BIOC I KEEP FORGET

PFK1 regulated by

x- ATP, citrate

✓- AMP, ADP, F26BP

pyruvate kinase regulated by

x- ATP, FA, acetyl COA, alanine

✓-F16BP buildup

total delta G glycolysis

-96

what holds glucokinase in the nucleus until glucose concentration high?

glucokinase regulatory protein

atp often acts as what kind of regulator?

neg/pos heterotropic

what extra regulation does liver pyruvate kinase isoform have?

glucagon→PKA→PK-p (inactive)

(makes glycolysis stop in liver when low blood sugar)

why does step 1 gluconeogenesis need to be so complicated

gluconeogenesis consimes NADH (glyceraldehyde 3 phsosphate dehydrogenase enzyme)

need to get this NADH from mitochondria to the cytoplasm so step 1 takes a long route to bring an NADH out of the mitochondria (if lactate feed gluconeogenesis it doesnt take this route because lactose dehydrogenase produces cytosollic NADH- so liver PEP carboxylase can directly produce PEP)

what cannot be used to make glucose?

FA and acetylcoA

what tissues is glucose 6 phosphatase expressed in?

kidney, liver, small intestine

on PFK2/FBPase2 in liver phosphorylation of _____ leads to F26BP activaton so no F26PB produced

Ser32

in the muscle/cardiac isozyme of F26BPase/PFK2 what effect does epinephrine→ PKA→ phosphorylation have and on what AAs

increases glycolysis by activating PFK2 and thus increasing F26BP

Ser483, Ser466, Thr475

in step 1 gluconeogenesis

____ inhibits PEP carboxylase

____ inhibits pyruvate carboxylase

____ activates pyruvate carboxylase

ADP

ADP

acetyl COA

oxidative PPP produces

ribulose-5-phosphate and NADPH (by oxidating glucose-6-p)

what xyulose 5-phosphate do?

modulate PP in the liver (PP→ dephosphorylated Ser32→ active PFK2→ increased F26BP→increased glycolysis)

non-oxidative PPP for what?

replenish glycolytic intermediates, glucose-6-p or produce xyulose-5-p, (lots of isomerizations and rearrangments)

transketolase

trans aldolase

move 3C

move 3 C

NADPH for FAS comes from

phosphogluconate

glucose-6-p→glucose-1-p by _______

glucose-1-p +UTP → UDP-glucose + ppi by _____

phosphoglucomutase

UDPglucose phosphorylase

glycogen phosphorylase b kinase is activated by

PKA (camp/glucagon in liver)

explain high glucose and insulin effect on an active liver glycogen phosphorylase?

high glucose allosterically binds to GP and causes its 2 phsophoserines to stick out

the phosphoserines are now a better target for inslulin activated PP and the GP becomes inactive (no more breaking down gycogen)

what glucogenic enzyme do muscles lack?

glucose-6-phosphatase

PART D

PART D

glucose/FA

glycerol

amino acids

triacylglycerol

400

4000

100 000

600 000

when perilipin is phosporylated by PKA it activates and releases ____ which activates ____

CGI58, ATGL- adipose TAG lipase

glucagon is the hormone that triggers adipose release of FAs, what kind of receptor does it bind?

binds G protein coupled receptor, G protein activates adenylyl cyclase to produce cAMP and activate PKA

FA +CoA→FA-CoA by ___________

fatty acyl CoA synthetase

carnitine acyl transferase I is inhibited by __________

malonyl CoA (the FA syntheiss precursor)

need linoliate for

prostanglinds

what is citrate lyase activated by?

insulin

what is acetyl COA carboxylase regulated by?

x- metabolites: palmitoyl COA (neg feedback) hormones: glucagon, epinephrine phosphorylate, AMP

✓-metabolites: citrate, hormone: insulin dephosphorylates and polymerizes

what hormones act on adipose and muscle

epinephrine, insulin

hormones that bind surface receptor

hormones that bind nuclear receptor

peptide/ amide (fast)

steroid/thyroid (slow)

insulin GLUT4 effect

move to membrane to transport more glucose in

is cortisol fast or slow acting? what tissues does it act on?

slow

liver and adipose

effects of diabeties

basically no insulin so only glucagon so even when blood sugar high:

• GLUT 4 do not move to cell membrane, so cell cannot uptake glucose

• in liver glucagon signals for FBPase2 to be active so no F26BP produced so liver does gluconeogenesis and uses up oxaloacetate

• oxaloacetate depletion causes acetyl CoA buildup and then acetylCoA made to ketone bodies

• excessive ketone bodies cause ketosis which makes blood dangerously acidic

what does GSK3 do?

phosphorylates active glycogen synthase and makes it inactive

what needs to occur before GSK3 can take action?

casein kinase II has to phosphorylate Ser on the +4 position of GSa

after casein kinase II phosphorylates GSa, what residues does GSK3 phosphorylate?

serines at 0, -4, -8

what AA residues in GSK3 bind teh negative charges of the +4 phosphate group put on GSa by casein kinase II?

Arg96, Arg180, Lys205

how is GSK3 inhibited?

PKB phosphorylates pseudosubstrate on GSK3 at +4 proline and GSK3 binds itself, blocks catalytic activity as it is a proline not ser/thr

PM composition by weight

45% lipid, 50% protein, 5% carb

(lipids take up surface area, but not weight)

spingolipids have what kind of attachment to FA?

glycerophospholipids?

amide

ester

storage lipid-

membrane lipids: phospholipids- and glycolipids-

storage: TAG (3 FA, 1 glycerol)

phospholipids: glycerophospholipids(2 FA, 1 glycerol, 1 phosphate, head group alc derived), sphingolipids (1 sphingosine, 1 FA, head group)

glycolipids: galactolipids/ or sulfolipids (glycerol, FA, FA, saccharide, sometimes SO4), sphingolipids (1 sphingosine, 1 FA, head group carb)

what does GPI in GPI anchored protein stand for?

how are this type of protein removed from membrane?

glycosylphosphatidylinositol

phospholipase C (leaves a protein glycan)

hydropathy plot

predicts TMD >20 hydrophobic AA in a row- prolly a TMD

Bacteriorhodopsin

7 tmd, GPCR

3 mentioned B barrel outer membrane proteins (bacteria or mt)

FepA, OmpLA, maltoporin

N linked (asn)

O linked (ser/thr)

N linked- GlcNAc N-acetylglucosamine

O linked- GalNAc N-acetylgalactosamine

catalyzed trans bilayer translocations

flippase

floppase

scramblase

to inner, ATP, NH3+ selective (only PE and PC), p type ATPase

to outer, ATP, ABC transporter

both ways with gradient

transporter:

channel:

transporter: not just a continuous pore, highly selective (stereospecific) limited by saturability

channel: (ex. aquaporin, glycerol, urea) limited by nothing but diffusion (nonsaturable), often gated and “timed”

aquaporin significant AAs and functions

His180- prevent large molecule entry

Arg195- electrostatic H3O+ and ion repulsion (only water come through)

Asn192 and Asn76- water dipole reorientation and prevents a newton cradle effect of H+ transfers

GLUT1 vs GLUT2 vs GLUT4

GLUT1-export in liver (D-glucose)

GLUT2- import in RBC (erythrocytes)

GLUT4- import in muscle/fat

move with gradient

(T1 and T2 conformations)

Given the transport equation:
ΔG = RT ln (c 2/c 1)
Which of the following about Na+ transport
across the cell membrane is true?
1) It will move down its concentration gradient
2) It will move up its concentration gradient
3) It will always be at equilibrium
4) None of the above

none, need to account for charge

what is the sequence of AA in the K+ voltage gated channel that have C=O carbonyls that replace the hydration layer around the ion and help with size exclusion and selectivity

GYGVT

(note tetramer with 2TMD, 1 selectivity helix per unit)

sodium channel has 4 domain, 6TMD each, what do helix 6 an d4 do, where is the inactivation gate

6- forms pore

4- voltage sensor

inactivation gate between III and IV domain (connect III6 to IV1) (close to C term)

the helix 4 of Na+ channel is voltage sensor with what charge? what state of membrane causes it to move up and channel open due to helix 6 coupled movements?

positive, when membrane depolarizes, moves up and causes short channel opening before inactivation loop shuts off

conserved mechanisms of signaling (5)

• specificity

• amplification

• modularity

• desensitization/adaptability (ex.neg feedback)

• integration

what receptor functions at the neuromuscular junction

nicotinic acetylcholine receptor (acetylcholine from nerve intoo muscle cell)

the acetylcholine receptor is found on the muscle cell surface, this is a ligand gated channel, what is the ligand? what flows through the channel ?

ligand- acetylcholine (from the nerve)

flows into myocyte- Na+, Ca2+ (triggers contraction)

explain the process of the nerve signal traveling down an axon

acetylcholine binds acetylcholine receptor causing Na+ to flow in and raise membrane potential from -60mV to +30mV (1ms)

then Na+ channels close and K+ channels open and K+ flows out until a hyper polarized -75mV (2ms)

the K+ channels close and in about 3ms the cell resets to -60mV contributed to by the Na+/K+ ATPase normal pumping of ions to maintain the -60mV normal state

big and bulky ______ on M2 helix of the nicotinic Ach receptor blocks the opening of the channel, but ligan binding of 2 Ach twists the structure so that _____ line the channel (Ach receptor has 5 subunits a, a, B, y, d, each with 4 helixed one being M2 lining the pore)

leucines

small polar residues

glucagon and epinephrine bind what kind of receptor?

G protein coupled receptor

3 components of the g protein system?

3 second messengers

GPCR (7 TMD helices), G protein, intracellular enzyme that produces second messenger

cAMP, cGMP, inositol 1,4,5 triphosphate

GTP in G proteins acts as a _____

timer (hydrolysis turns it off)

what are the 3 GTP-GDP exchange factors (GEFs)

SOS, Rh, B-AR

what parts of the guanosine binding protein (G-protein) are embedded in lipid layer?

y and a (not B, which is attached to y)

explain what happens when adrenaline/epinephrine binds GPCR? (B-adrenergic pathway)

the G protein dissociates and Ga (stimulatory) moves to activate adenylyl (adenylate) cyclase and this trigger production of cAMP which generally then activates PKA which goes on to phosphorylate stuff

what degrades cAMP?

cyclic nucleotide phosphodiesterase

besides adenylyl (adenylate) cyclase what else does Gprotein activate?

cGMP, RAF, PDE

2 levels of control to the B-adrenergic GPCR (epinephrine receptor)

• GTP→GDP stops signal

• internalization (endocytosis) of the receptor stops signal from re-occuring

describe internalization process of epinephrine GPCR

B-ARK binds the receptor and phsophorylates the C term

B-arrestin binds the phsophorylated C term and then the complex is endocytosed

in vessicle- B-arrestin dissociates and receptor dephosphorylated

receptor returns to membrane when needed i guess

is a GPCR an enzyme? what about RTK?

no, yes

receptor enzymes can have ____ or ____ activity

tyrosin kinase or guanylyl cyclase activity

the insulin receptor is a receptor enzyme with 4 subunits (2a, 2B) what kind?

RTK (B-domains autophosphorylate)

when not phosphorylated the RTK active site is blocked by activation loop which has three Tyr ___, ___, ____ and one makes bind to Asp_____ for activation when phsophorylated

Tyr1162, Tyr1163, Typ1158- Asp1132 (H-bond)

describe the MAPK pathway start from insulin and end with transcription of genes for cell division

insulin binds cytoplasic domain (a) of RTK

RTK autophsophorylates (Tyr1162, Try1163, Tyr1158-Asp1132)

catalytic domain phsoporylates Tyrosine on IRE-1

SH2 domain of GRB2 binds Tyr-P on IRE1, SH3 domain on GRB2 binds prolines on SOS

SOS (GEF) binds Ras and GDP→GTP activated Raf

Raf binds and activates Raf1

Raf1 phosphorylates mek

mek phsoporylates erk

erk moves to nucleus and phsoporylates elk

elk acts as transcription factor with srf to increase transcription of cell division genes (therefore insulin can regulate gene expression)

what other three functions besides the TF and MAPK pathway does insulin have after binding to RTK?

1. GS activation

RTK phosphorylates IRS-1 on tyrosine

PI3K SH2 domain binds the p-Tyr and converts pip2→pip3

pip3 is phosphorylated by PDK1 and PKB attached to it is activated

PKB phsophorylates GSK3 on Ser residue and inactivates it, with GSK3 inactivated, GS is no longer phosphorylated and thus active to make glycogen

2. movement of GLUT4 transporters to membrane to import glucose

RTK phosphorylates IRS-1 on tyrosine

PI3K (phosphoinositide 3-kinase) SH2 domain binds the p-Tyr and converts pip2→pip3

pip3 is phosphorylated by PDK1 and PKB attached to it is activated PKB

PKB through G proteins Rab and Rac1 causes GLUT4 to move form vesicles to the PM to increase glucose uptake

3. increased hexokinase synthesis

summary of everything insulin does through RTK

• increase hexokinase synthesis

• move GLUT4 to PM

• activate GS by inactivating GSK3

• increase transcription of cell divison genes

steroid hormones

thyroid hormones

progesterone, estrogen, cortisol (4 rings)

iodinated tyrosine (thyroxine)