Question

(a) Describe the primary, secondary, and tertiary structures of proteins. (b) Quaternary structures of proteins arise if two or more smaller polypeptides or proteins associate with each other to make an overall much larger protein structure The association is due to the same hydrogen bonding, electrostatic, and dispersion forces we have seen before. Hemoglobin, the protein used to transport oxygen molecules in our blood, is an example of a protein that has quaternary structure. Hemoglobin is a tetramer; it is made of four smaller polypeptides, two "alphas" and two "betas." (These names do not imply anything about the number of alpha helices or beta sheets in the individual polypeptides.) What kind of experiments would provide sound evidence that hemoglobin exists as a tetramer and not as one enormous polypeptide chain? You may need to look into the chemical.literature to discover techniques that chemists and biochemists use to make these decisions.

Short answer

The primary structure of proteins refers to the sequence of amino acids connected by peptide bonds, forming a polypeptide chain. The secondary structure involves patterns of amino acids and spatial arrangement in the polypeptide chain, primarily due to hydrogen bonding, forming structures such as alpha helices and beta sheets. The tertiary structure refers to the overall three-dimensional shape of the protein, determined by the spatial arrangement of amino acid residues and stabilized by various interactions. The quaternary structure involves the association of multiple polypeptide chains into a single protein complex, such as hemoglobin, which is composed of four smaller polypeptide chains (two alphas and two betas). To determine that hemoglobin exists as a tetramer, experiments such as gel filtration chromatography, electrophoresis under denaturing conditions, X-ray crystallography, and proteolysis with peptide mapping can be used to provide evidence of its molecular weight, distinct polypeptide chains, detailed three-dimensional structure, and peptide sequences, respectively.

Step-by-step solution

Primary Structure of Proteins

The primary structure refers to the sequence of amino acids that make up the protein. It is the simplest level of protein structure. The amino acids are connected by peptide bonds, forming a polypeptide chain. The specific sequence of amino acids in the primary structure directly affects the protein's higher-level structures and functions.

Secondary Structure of Proteins

The secondary structure involves regularly repeating patterns of amino acids and spatial arrangement of the polypeptide chain, primarily due to hydrogen bonding interactions between backbone atoms. There are two main types of secondary structures: alpha helices and beta sheets. In an alpha helix, the polypeptide chain forms a right-handed spiral, while beta sheets involve linear strands of amino acids that are arranged side by side and are linked by hydrogen bonds.

Tertiary Structure of Proteins

The tertiary structure refers to the overall three-dimensional shape of the protein. This structure is determined by the spatial arrangement of amino acid residues that are far apart in sequence but form interactions in the folded protein. The folding and stabilization of tertiary structure are mainly due to hydrophobic interactions, hydrogen bonding, ionic interactions, and disulfide bridges between cysteine residues.

Quaternary Structure of Proteins

The quaternary structure involves the association and assembly of multiple polypeptide chains into a single functional protein complex. These polypeptide chains, or subunits, are held together by non-covalent interactions, including hydrogen bonding, ionic forces, and dispersion forces. Hemoglobin is an example of a protein with a quaternary structure, composed of four smaller polypeptide chains (two alphas and two betas).

Experiments to Determine Hemoglobin's Tetrameric Structure

The following experiments can provide evidence that hemoglobin exists as a tetramer and not a single large polypeptide chain: 1. Gel filtration chromatography: Size-exclusion chromatography can be used to separate protein molecules based on their size and shape. By comparing the elution profile of hemoglobin against protein standards with known molecular weights, we can estimate hemoglobin's molecular weight, which should correspond to a tetramer. 2. Electrophoresis under denaturing conditions: Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) can separate polypeptide chains based on their molecular weight. By analyzing the bands on the gel, we can identify the presence of four distinct polypeptide chains (two alphas and two betas). 3. X-ray crystallography: This technique provides a detailed three-dimensional structure of a protein in its crystalline form. By examining the high-resolution structure of hemoglobin, we can determine that it is composed of four separate polypeptide chains. 4. Proteolysis and peptide mapping: Proteolytic enzymes can be used to cleave hemoglobin into smaller fragments. The resulting peptide fragments can be analyzed by techniques such as mass spectrometry to define their amino acid sequences. By comparing these peptide sequences to the known amino acid sequences of the alpha and beta chains of hemoglobin, we can confirm hemoglobin's tetrameric structure.

Key concepts

Primary Structure

The primary structure of a protein is its most foundational level. It refers to the specific sequence of amino acids that are linked together like beads on a string by peptide bonds. These amino acids are ordered in a unique sequence that is crucial, because even a single change in the sequence can significantly affect a protein's higher-level structures and its eventual function.

The process by which proteins are synthesized is directed by the genetic code in the DNA. It is this sequence that determines how the protein will eventually fold and what tasks it can perform in the body. Correct folding is essential for the protein's biological activity. When examining or discussing proteins, the primary structure is often denoted as a simple linear string of letters, each representing an amino acid.

Secondary Structure

As we move from the primary to the secondary structure of proteins, we start to explore patterns in the folding of the protein chain. Secondary structures arise from the way hydrogen bonds form between the backbone atoms in the chain.

Two major types of secondary structures are the alpha helix and the beta sheet. In the alpha helix, the chain twists into a helical shape stabilized by hydrogen bonds every four amino acids. This creates a tightly coiled "spring-like" structure.

• Alpha Helices: Right-handed coils that look like a corkscrew.
• Beta Sheets: These are formed when polypeptide chains lie alongside each other in such a way that they are able to form hydrogen bonds with each other, creating a pleated sheet.

These structures are foundational to a protein’s overall shape and function.

Tertiary Structure

The tertiary structure is where proteins get their overall three-dimensional shape. This level results from interactions among the side chains (R groups) of the amino acids.

Key interactions include:

• Hydrophobic Interactions: Non-polar side chains tend to cluster together away from water.
• Hydrogen Bonds: These bonds occur between polar side chains.
• Ionic Bonds: Charged side chains can bond together.
• Disulfide Bridges: Covalent linkages between sulfur atoms in cysteine residues add stability.

Each protein has a unique tertiary structure, which determines its functionality, as the specific shape allows the protein to interact precisely with other molecules.

Quaternary Structure

The quaternary structure is the arrangement of multiple polypeptide chains into a single functional complex. This is the structure seen in proteins composed of more than one peptide chain or "subunit."

These subunits usually assemble through non-covalent interactions like hydrogen bonds and ionic or hydrophobic interactions.

Hemoglobin serves as a classic example of quaternary structure. It comprises four subunits: two alpha chains and two beta chains. Each subunit can bind an oxygen molecule, allowing hemoglobin to carry oxygen efficiently through the bloodstream.

Hemoglobin

Hemoglobin is a well-known protein with a distinctive quaternary structure. Its primary function is to transport oxygen from the lungs to tissues throughout the body.

As a tetramer, hemoglobin is composed of four polypeptide chains, giving it a robust structure necessary for its oxygen-carrying role. Each subunit in hemoglobin can bind to one oxygen molecule, meaning a single hemoglobin protein can carry up to four oxygen molecules at a time.

The structure of hemoglobin changes slightly when it binds oxygen, a property known as cooperativity, which increases its efficiency in oxygen uptake and release, making it a pivotal protein in respiration.

Biochemical Techniques

Biochemical techniques are essential to study and verify the structure of proteins like hemoglobin. Techniques that are often employed include:

• Gel Filtration Chromatography: Used to determine the size and mass of protein complexes by separating them based on size as they travel through a gel matrix.
• Electrophoresis: SDS-PAGE is commonly used to separate proteins based on their molecular weight, helping identify distinct subunits.
• X-ray Crystallography: This method visualizes the precise three-dimensional structure of proteins by analyzing the diffraction pattern of X-rays passing through protein crystals.
• Mass Spectrometry: Used to analyze complex peptide mixtures, allowing scientists to determine the sequence of amino acids in proteins.

These techniques play a crucial role in understanding protein structure and function, enabling discoveries that impact fields ranging from medicine to biochemistry.