Studying and experimenting on proteins have become a mainstay of modern bioscience.
In this article we will take a quick glance at the fundamentals of protein biochemistry.
In this article:
Peptide bond: the road to polypeptide formation
Protein structure: folding of the polypeptide chain into a specific architecture
What are proteins?
Chemically, proteins are long chains of amino acids.
Akin to how single brick pieces together make up a large wall, each constituent amino acid is a monomer that together builds up the polymer i.e., protein. Consequently, a protein has a very high molecular weight. Being large molecules, they are thus termed ‘macromolecules’.
Individual amino acids in a protein are technically called ‘residues’.
A word on amino acids
Amino acids are a type of organic compound.
If we recap our high school chemistry, the carbon atom (C) is tetravalent. That is, a carbon atom can make four bonds. Further, C can bond with both positively charged atoms or groups such as hydrogen (H+), (-NH3+) etc., as well as with negatively charged atoms or groups like oxygen (O2-), sulfur (S2-) and carboxylate (-CO2-).
In an amino acid molecule, the central carbon atom, known as the α-carbon (C- α), is bonded to these four groups (moieties):
The first three moieties are present in all amino acids. Since
both the ‘amino’ as well as the carboxylic ‘acid’ groups are present for this
class of compounds, they are termed ‘amino acids.'
Figure 1. Schematic representation of the generic structure of an amino acid.
The variations in amino acids lie in their “R groups”, which is unique for each amino acid. Amino acids are classified based on these respective side chains. R groups can be as simple as a single hydrogen atom. This is the case for glycine, the amino acid with the simplest structure.
As the next level of complexity, the R group can be aliphatic (organic compounds without a ring structure. They can be straight/ branched chains but should not have rings). Alanine, valine, leucine and isoleucine comprise this class of amino acids.
Figure 1.3. In contrast to glycine whose R group is a single hydrogen, alanine, valine, leucine and isoleucine are examples of having more complex R- groups.
Proline, though considered to be an
aliphatic amino acid, nevertheless is an aberration in this group. Here the
aliphatic side chain connects with N of the amino group bonded to the C- α,
forming a loop.
Figure 1.4. Proline contains a ring and is an example of an aliphatic amino acid.
For two amino acids, serine and threonine, the R group
contains an alcohol group (-OH)
As a slight variation, if the -OH is changed to a thiol group (-SH), that forms a distinct class of amino acids that contain sulfur. As we will see later, these amino acids have distinct physiological properties owing to the constituent S atom. Members of this amino acid type are cysteine and methionine.
If an R group contains an amide (-CO(NH2)) functional group, that constitutes another class of amino acids. Examples are glutamine and asparagine.
For amino acids tryptophan, tyrosine and phenylalanine, the R group has an aromatic ring. They form the category- aromatic amino acids (organic compounds with a ring structure).
For two amino acids, aspartic acid and glutamic acid, the R group has a carboxylic (COO -) functional group. They are classified as negatively charged (anionic) side chain amino acids.
Alternatively, the R group is positively charged
(cationic) for lysine, arginine and histidine owing to the presence of a
positively charged N atom in their R group.
Figure 1.9. Lysine, arginine and histidine are examples of amino acids with a positively charged R group.
Table 1. is a quick, simple guide to the structures of
amino acids commonly seen in proteins.
| Simplest R | |
| Amino Acid | Structure |
| Glycine | 
|
|
|
|
|
|
|
|
Simple Aliphatic R |
|
|
Alanine |
|
|
Valine |
|
|
Leucine |
|
|
Isoleucine |
|
|
Proline |
|
|
-OH containing R |
|
|
Serine |
|
|
Threonine |
|
|
-SH containing R |
|
|
Cysteine |
|
|
Methionine |
|
|
-CONH2 containing R |
|
|
Glutamine |
|
|
Asparagine |
|
|
Aromatic group containing R |
|
|
Tryptophan |
|
|
Tyrosine |
|
|
Phenylalanine |
|
|
COO- group in R |
|
|
Aspartate (Aspartic Acid) |
|
|
Glutamate (Glutamic Acid) |
|
|
N group in R |
|
|
Lysine |
|
|
Arginine |
|
|
Histidine |
|
Peptide bond: the road to polypeptide formation
Now that we are familiarized with the individual building blocks (amino acid residues) of proteins, let us understand how amino acids get joined to each other to form a protein.
As depicted in Figure 2, two amino acids are in close proximity to each other and the functional groups readily react.
Whenever the carboxylic acid functional group of amino acid 1 (represented with side chain R1) is near the amino group of the second amino acid (represented with side chain R2), these two moieties react. The -COOH group of one amino acid loses an OH and the -NH2 group from the other amino acid loses a H, which combine to form a water (H2O) molecule byproduct.
Meanwhile, the two amino acids participating in the reaction gets joined via a -CO-NH- bond between the carboxy terminus of one amino acid and the amino terminus of the second amino acid. This linkage is called the ‘peptide bond’.
Figure 2. Illustrates the peptide bond formation between amino acids.
This new molecule (two amino acids joined to each other with a peptide bond) is a ‘peptide’.
At one end of this molecule is a free carboxyl group. At the other end is a free amino group.
When two amino acids are joined, the corresponding peptide bond is termed as dipeptide (‘di’=two). When a third amino acid participates and three are joined together, it now becomes a tripeptide (‘tri’=three). As the length increases to four amino acids, the resultant product is consequently a tetrapeptide (‘tetra’=four) and so on.
- Two amino acids – Dipeptide
- Three amino acids – Tripeptide
- Four amino acids – Tetrapeptide
- Five amino acids – Pentapeptide
- Six amino acids – Hexapeptide
- Seven amino acids – Heptapeptide
When the number of amino acids linked together is 2-20, it can also be called an ‘oligopeptide’.
However, as with most common proteins, the number of constituent amino acids is way beyond twenty. In such cases, the term used is ‘polypeptide’ (‘poly’=many).
The important thing to note is that irrespective of whether the number of amino acids is as low as 2 or as high as innumerable, there will always be a free carboxyl group at one end and a free amino group at the other end of the molecule.
The end containing the carboxyl group is termed as “C terminus”: C from ‘Carboxyl’ and ‘terminus’ means ‘end’.
The opposite end with a free amino group is called “N terminus”. ‘N’ here signifies the N-atom of the terminal amino group.
Thus, every polypeptide has a C and a N terminus.
Most importantly, all proteins are polypeptides, in their most simplistic terminology.
How does the polypeptide chain fold into higher levels of protein structure?
The most basic or ‘primary’ structure of a protein is its sequence of amino acids forming the polypeptide chain.
To understand the next level of complexity in the structure of proteins, let us again get back to high school chemistry and refresh our memories on Hydrogen bonds.
In a polypeptide backbone, there will be innumerable carboxyl oxygen atoms and hydrogen atoms from the amino groups. Hydrogen bonds forms between them in close proximity. As a result, in local segments of the polypeptide chain, three dimensional structural patterns develop. This represents the secondary structure of proteins.
Two secondary structures most commonly seen in proteins are alpha helix and beta sheet. A schematic representation of an alpha helix is depicted in Figure 3.
Figure 3. Representation of an alpha-helix
The secondary structural features in proteins pave the way for the next level of protein architecture - the tertiary structure. This is the final three-dimensional structural organization in which a single protein exists in its biological niche, like the cell cytoplasm for example.
The amino and carboxy functional groups of the amino acids are sequentially bonded to each other such that only a terminal carboxy and a terminal amino group are left free. However, the side chains of constituent amino acids in a protein are free to interact in a variety of ways owing to their specific chemical natures.
For example, consider the sulfur atoms in cysteines. These can form disulfide bridges between two cysteine residues in a protein.
Other such type of interactions between amino acid side chains in the polypeptide backbone drives formation of the protein tertiary structure.
Figure 4. Protein folding. Amino acids are represented by the letter ‘A.'
Often the secondary structural elements facilitate the polypeptide adopting its tertiary architecture. Let us look at one very common example.
Alpha helices and beta sheets form in a way that they have certain specific regions which are hydrophobic and others hydrophilic. This happens because amino acids may have both non-polar (such as aliphatic) as well as polar (such as carboxyl groups) moieties. Just to recall, non-polar molecules are hydrophobic while polar ones are hydrophilic
Once this type of secondary structural organization happens, the architecture is adopted such that the hydrophobic regions of the protein are buried inside, while the hydrophilic regions face the outward environment such as the cell cytoplasm which is rich in water.
Some proteins, hemoglobin for example, are made up of more than one polypeptide chain. The intricate and precise architecture of how these multiple polypeptides (each of them having their own structural organizations up to tertiary levels) are structurally organized determines the quaternary structure of a protein.
In real physiological circumstances, proteins are often found in a complex with metals (think about iron in hemoglobin) or other biomolecules such as nucleic acids (chromosomes – complex of DNA and proteins). These kinds of structural organizations also qualify as quaternary.
.
References
- Alberts B et al. (2002). The shape and structure of proteins. Molecular biology of the cell.
- Sun et al. (2004). Overview of protein structural and functional folds. Curr Protoc Protein Sci. 35(1):1711-171189
- Rayment. (2003). Protein structure. Encyclopedia of physical science and technology. 191-218
