determining protein folding

Question 1

amino acid sequences determine

Answer 1

native (proper 3D) structure and folding pathway to that native structure

Question 2

FOlding

Answer 2

balances several thermodynamic parameters in order to get negative delta G

Question 3

conformational entropy

Answer 3

works against folding because delta S is negative (less conformational choices as a ball rather than a string)

Question 4

Why is delta H favorable for folding?

Answer 4

noncovalent interactions… When these interactions occur during protein folding, they release energy, making the process energetically favorable overall. The protein folds into a structure where these interactions are maximized, leading to a lower enthalpy and a more stable state.

Question 5

How are salt bridges broken?

Answer 5

add ions, change the protonation state by adding acid or base which would destroy tertiary structure

Question 6

proteins H bonds, how are they broken?

Answer 6

NH, OH, SH?
pH change, agitation

Question 7

Dispersion forces what amino acids are involved?

Answer 7

most important are the nonpolar

Question 8

how are dispersion forces destroyed

Answer 8

with fatty acid detergents, it will pull it apart

Question 9

How does heat affect folding?

Answer 9

as you heat something molecular motion increases, which may typically break interactions

Question 10

how does urea affect folding?

Answer 10

urea = chaotropic agent (disripts the structure of and denatures macromolecules such as proteins)
- introduce chaos, disrupts interactions

Question 11

hydrophobic effect how is that key to entropy of folding?

Answer 11

need protein to fold hydrophobic residues inside, referred to as hydrophobic collapse

Question 12

protein stability

Answer 12

proteins are only slightly stable

Question 13

protein denaturation

Answer 13

occurs over a narrow temperature range

Question 14

Tm

Answer 14

is the melting temperature, halfway between the range of protein denaturation curve where 50% is folded and 50% is unfolded

Question 15

Why are disulfide bonds produced in proteins

Answer 15

to have stability, used extracellularly
ex: insulin, has disulfide bonds and proteins that need to be very strong
ex: superoxide dimutase (SOD1) copper zinc protein present to destroy free radicals, in a very reactive environment so uses disulfide bonds
(goes rogue in ALS)

Question 16

extracellular disulfide vs intracellular disulfide

Answer 16

extracellular: oxidized form predominates,
intracellualr: reduced form predominates

Question 17

more disulfide bonds mens that

Answer 17

there is a decrease in number of conformations possible in the unfolded state (ex, glue on a string)
- entropy decreases
- folded state is less affected as entropy is already low