4-tertiary&quaternary

Question 1

what composes quaternary structure

Answer 1

multiple subunits (>1 polypeptide) combining to form a protein

Question 2

what are subunits

Answer 2

individual polypeptides

Question 3

what is a protomer

Answer 3

a repeating unit in an oligomer

Question 4

what is a repeating unit in an oligomer

Answer 4

a protomer

Question 5

how many polypeptides compose a protomer

Answer 5

it can be more than 1

Question 6

what is a multimer

Answer 6

a protein consisting of many subunits/monomer

Question 7

what are the protomer sin hemoglobin

Answer 7

1 alpha and 1 beta

Question 8

how critical are errors in translation in critical structure and why

Answer 8

less critical because you can just swap out one of the subunits, it doesnt have to be the whole protein

Question 9

what is a monomer

Answer 9

1 peptide chain

Question 10

how many peptide chains in 1 subunit

Answer 10

1

Question 11

what is global symmetry

Answer 11

where the whole protein is involved in symmetry

Question 12

what is local symmetry

Answer 12

where only some portions of the structure contain symmetry

Question 13

do you see reflectional symmetry and why or why not

Answer 13

no because that inverts stereochemistry

Question 14

what is pseudo-symmetry +example

Answer 14

when non-identical homologous subunits are related by symmetry (like alpha and beta subunits that are very similar)

Question 15

how can you describe cyclic symmetry (C and N)

Answer 15

CsubN is N promoters arranged around 1 rotation axis

Question 16

what does the n represent in rotational symmetry

Answer 16

n=amount of protomers

Question 17

how can you describe dihedral symmetry (C and N)

Answer 17

DN is 2N protomers arranged around 2 axes (2x CN)

Question 18

what are the folds of the 2 axes in dihedral symmetry

Answer 18

1 is N-fold

the other is 2fold

Question 19

how many protomers in tetrahedral symmetry

Answer 19

12

Question 20

how many protomers in octahedral symmetry

Answer 20

24

Question 21

how many protomers in icosahedral symmetry

Answer 21

60

Question 22

what is helical symmetry

Answer 22

when protomers are relaxted to eachother by rotation AND translation

Question 23

practice drawing the symmetries

Answer 23

ok

Question 24

can you have dihedral symmetry with 5 protomers

Answer 24

no, you need an even # of protomers

Question 25

what are 2 types of symmetry you can have with 6 protomers

Answer 25

C6 and D3

Question 26

what are most of the forces in protein folding like (2 things)

Answer 26

weak and non covalent

Question 27

what is denaturation

Answer 27

destroying the native state (unfolding)

Question 28

what are 4 ways to denature proteins

Answer 28

Heat pH detergents and organic solvents/molecules

Question 29

how do denaturants work (4 things)

Answer 29

water soluble, strong H bonding ability, disrupts hydrophobic interactions, effects entropy of system "chaotropic"

Question 30

what are 2 denaturant examples

Answer 30

guanidium ion, urea

Question 31

what do reducing agents do (2 things)

Answer 31

reduce disulfide bonds and become oxidized as part of the reaction

Question 32

what are 2 examples of reducing agents

Answer 32

BME and DTT

Question 33

what kind of process is denaturation

Answer 33

cooperative

Question 34

what does it mean for denaturation to be a cooperative process

Answer 34

as you continue to denature, it gets easier and easier

Question 35

what is denaturation (definition)

Answer 35

the transition from folded to unfolded

Question 36

what kind of range does the the transition from folded to unfolded occur

Answer 36

over a small range (not sure what that means)

Question 37

what is TM (what does it stand for and what its characteristic of)

Answer 37

midpoint transition, characteristic of both the denaturant and the protein

Question 38

why does it get easier and easier to denature the protein as time goes on

Answer 38

because unfolding part of it decreases the energy required to unfold the rest of the structure

Question 39

what shape is the thermal denaturation of protein curve

Answer 39

sigmoidal

Question 40

how does temperature work as a denaturant

Answer 40

it breaks weak non-covalent forces

Question 41

how can you track the transition between folded and unfolded proteins

Answer 41

spectroscopic markers

Question 42

what does TM mean on the graph

Answer 42

the midpoint between fully folded and fully unfolded

Question 43

what does increasing concentrations of urea affect denaturation

Answer 43

it increases it

Question 44

how does urea cause denaturation

Answer 44

disrupts hydrophobic interactions

Question 45

what does the value of Tm depend on (3 things)

Answer 45

which protein and denaturant is used, and their concentrations

Question 46

what happens once you remove denaturants

Answer 46

the protein may be able to refold into native structure if no covalent bonds have been affected

Question 47

what happens if the disulfide bonds reform before the denaturant is removed

Answer 47

the protein may be locked into the wrong conformation (if you remove the thing that broke disulfide bonds but didnt remove the denaturant)

Question 48

are disulfide bonds primary structure

Answer 48

no | they just help stabilize it

Question 49

what kind of process is protein folding

Answer 49

cooperative process (like unfolding)

Question 50

what are the 4 steps in protein folding (what forms in order after primary structure)

Answer 50

formation of 2ary structures, motifs, domains, final tertiary

Question 51

when is molten globule state acheived

Answer 51

after formation of secondary but prior to completion of tertiary structure

Question 52

what is the energy level of the molten globule state (compared to native and unfolded)

Answer 52

it is inbetween

Question 53

what are 3 characteristics of the molten globule state

Answer 53

hydrophobic core, secondary structures present, collection of dynamic structures

Question 54

what is the conformational entropy in unfolded states

Answer 54

large

Question 55

what is the conformational entropy in folded states

Answer 55

smallest

Question 56

what is the free entropy in unfolded states

Answer 56

relatively high

Question 57

what do the local minima represent in the free-energy funnel diagram

Answer 57

relatively stable states

Question 58

what happens to the number of states present as folding progresses

Answer 58

they decrease

Question 59

what happens to conformational entropy as folding increases

Answer 59

it gets smaller

Question 60

does a folded or unfolded protein have higher free energy

Answer 60

unfolded

Question 61

does a folded or unfolded protein have higher conformational entropy

Answer 61

unfolded

Question 62

what does it mean for the unfolded protein to have a high free energy

Answer 62

molecule is unstable, and flops easily between the different conformational states.

Question 63

what is the free energy of a folded native state protein

Answer 63

low

Question 64

what are amyloid fibres

Answer 64

very stable misfolded states

Question 65

what is misfolding

Answer 65

formation of stable structures which are not native

Question 66

what are 2 types of proteins that assist in protein folding

Answer 66

molecular chaperones and isomerases

Question 67

what are 2 types of molecular chaperones

Answer 67

head shock proteins and chaperonins

Question 68

what are 2 types of isomerases

Answer 68

PDI and PPI

Question 69

do chaperones change the final structure of protein

Answer 69

no but they help them get there

Question 70

what can aggregate in misfolded proteins

Answer 70

exposed hydrophobic groups

Question 71

what can happen with hydrophobic groups in misfolded proteins

Answer 71

they become exposed and may aggregate

Question 72

what do chaperones do to misfolded proteins

Answer 72

isolate them so that they are unable to interact

Question 73

what is required to unfold misfolded proteins

Answer 73

energy, typically ATP hydrolysis

Question 74

is the effect of chaperones kinetic or thermodynamic and why

Answer 74

kinetic because it doesnt change the fold of the protein but assists in formation

Question 75

is ATP hydrolysis linked to unfolding and why

Answer 75

yes because you need energy to unfold

Question 76

what does ATP hydrolysis do to the binding site for the protein substrate

Answer 76

it changes it

Question 77

what can the GroEL/GroES complex do

Answer 77

help refold misfolded things (along with ATP)

Question 78

what is PDI stand for

Answer 78

protein disulfide isomerase

Question 79

what are the 2 properties of PDI (protein disulfide isomerase)

Answer 79

isomerase property and oxidoreductase property

Question 80

what does PDI protein disulfide isomerase do

Answer 80

catalyzes the shuffling of disulfide bonds to form the correct bonds of the native conformation

Question 81

what does PPI stand for

Answer 81

peptide prolyl cis-trans isomerase

Question 82

what is the role of PPI (peptide prolyl cis-trans isomerase)

Answer 82

help proline adopt a cis peptide bond (only 10% are cis, its not spontaneous)

Question 83

why is PPI needed to help proline adopt a cis peptide bond

Answer 83

because that is not a spontaneous formation (only 10% are in the cis bond)

Question 84

what did Christian Afinsen say

Answer 84

the native conformation is determined by the totality of interatomic interactions and amino acid sequence in a given environment