Biochemistry Chapter 4: Protein Structure

Primary structure = The linear sequence of amino acids in a polypeptide chain. Secondary structure = The local three-dimensional folding of a polypeptide chain, such as α-helices and β-sheets. Tertiary structure = The overall three-dimensional shape of a single polypeptide chain. Quaternary structure = The arrangement of multiple polypeptide chains (subunits) in a protein complex.

Peptide bond = The covalent bond that links amino acids together in a polypeptide chain. Amino terminus = The end of a polypeptide chain that has a free amino group. Carboxyl terminus = The end of a polypeptide chain that has a free carboxyl group. Disulfide bond = A covalent bond that forms between two cysteine residues, linking different parts of a polypeptide chain or different polypeptide chains.

Receptor = A protein that binds to a specific molecule, triggering a cellular response. Enzyme = A protein that catalyzes a specific biochemical reaction. Structural protein = A protein that provides support and shape to cells and tissues. Hormone = A protein that acts as a chemical messenger, regulating physiological processes.

<p>The sequence of amino acids in insulin = Primary structure The α-helix in a protein = Secondary structure The three-dimensional shape of an enzyme = Tertiary structure The arrangement of subunits in hemoglobin = Quaternary structure.</p> Signup and view all the answers

<p>R-groups = Contribute to the unique properties and interactions of different amino acids. Side chains = Contribute to the overall three-dimensional shape of a protein by interacting with each other and with the environment. Polarity = Influences the solubility and interactions of amino acids within a protein. Hydrophobicity = Drives the folding of proteins into compact structures, often with hydrophobic residues buried in the interior.</p> Signup and view all the answers

<p>Hydrogen bonding = Interactions between polar groups, contributing to the stability of secondary structures and tertiary structure. Hydrophobic interactions = Interactions between nonpolar groups, driving hydrophobic residues inwards in protein folding. Ionic interactions = Electrostatic attractions between charged groups, contributing to protein stability. Van der Waals interactions = Weak, short-range interactions between atoms, contributing to the overall shape and packing of proteins.</p> Signup and view all the answers

<p>Temperature = Can disrupt weak interactions and cause protein denaturation. pH = Can alter the ionization state of amino acid side chains, affecting protein stability. Solvent = Can affect the solubility and stability of proteins through interactions with amino acid residues. Mutations = Can alter the sequence of amino acids, potentially affecting protein structure and function.</p> Signup and view all the answers

<p>Formation = Results from the oxidation of two cysteine residues. Location = Can occur between different parts of a polypeptide chain or different polypeptide chains. Role = Contribute to protein stability and structure by linking different regions together. Effect = Can affect protein conformation and function by stabilizing specific structures.</p> Signup and view all the answers

<p>α-Helix = A helical structure stabilized by hydrogen bonds between backbone atoms. β-Sheet = A sheet-like structure formed by hydrogen bonding between polypeptide chains. Coiled Coil = Two α-helices intertwined to form a left-handed superhelix. Triple Helix = Three intertwined helical polypeptide chains forming a superhelical cable.</p> Signup and view all the answers

<p>Planarity = Due to partial double bond character Trans configuration = Minimizes steric clashes between side chains Cis configuration = Rarely observed due to steric hindrance Proline = Disrupts helix formation due to its rigid ring structure</p> Signup and view all the answers

<p>Hydrogen Bonds = Interactions between polar groups, involving a hydrogen atom shared between two electronegative atoms. Ionic Bonds = Interactions between oppositely charged groups. Van Der Waals Forces = Weak attractions between nonpolar molecules. Disulfide Bonds = Covalent bonds between sulfur atoms in cysteine residues.</p> Signup and view all the answers

<p>Alpha helix = A coiled structure stabilized by intrachain hydrogen bonds Beta sheet = A sheet-like structure formed by hydrogen bonds between adjacent strands Turn = A sharp bend in the polypeptide chain, often involving proline Random coil = A region without a defined structure</p> Signup and view all the answers

<p>Primary Structure = The linear sequence of amino acids in a polypeptide chain. Secondary Structure = The local three-dimensional arrangement of amino acids, such as α-helices and β-sheets. Tertiary Structure = The overall three-dimensional shape of a single polypeptide chain. Quaternary Structure = The arrangement of multiple polypeptide chains (subunits) in a protein complex.</p> Signup and view all the answers

<p>α-Keratin = Structural protein found in hair, wool, and nails. Collagen = Structural protein found in skin, bone, tendons, and cartilage. Myoglobin = Oxygen-binding protein in muscle tissue. Hemoglobin = Oxygen-binding protein in red blood cells.</p> Signup and view all the answers

<p>Valine, Threonine, Isoleucine = Steric clashes destabilize the helix Serine, Aspartic acid, Asparagine = Hydrogen bonding interactions destabilize the helix Proline = Ring structure prevents bond rotation, disrupting helix formation Glycine = Small size allows for flexibility, potentially stabilizing the helix</p> Signup and view all the answers

<p>Parallel = Adjacent strands run in the same direction (N-terminus to C-terminus) Antiparallel = Adjacent strands run in opposite directions Mixed = A combination of parallel and antiparallel strands Twisted conformation = A common structural variation of the beta sheet</p> Signup and view all the answers

<p>Turns and Loops = Regions of polypeptide chains that change direction, often involved in protein interactions. Fibrous Proteins = Proteins with elongated, thread-like structures, providing structural support. Globular Proteins = Proteins with compact, spherical structures, often involved in enzymatic activity or signaling. Coiled Coil = A superhelical structure formed by two intertwined α-helices, often found in fibrous proteins.</p> Signup and view all the answers

<p>Intrachain hydrogen bonds = Stabilize alpha helices Interchain hydrogen bonds = Stabilize beta sheets Hydrogen bonds between side chains = Contribute to tertiary and quaternary structure Hydrogen bonds involving backbone atoms = Primary contributors to secondary structure</p> Signup and view all the answers

<p>Superhelix = A helical structure formed by the intertwining of multiple polypeptide chains. Disulfide Bond = A covalent bond between sulfur atoms in cysteine residues, stabilizing protein structure. Salt Bridge = An ionic interaction between oppositely charged groups, contributing to protein stability. Hydrophobic Interaction = Nonpolar interactions between amino acids, driving protein folding.</p> Signup and view all the answers

<p>Hydrophobic interactions = Drive the folding of proteins into compact structures Disulfide bonds = Stabilize tertiary and quaternary structure, particularly in extracellular proteins Electrostatic interactions = Contribute to the stability of protein-protein interactions and other interactions Van der Waals forces = Weak interactions that contribute to overall protein stability</p> Signup and view all the answers

<p>Hydrogen Bonding = Stabilizes secondary structure by interacting with backbone atoms. Hydrophobic Interactions = Drives the burial of nonpolar residues in the protein interior. Disulfide Bonds = Forms covalent cross-links, stabilizing tertiary structure. Ionic Interactions = Contributes to protein stability by forming salt bridges between oppositely charged groups.</p> Signup and view all the answers

<p>Primary structure = The linear sequence of amino acids in a polypeptide chain Secondary structure = Local three-dimensional structures formed by hydrogen bonding between backbone atoms Tertiary structure = The overall three-dimensional shape of a single polypeptide chain Quaternary structure = The arrangement of multiple polypeptide chains in a protein complex</p> Signup and view all the answers

<p>Hydrophobic Amino Acids = Found primarily in the interior of globular proteins, away from water. Polar Amino Acids = Found on the exterior of globular proteins, interacting with water. Charged Amino Acids = Found on the surface of globular proteins, contributing to protein-protein interactions.</p> Signup and view all the answers

<p>Temperature = High temperatures can disrupt hydrogen bonding and other weak interactions, leading to denaturation pH = Extreme pH values can disrupt electrostatic interactions and alter the ionization state of amino acids Salt concentration = High salt concentrations can shield electrostatic interactions, potentially destabilizing proteins Presence of denaturants = Substances like urea and guanidinium hydrochloride can disrupt hydrogen bonding and hydrophobic interactions, causing unfolding</p> Signup and view all the answers

<p>Primary structure = The linear sequence of amino acids in a polypeptide chain. Secondary structure = Regular, repeating patterns of amino acid chains, such as alpha-helices and beta-sheets. Tertiary structure = The three-dimensional shape of a single polypeptide chain, incorporating interactions between side chains. Quaternary structure = The arrangement of multiple polypeptide chains in a protein complex.</p> Signup and view all the answers

<p>Motifs = A combination of secondary structures, like a helix-turn-helix motif in DNA-binding proteins. Domains = Distinct, compact regions within a protein, often with specific functions, like a catalytic domain in an enzyme. Subunits = Individual polypeptide chains that associate to form a multimeric protein, like the subunits of hemoglobin. Quaternary structure = The arrangement of multiple subunits in a protein complex, like the tetrameric structure of hemoglobin.</p> Signup and view all the answers

<p>Urea = Disrupts non-covalent interactions, like hydrogen bonds and hydrophobic interactions. Mercaptoethanol = Reduces disulfide bonds, breaking covalent links between cysteine residues. Heat = Disrupts non-covalent interactions, causing unfolding and loss of structure. pH changes = Can disrupt ionic interactions and hydrogen bonds, leading to protein denaturation.</p> Signup and view all the answers

<p>Hydrophobic effect = The tendency of nonpolar amino acid side chains to cluster away from water, driving protein folding. Folding funnel = A conceptual model illustrating how proteins fold, with a landscape of energy states leading to the native, lowest-energy conformation. Anfinsen experiment = Demonstrated that the amino acid sequence of a protein determines its three-dimensional structure. Chaperone proteins = Assist in protein folding by preventing aggregation and promoting proper conformation.</p> Signup and view all the answers

<p>Nonpolar amino acids = Tend to be found in the interior of a protein, away from water. Polar amino acids = Often found on the surface of a protein, interacting with water. Disulfide bonds = Covalent bonds that stabilize the tertiary structure, particularly in proteins that encounter harsh environments. Hydrogen bonds = Non-covalent interactions that contribute to both secondary and tertiary structures, often between polar side chains.</p> Signup and view all the answers