Secondary, tertiary and quaternary protein structure Flashcards
What two secondary structures are found in proteins?
alpha helix and beta sheet
What stabilizes the alpha helix?
the interchain hydrogen bonds between the amide backbone and carbonyl groups four residues apart
in a right handed helix how many residues are there per turn?
3.6
How do the R groups project in an alpha helix?
outward
In beta sheets how are the chains connected? How do the R groups come out?
hydrogen bonds between the chains
R groups project from both faces
What are the two ways beta sheets can be orientated?
parallel or antiparallel
what is a beta bend?
where the polypeptide makes a 180° turn at the protein surface
Examples of conformational diseases?
Alzheimers and prions
diabetes (2), parkinsons
Alzheimers conformational explanation
human amyloid peptide usually helical transitions to beta sheet which causes nucleation into a giant fibre
Prions conformational explanation
normally alpha helixes when converted to beta sheets allows for nucleation
What are super secondary structures?
motifs and domains
what is a protein motif?
small regions with defined sequence or structure which often serve a common function in different proteins
what is a protein domain?
sub regions of single polypeptide chains that can fold and function independently (sometimes correlated with exons)
What do you see with a backbone representation of a protein?
Ca per residue
what do you see with a wireframe representation of a protein?
every bond and atom
use this if you know catalytic site or mutation
what do you see with a space fill representation of a protein?
shows van der waals forces
volume (radii)
what do you see with a ribbon representation of a protein?
highlights the secondary structure, which components are alpha helixes or beta sheets
What is the native structure stabilized by?
burying the non-polar side chains, hydrophobic effect
optimized hydrogen bonds
any inter chain S-S bonds
maximized side chain packing in interior due to VDW
What is the denatured state stabilized by?
increased conformational entropy of the unfolded chain
what can cause denaturation?
heat, chemicals, pH extremes, mutations that destabilize N
why is denaturation often irreversible?
because of exposure of proteolytic sites and non-polar residues
What did the Anfinsen experiment show?
native structure of protein only recovered if urea removed before reducing agent showing that it is not the S-S bonds that dictate protein folding but the primary structure
what is the Levinthal paradox?
if explored
randomly, all possible conformtions of
a 100-residue protein would take the age of the universe to sample…yet
proteins often fold within seconds!
because folding is directed by the rapid intial formation of 2° structure elements which prevent other possibilities
Some areas of the protein only fold when interacting with binding partners : T or F?
T
Some of the intermediates may promote misfolding and aggregation: T or F?
T
How is protein folding a free energy funnel?
as get closer the native structure the amount of free energy continually decreases
what is chaperon assisted folding?
heat shock proteins (chaperones) help larger molecules fold by providing a safe space allowing it to find the correct formation requires ATP and thus there is a loss of ADP and Pi
Quaternary structure is what
multiple polypeptide chains forming a functional protein
nomenclature
homodimer-two identical subunits
heterotetramer-4 different sub units
