Structural determinants of protein function Flashcards
(48 cards)
What does the protein 3D shape determine?
How protein works in the cell
What do loop, coil and random coil structures share?
They have no regular defining properties in structure
Not Alpha-helices and Beta-sheets
What is the structure of loop and coil?
In line
Ordered (not mobile), but not in a systematic or regular way
What is the structure of loop and coil?
American Lines
Disordered, mobile, fluctuating set of structures
What % of protein is alpha helix?
31%
What % of protein is beta sheet?
28%
What is the remaining part of the protein structure?
Doesn’t repeat
Rest is non repetitive structure
What are the supersecondary structures (motifs)?
Greeks put in their hair
B alpha Beta Motif
Beta Hairpin motif
Alpha Alpha Motif
Helical supersecondary structures have?
looped together
4 Helix bundle motif
Describe the structure of Beta Supersecondary Structures
The chain is a N to a C with 4 sections.
Beta Hairpin motif
the second and third section folds so it is ordered 3,2,1,4
What are the different folds for Beta supersecondary structures?
Immunoglobulin fold
Beta-Barrel fold
Alpha/Beta Barrel (TIM barrel) fold
What is the structure of the immunoglobulin fold?
N to C Beta Hairpin motif 4 folds 1 is bound to 2 2 is bound to 5 4 to 3 3 to 6 6 to 7
What is the structure of the Beta barrel fold?
N to C beta hairpin motifs
1,2,3,4,5,6, 7, 8
Wiggly line
What is the structure of the Alpha/Beta Barrel (TIM barrel) fold?
N to C
Each is folded with itself in a beta hairpin motif
1,2,3,4,5, 6,7 ,8
So 1 is adjacent to 2
Define and give an example of Protein tertiary structure
How the secondary structural elements come together
Each protein structure is different (Unlike DNA)
Whale myoglobin (first structure solved): Oxygen carrier, allows whales to store oxygen for long periods while they are diving
Teritary structures that build protein structures may contain?
Alpha-helices and or Beta-sheets or neither
What are the features of the side chain location in tertiary structure?
Water is largely excluded from interior
Hydrophobic “non-polar” amino acids in the core: Shielded from the aqueous solvent (water)
Hydrophillic “charged” amino acids on the exterior- in contact with the water in the solvant
Uncharged polar amino acids often on surface, but can be found in the inside, but usually buried hydrogen bond donors form bonds with acceptors (sort of neutralizing the polarity)
What amino acids face protein interior?
Phe
lle
Leu
What amino acids face protein exterior?
Ala Asp Lys Gly Glu Asn Arg Gln
What are protein domains?
Large polypeptides (200 or more amino acids) Usually fold up into a group of globular domains
E.g. Glyceraldehyde-3-phosphate
What helps protein folding?
Proteins aren’t a tangled mess because they are hierarchically organised, with domains often divided into subdomains
Thing that need to end up close in 3D start close in 2D
What are the common DNA folds?
Helix-turn-helix
Zinc finger
Leucine zipper
What is the structure of Helix-turn-helix?
DNA-binding helix is connected to a Dimer-binding helix (loop de loop) by a turn shaped like a upside down mountain
Explain the Amino acid sequence for Helix-turn-helix motif
20 AA’s per chain
One Alpha helix for recognition of DNA then beta turn, then another Alpha helix
For DNA-binding helix-turn-helix motifs in the lac repressor (tetramer)