Amino acids - Swag!

Alright! I'm in a spectacular feeling about this biology article!

This time, we are going to learn about the building blocks of proteins,

Amino Acids!

21 of these little Amino acids all have different things that it can do - 

And we, are going study the basics of this adventure!

                                        

First of all, I would like you to know where amino acids are even a part of the body. Let's give you an example of a protein called "Hemoglobin".

Hemoglobin is a protein that's inside the red blood cells, and it's job is to pick up oxygens and bring it to the tissues(cells) all over the body.

The tissues uses the oxygen to generate ATP, which makes energy in order to live. And Amino acids are the ones that makes this important hemoglobin.

Here is the structure of a amino acid:

Amino acids are made by containing amine(NH2) and a carboxylic acid(-COOH) and a R and H.

Can you see the letter R? That's the side chain of the amino acid.

It's difference is what makes the amino acids all different.

Also, if you learned chemistry, you would know that there is a Carbon in the center part of the others. 

The carbon that is bonded with the NH2, R, and another carbon (alongside with a H atom that is not seen) is called the (chiral) alpha carbon.

"Chiral" means a carbon atom bonded to four unique other elements.

And the other carbon that's connected to the O, OH, and the alpha carbon is the carbonyl carbon.

Now, in order for these individual amino acids to become into a protein, The AAs should be linked together. A bond of two amino acids are called a "Peptide bond".

As you can see in the picture above, the first step is to "pluck" off the H from the N and combine it with OH-.

With the formation of a water molecule, connect the NH+ and the carbonyl C. Then a bond will show between the carbonyl carbon and the nitrogen. That's a peptide bond. And the molecule that's been formed is called a Dipeptide.

When these AAs join together, a polypeptide chain is formed.

For simplicity, We only write the N, alpha C and carbonyl C.

And so the polypeptide chain is like this: N-C-C-N-C-C-N-C-C

The side that the N is on is called the N terminal.

And the side that the carbonyl C is the C terminal.

We can imagine that the N-C-C to act as a "group" and call it a residue.

                                        

Just like AAs can make peptide bonds, you can also break down the peptide bond as well. in order to do that, we need to use a way called Hydrolysis.

There are two ways of Hydrolysis:

One is called "Acid Hydrolysis". And just like the name, we use strong acids with heat to break the peptide bonds.

The other one is called "Proteolysis". And for that, we use a special enzyme called protease. Unlike acid hydrolysis, proteolysis can let you pick which peptide bond to break.

For example, a protease called Trypsin cuts the C term of arginine and lysine. So if we have a polypeptide chain like this:

***- ^^^- arginine - @@@- !!! - lysine - &&& And input trypsin inside,

we would have it like this: ***- ^^^- arginine   @@@- !!! - lysine  &&&

Using proteolysis has a big advantage for experiments because you can cut wherever you want for the research. Pretty cool, right?

                                           

Now, we will talk about our most special Amino acids of them all - The AA show!

It looks like our contestants are Histidine, Proline, Glycine, and Cysteine.

What could possibly make them special?  

Well, let's look at our first stop, Histidine!

The thing that makes Histidine special is that it's pKa is approximately 6.5 which is close to physiological PH.

Now you might say "Umm, ok, the pka and ph is close.. So what?"

According to the Henderson - Hasselbalch equation, the pKa = PH + log [HA] / [A-].

If we make pKa > PH, or making the solution more acidic, the log [HA] / [A-] > 0. Which means that [HA] > [A-]. Meaning that a stronger acid will cause the formation of [HA], the protonated form.

If we make pKa < PH, AKA making the solution more basic, the log [HA] / [A-] < 0. So [HA] < [A-], meaning a stronger base will cause the formation of [A-], the deprotonated form.

Look here for more: 

http://www.mhhe.com/physsci/chemistry/carey5e/Ch27/ch27-1-3.html

For Histidine, since it's pKa is close to physiological PH, it can switch from protonated to deprotonated from and vice versa with just small changes of PH. Making it to a H+ donor/acceptor without wasting energy and Enable things like transporting protons to one molecule to another.  

                                             

Next is Proline and Glycine, the alpha(α) helix breakers!

Let's look at Proline first.

Unlike all the other Amino acids, you can see that proline has its R group to have a cyclic structure that has a bond with the amine(NH2).

So we say that Proline has a secondary alpha amino group.

Because of it's odd side chain, proline is very rigid then others. So it doesn't have a free rotation alongside the other atoms.

On the other hand, Glycine is the opposite of proline's structure.

Glycine's side chain is DA most simplest side chain in the HISTORY of side chains! It only has a H for it's side chain!

Because of it's simple side chain, it's very flexible then others.

But there is a catch for that simple side chain as well.

Remember the part where I told you about the "Chiral" alpha carbon?

Like I said, "Chiral" means four different elements bonded into a C.

But for Glycine, since it's side chain is a H atom, we have a double H for the alpha carbon. So we cannot say that the carbon is chiral for glycine.

                                        

Now, about this time now, I think you should know what an alpha helix is.

An alpha helix is a coiled up polypeptide chain. It kinda looks like this:

Even though Proline and Glycine has a role of forming alpha helixes, they introduces a Beta turn to the alpha helix.

A beta turn is a bend(or turn) in the primary structure.

For Proline, because of it's odd secondary alpha amino group, it makes a bend when making peptide bonds. Glycine also makes bends because of it's flexibility,

                                          

Our last Amino acid is Cysteine!

And so, what cysteine has is this little trick on it's sleeve to form a disulfide bridge when each of them are close to each other as a polypeptide chain.

It would be good to learn redox reactions before this.

https://www.khanacademy.org/science/chemistry/oxidation-reduction/redox-oxidation-reduction/v/introduction-to-oxidation-and-reduction

Now, you can see that Cysteine has a thiol group( C - SH) as it's side chain.

The Cysteine molecules are in a reduced environment. So if we put this in a oxidizing environment, the side chains will lose an H and the S will form a bond.

We call that bond a Disulfide bridge.

And I should really say - Cysteine has name issues!

Some are asking is "Cysteine" or "Cystine" the correct way to spell the name.

And the thing is, both of them are right.

The name "Cysteine" is used for it's usual form, where the disulfide bridge is not formed yet.

The name "Cystine" is used when it has a disulfide bridge, in an oxidized state.

So, you can think about it like this:

1, Cysteine is used for it's usual form, and inside it's reduced - intracellular space.

2, Cystine is used for it's bonded form, and inside it's oxidized - extracellular space.

                                                                   

And with that, the Amino acids show will end.

Amino acids are pretty fun, right?

I asked a question to my dad about why Amino acids are left out of the central dogma. (Because I was curious)

And the answer was simple - Since Amino acids makes proteins, we can say that they are the smallest protein unit. So it's not "left out".

Well, that's it for today's article. And I hope to see you again in the next one about Amino acids - DA protein makers! Swag! 

                                      2015, 12/30   

                                   Jane Kim (김해인)