Lecture 3: Structure/Function Relationships of Proteins: Myoglobin & Hemoglobin

Question 1

What is a molecule that binds?

Answer 1

ligand

Question 2

What is the small region where the ligand binds?

Answer 2

binding site

Question 3

What forces are used during non-covalent binding?

Answer 3

non-covalent forces

Question 4

What is K?

Answer 4

Equilibrium Constant

Question 5

What is k?

Answer 5

Rate constant

Question 6

What is another name for the ligand-binding site?

Answer 6

Catalytic (Active) site

Question 7

Are the Kd and Ka inverse?

Answer 7

Yes

Question 8

True or False; Better drugs have a larger kd

Answer 8

False; Better drugs have a smaller kd (disassociation constant) which means they have a higher association constant and high affinity.

Question 9

Which will have the highest affinity?

ka= 10^5
ka= 10^-5

Answer 9

ka= 10^5

Question 10

What are (3) notes to remember about binding? (Exam review)

Answer 10

1) Binding occurred at Eq
2) Binding is reversible
3) Total [L]= Pre[L] because protein is saturated with ligand

Question 11

What is kd in reference to [L]?

Answer 11

[L] at which 1/2 protein bound to ligand

Question 12

What can we assume at y-max as it relates to protein availability?

Answer 12

All of protein is bound to ligand

Question 13

What is the Langmuir Isotherm Equation

Answer 13

[PL]= [P]total [L] total/ Kd + [L] Total

*Shows difference bt amounts of protein/ligand

Question 14

What are suicide inhibitors?

Answer 14

They induce a lot of side effects and are very reactive

Question 15

Which model only allow certain ligands to bind?

Answer 15

Lock & Key Model

Question 16

What are (3) ways Lock & Key Model complement?

Answer 16

size shape charge hydrophobic/hydrophilic character

Question 17

Which model occurs upon ligand binding and causes a conformational change

Answer 17

Induced Fit Model

Question 18

True or False: Induced Fit allows for loose binding of the ligand

Answer 18

False; Induced Fit allows for tight binding of the ligand.

Question 19

True or False: Induced fit can increase the affinity of the protein for a second ligand

Answer 19

True

Question 20

True or False; only the ligand can change their conformations in Induced Fit

Answer 20

False; Both the ligand and protein can change their conformations

Question 21

What is a goal of Myoglobin?

Answer 21

need to store O2 for metabolism but protein side chains lack an affinity for O2

Question 22

How does Myoglobin store O2?

Answer 22

Capture molecule with Heme moiety,

Question 23

True or False; Myoglobin is the main O2 storage in bacteria

Answer 23

False; Main O2 storage in Mammals.

Question 24

True or False; Increase in Delta G means an unfavorable and increase in kd

Answer 24

True; increase in kd means decrease in affinity and unfavorable reaction

Question 25

True or False; Transition metals that bind to Myoglobin cause free radicals

Answer 25

True

Question 26

True or False; O2 binds to myoglobin irreversibly

Answer 26

False; binds to myoglobin reversibly

Question 27

How many subunits does Heme contain?

Answer 27

2

Question 28

What are the subunits that Heme contain

Answer 28

Alpha2-Beta2

Question 29

True or False; Heme is a weak chromophore

Answer 29

False; it is a strong chromophore

Question 30

What is the prosthetic Group of Hemoglobin

Answer 30

Heme

Question 31

What are the 2 interchangable structural states of Hemoglobin

Answer 31

T/R

Question 32

What do we know about T structural states?

Answer 32

Most stable when NOT bound to O2

Question 33

What do we know about R structural states?

Answer 33

O2 binding promotes transitioning

Question 34

True or False; O2 binding is allosteric and cooperative

Answer 34

True

Question 35

True or False; Hemoglobin has a few binding sites

Answer 35

False; Hb has multiple binding sites

Question 36

What is it called when binding sites are able to interact with each other?

Answer 36

Cooperatively

Question 37

What is bound to iron in Heme?

Answer 37

4- Pyrole Rings Proximal His O2

Question 38

What does R in R-state stand for?

Answer 38

Relaxed State

Question 39

What does T in T-State stand for?

Answer 39

Tense state

Question 40

T transforms to R when what happens

Answer 40

O2 binds to T causing a conformational change

Question 41

Which state has a high affinity for O2>

Answer 41

R-state

Question 42

True or false: Blood in lungs has a higher pH than blood in tissues

Answer 42

True; The blood is most acids in the tissues

Question 43

True or false; O2 has a higher affinity for a lower pH

Answer 43

False; O2 has a higher affinity for a higher pH

Question 44

When is O2 released? at higher or lower pH?

Answer 44

Lower pH

Question 45

What is the Bohr Effect

Answer 45

the pH difference between the lungs and metabolic tissues increasing the O2 transfer efficiency

Question 46

Explain how Hb picks up and distributes O2?

Answer 46

Hb pick up O2 from Lungs (high affinity/high pH) and distributes it to the tissues of the body (low affinity/low pH)

Question 47

True or False; When protonated, His favors the T-state

Answer 47

True (lower pH) pronated (acidic)

Question 48

True or False; When deprotonated, His favors the T-state

Answer 48

False; depronation= His favors R-state depronated (higher pH)

Question 49

What AA contributes to the Bohr Effect

Answer 49

Histidine

Question 50

How is CO2 exported via Hemoglobin?

Answer 50

1) Dissolved bicarbonate in the blood | 2) In the form of a carbamate on the Amino Terminal Residue of each Hb polypeptide subunit

Question 51

True or False; When Hb binds to O2 in the lungs, CO2 is released

Answer 51

True

Question 52

BPG is found where?

Answer 52

RBC;

Question 53

Where does BPG bind to O2?

Answer 53

Between the Beta subunits

Question 54

True or False; BPG stabilizes the R-State

Answer 54

False; it stabilizes the T-state

Question 55

True or False; purified HB has a lot of BPG in the blood>

Answer 55

True

Question 56

How can you force a drug to bind to a protein if it has a very high Kd?

Answer 56

Increase amount of ligand present; downside will give you lots of side effects

Question 57

What does Kd depend on?

Answer 57

pH specificity between the protein and ligand

Question 58

What are (3) assumptions about Langmur Equation?

Answer 58

1) Binding is at eq 2) Binding is reversible 3) Total [L] > Total [P] meaning protein is saturated with ligand. So most of the ligand is NOT bound to the protein.

Question 59

True or False; Fractional occupancy of the protein receptor increases as the binding affinity increases

Answer 59

True

Question 60

True or False; Heme group has a porphyrin ring with a Fe atom

Answer 60

True

Question 61

Is Hb tetrameric or monomeric?

Answer 61

tetrameric

Question 62

Is Mb tetrameric or monomeric?

Answer 62

Monomeric

Question 63

How many O2 can Hb bind to?

Answer 63

4-O2

Question 64

How may O2 can Mb bind to?

Answer 64

1-O2

Question 65

How many peptide chains does Mb consist of?

Answer 65

single

Question 66

Where is Mb found

Answer 66

tissues

Question 67

What is bound to iron in Heme?

Answer 67

4-Pyrole rings, Distal histidine, O2

Question 68

Wha type of binding does Hb bind?

Answer 68

Cooperative Binding

Question 69

What type of bonds does 2,3-BPG form with the R-state?

Answer 69

None. It only binds to the T-state/stabilizes it. (via ion interactions)