Study BMB 401H Chapter 8 Flash Cards

 
Pile Management Card
BMB 401H Chapter 8

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a-b barrels (the TIM fold)
-8 stranded parallel b barrel concentric with 8 outer a helices
-loop region of the C terminal side of b strands is active site
b barrels
-Diverse group
-4 to over 10 antiparallel strands
-typically 2 b sheets that pack against each other
-twist-like barrel
globin fold
-in myoglobin, hemoglobin
-bundle of 8 a helices
-helices forms a pocket for the active site
-heme for oxygen binding
-Protects heme from contacting other heme
Four helix bundles
-simplest
-4 a helices in a bundle
-residues contacting each other in the bundle are hydrophobic
a-a motifs
-Four helix bundles
-globin fold
b-a-b motif
-parallel b-sheets connected by a-helix
-common
-helix packs against B sheet to shield its hydrophobic residues
-loop regions vary in length
-loop connecting C end of B sheet to a-helix is often binding site or active site
-right handed
Hairpin b motifs
-2adjacent antiparallel strands joined by a loop (2-5 aas)
-hairpin or a b-b unit
Supersecondary structure
-Building blocks for proteins:
bab motif
b hairpin motif
aa motif
Greek key motif
domains
-globular structures
-a polypeptide usually wanders back and forth within domain.
-Neighboring domains typically connected by one or two segments.
-Domains often have specific function (ex: binding site for NAD)
Side chain location trends
-tendency to hide hydrophobic residues
-When in interior, always hydrogen bonded.
-H bond ‘neutralizes’ charge so that it can go to interior
tertiary structure
-folding of secondary structure with the side chains spatially oriented
how to read 2-D NMR
-off diagonal peaks arise from interaction of two protons that are < 5 Angstroms apart
-molecule to be assembled in space.
-Inter-proton distance not precise
2D-NMR
-Nuclear magnetic resonance
-monitor protons
-apply large external magnetic field
-separates nuclear spin energies
-flips spin from lower to higher energy state
protein crystals
-protein crystals mostly water (60%)
-jello-like matrix limits resolution
-Leu, Ile and Thr can't be distinguished, so primary structure needed
-catalytically active--> shows protein is native
X-ray crystallography
-X-rays are approximately 1.5 Angstroms (covalent bonds are 1.5 A)
-need crystal lattice
-electron density affects intensity
-produces electron density map
-atoms are fitted to map
Globular proteins
-spherical
-structures studied via X-ray and NMR studies
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