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Lecture 2, protein structure
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- 1protein function is determined by it3D structure
- 2The 3D structure of a protein is called itNative fold, The native fold has a large number of favorable interactions within the protein
- 3when a protein is denatured, it loosesits native fold
- 4Hydrophobic effectRelease of water molecules from the structured solvation layer around the molecule
- 5Hydrogen bonds give rise to what structuresInteraction of N-H and C=O of the peptide bond leads to local regular structures such as alpha-helices and beta-sheets
- 6London dispersionMedium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein
- 7Electrostatic interactionsLong-range strong interactions between permanently charged groups.
Salt-bridges, esp. buried in the hydrophobic environment strongly stabilize the protein - 8The amino acids sequence, peptide bond and disulfide binds are the _______ structureprimary
- 9The 3D structure is the _______ structuretertiary
- 10Tertiary structureTertiary structure of the protein is a three-dimensional combination of α-helices and β-sheets that fold next to each other as a result of noncovalent interactions between amino acids' side groups and the environment surrounding the single polypeptide.
- 11A quandary structure has two or more ______ structurestertiary
- 12Structure of the protein is partially dictated by the properties of thepeptide bond
- 13The peptide bond is a resonance hybrid of twocanonical structures
- 14resonance of two canonical structures in the peptide causes the peptide bondsto be less reactive compared to esters, for example
to be quite rigid and nearly planar
to exhibit a large dipole moment in the favored trans configuration - 15a polypeptide chain (3D) is a _____ structuretertiary
- 16in a polypeptide, where are rotations permitted and not permittedRotation around the peptide bond is not permitted
Rotation around bonds connected to the alpha carbon is permitted - 17why is the C-N bond in the polypeptide bond shorter than that of typical amidesdue to the resonance of the two canonical structures and the sharing of two pairs of electrons, it creates a partial double bond that cannot rotate freely
- 18what is a secondary structurea local spatial arrangement of the polypeptide backbone, the two regular are alpha-helix and beta-sheets
- 19alpha helix is stabilized bystabilized by hydrogen bonds between nearby residues
- 20the beta sheet is stabilized bystabilized by hydrogen bonds between adjacent segments that may not be nearby
- 21Irregular arrangement of the polypeptide chain is calledthe random coil
- 223 key features of an alpha-helix1. Right-handed helix with 3.6 residues (5.4 Å) per turn (axial length of one loop)
2. Peptide bonds are aligned roughly parallel with the helical axis
3. Side chains point out and are roughly perpendicular with the helical axis, interaction of side chains 3-4 AA apart affect formation - 23what is the inner and outer diameter of an alpha-helixinner= 4-5 A
outer= 10-12 A - 24what two small hydrophobic AA are string helix formers?alanine, and leucine
- 25what two AA act as helix breakers and why?Proline acts as a helix breaker because the rotation around the N-Ca bond is impossible
Glycine acts as a helix breaker because the tiny R-group supports other conformations - 26in the structure of a alpha-helix, where are the positive and negative interaction of the backbone foundThe between the carbonyl-oxygen (-), and the hydrogen(+) of the the amide.
- 27in beta sheets, Sheet-like arrangement of backbone is held together byhydrogen bonds between the backbone amides in different strands
- 28where do the side chains sit in beta sheetsSide chains protrude from the sheet alternating in up and down direction
- 29In parallel b sheets the H-bonded strands run in the ________ direction, resulting inIn parallel b sheets the H-bonded AA strands run in the same direction
Resulting in bent H-bonds (weaker) - 30In antiparallel b sheets the H-bonded strands run in _______ directions Resulting inIn antiparallel b sheets the H-bonded AA strands run in opposite directions
Resulting in linear H-bonds (stronger) - 31how many AAs in a beta turn4
- 32beta turns are stabilized byThe turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence, Proline in position 2 or glycine in position 3 are common in beta turns
- 33two major classes of proteinsfibrous and globular
- 34Fibrous protein arrangementpolypeptide chains arranged in long strands or sheets
- 35Globular proteins arrangementpolypeptide chains arranged in spherical or globular shapes
- 36typical secondary structures of fibrous proteins includealpha helix crosslinked by disulfide bonds, beta confromation, and collagen tripple helix
- 37describe the structure of keratinalpha helix linked by disulfide bonds, tough, insoluble protective structures of varying hardness and flexibility
- 38describe the structure of silk fibroinmade of beta conformations, soft, flexible filaments
- 39describe the structure of collagen of tendonscontains collagen triple helix, high tensile strength, without stretch
Each collagen chain is a long Gly- and Pro-rich left-handed helix
Three collagen chains intertwine into a right-handed superhelical triple helix - 40Fibroin is the main protein insilk from moths and spiders
- 41describe the structure of fibroinAntiparallel beta sheet structure
Small side chains (Ala and Gly) allow the close packing of sheets
Structure is stabilized by
hydrogen bonding within sheets
London dispersion interactions between sheets
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- biochem Fichas sobre Lecture 2, protein structure, creado por Ashlin Deatherage el 03/09/2023.
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- Ashlin Deatherage
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