LEC3: Protein Structure and Ligand Binding

Question 1

why is the binding of a ligand to its binding partner not a permanent interaction?

Answer 1

because binding sets off a signaling pathway - do not want this always turned on

need binding to re-occur to signal again

Question 2

For a drug that binds to a receptor to be efficacious, should it have a lower or higher K_D than the natural ligand? Why?

Answer 2

drug should have a lower K_D

because K_D is dissociation constant - so a lower K_D means greater affinity

Question 3

How would removing the tetramerization domain from a protein that forms a four-subunit complex affect its function?

Answer 3

it woudl become nonfunctional or less effective?

Question 4

Explain why cooperative binding of oxygen to hemoglobin is important for the normal transport of oxygen from lungs to tissues.

Answer 4

because it allows for most efficient delivery of oxygen to tissues

Question 5

What is an allosteric effector?

Answer 5

molecule that binds to a protein on 1 site, causing a conformational change in the protein that affects its fxn at a distant site

Question 6

what is tertiary structure of a protein? what does it enable?

Answer 6

the overall 3D conformation of a protein

enables protein to become function

i.e. amino acid side chains in a particular region of the protein can form a binding pocket for a ligand

Question 7

what is a ligand, and what does it do? examples of types of ligands?

Answer 7

ligand: molecule that binds reversibly to specific site in proteins, with extremely high specificity

protein, lipid, small molecules, ions, gases

Question 8

what is the beta-adrenergic receptor?

what binds to what?

what is the effect?

Answer 8

example of a ligand-receptor interaction

hormone, epinephrine (aka adrenaline) binds to its cell surface receptor, the beta-adrenergic receptor

b-adrenergic receptor is a **transmembrane protein **w/ 7 membrane-spanning regions of **alpha-helices **

epinephrine-receptor binding activates signaling pathway that controls: blood prssure, cardiac output, breakdown of energy stores

Question 9

what is the equilibrium reaction re: ligand-binding partner?

Answer 9

protein (P) + ligand (L) (PL)

Association: P + L PL

Dissociation: PL P + L

K_D = [P] [L] / [PL]

Question 10

what is K_D? definition, meaning

what does a low K_D mean?

Answer 10

K_D: is the dissociation constant for the dissociation reaction between a ligand & its binding partner

the concentration of the ligand at which 1/2 of the protein is bound to the ligand

lower K_D = higher affinity of ligand for protein, because it takes smaller amt of ligand to 1/2 saturate the binding partner

Question 11

what is oxygen-hemoglobin binding an example of?

Answer 11

ligand binding

it’s reversible

Question 12

what is the structure of adult hemoglobin?

Answer 12

4 globin chains: 2 alpha-globin chains + 2 beta-globin chains

each chain has heme as a tightly bound prosthetic group

Question 13

how does oxygen bind to hemoglobin?

Answer 13

ferrous iron (Fe²⁺) in heme group can form 6 potential bonds

oxygen binds to Fe²⁺ in heme group and it H-bonds w/ histidine in globin

Question 14

what is the structure of myoglobin?

Answer 14

only 1 subunit, rather than a quarternary structure, like hemoglobin

has oxygen-binding site

Question 15

how do oxygen-hemoglobin bind? what does this mean? what does it enables?

Answer 15

example of cooperative binding/allosteric effect/allosteric binding

binding of an oxygen molecule to 1 heme group increases oxygen affinity of remaining heme groups in the same hemoglobin molecule (4th oxygen has 100x affinity as 1st)

enables hemoglobin to very efficiently combine oxygen in the lungs & release it into the tissues

Question 16

how much of oxygen from lungs by myoglobin, hemoglobin, or hypothetically no cooperative binding oxygen is released into tissue?

what does this demonstrate?

what is the shape of this relationship’s curve?

Answer 16

myoglobin: 7%
hemoglobin: 66%
hypothetical: 38%

demonstrates that cooperative binding allows hemoglobin to most efficiently uptake oxygen from lungs, release it in the tissues

SIGMOIDAL relationship

Question 17

in which state does hemoglobin bind to oxygen? when doesn’t it bind to oxygen?

Answer 17

binds in the relaxed (R) state

does not bind in the taut (T) state

Question 18

explain this:

Answer 18

binding of oxygen to hemoglobin

partial pressure of oxygen pO₂ (torr) (x) vs. fractional saturation of hemoglobin (y)

when binding occurs in a cooperative manner, plot produces a sigmoidal curve

cooperative binding allows hemoglobin to become completely saturated w/ oxygen in the lungs, release it in the tissues

Question 19

what are allosteric effectors?

Answer 19

molecules that bind to a protien on a site, & cause a conformational change in the protein that affects its function at a distant site

Question 20

what molecules are allosteric effectors of oxygen-hemoglobin interaction?

Answer 20

1) oxygen itself affects binding of oxygen thru cooperative binding
2) Bohr effect: Low pH
3) High CO₂
4) 2,3-biphosphoglycerate (2,3-BPG)

Question 21

What is the Bohr effect? How does it work?

Answer 21

High concentration of dissolved CO₂shifts equilibrium toward bicarbonate plus protons, aka lowered pH

**Lowered pH causes decrease in affinity of hemoglobin for oxygen **(therefore increased K_D)

This effect allows more oxygen to be released from hemoglobin in active tissues where pH is low

Question 22

what is this?

Answer 22

Bohr effect

higher CO₂ > lowered pH > increased K_D / less hemoglobin-oxygen affinity > more oxygen released to O₂-deficient tissues

Question 23

how does CO₂ have an allosteric effect on hemoglobin?

when does this occur?

Answer 23

CO₂ can bind directly to hemoglobin, stabilize a conformation w/ a lower affinity for oxygen

occurs in conditions of lower pH, were K_D is higher

allows for more release of oxygen into tissues (88%)!

Question 24

what is 2,3-BPG? its allosteric effect on hemoglobin? the result?

Answer 24

2,3-BPH is a highly negative molecule, a metabolic product of glucose breakdown

it binds to positive part of B-chain of hemoglobin

binding of 2,3-BPG decreases the affinity of hemoglobin for oxygen

Question 25

what pathological conditions does 2,3-BPG matter for? why?

Answer 25

high levels of 2,3-BPH in individuals w/ anemia or chronic hypoxia due to lung disease

2,3-BPH causes decreased hemoglobin-oxygen affinity, aka

presence of 2,3-BPH results in relase of oxygenf rom hemoglobin at higher partial pressures of oxygen

Question 26

how does 2,3-BPG impact individuals at high altitude?

Answer 26

2,3-BPH increases in reponse to decrease in partial pressure of oxygen in the air

so it allows adaptation at high altitudes

presence of 2,3-BPH results in relase of oxygenf rom hemoglobin at higher partial pressures of oxygen

Question 27

is hemoglobin structure the same throughout development?

Answer 27

no

diff types of hemoglobin are expressed at diff times during development

Question 28

what is the structure of fetal hemoglobin (HbF)?

what is its affinity for oxygen like re: adult hemoglobin (HbA)

Answer 28

HbF= 2 alpha-globin chains, 2 gamma-globin chains

does not bind strongly to 2,3-BPH, therefore has a **higher affinity for oxygen **than HbA

means oxygen is efficiently transferred from maternal RBC > fetal RBC

Question 29

explain this:

Answer 29

fetal hemoglobin does not bind 2,3-BPG

it therefore has a higher affinity for oxygen than adult hemoglobin

it therefore transfers O₂ more efficiently to RBC

O₂ flows from maternal oxyhemoglobin > fetal deoxyhemoglobin

Question 30

genetic basis for sickle cell anemia?

Answer 30

single ntd change from** **in beta-globin gene

results in single amino acid change from glutamate to valine in beta-globin protein

glutamate = positively charged, usually on outside, vs valine = hydrophobic, usually in center of globulin

valine on outside of

Question 31

why do sickled cells manifest?

Answer 31

amino acid change in B-globin protein from glutamate to valine promotes **polymerization **of variant hemoglobin (HbS) b/c of hydrophobic interactions btwn B-globin subunits per valine

HbS polymerization produces long fibers, which distory shape of RBC into curved, sickled appearance

Question 32

how does RBC change shape in sickle cell anemia? what is the result?

Answer 32

usually flexible, compact, round RBC can go through capillaries easily

sickled RBC cannot, clogs small capillaries