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Biochem > Lecture 5 Information > Flashcards

Lecture 5 Information Flashcards

1
Q

Why do humans need more hemoglobin than earthworms?

A

Earthworms do not move as much as humans and therefore have a slower rate of metabolism and do not need as much O2

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2
Q

Is ligand binding always good?

A

No

if a toxin binds to a protein and is brought into the cell through endocytosis, the toxins can integrate themselves into the cell membrane and can potentially cause paralysis

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3
Q

How does insulin work as a ligand?

A

insulin binds to protein on the cell’s membrane which triggers the cell to uptake glucose for metabolism

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4
Q

Induced fit

A

the structure that a protein assumes as it binds its ligand

maxmizes interactions between the ligand and the protein

conformational change

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5
Q

What does induced fit have to be?

A

reversible

want to be able to reuse the proteins that are binding the ligand

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6
Q

Dissociation constant (Kd)

A

=reactants / products

*opposite of Keq

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7
Q

What does a lower Kd mean?

A

a stronger binding affinity

more likely to have products than reactants

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8
Q

Theta

A

the fraction of binding sites that are occupied

[PL] / [PL] + [L]

how many sites are occupied out of the total number of sites

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9
Q

What happens as ligand concentration increases to theta?

A

Theta generally increases as more ligand sites are occupied

Eventually theta will reach a max and plateau

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10
Q

How can you graphical find Kd?

A

plot Theta versus Ligand Concentration

look at where the graph crosses 0.5 theta

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11
Q

Why doesn’t theta ever reach 1 and all binding sites occupied?

A

this would require so many ligands that you would exceed the solubility of the ligands

the ligands would not be soluble at that high of a concentration and actually start precipitating out

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12
Q

why do we need a delivery system for O2?

A

O2 is not very soluble in water

will cause harmful bubbles in the blood rather than dissolve

need myoglobin to carry this gas through the blood

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13
Q

Why do we use Fe and Cu to bind O2?

A

these metals bind O2 reversibly

amino acids do not bind O2 reversibly

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14
Q

How is Fe coordinated in myoglobin?

A

Fe is attached to histidine residue on one side and directly across the O2 binds

This forms a straight line which allows O2 to bind more tightly

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15
Q

How is O2 allowed into the myoglobin complex?

A

through H-bonding interactions with histidines

CO does not have this same interaction and cannot get into the complex as easily

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16
Q

What is the shape of the curve of binding of myoglobin to oxygen?

A

hyperbolic curve

increases, reaches a max, and then flattens out

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17
Q

How are hemoglobin’s 4 subunits held together?

A

by noncovalent interactions

hydrogen bonds, hydrophobic interactions, ionic bonds, some disulfide, etc.

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18
Q

T state of hemoglobin

A

low O2 affinity conformation

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19
Q

R state of hemoglobin

A

high O2 affinity conformation

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20
Q

What does the binding of O2 to hemoglobin do?

A

changes the conformation of the molecule

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21
Q

Cooperative binding

A

the binding of one ligand to a subunit affects the structure and the binding affinity of other sites

*same with reverse direction when O2 is lost

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22
Q

What type of curve indicates cooperative binding?

A

Sigmoid binding curve

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23
Q

Allostery

A

binding at one site affects the shape of another site

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24
Q

Why do we use hemoglobin and not myoglobin as our primary oxygen carrier?

A

Myoglobin has a higher affinity for oxygen

Would not release oxygen in deep tissues where it is needed

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25
Q

What 4 things contribute to the binding of hemoglobin to oxygen?

A

1) pO2
2) pH
3) CO2 concentration in the tissues
4) Binding of BPG

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26
Q

What state does hemoglobin arrive to the lungs in?

A

arrives in the T-state with BPG attached in central area

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27
Q

What happens when hemoglobin picks up O2 in the lungs?

A

it switches from T-state to R-state

*BPG is also released before picking up O2

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28
Q

BPG

A

2,3-bishosphoglycerate

highly negatively charged and binds to positive residues in the central portion of the hemoglobin molecule

allows subunits to be held in the T state

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29
Q

How does pH influence the conformation of hemoglobin?

A

when CO2 concentration is high (like in the lungs), it becomes HCO3- and H+. These H+ protons lower the pH and can attach to histidine residues on hemoglobin

The histidine residues become positively charged and stabilize a negatively charged aspartate

these interactions help stabilize the T-state

So t-state is favored a lower pHs and O2 will be released

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30
Q

How does CO2 get transported to the lungs?

A

around 25-30% of CO2 gets transported to the lungs through hemoglobin

CO2 binds to the amino terminus and converts the terminus into a carbonyl group

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31
Q

Why does fetal hemoglobin have a higher affinity for oxygen than maternal hemoglobin?

A

this facilitates the transfer of oxygen from the mother to the fetus

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32
Q

What is fetal hemoglobin made out of?

A

gammaglobin, higher O2 affinity

33
Q

Bohr effect

A

hemoglobin binds more tightly to oxygen at high pHs

hemoglobin binds less tightly to oxygen at low pHs

34
Q

pH of the lungs

A

7.6

35
Q

pH of the deep tissues

A

7.2

36
Q

Altitude and binding affinity

A

at high altitude, pO2 is much lower and you do not get as much oxygen in the lungs

this means there is less oxygen to drop off in the tissues

need to increase the amount of BPG so the T-state is favored and oxygen will be dropped off

37
Q

Why do we never give up all the oxygen?

A

need to keep a reserve for emergency situations

38
Q

Sickle Cell Anemia

A

Mutation on the B-subunit of hemoglobin and Glu is converted to Val

Val can generate hydrophobic patches that come together and form a chain of hemoglobin

This distorts the shape of the red blood cell

39
Q

Are muscle fibers made up of multiple cells?

A

no

they are actually a single cell with multiple nuclei

40
Q

Sarcomeres

A

sections of myofibrils in muscle cells

individual contractile units in muscle fibers

include the tissue between one I-band and another

41
Q

Thick filament

A

made of myosin proteins that come together

intertwined dimers make up the thick filament

42
Q

Thin filament

A

made up of actin monomers that have polymerized into a chain

ATP is needed to combine actin monomers

43
Q

I-band

A

region of thin filament without any thick filament present

contracts in muscle contraction

44
Q

A-band

A

center of the thick filament that holds myosins together

45
Q

Z disks

A

found on either end of a sacromere

are pulled together as the muscle contracts

46
Q

What does each actin monomer have on it?

A

ADP and a region to bind to myosin

47
Q

Troponin subunits

A

found on the thin filaments

prevent actin from binding to myosin

48
Q

Calcium and muscle contraction

A

Calcium triggers a conformational change in troponin to unbind it and myosin can bind to actin

An electrical signal releases calcium

49
Q

What state does myosin start in?

A

begins in a rigor state that has no bound nucleotide and myosin is tightly bound to actin

no movement of muscle

50
Q

How does myosin work?

A

ATP binds to myosin and releases it from actin
Myosin then uses ATP to be in an activated state (changes conformation)
Rebinds to another actin filament and releases Pi
Pi triggers a “power stroke” that moves actin one unit forward

51
Q

Power stroke

A

conformational change back to the original state that causes ADP to be released

move one actin molecule further along the chain

ADP is released and we return to the rigor state

52
Q

A prothestic group

A

is permanently associated with a protein

an example is the heme group

53
Q

What is the relationship between Ka and Kd?

A

they are inverses

as one increases, the other decreases

54
Q

What are the similarities between myoglobin and hemoglobin’s subunits?

A

myoglobin and hemoglobin’s subunits have a very similar tertiary structure, but different primary structure

55
Q

What is the defining secondary structure of myosin?

A

alpha helices

these coil around each other in a left-handed helix

56
Q

What is the energy released by ATP by actin used for?

A

actin filament assembly

actin requires energy to polymerize

57
Q

What binds stronger to the heme group, O2 or CO?

A

CO

so, have to prevent CO from entering the complex

58
Q

Which ions/molecules does hemoglobin transport?

A

CO2, O2, and H+

59
Q

What converts CO2 to HCO3-?

A

carbonic anhydrase

60
Q

What do the nitrogens in the heme group do?

A

they have electron donating character that prevents Fe2+ from transitioning to Fe3+

61
Q

Why does the sickle cell anemia trait continue?

A

the trait prevents people from getting malaria infection

62
Q

When can you find Kd?

A

when half the binding sites are occupied

0.5 theta

63
Q

What would happen if histidine changed into a nonpolar group in heme?

A

the iron would not be coordinated to histidine

64
Q

How does CO bind more strongly to the heme group than O2?

A

CO binds perpendicular to the heme group’s ring

allows maximum overlap between CO and Fe2+

65
Q

What reduces CO from binding to heme groups?

A

histidine residues

66
Q

What triggers a power stroke?

A

the release of Pi

67
Q

Titins

A

the largest single polypeptide chair discovered thus far

link thick filaments to the Z disk

regulates the length of the sacromere itself and prevents overextension

68
Q

Relationship between Kd and [L]

A

Kd=[L] when 1/2 of the binding sites are occupied (theta=0.5)

69
Q

When do you use a Scathard plot?

A

when you want a more preside measurement of Kd

70
Q

What does Scathard plot graph?

A

Bound/Free versus Bound

71
Q

How to find Kd from Scathard plot?

A

Slope = -1/Kd

72
Q

Bmax

A

all the possible binding sites

[L] + [PL]

73
Q

How can you express the number of unbound sites?

A

[P] = Bmax - [PL]

74
Q

What is the binding pattern of myoglobin to oxygen?

A

hyperbolic

75
Q

What is the binding pattern of hemoglobin to oxygen?

A

sigmoidal

when concentrations of the ligand are low, don’t bind as well as when concentrations of the ligand are high

there is cooperative binding taking place

76
Q

Why can’t you use Edman degradation in the deep tissues?

A

CO2 is bound to the N-terminus of hemoglobin

77
Q

Why do you need capillaries in the muscles?

A

need them to exchange O2 with CO2

78
Q

Sarcoplasmic reticulum

A

stores calcium which can be released to remove troponin

79
Q

H-zone of the sarcomere

A

lacks thin filaments when extended

center of the sarcomere

as myosin crawls along the thin filaments, the thin filaments get pulled towards the middle of the H-Zone

Biochem (20 decks)

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