exam 3 Flashcards

(135 cards)

1
Q

What is the cell cycle

A

A process in which cells reproduce by duplicating their contents + dividing it into 2: cell growth + chromosome duplication, chromosome segregation, cell division

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2
Q

3 main transition points of the cell cycle

A

G1>S: confirms env is favorable for proliferation before commiting to DNA replication

G2>M: confirms that the DNA is undamaged and fully replicated

M: ensures that the duplicated chromosomes are properly attached to the mitotic spindle

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2
Q

What is the cell-cycle control system

A

ensures that key processes occur in the proper sequence
control system is regulated at certain critical points of the cycle by feedback from the process currently being performed
has checkpoints to pause the cycle at certain points + does not trigger next step unless cell is prepared

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2
Q

What are the phases of the cell cycle

A

Interphase: cell grows continuously (otherwise it would shrink w/ each division)
> G1, S, G2
G1, G2 - gap phases, cell monitors internal state + external env
S - DNA replication

M: mitosis (nuclear division) + cytokinesis (cytoplasmic division)

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3
Q

Progression through the cell cycle depends on..

A

Cdks - cyclin-dependent protein kinases

must bind a cyclin (a regulatory protein) before it can become enzymatically active (where it then phosphorylates key proteins that are required to initiate particular steps in the cell cycle)

distinct Cdks associate w/ different cyclins to trigger diff events

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4
Q

changes in cyclin concentration

A

gradual increase in cyclin conc (due to transcription of cyclin genes + synthesis of cyclin protein)
rapid fall in cyclin conc (due to full-scale targeted destruction of protein)

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5
Q

cyclin-cdk complexes

A

G1-Cdk: cyclin D + Cdk4/6
G1/s-Cdk: cyclin E + Cdk2
S-Cdk: cyclin A + Cdk2
M-Cdk: cyclin B + Cdk1

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6
Q

Active cyclin-cdk complex > inactivation (cell-cycle control system)

A

active cyclin-cdk comples > ubiquitylation of cyclin by APC/C > destruction of cyclin in proteasome > inactive cdk + destructed cyclin

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7
Q

how to activate cdks (e.g M-cdk) (cell-cycle control system)

A

M-cdk complex forms + is immediately phosphorylated by an inhibitory protein kinase (Wee1)

this keeps m-cdk inactive until…

phasphates are removed by an activating protein phosphatase (Cdc25) = active M-Cdk

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8
Q

How can cdk activity be blocked (cell-cycle control system)

A

by the binding of a cdk inhibitor protein to an activated cyclin-Cdk complex

attachment prevents Cdk from phosphorylating target proteins + maintains complex in an inactive state

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9
Q

Which mechanisms are used to pause the cell cycle at which transition points

A

G1>S: Cdk inhibitors blocking entry to S phase (bc env is not favorable)

G2>M: inhibition of activation phasphatase (Cdc25) blocks entry to mitosis (bc DNA replication not complete + DNA damage)

Exit of mitosis: inhibition of APC/C activation delays exit from mitosis (bc chromosomes are not properly attached to spindle)

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10
Q

G1 phase overview: pathways + cdk inhibitors?

A

inhibitors: p15, p16, p18, p19
inhibit CDK4/6 + Cyclin D
cyclin D is produced/upregulated by: MAPK, PI3K, Wnt, NFkB
CDK4/6 + Cyclin D complex phosphorylates Rb = releases transcription regulator (E2F) = transcription of genes producing equired for S-phase entry (e.g cyclin A/E)

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11
Q

mitogens

A

extracellular signals produced by other cells that stimulate a cell to multiply

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12
Q

One way in which mitogens stimulate cell proliferation (G1)

A

inhibition of the Rb protein

absence of mitogens: dephosphorylated Rb hold specific transcription regulators in an inactive state

mitogens binding to cell-surface receptors activate intracellular signalling pathways that lead to the formation + activation of G1-Cdk and G1/S-Cdk complexes

Complexes phosphorylate = inactivate Rb protein = release transcription regulators = activate transcription of genes req for entry into S

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13
Q

DNA damage: Halt progression through G1

A

DNA damage > activation of protein kinases that phosphorylate p53 protein, stabilizing + activating it > activated p53 accumulated + stimulates transcription of the gene that encodes the Cdk inhibitor protein (p21) > p21 protein binds to G1/S-Cdk and S-Cdk and inactivates them = cell cycle arrests in G1

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14
Q

permanent vs temporary withdrawl from cell cycle

A

permanent: terminally differentiated cells = cell-cycle control system is dismantled completely + genes encoding relevant cyclins + Cdks are irreversibly shut down

temporary: absence of appropriate signals = enter an arrested state called G0. They retain the ability to reassemble the cell-cycle control system quickly + divide again

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15
Q

S phase overview: inhibitors + proteins

A

inhibitors: p21, p27, p57

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16
Q

Initiation of DNA replication: S phase steps

A

During G1, Cdc6 binds to the ORC (origin recognition complex), together these load a pair of DNA helicases on the DNA + the Cdc6 dissociates = forms the prereplicative complex.

At the start of S phase, S-Cdk triggers the firing of this loaded replication origin by guiding the assembly of the DNA polymerase + other proteins that initiate DNA synthesis at the replication fork.

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17
Q

how can S-Cdk block re-replication

A

by phosphorylating Cdc6 and the ORC = keeps these proteins inactive + prevents the reassembly of the prereplicative complex until the Cdks are turned off in the next G1

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18
Q

What happens if there is incomplete replication

A

Activity of M-Cdk is inhibited
DNA damage response is triggered:
Inhibition of phosphatase Cdc25 = prevents removal of the inhibitory phosphates from M-Cdk = M-Cdk remains inactive

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19
Q

Role of M-Cdk

A

helps prepare the duplicated chromosomes for segregation + induces the assembly of the mitotic spindle

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20
Q

How is M-Cdk activated

A

Activating phosphatase Cdc25 removes the inhibitory phosphates holding M-Cdk in an inactive state
self-reinforcing process: M-Cdk phosphorylates + activates more Cdc25 (positive feedback increasing M-Cdk activity which drives G2 into M phase)

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21
Q

Stages of mitosis

A

prophase, prometaphase, metaphase, anaphase A, anaphase B, telophase

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22
Q

Going from metaphase to anaphase

A

APC/C triggers the separation of sister chromatids by promoting the destruction of cohesins.

APC/C indirectly triggers the cleavage of the cohesins that hold sister chromatics together. It catalyzes the ubiquitylation and destruction of an inhibitory protein called securin, which blocks the activation of separase (a protease). When freed from securin, separase cleaves the cohesion complexes, allowing the mitotic spindle to pull the sister chromatids apart

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23
Two processes segregate chromosomes at anaphase
Anaphase A: (kinetochore microtubules shorten + chromosomes move poleward) sister chromatids are pulled toward opposite poles as the kinetochore microtubules depolymerize Anaphase B: spindle poles move apart as a result of 2 separate forces: 1) elongation + sliding of the interpolar microtubules past one another pushes the 2 poles apart 2) forces exerted on the outward-pointing astral microtubules at each spinfle pole pull the poles away from each other, toward the cell cortex
24
Nuclear envelope break down + re-forming
Phosphorylation of nuclear pore proteins + lamins help trigger the disassembly of the nuclear envelope at prometaphase. Dephosphorylation of nuclear pore proteins + lamins at telophase help reverse the process (continued fusion of nuclear envelope vesicles)
25
What is Metaphase checkpoint
Prevents premature segregation of sister chromatids by delaying anaphase onset until all chromosomes are correctly attached to the spindle apparatus If any chromosome is improperly attached, SAC proteins inhibit APC/C activation. Once all kinetochores are properly attached, SAC inhibition is lifted, APC/C degrades Cyclin B1 and Securin, and anaphase proceeds.
26
When does the mitotic checkpoint activate
during prometaphase
27
the process of achieving stable microtubule attachments at the kinetochores
Unstable Attachments: Microtubules initially bind kinetochores in incorrect or unstable orientations. These unstable attachments are corrected through trial-and-error (via tension sensing) Stable Attachment: When microtubules attach properly (with tension generated between sister kinetochores), the attachments are stabilized. Stable attachments satisfy the SAC, allowing progression to anaphase.
28
Cells + DNA content levels
G1: 2N (normal diploid amount of DNA, has not replicated its DNA yet) S: DNA replication occurs = DNA content gradually increases to 4N G2: 4N (replication is fully complete)
29
Summary of cell cycle
Initiation of cell cycle progression by RAS/NOTCH/WNT pathways G1 phase: Restriction point and preparation for DNA replication S phase: DNA replication G2 phase: DNA damage checkpoint and preperation for mitosis M phase: Mitotic checkpoint and mitosis Cell cycle analysis using Flow cytometry
30
What are the 3 types of protein filaments that form the cytoskeleton
intermediate filaments, microtubules (largest), actin filaments (smallest)
31
Intermediate filaments
Ropelike, withstand mechanical stress, Makes cell rigid, tent poles Monomer: alpha-helical central rod domain w/ unstructured terminal domains at either end. Form stable dimers by wrapping around each other (coiled) Dimers running in opposite directions = form staggered tetramer (where both ends of tetramer are the same = no structural polarity) Tetramers assiociate w/ eachother = final ropelike intermediate filament
32
What are the 4 classes of intermediate filaments?
Cytoplasmic: Keratin filaments (in epithelial cells + distribute the stress tat occurs when skin is stretched) Vimentin / vimentin-related filaments (in connective-tissue cells, muscle cells, glial cells) Neurofilaments (in nerve cells + provide strength / stability) Nuclear: Nuclear Lamins (in all animal cells + provides rigidity of the nucleus)
33
Effects of a defective nuclear lamin
Progeria: aging @ young age
34
Effect of mutations in keratin genes
Epidermolysis Bullosa Simplex - skin is highly vulnerable to mechanical injury - Keratin 5 + 14 are affected
35
Microtubules
Transport system Can rapidly disassemble in one location + reassemble in another They extend from organizing centers
36
Microtubuli: organizing centers
Where growth and shrinkage occurs Centrosomes (nondividing cell) Two poles of a mitotic spindle (disassemble from centrosome + reassemble there during mitosis) or the basal body of a cilium (form the hairlike structures) Growth and shrinkage: see later on Motor proteins: required for transport. Dynamic instability: be able to describe it.
37
Microtubuli: α and β tubulin
Microtubles are hollow, Tubulin heterodimer: alpha and beta Heterodimers join to form protofilaments which join together to form a tube Structural polarity: there is a + and - end
38
Microtubuli: orientation
Centrosome w/ attached microtubules: - end embedded in centrosome, grown from a gamma-tubulin ring complex + end extends into cytoplasm gamma-tubuliin ring complexes serve as a starting points (nucleation site) for the growth of one microtubule
38
Microtubuli: Dynamic Instability
Dynamic instability is the switching back and forth between polymerization and depolymerization (allows microtubules to undergo rapid remoldelling) GTP hydrolysis controls dynamic instability Growing microtubule > Tubulin dimers carrying GTP bind more rightly to one another than tubulin dimers carrying GDP Rapidly growing + ends tend to keep growing Shrinking microtubule > Time to time (esp if microtubulin growth is slow = GTP hydrolysis is faster than addition of new GTP-tubulin dimers) the dimers in this GTP cap will hydrolyze their GTP to GDP before fresh dimers loaded w/ GTP have time to bind = GTP cap is lost GDP-carrying dimers less tightly bound = protofilaments peel away from + end and dimers are released = microtubule shrinks GTP cap is the driving force
38
Role of motor proteins in intracellular transport
Saltatory movements driven by motor proteins Motor proteins move along microtubules using their globular heads Kinesins + cytoplasmic dyneins: - microtubule motor proteins that move in opposite directions along a microtubule - kinesins move towards + end, dyneins move toward - end - Each is a dimer composed of 2 identical subunits - Each dimer has 2 globular ATP-binding heads and a single tail - Heads interact with microtubules - tail interacts with cargo (directly or indirectly through adaptor proteins)
38
How does a cilium beat
by performing a repetitive cycle of movements, consisting of a power stroke followed by a recovery stroke
38
How do the heads of kinesins and dyneins move these proteins?
Heads are enzymes w/ ATPase activity ATP hydrolysis and phosphate release by rear head = loosens its attachment to the microtubule. ADP release + ATP binding by the front head = conformational change that flips the rear motor head to the front = complete single step
39
Dynein movement - flagellum
Dynein (movement towards minus side) causes sliding in a flagellum Intact flagellum: doublets are tied to each other by flexible protein links so that the action of the system produces bending rather than sliding
39
Microtubules in a cilium or flagellum
Arranges in a "9+2" array 9 outer microtubules carry 2 rows of dynein molecules Dynein heads periodically make contact with the adjacent doublet microtubule and move along it = produce force for ciliary beating
39
Forms of actin
Microvilli, contractile bundles (cytoplasm), filopodia (protrude from edge of a moving cell), contractile ring (during cell division)
39
Actin filaments
smallest diameter, thin flexible protein threads Subunit: actin monomer A cleft in the monomer = the binding site for ATP or ADP Each actin filament: 2 stranded helix Structural polarity: have a + end and - end
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Growth + shrinkage of actin
Actin monomers in the cytosol carry ATP (which is hydrolyzed to ADP after actins assembly onto a growing filament) ADP molecules remain trapped within actin filament until the actin monomer that carries them dissociates from the filament When ATP-actin adds to the + end of the filamane tat the same rate that ADP-actin is lost from - end treadmilling occurs When rates of addition and loss are equal, the filament stays the same length
40
Actin-binding proteins
They control the behavior of actin filaments in vertebrate cells most known is myosin
41
Actin movement
Forces generated in the actin-filament-rich cortex help move a cell forward Actin polymerization at the leading edge of the cell pushes the plasma membrane forward New points of anchorage are made between the bottom of the cell and the surface on which the cell is crawling (substratum) Contraction at the rear of the cell (mediated by myosin motor proteins moving along actin filaments) draws the body of the cell forward New anchorage points established at front + old ones released at the back as the cell crawls forward Cycle repeats
42
What can have a dramatic effect on the organization of actin filaments in fibroblasts
Activation of Rho-family GTPases > behave as molecular switches that control intracellular processes by cycling between an active GTP-bound state and an inactive GDP-bound srarwe
43
Role of myosin
myosin II filament can slide two actin filaments past each other > myosin II head group walks toward the + end of the actin filaments with which it interacts > myosin filament slides sets of oppositely oriented actin filaments past one another If organized in a bundle it can generate a strong contractile force Myosin II is bipolar
44
Sarcomeres
the contractile units of the muscle Z discs at either end of the sarcomere are the arrachment points for the + ends of actin filaments Centrally located thick myosin II filaments
45
Muscle contraction
Performed by a sliding-filament mechanism Actin and myosin filaments slide past each other Filaments themselves remain the same length Sarcomere shortens Sliding motion is driven by the myosin heads walking toward the + ends of the adjacent actin filaments
46
Macrophages are treated with a substance colchicine that blocks the formation of microtubuli. Do you expect an effect on phagocytosis, and on the digestion of the material?
No effect on phagocytosis, but on intracellular transport Transport of lysosomes to phagosome cannot take place
47
What controls skeletal muscle contraction
Tropomyosin and troponin complexes Tropomyosin binds in the groove of the actin helix + prevents the myosin heads from associating with the actin filament Troponin is a Ca2+ sensitive protein associated with the end of a tropomyosin molecule When conc of Ca2+ in cytosol rises, Ca2+ binds to troponin = conformational change = causes tropomyosin molecules to shift = allows myosin heads to bind to actin filaments = initiates contraction
48
When treating macrophages with a substance that inhibits the actin filament system, what process is blocked?
phagocytosis
49
Effect of a protein that were to increase dynamic instability of microtubules
You would expect an increase in #no. of shrinking microtubules + #no. of growing microtubules
50
Each epithelial type contains a specific repertoire of of keratins. Name a very important diagnostic tool to elucidate for instance the origin of metastases
Keratin staining
51
Mode of action of taxol
interferes with the spindle figure of dividing cells
52
What is delta G at equilibrium
for both forward and backward reactions it is 0
53
Calculating the equilibrium constant K
K = Kon/Koff = [AB]/[A][B] At equilibrium: association rate = dissociation rate Kon[A][B] = Koff[AB]
54
Terminal phosphate of ATP
Terminal phosphate of ATP can be readily transferred to other molecules because energy-rich phosphoanhydride bond in ATP is converted to a less energy-rich phosphoester bond in the phosphate-accepting molecule (this reaction is energetically favorable + large negative delta G)
55
What can drive an energetically unfavorable biosynthetic reaction?
ATP hydrolysis. 1) activation step: ATP transfers a phosphate to A-OH to produce a high-energy intermediate, A-O-PO3 2) condensation step: activated intermediate interacts with B-H to form A-B net products: A-B, ADP, P
56
Role of NADPH
NADPH accepts and donates e- via its nicotinamide ring NADPH donates its e- together w/ a proton (this oxidation of NADPH to NADP+ is energetically favorable bc nicotinamide ring is more stable when these e- are absent)
57
Breakdown of food molecules in animals
Stage 1: mostly occuring outside cells, breakdown of large food molecules in the mouth and gut (intracellular lysosomes can also digest such large molecules) Proteins > amino acids, polysaccharides > simple sugars, fats > fatty acids and glycerol Stage 2: intracellular, glycolysis in the cytosol > conversion of pyruvate to acetyl groups on acetyl CoA in the mitochondrial matrix Stage 3: citric acid cycle in mitochondrial matrix > oxidative phosphorylation on the mitochondrial inner membrane NADH generated in stage 2 adds to the NADH produced by the citric acid cycle = drives the production of large amounts of ATP by oxidative phosphorylation NET RESULT: ATP, NADH, CO2, H2O
58
Glycolysis
Anaerobic conditions: Fermentation in an active muscle cell: Glucose undergoes glycolysis = pyruvate + NADH > converted into lactate in the cytosol (NADH gives up its e- and is converted back to the NAD+ required to maintain the reactions of glycolysis) Fermentation in yeast: Pyruvate is converted into CO2 and ethanol (also regenerates NAD+ from NADH) 1 molecule of glucose = 2 molecules of pyruvate = 2 molecules of lactate or 2 of CO2 and ethanol, 2 of NAD+ Anaerobe glycolysis: ATP generation and recycling NADH: Very fast but inefficient use of glucose and leads to acidification
59
What drives the energetically unfavorable formation of NADH and ATP in glycolysis
Step 6: energy released by the energetically favorable oxidation of a C-H bond in glyceraldehyde 3-phosphate is large enough to drive two energetically costly reactions: namely the formation of both NADH and a high-energy phosphate bond in 1,3-bisphosphoglycerate Subsequent energetically favorable hydrolysis of that high-energy phosphate bond in step 7 = drives the formation of ATP (energetically unfavorable)
60
What is the citric acid cycle
series of reactions in the mitochondrial matrix that catalyze the complete oxidation of the carbon atoms of the acetyl groups in acetyl CoA Acetyl-group carbons are transferred from acetyl CoA to an oxaloacetate = forms citric acid > progressively oxidized (this energy is used to produce activated carriers e.g NADH) Reaction of Acetyl CoA (from pyruvate) with oxaloacetate + citric acid
61
Fatty acids: conversion into acetyl CoA
Fats are stored in a triacylglycerol (glycerol joined by an ester bond to 3 fatty acid tails) Lipases hydrolyze these ester bonds when fatty acids are needed for energy Released fatty acids are coupled to CoA in a reaction requiring ATP. Activated fatty acids (fatty acyl CoA) are oxidized in a cycle containing 4 enzymes Each turn of the cycle shortens the fatty acyl CoA by 2 carbons + generated 1 molecule each of FADH2, NADH, and acetyl CoA
62
Oxidative phosphohrylation
Chemical energy captured by the activated carriers (produced during glycolysis and the citric acid cycle) is used to generate ATP NADH and FADH2 transfer their e- to the electron transport chain in the innter mitochondrial membrane As e- pass through the series of e- acceptor and e- donor molecules they fall to lower energy states The energy released is used to drive protons (H+) across the inner membrane(from mitochondrial matrix to intermembrane space) = generates a proton gradient = this is used to drive the synthesis of ATP
63
Role of mitochondria
Energy production, Apoptosis, Fat metabolism (Cholesterol and fatty acid metabolism), Ca2+ storage
64
Membrane-based process for making ATP
Stage 1: Sets up an electrochemical proton gradient. Energy of electron transport is used by proton pump to pump protons across membrane Stage 2: Use of proton gradient to generate ATP. Energy in the proton gradient is harnessed by ATP synthase to made ATP
65
Mitochondrion division
divides like a bacterium Undergoes a fission process
66
Mitochondrial DNA (mtDNA)
Total genome length: 16,569 base pairs Protein coding regions: e.g subunits of NADH dehydrogenase, cytochrome oxidase, and ATP synthase tRNA genes, rRNA genes
67
Mitochondrial morphology
Matrix, inner membrane, outer membrane, intermembrane space
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Dynamic processes of mitochondria
Fission and fusion Fission: a single mitochondrion divides into two or more smaller mitochondria Can remove damaged parts of mitochondria, even distribution to daughter cells, Adaptation to energy needs Fusion: two or more mitochondria merge to form a single, larger mitochondrion Compensates for damage, Energy optimization, Maintains mtDNA integrity Mitochondria constantly undergo cycles of fission and fusion to adapt to the cell's metabolic needs
69
Which food-derived molecules are converted to acetyl CoA
Polysaccharides (sugars) > glucose > pyruvate > acetyl CoA Fats (fatty acids) > Acetyl CoA Enter the mitochondrion from the cytosol Acetyl CoA then oxidized to CO2
70
Metabolic roads to Acetyl-CoA
Pyruvate (from glucose or alanine), Ethanol, palmitate (fatty acid), acetoacetate,
71
Citric acid cycle: energy for electrons
Acetyl groups from acetyl CoA are oxidized to Co2. Some of the energy from this is saved in the form of high-energy e- held by activated carriers NADH and FADH2 (they can then donate their e- to the ETC) Hydride ion is removed from NADH and is converted into a protin + 2 e-
72
Chemiosmotic coupling
Stage 1: as e- are transferred from activated carriers to oxygen (to form water), protons are pumped across the inner mitochondrial membrane stage 2: proton gradient used to drive ATP synthesis
73
net equation of oxidative phosphorylation
2NADH + O2 + 2H+ ----> 2NAD+ + 2H2O
74
Electron transport chain: enzyme complexes
high-energy e- are transferred through 3 respiratory enzyme complexes in the inner mitochondrial membrane During transfer of e- from NADH to oxygen, protons derived from water are pumped across the membrane from the matrix into the intermembrane space by each of the complexes Ubiquinone and cytochrome c are mobile carriers that ferry e- from one complex to the next NADH dehydrogenase comples > ubiquinone > cytochrome c reductase complex > cytochrome c > cytochrome c oxidase complex
75
Proton-motive force
The electrochemical proton gradient induces a large force due to the membrane potential (delta V) + a smaller force due to the H+ conc grad (the pH gradient, delta pH) Intermembrane space is slightly more acidic than matrix (bc of higher proton conc) Membrane potential + pH gradient = proton-motive force which pulls protons back into the mitochondrial matrix
76
How does ATP synthase use the energy of the proton gradient
ATP synthase (a large multisubunit protein) is composed of a stationary head (F1 ATPase) + a rotating portion called F0 (transmembrane proton carrier + a central stalk) F1 and F0 are formed from multiple subunits Driven by the proton gradient F0 spins rapidly within the stationary head of the F1 = generates ATP from ADP and Pi The stationary head is secured to the inner membrane by an elongated protein "arm" called the peripheral stalk F1 ATPase can carry out the reverse reaction (hydrolysis of ATP to ADP and Pi) when detatched from the F0 portion
77
ATP synthase: reverse coupling device
It can either A) synthesize ATP or B) pump protons against this gradient by hydrolyzing ATP (Protons flow back into the mitochondrial matrix) The direction of operation (and rotation) at any given instant depends on the net free-energy change (delta G) for the couples processes of H+ translocation across the membrane and the synthesis of ATP from ADP and Pi E.g if the electrochemical proton gradient falls below a certain level, the delta G for H+ transport into the matrix will no longer be large enough to drive ATP production; instead, ATP will be hydrolyzed by ATP synthase to rebuild the proton gradient
78
How are pyruvate, ADP and Pi transported into the matrix
Pyruvate and Pi are moved into the matrix along w/ protons (as they move down their electrochem grad) Both are -vely charged so their movement is opposed by the negative membrane potential. however, the proton conc grad (pH gradient) drives their inward transport ADP is pumped into the matrix and ATP is pumped out by an antiport process that uses the voltage gradient across the membrane to drive the exchange The outer mitochondrial membrane is freely permeable to all of these compounds due to the presence of porins
79
Redox in the ETC
Redox potential increases along the mitochondrial ETC. The biggest increases in redox potential occur across each of the 3 respiratory enzyme complexes, whicih allows each of them to pump protons
80
What happens if all ADP is converted into ATP
NADH can not be recycled to NAD+ > block TCA cycle High NADH levels > citrate accumulation in mitochondrion > citrate transport to cytosol > used for fatty acid production
81
Protons can also be transported by uncoupling proteins
uncoupling of oxidative phosphorylation (OXPHOS) ETC continues to transfer electrons and pump protons across the inner mitochondrial membrane, but the energy stored in the proton gradient is not used to produce ATP. Instead, this energy is released as heat. Activated uncoupling protein (UCP2, UPC3) (a family of proton transporters) may cause increased thermogenesis (heat production) which leads to reduced storage of fat (particularly brown adipose tissue)
82
NET equations
Glycolysis: C6H12O6 + 2 NAD + 2 ADP + 2 P → 2 pyruvate + 2 NADH + 2 ATP Decarboxylation: 2 pyruvate + 2 HSCoA + 2 NAD → 2 acetyl-CoA + 2 NADH + 2 CO2 TCA cycle: 2 Acetyl-CoA + 6 H2O + 6 NAD + 2 FAD + 2 ADP + 2 P → 2 CoA + 6 NADH + 2 FADH2 + 2 ATP + 4 CO2 Oxidative Phosphorylation: 10 NADH2 + 2 FADH2 + 34 ADP + 34 P + 6 O2 → 34 ATP + 12 H2O + 10 NAD + 2 FAD * Aerobic situation: C6H12O6 + 6 O2 + 38 ADP + 38 P → 6 CO2 + 6 H2O + 38 ATP Anaerobic situation: Only 2 ATP
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By-products of oxidative phosphorylation in mitochondria
ROS (superoxide, hydrogen peroxide, hydroxyl radical) Occasionally, some electrons escape from ETC at CoEnzym-Q and react with oxygen, forming superoxide which is then converted into different ROS (oxygen radicals with unpaired electron(s)) Cause oxidative stress
84
How can mitochondria protect against oxidative damage
mitochondria are equipped with antioxidant enzymes that neutralize ROS e.g A) Superoxide Dismutase (SOD): Converts superoxide anions (O₂⁻·) into hydrogen peroxide (H₂O₂) and oxygen (O₂) B) Catalase: (found primarily in the peroxisomes) Converts hydrogen peroxide (H₂O₂) into water (H₂O) and oxygen (O₂).
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Effect of ROS on biological macromolecules
ROS can react with biological macromolecules + cause oxidative damage e.g hydroxyl radicals (OH·), are highly reactive and can directly modify nucleobases in DNA. Guanine, being the most oxidizable of the DNA bases, is a primary target for ROS-induced damage. Forms a hydroxyl group on the guanine = 8-hydroxyguanine mutagenic because: It can mispair with adenine (A) during DNA replication instead of cytosine (C). This leads to a G→T transversion mutation in the next replication cycle
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Why is mitochondrial DNA is highly susceptible to damage
mtDNA lacks protective histones No efficient ‘repair’ mechanism In vicinity of OxPhos (ROS)
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Mitochondrial diseases
Caused by mtDNA mutations/deletions Leber’s heridatry optic neuritis (LHON) Myoclonic Epilepsy with Ragged Red Fibers (MERFF syndrome) Mitochondrial encephalomyopathy, lactic acidosis, and stroke (MELAS) Caused by nuclear genetic defects Friedrich’s ataxia Dominant optic atrophy Charcot-Marie-Tooth disease 2a Hereditary spastic paraplegia Familial Parkinson’s Disease Diseases associated with severe mitochondrial dysfunction (Aging), Obesity, Diabetes Mellitus, Cardiovascular disease, Stroke, Epilepsy, Alzheimer’s Disease, Huntington’s disease, Schizophrenia, Autism
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Multiple sclerosis
Usually starts between 20 and 40 yrs of age women affected twice as often as men Northern European background 1 in every 1,000 people
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Risk factors of MS
Infectious agent (e.g EBV) Genetic predisposition Environmental factors (e.g vitamin D)
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MS: diagnosis
Neurological examination, lumbar puncture, MRI (you can see active lesions)
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Multiple sclerosis clinical patterns
Relapsing-remitting (~75%) Secondary-progressive Primary-progressive (~15%) Progressive-relapsing
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Chronic active lesions
Ongoing demyelination at the rim Activated microglia and some foam cells at the edge of the lesion (MHC class II presenting antigen, myelin fragments)
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Oxygen + Mitochondria in multiple sclerosis
Adult brain oxygen consumption: 20% of total oxygen Highly dependent on aerobic respiration Neurons contain many mitochondria Na+/K+ ATPase consumes 90% of energy in brain (action potential) Action potential: very efficient in myelinated axon Loss of myelin increases the energy demands of axons because: Sodium-potassium ATPase must work harder to restore ionic gradients disrupted by inefficient conduction. Voltage-gated sodium channels become redistributed, requiring more ATP to maintain membrane potential
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Tissue
Cells > tissues > organs Tissue is an assembly of cells held together by cell-cell adhesions, extracellular matrix, or both
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Bone
calcified connective tissue Bone is also considered a connective tissue. Slice image: concentric circular structures: middle contains a blood vessel. Dark spots are osteocyte lacunae, which are all connected by very tiny canaliculi, canals that run through bone and sense loading.
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Structure of collagen
single collagen polypeptide chain > triple-stranded collagen molecule > collagen fibril > collagen fiber
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Collagen synthesis
Procollagen precursor: has unstructured peptides at either end. These peptides prevent collagen fibrils from assembling inside the fibroblast. When the procollagen is secreted, extracellular procollagen proteinases remove its terminal peptides, producing mature collagen molecules. These molecules can then self-assemble into ordered collagen fibrils
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Ehlers-Danlos syndrome
hyperextensible skin, joints Incorrect assembly of collagen Either due to: a lack of an enzyme that converts procollagen to collagen or a defect in procollagen itself
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Integrins + fibronectin
Fibronectin and transmembrane integrin proteins help attach a cell to the extracellular matrix Fibronectin has 2 sites: extracellular matrix binding site (e.g for collagen), cell attachment site (e.g for integrin) Fibronectin molecules bind to collagen fibrils outside the cell. Integrins in the plasma membrane bind to the fibronectin and tether it to the cytoskeleton inside the cell. (transmembrane linkage) The integrin molecule transmits tension across the plasma membrane: it is anchored inside the cell via adaptor proteins to the actin cytoskeleton and externally via fibronectin to other extracellular matrix proteins, such as the collagen fibril shown. The integrin shown here links fibronectin to an actin filament inside the cell. Other integrins can connect different extracellular proteins to the cytoskeleton Recognition sequence on extracellular matrix molecules for integrins: RGD (a sequence of three amino acids)
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Integrins: activation / inactivation
An integrin protein consists of two different subunits, α and β, both of which can switch between a folded, inactive form and an extended, active form. Switch to activated state: triggered by binding to an extracellular matrix molecule (such as fibronectin) or to intracellular adaptor proteins that then link the integrin to the cytoskeleton. In both cases, the conformational change alters the integrin so that its opposite end rapidly forms an attachment to the appropriate structure. (e.g binding to extracellular matrix = strong binding to cytoskeleton, binding to cytoskeleton = strong binding to extracellular matrix)
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Variation in alpha beta subunits of integrins
Various alpha and beta chain combinations possible, often cell type dependent. Some are specific for specific cell-matrix interactions, for instance alpha2beta1 for collagen, alpha6beta1 for laminin etc. Some, like CD11c, the combination of beta2 and alphaX, are specific for dendritic cells, or beta2 and alphaM for monocytes.
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How are integrins involved in actin protrusion
Integrins attach and accumulate at focal contacts, where adhesion to collagen or other substratum is made. (very front region) These integrins INTEGRATE with the actin network in the cell. The contact at focal adhesions may push the cell forward, pushing forward a blob of actin
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Osteoclast precursors grown on bone slices
Osteoclast precursors grown on bone slices express markedly more IL-1 than those cultured on plastic plates. GFP or c-Fos retrovirus-infected WT MDS were cultured on plastic or bone slices in the presence of M-CSF for 9 days. total RNA was extracted and subjected to real-time RT-PCR to determine the expression levels of IL-1 and TNF. IL-1β protein concentrations were measured by enzyme-linked immunosorbent assay in the culture medium collected from the cultures described in A at the end of the culture. Bone matrix components stimulate osteoclast precursors to express higher levels of IL-1 and potentially TNF, likely through interactions with matrix proteins Extracellular matrix proteins can evoke expression of IL-1β by adherent osteoclast precursors Here it is shown that adhesion to certain bone matrix proteins, DSP and OPN and NOT DPP or TGF-beta give rise to elevated IL-1 expression, which induces c-Fos-expressing precursors to form osteoclasts. This, then also corresponds to increased osteoclast numbers that form in the presence of DSP and OPN, which can be blocked by adding an inhibitor to IL-1, IL-1Ra.
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Distinct Responses of Osteoclast Precursors to IL-17A and Their Bone Resorption Activity
Bone resorption by osteoclasts originating from the different monocyte subsets Classical Monocytes: Main contributors to bone resorption, forming the highest number of bone-resorbing osteoclasts. Their numbers and resorption activity are not affected by IL-17A treatment. Intermediate Monocytes: Show significant bone resorption activity. IL-17A inhibits their fusion on bone but increases their resorption activity. Non-Classical Monocytes: Rarely form osteoclasts on bone, and these osteoclasts lack resorption capability. IL-17A enhances osteoclast formation but does not induce bone resorption. Classical monocytes adhere most effectively to bone > intermediate monocytes > non-classical monocytes showing the lowest adhesion. Correlates with the expression of integrins: Classical and intermediate monocytes express αMβ2 integrins (alpha M and beta-2 subunits), crucial for bone adhesion. Non-classical monocytes do not express αMβ2, explaining their poor bone adhesion and lack of resorption activity. Conclusion: ability to adhere to bone, mediated by αMβ2 integrins, is critical for osteoclast activity. Classical and intermediate monocytes are the primary contributors to bone resorption, with IL-17A modulating intermediate and non-classical monocyte behavior. Non-classical monocytes fail to adhere effectively or resorb bone due to the lack of αMβ2 integrins, underscoring their limited role in bone resorption.
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Glucosaminoglycans
Resist compression, attracts water, important in cartilage, Shock absorber Chains of Glucosaminoglycans are usually linked to a core protein to form Proteoglycans
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What structure is between epithelial cells + connective tissue
Basal lamina
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Tight junctions
allow epithelial cell sheets to serve as barriers to solute diffusion (they cannot traverse the junctions that seal adjacent cells together) sealed together by branching strands of transmembrane proteins, called claudins and occludins Found near apical face of cells
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Cadherin proteins
Adherens junctions and desmosomes are built around proteins belonging to the cadherin family Identical cadherin molecules in the plasma membranes of adjacent cells bind to eachother extracellularly. Inside the cell, they are attached via linker proteins to cytoskeletal filaments (actin filaments or keratin intermediate filaments) When epithelial cells in culture touch one another, their cadherins become concentrated at the point of attachment, leading to the formation of adherens junctions
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Epithelial cell junctions: 3 main types
Adherens junctions and desmosomes, hemidesmosomes, and gap junctions
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Adherens junctions
They form adhesion belts around epithelial cells in the small intestine A contractile bundle of actin filaments runs along the cytoplasmic surface of the plasma membrane near the apex of each cell. These bundles are linked to those in adjacent cells via transmembrane cadherin molecules
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Desmosomes
Desmosomes link the keratin intermediate filaments of one epithelial cell to those of another On the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular linker proteins. A bundle of keratin filaments is attached to the surface of each plaque. The cytoplasmic tails of transmembrane cadherin proteins bind to the outer face of each plaque, their extracellular domains interact to hold the cells together
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Hemidesmosomes
Hemidesmosomes anchor the keratin filaments in an epithelial cell to the basal lamina The linkage is mediated by a transmembrane attachment complex containing integrins, rather than cadherins Keratin filaments > plaque of linker proteins > integrin proteins (transmembrane) > basal laminal
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Gap junctions
Gap junctions provide neighboring cells with a direct channel of intercytosolic communication pores of the cell, passage of small molecules between cells The apposed membranes are penetrated by protein assemblies called connexons, each of which is formed from 6 identical protein subunits 2 connexons join across the intercellular hap to form an aqueous channel connecting the cytosols of the 2 cells
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Skin: an example of a mixture of cell types
Composed of 2 main tissues: epithelial tissue (the epidermis) on the outside, and connective tissue on the inside The outermost layer of the epidermis consists of flat, dead cells, whose intracellular organelles have disappeared. The underlying connective tissue consists of the tough dermis and the deeper, fatty hypodermis. The dermis and hypodermis are richly supplied with blood vessels and nerves (some nerves extend into the epidermis) All tissues are dynamic and renew: All tissues must contain certain progenitor cells or there must be an influx of progenitor cells to restore cells that are at the end of their life span
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Stem cells
Stem cells in tissue: self renewal Different kinds: hematopoietic, gut, skin Proliferate and receive differentiation signals Each cell type/ tissue each own type
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Stem cell division
When a stem cell divides, each daughter can either remain a stem cell (self-renewal) or go on to become terminally differentiated Terminally differentiated cells usually develop from proliferating precursor cells that divide a limited number of times before they terminally differentiate. Stem-cell divisions can also produce 2 stem cells or 2 precursor cells, as long as the pool or stem cells is maintained
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Cell differentiation in lumen of the gut
Cell differentiation takes place from the bottom of the crypts Stem cells can give rise to: Proliferating precursor cells (continuously slide upward) and terminally differentiate into secretory (goblet) Terminally differentiated paneth cells, which move down to the bottom of the crypt
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Stem cells: Skin
Epidermis is a stratidies epithelium renewed from stem cells in its basal layer Stem cells are at the lower layers that rest on the basal lamina Precursor cells move outward, progressively differentiation as they go, eventually the cells undergo cell death (shed on the skin surface)
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hemopoietic stem cell
A hemopoietic stem cell divides to generate more stem cells, as well as various types of precursor cells that proliferate and differentiate into the mature blood cell types found in the circulation. Note that monocytes give rise to both macrophages, which are found in many tissues of the body, and osteoclasts, which eat away bone matrix. Megakaryocytes give rise to blood platelets by shedding cell fragments
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Mouse ES cells
Mouse ES cells can be induced to differentiate into specific cell types in culture ES cells are harvested from the inner cell mass of an early mouse embryo and can be maintained indefinitely as pluripotent stem cells in culture. If they are allowed to aggregate + are exposed to the appropriate extracellular signal molecules, they can be induced to differentiate into specific cell types of interest
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Cancer: what are similarities and differences with stem cells?
Similarity: self-renewal. Difference: malignant vs. somatic/ non-malignant. Invasive (cancer) vs. non-invasive. Stop vs. no stop on cell division.
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Evolution of tumors
Tumors evolve by repeated rounds of mutation, proliferation, and natural selection.
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Which pathways are altered in cancer
Cell proliferation, cell growth, damage response, cell survival
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Polyp in epithelial lining of the colon or rectum
Polyp in epithelial lining of the colon or rectum, caused by loss of both copies of the APC gene = can progress to cancer by accumulation of additional driver mutations: Excessive proliferation of the mutant cells > One copy of protooncogene (Ras) activated Small tumor > sequential inactivation of both copies of another tumor suppressor gene Large tumor > sequential inactivation of both copies of a 3rd tumor suppressor gene (p53) Tumor becomes invasive cancer > rapid accumulation of other driver mutations Metastasis
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Factors that can contribute to genetic instability
Defects in: Dna replication, Dna repair, cell-cycle checkpoint mechanisms Mistakes in mitosis Abnormal chromosome numbers