Amino Acids and Protein Structure.mp4

Amino Acids and Protein Structure.mp4


In the tutorial on hemoglobin, we explored
hydrophilicity and hydrophobicity. Show Hydrophilic. We saw that molecules made primarily of atoms
with full or partial charges can typically interact favorably with water, because the
atoms of water are partially charged. These molecules are called hydrophilic or polar
molecules, and they contain ionic and/or polar covalent bonds. Show Hydrophobic. Molecules
made primarily of uncharged atoms typically do not interact favorably with water, and
these molecules are called hydrophobic or nonpolar molecules. They contain mainly nonpolar
covalent bonds. Show Hydrophobic effect + Illustration. Any hydrophilic molecules that
neighbor hydrophobic molecules must forgo favorable interactions with other hydrophilic
molecules. This is what causes the hydrophobic effect: in order to maximize favorable interactions
between hydrophilic molecules, hydrophobic molecules clump together, which decreases
hydrophobic surface area. Let’s see how hydrophilicity and hydrophobicity
apply to amino acids and proteins. Proteins are polymers made up of amino acids, which
are the monomers. Amino acids are like pearls on a string, and the protein is the necklace.
Here’s the basic structure of an amino acid: This group of atoms is called an amino group;
and this group of atoms is called a carboxylic acid group. These groups together give amino
acids their name. This basic structure makes up the backbone of a chain of amino acids,
highlighted in orange. The R group stands for a variable chain or side chain that is
covalently bonded to the backbone of the amino acid. There are 20 different side chains,
and thus 20 different amino acids, that are encoded by DNA. Remember from the Representing
Molecules tutorial that this is an equivalent way to draw an amino acid. Because all amino acids have the same backbone,
we classify them based on their R group to highlight the differences between them. Here
are the twenty amino acids, and these top ones are the hydrophobic, or nonpolar, amino
acids. Despite the fact that the backbone contains partially charged atoms, amino acids
with hydrophobic or nonpolar side chains are considered hydrophobic or nonpolar amino acids.
Note that the only atoms in these side chains are carbon, hydrogen, and sulfur, all of which
have very similar electronegativities and thus form nonpolar covalent bonds, resulting
in atoms with no charge. Here are the hydrophilic amino acids. We can
further divide them into amino acids with only partially charged atoms because of polar
covalent bonds, and amino acids with fully charged atoms, which can form ionic bonds. Amino acids join together through covalent
bonds to form a chain of amino acids, called a polypeptide. The reaction that creates this
covalent bond is a condensation reaction. A condensation reaction is the joining of
two molecules and the loss of a small molecule, in this case water. A condensation reaction
that involves the loss of water is often called a dehydration reaction. The bond formed between
the two amino acids is a peptide bond, highlighted in orange. The peptide bond is between the
carbon, that is also double bonded to an oxygen, and the nitrogen atom. The repeating basic
structure of a polypeptide chain is called the backbone. Amino acids that are bonded
together through peptide bonds are often referred to as amino acid residues. As you’ve seen in molecular genetics, the
order of amino acids in a protein is determined by the DNA sequence of the gene encoding that
protein. This amino acid sequence is especially important for the protein’s function, because
each amino acid has slightly different properties. The sequence of amino acids is called the
primary structure of a protein. Note that the type of bond that creates the primary
structure is the peptide bond, because this joins amino acids together. Regardless of the side chain, each amino acid
has some partially charged atoms. In particular, there are partially positive hydrogen atoms
and partially negative atoms. This allows the backbone to form hydrogen bonds not only
with water but also with other parts of the backbone. A fully or partially charged atom
that is not interacting with an oppositely charged atom is foregoing favorable interactions,
so it is most favorable for these partially charged atoms to maximally interact with oppositely
charged atoms. Hydrogen bonds that involve only the backbone
and not atoms from the side chain make up the protein’s secondary structure. Because
every protein has the same backbone but the sequence of side chains is unique, secondary
structures are common motifs seen in many different proteins. The two major formations
that fall in the category of secondary structure are alpha helices and beta sheets. An alpha helix involves a series of hydrogen
bonds within one polypeptide strand. The backbone, which is highlighted in blue, coils around
to allow hydrogen bonding between amino acids of the same strand. The partially negative
oxygen of one amino acid forms a hydrogen bond with the partially positive hydrogen
of an amino acid that’s four away. I’ve outlined the amino acids, so you can see amino
acids 1, 2, 3, 4, 5, and 6. And you can see that there’s a hydrogen bond between amino
acids 2 and 6. There’s also a hydrogen bond between 1 and 5, and 3 and 7, and so on. This
is one way to maximize favorable interactions between partially charged atoms of the backbone.
Alpha helices also bring together side chains from non-neighboring amino acids; you can
see that these R groups are now relatively close together. A beta sheet, also called a beta strand, also
involves hydrogen bonds between atoms of the backbone, but not from a strand that is coiled
around itself. Instead, beta sheets are formed from polypeptide strands that lie side by
side. These can be parallel beta sheets, in which the strands involved run in the same
direction, like these first two strands; or they can be antiparallel beta sheets, in which
the strands run in the opposite direction, like these second two strands. Here’s a cartoon model of a small protein
called ubiquitin. In these models, alpha helices are represented by spirals, and beta sheets
are represented by strands with arrows to show direction. The type of bond that creates a protein’s
secondary structure is the hydrogen bond, and only between atoms of the backbone. But a polypeptide chain can also interact
in other ways, which make up the tertiary structure. Random coils may exist due to irregular
hydrogen bonding between the backbone. And the side chains can participate in bonding
of a variety of types: hydrogen bonding, ionic bonding, and covalent bonding. As you might
expect, side chains with polar covalent bonds participate in hydrogen bonding and charged
side chains participate in ionic bonding. The covalent bond that is seen between side
chains is the disulfide bond, which forms between two cysteine side chains. Here are
two cysteine side chains, and the disulfide bond they can form looks like this. These interactions, along with the secondary
structure, give the polypeptide chain its overall three-dimensional shape, which is
called the tertiary structure. So the types of bonds that create a protein’s tertiary
structure include hydrogen bonds, ionic bonds, and covalent bonds. Another force that contributes
to tertiary structure is the hydrophobic effect. If a protein exists in the watery environment
of the cytoplasm, then any hydrophobic surface area is unfavorable, because it forces hydrophilic
molecules to forgo favorable interactions. As a result, any hydrophobic side chains,
shown here in black, are tucked into the interior of the protein, away from the protein’s
surface, and thus away from the hydrophilic cytoplasm. Finally, some proteins are made of more than
one polypeptide chain. An example is hemoglobin, which is made of four polypeptide chains.
The interaction of all these chains together is called the quaternary structure. The types
of bonds that can bring chains together and thus form the quaternary structure are the
same as those seen in the tertiary structure – hydrogen bonds, ionic bonds, and covalent
bonds (specifically, disulfide bonds). The hydrophobic effect also plays a role in quaternary
structure. Because not all proteins are made of more than one chain, not all proteins have
a quaternary structure.