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Glossary of Biochemistry (Energetics) Glycolysis, Glycogenolysis, Glycogenesis

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In enzyme classification: What does it mean to be a Dehydrogenase?
enzymes which oxidize substrate with cofactors (NAD)as electron acceptors.
In enzyme classification: What does it mean to be a REDUCTASE?
add electron from a reduced cofactor.
In enzyme classification: What does it mean to be a Kinase?
Phosphorylate substrate.
In enzyme classification: What does it mean to be a Isomerase?
Enzymes which mediate interconversions between isomers.
In enzyme classification: What does it mean to be a Carboxylase?
Add carboxyl groups (C02)
In enzyme classification: What does it mean to be a Decarboxylase?
remove carboxyl group (CO2)
In enzyme classification: What does it mean to be a Synthetase?
synthesis of products using ATP.
In enzyme classification: What does it mean to be a Synthase?
synthesis of product WITHOURT ATP requirement.
What is it important to recall about opposed pathways?
Opposed pathways (glycolysis vs gluconeogenesis) are not just simply reverse steps, even if they share a common intermediate or enzyme. Each process is regulated to avoid a futile cycle.
Biological regulation:
3 ways to control the amount of enzyme...
1.) Compartmentilization: regulates the metabolism by keeping enzymes in certain locations.

2.) Hormonal Control: Hormones by 2 different mechanisms can bind to the genetic materal or activate signal transduction pathways to regulate enzyme production

3.) Tissue specialization- keeping allthe enzymes in a particular cell assures that a pathway is not carried out if it is not necessary.
Biological Regulation... 3 ways to regulate the catalytic activity of enzymes.
1.) allosteric effects- changes in structure can effect the activation of enzymes.

2.) Inhibitors- stop pathways by inhibiting an enzyme in the pathway.

3.) Covalent modification: Addition of groups to enzymes in order to activate/deactivate them (phophorylation/methylation)
Biological Pathway regulation. 2 ways accessibility to substrate regulates pathways.
1.) Compartmentilization- control of pathways can occur by changing the accessibility to necessary substrates.

2.) Ratios of energy producers (NADH/NAD or ATP/ADP + AMP)... when ratios are low catabolic pathways are induced and when they are high they are inhibited.
Glycogen mobilization or glycogenolysis is a process that is carried out by what kind of pathway? and what substance in the liver vs what substance in the muscles?
Signal transduction pathway; Glucagon (from pancreas to liver) and epinephrine (adrenaline) in muscles.
In the signal transduction pathway of glucogenolysis, what are the first messengers? What IS the second messenger? 3 protein components used in the process what are they? the transducer is? The effector enzyme is? What is the final result of the pathway?
Glucagon (liver), epinephring (muscles); cAMP; receptor, transducer (G-protein), effector (enzyme- adenylate cyclase); conversion of ATP to cAMP (second messenger).
The more highly reduced a substrate is the (lower/higher) its potential for generating biological energy
Higher
which stores more energy fat or carbohydrates? why?
Fats; more highly reduced (saturated hydrocarbons).
The first step of glycolysis is glucose to ___________. Using the enzyme _____________ and requires __________.
Glucose ------> Glucose 6-phosphate; hexokinase; 1 ATP (irreversible step).
The first enzyme of glycolysis, hexokinase is found ___________. has what kind of specificity for sugars? what kind of affinity for sugars? catylizes an exothermic/endothermic rxn?
INHIBITED BY?
found in ALL CELLS.

LOW specificity for sugars (phosphorylates many hexoses)

High affinity for sugars

exothermic (irreversible)

Glucose 6 phosphate (product of the rxn it catylizes)
The first step of glycolysis is Glucose to glucose 6 phosphate using what enzyme other than hexokinase? found in? affinity for glucose? induced by? inhibited by G6P?
Glucokinase

found in LIVER

Low affinity for glucose (highly specific for glucose)

large carbohydrate meals (glucose surge)

NOT inhibited by G6P whereas hexokinase was. (key distinction)
The second step of glycolysis is the conversion of glucose 6-phosphate to Fructose 6-phosphate using the enzyme? the isomerization requires no chemistry (movement of e-) from _________ sugar to ________ sugar.
Phosphoglucoisomerase; aldose sugar to ketose sugar (Carbonyl moves to internal position.)
the third step of glycolysis is the conversion of Frucose 6-phosphate to Fructose 1,6 bisphosphate using the enzyme? this step requires? what is known of the enzymes regulation?
phosphofructokinase

ATP (highly exothermic;irreversible)

HIGHLY regulated to modulate carbon flow through Glycolysis (KEY POINT)
The fourth step of glycolysis takes Fructose 1,6 bisphosphate and forms what two products using what enzyme? this enzyme functions to do what? reversible/irreversible?
Dihydroxyacetone phosphate & Glyceraldehyde 3 phosphate; Aldolase; cleaves 6 carbon rings to 2 3-membered products (aldol condensation); reversible.
In the fifth step of glycolysis all of the dihydroxyacetone phosphate from the previous step is converted to the other product of the fourth step G3P. by what enzyme? which converts all sugar from its ______ form to ______ form. reversible/irreversible?
triose phosphate isomerase; ketose to aldose; reversible
the sixth step of glycolysis is the conversion of 2-G3P to 1,3 BiPG by the enzyme? this conversion begins what? what is done with lossed e-? this step thus requires what?reversible/irreversible?
G3P dehydrogenase; the energy yielding processes; they are put on e- carriers; Pi & NAD which becomes reduced to NADH; reversible.

FOR MECHANISM SEE PG 74 in notes. (Thiolhemiacetal, thioester, finally large energy stored in phosphoanhydride bond of 1,3 BPG)
in the seventh step of glycolysis 1,3BPG is converted to 3 phosphoglycerate by what enzyme? this process requires _____ and gives off ______? reversible/irreversible? this is known as what kind of ATP production? at this point what is the net energy cons
Phosphoglycerate kinase; ADP to 2 ATP each glucose; reversible; substrate level phosphorylation. Net= 0= 2 consumed + 2 just made.
Step 8 in the glycolysis pathway is the conversion of 3 phosphoglycerate to 2 phosphoglycerate by what enzyme? what actually happens? intermediate? reversible/irreversible?
phosphoglycerate mutase; the enzyme puts its phosphate at C2 and takes the phosphate from C3. intermediate= 2,3 BPG, reversible.
the ninth step of glycolysis is the conversion of 2-phosphoglcerate to phosphoenylpyruvate using what enzyme? what kind of process? what other product? irreversible/reversible? is the final product more or less stable (more or less energy)?
enolase; Keto-Enol tautomerization; H20; reversible; less stable (reversible) enol is less stable and has more energy.
the tenth and final step of glycolysis, phosphoenylpyruvate is converted to pyruvate by what enzyme? produced what? by what process is it produced? what is known of its regulation? reversible/irreversible?
pyruvate kinase; 2 ATP; substrate level phosphorylation; highly regulated step; irreversible (highly exothermic).

PRODUCES THE NET 2 ATP's!
Steps 7, 9 and 10 all require Mg ion (10 also requires K ion). Where are these ions from?
Complexed to the ADP that has come in and by substrate level phosphorylation becomes ATP. Recall AMP, ADP and ATP are usually complexed to Metal ions, namely Mg2+.
What is the net overall reaction of glycolysis?
Glucose + 2 ATP -----> 4 ATP + 2 NADH + 2 Pyruvate
Glycolysis is highly inefficient what are the statistics that prove this...
61 kj/mol stored in 2 ATP/ 2840 kj/mol in glucose

= 2% of energy in glucose has been stored in ATP.

Glucose's energy is effectively 95% unused.
After glycolysis pyruvate suffers one of 3 fates what are they..
1.) Anaerobic metabolism
2.) Alcoholic fermentation (also anaerobic)
3.) Aerobic metabolism
Anaerobic metabolism takes the glycolytic pyruvate and converts it to ____________ by what enzyme? its MAIN PURPOSE IS TO...? Why is this step reversible?
Lactate; Lactate dehydrogenase;

to reoxidize NADH to NAD+ to continue the minimal gain of 2 ATP by glycolysis

The step is reversible because 2 ATP is not good output and when Oxygen becomes available lactate is better served as pyruvate through aerobic respiration (more ATP/glucose).
Another fate of pyruvate under anaerobic conditions is alcoholic fermentation. The first step takes pyruvate to ________ by what enzyme? the second step uses what reagent and what enzyme to form the final product Ethanol. WHAT IS THE MAIN PURPOSE OF THIS
acetaldehyde; pyruvate decarboxylase

NADH and Alcohol dehydrogenase.

To reoxidize NADH for continued glycolysis.

so when Oxygen becomes available the organism can use that route instead (more ATP).
Glycolysis inhibition occurs at the following steps...
Hexokinase is regulated by its catlylized product Glucose 6 phosphate

Every step that makes ATP (including later aerobic metabolism) regulates the phosphofructokinase enzyme and makes F2,6BP instead of F1,6BP.

Acetyl CoA the next step in aerobic metabolism inhibits the formation of more acetyl CoA and an accumulation of pyruvate which then inhibits phosphofructokinase.
glycolysis promoted reactions...
When ADP levels are high (ATP levels are low) the phosphofructokinase step is highly promoted to convert Fructose 6 phosphate to Fructose 1,6 phosphate.
The glycogen molecule has many nonreducing terminals but only one reducing terminal to which (glucose's are added).. how are they found?
Non reducing terminals all come off a branch. The reducing terminal is found as the end of the main chain (not in the center of the molecule).
What is the enzyme required to cleave glycogen for glucose consumption? how many ATPs are used? Where are the glucose removed from? what bond is cleaved to remove a single glucose?
Glycogen phosphorylase; none the energy used is from the breaking of the glycosidic bonds; from the non-reducing end; the alpha 1-4 bond (alpha because it is below the plane of the main chain.
recall that glycogen phosphorylase (in glycogenolysis) stops breaking gluose 4 residues from the 1,6 branch point. What then is the dual role of DEBRANCHING ENZYME?
See pg 473 Figure 13.17
acts as a TRANSFERASE. it transefers non-reducing glucose (those glycogen phosohorylase cannot reduce) to the end of an adjoining chain (so it can continue) AND it cleaves off the 1,6 linked glucose.
Recall the product of glycogenolysis is the cleavage of a 1 phosphoglucose residue. How does this enter glycolysis?
The Glucose 1 phosphate is converted to Glucose 6 phosphate by Phosphoglucomutase (not to be confused with phosphoglyceromutase or phosohoglucoseisomerase)
Excess glucose is converted to glycogen. (Glycogenesis, 572, 84) What is the process?
1.)Excess glucose is converted to glucose 6 phosphate (by hexokinase or glucokinase as in glycolysis.)
2.) Then phosphoglucomutase converts G6P to Glucose 1 Phosphate. (reverse in glycogenolysis)
3.) Then a nucleotide UTP (uridine triphosphate) and G1P are converted to UDGP (uridine diphosphate and diphosphate (2 ionorganic phosphates) enzyme: UPD-glucose pyrophosphorylase.
4. Finally glycogen synthase (acts as a glycosyltranderase- transfers sugars to nonreducing sugar hydroxyl groups) adds glucose to the non-reducing end @ carbon 4.

THIS METHOD ONLY WORKS TO ADD GLUCOSE TO A BRANCH WITH 4 OR MORE ALREADY ON IT (SAME IN REVERSE). In other words all that can be done without branching enzyme!
How is glycogenesis different in the presence of branching enzyme? (573, 85)
makes 2 non reducing terminals to which glycogen ynthase can then continue to add glucose to.
Recall that when epinephrine or glucagon are released they inhibit glycogenesis. What two ways does this process cease?
by activating glycogen phosphorylase (not only stops glycogen production but breaks glycogen for necessary glucose) and inhibiting glycogen synthase.
Glycogen regulation see page 475 and page 86 in notes.
1.) Epinephrine/glucagon bind to receptor in cellmembrane.
2.) message sent from G protein to Adenate cylase which when activated converts ATP to Cyclic AMP and di inorganic phosphate.
3.) cAMP activates protein kinase A.
4.) The activation of protein kinase A inhibits glycogen SYNTHASE meanwhile activating GLYCOGEN PHOSPHORYLASE.
How does protein kinase A become inactive to shut off glycogen phosphorylase?
Recall that adenylate cyclase + ATP = cAMP + PPi (protein phosphotase). With high concentrations of PPi, Protein kinase is inactivated stopping glycogen phosophorylase activity. glycogenesis resumes.
Other comments about glycogenolysis and glycogenesis regulation:
1.) Liver has primary receptors for glucagon (Does not need to stop glycogen phosphorylase hormonally through cAMP (too slow)).

2.) Muscles have primary receptors for epinephrine. Under hormonal regulation.

3.) glycogen phorphorylase is sensitive to AMP (lack of ATP) and glycogen is then broken down.

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