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Biochemistry > Chapter 6.1 and 6.2 > Flashcards

Chapter 6.1 and 6.2 Flashcards

1
Q

what are the 5 major protein classes?

A
  1. enzymes
  2. structural
  3. cell signalling
  4. genomic caretaker
  5. transport
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2
Q

what do enzymes do?

A

catalyze biochemical reactions

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3
Q

how do enzymes catalyze biochemical reactions? (3)

A
  1. lower activation energy
  2. increase rate of product formation
  3. involved in energy conversion pathways
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4
Q

do enzymes alter the equilibrium concentration of products and reactants?

A

HELL NO

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5
Q

how do enzymes work?

A

mostly as complexes of 2-60 subunits

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6
Q

what are eznymes responsible for?

A

the synthesis and degradation of macromolecules as they convert one to another

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7
Q

where are enzymes found?

A

often found in the cytoplasm

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8
Q

give an example of an enzyme

A

malate dehydrogenase

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9
Q

what do structure proteins do?

A

maintain cell structure and shape

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10
Q

what do structural proteins provide?

A

a framework for cells, tissue, and organs

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11
Q

what are the most abundant type of proteins?

A

structural proteins

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12
Q

what do structural protein often form?

A

polymers (often fibrous)

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13
Q

where are structural proteins found

A

through membranes

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14
Q

what is a type of structural protein responsible for cell shape, cell migration, and cell signaling?

A

cytoskeletal proteins

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15
Q

give 3 examples of cytoskeletal proteins

A
  1. actin
  2. tubulin
  3. collagen
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16
Q

where is actin abundant?

A

in animal cells

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17
Q

where is actin found?

A

in muscle

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18
Q

what do actin subunits form?

A

self-assemble from actin monomers to form long polymers called thin filaments

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19
Q

what are the 2 forms of actin?

A
  1. g-actin
  2. f-actin
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20
Q

describe g-actin

A

the inactive, globular, monomer form of actin

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21
Q

describe f-actin

A

the active, filament, polymer form of actin

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22
Q

where is tubulin abundant?

A

in animal cells

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23
Q

what do tubulin monomers form?

A

seld-assemble to form polymers called microtubules

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24
Q

what do microtubules do?

A

act as roads for movement of organelles and chromosomes during cell division

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25
Q

what is the major structural protein in animals?

A

collagen

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26
Q

what is collagen a primary component of?

A

connective tissue

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27
Q

what does collagen do? (3)

A
  1. provides skin elasticity
  2. bolsters joint health
  3. promotes bone health
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28
Q

describe collagen structure (4)

A
  1. every 3rd residue is glycine
  2. contains many proline and hydroxyprolines
  3. repetitive motif
  4. special left-handed helix secondary structure
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29
Q

describe the repetitive motif of collagen

A

either Gly-Pro-X or Gly-X-Hyp (X is any other amino acid)

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30
Q

what do 3 collagen chains form?

A

a triple helix structure

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31
Q

where are the glycine side chains in the triple helix structure and why?

A

in the middel! they have no side chain therefore no hinderance in any way (steric or electrical)

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32
Q

what would happen if you replaced glycine in collagen with any other amino acid?

A

the triple helix would break

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33
Q

how are the triple helices of collagen stabilized?

A

through hydrogen bonding between the backbone N on glycine hydrogen bonding to the backbone carbonyls of the adjacent residues

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34
Q

what do cell signaling proteins do?

A

transmit extracellular and intracellular signals

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35
Q

what do signaling protein exist as?

A

molecular switches, with one “on” active conformation and one “off” inactive conformation

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36
Q

what are the 3 types of cell signaling proteins and where are they found?

A
  1. membrane receptors in membranes
  2. intracellular signaling proteins in the cytoplasm
  3. nuclear receptors in the nucleus
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37
Q

give 3 examples of membrane receptos cell signaling proteins

A
  1. g-couple protein receptors
  2. receptor tyrosine kinases
  3. growth hormone receptors
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38
Q

describe the general structure of a cell signaling protein (3)

A
  1. extracellular component receives signal
  2. transmembrane/membrane component transmits the signal
  3. intracellular component does the thing with the signal
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39
Q

how do intracellular proteins exist?

A

as molecular switches; change conformation in response to incoming signals

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40
Q

what is receptor activation for intracellular proteins?

A

when they change conformation in response to incoming signals, since they exist as molecular switches

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41
Q

what are 2 examples of intracellular signaling proteins?

A
  1. adenylate cyclase
  2. protein kinases
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42
Q

what do protein kinases do? how ? (2)

A

reversibly phosphorylate proteins at Ser and Thr
1. use ATP
2. activate downstream target proteins in response to upstream receptor activation

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43
Q

what do nuclear receptors function as?

A

transcription factors

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44
Q

what do nuclear receptors, acting as transcription factors, do?

A

regulate gene expression in response to ligand binding

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45
Q

where are nuclear receptor proteins found?

A

in the nucleus

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46
Q

give an example of a nuclear receptor protein

A

thryoid receptor

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47
Q

what is the implication of most ligands for nuclear receptors being hormones?

A

they are susceptible to imbalances and disorders

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48
Q

what do genomic caretaker proteins do?

A

maintain the integrity and accessibility of genomic info

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49
Q

where are genomic caretaker proteins found?

A

in the nucleus

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50
Q

give 4 specific functions of genomic caretaker proteins

A
  1. DNA replication
  2. DNA repair
  3. DNA recombination
  4. gene expression
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51
Q

give 4 examples of genomic caretaker proteins and then say generally what they make up

A
  1. DNA polymerase
  2. DNA ligase
  3. DNA helicase
  4. topoisomerase
    make up the replication fork
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52
Q

what do transport proteins do?

A

facilitate movement of molecules within and between cells

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53
Q

where are transport proteins abundant?

A

in the plasma membrane

54
Q

what do transport proteins allow?

A

permit polar and charged molecules to enter and exit the cell

55
Q

what are the 2 membrane-bound transport protein classes?

A
  1. passive transporters
  2. active transporters
56
Q

what do passive transport proteins do?

A

allow molecules to move across a membrane DOWN a concentration gradient

57
Q

describe passive transport proteins’ energy relationship

A

energy independent

58
Q

give two examples of passive transport proteins

A
  1. porins
  2. ion channels
59
Q

what are porins?

A

specific holes; allow easy access but only for desired molecules

60
Q

describe active transport proteins’ energy relationship

A

require energy

61
Q

why do active transport proteins require energy?

A

the energy causes a conformational change that opens or closes the channel

62
Q

what do active transport proteins do?

A

pump small molecules UP a concentration gradient

63
Q

describe where the energy for pirmary and secondary active transport proteins comes from

A
  1. primary active transport proteins do ATP hydrolysis (ATP dependent)
  2. secondary active transport proteins couple with primary and utilize the ionic gradient formed by the primary proteins
64
Q

give 2 examples of globular transport proteins

A
  1. myoglobin
  2. hemoglobin
65
Q

is myoglobin a monomer or a polymer?

A

monomer

66
Q

describe the size of myoglobin

A

small and compact; 153 amino acids

67
Q

where is myoglobin found?

A

in muscle tissue

68
Q

what is the function of myoglobin?

A

oxygen storage; reversibly binds O2

69
Q

what is myoglobin composed of, secondary structurally?

A

8 alpha helices (A-H)

70
Q

what does myoglobin contain?

A

a prosthetic heme group (added after translation, like a prosthetic limb added after birth)

71
Q

describe the structure of heme

A

porphyrin ring system

72
Q

where is the heme group in myoglobin?

A

placed in a hydrophobic pocket between helices E and F

73
Q

what is at the center of the heme group?

A

an iron atom

74
Q

what is the role of the iron atom at the center of the heme group?

A

coordinate covalent bonds with electronegative atoms

75
Q

what are the 2 forms of the iron atom at the center of the heme group? which one do you want and why?

A

can be Fe2+ (ferrous) or Fe3+ (ferric); want Fe2+ because only ferrous REVERSIBLY binds O2 (Fe3+ irreversibly binds=bad news bears)

76
Q

how many coordination sites does Fe2+ at center of heme group have? what goes there?

A

6
4 bonds to pyrrole N’s
1 goes to the proximal histidine (His F8)
1 binds to O2

77
Q

what does the distal histidine of the heme group binds to? (this is His E7)

A

O2

78
Q

contrast the distal and proximal histidines of the heme group of myoglobin and how they bind to iron

A

proximal histidine directly binds to iron
distal histidine binds to the O2 bound to the iron (indirect)

79
Q

what does the heme-O2-heme complex do?

A

oxidized Fe2+ to Fe3+ and causes nonreversible O2 binding

80
Q

what does the proximal histidine do for the heme?

A

keeps the heme coordinated to the protein

81
Q

what does the distal histidine do for the the heme? how?

A

prevents other hemes from binding Fe2+ to O2 becuase its steric hindrance disallows a second heme from entering the O2 binding site

82
Q

what is the equation for the binding of any ligan (L) to any protein (P)?

A

P + L double arrow PL

83
Q

what is Kd?

A

the dissociation constant of ligands and proteins

84
Q

give the equation for Kd

A

[P]][L]/[PL]

85
Q

what are the units of Kd?

A

Molarity

86
Q

what is Ka?

A

the association constant of proteins and ligands

87
Q

give the equation for Ka

A

[PL]/[P][L]

88
Q

how is Ka related to binding affinity?

A

Ka is directly related to binding affinity

89
Q

what does a higher or lower Ka mean?

A

higher Ka means stronger binding, lower Ka means weaker binding

90
Q

how is Kd related to binding affinity?

A

Kd is inversely related to binding affinity

91
Q

what does a higher or lower Kd mean?

A

higher Kd means weaker binding and lower Kd means stronger binding

92
Q

how is fraction saturation (theta) related to Kd?

A

fractional saturation is inversely related to Kd

93
Q

what is the equation for fractional saturation?

A

[L]/[L]+Kd

94
Q

how is ligand concentration related to fractional saturation?

A

the higher concentration of ligand [L], the higher the fractional saturation because there are more ligands to bind (saturate)

95
Q

what is the standard value of fractional saturation used to compare binding affinities between proteins? why?

A

0.5; past that it’s hard to measure anything about the protein

96
Q

what will a stronger binding curve look like? describe L and Kd

A

will curve left, with a lower Kd and less [L] needed to reach half saturation

97
Q

what will a weaker binding curve look like? describe L and Kd

A

will curve right with a higher Kd and with more [L] needed to reach half saturation

98
Q

how do you calculate fractional saturation in terms of proteins and ligands

A

occupied binding sites/ total binding sites, so [PL]/[PL]+[P]

99
Q

for the equation Mb + O2 double arrow MbO2, how would you calculate fractional saturation?

A

[MbO2]/[MbO2]+[Mb]

100
Q

what is the shape of the myoglobin binding curve?

A

hyperbolic

101
Q

what is Kd on the myoglobin saturation curve? why?

A

the concentration of O2 when half of Mb bind to O2, but is hard to measure the concentration of gases, so we use partial pressure instead (on all gases!), so Kd=P50

102
Q

where is hemoglobin found?

A

in red blood cells

103
Q

describe the structure of hemoglobin

A
  1. a heterotetramer
  2. secondary and tertiary structures similar to myoglobin
  3. quarternary structure is 2 alpha chains and 2 beta chains
  4. each subunit has a heme group
104
Q

describe the O2 capacity of hemoglobin compared to myoglobin and why?

A

hemoglobin has 4x the O2 capacity of myglobin because it has 4 subunits instead of 1

105
Q

describe the shape of hemoglobin’s binding curve

A

sigmoidal

106
Q

what does a sigmoidal binding shape indicate? describe

A

cooperative binding: binding of one ligan to one site increase binding affinity for another ligand at another site; also works in reverse as release of one ligand at one site decreases binding affinity for another ligand at another site

107
Q

why doesn’t myoglobin have cooperative binding?

A

it only has one binding site, no one to cooperate with

108
Q

why does hemoglobin have a lower fractional saturation in tissues than myoglobin?

A

so that it is able to drop its O2 off easier thaan myoglobin

109
Q

what is the Hill coefficient?

A

a measure of cooperativity, n

110
Q

what do the signs of the Hill coefficient, n, mean?

A

n=1: no cooperativity
n>1: positive cooperativity (easier for next ligand to bindor dissociate)
n<1: negative cooperativity (harder for next)

111
Q

what are the 2 states of hemoglobin?

A
  1. deoxygenated
  2. oxygenated
112
Q

what does the proximal histidine do to the Fe of hemoglobin when it is deoxygenated?

A

pulls Fe up and out of plane of the rest of the ring, resulting in a domed/puckered conformation

113
Q

what does the bound oxygen to the Fe do to the shape of hemoglobin when it is oxygenated?

A

pulls the ring back to planar conformation

114
Q

describe dexoygenated hemoglobin (3)

A
  1. No bound O2
  2. heme ring is not planar, in T or Tense conformation
  3. Fe lies approx 0.6A out of plane
115
Q

describe oxygenated hemoglobin (3)

A
  1. O2 is bound
  2. heme ring is planar
  3. in R or Relaxed conformation
116
Q

describe the conformational switch between deoxygenated and oxygenated hemoglobin

A
  1. O2 binding pulls Fe into plane of heme
  2. His F8 is pulled with Fe
  3. entire F helix moves toward the heme
117
Q

what is the concept of allostery?

A

conformational switches underlie cooperativity

118
Q

what does allostery do?

A

transmits changes in one subunit across the interface to the next subunit

119
Q

what are the 2 models to explain allostery?

A
  1. concerted
  2. sequential
120
Q

describe the concerted model to explain allostery (3)

A
  1. protein found in either ALL T or ALL R conformations
  2. binding to a single subunit helps stabilize the R state
  3. the whole molecule is affected at the same time at different levels of probability
121
Q

describe the sequential model to explain allostery (3)

A
  1. protein found in a mix of T and R
  2. binding doesn’t convert the entire complex to the R state, just alters the affinity of ADJACENT subunits
  3. each neighbor is affected by the previous switch
122
Q

describe positive allosteric effectors for hemoglobin (2)

A

increase Hb affinity for O2, shift equilibrium to the R state

123
Q

what is the positive allosteric effector?

A

O2

124
Q

describe negative allosteric effectors for hemoglobin (2)

A

decrease Hb affinity for O2, shift equilibrium toward the T state

125
Q

what are the 3 negative allosteric effectors for hemoglobin?

A
  1. 2,3-BPG
  2. H+ (protons/lower pH)
  3. CO2
126
Q

what does BPG stand for?

A

bisphosphoglycerate

127
Q

how does 2,3-BPG work as a negative allosteric effector for Hb?

A

binds deoxygenated hemoglobin (T state) and stabilizes that T state

128
Q

what would happen without 2,3-BPG?

A

Hb would bind O2 too tightly and not drop it off in tissues

129
Q

describe fetal Hb binding affinity for BPG

A

fetal Hb binds BPG poorly, so fetal Hb binds O2 super strong to make sure gets O2 from mom

130
Q

describe the Bohr effect decreasing binding affinity of Hb for O2

A

as pH drops, the binding affinity of Hb for O2 also drops because H+ and CO2 weaking binding affinit

131
Q

describe how H+ and CO2 weaked Hb binding affinity

A
  1. residues on Hb can be protonated, which causes conformational changes to stabilize the T state
  2. increased CO2 increase H+ via carbonic anhydrase
  3. CO2 bunds to Hb at the N terminus, which stabilize the T state and produces H+

Biochemistry (20 decks)

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