1. crowded 2. rough-and tumble(constantly colliding) 3. viscous （Re： Reynold's number） 4. elastic 5. meshwork (网状组织) 6. active material

Energy Flashcards by Cathy Xie

（）% genome related to metabolism

20%

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ATP binding/hydrolysis can () of protein

distort 3D structure

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distortion () energy, relaxation () energy

store, use

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NAD+ to NADH

G >0

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NAD+ is electron ()

acceptor

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() bring NAD+ into the position to be reduced

GAPDH

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FAD need () energy to be reduced than ()

less, NAD

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thermal energy equation

E=(3/2)(Kb)(T)

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1 Kb T=

0.6 Kcal/mol

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ATP hydrolysis

20 KbT

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()molecule has () D, what is D

smaller, larger, diffusion coefficient

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Brownian motion

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Mean-square displacement

X^2=2Dt

t: time
X: displacement

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covalent bond>NADH oxidation>photon>enzyme activation>ATP hydrolysis>non-covalent bond（ex. H-bond）>mechanical force

photon: 80 KbT
noncovalent bond:2-12
mechanical force: 1

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energy of molecule fluctuate

P=e^(-E/(KbT))
E=()KbT
ln(P)=-E/(KbT)

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cytoplasm

crowded
rough-and tumble(constantly colliding)
viscous （Re： Reynold’s number）
elastic
meshwork (网状组织)
active material

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Reynold’s number

intertial forces/viscous forces=pvl/u

density velocity length/dynamic viscosity

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carbon starvation or ATP depletion can “freeze the cytoplasm”

turn to “glass”

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cytoskeleton function

1.shape, struture, stability
2.intracellular support
3.spatial organization
4.contraction adn motility

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Actin is ATPase

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actin polymerization

nulceation
elongation
steady state

net growth=

Kon-Koff

Cc=

Kon/Koff

formin

control growth rate of actin
FH2 domain: dimer (donate shape)
FH1 domain: bind profilin actin
highly processive

cofilin/ADF

cut actin filament twist actin filament and unwind

capping protein

stop growth (+)end: CapZ (-)end: tropomodulin (in muscle)

Arp2/3

activate by WASp form branch

alpha-actinin

cross link 1 binding domain wider than fimbrin in stress fiber, filopodia, muscle Z line

fimbrin

2 binding actin domain microvilli, filopodia, focal adhesion

Spectrin

heterodimer, 1 actin binding domain 2 polypeptide, beta and alpha in cell cortex

filamin

single polypeptide, 2 actin binding domain flexible

WASp

3 domains: W, C, A WH2 domain: bind actin monomer Acidic domain: induce conformational change in Arp 2/3 and bind with it

ActA

protein mimic WASp

profilin

recycle actin monomer and block (-) end polymerization bind with the smooth end accelerate the exchange rate of ATP, cause rapid lose of ADP

myosin

actin binding site+nucleotide binding site+arm can transfer and produce force move toward the (-)end of actin

myosin class I II V

I : membrane associated, 1 head, to + end II: bundle, contraction, 2 head V: organelle transport 2 head, to + end

Rho family protein

membrane associated GTPase Rho: stress fiber Rac: lammelopodia Cdc42: filopodia

Rho-GTP, GDP GDI GEF GAP

GEF: GDP-->GTP GAP: GTP-->GDP GDI: bind Rho-GDP

Rho activate() by ()

formin relieving auto-inhibition RBD: rho-binding domain

cdc 42 activate () by ()

Arp2/3 opening WASp

cell motility process

1.extracellular signal 2.cdc42: activate WASp, activate Arp2/3, form filopodia in the front 3.cdc42 activate GEF of Rac 4.Rac activate WAVE, activate Arp 2/3, form lamellipodia 5.Rac activate GEF of Rho 6.Rho inhibit Rac at back, activate formin and myosin, form stress fiber to do contraction

extracellular signal create zone of different Rho activity

centrosome

centrioles, pericentriolar material, gama TURCs

gama TURC

provide template for nucleation of mictrotubule TURC+accessory proteins form ring structure at (-)end

arrange monomers to nucleate polymer

spire: 4 WH2 domain to bind 4 actin MAPs: bind tubulin

serving enzyme

ATPase, cut microtubule karanin other protein help to stable the fragment

+TIP protein

bind GTP cap ex. EB1

depolymerase of microtubule

kinesin-13: MCAK ATPase remove tubulin from the end

polymerase of microtubule

XMAP 215 5 tubulin binding domain increase rate constant 1 domain bind to tubulin dimer catalyzes the reverse reaction, stabilize the attachment of tubulin dimer