Biochem Protein Lecture 10

Question 1

Is oxygen highly soluble in H2O?

What does this mean for transport to bodily tissues?

Answer 1

No, it has limited solubility

It can’t be transported to bodily tissues by dissolving it in blood serum or diffusion through tissues

Question 2

What are needed to transport and store O2 in the body?

Answer 2

Proteins

Question 3

Reversible binding of O2 requires….

Answer 3

A transition metal

Question 4

Can AA side chains reversibly bind O2?

Answer 4

No.

Question 5

What is incorporated to heme to reversibly bind O2?

Answer 5

Iron

Question 6

This is a complex of protoporphyrin and iron

Answer 6

Heme

Question 7

Free heme (not bound to protein) leaves Fe2+ with how many open coordination bonds?

Answer 7

2

Question 8

Where is heme located in heme-containing proteins? Why?

Answer 8

Deep within the protein structure to prevent conversion to Fe3+ (via the air)

Question 9

In a free heme, one of the two open sites is occupied by a ______

What is the other open site?

Answer 9

His (F8) residue (proximal his)

The Open O2 binding site

Question 10

The imidizole group of a second His (E7) called _______ is located on the O2 binding site of heme

Answer 10

Distal His

Question 11

How does the distal His assist in O2 binding?

Answer 11

H-bonds

Question 12

A single polypeptide with one molecule of heme

Answer 12

Myoglobin

Question 13

The helical segments of myoglobin are labeled __ through ____

Answer 13

A through H

Question 14

This refers to the 8th residue in α helix F

Answer 14

His F8

Question 15

The bends of myoglobin are labeled AB, CD, etc, indicating the α helical segments they connect

Answer 15

!

Question 16

Oxygen is removed from the air in the lungs, transported by ______ in red blood cels to tissues of the body, and then delivered to cells at a pressure not much lower than that found in the atmosphere

Answer 16

Hemoglobin

Question 17

Part of oxygen transported to tissues by Hb is used for _____ in mitochondria

There rest of the oxygen may be stored by ____ and saved for when oxygen demand increases

Answer 17

Aerobic metabolism

Myoglobin

Question 18

Within cells, dissolved oxygen diffuses, or it is bound to _____ which helps transport oxygen to the mitochondria

Answer 18

Myoglobin

Question 19

Carbon dioxide, released from oxidative processes in tissues, is carried back to the lungs by ___ and expired

Answer 19

Hemoglobin

Question 20

As shown in the aerobic metabolism figure 7.4, oxygen is carried by hemoglobin circulatin gin the ____ to the tissues

Answer 20

Capillaries

Question 21

Oxygen diffuses into the muscle cells through the

Answer 21

Capillaries

Question 22

______ is found inside muscle cells. It binds the oxgen and delivers it to the mitochondria

Answer 22

Myoglobin

Question 23

Myoglobin must release O2 when and where it is needed, what two muscle types have higher energy needs and require rapid transport from Hb to mitochondria in the respiring cells. Mb aids in this process

Answer 23

Heart and skeletal muscle

Question 24

What is the equilibrium expression for the reversible binding of a proteins to a ligand?

Apply this concept to Mb and O2

Answer 24

P + L —> PL

Mb + O2 —> MbO2

Question 25

What equation characterizes the equilibrium expression for the reversible binding of Mb and O2?

Answer 25

Ka = [MbO2]/[Mb][O2]

Question 26

This equilibrium constant provides a measure of the affinity of oxygen for Mb A higher Ka means a HIGHER/LOWER affinity of O2 for Mb

Answer 26

Ka Higher

Question 27

The fraction of Mb molecules that are oxygenated can be determined by differences in the _______ of Mb in the presence and absence of O2

Answer 27

Absorption spectra

Question 28

Θ (peta) = ?

Answer 28

Θ = [MbO2]/([MbO2]+[Mb]) Θ = binding sites occupied/total binding sites

Question 29

When substituting Ka values for the Θ equation, what is the final equation after derivation?

Answer 29

Θ = [O2]/([O2]+1/Ka)

Question 30

The value of Ka can be determined from a plot of Θ vs. ____

Answer 30

[O2]

Question 31

Any equation of the form x=y/(y+z) describes a ____ shape

Answer 31

Hyperbola

Question 32

The [O2] at which Θ = ______ corresponds to 1/Ka

Answer 32

Θ = 0.5 (half-occupied)

Question 33

What is the equation for the dissociation constant, Kd? Then, Θ = what?

Answer 33

Kd=1/Ka Θ = [O2]/([O2]+Kd)

Question 34

A lower value of Kd indicates a HIGHER/LOWER affinity of protein for ligand

Answer 34

Higher | there is an inverse relationship between Kd and Ka

Question 35

Kd= [O2] at which one half or the binding sites are occupied, or [O2](0.5)

Answer 35

Θ= [O2]/ [O2] + [O2]0.5

Question 36

In experiments, the partial pressure of oxygen (pO2) in the gas phase above the solution is varied because it is easier to measure than the concentration of dissolved oxygen in solution

Answer 36

[O2] = P(50)

Question 37

What is the equation for Θ in terms of partial pressure

Answer 37

Θ= pO2/pO2 + P(50)

Question 38

The P(50) is very HIGH/LOW, corresponding to a HIGH/LOW oxygen affinity

Answer 38

Low P50, corresponds to high oxygen affinity

Question 39

The protein/ligand interaction is affected by protein structure and is often accompanied by _____

Answer 39

Conformational changes

Question 40

What molecule binds to free heme molecules >20,000 times better than O2? When heme is bound in myoglobin, the binding of the above molecule is only 200 times better

Answer 40

CO

Question 41

What explains the difference in binding affinity for CO that heme has when free and bound to Mb? What else may affect bonding of CO?

Answer 41

Steric Effects of ligands bound to the heme of Mb H-bonding of O2 to distal His

Question 42

Binding of O2 to the heme in Mb also depends on molecular motion known as _______ Rapid molecular flexing of aa side chains produces transient cavities in protein structure ----> what enters?

Answer 42

Breathing O2

Question 43

Mb has a ____ binding curve for oxygen It's relatively SENSITIVE/INSENSITIVE to small changes in the concentration of oxygen, making it function well for oxygen sorage

Answer 43

Hyperbolic Insensitive

Question 44

Is the hyperbolic binding curve of myoglobin for O2 make it a good O2 transporter?

Answer 44

No, it doesn't.

Question 45

Why does Mb not provide efficient transport of O2 from the lungs to the tissues?

Answer 45

The partial pressure of O2 in the lungs is 3x that in the tissue, at either pressure, most of the protein is in the bound form. It wouldn't release enough O2

Question 46

Oxygen is transported in blood by

Answer 46

Hemoglobin

Question 47

These cells, aka red blood cells, survive for ~ 120 days Their main function is to carry

Answer 47

Erythrocytes Hb

Question 48

In arterial blood passing from lungs through the heart to tissues, Hb is how saturated with oxygen? What color is it?

Answer 48

96% Red

Question 49

In venous blood that is returning to the heart, Hb is only ____ % saturated What color is it? How much oxygen does 100ml of blood release? Percent total and volume.

Answer 49

64% Dark purple 1/3, or 6.5mL

Question 50

Hemoglobin has multiple subunits and O2 binding sites

Answer 50

!

Question 51

Which can respond to changes in ligand concentration and changes in oxygen demand by tissues: Hb or Mb?

Answer 51

Hb (good for transport)

Question 52

Hemoglobin is a ____ that contains 4 heme groups, one for each polypeptide chain It is also called a dimer of _____ protomers

Answer 52

Tetramer αβ

Question 53

When Hb dissociates in urea, the closest and strongest contacts are between α-α and β-β or α-β?

Answer 53

α-β Hence, dimer of α-β protomers

Question 54

Fewer than what percent of aa residues of α and β subunits are identical, even? Do the non-identical ones have similar structure?

Answer 54

Fewer than 50% Yes

Question 55

Do Mb and Hbα and Hbβ have similar subunit structure?

Answer 55

Yes, even though they're only identical at 27 positions

Question 56

When considering quaternary structure of Hb, there are a few H bonds and salt bonds between chains, but most of the interactions between chains are

Answer 56

Hydrophobic

Question 57

Because Hb is a tetramer, each Hb molecule can bind how many oxygens? What quality does each site display in binding?

Answer 57

4 Cooperativity

Question 58

There are two major conformations of Hb which have been confirmed by X-ray crystal structures. ____ means tense and ____ means relaxed

Answer 58

T= tense R= Relaxed

Question 59

Which has higher oxygen affinity, the R state of Hb or the T state?

Answer 59

R state

Question 60

Does the binding of oxygen to the R state stabilize or destabilize it?

Answer 60

Stabilizes the R state

Question 61

Which state is the predominant conformation of oxyHb, T or R?

Answer 61

R state (what's oxyHb?)

Question 62

The absence of oxygen stabilizes which state?

Answer 62

T state

Question 63

Which state is the predominant conformation of deoxyHb, R or T?

Answer 63

T state

Question 64

The T state is stabilized by what at many of the α-β interfaces?

Answer 64

Ion pairs

Question 65

The binding of O2 to Hb in the T state promotes a change in conformation to the ________ _______ are broken and formed, important for structure and function

Answer 65

R state Ion Pairs