lecture 6 - protein structure & folding Flashcards
What is protein super secondary structure?
Elements of secondary structure, e.g. alpha helices, beta sheets and turns are connected to make up a part of the entire protein chain.
What are the 4 most common motifs of protein super-secondary structure?
Helix-turn-helix, Beta hairpin, greek key, strand-helix-strand
What is the structure of a ‘helix-turn-helix’?
2 alpha helices connected by a turn.
An EF hand protein is an example of what type of super-secondary motif?
Helix-turn-helix
What does an EF hand protein bind?
Calcium - the loop acts as a binding site
In a Beta hairpin, are the strands parallel of anti parallel?
Antiparallel
What is the overall structure of a greek key super-secondary motif?
4 antiparallel Beta strands connected by turns and folded into a ‘U’ shape
What is the structure of strand-helix-strand super-secondary structure?
A Beta strand, then alpha helix then Beta strand, connected by turns. The strands are therefore parallel with a helix between them.
What are protein domains, and what overall level of structure do they come under?
A combination of super secondary structures that combine to form a larger part of a protein strand, but do not include the entire polypeptide so are not tertiary.
What are the 3 main protein domain families?
Alpha-domain, alpha/beta, antiparallel beta
What does amphipathic mean, in terms of a protein?
A whole, or part of, a protein has both hydrophobic and hydrophilic components, with closely packed chains at the core.
What is the structure of an alpha-domain?
Domain is mostly helical, and is amphipathic, with a hydrophobic core and hydrophilic outer
The 4 helix bundle is an example of which domain?
alpha-domain
What is the structure of alpha/beta domain?
Contains a combination of alpha helices and beta sheets
What were the overall steps of the Antinsen experiment?
A protein was denatured using chemicals that made it unfold, losing its tertiary structure. However, once the chemicals were removed, the protein spontaneously refolded itself.
What does the Antinsen experiment prove?
The only instructions proteins need to fold are imbedded in the amino acid sequence
What is the likely sequence of events in the folding of a protein?
Short secondary elements form, subdomains form then combine to form a globule (partly folded domain), tertiary and/or quaternary structure emerge.
What are the non-covalent interactions that stabilise protein folding?
Hydrophobic interactions, metal ion coordination, hydrogen bonds, electrostatic interactions.
What type of covalent bond is involved in protein folding?
Disulphide bond.
What are the 3 types of protein, in terms of their dependence on a chaperone to fold?
Chaperone independent, Chaperone dependent, chaperonin-dependent
What percentage of proteins are chaperone dependent or independent (do not require chaperonin)?
85%
What are some examples of conditions/chemicals that will cause a protein to denature?
extreme pH, heat, organic solvents, urea, detergents,
What is a prion?
A mis folded protein that has the ability to transmit its misfolded shape into similar proteins.
Bovine spongiform encephalopathy - ‘Mad Cow Disease’ is caused by what?
Prions that cause brain damage
What protein phenomena causes Creutzfeldt-Jacob disease?
Prions
What protein phenomena causes Alzheimer’s Disease?
Protein aggregation in the brain
What structural change causes prions to fold abnormally?
transformation of alpha helix to beta strand
