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.