lecture 6 - protein structure & folding

Question 1

What is protein super secondary structure?

Answer 1

Elements of secondary structure, e.g. alpha helices, beta sheets and turns are connected to make up a part of the entire protein chain.

Question 2

What are the 4 most common motifs of protein super-secondary structure?

Answer 2

Helix-turn-helix, Beta hairpin, greek key, strand-helix-strand

Question 3

What is the structure of a ‘helix-turn-helix’?

Answer 3

2 alpha helices connected by a turn.

Question 4

An EF hand protein is an example of what type of super-secondary motif?

Answer 4

Helix-turn-helix

Question 5

What does an EF hand protein bind?

Answer 5

Calcium - the loop acts as a binding site

Question 6

In a Beta hairpin, are the strands parallel of anti parallel?

Answer 6

Antiparallel

Question 7

What is the overall structure of a greek key super-secondary motif?

Answer 7

4 antiparallel Beta strands connected by turns and folded into a ‘U’ shape

Question 8

What is the structure of strand-helix-strand super-secondary structure?

Answer 8

A Beta strand, then alpha helix then Beta strand, connected by turns. The strands are therefore parallel with a helix between them.

Question 9

What are protein domains, and what overall level of structure do they come under?

Answer 9

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.

Question 10

What are the 3 main protein domain families?

Answer 10

Alpha-domain, alpha/beta, antiparallel beta

Question 11

What does amphipathic mean, in terms of a protein?

Answer 11

A whole, or part of, a protein has both hydrophobic and hydrophilic components, with closely packed chains at the core.

Question 12

What is the structure of an alpha-domain?

Answer 12

Domain is mostly helical, and is amphipathic, with a hydrophobic core and hydrophilic outer

Question 13

The 4 helix bundle is an example of which domain?

Answer 13

alpha-domain

Question 14

What is the structure of alpha/beta domain?

Answer 14

Contains a combination of alpha helices and beta sheets

Question 15

What were the overall steps of the Antinsen experiment?

Answer 15

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.

Question 16

What does the Antinsen experiment prove?

Answer 16

The only instructions proteins need to fold are imbedded in the amino acid sequence

Question 17

What is the likely sequence of events in the folding of a protein?

Answer 17

Short secondary elements form, subdomains form then combine to form a globule (partly folded domain), tertiary and/or quaternary structure emerge.

Question 18

What are the non-covalent interactions that stabilise protein folding?

Answer 18

Hydrophobic interactions, metal ion coordination, hydrogen bonds, electrostatic interactions.

Question 19

What type of covalent bond is involved in protein folding?

Answer 19

Disulphide bond.

Question 20

What are the 3 types of protein, in terms of their dependence on a chaperone to fold?

Answer 20

Chaperone independent, Chaperone dependent, chaperonin-dependent

Question 21

What percentage of proteins are chaperone dependent or independent (do not require chaperonin)?

Answer 21

85%

Question 22

What are some examples of conditions/chemicals that will cause a protein to denature?

Answer 22

extreme pH, heat, organic solvents, urea, detergents,

Question 23

What is a prion?

Answer 23

A mis folded protein that has the ability to transmit its misfolded shape into similar proteins.

Question 24

Bovine spongiform encephalopathy - ‘Mad Cow Disease’ is caused by what?

Answer 24

Prions that cause brain damage

Question 25

What protein phenomena causes Creutzfeldt-Jacob disease?

Answer 25

Prions

Question 26

What protein phenomena causes Alzheimer’s Disease?

Answer 26

Protein aggregation in the brain

Question 27

What structural change causes prions to fold abnormally?

Answer 27

transformation of alpha helix to beta strand