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BI203 > Midterm #4 > Flashcards

Midterm #4 Flashcards

1
Q

where does glycolysis occur?

A

the cytoplasm

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2
Q

pyruvate is made in both ____ and ____

A

glycolysis; fatty acid metabolism

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3
Q

what is the net gain in glycolysis?

A
  • 2 ATP
  • 2 NADH
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4
Q

the citric acid/krebs cycle uses ____ and transforms it into ____

A

pyruvate; acetyl-coA

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5
Q

where does the citric acid/Krebs cycle occur?

A

the matrix of the mitochondria

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6
Q

what is the net gain from the citric acid/Krebs cycle?

A
  • 2 ATP
  • 8 NADH
  • 2 FADH2
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7
Q

oxidative phosphorylation generates about ____ molecules of ATP

A

32

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8
Q

the outer membrane of the mitochondria is ____ versus the inner membrane which is ______

A

permeable; impermeable

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9
Q

where is the mitochondria genome located?

A

matrix of the mitochondria

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10
Q

what is cardiolipin?

A

a mitochondrial lipid exclusive to the inner membrane

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11
Q

what are the functions of cardiolipin?

A
  • plays a role in electron transport chain efficiency
  • essential for the curvature of the inner membrane
  • facilitates protein import into the mitochondria
  • involved in apoptosis
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12
Q

what is mitochondrial fusion?

A

the process where two mitochondria merge into a single organelle

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13
Q

why is mitochondria fusion significant?

A

it promotes healthy mitochondria by compensating for damaged components

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14
Q

which proteins help regulate mitochondrial fusion?

A

Mfn1 and OPA1

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15
Q

what is mitochondrial fission?

A

the process where a single mitochondrion divides into two serperate organelles

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16
Q

what is the significance of mitochondrial fission?

A
  • facilitates cellular distribution of mitochondria during cell division
  • allows for isolation and removal of damaged mitochondrial segments
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17
Q

which proteins regulate mitochondrial fission?

A

DRP1

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18
Q

explain the steps of oxidative phosphorylation using NADH

A
  1. NADH is converted into NAD+, releasing 1 electron - these e- change the shape of compex I
  2. protons are pumped across the membrane at the same time
  3. Coenzyme Q (ubiquinone) gets reduced which allows it to transfer the e- to complex III
  4. same process occurs at complex III
  5. cytochrome C transfers the e- to complex IV which pumps more protons across the membrane
  6. cytochrome C also uses the energy from e- to facilitate rxn between molecular oxygen and hydrogen to create water
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19
Q

explain the steps of oxidative phosphorylation using FADH2

A
  1. FADH2 is converted into FAD, releasing 2 electrons - these e- change the shape of compex II
  2. Protons are pumped across the membrane at the same time
  3. Coenzyme Q (ubiquinone) gets reduced which allows it to transfer the e- to complex III
  4. same process occurs at complex III
  5. cytochrome C transfers the e- to complex IV which pumps more protons across the membrane
  6. cytochrome C also uses the energy from e- to facilitate rxn between molecular oxygen and hydrogen to create water
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20
Q

what are the overall steps of oxidative phosphorylation?

A
  1. establish an electrochemical gradient across the inner membrane
  2. electron transport through the complexes
  3. ATP synthesis (complex V)
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21
Q

What is ATP synthase?

A

an enzyme that couples the flow of protons down their chemical gradient to the synthesis of ATP

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22
Q

how many proteins are coded by the mitochondrial proteome?

A

1000-1500

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23
Q

what is the purpose of the mitochondrial replacement theory?

A

to prevent transmission of mitchondrial diseases from mother to offspring

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24
Q

what is the method of the mitochondrial replacement theory?

A
  • combine nuclear DNA from mothers egg with healthy mitochondria from donor egg
  • resulting egg has nucelar DNA from mother and mitochondrial DNA from donor
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25
Q

what are the techniques for mitochondrial replacement theory?

A
  • maternal spindle transfer (MST) = transfer mothers nuclear DNA into donor eggs w/ health mitochondria
  • pronuclear transfer (PNT) = transfer nuclear DNA of fertilized mothers egg into fertilized donor egg w/ healthy mitochondria
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26
Q

what are presequences?

A

positively charged, helical structures that direct proteins to the mitochondria

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27
Q

what is the translocase of the outer membrane (TOM) complex?

A

main entry gate for nuclear encoded proteins that recognizes presequences and faciliates protein import

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28
Q

what is the translocase of the inner membrane (TIM) complex?

A

entry gate that transports proteins from the intermembrane space into the matrix

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29
Q

what is the import mechanism for mitochondrial proteins with presequences?

A
  1. presequence binds to receptor site on TOM complex
  2. protein is threaded through the TOM channel
  3. presequence interacts with TIM 23 complex
  4. protein is translocated into the matrix and the presequence is cleaved by the matrix processing protease (MPP)
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30
Q

what is the function of the TIM9-TIM10 complex?

A

acts as a chaperone protein that binds and stabilizes hydrophobic proteins after passing through the TOM complex

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31
Q

where is the TIM9-TIM10 complex located?

A

in the innermembrane space

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32
Q

what is the function of the TIM22 complex?

A

specializes in the insertion of carrier proteins into the innermembrane

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33
Q

what is the function of the OXA1 translocase?

A

integration of proteins synthesizes by mitochondrial ribosomes and importation of some nuclear-encoded protiens into the innermembrane

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34
Q

what is the import mechanism for presequence independent protein targeting to the mitochondrial inner membrane?

A
  1. hydrophobic proteins enter the TOM complex
  2. proteins are then transiently bound to by the TIM9-TIM10 complex
  3. transferred to TIM22 for insertion into the inner membrane
  4. some proteins further inegrated by OXA1
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35
Q

what are single transmembrane domain proteins?

A

proteins who destination is the outer membrane

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36
Q

what is the function of Mim1?

A

inserts single transmembrane domain proteins into the outer membrane

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37
Q

what are β barrel proteins?

A

protein that is inserted into the outer membrane

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38
Q

what is the sorting and assembly machinery (SAM) complex?

A

complex that inserts β barrel proteins into the outer membrane

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39
Q

what is the process for β barrel protein insertion?

A
  1. transfered through the TOM complex
  2. bound by TIM9-TIM10 chaperone proteins in innermembrane space
  3. directed to the SAM complex
  4. inserted into the outer membrane
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40
Q

what is the function of phospholipid transfer proteins?

A

extract and transport phospholipids

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41
Q

where is the transfer site for phospholipid transfer proteins?

A

occur at regions of close contact between the ER and the mitochondria

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42
Q

what is the significance of the phospholipid transfer protein?

A
  • ensures proper lipid composition of membranes
  • facilitates lipid exchange between organelles
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43
Q

what are peroxisomes?

A

small membrane bound organelles present in nearly all eukaryotic cells

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44
Q

what is a plasmalogen?

A

a specialized phospholipid

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45
Q

what are the functions of plasmalogens?

A
  • contribute to structual integrity of cell membranes
  • acts as antioxidants protecting cells from oxidative stress
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46
Q

what is the process of assembly of peroxisomes?

A

V1 and V2 vesicles fuse together
*these vesicles have distinct membrane proteins

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47
Q

what is the process of importing peroxisomal matrix proteins?

A
  • protein that contains PTS1 targeting signal is recognized by Pex5
  • this complex binds to the docking complex on the peroxisomal membrane
  • Pex5 and Pex14 form a membrane pore
  • cargo protein is translocated into the peroxisome
  • Pex5 is recycled back to cytosol after translocation
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48
Q

what are the two ways a peroxisome can be formed?

A
  • de novo formation - fusing of vesicles from ER
  • alternative formation - growth and divison of already existing peroxisomes
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49
Q

what is the signficance of globular actin?

A

have binding sites that that mediate head to tail interaction

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50
Q

what is the significance of filamentous actin?

A

can grow at both ends and has polarity

51
Q

actin is _ when bound to ATP and _ when bound to ADP

A

more stable; less stable and more likely to fall apart

52
Q

what is treadmilling?

A

when ATP actin is added at the barbed end while ADP-actin dissociates from the pointed end

53
Q

what is the function of formin in actin filament formation?

A

formin dimers bind to ATP-actin initiating the polymerization of long unbranched actin filaments

54
Q

what is the function of profilin in actin filament formation?

A

binds to actin monomers and stimulates the exchange of bound ADP for ATP, increasing the local concentration of ATP actin

55
Q

what is the function of Arp2/3 in actin formation?

A

makes the actin branches

56
Q

what is the function of tropomyosin?

A

stabilizes the actin filaments by binding lengthwise along the growth of the filament

57
Q

what is the function of capping proteins?

A

stabilize actin by binding to the barbed or pointed ends

58
Q

actin bundles are supported by _

A

crosslinking proteins

59
Q

actin networks are connected by _

A

large, flexible proteins that crosslink orthogonally (90°)

60
Q

actin bundles give rigidity and shape to cell protrusions for _ versus actin networks offer mechanical support and are involved in cellular activities such as _

A

interactions w/ the environment; mobility and shape changes

61
Q

what is the function of spectrin?

A

associates with actin contributing to the elasticity and mechanical stability of the plasma membrane

62
Q

what is the composition of spectrin?

A

tetramertic stucture with 2α and 2β domains

63
Q

where are the actin binding domains located on spectrin?

A

on the amino (N) terminus

64
Q

what is the function of ankyrin?

A

severs as a link between the spectrin and actin network and the plasma membrane by binding to the spectrin and band 3 (transmembrane protein)

65
Q

what is the role of protein 4.1 in erythrocyte cytoskeletons?

A

reinforces the cytoskeleton membrane linkage by associating with spectrin/actin juntions and connecting to glycophorins

66
Q

what are actin stress fibers?

A

bundles of actin filaments that provide structural integrity

67
Q

what are focal adhesions?

A

points that indicate contact with the extracellular matrix

68
Q

what is the function of viniculin?

A

a protein that helps anchor the actin filaments to the cell membrane

69
Q

what is the role of viniculin

A

plays a role in cell adhesion and and signal transduction

70
Q

what is the compostion of focal adhesions?

A

comprised of integrins binding to the extracellular matrix (ECM)

71
Q

what is the role of stress fibers?

A

provide tensile strength and are crucial for contractability

72
Q

what is the function of talins with focal adhesions?

A

links integrins to viniculin and actin

73
Q

what are cadherins?

A

transmembrane proteins that mediate cell-cell contacts at adherens junctions

74
Q

what are the protein interactions in adherens junctions?

A
  • β-catenin links caherins to α-catenin
  • α-catenin interacts with actin filaments and viniculin anchoring junction to the cytoskeleton
75
Q

actin filaments with microvilli and crosslinked by _

A

villin, fimbrin, and epsin

76
Q

how are microvilli attached to the plasma membrane?

A
  • myosin I attaches actin filaments to the plasma membrane along their length
  • myosin VI is responsible for the attachment at the base of the actin bundle
77
Q

what are the stages of cell migration?

A
  • extension of the leading edge - the cell projects forward through the formation of lumellipodia or filopodia
  • attachment of the leading edge - newly extended protrusions ashere to the substratum via focal adhesions
  • retraction of the rear - the cells rear contracts and attches, pulling the trailing end forward into the cell body
78
Q

actin polymerization is used for _ , integrin-mediated adhesion for _ , and actomyosin contraction for _ in cell movement

A

protrusion; attachment; retraction

79
Q

why is actin filament remodelling significant?

A

crucial for cell movement, especially at the leading edge during migration

80
Q

what are Rho family GTPases?

A

a family of small GTP binding proteins primarily associated with the regulation of the actin cytoskeleton and cell mobility

81
Q

what is profilins role in actin filament remodelling?

A

facilitates the ADP to ATP exchange on actin monomers, promoting actin filament extension

82
Q

what is cofilins role in actin filament remodelling?

A

slices existing actin filaments, generating new (+) ends for further filament growth

83
Q

what is a sarcomere?

A

an individual unit of muscle fiber

84
Q

what is the composition of the sarcomere?

A

thick filaments of myosin and thin filaments of actin

85
Q

what are the ends of the sarcomere called?

A

z-discs

86
Q

what is the middle of the sarcomere called?

A

the m-line

87
Q

_ filaments are anchored to the m-line and project out in both directions

A

myosin

88
Q

what is the sliding filament model?

A

contraction entails the sliding of actin and myosin filaments past each other

89
Q

what is the function of myosin II?

A

drives filament sliding

90
Q

describe the steps of muscle contraction in terms of the filaments

A
  1. ATP binds to myosin, causing the myosin head to undergo a shape change causing it to dissociate
  2. the myosin head binds to a new position on actin
  3. when ADP is bound to the myosin head returns to its original position
91
Q

when there is low [Ca2+] _

A

the tropomyosin-tropinin complex masks the myosin binding site on actin preventing it from binding

92
Q

when there is high [Ca2+] _

A

Ca2+ binds to troponin which shifts the tropomyosin/troponin complex and the myosin binding site is unmasked which means it can bind to actin

93
Q

what are the differences between muscle and non-muscle contraction?

A
  • muscle cells have highly organized microfibrils w/ repeating sarcomeres
  • non muscle cells have less organization
  • muscle cell contraction is often synchronous and rapid
  • non-muscle cell contraction can be asynchronous and varied in pace
94
Q

what is cyokinesis?

A

division of the cell after mitosis

95
Q

how is myosin II activated?

A

through phosphorylation

96
Q

what is calciums role in activation of myosin II?

A

calcium ions binds to calmodulin, initiating the activation process

97
Q

what happens to calmodulin when it binds with Ca2+?

A

it undergoes a conformational change

98
Q

what is the MLCK?

A

the myosin light chain kinase

99
Q

what are unconventional myosins?

A

myosins that do not form filaments

100
Q

what is the structure of microtubules?

A

composed of dimers of α-tubulin and β-tubulin that polymerize w/ 13 protofilaments each

101
Q

what is the process of polymerization of microtubules?

A
  1. tubulin dimers w/ GTP bound tubulin asscoate with the growing (+) end while in a flat sheet
  2. the flat sheet then zips up into the mature MT just behind the region of growth
  3. the GTP bound β tubulin is the hydrolyzed to GDP tubulin which are less stable and lead to dissociation at the (-)
102
Q

what is dyanmic instability?

A

microtubule shrinkage due to insufficient GTP-tubulin

103
Q

what are the functions of microtubule associated proteins (MAPs) in dynamic instabilty?

A

regulation of the dynamic behavior of microtubules by binding to their (+) ends

104
Q

what are the functions of microtubule polyermerases?

A
  • accelerate growth of microtubules
  • increase the incorporation of GTP-bound tubulin into the microtubule
105
Q

what are the functions of microtubule depolymerase?

A
  • induce microtubule shrinkage or catastrophe
  • dissociation of GTP bound tubulin from (+) end
106
Q

what are clasp proteins?

A

proteins that stop disassembly and promote the restart of microtubule growth

107
Q

the (-) ends of MT are anchored to the _ in mitosis

A

centrosome

108
Q

dendrites contain microtubules that are oriented in which direction?

A

they are oriented in both directions with the (+) end pointing away from the body

109
Q

in which direction are the microtubules in axons oriented?

A

uniformily oriented with the (+) end pointed towards the axon tip

110
Q

which MAPs cap dendrites?

A
  • MAP2
  • Tau
111
Q

what are kinesin and dyneins?

A

molecular motors that move along MT and are powered by ATP hydrolysis

112
Q

most kinesins move towards the _ end which is also considered _ transport

A

(+); anterograde

113
Q

most dyneins move towards the _ end which is also considered _ transport

A

(-); retrograde

114
Q

what are kinetchore microtubules?

A

MT that attach to kinetechores on condensed chromosomes

115
Q

what are interpolar microtubules?

A

MT that overlap at the cell center, helping stabilize the spindle

116
Q

what are astral microtubules?

A

MT that extend from chromosomes to the cell periphery, aiding in spindle orientation

117
Q

What causes chromosome movement in Anaphase A?

A

the kinesin motor proteins help depolarize the MT which shortens them

depolarization causes degredation of MT

118
Q

what are the two movements for spindle seperation in Anaphase B?

A
  • (+) end directed motor proteins
  • (-) end directed motor proteins
119
Q

describe what happens during the movement of (+) end directed motor proteins?

A
  • push the spindle poles apart to elongate the cell
  • drive the sliding of interpolar microtubules
120
Q

describe what happens during the movement of (-) end directed motor proteins?

A
  • facilitate the pulling of astral microtubules
  • are anchored to the cell cortex for traction
121
Q

what is the function of intermediate filaments?

A

provide tensile strength to cells preventing them from being torn apart under tension

122
Q

what is a desmosome?

A

molecular complexes of cell adhesion proteins and linking proteins that attach the cell surface adhesion proteins to intracellular keratin intermediate filaments

123
Q

what is a hemidesmosome?

A

molecular complexes that link intermediate filaments to the extracellular matrix through plectin and integrins

124
Q
A

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