Protein Structure Overview
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Questions and Answers

What is the average width of a b-sheet?

  • 30 Å
  • 35 Å
  • 25 Å (correct)
  • 20 Å
  • Which type of b-sheet is considered less stable?

  • Antiparallel
  • Tandem parallel
  • Crossover
  • Parallel (correct)
  • Where do non-polar sidechains primarily reside within a protein?

  • In the interior away from water (correct)
  • On the surface in contact with water
  • At the ends of the protein
  • Evenly distributed throughout
  • What characteristic feature is required for antiparallel b-sheets?

    <p>Hairpin turn</p> Signup and view all the answers

    Which of the following amino acids is considered a charged polar residue?

    <p>Aspartic acid</p> Signup and view all the answers

    What does 'N' represent in the Nm Helix Nomenclature?

    <p>Number of repeating units per turn</p> Signup and view all the answers

    Which of the following best defines an unfavorable steric hindrance?

    <p>When there is too little space leading to energy depletion</p> Signup and view all the answers

    How many atoms complete the hydrogen bond cycle in an alpha helix as represented by 'M'?

    <p>2</p> Signup and view all the answers

    What is the primary characteristic of an alpha helix concerning its structural configuration?

    <p>It exhibits a rigid and favorable conformational stability</p> Signup and view all the answers

    Which of the following statements about the alpha helix is incorrect?

    <p>The alpha helix does not involve hydrogen bonding</p> Signup and view all the answers

    What is the main objective of X-ray crystallography?

    <p>To determine the 3D structure of a protein</p> Signup and view all the answers

    Which of the following accurately describes an advantage of X-ray crystallography?

    <p>Proteins in crystalline form often maintain conformations similar to those in solution.</p> Signup and view all the answers

    What is created from the diffraction pattern of X-rays in X-ray crystallography?

    <p>An electron density map</p> Signup and view all the answers

    Which experimental technique is NOT used for protein structure determination?

    <p>Mass spectrometry</p> Signup and view all the answers

    How do different atoms respond to X-rays during X-ray crystallography?

    <p>Variable intensities are produced based on electron density.</p> Signup and view all the answers

    What is likely true about enzymes in their crystalline state, according to X-ray crystallography?

    <p>They are often catalytically active.</p> Signup and view all the answers

    Which statement best describes the electron density map produced in X-ray crystallography?

    <p>Amino acid structures can be fit into it.</p> Signup and view all the answers

    Which term describes the structure a crystalline protein assumes in X-ray crystallography?

    <p>Near-native structure</p> Signup and view all the answers

    What is the primary driving force behind the global conformation of proteins?

    <p>Hydrophobic effects</p> Signup and view all the answers

    Which factor contributes to protein denaturation when heating proteins?

    <p>Disruption of thermal vibrations and weak bonds</p> Signup and view all the answers

    What role do chaotropic agents like Urea play in protein denaturation?

    <p>They increase the solubility of nonpolar groups</p> Signup and view all the answers

    In which manner do proteins generally fold into their native states?

    <p>Via directed pathways</p> Signup and view all the answers

    Which of the following statements is incorrect regarding protein denaturation?

    <p>Detergents increase water interactions.</p> Signup and view all the answers

    What is a notable advantage of Cryo-EM in protein structure analysis?

    <p>No need for a crystal</p> Signup and view all the answers

    Which limitation of Cryo-EM involves the orientation of the molecules?

    <p>Molecules are detected in unknown orientations</p> Signup and view all the answers

    How does resolution in Cryo-EM compare to other structural biology methods?

    <p>Inferior to both NMR and X-Ray crystallography</p> Signup and view all the answers

    What methodology does 'Fold recognition' fall under when predicting protein structures?

    <p>Computationally based methods</p> Signup and view all the answers

    Which of the following is NOT a limitation of Cryo-EM?

    <p>Inability to detect different conformational states</p> Signup and view all the answers

    What stabilizes protein structures at tertiary and quaternary levels?

    <p>Electrostatics, hydrogen bonds, and van der Waals forces</p> Signup and view all the answers

    What aspect of protein structure prediction does homology modeling rely on?

    <p>Proteins with the same function have the same folding</p> Signup and view all the answers

    Which of the following factors could stabilize peptide chains in proteins?

    <p>Cross-linking by disulfides</p> Signup and view all the answers

    Study Notes

    Protein Structure

    • The outside of the protein is composed of Gly
    • The conformation of a protein can be favorable with little steric hindrance
    • Incorrect conformations occur with too many amino acids in a small space
    • The conformation of a protein can be unfavorable due to steric hindrance
    • The number of repeating units per turn and the number of atoms that complete the H-bond cycle is used to classify helices.
    • The alpha helix is considered a 3.61 helix
    • There are multiple types of helices including the 4.11 and 6-helix
    • Beta strands are straight, but can be wonky.
    • Beta sheets are composed of beta strands
    • The repeat distance of beta sheets is 7.0 Angstroms
    • Amino acid side chains alternate above and below the plane of the sheet.
    • Beta sheets are typically 2 to 15 residues long
    • A beta sheet can have 2 to 22 strands
    • Beta sheets can have parallel and antiparallel orientations
    • Antiparallel beta sheets are more stable than parallel beta sheets
    • Antiparallel beta sheets need a hairpin turn
    • Tandem parallel beta sheets need a crossover connection with a right-handed sense
    • Non-polar side chains tend to occur in the interior of a protein
    • Uncharged polar residues tend to occur on the surface of a protein, but can occur in the interior
    • Charged polar residues tend to occur on the surface of a protein
    • The Hydropathy scale can be used to predict whether a residue occurs on the surface or interior of a protein
    • Hydrophobic effects are important for transmembrane proteins

    Protein Structure Determination Methods

    • Protein structure can be determined experimentally through:
      • X-ray crystallography
      • Nuclear Magnetic Resonance (NMR)
      • Cryogenic electron microscopy (cryo-EM)

    X-ray Crystallography

    • X-ray crystallography is a method used to determine the 3D structure of a protein.
    • X-rays are bounced off of the protein and deflected by electrons in the various atoms/bonds
    • The intensity of the x-ray is dependent upon the electron density of the atom/bond
    • The diffraction pattern of the x-ray is measured and an electron density map is created
    • Amino acid structures are fit into the electron density maps
    • Higher resolution is achieved with smaller scattering amplitudes

    X-ray Crystallography Advantages

    • Crystalline proteins assume a structure that is similar to the protein in solutions
    • Different X-ray crystallography experiments typically produce the same conformation (reproducibility)
    • Many enzymes are catalytically active in the crystalline state

    Cryo-EM Advantages

    • No need for crystals
    • Requires small amounts of sample (~0.1 mg)
    • Does not have a size or weight limit to the macromolecule
    • Protein conformations are in their native states
    • Multiple conformations can be captured

    Cryo-EM Limitations

    • Molecules are detected in unknown orientations
    • Resolution of the raw data can be very noisy
    • Different “shapes” might reflect the same conformation
    • Similar “shapes” might reflect different conformations
    • Resolution is inferior to both NMR and X-ray crystallography

    Protein Structure Prediction

    • Protein structure can be predicted computationally through:
      • Ab Initio
      • Fold recognition (Threading)
      • Homology modeling
    • Ab Initio method predicts a protein's structure from its sequence
    • Fold recognition uses known protein structures as references to determine possible folds for other proteins
    • Homology modeling relies on sequence similarity to known structures
    • Protein structure prediction methods are based on the sequence of a protein and the chemical and physical properties of amino acids.

    Protein Structure Stabilization

    • Electrostatic, hydrogen bonds, and van der Waals forces hold a protein together
    • Peptide chains can be cross-linked by disulfide bonds, salt-bridge networks, metal ions, prosthetic groups, and other ligand compounds
    • Proteins fold quickly and generally in only one stable conformation
    • Hydrophobic effects are the most important driving force for protein folding

    Protein Denaturation

    • High temperatures can cause protein denaturation
    • Changes in pH can cause protein denaturation
    • Detergents can denature proteins
    • Chaotrophic agents, such as urea and guanidinium ions, disrupt hydrophobic interactions and cause protein denaturation

    Protein Folding

    • Proteins fold in a hierarchical manner
    • Proteins fold spontaneously into their native states
    • Folding is directed through specific pathways
    • Folding does not occur through random conformational searches
    • Hydrophobic effects are the most important factor in protein folding and stability

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    Description

    This quiz covers key concepts related to protein structure, focusing on the characteristics of alpha helices and beta sheets. Participants will explore the factors affecting protein conformation, the stability of various helices, and the arrangement of amino acids in beta sheets. Perfect for students of biochemistry and molecular biology.

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