biochem exam 1 chap 14 &15

Question 1

Storage Homopolysaccharides – Starch (Glycogen)

Answer 1

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?

Question 2

Glycogen

Answer 2

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?)

Question 3

Glycogen – Why Branching?

Answer 3

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

Question 4

Glycogen Synthesis

Answer 4

• 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

Question 5

Glycogen Synthesis

Answer 5

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

Question 6

what is the function of UDP-glucose?

Answer 6

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

Question 7

Glycogen Synthesis

Answer 7

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

Question 8

Initiation of Glycogen Synthesis

Answer 8

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

Question 9

Continuation of Glycogen Synthesis

Answer 9

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

Question 10

Glycogen Branch Synthesis

Answer 10

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!

Question 11

Glycogen Catabolism (Breakdown)

Answer 11

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!

Question 12

glycogen breakdown w phosphorylase

Answer 12

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

Question 13

exergonic, regulated, by passes through gluconeogenesis:

Answer 13

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

Question 14

general principles of metabolic regulation

Answer 14

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

Question 15

controlling enzyme activity

Answer 15

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!!!

Question 16

factors effecting activity

Answer 16

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

Question 17

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

Answer 17

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

Question 18

So, for example…

Answer 18

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!

Question 19

Regulation of Glycolysis & Gluconeogenesis

Answer 19

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 :)

Question 20

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

Answer 20

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

Question 21

Insulin, Glucagone

Answer 21

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

Question 22

Regulation of Glycolysis & Gluconeogenesis

Answer 22

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

Question 23

glycolysis step 1

Answer 23

glucose + hexokinase + ATP = glucose 6-phosphate

delta G = -16.7kJ/mol

Question 24

regulation of step 1 glycolysis

Answer 24

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!

Question 25

regulation of step glycolysis

Answer 25

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)

Question 26

glycolysis (step 3) and gluconeogenesis

Answer 26

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

Question 27

Regulating Glycolysis: Step 3

Answer 27

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!!!!!!!

Question 28

We gotta be careful with this “coordinate regulation” thing... glycolysis (step3) and gluconeogenesis

Answer 28

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

Question 29

PFK-1 & FBPase-1

Answer 29

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

Question 30

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

Answer 30

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!!!!!

Question 31

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

Answer 31

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

Question 32

what does F 2,6 BP do

Answer 32

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

Question 33

enzymes to know and are regulated

Answer 33

step 1: hexokinase, by glucose (liver) or G6P (muscle) step 3: PFK step 10: pyruvate kinase

Question 34

Regulating Glycolysis: Step 10

Answer 34

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

Question 35

Regulating Glycolysis: Step 10

Answer 35

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

Question 36

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

Answer 36

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

Question 37

regulation of gluconeogenesis by controlling the fate of pyruvate

Answer 37

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 :)

Question 38

Regulation of Glycogen Metabolism

Answer 38

breakdown involves glycogen phosphorylase synthesis involves glycogen synthase we need to regulate both enzymes stimulate breakdown, inhibit synthesis inhibit breakdown, stimulate synthesis

Question 39

regulation of glycogen phosphorylase

Answer 39

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)

Question 40

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

Answer 40

B Activation, inactivation YESSSSS THANK YOU JESUS IN JESUS NAME AMEN!!!

Question 41

Glucose ___ glycogen breakdown, and glucagon ___ glycogen synthesis A Promotes, promotes B Promotes, inhibits C Inhibits, promotes D Inhibits, inhibits

Answer 41

D Inhibits, inhibits JESUS! THANK YOU I PRAY FOR AN A ON THIS EXAM IN JESUS NAME AMEN!!!

Question 42

what does F 2,6-BP do

Answer 42

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

Question 43

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

Answer 43

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

Question 44

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

Answer 44

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

Question 45

regulation of glycogen phosphorylase

Answer 45

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)

Question 46

regulation of glycogen synthesis

Answer 46

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

Question 47

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

Answer 47

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!

Question 48

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

Answer 48

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

Question 49

regulation of glycogen synthase

Answer 49

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 :)