ilovehaein

Welcome back everyone! Long time no see!

You know, I had to come in this late and write the article.... Because I wanted to tell you about the many things I've learned! 

Amino acid's left/right hand, a fact that has PH within it, and the one you have been longing to wait for.... How does AA's turn into well - shaped proteins?

We will be learning those soon and see some others as well!

Alright, Let's go! Into this wonderfully small world!

The first thing I want you to know is something called "Fischer Projection".

Fischer Projection is a 2D model for a 3D structure.

In Fischer projection, there are two types of AA's - The L and D types!

As you can see in the picture above, the fischer projection shows amino acids in four spots. The Amino group(Amine, or NH2), the carboxylic acid group(COOH), the side chain(R), and the bonded Hydrogen atom.

The L and D amino acids are like our left and right hands. 

Try to overlap your hands together. Do they overlap them perfectly? 

The answer is NO, and just like our hands, L/D AA's also cannot overlap each other perfectly. So we can say that L/D AA's are Non - superimposable to each other. 

The difference in structure is that the NH2 is on the left side for the L - AA while the NH2 is on the right side for the D - AA.

This makes the L amino acid to act as part of the system of proteins, enzymes, and lots of others that has to do with living things.

But for D amino acids, however, are not yet well - known. So it's hard to tell.

(If I get some more info, I'll tell you about it. Ok?) 

Now, here is the time I can tell you about Iso - electric point and zwitterions!

If we take a glycine molecule and show it, you will normally have NH2 and COOH. However, there can be a slight change to the structure. That is, when the COOH "knocks off" or donate the H+ to the NH2, making it into COO- and NH3+. This new glycine molecule has both positive and negative charge, while having a net charge of 0.(1 - 1) 

Like form B, we call this a Zwitterion!

Now, let me do a quick review of the difference between PH, PKa, and Ka.

Ka is the strength of an acid, or the "Degree of acid dissociation". 

PKa is the negative log of Ka, so the stronger the acid, the larger the Ka, the smaller the PKa, and vice versa.

PH is the measure(amount) of H+ in the solution. It is described as the negative log of [H+] ---> (The concentration of H+).

If you go back to the picture, you can see that the zwitterion can change it's 'form' depending on the value of PKa.

For form A, it has a PKa of 2.34, which means it's in a acidic solution.

This also tells us that the concentration of H+ has increased as well too.

Because a lot of H+ is in the area, the COO- can form a bond with the H+, making it back to COOH. And the net charge result is 1. (0 + 1)

On the other hand, for form C, it has a PKa of 9.6. 

This means it's in a basic - solution, and has a high PH which means that the concentration of OH- has increased.

Because of the OH- in the solution, the NH3+ can give it's H+ and become into NH2 again. So it's net charge is -1. (0 - 1)

Here's the fun part, you can now know at what PH can this glycine molecule become into a zwitterion! 

How do we do it? By using something called a Iso - electric point!

The Iso - electric point, also named PI for short, and this is the PH point where the AA has a net charge of 0.

How do we find PI? By calculating the total of our PKa's!

PI = (PKa1 + PKa2) / 2

With this equation, let's find the PI of glycine!

The equation is like this: (2.34 + 9.6) / 2 = 11.94 / 2 = 5.97

So we can see that 5.97 is our PI! Yay!

Oh, and one more thing. Different side chains(Acidic/basic) can change the PKa's to be different. And that's why all of the AA's PI's are different.

As we all know, we have 21 Amino acids in nature. 

Then, how do we sort these individual AAs in groups?

There's a lot of ways to classify Amino acids, but in this case, i'm gonna use it as this way:     

Amino acids --> Hydrophobic / Hydrophilic

Hydrophobic: Aliphatic group, Aromatic group, cyclic group.

Hydrophilic: Amide, S or Se containing group(neutral group), acidic, and basic group.  

Hydrophobic AAs are non - polar and does not like to form a bond with water while Hydrophilic AAs are polar and likes to bond and hang out with water.

We can split hydrophobic AAs to Aliphatic and aromatic groups. 

Both Aliphatic and aromatic groups has side chains are made out of Carbon and Hydrogen. the difference is - Aromatic groups has a cyclic hexagon - like structure(ex: benzene) while aliphatic groups doesn't.

Aliphatic groups includes Amino acids Glycine, Alanine, Valine, Methionine, Leucine, Isoleucine. Even though Methionine does have a sulfur atom, it is bonded to two Carbon atoms instead of an R - S - H bond. Making it nonreactive and non polar.

Aromatic groups includes AAs Phenylalanine, Tryptophan, Histidine ,and Tyrosine(Non polar because of it's benzene).

The Cyclic group includes one Amino acid - Proline. (Because of its odd, cyclic structure)

For the Neutral - or Hydroxyl, Alcohol, Amide, Sulfur, Selenium containing group, is in the hydrophilic group. Neutral groups includes Serine, Threonine, Asparagine, Glutamine, Cysteine(Cystine), and Tyrosine(slightly polar because of it's OH). 

Acidic groups have carboxylic acid(COOH) on their side chain, which is very acidic(strong hydrogen donor). Acidic members are Aspartic acid and Glutamic acid. In their deprotonated state, they become Aspartate and Glutamate.

Basic groups contain Amine groups as their side chain, which is basic.

Basic groups are amino acids Histidine(It's side chain is basic and aromatic), Lysine, Arginine.

These are the ways of classifying AAs in my way.

Say, after listening to all this amino acid stuff, doesn't it make you wonder?

About how does Amino acids turn and become proteins.

As it turns out, they go into a four step process for their well done protein structure - Primary, Secondary, Tertiary, and Quaternary!

Primary structure is about everything we learned - Amino acids, linked in peptide bonds. The very basics of proteins lives in here.

Secondary structure is where these primary structures folds themselves into Alpha helix(α helix) and Beta sheets.(β sheet)

An Alpha helix gets folded in a way that the C = O bond of the "nth" amino acid can form a Hydrogen bond with the N - H of the "n + 4 th" amino acid.

Which makes the Hydrogen bonds, drawn in dotted lines in the structure above.

For Beta sheets, however, they form a Hydrogen bond with the amino acid that's on the different strand (or "team") rather then the amino acid that's on the same strand.

Each of the chain of AAs in beta sheets are called Beta strands.

There are two kinds of Beta sheets - Parallel and Antiparallel.

Parallel Beta sheets has beta strands that starts and ends on the same side, while Antiparallel Beta sheets has beta strands that starts at a different side.

Just like on the Beta sheet picture above.

Now, what happens if a beta sheet is on 3D?

The Beta strands will be shown as arrows in the direction Nterm -> Cterm

and each Beta sheets will be shown as arrows more or equal to two.

The picture above is one of the beta sheets in 3D. Kinda looks like a hairpin, right? Well, just like that, the structure's name is called a Beta hairpin!

This Beta hairpin occurs when two antiparallel beta strands are together.

Do you see the paperclip - like loop in the 3D picture? That's called a Beta turn. It's made out of 2 ~ 5 amino acids and mostly consists Proline or Glycine.

These loops are important to keep the beta strands to be holded together and even to link with alpha helices. If they fold more, then what forms is called the Tertiary structure.

In Tertiary structure, there are two kinds - Globular and Fibrous. We are going to learn about Globular Tertiary structure. (Because I did not learn deeply to Fibrous Tertiary structures yet.)

Starting from Tertiary structure, you can call the whole thing a protein from now on. Globular proteins fold themselves as a ball shape in order to let it's hydrophobic stuff to the inside and the hydrophilic stuff on the outside.

This is called Hydrophobic interactions.

As well as the Hydrogen bond from the secondary structure, there are other bonds in tertiary structure to keep it stable.

This include Ionic bonds, and Disulfide bridges.(which is pretty hard to make, since they only happen in oxidizing environments) 

Quaternary structure are multiples of these tertiary proteins that are together.

Quaternary structures use the bonds that stabilizes tertiary structures.

An Example of a Globular quaternary structure is Hemoglobin. Which is a four - protein quaternary structure.

In quaternary structures, each protein that makes the quaternary structure is called a Subunit. When two of them are together, we call it a dimer.

For three of them, it's a trimer. Four is tetramer. And more then that are all called multimers. Each with their own name.

Normal proteins are formed with the steps above. But sometimes there can be an error in the step that causes the protein to be "Denatured".

Denaturation occurs if the protein gets enough "stress" to make it's structures to be broken and lowered down to the previous structure.

One thing to note though, Denaturation does not effect the Primary structure.

Now here are the Top 3 ways to Denature a protein:

Number 1: Heat.

Heat makes a lot of (Kinetic) energy that is strong enough to make the molecules vibrate rapidly. This breaks the Hydrogen bond of the secondary, tertiary, quaternary structure.

Number 2: Acid/Bases.

If an acid makes the solution to go below the PI, the concentration of H+ will increase. Making the negatively charged anion to be neutral.(Same with bases) Breaking the ionic bond of the tertiary, quaternary structure.

Number 3: Alcohols.

Alcohols like ethanol(CH3CH2OH), has this OH(Hydroxyl group) that can break the old hydrogen bond and form a new one. Making the secondary, tertiary, and quaternary structure to be denatured.

This is it, The end of this article!

The next one will be all about Enzymes.

Happy new year everyone, and happy studying!

NOTE: All pictures from Khan academy and Wikipedia. 

I do not own this picture nor site.

If you want more information, go to this link: 

https://www.khanacademy.org/test-prep/mcat/biomolecules

https://en.wikipedia.org/wiki/Main_Page

                                    2016 1/05

                                    By Jane Kim

                                    <해인이가>

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)