Lecture 3: protein structure Flashcards
protein is a linear polymer of _____ linked to one another by peptide bonds
protein is a linear polymer of L-alpha-AA’s linked to one another by peptide bonds
primary structure (1)
- linear sequence of AA’s with no higher order structure
secondary structure [define; how is it stabilized? ex (2)]
- spatial arrangement of AA’s that are close to each other in the primary sequence
- structure stabilized by backbone H-bonds
ex) alpha-helix and beta-strand
tertiary structure [define; how is it stabilized? (3)]
- folding of secondary structural units to minimize molecular volume and pack interior
- stabilized by side-chain H-bonding, salt bridges and hydrophobic effect
quaternary structure [define]
interaction of multiple individual polypeptide chains in a multi-subunit protein complex
from primary to quaternary the structure becomes more ____ and ____
the structure becomes more compact and ordered
what kind of rxn is a peptide bond formation?
dehydration rxn
the Ramachandran plot identifies ____, with the white regions showing _____
identifies different allowed geometries, with the white regions showing the range of the most favorable
secondary structure requires the ____ geometry
requires the trans geometry
how is the alpha helix structure stabilized? [n+?]
stabilized by backbone H-bonds between residues within the helix chain [n+4]
all side chains of the alpha helix face (in/outwards)
all side chains face outwards
why does proline disrupt the alpha helix? what can it identify?
- during the dehydration rxn, the N loses both of its H’s so it has no stable backbone
- identifies 2 separate alpha helices
hydrophobic effect drives ____ regions together to establish the overall protein fold
hydrophobic effect drives non-polar regions together to establish overall protein fold
alternate side chains in a beta chain points in ____ directions
alternate side chains point in opposite directions
difference in type 1 and 2 beta turn
the change in orientation
how is a beta turn stabilized? [n+?]
stabilized by H-bonds between residues [n+3]
where are beta turns and what is their purpose?
beta turns are on the edges of globular proteins and allow for a change in direction (180° turn) of the polypeptide chain
what amino acids will not form an alpha helix or a beta sheet and why? (2)
- proline; rigid, forms a covalent bond with itself
- glycine; has too small of a side chain, not able to interact with other residues to stabilize either forms
intrinsically disordered proteins (IDP’s) [define; ex (1)]
- protein that can’t retain a structure past primary or secondary [very little overall fold]
ex. protein tau = stabilizes protein structure of tubule
