Protein Structure and Denaturation Basics

Introduction to Protein Structure

Ever wondered why egg whites turn from clear to opaque when cooked? This is due to protein denaturation. Egg whites contain albumins, proteins with a specific 3D shape maintained by bonds between amino acids. Heating breaks these bonds, exposing hydrophobic amino acids. These amino acids then clump together to avoid water, forming a network that gives the egg white its new structure.

The shape of a protein is crucial to its function. To understand how proteins achieve their final shape, we need to explore the four levels of protein structure: primary, secondary, tertiary, and quaternary.

🧬 Primary Structure

The primary structure is the simplest level of protein structure and refers to the sequence of amino acids in a polypeptide chain.

For instance, the hormone insulin consists of two polypeptide chains, A and B, each with its own unique amino acid sequence. The A chain starts with glycine at the N-terminus and ends with asparagine at the C-terminus, differing from the B chain's sequence.

The sequence of a protein is dictated by the DNA of the gene that encodes it. Alterations in the gene's DNA sequence can lead to changes in the amino acid sequence of the protein, potentially affecting its overall structure and function. Even a single amino acid change can have significant consequences.

For example, sickle cell anemia results from a single amino acid change in hemoglobin, the protein that carries oxygen in the blood.

The image depicts the molecular structure of normal vs. sickle cell hemoglobin. In sickle cell anemia, glutamic acid is substituted with valine, altering the structure and function of hemoglobin.

In this condition, glutamic acid, the sixth amino acid in the hemoglobin β chain, is replaced by valine. Hemoglobin consists of two α chains and two β chains, each containing approximately 150 amino acids. The difference between normal and sickle cell hemoglobin is only two amino acids out of about 600. Individuals with only sickle cell hemoglobin experience symptoms of sickle cell anemia. The amino acid change causes hemoglobin molecules to assemble into long fibers, distorting red blood cells into crescent shapes.

The image shows a microscopic view of sickled red blood cells. These cells are irregularly shaped and can obstruct blood vessels, leading to serious health issues.

These sickled cells get stuck in blood vessels, impairing blood flow and causing health problems such as breathlessness, dizziness, headaches, and abdominal pain.

🌀 Secondary Structure

Secondary structure refers to local folded structures within a polypeptide chain, resulting from interactions between atoms of the backbone.

The most common types of secondary structures are the α helix and the β pleated sheet. Both structures are stabilized by hydrogen bonds between the carbonyl O of one amino acid and the amino H of another.

The image provides a visual representation of alpha helices and beta pleated sheets, highlighting the hydrogen bonds that stabilize these structures.

Alpha Helix

In an α helix, the carbonyl (C=O) of one amino acid forms a hydrogen bond with the amino H (N-H) of an amino acid four positions down the chain. This bonding pattern pulls the polypeptide chain into a helical shape, resembling a curled ribbon, with each turn containing 3.6 amino acids. The R groups extend outward from the α helix, allowing them to interact with other molecules.

Beta Pleated Sheet

In a β pleated sheet, two or more segments of a polypeptide chain align next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of the backbone, while the R groups extend above and below the plane of the sheet. Strands can be parallel (N- and C-termini match up) or antiparallel (N-terminus of one strand is next to the C-terminus of the other).

Certain amino acids are more likely to be found in α-helices or β pleated sheets. For example, proline is often called a "helix breaker" due to its unique R group, which creates a bend in the chain and disrupts helix formation. Amino acids with large ring structures in their R groups, such as tryptophan, tyrosine, and phenylalanine, are commonly found in β pleated sheets.

Many proteins contain both α helices and β pleated sheets, while some contain only one type of secondary structure or neither.

🧱 Tertiary Structure

The tertiary structure is the overall three-dimensional structure of a polypeptide. It is primarily determined by interactions between the R groups of the amino acids.

R group interactions that contribute to tertiary structure include:

• Hydrogen bonding

• Ionic bonding

• Dipole-dipole interactions

• London dispersion forces

Hydrophobic interactions are also crucial, where amino acids with nonpolar, hydrophobic R groups cluster together inside the protein, while hydrophilic amino acids interact with surrounding water molecules.

Disulfide bonds, which are covalent linkages between the sulfur-containing side chains of cysteines, act as molecular "safety pins," holding parts of the polypeptide together.

This image displays a protein embedded in a cell membrane, illustrating hydrophobic and hydrophilic regions as well as a disulfide bridge, all contributing to the protein's tertiary structure.

🔗 Quaternary Structure

Quaternary structure arises when multiple polypeptide chains, or subunits, come together to form a protein.

Examples include:

• Hemoglobin: Carries oxygen in the blood and consists of two α and two β subunits.

• DNA polymerase: Synthesizes new DNA strands and is composed of ten subunits.

Generally, the same types of interactions that contribute to tertiary structure (such as hydrogen bonding and London dispersion forces) also hold the subunits together in quaternary structure.

The image shows the four levels of protein structure, from the amino acid sequence (primary) to the final complex arrangement of subunits (quaternary).

🌡 Denaturation and Protein Folding

Each protein has a unique shape that is essential to it's function. If the temperature or pH of a protein's environment changes, or if it is exposed to certain chemicals, these interactions can be disrupted. When a protein loses its higher-order structure but maintains its primary sequence, it is said to be denatured. Denatured proteins are usually non-functional.

In some cases, denaturation can be reversed, allowing the protein to refold into its functional form when returned to its normal environment. However, in other cases, denaturation is permanent. Frying an egg is an example of irreversible protein denaturation, where the albumin protein in the egg white becomes opaque and solid due to heat and cannot return to its original state.

Some proteins can refold after denaturation on their own, indicating that their amino acid sequences contain all the necessary information for folding. However, not all proteins can do this, and protein folding in a cell often requires assistance from chaperone proteins (chaperonins).