🔬biological chemistry i review
3.3 Secondary, tertiary, and quaternary protein structures
Last Updated on August 7, 2024
Proteins are like intricate origami sculptures, folding into complex shapes. Secondary structures, like alpha helices and beta sheets, form the basic folds. These are held together by hydrogen bonds, creating stable local structures within the protein.
Tertiary and quaternary structures add layers of complexity. Tertiary structure involves the overall 3D shape, stabilized by various interactions. Quaternary structure occurs when multiple protein chains come together, forming functional complexes essential for life.
Secondary Structure Elements
Alpha Helix and Beta Sheet Structures
Top images from around the web for Alpha Helix and Beta Sheet Structures
.png&w=828&q=75)
Alpha helix - Wikipedia View original
Is this image relevant?
Proteins | Microbiology View original
Is this image relevant?
Proteins | Biology for Majors I View original
Is this image relevant?
Alpha helix - Wikipedia View original
Is this image relevant?
Proteins | Microbiology View original
Is this image relevant?
1 of 3
Top images from around the web for Alpha Helix and Beta Sheet Structures
Alpha helix - Wikipedia View original
Is this image relevant?
Proteins | Microbiology View original
Is this image relevant?
Proteins | Biology for Majors I View original
Is this image relevant?
Alpha helix - Wikipedia View original
Is this image relevant?
Proteins | Microbiology View original
Is this image relevant?
1 of 3
- Secondary structure refers to the local three-dimensional structure of a protein segment formed by hydrogen bonding between amino acid residues
- Alpha helix is a common secondary structure element where the polypeptide chain coils into a right-handed spiral stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amino hydrogen of another amino acid located four residues away (i+4 residue)
- Beta sheet is another common secondary structure element formed by two or more extended polypeptide chains (beta strands) that lie side-by-side and are held together by hydrogen bonds between the carbonyl oxygen of one amino acid and the amino hydrogen of another amino acid on an adjacent strand
- Hydrogen bonding plays a crucial role in stabilizing secondary structures by forming non-covalent interactions between the carbonyl oxygen and amino hydrogen of the peptide backbone
Importance of Hydrogen Bonding
- Hydrogen bonds are relatively weak interactions compared to covalent bonds but their cumulative effect contributes significantly to the stability of secondary structures
- The regular pattern of hydrogen bonding in alpha helices and beta sheets allows for the formation of compact and stable local structures within a protein
- Disruption of hydrogen bonds can lead to the destabilization and unfolding of secondary structure elements affecting the overall structure and function of a protein
Tertiary Structure Interactions
Disulfide Bonds and Hydrophobic Interactions
- Tertiary structure refers to the three-dimensional arrangement of all the amino acid residues in a polypeptide chain including the secondary structure elements and other interactions that stabilize the overall fold
- Disulfide bonds are covalent linkages formed between the sulfhydryl groups (-SH) of two cysteine residues in a protein contributing to the stability of the tertiary structure (insulin)
- Hydrophobic interactions occur between nonpolar amino acid side chains that cluster together in the interior of a protein away from the aqueous environment minimizing their contact with water molecules (globular proteins)
Ionic Interactions and Their Contributions
- Ionic interactions also known as salt bridges are attractive forces between oppositely charged amino acid side chains (lysine and glutamate) that help stabilize the tertiary structure
- The combination of various non-covalent interactions including hydrogen bonds hydrophobic interactions and ionic interactions collectively contribute to the overall stability and unique three-dimensional shape of a protein
- The tertiary structure of a protein is critical for its biological function as it determines the positioning of functional groups and binding sites necessary for catalytic activity ligand binding and protein-protein interactions
Quaternary Structure and Folding
Subunits and Their Assembly
- Quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) that associate to form a functional protein complex
- Subunits are individual polypeptide chains that can be identical (homooligomers) or different (heterooligomers) and assemble through non-covalent interactions to form the quaternary structure (hemoglobin)
- The assembly of subunits into a quaternary structure can confer several advantages such as increased stability regulated activity and the formation of cooperative binding sites
Protein Folding and Its Importance
- Protein folding is the process by which a polypeptide chain acquires its native three-dimensional structure through the formation of secondary tertiary and quaternary structures
- Proper folding is crucial for a protein to attain its functional state as misfolded proteins can lead to aggregation and the formation of insoluble deposits associated with various diseases (Alzheimer's disease)
- Chaperone proteins assist in the folding process by preventing aggregation and guiding the polypeptide chain towards its native conformation
- The folding process is driven by the minimization of free energy as the protein reaches its most thermodynamically stable state under physiological conditions
Key Terms to Review (18)
X-ray crystallography: X-ray crystallography is a powerful technique used to determine the atomic and molecular structure of a crystal by diffracting X-ray beams through the crystal. This method provides detailed information about the arrangement of atoms in proteins and other biological molecules, revealing essential insights into their secondary, tertiary, and quaternary structures, as well as their classification and functional diversity.
Prion: A prion is an infectious protein that can cause neurodegenerative diseases by inducing abnormal folding of normal cellular proteins, primarily in the brain. Unlike conventional pathogens, prions lack nucleic acids and propagate by converting healthy proteins into misfolded forms. This abnormal protein conformation disrupts normal cellular functions and leads to tissue damage.
Myoglobin: Myoglobin is a protein found in muscle tissue that binds oxygen, allowing for oxygen storage and transport within muscles. This globular protein consists of a single polypeptide chain and a heme group, which contains an iron atom capable of binding oxygen. Myoglobin's structure enables it to efficiently store oxygen in muscle cells, particularly during intense physical activity when oxygen demand increases.
Amyloidosis: Amyloidosis is a group of diseases characterized by the abnormal deposition of amyloid proteins in tissues and organs, leading to dysfunction and damage. This misfolding of proteins often relates to alterations in secondary, tertiary, and quaternary protein structures, which can trigger conformational changes that result in amyloid fibril formation. Understanding amyloidosis requires insight into how these structural abnormalities disrupt normal protein dynamics and lead to disease states.
Enzyme active site: The enzyme active site is a specific region on an enzyme where substrate molecules bind and undergo a chemical reaction. This site is crucial for the enzyme's functionality and is intricately shaped to complement the substrate, allowing for a precise interaction that facilitates the conversion of substrates into products. The structure and properties of the active site are influenced by the enzyme's secondary, tertiary, and quaternary protein structures, which determine the overall folding and stability of the enzyme.
Denaturation: Denaturation is the process in which proteins lose their native structure and function due to the disruption of non-covalent interactions and the unfolding of their secondary, tertiary, or quaternary structures. This alteration can occur due to various factors such as temperature changes, pH fluctuations, or exposure to chemicals. The loss of structure directly affects a protein's ability to perform its biological functions, leading to potential implications in protein classification, stability, and even nucleic acid organization.
Binding affinity: Binding affinity refers to the strength of the interaction between a molecule, such as a ligand, and its target, typically a protein or receptor. A high binding affinity means that the ligand binds tightly to the target, while a low binding affinity indicates weaker interactions. This concept is crucial for understanding how proteins adopt their secondary, tertiary, and quaternary structures, as well as how they interact with each other to form complexes that carry out various biological functions.
Protein conformation: Protein conformation refers to the three-dimensional shape of a protein, which is crucial for its function and activity. This shape is determined by the sequence of amino acids and the interactions between them, including hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces. Proper protein conformation is essential because it influences how proteins interact with other molecules and perform their biological roles.
Beta sheet: A beta sheet is a common secondary structure in proteins, characterized by two or more polypeptide chains lying side by side, connected by hydrogen bonds. This arrangement creates a sheet-like structure that contributes significantly to the overall stability and shape of the protein. Beta sheets can be parallel or antiparallel, depending on the orientation of the adjacent polypeptide strands, influencing how the chains interact and ultimately affecting the protein's tertiary structure.
Alpha helix: The alpha helix is a common structural motif in proteins characterized by a right-handed coiled shape, where the backbone of the polypeptide chain forms a helical structure stabilized by hydrogen bonds. This structure is crucial for the overall stability and functionality of proteins, playing a significant role in their secondary, tertiary, and quaternary arrangements.
Quaternary Structure: Quaternary structure refers to the complex assembly of multiple polypeptide chains or subunits into a single functional protein complex. This level of structure is critical because it can significantly impact a protein's function, stability, and interactions with other molecules, demonstrating the importance of multimeric arrangements in biological systems.
Secondary Structure: Secondary structure refers to the local folding of a protein's polypeptide chain into specific shapes, primarily stabilized by hydrogen bonds between the backbone amide and carbonyl groups. This structural feature includes common patterns like alpha helices and beta sheets, which are crucial for the overall three-dimensional arrangement of proteins and influence their stability and function.
Hydrogen Bonds: Hydrogen bonds are weak attractions that occur between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom. These interactions are crucial for maintaining the structure and stability of biomolecules, influencing the folding of proteins, the formation of protein complexes, and the overall organization of nucleic acids.
Disulfide Bridges: Disulfide bridges are covalent bonds formed between the sulfur atoms of two cysteine amino acids within a protein. These bridges play a critical role in stabilizing the three-dimensional structure of proteins by linking different parts of the polypeptide chain or even different polypeptide chains together. By forming these strong bonds, disulfide bridges contribute significantly to the overall stability and integrity of proteins, impacting their secondary, tertiary, and quaternary structures.
Tertiary structure: Tertiary structure refers to the overall three-dimensional shape of a polypeptide chain, resulting from the interactions between the side chains (R groups) of amino acids. This level of structure is crucial for the protein's functionality, as it determines how proteins fold and how they interact with other molecules. Understanding tertiary structure is vital because it connects the properties of individual amino acids to the larger context of protein folding, stability, and function in biological systems.
Hemoglobin: Hemoglobin is a specialized protein found in red blood cells that binds oxygen and facilitates its transport throughout the body. This essential biomolecule plays a crucial role in cellular respiration and energy production by enabling the delivery of oxygen to tissues while also aiding in the removal of carbon dioxide, a metabolic waste product.
NMR Spectroscopy: NMR spectroscopy, or Nuclear Magnetic Resonance spectroscopy, is a powerful analytical technique used to determine the structure and dynamics of molecules by observing the magnetic properties of atomic nuclei. This method is essential for understanding the interactions and conformational states of biomolecules, making it invaluable in studying proteins, nucleic acids, and other key biomolecules in cellular processes.
Hydrophobic interactions: Hydrophobic interactions are the forces that drive non-polar molecules to aggregate in aqueous environments, minimizing their exposure to water. This phenomenon is crucial for the folding of biomolecules and plays a significant role in various biological processes, including protein structure formation and stability.