BCHM 4720: Exam III

A fatty acid composed of 18 carbon atoms undergoes b oxidation. How many acetyl CoA, FADH2}, and NADH does b oxidation of this fatty acid generate? Calculate the net ATP generated by the B oxidation of the 18 carbon fatty acid. Assume that each FADH2 generates 1.5 ATP and each NADH generates

-9 acetyl CoA, 8 FADH2, 8 NADH -120 ATP

Cori Cycle

-1947 Nobel prize in medecine -Gerty was the first American Woman to win a nobel prize in science -Lactate and alanine formed by contracting muscles are used by other organs -Muscle and liver display interorgan cooperation in a series of reactions called the Cori cycle -Liver takes up lactate and converts it into glucose --> blood -Pyruvate accepts NH2 from amino acids --> alanine -muscle wasting disease -Alternately in the liver: alanine --> pyruvate -Alanine aminotransferase ALT (diagnostic) -abundant liver enzyme

how is cAMP-dependent protein kinase activated by cAMP?

-4 cAMP bind to the 2 regulatory subunits which then change conformation releasing 2 catalytic cAMP dependent protein kinase residues

Diagram of Fat Metabolism Through Various Organs

(1) Bile salts emulsify dietary fats in the small intestine making micelles (2) Intestinal lipases degrade triacylglycerols -(water-lipid interface) (3) Fatty acids and other breakdown products are taken up by the intestinal mucosa and converted into triacylglycerols (4) Triacylglycerols are incorporated with cholesterol and apolipoproteins into chylomicrons (5) Chylomicrons move through the lymphatic system and bloodstream to tissues (6) Lipoprotein lipase activated by apoC-II in the capillary converts triacylglycerols to fatty acids and glycerol (7) Fatty acids enter cells through diffusion (8) Fatty acids are oxidized as fuel or reesterified for storage -Myocyte: storage for muscle cells -Adipocyte: storage for fat cells

Sources of Fat

(1) Dietary Fats: -fatty acids --> acetyl CoA or triglycerides -fatty acids --> muscle --> fatty acids --> Acetyl CoA (through b oxidation) --> CO2, H2O, and ATP (through TCA and Oxidative phosphorylation) -fatty acids --> adipose (fat cells) --> fatty acids --> triglycerides (storage) (2) Stored Fats: -glycerol --> glycolysis -Triglycerides --> fatty acids (through lipases) --> Blood (hormonal control here) --> skeletal and cardiac muscle (3) De Novo Synthesis (liver): - carbohydrates + amino acids --> acetyl CoA - --> ketone bodies (source of energy) --> blood - --> fatty acids --> triglycerides --> lipoproteins --> blood -Everything is more clear in the image

Fate of pyruvate / TCA cycle at high acetyl CoA, NADH, ATP; at low acetyl CoA, NADH, ATP; and at high acetyl CoA, low NADH and low ATP.

(1) High: Acetyl CoA, NADH, and ATP -Lots of energy -pyruvate --> glucose is enhanced and excess glucose is made into glycogen (storage) -TCA down -Pyruvate decarboxylase up (acetyl CoA) (2) Low: Acetyl CoA, NADH, and ATP -low energy -pyruvate --> glucose is suppressed -Pyruvate carboxylase down -TCA up (PDH) (3) High: Acetyl CoA Low: NADH and ATP -pyruvate carboxylase (PC) up (acetyl CoA) -acetyl CoA --> OAA --> TCA cycle -TCA up -No glucogenesis

GPCR: what are they, how do they work. Remember that there are MANY different GPCR, activated by a wide variety of hormones

- Heterotrimeric G-protein coupled receptor -Substrate binds to the G protein receptor and GTP is released -GTP to coupled enzyme and it is activated -G-protein hydrolyzes GTP to GDP and goes back to inactive state

how are ketone bodies converted into energy? How does liver avoid consuming ketone bodies

-"selfless liver" -CoA transferase is not in the liver so the liver cannot consume ketone bodies -Can only produce ketone bodies -Liver cannot convert ketone bodies back into acetyl CoA -Liver does not have OAA so it cannot process acetyl CoA

Phosphorylase Kinase Structure

-(alpha, beta, gamma, delta)4 composition -active site on gamma subunit -Phosphorylase kinase is activated first by Ca2+ binding and then by phosphorylation (by PKA) -delta subunit (calmodulin) is the calcium sensor -Phosphorylase kinase is maximally effective when phosphorylated and Ca2+ is bound

Glucose-alanine cycle to transport more carbon to the liver for gluconeogenesis

-1 Glucose is made into 2 pyruvate via glycolysis -pyruvate cannot be transported to it is made into alanine (can be transported) -2 alanine is then made back into 2 pyruvate in by alanine aminotransferase -2 Pyruvate is made into 1 glucose by guconeogenesis -alanine (at first pyruvate) transports more carbon to the liver

Overall B Oxidation of Palmitoyl CoA

-10.5 ATP formed from the 7 FADH2 (1.5*n FADH2) -17.5 ATP from the 7 NADH (2.5*n NADH) -80 from the 8 acetyl CoA molecules (10*n) (TCA cycle) -2 molecules are consumed and split into AMP and 2 molecules of orthophosphate -Complete oxidation yields 106 ATP

Cross Linked Polymer

-12 layers/fractals - ~60,000 glucose units/particle -Branch points separated by 8-12 glucose units -One reducing end -Many nonreducing ends (indicated as N in the image) -Stored in cytoplasm as glycogen granules Modeling: -Max # of glucose/volume -Max # of ends -Minimal repulsion

Concept of Substrate Cycles

-A pair of reactions such as phosphorylation of fructose 6 phosphate to fructose 1,6 biphosphate and back is called a substrate cycle. -Both reactions are not fully active at the same time because of reciprocal allosteric controls -There can be some detectable activity of opposing pathways futile cycle -Substrate cycles are biologically important -Enhance metabolic signals -A small change in two opposing cycles can lead to a large change in the net flux -20% change in activation on both sides leads to a 380% change in flux.

What is a second messenger - and name at least two

-A substrate made in response to hormones -cAMP -cGMP -DAG -IP3

two forms of ACC - regulatory role of ACC2 in making malonyl CoA to prevent the import of FA into mitochondria

-ACC1: In adipose -makes fatty acid -ACC2: most tissues -makes malonyl CoA for regulatory reasons -Inhibits fatty acid import into the mitochondria

activation of acetyl coA by ACC - role of biotin, why carboxylation, mechanism. what is the fate of the HCO3 that is being put on?

-ACC2: In most tissues it inhibits fatty acid transport into the mitochondria -ACC1: in adipose cells and makes fatty acids -biotin serves as the carboxy phosphorylate intermediate -allows for the transfer of HCO3- to acetyl CoA -HCO3- ends up on acetyl CoA and makes it into malonyl CoA

Fat Burns in the Flame of Carbohydrates

-Acetyl CoA + OAA --> citrate (TCA cycle) -If no OAA then OAA --> gluconeogenesis -Acetyl CoA is diverted into ketones -transport for acetyl CoA

Reciprocal Regulation of Gluconeogenesis

-Acetyl CoA is a feedback inhibitor of pyruvate dehydrogenase (PDH) -NADH and ATP suppress the TCA cycle -Isocitrate and aketoglutarase repression -produced inhibition (1) High: Acetyl CoA, NADH, and ATP -Lots of energy -pyruvate --> glucose is enhanced and excess glucose is made into glycogen (storage) -TCA down -Pyruvate decarboxylase up (acetyl CoA) (2) Low: Acetyl CoA, NADH, and ATP -low energy -pyruvate --> glucose is suppressed -Pyruvate carboxylase down -TCA up (PDH) (3) High: Acetyl CoA Low: NADH and ATP -pyruvate carboxylase (PC) up (acetyl CoA) -acetyl CoA --> OAA --> TCA cycle -TCA up -No glucogenesis

Glycogen Breakdown Overview

-All enzymes are bound to granules (1) glycogen(n+1) [a(1-->4)] + Pi --glycogen phosphorylase--> glycogen(n) + glucose 1 phosphate (2) Glucose 1 phosphate <--Phosphoglucomutase--> Glucose 6 phosphate (3) Glucose 6 Phosphate + H2O --glucose 6 phosphatase--> glucose + Pi (liver only) (4) Debranching enzyme [a(1-->6) linkage]

Two Types of Reciprocal Regulation

-Allosteric -Hormonal -Acetyl CoA activates pyruvate carboxylase

Ketone Bodies (Ketogenesis)

-Alternative fuel source when energy reserves are low -In the liver -Fatty acids --> Acetyl CoA - --> ATP (through TCA) - --> acetoacetate or 3-hydroxybutyrate (ketone bodies) --> [Muscle/brain] ketones --> acetyl CoA --> ATP -Transport system for acetyl CoA -Ketoacidosis: Overproduction of ketones -Ketosis: high levels of blood ketones -acidosis: decreased blood pH -acetone production from acetoacetate -Severe starvation: -Gluconeogenesis depletes OAA driving acetyl CoA to OAA -Juvenile Diabetes (type 1): -insufficient glucose uptake -elevated gluconeogensis -Elevated B oxidation -Blood ketones: -90mg/100ml (untreated) -3mg/100ml (normal) -A keto-diet does not cause ketoacidosis

steps of beta oxidation in mitochondria.

-An activated fatty acid is oxidized to introduce a double bond -The double bond is hydrated to introduce a hydroxyl -The alcohol is oxidized to a ketone -The fatty acid is cleaved by coenzyme A to yield acteyl CoA and a fatty acid chain 2 carbons shorter

Ketone bodies: what are they, when and where (which organ) are they generated? what is their purpose and fate?

-An alternative fuel source when energy reserves are low -ketogenesis -Made in the liver -Acetyl CoA is diverted into ketones (transport form of acetyl CoA) which is then transported to the muscle/brain -the ketones are then made into acetyl CoA in muscle or the brain which then is used to make ATP -Fate: ATP production in brain/muscle

What is trans-fat?

-An unsaturated fat, formed artificially during hydrogenation of oils, containing one or more trans double bonds.

Structure of Phosphofructokinase 2

-Bidirectional enzyme -Toggled by phosphorylation of serine

What are bile salts and what is their purpose

-Bile salts breakdown large globules of fat into smaller droplets of fat -essentially act as bodily detergents -Bile salts also help the body absorb those droplets

Arrange the four major steps in the elongation of fatty acid chains by fatty acid synthase.

-Binding of malonyl‑CoA to ACP -Condensation by B-ketoacyl synthase -Reduction by B-ketoacyl reductase -Dehydration by 3-hydroxyacyl dehydratase -Reduction by enoyl reductase -Butyryl group transfer from ACP to β‑ketoacyl synthase

(1) Glycogen Phosphorylase

-Binds to glycogen + Pi -acid-base catalysis --> cleavage of a(1-->4) link -pyridoxal phosphate (PLP) cofactor -Oxonium ion (oxygen ion with 3 bounds) intermediate that is resonance stabilized. -Group transfer to Pi (makes glucose 1 phosphate) -retention of configuration -We are making a high energy P bond by using the energy from breaking the glycosidic bond

How does CoA-SH resemble the phosphopantetheine prosthetic group in ACP?

-Both are covalently attached -Both prosthetic groups are the same -Allows for carrying (free transport) of active groups

Hormonal Regulation of Glycogen Phosphorylase by a Kinase Cascade

-Brain --> adrenal --> epinephrine --> muscle --> binds to epinephrine receptor -Pancreas --> a (fasting) or b (fed) cells --> glucagon or insulin (respective) --> respective receptor -insulin promotes cAMP hydrolysis (cAMP --> AMP) -phosphorylase kinase is activated by Ca2+ (calmodulin) -IP3 (inositol 1,4,5-triphosphate), Ca2+, cAMP/cGMP, and DAG (diacylglycerol) are secondary messenger made in response to hormones -

how does calcium binding to calmodulin change its properties? how does calcium binding to calmodulin relieve autoinhibition of a kinase? Is this a catalytic process?

-Ca2+ binds to calmodulin changing the exposure/alignment of the hydrophobic residue -This moves opens up the catalytic site which can then bind to target proteins -calmodulin blocks the catalytic site and auto-inhibits the kinase -Ca2+ then binds and opens up the catalytic site and relieves its auto-inhibition -This process is not catalytic since the kinase has no activity before Ca2+ binds

transport of fatty acid through inner mitochondrial membrane via carnitine (and energy balance)

-Carnitine binds to fatty acyl CoA (favorable) -A translocase (antiporter) can then transport acyl carnitine through the IMM -C8 and shorter can get through the IMM without a transporter

how can certain cells 'ignore' hormonal regulation, while others are very responsive to it?

-Certain cells do not have hormonal receptors -(e.g. no insulin/glucagon receptors) -i.e. liver/brain cells have no insulin receptors -Other cells have a high number of these receptors and are thus very responsive -i.e. liver/kidneys have a high number of glucagon receptors

odd chain fatty acid. what is the end product and what do we do with it? (no mechanism)

-Cis d^3-enoyl CoA which cannot be processed by acyl CoA dehydrogenase -Cis d^3-enoyl isomerase converts the double bond into trans d^2-enoyl CoA which is a normal B oxidation substrate

energy balance of the Cori cycle

-Cori cycle consumes 6 ATP and produces 2 ATP per molecule of glucose/lactate -That means it is energy balance negative

Understand the importance of coupling reactions in the UDP-glucose pyrophosphorylase mechanism and what drives this reaction Cont.

-Coupling the two reactions makes the group transfer favorable

Esterification Reactions are Catalyzed by Various Acyl Glycerol Transferase

-Diesterification is catalyzed by various lipases: -Monoglyceride lipase -diglyceride lipase -Triglyceride lipase -Phospholipase -Hormonally controlled with some specificity -Olestra: A fat substitute that cannot be digested -Sucrose octo-ester

Dietary Fats Ingested as Triglycerides

-Dietary fats are emulsified in the small intestine by bile salts -e.g. taurocholic acid -Hydrolysis of triglycerides to fatty acids, mono and diglycerides -These can then be absorbed into the intestinal mucosa (epithelial cells lining the intestine)

Glycogen Phosphorylase X-Ray Structure

-Dimer: monomers related by 2 fold symmetry -Catalytic site: G1P bound pyridoxal phosphate (P1P) -Pyridoxal S' phosphate: PLP, vitamin B6 -PLP phosphorylase: Schiff's base -Glycogen binding site: Maltoheptose bound -30 A from catalytic site -Allosteric effector site: -AMP: activator -ATP, G6P: inhibitors -Nucleotide inhibitor site: -adenosine, caffeine: inhibitors -Phosphorylation site: Ser14

(4) Branching Enzyme (amylo(1,4-->1,6)transglycosylase)

-Distinct from debranching enzyme -Cleaves a(1-->4) -Makes a(1-->6) -Length of transferred segments is roughly 7 residues -Creates new non-reducing ends -Branch points every 8-12 residues -This enzyme can count and measure

know that only C16 or shorter saturated FA are made by FAS, longer and unsaturated chains are made by elongases and desaturases, respectively Cont.

-Elognases use malonyl CoA or acetyl CoA -Cn --> Cn+2

Triacylglycerols, with their hydrocarbon-like fatty acids, have the highest energy content of the major nutrients. Answer the questions about energy reserves in adipose tissue. Assuming that 15% of the body mass of a 70.0 kg adult consists of triacylglycerols, calculate the total energy reserve, in units of kilojoules and kilocalories, that is available from triacylglycerols. If the basal energy requirement is approximately 8,400 kJ/day (2,000 kcal/day), calculate the amount of time that this 70.0 kg person could survive if the oxidation of fatty acids stored as triacylglycerols were this person's only source of energy. Calculate the weight loss in pounds per day under the starvation conditions in the previous part (1 lb=0.454kg)(1 lb=0.454kg) .

-Energy reserve: 398960 kJ = 95445 kcal -Time until reserves are gone: 47.72 -Weight loss per day: 0.485 lbs/day

all life form use glucose polymers for energy storage

-Eukaryotes, archea, and bacteria all use glycogen as a glucose polymer for energy storage -Plants uses starch as a glucose polymer for energy storage

Allosteric Control:

-F 2,6 biphosphate, AMP, citrate --> TCA cycle reactions -Acetyl CoA activates PDH kinase (remember TCA cycle) inactivates PDH

What is used as an electron acceptor for going from alkane to alkene (deja vu all over again)

-FAD is used as the electron acceptor from alkane to alkene

know that only C16 or shorter saturated FA are made by FAS, longer and unsaturated chains are made by elongases and desaturases, respectively

-FAS cannot make past C16 -mammals lack enzymes that induce double bonds past C9

Fat Metabolism Overview

-Fat esterification of OH will produce fatty acids -e.g.: glycerol --> monoacylglycerol --> diacylglycerol --> triacylglycerol -Same thing happens with phospholipids

What is fat, what are phospholipids?

-Fats are fatty acids used for energy storage -Phospholipids have a hydrophilic head group and form membranes and micelles for transport.

the pathway of dietary fat until it reaches its target tissue

-Fats ingested -Bile salts emulsify dietary fats in the small intestine -Fatty acids are taken up by the intestinal mucosa and converted into triacylglycerols -Triacylglycerols are made into chylomicrons -Lipoprotein lipase converts triacylglycerols to fatty acids and glycerol -Fatty acids can then enter the cell

Place the reactions and relevant locations of reactants for the degradation of an even‑chain saturated fatty acid in the proper order.

-Fatty acid in the cytoplasm -Activation of fatty acid by joining to CoA -Formation of carnitine ester -Acyl CoA in mitochondria matrix -FAD liked oxidation -Hydration by enoyl CoA hydratase -NAD+ linked oxidation -Thiolytic cleavage by B-ketothiolase -Acetyl CoA enters the citric acid cycle

overall similarities of fatty acid degradation (beta oxidation) and fatty acid synthesis

-Fatty acid synthesis and degradation are both four steps and the reverse of each other -Both deal in 2C subunits

Phosphorylase Mechanism

-Glycogen is the R group -A bound HPO42- donates a proton to the C4 oxygen of the departing glycosyl group -This is favored by the transfer of a proton from the protonated phosphate group of the bound PLP group -The carbonium ion and and glucose 1 phosphate combine to form glucose 1 phosphate -Mechanism is much clearer in the image -Glycogen phosphorylase removes >1 glucose 1 P while remaining bound -Schiff bases: primary amine + aldehyde

Fatty Acid Degradation and Synthesis Mirror Each Other in Their Chemical Reactions

-Fatty acid synthesis and degradation consist of four steps that are the revers of each other. -Fatty acid degradation: -an oxidative process that yields acetyl CoA -an activated fatty acid is oxidized to introduce a double bond -the double bond is hydrated to introduce a hydroxyl group -The alcohol is oxidized to a ketone -The fatty acid is cleaved by coenzyme A to yield acetyl CoA and a fatty acid chain 2 carbons shorter -Fatty acid synthesis: a reductive process that begins with malonyl CoA (a modified version of acetyl CoA) -activated acyl group is fused to activated malonyl group (C3) (coupled to decarboxylation --> CO2 to power the reaction) -Carbonyl group is reduced to a methylene group -Both deal in 2 carbon units

Fatty Acid Oxidation

-Fatty acids --> acetyl CoA -C16 --> 8C2 (1) Activation of fatty acids by addition of CoA -product in the cytosol -High energy activated bond (2) Transport of fatty acyl Coterm-271A to Mitochondria (3) Cleavage of Ca --> Cb bonds: -Products: acetyl CoA, NADH, FADH2 (4) Oxidative Phosphorylation coupled to electron transport -NADH, FADH2 --> ATP

Why are fatty acid more energy rich (per gram and per carbon) than glycogen?

-Fatty acids are more reduced than sugars and thus carry more energy -There are more electrons around each carbon -When electrons move to more electronegative atoms (i.e. C --> O) then energy is released. So the more electrons available the more energy is released

Packaging into Chylomicrons

-Fatty acids are reesterified into triacylglycerides Chylomicrons: -lipid protein aggregates -Outside: apoproteins, phospholipids, cholesterols, and cholesterol esters -Inside: Triglycerides -apoproteins are recognized by cell receptors - 100-500 nm in size -Similar to HDL and LDL -Polar head groups of phospholipids face to the outside -Chylomicrons are transported to the blood -Targeted to certain tissues (especially muscles and fat)

(2) Transport of Fatty Acyl CoA to the Mitochondria

-Fatty acyl CoA + Carnitine --> Fatty acyl carnitine -carnitine palmitoyl transferase I, II is the enzyme involved -This is a Favorable reaction -Carnitine is a zwitterion -Antiporter moves fatty acyl CoA into and out of the inner mitochondrial matrix -C8 and shorter can enter the IMM without a transporter

in broad steps, how are acetoacetate and hydroxybutyrate made from acetyl CoA?

-Formed from acetyl CoA in the liver (1) 3-ketothiolase (2) hydroxymethylglutaryl CoA synthase (3) hydroxymethylglutaryl CoA cleavage enzyme (4) d-3-hydroxybutyrate dehydrogenase -acetoacetate spontaneously decarboxylates to form acetone

How is protein kinase A (cAMP-dependent protein kinase) activated by cAMP?

-Four cAMP subunits bind to PKA regulatory subunits inducing conformational changes -This releases two catalytic (active) subunits

What is GTPase activity? What is the role of the GTPase function of heterotrimeric G-protein? why does the GTPase activity need to be slow?

-G-protein acts as a very slow GTPase hydrolyzing GTP to GDP. -The GTPase acts as an "egg timer" the enzyme/protein can work until GTP is finally hydrolyzed to GDP -If GTPase activity was too fast then the protein would not be able to do anything

How is Adenylate Cyclase activated by hormone

-GPCR: heterotrimeric G-protein coupled receptor -Roughly 800 in genome -1/3 of all drugs target the GPCR -receptor g-protein complex -Hormone receptor changes upon hormone binding -Hydrolyze GTP --> GDP -G-protein is a slow GTPase -activates adenylate cyclase to make cAMP -The GTPase activity of G-protein functions like an egg timer. -As soon as GTPis --> GDPi AC is inactive

how is the signal from glucagon amplified in the cell?

-Glucagon interacts with its receptor causing G protein conformational changes -This activates adenylate cyclase which produces a large number of cAMP from ATP which then amplifies the signal

what is glucagon, where is it made, and what is its effect?

-Glucagon is a hormonal peptide produced by pancreatic a cells. -It signals low blood sugar through hormonal regulation described above involving G protein coupled receptors. -Glucagon triggers a cAMP cascade that activates fructose biphosphatase 2 (FBPase 2) and inactivates PFK2. This activates gluconeogenesis and inactivates glycolysis.

Glycogen Structure

-Glucose linked by a(1 --> 4) linkages -a-D-glucose has an OH down at carbon 1 -opposite side as CH2OH -b-D-glucose has an OH up at carbon 1 -Same side as CH2OH -Glycogen grows and degrades from the nonreducing end (side with carbon 4 prominant) -Reducing end has carbon 1 and OH prominant -Crosslinks at a(1 --> 6) linkages: -Branches -Tollens reagent (ag) reacts with the a(1-->6) linkages

Primer for Glycogen Synthesis

-Glycogen Synthase: how does it get started -requires a primer to initiate glycogen chain -Glycogenin (~37 kDa) -primer function -Intrinsic glucosyl transferase activity -Linkage of C1 to Tyr194

Diagram of Phosphorylase a and b Structure

-Glycogen binding site is highlighted in pink -Green highlighted loop leaves the active site open in phosphorylase a (R) and covers the active site in phosphorylase b (T)

Glucagon secretion is stimulated when blood glucose concentration decreases. Select all of the carbohydrate pathways that glucagon stimulates in the liver. -Glycogen breakdown (glycogenoysis) -Gluconeogenesis -Glycolysis -Glycogen synthesis (glycogenesis) -Glucose uptake

-Glycogen breakdown -Gluconeogenesis

Epinephrine is released in response to stress, and is a fight or flight hormone. Select all metabolic pathways that epinephrine stimulates. -Glycogen breakdown (glycogenolysis) in the liver and muscle -Gluconeogenesis in the liver -Glycolysis in muscle -Lipolysis in adipose tissue -Glycogen synthesis (glycogenesis)

-Glycogen breakdown (glycogenolysis) in the liver and muscle -Gluconeogenesis in the liver -Glycolysis in muscle -Lipolysis in adipose tissue

Select the results that occur from having few or no a-1,6 linkages in glycogen

-Glycogen degradation would slow down -Maintaining proper blood sugar levels would be more difficult

Fed State Favors Glycogen Synthesis and Storage

-Glycogen is a glucose polymer -Glycogen is most abundant in the liver and muscle -Its function varies according to the tissue its located in -Archea, bacteria, and eukaryotes all use glycogen -Plants use starch

Glycogen in Skeletal Muscle

-Glycogen is utilized for ATP synthesis --> muscle contraction -Storage of glycogen, degradation to G6P consumption in glycolysis -Fed state: produces glycogen -Fasting state: produces ATP from glycogen (lactate byproducts)

Adrenalin / epinephrin, glucagon, insulin: where are they made, where do they act, and what effect do they have on glycogen metabolism?

-Glycogen metabolism shown in image -Organ: -where messengers released -stimuli -messenger -receptors -Vascular: -pituitary -Stress, low blood sugar -Vasopressin -a adrenergic receptors Liver: -Pancreas -Low blood glucose -glucagon -glucagon receptors Muscle/liver: -adrenal medulla -stress -epinephrine -epinephrine receptors Nervous system: -junction -nerve impulse -acetylcholine -Muscarinic receptors

Glycogen Phosphorylase Diagram

-Glycogen phosphorylase is bound to granules -Dimer -Glycogen binding site is 30 A ~5-6 glucose units big allowing it to phosphorolyze several glucose before rebinding -Each catalytic site includes a pyridoxal phosphate (PLP) group, linked to lysine 680 of the enzyme -The binding site for the phosphate (Pi) substrate is shown -The catalytic site lies between the C terminal domain and the glycogen binding site

what would the net outcome be if glycogen breakdown and synthesis were active at the same time?

-Glycogen synthesis and breakdown would occur at the same time. -Overall nothing would happen and body would just waste energy -"futile cycle"

Glycogen in the brain

-Glycogen utilized as a fuel source for G6P -Emergency supply of Glucose -Hypoglycemia (low blood glucose) -Hypoxia (low O2) -Majority of glucose is from the liver -Need a way to signal from the brain to the liver -Hormonal control (travels in the bloodstream)

Glycogen Synthase

-Glycogen(n) + UDP-Glucose --> glycogen(n+1) + glucose -Phosphorylating glycogen synthase: -Many glycogen synthase kinases -Protein phosphatase 1 (PP1) -Phosphorylated form inactive -Glycogen Synthase Kinases: -All kinases that activate phosphorylase deactivate synthase -cAMP dependent protein kinase: PKA inhibits synthase and activates phosphorylase kinase -phosphorylase kinase: inhibits synthase -Ca2+-calmodulin dependent protein kinase

familiarize yourself with glycogen storage diseases (Table 21-2) even though we didnt talk about it. think about how the clinical features might be explained.

-Google if need be -not worth it to list all explanations here

Effects of Regulatory Compounds on Gluconeogenesis and Glycolysis

-High AMP: -Energy state low -Favors glycolysis -High citrate: -TCA low -Favors gluconeogenesis F 2,6 biphosphate: -Favors glycolysis -low energy elevated by AMP -Low blood glucose lowered by glucagon (through cAMP) -Glucagon: peptidehormone -signals low blood sugar

Allostery Defined by MWC model (T<-->R) Cont.

-High Energy State: -ATP UP, Glycogen Phosphorylase: inactive (T) -G6P UP, Glycogen Synthase: active (R) -AMP DOWN, Favors net glycogen synthesis -Low Energy State: -ATP DOWN, Glycogen Phosphorylase: active (R) -G6P DOWN, Glycogen Synthase: inactive (T) -AMP UP, favors glycogen breakdown -We need hormonal control to control organs

Glycogen Synthesis Overview:

-High blood glucose (1) glucose 6P <--phosphoglucomutase--> glucose 1-P -Same enzyme for degradation (2) glucose 1 P + UTP -UDP-glucose pyrophosphorylase-> UDP-glucose + PPi -PPi = 2Pi -activated form of glucose (3) UDP-glucose + glycogen(n) -glycogen synthase-> UDP + glycogen(n+1) -elevated energy status (4) glycogen branching enzyme -Steps 2-4 are unique to this synthesis -Overall strategy: activate glucose by forming a high energy sugar nucleotide

how is the amount of F 2,6 bisphosphate determined / regulated?

-High in fed state and low in starved state -F 2,6 biphosphate is allosteric effector of PFK whereas F 6 phosphate is not. -F 2,6 biphosphate stimulates PFK (glycolysis) and inhibits F 1,6 biphosphatase (gluconeogenesis) -When blood sugar level is low F 2,6 biphosphate loses a phosphoryl group to form F 6 phosphate. -PFK2 forms F 2,6 biphosphate -Fructose biphosphatase 2 (FBPase 2) forms F 6 phosphate -Both enzymes on the same polypeptide chain... Bifunctional enzyme

(2) Covalent Modification by Protein Phosphorylation

-Highly regulated: kinase kinase -Glycogen phosphorylase: -phosphorylase b (inactive) --> phosphorylase a (active) through phosphorylase kinase -Phosphorylase a (active) --> phosphorylase b (inactive) through Pi protein phosphatase 1 (PP1) -phosphorylase a frees up glucose -pretty non-specific (not that highly regulated) -reversible modification -Independent control -Hormonal regulation -Phos a: Phos b ratio is determined by relative activities of kinase vs phosphatase

why does the breath of diabetics in crisis smell of acetone?

-In diabetes there is insufficient glucose uptake and elevated b oxidation/gluconeogenesis -In diabetes there are a large number of ketone bodies in the blood. -These ketone bodies are degraded to acetoacetate which then spontaneously decarboxylates to form acetone -The acetone can then be smelled in the breath of someone with diabetes

Metabolic Interrelationships between the brain, muscle, adipose tissue, liver, and kidneys

-In diagram -G6P Fates: -Lactate from pyruvate through glycolysis and subsequent usage in brain and muscle -NADPH through pentose phosphate pathway -To glucose through the liver and released into the blood for other tissues -Pink arrows indicate pathways that predominate in the well fed state when glucose, fatty acids, and amino acids are directly available from the intestines

steps of FA synthase, and movement of the growing FA chain from ACP to a cysteine on the enzyme and back.

-In image

steps of FA synthase, and movement of the growing FA chain from ACP to a cysteine on the enzyme and back. Cont.

-In image

steps of FA synthase, and movement of the growing FA chain from ACP to a cysteine on the enzyme and back. Cont. Cont.

-In image

mechanism of thiolysis (alpha-beta cleavage)

-In image -Uses coASH

mechanism of thiolysis (alpha-beta cleavage) Cont.

-In image again

(3) Alpha Beta Bond Cleavage

-Occurs in the mitochondria -ETF: electron transferring flavoprotein -membrane bound -Specific enzymes for fatty acid lengths: -long: 12-18 -medium: 6-12 -short: 4-6 -alkane --> keto: -Similar to TCA cycle (succinate --> oxaloacetate) -Different enzymes similar chemistry

Reciprocal regulation

-In the cell one pathway is relatively inactive whereas the other is highly active -Glycolysis will predominate when glucose is abundant -Gluconeogenesis will be highly active when glucose is scarce -Occurs in gluconeogensis and glycolysis -interconversion of 1,6-biphosphate and fructose 6-phosphate (2 enzymes) -interconversion of phosphophenolpyruvate and pyruvate -When both pathways are activated there is waste

(1) Activation of Fatty Acids

-In the cytoplasm -Fatty acid is activated by acetyl CoA synthase to form fatty acyl CoA -has a tetrahedral intermediate -Fatty acyl CoA has high energy bonds -Fatty acyl CoA is the activated form of fatty acids

Ketoacidosis is a potentially life‑threatening condition that can occur when there is inadequate cellular glucose uptake, such as in uncontrolled diabetes. Order the steps that would lead to the development of ketoacidosis.

-Inadequate -Glucose metabolism decreases -Ketone bodies are produced in the liver -Ketone bodies are used as fuel for tissues -Ketone bodies accumulate in the blood, causing the pH to decrease -Ketoacidosis

Insulin Receptor Signaling

-Insulin stimulates glycogen by inactivating glycogen synthase kinase -ISPK: insulin stimulated protein kinases Insulin receptor: -Receptor consists of 2 units each with an a and b subunit -2 a units on the outside of the cell come together and form the insulin binding site -b units lie on the inside of the cell and include a protein kinase domain

Hormonal Control of Fructose 2,6 Biphosphatase

-Integration of signals from other organs -if no insulin receptor then you are oblivious to insulin -(i.e. liver cells) -Pancreas produces a cells under low blood glucose (fasting) which interact with glucagon receptors -pancreas produces b cells under high blood glucose (fed) which interact with insulin receptors -Hormonal controls is mediated through G-proteins -(cascade effects) -Secondary messenger amplification -cAMP dependent protein kinase A (cAK) is roughly PKA -Catalytic substrates (C) are bound to regulatory substrates (R) and become active when separated

Glycogen Synthase Cont.

-Interlaced regulatory pathways -allosteric (dense energy status of cell) -hormonal regulation to integrate signals throughout the body -opposite to phosphatase

how is cAMP made, why is this favorable, and how is it removed?

-Is produced from ATP by adenylate cyclase (on G protein) -Glucagon trigger a cAMP cascade -cAMP is degraded by phosphodiesterase (PDE) to form AMP (inactive) -Glucagon binds favorably to the its receptor on the G protein. This causes conformational changes that activate adenylate cyclase to form cAMP

Lipase Figure

-Lipases convert triacylglycerides --> diacylglycerides --> monoacylglycerides

Fuel Reserves in a 70 Kg Human

-Liver exports most of is glucose and glycogen stores -Muscle has a large amount of all stores (mostly protein) -Adipose tissue is almost exclusively triglycerides -Brain has only minimal fuel reserves (a tiny amount of glycogen and glucose)

(3) Glucose 6 Phosphatase

-Liver not muscle -Favorable dG0' ~= -14 kJ/mol

Hormonal Control:

-Low blood glucose makes more glucagon which amplifies the signal -cAMP is then produced and amplifies the signal further to fructose 6 biphosphatase -PFK is less activated so less glycolysis -Less inhibition of FBP 2 leads to more gluconeogenesis -Gluconeogenesis mainly takes place in the liver -specialized compartments: -Glucose 6 p'tase -Glucagon receptors -Organs without receptors will not respond

Regulation of glycogen synthase

-Many glycogen synthase kinases phosphorylate (inactivate) glycogen synthase -Protein phosphatase-1 dephosphorylate (activate) glycogen synthase

Heterotrimeric G-protein and how it activates adenylate cyclase in response to hormone binding to GPCR.

-Mechanism as depicted above with adenylate cyclase acting as the enzyme making cAMP through hydrolysis

(1) Allostery described by the MWC model (T <--> R)

-Monod-Wyman-Changeux model -Protein can exist in at least two functional states: tense and relaxed. State is determined by thermal equilibrium -Binding of effectors only shifts the probability that the protein will be in one state or the other. -Effectors will not make the conformational change but shift towards the other conformation. Glycogen Phosphorylase: -glycogen(n+1) --> glycogen(n) + G1P -T(inactive) <--> R(active) -tense effectors: glucose, G1P, ATP -relaxed effectors: AMP Glycogen Synthase: -glycogen(n) + UDP-Glucose --> glycogen(n+1) + UDP -T(inactive) <--> R(active) -tense effectors(?): adenosine, caffeine -relaxed effectors: G6P -All effectors above are allosteric effectors

how does insulin act in response to high blood glucose level?

-More insulin is released

where is glycogen stored (organ / where in the cell)?

-Mostly stored in the liver and muscles -Glycogen is stored as granules in the cytoplasm -Stored as a cross linked polymer

To answer this question, you may reference the Metabolic Map. Which molecules directly participate in fatty acid synthesis by acting as energy sources? Ethanol consumption inhibits gluconeogenesis by causing an increase in the concentration of NADH. NADH is a substrate for malate dehydrogenase, the enzyme that produces malate. An accumulation of malate favors the activity of malic enzyme. Thus, an increase in NADH concentration increases the enzymatic activity of malic enzyme.

-NADPH and ATP -Increase in NADPH concentration, stimulates fatty acid synthesis, ethanol consumption in a fasting state increases the risk of hypoglycemia

is food that contains mono- and diacylglycerols really 'low fat', 'low calory'?

-No a food containing mono and diacylglycerols still has all the energy associated with those fats -The "low fat" moniker is just due to the definition of fats not including mono and diacylglycerols

Allosteric control of fructose 1,6 biphosphate

-Occurs through the control of fructose 1,6-biphosphate (FBP) by AMP, citrate, and fructose 2,6 biphosphate -Gluconeogenesis and glycolysis are linked through these substrates -PFK-2: phosphofructokinase 2 -FBP-2: Fructose biphosphatase 2 -Gluconeogenesis: F 1,6 BP to F6P -Glycolysis: F6P to F 1,6 BP

Reciprocal regulation of F1,6 bisphosphatase and Phoshopfructokinase by AMP, Citrate, and F2,6 bisphosphate

-Occurs through the control of fructose 1,6-biphosphate (FBP) by AMP, citrate, and fructose 2,6 biphosphate -Gluconeogenesis and glycolysis are linked through these substrates -PFK-2: phosphofructokinase 2 -FBP-2: Fructose biphosphatase 2 -Gluconeogenesis: F 1,6 BP to F6P -Glycolysis: F6P to F 1,6 BP Low AMP: Glycolysis (Phosphofructokinase) High AMP: Gluconeogenesis (F 1,6 biphosphatase) Low Citrate: Glycolysis (Phosphofructokinase) High Citrate: Gluconeogenesis (F 1,6 biphosphatase) Low F 1,6 bP: gluconeogenesis (F 1,6 biphosphatase) High F 1,6 bP: glycolysis (Phosphofructokinase)

Issues with unsaturated FA degradation. what if the double bond is at an even-numbered carbon? what has to happen if it is on an odd-numbered carbon?

-Odd chain fatty acids: -yields 1 propionyl CoA -B oxidation alone cannot degrade unsaturated fatty acids -Unsaturated fatty acids with an odd number of double bonds need only isomerase -Unsaturated fatty acids with an even number of double bonds need both isomerase and reductase

Why is sucrose-octaester (olestra) a low-calory fat substitute?

-Olestra cannot be digested yet tastes and feels like fat. -Therefore olestra has very little to no calories associated with it

UDP-Glucose Pyrophosphorylase Cont.

-Overall -19 kJ/mol -First reaction is non-favorable (dG0' = 0) -Second reaction is favorable (dG0' = -19) -When the two reactions are coupled the overall reaction is favorable

how are odd chain fatty acids synthesized (and remember how they are broken down, as well!) Cont.

-Oxidized (metabolized) with 3 enzymes: (1) propionyl CoA carboxylase (2) Methylmalonyl-CoA epimerase (3) Methylmalonyl-CoA mutase

Table of Regulators of Gluconeogenic Enzyme Activity

-PFK 2 and FBPase 2 are bifunctional enzymes

Protein Phosphatase 1 (PP1)

-PP1 active: -glycogen synthase on -glycogen phosphorylase off -Glucose storage favored -Made specifically by interchange? proteins (~2200) -Quite non-specific... many targets -Removes P signals -Bound to glycogen particles via G subunit (~160 kDa) -G is phosphorylated at 2 serines (site 1 and site 2) by cAMP dependent protein kinase -G is phosphorylated at site 1 by "insulin-stimulated protein kinase" (ISPK) -ISPK as stimulates phosphodiesterase which destroys cAMP -ISPK also activates glycogen synthesis and inhibits glycogen degradation -More glucose uptake -Insulin stimulates glycogen synthesis by activating a signal transduction pathway that results in the phosphorylation and inactivation of glycogen synthase kinase. -PP1 subsequently dephosphorylates glycogen synthase (generates the active a form) -Insulin also facilitates glycogen synthesis by increasing the number of glucose transporters (GLUT4) in the plasma membrane... increases the uptake of glucose

regulation of protein phosphatase through G-protein.

-PP1 is bound to glycogen via G subunits -G subunit is phosphorylated at two serines (site 1 and 2) by cAMP dependent protein kinase -G subunit is phosphorylated at site 1 by ISPK

Signal Integration Diagram

-Phosphodiesterase also acts in the same way as insulin stimulated protein kinase Organ: -where messengers released -stimuli -messenger -receptors -Vascular: -pituitary -Stress, low blood sugar -Vasopressin -a adrenergic receptors Liver: -Pancreas -Low blood glucose -glucagon -glucagon receptors Muscle/liver: -adrenal medulla -stress -epinephrine -epinephrine receptors Nervous system: -junction -nerve impulse -acetylcholine -Muscarinic receptors

Identify the enzymes that are required for the synthesis of a glycogen particle starting from glucose 6-phosphate

-Phosphoglucomutase -Pyrophosphatase -Glycogenin

(4) Debranching Enzyme

-Phosphorylase catalyzes processive cleavage to 4-5 residue from the branch point a(1-->6) -Has 2 active sites an a-1,4 glucanotransferase (GT) and an a-1,6 glucosidase (GC) -bifunctional enzyme -When the limit branch is reached a-1,4 glucanotransferase (GT) transfers the "stub" to a nonreducing end - a-1,6 glucosidase (GC) thens cleaves the "stub" forming glucose and a debranched glycogen

Understand the importance of coupling reactions in the UDP-glucose pyrophosphorylase mechanism and what drives this reaction

-Powered by PPi to 2Pi (hydrolysis) -Group transfer and phosphoanhydride exchange

Overall glycogen Synthesis and Breakdown Cont.

-Problem futile cycle -solution: reciprocal regulation at glycogen phosphorylase and synthase Glucose utilization: -glycogen synthase: down -glycogen phosphorylase: up -fasting (liver) -exercising (muscle) Excess Glucose: -glycogen synthase: up -glycogen phosphorylase: down -Feeding Mechanisms: -allosteric effectors -Hormonal control -covalent modification through phosphorylation

Prosthetic group of ACP

-Reaction driven by decarboxylation of malonyl ACP -Tail to head

how is this outcome avoided?

-Reciprocal regulation at glycogen phosphorylase and synthase -In glycogen phosphorylase: -phosphorylation and dephosphorylation to form tense and relaxed forms -In glycogen synthase: -regulated through G6P

Multicyclic Cascades

-Results in amplification of signal -chemical -sensitivity -Divergence in pathways -Epinephrine and glucagon are hormones -1 enzyme can turn out many substrates -enzyme goes through cycles of glycogen --> G1P until glycogen concentration gets too low

how is cAMP-dependent protein kinase activated by cAMP (release of catalytic subunit through cAMP binding to regulatory subunit.

-Same process as with G proteins -4 cAMP residues bind to the 2 regulatory domains causing conformational change. This releases the 2 active catalytic subunits

Common Biological Fatty Acids Table

-Saturated fatty acids have no double bonds -Unsaturated have various number and position of double bonds -Cis: H are on the same side of the double bond -Trans: H are on opposite sides of the double bond

Overall Glycogen Synthesis and Breakdown

-Separate pathways, independent control, both directions are energetically favorable Overall: -glycogen(n+1) + H2O --> glycogen(n) + glucose (-18 kJ/mol) -Glucose + ATP + UTP + glycogen(n) + H2O --> glycogen(n+1) + ADP + UDP + 2Pi (-42 kJ/mol) -Overall: ATP + UTP + 2H2O --> ADP + UDP + 2Pi

Reaction catalyzed by 'malic enzyme', and fate of pyruvate and NADPH that is produced by it.

-Sequential activation of cytoplasmic malate dehydrogenase and malic enzyme -Malic enzyme catalyzes malate --> pyruvate + NADPH -pyruvate enter the mitochondria and then is converted to oxaloacetate by pyruvate carboxylase

Energy balance of making a fatty acid

-Shown in image

location of fatty acid synthesis and degradation (organ / in the cell)

-Shown in image

overview of energy utilization. what happens in the main organs during fed, fasting and starving fate? which metabolites are taken up / exported?

-Shown in image

Role of PLP in glycogen phosphorylase reaction, overall mechanism.

-Shown in image -schiff base -acts as a proton acceptor

what are chylomicrons, and what is their architecture?

-Similar to HDL and LDL -Lipid protein aggregates -apoprotein, phospholipids, cholesterol, and cholesterol esters on the outside of the chylomicrons -Triglycerides on the inside -Essentially triglyceride transports in the blood and can be targeted to certain tissues -apoproteins can be recognized by cell receptors

(2) UDP-Glucose Pyrophosphorylase

-Step 1 is covered in glycogen degradation (above) -UTP: the three phosphates are labeled a, b, g from outside to inside -UDP-glucose: uridine diphosphate glucose -Group transfer of G1P for PPi on UMP -Phosphoanhydride exchange -Powered by PPi --> 2Pi -dG0' = -30 kJ/mol

During ketogenesis, the liver synthesizes ketone bodies that can be used as an energy source. Put the statements regarding ketogenesis in the correct order, beginning with a stimulus for ketogenesis.

-Stimulus -low blood glucose levels stimulate the breakdown of fatty acids to acetyl CoA -Two acetyl CoA condense to form the four carbon acetoacetyl-CoA -A condensation reaction with acetyl-CoA produces the 6 carbon HMG-CoA -HMG-CoA loses acetyl-CoA, forming a 4 carbon ketone body -3-Hydroxybutyrate and acetoacetate can cross the blood brain barrier to provide fuel for the brain.

bifunctional enzyme - which part of it is regulated by glucagon and thus by cAMP?

-The activity of either enzyme is reciprocally controlled by the phosphorylation of a serine residue. -In a fasting state glucose is scarce and glucagon rises -Glucagon triggers a cAMP cascade -Protein kinase A (PKA) phosphorylates that serine residue activating FBPase 2 and inhibiting PFK2

Identify the true statements regarding a-1,6 linkages in glycogen

-The enzyme that forms a-1,6 linkages is catalyzed by a branching enzyme

Final step of Gluconeogenesis:

-The generation of free glucose in the liver -Only occurs in the liver -Glucose 6 phosphate is transported into the lumen of the endoplasmic reticulum -Glucose 6 phosphatase catalyzes the formation of glucose from G6P -An integral membrane protein on the inner side of the endoplasmic reticulum -In tissues that do not dephosphorylate glucose, G6P is converted into glycogen for storage. -liver has a special form of hexokinase called glucokinase -Km(glucose) ~= 5 uM glucose

what determines the melting point of a fatty acid? (number of double bonds)

-The more double bonds in a fatty acid the lower the melting point. -e.g. EPA has 5 double bonds and a melting point of -54 C

Remember that this enzyme is not very specific. what confers specificity to targets?

-The shape of the catalytic site to the substrate it attempts to bind to

what is a multicyclic cascade, and what purpose does it have?

-Through multiple cycles 1 enzyme can degrade many substrates -Allows for the amplification of signals and divergence in pathways

Fatty Acid Overview

-Triacylglycerol (triglyceride): fat storage -Fatty acids have six times the energy content than hydrated glycogen per gram -Twice the energy produced per carbon (38 vs 17 kJ/g) -esterified with glycerol to form acyl glycerols, glycerides, or glycerophospholipids In a 150 lbs person: -420,000 kJ (11 kg) in reserve fat -Stored in cytoplasm of adipose cells Four main roles of fatty acids: -fuel storage -building blocks for phospholipids -Many proteins are modified by covalent attachment of fatty acid(s) -Fatty acid derivatives --> hormones and intracellular messengers

Place the steps regarding fat digestion and absorption in the correct order. The abbreviation TAG is used for triacylglycerol (triglyceride).

-Triacylglycerols enter stomach -Undigested fats enter the small intestine -The gallbladder secretes bile into the small intestine -Pancreatic lipase hydrolyzes TAGs into lipid droplets -Insoluble lipids, in micelles, are absorbed through the lining of the small intestine -TAGs in chylomicrons enter the lymph system -TAGs in chylomicrons enter the blood stream -Triacylglycerols absorbed into cells

Transport of Acetyl CoA from mitochondria into cytosol.

-Tricarboxylic acid carrier -Acetyl CoA + OAA --> citrate -citrate can then be transported into the cytosol -ATP citrate lyase: citrate --> acetyl CoA + OAA

why might ACC or FAS be good targets for cancer drugs?

-Tumors require a large amount of fatty acid synthesis to produce precursors for membrane synthesis -FAS inhibitors prevent the cell from synthesizing fatty acids ACC inhibitors prevent the cell from transporting ketone bodies and thus will not be able to transport energy out of the mitochondria

Calmodulin Structure

-Very common Ca2+ sensor -Sometimes works alone, but more often as a subunit of protein complexes -relieves auto-inhibition of phosphorylase kinase -Two similar globular domains connected by an alpha helix -When Ca2+ is bound to calmodulin it becomes more ordered -different binding properties occur -Hydrophobic residue is exposed -Can then bind to target protein -Ca2+ binding --> ordered ea segment --> Moves hydrophobic segment --> can now bind to other proteins -Once Ca2+ binds it relieves the auto-inhibition of phosphorylase kinase (makes it active)

Remember that Viagra's application to treat ED was discovered by 'accident' - it is a phosphodiesterase inhibitor.

-Viagra inhibits phosphodiesterase and thus cAMP cannot be degraded

(3) Hormonal Control through Phosphorylation

-Whats regulates the regulator? "kinase kinase" Phosphorylase kinase (alpha, beta, gamma, delta)4: -gamma catalytic subunit (kinase) -Activated by Ca2+ (delta = calmodulin) -calmodulin: calcium binding module -Activated by phosphorylation (alpha, beta, regulatory subunits) -PKA: cAMP dependent protein kinase ("kinase kinase") -phosphorylates phosphorylate kinase -Makes active form -PP1: protein phosphatase 1 -dephosphorylates phosphorylase kinase -makes inactive form

cAMP Dependent Protein Kinase Activation

-When active gluconegenesis wins -Low blood glucose --> increased gluconeogenesis -Amplification: -1 glucagon --> many cAMP -Many PKA activated -PKA phosphorylates many targets SUMMARY: Glucogenesis is favored in a fasting state

Glycolysis and Gluconeogenesis Reciprocal Regulation Diagram

-When citrate is high energy is high -Citrate proportional to energy -Citrate forms in the TCA cycle

Control of the Synthesis and Degradation of Fructose 2,6 biphosphate

-When glucose is abundant fructose 2,6 biphosphate is high -when glucose is scarce fructose 2,6 biphosphate is low -The enzyme is regulated through phosphorylation and dephosphorylation

what is a substrate cycle, and why does it help when it is 'leaky'?

-When two metabolic pathways run simultaneously in opposite directions -e.g. the phosphorylation of F 6 P to F 1,6 bP and back to F 6 P -Sometimes called futile cycles -Neither metabolic pathway is fully active so one wins over slightly. (one leaks over the other) -These pathways enhance metabolic signals -A small change in the rates of the opposing reactions leads to a massive change in the net flux -A 20% in activation on both sides leads to a 380% change in net flux

How are the levels of cAMP determined (activity of adenylate cyclase : phosphodiesterase)

-adenylate cyclase hydrolyzes (produces) cAMP -Phosphodiesterase degrades cAMP -?

mechanism of phosphoglucomutase (how is the high-energy phosphate bond conserved?) Cont.

-another image

Hormonal Control through Phosphorylation Cont.

-cAMP dependent protein kinase -PKA -regulated by cAMP (talked about above) -cAMP dependent kinase is a "kinase kinase" -cAMP inhibited by Viagra

Phosphorylase kinase: how is it activated by cAMP dependent protein kinase, and by calcium (calmodulin)

-cAMP dependent protein kinase phosphorylates phosphorylase kinase making 2 catalytic subunits -this activates phosphorylase kinase -Calmodulin changes conformation around Ca2+ and opens the catalytic domain of phosphorylase kinase -This conformational change allows phosphorylase kinase to bind to substrates

Glycogen in the liver

-exports glucose to other tissues -storage of glycogen and degrades it to glucose -Synthesis of glucose by gluconeogenesis -synthesis and storage/degreadtion of glycogen are 2 separate events -Fed state: produces glycogen -Fasting state: produces glucose from glycogen Cori cycle produces glucose from lactate

Glycogen synthesis is primed by glycogenin - what does it do, and how? what are its substrates?

-glycogenin is a primer to form glycogen -all glycogen granules have glycogenin at center -Has intrinsic glucosyl transferase activity -Links C1 to Tyr194 -Glycogenin binds UDP-glucose (UDPG) which then binds glycogen synthase. Glycogen synthase then extends the primer cleaving off UDP Substrates: -UDPG

Glycogenin and Glycogen Synthesis Overview

-glycogenin: dimer -glycogenin's nonreducing enol catalyzes the addiction (1) Glucosyl transfer from UDPG to Tyr194 (2) Binds glycogen synthase (3) glycogenin extends primer -UDP-Glucose --> UDP (4) glycogen synthase extends glycogen (5) branching enzyme branches -glycogen synthase binds after step 3 -Every glycogen granule has glycogenin at center

Where are Pyruvate carboxylase and pyruvate dehydrogenase located

-in the same compartment (mito) on the same substrate

What is the Cori cycle, and what purpose does it have?

-lactate produced by muscle glycolysis is transported to the liver via the bloodstream where it is converted to glucose by gluconeogenesis. -Blood stream carries glucose back to the muscles where it is stored as glycogen -Mobilization of glucose from lactate -Produces useful energy source from waste byproduct

how is this pathway linked into isoprenoid synthesis (Mevalonate pathway)

-mevalonate pathway effects hydroxymethylglutaryl CoA synthase through isoprenoids

mechanism of phosphoglucomutase (how is the high-energy phosphate bond conserved?)

-phosphate binds to glucose and then rebinds to the enzyme

how are odd chain fatty acids synthesized (and remember how they are broken down, as well!)

-propionyl CoA is used as a primer in place of acetyl CoA

A few days after starting an extremely restrictive "no‑carb" fat‑based diet, an otherwise healthy man begins to feel tired and weak. You suggest that the man add some carbohydrates to his diet. Despite your explanation that "fats burn in the flame of carbohydrates," the man still refuses to consume carbohydrates. Consider other ways in which the man could supplement his diet to improve his metabolic health. Select all the compounds that could improve this man's ability to metabolize fats.

-pyruvate -glycerol -succinyl CoA

What are the reactions that allow the conversion of cytosolic NADH into NADPH during fatty acid biosynthesis? What enzymes are required? What is the sum of these reactions?

-pyruvate + CO2 + ATP + H2O ⟶ oxaloacetate + ADP + Pi + 2H+ -oxaloacetate + NADH + H+↽−−⇀ malate + NAD+ -malate + NADP+ ⟶ pyruvate + CO2 + NADPH -pyruvate carboxylase -malate dehydrogenase -malic enzyme -NADP+ + NADH + ATP + H2O ⟶ NADPH + NAD+ + ADP + Pi + H+

(2) Phosphoglucomutase

-remains bound on enzyme -similar to phosphoglycerate mutase 3PG <--> 2 PG -Both use hydrolysis -Would need ATP -Saves the high energy bond

energy balance of fatty acid oxidation (dont forget expenditure for initial activation of fatty acid) - how much ATP can we make, for example, from a C20 fatty acid? how would this look like if we started from a triglyceride?

-repetitions (n carbons/2 -1) -acetyl-SCoA (carbons/2) -1 NADH and 1 FADH2 per repetition - (I) repetitions(NADH*2.5) + repetitions(FADH2*1.5) - acetyl-SCoA(1 ATP + (2.5 ATP/NADH * 3NADH) + (1.5 ATP/FADH2 * 1 FADH2)) (II) acetyl-SCoA(10 ATP) -(I) + (II) -2 ATP (energy cost) = net ATP -example in the problem: -9 repetitions, 10 acetyl-SCoA -9(2.5) + 9(1.5) = 36 ATP -10(10) = 100 ATP - 36 + 100 -2 = 134 ATP for a C20 fatty acid -Rule of thumb: an extension of a fatty acid chain by 2 carbons allows it to make 14 more ATP -e.g. C16 = 104, C18 =120, C20 =134... -For a triglyceride: -multiply the number of ATP produced by each chain (like above) by 3 -add 15 ATP to account for pyruvate holding the chains together

similarities and differences between fatty acid beta oxidation and biosynthesis

-shown in image above -Synthesis partially shown in image

Alpha Beta Bond Cleavage Cont.

-thiolase ~= hydrolysis -Reverse claisen condensation in step one -Enolate anion is resonance stabilized in step 2 -tetrahedral intermediate in the last step -Fatty acyl CoA(n) + CoA + NAD+ + FAD + H2O --> Fatty acyl CoA(n-2) + acetyl CoA + NADH + FADH2

Calculate the number of ATPs generated from one saturated 18-carbon fatty acid. For this question, assume that each NADH molecule generates 2.5 ATPs and that each FADH2 molecule generates 1.5 ATPs.

120 ATPs

Select the results from having few or no a 1,6 linkages in glycogen: -Glycogen solubility would increase -Glycogen degradation would slow down -Glycogen synthesis would be faster -maintaining proper blood sugar levels would be more difficult

2 and 4 ( the alpha 1,6 linkages are the crosslinks that allow branching to occur) -Glycogen degradation would slow down -Maintaining proper blood sugar levels would be more difficult

On average, how many glucose 1‑phosphate molecules will be released from a single glycogen branch at its nonreducing end before glycogen phosphorylase cannot cleave that branch any further?

6

Calculate the number of repetitions of the β‑oxidation pathway required to fully convert a 18-carbon activated fatty acid to acetyl‑SCoA molecules. Calculate the number of acetyl‑SCoA molecules generated by complete β oxidation of a 18-carbon activated fatty acid.

8 repetitions (n carbons/2 -1) 9 acetyl-SCoA (carbons/2)

what is a processive enzyme?

An enzyme that can catalyze subsequent reactions before releasing its substrate. -e.g. glycogen phosphorylase binds 4-5 units of glycogen and can phosphorylate several glucose units before it must rebind

Where does beta oxidation occur, which cellular compartment? Where does FA synthesis occur? Where are ketone bodies made, both body organ and cellular compartment?

Beta oxidation occurs in the mitochondria, FA synthesis happens in the cytosol. Ketone body synthesis happens in the mitochondria of the liver.

Understand the two enzymatic activities of glycogen debranching enzyme and why both are important.

Bifunctional -Two active sites: -a-1,4 glucanotransferase (GT) -shifts a block of 3 glucosyl residues from an outer branch to an inner one -Essentially takes the glucosyl residues in front of a branch point and moves them to an inner branch. think about cleaving little branches and adding them to the trunk of a tree until you get to the stump. -a-1,6 glucosidase (GC) -cleaves the glucose residue from the branch to form a linear branch and a glucose -Essentially removes the nubs of the branches so you have a linear branch

Branching and debranching enzyme - what do they do?

Branching enzyme: -Creates new non-reducing ends -Can count and measure glucosyl residues -Branches glycogen granules Debranching enzyme: -Debranches glycogen to free up glucose (last residue of the branch) and add glucosyl residues to main branch -This allows for further breakdown of glycogen -Like debranching a tree.

Glucagon secretion is stimulated when blood glucose concentration decreases. Select all of the carbohydrate pathways that glucagon stimulates in the liver.

Carbohydrate pathways that glucagon stimulates in the liver: -Glycogenolysis (glycogen breakdown) -Gluconeogenesis

Cori Cycle Cont.

Cori Cycle: -Mobilization of glucose from lactate produced in skeletal muscle via gluconeogenesis in the liver -Liver: -Synthesis/storage of glycogen -Degradation of glycogen to glucose -Synthesis of glucose by gluconeogenesis Skeletal Muscle: -Storage of Glucose as Glycogen -Glycogen --> g6P --> glycolysis -Gluconeogenesis via the cori cycle -Glucose --> lactate (in skeletal muscle) generates 2 ATP -Lactate --> glucose (in liver) consumes 6 ATP -Both are NADH neutral Glucose alanine cycle: -Muscle: pyruvate --> alanine -Liver: alanine --> pyruvate (urea excreted as a by product... urea cycle) -Cooperation between glycolysis and gluconeogensis during a sprint in the diagram on the left.

flux of carbon between skeletal muscle, heart muscle, and liver

Cori cycle: mobilization of glucose from lactate produced in skeletal muscle via glucogenesis in the liver. glucose alanine cycle: mentioned above flux of carbon in fed and fasting states is well indicated in the diagram

Pathway of Gluconeogenesis

Diagram in image

What are the products of each round of beta oxidation? What are the total products for the complete oxidation of palmitoyl CoA?

Each round of beta-oxidation yields 1 Acetyl-Coa, 1 FADH2, and 1 NADH. For complete oxidation of 16C FA we get 8 Acetyl-Coa, 7 FADH2, and 7 NADH

In exercising muscle, glycogen degradation supplies the muscle with glucose‑6‑phosphate. In order to stimulate muscle glycogen degradation, protein phosphatase 1 (PP1) must be inhibited. Four of the five events are involved in the inactivation of PP1 in exercising muscle.

Event not involved in the inactivation of PP1 in exercising muscle: -Insulin initiates a protein kinase cascade that utilizes glycogen synthase kinase. Events involved in the inactivation of PP1 in exercising muscle: -Epinephrine initiates a cAMPcAMP signal transduction cascade that utilizes protein kinase A. -Protein kinase A phosphorylates an inhibitor of PP1. -Protein kinase A phosphorylates GM in the GM-PP1 complex, resulting in its dissociation. -Phosphorylated PP1 inhibitor binds to PP1, facilitating glycogen degradation by phosphorylase a.

Regardless of its efficacy, what is the reasoning behind carbohydrate loading

Excess glucose is stored as muscle or liver glycogen, which can be broken down to supply energy during the event

What is the electron acceptor used for going from an alkane to an alkene?

FAD

Match each characteristic to the synthesis or oxidation of fatty acids.

Fatty acid synthesis: -occurs in the cytoplasm -Uses NADPH -Acyl carrier protein is the acyl carrier -involves the conversion of a carbonyl to a methylene -Enzymes are organized in a multienzyme complex Fatty acid oxidation: -Uses NAD+ -Uses FAD -Occurs in the mitochondria -Coenzyme A is the acyl carrier -Involves the conversion of a methylene to a carbonyl

What are the four main roles of fatty acids?

Fuel storage, building blocks for phospholipids, protein modifications, and to create fatty acid derivatives such as hormones and intracellular

Glycogen synthase may be regulated by covalent modification and/or allosteric control. Label the diagram with the appropriate terms to describe glycogen synthase regulation. Note that some texts use glycogen synthase I instead of glycogen synthase a and glycogen synthase D instead of glycogen synthase b.

In the image on the right

Under conditions of low blood sugar, what hormone will predominantly be released? What does this cause to happen to beta oxidation and FA synthesis?

Glucagon is released. Increases beta oxidation, decreases FA synthesis

The hormone glucagon and the hormone and neurotransmitter epinephrine aid in maintaining blood glucose levels. Classify the statements as describing glucagon only, epinephrine only, or both glucagon and epinephrine.

Glucagon: -secreted by pancreatic a cells -polypeptide Epinephrine: -derived from tyrosine -stimulates muscle cells to break down glycogen -released in response Both: -released in response to a drop in blood glucose levels -inhibits glycolysis and stimulates gluconeogenesis in the liver -the receptor has seven transmembrane a helices

two fates of pyruvate in mitochondria, and how its fate is determined based on energy levels and needs of the cell

Gluconeogenesis: -Pyruvate is carboxylated to form oxaloacetate by pyruvate carboxylase -OAA is then reduced to malate and shuttled to the cytoplasm to produce phosphophenolpyruvate Glycolysis: -Pyruvate is converted to Acetyl CoA by PDH -Pyruvate is converted to OAA in the fed state and converted to acetyl CoA in a fasting state -PDH is suppressed when carbohydrate levels are low promoting gluconeogenesis

Energetics of Glycogen Synthesis

Glucose + ATP --> G6P + ADP (-17 kJ/mol) G6P --> G1P (7 kJ/mol) G1P + UTP + H2O --> UDPG + 2Pi (-19 kJ/mol) Glycogen(n) + UDPG --> glycogen(n+1) + UDP (-13 kJ/mol) Overall: -Glucose + ATP + UTP + glycogen(n) + H2O --> glycogen(n+1) + ADP + UDP + 2Pi (-42 kJ/mol) -Favorable -addition of each glucose costs 2 ATP -UDP + ATP <--> UTP + ADP (dG0' ~ 0) -nucleoside diphosphatekinase is the enzyme -Sugar nucleotide intermediate

'balance the reaction' - going from glucose to glycogen n+1 and from glycogen to glucose, n-1

Glucose --> glycogen(n+1): Glucose + ATP + UTP + glycogen(n) + H2O --> glycogen(n+1) + ADP + UDP + 2Pi (-42 kJ/mol) Glycogen(n) --> glycogen(n-1) + Glucose: Glycogen(n+1) + H2O --> glycogen(n) + glucose (-18 kJ/mol) Overall: ATP + UTP + 2H2O --> ADP + UDP + 2Pi (-24 kJ/mol?)

Glycogen phosphorylase catalyzes a __________ reaction that breaks __________ in glycogen. Phosphorylase is one of the enzymes of glycogenolysis that directly generates __________ In the fasting state, the hormone glucagon ________ the enzyme, resulting in __________ in blood glucose levels.

Glycogen phosphorylase catalyzes a phosphorolysis reaction that breaks α‑1,4 linkages in glycogen. Phosphorylase is one of the enzymes of glycogenolysis that directly generates glucose 1‑phosphate. In the fasting state, the hormone glucagon stimulates the enzyme, resulting in an increase in blood glucose levels.

(3) Glycogen Synthase

Glycogen(n) + UDP-G --> glycogen(n+1) + UDP -Group transfer of glucose dG0' ~= -13 kJ/mol -Driven by the hydrolysis of the sugar nucleotide

What is the purpose of ketone bodies? How are ketone bodies synthesized? How many Acetyl-CoA units does it require?

Ketone bodies provide an additional energy source when glucose levels are low, especially for tissues that can't metabolize triglycerides like the brain. It takes 3 Acetyl-Coa units to synthesize HMG-CoA.

What is the driving force for ADP-glucose pyrophosphorylase reaction

Hydrolysis of pyrophosphate

Identify the characteristics of allosteric regulation of glycogen phosphorylase in the muscle and liver

In Muscle: -Activation generates glucose for the cell. -b form is the default state. -AMP binding induces R state. In Liver: -Activation liberates glucose for export. -a form is the default state. -Glucose binding induces T state.

Balance the equations for glycogen degradation

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Complete the reactions which show the transfer of glucose to a growing glycogen chain.

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Complete the sentences to correctly describe steps in fatty acid synthesis.

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During glycogenolysis, glycogen is broken down and converted to glucose 6‑phosphate, which can enter glycolysis or be used by the liver to raise blood glucose levels. Complete the sentences describing glycogen breakdown. Some terms will be used more than once, and two terms will not be used at all.

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Insulin receptor: dimerizes upon binding of insulin --> activates insulin stimulated protein kinases (ISPK), and many other insulin receptor substrates (IRS) through phosphorylation of tyrosine. Remember that insulin receptor is a tyrosine kinases

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Phosphorylation and Dephosphorylation Systems of Glycogen Metabolism in Muscle

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Table of Glycogen Storage Diseases

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The diagram shows the reactions of the β‑oxidation pathway. Label the reaction types on the diagram.

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Water is prevented from entering the active site of glycogen phosphorylase. What are the advantages of excluding water from the active site

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Glycogen synthase catalyzes glycogen synthesis. Determine whether each example is associated with an increase or decrease in glycogen synthase activity.

Increased glycogen synthase activity -insulin -activation of phosphoprotein phosphatase (PP1) -phosphorylation of glycogen synthase kinase (GSK, or GSK3) Decreased glycogen synthase activity -phosphorylation of glycogen synthase -subunit dissociation of cAMP-dependent protein kinase (PKA) -phosphorylation (inactivation) of phosphoprotein phosphatase 1 (PP1) by PKA

When blood glucose is low, the pancreas releases glucagon, a peptide hormone which stimulates the liver to produce and excrete glucose. Binding of the hormone to its receptor triggers a "second messenger" cascade pathway that results in a change in the concentration or activity of many enzymes and signaling intermediates. The activity of some pathway enzymes is altered, as is the direction of net flow through some pathways. How does glucagon stimulation affect the concentration or activity of the given signaling intermediates and enzymes?

Increases: -adenyl cyclase -[3',5'-cyclic AMP] -protein kinase A -phosphorylase b kinase -glycogen synthase kinase -fructose-2,6-biphosphatase Decreases: -[fructose-2,6-biphosphate] -phosphofructokinase-2 Glucagon stimulation decreases which pathway enzymes? Select all that apply: -glycogen synthase -pyruvate kinase -phosphofructokinase-1 Glucagon stimulates which pathways? Select all that apply. -gluconeogenesis -glycogenolysis (glycogen breakdown)

Under conditions of high blood sugar, what hormone will predominantly be released? What does this cause to happen to beta oxidation and FA synthesis?

Insulin. Decreased beta oxidation, increased FA synthesis.

What is the advantage of phosphorylation having opposite effects on glycogen synthesis and breakdown?

It prevents useless expenditure of energy

What would happen if G-protein hydrolyzed GTP at a fast rate? -It would get degraded rapidly -It would waste energy -It would not be able to stay bound to the GPCR -It would not be able to activate AC (adenylate cyclase)

It would not be able to activate AC (adenylate cyclase)

fatty acid esterification and de-esterification by acyl glycerol transferases and lipases, phospholipases

Lipases: -Deesterification -removes acyl groups -tri --> di --> monoacylglycerol Transferases: -Esterification -Adds acyl groups -mono --> di --> tri

fundamental difference between liver, muscle, and brain in their glycogen metabolism / storage capacity

Liver: makes and mostly exports glycogen while storing some Muscle: Stores glycogen and glucose but mostly protein Brain: almost no energy stores (emergency only) consumes glucose and glycogen at a high rate

Diagrams of Glycogen Phosphorylase a/b ratios

Liver: phosphorylase b (dephosphorylated) is active Muscle: phosphorylase a (phosphorlated) is active -In both cases the relaxed state is active

Fates of glucose 6 P.

Liver: to glucose through glucose 6 phosphatase -glucose is then treleased in the blood for use in other tissues Muscle/brain: to pyruvate through glycolysis -pyruvate is then converted to lactate during muscle contraction Pentose Phosphate Pathway: ribose and NADPH

Epinephrine is released in response to stress, and is a fight‑or‑flight hormone. Select all metabolic pathways that epinephrine stimulates:

Metabolic Pathways that epinephrine stimulates: -Glycolysis in muscle -glycogen breakdown (glycogenolysis) in liver and muscle -Gluconeogenesis in the liver -Lipolysis in adipose tissue

How does the regulation of protein phosphatase activity differ in muscle and liver? Why is it different?

Muscle: the interaction of the phosphatase with the glycogen granule is enhanced by cAMP, but inactivated by camp-dependent protein kinase, PKA, (through phosphorylation of M protein). then, an inhibitor (also activated by protein kinase, binds and shuts down the phosphatase for good. In liver: inhibited by binding to the active glycogen phosphorylase. When glucose is abundant, that shifts to the T state, which no longer binds the particles. PP1 is then free to activate glycogen synthase by dephosphorylation, and inactivate the T-state (already pretty dead) of glycogen phosphorylase by removing the P now P'lase b.

Which of the following mutations in muscle glycogen phosphorylase could result in a condition similar to McArdle disease

Mutant glycogen phosphorylase is unable to bind to AMP

Source of reducing power for fatty acid synthesis

NADH and NADPH are the source of reducing power for fatty acid synthesis

Is food that contains mono- and diacylglycerols really 'low fat', 'low calorie'?

No, Chemically, all these glycerides are esters of glycerol and fatty acids which are metabolized in exactly the same way. Monoglycerides and diglycerides, like normal fats, also have 9 Calories per gram. The FDA regulations require reporting fatty acids expressed as triglycerides. In a strict interpretation, monoglycerides and diglycerides are not considered "fat", and information about the saturation of their fatty acid components is omitted from the nutrition label.

why do we need glycogen / branched glycogen; know the concepts of 'reducing end' and 'nonreducing end'

Non-reducing ends: glycogen grows and degrades from those ends (C4) Reducing ends: these ends can oxidize and reduce other molecules (C1)

If skeletal muscle cells had the same mutation, what would be the effects on skeletal muscle cells?

Nothing. Skeletal muscle cells lack glucose-6-phosphatase.

Arrange in proper order the events of the signal‑transduction cascade for glycogen degradation in muscle.

Order of signal transduction pathway for glycogen degradation in muscle: -Contraction begins -phosphorylase kinase is partly activated by binding Ca2+ -epinephrine is released and binds to muscle B-andrenergic receptors. -The simulatory Ga protein dissociates and activates adenylate cyclase -Intracellular cAMP levels increase, which activates protein kinase A -phosphorylase kinase is phosphorylated on its a and b subunits -Glycogen phosphorylase b is converted to glycogen phosphorylase a -phosphorylysis of glycogen yields glucose 1-phosphate

Know the involved organs / enzyme and remember a bit about the Coris.

Organs involved: -Liver: gluconeogenesis (lactate --> glucose) -Muscle: makes lactate through contraction, stores glucose as glycogen enzyme involved: alanine aminotransferase (ALT) -High ALT level in the blood signals liver damage -Abundant liver enzyme Coris: -Immigrated to the U.S. in 1922 -Gerty was the first U.S. woman to win nobel prize in science (1947: medicine) -Gerty worked with her husband Carl and directors of the institute did not want that.

Glycogen phosphorylase a and b, T and R.

Phosphorylase a: -liver -(T): inactive -(R): active Phosphorylase b: -muscle -(T): inactive -(R): active -Phosphorylase a is phosphorylated and phosphorylase b is unphosphorylated

Allosteric regulation of glycogen phosphorylase - what is the structural basis (Km effect)

Phosphorylase b (unphosphorylated): -ATP, G6P, and caffeine favor phosphorylase b (T) (inactive) -AMP favors (R) (active) Phosphorylase a (phosphorylated): -glucose favors (T) (inactive) Allosteric effector site: -AMP: activator -ATP, G6P: inhibitors

If you were to design a low calorie fat substitute, what key features would you want? Hint: Why is sucrose-octaester (olestra) a low-calory fat substitute?

Similar features to fatty acids but make it indigestible

Energetics of glycogen synthesis and breakdown

Synthesis: - -14 kJ/mol -favorable Breakdown: - -18 kJ/mol -favorable -Energetics of partial reactions are shown in the image

the direction of glycogen synthesis and breakdown.

Synthesis: fed state -glycogen to G1P Breakdown: fasting state -Activates glucose by forming a high energy sugar nucleotide -Glucose to branched glycogen

We have encountered reactions similar to the sequential oxidation, hydration, and oxidation reactions of fatty acid degradation earlier in our study of biochemistry. What other pathway employs this set of reactions?

TCA Cycle

Why is water excluded from the active site of glycogen phosphorylase, and how do you think this could be achieved?

The active site closes in order to prevent hydrolysis resulting in glucose rather than G6P

Andersen's disease is a deficiency of the glycogen branching enzyme (amylo(1,4 1,6) transglycosylase). This is one of the most severe glycogen storage diseases, resulting in death before age of 2 from progressive cirrhosis of the liver. Explain what the glycogen would look like, and speculate why this results in progressive liver damage.

This would cause the glycogen to be super long chains without any branching. It is recognized by the immune defense system and therefore results in liver damage.

how is the first oxidative step integrated in the electron transport chain?

Through the use of NADH and FADH2 to form ATP

In glycogen metabolism, which molecule's synthesis reaction is by the hydrolysis of pyrophosphate

UDP-glucose

You have identified a patient whose heterotrimeric G protein has a 10-fold higher turnover rate in its GTPase activity. Its interaction with hormone-bound receptor is normal. Explain the downstream effect.

Very little cAMP would be made because the adenylate cyclase wouldn't remain active for very long. There would be less activation of glycogen breakdown as a result.

Debranching enzyme allows for the complete degradation of glycogen by glycogen phosphorylase. In eukaryotes, debranching enzyme is a bifunctional enzyme containing transferase and α‑1,6‑glucosidase activity. Transferase transfers three glucosyl residues from a limit dextrin to another part of the glycogen molecule. α‑1,6‑Glucosidase hydrolyzes the α‑1,6 bond that links the single glucosyl residue remaining at the branch point after the limit dextrin has been transferred. What is the product of α‑1,6‑glucosidase activity?

What is the product of α‑1,6‑glucosidase activity? -Glucose

In a skeletal muscle cell without any mutations, is any glucose generated from the breakdown of glycogen? If yes, does it accumulate?

Yes, skeletal muscle cells also have the glucosidase activity of glycogen debranching enzyme, but since hexokinase has such a low Km, they readily grab the glucose and send it down the glycolytic pathway.

In the liver, if we had a mutation that completely blocked glucose-6-phosphatase activity Would any glucose be generated from glycogen degradation?

Yes, the glucosidase activity of glycogen debranching enzyme hydrolyzes off the last glucose residue instead of phosphorylating off the last residue and according to the book, about 10% of the glucose residues are hydrolyzed off

structures of alpha-D and beta-D glucose, and the two types of linkages in glycogen

alpha D: -"away" -The C1 OH is down beta D: -"Both" -The C1 OH is up (same plane as CH2OH)

Answer the question using only your knowledge of glycogen metabolism enzymes. An infant is brought to a physician after having seizures. The infant had been noted as being very small for her age (below the 5th percentile for weight). During examination, the physician noted an enlarged abdomen (due to an enlarged liver). Tests show fasting hypoglycemia (low blood glucose concentration) and increased serum lipid levels. Liver and muscle biopsy revealed an increased amount of glycogen with short branches.

amylo-α-1,6-glucosidase (debranching enzyme)

Which of these is a second messenger? -Epinephrine -G-protein -cAMP -Adenylate cyclase

cAMP

Suppose a researcher introduces a mutation into the glucosidase domain of the mammalian glycogen debranching enzyme. The mutation inhibits the activity of the glucosidase but does not affect the other functions of the enzyme. The researcher then introduces the mutated enzyme into mammalian cells that do not express wild type glycogen debranching enzyme. Predict the effect of the mutation on glycogen metabolism

glycogen molecules with branches containing a single glucose residue

Energetics of Glycogen Breakdown

glycogen(n+1) + Pi + --> glycogen(n) + G1P (dG0' ~= 3 kJ/mol) G1P --> G6P [in liver] (-7 kJ/mol) G6P + H2O --> glucose + Pi (-14 kJ/mol) Overall: -glycogen(n+1) + H2O --> glycogen(n) + glucose (-18 kJ/mol) -Favorable

Glycogen breakdown in image

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Table of Gluconeogensis Reactions

in image -G6P --> glucose (only in liver)

How would the following changes affect the rates of glycogen synthesis and glycogen breakdown? Write down which enzymes are regulated, and how.

increased cytosolic Ca2+: -Calcium activates calmodulin subunit in phosphorylase kinase and partially activates the enzyme. Phosphorylase kinase then phosphorylates phosphorylase to activate it. Phosphorylase kinase also phosphorylates glycogen synthase to inactivate it. This essentially turns on glycogen breakdown and inhibits glycogen synthesis. increased plasma insulin: -Insulin binds the insulin receptor which allows the phosphorylation of a number of target proteins including: phosphodiesterase and protein phosphatase 1. Activated phosphodiesterase hydrolyzes cAMP. As a result, cAMP can no longer activate PKA and glycogen breakdown is inhibited. When protein phosphatase 1 is phosphorylated, it dephosphorylates glycogen synthase which activates it and phosphorylates phosphorylase to inactivate it. Basically turns glycogen synthesis on and glycogen breakdown off.