3. Protein

Proteins

Proteins are complex molecules found in all living things and are essential for life. They are built from chains of amino acids linked together by a type of chemical bond called peptide bonds. The order and type of amino acids determine a protein’s unique shape and function.

Proteins have an incredibly diverse function in the body; some examples include:

• Enzymes: They act as biological catalysts, speeding up metabolic reactions throughout the body.
• Structural support: Provide structure and support to tissues, like collagen in skin and bones.
• Transport: Facilitate the movement of molecules across cell membranes and throughout the body.
• Immune function: antibodies are proteins that help defend the body against pathogens.
• Hormones: Some hormones, like insulin, are proteins that regulate various physiological processes.

Amino acids

Amino acids are made up of a carbon atom in the middle that is connected to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a side chain (R group) that is different for each amino acid.

There are 20 different standard amino acids commonly found in living organisms. The specific properties of the R group determine the amino acid’s function and it’s role in protein formation. 

Primary structure

Two amino acids can be connected via a covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid. This covalent bond is a so-called peptide bond. Further peptide bonds (to the third and fourth and so on) eventually form a chain of amino acids, which is the basic structure of the protein.

This protein's basic configuration, which consists of a series of amino acids connected by peptide bonds, is called “primary structure.”

Secondary structure

Primary structure only explains a chain of amino acids. However, the real proteins in the cell have a 3-dimentional conformation. The amino acid chains must be folded in a certain way—not at random—in order to accomplish this. This specificity of folding is ensured by carrying out folding in multiple steps. 

The secondary structure is the most basic three-dimensional structure of a protein. This structure is created through a hydrogen bond between the carbonyl oxygen (C=O) of one amino acid and the amino group (N-H) of another amino acid. As a result of this interaction, the polypeptide chains will be shrunk and then coiled or folded. If coiling, the structure is called alpha-helix structure, and if folded, it is called beta-sheet structure.

You may notice that the functional groups involved in the hydrogen bond are universal for all parts of the polypeptides because those parts are included in the peptide bonds, which are the common structure for all amino acids in a polypeptide chain. Due to this, the secondary structures are regular and repeating arrangements in the whole structure of the protein, and we can find alpha-helix structures and beta-sheet structures in most of the proteins repeatedly. 

The secondary structure of a protein plays a crucial role in its function. For example, the alpha helix is often found in proteins that need to bind to other molecules, while beta sheets are common in structural proteins that provide rigidity.

The secondary structure of a molecule is dictated by its primary structure, which refers to the specific arrangement of amino acids in the sequence. This is because certain amino acid sequences have a higher propensity to fold into specific secondary structures.

Tertiary structure

After the secondary structure is formed, the tertiary structure will be formed. The tertiary structure of a protein refers to the complete three-dimensinoal shape of a single polypeptide chain, including all its folds and arrangements. It is the most complex level of protein structure and is critical for its function.

Unlike the secondary structure, which pertains to the hydrogen bonds within the polypeptide's backbones, the tertiary structure considers the interactions among the side chains (R groups) of amino acids. Additionally, there are some variations in the type of interaction. 

Types of interaction

• Hydrophobic interactions: nonpolar (hydrophobic) side chains tend to cluster together towards the interior of the protein away from water, a principle known as the hydrophobic effect. Due to this effect, hydrophobic parts of the polypeptide are attracted to each other.
• Hydrogen bonding: This can occur between side chains with suitable functional groups, further stabilizing the folded structure.
• Ionic bridge: interactions between oppositely charged side chains (e.g., positively charged lysine and negatively charged glutamate) can contribute to folding.
• Disulfide bridges: Covalent bonds formed between the sulfur atoms of cysteine side chains can create a more rigid structure.

The tertiary structure is essential for a protein’s function. It determines how the protein interacts with other molecules, such as substrates, enzymes, or regulatory molecules. Specific regions of the folded protein may form pockets or grooves that serve as binding sites for other molecules.

Quaternary structure

The quaternary structure of a protein refers to the arrangement and interaction of multiple polypeptide chains that come together to form a functional protein complex. Not all proteins have a quaternary structure; many proteins function perfectly well with a single polypeptide chain folded into their tertiary structure.

Proteins with quaternary structure consist of two or more polypeptide chains, also called subunits, that associate with each other. These subunits can be identical or different. The interactions between subunits are primarily non-covalent bonds such as hydrogen bonds, ionic bonds, and hydrophobic interactions. In some cases, disulfide bridges might also play a role. Disulfide bridges are formed between two thiol groups in different amino acid side chains. The only amino acid that has a thiol group is cysteine. (So, the disulfide bridge can be formed between two cysteines.)

The quaternary structure creates a complete and often much more complex functional protein complex. The arrangement of subunits can create specific binding sites, cavities, or channels that are essential for the protein’s function. For example, hemoglobin, the oxygen-carrying protein in red blood cells, has a quaternary structure that allows it to bind to four oxygen molecules.

Denaturation

Denaturation of a protein is the process by which a protein loses its native three-dimensional structure and unfolds, rendering it unable to function properly. It’s like a carefully constructed origami figure being flattened or crumpled.

Several factors can cause protein denaturation, including:

• Heat: High temperatures can disrupt the hydrogen bonds and other weak interactions stabilizing the protein structure. Cooking an egg is a common example of heat-induced denaturation.
• pH changes: Extremely acidic or basic environments can alter the changes in amino acid side chains, disrupting the ionic interactions that contribute to protein folding.
• Organic solvents: Organic solvents like alcohol can dissolve the hydrophobic interactions that hold the protein together within its folded state.
• Heavy metals: Metal ions can bind to protein side chains, interfering with the interactions that maintain the folded structure.

Denaturation typically disrupts the protein’s structure to the point where it cannot refold back into its functional form. However, in some cases, under specific conditions, some proteins may be able to renature if the denaturing agent is removed.

Protein denaturation can have significant consequences for cells. If essential proteins lose their function, it can disrupt cellular processes and potentially lead to cell death.