Lecture 2: Protein Function

Question 1

list the 6 key principle of proteins that fuction through reversible interaction

Answer 1

1. The functions of many proteins involve the reversible binding of other molecules.
2. A ligand binds a protein at a binding site complementary in size, shape, charge, and hydrophobic or hydrophilic character.
3. proteins are flexible
4. binding of a protein and a ligand is coupled to a conformational change in the protein that makes the binding site more complementary to the ligand, permitting tighter binding (Induced fit)
5. In a multisubunit protein, a conformational change in one subunit often affects the conformation of other subunits
6. Interactions between ligands and proteins may be regulated.

Question 2

Explain reversible interactions in the function of proteins?

Answer 2

interactions in which neither the chemical configuration nor the composition of the bound molecule is changed

oxygen transport, nerve impulse transmission and immune function

Question 3

myoglobin

Answer 3

• consists of alpha helices linked together by turns to form a globular structure
• oxygen binding facilitated by heme group
  -contains organic component called PROTOPORPHYRIN with a central Fe 2+ ion

Question 4

Oxygen binding changes the position of the iron, Explain?

Answer 4

• iron ion lies slightly outside the plane of the porphyrin in deoxymyglobin
• Binding of oxygen rearranges the electrons in the iron, making it smaller and allowing it to move within the plane of the porphyrin

Question 5

Oxygen binding changes the position of the iron, Explain?

Answer 5

• iron ion lies slightly outside the plane of the porphyrin in deoxymyglobin heme but moves into the plane of the heme on oxygenation
• it consist of the 5th and 6th coordination sites where 2 additional bonds are formed on each side of the heme plane.
• the 5th c site is occupied by imidazole ring of histidine in myoglobin hence oxygen binding occurs on the 6th c site
• in deoxymyoglobin this site is unoccupied
• binding of oxygen rearranges the electrons in the iron making it smaller thus allowing it to move within the plane of porphyrin

Question 6

hemoglobin

Answer 6

• is an assembly of 4 myoglobin like subunits
• has 4 polypetide chains 2 alpha and 2 Beta chains
• is a dimer of 2 alphabeta protomers

Question 7

protomer

Answer 7

is the structural unit of a protein containing quartenary structure

Question 8

describe the oxygen binding curves of myoglobin and hemoglobin

Answer 8

• fractional saturation against oxygen partial pressure
• curve sharply rises as pO2 rises for myoglobin showing it has a high affirnity for O2
• the oxygen binding curve is a sigmoidal shape for hemoglobin
• half saturation is at 26 mmHg showing the binding is weaker compared to myoglobin
• the shape suggest that binding of oxygen to one site on the hemoglobin increases the likelihood of oxygen binding to the remaining unoccupied sites, this behaviour is referred to as cooperative

Question 9

Explain the physiological significance of cooperative binding?

Answer 9

• the cooperative release of oxygen favors more complete unloading of oxygen in tissues
• if myoglobin were employed, due to its high affirnity, the oxygen would tightly bind to the myoglobin and this would deprive tissues of oxygen

Question 10

T (tense) state

Answer 10

• quaternary structure in deoxyhemoglobin
• molecule is constrained by subunit subunit interactions

highly unstable

Question 11

R (relaxed state)

Answer 11

• quartenary structure of oxyhemoglobin
• oxygen binding sites are free of strain
• hence they bind to oxygen with higher affirnity than sites in the T state

Question 12

Oxygen binding changes the quatenary structure of hemoglobin, explain?

Answer 12

• Cooperative binding requires that binding of oxygen at one site in the tetramer influence the oxygen binding at other sites
• The α1β1 and α2β2 dimers rotate approximately 15 degrees with respect to one another
• making them freer to move with respect to one another in oxygenated state than in the deoxygenated state

Question 13

co

concerted model

Answer 13

• Overall assembly can exist in 1 of 2 forms
• Binding of Oxygen at one shifts the equilibrium towards the R state.

Question 14

explain the difference in sequential model and concerted model in explaining Hemoglobin cooperativity

Answer 14

• in the concerted model the overal assembly can only exist in one of 2 states, T state and the R state
  where as in the sequetial model individual subunits can have different conformations.

Question 15

Fetal Hemoglobin

describe the structure and give reasons?

Answer 15

• fetal hemoglobin tetramers include 2 alpha chains and 2 gamma chains
• due to substitution of a serine residue for His 143 in the beta chains
• therefore oxygen binding affirnity of fetal hemoglobin is higher than that of maternal hemoglobin
• allowing for effective transfer of oxygen from maternal to fetal blood.

Question 16

fractional saturation

Answer 16

fraction of possible binding sites that are bound to oxygen

from 0 - 1

Question 17

sequential model

Answer 17

• binding of oxygen to one site in an assembly increases the binding affinity of neighboring sites without inducing full conversion from T into the R state

Question 18

2,3 Biphosphoglycerate molecule

Answer 18

• stabilizes the T state until binding of sufficient Oxygen converts it to R state
• crucial in determining oxygen affirnity to hemoglobin

Question 19

Fetal hemoglobin

Answer 19

• 2 alpaha chains and 2 gamma chains
• serine residue is substituted for His 143
• reducing the affirnity of 2,3 BPG for fetal hemoglobin
• hence oxygen binding affirnity of fetal hemoglobin is higher than maternal hemoglobin

Question 20

effect of carbon monoxide

Answer 20

• binds to hb at the same site as oxygen
• binds 200-fold more tightly
• hence can displace oxygen from Hb even at low partial pressures
• preventnting oxygen delivery to tissues hence suffocation.

treatment- hyperbaric oxygen therapy

CO2 bound to one site increases the stability of the R state preventing delivery of Oxygen to tissues

Question 21

Bohr Effect

Answer 21

• CO2 and H+ from metabolism influence oxygen release
• H+ and CO2 are allosteric cofactors, binds in sites distinct from oxygen binding site
• oxygen affirnity of Hb decreazes as PH drops(tendency to release oxygen)
• aa residue within the subunits of hemoglobin form salt bridges (Ionic interactions).
• stabilizing the T state hence oxygen is released

Question 22

sickle cell anaemia

Answer 22

• red blood vessels are sickle shaped
• due to mutated

Question 23

Carbon dioxide effect

Answer 23

• lead to the formation of carbonic acid
• This drops the PH which the stabilizes the T state

Question 24

sickle cell anaemia

Answer 24

• molecular defect is a single amino acid substitution in the β chain of hemoglobin.
• Glutamate is replaced by valine.
• reduces the solubility of hemoglobin.

Question 25

alpha thallasemia

Answer 25

• loss or reduction of a single hemoglobin chain.
• result is low levels of functional hemoglobin
• decreased production of red blood cells

Question 26

beta thallasemia

Answer 26

• β chain of hemoglobin is not produced in sufficient quantity
• hence alpha chains form insolunle aggregates that precipitate inside immature red blood cells
• loss of RBC causes anaemia