Podcast
Questions and Answers
What is the average width of a b-sheet?
What is the average width of a b-sheet?
Which type of b-sheet is considered less stable?
Which type of b-sheet is considered less stable?
Where do non-polar sidechains primarily reside within a protein?
Where do non-polar sidechains primarily reside within a protein?
What characteristic feature is required for antiparallel b-sheets?
What characteristic feature is required for antiparallel b-sheets?
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Which of the following amino acids is considered a charged polar residue?
Which of the following amino acids is considered a charged polar residue?
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What does 'N' represent in the Nm Helix Nomenclature?
What does 'N' represent in the Nm Helix Nomenclature?
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Which of the following best defines an unfavorable steric hindrance?
Which of the following best defines an unfavorable steric hindrance?
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How many atoms complete the hydrogen bond cycle in an alpha helix as represented by 'M'?
How many atoms complete the hydrogen bond cycle in an alpha helix as represented by 'M'?
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What is the primary characteristic of an alpha helix concerning its structural configuration?
What is the primary characteristic of an alpha helix concerning its structural configuration?
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Which of the following statements about the alpha helix is incorrect?
Which of the following statements about the alpha helix is incorrect?
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What is the main objective of X-ray crystallography?
What is the main objective of X-ray crystallography?
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Which of the following accurately describes an advantage of X-ray crystallography?
Which of the following accurately describes an advantage of X-ray crystallography?
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What is created from the diffraction pattern of X-rays in X-ray crystallography?
What is created from the diffraction pattern of X-rays in X-ray crystallography?
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Which experimental technique is NOT used for protein structure determination?
Which experimental technique is NOT used for protein structure determination?
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How do different atoms respond to X-rays during X-ray crystallography?
How do different atoms respond to X-rays during X-ray crystallography?
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What is likely true about enzymes in their crystalline state, according to X-ray crystallography?
What is likely true about enzymes in their crystalline state, according to X-ray crystallography?
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Which statement best describes the electron density map produced in X-ray crystallography?
Which statement best describes the electron density map produced in X-ray crystallography?
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Which term describes the structure a crystalline protein assumes in X-ray crystallography?
Which term describes the structure a crystalline protein assumes in X-ray crystallography?
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What is the primary driving force behind the global conformation of proteins?
What is the primary driving force behind the global conformation of proteins?
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Which factor contributes to protein denaturation when heating proteins?
Which factor contributes to protein denaturation when heating proteins?
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What role do chaotropic agents like Urea play in protein denaturation?
What role do chaotropic agents like Urea play in protein denaturation?
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In which manner do proteins generally fold into their native states?
In which manner do proteins generally fold into their native states?
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Which of the following statements is incorrect regarding protein denaturation?
Which of the following statements is incorrect regarding protein denaturation?
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What is a notable advantage of Cryo-EM in protein structure analysis?
What is a notable advantage of Cryo-EM in protein structure analysis?
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Which limitation of Cryo-EM involves the orientation of the molecules?
Which limitation of Cryo-EM involves the orientation of the molecules?
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How does resolution in Cryo-EM compare to other structural biology methods?
How does resolution in Cryo-EM compare to other structural biology methods?
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What methodology does 'Fold recognition' fall under when predicting protein structures?
What methodology does 'Fold recognition' fall under when predicting protein structures?
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Which of the following is NOT a limitation of Cryo-EM?
Which of the following is NOT a limitation of Cryo-EM?
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What stabilizes protein structures at tertiary and quaternary levels?
What stabilizes protein structures at tertiary and quaternary levels?
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What aspect of protein structure prediction does homology modeling rely on?
What aspect of protein structure prediction does homology modeling rely on?
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Which of the following factors could stabilize peptide chains in proteins?
Which of the following factors could stabilize peptide chains in proteins?
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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.
