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BMSC 200 > Chapter 5 > Flashcards

Chapter 5 Flashcards

1
Q

why can many proteins undergo reversible interactions with other molecules

A

the interactions serve to regulate protein function

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2
Q

what is a molecule reversibly bound by the protein called

A

ligand

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3
Q

what can a ligand be

A

any kind of molecule including another protein another protein

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4
Q

what does a target + ligands create

A

through docking it creates a complex

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5
Q

where does the ligands bind to

A

a specific site on the protein called the binding site

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6
Q

how is the binding site complementary to the ligands

A

interms of shape, charge, hydrophobicity, hydrogen bonding potental

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7
Q

can a protein only have one binding site for ligands

A

no a given protein may have multiple binding sites for multiple ligands
i.g. ligands of hemoglobin include oxygen and 2,3 bisphosphoglycerate (2,3 BPG)

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8
Q

what can the binding of a ligand change

A

it can cause conformational change in the protein

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9
Q

what can the induced fit of a binding of a ligands change

A

it can change the properties of the protein
these chanes in protein structure often relate to changes on function

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10
Q

what is an example of an element that has a affinity for O2

A

Fe

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11
Q

what are the challenges of oxygen delivery and storage

A

every cell requires a constant supply of oxygen

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12
Q

what are the obstacles for oxygen delivery and storage

A

-for many multi-cellular organsims the solubility of oxygen is too low to meet oxygen requirements through passive diffusion
-amino acid side chains not well suited for reversible binding of oxygen
-transition state metals have a strong tendency to bind oxygen but produce damaging free radicals

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13
Q

what are the solutions for the challenges of oxygen delivery and storage

A

-specialized proteins for oxygen storage and delivery
-heme groups to safely harness irons oxygen binding properties

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14
Q

what is myogobin (Mb)

A

monomeric protein that facilitates oxygen storage in peripheral tissue

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15
Q

what kind of structure is myoglobin (Mb)

A

tertiary structure

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16
Q

how does myoglobin bind to O2

A

has a single heme group that binds to single O2 molecule
(strong affinity for O2 to make it harder to strip away)

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17
Q

what is hemoglobin (Hb)

A

a tetrameric protein found in red blood cells that transports oxygen from lungs to the periphery

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18
Q

what has a stronger afinity for O2 Hb or Mb

A

myoglobin

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19
Q

what can the amount of available oxygen do to an organism

A

it can limit its size. (availability of O2 limits size)

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20
Q

when is oxygen poorly soluble

A

in aqueous solutions

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21
Q

what did the emergence of larger multicellular organism depend on

A

the evolution of proteins that could transport and store oxygen

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22
Q

what forms is cellular iron bound in

A

forms that sequester it and/or make it less reactive

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23
Q

what does heme consist of

A

a protoporphyrin ring system bound to a singe (Fe2+) iron atom

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24
Q

why does heme contain Fe 2+ and not 3+

A

because Fe2+ binds O2 reversably Fe3+ does not

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25
Q

how does the ring system in a heme provide four coordinating interactions with the iron atom

A

the electron donating characteristic of nitrogen (found in the ring) prevents the conversion of Fe2+ to Fe3+

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26
Q

who uses heme

A

both myoglobin and hemoglobin

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27
Q

how is heme bound with myoglobin and hemoglibin

A

with discrete pockets

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28
Q

how many coordinating interactions does Fe 2+ seek

A

6

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29
Q

where does the six coordinating interactions for Fe 2+ come from

A

-4 from interactions with heme
-a 5th from interactions with imidazole group of s proximal histidine residue
-six positioning for O2 binding

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30
Q

what provides a stabilizing interaction for bound O2 (that is off the Fe2+)

A

a distal histidine provides a stabilizing interaction

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31
Q

what is the difference in structure of deoxyhemoglobin and oxyhemoglobin

A

the Fe has a O2 off it on oxyhemoglobin

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32
Q

how can one get CO poisoning

A

-CO has a simular structure to CO2
-CO exerts its deadly effects by competing with O2 for binding to heme
-CO binds heme withe 200x greater affinity than O2

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33
Q

how does Mb compare to Hb in terms of structure

A

-myoglobin with a single subunit is a tert structure
-hemoglobin, with 4 sub-units is an example of a quartinary structure

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34
Q

how does Mb compare to Hb in terms of oxygen binding

A

-with single heme group myoglobin can bind one oxygen molecs
-with four heme roups hemoglobin can bind 4 O2 molecs

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35
Q

what does each sub unit of hemoglobin resemble

A

myoglobin

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36
Q

how does Mb compare to Hb in terms of O2 affinity (graph)

A

-myoglobin has a higher affinity for oxygen than hemoglobin

-myoglobin has a hyperbolic curve of oxygen bonding
-binding of oxygen by hemoglobin displays sigmoidal behavior (indicating coopertivity of oxygen bonding)

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37
Q

what does hemoglobin not have to be 100% saturated

A

is can for example be 25% saturated because it has 4 subunits

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38
Q

can myoglobing be 50% saturated

A

no its either saturated or its not

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39
Q

how many torr of O2 would be required to saturate 50% of heme and myoglobin(even though it cant be)

A

around 3 torr for myoglobin and 30 torr for hemoglobin

(myogobins affinity for O2 is about 10x higher them hemoglobin)

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40
Q

what does myoglobin consist of

A

-a single poly peptide of 153 residues arranged in 8 alpha helicies
-a heme (iron porphyrin) prostetic group

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41
Q

what was the first protein structure determined

A

sperm whale myoglobin. determined by x-ray crystallography

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42
Q

why did they look for myoglobin in a sperm wale

A

because they would be very high in it

43
Q

what is the oxygen saturation curve of myoglobin

A

it is hyperbolic, indicating a single O2 binding constant

44
Q

what is the P50

A

they way to quantify the amount of O2 required to half saturate a protein

45
Q

what is the P50 of myoglobin

A

3 torr

46
Q

where is the physiolgical O2 concentration highest and lowest. and whats the torr

A

-the lungs is the highest (typically 100 torr)
-the periphery is the lowest (typically 20 torr)

47
Q

how is the fraction of myoglobin saturated with oxygen at a given partial pressure of oxygen calculated by

A

0=[pO2]/([pO2]+[P50])

i.g pp of O2 in peripheral tissue is around 20 torr
0=20/(20+3)=87% saturation

48
Q

what are erthrocytes

A

red blood cells

49
Q

how many sub units does hemoglobin have

A

4

50
Q

what does it mean that hemoglobin is a allosteric protein

A

-its oxygen affinity is regulated through various physiological signals
-it can adopt 2 different conformations
-can transition from T states and R states

51
Q

what kind of forms do allostatic proteins have

A

they have T (inactive) and R (active) forms
they are in rapid equilibrium

52
Q

what has a higher affinity for oxygen the T state or R state of hemoglobin

A

T state has a lower affinity
(deoxyhemoglobin)
R state has a higher affinity (oxyhemoglobin)

53
Q

what would happen if hemoglobin only has a high or low affinity for O2
how does hemoglobin fix this

A

-a protein with high affinity would saturate effectively with O2 in the lungs but not release it in the tissue
-a protein with low affinity would be able to release O2 to tissue but would not have sufficient affinity to saturate in the lungs
-hemoglobin solves this by undergoing transitions from high to low affinity states

54
Q

can myoglobing undergo transitions from high to low affinity states

A

no it only has a single ligand binding site

55
Q

what state would hemoglobin be in the lungs

A

the R state so it can fully saturate

56
Q

what state is hemoglobin when delivering O2

A

in the T state so it can release the O2

57
Q

how many of the the hemes just go for a ride and why

A

50% just go for a ride around the circulatory system. they are there to be something to count on in a time of need

58
Q

what are allosteric effectors (modulators)

A

they bind allostatic proteins at specific sites

59
Q

are allosteric effectors activators or inhibitors

A

they and be either or

60
Q

what do allosteric activators and inhibitors stabilize

A

-activators stabilize the R state
-inhibitors stabilize the T state

61
Q

what does it mean if the interaction is homotrophic

A

when the normal ligans and modulator are the same the interaction is homotrophic

62
Q

what does it mean if the interaction is heterotrophic

A

the modulator is different from the normal ligand

63
Q

what is the binding and release of O2 regulated by

A

they are allosterically regulated

64
Q

what is an example of how the binding and release of O2 in allosterically regulated

A

-for example O2 is a homotrophic allosteric activator of hemoglobin
-binding the first O2 by hemoglobin causes a conformational change making easier to bind subsequent O2 (positive cooperation)
-O2 binding promotes and stabilizes the R state of hemoglobin which has higher O2 affinity the the T state

65
Q

where is the iron atom on a T and R state hemoglobin

A

-on a T state it is just out side the plane of the heme ring
-in the R state (O2 bound) the iron moves into plane of the ring

66
Q

when the iron is just out side the plane vs in the plane of ring (in R vs T state) what does this effect

A

the minor movement within one sub unit causes structural changes that are translated to quantinary structure of the protein

67
Q

at partial pressure on oxygen found in the periphery what does hemoglobin do

A

the hemoglobin realeases over half of its O2 load

68
Q

at partial pressure on oxygen found in the lungs what does hemoglobin do

A

hemoglobin completely saturates with O2

69
Q

what partial pressure does the p50 of hemoglobin match

A

the partial pressure of O2 found in periphery

70
Q

where is Hb most sensitive for O2 release

A

at the partial pressure of O2 found in the periphery

71
Q

why is it goos Hb is most sensitive for O2 release at the partial pressure of periphery

A

because this allows Hb to sense and respond to changes in O2 levels in regions at greatest risk for hyooxia

72
Q

what is 2,3 bisphosphoglycrate

A

its a heterothrophic allostaric inhibitor of hemoglobin

73
Q

what would happen if we had highly purified hemoglobin

A

it would have an extremely high affinity for oxygen
which would limit the ability of the protein to release a O2 to the periphery

74
Q

what did replacing various components of blood reveal

A

that 2,3 biphosphoglycrate decreases hemoglobins affinity for oxygen

75
Q

what charges does 2,3 BPG carry

A

five units of negative charge

76
Q

what does the pocket formed at the interface between the subunits of DOHb contain

A

six + charged residues

77
Q

how does a fetus get its O2

A

-needs to pull O2 away from the mothers blood
-fetal heme needs higher affinity for O2 then mother
-has one amino acid change for this to happen

78
Q

how does the fetus have a stronger affinity for O2

A

-adult Hb has 6+ residues at the 2,3BPG binding site, Fetal Hb has 4+
-decreasing affinity for 2,3 BPG translates into higher O2 affinity for fetal Hb
-(lower affinity for the allosteric inhibitor bestows higher affinity form O2)

79
Q

how does altitude change O2 conc

A

there is less O2 at higher altitudes

80
Q

why is it hard to adapt to O2 conc at higher altitudes

A

-adaption to high alts can rapidly occur through increased production of 2,3 BPG
-increased 2,3 BPG decreases Hb’s O2 affinity to ensure sufficent O2 delivery to periphery

81
Q

what does activity at extremely high altitudes require

A

artificial means to provide O2

82
Q

why do you need to drink lots of water at high altitudes

A

because when you sleep you begin to pants which leads to loss of water

83
Q

what does the borh effect describe

A

the pH dependence of hemoglobins affinity of O2

84
Q

what is hemoglobins affinity for O2 at a decreased pH

A

it has a lower affinity

85
Q

why does active tissue have a lower pH

A

-increased muscle activity increases production of CO2. this CO2 eventually decreases pH
-in extreme exercise muscles produce lactic acid to further decrease pH

86
Q

what does the bohr effect serve to do

A

to coordinate increased release of O2 to active tissue

87
Q

what are the two primary challenges to cellular respiration and metabolism

A

-delivering sufficient O2 to the the tissue
- removing CO2 (the “exhaust” of metabolism) from the pariphery

88
Q

what happens with increased muscle activity

A

both O2 and CO2 requirements increase with increased muscle activity

89
Q

what does the the enzyme carbonic anhydrase do

A

once CO2 is taken up into the RBC it converts it into bicarbonate and a proton

90
Q

what things happen as a result of carbonic anhydrase converting CO2

A

-CO2 is converted into a soluble form for transport to the lungs
-the decreased pH decreases hemoglobins O2 affinity to promote O2 release to active tissue

91
Q

how does CO2 form a carbaminohemoglobin

A

the CO2 can form a covalent carbomate linkage to the N terminus of each chain of hemoglobin chain to form it

92
Q

what are the 3 important out comes of the carbaminohemoglobin reaction

A

-converts CO2 into a more stable form to assist in its transport to the lungs
-carbamino hemoglobin has a lower O2 affinity than hemoglobin to promote O2 release
-the released proton promotes O2 release through the bohr effect

93
Q

what is anorobic metabolism

A

when your working out and can still have a convorsation

94
Q

what is anaerobic metabolism

A

working out to a point of burning more O2 then body can deliver (can only be done for a short period of time)

95
Q

what happens of your body goes into O2 dept

A

it starts to produce lactic acid

96
Q

what does lactic acid do

A

-it enables muscles to be able to preform for awhile in absence of insufficient O2
-it causes a pH drop within the tissue

97
Q

what happens when your work out a particular muscle

A

the partal pressure of O2 drops in that tissue the hemoglobin will automatically release more O2 to that tissue

98
Q

biologically what causes sickel cell anemia

A

results from a single amino acid change (Glu6Val)

99
Q

what biologically happens when a single amino acid change causes sickle cell anemia

A

-formation of fibers from the deoxy form of HbS
-fibers tend to form in the capillaries (where the O2 concentration is the lowest) which blocks blood flow to the extremities of the body

100
Q

what are red blood cells like if one has sickle cell anaemia

A

they become very ridged

101
Q

where is sickle cell anemia prone

A

in places with malaria like Africa and South america. it is selected for

102
Q

what is a theory as to why sickle cell anemia is selected for in parts of the world

A

-malaria infects RBC
-infection decreses pH in RBC
-decreaseed pH causes release of O2 from Hb
-ppl with SCA, detox HbS forms fibers deforming the redblood cell
-these deformed RBC (which contain malaria) are selectively destroyed by the spleen

103
Q

what is hemocyanin

A

another kind of O2 carrier that invertebrates (like horseshoe crab) use

104
Q

how is hemocyanin distinct form hemoglobin

A

-hemocyanin uses copper rather than iron(blue blood instead of red)
-2 Cu atoms bind a single O2
-no heme ring group, Cu atom is coordinated through histidine residues
-hemocyanin is not localized within specialized O2 transport cells

BMSC 200 (10 decks)

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