Globular Proteins

Question 1

ligand

Answer 1

molecule that reversibly binds to a protein

Question 2

binding site

Answer 2

• site where ligand docks
• specific size, shape, charge, hydrophilic/hydrophobic
• noncovalent forces

Question 3

induced fit

Answer 3

binding results in conformational change

Question 4

myoglobin: function

Answer 4

• store O2 for metabolism
• protein side chains lack affinity for O2

Question 5

myoglobin: structure

Answer 5

• peptide bond in trans-config.
• all a-domain: 8 a-helices (A-H)
• 3 or 4 proteins at bends
• hydrophobic residues interior
• Fe(II) at center of heme coordinated by 4 porphyrin bond to Fe, O2-Fe

Question 6

Ka equation

Answer 6

[PL]/[P][L]

Question 7

Kd equation

Answer 7

[P][L]/[PL]

Question 8

fractional saturation equation

Answer 8

θ=protein occupied by ligand/total protection
= [PL]/[P]+[PL]

Question 9

hyperbolic curve equation

Answer 9

θ=[L]/Kd+[L]

Question 10

carbon monoxide

Answer 10

• binds 20,000x better than O2 because of lone electron pair that donates to Fe 3+
• similar size and shape to O2 because of lone electron pair
• blocks myoglobin and hemoglobin

Question 11

myoglobin as O2 transporter

Answer 11

• pO2 in lungs is ~13 kPa (100 mmHg)
• myoglobin binds oxygen well
• pO2 in tissues is ~ 4 kPa (20 mmHg)
• myoglobin won’t release oxygen

Question 12

hemoglobin as O2 transporter

Answer 12

• affinity has to vary with pO2 for effective transport
• hemoglobin binds in lungs well, releases about 1/2 of O2 in tissues

Question 13

hemoglobin: physiochemical info

Answer 13

• tetrameric protein (a2B2)
• Mr 64,000 (subunit 16,000)
• 4 total

Question 14

hemoglobin: function

Answer 14

• sensitive response to changes in [O2], [CO2], [H+], [BPG]

Question 15

cooperativity

Answer 15

positive
- first binding event increases affinity at remaining sites (hemoglobin is positive)

Question 16

hemoglobin: quaternary structure

Answer 16

• a2B2 dissociates to two aB dimers in presence of urea
• strong interactions between unlike subunits
• conformations
  
  • oxyhemoglobin
  • deoxyhemoglobin

Question 17

oxyhemoglobin

Answer 17

HbO2
- R (relaxed) state
- greater affinity for O2

Question 18

Deoxyhemoglobin

Answer 18

Hb
- T (tense) state
- lower affinity for O2
- stabilized by greater number of ion pairs than R-state

Question 19

T to R transition

Answer 19

1. movement of heme iron by 0.039 nm (0.39 Å)
2. O2 binds, Fe2+ pulled into heme plane, dragging HisF8 and F helix in
   
   • spin state high to low
3. upon O2 binding, F helix tilts and translates by ~ 1Å to avoid crashing into heme
   
   • subunits tightly coupled, large tertiary changes in subunit cannot occur with full molecule quaternary changes
4. one O2 in each aB: strain sufficient to tear away C-terminal

Question 20

allosteric proteins: concerted

Answer 20

• 2 conformations in equilibrium
• ligand can bond to either
• molecular symmetry conserved

Question 21

allosteric proteins: sequential

Answer 21

• ligand binding to subunit causes conformational change
  
  • may cause changes in adjacent subunits
• the more ligand bound, the more likely subsequent conformational changes will occur

Question 22

bohr effect

Answer 22

• affinity for O2 decreases with decreasing pH
• Hb releases 10% more O2 at pH 7.2 than 7.4
• increased [H+] favors in pair conformation, driving R–>T transition and releasing O2

Question 23

bohr effect in tissues

Answer 23

H+ is generated as a consequence of HCO3- formation

Question 24

bohr effect in lungs

Answer 24

O2 binds, driving T–>R, releasing H+ and driving CO2 evolution

Question 25

hemoglobin variants: HbS

Answer 25

• Glu6 is Val6 in beta-subunit
• interactions between hydrophobic val side chains at position B6 and hydrophobic pockets of neighboring side chains

Question 26

hemoglobin variants: HbA

Answer 26

adult hemoglobin
- a2B2

Question 27

hemoglobin variants: HbF

Answer 27

fetal hemoglobin
- a2Y2
- His143 is Ser143
- BPG binds to T-state, interacts with His143 well, not Ser143 (lower affinity in HbF)