Protein function

Question 1

what determines a proteins 3D structure?

Answer 1

its primary structure

Question 2

what is the structure of myglobin?

Answer 2

tertiary structure

Question 3

what is the structure of hemoglobin?

Answer 3

quaternary structure

Question 4

where does hemoglobin bind to and where is it released?

Answer 4

binds to O2 in the lungs and is released in tissues

Question 5

where does myoglobin bind to? what is it’s function?

Answer 5

binds to O2 in muscles

-O2 reserve during exercise
-facilitates O2 diffusion in muscle tissue
-stores O2 in aquatic animals

Question 6

what is the relationship between protein function and ability to bind?

Answer 6

the function of many proteins depends on their ability to bind other small molecules (ligands) reversibly

Question 7

what does a high Kd signify?

Answer 7

a low affinity

Question 8

what does a low Kd signify?

Answer 8

a high affinity

Question 9

what is the relationship between ligand-protein complex and the [ligand] and [protein]?

Answer 9

the affinity of Y for X greatly influences the extent to which the (XY) complex is formed, regardless of the concentrations of X or Y. Higher affinity results in a greater proportion of complex formation, while lower affinity leads to less complex formation.

Question 10

which numbers show a higher affinity? which ones show lower?

Answer 10

1 and 2- higher
3 and 4- lower

Question 11

what is Kd ?

Answer 11

It’s a measure of the affinity of a ligand for its receptor. In other words, it represents the concentration of a ligand at which half of the available binding sites on the receptor are occupied by the ligand

Question 12

which ligand will have a higher Kd? what would the binding curve look like?

Answer 12

Kd (z) will be higher due to its lower affinity

Question 13

what helices is the heme group between for myoglobin?

Answer 13

between helices E and F

Question 14

what are the structural differences between hemoglobin and myoglobin?

Answer 14

hemoglobin - quaternary structure
myoglobin - tertiary structure

Question 15

what is the structure of heme?

Answer 15

-circular and planar
-Fe2+ ring between four N atoms

Question 16

is heme hydrophobic or polar?

Answer 16

largely hydrophobic with 2 polar charged groups

Question 17

what state must the Fe atom be inside the heme group?

Answer 17

Fe must be maintained as Fe2+

Question 18

what position is the O2 at in regards to heme?

Answer 18

6th

Question 19

what position is the Histidine at in regards to the heme group?

Answer 19

5th

Question 20

what interactions are important for the heme to fit in the bidning pocket?

Answer 20

hydrophobic interactions

Question 21

what positions is the heme group at?

Answer 21

1-4

Question 22

what forces hold the hemoglobin porphyrin ring in place?

Answer 22

hydrophobic interactions and coordination bond between Fe2+ and a His (F8 or proximal)

Question 23

what is the function of the proximal His?

Answer 23

1) bind heme into heme-binding pocket
2) prevent oxidation of iron atom

Question 24

what is the proximal His reffered to as?

Answer 24

His F8

Question 25

what is the distal His reffered to as?

Answer 25

His E7

Question 26

what is the function of the Distal His (His E7)?

Answer 26

1) increases O2 binding affinity 2) lowers affinity of other molecules (CO) 3) creates increased specificity for O2 -anchors heme and doesn't interact with Fe2+ at all

Question 27

what factors are important in O2 binding?

Answer 27

specificty and affinity

Question 28

what is the realtionship between reactions and affinity?

Answer 28

favourable rxn's - increase affinity unfavourable rxn's - decrease affinty -in this example CO is blocked by the distal His in order to prevent binding

Question 29

what is the difference on the dissociation curve of myoglobin vs hemoglobin?

Answer 29

-higher affinity of O2 to bind to myoglobin -sigmoidal shape for hemoglobin

Question 30

what subunits does hemoglobin have?

Answer 30

2 alpha 2 beta

Question 31

what is the affect of a conservative substitution?

Answer 31

they have minor effects on structure / function due to simalar AA structure

Question 32

how does the binding of O2 change for hemoglobin as opposed to myoglobin?

Answer 32

the binding is the same

Question 33

what does a hyperbolic curve indicate about affinity?

Answer 33

is tells us that affinity is constant -Kd doesnt change -myoglobin

Question 34

what does a sigmoidal curve tell us about affinity?

Answer 34

it tells us that binding affinity is cooperative -ligand affinity changes as more ligands bind -hemoglobin

Question 35

what structural changes allow for Hb to change its affinity for O2?

Answer 35

change in tense vs relaxed state -tense has low affinity -relaxed has high affinity

Question 36

what residues is the His group located between in the T state (deoxyhemoglobin)?

Answer 36

Between Thr and Pro

Question 37

what residues is the His group located between in the R state (oxyhemoglobin)?

Answer 37

between 2 Thr groups

Question 38

explain the differences between the T and R state of hemoglobin in regards to its affinity, O2 binding and central cavity size

Answer 38

Question 39

what does the word allostery mean?

Answer 39

other space

Question 40

what is the function of an effector?

Answer 40

alters binding affinity based apon binding

Question 41

what is a homoallosteric effector?

Answer 41

binding affects further binding of the same compound

Question 42

what is a heteroallosteric effector?

Answer 42

binding affects further binding of a different compound

Question 43

what does an activator do to affinity?

Answer 43

increases binding affinity -positive effector

Question 44

what does an inhibitor do to affinity?

Answer 44

decreases binding affinity -negative effector

Question 45

what kind of effector is O2 to Hb?

Answer 45

homoallosteric activator

Question 46

what events occur in O2 binding?

Answer 46

1) O2 binds to a subunit 2) Fe2+ moves into plane of heme -His F8 moves with Fe -Helix F moves 3) Subunit interface change affects other subunits -Helix F / His F8 / Fe2+ movement -O2 binding site becomes high-affinity (R), oxygen binds more readily to other binding sites

Question 47

what 2 molecules are allosteric effectors for Hb?

Answer 47

O2 -homoallosteric activator BPG (2,3-bisphosphoglycerate) -heteroallosteric inhibitor for O2 H+ -heteroallosteric inhibitor for O2

Question 48

what is BPG essential for in regards to Hb?

Answer 48

BPG is small and highly negative, it is essential in formation of the T state -negative allosteric effector of O2 binding -increased [BPG] = decreased O2 binding

Question 49

where does BPG bind to?

Answer 49

binds in the central cavity of deoxyhemoglobin (T-state)

Question 50

what does BPG interact with in the binding cavity?

Answer 50

the (-) charges on BPG interact with the (+) charged groups on the protein

Question 51

why does BPG not bind in the R state?

Answer 51

the central cavity is too small

Question 52

what does metabolism do to [H+]? how does this affect side chains on Hb?

Answer 52

increases proton concentration and lowerd pH -these causes protonation of side chains and functional groups

Question 53

what affect does BPG have on protonation of side groups?

Answer 53

groups associated with BPG binding become protonated (Bohr effect) -enhance BPG binding -Reduce O2 binding -subunit interface effected by new electrostatic interactions

Question 54

what does the position state of Hb depend on?

Answer 54

BPG presence, [H+], and ppO2

Question 55

what Hb state is favoured in the lungs?

Answer 55

R state is favoured due to high ppO2 and high pH -higher pH = higher affinity

Question 56

what state do actively respiring tissues favour?

Answer 56

they favour the T-state due to their low pH and low ppO2 -oxygen is released

Question 57

explain the path of O2 transport by Hb

Answer 57

deoxyHb -BPG bound; T-state ---> Lungs bind O2 and Hb switches to R-state -BPG not bound ---> peripheral tissues release O2 -BPG bound

Question 58

what is the effect of CO2 On oxygen?

Answer 58

CO2 promotes release of O2 -CO2 dissociates into HCO3- and H+ -increased H+ will decrease pH and decrease affinity

Question 59

what is the effect of salt bridges on Hb?

Answer 59

salt bridges stabilize the deoxy form (T-state) of Hb -CO2 binds to the N-terminus of Hb, HbNH-COO-, this forms a salt bridge stabilizing the T state.

Question 60

what substitution causes sickle cell disease?

Answer 60

Glu6 for Val

Question 61

how does the substitution of Glu6 for Val affect O2 binding to Hb?

Answer 61

the binding of Val to the hydrophobic surface exposed between E and F helices during transition from T to R causes Hb molecules to aggregate into long polymers / fibres

Question 62

how does affinity differ from fetal Hb, adult Hb and Mb?

Answer 62

adult Hb < Fetal Hb < Mb

Question 63

what is the His residue involved in fetal Hb binding?

Answer 63

His 143

Question 64

what are the 4 main roles for His in relation to Hb function?

Answer 64

1) His F8 - proximal 2) His E9 - distal 3) 4 His in central cavity 4) subunit interface