Hello everyone! My name is Eman, and welcome back to my YouTube channel.

Today, we’re
kicking off a brand new, improved, and fully updated MCAT biochemistry series. If you’ve been
here before, you know that I’m always working to improve the clarity, structure, and depth of
these lessons. I take your feedback seriously because I want to make sure you have everything
you need to truly understand the material and feel confident going into the MCAT. Everything I
share here is freely available because I believe that education should never be gated behind a
paywall. Everyone deserves access to quality science education, no matter their background or
resources. You’ll find a link to the notes and a full transcript for this video in the description
below.

With that being said, let us get started with Chapter 1 which is titled Amino Acids, Peptides, and
Proteins**.** In this chapter, we’ll cover six main objectives.

1. First, we’ll begin with the amino acids found in proteins. We’ll go over basic terminology,
the stereochemistry of amino acids, their structures, and how to classify them as
hydrophobic or hydrophilic. We’ll also review the one-letter and three-letter abbreviations
that you’ll need to recognize on the MCAT.
2. Second, we’ll dive into the acid-base chemistry of amino acids. This includes how they
gain or lose protons depending on pH, how to interpret pKa values, and how to analyze
titration curves—especially the isoelectric point.
3. Third, we’ll look at peptide bond formation and hydrolysis. You’ll learn how amino acids
are linked together, how peptide bonds are broken, and how this process fits into protein
synthesis and degradation.
4. Fourth, we’ll cover primary and secondary protein structure. That means understanding
the sequence of amino acids and how they fold into alpha helices or beta sheets through
hydrogen bonding.
5. Fifth, we’ll explore tertiary and quaternary structure. Tertiary structure is the full three-
dimensional shape of a single polypeptide. Quaternary structure applies when multiple
chains come together to form a functional protein. We’ll also talk about conjugated
proteins, which have extra chemical groups called prosthetic groups that help them
function.
6. And finally, sixth, we’ll finish with denaturation. That’s when a protein loses its structure,
often due to heat or chemical stress, and as a result, loses its function too.

Let’s begin with the first major topic: amino acids found in proteins.

● Proteins are some of the most versatile molecules in biology. They come in an incredible
variety of structures, which allows them to perform a wide range of functions. Everything
from carrying oxygen, to speeding up reactions, to fighting infections—proteins are at the
center of it all.
● The first protein to have its three-dimensional structure determined was myoglobin. This
was a major scientific milestone, and it was made possible through a technique called X-
ray crystallography. That structure gave us our first real view of what proteins look like at
the atomic level, and it laid the groundwork for understanding how protein structure
relates to function.
● Now, depending on the role a protein plays, we can group them into different categories.
○ First, we have enzymatic proteins. These are proteins that act as catalysts. They
speed up chemical reactions by lowering the activation energy needed. A classic
example is digestive enzymes. For instance, enzymes in your digestive system
help break down large molecules in food by catalyzing the hydrolysis of chemical
 bonds. That means they use water to break those bonds and make the nutrients
easier to absorb.
○ Next, we have defensive proteins. These are involved in protecting the body
against disease. Antibodies are a great example. They recognize and bind to
foreign invaders like viruses or bacteria, inactivating them and tagging them for
destruction by the immune system.
○ Then we have storage proteins. As the name suggests, these proteins store
amino acids or other important molecules for later use. One example is
ovalbumin, which is the main protein found in egg white. It serves as a reservoir
of amino acids for the developing embryo.
○ We also have transport proteins. These move substances throughout the body or
across cell membranes. Hemoglobin is a classic example. It’s found in red blood
cells and carries oxygen from the lungs to tissues all around the body. Without it,
oxygen wouldn’t reach where it’s needed.

Now all of these proteins, no matter how different their functions seem, are built from the same
basic building blocks. And that brings us to the big question: what are proteins actually made
of?

● The answer is amino acids. Amino acids are the building blocks of proteins. Each one
contains four essential components bonded to a central carbon atom, which we call the
alpha carbon. These four groups are: an amino group, a carboxyl group, a single
hydrogen atom, and a variable group known as the R group, or side chain. It’s this R
group that gives each amino acid its unique chemical properties.
● When we study amino acids for the MCAT, we focus on the twenty standard amino acids
that are directly encoded by the genetic code. These are called the proteinogenic alpha-
amino acids. There is a 21st amino acid, selenocysteine, and while it plays a role in
specialized proteins, it’s not something you need to memorize for the MCAT.
● Now these twenty amino acids are all alpha amino acids, meaning the amino group is
attached to the same carbon that holds the carboxyl group—the alpha carbon.
● To keep everything organized, each amino acid has a full name, a three-letter
abbreviation, and a one-letter code. On the MCAT, these show up in figures, in tables,
and in passage text. So throughout this lesson, I’ll make sure to clearly say all three for
each amino acid as we walk through them.
● Let’s start with the nonpolar, nonaromatic amino acids. These amino acids have side
chains that are hydrophobic. They don’t interact well with water and are usually found in
the interior of folded proteins, where they help stabilize the overall structure.
○ First is Glycine, abbreviated as Gly, with the letter G. Glycine is special because
its side chain is just a single hydrogen atom. That makes it the smallest amino
acid and the only one that is not chiral. Because it’s so small, glycine is highly
flexible, and you’ll often find it in regions of the protein where the backbone
needs to bend or turn.
○ Next is Alanine, Ala, letter A. Its side chain is a simple methyl group. It’s
compact, nonpolar, and hydrophobic.
○ Then we have Valine, Val, letter V, which has a branched isopropyl side chain.
This adds bulk and makes it more strongly hydrophobic.
○ Leucine, Leu, letter L, and Isoleucine, Ile, letter I, are also branched-chain amino
acids. They are hydrophobic, and they’re commonly found packed in the cores of
folded proteins.
○ Next is Proline, Pro, letter P. Proline has a distinctive ring structure that connects
back to its own amino group. This creates a rigid backbone that limits flexibility.
 Because of this rigidity, proline often disrupts alpha helices and creates turns or
kinks in protein structures.
○ And finally, we have Methionine, Met, letter M. Methionine has a sulfur-containing
thioether in its side chain. Despite the sulfur, it remains nonpolar and
hydrophobic. Methionine is also notable because it’s the first amino acid
incorporated during translation in eukaryotic proteins.
● Let’s move on to the aromatic amino acids. These amino acids contain ring structures
with conjugated pi electrons, which allows them to absorb ultraviolet light. This makes
them useful for detecting proteins using spectrophotometry.
○ First is Phenylalanine, Phe, letter F. It has a benzyl side chain, which is highly
hydrophobic and nonpolar.
○ Next is Tyrosine, Tyr, letter Y. It has a hydroxyl group attached to its aromatic
ring. That hydroxyl group makes tyrosine slightly polar and capable of forming
hydrogen bonds.
○ Then we have Tryptophan, Trp, letter W. Tryptophan has a bulky double-ring
structure. While it’s generally nonpolar, it is more hydrophilic than phenylalanine.
● The next category to cover is polar, uncharged amino acids. These amino acids have
side chains that can form hydrogen bonds, so they’re hydrophilic, but they don’t carry a
formal charge at physiological pH.
○ Serine, Ser, letter S, has a hydroxyl group on a short side chain. It’s small and
highly polar.
○ Threonine, Thr, letter T, also has a hydroxyl group, but it’s attached to a slightly
larger side chain. Like serine, it can form hydrogen bonds and is polar.
○ Asparagine, Asn, letter N, and Glutamine, Gln, letter Q, both have amide groups
in their side chains. These amides are polar and excellent at forming hydrogen
bonds, which helps stabilize protein surfaces.
○ And we should also include Cysteine, Cys, letter C. Cysteine has a thiol group on
its side chain, which makes it polar. The key feature of cysteine is that two
cysteine residues can form a covalent disulfide bond, which helps stabilize the
three-dimensional shape of a protein.
● Moving on to negatively charged amino acids, also called the acidic amino acids. These
amino acids have side chains that are deprotonated at physiological pH, giving them a
negative charge. There is two amino acids to cover in this category.
○ Aspartic acid is the protonated form, while aspartate is its conjugate base—the
deprotonated form that predominates at physiological pH. It’s abbreviated Asp,
letter D, and has a carboxylic acid group attached just one carbon away from the
alpha carbon.
○ Glutamic acid and glutamate follow the same pattern: glutamic acid is the
protonated form, and glutamate is the deprotonated conjugate base. Abbreviated
Glu, letter E, it’s very similar to aspartate but has an extra carbon in the side
chain before the terminal carboxylic acid group.
○ Both are strongly hydrophilic and frequently involved in ionic interactions, such as
salt bridges, that help stabilize folded proteins.
● Finally, let’s talk about the positively charged amino acids, also known as the basic
amino acids. These amino acids have side chains that are protonated at physiological
pH, which gives them a net positive charge.
○ Lysine, Lys, letter K, has a long side chain ending in a positively charged amino
group. It’s strongly basic and highly hydrophilic.
○ Arginine, Arg, letter R, has a guanidinium group at the end of its side chain. This
group is resonance-stabilized and carries a positive charge, making arginine one
of the strongest basic amino acids.
 ○ And lastly, we have Histidine, His, letter H. Histidine has an imidazole side chain
with a pKa close to physiological pH. That means it can shift between being
protonated or unprotonated depending on the environment, which makes it
especially useful in enzyme active sites where acid-base chemistry is involved.
● With that, we have introduced our 20 amino acids. In addition, we can classify amino
acids based on how they behave in wate along a spectrum from hydrophobic to
hydrophilic.
○ On the hydrophobic end, we have amino acids like alanine, isoleucine, leucine,
valine, and phenylalanine. These side chains tend to avoid water and prefer to be
tucked away inside the folded protein.
○ On the hydrophilic side, we have histidine, arginine, lysine, glutamate, and
aspartate. These amino acids have polar or charged side chains that readily
interact with water and are usually found on the outside of proteins where they
can interact with the aqueous environment.
○ Everything else—meaning most of the remaining amino acids—falls somewhere
in the middle. Their behavior depends on the specific context, like pH, nearby
residues, or whether they’re exposed to water or buried in the protein core.
● There are also two structural facts that are also important to keep in mind:
○ First, all amino acids are chiral, except for glycine. Since glycine’s side chain is
just a hydrogen atom, its alpha carbon is bonded to two identical groups, so it
lacks chirality.
○ Second, all amino acids have S absolute configuration, with the exception of
cysteine. Even though cysteine is still L in biological systems, its sulfur atom
changes the priority order in its side chain, giving it R configuration instead of S.
● So to wrap up this section, amino acids can be grouped in several different ways—by
polarity, by charge, by aromaticity, and by whether they’re hydrophobic or hydrophilic.
These properties directly affect how they behave in water, how they fold into proteins,
and how they interact with other molecules. And remember, for the MCAT, it’s essential
that you can recognize the name, structure, three-letter abbreviation, and one-letter code
for each of these amino acids.

Now let’s move into Objective 2: the acid-base chemistry of amino acids.

● Amino acids are amphoteric, which means they can act as both acids and bases. In
other words, they have the ability to either accept a proton or donate a proton. How they
behave depends entirely on the pH of their environment.
● At the most basic structural level, every amino acid has at least two groups that can gain
or lose protons—a carboxyl group and an amino group. These groups respond
differently depending on whether the pH is acidic, neutral, or basic.
● Let’s start by imagining an amino acid that hasn’t gained or lost any protons yet. In this
state, the carboxyl group is written as COOH, and the amino group is written as NH₂.
● But in water—and especially around physiological pH—that exact form usually doesn’t
exist. Instead, amino acids tend to exist in a structure called a zwitterion. A zwitterion is
a molecule that carries both a positive and a negative charge on different atoms, but has
no net charge overall.
● Here’s how that happens:
○ In water, the carboxyl group tends to lose a proton and becomes negatively
charged, forming COO⁻.
○ At the same time, the amino group tends to gain a proton and becomes positively
charged, forming NH₃⁺.
 ○ So even though the molecule carries both charges, they cancel each other out.
This results in a zwitterionic form—electrically neutral overall.
● Now, to understand how amino acids behave as acids and bases, there are two key
rules you need to remember:
○ Ionizable groups tend to gain protons under acidic conditions and lose them
under basic conditions. So in general, at low pH, ionizable groups tend to be
protonated, and at high pH, they tend to be deprotonated.
○ The pKa of a group is the pH at which half of the molecules of that group are
deprotonated. So, if the pH is lower than the pKa, most of that group will be
protonated. If the pH is higher than the pKa, it will be deprotonated.
● Every amino acid has at least two groups that can gain or lose protons—the amino
group and the carboxyl group—which means they all have at least two pKa values:
○ The first pKa, usually around 2, corresponds to the carboxyl group.
○ The second pKa, usually around 9 to 10, corresponds to the amino group.
○ And if an amino acid has an ionizable side chain, it will have a third pKa specific
to that group.
● Let’s apply those ideas in different pH environments:
○ At a low pH, meaning in highly acidic conditions, the solution contains lots of free
protons. In this environment, the amino acid becomes fully protonated. The
carboxyl group stays in its protonated form as COOH, and the amino group is
NH₃⁺. This gives the molecule a net positive charge.
○ As we raise the pH and approach neutrality, the carboxyl group loses its proton
first—because its pKa is lower, around 2. At this point, the carboxyl group is
COO⁻, while the amino group remains NH₃⁺. Now the molecule carries both a
negative and a positive charge, making it a zwitterion. This is the dominant form
at physiological pH, which is about 7.4.
○ If we continue to raise the pH into basic territory, the amino group eventually
loses its proton too. NH₃⁺ becomes NH₂. Now both functional groups are
deprotonated, and the overall charge on the amino acid is negative.

So to summarize this trend:

● At low pH, amino acids carry a positive charge.

Because amino acids have both acidic and basic groups, they’re excellent candidates for
titration experiments. Their ability to gain and lose protons at specific pH values allows us to
study how their charge changes across the pH scale.

● Let’s take a closer look at the titration curve of glycine, the simplest amino acid. In this
case, we’re starting with a 1 molar glycine solution and gradually adding base—in the
form of hydroxide ions. On the x-axis, we track the amount of base added, measured in
equivalents. On the y-axis, we monitor the pH of the solution.
● Glycine contains two ionizable groups: a carboxylic acid group (–COOH) and an amino
group (–NH₂). At the start of the titration, the solution is very acidic, and glycine is fully
protonated. The carboxyl group is in its –COOH form, and the amino group is in its
positively charged –NH₃⁺ form, giving the molecule a net positive charge.
● As we begin to add base, the carboxyl group is the first to lose a proton. This is because
its pKa is lower than that of the amino group, meaning it is more acidic. When the pH
reaches 2.34—glycine’s first pKa—the concentrations of the protonated and
 deprotonated forms of the carboxyl group are equal. This is a key concept: at the pKa of
a group, its conjugate acid and conjugate base are in equilibrium. At this stage, glycine
exists as a mixture of two forms: the fully protonated form and the zwitterion. This region
of the curve is relatively flat because glycine acts as a buffer around its pKa.
● As we continue adding base, we eventually reach the isoelectric point, or pI, at a pH of
5.97. This is the pH at which glycine exists entirely in its zwitterionic form. Because the
molecule is electrically neutral, it no longer buffers the solution, and the titration curve
becomes steep—meaning the pH rises rapidly with each additional amount of base.
● Beyond the pI, further addition of base begins to deprotonate the amino group. Around
pH 9.60—the second pKa—the NH₃⁺ group loses its proton and becomes NH₂. Here ,
both the zwitterion and the fully deprotonated form exist in equilibrium.
● Now, an important question to ask is how do we calculate the pI for a neutral amino acid
like glycine? Since it only has two ionizable groups—the amino and carboxyl—we take
the average of the two pKa values. That’s (2.34 + 9.60) divided by 2, which gives us
5.97.
● But for amino acids that have ionizable side chains, like glutamic acid or lysine, the
titration curve has an extra step. That’s because they have three ionizable groups, not
just two. But the same principle still applies.
○ Let’s take glutamic acid as an example. It has two carboxyl groups—one on the
backbone and one on the side chain—and one amino group. The zwitterion of
glutamic acid forms after the first carboxyl group deprotonates, but before the
side chain carboxyl group does. So, to find the pI, we average the pKa values of
the two carboxyl groups—those are the two deprotonation steps on either side of
the neutral zwitterion. This gives a pI of about 3.2.
○ Now consider lysine, which has two amino groups—one on the backbone and
one on the side chain—and a single carboxyl group. In this case, the zwitterion
exists after the carboxyl group deprotonates but before either amino group does.
So, to calculate the pI, we average the two highest pKa values: the one for the
backbone amino group and the one for the side chain. Those are the steps that
surround the zwitterionic form. The result is a pI of about 9.75.
● So in summary:
○ For amino acids without ionizable side chains, the pI is the average of the
backbone pKa values (amino and carboxyl groups).
○ For amino acids with ionizable side chains, the pI is calculated by averaging the
two pKa values that flank the zwitterionic (neutral) form.

Let’s move on to Objective 3: Peptide Bond Formation and Hydrolysis.

● Peptides are chains made up of amino acid subunits. When we link amino acids
together, we form a peptide. If the chain is shorter than about fifty amino acids, we call it
a peptide. If it’s longer than fifty amino acids, we typically refer to it as a protein.
● Now, the bond that links one amino acid to the next is called a peptide bond. Let’s walk
through how it forms.
○ Peptide bond formation is a type of condensation reaction, also known as a
dehydration reaction. That means two molecules are joined together, and in the
process, a water molecule is removed.
○ Specifically, the carboxyl group of one amino acid reacts with the amino group of
another amino acid. The hydroxyl group from the carboxylic acid and a hydrogen
from the amino group are removed—together forming water. What’s left is a new
bond between the carbon of the carboxyl group and the nitrogen of the amino
group. That bond is what we call the peptide bond.
 ○ This type of reaction requires energy, and in cells, it’s catalyzed by ribosomes
during protein synthesis.
● Now, once that peptide bond is formed, we can refer to the two ends of the peptide chain
using specific terms.
○ The end of the chain that still has a free amino group is called the N-terminus, or
amino terminus. The other end, which has a free carboxyl group, is called the C-
terminus, or carboxy terminus.
○ So when we talk about the direction of a peptide or protein, we always read it
from the N-terminus to the C-terminus.
○ Just as peptide bonds can be formed, they can also be broken. The reverse of
this process is called hydrolysis, and it involves the addition of water to break the
bond between two amino acids. This reaction can happen under acidic or basic
conditions, or with the help of specific enzymes, such as proteases.
● So again:
○ Peptide bond formation is a condensation reaction that removes water.
○ Peptide bond hydrolysis is the reverse—it adds water to break the bond.

With that, we’re moving into Objective 4, which covers protein structure—starting with primary
and secondary structure.

● Proteins are long chains of amino acids, and all proteins have a specific hierarchical
structure that determines how they fold and function.
● We organize protein structure into four levels: primary, secondary, tertiary, and
quaternary.
● You can think of this progression the same way we build meaning in language. The
primary structure is like letters of the alphabet. The secondary structure is like words.
The tertiary structure is like full sentences. And the quaternary structure, which only
applies to some proteins, is like paragraphs—multiple units coming together to express
something more complex.
● Let’s start with the first level: primary structure.
○ The primary structure is the exact linear sequence of amino acids, connected by
peptide bonds. This sequence is determined by the DNA that codes for the
protein, and it’s always written from the N-terminus, which has the free amino
group, to the C-terminus, which has the free carboxyl group.
● The secondary structure is the local folding that happens between neighboring amino
acids. These folds are stabilized by hydrogen bonds, but specifically between atoms in
the backbone—not the side chains. This level of structure includes recurring patterns
that we see over and over in proteins. There are two common types of secondary
structure:
○ First is the alpha helix. This is a right-handed coil where the peptide backbone
spirals around itself. Hydrogen bonds form between the carbonyl oxygen of one
amino acid and the amide hydrogen a few residues ahead. This gives the helix a
stable and compact shape.
○ The second is the beta-pleated sheet. In this structure, strands of the polypeptide
chain lie next to each other, either in the same direction or in opposite directions.
Hydrogen bonds form between the strands, giving the sheet a flat, extended
appearance. These can be parallel or antiparallel, depending on the orientation
of the strands.
○ A fun little fact I’d like to mention here is how proline behaves in secondary
structures. Proline has a unique, rigid ring structure that connects back to its
backbone nitrogen, which restricts its flexibility. Because of this, proline
 introduces a kink in the polypeptide chain when it's found in the middle of an
alpha helix. It disrupts the helical geometry and breaks the hydrogen bonding
pattern. For that reason, it's rarely found within alpha helices—though it may
appear at the start of one to help cap or terminate the helix. Similarly, proline is
also uncommon in beta sheets, where the extended conformation and regular
hydrogen bonding make it an unfavorable fit. So when you see proline in a
protein sequence, it usually signals a bend or turn, rather than a clean alpha helix
or beta sheet.

Now, objective five which dives into tertiary and quaternary structure.

● The tertiary structure of a protein refers to its overall 3D shape. This folding happens as
a result of interactions between the R groups, or side chains, of the amino acids—not
just the backbone. These interactions include hydrophilic and hydrophobic interactions,
hydrogen bonds, ionic bonds, and disulfide bridges.
1. Hydrophobic interactions play a big role. Nonpolar side chains tend to get buried
in the interior of the protein, away from water. This increases the entropy of the
water molecules around the protein and leads to a decrease in Gibbs Free
Energy, which makes the folding process favorable.
2. On the other hand, polar or charged side chains tend to stay on the outside,
where they can interact with water or with each other. We also see salt bridges
form—those are ionic interactions between oppositely charged side chains. And
finally, we have disulfide bonds, which are covalent bonds that form between two
cysteine residues. When they come together, they form a bridge which helps
stabilize the folded structure.
● For some proteins, tertiary structure is the highest structure present. But for others,
there’s a final level: quaternary structure.
● Quaternary structure only applies to proteins that are made of more than one
polypeptide chain.
● These multi-subunit proteins arrange their subunits in a very specific way to become
functional. Forming a quaternary structure can do a few things:
1. It can increase the overall stability of the protein.
2. It can reduce the amount of DNA needed to encode a large functional protein
complex.
3. It can allow for more efficient catalysis by bringing active sites closer together.
4. And it enables cooperativity, where binding at one subunit affects the behavior of
the others—this is common in proteins like hemoglobin.
● One final point here—some proteins are called conjugated proteins. These are proteins
that require a prosthetic group to function. A prosthetic group is a non-protein molecule
that’s covalently attached and critical to the protein’s role. If the prosthetic group is a
lipid, we call it a lipoprotein. If it’s a carbohydrate, it’s a glycoprotein. And if it’s a nucleic
acid, it’s called a nucleoprotein.
● So, to wrap this up: primary structure is the amino acid sequence. Secondary structure is
local folding into alpha helices and beta sheets. Tertiary structure is the full 3D fold of a
single chain. And quaternary structure is when multiple chains come together into a
single, functional unit. That’s the full hierarchy of protein structure.

We can now wrap up this chapter with our final objective which is about denaturation and this is
essentially the reverse of protein folding.
● When a protein folds, it adopts a very specific three-dimensional shape that allows it to
function properly. But if the protein is exposed to the wrong conditions—like too much
heat or certain chemical solutes—it can lose that shape. This process is called
denaturation.
● During denaturation, the tertiary and quaternary structure of the protein are disrupted.
The protein unfolds, losing the stabilizing interactions like hydrogen bonds, hydrophobic
interactions, salt bridges, and disulfide bonds. It’s important to note that the primary
structure—the sequence of amino acids—usually stays intact.
● Common causes of denaturation include:
○ Heat, which increases molecular motion and breaks non-covalent interactions.
○ Solutes like urea or detergents, which interfere with hydrogen bonding or disrupt
hydrophobic environments.
● Denaturation inactivates the protein because function is directly tied to structure. For
example, enzymes lose their active site shape and can no longer catalyze reactions.
● In some cases, denaturation is reversible if the damaging agent is removed and the
protein refolds correctly. But often, especially in the case of extreme heat or strong
chemicals, denaturation is irreversible, and the protein is permanently nonfunctional.
● So, while folding is how proteins gain structure and function, denaturation is what strips
that away, leaving the protein unfolded and biologically inactive.