26.9 Protein Structure
3 min read•may 7, 2024
Proteins are the workhorses of life, performing countless functions in our bodies. Their structure is key to their function, with four levels of organization: primary, secondary, tertiary, and quaternary. Each level builds upon the previous, creating complex 3D shapes.
Understanding protein structure is crucial for grasping how they work and what happens when things go wrong. From to beta sheets, various forces hold proteins together. When these structures break down, it can lead to serious health issues.
Protein Structure
Four levels of protein structure
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- Unique sequence of linked together by
- Determined by the gene that codes for the protein
- Amino acid sequence is specific to each protein (, )
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- Local patterns of the stabilized by
- Occurs between the backbone atoms of nearby amino acids
- Two main types are alpha helices and (, )
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- Three-dimensional shape of the entire polypeptide chain
- Stabilized by various interactions between amino acid
- Determines the overall structure and function of the protein (, )
- May consist of multiple , which are distinct functional or structural units
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- Arrangement of multiple folded polypeptide chains into a larger protein complex
- Held together by the same types of interactions as
- Not all proteins have (hemoglobin, )
Alpha helices vs beta-pleated sheets
- Alpha helices
- Spiral conformation of the polypeptide chain that coils to the right
- Stabilized by hydrogen bonds between the carbonyl oxygen and amino hydrogen of amino acids spaced 4 residues apart
- Each turn of the helix contains 3.6 amino acid residues with a rise of 1.5 Å per residue
- Found in () and ( in hair)
- Beta-pleated sheets
- Extended conformation of the polypeptide chain with amino acids spaced 3.5 Å apart
- Stabilized by hydrogen bonds between the backbone atoms of adjacent polypeptide strands
- Can be parallel with N-termini aligned or antiparallel with alternating N- and C-termini
- Found in fibrous proteins () and the core of many globular proteins ()
Forces in tertiary structure
- Hydrogen bonds form between side chains and backbone atoms
- created by the oxidation of residues (insulin)
- occur between positively and negatively charged side chains ()
- between nonpolar side chains that avoid water (protein cores)
- arise from close packing of atoms
- causes loss of tertiary structure by disrupting the stabilizing forces
- Changes in temperature (heating)
- Changes in pH (acid or base)
- Exposure to chemicals (urea, detergents)
- Denaturation often results in loss of protein function (enzyme inactivation)
- Some proteins can refold to their native state when denaturing conditions are removed ()
Protein Folding and Misfolding
- Protein folding is the process by which a polypeptide chain assumes its functional three-dimensional structure
- are proteins that assist in the folding process, preventing misfolding and aggregation
- Misfolded proteins can form aggregates, leading to various diseases
- are misfolded proteins that can induce misfolding in other proteins, causing neurodegenerative disorders
Key Terms to Review (46)
Alpha Helices: Alpha helices are a common secondary structure found in proteins, where the polypeptide chain coils into a spiral shape stabilized by hydrogen bonds. This structure is crucial for the overall three-dimensional folding and function of many proteins.
Alpha-Keratin: Alpha-keratin is a structural protein found in the cytoskeleton of epithelial cells, particularly in the hair, nails, and outer layer of the skin. It is a key component of the intermediate filaments that provide strength and flexibility to these tissues.
Amino Acids: Amino acids are the fundamental building blocks of proteins, which are essential macromolecules that perform a vast array of functions in living organisms. These organic compounds contain an amino group (-NH2), a carboxyl group (-COOH), and a side chain (R-group) that varies among the different types of amino acids. The unique combination and sequence of amino acids give rise to the diverse structures and functions of proteins.
Antibodies: Antibodies are specialized proteins produced by the immune system to recognize and neutralize foreign substances, such as bacteria, viruses, and toxins, that enter the body. They play a crucial role in the body's defense against infection and disease.
Beta-Pleated Sheets: Beta-pleated sheets are a secondary structure of proteins, characterized by a zigzag pattern of hydrogen-bonded polypeptide chains. This structure is formed when the polypeptide backbone folds in a way that maximizes the number of hydrogen bonds between adjacent strands, creating a stable and rigid structure.
Chaperones: Chaperones are proteins that assist in the proper folding and assembly of other proteins within cells. They play a crucial role in ensuring that proteins attain their correct three-dimensional structure, which is essential for their proper function and stability.
Collagen: Collagen is the most abundant protein in the human body, found in the connective tissues of skin, bones, cartilage, tendons, and ligaments. It provides structural support and strength to these tissues, playing a crucial role in maintaining the integrity and function of the body's systems.
Cysteine: Cysteine is a sulfur-containing amino acid that plays a crucial role in the structure and function of proteins. It is one of the 20 standard amino acids found in proteins and is known for its unique chemical properties that contribute to various aspects of biochemistry covered in this chapter.
Denaturation: Denaturation is a process that occurs when the native structure of a protein or nucleic acid is disrupted, leading to the loss of its biological function. This structural change can be induced by various factors, such as temperature, pH, or the presence of certain chemicals.
Denatured: In the context of proteins, denaturing refers to the process whereby a protein loses its native 3D structure due to external factors such as changes in pH, temperature, or chemical exposure. This alteration can lead to the loss of biological activity or function.
Disulfide Bridges: Disulfide bridges are covalent bonds formed between two sulfur atoms from the side chains of two cysteine amino acid residues within a protein structure. These bridges help stabilize and maintain the three-dimensional shape of proteins, contributing to their overall structural integrity.
DNA Polymerase: DNA polymerase is a crucial enzyme responsible for the replication and repair of DNA molecules. It plays a vital role in ensuring the accurate duplication of genetic information during cell division, as well as the maintenance of genomic integrity through DNA repair processes.
Enzymes: Enzymes are biological catalysts that speed up chemical reactions in living organisms without being consumed in the process. They play a crucial role in facilitating various biochemical reactions necessary for life, including those involved in metabolism and DNA replication.
Enzymes: Enzymes are biological catalysts that accelerate chemical reactions in living organisms. They are essential for a wide range of processes, from digestion to energy production, and play a crucial role in maintaining the delicate balance of biochemical reactions that sustain life.
Fibrous proteins: Fibrous proteins are a class of proteins that are elongated, insoluble, and structural in nature, characterized by a repetitive amino acid sequence that forms rigid, rod-like structures. They play critical roles in the structure and support of cells and tissues.
Folding: Folding refers to the process by which a protein structure assumes its functional three-dimensional shape from a linear sequence of amino acids. This complex process is critical for the protein to carry out its intended biological activities within the cell.
Globular proteins: Globular proteins are spherical, water-soluble proteins with a compact and densely folded structure. They play a wide variety of roles in biological processes, including as enzymes, hormones, and antibodies.
Hemoglobin: Hemoglobin is the iron-rich protein found in red blood cells that is responsible for transporting oxygen from the lungs to the body's tissues and carbon dioxide from the tissues back to the lungs. It is a crucial component in the processes of protein structure and DNA sequencing.
Hydrogen Bonds: Hydrogen bonds are a type of noncovalent interaction that occurs when a hydrogen atom covalently bonded to a highly electronegative element, such as nitrogen, oxygen, or fluorine, is attracted to another nearby highly electronegative element. This attractive force is significantly stronger than a typical dipole-dipole interaction and plays a crucial role in the structure and properties of various molecules and biological systems.
Hydrophobic Interactions: Hydrophobic interactions are non-covalent attractive forces that arise between non-polar, hydrophobic regions or molecules in an aqueous environment. These interactions are driven by the tendency of water molecules to minimize contact with non-polar substances, resulting in the clustering of hydrophobic groups to exclude water and maximize entropy.
Immunoglobulins: Immunoglobulins, also known as antibodies, are large, Y-shaped glycoproteins produced by plasma B cells that play a crucial role in the adaptive immune response. They are capable of recognizing and binding to specific foreign antigens, initiating a series of immune reactions to neutralize or eliminate the threat.
Insulin: Insulin is a hormone produced by the pancreas that regulates blood sugar levels by facilitating the uptake and utilization of glucose by cells. It is a critical component in the metabolic processes of protein structure, DNA sequencing, fatty acid biosynthesis, and carbohydrate metabolism through gluconeogenesis.
Ionic Interactions: Ionic interactions are electrostatic attractions between oppositely charged ions or molecules. These interactions play a crucial role in the structure and function of proteins, which are the fundamental building blocks of living organisms.
Myoglobin: Myoglobin is an oxygen-binding protein found in the muscle cells of vertebrates, including humans. It plays a crucial role in the storage and transport of oxygen within muscle tissues, enabling them to function efficiently during physical activity and periods of increased oxygen demand.
Peptide Bonds: A peptide bond is a covalent chemical bond formed between the carboxyl group of one amino acid and the amino group of another amino acid, resulting in the creation of a polypeptide chain. These bonds are central to the structure and function of proteins, which are essential macromolecules in biological systems.
Polypeptide Chain: A polypeptide chain is a linear sequence of amino acids covalently linked together by peptide bonds, forming the fundamental structural unit of proteins. This chain serves as the backbone upon which the complex three-dimensional structure of proteins is built.
Primary structure: The primary structure of a protein is the specific sequence of amino acids in a polypeptide chain, determined by covalent peptide bonds. It dictates the protein's overall shape and function.
Primary Structure: The primary structure of a protein refers to the linear sequence of amino acids that make up the polypeptide chain. It is the most fundamental level of protein structure and forms the foundation for the higher-order structures that give proteins their unique functional properties.
Prions: Prions are infectious, misfolded proteins that can induce normal, properly folded proteins to misfold and aggregate, leading to progressive neurodegeneration. They are the causative agents of a group of rare and fatal neurodegenerative disorders known as transmissible spongiform encephalopathies (TSEs) or prion diseases.
Protein Domains: Protein domains are distinct, three-dimensional structural and functional units within a larger protein molecule. These modular segments of a protein often fold independently and can be found in a variety of different proteins, performing specific tasks or interacting with other molecules.
Quaternary structure: The quaternary structure of a protein describes the arrangement and interaction of multiple polypeptide chains (subunits) in a multi-subunit complex. It is the highest level of protein structure, determining the overall 3D arrangement of subunits that are individually folded into their tertiary structures.
Quaternary Structure: Quaternary structure refers to the three-dimensional arrangement of multiple polypeptide chains or subunits that come together to form a functional protein. It is the highest level of protein structure and is crucial for the proper functioning of many complex proteins.
Renaturation: Renaturation is the process by which a denatured protein regains its native three-dimensional structure and biological activity. This occurs when the disrupted non-covalent interactions that maintain the protein's folded state are restored, allowing the polypeptide chain to refold into its original conformation.
Salt bridge: A salt bridge in the context of protein structure refers to a bond formed between oppositely charged side chains of amino acids, stabilizing the protein's tertiary or quaternary structure. These electrostatic interactions are crucial for maintaining the specific three-dimensional shape necessary for the protein's function.
Salt Bridges: Salt bridges are non-covalent interactions that form between oppositely charged functional groups, typically between the positively charged amino group of a lysine or arginine residue and the negatively charged carboxylate group of an aspartic acid or glutamic acid residue. These interactions help stabilize the three-dimensional structure of proteins.
Secondary structure: In the context of protein structure, the secondary structure refers to the specific geometric shape or conformation that segments of a protein's polypeptide chain assume, primarily as a result of hydrogen bonding. These shapes include alpha-helices and beta-pleated sheets, which are fundamental to the protein's overall structure and function.
Secondary Structure: Secondary structure refers to the local three-dimensional structure of proteins, specifically the regular, recurring patterns formed by hydrogen bonding between the backbone atoms of the polypeptide chain. It is one of the key levels of protein structure that determines the overall shape and function of the protein molecule.
Side Chains: Side chains are the branching structures attached to the main backbone of amino acid residues that make up proteins. These side chains contribute to the unique chemical and physical properties of each amino acid, influencing the overall structure and function of the protein.
Silk: Silk is a natural protein fiber produced by certain insect larvae, primarily the silkworm. It is renowned for its lustrous, smooth, and durable properties, making it a highly valued material in the textile industry and beyond.
Silk Fibroin: Silk fibroin is a natural protein fiber produced by silkworms, known for its exceptional strength, luster, and versatility. It is the main structural component of silk, making up the core of silk threads spun by silkworms to create their cocoons.
Tertiary structure: The tertiary structure of a protein refers to the overall three-dimensional shape formed by the folding and coiling of its peptide chain, stabilized by various interactions among its amino acids. This structure is crucial for the protein's function and specificity.
Tertiary Structure: Tertiary structure refers to the three-dimensional folding and spatial arrangement of a protein molecule. It is the highest level of protein structure and is crucial for determining a protein's overall shape and function.
Van der Waals forces: van der Waals forces are weak intermolecular attractive forces that arise between neutral molecules. These forces, while individually weak, can collectively contribute to the physical and chemical properties of substances.
α Helix: An α Helix is a common structural motif in proteins, characterized by a right-handed coil where each amino acid corresponds to a 360-degree turn every 3.6 residues. The structure is stabilized by hydrogen bonds between the backbone atoms of the amino acids.
α-Amino acids: α-Amino acids are the building blocks of proteins, consisting of a central carbon atom (the α-carbon) to which an amino group, a carboxyl group, a hydrogen atom, and a distinctive side chain (R group) are attached. They play a crucial role in biochemistry as they polymerize to form peptides and proteins.
β-Pleated sheet: A β-pleated sheet is a type of secondary structure found in proteins, characterized by rows of amino acids folded into a zigzag pattern that are then aligned side by side and held together by hydrogen bonds. This structure lends stability and rigidity to the overall protein shape.