets its own 5, plus 3 (one from each hydrogen). That makes 8.

 

Next lesson is perhaps functional groups. The amino acid got its name from the amine group, and the carboxylic acid group. But if you never had chemistry lessons, then I think you have enough to disgest in 1 day already.

Edited by CaptainPanic
structuring the text a little
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i get it :D

 

So the N has a + next to it becasue it HAD 8 electons in its covalance shell due to the 3 hydrogen, but then the carbon took one.. so now it has 7.. which means it has 9 electrons and 10 protons.. which gives it a positive charge...

 

correct?

 

For the sake of simplicity, it is easiest to consider only the outer eight electrons.

 

I think your confusion on this stems partially from the fact that there is more than one way to account for electrons.

 

The "+" that you see is what is known as a "formal charge". A formal charge is the number of electrons an atom usually has minus the number of electrons that the atom actually has. Consider the nitrogen. As Captain posted, nitrogen usually has 5 electrons (considering only the outer shell). When accounting for how many electrons the atom has, you split each bond in half. One electron in the bond goes to one atom, the other to the other atom. So the nitrogen has 4 bonds, and therefore 4 electrons assigned to it. Therefore, 5 - 4 = +1, which is the formal charge of the nitrogen.

 

The octet rule is another way to account for electrons. The nitrogen has 4 bonds. In this method of counting, both electrons count for both atoms in the bond. Therefore, the nitrogen has 4 bonds, which comes out to eight electrons. The octet rule is satisfied.

 

The octet rule is used for drawing structures.

 

Formal charges help identify sites of positive and negative charge in the atom.

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i get it :D

 

So the N has a + next to it becasue it HAD 8 electons in its covalance shell due to the 3 hydrogen, but then the carbon took one.. so now it has 7.. which means it has 9 electrons and 10 protons.. which gives it a positive charge...

 

correct?

 

You were almost correct. The N has a + next to it because it has 4 bonds, and not 3. The reason is that at first it was neutral. It had 8 electrons in the outer shell with a bond to the carbon, and to 2 hydrogen. Then a 3rd hydrogen came along, and squeezed itself in... This particular hydrogen that came along was a proton (a hydrogen atom that had completely lost its electron). The nitrogen was already sharing 3 of its 5 electrons with the 3 neighbours. It then shared both of the free electrons with the proton.

 

As it happens to be, I am sure that the hydrogen originated at the oxygen which is now negatively charged. The hydrogen broke off, and left its electron on the oxygen atom.

 

i always feel foolish to talk about happy atoms and unhappy atoms, but at the start of chemistry lessons it seems easiest to explain it like that. 8 electrons-in-the-outer-shell-atoms are happy. Later you realize it has to do with energies... but thermodynamics of acid/base reactions don't belong in this thread... yet.

 

For now: 8 electrons in the outer shell makes an atom happy. Hydrogen just needs 2 to be happy.

 

And to count charge, you need to know:

How many protons does an atom have. How many electrons does an atom have. How many is it sharing with its neighbours (all shared electrons, whether they come from the atom itself, or from the neighbours, count as 0.5).

So, the positively charged nitrogen has: 7 protons. 2 non-shared electrons. 5 shared electrons originating from itself. 3 shared electrons from other atoms (1 from the carbon, 2 from the hydrogen) and 0 shared electrons from the positively charged hydrogen.

So the total is: 7 protons, and 2 + 0.5*8 = 6 electrons. Result: a positive charge.

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Perfect!!!

 

my only question is.......... where in science can we just look at a diagram and guess out of the blue that "hey look, that hydrogen doesnt have an electron".

 

how is anyone saposed to know that one of the Hydrogen hasnt an electron? How can i recognizethis for future reference

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There are 2-and-a half ways:

 

1: The hydrogen that has lost an electron (but has not yet joined up with another molecule) is written as [ce]H+[/ce]. The + shows it's positively charged. So there's pretty little guessing here. It's just reading.

 

2: In case the hydrogen joined up with another molecule, you must count the electrons/protons. If there is a positive charge, then you can bet that some atoms lost an electron (why else would it have a positive charge?).

 

3: Acids -by definition- lose protons (they get rid of the positively charged hydrogen atom, keeping the electron). The fact that they do this makes them an acid. It is the definition of acid. Strong acids do it always, weak acids do it sometimes (and you will learn later to calculate exactly how much). So if you notice that you're dealing with an (amino)acid, then you just search until you find it.

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