MTY1107: BIOCHEMISTRY | LECTURE

MODULE 1: REVIEW ON CHEMISTRY (THERMODYNAMICS)

NAME OF LECTURER: MS. LENZIE SANTILLAN
DATE: AUGUST 23, 2021

TABLE OF CONTENTS TYPES OF SYSTEMS

Open free to exchange matter and energy with
I. INTRODUCTION …………………………………………….…… 1 the surroundings.
II.THERMODYNAMICS…………..……….…………………….… 1 Closed can exchange energy, but not matter, with
the surroundings.
A. Systems and Surroundings ……..…………………….. 1
Isolated cannot exchange matter or energy with
B. Laws of Thermodynamics ……..………………………. 1 the surroundings.
III. GIBBS FREE ENERGY ………………….……………..……… 2
A. EXERGONIC AND ENDERGONIC PROCESSES ….. 3 • Surrounding
QUICK REVIEW ………………………………………………….… 4 o Everything else that is not the system defined
Review questions ………………………………………..…..
REFERENCES ……………………………………………………….. 4

INTRODUCTION
• The processes occurring inside the cell all require
energy. These processes, essential to life, are not
exempt from the natural laws that govern how energy
is transformed and transferred in the universe
• Different biological reactions occurring in a cell require
energy, and therefore obey the laws of Figure 1.1. Diagram explaining a system and its
thermodynamics. surroundings

THERMODYNAMICS
• The language used to describe the principles that
govern how energy flows in the universe, how is used
and transformed.
• The science of heat and work.
• Interconversion of heat and other kinds of energy. Figure 1.2. Examples of types of system
o Energy – the capacity to do work; directed energy
change resulting from a process. LAWS OF THERMODYNAMICS
o Heat – lowest or last form of energy; disordered • 1ST LAW: Energy can neither be created nor
and cannot be converted back to useful energy destroyed. The energy of the universe is constant.
o Work – any form of processes that produce o Energy can neither be lost nor gained in a system.
energy. It can only transform into another form of energy.
▪ Example: Heat emitted from a campfire.
SYSTEMS AND SURROUNDINGS (Radiant to chemical energy)
• In thermodynamics, we often separate the universe o Esystem + Esurroundings = Euniverse =
(that is, everything that exists) into 2 parts: CONSTANT
• System ▪ E = energy
o An object is of interest; the portion that is singled • 2ND LAW: The total entropy of the universe is
out for study continuously increasing.
▪ Example: Substances involved in chemical or o All systems in the universe tend to attain
physical change equilibrium, a thermodynamically most stable
▪ Example: A beaker with 50mL of hydrochloric state at a given set of conditions, which can only
acid and 50mL of sodium hydroxide necessary be reached when all molecules within a system
for neutralization reaction

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. | LASAC, R. | SALGADO, R. 1

 exist in the most random or disordered state
possible, defined as entropy.
o Entropy increases as randomness increases and
has the maximum value when the system is at
equilibrium.
o “The entropy of a system can decrease as long as
the entropy of the surroundings is increased by a
greater amount”
▪ Because what is noted is the SUM of the
entropy of the system and surroundings
(total entropy of the universe) Figure 3.1. Examples of synthetic, mechanical, and
o “An increase in the no. of particles […] an concentration work
increase in volume […] changing state increases
entropy”

Figure 3.2. Examples of synthetic, mechanical, and

concentration work

Figure 2.1. Factors that increase entropy • Gibbs Free Energy (G)
o Enthalpy (H) - heat content of the system under
o To reach entropy, and therefore equilibrium, the study, closely approximated by the number and
process must be spontaneous (automatic). kinds of bonds and interaction present between
▪ Example: Hot coffee becoming cold over time. molecules and molecule groups.
▪ Needs an outside source (“trigger”)
Gibbs Free Energy (G) ▪ Non-spontaneous reaction
• The energy associated with a chemical reaction that o Entropy (S) - a measure of the randomness or
can be used to do work. disorder of the system.
o Glucose to ATP (energy) which occurs in ▪ “Hotter to colder movement”
mitochondria ▪ Releases energy, without outside source,
o Amount of energy that is available to: to another system
▪ Move heat o The relationship of both gives the value of free
▪ Metabolize cell energy, as shown in this equation:
▪ Produce mechanical energy
• “Disorder is more probable than order. Work is G = H – TS
generally required to produce order out of disorder,
so energy must be used to produce a highly ordered G – Gibbs Free Energy
state.” H – enthalpy (heat content)
T – temperature
TYPES OF WORK AND THEIR EXAMPLES S – entropy
Synthetic The process of photosynthesis
Mechanical The concentration of a weightlifter’s • It is easier to measure changes (∆) in H and S during a
muscles
process, hence why ∆G is more typically known that G.
Concentration The accumulation of molecules in a cell
Heat production Shivering in the cold
Therefore, what is more known and preferable is:
Bioluminescence The courtship of fireflies
Electrical The membrane potential of a
mitochondrion

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. | LASAC, R. | SALGADO, R. 2

 ∆G = ∆H – T∆S

∆G – change in Gibbs Free Energy

∆H – change in enthalpy (heat content)
T – temperature
∆S – change in entropy

EXERGONIC AND ENDERGONIC PROCESSES

• ∆G can be negative or positive.
o Negative (-) value – chemical reaction RELEASED
energy.
▪ Towards entropy Figure 4.2. Summary of possible spontaneous and non-
▪ Energy can be used to do work somewhere else spontaneous reactions
▪ Example: Room becomes cluttered overtime
o Positive (+) value – reaction USED up energy and • An endergonic reaction can be “mechanically joined”
work had to be done to provide the energy used. to a separate, exergonic reaction via a shared
▪ Towards enthalpy intermediate to drive the unfavorable reaction.
▪ Example: Synthesis of high-energy molecules o In other words, combining an endergonic reaction
or the creation of ion gradient in cells with an exergonic reaction will result in a
• A reaction is thermodynamically favorable if… thermodynamically favorable reaction (negative
o It occurs without the need for additional energy ∆G)
input after the reactants are mixed and the reaction is
initiated.
o ∆G has a negative value
o More products than reactants present in the
equilibrium mixture
• Exergonic processes/reactions
o SPONTANEOUS processes where ∆G is negative.
o Spontaneity is not indicative of reaction rate, only
whether the reaction will proceed as written Figure 4.3. Synthesis of ATP from ADP coupled to the
(“whether w/o work or w/ work”). production of pyruvate from phosphoenol pyruvic acid
▪ Under thermodynamic control, while reaction (PEP)
rate is under kinetic control
• Endergonic processes/reactions
o NON-SPONTANEOUS processes where ∆G is
positive. (Needs a trigger)

Figure 4.4. The pyruvate kinase reaction (same reaction as

with figure 4.3)

o Many metabolic processes are full of coupled

reactions like this, where cells couple unfavorable
(endergonic, positive ∆G, non-spontaneous)
metabolic process with favorable (exergonic,
negative ∆G, spontaneous) ones so that the net
change in free energy is negative
(thermodynamically favorable, see figure 4.3).

Figure 4.1. Diagram showing the difference between

endergonic and exergonic reactions

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. | LASAC, R. | SALGADO, R. 3

 QUICK REVIEW

1. How is the science of thermodynamics related to

biological processes?
2. Explain systems and surroundings. Give an
example.
3. What are the different types of systems?
4. According to the first law of thermodynamics, how
is the energy of the universe constant?
5. What does the second law of thermodynamics
dictate? Explain.
6. What is Gibbs Free Energy? What is its
relationship to work?
7. Differentiate enthalpy from entropy. Explain their
relationship to Gibbs Free Energy.
8. How should we measure Gibbs Free Energy?
9. ∆G can yield either positive or negative results.
What does each result indicate?
10. How do we know if a reaction is
thermodynamically favorable and unfavorable?
11. Describe exergonic and endergonic processes.
12. What is the result of ∆G if:
a. (∆H-) – ⬆T(∆S+)
b. (∆H+) – ⬆T(∆S-)
c. (∆H-) – ⬆T(∆S-)
d. (∆H+) – ⬆T(∆S+)
13. Why are metabolic processes full of coupled
reactions (endergonic reaction “mechanically
joined” to an exergonic reaction?

REFERENCES

1. Biochemistry for Medical Technology (Lecture) Canvas.

Review on Chemistry Concepts: Thermodynamics.
PowerPoint Presentation
2. Review on Chemistry Concepts: Thermodynamics
lecture. Prepared by Ms. Lenzie Santillan
3. Review on Chemistry Concepts: Thermodynamics.
Prepared by Ms. Marie Juneau Mallari
4. Rafelson, M., Hayashi, J., & Bezkorovainy, A. (1980).
Basic biochemistry (4th ed., pp. 11-12). Macmillan

Goodluck, MT Tams! Road to RMT on 2024. Kaya natin ‘to.

“Knowing is better than wondering, waking is better than
sleeping, and even the biggest failure, even the worst, beats
the hell out of never trying.” - Meredith Grey

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. | LASAC, R. | SALGADO, R. 4

 MTY1107: BIOCHEMISTRY | LECTURE
MODULE 2: CARBOHYDRATES
NAME OF LECTURER: Ms. Lenzie Santillan
DATE: September 2, 2021

TABLE OF CONTENTS o Simpler members of the carbohydrate family

o Named for sweet taste (Latin: saccharum, “sugar”)
I. CARBOHYDRATES 1 o Classified as such depending on the no. of simple sugar
units:
II. MONOSACCHARIDES 1
▪ Monosaccharides (1)
A. Aldoses and Ketoses 1 ▪ Dissacharies (2)
B. Tautomer 2 ▪ Oligosaccharides (3-10)
III. FISCHER PROJECTIONS 2 ▪ Polysaccharides (more than ten)
IV. CYCLIZATION OF CARBOHYDRATES 3
A. Types of Cyclic Carbohydrates 3
B. Haworth Projections 4
V. Classification of Carbohydrates 5
REFERENCES ……………………………………………………….. 8

CARBOHYDRATES
• “Sugar” in layman’s term. In nutrition, it refers to the
nutrients that provide energy for the body to enable it to
perform work and maintenance of body processes.
• Polyhydroxyaldehydes, polyhydroxyketones, or substances
that give these compounds on hydrolysis.
• The most abundant organic compounds in the world. They Figure 1.2. Carbohydrates family
act as:
o Storehouses of chemical energy MONOSACCHARIDES: STRUCTURE AND
o Components of supportive structures in plants and NOMENCLATURE
crustacean shells, and connective tissues in animals • General formula: CnH2nOn
o Essential components in nucleic acids • Cannot be hydrolyzed to a simpler compound
• The word carbohydrate means “hydrate of carbon”, • Common monosaccharides have 3 to 9 carbon
derived from the formula Cn(H2O)m atoms
o In other words, molecules with several carbon atoms
• Tested with Benedict’s and Tollens’
that bear a hydrogen (H) and a hydroxyl group (-OH)
• Nomenclature:
▪ Example: Glucose – C6H12O6 as C6(H2O)6
o Suffix: -ose; indicates that molecule is a
carbohydrate
o Prefixes: tri-, tetr-, pent-; indicates number of
carbon atoms in the chain
▪ Example: Triose (3 carbon atoms)

Figure 1.1. Carbohydrate

Figure 2.1. Triose
o Not all carbohydrates have this general form.
o The term carbohydrate has become so firmly rooted in A. ALDOSES AND KETOSES
the chemical nomenclature that it persists as the name • Monosaccharides either contain an aldehyde or
for this class of compounds despite not being ketone group, and are classified as:
completely accurate. o Aldoses
• Saccharides

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 1

 ▪ Monosaccharides containing an aldehyde (- oIsomers – structures that have same chemical
CHO) group formula but different structure/connectivity
o Ketoses o Tautomerization – process of relocation of a
▪ Monosaccharides containing a ketone proton
(R2C=O) group • D-Glyceraldehyde is usually involved in a metabolic
pathway and is converted to the more stable
Dihydroxyacetone, which is more readily convertible
by our cells

Figure 2.2. Aldose (6 carbon + aldehyde group -

aldohexose) and ketose (5 carbon + ketone group -
ketopentose)

• Designations aldo- and keto- are added to the

name of monosaccharide, but they are often
omitted, and these molecules are simply
referredto as trioses, tetroses, and so on.

FISCHER PROJECTIONS
• A two-dimensional representation for showing the
configuration of tetrahedral stereocenters.
o Horizontal lines represent bonds projecting
forward from the stereocenters
o Vertical lines represent bonds projecting the rear
o Only the stereocenter is in the plane

Figure 2.3. Aldose Groups

• In 1891, Emil Fischer made the arbitrary

assignments of D- and L- to the enantiomers of
glyceraldehyde.
o D-monosaccharide (dextrorotary,
Figure 2.4. Ketose Groups clockwise)): -OH on its penultimate
carbon is on the right in a Fischer
B. TAUTOMERS Projection
• Structural isomers of chemical compounds that
readily interconvert.

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 2

 o L-monosaccharide (levorotary, counter-
clockwise): -OH on its penultimate
carbon is on the left in a Fischer
Projection

Figure 5.3. Anomeric carbon of α -D-Fructofuranose and

β-D-Fructofuranose (ketose) is at C-2

• Anomeric carbon
• D enantiomeric forms are most abundant in o The new chiral center (carbon stereocenter)
nature, while L isomers are rare. created in forming the cyclic structure.
• R, S system is more widely accepted today as a o Also known as epimeric carbon or anomeric
standard for designating configuration, however center.
the D, L system is more commonly used.

CYCLIZATION OF CARBOHYDRATES
• Formation of a new chiral center, leading to the
formation of anomers designated as α (alpha, OH
below the ring, trans) or β (beta, OH above the ring,
cis).
o In nature, carbohydrate molecules form ring
structures through the reaction between Figure 5.4. Anomeric carbon of α-D-glucopyranose
hydroxyl (-OH) and carbonyl groups (C=O). and β-D-glucopyranose

A. TYPES OF CYCLIC CARBOHYDRATES

• Sugars in ring conformation may adopt a five- or
six-membered closed structures which resemble
furan or puran rings.

Figure 5.1. Haworth projections for α-D-glucopyranose

and β-D-glucopyranose Figure 5.5. Furan and Pyran

• Anomers • Five-membered hemiacetal ring = -furan-

o Stereoisomers that differ in configuration at only o Furanose - five-membered cyclic hemiacetal
the anomeric carbon. form of monosaccharide
o They are epimers as they differ from each other
at only C-1 if they are aldoses and only C-2 if they
are ketoses.

Figure 5.2. Anomeric carbon of β-D-glucopyranose

(an aldose) is at C-1

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 3

 o Formation of a hemiketal in a ketose forms a
furanose ring in cyclization

• An abbreviated Haworth projection only shows

the hydroxyls in each carbon. Full Haworth
• Six-membered hemiacetal ring = -pyran- projections include the hydrogens.
• Pyranose - six-membered cyclic hemiacetal form
of monosaccharide HOW TO DRAW HAWORTH PROJECTIONS (ALDOSE)
• Formation of a hemiacetal in an aldose forms a
pyranose ring in cyclization 1 2 3

1. At the penultimate carbon (chiral center furthest

away from the functional group), rotate CH2OH, -OH,
and hydrogen so they are positioned as such:
2. Label each carbon, with the carbon of the functional
group as 1 and CH2OH as the last number. This will
serve as your guide when forming the Haworth
projection. Remember: Left on Fischer, Up on
Haworth; Right on Fischer, Down on Haworth.
3. Proceed to draw the Haworth projection, with
attachments on their appropriate position on the
• Aldopentoses also form cyclic hemiacetals. ring. C-1 is always on the left, then proceed to
o D-ribose and other pentoses in the biological clockwise from there.
world are furanoses. 4. Label with the appropriate designation (α or β)
• Fructose also forms five-membered cyclic
hemiacetals. HOW TO DRAW HAWORTH PROJECTIONS (KETOSE)

B. HAWORTH PROJECTIONS 1. Since the -OH of the highest chiral center will
• A common way of representing the cyclic structure “attack” the ketone, the anomeric carbon will be
(ring form) of carbohydrates. found in C-2. CH2OH (C-1) will be attached to C-2.
o Named after Sir Walter N. Haworth, an English
chemist who won the 1937 Nobel Prize in
Chemistry.
o A five- or six-membered cyclic hemiacetal
represented as a planar pentagon or hexagon.

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 4

 2. Proceed to draw the Haworth projection, with CLASSIFICATION OF CARBOHYDRATES
attachments on their appropriate position on the MONOSACCHARIDES
ring. C-1 is always on the left, then proceed to • Composed of one (1) sugar unit
clockwise from there. C-6 CH2OH is still attached • Monosaccharide derivatives also abound in nature.
to C-5. Remember: Left on Fischer, Up on This includes the diverse groups of monomeric sugars
Haworth; Right on Fischer, Down on Haworth. with additional substituents.

3. Label with the appropriate designation (α or β)

A. MONOSACCHARIDE DERIVATIVES
• Sugar Acids
o Sugars with free anomeric carbons are good
reducing agents and can reduce hydrogen
peroxide, ferricyanide, certain metals (Cu2+ and Ag)
and other oxidizing agents.
▪ Addition of Fehling’s solution (alkaline CuSO4)
C. CHAIR CONFIGURATIONS to aldose sugar produces red cuprous oxide
• For pyranoses, the six-membered ring is more (Cu2O) precipitate, converting aldose to aldonic
accurately represented as a Strain-free chair acid (Ex. gluconic acid).
conformation, compared to furanoses that are more o Oxidation at C-6 yields uronic acids
accurately represented by Haworth projections due ▪ D-glucoronic acid, L-iduronic acid
being close to a planar shape. o Oxidation at both C-1 and C-6 yields aldaric acids
• In both Haworth projections and chair ▪ D-glucaric acid
conformations, the orientations of groups on • Sugar Alcohols (Alditols)
carbons 1- 5 of b-D-glucopyranose are up, down, up, o The products formed when the carbonyl group
down, and up and all are equatorial. of a monosaccharide is reduced to a hydroxyl
• Hydrogen atoms bonded to the ring are not shown group by a variety of reducing agents, such as
in chair conformations. hydrogen in the presence of sodium
borohydride (NaBH4) or similar agents.
▪ Glucitol (Sorbitol) – found in many berries
and cherries, plums, pears, apples, seaweed,
and algae; used as sugar substitute for
diabetics, moisturizing agent in food and
cosmetics.
▪ Mannitol – injection for those with
kidney/renal failure
▪ Xylitol – sweetening agent in “sugarless”
gum candy, and sweet cereals
Figure 5.6. Haworth projection and chair conformation ▪ Glycerol - used for constipation, improving
of β-D-glucopyranose hydration and performance in athletes, and
for certain skin conditions; used in industry
machinery.
▪ Myo-inositol (vitamin B8) - found naturally in
cantaloupe, citrus fruit, and many fiber-rich
foods; sold in supplement form and used as
a complementary therapy to treat a wide
range of medical conditions, including
metabolic and mood disorders.

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 5

 ▪ Ribitol - occurs naturally in the plant Adonis o Used to differentiate blood types
vernalis and in the cell walls of Gram positive o Six-membered cyclic form
bacteria
o Designated by adding the suffix -itol to the
name of the parent sugar.
o The alditols are linear molecules that cannot
cyclize in the manner of aldoses.
• Deoxy Sugars
o Monosaccharides with one or more hydroxyl
groups replaces by hydrogens.
▪ 2-deoxy-D-ribose (2-deoxy-D-
erythropentose) – prefix 2-deoxy indicates
absence of oxygen at carbon 2; units of this
in nucleic acids and most other biological • Fructose
molecules are found almost exclusively in β o Ketohexose
configuration. o Sweetest tasting of all sugars
▪ L-Fucose, L-rhamnose – 6-deoxy sugars o Five-membered cyclic form
included in the composition of some cell
walls. Rhamnose is a component of ouabain,
a toxic carbon glycoside found in the bark
and root of ouabaio trees; used as arrow
poison in East Africa.
• Sugar Esters
o Important metabolic intermediates of
monosaccharides.
▪ Glucose 6-phosphate – product of first step
of glycolysis, the conversion of glucose.
• Amino Sugars
o Contain an amino group (-NH2) in place of a • Ribose
hydroxyl group at C-2. o Part of a variety of complex molecules which
▪ N-Acetyl-D-glucosamine – found in chitin include RNA, DNA, ATP
and cartilage; muramic acid, neuramic acid o Five-membered cyclic form
in cell membranes of higher organisms and
bacterial cell walls
▪ D-mannosamine
▪ D-galactosamine
o Found in naturally-occurring antibiotics

B. ESSENTIAL MONOSACCHARIDES
• Glucose
o Also known as grape sugar, blood sugar, and
dextrose
o Six-membered cyclic form
o Important in human nutrition
DISACCHARIDES
• Composed of two (2) sugar units joined by a
glycosylic bond

• Galactose
o Also known as brain sugar or milk sugar

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 6

A. FORMATION OF GLYCOSYLIC BONDS o Formed by an β -1,4-glycosydic bond between C-
• An anomeric carbon of one sugar unit bonds to the - 1 of β -D-galactopyranose and C-4 of β -D-
OH group of the other unit, forming α -or β- glucopyranose.
glycosidic linkage; also occurs in oligosaccharides. o Reducing sugar

Figure 6.3. α (1-4) Glycosidic bond

• Maltose
o Present in malt, the juice from sprouted barley
and other cereal grains.
o Formed by an α -1,4-glycosydic bond between
two units of D-glucopyranose.
o Reducing sugar

Figure 6.3. β (1-1) Glycosidic bond

• Cellobiose
o Contains two D-glucose monosaccharide units,
one of which must have a β configuration, linked
through a β-1,4-glycosidic linkage.
o Cannot be digested by humans.

Figure 6.4. Summary of glycosylic bonds

B. EXAMPLES OF DISACCHARIDES
• Sucrose
o Table sugar; most abundant disaccharide in the
biological world OLIGOSACCHARIDES
o Obtained from the juice of sugar cane and sugar
• Carbohydrates that contain 3–10 monosaccharide
beets. units bonded to each other via glycosidic linkages.
o Formed by an α -1,2-glycosydic bond between C-
• Commonly found in onions, cabbage, broccoli, and
1 of α-D-glucopyranose and C-2 of α-D- whole wheat.
fructofuranose. • Can distinguish blood types.
o Non-reducing sugar

• Lactose
o Principal sugar in milk; accounts for 5%-8% of
human milk and 4%-6% of cow’s milk. POLYSACCHARIDES
• Polymers of many monosaccharide units bonded
with glycosidic linkages.

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 7

 o Not sweet and do not show positive tests with
Tollen’s and Benedict’s solutions, whereas
monosaccharides are sweet and show positive
tests.
o Limited water solubility.
• Starch
o Storage polysaccharide: Polysaccharide that is a
storage form for monosaccharides and used as an
energy source in cells.
• Hyaluronic acid
▪ Glucose is the monomeric unit.
o Composed of d-glucuronic acid joined by a β-
▪ Storage polysaccharide in plants.
1,3-glycosidic bond to N-acetyl-d-glucosamine,
o Types:
which is in turn linked to d-glucuronic acid by a
▪ Amylose - unbranched; α-1,4-glycosidic bonds
β -1,4-glycosidic bond.
▪ Amylopectin - branched; α-1,4 and α-1,6
o Highly viscous and serve as lubricants in the fluid
of joints as well as vitreous humor of the eye.

• Heparin
o Blood anticoagulant
o Acidic polysaccharide

• Glycogen
o Storage polysaccharide in humans and animals.
o Contains only glucose units.
o Branched chain polymer with α-1,4 glycosidic
REFERENCES
bonds in straight chains and α-1,6 in branches. 1. Biochemistry for Medical Technology (Lecture)
o Contains up to 1,000,000 glucose units. Canvas. Carbohydrates. PowerPoint Presentation
o Excess glucose in blood is stored in the form of 2. Carbohydrate lecture. Prepared by Ms. Lenzie
glycogen. Santillan
3. Carbohydrate lecture. Prepared by Ms. Marie Juneau
• Cellulose Mallari
o Linear homopolysaccharide with β-1,4 glycosidic 4. Bettelheim, F. (2016). Introduction to General,
bond. Organic, and Biochemistry. Cengage
o Humans do not have enzymes that hydrolyze β-
1,4 linkages and so they cannot digest cellulose. Goodluck MT Tams! Road to RMT on 2024. Kaya natin
‘to.
“There is no flight without a leap.” – Dr. Vijay Kapoor, New
Amsterdam

• Chitin
o Linear polymer with all β-1,4 glycosidic linkages.
▪ It has an N-acetyl amino derivative of glucose.

ABELA, J. | AIRANEL, J. | DESAHAGUN, E. 8

 MTY1107: BIOCHEMISTRY | LECTURE
MODULE 3: LIPIDS
NAME OF LECTURER: Ms. Lenzie Santillan
DATE: September 9, 2021

TABLE OF CONTENTS B. SAPONIFICATION REACTIONS

• Based on whether a lipid can be broken down into
I. LIPIDS 1 smaller units through basic hydrolysis, that is,
II. FATTY ACIDS 1 reaction with water under basic conditions.
III. TRIACYLGLYCEROLS 3 (Saponification)
IV. COMPLEX LIPIDS 4 o Saponifiable lipids - converted into two or more
V. LIPIDS AS MESSENGER 7 smaller molecules when hydrolysis occurs
REVIEW QUESTIONS ………………………………………….. 11 ▪ Triacylglycerols
REFERENCES ………………………………………………………. 12 ▪ Phospholipids
▪ Sphingoglycolipids
LIPIDS ▪ Biological waxes
• Family of substances that are insoluble in water, o Nonsaponifiable lipids – do not react to water
but soluble in nonpolar solvents and solvents with ▪ Cholesterol
low polarity (ex. diethyl ether) ▪ Steroid hormones
• Primarily hydrocarbons ▪ Bile acids
• Defined by property or solubility, and not in terms ▪ Eicosanoids
of structure.
o Unlike carbohydrates and most other classes of FATTY ACIDS
compounds, lipids do not have a common
structural feature that serves as the basis for
defining such compounds.

CLASSIFICATION OF LIPIDS
• The decision of which system to use is arbitrary;
both systems have their merits.

A. BIOCHEMICAL FUNCTIONS
• Energy-storage lipids
o Animals and humans find it more economical to
use fats for storage of energy because fats
produce more than twice as much energy (9
kcal/g) as the burning of an equal weight of
carbohydrates (4 kcal/g)
▪ Triglycerides (triacylglycerols) Figure 2.1. Fatty acid structure
o Most abundant
• Membrane lipids • Amphipathic compounds with a carboxyl (-COOH)
o Provide separate compartments containing group “head” at the polar end (hydrophilic) and a
aqueous solutions, such as cells or organelles hydrocarbon chain at the nonpolar “tail”
▪ Phospholipids, sphingoglycolipids, cholesterol (hydrophobic).
o Second most abundant • One of the several building blocks of lipids, as they are
• Messenger lipids structurally diverse.
o Act as chemical messengers • Common characteristics of fatty acids:
▪ Steroid hormones (PRIMARY) – deliver signals o Practically all unbranched carboxylic acids
from one part of the body to another o Range in size from about 10 to 20 carbon atoms or,
▪ Prostaglandins, thromboxanes (SECONDARY) in nature, 14-24 carbon atoms
– mediate hormonal response
• Emulsification lipids
▪ Bile acids
• Protective-coating lipids
▪ Biological waxes

ABELA, J. 1
 o Contain an even number of carbon atoms
▪ Body builds these acids entirely from acetate
units, therefore putting carbons two at a time.
o No functional groups aside from carboxylic (-
COOH) group, except for some that have carbon-
carbon double bonds, where cis configurations
predominate.
• Essential fatty acids
o Fatty acids that are not synthesized by
mammals and yet are necessary for normal
growth and life; must be obtained by mammals
in their diet (specifically from plant sources).
▪ Linoleic acid and -linolenic acids • Unsaturated fatty acids:
o Stereochemistry is usually cis than trans
SATURATED VS UNSATURATED FATTY ACIDS o Slightly more abundant in nature than saturated
• Saturated Fatty Acids (SFAs) fatty acids, especially in higher plants.
o Carbon chain in which all carbon–carbon bonds o Oleic acid – most common
are single bonds. (Zero carbon-carbon double o No. of double bonds varies typically from one to
bonds) four. In bacteria, this number rarely exceeds
o Free rotation around each of the carbon–carbon one.
bonds make saturated fatty acids extremely o Double bonds also tend to make fatty acids to
flexible molecules. Saturated fatty acids adopt bend or kink
the straight conformation. o Lower melting points than saturated ones.
▪ Plant oils are liquid at room temperature
because they have higher proportions of
unsaturated fatty acids.
• Notation of fatty acids:
o No. of carbon atoms : No. of carbon-carbon
double bonds
▪ Oleic acid, 18:1 – 18 carbons, 1 fatty acid
• How to name fatty acids:
o Common name
▪ Fatty acids are nearly always referred to
using their common names
o Systematic name
• Monounsaturated Fatty Acids (MUFAs) o Symbol denoting no. of carbon and no. of
o Carbon chain with the presence of one carbon– carbon-carbon double bonds
carbon double bond.

• Polyunsaturated Fatty Acids (PUFAs)

o Carbon chain with the presence of two or more
carbon–carbon double bond.
Figure 2.2. Common Biological Fatty Acids

ABELA, J. 2
 STRUCTURE
• Triesters of glycerol (alcohol) and long-chain
carboxylic acids (fatty acids)
o Esters are made up of an alcohol part and an
acid part.
o The alcohol of triacylglycerols is always glycerol,
a simple compound that contains three hydroxyl
groups.
o When all three of the alcohol groups (one
glycerol molecule) form ester linkages with fatty
acids, the resulting compound is a triacylglycerol
(older name: triglyceride).

Figure 2.3. Selected Fatty Acids of Biological Importance

• Simple triacylglycerol
o Triester of glycerol and three identical fatty
acids

Figure 2.4. Classification Schemes for Fatty Acid Residues

Present in Triacylglycerols

TRIACYLGLYCEROLS (TRIGLYCERIDES)
• Lipids formed by esterification of three fatty acids • Mixed triacylglycerol
to a glycerol molecule. o Triester of glycerol and more than one kind
o In other words, three fatty acid residues (three of fatty acid molecule
acyl groups) attached to a glycerol residue.
o The “acyl” refers to the acyl group, the portion
of a carboxylic acid that remains after the -OH
group is removed from the carboxyl carbon
atom

PHYSICAL PROPERTIES
• Fat
o Mixtures of triglycerides containing a high
• Triacylglycerols are concentrated primarily in proportion of long-chain, saturated fatty
special cells (adipocytes) that are nearly filled with acids
the material. o Generally semisolids or solids at room
o More efficient at storing energy than is glycogen temperature
because large quantities of them can be packed o From animals = solid; from plants and fish =
into a very small volume. usually liquids
o Triacylglycerols in animals are found primarily in • Oils
the adipose tissue (body fat), which serves as a o Mixtures of triglycerides containing a high
depot or storage site for lipids. proportion of long-chain, unsaturated fatty
acids OR short-chain, saturated fatty acids
o Liquid fats, even though they are esters of
glycerols like solid fats; should not be

ABELA, J. 3
 confused with petroleum, which are mostly • Partial hydrogenation
alkanes. o Results in a product with just the right
o Generally liquid at room temperature consistency for cooking.
• Degree of unsaturation is the structural ▪ Margarine – made by partial hydrogenation
difference between fats and oils because the of vegetable oils; contains more unsaturation
physical properties of fatty acids are carried over than fully hydrogenated shortenings.
to the physical properties of triglycerides. ▪ Peanut butter – partial hydrogenation of
• Melting points of fatty acids increases as the peanut oil.
number of carbons in the hydrocarbon chains o In practice, the degree of hardening is carefully
increases and as the number of double bonds controlled to produce fats of a desired
decreases. consistency.
• Pure fats and oils are colorless, odorless, and
tasteless. SAPONIFICATION
o The taste and color on butter, olive oil, and • The base-promoted hydrolysis of fats and oils in
other fats and oils are caused by small aqueous NaOH (sodium hydroxide), producing
amounts of other substances dissolved in the glycerol and a mixture of fatty acid sodium salts
fat or oil. called soaps.
o Hydrolysis of a triacylglycerol is the reverse of
the esterification reaction by which it was
formed.
▪ Under acidic conditions, products are
glycerol and fatty acids.
▪ Under basic conditions, the hydrolysis
products are glycerols and fatty acid salts.
o First step: Hydrolysis of the ester linkages to
produce glycerol and three fatty acid
molecules

Figure 3.1. Average Percentage of Fatty Acids of Some o Second step: Reaction between the fatty acid
Common Fats and Oils molecules and the base (usually NaOH) in the
alkaline solution.
HYDROGENTATION
• Conversion of unsaturated liquid oils to solid fats.
o Reduction of carbon–carbon double bonds to • Saponification is one of the oldest known
single bonds by treating them with hydrogen chemical reactions.
and a catalyst, decreasing the level of
unsaturation in the fatty acid.

• Carried out on a large scale to produce the solid

shortening sold in stores and other fats for kitchen Figure 3.2. Example of the saponification of a typical fat
use.
o Shortening - any fat that is solid at room COMPLEX LIPIDS
temperature and used in baking, such as lard. • Constitute the main components of membranes.
o Manufacturers must be careful not to • Classified into two groups:
hydrogenate all double bonds, as a fat with no o Phospholipids
double bonds would be too solid. o Glycolipids
• Source of trans fatty acids
o Diets that contain large amounts of this tend to PHOSPHOLIPIDS
lead to (1) high serum cholesterol levels, (2) • Contains one or more fatty acids, a phosphate
higher low-density lipoprotein (LDL) to high- group, a platform molecule to which the fatty
density lipoprotein (HDL), which are risk factors acid(s) and the phosphate group are attached, and
for development of heart disease. an alcohol that is attached to the phosphate group.

ABELA, J. 4
 • Two types: o Triacylglycerols – three (3) ester linkages
o Glycerophospholipids (phosphoglycerides) –
platform molecule is the alcohol glycerol
o Sphingolipids – platform molecule is the alcohol
sphingosine (C18 aminodialcohol, which contains
two hydroxyl groups, -OH, and an amino group, -
NH2)

Figure 4.2. Comparison of ester linkages in

glycerophospholipids and triacylglycerols

• Phosphotidate
o Simplest phosphoglyceride containing an
unmodified phosphate group and is found in the
Figure 4.1. General block diagrams for a cell membrane in small quantities.
glycerophospholipid and a sphingophospholipid

• The fatty acid(s) give the phospholipid hydrophobic

properties while the phosphate and alcohol group
give it hydrophilic properties; thus, phospholipids
are amphipathic.

Figure 4.3. Structure of phosphotidate

• Phosphatidic acid

Figure 4.2. Schematic diagram of simple and complex

lipids Figure 4.4. Structure of phosphatidic acid

A. GLYCEROPHOSPHOLIPIDS o A molecule in which glycerol is esterified with

• Contains two fatty acids and a phosphate group two molecules of fatty acid and one of
esterified to a glycerol molecule and an alcohol phosphoric acid.
esterified to the phosphate group. ▪ Phosphatidyl group - fatty acid, glycerol, and
o C1 and C2 of the glycerol backbone are esterified phosphate portions of the
to two fatty acids while the C3 of the glycerol is glycerophospholipid
esterified to the phosphate group. ▪ The fatty acid on carbon 2 of glycerol is
o The alcohol attached to the phosphate group in a always unsaturated (Oleic acid in the
glycophospholipid is usually one of three amino structure)
alcohols: choline, ethanolamine, or serine. ▪ Phosphoric acid is the parent source for the
▪ The phosphate, together with such esterified minus one charged phosphate group used in
entities (amino alcohols), is referred to as a the formation of glycerophospholipids.
polar “head” group.
▪ The two fatty acids are the nonpolar “tail”.
o Function almost exclusively as components of
cell membranes and are not stored.
• All attachments (bonds) between groups in a
glycerophospholipid are ester linkages, a situation
similar to that in triacylglycerols. o Found in small amounts in most natural systems
o Glycerophospholipids – four (4) ester linkages and is an important intermediate in the

ABELA, J. 5
 biosynthesis of the more common o Important in blood clotting
glycerophospholipids.
▪ Because further esterification with a low-
molecular-weight alcohol gives a
glycerophospholipid.
o The most abundant glycerophospholipids are
derived from phosphatidic acid
o The three most abundant fatty acids in
phosphatidic acids are palmitic (16:0), stearic
(18:0), and oleic (18:1)
• Lecithin (phosphatidylcholines)
o Amino alcohol attached to phosphate group is Figure 4.7. Structure of cephalins, one with
choline. ethanolamine and the other with serine

• Glycerophospholipids are found almost exclusively in

plant and animal membranes, which typically consist
of 40% -50% phosphoacylglycerols and 50% - 60%
proteins.

Figure 4.5. Structure of the alcohol choline B. SPHINGOLIPIDS

• A lipid that contains one fatty acid and one
phosphate group attached to a sphingosine
molecule and an alcohol attached to the phosphate
group.
o Sphingosine - a complex alcohol that contains an
amino group (-NH2) and a long, unsaturated
hydrocarbon component

Figure 4.6. Structure of phosphatidylcholine

o Typical lecithin molecule has stearic acid on one

end and linoleic acid in the middle. Figure 4.8. Structure of sphingosine
▪ Other lecithin molecules contain other fatty
acids, but the one on the end is always
saturated and the one in the middle is always
unsaturated.
o Waxy solids that form colloidal suspensions in
water
o Egg yolks and soybeans are good dietary sources
of these lipids. Within the body, they are
prevalent in cell membranes. Figure 4.9. General block diagram for a
o The food industry uses these as emulsifiers to sphingophospholipid
promote the mixing of otherwise immiscible
materials. o The fatty acid is one of the tails, and the
▪ Found in mayonnaise, ice cream, and long carbon chain of sphingosine itself is the
custards. other tail.
• Cephalins (phosphatidylethanolamines and o The polar head is the phosphate group with
phosphatidylserines) its esterified alcohol.
o Amino alcohol attached to phosphate group is • Sphingomyelins
either ethanolamine or serine. o Sphingophospholipids in which the alcohol
o Found in heart and liver tissue and in high esterified to the phosphate group is choline
concentrations in the brain o Found in all cell membranes and are important
structural components of the myelin sheath, the
protective and insulating coating that surrounds
nerve axons.

ABELA, J. 6
 • Gangliosides
o Contain more complex carbohydrate structure
o Contain a branched chain of up to seven (7)
monosaccharide residues
o Occur in the gray matter of the brain and the
myelin sheath

Figure 4.10. Structure of sphingomyelin molecule

o Ceramide portion of the molecule: Fatty acid

and sphingosine
▪ May contain different fatty acids
▪ Stearic acid occurs mainly in sphingomyelin
▪ Found in many cerebrosides

Figure 4.12. Terminology for and Structural

Relationships Among Various Types of Fatty-Acid-
Containing Lipids

LIPIDS AS MESSENGER
STEROIDS
• A group of plant and animal lipids that contain a
tetracyclic ring structure: Three (3) cyclohexane
Figure 4.11. Ceramide portion of sphingomyelin and its rings (A, B, and C) fused with a cyclopentane ring
schematic diagram (D).
o Also called steroid nucleus:
o Most important lipids in the myelin sheaths
o Associated with diseases such as multiple
sclerosis

GLYCOLIPIDS
• Contain carbohydrates and ceramides
• Cerebrosides
o Consists of ceramide mono- or oligosaccharides
o Fatty acid of ceramide part may contain either • Not necessarily esters, though some of them are
18-carbon or 24-carbon chains
o Glucose of galactose forms a beta-glycosidic A. CHOLESTEROL
bond with the ceramide portion • Most abundant steroid in the human body and the
o Occur primarily in the brain (7% of brain’s dry most important
weight) and nerve synapses o Found in cell membranes (up to 25% by mass),
in nerve tissue, in brain tissue (about 10% by dry
mass), and in virtually all fluids.
• Functions
o Plasma membrane component in all animal cells
▪ Red blood cells
o Raw material (precursor) for synthesis of other
steroids such as:
▪ Sex and adrenocorticoid hormones
▪ Bile salts
• Exists both in free form and esterfied with fatty
acids.

ABELA, J. 7
• Most of it is biosynthesized by the liver and (to a 3. Once VLDL reaches muscle or fat tissues,
lesser extent) the intestine even without dietary triglycerides and proteins are removed from the
intake. VLDL
o Cholesterol synthesis in liver is reduced to half 4. As fat is removed, its density increases and it
the normal rate of production when cholesterol becomes LDL
levels in the blood exceeds 150 mg/100 mL. 5. LDL carries cholesterol to cells, where specific LDL
• 10-15% of the cholesterol in our systems those receptors bind it.
ingested from diet; however, total body cholesterol 6. apoB-100 protein on the surface of the LDL binds
levels increase with increased dietary intake of specifically to the LDL-receptor molecules in the
cholesterol because ingested cholesterol decreases coated pits.
biosynthetic cholesterol production. 7. After such binding, the LDL is taken inside the cell
o Excess, not presence, of cholesterol is the one (endocytosis), where enzymes break down the
associated with disease. lipoprotein.
• Lipoproteins 8. In the process, they liberate free cholesterol from
▪ Spherically shaped clusters containing both lipid cholesteryl esters
molecules and protein molecules.
▪ Core of hydrophobic lipid molecules REVERSE CHOLESTEROL TRANSPORT
surrounded by a shell of hydrophilic 1. High-density lipoproteins (HDL) transport
molecules such as proteins and cholesterol from peripheral tissues to the liver and
phospholipids. also transfer cholesterol to LDL.
▪ Protein carrier system for biosynthetic 2. While in the serum, free cholesterol in HDL is
cholesterols, which are only sparingly soluble in converted to cholesteryl esters.
water (blood). 3. In the liver, HDL binds to the liver cell surface and
▪ LDLs (low-density lipoproteins) - carry transfers its cholesteryl esters to the cell.
cholesterol from the liver to various tissues. 4. These esters are used for the synthesis of steroid
▪ HDLs (high-density lipoproteins) - carry hormones and bile acids.
excess cholesterol from tissues back to the 5. After HDL has delivered its cholesteryl esters to
liver. liver cells, it reenters circulation.
▪ High-density lipoprotein HDL (“good
cholesterol”), which consists of about B. STEROID HORMONES
33% protein and about 30% cholesterol • Hormones that are cholesterol derivative
and cholesteryl esters • Two types
▪ Low-density lipoprotein LDL (“bad o Adrenocorticoid hormones
cholesterol”), which contains only 25% o Sex hormones
protein but 50% cholesterol and
cholesteryl esters ADRENOCORTICOID HORMONES
▪ Very-low-density lipoprotein (VLDL), Function Major Hormone
which mostly carries triglycerides (fats) Mineralocorticoids control the Aldosterone
synthesized by the liver balance of Na+
▪ Chylomicrons, which carry dietary lipids and K+ ions in
synthesized in the intestines cells and
body fluids

Glucocorticoids control glucose Cortisol

metabolism and (hydrocortisone)
counteract
inflammation *Hormone
synthesized in the
largest amount by the
adrenal glands

*Used as prescription
drugs to control
inflammatory diseases
CHOLESTEROL TRANSPORT such as rheumatoid
arthritis
1. Transport of cholesterol from the liver starts out as
a large VLDL particle.
2. VLDL contains triglycerides and cholesteryl esters

ABELA, J. 8
 SEX HORMONES
Function Location of Synthesis
Estrogen Development of Ovaries
(female) female secondary Adrenal cortex
sex characteristics
at the onset of
puberty

Figure 5.1. Structure of mineralocorticoids (left) and Regulation of the

glucocorticoids (right) menstrual cycle

Stimulate the
development of the
mammary glands
during pregnancy

Induce estrus (heat)

in animals
Estradiol Primary estrogen; Ovaries
(female) most important
female sex
hormone

Responsible for
secondary
female
characteristics
Androgens Promote the Testes
(male) development of Adrenal cortex
male secondary sex
characteristics

Promote muscle
growth
Testosterone Most important Testes
(male) male sex hormone;
promotes the
normal growth of
the male genital
organs

Primary androgen
Progestins Prepare the lining Ovaries
(pregnancy) of the uterus for Placenta
implantation of the
fertilized ovum.

Suppress ovulation
Progesterone Primary progestin Ovaries

Prepares the uterus

for
pregnancy

• Synthetic steroids
o Mimic those of the natural steroid hormones.
▪ Oral contraceptives - used to suppress
ovulation as a method of birth control; mix of
Figure 5.2. Structure of selected sex hormones synthetic estrogen and progestin
▪ RU-486 (“morning after pill”) - interferes with
gestation of a fertilized egg and terminates a

ABELA, J. 9
 pregnancy within the first nine weeks of ▪ Inhibiting the secretion of gastric juices
gestation more effectively and safely than ▪ Increasing the secretion of a protective
surgical methods mucus layer into the stomach
▪ Anabolic steroids - illegal steroid drugs used ▪ Relaxing and contracting smooth muscle
by some athletes to build up muscle strength ▪ Directing water and electrolyte balance
and enhance endurance ▪ Intensifying pain
▪ Enhancing inflammation responses
▪ Control blood flow
▪ Formation of blood clots
▪ Induction of labor
o Aspirin reduces inflammation and fever
because it inactivates enzymes needed for
prostaglandin synthesis
Figure 5.3. Structure of selected synthetic steroids o Cyclooxygenase (COX)
▪ Catalyst enzyme for synthesis of
C. EICOSANOIDS prostaglandins from arachidonic acid
• An oxygenated C20-fatty-acid derivative that ▪ COX-1 catalyzes the normal physiological
functions as a messenger lipid. production of prostaglandins
o Eikos (Greek) – “twenty” ▪ COX-2 is responsible for the production of
o Metabolic precursor: Arachidonic acid (20:4) prostaglandins in inflammation
• Hormone-like molecules rather than true hormones ▪ When a tissue is injured or damaged,
because they are not transported in the special inflammatory cells invade the
bloodstream. injured tissue and interact with resident
• Exert their effects in the tissues where they are cells, for example, smooth muscle cells.
synthesized ▪ This interaction activates COX-2 and
• Usually have a very short “life,” being broken down, prostaglandins are synthesized
often within seconds of their synthesis, to inactive
residues.
• Mediates:
o The inflammatory response, a normal response
to tissue damage
o The production of pain and fever
o The regulation of blood pressure
o The induction of blood clotting
o The control of reproductive functions, such as
induction of labor
o The regulation of the sleep/wake cycle

• Prostaglandin
o A family of compounds that have the 20-
carbon skeleton of prostanoic acid
▪ Not stored in tissues as such, but are
synthesized from membrane-bound 20-
carbon polyunsaturated fatty acids (e.g. Figure 5.4. Action of cyclooxygenase
arachidonic acid) in response to specific
• Thromboxane
physiological triggers
o C20-fatty-acid derivative that contains a
o Prostaglandins are named after the prostate
gland, which was first thought to be their cyclic ether ring and oxygen-containing
only source. functional groups
o Promote the formation of blood clots
▪ Detected in the seminal fluid, which is
o Promote platelet aggregation and
produced by the prostate gland
o Made at sites of tissue damage or infection
vasoconstriction (Thromboxane A2)
that are involved in dealing with injury and
illness
o Regulatory functions:
▪ Raising body temperature

ABELA, J. 10
 c. They almost always contain an odd number of
carbon atoms.
d. no correct response

5. In which of the following pairs of fatty acids are

both members of the pair polyunsaturated fatty
acids?
o Produced by blood platelets a. 18:0 acid and 18:1 acid
o Aspirin and other nonsteroid anti- b. 18:1 acid and 18:2 acid
inflammatory drugs (NSAIDs) inhibit the c. 18:2 acid and 18:3 acid
synthesis of thromboxanes by inhibiting the d. no correct response
COX enzyme
• Leukotrienes 6. The double bond present in a monounsaturated
o C20-fatty-acid derivative that contains three fatty acid almost always
conjugated double bonds and hydroxy groups a. is in a cis-configuration
o Various inflammatory and hypersensitivity b. involves the second carbon from the carboxyl
(allergy) responses are associated with end of the carbon chain
elevated levels of leukotrienes. c. involves the second carbon from the methyl
o Produce muscle contractions, especially in end of the carbon chain
the lungs and thereby can cause asthma-like d. no correct response
attacks. 100x more potent than histamine.
o Found in leukocytes 7. How many structural “subunits” are present in
the block diagram for a triacylglycerol?
a. two
b. three
c. four
REVIEW QUESTIONS d. no correct response
1. A lipid is any substance of biochemical origin
that is 8. How many ester linkages are present in a
a. soluble in water but insoluble in nonpolar triacylglycerol molecule?
solvents a. zero
b. insoluble in water but soluble in nonpolar b. two
solvents c. four
c. soluble in both water and nonpolar solvents d. no correct response
d. no correct response
9. Which of the following is a distinguishing
2. Which of the following is not a biochemical characteristic between fats and oils?
function classification for lipids? a. physical state at room temperature
a. membrane lipid b. number of structural subunits present
b. messenger lipid c. number of fatty acid residues present
c. emulsification lipid d. no correct response
d. no correct response
10. Which of the following are the expected
3. The saponifiable/nonsaponifiable classification products when a fat undergoes saponification?
system for lipids is based on a. glycerol and fatty acids
a. lipid behavior in acidic solution b. glycerol and fatty acid salts
b. lipid behavior in basic solution c. fatty acids and fatty acid salts
c. ability of lipids to react with alcohols d. no correct response
d. no correct response
11. The effect of partial hydrogenation of a fat or oil
4. Which of the following statements concerning is which of the following?
fatty acids is correct? a. decrease in the degree of fatty acid
a. They are naturally occurring dicarboxylic unsaturation
acids. b. decrease in melting point of the fat or oil
b. They are rarely found in the free state in c. increase in the number of fatty acid residues
nature. present in a molecule

ABELA, J. 11
 d. no correct response a. Some, but not all of them, are cholesterol
derivatives.
12. Based on biological function, phospholipids are b. Some, but not all of them, are glucose
classified as derivatives.
a. energy-storage lipids c. All of them are cholesterol derivatives.
b. membrane lipids d. no correct response
c. messenger lipids
d. no correct response 19. Which of the following substances is associated
with Na+/K+ balance in the human body?
13. Which of the following types of lipids contain a. aldosterone
both ester and amide linkages? b. cortisol
a. triacylglycerols c. prednisolone
b. sphingophospholipids d. no correct response
c. glycerophospholipids
d. no correct response 20. The metabolic precursor for the production of
most eicosanoids is
14. Which of the following statements about the a. cholesterol
molecule sphingosine is correct? b. arachidonic acid
a. Two amino groups and one hydroxyl group c. sphingosine
are present. d. no correct response
b. Two hydroxyl groups and one amino group
are present. 21. Aspirin reduces inflammation and fever by
c. Two hydroxyl groups and two amino groups inhibiting the formation of which of the
are present. following types of messenger lipids?
d. no correct response a. prostaglandins
b. thromboxanes
15. In terms of the “head and two tails” model for c. leukotrienes
phospholipids d. no correct response
a. both tails are hydrophobic.
b. both tails are hydrophilic. REFERENCES
c. one tail is hydrophilic and the other 1. Bettelheim, F. (2016). Introduction to General,
hydrophobic. Organic, and Biochemistry. Cengage
d. no correct response 2. Stoker, H. S. (2016). General, Organic, and
Biochemistry. Cengage
16. The “steroid nucleus” common to all steroid 3. Lipids lecture. Prepared by Ms. Lenzie Santillan
structures involves a fused-ring system that
contains Goodluck MT Tams! Road to RMT on 2024. Kaya natin
a. four 6-membered rings ‘to.
b. four 5-membered rings "Have some fire. Be unstoppable. Be a force of nature. Be
c. three 6-membered rings and one 5- better than anyone here and don't give a damn about what
membered ring anyone thinks." – Cristina Yang, Grey’s Anatomy
d. no correct response

17. Which of the following statements concerning

cholesterol is correct?
a. An alcohol functional group is present in its
structure.
b. The lipoprotein HDL distributes cholesterol to
various parts of the human body.
c. The cholesterol associated with LDL is often
called “good cholesterol.”
d. no correct response

18. Which of the following statements concerning

steroid hormones is correct?

ABELA, J. 12
 MTY1107: BIOCHEMISTRY | LECTURE
MODULE 4: PROTEINS
NAME OF LECTURER: Ms. Lenzie Santillan
DATE: September 16, 2021

TABLE OF CONTENTS • α-amino acid

o An amino acid in which the amino group and the
I. FUNCTIONS OF PROTEINS 1 carboxyl group are attached to the α -carbon
II. AMINO ACIDS 1 atom.
III. PEPTIDE BONDS 4 o Amino acids found in proteins are always α-
IV. SIDE CHAINS 5 amino acids.
V. LEVELS OF PROTEIN STRUCTURES 6 o Contains the following chemical groups:
VI. PROTEIN DENATURATION 11 ▪ Amino group
REFERENCES ………………………………………………………. 12 ▪ Carboxyl group
▪ Side chain (R) - distinguishes α-amino acids
FUNCTIONS OF PROTEINS from each other, both physically and
• Structure. Structural proteins, such as keratin and chemically.
collagen, are the chief constituents of skin, bones, • There are only 20 standard amino acids.
hair, and nails for animals. o Standard amino acid - one of the 20 α-amino
• Catalysts. Enzymes catalyze virtually all reactions in acids normally found in proteins.
living organisms. o Grouped according to side-chain polarity:
• Movement. Muscles are made up of protein ▪ Nonpolar amino acids - contains a nonpolar
molecules myosin and actin. side chain; hydrophobic and generally found
• Transport. Transport molecules across cell in the interior of proteins.
membranes. ▪ Polar neutral amino acids – contains a polar
o Hemoglobin – blood protein that transports but neural side chain, neither acidic nor basic
oxygen from lungs to the cells, and CO2 from in solution at physiological pH. More soluble
cells to lungs. in water.
• Hormones. Insulin, erythropoietin, and human ▪ Polar acidic amino acids - contains one amino
growth hormone are proteins that serve as group and two carboxyl groups, the second
hormones. carboxyl group being part of the side chain.
• Protection. Blood clotting and protection from Side chain bears negative charge in solution
foreign substances. at physiological pH as the side-chain carboxyl
o Antibodies – production of this protein is one of group has lost its acidic hydrogen atom.
the major mechanisms of the body to fight ▪ Polar basic amino acids - two amino groups
disease. and one carboxyl group, the second amino
o Fibrinogen – blood clotting protein group being part of the side chain. Side chain
• Storage. Stores materials in the way starch and bears positive charge in solution at
glycogen store energy. physiological pH as nitrogen atom of side-
o Casein (milk) and ovalbumin (eggs) – stores chain amino group has accepted a proton.
nutrients for newborn mammals and birds • Essential amino acid
o Ferritin (liver) - iron o Standard amino acid needed for protein
• Regulation. Controls the expression of genes and synthesis that must be obtained from dietary
dictate when protein manufacture takes place. sources.

AMINO ACIDS ▪ arginine* ▪ methionine

• An organic compound that contains an amino group ▪ histidine ▪ phenylalanine
(-NH2) and a carboxyl group (-COOH); serve as the ▪ isoleucine ▪ threonine
building block for proteins. ▪ leucine ▪ valine
▪ lysine ▪ lysine

*Required for growth in children, but is not an

essential acid for adults

ABELA, J. 1
• Uncommon amino acids
o Aside from the common/standard amino
acids, there are others that occur in some but
not all proteins.

EXAMPLES OF UNCOMMON AMINO ACIDS

Parent Amino
Acid and Side- Uncommon
Function/Use
Chain Functional Amino Acid
Group Present
▪ Found in connective
Proline, Hydroxyl tissue protein such as
Hydroxyproline
group collagen

▪ Found in connective
Lysine, Hydroxyl tissue protein such as
Hydroxylysine Figure 2.2. Names and Abbreviations of the 20 Standard
group collagen
Amino Acids
▪ Found only in the
Tyrosine, extra thyroid
iodine-containing Thyroxine ▪ Ramps up
CHIRALITY OF AMINO ACIDS
aromatic group metabolism for
animals and humans • 19 of the 20 standard amino acids possess a chiral
center, therefore two enantiomeric forms (D- and L-
isomers) exist for each of these amino acids.

o Four different groups are attached to the a-

carbon atom in all of the standard amino acids
except glycine, where the R group is a hydrogen
atom.

• Amino acids in nature and in proteins are L isomers.

(L-configuration at the α -carbon)
o Unlike in monosaccharides, D isomers are rare.
Some are found in the cell walls of bacteria.

Figure 2.1. The 20 Standard Amino Acids, Grouped

According to Side-Chain Polarity
CLASSIFICATIONS OF AMINO ACID
• Aside from side chain polarity, amino acids can be
grouped under different classifications.

ABELA, J. 2
 POLARITY TYPE OF SIDE CHAIN (R)
UNCHARGED • Alanine (Ala, A) NEUTRAL with aliphatic • Glycine (Gly, G)
NONPOLAR • Valine (Val, V) hydrocarbon group • Alanine (Ala, A)
• Isoleucine (Ile, I) • Valine (Val, V)
• Leucine (Leu, L) • Isoleucine (Ile, I)
• Proline (Pro, P) • Leucine (Leu, L)
• Phenylalanine (Phe, F) • Proline (Pro, P)
• Methionine (Met, M) NEUTRAL with sulfur- • Cysteine (Cys, C)
• Tryptophan (Trp, W) containing side chain • Methionine (Met, M)
UNCHARGED POLAR • Cysteine (Cys, C) NEUTRAL with hydroxyl • Serine (Ser S)
• Glycine (Gly, G) group • Threonine (Thr, T)
• Serine (Ser S) NEUTRAL with aromatic • Tyrosin (Tyr, Y)
• Threonine (Thr, T) ring
• Tyrosin (Tyr, Y) NEUTRAL with amide • Asparagine (Asn, N)
• Asparagine (Asn, N) group • Glutamine (Gln, Q)
• Glutamine (Gln, Q) ACIDIC • Aspartic acid (Asp, D)
CHARGED POLAR • Lysine (Lys, K) • Glutamic acid (Gln, E)
• Arginine (Arg, R) BASIC • Lysine (Lys, K)
• Histidine (His, H) • Arginine (Arg, R)
• Aspartic acid (Asp, D) • Histidine (His, H)
• Glutamic acid (Gln, E)
FROM UN-IONIZED TO ZWITTERION

NUTRITIONAL REQUIREMENT
NON-ESSENTIAL • Alanine (A, A)
• Asparagine (Asn, N)
• Glutamine (Gln, Q)
• Aspartic acid (Asp, D) Above is an un-ionied α-amino acid. In neutral solution,
• Cysteine (Cys, C)
carboxyl groups ten to lose protons (H+), producing a
• Glutamic acid (Gln, E)
• Glycine (Gly, G) negatively charged species:
• Proline (Pro, P)
• Serine (Ser S) Amino groups,
• Tyrosin (Tyr, Y) on the other hand, tend to accept protons (H+),
• producing a positively charged species.
ESSENTIAL • Histidine (His, H)
• Isoleucine (Ile, I)
• Leucine (Leu, L)
• Lysine (Lys, K)
Therefore, in neutral solution, the -COOH group
• Methionine (Met, M)
• Phenylalanine (Phe, F) of an amino acid donates a proton to the -NH2 of the
• Threonine (Thr, T) same amino acid, the net result is a zwitterion.
• Tryptophan (Trp, W)
• Valine (Val, V)
• Arginine (Arg, R)

ZWITTERION
• Ionic compounds (internal salts) that have both a • Amino acids are zwitterions both in water and solid
negative and positive atom, but which has no net state, and being such a compound gives them their
charge. physical properties, such as:
• α-amino acids are commonly written in the un-ionized o High melting points
form, however since carboxylic acids cannot exist in o Solubility in water
the presence of a moderately weak base (NH3), they • Note that the net charge on a zwitterion is zero even
donate a proton to become carboxylic ions (COO-); though parts of the molecule carry charges.
therefore, they are more properly written as • Zwitterion structure changes when the pH of the
zwitterions. solution containing an amino acid is changed to acidic
(low pH) or basic (high pH).

ABELA, J. 3
 o Addition of acid, such as H3O+ (low pH, like 0) – o Amide – carboxylic acid + amine
positively charged ion, since -COO- receives a
proton H+ from H3O+

•
Classification of peptides by no. of amino acids in the
chain linked by a peptide bond:
o Addition of base, such as NaOH (high pH, like pH o Peptide – shortest chains of amino acids
14) – negatively charged ion, since -NH3+ donates a ▪ Dipeptide – contains two amino acids
▪ Tripeptide – contains three amino acids
▪
o Polypeptide – longest chains of amino acids; a
macromolecule
o Protein – biological macromolecule/polypeptide
chain containing at least 30 to 50 amino acids
proton to the OH- • Residues
o In solution, three different amino acid forms can o Individual amino acid units in the chain
exist: zwitterion (neutral), negative ion, and o Portion of an amino acid structure that remains,
positive ion after the release of H2O, when an amino acid
participates in peptide bond formation as it
becomes part of a peptide chain.

• Isoelectric point (pI)

o pH at which an amino acid exists primarily in its
zwitterion form (no net charge). • C-terminus (C-terminal amino acid) – amino acid at
o All molecules have equal positive and negative the end of the chain having the free -COO- group
charges. • N-terminus (N-terminal amino acid) – amino acid at
o 15/20 standard amino acids have pI near 6 (ranging the end of the chain having the free -NH3+ group
from 4.8 to 6.3). Figure 3.1. Example of N-terminus (Glycine) and C-
o 3/20 basic standard amino acids have higher pI
o 2/20 acidic standard amino acids have lower pI
• Amphiprotic
o Compound that is both an acid and a base
o Amino acids are amphiprotic because they have an
acid (COO-) and a base (NH3+)
• Buffers
o Recall that buffers neutralize both acid and base. It terminus (Serine) in tripeptide Gly-Ala-Ser
is an aqueous solution consisting of a mixture of a
weak acid and its conjugate base, or vice versa. Its • It is the universal custom to write polypeptide chains
pH changes very little when a small amount of with the N-terminal residue on the left because
strong acid or base is added to it. proteins are synthesized from left to write.
o Aqueous solutions of amino acids are buffers
because they have an acid and a base, and in
addition of a strong acid/base, will result in a
conjugate acid/base.
PEPTIDE BONDS (PEPTIDE LINKAGE)
• The special name given to the amide bond between
the α-carboxyl group of one amino acid and the
αamino group of another.
Figure 3.2. Small peptide showing the direction of the
peptide chain

ABELA, J. 4
• Backbone of a peptide: Repeating sequence of PHYSIOLOGICALLY IMPORTANT AMINO ACID
peptide bonds and α-carbon in a peptide DERIVATIVES
Amino Acid Derivative/Relat Function/Use
ed proteins
▪ Calming effect
▪ Low levels –
depression
▪ High levels – manic
5-hydroxytryptamine state
(serotonin) ▪ Controlled levels
o The side chains (R group) are considered manage manic-
substituents rather than part of the actual depressive (bipolar)
backbone. disorder
o Structurally, a peptide has: Tryptophan
▪ Helps in inducing
o Backbone – regularly repeating part sleep due to high
o R group – variable part levels of tryptophan

• Peptide Nomenclature Milk protein

Example: Gly-Tyr-Leu-Val
o Rule 1: The C-terminal amino acid residue
(located at the far right of the structure) keeps its
full amino acid name. ▪ Neurotransmitter
▪ In Gly-Tyr-Leu-Val, valine (Val) remains valine class
o Rule 2: All of the other amino acid residues have ▪ Stimulatory
names that end in -yl. The -yl suffix replaces the - hormones
Catecholamines, such (epinephrine and
ine or -ic acid ending of the amino acid name,
as epinephrine norepinephrine)
except for tryptophan (tryptophyl), cysteine (adrenalin) and ▪ Epinephrine – “fight
(cysteinyl), glutamine (glutaminyl), and norepinephrine or flight”, release of
asparagine (asparaginyl). glucose and other
▪ Glycine (Gly) becomes glycl; tyrosine (Tyr) nutrients into the
blood and stimulates
become tyrosyl; leucine (Leu) becomes leucyl brain function
o Rule 3: The amino acid naming sequence begins L- ▪ Intermediate in the
at the N-terminal amino acid residue dihydroxyphenylalanine conversion of
▪ Beginning with glycyl, the complete name for tyrosine to
epinephrine
this tetrapeptide is glycyltyrosylleucylvaline. Tyrosine and
▪ Precursor of
Phenylalanine
dopamine
SIDE CHAINS (R GROUP) AND THE PROPERTIES OF ▪ Lower than normal
AMINO ACIDS AND PROTEINS levels associated with
• The functions of amino acids, their polymers, Parkinson’s disease
▪ Supplements of this
proteins, are determined by side chains because are prescribed as it
these are the only difference between amino acids. passes quickly
o Particular emphasis on the functional group through the blood-
within these side chains. brain barrier and into
the brain
▪ Glutamine : Amide functional group
Aspartame ▪ Contains
phenylalanine
▪ Artificial sweetener
found in softdrinks
▪ Gives headache for
some people

PROPERTIES OF AMIINO ACIDS DUE TO SIDE CHAINS

• Acid-base properties
o Glutamic and aspartic acid – side-chain carboxylic
group (acidic at near at or neutral pH)
o Histidine, lysine, arginine – basic side chain at or
near neutral pH
• Interaction with other amino acids for 3D shape of
protein
o Due to polarity and charge of the side chains

ABELA, J. 5
• Location and measurement of concentration of ▪ At any pH above isoelectric point (basic) –
proteins net negative charge
o Tyrosine, phenylalanine, and tryptophan – side- ▪ Example: Serum albumin (pH 4.0)
chain aromatic rings absorb ultraviolet light at 280 o Act as buffers
nm o Proteins are least soluble in water at their
isoelectric points and can be precipitated from their
PROPERTIES OF PROTEINS solutions
• Based on: ▪ Water solubility of large molecules such as
o Properties of peptide backbone proteins often depends on the repulsive forces
o Properties of side chains between like charges
• Peptide linkages are essentially planar o Net positive or net negative charges – presence of
o Amide plane – two amino acids linked through a repulsive forces, protein molecules become
peptide linkage, six atoms lie in the same plane: soluble
the α-carbon atom and the C=O group from the o No net charge – no repulsive forces; protein
first amino acid and the N-H group and the α- molecules clump together to form aggregates,
carbon atom from the second amino acid. reducing solubility

LEVELS OF PROTEIN STRUCTURES

PRIMARY STRUCTURE
o The sequence of amino acids in a polypeptide chain.
o Read from N-terminus to C-terminus
o Linear with amide planes in the peptide bond

o Within a peptide linkage, the carbon-nitrogen

bond has some double-bond character (40%)
because of resonance. • The number peptides possible from the 20 protein-
▪ Causes the planar structure of the peptide derived amino acids is enormous.
linkage because the carbon-nitrogen bond o The number of peptides possible for a chain of n
is rigid, limited by its double bond amino acids is 20n. n = no. of amino acids in chain
character. o 202 = 20 x 20 = 400 dipeptides
▪ The net effect of “peptide bond planarity” is o 203 = 20 x 20 x 20 = 8000 tripeptides
the zigzag arrangement of atoms within a o For a small protein of 60 amino acids, the number
protein backbone, making the amide plane of proteins possible is 2060 = 1078
look like playing cards. o Slight change of sequence may make little to no
difference, but most of the time the sequence is
highly important.
o Human insulin is far too small to meet the need of
people with sever diabetes, so bovine, hog, or
sheep insulin can be used as an alternative,
despite being different only at the 8, 9, and 10
positions of the A chain and C-terminal position.
o Behaves like zwitterions
o Side chains of amino acids causes acid-base
behavior
▪ Glutamic and aspartic – acidic groups
▪ Lysine, arginine, histidine – basic groups
o Net charges
▪ At or near isoelectric point of protein – no
net charge (equal positive and negative ▪ However, human insulin is still best, so
charges) recombinant DNA techniques are now being
▪ Example: Hemoglobin (pH 6.8) used to synthesize this via bacteria.
▪ At any pH below isoelectric point (acidic) –
net positive charge

ABELA, J. 6
 o Nonapeptides oxytocin and vasopressin have
identical structures and disulfide bond, yet
their difference of amino acids in positions 2
and 7 makes their biological functions differ.
▪ Vasopressin - antidiuretic hormone
▪ Oxytocin - helps with contractions of the
uterus during childbirth and muscles of the
breast for milk
Figure 5.2. α-helix and β-pleated sheet

A. α-HELIX
• A protein secondary structure in which a single
protein chain adopts a shape that resembles a
coiled spring (helix), with the coil configuration
maintained by hydrogen bonds.
• The twist of the helix forms a right-handed, or
clockwise, spiral.
• The hydrogen bonds between C=O and N-H
entities are orientated parallel to the axis of
the helix.
• Each turn of the spiral includes 3.6 amino acid
residues.
o One change in the sequence of hemoglobin • The N-H groups of peptide bonds point in the
causes the fatal sickle cell anemia. same direction, roughly parallel to the axis of
the helix.
SECONDARY STRUCTURE • The C=O groups of peptide bonds point in the
• Conformations of amino acids in localized regions of opposite direction, also roughly parallel to the
a polypeptide chain axis of the helix.
• Hydrogen bonding between a carbonyl oxygen • All of the amino acid R groups extend outward
atom of a peptide linkage and the hydrogen atom from the spiral. There is not enough room for
of an amino group of another peptide linkage the R groups within the spiral.
farther along the protein backbone is responsible
for the conformations

Figure 5.1. The hydrogen bonding between the carbonyl

oxygen atom of one peptide linkage and the amide Figure 5.3. Four representations
hydrogen atom of another peptide linkage of the α-helix protein secondary
structure
• The most common types of secondary structure
are α-helix and β-pleated sheet. • Factors that can disrupt an α-helix
o Proline creates a bend because of (1) the
restricted rotation due to its cyclic structure
and (2) its amino group has no N-H for
hydrogen bonding.

ABELA, J. 7
 o Strong electrostatic repulsion caused by the
proximity of several side chains of like
charge, e.g., Lys and Arg or Glu and As.
o Steric crowding caused by the proximity of
bulky side chains, e.g., Val, Ile, Th
• Keratin - predominantly α-Helix

B. β-PLEATED SHEET
• A type of secondary structure in which two
polypeptide chains or sections of the same
polypeptide chain align parallel to each other; the
chains may be parallel or antiparallel
• Hydrogen bonds form between oxygen and
hydrogen peptide linkage atoms that are either:
o Intrachain (intramolecular) – in different parts of
a single chain that folds back on itself, meaning
between segments of the same polypeptide
o Interchain (intermolecular) – in between atoms
in different peptide chains in those proteins that
contain more than one chain, meaning between
separate polypeptide chains.

Figure 5.5. Parallel and antiparallel β-pleated sheets

• Features of a β-pleated sheet

o The six atoms of each peptide bond of a β-
pleated sheet lie in the same plane.
o The C=O and N-H groups of the peptide bonds
from adjacent chains point toward each other
and are in the same plane so that hydrogen
bonding is possible between them.

Figure 5.4. β-pleated sheet secondary structure

• Occur between molecules when polypeptide

chains run parallel (all N-terminal ends on one
side) or antiparallel (neighboring N-terminal
ends on opposite sides)
• In molecules where the β-pleated sheet involves
a single molecule, several U-turns in the protein
chain arrangement are needed to form the
structure.
o “U-turn structure” is the most frequently o All R- groups on any one chain alternate, first
encountered type of β-pleated sheet above, then below the plane of the sheet, etc
structure.
▪ Like a hairpin
▪ Runs antiparallel

ABELA, J. 8
 • β-bulge
• A common non-repetitive irregular 2˚ motif
in anti-parallel structure

o Greek key - a repetitive supersecondary

structure formed when an antiparallel
sheet doubles back on itself

• Structure of reverse turns

• Glycine and proline are encountered
o β-barrel – created when β-sheets are
• Spatial (steric) reasons
extensive enough to fold back on themselves
• Polypeptide changes direction

• Fibroin (in silk) – mainly β-Pleated Sheet

C. SUPERSECONDARY STRUCTURES
• The combination of α- and β-sections
o βαβ unit - two parallel strands of b-sheet D. RANDOM COIL
connected by a stretch of a-helix • A polymer conformation where the monomer
subunits are oriented randomly while still being
bonded to adjacent units.

o αα unit - two antiparallel a-helices

• Most proteins, especially globular ones, have

o β-meander - an antiparallel sheet formed by only certain portions of their molecules in these
a series of tight reverse turns connecting conformations.
stretches of a polypeptide chain

ABELA, J. 9
 o Many contain all three: α-helix, β-pleated F. TYPES OF PROTEINS
sheet, and random coil: • Fibrous proteins
o Contain polypeptide chains organized
approximately parallel along a single axis
o Characteristics:
▪ Consist of long fibers or large sheets
▪ Tend to be mechanically strong
▪ Insoluble in water and dilute salt
solutions
▪ Play important structural roles in nature
o Examples:
▪ Keratin (hair, wool)
▪ Collagen
• Globular proteins
o Proteins which are folded to a more or less
Figure 5.6. Schematic structure of the enzyme
spherical shape
carboxypeptidase. o Characteristics:
▪ Soluble in water and salt solutions
E. COLLAGEN TRIPLE HELIX (EXTENDED HELIX) ▪ Most of polar side chains are outside and
• Three polypeptide chains wrapped around each interact with the aqueous environment
other in a ropelike twist to form a triple helix ▪ Most of their nonpolar side chains are
called tropocollagen. MW approx. 300,000 buried inside
▪ Nearly all have substantial sections of α-
helix and β-pleated sheet

TERTIARY STRUCTURE
• The overall conformation of an entire polypeptide
chain. 3-dimensional arrangement of atoms in the
molecule.
o In fibrous protein, backbone of protein does not
fall back on itself, it is important aspect of 3˚ not
specified by 2˚ structure
o In globular protein, more information needed.
3k structure allows for the determination of the
way helical and pleated-sheet sections fold back
on each other.
• Interactions between side chains also plays a role
• Five ways to stabilize tertiary protein structure
o Covalent bonds. The formation of disulfide
bonds between cysteine side chains.
• 30% proline and hydroxyproline; also include ▪ Disulfide bond is the one most often involved
hydroxylysine in stabilizing tertiary structure and is the
o The three strands are held together by strongest.
hydrogen bonding involving hydroxyproline ▪ Human insulin
and hydroxylysine o Hydrogen bonding. Between polar groups on
• Each strand consists of repetitive strands of Gly- side chains or between side chains and the
X-Y. peptide backbone.
o Every third position is Gly (shortest side ▪ Between -OH groups of serine and threonine
chain) and repeating sequences are X-Pro-Gly o Salt bridges (Electrostatic attractions). Occur
and X-Hyp-Gly between two amino acids with ionized side-
• Each polypeptide chain is a helix but not an a- chains: acidic (-COO-) and basic (-NH3+ or =NH2+).
helix Held together by ion-ion attraction.
▪ Attraction of the -NH3+ group of lysine and -
COO- group of aspartic acid
o Hydrophobic interactions. Globular proteins in
aqueous solution turn their polar groups

ABELA, J. 10
 outward toward the aqueous solvent, and • Collagen
nonpolar groups turn inward away from the o Consists of many tropocollagen units, only found
water molecule. Nonpolar groups prefer to in fetal or young connective tissues. They are
interact with each other, resulting in this soluble.
interaction. o As one ages, the triple helixes organize
▪ Weaker than hydrogen bonding and salt themselves into fibrils cross-link and form
bridges but acts over large surface areas. This insoluble collagen.
makes the interactions collectively strong • Integral membrane protein
enough to stabilize. o Quaternary structures in which the outer
o Metal ion coordination. Two side chains with surface is largely nonpolar (hydrophobic) and
like charges would repel each other, but can interacts with the lipid bilayer.
also be linked via a metal ion,
▪ Two glutamic acid side chains would both
be attracted to a magnesium ion, forming
a bridge.
▪ This is why the human body requires
certain trace minerals.

QUATERNARY STRUCTURE
• The arrangement of polypeptide chains into a
noncovalently bonded aggregation.
Individual chains are held together by hydrogen
o
bonds, salt bridges, hydrophobic interaction
• Hemoglobin
o Adult hemoglobin – Two α chains, 141 amino Figure 5.8. (a) Integral membrane protein of
acids each; two β chains, 146 amino acids each rhodopsin, made of α-helices (b) Integral
o Fetal hemoglobin - Two α chains and two membrane protein from the out mitochondrial
gamma chains. Has greater affinity for oxygen membrane forming a β-barrel from eight β-pleated
than adult hemoglobin. sheets
▪ Alleviates some of the symptoms of sickle cell
anemia
o Each chain surrounds an iron-containing heme
unit.
▪ Globins – amino acid
▪ Heme units – prosthetic groups
o Conjugated proteins – non-amino acid portions
of protein
o Prosthetic group – non-amino acid portion of
conjugated proteins.

Figure 5.9. Protein structure at a glance

PROTEIN DENATURATION
• The process of destroying the native conformation
of a protein by chemical or physical means.
Figure 5.7. (a) Quaternary structure of heme (b) • The partial or complete disorganization of a
Structure of heme protein’s characteristic three-dimensional shape as
a result of disruption of its secondary, tertiary, and
quaternary structural interactions.

ABELA, J. 11
 o The result of denaturation is loss of biochemical
activity of a protein, which is dependent on its
3D shape.
o Some are reversible, some permanently damage
the protein
▪ Boiling of protein solution will destroy the a-
helical and B-sheet structure because heat
cleaves hydrogen bonds
▪ Permanent: Heat denatures the protein in
egg white, producing a white jellylike solid.
▪ Reversible: Waving hair by treating it with
reducing agent that breaks its disulfide
linkages. The reduced and rearranged hair is
treated with an oxidizing agent (potassium
bromate) to form disulfide linkages at new
locations within the hair. Figure 6.1. Selected Physical and Chemical
o Does not affect the primary structure of a Denaturing Agents
protein.
o “Unfolding”

• Noncovalent interactions that stabilize proteins are

weak and can be disrupted.
• Denaturing Agents:
▪ Heat - disrupt hydrogen bonding; in globular
proteins, it can cause unfolding of polypeptide
chains with the result that coagulation and
precipitation may take place.
▪ 6 M aqueous urea - Disrupts hydrogen bonding.
▪ Surface-active agents - Detergents such as
sodium dodecylbenzenesulfate (SDS) disrupt
hydrogen bonding.
▪ Reducing agents - 2-Mercaptoethanol
(HOCH2CH2SH) cleaves disulfide bonds by
reducing -S-S- groups to -SH groups.
▪ Heavy metal ions - Transition metal ions such as
Pb2+ , Hg2+ , and Cd2+ form water-insoluble salts
with -SH groups; Hg2+ for example forms -S-Hg-S-
▪ Alcohols - 70% ethanol penetrates bacteria and
kills them by coagulating their proteins. It is used
Figure 6.2. Denaturation and Refolding
to sterilize skin before injections.
in Ribonuclease

ABELA, J. 12
 REFERENCES
1. Bettelheim, F. (2016). Introduction to General,
Organic, and Biochemistry. Cengage
2. Stoker, H. S. (2016). General, Organic, and
Biochemistry. Cengage
3. Proteins lecture. Prepared by Ms. Lenzie Santillan

Goodluck MT Tams! Road to RMT on 2024. Kaya natin

‘to.
"I’m sure it must feel as though everything is coming apart,
but you can get through this." –Grey’s Anatomy

ABELA, J. 13
 MTY1107: BIOCHEMISTRY | LECTURE
MODULE 5: ENZYMES
NAME OF LECTURER: Ms. Lenzie Santillan
DATE: September 23, 2021

TABLE OF CONTENTS ▪ Oxidation of glucose occurs within seconds in

the human body compared to exposure to
I. CLASSIFICATIONS OF ENZYMES 1 oxygen in sterile conditions.
A. Nomenclature 1 o Extremely specific. Speeds up only one particular
B. Classification 2 reaction or class of reactions. This also extends to
C. Terminology 3 stereospecificity.
II. ENZYME KINETICS 3 ▪ Urease catalyzes only the hydrolysis of urea.
A. Models of Enzyme Activity 3 ▪ Trypsin only catalyzes the hydrolysis of peptide
B. Enzyme Specificity 4 bonds on the carboxyl side of lysine and
C. Factors That Affect Enzyme Activity 4 arginine residues.
D. Enzyme Inhibition 5 ▪ Carboxypeptidase only catalyzes the hydrolysis
V. ENZYME REGULATION 6 of the amino acid at the C-terminal end.
VI. USES OF ENZYMES IN MEDICINE 8 ▪ Lipases catalyze the hydrolysis of any
A. Enzyme Inhibitors Used in Medicine 8 triglyceride, but no effect on carbohydrates or
VI. TRANSITION-STATE ANALOGS 9 proteins.
REFERENCES ………………………………………………………. 11 ▪ Arginase hydrolyzes only L-arginine to L-
ornithine and urea but has no effect on D-
ENZYMES arginine.
• A large molecule, usually a protein, that increases the o Localized according to the need for specific
rates of chemical reactions without undergoing reactions. Distributed according to the body’s
change. need to catalyze specific reactions. Localization
o Act as biological catalysts also occurs within cells.
o Without these, most biochemical reactions ▪ Proteases – blood, to promote blood
would occur so slowly that they would not clotting.
occur under the mild conditions of ▪ Digestive enzymes – secretions of the
temperature and pressure that are compatible stomach and pancreas.
with life. ▪ Enzymes that catalyze oxidation of
o Vast majority are globular proteins, however not compounds that are part of the citric acid
all are. Some are simple proteins; some are cycle – mitochondria
conjugated proteins. ▪ Lysozyme – lysosomes
▪ Ribozymes – made of ribonucleic acid o Undergo all the reactions of proteins. This
▪ Catalyze the self-cleavage of certain portions includes denaturation.
of their own molecules ▪ Slight alterations in pH or temperature
▪ Implicated in the reaction that generates affect enzyme activity dramatically.
peptide bonds ▪ A person suffering from a high fever
▪ Many biochemists believe that RNA catalysts (greater than 106°F) runs the risk of having
emerged first, with protein enzymes arriving cellular enzymes denatured
later during evolution ▪ Overheating yeast kills the action of the
• Extreme caution must be exercised in handling yeast
enzymes to avoid the loss of their activity. Even
vigorous shaking of an enzyme solution can destroy NOMENCLATURE
enzyme activity • Most commonly named by using a system that
• General Characteristics attempts to provide information about the function
o Do not change the position of equilibrium. (rather than the structure) of the enzyme. Focal
o Extremely effective. Increase the rates of points are:
biochemical reactions by factors of 109 to 1020 o Reaction catalyzed
over uncatalyzed reactions. This is done by o Substrate identity
lowering the activation energy. ▪ Example: Lactate dehydrogenase speeds up
the removal of hydrogen (reaction catalyzed)
from lactate (substrate)
• Three important aspects of enzyme-naming:

ABELA, J. 1
 oThe suffix -ase identifies a substance as an o Examples:
enzyme. ▪ Carbohydrases - effect the breaking of
o The type of reaction catalyzed by an enzyme is glycosidic bonds in oligo- and polysaccharides
often noted with a prefix. ▪ Proteases - effect the breaking of peptide
▪ Oxidase – oxidation reaction linkages in proteins
▪ Hydrolase – hydrolysis reaction ▪ Lipases - effect the breaking of ester linkages
o The identity of the substrate is often noted in in triacylglycerols
addition to the type of reaction.
▪ Glucose oxidase
▪ Infrequently, the substrate but not the
reaction type is given. (Ex. Lactase)
• Enzymes of the digestive tract—pepsin, trypsin, and
chymotrypsin—are some of the enzymes that have • Lyases. Catalyzes the addition of a group to a double
older names, assigned before their actions were bond or the removal of a group (C–C, C–S, and
clearly understood. certain C–N bonds) to form a double bond in a
manner that does not involve hydrolysis or oxidation.
CLASSIFICATION OF ENZYMES o Dehydratase – removal of the components of
• Enzymes are classified into six major group based on water from a double bond
the type of reaction they catalyze. o Hydratase – addition of the components of water
• Oxidoreductases. Catalyze oxidation-reduction to a double bond.
reaction. Requires a co-enzyme that is oxidized or
reduced as the substrate is reduced or oxidized.
o Lactate dehydrogenase

• Isomerases. Catalyzes the isomerization

(rearrangement of atoms) of a substrate in a
• Transferases. Catalyzes the transfer of a functional reaction, converting it into a molecule isomeric with
group (C-, N-, or P) from one molecule to another. itself.
o Two major subgroups: o Only one reactant and one product in the
▪ Transaminases - transfer of an amino group reaction.
from one molecule to another
▪ Kinases - transfer of a phosphate group from
adenosine triphosphate (ATP) to give
adenosine diphosphate (ADP) and a
phosphorylated product; major role in
metabolic-energy production reactions.

• Ligases (or synthetases). Catalyzes the bonding

together of two molecules into one with the
participation of ATP.

• Hydrolases. Catalyzes a hydrolysis reaction in which

the addition of a water molecule to a bond causes
the bond to break.
o Hydrolysis reactions are central to the process of
digestion.

ABELA, J. 2
 such as amino acid side chains, to accommodate
the substrate.

• Enzyme-substrate complex
o The intermediate reaction species that is formed
when a substrate binds to the active site of an
enzyme.
▪ The substrate encounters more favorable
reaction conditions than if it were free. The
result is faster formation of product.
• Activation. Any process that initiates or increases
the action of an enzyme.
ENZYME TERMINOLOGY o Simple addition of a cofactor to an apoenzyme
• Apoenzyme. Protein (polypeptide) portion of the o Cleavage of a polypeptide chain of a proenzyme
enzyme. • Inhibition. Any process that makes an active
• Cofactor. Nonprotein portions of the enzymes enzyme less or inactive.
necessary for catalytic function, such as metallic o Inhibitors – compounds that accomplish
ions Mg2+ and Zn2+ inhibition.
o An apoenzyme cannot catalyze a reaction
without its cofactor and vice versa. ENZYME KINETICS (ENZYME ACTIVITY)
• Coenzyme. Organic molecules that act as cofactors. • Enzyme activity
o B vitamins are an important group of coenzymes o Measure of the rate at which an enzyme
that are essential to the activity of many converts substrate to products in a biochemical
enzymes. reaction
o Heme is an important coenzyme that is part of
o There is no difference in the free energy of the
several oxidoreductases as well as hemoglobin. overall reaction (energy of reactants minus
• Substrate – reactant in an enzyme-catalyzed energy of products) between the catalyzed and
reaction; substance upon which the enzyme “acts” uncatalyzed reactions.
o Enzymes provide an alternate, energetically
favorable reaction pathway different from the
uncatalyzed reaction.
o Factors:
▪ Temperature
▪ pH
▪ Substrate and enzyme concentration

MODELS OF ENZYME ACTION

• Models that account for the highly specific way
an enzyme recognizes a substrate and binds it
to the active site.
• Lock-and-Key Model
o The active site has fixed, rigid geometrical
conformation
o Only substrates with a complementary geometry
• Active site. A three-dimensional cavity (special
pocket or cleft) with specific chemical properties, and chemical nature can be accommodated.

ABELA, J. 3
 o There are weak binding forces (R group • Cofactors such as positively charged metal ions
interactions) between parts often help bind substrate molecules.
o Simplest and most frequently referenced model,
though considered too restrictive
o Analogy: Lock and key

• Induced-Fit Model
o Allows for small changes in the shape or
geometry of the active site of an enzyme to ENZYME SPECIFICITY
accommodate a substrate, result of enzyme’s • Substrate specificity
flexibility. o Limitation of an enzyme to catalyze specific
▪ Enzyme molecules are in dynamic state, not reactions with specific substrates
static. o Basis of enzyme action models
o Adapts to accept the incoming substrate. There o Types:
are weak binding forces (R group interactions) ▪ Absolute specificity
between parts ▪ Group specificity
o Simplest and most frequently referenced model ▪ Linkage specificity
o Analogy: Hand to glove ▪ Stereochemical specificity
• Absolute specificity. Catalyze only one reaction
o Most restrictive specificity, not common
▪ Catalase – absolute specificity for hydrogen
peroxide (H2O2)
• Group specificity. Only act on molecules that have a
specific functional group, such as hydroxyl, amino,
or phosphate groups.
• Both lock-and-key and induced-fit models explain o Carboxypeptidase – cleaves amino acids from
competitive inhibition. the carboxyl end of a peptide chain
o Inhibitor molecule fits into the active site cavity • Linkage specificity. Particular type of chemical
in the same way the substrate does. bond, rest of the molecular structure is not
o Maximum rate is achieved at: considered.
▪ Low substrate concentration, no inhibitor o Most common specificity
▪ High substrate concentration, inhibitor is ▪ Phosphatases – hydrolyze phosphate-ester
present bonds in all types of phosphate esters.
• Noncompetitive inhibition explained by induced-fit • Stereochemical specificity. Act on a particular
model stereoisomer.
o L-amino acid oxidase - catalyze the oxidation
of the l-form of an amino acid but not the d-
form of the same amino acid.

FACTORS THAT AFFECT ENZYME ACTIVITY

• Temperature
oMeasure of the kinetic energy of molecules
oChanges the conformation of the enzyme
oOptimum temperature
▪ The temperature at which an enzyme
• Electrostatic interactions, hydrogen bonds, and exhibits maximum activity
hydrophobic interactions all help attract and bind ▪ pH 7.0 to 7.5 for most enzymes except pepsin
substrate molecules, the same forces that maintain (pH 2.0) and trypsin (pH 8.0)
tertiary structure in the folding of peptide chains. • ↑ temperature, ↑ increase in rate of enzyme
reaction
o Any further increase alters conformation:

ABELA, J. 4
 ▪ Small temperature increase above optimum: substrate molecules due to saturation, the
↓ rate of enzyme reaction reaction rate will stay the same even if we
▪ Within narrow temperature range: Could be increase the substrate concentration
increased again by lowering temperature further.
because changes in conformation are ▪ This is presented by a saturation curve:
reversible
o Higher temperature above the optimum =
protein denaturation = irreversible change in
conformation = enzyme inactivated
• ↓ optimum temperature, ↓ rate of enzyme
reaction
o Used in preservation of food by refrigeration
• Optimal temperature of enzymes in other
organisms
o Most enzymes from bacteria and higher ▪ Each substrate must occupy an enzyme
organisms – 37°C active site for a finite amount of time, and
o Organisms that live in the ocean floor - 2°C the products must leave the site before the
o Hyperthermophile organisms – 90 to 105°C cycle can be repeated.
(100 atm, pH 1 to 4) ▪ Turnover time - the number of substrate
• pH molecules transformed per minute by one
o Changes the conformation of a protein molecule of enzyme under optimum
▪ Effects resemble those observed when the conditions of temperature, pH, and
temperature changes saturation
o Within narrow pH range, changes are reversible
by changing back to optimal pH ENZYME INHIBITION
o Extreme pH values (either acidic or basic), • Irreversible inhibitors
denaturation = irreversible o Bind to enzymes forming a strong covalent bond
• Substrate and enzyme concentration to an amino acid side-chain group at the
o Constant substrate concentration, ↑ enzyme enzyme’s active site
concentration = rate increases linearly o Do not have structures similar to that of the
▪ In all enzyme reactions, substrate molecules enzyme’s normal substrate
> enzyme molecules o ↑ substrate concentration ≠ reversal of
inhibition
o Enzyme is permanently inactivated
▪ Chemical warfare agents (nerve gases)
▪ Organophosphate insecticides
• Reversible inhibitors
o Bind to enzymes through noncovalent bonds.
▪ Competitive inhibitors – bind to the active
site of the enzyme surface; can compete with
the substrate for the same active site
▪ Reaction rate increases because more because the molecule is similar to the actual
substrate molecules can be accommodated enzyme substrate in shape and charge
in a given amount of time distribution.
▪ The greater the enzyme concentration, ▪ Noncompetitive inhibitors (alloterism) – bind
the greater the reaction rate to some other portion of the enzyme surface,
o Constant enzyme concentration, ↑ substrate altering the tertiary structure of the enzyme
concentration = rate does not increase to eliminate catalytic effectiveness.
continuously (saturation)
▪ Saturation point – point where each
enzyme molecule is working at full capacity
and the incoming substrate molecules must
“wait their turn” for an empty active site.
▪ Since substrate molecules > enzyme
molecules, if all enzymes available are used
and occupied to their maximum extent by

ABELA, J. 5
 • Competitive inhibitor’s effect can be reversed by
↑ substrate concentration. At a sufficiently high
substrate concentration, the reaction velocity
reaches the maximum rate (Vmax) observed in the
absence of inhibitor.
• Noncompetitive inhibitor’s effect cannot be
reversed by ↑ substrate concentration. This
decreases the apparent maximum rate (Vmax) of the
reaction.

Figure 5.1 Feedback inhibition

o Alloterism
▪ Binding of a regulator to a site other than
the active site changes the shape of the
active site and the three dimensional
structure of the enzyme.
o Allosteric enzyme
▪ Any enzyme affected by alloterism
▪ Quaternary structure; composed of two or
more protein subunits.
▪ Two binding sites: those for substrate
ENZYME REGULATION (active site) and those for regulators
• Feedback Control (regulating site); distinct from each other
o Formation of a product controls the activation or in both location and shape.
inhibition an earlier reaction in the sequence. o Regulator
▪ Occurs especially in a complex system where ▪ Substance that binds to the allosteric
enzymes work cooperatively. enzyme at the regulatory site.
o See figure 5.1 (negative regulator): o If a substance binds noncovalently and
▪ ↓ concentration of final product (D) = reversibly to a site other than the active site,
reactions proceed rapidly it may affect the enzyme in either of two
▪ ↑ concentration of final product (D) = action ways:
of enzyme 1 becomes inhibited and ▪ Negative modulation - inhibit enzyme
eventually stops because cell has enough of action
final product for its needs. ▪ Positive modulation – stimulate enzyme
o Regulators of an allosteric enzyme may be: action
▪ Products of different pathways of reaction
within the cell
▪ Compounds produced outside the cell
(hormones)
o The inhibition may be competitive or
noncompetitive.

ABELA, J. 6
 o Allosteric enzymes have two kinetic states to/from a particular amino acid within the
▪ R form (relaxed) – more active enzyme’s structure
▪ T form (taut) – less active o Activation or inhibition of enzymes through the
▪ Substrate binds well and catalyze the addition (phosphorylation) or removal
reaction when enzyme is in R form. (dephosphorylation) of a phosphate group
▪ Allosteric regulators are seen to function by ▪ Phosphate group is derived from an ATP
binding to the enzyme and favoring one form molecule
vs. the other. ▪ Often bonded to a serine, tyrosine, or
threonine residue
▪ Example of enzyme activated by
phosphorylation: Glycogen phosphorylase
▪ Example of enzyme activated by
dephosphorylation: Pyruvate kinase (PK)
from the liver
o Protein kinase
▪ Effect the addition of phosphate groups
o Phosphatase
▪ Catalyze removal of the phosphate groups
▪ Example: When PK is not needed, it is
phosphorylated by pyruvate kinase phosphate
(PKP) using ATP as a substrate as well as a source
• Proteolytic Enzymes and Zymogens of energy. To reactivate it, the enzyme
phosphatase dephosphorylates it.
o Based on the production of enzymes in an
inactive form. These inactive enzyme precursors
are then “turned on” at the appropriate time.
o Proteolytic enzyme – catalyzes the breaking of
peptide bonds that maintain the primary
structure of a protein.
▪ Manufactured by the body in an inactive
form, else they destroy the tissues that
produce them.
▪ Converted to active form when needed.
▪ Example: Digestive and blood-clotting
enzymes
• Isoenzymes (Isozymes)
o Zymogen (Proenzyme) - the inactive precursor
o Different forms of the same enzyme appear on
of a proteolytic enzyme
different tissues, catalyzing the same reaction
▪ Small part of their polypeptide chain must be
▪ Lactate dehydrogenase (LDH) oxidates lactate
removed to activate them and become the
to pyruvate.
proteolytic enzyme
▪ It is a tetramer (has four subunits) of H and M
chains.
▪ H4 is predominant in the heart; allosterically
inhibited by high levels of pyruvate (its
product) and has a higher affinity for lactate
(its substrate) than does the M4 enzyme
▪ M4 is predominant in the liver and skeletal
muscles; optimized for the opposite reaction
than H4
▪ Heart – LDH convert lactate to pyruvate in
the heart; after a heart attack, the level of
the heart isozyme in blood is elevated. The
LDH assay is a standard way to diagnose
heart attack.
• Covalent Modification
▪ Liver and skeletal muscles - favors the
o Enzyme activity is altered by covalently
production of lactate
modifying the structure of the enzyme through
o Different chemical and physical properties:
attachment or removal of a chemical group
▪ Electrophoretic mobility

ABELA, J. 7
 ▪ Kinetic properties
▪ Amino acid sequence
▪ Amino acid composition

o ACE inhibitors medications block the action of

ACE, ↓ blood pressure.
▪ Lisinopril – compound heavily prescribed for
treatment of moderately elevated blood
pressure conditions; not metabolized in the
urine.
Figure 5.2 The isozymes of lactate dehydrogenase (LDH). ▪ First obtained from the jararaca, a Brazilian
The electrophoresis gel depicts the relative isozyme types pit viper.
found in different tissues. • Sulfa Drug
o Whole family of sulfanilamide derivatives; —the
USES OF ENZYMES IN MEDICINE first “antibiotics” in the medical field.
• The level of enzyme activity in these fluids can • Antibiotics usually inhibit specific enzymes
easily be monitored. essential to the life processes of the bacteria.
o Abnormal activity (either high or low) of o Sulfanilamide inhibits bacterial growth because
particular enzymes in various body fluids signals it is structurally similar to PABA (p-aminobenzoic
either the onset of certain diseases or their acid).
progression. • Many bacteria need PABA in order to
produce an important coenzyme, folic acid.
• Sulfa drugs selectively inhibit only bacteria
metabolism and growth because humans
absorb folic acid from their diet and thus do
not use PABA for its synthesis.

ENZYME INHIBITORS USED IN MEDICINE

• Common prescription drugs exert their mode of
Figure 6.1 Structures of selected sulfa drugs in use today
action by inhibiting enzymes
as antibiotics
• Angiotensin-Converting Enzyme (ACE) Inhibitors
o Angiotensin
• Penicillin
▪ Octapeptide hormone involved in blood
o One of the most widely used antibiotics
pressure regulation, ↑ blood pressure by
• Discovered by Alexander Fleming in 1928
narrowing blood vessels
• Isolated by Howard Flory and Ernst Chain in
o ACE converts angiotensinogen (zymogen,
pure form and proved its effectiveness as an
decapeptide) to angiotensin (active form,
antibiotic a decade later
octapeptide) in the blood
o Several naturally occurring penicillin have now
▪ Two amino acids are cleaved from the
been isolated, and numerous synthetic
zymogen structure
derivatives have been produced
• All have structures containing a four-
membered β-lactam ring fused with a five-
membered thiazolidine ring.

ABELA, J. 8
 • Derivatives of the basic structure differ • Pyrrole2-carboxylate
from each other in the identity of a o Proline racemase catalyzes a reaction that
particular R group. converts L-proline to D-proline.
o Pyrroe2-carboxylate is able to inhibit this
reaction because it mimics what proline would
look like at its planar transition state.
o Binds to proline racemase 160x more strongly
than proline does.

o Inhibit transpeptidase by covalent modification • Abzymes

of serine residue. o Immunoglobulins generated by using transition-
state analogs as an immunogen; has catalytic
activity.
▪ An antibody is a protein designed to bind to
specific molecules on the immunogen. The
antibody will, in essence, serve as a fake
active site.
▪ An immunogen (a molecule that elicits an
antibody response) would elicit antibodies
• Transpeptidase - catalyzes the formation with catalytic activity (abzymes) if it
of peptide cross links between mimicked the transition state properties
polysaccharide strands in bacterial cell (shape, charge) of the reaction.
walls. ▪ Example: The Na-(5’-phosphopyridoxyl)-l-
• Penicillin is highly specific in binding to the lysine moiety is a transition-state analog for
active site of transpeptidase (very highly the reaction of an amino acid with pyridoxal-
competitive inhibitor) 5’-phosphate. When this moiety is bonded to
• By inhibiting transpeptidase, penicillin a protein and injected into a host, it acts like
prevents the formation of a strong cell an antigen and the host produces antibodies
wall. Any osmotic or mechanical shock that have catalytic activity (abzymes). The
then causes lysis, killing the bacterium. abzyme is then used to catalyze the reaction.
o Some bacteria produce the enzyme penicillinase,
which protects them from penicillin.
• Semisynthetic penicillins, such as methicillin
and amoxicillin have been produced that are
resistant to penicillinase activity

TRANSITION-STATE ANALOGS
• Molecules that mimic the transition state of a
chemical reaction and are used as enzyme
inhibitors.
• Abzymes have recently found an exciting
o Enzyme lowers the activation energy for a
reaction, making the transition state more application in the fight against AIDS.
o The idea is to produce a catalytic antibody that
favorable.
o It does so by having an active site that actually
will cleave the gp120 protein, which is part of
fits best to the transition state conformation the HIV virus coat.
rather than to the substrates or the products.

ABELA, J. 9
 b. Mutase – introduction of a double bond within a
molecule
c. Protease – hydrolysis of amide linkages in a
protein
d. no correct response

6. An enzyme active site is the location in an enzyme

where the substrate molecules
a. are produced
b. are changed to catalysts
c. react to form product
d. no correct response

7. Which of the following statements concerning the

lock-and-key model for enzyme activity is incorrect?
a. The active site has a fixed, rigid geometry.
b. The active site has a geometry complementary to
that of substrate.
c. The active site has a geometry identical to that of
the substrate.
REVIEW QUESTIONS
d. no correct response
1. Which of the following statements concerning the
nature of enzymes is incorrect?
8. Which of the following enzyme properties is
a. Most, but not all, enzymes are globular proteins.
explained by the induced-fit model for enzyme
b. Some, but not all, enzymes are conjugated
activity?
proteins.
a. high specificity of an enzyme for a specific
c. Most, but not all, enzymes are catalysts.
substrate
d. no correct response
b. ability of an enzyme to accommodate more than
one kind of substrate
2. Which of the following statements concerning an
c. susceptibility of enzymes to deactivation
enzyme substrate is incorrect?
d. no correct response
a. It is the substance upon which the enzyme “acts.”
b. It is the reactant in an enzyme-catalyzed
9. The specificity of an enzyme that catalyzes the
reaction.
oxidation of several different alcohols is termed
c. It is the product in an enzyme-catalyzed reaction.
a. absolute specificity
d. no correct response
b. stereochemical specificity
c. group specificity
3. Most enzyme names end with the suffix –ase, but a
d. no correct response
few names end in the suffix
a. –ose
10. Linkage-specific enzymes will act on a particular
b. –ine
type of
c. –in
a. chemical bond
d. no correct response
b. functional group
c. stereoisomer (d- or l-)
4. Which of the following pairings of enzyme type and
d. no correct response
enzyme function is incorrect?
a. Lipase – hydrolysis of ester linkages in a lipid
11. The number of substrate molecules converted to
b. Hydratase – addition of water to a substrate
product per minute is a measure of
c. Carboxylase – removal of carbon dioxide from a
a. enzyme activity
substrate
b. enzyme concentration
d. no correct response
c. enzyme specificity
d. no correct response
5. Which of the following pairings of enzyme type and
enzyme function is incorrect?
12. Which of the following statements concerning a
a. Kinase – transfer of a phosphate group between
reversible competitive inhibitor is incorrect?
substrates
a. resembles the substrate in shape

ABELA, J. 10
 b. binds at a site other than the active site b. sulfa drugs
c. its effect can be decreased by increasing the c. penicillins
substrate concentration d. no correct response
d. no correct response
13. Which of the following statements concerning an 20. Measurement of blood levels for the enzymes
irreversible enzyme inhibitor is incorrect? LDH, CPK, and AST is useful in determining
a. forms a strong covalent bond to the active site a. extent of heart muscle damage in heart
b. permanently prevents normal substrate from attacks
entering the active site b. the location of blood clots
c. has a shape almost identical to that of normal c. urea levels in the blood
substrate d. no correct response
d. no correct response

14. Which of the following binds to an enzyme at a ANSWER KEY:

location other than the active site? (18) a. (19) c. (20) a.
a. irreversible inhibitor a. (11) a. (12) b. (13) c. (14) c. (15) b. (16) b. (17) a.
b. reversible competitive inhibitor (1) a. (2) c. (3) c. (4) c. (5) b. (6) c. (7) c. (8) b. (9) c. (10)
c. reversible noncompetitive inhibitor
d. no correct response
REFERENCES
15. Which of the following is an incorrect 1. Bettelheim, F. (2016). Introduction to General,
characterization for an allosteric enzyme? Organic, and Biochemistry. Cengage
a. possesses quaternary structure 2. Stoker, H. S. (2016). General, Organic, and
b. substrate and regulator compete for the same Biochemistry. Cengage
binding site 3. Enzymes lecture. Canvas
c. substrate and regulator occupy different binding
sites Goodluck MT Tams! Road to RMT on 2024. Kaya natin
d. no correct response ‘to.
"I’m sure it must feel as though everything is coming apart,
16. Enzyme activity regulation that involves a reaction but you can get through this." –Grey’s Anatomy
sequence product inhibiting an enzyme in an earlier
step in the reaction sequence is called
a. negative regulator control
b. feedback control
c. covalent modification
d. no correct response

17. Which of the following statements applies to a

zymogen?
a. inactive precursor of a proteolytic enzyme
b. active form of a proteolytic enzyme
c. substance that coverts an enzyme from an
inactive form to an active form
d. no correct response

18. Inhibition of angiotensin-converting enzyme by the

medication lisinopril is useful for
a. treating moderately high blood pressure
b. reducing inflammation
c. treating bacterial infections
d. no correct response

19. Inhibition of the enzyme transpeptidase is the

mode of action for
a. all antibiotics

ABELA, J. 11
 MTY1107: BIOCHEMISTRY | LECTURE
MODULE 6: CARBOHYDRATE METABOLISM
NAME OF LECTURER: Ms. Lenzie Santillan
DATE: October 28, 2021

TABLE OF CONTENTS GLYCOLYSIS

• An anaerobic linear metabolic pathway that
I. OVERVIEW OF DIGESTION PROCESS 1 occurs in the cell cytosol where glucose is
A. Carbohydrate Digestion and Absorption 1 converted to:
II. GLYCOLYSIS 2 o 2 molecules of pyruvate
III. FATES OF PYRUVATE 3 o Chemical energy in the form of ATP
IV. THE CORI CYCLE 6
o NADH-reduced coenzymes
V. GLUCONEOGENESIS 6
• Two stages
VI. GLYCOGENESIS AND GLYCOGENOLYSIS 7
o Six-carbon stage – energy-consuming
VII. PENTOSE PHOSPHATE PATHWAY 8
REVIEW ………………………………………………………. 9 o Three-carbon stage – energy-generating
REFERENCES ……………………………………………….. 11
SIX-CARBON STAGE OF GLYCOLYSIS (STEPS 1-3)
OVERVIEW OF DIGESTION PROCESS Step 1: Formation of glucose 6-phosphate
• Digestion • Glucose is converted to glucose 6-phosphate, a
o A biochemical process where food molecules,
through hydrolysis, are broken down into smaller
chemical units that can be used by cells for their
metabolic needs.
• Enzymes present:
o Mouth: SALIVARY α-AMLYASE
o Small intestine: PANCREATIC α-AMLYASE
o Intestinal mucosal cells: MALTASE, LACTASE,
reaction catalyzed by hexokinase.
SUCRASE Step 2: Formation of fructose 6-phosphate
• Primary site of carbohydrate digestion: SMALL • Glucose is isomerized by
INTESTINE phosphoglucoisomerase to fructose 6-

CARBOHYDRATE DIGESTION AND ABSORPTION

• Step 1: Salivary α-amylase in the mouth breaks
down present carbohydrates in the food mass to
smaller polysaccharides and maltose.
• Step 2: Food mass moves down the digestive
tract to the stomach, where carbohydrates are
unaffected by gastric juices due to the acidic phosphate, going from an aldose to a ketose.
environment inactivating salivary α-amylase and Step 3: Formation of fructose 1,6-biphosphate
lack of carbohydrate-digesting enzymes. • Fructose 6-phosphate is phosphorylated,
• Step 3: Carbohydrates are broken down in the receiving a phosphate from ATP. Reaction is
small intestine by pancreatic α-amylase into catalyzed by phosphofructokinase, which is
smaller chains until only disaccharides lactose, activated by Mg2+.
sucrose, and maltose remain.
• Step 4: The disaccharides are then converted to
their monosaccharide units glucose, galactose,
and fructose by maltase, lactase, and sucrase in
the outer membranes of intestinal mucosal cells.
THREE-CARBON STAGE OF GLYCOLYSIS (STEPS 4-10)
• Step 5: The monosaccharides are absorbed into
Step 4: Formation of two triose phosphates
the bloodstream via active transport (using ATP)
• Fructose 1,6-biphosphate is split to two trioses:
by the intestinal lining, which has villi that are
Dihydroxyacetone phosphate and glucose 3-
rich in blood capillaries.
phosphate. Reaction is catalyzed by aldolase.

ABELA, J. 1
 Step 6B: Formation of 1,3-biphosphoglycerate
• 3-Phosphoglycerate is phosphorylated by a free
high-energy phosphate group, attached to a
carbon atom participating in a carbon-carbon or
carbon-oxygen double bond. Reaction is
catalyzed by glyceraldehyde 3-phosphate
dehydrogenase.

Step 5: Formation of glyceraldehyde 3-phosphate

• Dihydroxyacetone phosphate is converted to
glyceraldehyde 3-phosphate, a reaction
catalyzed by triosephosphate isomerase. Step 7: Formation of 3-phosphoglycerate
• 1,3-biphosphoglycerate is converted back to 3-
phosphoglycerate by transferring a phosphate
group to ADP, yielding an ATP. Reaction is
catalyzed by phosphoglycerokinase.
o Substrate-level phosphorylation –
biochemical process whereby ATP is produced
from ADP by hydrolysis of a high-energy
compound (the substrate).
Step 6A: Formation of 1,3-biphosphoglycerate
• Glyceraldehyde 3-phosphate is oxidized to an
acid by NAD+, yielding 3-Phosphoglycerate and
NADH.

ABELA, J. 2
Step 8: Formation of 2-phosphoglycerate • Isomerization reactions occur in Steps 2, 5, and
• 3-phosphoglycerate is isomerized to 2- 8.
phosphoglycerate by moving the phosphate • Overall ATP change per glucose is Net +2,
group from C3 to C2. Reaction is catalyzed by meaning two ATP molecules for every glucose
phosphoglyceromutase. molecule converted into two pyruvates.

ENTRY OF GALACTOSE AND FRUCTOSE INTO

Step 9: Formation of phosphoenolpyruvate GLYCOLYSIS
• 3-phosphoglycerate undergoes an alcohol • Galactose enters the glycolytic pathway by
dehydration reaction, where a carbon-carbon being converted to glucose 1-phosphate, which
double bond into the molecule. The reaction is then converted to glucose 6-phosphate.
yields phosphoenolpyruvate, which contains a • Fructose enters the glycolytic pathway by being
high-energy phosphate group attached to the phosphorylated to produce fructose 1-
carbon-carbon double bond. Reaction is phosphate, then split into glyceraldehyde and
catalyzed by enolase, activated by Mg2+. dihydroxyacetone phosphate.
o Dihydroxyacetone phosphate enters
glycolytic pathway directly.
o Glyceraldehyde must be phosphorylated to
glyceraldehyde 3-phosphate before entry to
pathway.

REGULATION OF GLYCOLYSIS
• Glycolysis, like all metabolic pathways, must
have control mechanisms associated with it for
Step 10: Formation of pyruvate regulation.
• Phosphoenolpyruvate transfers its high-energy • PFK and PK are allosteric enzymes.
phosphate group to ADP, yielding ATP and
pyruvate. Reaction is catalyzed by pyruvate CONTROL POINTS
kinase, activated by Mg2+ and K+. o Step 1 – hexokinase enzyme activity is
inhibited by glucose 6-phosphate, the
product of the reaction.
o Step 3 – phosphofructokinase (PFK) is
inhibited by high concentrations of ATP and
citrate.
o Step 10 – pyruvate kinase (PK) is inhibited by
high ATP concentrations.
NOTES FATES OF PYRUVATE
• Keep in mind that from step 6 onward, two • After pyruvate is produced via glycolysis, it
molecules of each of the C3 compounds take undergoes three different paths depending on
part in every reaction for reach original C6 cellular conditions and nature of the organism:
glucose molecule. o Oxidation to acetyl CoA
• ATP molecules are involved in Steps 1, 3, 7, and o Lactate fermentation
10. o Ethanol fermentation
• Energy-rich compounds are produced in Steps
6 and 9.

ABELA, J. 3
 o Pyruvate is the only glycolysis intermediate
• The three pathways are significant because they that is not phosphorylated and can travel
provide in regenerating NAD+ from NADH so that from the cytosol to the mitochondrial
glycolysis can continue. matrix.
• Occurs in aerobic conditions in humans,
animals, and microorganisms.
• Most acetyl CoA molecules produced from
pyruvate enters the citric cycle.
o Citric acid cycle operations change more
NAD+ to NADH.
▪ NADH produced from glycolysis,
oxidation of pyruvate, and from the citric
acid cycle enter the electric transport
chain, where electrons from NADH are
OXIDATION TO ACETYL CoA transferred to O2, and the NADH
becomes NAD+.
▪ Not all pyruvate-based acetyl CoA enters
the citric acid cycle. Some serve as
• Pyruvate formed in the cytosol through glycolysis starting material for producing the fatty
crosses the two mitochondrial membranes and acids needed for fat formation.
enters the mitochondrial matrix, where the • Reactants: Pyruvate, CoA-SH, NAD+
oxidation takes place. • Products: Acetyl CoA, NADH, CO2
o CO2 is formed through decarboxylation.

ABELA, J. 4
 ▪ Muscle soreness
▪ Muscle cramping
▪ Fatigue
• There is a net gain of two ATP for the
conversion of glucose to two lactates.
o Glucose yields two pyruvates, therefore
there are two lactates.
• Enzyme: Pyruvate dehydrogenase
• RBCs have no mitochondria and therefore
always process pyruvate to lactate.
FERMENTATION PROCESSES
• Fermentation
o Oxidation of NADH to NAD+ without the need
for oxygen
• Both lactate and ethanol fermentation occur
within the cellular cytosol.

LACTATE FERMENTATION

• Enzymatic anaerobic reduction of pyruvate to

lactate. ETHANOL FERMENTATION
o Sole purpose is conversion of NADH to NAD + • Enzymatic anaerobic conversion of pyruvate to
to replenish those that are needed for Step 6 ethanol and carbon dioxide.
of glycolysis. • Occurs in several simple organisms, including
yeast, that possess the ability to regenerate
NAD+ through ethanol, rather than lactate
production.
• Ethanol fermentation involving yeast causes
bread and other related products to rise as result
of CO2 bubbles being released during baking.
• Alcoholic drinks are produced via ethanol
fermentation of sugars in grain and fruit
products.
• Occurs in two steps:
o Step 1: Decarboxylation reaction of pyruvate
to produce acetaldehyde, catalyzed by
pyruvate decarboxylase.

o Lactate is converted back to pyruvate once

aerobic cellular conditions are established.
• Occurs in humans, animals, and microorganisms. o Step 2: Acetaldehyde is reduced to produce
• Lactate’s structure closely resembles of pyruvate ethanol, catalyzed by alcohol dehydrogenase.
and glycerate, and all three are derivatives of
propionic acid (C3 saturated monocarboxylic
acid)
• Reactants: Pyruvate, NADH, H+
• Products: Lactate, NAD+
• Enzyme: Lactate dehydrogenase • Acetaldehyde is a toxic substance responsible for
• Working muscles often produce lactate. much of the damage in fetal alcohol syndrome,
o Continuous strenuous work or exercise where transfer of nutrients and oxygen to fetus
creates lactate buildup, which contributes to: is depressed, leading to tragic consequences.
ABELA, J. 5
 THE CORI CYCLE
• A cyclic biochemical process in which glucose is
converted to lactate in muscle tissue, the lactate
is reconverted to glucose in the liver, and the
glucose is returned to the muscle tissue.
o Named in honor of 1947 Nobel Prize-winning
husband-and-wife team, Gerty Radnitz Cori
and Carl Cori.

• In the Cori cycle, there is a net gain of:

o 2 ATP in the glycolytic part
o 6 triphosphates (4 ATP, 2 GTP) in the o In steps 9 and 11 (steps 1 and 3 of glycolysis),
liver (gluconeogenesis portion) the new enzymes are fructose 1,6-
• Overall net loss of 4 nucleotide triphosphates biphosphatase and glucose 6-phosphate.
o In step 5 of gluconeogenesis
(reverse of step 7 of glycolysis), the
same enzyme is operative in both
directions; however, ATP is required
in gluconeogenesis but not in
glycolysis.
o Glycolysis ATP production
occurs in Steps 7 and 10. The reverse
of these two steps in
GLUCONEOGENESIS gluconeogenesis, Step 5 and Steps 1 and 2,
• The metabolic pathway by which glucose is are the steps where ATP is needed.
synthesized from noncarbohydrate materials. o Glycolysis is a catabolic process
o Pyruvate (the initial substrate) (energy-generating) and
o Lactate from muscles and RBCs gluconeogenesis is an anabolic
o Glycerol from triacylglycerol hydrolysis process (energy is needed for it to
o Glucogenic amino acids from dietary protein occur).
hydrolysis or from muscle protein during ▪ Glycolysis has a net production
starvation of 2 ATP (Section 24-2).
• 90% of this takes place in the liver and helps Gluconeogenesis has a net
maintain normal blood-glucose levels in times of expenditure of 4 ATP and 2 GTP,
inadequate dietary carbohydrate intake, like in which is equivalent to the
between meals. expenditure of 6 ATP.
• It is the reverse of glycolysis, converting pyruvate • Gluconeogenesis, because of its ATP-
to glucose. Both pathways are similar, but not consuming nature, occurs only under
identical: specific conditions, which include:
o Step 1 of gluconeogenesis (reverse of step 10 o Replenishing depleted liver
in glycolysis) occurs in two steps, making the glycogen stores.
overall steps of the process 11 instead of 10. o Converting lactate, produced by
▪ Pyruvate is converted to an oxaloacetate strenuous exercise, back to
intermediate, which is then converted to glucose.
phosphoenolpyruvate.
ABELA, J. 6
 o Maintaining blood glucose level • In a subsequent reaction, the UDP produced
when glycogen stores have been in Step 3 is converted back to UTP, which
depleted. can then react with another glucose 1-
phosphate (Step 2). The conversion reaction
GLYCOGENESIS AND GLYCOGENOLYSIS requires ATP.

GLYCOGENESIS
• The metabolic pathway by which glycogen is • Adding a single glucose unit to a growing
synthesized from glucose 6-phosphate. glycogen chain requires the investment of
• Involves three steps: two ATP molecules: one in the formation of
o Step 1: Glucose 6-phosphate is isomerized to glucose 6-phosphate and one in the
become glucose 1-phosphate, a reaction regeneration of UTP.
catalyzed by phosphoglucomutase.
GLYCOGENOLYSIS
• The metabolic pathway by which glucose 6-
phosphate is produced from glycogen.
o Not the reverse of glycogenesis because it
does not require UTP or UDP.
• A two-step process:
o Step 1: Glucose 1-phosphate is formed via
o Step 2: Glucose 1-phosphate is activated by the removal of an end glucose unit from a
high-energy compound uridine triphosphate glycogen molecule. Reaction is catalyzed by
(UTP). Uridine monophosphate (UMP) is glycogen phosphorylase.
transferred to glucose 1-phosphate, and the
resulting PPi is hydrolyzed to 2Pi .

o Step 2: Glucose 6-phosphate is formed by

moving the phosphate group from C1 to C6.
Reaction catalyzed by phosphoglucomutase.
• Neither ATP nor any of the other

nucleotide triphosphates is needed

• An immediate need for energy in the
muscle and brain cells is the stimulus for
glycogenolysis.
o Muscle and brain cells lack glucose 6-
phosphatase, they cannot form free
glucose from glucose 6-phosphate.
▪ UDP-glucose is the activated carrier of Thus, muscle and brain cells can use
glucose in glycogen synthesis glucose 6-phosphate from glycogen for
(glycogenesis) energy production only.
• A low level of glucose is the stimulus that
o Step 3: The glucose unit of UDP-glucose is initiates glycogenolysis in liver cells.
then attached to the end of a glycogen chain. o The glucose 6-phosphate produced must be
converted to free glucose before it can enter
the bloodstream, as glucose 6-phosphate
cannot cross cell membranes.
▪ Effected by glucose 6-phosphatase
o The liver, however, with this enzyme
present, has the capacity to use
ABELA, J. 7
 glucose 6-phosphate obtained from ▪ Two NADPH molecules per glucose 6-
glycogen to supply additional glucose phosphate is processed during this stage.
to the blood.
• When glycogen rather than free glucose is
the starting material for glycolysis, the net
gain in ATP is three molecules rather than
two for each glucose processed.
o Glucose from glycogen enters glycolysis
at Step 2, as glucose 6-phosphate, and
thus bypasses ATP-consuming Step 1. o Nonoxidative stage
• Glycogen is a more effective energy source ▪ First step of this stage is that ribulose 5-
than is free glucose. However, it costs the phosphate (ketose) is isomerized to ribose
equivalent of two ATP to incorporate a 5-phosphate (aldose).
glucose molecule into glycogen
(glycogenesis).

▪ Pentose ribose is a component of ATP,

GTP, UTP, CoA, NAD+/NADH, FAD/FADH2,
and RNA
▪ Further steps in the nonoxidative stage
contain provision for the conversion of
PENTOSE PHOSPHATE PATHWAY ribose 5-phosphate to numerous other
• Glucose 6-phosphate is used to produce NADPH, sugar phosphates.
ribose 5-phosphate (a pentose phosphate), and o Glyceraldehyde 3-phosphate and
numerous other sugar phosphates fructose 6-phosphate are formed.
• Significant in cells that produce lipids: • The pentose phosphate pathway, with its
o Fatty tissue many intermediates, helps meet cellular
o Liver needs in numerous ways:
o Mammary glands o When ATP demand is high, the pathway
o Adrenal cortex (active producer of steroid continues to its end products, which
lipids) enter glycolysis.
• NADPH coenzyme is reduced to NADP+ o When NADPH demand is high,
(nicotinamide adenine dinucleotide phosphate) intermediates are recycled to glucose 6-
o Phosphorylated version of NAD +/NADH phosphate (the start of the pathway), and
▪ The nonphosphorylated version (mainly further NADPH is produced.
NAD+) is involved in the common metabolic ▪ Glutathione is the main antioxidant
pathway used by the body to keep hemoglobin
▪ Phosphorylated version (mainly NADPH) is in its reduced form. NADPH is needed
involved in the synthesis of unsaturated for the regeneration of depleted
fatty acids, cholesterol, amino acids, glutathione.
photosynthesis, and reduction of ribose to ▪ Insufficient supply of NADPH, leading
deoxyribose for DNA. to lack of regeneration of glutathione,
• Two stages: leads to the destruction of
o Oxidative stage hemoglobin-containing RBCs, resulting
▪ Involves three steps through which glucose in severe anemia.
6-phosphate is converted to ribulose 5- • When ribose 5-phosphate demand is
phosphate and CO2 high, for nucleic acid and coenzyme
ABELA, J. 8
 production, most of the nonoxidative 5. Which of the following substances is needed
stage is nonfunctional, leaving ribose 5- for monosaccharides to enter the
phosphate as a major product. bloodstream?
a. ATP
b. α-amylase
c. Sucrase
d. No correct response
6. Indicate what step in the glycolysis pathway
each of the following events occurs:
▪ First phosphorylation of ADP occurs
▪ First “energy-rich” compound is produced
▪ Second “energy-rich” compound is
produced
▪ Third isomerization reaction occurs

a. Step 7, Step 9, Step 10, Step 5

b. Step 9, Step 5, Step 2, Step 3
c. Step 7, Step 6, Step 9, Step 8
d. Step 1, Step 4, Step 8, Step 10

7. Relate the names and functions of the

following glycolytic enzymes to steps in the
process of glycolysis:
REVIEW ▪ Phosphofructokinase
1. The primary site within the human body ▪ Phosphoglyceromutase
where carbohydrate digestion occurs is the ▪ Triosephosphate isomerase
a. Mouth ▪ Enolase
b. Stomach
c. Small intestine a. Step 8, Step 9, Step 10, Step 5
d. No correct response b. Step 6, Step 5, Step 1, Step 3
2. What is the first site within the human body c. Step 7, Step 6, Step 9, Step 8
where breaking of polysaccharide glycosidic d. Step 3, Step 8, Step 5, Step 9
bonds occurs?
a. Mouth 8. Which of the following statements
b. Stomach concerning glycolysis is correct?
c. Small intestine a. The pathway for the process is a
d. No correct response cyclic pathway.
3. What effect does gastric juice in the b. It occurs in the mitochondrial matrix.
stomach have on dietary polysaccharides? c. Molecular O2 is not needed for the
a. Converts polysaccharides to process to occur.
disaccharides d. No correct response
b. Converts polysaccharides to 9. The overall process of glycolysis converts a
monosaccharides C6 molecule into
c. Has no effect on polysaccharides a. Two C3 molecules
d. No correct response b. Three C2 molecules
4. The enzymes that convert disaccharides to c. A different C6 molecule
monosaccharides are associated with d. No correct response
a. Intestinal villi 10. The first two intermediates in the process of
b. Intestinal mucosal cells glycolysis are, respectively
c. Pancreas a. Glucose 6-phosphate and glucose 1-
d. No correct response phosphate

ABELA, J. 9
 b. Glucose 1-phosphate and fructose 6- 18. When gluconeogenesis and glycolysis are
phosphate compared in terms of reaction steps
c. Glucose 6-phosphate and fructose 6- a. Gluconeogenesis has one more step
phosphate b. Glycolysis has one more step
d. No correct response c. Both processes have the same
11. When one glucose molecule is processed number of steps
through the glycolysis pathway, relative to d. No correct response
ATP production/consumption, there is a 19. Which of the following intermediates is
a. Net loss of two ATP involved in gluconeogenesis but not in
b. Net gain of two ATP glycolysis?
c. Net gain of four ATP a. Glucose 1-phosphate
d. No correct response b. Pyruvate
12. In what two steps of glycolysis is ATP c. Oxaloacetate
converted to ADP? d. No correct response
a. Steps 1 and 2 20. Which of the following statements about
b. Steps 1 and 3 ATP equivalents in gluconeogenesis is
c. Steps 7 and 10 correct?
d. No correct response a. 4 ATP equivalents are expended
13. In the human body, under oxygen-rich and b. 6 ATP equivalents are expended.
oxygen-po or conditions, respectively, c. 4 ATP equivalents are produced.
pyruvate is converted to d. No correct response
a. Lactate and ethanol 21. Which of the following substances are
b. Lactate and acetyl CoA participants in the reactions encompassed
c. Acetyl CoA and lactate by the Cori cycle?
d. No correct response a. Pyruvate and acetyl CoA
14. NAD+ is needed as an oxidizing agent for this b. Pyruvate and lactate
pathway c. Pyruvate, lactate, and acetyl CoA
a. Acetyl CoA formation d. No correct response
b. Lactate fermentation 22. Which of the following statements
c. Ethanol fermentation concerning metabolic processes that involve
d. Glycolysis glucose is correct?
15. In which of the following conversions is CO 2 a. Pyruvate is the initial reactant in
produced? glycogenolysis.
a. Lactate to pyruvate b. Glycogen is the final product in
b. Pyruvate to acetyl CoA glycogenesis.
c. Pyruvate to lactate c. Glucose is the final product in
d. No correct response glycolysis.
16. The major purpose of lactate fermentation d. No correct response
is the production of 23. Which of the following pairs of processes
a. Acetyl CoA are the reverse of each other in terms of
b. O2 initial reactant and final product?
c. NAD+ a. Glycolysis and gluconeogenesis
d. No correct response b. Glycogenesis and gluconeogenesis
17. Accumulation of which of the following c. Glycolysis and glycogenolysis
substances in muscle cells is the cause of d. No correct response
stiffness and soreness after vigorous 24. Glucose 6-phosphate is the initial reactant.
exercise? a. Glycogenesis
a. Pyruvate b. Gluconeogenesis
b. Lactate c. Glycolysis
c. Acetyl CoA d. No correct response
d. No correct response 25. Glucose 6-phosphate is produced in the first
step.
ABELA, J. 10
 a. Glycogenesis
b. Gluconeogenesis
c. Glycolysis
d. No correct response
26. Glucose is the final product.
a. Glycogenesis
b. Gluconeogenesis
c. Glycolysis
d. No correct response
27. UTP is involved in this process.
a. Glycogenesis
b. Gluconeogenesis
c. Glycolysis
d. No correct response
28. A major purpose of the first stage of the
pentose phosphate pathway is the
production of
a. NADP+
b. NADPH
c. NADH
d. No correct response
29. A major purpose of the second stage of the
pentose phosphate pathway is the
production of
a. Ribulose 5-phosphate
b. Ribose 5-phosphate
c. Glucose 6-phosphate
d. No correct response
30. The pentose phosphate pathway when run
to its completion produces
a. Glycogen
b. Two glycolysis intermediates
c. Lactate
d. No correct response
ANSWER KEY:
(25) c. (26) b. (27) a. (28) b. (29) b. (30) (b.)
b. (18) a. (19) c. (20) b. (21) b. (22) b. (23) a. (24) a.
(10) c. (11) b. (12) b. (13) c. (14) a. (15) b. (16) c. (17)
(1) c. (2) a. (3) c. (4) b. (5) a. (6) c. (7) d. (8) c. (9) a.

REFERENCES
1. Stoker, H. S. (2016). General, Organic, and
Biochemistry. Cengage
2. Bettelheim, F. (2016). Introduction to General,
Organic, and Biochemistry. Cengage

Goodluck MT Tams! Road to RMT on 2024. Kaya natin

‘to.
"I’m sure it must feel as though everything is coming apart,
but you can get through this." –Grey’s Anatomy

ABELA, J. 11