biochem exam 1 chap 14 &15 Flashcards

1
Q

Storage Homopolysaccharides – Starch (Glycogen)

A

Main storage polysaccharide in animals
* Greatest abundance in liver (100g) and muscle cells (400g)
* Similar in structure to amylopectin, but with more branch points
* Unbranched glucose polymer (α1→4 linkage)
* Branches out every 8-12 residues (glucoses) using α1→6 linkages
* It is more compact. Why?

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2
Q

Glycogen

A

Not as energy rich as fatty acids, why?
* What are the advantages of glycogen?
* Maintains blood-glucose levels between meals
* Keeps brain supplied with glucose
* Energy for sudden, strenuous activity (fast breakdown) * Energy in the absence of O2
* Helps maintain osmotic balance in cells (remember?)

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3
Q

Glycogen – Why Branching?

A
  1. to use polysaccharides as sources of energy, degradative enzymes must degrade polymers into monomers
  2. these degradative enzymes act only on non-reducing ends
  3. each branch ends with a non-reducing sugar
  4. branching makes possible more rapid degradation
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4
Q

Glycogen Synthesis

A
  • Glycogen breakdown and synthesis are controlled primarily by three hormones that, in turn, control several sets of enzymes

these 3 hormones are:
- insulin - there is lots of glucose in the blood and so insulin pushes glucose into the cells so that it can be stored into glycogen for when the body needs energy – indicative of a high energy state
- glucagon (making glycogen gone by it being broken down into glucose) – indicative of a low energy state
- epinephrine - you need quick energy to run away so glycogen is broken down quickly into glucose to be used for energy – indicative of a low energy state

  • Insulin (“well-fed” hormone) – favors glycogenesis (what happens to blood glucose?- gets lowered!) - works right after a meal =- insulIN brings glucose in when too much of it is in the bloodstream and this results in a lower blood sugar. It favors glycogenesis because it can use the glucose that you just ate to build more glycogen for when you haven’t eaten in a while
  • Glucagon”e” (“hunger” hormone) – favors glycogenolysis (blood glucose?- is raised)- works when you haven’t eaten a while and makes your blood glucose rise because it puts glucose into the blood (right?). Favors glycogenolysis because it will break off the glucose bits off of glycogen to put into your bloodstream
  • Epinephrine (“fight-or-flight” hormone) – favors glycogenolysis (why?) because it will be able to break off glucose from glycogen in order to use it for quick energy
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5
Q

Glycogen Synthesis

A

Enter…UDP-Glucose!
* The biosynthesis of many polysaccharides involves sugar nucleotides

  • For the synthesis of glycogen, the intermediate is UDP-glucose
  • Why? Energetics of course! Reaction coupling! because this is an anabolic rxn we need ann exergonci rxn to drive this process forward
  • The formation of glycosidic linkages is ender or exergonic? - it is endergonic
  • So that energy must come from somewhere! Hydrolysis
    of UTP→UDP
  • so the formation of the glycosidic linkages in glycogen is endergonic and so it needs energy to be put in to move forward and that energy is from the hydrolysis of UTP to UDP!
  • What is it?
  • A high-energy sugar ready to be transferred to an existing glycogen chain or to start the growth of one.

The function of UDP-glucose: starts or adds to the glycogen chain from glycogenin

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6
Q

what is the function of UDP-glucose?

A

it provides the glucose to a growing glycogen polymer

the final step is essentially irreversible (because it is exergonic)

cells carry out this rxn only when glycogen is to be synthesized

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7
Q

Glycogen Synthesis

A
  1. glucose enters a cell and is phosphorylated to glucose-6-phosphate by hexokinase
  2. glucose-6-phosphate is then converted to glucose-1-phosphate by phosphoglucomutase
  3. synthesis of UDP-glucose. Glycogen can now be synthesized from UDP-glucose using 3 enzymes:
    - glycogenin: an enzyme that generates glycogen. It is the starting point for glycogen synthase to be added to glycogenin
    - glycogen synthase: adds to glycogenin
    - branching enzymes: used to form the branches of glycogen
  4. initiation of glycogen synthesis via glycogenin (primer and enzyme)
  5. continuation of synthesis via glycogen synthase
  6. branch synthesis via branching enzyme
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8
Q

Initiation of Glycogen Synthesis

A

Glycogenin is the seed that nucleates
glycogen growth. It is a dimer.

Glycogen can’t grow spontaneously, we have to attach glucose molecules to something, and that something is glycogenin

That something is Glycogenin

Here, at least 8 glucose molecules via UDP- glucose, are added to glycogenin

glycogenin is a primer and an enzyme, primer must have at least 8 glucose residues

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9
Q

Continuation of Glycogen Synthesis

A

Glycogen synthase breaks the phosphodiester linkage of UDP-glucose and forms an α(1→4) glycosidic bond between glucose and the growing glycogen chain at nonreducing ends (OR, H, H, OH) ****go over

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10
Q

Glycogen Branch Synthesis

A

The branching enzyme removes terminal 6-7 glucose molecules from the nonreducing end and makes the α(1→6) linkages for branches in the glycogen molecule somewhere else

This allows glycogen synthase to add new glucose molecules to the nonreducing end of either branch – faster!

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11
Q

Glycogen Catabolism (Breakdown)

A

remove monomers sequentially, producing glucose 1-phosphate

debranch, producing glucose

convert glucose 1-phosphate to glucose6-phosphate, happens in muscles when you need energy

in the liver: glc 6-p goes to glucose and maintains blood glucose

the hormones that stimulate glycogen catabolism: glucagon and epinephrine

the hormone that inhibits glucagon catabolism is insulin

also during glycogen sunthesis, G6P is turned into G1P and that G1P is added to glycogen
but during glycogen breakdown G1P is turned back into G6P and that will be able to go into glycolysis for breakdown into pyruvate and energy!

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12
Q

glycogen breakdown w phosphorylase

A

G 6-P to glucose - happens in the liver to maintain blood sugar

G 6-P to glycolysis - happens in the muscle to be broken down into pyruvate and energy

enzyme for glycogen breakdown: glycogen phosphorylase

enzyme for glycogen synthesis: glycogen synthase

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13
Q

exergonic, regulated, by passes through gluconeogenesis:

A

1, 3 & 10 you have to know the enzyemes of rxns 1, 3 & 10

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14
Q

general principles of metabolic regulation

A

extremely important to balance & regulate
- breakdown, yielding usable energy (ex: ATP)
- synthesis, requiring energy

remember: dynamic steady state (equal rates of formation and breakdown)

net effect: homeostasis (constant concentration can be disturbed)

key molecules: the energy molecules
- ATP/ADP/AMP
- NADH/NAD+
- NADPH/NADP+
- acetyl-COA

involved in many rxns, so changes have broad impact

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15
Q

controlling enzyme activity

A

by changing the # of active enzyme molecules in a cell (slow: second - hours
- synthesis (transcription, translation)
- activation of inactive precursors (proenzymes)

covalent modification (ex: phosphorylation & dephosphorylation; takes second to minutes)

by allosteric effectors (takes milliseconds). - this will be sigmoidal

covalent modification is phosphorylation!!!

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16
Q

factors effecting activity

A

enzyme:
binds ligand
binds substrate
undergoes phosphorylation
combines with regulatory protein

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17
Q

Additionally (remember?)… we can control reactions by controlling concentrations

A

recall: delta G is ~constant, but delta G depends on a concentration of metabolites

if the metabolite concentrations = equilibrium concentration, the rxns is near equilibrium so delta G is relatively small: rxn proceeds to a limited extent

the greater the difference between Keq and Q the greater the tendency to proceed so this rxn will be exergonic!!!!!!

if we make the [ ] far from equilibrium the rxn will go
is that why AMP will make energy producing rxns go? yes
AMP is far from equilibrium and so it will make the rxn go forwrad and so it has a negative delta G
ATP is also far from equilibrium but in the right direction so it will make the rxn go backward which we do not want want if we have a lot of energy and so it has a positve delta G probably

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18
Q

So, for example…

A

the key role of AMP
- as an indicator of metabolic status

its energy state moves very far from equilibrium and thus will drive the rxn forward yes!!!! great job
YOU WILL GET AN A ON THIS EXAM IN JESUS NAME AMEN!

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19
Q

Regulation of Glycolysis & Gluconeogenesis

A

Goal: Regulate [ATP] (homeostasis)

Regulate the far from equilibrium, exergonic, rate-limiting (irreversible steps)…which are? 1, 3, 10

Steps catalyzed by enzymes, so how do we regulate them?

Usually controlled by allosteric regulators, hormones, and the regulation of [substrate]

Regulation is coordinated…regulate both at the same step

the very largely exergonic and irreversible steps are 1, 3 & 10 and are therefore regulated :)

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20
Q

We gotta be careful with this “coordinate regulation” thing…

A

if opposing rxns of glycolysis and gluconeogenesis are coupled, they can simply burn (waste) energy without putting it to good use

ordinarily, this is prevented by coordinate reciprocal regulation

but in some circumstances this coupling can be allows to proceed for a good reason

futile (substrate) cycle
- happens when we cancel both sides of the arrow
- we cancel the fru-6-p and fru-1,6-bisp on both sides
- takes place in bees to keep them warm

21
Q

Insulin, Glucagone

A

insulin
- during High blood sugar: Glucose moves from the blood to the cells/formation of glycogen
- this lowers the blood sugar; insulin used to lower blood sugar

glucagone
- during Low blood sugar: Glucose moves from glycogen/cells to the blood (for later import into cells)
- this raises the blood sugar; sed to raise blood sugar

22
Q

Regulation of Glycolysis & Gluconeogenesis

A

When you have paired anabolic (gluconeo) and catabolic (glycolysis) pathways, enzymes used are common to both

At points of regulation, different enzymes are used! Specificity, and can go in both directions (ana and cat)

1, 3, 10 – So exergonic, essentially irreversible, needs to be well regulated!

step 1: hexokinase
step 3: Phosphofructokinase-1 (PFK-1)
step 10: Pyruvate kinase

they are all kinases so they add pi

23
Q

glycolysis step 1

A

glucose + hexokinase + ATP = glucose 6-phosphate

delta G = -16.7kJ/mol

24
Q

regulation of step 1 glycolysis

A

enyzme: hexokinase (4 isozymes) - so there are 4 diifferent hexokinases

in muscle (hexokinase I-III) primary regulation is by feedback inhibition of hexokinase by the rxn product glucose 6 phos.
- allosteric regulation of enzyme by product - prevents use of more than is needed
- this is allosteric inactivation

role of muscle: consume glucose when it is needed

glucose 6 phosphate binds to hexokinase when there is too much so that no more of glucose 6 phosphate can be made It blocks glucose from entering the active site

must occur in high energy state right?- yes!

25
Q

regulation of step glycolysis

A

in the liver (hexokinase-IV)

primary regulation is by glucose (substrate) concentration - high [glc] activates the enzyme; low [glc] decreases activity

not inhibited by product, G6P, like muscle

role of liver: regulate blood glucose level

more glucose, hexokinase catalyzes more rxns so the activity of it increase in the presence of glucose
so is this allosteric activation

regulates hexokinase in muscle: G6P, allosteric inactivation
regulates hexokinase in liver: glucose, allosteric activation

L-IV-ER

hexokinase I-III in muscle is regulated by G6P (product)
hexokinase IV in liver is regulated by glucose (substrate)

26
Q

glycolysis (step 3) and gluconeogenesis

A

will things have opposite effects on each enzyme?

fru 6 phos. + ATP + PFK-1 = to fru 1,6-bisp
- this is glycolysis

fru 1-6 bisphos. + FBPase-1 = to fru 6-p
- this is gluconeogenesis

insulin and glucagon is related via hormonal inhibition

27
Q

Regulating Glycolysis: Step 3

A

First “committed step”→must degrade glucose now.

PFK activity increases when energy status is low [ATP] so that more energy can be made! - low energy state, yes so we can break glucose down into energy

PFK activity decreases when energy status is high [ATP] so that no more energy can be made! - high energy state

Inhibited by reaction products:
- fructose-1,6-biphosphate
- ATP
- Citrate (Citric Acid Cycle intermediate = lots of energy) - citrate is indicative of a high energy state
all of these are PFK products and so when no more energy is needed, it can feedback and prevent it

These molecules signal that the cell has sufficient energy reserves.

Stimulated by:
- Fructose 2,6-bisphosphate (later)
- AMP - low energy state
- insulin

So: regulated by [substrate] and ATP
- ATP, F 1 phosphate & citrate

at high energy state, we are not doing glycolysis but we are doing gluconeogenesis - so we can use the energy we have to make glucose

at low energy state we are doing glycolysis (glucose to pyruvate) but not gluconeogenesis (pyruvate to glucose) - so we can make energy

glycolysis: make energy when energy is low
gluconeogenesis: use energy to make glucose

[AMP] means low energy so need
to do glycolysis so we need to increase PFK-1 activity
FBPase is for gluconeogenesis which we want to
decrease the activity of when we need energy

high [AMP], low ATP
- active PFK-1 ( for glycolysis)
- deactive FBPase (for gluconeogenesis)

low [AMP], high ATP
- inactive PFK-1 (for glycolysis)
- active FBPase (for gluconeogenesis) - YES now we can use the 6 energy equivalents to make more glucose for when we need it!!!!!!!

28
Q

We gotta be careful with this “coordinate regulation” thing…

glycolysis (step3) and gluconeogenesis

A

fru 6 phos. + ATP + PFK-1 = to fru 1,6-bisp
- this is glycolysis

fru 1-6 bisphos. + FBPase-1 = to fru 6-p
- this is gluconeogenesis

29
Q

PFK-1 & FBPase-1

A

Note: PFK-1 (glycolysis) and FBPase-1 (gluconeogenesis) are actually two separate domains on a single protein

30
Q

Hormonal Regulation of PFK-1/FBPase-1 (Gly Step 3)

A

after lunch
- high blood sugar
- increase insulin
- increase fru 2,6 BP
- PFK-1 more active = glycolysis
- FBPase-1 less active = less
gluconeogenesis

high blood sugar
increase insulin
increase fru 2,6 BP
make PFK more active and go towards
glycolysis
make FBPase-1 lesss active

use the energy that is released in this process (since it is exergonic) to push the glycolysis process along!!!!!

31
Q

Hormonal Regulation of PFK-1/FBPase-1 (Gluconeo)

A

if fasting
- low blood sugar
- increase glucogon
- decrease fru 2,6 BP
- PFK-1 less active = glycolysis
- FBPase-1 more active = more
gluconeogenesis

high blood sugar
increase insulin
increase fru 2,6 BP
make PFK more active and go towards
glycolysis
make FBPase-1 less active

32
Q

what does F 2,6 BP do

A

activates PFK-1 and inhibits FBPase-1

so then there is more of it then PFK-1 is more active and FBPase-1 is less active
so then there is less of it then PFK-1 is less active and FBPase-1 is more active

33
Q

enzymes to know and are regulated

A

step 1: hexokinase, by glucose (liver) or G6P (muscle)

step 3: PFK

step 10: pyruvate kinase

34
Q

Regulating Glycolysis: Step 10

A

if a lot of acetyl-COA, which is an indicator of high energy

enzyme: pyruvate kinase

allosterically inhibited by indicators of abundant energy supply:
- ATP
- acetyl-COA
- long fatty acids

also regulated by covalent modification - when it is phosphorylated by PKA (which is triggered by glucagonn) it will be deactivated and so it will not be able to turn PEP into pyruvate

pyruvate kinase does: PEP to pyruvate

where does pyruvate go: to the citric acid cycle to make ATP, so if we have a lot energy (either ATP, acetyl-COA or long fatty acids) then we do not need more energy and that is why the high energy indicators inhibit pyruvate kinase

if pyruvate kinase is inhibited then it will not make pyruvate from PEP and so pyruvate cannot go into the citric acid cycle to make more ATP

35
Q

Regulating Glycolysis: Step 10

A

liver only
- elevated glucagon slows down glycolysis in the liver

  • glucagon will stimulate the phosphorylation of PKA to put the phosphate group (from atp) onto pyruvate kinase which will inactivate it so it cannot catalyze rxn
  • then protein phosphatase removes the phosphate group off of pyruvate kinase and now is active which can now catalyze rxn from PEP to pyruvate which happens in all glycolytic tissue including the liver

note: glucagon again! (can regulate steps 3 and 10!) of glycolysis
- in step 3:
- Glucagon blocks glycolysis by decreasing the [Fru 2,6-bp] and will activate FBP1-ase so that gluconeogenesis can proceed

  • here it blocks glycolysis by getting pyruvate kinase L phosphorylated (inactivated) so no pyruvate can be made from PEP

we see glucagon twice!

oh so pyruvate kinase is regulated through covalent modification, so it will be phosprylated by PKA when PKA is stimulated by glucagon to do that. when pyruvate kinase is phosphorylated it is inactivate it

when pyruvate kinase is dephosphorylated by protein phosphatase, it will be activated to turn PEP into pyruvate

36
Q

In the liver, increased blood [glucagon] leads to…

A
Allosteric activation of pyruvate kinase

B
Allosteric inactivation of pyruvate kinase

C
Covalent activation of pyruvate kinase

D
Covalent inactivation of pyruvate kinase

A

D
covalent inactivation of pyruvate kinase
- because adding a pi is Covalent inactivates it

allosteric is acetyl-COA, long fatty acids and ATP

adding a pi is a covalent modulation

37
Q

regulation of gluconeogenesis by controlling the fate of pyruvate

A

acetyl COA (indicator of high energy state) in abundance can stop pyruvate from going into the CAC (by the acetyl-COA going into the pyruvate dehydrogenase complex) but now will go to gluconeogenesis

low acetyl-COA, go into CAC because we need more energy

high acetyl-COA, go into gluconeogenesis because we have a lot of energy to use to make more glucose molecules

if stored energy is abundant, synthesize glucose. If energy is needed catabolize acetyl-COA in the CAC

so acetyl-COA can make pyruvate go into the CAC when we need energy but if there is enough energy it will make pyruvate go into gluconeogenesis to make glucose :)

38
Q

Regulation of Glycogen Metabolism

A

breakdown involves glycogen phosphorylase

synthesis involves glycogen synthase

we need to regulate both enzymes

stimulate breakdown, inhibit synthesis
inhibit breakdown, stimulate synthesis

39
Q

regulation of glycogen phosphorylase

A

exists in two states a (active), b (less active)

this is a covalent modification

glycogen phosphorylase can exist in a more active (a, phosphorylated) or less active (b, not phosphorylated) state

a kinase enzyme phosphorylates the enzyme, thereby activating it

a phosphatase enzyme de-phosphorylates the enzyme thereby de-activating it

Kinase (phosphorylates → activates)

Phosphatase (de-phosphorylates → deactivates)

40
Q

Which of the following is correct about the regulation of glycogen phosphorylase? AMP promotes___; ATP promotes___

A
Activation, Activation

B
Activation, inactivation

C
Inactivation, activation

D
Inactivation, inactivation

A

B
Activation, inactivation

YESSSSS THANK YOU JESUS
IN JESUS NAME AMEN!!!

41
Q

Glucose ___ glycogen breakdown, and glucagon ___ glycogen synthesis

A
Promotes, promotes

B
Promotes, inhibits

C
Inhibits, promotes

D
Inhibits, inhibits

A

D
Inhibits, inhibits

JESUS! THANK YOU
I PRAY FOR AN A ON THIS EXAM
IN JESUS NAME AMEN!!!

42
Q

what does F 2,6-BP do

A

activates PFK-1 and inhibits FBPase-
1

insulin will activate F 2,6 BP to activate PFK and inhibit FBPase and promote glycolysis
glucagon will inhibit F26BP to activate FBPase to promot gluconeogenesis

43
Q

Regulation of “the Kinase” of glycogen phosphorylase (b → a)

A

remember, the kinase activates glycogen phosphorylase → glycogen → glucose

so the kinase adds a pi onto glycogen phosphorylase, making glycogen phosphorylase active which will stimulate the breakdown of glycogen into glucose

this enzyme phosphorylates phosphorylase b (which catalyzes the breakdown of glycogen)

epinephrine (in muscle) and glucagon (in the liver) acting through cAMP (2nd messenger) activate this kinase
- in muscle: fuel for glycolysis
- in liver: helps restore [glucose]

allosteric regulation: in muscle, Ca2++ and AMP can further activate phosphorylase - AMP because glycogen would be broken down into glucose to be used for energy, and if we do not have enough energy then we do need more

ATP blocks/prevents activation - because glycogen is broken down into glucose to be used for energy and if we have enough energy then we do not need any more

44
Q

Regulation of “the Phosphatase” of glycogen phosphorylase (a→b)

A

Remember, the phosphatase deactivates glycogen phosphorylase and will stop glycogen→glucose

phosphatase de-phosphorylates phosphorylase a, thereby de-activating it

in the liver, glucose induces a conformational change in phosphorylase a so that the phosphatase enzyme can inactivate the phosphorylase a

insulin activates the phosphatase - to inhibit glycogen breakdown!!!!!!!!
- so if it activates phosphatase, then phosphatase can remove the pi from phosphorylase a and thus phosphorylase a will not remain in the a active form but will go to the b less active form.
- if in the less active form, phosphorylase a can not stimulate the breakdown of glucose and thus promoting the synthesis of glycogen

45
Q

regulation of glycogen phosphorylase

A

glycogen phosphorylase stimulates the breakdown of glycogen into glucose when we need energy!

activated by a low-energy state:
- glucagon (liver)
- epinephrine (muscle)
- Ca2+, AMP (muscle)

inactivated by
- glucose (liver)
- insulin (liver)
- activation prevented by ATP

THROUGH the activation of glycogen phosphorylase kinase
(b→a)

THROUGH the activation of glycogen phosphorylase kinase
(b→a)

THROUGH the activation of glycogen phosphorylase phosphatase (INSULIN does this)
(a→b)

46
Q

regulation of glycogen synthesis

A

glycogen synthase can exist in an active (a) or an inactive(b) form

the active form not phosphorylated

the inactive form is phosphorylated

its flipped!

Glycogen phosphorylase was active if phosphorylated and inactive if dephosphorylated

Kinase (phosphorylates → deactivates)
- that kinase is called GSK3

Phosphatase (de-phosphorylates → activates)
- which is phosphoprotein phosphatase

47
Q

Regulation of “the Kinase” of glycogen synthase (a→b)

A

Remember, the kinase deactivates glycogen synthase X glucose→glycogen

inactivated by many protein kinases, the most important of which is glycogen synthase kinase 3 (GSK3)

GSK3 is inhibtied by insulin
- keeps GSK active
- now glucose can go to glycogen

GSK3 keeps glycogen synthase off by adding a pi onto it

insulin inhibits GSK3 so it can’t turn glycogen
syn. off by turning it into the inactive form so glycogen syn. is still on! to keep turning glucose into glycogen

insulin blocks GSK3 from turning glycogen synthase off so then glycogen synthase is left on!

48
Q

Regulation of “the phosphatase” of glycogen synthase (b→a)

A

Remember, the phosphatase activates glycogen synthase glucose→glycogen

phosphoprotein phosphatase 1 (PP1) activates glycogen synthase by depohsoprylating is thus putting it in the active form

glycogen synthase makes glycogen

activated: store glycogen

insulin: high energy state

glucagon: low energy state

PP1 is:
- activated by glucose
- activated by G6P
- activated by insulin
- inhibited by glucagon
- inhibited by epinephrine
the same enzyme that inactivates glycogen phosphorylase

PP1
- is the enzyme that inactivates glycogen phosphorylase so now if glycogen phosphorylase is inactivated then glycogen breakdown is inhibited and glycogen synthesis is promoted!!!

what would happen if PP1 was not working/inhibited:
- it will not be able to dephosphorylate glycogen phosphorylase a so glycogen phosphorylase a will stay on and promote glycogen breakdown
- it will not be able to dephosphorylate glycogen synthase b so glycogen synthase will remain in the inactive state and will not be able to do glycogen synthesis

49
Q

regulation of glycogen synthase

A

activated by PP1 by:
- glucose
- G6P
- insulin
all of these activate glycogen synthase by activating PP1 which actually activates glycogen synthase - which makes sense because PP1 removes the pi from glycogen synthase b and that dephosphorylation makes it active

inactivated by GSK3 blocked by
- insulin
because it stops GSK3 from turning glycogen synthase off so then insulin lets glycogen synthase stay on

activation by PP1 blocked by
- glucagon
- epinephrine

!
Glucagon and epinephrine stimulate phosphorylase and inhibit synthase
Insulin inhibits phosphorylase and stimulates synthase Think about it!

Glycogen synthase kinase 3 (adds a pi onto glycogen synthase) which inactivates glycogen synthase
- insulin turns Glycogen synthase kinase 3 off so that Glycogen synthase kinase 3 will not turn glycogen synthase off
- once insulin turns Glycogen synthase kinase off, Glycogen synthase will stay on because Glycogen synthase kinase 3 will not turn it off anymore :)