BIOC 212 Final Exam Lectures 16-37

Ames test

Reversant His- mutant Salmonella

Aflatoxin B1

Reacts with oxidases to form Aflatoxin-2,3-epoxide which binds to G in DNA

Oncogenes

Dominant, GoF, 1 event

Tumour-suppressors

Recessive, LoF, 2 events

Rb & cell proliferation

Rb inhibits entry into S phase when unphosphorylated, phosphorylated by cyclinD1-Cdk4 to increase proliferation, p16 inhibits formation of active cyclinD1-Cdk4

Papillomavirus tumour-causing proteins

E6 & E7 sequester & Ub host p53 & Rb respectively

Conditions for angiogenesis sprouting

Anoxia, high HIF, VGEF secretion

Angiogenesis steps

Sprouting, pseudopodia, hollow tube

VHL mutation

pVHL/elongin BC/hUCL-2 cannot Ub substrates p220 & p100

RYK cascade

Growth factor binding, dimerisation, receptor Y transphosphorylation, p-T docking sites for SH2-proteins

Ras cascade

Phosphorylation or GTP-binding, Sos promotes GDP release, Ras activation, GAPs increase Ras GTPase

COP-II vesicle pathway

ER to Golgi, anteretrograde

COP-II initiator(s)

Sar1-GDP

COP-II adaptor(s)

Sec23, Sec24

COP-II coat protein(s)

Sec13, Sec31

COP-II fission protein(s)

Coat proteins

COP-II uncoating protein(s)

Adaptor GAPs

COP-II TM protein signal

ER exit signals C-terminal FF, DXE

COP-II lumenal protein signal

TM cargo receptors FF

COP-I vesicle pathway

Golgi to ER, retrograde

COP-I initiator(s)

Arf1-GTP

COP-I adaptor(s)

Alpha/beta and gamma/zeta subunits

COP-I coat protein(s)

alpha/beta’ subunits

COP-I fission protein(s)

Coat proteins

COP-I uncoating protein(s)

Adaptor GAPs

COP-I type 1 TM signal

Cytosolic C-term KKXX

COP-I type 2 TM signal

Cytosolic N-term MXXRR

COP-I lumenal protein signal

KDEL for TM receptors KKXX

CCV pathway

Golgi/PM to endosomes

CCV initiator(s)

PI(4,5)P2 in PM, PI(4)P in Golgi

CCV adaptor(s)

AP-1, AP-2

CCV coat protein(s)

Clathrin triskelins

CCV fission protein(s)

Dynamin-GTP

CCV uncoating protein(s)

Auxilin & HSC70-ATP

TRAPPI pathway

ER to Golgi, within Golgi

TRAPPI cycle

Rab-GTP binds p115 coiled-coil tether, coiled-coil tether binds vesicle & transfers to TRAPPI, SNARE fusion

Exocyst/CATCHR pathway

Golgi to PM

Exocyst/CATCHR cycle

Rab-GTP binds to hexamer, binds target membrane proteins, forms octamer

Endocystosis pathway

PM & early endosomes to Golgi

Endocystosis cycle

Rab5-GTP vesicle + Rab5-GTP/CORVET early endosome, maturation to MVB & late endosome, Rab7-GTP late endosome + Rab7-GTP/HOPS lysosome

SNARE fusion cycle

SNAREs form ring, zippering, apposition, hemifusion stalk, hemifusion diaphragm, expansion, strain relief & inactivation

NSF cycle

Binds v-/t-SNAREs via alpha-SNAP, separates SNAREs, t-SNARE reactivated & v-SNARE recycled

Synaptic vesicles cycle

Docking, partial SNARE tetramer, complexin priming, Ca2+ signal, synaptogamin displaces complexin, stable SNARE & fusion

Retromer vesicle pathway

Endosomes, retrograde

Retromer initiator(s)

Rab5-GTP, Rab7-GTP

Retromer adaptor(s)

Vps26, Vps29, Vps35

Retromer coat

SNX, PI(3)P

Retromer fission protein(s)

Dynamin & cytoskeleton

Retromer uncoating protein(s)

GAPs

MVB cycle

ESCRT-0 binds PI(3)P & mono-Ub cargo, ESCRT-I binding, ESCRT-I/II push membrane in, ESCRT-III multimer ring, bending & pinching

Autophagy cycle

Vesicle nucleation, phagophore, fusion, autophagosome, lysosome fusion, digestion

Autolysosome cycle

ATG8 recruit receptor-cargo to vesicle, coalesce, phagophore, autolysosome

Actin filament growth

NPF activated at leading edge, activates Arp2/3 7-mer, conf change, nucleation, profilin-bound actin addition, + end growth & 70° network formation

Actin nucleating proteins

Arp2/3, formin

Actin monomer binding proteins

Profilin (promotes recruitment), thymosin (prevents assoc)

Actin filament binding proteins

CapZ (end binding), cross-linking: fimbrin (tight filopodia), alpha-actinin (loose stress-fibres), filamin (gel-like lamellipodia)

Actin filament severing proteins

Gelsolin, cofilin

Gamma-tubulin nucleation

gamma-TuSC (2 copies) + gamma-TuRC (7 copies) = 13 copy spiral

Microtubule nucleating proteins

gamma-tubulin, augmin

Tubulin sequestering proteins

Strathmin

End-binding MAPs

Kinesin-13 (collapse), XMAP215 (growth)

Microtubule severing proteins

Katanin

Kinesin directions

N-term + end, C-term - end

Dyneins

-end directed

Cascade in inner cells

Cell contact, LATS1/2 phosphorylate YAP, no TEAD4 inhibition, no Cdr2 expression

Cascade in outer cells

No cell contact, F-actin sequesters LATS1/2, no YAP phoshorylation, TEAD4 inhibition, Cdr2 expression

P/A PCP proteins

Van Gogh/Strabismus, Prickle

D/P PCP proteins

Frizzled/Dishevelled, Diego

Neural tube morphogens

Dorsal BMP gradient, ventral Shh gradient

Later dev cascade

LATS1/2 regulate Yorkie/Yap, Myc (growth) + cyclin E (div) + Diap/Batman (survival), tissue growth

Glycolysis step 1

Phosphorylation, glucose to G6P by hexokinase (-1 ATP)

Glycolysis step 2

Isomerisation, G6P to F6P by G6P isomerase

Glycolysis step 3

Phosphorylation, F6P to FBP by PFK (-1 ATP)

Glycolysis step 4

Cleavage, FBP to GAP & DHAP by aldolase

Glycolysis step 5

Isomerisation, DHAP to GAP by TIP

Glycolysis step 6

Ox-Phos, GAP to BPG by GAPDH (+2 NADH)

Glycolysis step 7

Substrate-level phosphorylation, BPG to 3PG by PGK (+2 ATP)

Glycolysis step 8

Isomerisation, 3PG to 2PG by PGM

Glycolysis step 9

Dehydration, 2PG to PEP by enolase (+2 H2O)

Glycolysis step 10

Substrate-level phosphorylation, PEP to pyruvate by pyruvate kinase (+2 ATP)

Glycolysis irrev steps

1, 3, 10

Glycolysis E-investment phase

1-5

Glycolysis E-gen phase

6-10

Glycolysis net E production

7 ATP

Hexokinase regulation

Product inhibition by G6P

PFK regulation

Adenylate charge, inhibition by ATP/citrate, activation by F2,6BP/ADP/AMP

Pyruvate kinase regulation

Inhibition by ATP/acetyl-CoA/Ala, feedforward activation by F1,6BP

PDC cycle

CO2 removed, PDE1 to hydroxyethyl-TPP, E2 acetyl-dihydroliponamide + CoA, E3 redu FAD/NAD+

PDC regulation

E1 phosphorylation & allosteric product inhibition by acetyl-CoA/NADH

CAC overall formula

OAA + acetyl-CoA + 3NAD+ + FAD + GDP + Pi —> OAA + CoA + 3NADH + FADH2 + GTP + CO2

CAC cycle

Acetyl-CoA, citrate, isocitrate, alpha-KG, succinyl-CoA, OAA

E gen for 1 CAC turn

10 ATP

ATP per NADH

2.5

ATP per FADH2

1.5

ATP per GTP

1

CAC flux regulation

E state (allosteric activation), redox state (mitoch NADH:NAD+), E-rich compound availability (acetyl/succinyl-CoA)

Citrate synthase regulation

Inhibition by NADH/succinyl-CoA

Isocitrate DH regulation

Inhibition by NADH/ATP, activation by ADP/Ca2+

alpha-KG DH regulation

Inhibition by succinyl-CoA/NADH, activation by Ca2+

H+ per NADH

4 H+ (complex I) + 4 H+ (complex III) + 2 H+ (complex IV)