The document discusses key aspects of carbohydrate metabolism, focusing on glycolysis. It describes the 10 steps of glycolysis in detail, including the investment and payoff phases. Regulation of glycolysis is also summarized, highlighting control points such as phosphofructokinase and factors that influence its activity like ATP/AMP ratios. The fate of pyruvate and processes like gluconeogenesis are briefly outlined. Finally, the pyruvate dehydrogenase complex and its role in aerobic metabolism is examined.

1. 5. The respiratory chain. Oxidative phosphorylation.
7. Citric acid cycle, amphibolic character, course, regulation.
17. Glycolysis, regulation, oxidation of pyruvate, pyruvate
dehydrogenase complex.
18. Gluconeogenesis, regulation.
19. Synthesis and degradation of glycogen, regulation.
20. Pentose phosphate cycle, regulation.
21. Metabolism of galactose and fructose, disorders.
22. Metabolism of glucuronic acid and its significance in organism.
Biochemistry final questions:
Carbohydrate Metabolism
questions

2. • Glycolysis is a metabolic pathway that is common to virtually all cells, both eukaryotic and
prokaryotic.
• Glycolysis occurs in the cytosol.
• In glycolysis: 1 glucose molecule  2 pyruvate molecules. Net gain of 2 ATP molecules.
• The process of glycolysis can be divided into 2 stages:
1. Energy investment stage (ATP “lost”)- the first 5 reactions, form phosphorylated
compounds, which are readily cleaved into 3 carbon phosphorylated compounds.
2. Energy gain stage (ATP gained)- the last 5 reactions.
Stage 1: Energy investment stage
1st reaction: glucose phosphorylation
• After glucose enters the cell via specific transport proteins, it is phosphorylated to glucose-6-
phosphate. This reaction is an important regulatory step in glycolysis.
• This reaction is Irreversible. This reaction is mediated by the enzyme Hexokinase.
• In this reaction 1 ATP is “lost” (kinase enzyme).
• This reaction causes 2 things:
1. Glucose-6-phosphate cannot leave the cell (can’t pass through the membrane- no
corresponding membrane protein). Also maintains gradient for glucose entry.
2. Glucose-6-phosphate commits to go through further metabolism in the cell.
2nd reaction: glucose-6-phosphate isomerization
• This reaction occurs using the enzyme phosphoglucose isomerase.
• Isomerization: Aldose -> ketose. glucose -> fructose.
• The reaction is reversible.
• The reaction is not rate-limiting or a regulated step.
• No ATP needed for the reaction.
17. Glycolysis, regulation, oxidation of pyruvate, pyruvate dehydrogenase
complex.

3. 3rd reaction: fructose-6-phosphate phosphorylation
• This reaction is irreversible.
• In this reaction 1 ATP is “lost” (kinase enzyme).
• This reaction occurs using the allosteric enzyme phosphofructokinase-1.
• This reaction is the most important rate-limiting, regulatory step in glycolysis.
4th reaction: fructose-1,6-biphosphate cleavage
• This reaction occurs using the enzyme
aldolase.
• This reaction is reversible.
• The reaction is not rate-limiting or a
regulated step.
• No ATP needed for the reaction.
5th reaction: Dihydroxyacetone phosphate isomerization
• This reaction occurs using the enzyme triose phosphate isomerase.
• This reaction is reversible.
• The reaction is not rate-limiting or a regulated step.
• No ATP needed for the reaction.
• DHAP can’t be used further in the glycolytic pathway, thus isomerized to GAP, in order for both
cleavage products to be used for energy production.

4. Stage 2: Energy gain stage
• This stage begins with 2 molecules of glyceraldehyde-3-phosphate (GAP) formed from each
molecule of glucose.
• Until this point energy was only “wasted” and not produced. From this point there is only
energy gain and no loss.
6th reaction: glyceraldehyde-3-phosphate oxidation
• This reaction occurs using the enzyme glyceraldehyde-3-phosphate dehydrogenase.
• This reaction can be divided into 2 parts:
1. Redox- GAP aldehyde group oxidation to carboxylic acid and NAD+ reduction.
2. Phosphate group attachment.
• The first part is energetically favorable (ΔG < 0), but the second part isn’t. Thus, an intermediate
form involves a covalent thioester bond with the enzyme is needed (cysteine residues on enzyme).
This intermediate form is required for the second part to be energetically favorable as well.
• NAD+ which serves as a co-enzyme is released after reduction to NADH and a “new” NAD+ replaces
it in the enzyme.
• The need in “new” NAD+ after this reaction, means there should be always available new NAD+s (a
molecule that has a limited amount of in the cell). Thus, the NADH formed must be oxidized back
to NAD+, which occurs either in pyruvate -> lactate (anaerobic), or in the electron transport chain
in the mitochondria (aerobic).
*** Arsenate (arsenic) poising- arsenate is very similar to phosphate group and can compete for binding the GAP. After arsenate
binding the new form skips a step in glycolysis (converts spontaneously to 3-phoshoglycerate) without any gain of ATP. Thus,
glycolysis continues but the process doesn’t gain a net ATP product.

5. 7th reaction: 3-phosphoglycerate synthesis and ATP production
• This reaction occurs using the enzyme phosphoglycerate kinase.
• Unlike most kinases, this reaction is physiologically reversible.
• In this reaction the phosphate group from C1, is transferred to ADP (ATP produced). This occurs
because 1,3-bisphosphoglycerate has a higher phosphoryl-transfer potential than the ADP.
• After this point 2 ATPs produced and 2 are lost from 1 glucose molecule. Thus, net ATP= 0.
8th reaction: phosphate group shift
• This reaction occurs using the enzyme
phosphoglycerate mutase.
• The phosphate group is transferred
from Carbon 3 to Carbon 2.
• The reaction is reversible.
9th reaction: 2-phosphoglycerate dehydration
• This reaction occurs using the enzyme enolase (enol form).
• The dehydration reaction, rearranges the molecule into an enol form (double bond between
Carbons).
• The enol form is less stable (higher energetic level). The phosphoryl-transfer potential now is
higher than the one of ADP (important for the next reaction).
• Despite the high energy state of the product, the reaction is reversible.
*** fluoride (F-) inhibits enolase activity. This property is one of the reasons fluoride is added to water, to inhibit the metabolism of
bacteria on the teeth, decreasing dental caries.

6. 10th reaction: pyruvate synthesis and ATP production
• This reaction occurs using the enzyme pyruvate kinase.
• The reaction is irreversible.
• This reaction is an important regulatory step in glycolysis.
• ATP is produced.
• 2 ATPs are gained in this reaction per glucose molecule. Net gain = 2 ATP.
Pyruvate will continue to metabolized to either:
• Lactate (anaerobic conditions, because of NAD+ balance). Humans (skeletal muscles) and some
bacteria (fermentation).
• Acetyl-CoA (aerobic conditions) -> Krebs cycle -> electron transport chain.
• Oxaloacetate- provides substrates for gluconeogenesis and replenishes intermediates of Krebs cycle.
• Ethanol- fermentation in some yeast and bacteria. Not in humans.
Net reaction of glycolysis

7. Summary of all glycolysis reactions

9. Regulation of glycolysis
• The glycolytic pathway has a dual role:
1. degenerate glucose for ATP production.
2. It provides building blocks for biosynthetic reactions as formation of fatty acids or amino acids.
• Thus, this process is highly regulated to meet the cellular needs. Reactions which are
irreversible are potential regulatory points in metabolic pathways.
• In glycolysis the irreversible reactions mediated by the enzymes: hexokinase,
phosphofructoskinase-1, and pyruvate kinase, are regulatory points.
Phosphofructokinase-1 regulation in skeletal muscle
• Most important regulatory point in glycolysis.
• ATP and AMP are allosteric effectors of the enzyme. ATP inhibits the enzyme activity
(negative effector), while AMP activates the enzyme (by competing for the allosteric site with
ATP, without having the inhibiting effect).
• Thus, ATP/AMP ratio plays a significant role in the enzyme activity.
• Why AMP stimulates and not ADP? When ATP is consumed rapidly, the enzyme adenylate
kinase forms ATP by the following reaction ->
• PH also plays a role is the regulation. Decrease in PH enhances the inhibitory activity of ATP,
such a decrease occurs when lactic acid accumulates in the muscle. This mechanism is one of
the reasons causing muscle fatigue during intense anaerobic exercise, and it protects the
tissue from damage.

10. Phosphofructokinase-1 regulation in the liver
• ATP/AMP ratio has an effect on phosphofructokinase-1 activity (PFK-1), but it’s less significant
in the liver, because the liver doesn’t experience sudden ATP needs that skeletal muscle do.
• Lactic acid is not normally produced in the liver, thus the PH level doesn’t change much and
doesn’t really affect the enzyme activity.
• Glycolysis in the liver forms building blocks for biosynthesis of different molecules. Thus, a
signal indicating if these building blocks are abundant or scarce is useful.
• In the liver, citrate (part of the citric acid/Krebs cycle) enhances the inhibitory effect of ATP.
In this way it indicates that there are enough precursor for biosynthetic activity. This inhibition
stimulates glycogen synthesis (glycogenesis).
• The key regulator of glycolysis in the liver following an increase in blood glucose level, is the
molecule Fructose 2,6-bisphosphate (don’t confuse with fructose 1,6-bisphosphate- which is
the product of phosphofructokinase-1). Fructose 2,6-bisphosphate increases PFK-1 affinity
for fructose-6-phosphate (F6P), diminishing the ATP’s inhibitory effect.
• Fructose 2,6-bisphophate is produced by the enzyme phosphofructokinase-2 (PFK-2), this
enzyme is a bifunctional protein, under certain conditions it acts as a kinase (phosphorylating
the substrate) and under different conditions it acts as a phosphatase (dephosphorylating the
substrate).
• When fructose-6-phosphate levels are high, PFK-2 acts as a kinase converting F6P -> F-2,6-BP.
F-2,6-BP activates PFK-1 to form F-1,6-BP.
• On the contrary, Glucagon secretion when blood glucose levels are low, causes the enzyme to
function as a phosphatase, inhibiting glycolysis -> activating gluconeogenesis instead.

11. Hexokinase regulation
• Hexokinase exist as isozymes I-III in most tissues of the body (isozymes- same function, different
amino acid sequences).
• These enzymes have high affinity to glucose (low Km). This allows efficient phosphorylation in
small glucose concentrations.
• They also have a low Vmax. Which means that these enzymes don’t phosphorylate more glucose
than needed for the cell.
• Also, hexokinases I-III are inhibited by their product, glucose-6-phosphate.
• Phosphofructokinase-1 inhibition (further in the glycolytic pathway) leads to increase of G6P
(isomerization of G6P to F6P is reversible, and aspires to reach equilibrium). Thus, PFK-1 inhibition
leads to hexokinase inhibition.
Hexokinase (glucokinase) regulation in liver
• Liver cells and pancreatic β-cells use the enzyme glucokinase for this reaction (also called
hexokinase IV).
• Glucokinase acts as a glucose sensor in the pancreatic β-cells (involved in insulin secretion) and
hypothalamic neurons (involved in stimulating adrenergic response in hypoglycemia).
• Glucokinase has a high Vmax and lower affinity (higher Km) than the other hexokinases. Prevents
flooding of the blood with glucose after a sugar-rich meal (minimizing hyperglycemia).
• The low-affinity of glucokinase compared to the other hexokinases, also priorities glucose
metabolism for the brain and muscles during low blood glucose levels.
• Unlike the other hexokinase, glucokinase is not inhibited by its product (G6P).
• Glucokinase activity is regulated by GKRP (glucokinase regulatory protein). When fructose-6-
phosphate (a step in glycolysis) levels rise GKRP binds glucokinase and moves into the nucleus.
Rising glucose levels facilitate the release of glucokinase from GKRP and movement into the
cytosol.
• The specificity of all hexokinases (including glucokinase
despite the name) is relatively broad, and they can
phosphorylate other hexoses in addition to glucose.
• Why is the PFK-1 regulatory
point is the most important
and not the hexokinase?
• Because G6P can go through
glycogenesis and isn’t fully
committed to glycolysis. PFK-1
is fully committed.

12. Pyruvate kinase regulation
• ATP inhibits pyruvate kinase activity.
• Fructose-1,6-bisphosphate (F-1,6-BP = product of PFK-1) activates pyruvate kinase. This activation
is referred to as feedforward activation.
Pyruvate kinase regulation in liver
• The liver cells contain an isozyme of the pyruvate kinase found in other tissues (liver= L form,
muscle + brain= M form).
• The liver isozyme can be inhibited by 2 mechanisms which doesn’t apply for the “regular” pyruvate
kinase.
• Alanine inhibits pyruvate kinase activity (only in liver).
• Glucagon (low blood glucose levels) leads to phosphorylation of pyruvate kinase (only in liver)
inactivating pyruvate kinase. This mechanism induces PEP (phosphoenolpyruvate) to enter
gluconeogenesis.
• The effect of insulin and
glucagon on gene expression
of the glucokinase, PFK-1, and
pyruvate kinase enzymes in
the liver.

13. Pyruvate dehydrogenase complex (also PDH complex or PDHC)
• Under aerobic conditions the pyruvate enters the mitochondrial matrix, where it is converted
into acetyl-CoA. This reaction is irreversible.
• The pyruvate dehydrogenase complex is a large, highly integrated complex of multiple copies
of 3 enzymes, each with its own active site.
• The 3 enzymes are:
1. pyruvate dehydrogenase (E1)
2. dihydrolipoyl transacetylase (E2)
3. dihydrolipoyl dehydrogenase (E3)
• The physical association of these enzymes links the reactions in proper sequence without the
release of the intermediates.
• 5 coenzymes are also involved in the enzymatic activity:
1. Thiamine pyrophosphate (TPP- vitamin B1 derivative). Used by E1.
2. Lipoic acid. Used by E2.
3. CoA. Used by E2.
4. FAD. Used by E3.
5. NAD+. Used by E3.
• The net reaction mediated by the pyruvate dehydrogenase complex is:
• The conversion of pyruvate into acetyl-CoA consists of 3 steps:
1. Decarboxylation (by E1): pyruvate combines with the ionized form of
TPP and is decarboxylated. Result= hydroxyethyl-TPP. This reaction is
a rate-limiting step in the synthesis of acetyl-CoA. 1 CO2 is released
in this reaction.

14. 2. Oxidation (by E2 and E1): in this reaction the hydroxyethyl group is oxidized to acetyl (from
the original pyruvate- pink) and the lipoamide (lipoic acid derivative) is reduced to break the
disulfide bond. The acetyl group is transferred to form acetyl-lipoamide.
3. Formation of acetyl-CoA (by E2): in this reaction the acetyl group is transferred from
acetyl-lipoamide to Co-A, forming acetyl-CoA.
• Although acetyl-CoA is already formed, another reaction needs to take place in order for the
complex to return to its initial structure.
• Redox: dihydrolipoamide oxidized to lipoamide, FAD reduced to FADH2.
• Later FADH oxidized and NAD+ is reduced -> resulting in NADH.
• The net reaction mediated by the pyruvate dehydrogenase complex is:

15. Regulation of the PDH complex
• The irreversible reaction in the PDH complex commits the C atoms of the pyruvate into one of
2 fates: 1. oxidation to CO2 in Krebs cycle. 2. incorporation into lipids (acetyl-CoA is a key
precursor lipid synthesis).
• Key regulatory mechanism: 2 regulatory enzymes- PDH kinase and PDH phosphatase.
• Dephosphorylation of PDH complex (specifically E1) by PDH phosphatase, activates the PDH
complex.
• Calcium is a strong activator of PDH phosphatase. Important in skeletal muscle where Ca
release during contraction stimulates also the PDH complex (energy production).
• Phosphorylation of PDH complex (specifically E1) by PDH kinase, inactivates the PDH
complex.
• PDH kinase is allosterically inhibited by pyruvate, and allosterically activated by ATP, NADH
and acetyl-CoA.
• Also the PDH complex itself, is allosterically inhibited by high concentrations of acetyl-CoA
and NADH (the products).
• Hormonal regulation of PDH complex:
 Adrenaline- increases Calcium levels in liver cells, activating PDH complex for energy
production.
 Insulin- stimulates PDH phosphatase in liver and adipose cells, activating PDH
complex to form acetyl-CoA. In this case the acetyl-CoA is used for lipid synthesis.
*** Arsenite (not arsenate) poisoning- arsenate binds to the lipoic acid, preventing from it to serve as a coenzyme ->
thus acetyl-CoA fails to form. Mercury also acts similarly. Aresante causes a failure in the glycolysis.

17. 21. Metabolism of galactose and fructose, disorders.
• Glucose is not the only monosaccharide we consume, as fructose and galactose are also
significant part of our diet. Thus, there should be a way to metabolize these molecules as well.
• Both fructose and galactose are converted to intermediates in the glycolytic pathway.
Fructose
• There are 2 possible pathways by which the fructose can enter glycolysis. One pathway occurs
in the liver, kidney and intestine, while the second occurs in most of the other tissues (e.g.
adipose tissue).
• Liver, kidney, intestine pathway:
1. Fructose -> fructose-1-phosphate (enzyme- fructokinase).
2. Fructose-1-phosphate is cleaved by the enzyme fructose-1-phosphate aldolase (also
called aldolase B). Result- DHAP (dihydroxyacetone phosphate) + glyceraldehyde.
DHAP is an intermediate of glycolysis.
3. Glyceraldehyde -> glyceraldehyde-3-phosphate (enzyme- triose kinase).
Glyceraldehyde-3-phosphate is an intermediate of glycolysis.
• Second pathway: fructose -> fructose-6-phosphate.
o Enzyme: Hexokinase.
• Hexokinase has a low affinity (high Km) for fructose, thus
unless the intracellular fructose levels become high most of
the fructose will be metabolized by the liver (fructokinase).
• That’s because fructokinase has a high affinity (low Km)
for fructose.

18. The polyol pathway
• Most sugars are phosphorylated when enter the cells to prevent them to “escape” back to the
blood. However, the polyol pathway is an alternative to this phosphorylation.
• In the polyol pathway the sugars are converted into sugar alcohols (polyol), by reduction of
their aldehyde group. This reduction is done by the enzyme aldose reductase.
• Aldose reductase is located in many tissues, and it has a high Km (low affinity), thus it needs
high levels of its substrates in order to be very active.
• The seminal vesicles, liver and ovaries use this pathway to convert glucose into fructose. In
these organs glucose converts to sorbitol (also glucitol) by the aldolase reductase. Then a
second enzyme sorbitol dehydrogenase (special only for these organs) converts sorbitol into
fructose.
• Hyperglycemia and polyol pathway: when hyperglycemia occurs and NADPH is available, aldolase
reductase activity increases leading to increased sorbitol levels in some tissues like retina and lens.
The sorbitol is “stuck” in these cells because there is no sorbitol dehydrogenase. This leads to cell
swelling (by osmotic pressure). This is one of the mechanisms by which diabetes leads to
retinopathies and cataracts, it is also one of the mechanisms in which beta cells die in the pancreas
and insulin secretion is reduced in DM type 2.

19. Galactose
• Galactose is converted into glucose-6-phosphate in 4 steps (occurs in most tissues).
1. Galactose -> galactose-1-phosphate (enzyme – galactokinase).
2. Galactose-1-phosphate acquires a uridyl group from UDP-glucose (enzyme: galactose-1-
phosphate uridyl transferase, or GALT). Result: UDP-galactose (UDP= uridine diphosphate).
3. The enzyme UDP-galactose-4-epimerase inverts the OH group on carbon 4.
Result: UDP-glucose + glucose-1-phosphate.
4. The glucose-1-phosphate produced can be converted into glucose-6-phosphate
(enzyme- phosphoglucomutase). Glucose-6-phosphate is a glycolysis intermediate.
• The “new” UDP-glucose produced (from UDP-galactose) can be used as a UDP donor for
further reactions of galactose-1-phosphate uridyl transferase (also called GALT).
• The UDP-glucose can also be
used in glycogen synthesis.
• The UDP-galactose
intermediate can be used as
a galactose donor in the
synthesis of different
glycoproteins, glycolipids,
and GAGs.

20. Fructose disorders
• Fructokinase deficiency- leads to fructosuria and high fructose levels in the blood after
fructose ingestion. However, this condition is asymptomatic. This disease is also called
essential fructosuria (it is an autosomal recessive disorder).
• Hereditary fructose intolerance- is a aldolase B deficiency, an autosomal recessive disorder.
This condition leads to accumulation of fructose-1-phosphate in the liver. This accumulation
leads to low phosphate levels in the cell -> low ATP production. The liver functions decrease
leading to hypoglycemia, jaundice, vomiting ,clotting problems, etc.
Galactose disorders
• Classic galactosemia- caused by GALT deficiency, an autosomal recessive disorder. This leads
to galactose-1-phosphate accumulation, which is also accompanied with galactose
accumulation. The accumulation of galactose-1-phosphate has a similar effect as the
hereditary fructose intolerance, just the effect is on a broader spectrum of tissues.
o In addition, the increased level of galactose is converted by aldose reductase (polyol
pathway) to galactitol. Galactitol leads to cataract and reduced intellectual ability
(the galactitol is “stuck” in the cells and leads to osmosis of water inside).
• Deficiencies in galactokinase or epimerase result in less severe symptoms than GALT
deficiency (but cause cataracts).

21. 7. Citric acid cycle, amphibolic character, course, regulation.
• The citric acid cycle is also called Krebs cycle or TCA cycle (Tri-carboxylic Acid cycle).
• The cycle is the major energy-producing pathway in the body (leads to the oxidative phosphorylation).
• The cycle also plays a role in synthesis of fatty acids, amino acids and gluconeogenesis.
• The cycle occurs in the mitochondrial matrix.
• The TCA cycle begins with the combination of oxaloacetate and acetyl-CoA to form citrate.
• The cycle includes a series of 8 reactions that result with the emission of the acetyl groups as
2 CO2 molecules and regeneration of oxaloacetate.
• In this process 3 NADH and 1 FADH2 molecules are produced. Which will produce ATP later in the
process of oxidative phosphorylation.
• The TCA cycle can be divided into 2 stages:
1. Oxidation of carbon atoms into CO2 (first 4 reactions)
2. Regeneration of oxaloacetate (last 4 reactions)
• All the enzymes in the TCA cycle are in the mitochondrial matrix with the exception of succinate
dehydrogenase, which is an integral protein of the inner mitochondrial membrane.
Net reaction in TCA cycle:

22. Stage 1- oxidation of C atoms to CO2
1st reaction: citrate synthesis
• The reaction is an irreversible condensation.
• Enzyme: citrate synthase.
• The reaction has 2 parts: first- combination of the oxaloacetate and acetyl-CoA to form citryl-CoA.
• The thioester bond in the Citryl-CoA is very energetic. Thus, its hydrolysis is energetically favorable
(ΔG < 0). This hydrolysis forms citrate.
• The binding of oxaloacetate to the enzyme increases the enzyme’s affinity to acetyl-CoA greatly.
2nd reaction: citrate isomerization
• Citrate is isomerized to isocitrate -> the OH group changes position.
• Enzyme: aconitase (named after the intermediate for cis-aconitate).
• This isomerization is needed for further oxidation reactions (tertiary -> secondary alcohol).
3rd reaction: isocitrate oxidative decarboxylation
• The reaction is irreversible. Thus, it is one of the regulatory steps in the TCA cycle.
• Enzyme: isocitrate dehydrogenase.
• Firstly, Isocitrate is oxidized and NAD+ is reduced. This redox reaction results in oxalosuccinate
which is unstable and goes through decarboxylation to α-ketoglutarate.
• In this step: gain of 1 NADH and loss of 1 CO2.

23. 4th reaction: oxidative decarboxylation of α-ketoglutarate
• The reaction is irreversible. Thus, it is one of the regulatory steps in the TCA cycle.
• The reaction is catalyzed by α-ketoglutarate dehydrogenase complex.
• This complex is very similar both structurally and functionally to the PDH complex (pyruvate
dehydrogenase complex), and is also composed of multiple copies of different enzymes.
• The α-ketoglutarate dehydrogenase complex uses the same coenzymes used by the PDH complex
(thiamine pyrophosphate, lipoic acid, CoA, NAD+, FAD) and employs a same mechanism for the
reaction.
• In this reaction: gain of 1 NADH and loss of 1 CO2.
• Comparison between the reactions of the 2 complexes:
Stage 2- regeneration of oxaloacetate
• From this point no more CO2 is produced.
5th reaction: cleavage of succinyl-CoA
• In this reaction the highly energetic thioester bond formed in the previous reaction is cleaved to
phosphorylate ADP or GDP. Thus, there is 1 ATP molecule gain here.
• Enzyme: succinate thiokinase (thio- for thioester bond, kinase for phosphorylating ADP/GDP)
• Also called succinyl-CoA synthetase for the reverse reaction.
• There are 2 forms of the enzyme in humans, one specific for ADP and another for GDP.
• In tissues that perform large amounts of cellular respiration (like skeletal and cardiac muscles) the
ADP form predominates
• In tissues that perform many anabolic
reactions (like liver) the GDP form
predominates. This type is believed to
work in the reverse direction (synthesis
of succinyl-CoA) for Heme synthesis.

24. 6th reaction: succinate oxidation
• Redox: succinate oxidized, FAD reduced to FADH2.
• Enzyme: succinate dehydrogenase.
• This enzyme differs from the other enzymes in the TCA cycle, because it is an integral protein in
the inner mitochondrial membrane.
• This is important because the FADH2 formed doesn’t dissociate from the enzyme (as occurs
with enzymes that use NAD+).
• The FADH2 transfers the H2 to coenzyme Q which is part of the oxidative phosphorylation.
• FAD is used instead of NAD+ because succinate dehydrogenase doesn’t have enough reducing
power to reduce NAD+.
7th reaction: fumarate hydration
• Enzyme: fumarase
• The hydration forms specifically L-malate
(not the enantiomer D).
8th reaction: malate oxidation
• Redox: L-malate oxidized, NAD+ reduced to NADH.
• Enzyme: malate dehydrogenase.
• This reaction is not favorable energetically (ΔG significantly positive). However, the oxidation of
malate is driven forward by the use of its products, oxaloacetate by citrate synthase and NADH by
the electron-transport chain.

25. Net reaction in TCA cycle:

26. Regulation of citric acid cycle
• 2 regulatory points by allosteric effect on the enzymes: isocitrate dehydrogenate and
α-ketoglutarate dehydrogenase complex. Both enzymes catalyze irreversible reactions.
• Isocitrate dehydrogenase:
 Allosteric inhibitors- ATP and NADH.
 Allosteric activators- ADP and calcium (Ca++ important in muscles).
• α-ketoglutarate dehydrogenase complex regulation:
 Similar to the regulation of the PDH complex (complex structurally similar too).
However, it’s not regulated covalently by other enzymes, only allosterically.
 Allosteric inhibitors- succinyl-CoA (product), ATP and NADH.
 Allosteric activators- calcium (Ca++ important in muscles).

27. Amphibolic character of the TCA cycle and its role in biosynthesis
• Amphibolic pathway is a pathway that has both catabolic and anabolic functions. Amphi- 2
sides, bolic- from metabolism.
• The catabolic nature of the cycle is in the oxidative decarboxylation resulting in energy
production (although, the first reaction forming citrate is anabolic).
• The anabolic nature of the cycle is in the fact it plays a role in biosynthesis of precursor
molecules and gluconeogenesis.
• The picture below shows how TCA cycle intermediates can be used for biosynthesis of amino
acids, fatty acids, Heme groups, purines and others.
• Similar reactions in the reverse direction can be used for gluconeogenesis.
• The regulatory points in the cycle correspond to the cycle’s “exit points”.
• Inhibition of isocitrate dehydrogenase leads to citrate accumulation, which can enter the
cytosol. The citrate then inhibits glycolysis (PFK-1 enzyme) and serves as a source for acetyl-
CoA needed for fatty acid synthesis.
• Inhibition of the α-ketoglutarate dehydrogenase complex, leads to α-ketoglutarate
accumulation. This molecule can be converted into some amino acids and purines.
Replenishing of oxaloacetate- an anaplerotic reaction
• The dual functions of the cycle presents a problem in that the molecules “exiting” the cycle for
biosynthesis of other molecules “steal” the oxaloacetate molecules needed for its initiation.
• Anaplerosis is the act of replenishing TCA cycle intermediates that have been extracted for
biosynthesis (in what are called anaplerotic reactions).
• The oxaloacetate levels are maintained by the reaction (enzyme- pyruvate carboxylase):
• This reaction also plays an important role in gluconeogenesis.

29. 5. The respiratory chain. Oxidative phosphorylation.
• The respiratory chain is the major source of ATP in the human body.
• It provides 26 out of 30 ATP molecules that are formed from 1 glucose molecule (2 from glycolysis
and 2 from TCA cycle).
• An average energy consumption of a person (2000 Kcal) = 83 kg of ATP. In the human body there
are about 250 gr of ATP which are constantly used and recycled by the respiratory chain.
• This process uses the electron-carriers NADH and FADH2 from the previous stages in metabolism
for the production of ATP.
• These molecules release their electrons in the respiratory chain, and their protons are pumped
across the inner mitochondrial membrane, creating H+ gradient across the membrane. This
gradient enables ATP production.
• The process of oxidative phosphorylation requires oxygen (is actually the truly aerobic part of
energy production). This process produces H2O as a by-product.
• The electron transport chain (also respiratory chain) is located in the inner mitochondrial
membrane. This chain is a series of protein complexes that act as electron carriers.
Mitochondria
• The outer mitochondrial membrane contains special channels called porins. These porins, make
the membrane freely permeable to most ions and small molecules.
• The inner mitochondrial membrane is impermeable to small ions, including H+ (important for the
electron transport chain). Specialized carriers and transporters are required to move molecules
across this membrane.
• The inner mitochondrial membrane is unusually rich in protein. About 50% of which participate in
oxidative phosphorylation. The membrane also has convolutions called cristae, that greatly
enlarge the membrane surface area.
• Matrix content- rich in proteins (enzymes),
ATP/ADP, free phosphates, NAD/NADH,
ribosomes, mtRNA, mtDNA.

30. Respiratory chain = electron transport chain (ETC)
• The inner mitochondrial membrane contains 4 separate protein complexes, called
complexes I, II, III, and IV. These complexes donate electrons to the relatively mobile Coenzyme Q
(not a protein) and to Cytochrome C.
Complex I NADH-Q oxidoreductase (also called NADH dehydrogenase)
Complex II Succinate-Q reductase
Complex III Q-cytochrome C oxidoreductase
Complex IV Cytochrome C oxidase
The reaction
• Transport of electrons from NADH -> FMN -> several
consecutive Fe-S centers -> Coenzyme Q.
• As the electron flow through Complex I, they lose
energy , this energy is used to pump H+ outside
across the inner mitochondrial membrane (4H+ per
NADH).
• When NADH is oxidized it releases 2 e- and 1 H+,
thus one H+ comes from the matrix to reduce FMN
(to FMNH2).
Complex I (NADH-coenzyme Q reductase):
• The largest protein complex in the electron-transport chain
(more than 40 subunits).
• This complex contains the coenzyme FMN (flavin mono-
nucleotide). FMN resembles FAD structurally and functionally.
• This complex also contains Fe-S centers (cofactors), in these
centers the iron is in Fe+3 form and can be reduced into Fe+2
form.

31. Complex II (succinate-Q reductase):
• Much smaller than complex I. Has only 4 subunits.
• Contains the enzyme succinate dehydrogenase, part of the citric acid cycle. During the citric acid
cycle, succinate dehydrogenase reduces its FAD coenzyme to FADH2.
• The complex also contains Fe-S centers.
Reaction
• Transport of electrons from FADH2 -> Fe-S
centers -> Coenzyme Q.
• Unlike the other complexes, the electron flow
through the complex doesn’t pump H+ out.
Coenzyme Q
• Not a protein! It is a quinone derivative with a long hydrophobic isoprenoid tail. It is made from
an intermediate of cholesterol synthesis.
• Also called ubiquinone.
• Coenzyme Q is mobile and can move laterally through the membrane.
• Function- an electron carrier that transfers e- from complexes I and II to Complex III.
• When CoQ is activated, it receives 2H+ from the matrix and 2e- from Fe-S centers. Result- CoQH2.
• CoQ can also transfer electrons from the enzymes acyl-CoA dehydrogenase and glycerol-3-
phosphate dehydrogenase (important in some metabolic pathways).

32. Complex III (Q-cytochrome C oxidoreductase)
• Has 11 subunits and Contains Fe-S centers.
• Also Contains cytochromes. Cytochrome is a protein that contains a heme group. A Heme group
has a porphyrin ring with a Fe atom at its center. The Fe atom is capable of reversible reduction
and oxidation (Fe+3 <----> Fe+2).
• Unlike the heme of hemoglobin, where the Fe normally shouldn’t be oxidized.
• There are 2 cytochromes in complex III: cytochrome b and Cytochrome c1.
Reaction:
• CoQH2 transfers the electrons to complex III. Complex III moves the electrons as in the picture
until they are transferred to cytochrome C.
• The flow of e- through the complex is accompanied by pumping 4H+ out.
Cytochrome c
• Cytochrome C is a mobile electron carrier, meaning it can move laterally through the membrane.
• Function- transfers the electrons from complex III to complex IV.
Complex IV (Cytochrome C oxidase)
• Has 13 subunits, including 2 cytochromes: cytochrome a and cytochrome a3.
• Each of the cytochromes has a Cu ions associated with it (in addition to the Fe).
• The Cu ions are reduced and oxidized (Cu+2 <----> Cu+).
• In the final step of the electron transport chain, complex IV reduces O2 molecules into H2O, using
the electron flow from the complex and free H+ from the matrix.
• The flow of e- through the complex is accompanied by pumping 2H+ out.

33. • Inhibitors of the ETC. Bind to a component in
the chain blocking redox reactions for electron
transport.
• Inhibits ATP production.

34. ATP synthase
• The electron flow through the electron transport chain, led to the pumping of H+ from the matrix
into the intermembrane space.
• The pumping causes an H+ concentration difference on the 2 sides of the inner membrane. This
causes a electro-chemical gradient that is used by the ATP synthase complex to generate ATP.
• ATP synthase structure: F0 domain- inside the inner mitochondrial membrane.
F1 domain- protrudes into the matrix.
• Protons from the intermembrane space re-enter the matrix via an H+ channel at the F0 domain.
The passage of H+ through this domain rotates the c ring in it.
• This rotation leads to conformational changes in the β units in F1 domain. F1 domain
phosphorylates ADP + Pi --> ATP.
• The ATP production by the ATP synthase and the electron transport chain are coupled. Meaning
that increasing (or decreasing) one process leads to the same effect on the other process.
• Uncoupling proteins- are proteins that occur on the inner mitochondrial membrane, they allow
passage of H+ into the matrix without production of ATP. However, this passage releases energy
in the form of heat (non-shivering thermogenesis).

35. Membrane transport systems
• ADP and ATP transport: the ATP produced needs to be transported into the cytosol for the cell
functions, while ADP needs to be enter the mitochondrial matrix for conversion by ATP synthase.
Thus, the inner mitochondrial membrane contains ADP/ATP translocase, an antiporter that
transfers 1ADP inside and 1ATP outside.
• Pi transport: done by phosphate translocase a symporter of 1H+ and 1Pi, on the inner
mitochondrial membrane.
• NADH transport via substrate-shuttles: the NADH produced in the glycolysis needs to be used by
the ECT for ATP production, but the membrane has no NADH transporters. Thus, the glycerol-3-
phosphate and malate-aspartate shuttles are used.
o Glycerol-3-phosphate: in the cytosol NADH is oxidized into NAD+ and DHAP is reduced
into glycerol-3-phosphate. The reaction is catalyzed by cytosolic glycerophosphate
dehydrogenase. Glycerol-3-phosphate can be transported into the matrix. In the matrix
mitochondrial glycerophosphate dehydrogenase reconverts G3P into DHAP, coupled with
FAD->FADH2. FADH2 transfers its electrons to coenzyme Q.
o Malate-aspartate shuttles: shown in the picture, forms NADH in matrix (not FADH2). The
NADH is oxidized by complex I. Video explaining:https://www.youtube.com/watch?v=tTHsED20s1o

37. 18. Gluconeogenesis, regulation
• The brain’s major fuel is glucose and RBC only fuel is glucose. Thus, the ability to synthesize
glucose from non-carbohydrate precursors is important. This process is called
gluconeogenesis.
• This process is especially important at times of prolonged fasting. The glycogen stores can
sustain the glucose levels for about a day, but for longer fasting periods gluconeogenesis is
essential.
• The major site of gluconeogenesis is the liver. The kidney is also able to perform significant
amounts of gluconeogenesis (up to 40% of total gluconeogenesis in very prolonged fasting).
• The major precursors for gluconeogenesis are lactate, amino acids and glycerol.
Remember: Fatty acids cannot convert to glucose, convert to acetyl-CoA and later to ketone bodies.
• Gluconeogenesis involves a pathway from pyruvate -> glucose. The non-carbohydrate
precursors of gluconeogenesis are converted to pyruvate or to another intermediate in the
pathway in order to synthesize glucose.
• Gluconeogenesis is not a complete reversal of glycolysis, because the reactions of hexokinase,
phosphofructokinase and pyruvate kinase are irreversible. Thus, these reactions need to be
bypassed.
The pyruvate -> glucose pathway
1st reaction – pyruvate carboxylation
• Enzyme: pyruvate carboxylase. Co-enzyme: biotin (vitamin B7).
• This reaction occurs in the mitochondria of kidney and liver cells.
• This reaction can have 2 purposes:
1. Initiation of gluconeogenesis.
2. Replenishing oxaloacetate stores for the citric acid cycle (anaplerotic reaction).
• The ATP hydrolysis is needed to bind CO2 to the enzyme-biotin complex (CO2 from HCO3-).
Then the CO2 is transferred to the pyruvate as a carboxyl group.

38. 2nd reaction – oxaloacetate transport into cytosol
• In order to transport oxaloacetate to the cytosol it has to be converted into malate
(oxaloacetate can’t cross the mitochondrial membrane).
• In the cytosol malate is converted back to oxaloacetate.
• Oxaloacetate -> malate enzyme: mitochondrial malate dehydrogenase (part of citric acid cycle).
• Malate -> oxaloacetate enzyme: cytosolic malate dehydrogenase (in cytosol).
• The cytosolic reaction involves reduction of NAD+ -> NADH. This NADH is needed for further
reactions in the pathway.
3rd reaction – phosphoenolpyruvate (PEP) formation
• Enzyme: phosphoenolpyruvate carboxykinase
• This enzyme both phosphorylates and decarboxylates the
oxaloacetate to form phosphoenolpyruvate (a glycolysis
intermediate).
• The phosphate donor is GTP.
• The aim of all the reactions until now was to bypass the
unidirectional pyruvate kinase reaction from glycolysis.

40. • From phosphoenolpyruvate the pathway continues as a reverse glycolysis until it gets to
fructose 1,6-bisphosphate.
Dephosphorylation of fructose 1,6-bisphosphate
• Enzyme: fructose-1,6-bisphosphatase
• Product: fructose-6-phosphate
• This enzyme bypasses the unidirectional reaction of
phosphofructokinase in glycolysis.
Glucose formation
• Fructose-6-phosphate converts into glucose-6-phosphate (reverse of glycolysis, by
phosphoglucose isomerase).
• Then the glucose-6-phosphate is converted into glucose.
• Enzyme: glucose-6-phosphatase. The enzyme is bound to the endoplasmic reticulum
membrane (thus the reaction is in the ER, not cytosol).
• This enzyme bypasses the action of the irreversible hexokinase/glucokinase enzymes in
glycolysis.
• The transport proteins in the ER membrane are called glucose-6-phosphate translocase.
• This step is also a part of liver glycogenolysis.

41. Precursors conversion into gluconeogenesis pathway intermediates
• Glycerol- released during TAG hydrolysis in adipose tissue. In the liver, glycerol is
phosphorylated into glycerol-3-phosphate and then it’s oxidized into DHAP (dihydroxyacetone
phosphate). DHAP can enter both glycolysis and gluconeogenesis.
• Amino acids- glucogenic amino acids (all except leucine and lysine), can convert into
intermediates of the citric acid cycle. Thus, they can become oxaloacetate and enter the
gluconeogenesis pathway.
• Lactate- produced by skeletal muscles and RBC in anaerobic respiration. The lactate is taken
up by the liver and converted back into pyruvate (by lactate dehydrogenase). Then the
pyruvate goes through the gluconeogenesis pathway and is released as glucose into the blood.
This process is the Cori cycle.
o Some slow-twitch skeletal muscle fibers and some cardiac muscle cells have carriers
for lactate and they can use lactate as a fuel. They convert the lactate into pyruvate
and then metabolize it in the citric acid cycle.

42. Regulation of gluconeogenesis
• Gluconeogenesis and glycolysis are regulated in a way that they cannot be highly active at the
same time. If glycolysis is highly active gluconeogenesis is inactive and vice versa.
• The basic principle is that when glucose is abundant, glycolysis predominates. While, when
glucose is scarce, gluconeogenesis takes over.
• In gluconeogenesis the activity of the enzymes pyruvate carboxylase, PEP carboxykinase, and
fructose-1,6-bisphosphatase is regulated.
Fructose-1,6-bisphosphatase
• The main regulatory enzyme.
• Activated by citrate, which its presence in the cytosol with high levels signals an energy-rich
situation. Citrate also deactivates phosphofructokinase from glycolysis.
• Inhibited by AMP, which its presence indicates an energy shortage in the cell. AMP also
activates phosphofructokinase from glycolysis.
• Inhibited by fructose-2,6-bisphosphate, a molecule that its levels are regulated by the
insulin/glucagon ratio. Fructose-2,6-bisphosphate also activates phosphofructokinase in
glycolysis.

43. Pyruvate carboxylase
• Allosterically regulated by Acetyl-CoA levels in the mitochondria.
• Higher levels of acetyl-CoA -> increase oxaloacetate formation by pyruvate carboxylase (these
levels also inhibit the PDH complex for citric acid cycle).
• Low levels of acetyl-CoA -> inactivate pyruvate carboxylase, and the pyruvate is oxidized by
the PDH complex and enters the citric acid cycle.
Glucagon influence on gluconeogenesis
• Glucagon reduces fructose-2,6-phosphate levels, due to its effect on phosphofructokinase-2.
• This enzyme is a bifunctional protein with a phosphofructokinase domain and
a fructose-2,6-phosphatase domain.
• High glucagon -> cAMP -> protein kinase A activated -> the phosphatase domain activated ->
low fructose-2,6-phosphate (converted to fructose-6-phosphate).
• In addition, protein kinase A deactivates pyruvate kinase from glycolysis. This diverts PEP into
the gluconeogenic pathway.
• Glucagon (cortisol too) also increases the gene expression of PEP carboxykinase. Insulin
inhibits this gene expression.
• During fasting, lipolysis occurs and fatty acids are
metabolized into acetyl-CoA in the liver. This flooding of
the liver with acetyl-CoA drives pyruvate into
gluconeogenesis.
• ADP inhibits pyruvate carboxylase activity and it also
inhibits the activity of PEP carboxykinase.

44. As seen in the picture, the “price” for bypassing the irreversible reactions of the glycolysis is to
“spend” 4 more phosphate carrier molecules.
Summary

45. 19. Synthesis and degradation of glycogen, regulation.
• Glycogen acts as a glucose storage molecule. Since glucose is essential for some cells like the
brain and RBC, its levels in the blood need to be maintained even under fasting conditions.
• The main glycogen stores in the body are the liver and skeletal muscles.
• The liver stores about 100g of glycogen. This glycogen is used to maintain the blood glucose
levels during fasting. This glycogen is able to sustain the glucose levels for about 24 hours.
• The glycogen in the skeletal muscle supplies the muscles metabolic needs during anaerobic
respiration. Thus, it doesn’t release glucose into the blood. The muscles contain about 400g of
glycogen.
Glycogen Synthesis
UDP-glucose formation
• The glucose donor for glycogen synthesis is UDP-glucose (UDP= uridine diphosphate).
• UDP-glucose is synthesized from UTP + glucose-1-phosphate, by the enzyme UDP-glucose
pyrophosphorylase.
• The hydrolysis of pyrophosphate (a product of the UDP-glucose formation) drives the reaction
forward. This hydrolysis is done by the enzyme pyrophosphatase.
• Glucose-1-phosphate is formed by isomerization of glucose-6-phosphate, by the enzyme
phosphoglucomutase.

46. Glycogen synthase
• Glycogen synthase is the enzyme that polymerizes the glycogen with adding new glucose units.
The glucose donor is UDP-glucose.
• The enzyme needs a fragment of glycogen to serve as a primer for polymerization.
• In the absence of a glycogen primer, the enzyme glycogenin adds glucose units to itself. Addition
of glucose to glycogenin occurs on the OH group of a specific tyrosine residue. In this way at least 4
glucose molecules are polymerized to the tyrosine residue.
• Glycogen synthase is able to add glucose molecules to the glucose chain bound to the glycogenin.
• Thus, it can be understood that glycogenin is the core of each glycogen molecule
• Glycogen synthase forms new α-1,4 glycosidic bonds. The action of glycogen synthase is in the
nonreducing end of the glucose chain polymerized.
• Reminder: nonreducing end = the glucose unit that its anomeric carbon is a part of a glycosidic
bond (anomeric carbon = chiral carbon in sugar molecule).
• The glycosidic bond involves C1 of the UDP-glucose and C4 of the glucose chain.
Branching of glycogen
• Formation of α-1,6 glycosidic bonds forms branches in the
glycogen molecule.
• These branches make the glycogen more soluble, and it increases
the nonreducing ends in the molecule that can be elongated.
• The enzyme responsible for this branching is called 4:6 transferase
(or just branching enzyme). This enzyme removes a set of 6-8
glucose units from the chain and attaches it to a nonterminal
glucose in the chain (by forming α-1,6 glycosidic bond)

47. Glycogenolysis (glycogen degradation)
Glycogen phosphorylase
• Glycogen phosphorylae is an enzyme that cleaves a glucose molecule from glycogen by adding a
phosphate group to it. The product is glucoe-1-phosphate.
• Coenzyme: pyridoxal phosphate (vitamin B6 derivative).
• The enzyme cleaves α-1,4 glycosidic bonds.
Glycogen debranching and remodeling
• The glycogen phosphorylase enzyme cannot cleave α-1,6 glycosidic bonds. Thus, at some point it
will stop cleaving due to the branching points with these types of bonds. The point in which the
enzyme stops cleaving is 4 glucose units away from the branch point.
• Thus, there is a need in remodeling the glycogen so glucose cleavage could continue.
• The first step in remodeling is to transfer a set of 3 glucose units from the 4 units branch to
another branch. This action is done by the enzyme 4:4 transferase.
• The 4:4 transferase cleaves the 3 glucose chain and adds it to another chain by forming a new
α-1,4 glycosidic bond.
• The enzyme α-1,6 glucosidase hydrolyzes the α-1,6 glycosidic bond, releasing the last glucose unit.
This unit is released in the form of a free glucose molecule.
• The glucose-1-phosphate molecules released by glycogen phosphorylase are converted to
glucose-6-phosphate (glycolysis and gluconeogenesis intermediate) by the enzyme
phosphoglucomutase.
• Free glucose molecules are released by the liver after glucose-6-phosphate is converted back to
glucose. This conversion is done by the ER enzyme glucose-6-phosphate phosphatase (like in
gluconeogenesis). Muscle cells lack this enzyme thus they don’t release glucose into the blood.

48. Regulation of glycogenolysis
• The main regulatory point is the activity of glycogen phosphorylase.
• Glycogen phosphorylase is regulated both by allosteric effectors that signal the energy state
of the cell, and by reversible phosphorylation. The phosphorylation is a result of hormonal
regulation by glucagon, epinephrine and insulin.
• Glycogen phosphorylase exists in 2 isozymes, a liver isozyme and a muscle isozyme.
• The regulation of each isozyme is somewhat different (makes sense, the function of
glycogenolysis differs between the tissues).
Allosteric regulation
• The liver isozyme (phosphorylase a) is generally in R state (R for relaxed, more active state).
This enzyme is allosterically inhibited by glucose. Thus, when the glucose levels in the cell are
sufficient there is no need to degrade glycogen. The glucose binding shifts the enzyme to the
T state (tensed, less active).
o The liver isozyme is also allosterically inhibited by ATP and glucose-6-phosphate.
• The muscle isozyme (phosphorylase b) is generally in T state (less active). This enzyme is
allosterically activated by AMP. Thus, when there is shortage in energy, glycogenolysis
is activated. The binding of the AMP shifts the enzyme to the R state.
o The muscle isozyme is allosterically inhibited by ATP and glucose-6-phosphate. These
molecules compete with AMP on the same allosteric binding site.

49. Hormonal regulation
• Glucagon and epinephrine: bind receptors (G-protein coupled receptors) -> cAMP ->
Protein kinase A is activation -> phosphorylase kinase a activation -> glycogen
phosphorylase is activated.
• Insulin: activates protein phosphatase-1. This protein dephosphorylates phosphorylase
kinase and glycogen phosphorylase, inhibiting glycogenolysis.

50. Regulation of glycogen synthesis
• The main regulatory point is the activity of glycogen synthase.
• Like glycogen phosphorylase it is regulated by both allosteric effectors and hormones (via
phosphorylation).
• Glycogen synthase exists in 2 isozymes (as glycogen phosphorylase), a liver isozyme and a
muscle isozyme.
Allosteric regulation
• Both the liver and muscle glycogen synthase isozymes are
allosterically activated by glucose-6-phosphate.
Hormonal regulation
• Epinephrine and glucagon: same pathway as in the
previous page. This pathway activates (by cAMP) protein
kinase A, and also activates glycogen synthase kinase.
• These enzymes phosphorylate glycogen synthase.
• Unlike glycogen phosphorylase, the phosphorylated form
of glycogen synthase is the inactive form.
• Thus, glucagon and epinephrine inhibit glycogen synthesis.
• Insulin: activates protein phosphatase-1, which
dephosphorylates glucagon synthase. Thus, activating it
and initiating glycogen synthesis.
• These regulatory mechanisms make sure that glycogen
synthesis and glycogenolysis cannot be activated
simultaneously.

52. 20. Pentose phosphate cycle, regulation.
• The function of the pentose phosphate cycle is to produce NADPH from glucose-6-phosphate,
and it also enables the production of pentose sugars (5-carbon) from 3-carbon and 6-carbon
sugars. The pentose sugars are required for DNA and RNA synthesis.
• The pentose phosphate cycle can be divided into 2 parts: irreversible oxidative reactions and
reversible nonoxidative reactions.
Irreversible oxidative reactions
• Overview of the irreversible oxidative reactions:
1st reaction: glucose-6-phosphate dehydrogenation
• Enzyme: glucose-6-phosphate dehydrogenase. Product: 6-phosphogluconolactone.
• The reaction converts NADP+ -> NADPH.
• This reaction commits for the formation of ribulose-5-phosphate.
2nd reaction: hydrolyzation
• Enzyme: gluconolactonase.
• Product: 6-phosphogluconate.
3rd reaction: Ribulose-5-phosphate formation
• Enzyme: 6-phosphoglutonate dehydrogenase.
• The reaction converts NADP+ -> NADPH.
• The reaction releases a CO2 molecule.

53. Regulation of the irreversible oxidative reactions
• Because glucose-6-phosphate is a component of both glycolysis and the pentose phosphate
pathway, there is a regulatory mechanism that “decides” which pathway it should take.
• NADPH is a competitive inhibitor of NADP+ for binding the glucose-6-phosphate
dehydrogenase.
• Thus, when NADPH concentration is high the irreversible oxidative reactions are inhibited.
• When there is demand for NADPH in the cells and the NADP+ levels increase the pathway is
activated.
NADPH uses
• NADPH acts as an electron donor for several metabolic processes. Like: fatty acid synthesis,
cholesterol synthesis and steroid hormones synthesis.
• In addition, NADPH is an electron donor that reduces oxidized glutathione. Thus, it maintains
the levels of reduced glutathione, an anti-oxidant that protects cells from ROS (reactive
oxygen species).
• NADPH is an electron donor needed for the activity of cytochrome P450 enzymes. These
enzymes are needed for the detoxification of drugs, toxins and other foreign compounds.
• NADPH is also an electron donor needed for the activity of phagocytotic leukocytes. The
NADPH is needed (electron donor) for the activity of NADPH oxidase, a lysosomal enzyme that
produces superoxide radical that breaks down the ingested bacteria.

54. Reversible nonoxidative reactions
• The nonoxidative reactions occur in all nucleotide synthesizing cells.
• In this reactions ribulose-5-phosphate is converted to ribose-5-phosphate.
• Ribose-5-phosphate can be used for nucleotide synthesis, or it can be converted into
intermediates of glycolysis.
1st reaction: formation of ribose-5-phosphate
• Enzyme: phosphopentose isomerase
• Many tissues (the ones from the previous
page) need NADPH much more than they
need ribose-5-phosphate. Thus, they
convert the ribose-5-psphate into glycolysis
intermediates instead to use it for
nucleotide synthesis.
Formation of glycolysis intermediates
• The net result of this process is formation of 2 hexoses and 1 triose from 3 pentoses.
• The triose is glyceraldehyde-3-phosphate and the hexoses are fructose-6-phosphate.
• The process involves isomerization of ribulose-5-phosphate into xylulose-5-phosphate
(enzyme-phosphopentose epimerase).
• This process involves the enzymes transketolase and transaldolase.

57. 22. Metabolism of glucuronic acid and its significance in organism.
Structure of glucuronic acid
• Glucuronic acid is the sugar acid of glucose, meaning it has a carboxyl group in carbon 6.
• Not to be confused with gluconic acid !!!, where the carboxyl is in carbon 1.
• Like glucose, glucuronic acid can exist as a linear compound (1%) or as a cyclic hemiacetal (99%).
Glucuronic acid synthesis and functions
• Glucuronic acid is synthesized from UDP-glucose by the enzyme UDP-glucose dehydrogenase.
The reaction involves the conversion of 2NAD+ -> 2NADH.
• The product is UDP-glucuronic acid which is an activated carrier than can attach the
glucuronic acid to other molecules.
• The pathway for producing UDP-glucose is explained in the glycogen synthesis question.
• Glucuronic acid has 2 major metabolic functions in the body:
1. Glucuronidation, is a process in which glucuronic acid is
conjugated to lipophilic compounds to make them much more
polar, for their excretion from the body.
o It occurs mainly in the liver, but occurs also in other tissues to
lesser extent (e.g. kidney, intestine, etc.).
o This is done to bilirubin, steroid hormones, and for
detoxification of certain drugs.
o The glucuronic acid is conjugated by
UDP-glucuronosyltransferase enzymes.
o The UDP-glucuronic acid is associated with some of the
Cytochrome P450 enzymes.
2. Glucuronic acid is used for the synthesis of GAGs
(glycosaminoglycans) and proteoglycans. Examples: hyaluronic
acid, chondroitin sulfate, heparin etc.
** in other animals and plants glucuronic acid is a precursor of ascorbic acid.
Humans lack the enzyme gulonolactone oxidase for ascorbic acid synthesis.

58. Catabolism of glucuronic acid
• Free glucuronic acid can be obtained from the diet or from lysosomal degradation of GAGs.
• Using the uronic acid pathway, glucuronic acid can be catabolized into xylulose-5-phosphate
and be incorporated into the pentose phosphate pathway, in order to produce intermediates
of glycolysis (F6P or GAP).
• This pathway is also used for dietary xylulose.