BioChemistry

Biochemical Energy
Introduction to the metabolism
and Enzymes

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 All living things do mechanical work.
• Microorganisms engulf food
• Plants bend toward the sun
• Animals move about.

Needed

In animals, it is the energy extracted from food and

released in the exquisitely
‫ رائع‬reactions of metabolism that allows work to be
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 All animals are powered by the cellular oxidation of
biomolecules containing mainly carbon, hydrogen,
and oxygen.

The products of this biological oxidation are :

Living organisms energy comes from the

sun. Photosynthesis in plants converts
sunlight to potential energy stored as
carbohydrates.
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 Carbohydrates are synthesized by green plants
during photosynthesis.

A complex process in which sunlight provides the

energy to convert CO2 and H2O into glucose plus
oxygen.

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 Organization of the Chemistry of Life
into Metabolic Pathways
• A metabolic pathway has many steps
– That begin with a specific molecule and end with a
product
– That are each catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3

A B C D
Reaction 1 Reaction 2 Reaction 3
Starting Product
molecule
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The sum of organic reactions that take place in
cells is called metabolism.
These reactions usually occur in long sequences
either linear or cyclic.
✓ In a linear sequence, the product of one reaction
serves as the starting material for the next.
✓ In a cyclic sequence, a series of reactions
regenerates the first reactant and produces other
products along the way.

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 Enzymes
• Enzymes are usually proteins that
increase the rate of reactions without
being changed in the overall process.
• Enzymes, in general, provide:
1- speed.

2- specificity.

3- regulatory control to reactions in the body.

• Among the many biologic reactions that

are energetically possible, enzymes
 selectively channel reactants called
substrates into useful pathways.
• Emil Fischer proposed that a substrate
molecule fits into the enzyme active site
like a key in a lock. This simple idea has
been widely embraced, in part because it
appears to explain the exquisite
substrate specificity of enzymes.
Enzyme-catalyzed reactions have three basic
steps:
 1. Binding of substrate: E + S ES.
2. Conversion of bound substrate to bound product:
ES EP.
3. Release of product: EP E+P

An enzyme binds the substrates of the reaction it

catalyzes and brings them together at the right
orientation to react very efficiently. The enzyme
then participates in the making and breaking of
bonds required for product formation, releases the
 products, and returns to its original state once the
reaction is completed.

Hydrolysis is using water to (break) a bond.

Proteolysis is the hydrolysis of a peptide bond in a
protein, a reaction catalyzed by enzymes called
proteases.
Chymotrypsin is an enzymes that utilize to hydrolysis
reaction, an OH- from water is added to the carbonyl
carbon of the peptide bond, and an H+ to the N, thereby
cleaving the bond.
 Chymotrypsin also can catalyze the hydrolysis of ester
bonds. An artificial substrate such as p-nitrophenylacetate
(an ester) is readily hydrolyzed by the action of
chymotrypsin:
The p-nitrophenolate reaction product is bright yellow, so
the progress of the reaction can be easily monitored in a
spectrophotometer at 410 nm.
Keep in mind that even within an organism,
more than one protein may catalyze a given
chemical reaction.
Multiple enzymes catalyzing the same reaction
are called isozymes. Although they usually
share a common evolutionary origin, isozymes
differ in their catalytic properties. Consequently,
the various isozymes that are expressed in
different tissues or at different developmental
stages can perform slightly different metabolic
functions.

Energy changes occurring during the reaction

All chemical reactions have an energy barrier
separating the reactants and the products. This
barrier called the free energy of activation or
activation energy. A enzymatic catalyst,
decreases the activation energy barrier (delta
G‡) of a reaction. It does so by interacting with
the reacting molecules such that they are more
likely to assume the transition state.
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 Al- Bayan University Biochemistry
2nd Year Dr. Mustafa saleem
2024 / 2025 Chemistry of Carbohydrates
Lec 3

CHEMISTRY OF CARBOHYDRATES
INTRODUCTION

• The carbohydrates are widely distributed both in animal and plant tissues.
• Chemically, they contain the elements carbon, hydrogen and oxygen.
• The empirical formula of many simple carbohydrates is [CH2O]n.
• The name “carbohydrate”, i.e. hydrated carbon. They are also called
“saccharides”. In Greek, saccharon means sugar.
• Although many common carbohydrates confirm the empirical formula [CH2O]n,
others like deoxyribose, rhamnohexos do not.
• Some carbohydrates also contain nitrogen, phosphorus or sulfur.

DEFINITION, CLASSIFICATION AND FUNCTIONS OF CARBOHYDRATES

• Carbohydrates may be defined chemically as aldehyde or ketone derivatives of

polyhydroxy (more than one hydroxy group) alcohols or as compounds that
yield these derivatives on hydrolysis.

FUNCTIONS OF CARBOHYDRATES

• Carbohydrates have a wide range of functions. The following are few of them:
➢ Source of energy for living beings, e.g. glucose
➢ Storage form of energy, e.g. glycogen in animal tissue and starch in plants
➢ Serve as structural component, e.g. glycosaminoglycans in humans, cellulose in
plants and chitin in insects
➢ Non-digestable carbohydrates like cellulose, serve as dietary fibers
➢ Constituent of nucleic acids RNA and DNA, e.g. ribose and deoxyribose sugar
➢ Play a role in lubrication, cellular intercommunication and immunity
➢ Carbohydrates are also involved in detoxification, e.g. glucuronic acid.

CLASSIFICATION OF CARBOHYDRATES

• Carbohydrates are classified according to the hydrolysis products into four

main groups as follows:
➢ Monosaccharides: contain one monosaccharide unit.
➢ Disaccharides: contain 2 monosaccharide units per molecule.
➢ Oligosaccharides: contain from 3 to 10 monosaccharide units per molecule.
➢ Polysaccharides: contain more than 10 monosaccharide units per molecule.

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 Al- Bayan University Biochemistry
2nd Year Dr. Mustafa saleem
2024 / 2025 Chemistry of Carbohydrates
Lec 3

Figure 1: Carbohydrates Classification

MONOSACCHARIDES (Greek: Mono = one)

• Monosaccharides are also called simple sugars.

• The term sugar is applied to carbohydrates that are soluble in water and sweet
to taste.
• They consist of a single polyhydroxy aldehyde or ketone unit, and thus cannot
be hydrolyzed into a simpler form.
• They may be subdivided into two groups as follows:

1. Depending upon the number of carbon atoms they possess, e.g.

➢ Trioses ➢ Hexoses
➢ Tetroses ➢ Heptoses.
➢ Pentoses

2. Depending upon the functional aldehyde (CHO) or ketone (C=O) group present:
➢ Aldoses
➢ Ketoses.

NOTE: The most abundant monosaccharide in nature is the six carbon sugar-D-glucose.

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 Al- Bayan University Biochemistry
2nd Year Dr. Mustafa saleem
2024 / 2025 Chemistry of Carbohydrates
Lec 3

Table 1: Biologically important monosaccharides

DISACCHARIDES

• Disaccharides consist of two monosaccharides united together by glycosidic

linkage, are the most abundant in nature
• They are crystalline, water soluble and sweet to taste.
• They are sub classified on the basis of the presence or absence of free reducing
(aldehyde or ketone) group.
➢ Reducing disaccharides with free aldehyde or keto group, e.g. maltose, lactose
➢ Non-reducing disaccharides with no free aldehyde or keto group, e.g. sucrose.
1. Sucrose (Sucrose contains glucose and fructose)
2. Maltose and isomaltose (Maltose contains two glucose residues).
3. Lactose. (Lactose contains glucose and galactose)

OLIGOSACCHARIDES (Greek: oligo = few)

• Oligosaccharides consist of a short chain of monosaccharide units (3 to 10

units), joined together by a characteristic bond called glycosidic bond.
• On hydrolysis, gives three to ten molecules of simple sugar (monosaccharide)
units.

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 Al- Bayan University Biochemistry
2nd Year Dr. Mustafa saleem
2024 / 2025 Chemistry of Carbohydrates
Lec 3

• Oligosaccharides are subdivided into different groups based on the number of

monosaccharide units present.
• Oligosaccharides with more than three subunits are usually found in
glycoproteins; such as blood group antigens.

POLYSACCHARIDES (Greek: Poly = many) or GLYCANS

• Polysaccharides are polymers consisting of hundreds or thousands of

monosaccharide units.
• They are also called glycans or complex carbohydrates.
• They may be either linear, (e.g. cellulose) or branched, (e.g. glycogen) in
structure.
• Polysaccharides have high molecular weight and are only sparingly soluble in
water.
• They are not sweetish and do not exhibit any of the properties of aldehyde or
ketone group. Polysaccharides are of two types.
➢ Homopolysaccharides (homoglycans): are composed of single kind of
monosaccharides, e.g. starch, glycogen and cellulose.
➢ Heteropolysaccharides (heteroglycans): are composed of two or more different
monosaccharides, e.g. hyaluronic acid, chondroitin sulfate, Glycosaminoglycans
or Mucopolysaccharides

GLYCOSIDE FORMATION

• A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a

carbohydrate (sugar) molecule to another group, which may or may not be
another carbohydrate.
• Glycosides are formed when the hydroxyl group of anomeric carbon of a
monosaccharide reacts with OH or NH group of second compound that may or
may not be a carbohydrate. The formed bond is known as glycosidic or glycosyl
bond
• There are two types of glycosidic bonds - 1,4 alpha and 1,4 beta glycosidic
bonds.
• The monosaccharides are joined by glycosidic bonds to form disaccharides,
oligosaccharides and polysaccharides.

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 Al- Bayan University Biochemistry
2nd Year Dr. mustafa
2022 / 2023 Chemistry of Carbohydrates

• In disaccharides, the glycosidic linkage may be either α or β depending on the

configuration of the atom attached to the anomeric carbon of the sugar (Figure 2).
• The formation of an acetal (or ketal) bond between two monosaccharides is called
a glycosidic bond or glycosidic linkage. Therefore, disaccharides are sugars
composed of two monosaccharide units that are joined by a carbon–oxygen-
carbon linkage known as a glycosidic linkage.

Figure 2: glycosidic or glycosyl bond.

STRUCTURE OF GLUCOSE

• Physiologically and biomedically, glucose

is the most important monosaccharide.
• The structure of glucose can be
represented in the following ways (Figure 3):
1. The straight chain structural formula
(Fisher projection).
2. Cyclic formula (Ring structure or Haworth
projection)
• Monosaccharide in solution is mainly
present in ring form. In solution, aldehyde
(CHO) or ketone (C=O) group of
monosaccharide react with a hydroxy (OH)
group of the same molecule forming a bond
Figure 3: Structure of D-Glucose
hemiacetal or hemiketal respectively.
• The aldehyde group of glucose at C-1 reacts
with alcohol (OH) group of C-5 or C-4 to form either six membered ring
called glucopyranose or five membered ring called glucofuranose, respectively.
(Figure 3)

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 Al- Bayan University Biochemistry
2nd Year Dr. mustafa
2022 / 2023 Chemistry of Carbohydrates

ISOMERISM

• The compounds possessing identical molecular formula but different structures

are referred to as isomers.
• The phenomenon of existence of isomers is called isomerism. (Greek ‘isos’ means
equal, ‘meros’ means parts).
• The five types of isomerism exhibited by sugar are as follows:
1. Ketose-aldose isomerism
2. D and L isomerism
3. Optical isomerism
4. Epimerism
5. Anomerism.

Ketose-Aldose isomerism

• Glucose and fructose are isomers of each other

having the same chemical (molecular) formula
C6H12O6, but they differ in structural formula with
respect to their functional groups.
• There is a keto group in position two of fructose
and an aldehyde group in position one of glucose Figure 4: Ketose-Aldose
(Figure 4). This type of isomerism is known as isomerism
ketose-aldose isomerism.

D and L isomerism

• D and L isomerism depends on the

orientation of the H and OH groups
around the asymmetric carbon atom
adjacent to the terminal primary alcohol
carbon, e.g. carbon atom number 5 in
glucose determines whether the sugar
belongs to D or L isomer.

Figure 5: D and L isomers (enantiomeric

pairs) of glyceraldehyde and glucose
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 Al- Bayan University Biochemistry
2nd Year Dr. mustafa
2022 / 2023 Chemistry of Carbohydrates

• When OH group on this carbon atom is on the right, it belongs to D-series,

when it is on the left; it is the member of the L-series.
• The structures of D and L glucose based on the reference monosaccharide, D and
L glyceraldehyde, a three carbon sugar (Figure 5).
• D and L isomers are mirror images of each other. These two forms are called
enantiomers.
• Most of the monosaccharides in the living beings belong to the D-series.

Optical Isomerism

• The presence of asymmetric carbon atoms exhibits optical activity on the

compound. Optical activity is the capacity of a
substance to rotate the plane polarized light
passing through it.
• When a beam of plane-polarized light is passed
through a solution of an optical isomer, it will be
rotated either to the right and is said to be
dextrorotatary (d) or (+) or to the left and is said
to be, levorotatory (l) or (-).
• When equal amount of D and L isomers are
present, the resulting mixture has no optical
activity.
• Since the activity of each isomer cancel one
another, such a mixture is said to be a racemic or
dl mixture. Epimerism
• When two monosaccharides differ from each Figure 6: Epimers of glucose
Other in their configuration around a single
asymmetric carbon (other than anomeric carbon) atom, they are referred to as
epimers of each other.
• For example, galactose and mannose are two epimers of glucose (Figure 6). They
differ from glucose in the configuration of groups (H and OH) around C-4 and C-2
respectively.
• Galactose and mannose are not epimers of each other as they differ in
configuration at two asymmetric carbon atoms around C-2 and C-4.

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 Al- Bayan University Biochemistry
2nd Year Dr. mustafa
2022 / 2023 Chemistry of Carbohydrates

GLYCOPROTEINS

• Glycoproteins are proteins to which oligosaccharides are covalently attached to

their polypeptide chain.
• Glycoproteins contain much shorter carbohydrate chain than proteoglycans.
• The distinction between glycoproteins and proteoglycans may be based on the
amount of carbohydrate.
➢ Glycoproteins contain less than 4 percent carbohydrate in the molecule.
➢ Proteoglycans contain more than 4 percent carbohydrate.

FUNCTIONS OF GLYCOPROTEINS

• Almost all the plasma proteins of humans are glycoproteins, except albumin.
• Many integral membrane proteins are glycoproteins.
• Most proteins that are secreted, such as antibodies, hormones and coagulation
factors are glycoproteins
• Glycoproteins serve as lubricant and protective agent, e.g. mucin of
gastrointestinal and urogenital tracts.
• Glycoproteins also serve as transport molecules, such as transferrin and
ceruloplasmin

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 Dr, Mustafa Saleem ./ 2nd year
Dr. Abbas A. S
Biochemistry. Lecture 4&5

GLUCOSE METABOLISM & GLYCOLYSIS

Yeast have been used in brewing and baking for thousands of years.

Recently, their ability to produce bubbles (CO2 gas) and alcohols (ethanol)

was believed to be a unique property of living things that possessed a “vital

force.” However, in the mid- 1800s, scientists began developing techniques

for preparing cell extracts and isolating individual enzymes, and it became

clear that the conversion of glucose to CO2 and ethanol.

Yeast

• Glucose occupies a central position in the metabolism of most cells. It

is a major source of metabolic energy (in some cells, it is the only
source).
• It provides the precursors for the synthesis of other biomolecules.
• Glucose is stored in polymeric form as starch in plants and as
glycogen in animals.
• The breakdown of these polymers provides glucose monomers that
can be catabolized to release energy.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

• The conversion of the six-carbon glucose to the three-carbon

pyruvate, a pathway we now call glycolysis, occurs in ten steps.

Glycolysis

Glucose Pyruvate Pyruvate

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 Dr, Mustafa Saleem ./ 2nd year
Dr. Abbas A. S
Biochemistry. Lecture 4&5

GLYCOLYSIS
✓ Glycolysis, occurs, at least in part, in almost every living cell. This series
of reactions is believed to be among the oldest of all the biochemical
pathways. Both the enzymes and the number and mechanisms of the
steps in the pathway are highly conserved in prokaryotes and
eukaryotes.
✓ The free energy consumed or released in certain reactions is
transferred by molecules such as ATP and NADH.

Glycolysis is one of the principle pathways for generating ATP in cells.

✓ Each step of the pathway is catalyzed by a distinct enzyme.

✓ The central role of glycolysis in fuel metabolism is related to its ability to

generate ATP with and without oxygen (O2).
✓ The oxidation of glucose to pyruvate generates ATP from substrate-level
phosphorylation (the transfer of phosphate from high-energy
intermediates of the pathway to ADP) and NADH.
✓ Subsequently, the pyruvate may be oxidized to carbon dioxide (CO2) in
the TCA cycle and ATP generated.

✓
✓ Sources of glucose available from:
1- Our diet.
2- Internal glycogen stores.
3- The blood.
4- Other dietary sugars, such as fructose and galactose, are oxidized by
conversion to intermediates of glycolysis.
✓ Glucose is stored in cells as glycogen, which can provide an
internal source of fuel for glycolysis in emergency situations.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

Figure: Major Pathways in Carbohydrate Metabolism

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

The net equation for the pathway of glycolysis (ignoring water and
protons) is:

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

✓ It is convenient to divide the 10 reactions of glycolysis into two phases.

✓ In the first (Reactions 1–5), the hexose is phosphorylated and cleaved in
half. In the second (Reactions 6–10), the three-carbon molecules are
converted to pyruvate.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

Reactions 1– 5 are the energy-investment phase of glycolysis

1. Hexokinase
In the first step of glycolysis, the enzyme hexokinase transfers a
phosphoryl group from ATP to the C6 OH group of glucose to form
glucose-6-phosphate:

A kinase is an enzyme that transfers a phosphoryl group from ATP

(or another nucleoside triphosphate) to another substance.
The hexokinase active site closes around its substrates so that a
phosphoryl group is efficiently transferred from ATP to glucose.
The standard free energy change for this reaction, which cleaves on of
ATP’s phosphoanhydride bonds, is -16.7 kJ.mol-1(G). That means the
reaction proceeds in only one direction; the reverse reaction is extremely
unlikely. hexokinase is said to catalyze a metabolically irreversible reaction
that prevents glucose from backing out of glycolysis.

2. Phosphoglucose Isomerase
The second reaction of glycolysis is an isomerization reaction in which
glucose-6- phosphate is converted to fructose-6-phosphate:

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

✓ The standard free energy change for this reaction is + 2.2 KJ.mole-1

3. Phosphofructokinase
The third reaction of glycolysis consumes a second ATP molecule in the
phosphorylation of fructose-6-phosphate to yield fructose-1,6-
bisphosphate.

Phosphofructokinase operates in much the same way as hexokinase.

The reaction is irreversible.

The concentration of ADP in the cell is a good indicator of the need for ATP,
which is a product of glycolysis.
The activity of phosphofructokinase is hormonally stimulated when the
concentration of glucose in the blood is high. The resulting increase in
fructose-2,6-bisphosphate concentration activates phosphofructokinase to
increase the flux of glucose through the glycolytic pathway.

4. Aldolase
Reaction 4 converts the hexose fructose-1,6-bisphosphate to two three-
carbon molecules, each of which bears a phosphate group.

In another word, the enzyme Aldolase splits fructose 1, 6-bisphosphate into two
sugars that are isomers of each other.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5

This reaction is the reverse of an aldol (aldehyde–alcohol) condensation,

so the enzyme that catalyzes the reaction is called aldolase.

5. Triose Phosphate Isomerase

The products of the aldolase reaction are both phosphorylated three-
carbon compounds, but only one of them—glyceraldehyde-3-phosphate
proceeds through the remainder of the pathway. Dihydroxyacetone
phosphate is converted to glyceraldehyde-3-phosphate by triose
phosphate isomerase:

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture 4&5
The reaction proceeds because glyceraldehyde-3- phosphate is quickly
consumed in the next reaction, so more dihydroxyacetone phosphate is
constantly being converted to glyceraldehyde-3-phosphate.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5

Reactions 6–10 are the energy-payoff phase of glycolysis

So far, the reactions of glycolysis have consumed 2 ATP, but this
investment pays off in the second phase of glycolysis when 4 ATP are
produced, for a net gain of 2 ATP. All of the reactions of the second phase
involve three-carbon intermediates, but keep in mind that each glucose
molecule that enters the pathway yields two of these three-carbon units.

6. Glyceraldehyde-3-Phosphate Dehydrogenase
In the sixth reaction of glycolysis, glyceraldehyde-3-phosphate is both
oxidized and phosphorylated:

✓ Glyceraldehyde-3- phosphate dehydrogenase does not use ATP as a

phosphoryl-group donor.
✓ It adds inorganic phosphate to the substrate.
✓ This reaction is also an oxidation–reduction reaction in which the
aldehyde group of glyceraldehyde-3-phosphate is oxidized and the
cofactor NAD+ is reduced to NADH.
✓ Note that the reaction product NADH must eventually be reoxidized to
NAD+, or else glycolysis will come to a halt.
✓ In fact, the re-oxidation of NADH, can generate ATP.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5
✓ (AsO43-), which competes with Pi (PO32- ) for binding in the
enzyme active site.

7. Phosphoglycerate Kinase
The product of Reaction 6, 1,3-bisphosphoglycerate, is an acyl phosphate.

The subsequent removal of its phosphoryl group releases a large amount

of free energy in part because the reaction products are more stable (the
same principle contributes to the large negative value of (delta-G) for
reactions involving cleavage of ATP’s phosphoanhydride bonds. The free
energy released in this reaction is used to drive the formation of ATP, as
1,3-bisphosphoglycerate donates its phosphoryl group to ADP:

Note that the enzyme that catalyzes this reaction is called a kinase since it
transfers a phosphoryl group between ATP and another molecule.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5

8. Phosphoglycerate Mutase
In the next reaction, 3-phosphoglycerate is converted to 2-
phosphoglycerate:

Although the reaction appears to involve the simple intramolecular transfer

of a phosphoryl group, the reaction mechanism is a bit more complicated
and requires an enzyme active site that contains a phosphorylated His
residue. The phospho-His transfers its phosphoryl group to 3-
phosphoglycerate to generate 2,3-bisphospho- glycerate, which then gives
a phosphoryl group back to the enzyme, leaving 2-phosphoglycerate and
phospho-His:

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5

9. Enolase
Enolase catalyzes a dehydration reaction, in which water is eliminated:

The enzyme active site includes an Mg2+ ion that apparently coordinates
with the OH group at C3 and makes it a better leaving group. Fluoride ion
and Pi can form a complex with the Mg2+ and thereby inhibit the enzyme. In
early studies demonstrating the inhibition of glycolysis by F-, 2-
phosphoglycerate, the substrate of enolase, accumulated.

10. Pyruvate Kinase

The tenth reaction of glycolysis is catalyzed by pyruvate kinase, which
converts phospho-enolpyruvate to pyruvate and transfers a phosphoryl
group to ADP to produce ATP:

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5

The reaction actually occurs in two parts. First, ADP attacks the phosphoryl
group of phosphoenolpyruvate to form ATP and enolpyruvate:

The Fate of Pyruvate

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5

Pyruvate kinas e deficiency:

Red blood cell pyruvate (PK) deficiency is a rare inherited disease
manifesting as hemolytic anemia that means the red blood cells break apart.
PK deficiency is a lifelong condition, with symptoms that range from mild to
severe.

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Dr. Abbas A. S./ 2nd year
Biochemistry. Lecture4&5

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