Lecture 3

Question 1

5 Functions of globular proteins

Answer 1

storage of ions and molecules, transport of ions and molecules, defense against pathogens, muscle contraction, and biological catalysis

Question 2

Ligand

Answer 2

molecule that binds to the protein

Question 3

Binding site

Answer 3

region in the protein where the ligand binds

Question 4

How do ligands typically bind?

Answer 4

Via non-covalent forces, which enables the interactions to be transient

Question 5

Suicide inhibitors

Answer 5

inhibitors that bind in a covalent manner.

Question 6

k(a)

Answer 6

association rate constant

Question 7

k(d)

Answer 7

dissociation rate constant

Question 8

K(a)

Answer 8

association constant at equilibrium

Question 9

K(d)

Answer 9

dissociation constant at equilibrium. 1/2 Vmax

Question 10

Large K(d)

Answer 10

Lots of free protein and ligand. Low affinity

Question 11

Low K(d)

Answer 11

Protein-ligand complex in high concentration. High affinity of protein

Question 12

Langmuir Isotherm Equation

Answer 12

[PL] = ( [P]t [L]t )/( K(d) + [L]t ).

describes association between a protein and its ligand

Question 13

3 assumptions for Langmuir Isotherm Equation

Answer 13

Binding is at equilibrium, binding is reversible, free ligand concentration = total ligand concentration if ligand concentration is much larger than protein concentration

Question 14

Fractional occupancy

Answer 14

ratio of the signal to the max signal.

= [L]t / (K(d) + [L]t)

Question 15

K(d) in relation to K(a)

Answer 15

K(d) = 1 / K(a)

Question 16

pH and K(d)

Answer 16

pH can change the protonation state and thus change the structure and affinity.

Question 17

Induced fit

Answer 17

conformational changes occur upon ligand binding. Allows for tights fit of binding. Increases affinity of the protein for a second ligand.

Question 18

Function of myoglobin

Answer 18

Store oxygen for metabolism in the tissues.

Question 19

Prosthetic group in myoglobin

Answer 19

Iron on a porphyrin ring (with Iron it is a Heme)

Question 20

Important residue in myoglobin

Answer 20

Proximal histidine

Question 21

Chromophore

Answer 21

the heme group absorbs light in UV and visible range

Question 22

Myoglobin light visibility appearance

Answer 22

deoxymyoglobin appears purplish (429 nm). oxymyoglobin appears red (414 nm).

Question 23

Hemoglobin structure

Answer 23

tetramer of two subunits (alpha and beta)

Question 24

partial pressure of oxygen in lungs and in tissues

Answer 24

lungs - 13kPa

tissues - 4 kPa

Question 25

type of graph for hemoglobin

Answer 25

sigmoidal. Hemoglobin has a much lower affinity in the tissues

Question 26

Positive cooperativity

Answer 26

first binding event increases affinity at remaining sites

Question 27

Negative cooperativity

Answer 27

first binding event reduces affinity at remaining sites

Question 28

3 important residues in deoxyhemoglobin

Answer 28

Lysine, Histidine, and aspartic acid

Question 29

T state

Answer 29

Tense state, has low affinity for oxygen

Question 30

R State

Answer 30

Relaxed state, has high affinity for oxygen

Question 31

Important residue for transition of T state to R state

Answer 31

Proximal histidine

Question 32

pH in lungs, blood, and tissues

Answer 32

lungs: 7.6
blood: 7.4
tissues: 7.2

Question 33

Bohr effect

Answer 33

the pH difference between lungs and metabolic tissues increases the oxygen transfer efficiency. When lower pH, the His (protonated) favors the T state

Question 34

CO2 export

Answer 34

some dissolved as bicarbonate. some exported as carbamate on the amino terminal residues of each hemoglobin subunit

Question 35

Carbamate formation

Answer 35

condensation that produces a hydrogen which will protonate the histidine and promote oxygen dissociation

Question 36

Allosteric effector for hemoglobin

Answer 36

BPG (2,3-biphosphoglycerate). Negatively charged and stabilizes it in the T state