Protein Structure and Protein Folding Flashcards
What is a super secondary structure?
Elements of secondary structures (helices and strands) are connected by turns or by regions of less ordered structure called loops or coils to make up super secondary structure
What is the helix-turn-helix supersecondary structure?
Two alpha helix connected by a turn or a loop, often found in DNA and calcium binding proteins aka EF-hand proteins
What is a beta-hairpin supersecondary structure?
Common
Antiparallel - B sheet connected by a turn
Length varies
e.g. snake venom toxin
What is the greek key supersecondary structure?
4 Beta strands connected by turns, each individual arrow is a B-strand, whole structure is a B-sheet
If we have a B-sheet all B-strands are on the same polypeptide
What is a strand, helix, strand?
Combination of beta strand and alpha helix connected by turns. Very common, strands run parallel to each other. Helix and strands on a different plane so hydrogen bonding can still occur
What are protein domains?
Collections of supersecondary structures that each have a specific structure, combine to form domains
Independently folded regions that often posses a specific function
Hydrophobic core, hydrophilic parts on surface or near solvent
Small proteins usually have one domain, large may have many
What is an a-domain family protein domain?
Mostly helical structure, side chains packed closely together within a hydrophobic core and hydrophilic bits pointing outwards
Packing can occur between non adjacent helices in globin folds
What is an a/B family protein domain?
Mixture of alpha helix and beta sheet, common in enzymes, can have long coils which change the path of polypeptides
Can also take shape of a horseshoe when there are 16 strands
What is an antiparallel B family protein domain?
Mostly antiparallel B structure, can take shape of a barrel, hydrophobic inside barrel, water soluble used to bind hydrophobic things and transport them e.g. vitamin A
What is protein folding?
Proteins are synthesised as linear polymers that must fold into 3D structures, made at the ribosome and generally fold spontaneously
Instructions to fold embedded in the aa sequence
Directed largely by internal hydrophobic residues (hydrophobic core) while hydrophilic residues are solvent exposed
Protein folding sequence of events
Polypeptide emerges from ribosomes -> secondary structure form (alpha helix and beta structure) -> supersecondary structures form -> domains form but not in the best compact shape -> final adjustments made to form compact tertiary structure
How is protein folding stabilised?
Non-covalent interactions (weak in proteins individually), in some proteins additional covalent bonds (e.g. disulfide bonds) may be present, hydrophobic core is most important noncovalent contributor to protein stability
What are the three protein folding helpers?
Chaperone-independent (folds alone)
Chaperone-dependent e.g. Hsp70
Chaperonin-dependent e.g. GroEL-GroES
If these do not help proteins aggregate -> misfolding
How does unfolding of proteins occur?
Occurs if the non-covalent bonds break usually because of change in pH, heating (kinetic energy gain) etc.
What is the misfolding of proteins?
Proteins in living organisms that are folded normally can sometimes change their shape and become misfolded. Some misfolded proteins can cause other proteins to change their shape as well
