Leah here from leah4sci.com/mcat and in this video we'll start the introduction to Amino
Acids as you have to know them for the mcat and potentially your biochemistry class.
This video we'll look at the basics and the remainder of this series will break it down
step by step to make sure that you understand every single aspect.
The first question to ask yourself is What is an Amino Acid?
Every Amino Acid has a central carbon called the alpha carbon.
Then we have the amino portion which is an amine group NH2 and an acid portion which
is a carboxylic acid.
There is also a hydrogen atom and a variable group called the R-group which is the rest
of the molecule and this will change from amino acid to amino acid.
We said the central carbon is called the Alpha Carbon and this goes back to something you
learned in Organic Chemistry.
When you had a carbon chain with a carbonyl, that carbonyl was the starting carbon, like
the ground zero where you start counting.
The first carbon attached to that was called the Alpha carbon.
The second carbon attached was the beta carbon, the third is the gamma carbon, and then the
delta and so on, and so on.
For the amino acid, if the carboxylic acid has a carbonyl at zero, the central carbon
attached to the carbonyl is the first one and therefore the alpha carbon.
This form of drawing a neutral amino acid is technically incorrect because it can't
exist like this in nature.
The amino acid naturally exists as having two ions in the backbone that cancels each
other out.
This is called the dipolar ion or the zwitterion and this can change depending on the specific
ph, something we'll look at in this zwitterion tutorial.
For now, just realize that if we take away the hydrogen on the carboxyl, we get an Oxygen
with three lone pairs and a negative charge.
And if we add a hydrogen to the amino we get four bonds to Nitrogen, we took away its lone
pair and we get a positive charge.
We'll show the amino acid as AA for short.
And notice in the backbone we have 4 common atoms.
We have carbon, oxygen, nitrogen, and hydrogen.
Two of the R-groups also have sulfur and this is important for being able to distinguish
between amino acids and nucleotides which is another very important molecule in a living
system.
Nucleotides which make up DNA and RNA also have carbon, oxygen, nitrogen, and hydrogen
but they have a phosphorous in their backbone and they don't have sulfur so that's the qa
to distinguish which type of molecule it came from.
And why are amino acids so important?
They are the monomers, the single unit that make up a very important structure key to
the survival of a cell and that is proteins.
Proteins forms so many important critical structures of the cell, from holding it together
like the cytoskeleton, enzymes that catalyze reactions, structural components for example
in the cell membranes or holding proteins, dna, and different things together, transport
in signalling so we have proteins acting as carrier molecules, peptide hormones which
are made up of Amino Acids and we can even use it for energy on the cell if we need to.
And these are just some examples.
Amino acids are the building blocks of proteins.
And if you take the twenty most common amino acids, and you change the sequence in which
they're attached, and the link of the chain you get an infinite number of possibilities
of different types of proteins that can be formed.
There are twenty common amino acids that you need to know for the MCAT.
Understand that there can be more, through modification or rare ones, but the twenty
common ones are the ones you need to memorize.
These can be broken down into essential amino acids, meaning the body can't synthesize these
amino acids so you have to get it from your diet.
And then the non-essential amino acids which your body can synthesize using the essential
amino acids as the starting point.
You don't have to memorize this but the 9 essential amino acids are histidine, leucine,
isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
The non-essential include the conditionally essential but we'll just classify them as
non-essential in general which means that the body can make them depending on the circumstances.
That includes alanine, asparagine, aspartic acid, and arginine, glutamic acid, glutamine,
glycine, proline, serine, tyrosine, and cysteine.
What sets these amino acids apart?
It's the R-group.
The r-group is a variable group and this is what changes from amino acid to amino acid.
This group gives the amino acid its special characteristics, determines how it interacts
with other amino acids and ultimately determines how it interacts with this environment and
all the molecules around it.
The amino acids will be classified based on the chemistry of that R-group.
We can simply separate them into the hydrophobic and hydrophilic groups.
Instead of memorizing why an amino acid falls into a certain category, I want you to understand
what about the chemistry of the R-group makes it fall into that category.
That way when you look at the side chain, you'll be able to look at it and understand
what's going on.
If you break this word down, we have hydrophobic means fearing and philic means loving.
Water is a very common molecule.
Most of the world is made up of water and even most of your body is water.
Water has one oxygen atom and two hydrogen atoms.
Oxygen is highly electronegative, that means even though it's bound to hydrogen with a
covalent bond, a sharing bond, Oxygen is greedy and it tries to pull on the electrons from
the bond towards itself.
In pulling down those electrons we have a pulling or polar bond and this concentrates
the negativity of the bond around the oxygen taking it away from hydrogen.
That extra negativity around the oxygen makes it partially negative, and hydrogen having
its positive nucleus exposed is now partially positive.
That gives the oxygen portion of water a partial negative charge, the hydrogen portion, a partial
positive charge, and this polarity allows it to interact with other molecules, like
water molecules or amino acid side chains.
When you look at a side chain, ask yourself, does it want to interact with water?
Does it have a charge or partial charge that can associate with the partial negative oxygen
or partial positive hydrogen?
Or is it completely hydrophobic meaning it fears water because it has no way to interact
with it.
Hydrophobic is non-polar, there is no polarity to interact with water and hydrophilic side
chains will be polar, meaning they have partial charges or fully charged like your acidic
and basic side chains.
The hydrophobic side chains can be broken up into two categories, the Aliphatic, and
Aromatic side chains.
These are terms you should recognize from Organic chemistry.
Aliphatic is linear, non-cyclical.
It doesn't have aromaticity so think of these as your linear or non-aromatic side chains.
Aromatic side-chains have aromatic groups within them.
For example, benzene or even heterocyclic aromatic compounds.
See the link below if you need a review on aromaticity.
Hydrophilic side chains can also be broken down.
We said that hydrophilic side chains can be polar.
That means partial charges but not full charges.
And if we don't have a full charge, then the side chain is neutral.
What you're looking for in these side chains are oxygen and nitrogen atoms, but without
a protonation-deprotonation going on.
For the charged side chain, we're going to see acidic and basic components.
The charged side chains can get a charge by donating or accepting a proton.
Donating a proton acid or accepting a proton base.
And yes, we'll break them all down in the upcoming videos.
Another thing to keep in mind is that amino acids have chirality or stereochemistry.
In Organic Chemistry you learn this as R&S, but in biochemistry we'll use the configuration
of D&L.
The amino acid chirality video, we'll break it down and show you how to find the chirality
but for now keep this in mind, Eukaryotic organisms like the L form of amino acids and
they don't like the D form of amino acids.
If you're asking, does D&L convert to R&S?
the answer is, it can be both.
R&S does not specifically tell me D&L and I'll show you how to recognize this in the
amino acid chirality video.
And finally, in understanding amino acids as an essential component of protein, it's
critical to understand how they react.
Later in this series, we'll look at three important amino acid reactions.
When amino acids are brought together, they form a peptide bond and you can think of this
as dehydration synthesis because you're synthesizing the bond, you're bringing the two amino acids
together and in the process taking out a molecule of H2O.
If connecting amino acids takes out the water molecule, then you can imagine that to break
apart a peptide bond into the separate acids, you have to put the water back.
And this is called the hydrolysis reaction.
Which comes from the word, hydro, adding the water back in, and lysis to break.
Another critical reaction is Sulfur linkage creating disulfide bridges, and this is the
only covalent bond that forms between amino acid side chains to strengthen that three
dimensional tertiary or Quaternary protein structure.
Now that you have an idea of what you need to know, let's break it down step by step.
Make sure you download the amino acid cheat sheet so you can follow along as you watch
this entire series and then try the amino acid practice quiz.
You can find all of these on my website leah4sci.com/AminoAcids.