Biochemistry
LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY)
INTRODUCTION
- Biochemistry is sometimes called biological
chemistry.
- It can be seen as a study of the components and
composition of living things and how they come
together to become life.
- It is the study of chemical processes that give rise to
the complexity of life.
- It is also related to molecular biology that concerns
genetic information encoded in DNA as well as
understanding the structures, functions, and
interactions of biological macromolecules.
LESSON 11:: SIGNIFICANCE AND RELATION OF
BIO
BIOCHEMISTRY
CHEMISTRY TO OTH OTHERER FIELDS OF SCIENCES
WHAT IS BIOCHEMIS
BIOCHEMISTRY?TRY?
> Biochemistry is the study of the chemical
substances found in living organisms and the
chemical interactions of these substances with each
other.
> Biochemistry is a field in which new discoveries are
made almost daily about how cells manufacture the
molecules needed for life and how the chemical
reactions by which life is maintained occur. The
knowledge explosion that has occurred in the field of
biochemistry during the last decades of the twentieth
century and the beginning of the twenty-first is truly
phenomenal.
WHAT IISS BI
BIOCHEMIC
OCHEMIC
OCHEMICALAL SU
SUBSTANCE
BSTANCE
BSTANCE??
- a chemical substance found within a living organism
and are divided into two groups:
Bioinorganic Subst
Substances
ances Bioorganic Substances
- includes water and - includes carbohydrates,
inorganic salts lipids, proteins, and nucleic
acids
As isolated compounds, bioinorganic and bioorganic
substances have no life in and of themselves. Yet when
these substances are gathered together in a cell, their
chemical interactions are able to sustain life.
Figure: Mass composition for the human body in terms of types of
biochemical substances present.
Although the human body is usually thought of as
containing mainly organic (biochemical) substances,
such substances make up only about one-fourth of
total body mass. The bioinorganic substance water
constitutes more than two-thirds of the mass of the
human body, and another 4%–5% of body mass
comes from inorganic salts.
BIOCHEMICAL IMPORTANCE
Biochemistry and medicine enjoy a mutually
cooperative relationship. Biochemical studies have
illuminated many aspects of health and disease, and
the study of various aspects of health and disease has
opened up new areas of biochemistry. The medical
relevance of biochemistry both in normal and
abnormal situations is emphasized throughout this
module. Biochemistry makes significant contributions
to the fields of cell biology, physiology, pathology,
pharmacology, microbiology, immunology, nutrition,
forensic medicine, and toxicology, as well as the fields
of inflammation, cell injury, and cancer. These close
relationships emphasize that life, as we know it,
depends on biochemical reactions and
processes. Aside from medicine, biochemical
research is also applied in industry, agriculture, and
food production.
LESSON 2: PROPERTIES OF WATER AND CHEM CHEMICAL
ICAL
REACTIONS IN THE CELL
WHAT IS WATER?
- one of the most plentiful compounds on earth.
- major component of the cell (70-90% of its weight)
and is referred to as inert space filler in a living
organism.
- comprises 62% of an adult body weight, higher in
young children and lower in the elderly.
- has many important roles in human and all living
organisms.
- Every day we take up about 2700 mL of water from
various sources: drinking, water of metabolism and
preformed water in food.
HOW LONG CAN A PERSON LIVE WITHOUT WATER?
- we can live without food for weeks, but we could be
dead in about 3 days without water.
- death usually occurs when water loss is over 10% of
the person’s body weight.
- impossible to answer for many variable factors
determine a person’s survival time. Under the most
extreme conditions, death can come rather quickly.
Ex: a child left in a hot car / an athlete exercising on a
hot weather can dehydrate, overheat & die in a
period of a few a hours. An adult in a comfortable
surroundings, in contrast, can survive for a week or
more.
PROP
ROPERTIES
ERTIES OF WATER & BIOLOGICAL IMPORTANCE
1. Water a ass a SSolvent
olvent
- All of our body fluids (blood, urine, lymph, sweat, and
digestive juices) are mostly water.
- All the chemical reactions in the body take place in
water,
- UNIVER
UNIVERSALSAL SOLSOLVENT
VENT because it dissolves both
polar (like) and non-polar (unlike) substances.
- Used during digestion in a series of hydrolysihydrolysiss
reactions, i.e., breakdown of large compounds into
smaller, more easily absorbed compounds.
2. Water a ass a Transporter
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Biochemistry
LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY)
- Water in blood carries nutrients from the eaten Examp
Examples:
les:
foods to tissues throughout the body.
- Also transports waste products from cells to lungs,
kidneys, and skin to be discarded as CO2, urine or
sweat.
- Urine & sweat help eliminate excess nitrogen % salt,
are both over 95% water.
- Plasma (liquid portion of blood) caries hormones to
their specific target sites throughout the body.
- It is essential for blood circulation
- Also transports materials within cells.
3. Water a ass a Temperature R Regu
egu
egulator
lator
- Water retains heat better than most liquids. It takes
a great deal of heat to turn liquid water into vapor.
With that, a lot of heat is lost when we perspire, and
the body is greatly relief from that small amount of
sweat that has evaporated.
- INSENSIBLE PERSPIRA TION – water loss due to the
PERSPIRATION
constant evaporation of water from skin and the
lungs, even when temperatures are not very hot. We
don’t see/feel it, but it balances the heat produced
through metabolic processes in the cells in order that
our body temperature remains constant.
4. Water a ass a Lubricant
- Present in synovial fluid that helps the joints (knees
& elbows) to move easily; tears protects the surface
of the eyes; IN ALCOHOLS
- Lubricates thin spaces around internal organs; a. Primary (1° ) alcohols
alcohols are first oxidized to aldehydes
- In the chest, water serves as lubricant as the rib (RCHO), which are further oxidized to carboxylic
cage slides over several internal organs during acids (RCOOH) by replacing one and then two C–H
breathing. bonds by C–O bonds.
- Moistens food during digestion and ending with the
passage of water-softened feces through the anus.
- Principal component of mucus and every other
lubricant fluid in the body,

CHEMICAL REACTIONS IN THE CELL

1. OXIDATION
OXIDATION--REDUCTION (REDOX) REAC REACTIONS
TIONS
Oxidation-reduction (redox) reactions are important - Since the enzymes have a higher affinity for ethanol
because they are the principal sources of energy on than methanol, methanol poisoning is treated by
this planet, both natural or biological and artificial. giving ethanol to an individual. With both methanol
Most of the metabolic pathways that will be and ethanol in a patient’s system, the enzymes react
discussed in later modules are combinations of more readily with ethanol, allowing the methanol to
oxidation and reduction reactions. This is where be excreted unchanged without the formation of
mnemonics can be applied to remembering methanol toxic oxidation products.
important facts.
REDUCTION (VDGEHROA)
When the Valence / oxidation number of an element
Decreases that means it Gained
Electrons/Hydrogens, it (substance) was Reduce
Reduced d
and its compound is the Oxidizing Age
Agentnt.
OXIDATION (VILEHORA)
If the Valence / oxidation number of an element
Increases that means it Lost Electron/Hydrogen, it
(substance) was Oxidized and its compound acts as
the Reducing Agent.
Secondaryy ((22° ) alcohols are oxidized to ketones (R2
b. Secondar
CO), by replacing one C–H bonds by one C–O bonds.

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Biochemistry
LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY)
more molecule of H2O are eliminated.
Ex: Glucose + Glucose à Maltose
3. ISOMERIZATIO
ISOMERIZATION N
- In isomerization reactions, a single molecule is
rearranged such that it retains the same molecular
formula but now has a different bonding order of the
atoms forming a structural or stereoisomer.

c. Tertia ry (3°) alcohols have no H atoms on the

Tertiary
carbon with the OH group, so they are not oxidized.
EPIMIRIZATI
EPIMIRIZATION
ON
- Interconversion of two aldoses
- D-mannose / D-galactose à D-glucose

2. HYDROLYSIS AND CONDE

CONDENSATION
NSATION
HYDROLYSIS
- Greek “water loosening”
- A molecule of water, with the help of enzymes,
interacts with the reactant to break up the reactants’
TAUTOMERISM
bond;
- Water converts a complex substance to smaller / - Interconversion of aldose to ketose
- D-glucose à D-fructose (or vise versa)
simpler substances.

The first stage of catabolism, digestion, is the hydrolysis of large
molecules to small molecules; polysaccharides such as starch are
hydrolyzed to monosaccharides, proteins are hydrolyzed to their
component amino acids, and triacylglycerols are hydrolyzed to
glycerol and fatty acids. Each of these molecules enters its own
metabolic pathway to be further broken down into smaller
components, releasing energy.
- Hydrolysis is important to the body for large
molecules of protein, nucleic acid, and fats are broken
down into simpler, smaller, more usable molecules.
- Generally, almost all digestive and degradative
processes in the body occur by hydrolysis.
Examp
Examples:
les:
- Chemical reactions occurring in a living matter
a. C12H22O11 + H2O à C6H12O6 + C6H12O6
b. Sucrose + H2O à Glucose + Fructose
c. Maltose + H2O à Glucose + Glucose
d. Lactose + H2O à Glucose + Galactose
CONDENSATION / DEHYDRATIO
DEHYDRATION N
- Essentially hydrolytic reactions in reverse; small
molecules united into larger molecules and one or
PROP
ROPERTIES
ERTIES OF WATER & BIOLOGICAL IMPORTANCE
The pH Scale
- Measures how acidic or basic a substance is.
- Ranges from 0-14 related to the [H3O+] (hydronium)
of the solution.
- Scientists uses a pH number to show the strength of
an acid or base.
- A pH is measured by dipping litmus into solution
such as water and other liquids.
- First introduced by a Danish chemist Soren
Sorensen at the Carlsberg Laboratory in 1909.
- p exact definition is unknown.
- H stands for Hydrogen.
- For convenience, Sorensen suggested ‘pH’ as “power
of Hydrogen”
- Gave doctors, chemists, and technologists a
measurement that could tell them exactly how acidic,
alkaline or neutral a substance is.

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Biochemistry
LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY)
- All fluids in the human body is aqueous, the only
solvent present is water.
- Consequently, all body fluids have a pH value. Some
of them have narrow range, some are wide.
Ex: pH of blood = 7.35 – 7.7.45
45
pH of urine = 4.8 – 8.
8.44

pH and Buffer Computat

Computations
ions

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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)
INTRODUCTION b. Chitin – exoskeleton of crustacean
- Carbohydrates is the most abundant of all the c. Peptidoglycan – found in the cell wall of bacteria
organic compounds in nature. 3. Transport function
- About 65% of the foods in our diet consist of - Glycoproteins
carbohydrates.
- Each day, we utilize carbohydrates in foods such as
bread, pasta, potatoes, and rice. Other
carbohydrates called disaccharides include sucrose
in table sugar and lactose in milk.
- During digestion and cellular metabolism,
carbohydrates are converted into glucose, which is 4. Regulatory function
oxidized further in our cells to provide our bodies with - Follicle-stimulating hormones which regulates the
energy and to provide the cells with carbon atoms for development, growth, pubertal maturation and
building molecules of proteins, lipids, and nucleic reproductive process.
acids. 5.. Catalytic funct
function
ion
- In addition to providing the structural framework of - Ribonuclease
plants, cellulose has other important uses too. The 6. Anti
Anti--viral function
wood in our furniture, the pages in our book, and the - Interferon
cotton in our clothing are all made of cellulose. 7. Protective/Lubricating function
- Carbohydrates can be simple or complex, having as a. Hyaluronic Acid – most abundant acid
few as three or as many as thousands of carbon mucopolysaccharide found in connective tissue,
atoms. The glucose metabolized for energy in cells, vitreous humor of eye, synovial fluid
the sucrose of table sugar, and the cellulose of plant
stems and tree trunks are all examples of
carbohydrates.
- Carbohydrates on cell surfaces determine blood
type, and carbohydrates form the backbone of DNA, b. Mucin
the carrier of all genetic information in the cell. > Synovial Fluid – Multipurpose fluid surrounding
- Carbohydrates have many polar functional groups, all articular joints. Has both viscous (lubrication) and
whose structure and properties can be understood elastic (shock absorption) proportions (viscoelastic).
by applying the basic principles of organic chemistry. 8. Other Biological Function
a. Biological specificity of animal cell membrane. E.g.
LESSON 11:: DEFINITION, SOURCES, PROPERTIES AND Blood Typing
FUN
FUNCTIONS
CTIONS OF CARBOHYDRATE
CARBOHYDRATES S Focus on the Human Body Blood Type
WHAT ARE CARBOHYDRATES? - There are 4 blood types – A, B, AB, and O.
> Are polyhydroxy ketones (ketose) or polyhydroxy - It is based on 3 or 4 monosaccharides attached to
aldehydes (aldose) or compounds that can be a membrane protein of RBCs.
hydrolyzed from them; (CH2O)n ; Cn(H2O)y) ; carbon - Each blood type has the monosaccharides below:
hydrates; sometimes referred also as sugars. Type O N-acetyl D-glucosamine
D-galactose
L-fucose

Type A N-acetyl D-glucosamine

WHAT ARE ITS FUFUNCTIONS?
NCTIONS? N-acetyl D-glucosamine
1. Storage form of me
metabolic
tabolic fuel D-galactose
L-fucose

Type B N-acetyl D-glucosamine

D-galactose
D-galactose
2. Structural function / Supportive function L-fucose
a. Ce llulose – most abundant in nature, no nutritive
Cellulose
value, forms the cell wall of plants.

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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)
2. FURANOSE – five-membered ring resembling
furan; ketoses.

Type AB N-acetyl D-glucosamine

N-acetyl D-glucosamine
D-galactose
D-galactose
L-fucose
b. Components of clotting proteins CLASSIFICATIONS
- Heparin – an anti-clotting agent present in the ALDOSES
body. Aldotriose D-Glyceraldehyde
9. Precursors Aldopentetroses D-Erythrose
- Initiates biological processes for biosynthesis of: D-Threose
purine, pyrimidine, nucleotides, Vitamin C, and Aldopentoses D-Ribose (Rib)
certain amino acids. D-Arabinose (Ara)
D-Xylose (Xyl)
LESSON 22:: CLASSIFICATIONS OF CA
CARBOHYDRATES
RBOHYDRATES D-Lyxose (Lyx)
TYPES OF CARBOHYDRATES Aldohexoses D-Allose
A. ACCORDING TO NUMBER OF SIMPLE SUGARS D-Altrose
OBTAINED BY H HY
YDROLYSIS D-Glucose (Glc)
D-Mannose (Man)
D-Gulose
D-Idose
D-Galactose(Gal)
D- Talose
KETOSES
Ketotriose Dihydroxyacetone
Ketotetrose D-Erythrulose
Ketopentoses D-Ribulose
D-Xylulose
Ketohexoses D-Psicose
1. Monosaccharides D-Fructose
- Simplest form of sugar which cannot be further D-Sorbose
hydrolyzed; building blocks of carbohydr
carbohydrates
ates D-Tagatose
- Sweet tasting, with varying relative sweetness
- Polar compounds with high melting points 2. Oligosaccharides
- Solids at room temperature, very soluble in water - Polymers made up of 2-10 monosaccharides.
B. ACCORDING TO NUMBER OF CARBONS IN Disaccharides à 2 Monosaccharides.
MONOSACCHARIDES Maltose = Glucose + Glucose
1. TRIO SE – contains 3 carbon atoms
TRIOSE Lactose = Glucose + Galactose
2. TETROSE – contains 4 carbon atoms Sucrose = Glucose + Fructose
3. PENTOSE – contains 5 carbon atoms 3. Polysaccharides
4. HEXOSE – contains 6 carbon atoms - Polymers more than 10 saccharide units.
5. HEPTOSE – contains 7 carbon atoms a. HOMOPOLYSACCHARIDES – one kind of
C. ACCORDIN
ACCORDING G TO REACTIVE GROUP monosaccharide.
1. ALDOSE – monosaccharides with an aldehyde 1. Starch – Glucose
group. 2. Glycogen – Glucose
- Carbonyl at C1; like Glucose 3. Dextrin – Glucose
2. KETOSE – monosaccharides with a ketone group 4. Cellulose - Glucose
- Carbonyl at C2; like Fructose 5. Dextran - Glucose
6. Inulin - Fructose
b. HETERO
HETEROPOLYSACCHARIDES
POLYSACCHARIDES – two or more kind of
monosaccharides.
1. Hyaluronic Acid:
d-glucuronic acid + d-glucosamine + acetic pain
C. ACCORDIN
ACCORDING
G TO RING STRUCTURE 2. Hepari
Heparinn
1. PY
PYRANOSE
RANOSE – six-membered ring resembling pyran; - Six sugar residues + N-acetyl D-glucosamine + D-
aldoses. iduronate

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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)
4. Derived Carbohydrates
- Sugars with added with other substituents aside
from OH.
a. Sugar acid
b. Sugar alcohol
c. Amino sugar
d. Deoxy sugar
e. Phosphorylated sugar
D. ACCORDIN
ACCORDING G TO REDUCING POWER
1. REDUCING SUGARS – carbohydrates with free
aldehyde or ketone group.
- All monosaccharides and disaccharides except
sucrose.
2. NON
NON--REDUCING SUGARS– carbohydrates without
- Most biologically active monosaccharides are D
free aldehyde or ketone group
isomers.
- Sucrose and all polysaccharides. - Most monosaccharides occurring in mammals are
of the D-configuration and enzymes are responsible
LESSON 3 - ISOMERISM
ISOMERISM:: FISCHER STRUC
STRUCTURE
TURE AND
for their metabolism are specific for this
HAWORTH STRUCTURE
configuration.
DIF
DIFFERENT
FERENT FORMS OF ISOMERI
ISOMERISM
SM
3. Alpha & Beta Anomers
1. Optical Isomers
- Stereoisomers that differ configuration around an
a. De
Dextrorotator
xtrorotator
xtrorotatoryy – an optical isomer which rotates
anomeric carbon of a cyclic ring structure or ring
the beam of polarized light to the right or clockwise
structure.
and indicated by a (+) sign or smaller letter d.
a. Alpha (α) – the OH is written below the anomeric
Alpha
Ex: (+) glucose or d-glucose
carbon.
b. Levorotatory – an optical isomer which rotates the
beam of polarized light to the left or counter- - Most sugars are of α-anomers since our body can
clockwise and indicated by a (-) sign or small letter l. only utilize those of this anomers except in some
Ex: (-) glucose or l-glucose cases.
b. Beta (β ) – the OH is written above the anomeric
carbon.

> Pyranose – the anomeric carbon is C-1 and is

obtained by cyclization of an aldehyde and an alcohol
group.

2. D & L Enantiomers > Furanose – the anomeric carbon is C-2 and is

a. D – the enantiomer with the OH group on the right obtained by cyclization of a ketone and an alcohol
(dextro) side of the chiral carbon farthest from the group.
carbonyl group. Naturally occurring.
b. L – the enantiomer with the OH group on the left
(levo) side of the chiral carbon farthest from the
carbonyl group. Unnatural Enantiomer.

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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)
b. Hemiketal – the product of the addition of an
alcohol to the carbonyl group of a ketone.
a. b.

4. Epimers 3. New
Newman
man Pro
Project
ject
jection
ion
- Stereoisomers that differ in configuration around a - Boat and chair structures.
single carbon atom of a linear structure, using D-
glucose as reference.
- Two sugars which differs from one carbon only in the
configuration.

GENERAL RULE TO TRANSLATE A FISHCER

PROJECTION TO A HAWORTH PROJECTION
1. Classify given sugar as aldose (pyranose) or ketose
(furanose).
2. Determine whether the given sugar is α- anomer or
SUMMARY β- anomer. At the anomeric carbon, the α from is
Optic
Optical
al De
Dextro
xtro – right, Levo – left, (-), l indicated by the -OH being written below the plane;
Isomer (+), d, the β form has the -OH above the pl ane.
plane
D – OH group L – OH group on 3. The groups on the right side of the Fischer
on the right, the left, projection are written below the plane in the Haworth
Enantiomers
naturally unnatural projection. Those on the left side are written above
occurring the plane. Applicable for C2,C3, C4 for aldoses; C3, C4
Alp
Alpha
ha ( α) – OH Beta (β ) – OH for ketoses.
Anomers
written below written above 4. Exception to rule 3 occurs at carbon 4 in pentoses
Pyranose – 6- Furanose – 5- and at carbon 5 in hexoses because of the nature of
membered ring, membered ring, the reaction occurring there.
C-1, aldehyde + C-2, ketone + 5. In both projections, the CH2OH group in C6 for
alcohol alcohol aldoses and C1 & C6 in ketoses, which has no chiral
Stereoisomers that differ in carbon, is written as a unit.
Epimers configuration around a single
carbon atom of a linear structure. Try:

KINDS OF TWO DIMENSIONAL RE REPRESENTAT

PRESENTAT
PRESENTATION
ION
1. FFischer
ischer Pro
Project
ject
jectio
io
ion
n
- Straight chain or open chain structures.

2. Haworth Pro
Project
ject
jection
ion
- Ring or cyclic structures; hemiacetals or hemiketals.
a. Hemiace
Hemiaceta tall – the product of the addition of an
ta
alcohol to the carbonyl group of an aldehyde.

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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)
1. D-glucose

2. D
D--man
mannose
nose

3. Fructose – a ketohexose with 5-membered ring

and 2 anomers,

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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)
LESSON 44:: MONOSACCHARIDES, DISAC DISACCHARIDES,
CHARIDES,
POLYSACCHARIDES AND ARTIFICIAL SWEETENERS
USES OF DIFFER
DIFFERENT
ENT CARBOHYDRATES
(Monosacchari
Monosaccharides)des)
1. D
D--GLUCOSE
- Most important of all monosaccharide
- An aldose
- Usually found in the bloodstream and in tissue fluids
thus known as the blood sugar.
- Commercially known as Dex extrose
trose because it is
mostly dextrorotatory.
- Two hormones, insulin and glucagon, have
important roles in keeping it within normal range.
- Primary source of energy digesting by the cells.
- A 5% (m/v) glucose solution is often used in hospital
as a IV source of nourishment for patients who cannot
take food by mouth. The body can use it as an energy
source without digesting it.
- Excess glucose is stored as the polysaccharide
glycogen or as fat.
Associated Disease
> Diabetes – patient produce insufficient insulin to
adequately regulate blood sugar levels, so they must
monitor their diet and/or inject insulin daily.
- Glucose is found in the urine of a patient with
diabetes mellitus.
- Normal quantity of glucose present in blood taken
after a period of fasting is 70-110 mg/dL. This value is
called the Normal Fasting Blood Sugar.
- To evaluate blood glucose levels, GTT is ordered.
- The patient fasts for 12 hrs., and then a blood sample
is taken immediately.
> Hyp
Hyper
er
erglycemia
glycemia – if the blood glucose exceeds 100
mg/dL and remains high.
- An example of a disease that can cause
hyperglycemia is diabetes mellitus, which occurs
when the pancreas is unable to produce sufficient
quantities of insulin.
> Hypo glycemia – the blood glucose level rises and
Hypoglycemia
then decreases rapidly to levels as low 70mg/dL. In
some cases, it is cause by the overproduction of
insulin by the pancreas. Low blood glucose can cause
dizziness, general weakness, and muscle tremors
2. D-FRUCTOSE
- The only ketose sugar encountered in biochemistry.
- Sweetest common sugars; sweetness of fruits is due
to its presence; Fruit Sugar
- Occurs naturally in fruit juices and honey; the most
soluble of all sugars.
- Also known as Levulose because it is strongly
levorotatory in solution,
- The liver can convert D-fructose to D-glucose.
3. D-MANNOSE
- An aldose not found free in nature but is rather
widely distributed in the form of polysaccharide
called mannans.
- Found in silage, pineapples, important in explosives.
- The only carbohydrate with a bitter taste.
4. D-GALACTOSE
- Most common occurrence is in lactose (milk sugar)sugar);;
brain ssu
ugar found in brain and nerve tissue.
- Necessary for the synthesis of lactose in milk; made
in the mammary glands.
Associated Disease
> Lactose Into
Intolerance
lerance
- The disaccharide lactose is an important dietary
carbohydrate that is found in the milk of all
mammals.
- Lactose digestion occurs in the small intestine,
where the enzyme lactase (β-galactosidase)
hydrolyzes the molecule to form galactose and
glucose. Many adults, including most blacks and
almost all Asians, have a low level of this enzyme.
- The lactose in the milk travels through the small
intestine to the colon mostly undigested. In the colon,
bacterial fermentation of those lactose produces
large quantities of CO2, H2, and irritating organic
acids. This results in bloa
bloating,
ting, flflatulence,
atulence, abdominal
pain, and diarrhea from drinking milk. The diarrhea
results from fluids moving into the small intestine in
response to the osmotic pressure from the
undigested lactose.
> Galactosemia – a more serious disease. More than
one out of every 20,00 children is born with a
deficiency in certain enzymes necessary for the
metabolism of galactose, Their bodies can hydrolyze
lactose to form glucose and galactose. Thus
producing the toxic metabolic derivative D-
GALACTITOL (D-DULCITOL
DULCITOL))
- As the galactose accumulates in the blood and
urine, the body converts it to the other compounds
that can lead to cataract formation and mental
disorders. In more severe cases, some children have
died from liver damage resulting from the building of
galactose.
USES OF DIFFER
DIFFERENT
ENT CARBOHYDRATES
(Disaccharides)
- When this reaction occurs between two
monosaccharides the bond that joins them together
is called a glyco
glycosidic
sidic llinkage.
inkage.
- The glycosidic linkage joining the two rings can be
alpha or beta.
- If the bond is alpha
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Biochemistry
LECTURE | MODULE 2 (CARBOHYDRATES)

- If the bond is beta.

2. GLYCOGEN
- Also called Animal Starch
- Branched chain α-1,4 and α-1,6 glycosidic linkages in
every 12-18 glucose units; 3x more highly branched
than amylopectin.
- Hydrolysis cleaves the C–O glycosidic linkage and - Much larger with up to 1, 000, 000 glucose units.
forms to monosaccharides. -Found mostly in the liver as storage material and in
1. MALTOSE the muscle as source of energy.
- Glucose + Glucose (when hydrolyzed) 3. CELLULOSE
- α-1,4 glycosidic linkage is present. - Straight chain β-1,4 glycosidic linkage is present;
- Most common reducing disaccharide contains 5000 glucose units.
- Not found as free substance but as a constituent of
polysaccharides, starch and glycogen; MALT SUGAR . RELATIVE SWEETNESS OF SUGARS AND OTHE
OTHER
R
- Used as malt extract, sweetener and as a COMPOUNDS
fermentative agent. Glucose 74.3
- Common ingredient in baby foods. Fructose 173.3
2. LAC
LACTOSE
TOSE Mannose 0.0
- Glucose + Galactose (when hydrolyzed) Galactose 32.1
- β-1,4 glycosidic linkage is present. Maltose 32.5
- Milk Sug
Sugar
ar Lactose 16.0
Its main function is to furnish the galactose necessary Sucrose 100.0
for the synthesis of glycolipids of brain and nervous Starch
tissue. Glycogen Tasteless
- Hydrolyzed by lactase ; makes up of 4% lactose in Cellulose
cow’s milk. Aspartame 15, 000
3. SUCROSE Cyclamate 3, 000
- Glucose + Fructose (when hydrolyzed) Saccharin 35, 000
- α-1,2 glycosidic linkage is present. Sucralose 60. 000
- Commonly called as Cane Sugar and sometime
Saccharose.
- Ordinary sugar used in cooking and in the table;
Table Suga
Sugarr.
- A non-reducing sugar.
- Very sweet, but contains many calories.
- To reduce caloric intake, many artificial sweeteners
have been developed.

USES OF DIFFER
DIFFERENT
ENT CARBOHYDRATES
(Poly
Polysaccharides)
saccharides)
1. STARCH
- Storage form of energy in plants.
- One of the most important constituents of the
human diet, making about 50-70% of the solid
substances of most of the cereals.
- 2 forms of starch: Amylose (the linear form of
starch), and Amylopectin (the branched form of
starch).

JALN | 11
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
INTRODUCTION
- Have you ever wondered why oil and water do not
mix? Or what do butter, oil, fatty acids, cholesterol,
and vitamin A have in common? Lipids known as fats
provide a major way of storing chemical energy and
carbon atoms in the body. Fats also surround and
insulate vital body organs, providing protection from
mechanical shock and preventing excessive loss of
heat energy. Phospholipids, glycolipids, and
cholesterol (a lipid) are the basic components of cell
membranes. Several cholesterol derivatives function
as chemical messengers (hormones) within the body.
- Lipids are unique among organic molecules
because their identity is defined on the basis of a
physical property and not by the presence of a
particular functional group. Because of this, lipids
come in a wide variety of structures and have many
different functions. Common lipids include
triacylglycerols in vegetable oils, cholesterol in egg
yolk, and vitamin E in leafy greens.
Examples of Lipids:
LESSON 11:: INTRODUC
INTRODUCTIONTION TO LIPIDS: PRO
PROPEPE
PERTIES,
RTIES,
FUNCTIONS AND REACTION
REACTIONS S
WHAT ARE LIPIDS
LIPIDS??
- Lipids share no common chemical structure.
- They are not defined by a particular functional
group, thus they have a variety of structures and
functions.
- Include all biological compounds that are soluble in
organic solvent (chloroform, methanol, ether,
benzene, acetone, n-hexane, etc.) but not in water
and other ordinary solvents (dilute acids, dilute
alkaline, salt solutions, etc.).
- Include fats, vegetable oils, waxes, steroids, vitamins
and hormones.
- Organic (carbon-containing) compounds that are
poorly soluble in water.
PROPERTIES OF LIPIDS
- Heterogeneous group of compounds that are
related more by their physical than by their chemical
properties.
- They are not defined by a particular functional
group, thus they have a variety of structures and
functions.
- They are relatively insoluble in water and soluble in
a non-polar solvent.
- They are greasy to touch and leaves a permanent
oily stain on the paper.
- Lipids are lighter than water.
- Pure lipids are colorless with bland odor and taste.
- When heated strongly, undergoes decomposition
forming acrid flammable vapors and when ignited,
they burn with a sooty flame.
- Lipids are poor conductors of heat and electricity
and therefore serve as excellent insulators for the
body, slowing the loss of heat through the skin.
FUNCTIONS OF LIPIDS
- Lipids are a major source of energy for the body,
and they also provide the hydrophobic barrier that
permits the partitioning of the aqueous contents of
cells and subcellular structures.
- They serve additional functions in the body, for
example, some fat-soluble vitamins have regulatory
or coenzyme functions, and the prostaglandins and
steroid hormones play major roles in the control of
the body’s homeostasis.
- Lipids also act as precursors for other lipids and play
a role in the transport of other lipids in the body. They
also function as emulsifying agents in the
gastrointestinal tract.
- Deficiencies or imbalances of lipid metabolism can
lead to some of the major clinical problems
encountered by physicians, such as atherosclerosis
and obesity.
SIGNIFICANCES OF LIPIDS
1. Source of energy or fuel
1 g fat = 9 kcal
1 g protein = 4 kcal
2. Reserve supply of food and energy when stored in
adipose tissue; inert.
3. Protector of vital organs and nerve endings.
4. Heat and electrical insulators.
5. Component of cell membrane.
6. Confers palatability to the diet.
ATHEROSCLEROSIS
- A form of arteriosclerosis, a condition in which
deposits of lipid materials (cholesterol) accumulate in
the walls of the arteries to form bulges or plaques
which restricts blood flow.
- Consequences of dyslipidemia (atherosclerotic
disease): Myocardial infarction, angina, ischemic
stroke, peripheral arterial disease.
CHEMIC
CHEMICAL AL REACTIONS OF LIPIDS
1. Saponification/Alkaline Hydrolysis
- Fats and oils can be hydrolyzed in the presence of
an acid, a base, or specific enzymes known as lipases.
The hydrolysis of fats and oils in the presence of a
base is used to make soap and is called
saponification.
- The reaction of fats with strong bases producing
salts of fatty acids known as soap and glycerol.
JALN | 12
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
Fat / Oil + Strong Base à Glycerol + Salts (Soap) of
Fatty Acids
- Soaps are commonly sodium salts of carboxylic
acids and are almost completely soluble in water, In
every dilute solutions, soap exist as micelles. Micelles
behave as carboxylate ions containing both a
hydrophilic and a hydrophobic end. The hydrophobic
end of the micelles are the ones that attract the dirt,
forming an aggregate of dirt and micelle that is
soluble in water.
- Sodium st earate– Soap
stearate
- So dium lauryl sulfate– detergent
Sodium
- Hydrolysis of Tr
Triacylglycerol
iacylglycerol
iacylglycerolss (S
(Soap
oap Synthe
Synthesis)
sis)
> The nonpolar tails dissolve grease and oil and polar
head makes it soluble in water.
> Soaps are made from lard (from hogs), tallow (from
cows/sheep), coconut oil, or palm oil.
> All soaps work in the same way, but have different
properties depending in the lipid source, length of C
chain, and degree of unsaturation.
2. Hydrogenation
- The double bonds in fats and oils can undergo
hydrogenation. The hydrogenation of vegetable oils
to produce semisolid fats is an important process in
the food industry. Chemically, it is essentially identical
to the catalytic hydrogenation reaction described for
alkenes.
- In commercial processes, the number of double
bonds that are hydrogenated is carefully controlled
to produce fats with the desired consistency (soft and
pliable). In the preparation of margarine, for
example, partially hydrogenated oils are mixed with
water, salt, and nonfat dry milk, along with flavoring
agents, coloring agents, and vitamins A and D, which
are added to approximate the look, taste, and
nutrition of butter.
- Unsaturated fatty acids in triglycerides converts
double bonds into single bonds by the addition of
hydrogen. The hydrogen is bubbled through hot oil in
the presence of nickel catalyst.
a. Part
Partial
ial Hydrogenation: produces soft, semi-solid fat
Hydrogenation
(more preferable product)
Vegetable Oil + H2 à Vegetable shortening, Tub soft
margarine, Stick margarine
b. Complete Hydrogenation: produces hard, brittle
fats
3. Oxidation
Oxidation// Rancidity
- Fats and oils that are in contact with moist air at
room temperature eventually undergo oxidation and
hydrolysis reactions that cause them to turn rancid,
acquiring a characteristic disagreeable odor.
- One cause of the odor is the release of volatile fatty
acids by hydrolysis of the ester bonds. Butter, for
example, releases foul-smelling butyric, caprylic, and
capric acids. Microorganisms present in the air
furnish lipases that catalyze this process. Hydrolytic
rancidity can easily be prevented by covering the fat
or oil and keeping it in a refrigerator.
– a reaction in which a fat or oil becomes rancid when
its double bonds are oxidized by oxygen (oxidation)
and microorganisms (hydrolysis). The oxidation
products are short-chain aldehydes and fatty acids
that have very disagreeable odors and tastes.
1. Fat/oil turning rancid over a long period of time
will undergo oxidation to produce àshort-chain
aldehydes àshort-chain carboxylic acids giving
off an unpleasant odor.
2. Butter exposed at room temperature for too
long will undergo hydrolysis by the enzymes
produced by microorganisms in air àbutyric acid
giving an odor of rancid butter.
Body O
Odor
dor
- 3-methyl-2-hexenoic acid, as being largely
responsible for body odor.
- The bacteria (lipophilic diphtheroid) that
produce the most 3-methyl-2-hexenoic acid are
found in about 90% of male armpits but only
about 60% of females’.
- This fact led to the development of different
deodorant products for men and women.
JALN | 13
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
Antioxidants - Lipids containing fatty acids, alcohol, phosphoric
- Substances that retards the rancidity of fats/oils acid and a nitrogen compound.
by preventing oxidation to take place. Glycerophosphol
Glycerophospholipids
ipids
- Examples are Vitamins C and E. - The alcohol is glycerol
Sphin
Sphingophospholipi
gophospholipi
gophospholipidsds
LESSON 22:: CLASSIFICATION OF LI
LIPIDS
PIDS - The alcohol is sphingosine
BASED ON THEITHEIR
R REACTION WITH WATER b. Glycolipi
Glycolipids
ds
1. H
Hydrolyzable
ydrolyzable Lipi
Lipids
ds - Lipids containing a fatty acid, sphingosine, and
– These are compounds that can be converted into carbohydrate (either galactose or glucose).
smaller molecules by hydrolysis. c. Other complex llipids
ipids
– These are compounds that are derived from fatty - Lipids such as sulfolipids, aminolipids, lipoproteins
acids. and lecithin.
Examples: Fats, oils, waxes, phospholipids 3. Precursor and Derived Lipi
Lipids
ds
- Precursor Lipids – compounds produced when
simple and complex lipids undergoes hydrolysis. They
include such substances as fatty acids, glycerol,
sphingosine, and other alcohols.
- Derived Lipids – formed by metabolic
2. Nonh
Nonhydrolyzable
ydrolyzable Lipi
Lipids
ds transformation of fatty acids, They include ketone
– These are compounds that cannot be cleaved into bodies, steroids, fatty aldehydes, prostaglandins, and
smaller molecules by hydrolysis. lipid-soluble vitamins.
Examples: steroids, fat-soluble vitamins, eicosanoids
LESSON 3: FATTY ACIDS
WHAT ARE FATTY ACIDS?
- Building blocks of lipid.
- Long-chain carboxylic acids that typically have an
even number of carbon atoms ranging from 12-18
BASED ON THEIR STRUCTURE (most common).
- They contain a polar end and a non-polar end.
- Apart from the carboxylic acid (-COOH) group,
fatty acids have no functional groups, except that
some do have double bonds.

CLALASSIFICATION
SSIFICATION OF FATTY ACIDS
1. Satu
Saturated
rated Fatty Acid
- Contains only single bonds.
- Inert; unreactive
- Straight-chain structures; allow their molecules to fit
1. Simple Lipi
Lipids
ds
close together and form attractions,
– Lipids which yield fatty acids and alcohol upon
- Have no double bonds
hydrolysis. - Fatty/waxy solids at room temperature
- Are esters of fatty acids. - High boiling and melting point
- The hydrolysis of a simple lipid may be expressed - Ends with -ANOIC ACID
as: Ex: Stearic acid
Simple lipid + Water à Fatty acid(s) + Alcohol CH3(CH2)16COOH
Examples: triacylglycerols (fats and oils) and waxes 18:0
a. Fats & OOils
ils Octadecanoic acid
- 3 fatty acids + glycerol - Palmitic (16 carbons) and stearic (18 carbons) are
b. Waxes the major human saturated fatty acids.
- fatty acids + high molecular mass monohydric 2. Uns
Unsatu
atu
aturated
rated Fatty Acid
alcohol - Contains one or more double bonds
2. Comple
Complex/Compound
x/Compound Lipids - Most contain cis double bonds that cause one or
– Lipids which yield fatty acids, alcohol, and other more bends in the carbon chain; irregular shape.
compounds upon hydrolysis. - Do not fit closely; weaker bonds
– Found in cell membranes, brain, nervous tissues, - Liquid at room temperature
myelin sheaths of nerves, and blood platelets - Lower boiling points than room temperature
Examples: phospholipids, glycolipids, sphingolipids, - Ends in -ENOIC AC ACID
ID
and lipoproteins Ex: Oleic acid
a. Phospholipids CH3(CH2)7CH=CH(CH2)7COOH
18:1n-9

JALN | 14
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
9-Octadecanoic acid - Cell membranes release arachidonic acid in
response to a variety of circumstance / physiological
a. Monounsaturated Fatty Acid triggers, including infection and allergic reactions.
- Have 1 C–C double bond.
- Palmitoleic acid and Oleic acid are the major
human monounsaturated fatty acids.
- OLEIC ACID – possibly the most common fatty acids
in natural fats.
- Many plants and vegetable oils are
monounsaturated fatty acids, and therefore are good
for you.
- Most naturally occurring unsaturated fatty acids
occur in cis- configuration.
b. Poly
Polyunsaturated
unsaturated Fatty Acid
- Have more than 1 C–C double bond.
- Linoleic acid, linolenic acid, and arachidonic acid are 1. Prostacyclin – a prostaglandin that dilates blood
examples. vessels and inhibits the formation of blood clots.
2. Thromboxane – a prostaglandin that constricts
blood vessels and causes blood clotting.
3. Leukotrienes – a prostaglandin that produce
muscle contractions, especially in the lungs and
thereby cause asthma-like attacks /
inflammations. In this regards, they are 100 times
more potent than histamine.
DRUGS AND EICOSANOIDS
- Many drugs control one or more of the eicosanoids’
physiological effects.
- Non-steroidal anti-inflammatory drugs (NSAIDs)
block the oxidation of arachidonic acid to form
prostaglandins and thromboxane.
Ex: aspirin, ibuprofen, ketoprofen, celecoxib

Unsaturated fatty acids can be further classifi

classified
ed as
cis fatty acids or trans
trans--fatty acids.
- cis Fatty acids have two hydrogen atoms on the
same side of the double bond, which creates a kink in
the structure. (healthy; usually seen in oils)
- trans Fatty acids have two hydrogen atoms on the
opposite side of the double bond, which results in a
similar structure to that of saturated fatty acid (not
healthy; seen in margarine and repeated use of oil )

c. Ei
Eicosanoids
cosanoids
- The biochemicals derived from fatty acid
arachidonic acid.
- Prostaglandins are the best known of the eicosanoid HOW TO WRITE THE SHORT HAND CODE OF F ATTY
class, which also includes the leukotrienes, ACIDS?
prostacyclin, and thromboxane. A: Bn – C
Where:

JALN | 15
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
A = number of carbon atoms No. of C a toms: 18
atoms:
B = number of double bonds Formula
Formula:: CH3(CH2)16COOH
C = position of first double bond from the methyl end Short hand code: 18:0
of the molecule. 9. Arachidic acid
Sho
Short
rt hand cod
codee uses Omega des
designation:
ignation:starts with No. of C a toms: 20
atoms:
methyl group Formula
Formula:: CH3(CH2)18COOH
Short hand code: 20:0
IUPAC naname
me u ses Delt
Delta
a design ation: starts with
designation:
carboxyl group Unsa
Unsaturated
turated Acids
Acids::
- Fatty acids can be named using a shorthand 1. Palmitole
Palmitoleic ic acid
nomenclature. First, count the number of carbons. No. of C a atoms:
toms: 16
Next, count the number of double bonds and note Formula
Formula:: CH3 (CH2)5CH=CH(CH2)7COOH
their position: Delta – starting from the carboxylic Short hand code: 16:1n-9
end, and omega – starting from the methyl end. 2. Ole
leic
ic acid
No. of C a toms: 18
atoms:
Formula
Formula:: CH3 (CH2)7CH=CH(CH2)7COOH
Shortt hand code: 18:1n-9
Shor
3. Lino
Linole
le
leic
ic acid
- Write the number of carbons followed by a colon No. of C a atoms:
toms: 18
and the number of double bonds present, if any. For Formula:: CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH
Formula
unsaturated fatty acids, indicate if you started Short hand code: 18:2n-6
counting from the delta or omega end. For example: 4. Linol
Linolen
en
enicic acid
No. of C a atoms:
toms: 18
Formula
Formula:: CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7
COOH
Short hand code: 18:3n-3
2. Arachidoni
Arachidonicc acid
No. of C a atoms:
toms: 20
Formula:: CH3(CH2)4(CH=CHCH2)4CH2CH2COOH
Formula
Some of the Naturall
aturallyy Occurring Fatty Aci
Acids
ds Short hand code: 20:4n-6
Saturate
aturated d Acids:
1. B
Butyric
utyric acid ESSENTIAL FATTY ACIDS
No. of C a atoms:
toms: 4 - Fatty acids not synthesized by the body and are
Formula
Formula:: CH3CH2CH2COOH essential for the health and growth of tissues, esp. in
Short hand code: 4:0 infants. It includes alpha-linolenic acid (ALA) and
2. Caproic acid linoleic acid (LA).
No. of C a atoms:
toms: 6 1. Linoleic Acid
Form ula:: CH3(CH2)4COOH
Formula
ula - Called the nutritionally essential fatty acid; omega-
Short hand codecode:: 6:0 6 acid.
3. Caprylic acid
No. of C a toms: 8
atoms:
Formula
Formula:: CH3(CH2)6COOH
Short hand code: 8:0
4. Capr
Capricic acid
No. of C a atoms:
toms: 10
Formula
Formula:: CH3(CH2)8COOH - The parent fatty acid of the omega-6 family.
Short hand code: 10:0
5. Lau
Lauric
ric acid
No. of C a atoms:
toms: 12
Formula:: CH3(CH2)10COOH
Formula 18:
18:2n-6
2n-6
Short ha
handnd code: 12:0 2. Linolenic Acid
6. Myrist
Myristicic acid - Can be synthesized from synthesis of linolenic acid;
No. of C a toms: 14
atoms: called omega-3 acid.
Formula
Formula:: CH3(CH2)12COOH
Short hand code: 14:0
7. Palmit
Palmiticic acid
No. of C a atoms:
toms: 16
Formula
Formula:: CH3(CH2)14COOH - α-Linolenic acid is the parent fatty acid of the
Short hand code: 16:0 omega-3 family
8. Stea
Stearic
ric acid

JALN | 16
Biochemistry
LECTURE | MODULE 3 (LIPIDS)

18:3n
18:3n-3
-3
- Eicosapentaenoic acid (EPA) 20:5 ω3 20:5n
20:5n-3
-3
- Docosahexaenoic acid (DHA) 22:6 ω3 20:6n
20:6n-3
-3

3. Arachidon
Arachidonic
ic Acid Physical Properties of Fats and Oils
- Loss of weight 1. Generally white or yellow solids and liquids.
- Skin dermatitis 2. Odorless and tasteless.
- Eczema 3. Become rancid and then develop an unpleasant
- Adults usually have a deficiency in fatty acids. odor and taste.
Associated Disease: FATS
a. Dermatitis: inflammation of the skin from any - Solid triglycerides; solids at room temperature.
cause, resulting in a range of symptoms such as - Usually come from animal sources such as meat
redness, swelling itching or blistering. (lard and tallow), whole milk, butter, eggs and cheese.
b. Eczema: skin condition, an inflammation of the skin - Few come from plants: Palm Oil & Coconut Oil
characterized by reddening and itching and the (liquid – short bond)
formation of scaly or crusty patches that may leak - A mixture of triglycerides containing a high
fluid. proportion of long-chain, saturated fatty acids
- Fats have higher melting points
Ome
Omega ga
ga--3 Fatty Acids/Polyunsaturated FFatty
atty Aci
Acids
ds - Contain mostly saturated fatty acids.
> Eicosapentaenoic acid (EPA) 20:5n-3 - Mostly are shorter in length.
> Docosahexaenoic acid (DHA) 22:6n-3 - Also vegetable shortening.
- Usually derived from fishes coming from cold
countries/climate
- Have been linked to healthy aging.
- Added to infant formula for development of brain,
retina, and immune function.
- Recommended to woman who are breastfeeding or
pregnant to include these in their diet.
- Also known to prevent cardiovascular and
Alzheimer’s diseases.
OIL
OILSS
LESSON 44:: SIMPLE AND COMPLEX LIPIDS - Are liquid triglycerides from plant sources
SIMPLE LIPIDS - Contain mostly unsaturated fatty acids; liquid at
1. FFats
ats & Oil
Oilss room temperature.
- Neutral fats; simplest and most abundant form of - A mixture of triglycerides containing a high
lipid. proportion of long-chain, unsaturated fatty acids, or
- Esters of three fatty acids and glycerol. short-chain, saturated fatty acids
- Known as Triglycerides, an inaccurate term. - Oils have lower melting points
- Also referred to as Triacylglycerol/TAGS, a more - Mostly obtained from plants and fish
accurate term.
- Main form of fat storage in plants and the adipose
cells (fat cell of animals).
- An average man’s body is 21% fat in men and 26%
in women, enough fat to supply his body’s energy
needs for 2-3 months.
- It is recommended that no more than 20-25% of a
person’s caloric intake should come from lipids.
- Humans store energy as triglycerides in adipose
cells below the surface of the skin, in the breast area, - Olive oil, peanut oil, and avocado oil contain
and surrounding internal organs. monounsaturated fatty acids.
- Hydrolyzed by enzymes called lipases to produce - Omega
Omega--6 Polyunsaturated oils: Cottonseed,
energy. safflower, sunflower seeds, sesame, walnuts, corn and
- Complete metabolism of triglycerides yields: CO2, soybean oils.
H2O, and energy. - Omega
Omega-3-3 Polyunsaturated oils: Canola, soybean
oil, salmon, mackerel and walnut.

JALN | 17
Biochemistry
LECTURE | MODULE 3 (LIPIDS)

a. Glycerophospholipids / Phosphoacylglycerols
- Fatty acids, glycerol, phosphoric acid and a nitrogen
compound.
- Most abundant lipid in the cell membranes.
- Phosphoacylglycerols are the main component of
most cell membranes.
2. Waxes - Structurally, they
- Esters of fatty acid with high-molecular mass resemble a triacylglycerol,
monohydric alcohol. except a phosphodiester
- Usually contain 14-30 carbon atoms. bonded to an alcohol.
- Typically solids that melt easily. - Cephalin - one of the main types of
- Because of their long nonpolar C chains, waxes are phosphoacylglycerols.
very hydrophobic.
- Form protective coating on plants and fruits, and an
animal
- Flexible and non-reactive which makes them
excellent protective and water-repellant coatings.
- Have commercial use in cosmetics, floor waxes, - Le cithin - second of the main types of
Lecithin
furniture and car polishes, ointments and creams. phosphoacylglycerols.
Example:
a. Wax coat
coatings
ings in fruits and on leaves and st
stems
ems of - The two fatty acid side chains form two nonpolar
plants. It prevents water loss and damage from tails that lie parallel to each other.
pests. - The phosphodiester end of the
b. Waxes on skin, fur and feather of animals and molecule is a charged or polar
bird
birdss coatin
coating.
g. It provide a waterproof animals and head.
birds coating. b. Sphingo
Sphingophospholipids
phospholipids
phospholipids/Sphingomyelins
/Sphingomyelins
c. Lanolin, a wax obtained from wool (sheep’s hair). - Fatty acids, sphingosine, phosphoric acid and a
Used in creams and lotions to aid water retention nitrogen compound.
which softens the skin. - Group of phospholipids that are abundant in brain
d. Beeswax obtained from honeycomb and used in and nerve tissues.
furniture, car and shoe polishes and waxes. - Sphingomyel
Sphingomyelinsins do not
e. Carnauba obtained from palm tree. contain a glycerol backbone,
f. Spermacetti obtained from oil of sperm whale. It they have a sphingosine
is used in making candles and cosmetics. backbone instead.
- Sphingomyel
Sphingomyelins ins do not contain an ester; their single
COMPLE
COMPLEX X LIPIDS fatty acid is bonded to the backbone by an amide
- Lipids that, upon hydrolysis, yield fatty acids, an bond.
alcohol (either glycerol or sphingosine) and other
compounds (such as phosphate or sugar group).
1. Phospholipids
- Where x can be choline, ethanolamine, serine,
inositol; Ex: lecithin
- Lipids that contain P atom.
- Also called phosphoglycerides or - Myel
Myelin in sheath, the coating that surrounds nerve
glycerophospholipids cells, is rich in sphingomyelins.
- Long-chain fatty acids on a glycerol backbone
attached to a phosphoric acid molecule containing
an alcohol substituent. (usually amino alcohol)
- The essential components of cell membranes and
are found in small concentrations in other parts of the
cell. - Glyco lipids - Are complex lipids that contain a fatty
Glycolipids
2 Ty
Types
pes of Pho
Phospholipi
spholipi
spholipids
ds acid, sphingosine, and carbohydrate (either
galactose/glucose). Present in cell membranes. Often
called cerebrosides because of their abundance in
brain tissue

JALN | 18
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
2. Lipoproteins
- Lipoproteins are the primary means of transport of
cholesterol among tissues
- Secreted by the small intestine and liver into the
circulating blood
- Composed of lipids and special proteins
(apolipoproteins)
Chylomicron
- They are formed in the mucosal cell of the intestine.
- They deliver triglycerides to the adipose tissue and
muscle. They also deliver dietary cholesterol to the
liver
a. Very Low
Low--Density Lipoprotei
Lipoproteins
ns
They are formed in the liver for the export of
triglycerides. They transport triglycerides from the
liver to the muscle and adipose tissue for storage or
energy.
b. Low
Low--Density Lipoproteins
They are primary carriers of cholesterol in the blood
for delivery to the tissues.
c. High
High--Density Lipoprotei
Lipoproteins
ns
They are scavengers for cholesterol from peripheral
tissues. They also return cholesterol to the liver for
metabolism.
3. Other Comple
omplexx Lipids
- Lipids such as sulfolipid, aminolipid, lipoproteins and
lecithin.
CELL MEMBRANES
Structure of the Cell Membrane
- The basic unit of living organisms is the cell.
- The cell membrane surrounds the cytoplasm, the
aqueous medium inside the cell.
- The cell membrane acts as a barrier to stop the
passage of ions and molecules into or put of the cell.
- The other job of the membrane is to allow nutrients
in and waste out.
- In this way, a cell membrane is selectively
permeable.
- Phospholipids, the major component of cell
membranes, contain a hydrophilic polar head and
two hydrophobic non polar tails.
- When phospholipids are mixed with water, they
assemble in a lipid bilayer.
- Proteins and cholesterol molecules are embedded
in the lipid bilayer membrane.
- Peripheral pr proteins
oteins are embedded within the
membrane and extend outward on one side only.
- Integral proteinsextend through the entire bilayer.
- Sometimes carbohydrates are attached to the
exterior of the cell forming glycolipids and
glycopr
glycoproteins.
oteins.
Transport Acro
Across
ss the Cell Membrane
- Small molecules like O2 and CO2 can diffuse through
the cell membrane, travelling from higher to lower
concentrations.
- Large pol
polar
ar molecules need facilitated transport to
cross efficiently.
- Ions like Cl- or HCO3- travel through integral protein
channels.
- Other ions, Na+, K+, and Ca2+, move against the
concentration gradient; this requires energy input
called active transport.
LESSON 5: DERIVED LIPIDS
1. Steroids
- Steroids are a group of lipids whose carbon
skeletons contain several fused rings:
2. Sterols
- Also known as steroid alcohol
- Occur naturally in plants, animals, and fungi
- Plant sterols have cholesterol-lowering properties
a. Cholesterol
- Precursor for vitamins and hormones
- Elevated levels of cholesterol in the bloodstream
lead to coronary artery disease, heart attack, etc.
- Transported through the bloodstream by
lipoproteins.
3. Bile Salts
- Bile salts are oxidation products of cholesterol.
- Bile salts are powerful detergents.
- Responsible for fat emulsification
- The secretion of bile salts and cholesterol into the
bile by the liver is the only mechanism by which
cholesterol is excreted.
4. Fat
Fat--Soluble Vitamins
- Vitamins are organic compounds and vital nutrients
that an organism requires in limited amounts.
- They cannot be produced by the body.
- Fat-soluble vitamins are stored in the body for long
periods of time.
- They pose a greater risk of toxicity than water-
soluble vitamins.
- Vitamins A, D, E, K
5. Hormones
- Hormones are chemical messengers that are
secreted directly into the blood, which carries them to
organs and tissues of the body to exert their
functions.
- Cholesterol is the starting material for the synthesis
of steroid hormones.
a. Adrenocorticoid hormones
JALN | 19
Biochemistry
LECTURE | MODULE 3 (LIPIDS)
b. Sex hormones
c. Anabolic steroids
6. Ketone Bodies
- Ketone bodies serve as an energy source for the
heart, kidney, and skeletal muscles, thereby
preserving the limited glucose for use by the brain.
- Produced by the liver from the breakdown of fatty
acids during periods of low food intake, carbohydrate
restrictive diets, starvation, prolonged intense
exercise, or in untreated type 1 diabetes mellitus.
7. Eicosanoids
- Eicosanoids are metabolites of arachidonic acid.
- Responsible for inflammatory responses, on the
intensity and duration of pain and fever, and on
reproductive function.
- Inhibits gastric acid secretion
- Regulates blood pressure through vasodilation or
constriction
- Inhibits or activates platelet aggregation and
thrombosis.
a. Prostaglandins (PGs)
b. Thromboxanes (TXs)
c. Leukotrienes (LTs)
d. Lipoxins (LXs).

JALN | 20
Biochemistry

LECTURE | MODULE 4 (PROTEINS)

INTRODUCTION - The amino group is attached to the α-carbon, the C
- The word “protein” is derived from the Greek word atom adjacent to the carbonyl group.
proteios, meaning “first.” All proteins in humans are
large molecules made up from 20 different amino
acids.
- Each kind of protein is composed of amino acids
arranged in a specific order that determines the
characteristics of the protein and its biological action.
- An extraordinary number of different proteins, each
with a different function, exist in the human body. - GLYCINE – simplest amino acid,
- A typical human cell contains about 9000 different where R=H.
kinds of proteins, and the human body contains about - The R group, called the side chain,
100,000 different proteins. determines the identity of the amino
- Proteins provide structure in membranes, build acid.
cartilage and connective tissue, transport oxygen in - If R = a basic N atom, it is a basic amino acid.
blood and muscle, direct biological reactions as - If R = an additional COOH group, it is an acidic amino
enzymes, defend the body against infection, and acid.
control metabolic processes as hormones. - Since amino acid contain a base (NH2) and an acid
- They can even be a source of energy. (COOH), a proton transfers from the acid to the base
- The different functions of proteins depend on the to form a zwitterion.
structures and chemical behavior of amino acids, the
building blocks of proteins. We will see how peptide
bonds link amino acids and how the sequence of the
amino acids in these protein polymers directs the
formation of unique three-dimensional structures.
- Every second, thousands of chemical reactions
occur in the cells of the human body at rates that
meet our physiological and metabolic needs. To make NEUTRA
NEUTRALL COMMON AMINO ACID
this happen, enzymes catalyze the chemical Alanine (Ala) Proline (Pro)
reactions in our cells, with a different enzyme for
every reaction. Digestive enzymes in the mouth,
stomach, and small intestine catalyze the hydrolysis
of carbohydrates, fats, and proteins. Enzymes in the
Asparagine (Asn) Serine ((S
Ser)
mitochondria extract energy from biomolecules to
give us energy.

LESSON 11:: AMINO ACIDS: DEFINITION, GENERAL

STRUCTURE , FUNCTIONAL GROUP, AND THEIR Cy
Cyssteine (Cy
(Cys)
s) Th
Thre
re
reonine
onine (Thr)
SIGNIFICANCE
WHAT ARE PROTEIN
PROTEINS S?
- Are biomolecules that contain many amide bons,
formed by joining amino acids.
Glutamine (Gl
(Gln)
n) Valine (Val)

Tryptophan (Trp)
- Account for 50% of the dry weight of the human Gly
Glyci
ci
cine
ne (Gly)
body,
- Have many functions in the body.
- Unlike lipids and carbohydrates, proteins are not
stored, so they must be consumed daily.
- Current recommended daily intake for adults is 0.8 Isoleucine (Ile) Tyrosine (Tyr)
grams of protein per kg of body weight (more is
needed for children).
- Dietary protein comes from eating meat and milk.
Le
Leucine
ucine (L
(Leu)
eu) Aspartic acid (As
(Asp)
p)
WHAT ARE AMINO ACIDS
ACIDS??
- Contains two functional groups – an amino group
(NH2) and a carboxyl group (COOH).

JALN | 21
Biochemistry

LECTURE | MODULE
Methionine (Met) 4 (PROTEINS)
Glutamic aci
acidd ((Gl
Gl
Glu)
u) 2. Glutamate (Glu): E
Amidic Sid
Side
e Chains
1. Asparagine (Asn): N
2. Glutamine (Gln): Q
Phenylalanine (Phe) Ba
Basic
sic Amino Acids
1. Arginine (Arg): R
2. Histidine (His): H
3. Lysine (Lys): K
Imino Acid
1. Proline (Pro): P
- not an α-amino acid as the other 19 amino acids.
BASIC AMINO ACID
Arginine (Arg) Histidine (His
(His)) CLASSI
CLASSIFICATION
FICATION OF AMINO ACID BY FUN
UNCTIONAL
CTIONAL
GROUPS
Non
Non--polar Ami mino
no Acids
1. Alanine Ala A
2. Isoleucine Ile I
Lysine (Lys) 3. Leucine Leu L
4. Methionine Met M
5. Phenylalanine Phe F
6. Proline Pro P
7. Tryptophan Trp W
8. Tyrosine Tyr Y
9. Valine Val V
STEREOCHEMISTRY OF AMINO ACIDS
Polar Amimino
no Acids
- All amino acids (save glycine) have a chirality center 10. Asparagine Asn N
on the α carbon. 11. Cysteine Cys C
12. Glutamine Gln Q
13. Glycine Gly G
14. Serine Ser S
15. Threonine Thr T
Acidic Amimino
no Acids
16. Aspartic acid Asp D
17. Glutamic acid Glu E
Basic Amimino
no Acids
18. Arginine Arg R
- L amino acids have the -NH3+ group on the left.
- D amino acids have the -NH3+ group on the right. 19. Histidine His H
20. Lysine Lys K
LESSON 2: CLASSIFICATION OF AMINO ACIDS
CLASSI
CLASSIFICATION
FICATION OF AMINO ACID AS ESSENTIAL AND
BASED ON PHYSICAL AND CHEMICAL PROPERTIES
NON
NON--ESSENTIA
ESSENTIALL
CLASSI
CLASSIFICATION
FICATION OF AMINO ACID BY SIDE CHAINS
Essential Amino Acid
Aliphat
Aliphatic
ic Non
Non--polar Side Chains
1. Alanine (Ala): A - Are essential to the normal functioning of the human
body,
2. Glycine (Gly0: G
3. Isoleucine (Ile): I - Since the body is not capable of synthesizing them,
they must be supplied in our diet.
4. Leucine (Leu): L
5. Valine (Val): V 1. Phenylalanine 6. Methionine
2. Valine 7. Leucine
Aromatic Side Chains
1. Phenylalanine (Phe): F 3. Tryptophan 8. Lysine
4. Threonine 9. Histidine*
2. Tyrosine (Tyr): Y
3. Tryptophan (Trp): W 5. Isoleucine 10 Arginine*
*relatively essential
Hydroxyl
Hydroxyl--containing Side Chains
1. Serine (Ser): S - On a nutritional basis, proteins are classified as
complete or incomplete.
2. Threonine (Thr): T
Sulfur
Sulfur--containing Side Chains - A complete protein supplies all the essential amino
acids; usually from animal sources (except gelatin –
1. Cysteine (Cys): C
2. Methionine (Met): M absence of tryptophan HC Test).
- An incomplete protein is deficient in one or more
Acidic Amino Acid
Acidss
1. Aspartate (Asp): D essential amino acids; usually from plant sources.
Ex: Rice – low in lysine and threonine.

JALN | 22
Biochemistry
LECTURE | MODULE 4 (PROTEINS)
LESSON 33:: ESSENTIAL AMINO ACIDS AND THEIR
SIGNIFICANCE
ESSENTIAL AMINO ACIDS
- A standard amino acid needed for protein synthesis
that must be obtained from dietary sources because
the human body cannot synthesize it in adequate
amounts from other substances.
- There are nine essential amino acids for adults, and
a tenth one is needed for growth in children. The table
below shows the list of essential amino acids.
- The human body can synthesize small amounts of
some of the essential amino acids, but not enough to
meet its needs, especially in the case of growing
children.
COMPLETE DIETARY PROT PROTEIN
EIN
- A protein that contains all of the essential amino
acids in the same relative amounts in which the body
needs them.
- A complete dietary protein may or may not contain
all of the nonessential amino acids.
IN
INCCOMPLETE DIETARY PROTE
PROTEIN
IN
- A protein that does not contain adequate amounts,
relative to the body’s needs, of one or more of the
essential amino acids.
- Associated with the term incomplete dietary protein
is the term limiting amino acid.
LIMITING AMINO A ACID
CID
- An essential amino acid that is missing, or present
in inadequate amounts, in an incomplete dietary
protein
- Protein from animal sources is usually a complete
dietary protein. Casein from milk and proteins found
in meat, fish, and eggs are complete dietary proteins.
- There is one common incomplete dietary protein
that comes from animal sources. It is gelatin, a
protein in which tryptophan is the limiting amino acid.
- Protein from plant sources tends to be incomplete
dietary protein. With plant proteins, three amino
acids are often limiting: lysine (wheat, rice, oats, and
corn), methionine (beans and peas), and tryptophan
(corn and beans). Note that both corn and beans
have two limiting amino acids. Soy is the only
common plant protein that is a complete dietary
protein.
COMPLE
OMPLEMENTARY
MENTARY DIETARY PROTEIN
- Two or more incomplete dietary proteins that, when
combined, provide an adequate amount of all
essential amino acids relative to the body’s needs.
- A mix of plant proteins generally provides high-
quality (complete) protein. Rice by itself is an
incomplete dietary protein, as are beans. A serving of
rice and beans provides all of the essential amino
acids by protein complementation.
- Prior to the development of genetic engineering
procedures, the quality of a given plant’s protein was
something that could not be changed. Genetic
modification techniques can improve a plant’s
protein by causing it to produce increased amounts
of amino acids that it normally has in short supply.
Such genetic modification, if fully implemented in the
future, would be especially important in areas of the
world that rely heavily on one incomplete protein food
source (beans or corn or rice); a much higher quality
protein would be available to the people for
consumption.
LESSON 44:: ACID
ACID--BASE BEHAVIOR OF AMINO ACIDS -
ZWITTERION STRUCTURE
AMPHOTERISM
- Amino acids are amphoteric when they can react
either as an acid or a base.
ACID-BASE BEHAVIOR OF AMINO ACIDS
- An amino acids exists as a neutrally charged
zwitterion (dip
(dipola
ola
olar)
r) at a certain pH, the isoelectric pH.
JALN | 23
Biochemistry

LECTURE | MODULE 4 (PROTEINS) LESSON 5 - PEPTIDES: FORMATION,

NOMENCLATURE & THE BI BIOLOGICAL
OLOGICAL IMPORTANCE
WHAT ARE PEPTIDE
PEPTIDES?
S?
- Peptides and proteins are formed when amino
acids are joined together by amide bonds.
- Dipeptide - has two
- The amino acid can exist in different forms, amino acids joined
depending on the pH of the aqueous environment. together by one amide
bond.
ISO
ISOELECTRIC
ELECTRIC POINT - The amide bond is called
- pH at which there is no migration toward either a peptide bond.
electrode is called the isoelectric point; - Trip
Tripeptide
eptide – has three
- pH when an amino acid in solution has equal (+) and amino acids joined
(–) charges. together by one amide
- Electrically neutral bond.
- Does not migrate toward either the positive or - Polypeptides have many amino acids, while proteins
negative electrode when placed in an electrolytic cell. have more than 40 amino acids.
- The amino acids Ala and Ser can be combined this
pH OF AM
AMINO
INO ACI
ACIDS
DS way:

- Or they can combine with Ser first and Ala second:

- When the pH is < isoelectric pH, the carboxylate

anion gains a proton, and the amino acid has a net
positive charge.

- The amino acid with the free -NH3+ group is the N-

termi
terminal
nal amino acid and is written on the left.
- The amino acid with the free -COO- group is the C-
terminal amino acid and is written on the right.
- When the pH is > isoelectric pH, the ammonium
cation loses a proton, and the amino acid has a net
negative charge.

HOW TO DRAW A DIPEPTI

DIPEPTIDE
DE FROM 2 AMINO A ACIDS?
CIDS?
Ex: Draw the structure of the dipeptide Val-Gly, and
label the N-terminal and C-terminal amino acids.
Step 1
- Draw the structures of the individual amino acids
from left to right.
- Draw valine on the left, glycine on the right.

JALN | 24
Biochemistry
LECTURE | MODULE 4 (PROTEINS)
STEP 2
- Join the adjacent -COO- and -NH3+ groups.
FINAL ANSWER:
BI
BIOLOGICALLY
OLOGICALLY ACTIVACTIVEE PEPTIDES
Neu
europeptides
ropeptides - Enkephalins & Pain Relief
a. Enkephalins
Enkephalins,, pentapeptides made in the brain, acts
a s a pain killers and sedative by binding to pain
receptors.
- Addictive drugs morphine and heroin bind to these
same pain receptors, thus producing a similar
physiological response, though longer lasting.
b. Enkephalins belong to the family of polypeptides
called endorphins, which are known for their pain
reducing and mood enhancing effects,
- The other main enkephalin, leu- enkephalin:
Peptide Hormones - Ox
Oxytocin
ytocin & Vasopressin
- Oxytocin and vasopressin are cyclic nonapeptide
hormones, which have identical sequences except for
two amino acids.
- The slight different sequence gives the two peptides
vastly different effects on the body.
a. Oxytocin – stimulates the contraction of the uterine
muscles, and signals for milk production; it is often
used to induce labor.
b. Vasopressin – antidiuretic hormone (ADH) targets
the kidneys and helps limit urine production to keep
body fluids up during dehydration.
LESSON 6 - PROTEINS: COMPOSITION, PROPERTIEPROPERTIES S
AND BIOCHEMICAL SIG SIGNIFICANCE
NIFICANCE
COMMON PROTEIN IN THE HUMAN BODY
- Protein are generally classified according to their 3D
shapes.
- Fibrous proteins are composed of long linear
polypeptide chains that are bundled together to form
rods or sheets.
- Fibrous proteins are insoluble in water and serve
structural roles.
- Globular proteins are coiled into compact shapes
that are water soluble.
- Enzymes and Transport pro proteins
teins are globular.
1. α – Keratins
- The protein found in hair hooves nails, skin, and wool.
- They are made of two mainly α-helix chains coiled
around each other in a superhelix.
- These coils wind around other coils making larger
and stronger structures (like hair).
- Collage
Collagen
n – requires 3 chains in a superhelix.
- Vitamin C helps stabilize the chain, and, when
missing, poorly formed collagen fibers result.
2. Hemoglobin a and
nd Myoglob
Myoglobiin
- Both hemoglobin and myoglobin are globular and
conjugated proteins, meaning they contain both a
protein and non-protein component.
- Their non-protein unit is a heme heme,, an organic
complex surrounding a Fe+2 ion.
- The Fe+2 ion bind to O2 gas in the bloodstream.
- Then, the hemoglobin protein transports the O2 to
wherever it is needed in the body.
- Or, if needed, the myoglobin store O2 in tissues.
JALN | 25
Biochemistry

LECTURE
The | MODULE
heme unit: 4 (PROTEINS) (enzymes and transport proteins). These are bundles
formed by the folding and crumpling of protein
chains. e.g., pepsin, edestin, insulin, ribonuclease,
myoglobin, hemoglobin, transferrin, immunoglobulins,
etc.
b. Fibrous proteins
- Composed of long linear polypeptide chains that
are bundled together to form rods or sheets; are
- Myog
Myogllobin has 153 amino acids in 1 polypeptide insoluble in water and serve structural roles. e.g.,
chain: keratin, collagen, elastin, myosin, fibrin/fibrinogen, etc.
3. Molecula
Molecularr Weight
The proteins generally have large molecular weights
ranging between 5 × 103 and 1 × 106. It might be noted
that the values of molecular weights of many proteins
lie close to or multiples of 35,000 and 70,000.
4. Colloidal Nature
- Hemoglobin has 4 polypeptide chains, each Because of their giant size, the proteins exhibit many
carrying a heme unit. colloidal properties, such as; Their diffusion rates are
extremely slow and they may produce considerable
light-scattering in solution, thus resulting in visible
turbidity (Tyndall effect).
5. Denaturation
Denaturation refers to the changes in the properties
of a protein. In other words, it is the loss of biological
activity. In many instances, the process of
- Carbon monoxide (CO) is poisonous because it denaturation is followed by coagulation— a process
binds 200 times more strongly to the Fe+2 than does where denatured protein molecules tend to form
O2. large aggregates and to precipitate from solution.
- Hemoglobin complexed with CO cannot carry O2, 6. Amphoteric Nature
and cells will die from lack of O2. Like amino acids, the proteins are amphoteric, i.e.,
- Sickle cell anemiais a disease where a single amino they act as acids and alkalines both. These migrate in
acid is different in two of the subunits of hemoglobin. an electric field and the direction of migration
- Red blood cells containing these mutated depends upon the net charge possessed by the
hemoglobin units become elongated and crescent molecule. The net charge is influenced by the pH
(sickle) shaped. value. Each protein has a fixed value of the isoelectric
- These RBCs will rupture capillaries, causing pain and point (pl) at which it will move in an electric field.
inflammation, leading to organ damage, and 7. Io
Ion-
n-
n-Binding
Binding Capacity
eventually painful death. The proteins can form salts with both cations and
anions based on their net charge.
PHYSICAL PROPERTIES OF PROTEI
PROTEINS
NS 8. Solubility
The solubility of proteins is influenced by pH. Solubility
is lowest at the isoelectric point and increases with
increasing acidity or alkalinity. This is because when
the protein molecules exist as either cations or anions,
repulsive forces between ions are high since all the
molecules possess excess charges of the same sign.
Thus, they will be more soluble than in the isoelectric
state.
9. Optical AcActivity
tivity
1. Color and Taste All protein solutions rotate the plane of polarized light
Proteins are colorless and usually tasteless. These are to the left, i.e., these are levorotatory.
homogeneous and crystalline.
2. Shape and Size CHEMICA
HEMICALL PROPERTIES OF PROTEINS
The proteins range in 3D-shape from simple 1. Hydrolysis
crystalloid spherical structures to long fibrillar - Protein hydrolysis involves breaking the peptide
structures. Two distinct patterns of shape have been bonds by treatment with aqueous acid, base, or
recognized : certain enzymes.
a. Globular prote
proteins
ins - In the body, the enzyme pepsin in gastric juice
- These are spherical and coiled in compact shapes cleaves some of the peptide bonds of large proteins
that are water-soluble and with active functions to make smaller peptide chains.

JALN | 26
Biochemistry

LECTURE | MODULE
- In the intestines, 4 (PROTEINS)
enzymes trypsin and chymotrypsin
hydrolyze the remainder of the amide bonds resulting
in individual amino acids.

- Shorthand symbols on a protein ribbon diagram:

- If fresh pineapple is added to gelatin desserts, the

gelatin will not gel. Fresh pineapple contains an
enzyme that facilitates the hydrolysis of gelatin
peptide linkages. Canned pineapple can be added to 3. Ter
Tertiary
tiary and Quaternary Structure
gelatin without preventing it from gelling. The heat - The tertiary structure is the 3D shape adopted by
used in processing the canned pineapple has the entire peptide chain.
denatured the hydrolysis enzymes. - To maximize hydrogen bonding with water, the
2. Reactions with Other Chemical Reagents nonpolar side chains are stabilized by London
dispersion forces in the interior of the structure.
BIOCHEMICAL SIGNIFICANCE - Polar functional groups can be hy drogen bond to
hydrogen
Keratin, Collagen, Hemoglobin, Myoglobin, Enzymes, each other.
Pepsin, Trypsin and Chymotrypsin - Amino acids with charged side chains are attracted
by electrostatic inter
interactions.
actions.
LESSON 77:: STRUCTURE OF PROTEINS - Di sulfide bonds form covalent bonds that stabilize
Disulfide
1. Primary Struct
Structure
ure the tertiary structure.
- The sequence of amino acids joined together by
peptide bond.
- All bonds angles are 120o, giving the protein a zigzag
arrangement.

2. Seconda
Secondary
ry Struct
Structure
ure
- The 3D arrangement of localized regions of a
protein.
- These regions arise due to hydrogen bonding
between the N-H group of one amide with the C=O
group of another.
- Two stable arrangements are the α-helix and the β-
pleated sheet.
- Most protein have regions of α-helix and β-pleated - The quaternary structure if the protein is the shape
sheet, and other regions that are random adopted when two or more folded polypeptide chains
arrangements. come together into one complex.
- Insulin consists of 2 separate polypeptide chains
linked by intermolecular disulfide bonds.
- Hemoglobin consists of 4 subunits held together by
intermolecular forces into a compact 3D shape.

JALN | 27
Biochemistry
LECTURE | MODULE 4 (PROTEINS)
LESSON 88:: PROTEIN DENATURATION
Protein denaturation is the partial or complete
disorganization of a protein’s characteristic three-
dimensional shape as a result of disruption of its
secondary, tertiary, and quaternary structural
interactions. Because the biochemical function of a
protein depends on its three-dimensional shape, the
result of denaturation is the loss of biochemical
activity. Protein denaturation does not affect the
primary structure of a protein.
Loss of water solubility is a frequent physical
consequence of protein denaturation. The
precipitation out of a biochemical solution of
denatured protein is called coagulation.
1. Heat Disrupts Hydro
Hydrogen
gen Bonds
- Egg white, a substance containing a high percentage
of protein, coagulates on heating like frying or boiling.
- Cooking makes the protein in meat more tender to
chew and easily digested. And also kills
microorganisms/parasites present in meat.
- Heat coagulates and destroys protein present in
bacteria. Hence, sterilization of instruments and
clothing for use in operating rooms requires the use
of high temperatures.
- The presence of protein in the urine can be
determined by heating a sample of urine, which will
cause the coagulation of any protein material that is
present.
- Cauterization, in surgery, heat is often used to seal
small blood vessels.
- A temperature above 41 C causes the inactivation
of enzymes through denaturation. It can have lethal
effects on body chemistry.
2. Salts of Heavy Metals Disrupt Electrostati
Electrostaticc
Attraction and Disul
Disulfide
fide Bonds
- The antidote for mercuric chloride or silver nitrate
when these poisons are taken internally is egg white.
The heavy metal reacts with the egg white and
precipitates out. The precipitate thus formed must be
removed from the stomach by an emetic or the
stomach will digest the egg white and return the
poisonous material to the system.
- Presence of too much Hg in skin-
lightening/whitening magic creams.
- Dilute silver nitrate is used to prevent gonorrhea
infections in the eyes of newborn infants. Silver nitrate
is also used in the treatment of nose and throat
infections, as well as to cauterize wounds.
- Use of Merthiolate as a cheap antiseptic in wounds
from manicure/pedicure.
3. Alkaloidal Reagents Disrupt Electrostatic Attraction
and Hydrogen Bonds
- Picric acid has antiseptic and astringent properties.
For medical use, it is incorporated in a surface
anesthetic ointment or solution and in burn
ointments.
- Tannic acid has been extensively used in the
treatment of burns. When this substance is applied to
a burn area, it causes the protein to precipitate as a
tough covering, thus reducing the amount of water
loss from the area. It also reduces exposure to air.
Newer drugs have taken the place of tannic acid for
burns, but an old-fashioned remedy still in use for
emergencies involves the use of wet tea bags.
- A TCA (trichloroacetic acid) peel is a non-invasive
skin treatment used to treat skin discolorations,
scarring, and wrinkles. These peels are used to clear
away dead skin cells to reveal the newer and
smoother skin layers below.
4. Strong Acids and Bases Disrupt Electrostatic
Attraction and HHydroge
ydroge
ydrogenn Bonds
JALN | 28
Biochemistry

- Formation| of
LECTURE MODULE 4 (PROTEINS)
yellow stain as concentrate nitric acid
comes into contact with skin.
- Adding acids in making cheeses.
- The need to wear goggles in a chemistry laboratory
to avoid serious eye damage as clouded cornea.
5. Organic Solvent
Solventss (ethanol, 2-propanol, acetone,
phenol) Disrupt Hydrogen Bonds

- Use of ethyl and isopropyl alcohol as antiseptic and

as disinfectant.
- Use of phenol to denature the protein in the nail bed
that causes ingrown nail.
- The presence of water is a crucial factor in
destroying or inhibiting the growth of pathogenic
microorganisms with isopropyl alcohol. Extra water
content slows evaporation, therefore increasing
surface contact time and enhancing effectiveness.
- Alcohols are an important type of denaturing agent.
Denaturation of bacterial protein takes place when
isopropyl or ethyl alcohol is used as a disinfectant—
hence the common practice of swabbing the skin with
alcohol before giving an injection. Interestingly, pure
isopropyl or ethyl alcohol is less effective than the
commonly used 70% alcohol solution. Pure alcohol
quickly denatures and coagulates the bacterial
surface, thereby forming an effective barrier to
further penetration by the alcohol. The 70% solution
denatures more slowly and allows complete
penetration to be achieved before coagulation of the
surface proteins takes place.
6. Reducing Agents Disrupt DiDisulfide
sulfide Bonds

If oxidizing agents cause the formation of a disulfide

bond, then reducing agents, of course, act on any
disulfide bonds to split it apart. Reducing agents add
hydrogen atoms to make the thiol group, -SH.
7. Detergent
- Detergent affects R-group interactions.
8. Microwave radiati
radiation
on Disru
Disrupt
pt Hydroge
Hydrogen n Bonds
- This causes violent vibrations of molecules that
disrupt hydrogen bonds.
9. Ultraviolet radiation
- The effect of ultraviolet radiation from the sun, an
ionizing radiation, is similar to that of heat. Denatured
skin proteins cause most of the problems associated
with sunburn.
10. Violent whipping or shaking
- Violent whipping or shaking causes molecules in
globular shapes to extend to longer lengths, which
then entangle like beating egg white into a meringue.

JALN | 29
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
INTRODUCTION - Because a catalyst id not consumed in the reaction,
- Proteins that serve as biological catalysts for it can be used over and over again.
reactions in all living organisms. Like all catalysts, - Such compounds therefore need to be present in
enzymes increase the rate of reactions, but they only very small amounts.
themselves are not permanently changed in the Example: Without the enzyme in our digestive tract, it
process. Moreover, the position of equilibrium is not would take us about 50 years to digest a single meal.
altered by an enzyme, nor are the relative energies of Advantage: Economical
the starting material and product. Disadvantage: Fatal to eat again, no pleasure of
- Enzymes are crucial to the biological reactions that eating.
occur in the body, which would otherwise often
proceed too slowly to be of any use. In humans, NO
NOTES:
TES:
enzymes must catalyze reactions under very specific
physiological conditions, usually a pH around 7.4 and
a temperature of 37 °C.
- Every second, thousands of chemical reactions
occur in the cells of the human body at rates that
meet our physiological and metabolic needs. To make
this happen, enzymes catalyze the chemical
reactions in our cells, with a different enzyme for
every reaction. Digestive enzymes in the mouth,
stomach, and small intestine catalyze the hydrolysis
of carbohydrates, fats, and proteins. Enzymes in the
mitochondria extract energy from biomolecules to
give us energy.

LESSON 11:: GENERAL CHARACTERISTI

CHARACTERISTIC,
C, STRUCTURE
AND NOMENCLATURE OF ENZYMES

HOW ARE ENZYMES SUPERIOR TO OTHER CATALYSTS

IN SEVER
SEVERAL
AL WAY
WAYS?
S?
1. They have a much greater catalytic power than
inorganic catalysts.
- In general, enzymes increase the rate of reaction
from more than 1 million to more than 1 trillion (106 to
1012) times faster than a corresponding reaction
without an enzyme.
WHAT ARE EENZYMES?
NZYMES? 2. Enzymes are highly specific with varying degrees of
- Are proteins that increase the rate of biological specificity. Inorganic catalysts are non-specific in their
reactions within the cells of the body. reactions.
- Lower the activation energy an increase the rate of 3. The activity of enzymes is closely regulated,
reaction; biological catalyst that are very specific. whereas that of catalysts is difficult to control.
- Are the largest and most highly specialized class of
TERMINOLOGIES
proteins hence activity is lost of denatured.
Ex: Apoenzyme The protein / main part of the
Salivary amylase enzyme molecule.
Catalase Activators Additional chemical groups that are
Phenolase (water, cold temperature and acidic required for enzyme activity. It may
environment) consist of metal ions or complex
organic molecules. Some enzymes
WHAT ARE CATALYS
ATALYST?
T? require both types of cofactors.
- A compound which lowers the energy required for a Temporary:
reaction. a. Cofactor – inorganic substance
(metals) that tend to increase the
activity of an enzyme [iron, zinc].

JALN | 30
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
b. Coenzyme – complex organic
molecule other than a protein
[thiamine].
Permanent:
Prosthetic Group – if the activator
c. Prosthetic
becomes a permanent part of the
enzyme.
Active Site The specific area of enzyme to INACTIVE AND ACTIVE EENZYMES
NZYMES
which the substrate attaches during Zymogen Holoenzyme
the reaction. An enzyme molecule 1. Pepsinogen (stomach) Pepsin
can have several active site. 2. Trypsinogen (pancreas) Trypsin
Substrate The chemical substance/s on which 3. Prothrombin Thrombin
the enzyme acts.
Inhibitor A substance that will make an NO
NOTES:
TES:
enzyme less active or render it
inactive,

NO
NOTES:
TES:

ENZY
NZYMES
MES NOMENCLATURE
- Because enzymes are the largest class of proteins,
scientists have been able to isolate and describe a
great number of individual enzymes.
- Originally, enzymes were named simply by ending
with the suffix --in
in to indicate a protein.
Ex: Trypsin, Rennin, Pepsin
- However, such names give no indication of the
reaction being catalyzed by the enzyme of the
THE DIF
DIFFERENCE
FERENCE BETWEEN HOLOENZYME AND substrate involved.
PROENZYME/ZYMOGEN
ENZYMES UNDER THE OLD SYSTE SYSTEM
M
Holoenzyme
- An entire active enzyme, which consists of an Casein Rennin
apoenzyme and one or more factors. Protein Pepsin
Pro
Proenzyme
enzyme
enzyme/Zymogen
/Zymogen Carbohydrate Trypsin
- An enzyme in its inactive form. Ptyalin
- Enzymes (especially digestive) are often - In 1961, the Commission on Enzymes of the
synthesized in an inactive form, transported to the International Union of Biochemistry proposed a
place where activity is desired, and then converted to standard classification of enzymes.
their active forms. - They recommended that enzymes be divided into
six major classes, each with several subclasses, based
on the reactions they catalyze.

JALN | 31
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
- Enzymes are now named by adding an -ase suffix Oxidases Addition of oxygen to a
on the name of the substrate. substance/substrate.
SUBSTRATE/REACTION Dehydrogenases Removal of hydrogen from a
ENZYMES
TYPE substance/substrate.
Maltase Maltose Reductases Addition of hydrogen from a
Urease Urea substance/substrate.
Protease Proteins
Carbohydrases Carbohydrates Transferases
Lipases Lipids - Enzymes that catalyze reactions involved in the
Hydrolyses Hydrolysis reactions transfer of functional groups.
Deaminases Removing amines Tranaminase
Tranaminase/s /s Transfer of –NH2
Dehydrogenases Removing hydrogens Tra
Transmethylase
nsmethylase
nsmethylase/s/s Transfer of –CH3
Glucose oxidase Transacylase
Transacylase/s/s Transfer of
Lactate dehydrogenase
DNA polymerase
- However, in this text, the older names of the
enzymes will still be in use since they are much easier Transphosphat
Transphosphatase
ase
ase/s
/s Transfer of
to write. Like in the case of sucrase and a-
glucopyrano-ß-fructofuranohydrolase.

NO
NOTES:
TES:
Ly
Lyases
ases
- Enzymes that catalyze the elimination of groups to
form double bonds.
Decarboxylases Remove CO2
Dehydr
ehydrases
ases Remove H2O
Deaminases Remove NH3

Isomera
Isomerases
ses
- Enzymes that catalyze the interconversions of
isomers.
Isomerases Convert cis to trans; ketose to
LESSON 22:: CLASSIFICATION OF ENZ
ENZYMES
YMES
aldose (or vice versa)
Epimerases Convert D- to L- isomer (or vice
versa)

Lig
Ligaases
- Enzymes that, in conjunction with ATP, catalyze the
formation of new bonds.
TWO TYPES OF ENZYMES Combine two molecules
Synthetases
Simple Enzymes
Carboxylases Add CO2 to a substrate
- Simple proteins: amino acids
Comple
Complex/Conjugated
x/Conjugated Enzymes
LESSON 33:: ENZYME ACTIVITY AND INHIBITION
- Made up of more parts other than protein and/or
amino acids.

CLASS
CLASSIFICATION
IFICATION OF ENZYMES
Hydrolases (mos
(mostt common)
- Enzymes that catalyze hydrolysis reactions.
Carbohydrase Polysaccharides + H2O à
Monosaccharides + disaccharides
Esterases Ester + H2O à Carboxylic acid +
alcohol
Proteases Protein + H2O à Peptides + amino
acids
Nucleases Nucleic acids + H2O à Pyrimidines / ENZYME ACTIVITY
purines + sugar + phosphoric acid 1. Lock
Lock--and-Key Mod el (preferred model)
Model
- The substrate must fit into the active site the way a
Oxidoreductases key fits into a lock.
- Enzymes that catalyzes REDOX reactions.

JALN | 32
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
- With the substrate at the active site, chemical INHIBTIO
INHIBTIONN OF ENZYME ACTIVITY
reaction occurs that involves breaking or forming
bonds of the substrate.
- The products will no longer be attracted to the site
and leave the enzyme.
- The enzyme goes on to catalyze the same reaction
with other substrate molecules.
- Enzymes are specific to their substrate.

- The actions of many poisons and drugs is due to

their ability to inhibit specific enzymes.
E + S ó E –S à E + P - Enzymes can be inhibited by other molecules.
Where; - Inhibition can be competitive or non-competitive
E = Enzyme 1. Reversible Compe
Competitive
titive Inhibition
S = Substrate - Type of inhibition in which a substrate and an
E-S = Enzyme-Substrate Complex inhibitor compete for the active sites on the enzyme.
P = Product They are so similar in structure that the enzyme binds
Lock
Lock--and-Key Model Hypothesis to the inhibitor by mistake,
- The substrate and the active site match each other - As long as the competitive inhibitor occupies the
in 2 ways: active site, no reaction of the substrate can take
a. Str
Structurally
ucturally – The 3D place.
structure of the active site is - Can be reversed by adding more substrate that
specific to the substrate. competes with the inhibitor. The addition of large
Substrates that don’t fit, amounts of substrate can completely reverse the
won’t react. inhibition.
b. Chemically – Substrates that are not chemically
attracted to the active site won’t be able to react.
2. Induced-Fit Theory
- The substrate induces the active site to take on a
shape complimentary to the shape of the substrate
molecule. - A competitive inhibitor:
- The substrate may induce the enzyme to take on a > Has a structure similar to
shape that matches the substrate. substrate.
> Occupies active site.
> Competes with substrate for
active site.
> Has effect reversed by increasing
substrate concentration.
Example
Examples:s:
The induce
induced-
d-
d-fit
fit model better explain
explainss enzyme a. Overcoming al alcohol
cohol
coholism
ism
activity
- If the lock-and-key model were true, one enzyme
would only catalyze one reaction. In actuality, some
enzyme can catalyze multiple reactions.
- As the substrate approaches the enzyme, it induces
a conformational change in the active site – it - Antabuse (disulfiram competes with the aldehyde
changes shape to fit the oxidase and prevents acetaldehyde from becoming
substrate. an acetic acid.
- This stresses the - A build-up of acetaldehyde follows, resulting in a
substrate, reducing the strong feeling of nausea and other strong hangover
activation energy of the symptoms - a good deterrent from drinking.
reaction. - Antabuse is administered as a daily pill, so its
efficacy relies on the patient’s own motivation – if
they stop taking it, they can drink again.

JALN | 33
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
b. Et
Ethanol
hanol as antido
antidote
te in Methan
Methanol
ol Poisonin
Poisoningg 1. Nerve Gases
- Ethanol is administered intravenously (IV) a. Cholinesterase – enzyme that catalyzes a reaction
- It competes with the methanol as a substrate and taking place at the juncture of nerve cells.
inhibitor. - Necessary for normal transmission of nerve
c. Antihistamines impulses.
2. Reversible Non-competitive Inhibition - Nerve gases (occurs naturally in poisons and
- Type of inhibition wherein a noncompetitive inhibitor venoms) combine with the –OH group on a serine
binds to an enzyme, at a site other than the active molecule that is vital to the active site of the
site, cholinesterase enzyme, When this happens, the
- Its structure does not resemble that of the structure. enzyme loses its ability to transmit nerve impulses.
- When a noncompetitive inhibitor attaches to an - This is why animals/humans poisoned by nerve
enzyme, it alters the 3D structure of the enzyme as gases become paralyzed – eventually die.
well as the shape of its active site. In result, the b. Poisoning of Heavy Metal [[Hg,
Hg, Pb, Ag]
substrate cannot bind properly to form ES complex. - These heavy metals are toxic because they bid
- Adding more substrate will not reverse it for it is not irreversibly with free –SH functional groups on
competitive. enzymes.
c. Penicillin (and other antibiotic)
- An antibiotic that kills bacteria because it
irreversibly binds to glycopeptide transpeptidase for
the synthesis of bacterial cell wall.

- A noncompetitive inhibitor:
> Does not have a structure similar to substrate.
> Binds to the allosteric site not on the active site.
> Changes the shape of the
enzyme and active site.
> Substrate cannot fit to
altered active site. LESSON 44:: FACTORS THAT AFFECT ENZYME ACTIVITY
ENZYME
> No reaction occurs
> Effect is not reversed by
adding substrate but by
reducing the concentration of
the noncompetitive inhibitors.

DRUGS THAT INT INTERACT

ERACT WITH ENZYMES
1. P
Penicil
enicil
enicillin
lin
- Inhibits the enzyme that forms cell walls of bacteria,
destroying the bacterium
2. ACE Inhibi
Inhibito
to
tors
rs
- ACE (Angiotensin-converting Enzymes) causes
blood vessel to narrow, increasing blood pressure.
- ACE Inhibitors are given to those with high blood
pressure to prevent ACE’s synthesis from its
zymogen. 1. Enzyme Concent
Concentration
ration
3. HI
HIVV Protease Inhibi
Inhibitors
tors - The rate of an enzymatic reaction increases when
- HIV protease is an essential enzyme that allows the the concentration of enzyme is increased.
virus to make copies of itself. - Direct proportionality
- HIV Protease Inhibitors interfere with this copying,
decreasing the virus population in the patient. 2. Temperature
- An increase in temperature increases enzyme
2. Irr
Irreversible
eversible Inhibition activity up to its optimum temperature.
- A type of inhibition of enzyme activity which occurs -High temperatures can cause denaturation and loss
when a functional group in the active site or a of catalytic activity.
cofactor required for the activity of the enzyme is -Reaction rate increases temperature until the point
destroyed/modified. at which the protein is denatured and activity drops
- Also a noncompetitive inhibition for it does not have sharply.
a structure similar to the substrate. Optimum Tem perature – the temperature where
Temperature
- Cannot be removed from the protein without enzymes reach their greatest activity usually
destroying it. around 37 oC, also the normal body temperature.
Example
Examples: s:

JALN | 34
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
- 40 oC fever can cause loss of function of critical ENZYME USED IN MEDIC
MEDICINE
INE
enzymes, particularly those of the CNS, can result to - Most enzymes are confined within the cells of the
dysfunction sufficient to death. body.
- Sterilization of medical instruments and - However, small amounts of them can also be found
laundry/autoclave superheated steam. in body fluids such as blood, urine, and CSF.
- Herbal tea must be below the boiling point so that - The level of enzyme activity in these fluids can easily
the nutrients will not fade. be monitored.
- This information can prove extremely useful:
3. pH Abnormal activity (either high or low) of particular
- Enzymes are most active at their optimum pH. enzymes in various body fluids signals the onset of
-Values above or below optimum pH cause certain diseases or their progression.
denaturation of the enzyme and loss of catalytic - The table below lists some of the enzyme used in
activity, medical diagnosis and their activities in normal body
Optimu
Optimum m pH – pH at which enzymes are most fluids.
active. Enzyme
Normal Body Dise
Disease
ase
- Extremely high or low pH values generally result in Activity Flu
Fluid
id Diagnosed
complete loss of activity for most enzymes. Alanine
- pH is also a factor in stability of enzymes. aminotransferase Hepatitis /
(ALT) Liver &
- As with activity, for each enzyme there is also a
Old Name: SGPT 3 – 17 U/L Serum Kidney
region of pH optimal stability. Serum Glutamic health
- The optimum pH value will vary greatly from one Pyruvic condition
enzyme to another, as shown below: Transaminase
ENZYME OPTIMUM PH 2.5 – 12 Prostate
Ac
Acid
id phosph
phosphate
ate Serum
1. Lipa
Lipase
se (pancreas) 8.0 U/L cancer
2. Lipase (stomach
(stomach)) 4.0 – 5.0 Alkaline Liver or
13 – 38
3. Lipase ((castor
castor oil) 4.7 Serum Bone
phosphate U/L
4. Pepsin disease
1.5 – 1.6 19 – 80 Pancreatic
5. Tr
Trypsin
ypsin 7.8 – 8.7 Amylase Serum
U/L Disease
6. Urease 7.0 Aspartate
7. Invertase 4.5 aminotransferase 7 – 19 U/L Serum Liver
8. Maltase 6.1 – 6.8 (AST)
health or
9. Amylase (pancreas) 6.7 – 7.0 Old Name: SGOT
Heart
10. Amylase (malt) 4,6 – 5.2 Serum Glutamic
7 – 49 U/L CSF attack
Oxaloacetic
11. Catalase 7.0 Transaminase
Lactate
4. Substrate Con
Concent
cent
centra
ra
ration
tion dehydrogenate 100 – 350
Serum
- An increase in substrate concentration increases (LDH) WU/mL
the rate of an enzyme catalyzed action unit of all the Heart
Creatini
Creatinine
ne
7 – 60 U/L Serum attack
available enzyme has combined with substrate. phosphate (CPK)
Phosphohexose 15 – 75
isomer
isomerase
ase Serum
U/L
> U/L = International units per liter
> WU/mL = Wrobleski units per liter
- When a heart attack occurs, some heart muscles
are damaged/destroyed, and their enzymes leak into
the blood stream.
- Another name for aminotransferase is
transaminase.
Pr
Proteases
oteases
- Convert plasminogen to plasmin, a protease that is
capable of breaking apart fibrin molecules, thereby
LESSON 5
5:: USES OF ENZYMES
dissolving the clot.
- Given to patients to dissolve blood clot wherein
treatment last in 30-60 mins.

INDUTRIAL
INDUTRIAL--STREN
STRENGHT
GHT ENZYME
- Enzymes are increasingly important in industry,
- It offers two major advantages to manufacturing
processes and in commercial products.
Advantages:

JALN | 35
Biochemistry
LECTURE | MODULE 5 (ENZYMES)
1. Enzymes cause very large increase in reaction rates -Industrial enzymes are used most often as detergent
even at room temperature. additives.
2. Enzymes are relatively specific and can be used to - As a side benefit, detergents that are effective in
target selected reactants, mild condition and also save on water and electric
Disadvantages:
Disadvantages: bills.
1. Relative scarcity Proteases
2. Higher cost compared with traditional chemical - Added to digest the most difficult clothing stains
treatments. (Remedied by genetic engineering) such as grass, blood, and swear which contain
proteins,
DIGESTIVE (BREAKDOWN) F UNCTION – Lipases
HYDROLASES - Team up with soaps to remove greasy stains,
1. Proteases / Proteo- Amyla
Amylasesses
Proteins
lytic enzymes - Often added to digest starchy residues from foods
2. Lipases Lipids such as rice, oatmeal, chocolate, and mashed
3. Cellulases Cellulose potatoes.
4. Amylases Amylose Cell
Cellula
ula
ulases
ses
5. Lactases Lactose - Applied to remove these rough protuberances for
6. Pectinase Pectin smoother, glossier and brighter-colored fabric.

FOOD PROCESSING
Pectinase
- Enzyme that can effectively peel an orange,
dissolves the albedo (the white stringy material). The
industry markets pre-peeled citrus in perfect
condition to hospitals, airlines and restaurant.
- Also used to clarify fruit juices; also increases fruit
juice volume from banana, grapes and apples.
Lactase
- Enzyme given to people who are lactose intolerant;
ice cream made from lactase-treated milk tend to be
creamier; prolongs the shelf life of cottage-cheese
and yogurt.
α-Amylase, Glucosaminase & Glu cose Isomerase
Glucose
- Enzyme used to convert cornstarch into high-
fructose syrup that is equivalent in sweetness to
sucrose. More than 5 billion pounds are produced
annually.

TECHNOLOGY
Pectinase
- Enzyme used in “scouring” (to remove pectic
substance and cotton wax) cotton, more preferable
since it operates under milder conditions.
Cellulase
a. De nim – use cellulase to give a soft appearance to
Denim
its cotton fabric, “stonewashing” (pumice stones and
harsh chemical agents) or “biostoning” (enzymatic
process) the cloth.
- In this process, the cellulases digest some of the
cellulose on the surface of the cotton to achieve a
more uniform aged look for denim garment,
b, Paper – Use cellulases to complete the breakdown
of wood chips to paper pulp.
- The enzyme treatment form a better pulp and
paper can be produces with smaller amounts of
bleach, again easing environmental pollution.
- Also for removing inks in waste paper products.

CONSUMER GOODS

JALN | 36
Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
INTRODUCTION

- DNA molecules contain several million nucleotides

while RNA molecules only have a few thousand.
- DNA is contained in the chromosomes of the
nucleus, each chromosome having a different type of
DNA, while RNA can be found on the cytoplasm.
- Humans have 46 chromosomes (23 pairs), each
made up of many genes.
- A gene is the portion of the DNA molecule
Whether you are tall or short, fair-skinned or dark- responsible for the synthesis of a single protein.
complexioned, blue-eyed or brown-eyed, your unique
characteristics are determined by the nucleic acid WH
WHAT
AT ARE NUCLEOSIDES?
polymers that reside in the chromosomes of your - A nucleoside is formed by joining the anomeric
cells. The nucleic acid DNA stores the genetic carbon of the monosaccharide with a N atom of the
information of a particular organism, while the nucleic base.
acid RNA translates this genetic information into the
synthesis of proteins needed by cells for proper
function and development. Even minor alterations in
the nucleic acid sequence can have significant effects
on an organism, sometimes resulting in devastating
diseases like sickle cell anemia and cystic fibrosis. In
this module, we study nucleic acids and learn how the
genetic information stored in DNA is translated into
DNA RNA
protein synthesis.
Monosacchar
Monosaccharide
ide
LESSON 11:: TYPES OF NUCLEIC ACID, NUCL
NUCLEOTIDE
EOTIDE - Aldopentose D-2- - Aldopentose D-ribose
BUILDING BLOCKS AND NUCLEOTIDE FORMATION deoxyribose

Nitrogen
Nitrogen--containing base
Pyrimidine (C, U, TT))

WHAT ARE NUCLEIC ACIDS?

- Unbranched polymers composed of repeating Purine (A, G)
monomers called nucleotides.
TWO TYPES OF NUCLEIC ACIDS
a. DNA (deoxyribonucleic acid) – stores the genetic
information of an organism and transmits that
information from one generation to another.
b. RNA (ribonucleic acid) – translates the genetic
information contained in DNA into proteins needed - A, G, C, and T - A, G, C, and U
for all cellular function. - To name a nucleoside derived from a pyrimidine
base, use the suffix -idine.
MONOMERS OF D DNA
NA AND RNA - To name a nucleoside derived from a purine base,
- The nucleotide monomers that compose DNA and use the suffix -osine.
RNA consist of: a monosaccharide, a N-containing - For deoxyribonucleosides, add the prefix deoxy-.
base, and a phosphate group.

JALN | 37
Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
WH
WHATAT ARE NUCLEO
NUCLEOTI
TI
TIDES?
DES? - The identity and order of the bases distinguish one
- Formed by adding a phosphate group to the 5’-OH polynucleotide from another (primary structure).
of a nucleoside. - A polynucleotide has one free phosphate group at
the 5’ end and one free OH group at the 3’ end.
- In DNA, the sequence of the bases carries the
genetic information of the organism.

The namecytidine 5’ - m onop hosphate is

abbreviated as CMP

- The previous chain can be abbreviated: CATG

The name deoxya denosine 5’ -mono phosphate is
abbreviated as dAMP.
An example of diphosphate: ADP
- This polynucleotide would be named CATG, reading
from the 5’ end to the 3’ end.
THE DNA DOUBLE HELIX
- Initially proposed by Watson and Crick in 1953.
- Consists of two polynucleotide strands that wind
into a right-handed double helix.
- The two strand run in opposite directions; one runs
from 5’ end to the 3’ end and the other runs from the
3’ end to the 5’ end.
- The sugar-phosphate groups lie on the outside of
the helix and the bases lie on the inside.

An example of triphosphate: ATP

- The bases always line up so that a pyrimidine

NUCLEIC ACIDS
- Polymers of nucleotides joined by phosphodiester
linkages.
- A polynucleotide contains a backbone consisting of
alternating sugar and phosphate groups.
derivative can hydrogen bod to purine derivative on
the other strand.
- Thus, there are complimentary base pairs that
always hydrogen bond together in a particular
manner.
- Adenine pairs with thymine with 2 oxygen bonds to
form an A-T base pair.
- Cytosine pairs with guanine using 3 hydrogen bonds
to form a C-G base pair.

JALN | 38
Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
LESSON 22:: CHEMICAL COMPOSITION & Stable under produced, used,
STRUCTURES OF DNA AND RNA alkaline conditions degraded, and
While both DNA and RNA are used to store genetic recycled.
information, there are clear differences between Not stable under
them. This table summarizes the key points: alkaline
MAIN DIFFE
DIFFERENCES
RENCES BET
BETWEEN
WEEN DNA & RNA conditions
Comparison DNA RNA DNA is susceptible Compared with
DeoxyriboNucleic RiboNucleic Acid to UV damage. DNA, RNA is
Name Acid UV Damage relatively
Long-term Used to transfer resistant to UV
storage of genetic the genetic code damage.
information; from the nucleus
transmission of to the ribosomes LESSON 33:: CENTRAL DOGMA OF PROTEIN
genetic to make proteins.
SYNTHESIS – REPLICATION, TRANSCRIPTION AND
information to RNA is used to
make other cells transmit genetic
TRANSLATION
and new information in - The information stored in DNA is used to direct
Function organisms. some organisms synthesis of proteins.
and may have
been the
molecule used to
store genetic
blueprints in
primitive
organisms.
B-form double A-form helix. RNA
helix. DNA is a usually is a single-
double-stranded strand helix
Structural molecule consisting of
Replication The process by which DNA makes
Features consisting of a shorter chains of a copy of itself when a cell divides.
long chain of nucleotides. Transcription The ordered synthesis of RNA from
nucleotides. DNA; the genetic information
Deoxyribose Ribose sugar stored in DNA is passed onto RNA.
sugar Translation The synthesis of protein from RNA;
Phosphate the genetic information
Composition Phosphate backbone determined the specific amino
of bases backbone
adenine, guanine, acid sequence of the protein.
and sugars
adenine, guanine, cytosine, uracil
cytosine, thymine bases REPLICATION
bases - The original DNA molecule forms two new DNA
DNA is self- RNA is molecules, each of which contains a strand from the
replicating. synthesized from parent DNA and one new strand.
Propagation DNA on an as-
needed basis.
AT (adenine- AU (adenine-
thymine) uracil)
Base Pairing GC (guanine- GC (guanine-
cytosine) cytosine)
The C-H bonds in The O-H bond in
DNA make it fairly the ribose of RNA
stable, plus the makes the
body destroys molecule more
enzymes that reactive,
would attack compared with
DNA. The small DNA. RNA is not - Replication Fork – forms at two strands split apart.
Reactivity
grooves in the stable under Synthesis of Lagging Strand:
helix also serve as alkaline
protection, conditions, plus
providing minimal the large grooves
space for in the molecule
enzymes to make it
attach. susceptible to
enzyme attack.
RNA is constantly

JALN | 39
Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
- Replication proceeds in the 3’-to-5’ direction of the - The difference between mRNA and the information
template for both the leading and the lagging strands. DNA strand is that the base U replaces T on the
- The identity of the bases on the template strand mRNA.
determines the order of the bases on the new strand.
- A must pair with T, and G must pair with C.
- A new phosphodiester bond is formed between the
5’-phosphate of the nucleoside triphosphate and the
3’-OH group of the new DNA strand.
- Replication occurs in only one direction on the
template strand, from 3’ end to the 5’ end.
- The new strand is either a leading strand, growing
continuously, or a lagging strand, growing in small
fragments.

RNA
- In RNA, the monosaccharide is ribose.
- The T base is not present in RNA; instead, the U base
is used.
- RNA is a single strand, and smaller than DNA.
- The three types of RNA molecules are ribosomal
RNA (rRNA), messenger RNA (mRNA), and transfer
RNA (tRNA).
rRNA
- Provides the site where polypeptides are assembled
during protein synthesis.
mRNA
- Carries the information from DNA to ribosome.
tRNA
- Brings specific amino acids to the ribosomes for
protein synthesis.
- Drawn as a cloverleaf shape, with an acceptor stem
at the 3’ end, which carries the needed amino acid,
and an anticodon, which identifies the needed amino
acid.
THE GENETIC CODE
- A sequence of three nucleotides (a triplet) codes for
a specific amino acid.
- Each triplet is called a codon.
- For example, UAC is a codon for the amino acid
serine; UGC is a codon for amino acid cysteine.
- Codons are written from the 5’ end to the 3’ end of
the mRNA molecule.
TRANSLATION and PROTEIN SYNTHESIS
- mRNA contains the sequence of codons that
determine the order of amino acids in the protein.
- Individual tRNAs bring specific amino acids to the
peptide chain.
- rRNA contains binding sites that provide the
platform on which protein synthesis occurs.

RELATED CODONS, ANTICODONS, AND AMINO ACIDS

mRNA Codon tRNA Anticodon Amino Acid
ACA UGU Threonine
GCG CGC Alanine
AGA UCU Arginine
UCC AGG Serine
- The three main parts of translation are initiation,
elongation, and termination.

INITIATION
- Initiation begins with
mRNA binding to the
TRANSCRIPTION ribosome.
- The synthesis of mRNA from DNA. - A tRNA brings the first
- The DNA splits into two strands, the template amino acid, always at
strand, which used to synthesize RNA, and the codon AUG.
informational strand which is not used.
- Transcription proceeds from the 3’ end to the 5’ end ELON
ELONGATION
GATION
of the template. - Elongation proceeds as the next
- Transcription forms mRNA with a complementary tRNA molecule deliver the next
sequence to the template DNA strand and an exact amino acid, and a peptide bond
sequence as the informational DNA strand. forms between the two amino
acids.

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Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
TERMINATION Deletion Mutati
Mutation
on
- Translation continues until a - Occurs when one or more nucleotides is / are lost
stop codon (UAA, UAG, or from a DNA molecule.
UGA) is reached, which is called
termination; the completed
protein is released.

Insertion Mutation
- Occurs when one or more nucleotides is / are added
to a DNA molecule.

LESSON 4: THE GENETIC CODE
- A sequence of three nucleotides (a triplet) codes for
a specific amino acid,
- Each triplet is called a codon.
- For example, UAC is a codon for the amino acid
serine; UGC is a codon for the amino acid cysteine.
- Codons are written from the 5’ end to the 3’ end of
the mRNA molecule.
- A complete codon list is given below:
Silent Mutation
- A silent mutation has a negligible effect to the
organism, because the resulting amino acid is
identical.
- The mutation has no effect.
- A mutation that produces a protein with one
different amino acid usually has a small to moderate
effect on the protein overall.
- Some proteins, such as hemoglobin, substitution of
just one amino acid can result in the fatal disease
sickle cell anemia.
- If a mutation causes a big change, like producing a
stop codon , the remainder of the protein will not be
synthesized, which can have catastrophic results.

- When a mutation causes a protein deficiency or

defective protein synthesis and this mutation is
passed through generations, it is a genetic disease.
LESSON 5: MUTATION, RECOMBI
RECOMBINANT
NANT DNA AN
ANDD - Cystic fibrosis results from defective cystic fibrosis
POLYMERASE CHAIN REACTION transmembrane conductance regulator (CFTR); the
effects are extremely thick lung mucus and low
MUTAT
MUTATION
ION
IONSS AND GENETIC DISEASE pancreatic secretions.
- A mutation is a change in the nucleotide sequence - Galactosemia results from a deficiency of an
in a molecule of DNA. enzyme needed for galactose metabolism and can
- Some mutations are random, while others are cause mental retardation.
caused by mutagens.
Point Mutatio
Mutationn GENETIC DISEAS
DISEASES
ES
- The substitution of one nucleotide for another. DISEASE CHARACTERISTICS
Tay – Sachs disease Mental retardation;
caused by a defective
hexosaminidase A
enzyme

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Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
Sickle cell anemia Anemia; occlusion and Polymerase Chain Reaction (PCR)
inflammation of blood - Polymerase chain reaction (PCR) amplifies a
capillaries, caused by specific portion of a DNA molecule, producing millions
defective hemoglobin of exact copies.
Phenylketonuria Mental retardation; - Four elements are needed to amplify DNA by PCR:
caused by a deficiency 1. The segment of DNA that must be copied.
of the enzyme 2. Two primers – short polynucleotides that are
phenylalanine complementary to the two ends of the segment to
hydroxylase needed to be amplified.
convert the amino acid 3. A DNA polymerase enzyme to catalyze the
phenylalanine to synthesis of a complementary strand.
tyrosine. 4. Nucleoside triphosphates – the source of the A,
Galactosemia Mental retardation; T, C, and G needed to make the new DNA.
caused by a deficiency
of an enzyme needed How to use the PCR to amplify a ssample
ample of DNA?
for galactose Step 1: heat the DNA segment to unwind the double
metabolism. helix to form single strands.
Huntington’s disease Progressive physical
disability; caused by a
defect in the gene that
codes for Htt protein,
resulting in
degeneration in the Step 2: Add primers that are complementary to the
neurons in certain DNA sequence at either end of the DNA segment.
areas of the brain.

RECOMBINANT DNA
General Princ
Principles
iples
- Recombinant DNA is synthetic DNA that contains
segments from more than one source.
- Three key elements are needed to form
recombinant DNA:
a. A DNA molecule into which a new DNA segment
will be inserted.
b. An enzyme that cleaves DNA at specific
locations.
c. A gene from a second
organism that will be inserted
into the original DNA molecule.

- First, bacterial plasmid DNA is cut

by the restriction endonuclease
EcoRI, which cuts in a specific place.
Step 3: Use a DNA polymerase and added
- This gives a double strand of linear
plasmid DNA with two ends ready to nucleotides to lengthen the DNA segment.
bond, called sticky ends.
- Then, a second sample of
human DNA is cut with the
same EcoRI.
- This forms human DNA
segments with sticky ends - After each cycle the amount of DNA is doubled, so
that are complimentary to the after 20 cycles, 1,000,000 copies have been made.
plasmid DNA.
FOCUS ON THE HUMAN BOD BODY Y
- Combining the two pieces of DNA DNA Fingerprin
Fingerprinting
ting
(with DNA ligase enzyme) forms - The DNA of each individual person is unique, so DNA
DNA containing the new segment. can be used as a method of identification.
- This DNA chain is slightly larger - Any type of cell (skin, saliva, semen, blood, etc.) can
because of its additional segment. be used to obtain a DNA fingerprint.

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Biochemistry
LECTURE | MODULE 6 (NUCLEIC ACID)
- The DNA is first amplified by PCR, and then cut by - The viral DNA can then transcribe RNA, which then
restriction enzymes. directs protein synthesis (new retroviral particles to
- The DNA fragments are then separated by size by infect other cells).
gel electrophoresis. - Acquired immune deficiency syndrome (AIDS) is
- DNA fragments can be visualized on X-ray film after caused by the retrovirus human immunodeficiency
they have been separated: virus (HIV).

Example Questio
Question:n:
There was a mix-up in the nursery at the hospital and
there is a question as to which baby belongs to a set
of new parents. The given gel contains the DNA
fingerprint of the new mother (Lane 1), the new Father
(Lane 2), and two infants (Lane 3 and 4). The DNA
fingerprinting indicated that the infant tested in Lane
4 is the child of these parents.

Viruses
- A virus is an infectious agent consisting of a DNA or
RNA molecule that is contained within a protein
coating.
- It is incapable of replicating alone, so it invades a
host organism and makes the host replicate the virus.
- Many prevalent diseases like the common cold,
influenza, and herpes are viral in origin.
- A vaccine is an inactive form of a virus that causes
a person’s immune system to produce antibodies to
the virus to ward off infection.
- A virus with an RNA core is called a retrovirus.
- Retroviruses invade
a host and then
synthesize viral DNA
by reverse
transcription.

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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
INTRODUCTION starting material into an end product. Such pathways
may be linear, in which a series of reactions generate
a final product, or cyclic, in which a series of reactions
regenerates the first reactant.
- The major metabolic pathways for all life forms are
similar. This enables scientists to study metabolic
reactions in simpler life forms and use the results to
help understand the corresponding metabolic
reactions in more complex organisms, including
humans.

LESSON 1 - DIGESTION AND THE CONVERSION OF

FOOD INTO ENERGY

- Despite the wide diversity among living organisms,

virtually all organisms contain the same types of
biomolecules— carbohydrates, lipids, proteins, and
nucleic acids—and use the same biochemical
reactions. DIGESTION AND THE CONVERSION OF FOOD INTO
- Metabolism is the sum total of all the biochemical ENERGY
reactions that take place in a living organism. Human Metabolism
metabolism is quite remarkable. An average human - The sum of all the chemical reactions that take
adult whose weight remains the same for 40 years place in an organism.
processes about 6 tons of solid food and 10,000 Catabolism
gallons of water, during which time the composition of - The breakdown of large molecules into smaller ones;
the body is essentially constant. Just as gasoline is put energy is generally released during catabolism.
into a car to make it go or a kitchen appliance is Anabolism
plugged in to make it run, the human body needs a - The synthesis of large molecules from smaller ones;
source of energy to make it function. Even the energy is generally absorbed during anabolism.
simplest living cell is continually carrying on energy-
demanding processes such as protein synthesis, DNA METABOLIC PATHWAY
replication, RNA transcription, and membrane - The process of a series of consecutive reactions.
transport. Linear Pathway
- Metabolic reactions fall into one of two subtypes: - The series of reactions that generates a final
catabolism and anabolism. Catabolism is all product different from any reactants.
metabolic reactions in which large biochemical
molecules are broken down into smaller ones.
Catabolic reactions usually release energy. The
reactions involved in the oxidation of glucose are
catabolic. Anabolism is all metabolic reactions in Cyclic Pathway
which small biochemical molecules are joined - The series of reactions that regenerates the first
together to form larger ones. Anabolic reactions reaction.
usually require energy in order to proceed. The
synthesis of proteins from amino acids is an anabolic
process.
- The metabolic reactions that occur in a cell are
usually organized into sequences called metabolic
pathways. A metabolic pathway is a series of
consecutive biochemical reactions used to convert a

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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
MITOCHONDRIA STAGE 2: FORMATION OF ACETYL CoA
- Energy production occurs in the mitochondria.
- Mitochondria are organelles within the
cytoplasm of a cell.
- Mitochondria contain an outer membrane and
inner membrane with many folds.
- The area between two membranes is called the
intermembrane space.
- The area enclosed by the inner membrane is called
the matrix, where energy production occurs.

- Monosaccharides, amino acids and fatty acids are

degraded into acetyl groups, which are then bonded
to coenzyme A forming acetyl-CoA.

STAGE 3: CITRIC ACID CYCLE

AN OVERVIEW OF METABOLISM - The citric acid cycle is based in
STAGE 1: DIGESTION the mitochondria, where the
- The catabolism of food begins with digestion, which acetyl CoA is oxidized to CO2.
is catalyzed by enzymes in the saliva, stomach, and - The cycle also produces energy
small intestines. stored as a nucleoside
triphosphate and the reduced
coenzymes.
STAGE 4: ELECTRON TRANSPORT CHAIN & OXIDATIVE
PHOSPHORYLATION
- Within the mitochondria, the electron transport
a. Carbohydrates are hydrolyzed into chain and oxidative phosphorylation produce ATP
monosaccharides beginning with amylase enzymes (adenosine 5’-triphosphate).
in saliva and continuing in the small intestine. - ATP is the primary energy-carrying molecule in the
body.

b. Protein digestion begins when stomach acid

denatures the protein and pepsin begins to cleave the
large protein backbone into smaller peptides.
- Then, in the small intestines, trypsin and
chymotrypsin cleave the peptides into amino acids.
LESSON 22:: ATP AND ENERGY PRODUCTION

c. Triacylglycerols are emulsified by bile secreted by

the liver, then hydrolyzed by lipase into 3 fatty acids
and a glycerol backbone.

ATP AND ENERGY PRODUCTION

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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
General Features of ATP Hydrolysis
- Hydrolysis of ATP cleaves 1 phosphate group.
- This forms ADP and hydrogen phosphate (HPO42-),
releasing 7.3 kcal/mol of energy
- Phosphorylation is the reverse reaction, where a
phosphate group is added to ADP.
- Phosphorylation reforms ATP and requires 7.3
kcal/mol of energy.
- Any process (walking, running, breathing) is fueled
by the release of energy when ATP is hydrolyzed to
ADP.
- Energy is absorbed and stored in ATP when it is
synthesized from ADP.
Coupled Reactions in Metabolic Pathways
- Coupled reactions are pairs of reactions that occur
together.
- The energy released by one reaction is absorbed by
the other reaction.
- Coupling an energetically unfavorable reaction with
a favorable one that releases more energy than the
amount required is common in biological reactions.
- The hydrolysis of ATP provides the energy for the
phosphorylation of glucose.
LESSON 33:: COENZYMES IN METABOLISM
COENZYMES IN METABOLISM
Coenzymes NAD+ and NADH
- A coenzyme acting as an oxidizing agent causes an
oxidation reaction to occur, so the coenzyme is
reduced.
- When a coenzyme acts as an oxidizing agent, it
gains H+ and e-.
- A coenzyme acting as a reducing agent causes a
reduction reaction to occur, so the coenzyme is
oxidized.
- When a coenzyme acts as a reducing agent, it loses
H+ and e-.
- Coenzyme NAD+ (nicotinamide adenine
dinucleotide) is an oxidizing agent.
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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
- After gaining 1 H+ and 2 e-, - When the thioester bond is broken, 7.5 kcal/mol of
the reduced form of NAD+ is energy is released.
NADH.
LESSON 44:: CITRIC ACID CYCLE
- Curved arrows are often The citric acid cycle, a series of
used to depict reactions that enzyme-catalyzed reactions
use coenzymes as oxidizing that occur in mitochondria,
agents. comprises the third stage of the
catabolism of biomolecules—
carbohydrates, lipids, and
amino acids— to carbon
dioxide, water, and energy. The
citric acid cycle is the series of
- In this reaction, isocitrate is oxidized to biochemical reactions in which
oxalosuccinate while NAD+ is reduced to NADH. the acetyl portion of acetyl CoA
is oxidized to carbon dioxide
Coenzymes FAD and FADH2 and the reduced coenzymes
- Coenzyme FAD (flavin adenine dinucleotide) is FADH2 and NADH are produced. This cycle, stage 3
an oxidizing agent as well. of biochemical energy production, gets its name from
the first intermediate product in the cycle, citric acid.
It is also known as the Krebs cycle, after its discoverer
Hans Adolf Krebs, and as the tricarboxylic acid cycle,
in reference to the three carboxylate groups present
in citric acid.

- After gaining 2 H+ and 2 e-, the reduced form of FAD

is FADH2.

Reduced Coenzymes NADH and FADH2

- NAD+ and FAD both act as oxidizing agents.
- Their reduced forms, NADH and FADH2, both act
as reducing agents.

Coenzyme A
- Coenzyme A (HS-CoA) is neither an oxidizing nor a
reducing agent.

- When an acetyl group reacts with sulfhydryl end of

coenzyme A, the thioester acetyl CoA is formed.

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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
THE CITRIC ACID CYCLE
- The citric acid cycle is a cyclic metabolic pathway
that begins with the addition of acetyl CoA to a four-
carbon substrate.
- The cycle ends when the same four-carbon
substrate is formed as a product 8 steps later.
- The citric acid cycle produces high-energy
compounds for ATP synthesis in stage [4] of
catabolism.
Overview of the Citric Acid Cycle

Step 2
Step [2] isomerizes the 3o alcohol in citrate to the 2o
alcohol in isocitrate; it is catalyzed by aconitase.

- The citric acid cycle begins when 2 C’s of acetyl
CoA react with a four-carbon substrate to form a
six-carbon product (step [1]).
- 2 C atoms are sequentially removed to form 2 CO2
molecules (steps [3] and [4]).
- 4 molecules of reduced coenzymes (3 NADH’s and
1 FADH2) are formed (steps [3], [4], [6], and [8]).
- 1 mole of GTP is made in step [5]; GTP is similar to
ATP.
Specific Steps of the Citric Acid Cycle
Step 3
- Step [3] isocitrate loses CO2 in a
decarboxylation reaction catalyzed by
isocitrate dehydrogenase.
- Also, the 2o alcohol of isocitrate is
oxidized by the oxidizing agent NAD+ to
form the ketone a-ketoglutarate and
NADH.
Step 4
- Step [4] releases another CO2 with the oxidation of
a-ketoglutarate by NAD+ in the presence of
coenzyme A to form succinyl CoA and NADH.
- This step is catalyzed by a-ketoglutarate
dehydrogenase

Step 5
In step [5] the thioester bond of succinyl CoA is
hydrolyzed to form succinate, releasing energy that
converts GDP to GTP.

Step 1
Step [1] reacts acetyl CoA with oxaloacetate to form
citrate, and it is catalyzed by citrate synthase.

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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
Step 6
In step [6] succinate is converted to fumarate with
FAD and succinate dehydrogenase; FADH2 is
formed.

LESSON 5 5:: ELECTRON TRANSPORT CHAIN &

Step 7
In step [7], water is added across the
C=C; this transforms fumarate into
malate, which has 2o alcohol.
Step 8
- In step [8], the 2o alcohol of malate is
oxidized by NAD+ to form the ketone
portion of oxaloacetate and NADH.
- The product of step [8] is the starting
material for step [1].
OXIDATIVE PHOSPHORYLATION
- The NADH and FADH2 produced in the Citric Acid
Cycle pass to the Electron Transport Chain. The
Electron Transport Chain is a series of biochemical
reactions in which electrons and hydrogen ions from
NADH and FADH2 are passed to intermediate
carriers. Each electron carrier that participates in the
chain has an increasing affinity for electrons. Upon
accepting the electrons and hydrogen ions, the O2 is
reduced to H2O.
- Oxidative Phosphorylation is the biochemical
process by which ATP is synthesized from ADP as a
result of the transfer of electrons and hydrogen ions
from NADH or FADH2 to O2 through the electron
carriers involved in the Electron Transport Chain.
Oxidative phosphorylation is coupled to the reactions
of the electron transport chain. Oxidative
Phosphorylation is conceptually simple but
mechanistically complex.

Overall Reaction of the Citric Acid Cycle

Overall

The overall citric acid cycle yields:

- 2 CO2 molecules
- 3 NADH and 1 FADH2 molecules
- 1 GTP molecule
The main function of the citric acid cycle is to
produced reduced coenzymes (NADH and FADH2).
These molecules enter the electron transport chain
and ultimately produce ATP.

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Biochemistry
LECTURE | MODULE 7 (BIOENERGETICS: How the Body Converts Food to Energy)
ATP YIELD FROM OXIDATIVE PHOSPHORYLATION
- Each NADH entering the electron transport chain
produces enough energy to make 2.5 ATPs.
- Each FADH2 entering the electron transport chain
produces enough energy to make 1.5 ATPs.
- The citric acid cycle produces overall:

FOCUS ON HEALTH AND MEDICINE

THE ELECTRON TRANSPORT CHAIN
- The electron transport chain is a multistep process
using 4 enzyme complexes (I, II, III and IV) located
along the mitochondrial inner membrane.
Hydrogen Cyanide
- If any one step of the electron transport chain or
oxidative phosphorylation is disrupted an organism
cannot survive.
- Hydrogen cyanide (HCN) produces -CN, which
irreversible binds to the Fe3+ portion of the
cytochrome oxidase.
- Cytochrome oxidase is a key enzyme of complex IV
of the electron transport chain.
- This prevents Fe3+ from being reduced to Fe2+,
halting the electron transport chain and energy
production.
- ATP is not synthesized, and cell death occurs.

- The reduced coenzymes (NADH and FADH2) are

reducing agents, and can donate e- when oxidized.
- NADH is oxidized to NAD+ and FADH2 is oxidized to
FAD when they enter the electron transport chain.
- The e- donated by the coenzymes are passed down
from complex to complex in a series of redox
reactions, which produces some energy.
- These e- and H+ react with inhaled O2 to form
water.
- This process is aerobic because of the use of O2.

AT
ATPP SYNTHESIS BY OXIDATIVE PHOSPHORYLATION
- The electron transport chain provides the energy to
pump H+ ions across the inner membrane of the
mitochondria.
- The concentration of H+ ions in the intermembrane
space becomes higher than that inside the matrix.
- This creates a potential energy gradient, much like
the potential energy of water stored behind a dam.
- To return the matrix, H+ ions travel through a
channel in the ATP synthase enzyme.
- ATP synthase is the enzyme that catalyzes the
phosphorylation of ADP into ATP.
- The energy released by the H+ ions return to the
matrix is the energy stored in the ATP molecule.
- It is called oxidative phosphorylation because the
energy used to transfer the phosphate group results
from the oxidation of the coenzymes.

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Biochemistry
LECTURE | MODULE 8 (Carbohydrate, Lipid, and Protein Metabolism)
INTRODUCTION
- The metabolism of ingested food begins with the
hydrolysis of large biomolecules into small
compounds that can be absorbed through the
intestinal wall. In Module 7, we learned that the last
stages of catabolism, which produce energy from
acetyl coenzyme A (acetyl CoA) by means of the
Citric Acid Cycle, Electron Transport Chain, and
Oxidative Phosphorylation, are the same for all types
of biomolecules. The catabolic pathways that form
acetyl CoA are different, however, depending on the
particular type of biomolecule.
- In this last module, we will examine the specific
metabolic pathways for carbohydrates, lipids, and
proteins.
- Recall from Module 7 that we can conceptually
consider catabolism as the sum of four stages.
Catabolism begins with Digestion in stage [1] in which
polysaccharides, triacylglycerols, and proteins are
hydrolyzed to smaller compounds that can be
absorbed by the bloodstream and delivered to
individual cells. Each type of biomolecule is then
converted to acetyl CoA by different pathways in
stage [2]. Acetyl CoA enters the citric acid cycle and
produces reduced coenzymes, whose energy is
stored in ATP (stages [3] and [4]). Since we already
learned many important facts about stages [1], [3],
and [4] of catabolism, we now consider the metabolic
pathways that convert monosaccharides, fatty acids
and glycerol, and amino acids to acetyl CoA in stage
[2].
- In the catabolism of lipids, fatty acids are converted
into thioesters and then cleaved into many acetyl
CoA units.
- Amino acids are usually reassembled into new
proteins.
- Since excess amino acids are not stored in the body,
they can also be catabolized for energy.
- The amino groups (NH2) are converted to urea
[(NH2)2 C=O], which is excreted in urine.
UNDER
UNDERS STANDING BIOCHEMIC
BIOCHEMICALAL REACTIONS
The name of an enzyme is often a clue as to the type
of reaction it catalyzes:
> Carboxylase catalyzes the addition of a -COO-
(carboxylate).
> Decarboxylase catalyzes the removal of -COO-
> Dehydrogenase catalyzes the removal of 2H
Atoms
> Isomerase catalyzes the isomerization of one
isomer into another.
> Kinase catalyzes the transfer of a phosphate.
> The transfer of a phosphate unit from ATP to the
fructose 6-phosphate molecule is catalyzed by a
kinase enzyme.

LESSON 11:: UNDERSTANDING BIOCHEMICAL

REACTIONS AND GLYCOLYSIS
BIOCHEMICAL REACTIONS
- The biochemical reactions we learned in Module 7
and those we will examine in this Module 8 are often
challenging for a student to tackle. On the one hand,
cells use the basic principles of organic chemistry in
oxidation, reduction, acid-base, and other reactions.
On the other hand, the use of enzymes and
coenzymes allows cells to carry out transformations
that are not easily replicated or even possible in the
lab, so many reactions take on a new and different
appearance. Moreover, many substrates have
several functional groups and these reactions often
proceed with complete selectivity at just one of them.
- While it is often difficult to predict the exact product
of some reactions, it should be possible to understand
and analyze a reaction by examining the reactants
and products, the reagents (coenzymes and other
materials), and the enzymes. The name of an enzyme GLYCOLYSIS
is often a clue as to the type of reaction. Common - Glycolysis is the metabolic pathway by which
types of enzymes encountered in metabolisms, such glucose (a C6 molecule) is converted into two
as kinases and isomerases, will be included in our molecules of pyruvate (a C3 molecule), chemical
lessons. energy in the form of ATP is produced, and NADH-
CARBOHYDRATE
CARBOHYDRATE,, LIPID, AND P PROTEIN
ROTEIN METABOLISM reduced coenzymes are produced. Glycolysis is also
- In the catabolism of carbohydrates, glycolysis called the Embden-Meyerhof pathway after the
converts glucose into pyruvate, which is then German chemists Gustav Embden (1874–1933) and
metabolized into acetyl CoA.

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Biochemistry
LECTURE | MODULE 8 (Carbohydrate, Lipid, and Protein Metabolism)
Otto Meyerhof (1884–1951), who discovered many of Reactant Fructose 6-phosphate
the details of the pathway in the early 1930s. Products Fructose 1, 6-bisphosphate
- It is a linear rather than cyclic pathway that STEP 3 Enzyme Phosphofructokinase
functions in almost all cells. The conversion of glucose Rea
Reagent
gent ATP
to pyruvate is an oxidation process in which no Reaction Phosphorylation
molecular oxygen is utilized. The oxidizing agent is the Reactant Fructose 1, 6-bisphosphate
coenzyme NAD+. Metabolic pathways in which Dihydroxyacetone
molecular oxygen is not a participant are called phosphate,
anaerobic pathways. Pathways that require Products
STEP 4 Glyceraldehyde 6-
molecular oxygen are called aerobic pathways. phosphate
Glycolysis is an anaerobic pathway. Enzyme Aldolase
- Glycolysis is a ten-step process (compared to the Reaction Cleavage
eight steps of the citric acid cycle) in which every step Dihydroxyacetone
is enzyme-catalyzed. All of the enzymes needed for Reactant
phosphate
glycolysis are present in the cell cytosol, which is
2 Glyceraldehyde 6-
where glycolysis takes place. Products
STEP 5 phosphate
- Glycolysis, is a linear, 10-step anaerobic pathway
that converts glucose into two molecules of pyruvate. Triose Phosphate
Enzyme
Isomerase
- Steps [1] to [5] comprise the energy investment
phase, where 2 ATP molecules are hydrolyzed. Reaction Isomerization
- The 6-carbon glucose molecule is converted into 2 Glyceraldehyde 6-
Reactant
two 3-carbon segments. phosphate
- Steps [6] to [10] comprise the energy- generating Products 1, 3-bisphosphoglycerate
phase, producing 1 NADH and 2 ATPs for each Glyceraldehyde 3-
STEP 6 Enzyme
pyruvate formed. phosphate dehydrogenase
Coenzyme NAD+
Oxidation and
Reaction
Phosphorylation
Reactant 1, 3-bisphosphoglycerate
Products 3-phosphoglycerate
STEP 7 Enzyme Phosphoglycerate Kinase
Rea
Reagent
gent ADP
Reaction Phosphate Transfer
Reactant 3-phosphoglycerate
Products 2-phosphoglycerate
STEP 8
Enzyme Phosphoglycerate Mutase
Reaction Isomerization
Reactant 2-phosphoglycerate
Products Phosphoenolpyruvate
STEP 9
Enzyme Enolase
Reaction Dehydration
Reactant Phosphoenolpyruvate
Products 2 Pyruvate
STEP
Enzyme Pyruvate Kinase
10
Rea
Reagent
gent ADP
Reaction Phosphate Transfer

THE NET RESULT OF GLYCOLYSIS

- 2 ATPs are used in phase one of glycolysis and 4
THE STEPS IN GLYCOLYSIS ATPs are made in phase two glycolysis.
Reactant Glucose - The net result is the synthesis of 2 ATPs from
Products Glucose 6-phosphate glycolysis.
STEP 1 Enzyme Hexokinase - The 2 NADHs formed are made in the cytoplasm
Rea
Reagent
gent ATP and must be transported to the mitochondria to join
Reaction Phosphorylation the electron transport chain and make ATP.
Reactant Glucose 6-phosphate - The fate of 2 pyruvate molecules depends on O2
Pro
Products
ducts Fructose 6-phosphate availability.
STEP 2
Enzyme Phosphohexose Isomerase
Reaction Isomerization

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Biochemistry
LECTURE | MODULE 8 (Carbohydrate, Lipid, and Protein Metabolism)
GLYCOLYSIS AND OTHER HEXOSE
- Fructose is obtained by the hydrolysis of the
disaccharide sucrose, found in sugar beets and
sugarcane.
- It can be converted by muscle or kidney cells into
fructose 6-phosphate and enter glycolysis at step [3].
- Or, it can be converted by the liver to
glyceraldehyde 3-phosphate and enter glycolysis at
step [6].
- Galactose is obtained by the hydrolysis of the
disaccharide lactose in milk.
- Galactose is converted into glucose 6-phosphate
and then enters glycolysis in step [2].
- Patients with galactosemia lack the enzyme to
perform this conversion.
- Mannose is obtained from polysaccharides in fruits
such as cranberries and currants.
- Mannose is converted to fructose 6-phosphate, and
it enters glycolysis at step [3].
- Thus, all the common hexoses enter glycolysis and
are metabolized into pyruvate.
LESSON 2A
2A:: FATE OF PYRUV
PYRUVATE
ATE AND ATP YIELD
FROM GLUCOSE
Pyruvate is a versatile molecule that feeds into
several pathways. It is then converted to acetyl CoA
under aerobic conditions which have numerous
metabolic destinations including the TCA cycle. It can
also be converted into lactate under an anaerobic
condition that enters the Cori cycle to undergo
gluconeogenesis.
THE FATE OF PYRUVATE
- Pyruvate can be converted into three possible
products depending on the conditions and the
organism.
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- The ethanol in alcoholic beverages is obtained by

the fermentation of the sugars in grapes, barley malt,
corn, rye, rice, or potatoes.

THE ATP YIELD FROM GLUCOSE

CONVERSION TO ACETYL CoA

- Under aerobic conditions (when O2 is plentiful),
pyruvate is oxidized by NAD+ in the presence of
coenzyme A to form acetyl CoA.

- The NADH formed needs O2 to return to NAD+, so

without O2 no additional pyruvate can be oxidized.

CONVERSION TO LACTATE
- In anaerobic conditions (when O2 is lacking) there is
an abundance of NADH.
- The NADH acts as a reducing agent, reducing - First, glycolysis yields a net of 2 ATPs and 2 NADHs
pyruvate to lactate. (which will give 5 ATPs).

- During strenuous exercise, when ATP needs are high, - Second, oxidation of the 2 pyruvates yields 2 NADHs
there is not enough O2 being inhaled to re- oxidize (which will give 5 ATPs)
NADH in the electron transport chain.
- The lactate formed by anaerobic metabolism of
pyruvate builds up in muscle cells, resulting in
soreness and cramping.
- An “oxygen debt” is created, and when vigorous
activity decreases, the person must take deep
breaths of air to repay this debt. - Finally, the 2 acetyl CoAs proceed through the citric
- The lactate in the muscles is then re-oxidized to acid cycle, starting the electron transport chain and
pyruvate, which can return to acetyl CoA and muscle oxidative phosphorylation, yielding 10 ATPs x 2 = 20
soreness, fatigue, and shortness of breath resolve. ATPs.
- The pain felt during a heart attack is caused by an
increase of lactate in the heart and areas near the
heart cut off from oxygenated blood.
- A higher-than normal blood lactate level can
indicate lung disease, congestive heart failure, or
serious infection. - The final total is 1 glucose = 32 ATP.
- Blood glucose levels are carefully regulated by
CONVERSION TO ETHANOL two hormones.
- Fermentation is the anaerobic conversion of glucose - When blood glucose levels rise after a meal,
to ethanol and CO2 by yeast and other insulin stimulates the passage of glucose into
microorganisms. cells for metabolism.
- When blood glucose levels are low, the hormone

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glucagon stimulates the conversion of stored
glycogen to glucose.

LESSON 2B 2B:: GLUCONEOGENESIS AND THE CORI

CYCLE
- Gluconeogenesis is literally translated as ‘the
production of new glucose’. It is a metabolic pathway
that results in the generation of glucose from non-
carbohydrate carbon substrates such as lactate,
glycerol, and glucogenic amino acids.
- Gluconeogenesis occurs beyond around 8 hours of
fasting when liver glycogen stores start to deplete and
an alternative source of glucose is required. It occurs
mainly in the liver and the kidney (to a lesser extent
in the cortex).
- When carbohydrate intake is high (glucose is
plentiful), little use of the gluconeogenesis metabolic
pathway occurs. On the other hand, gluconeogenesis
becomes an important pathway for a person on a low
carbohydrate diet (glucose is available in only limited
amounts). Through gluconeogenesis, fat and even
proteins can be converted to glucose.
- There are three main precursors:
> Lactate from anaerobic glycolysis in exercising
muscle and red blood cells via the Cori Cycle;
> Glycerol which is released from adipose tissue
breakdown of triglycerides, and
> Amino acids (mainly alanine).
- Gluconeogenesis has a close relationship with
glycolysis. Glycolysis is the breaking of glucose, LESSON 22C:
C: CORI CYCLE
gluconeogenesis is the creation of glucose. However, - The Cori cycle is a cyclic biochemical process in
gluconeogenesis is not as simple as reversing which glucose is converted to lactate in muscle tissue,
glycolysis, as there are irreversible steps in glycolysis. the lactate is reconverted to glucose in the liver, and
the glucose is returned to the muscle tissue.
GLUCONEOGE
GLUCONEOGENESISNESIS - The Cori cycle, or glucose-lactate cycle, was
- Gluconeogenesis is the synthesis of glucose from discovered by Carl Ferdinand Cori and Gerty Theresa
noncarbohydrate sources-lactate, amino acids, or Radnitz, a husband-and-wife team, in the ‘30s and
glycerol. ‘40s of the last century. They demonstrated the
- Gluconeogenesis is an anabolic pathway since it existence of metabolic cooperation between the
results in the synthesis of larger molecules from skeletal muscle working under low oxygen conditions
smaller ones. and the liver. This cycle can be summarized as
follows:
> the conversion of glucose to lactic acid, or lactate,
by anaerobic glycolysis in skeletal muscle cells;
> the diffusion of lactate from muscle cells into the
bloodstream, by which it is transported to the liver;
> the conversion of lactate to glucose by hepatic
gluconeogenesis;
> the diffusion of glucose from the hepatocytes into
the bloodstream, by which it is transported back to
the skeletal muscle cells, thereby closing the cycle.
- Part of the lactate produced in skeletal muscle is
converted to glucose in the liver and transported
back to skeletal muscle.

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- The importance of this cycle is demonstrated by the
fact that it may account for about 40% of plasma
glucose turnover.
LESSON 3: CATABOLISM OF TRIACYL
TRIACYLGLYCEROLS
GLYCEROLS
AND ATP YIELD
- Lipid metabolism entails the oxidation of fatty acids
to either generate energy or synthesize new lipids
from smaller constituent molecules. Lipid metabolism
is associated with carbohydrate metabolism, as
products of glucose (such as acetyl CoA) can be
converted into lipids.
- Breakdown of Fatty Acids. During fatty acid
oxidation, triglycerides can be broken down into
acetyl CoA molecules and used for energy when
glucose levels are low.
- Acetyl CoA is used to create lipids, triglycerides,
steroid hormones, cholesterol, and bile salts.
KETOGENESIS
- If excessive acetyl CoA is created from the oxidation
of fatty acids and the Krebs cycle is overloaded and
cannot handle it, the acetyl CoA is diverted to create
ketone bodies. These ketone bodies can serve as a
fuel source if glucose levels are too low in the body.
Ketones serve as fuel in times of prolonged starvation
or when patients suffer from uncontrolled diabetes
and cannot utilize most of the circulating glucose. In
both cases, fat stores are liberated to generate
energy through the Krebs cycle and will generate
ketone bodies when too much acetyl CoA
accumulates.
- Ketones oxidize to produce energy for the brain.
beta (β)-hydroxybutyrate is oxidized to acetoacetate
and NADH is released. An HS-CoA molecule is added
to acetoacetate, forming acetoacetyl CoA.
- When ketones are produced faster than they can
be used, they can be broken down into CO2 and
acetone. The acetone is removed by exhalation. One
symptom of ketogenesis is that the patient’s breath
smells sweet like alcohol. This effect provides one way
of telling if a diabetic is properly controlling the
disease. The carbon dioxide produced can acidify the
blood, leading to diabetic ketoacidosis, a dangerous
condition in diabetics.
THE CATABOLISM OF TRIACYL
TRIACYLGLYCEROLS
GLYCEROLS
- The first step in the catabolism of triacylglycerols is
the hydrolysis of the three ester bonds to yield
glycerol and 3 fatty acids.
GLYCEROL CATABOLIS
CATABOLISM M
- The glycerol backbone is converted to
dihydroxyacetone phosphate, which can enter
glycolysis.
- The first step involves the phosphorylation of
glycerol to glycerol 3-phosphate.
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- In step [3], the B-alcohol is oxidized with NAD+
forming a B-carbonyl group and
NADH.

- The second step involve oxidation with NAD+ to yield

dihydroxyacetone phosphate and NADH.

- In step [4], the bond between a and b carbons is

cleaved with another coenzyme A.

- The product is an intermediate in both glycolysis

and gluconeogenesis, so two pathways are available.

FATTY ACID CATABOLISM BY B B--OXIDATION

- Fatty acids are catabolized by B-oxidation, a
process whereby acetyl CoA units are sequentially
cleaved from the fatty acid.
- First, the fatty acid is converted to a thioester with
coenzyme A, then B-oxidation begins.
- This requires energy, provided by the conversion of
ATP to AMP.
- The result is a new acyl CoA having 2 fewer C’s than
the original.
- This new acyl CoA can then proceed through B-
oxidation again, cleaving off two more C’s, until finally
only acetyl CoA molecules are present.
- For example, an 18-carbon acyl CoA is cleaved into
9 acetyl CoA molecules.
- A total of 8 cycles of B-oxidation are needed to
cleave the eight C-C bonds, such that every carbon
of the original fatty acids ends up in an acetyl CoA.

- In step [1], FAD removes 2 H’s to form FADH2, and a

double bond forms between a and b carbons.

- In step [2], water is added to the double bond; this

always makes a B-alcohol.

Complete B-oxidation of the acyl CoA derived from

an 18- carbon fatty acid (stearic acid) forms:
- 9 Acetyl CoA molecules

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- 8 NADH molecules
- 8 FADH2 molecules

HOW TO DETERMINE THE NUMBER OF ATPS FORMED

FROM A FATTY ACID
Example: How much ATP is formed by the complete
catabolism of stearic acid C18H36O2
Step 1: Converting the fatty acid into the fatty acyl
CoA uses up 2 ATP.
ATP Total = -2 ATP
Step 2: Next, add up the ATP from the reduced
coenzymes made during B-oxidation.
ATP Total = -2 ATP + 32 ATP
Step 3: Finally, add up the ATP synthesized from each
acetyl CoA. AMINO ACID METABOLISM
9 Acetyl CoA x 10 ATP = 90 ATP - The catabolism of amino acids can be divided into
ATP Total = -2 ATP + 32 ATP + 90 ATP ATP Total = 120 two parts.
ATPs from stearic acid - The first part concerns the fate of the amino group.
- The second part concerns the fate of the carbon
atoms.

FATE OF TTHE
HE AMINO GROUP
- The amino group of the amino acid is first removed
by transamination.
- Transamination is the transfer of an amino group
from an amino acid to an a-keto acid.

Lesson 44:: Amino Acid Metabolism and the Urea - Transamination often uses a-ketoglutarate as the
Cycle a-keto acid.
- Protein is the important tissue builder in the body
which can help in the cell structure, functions,
hemoglobin formation to carry oxygen, the enzyme
for metabolic reaction, and other functions in the
body. Also, it supplies the nitrogen for the DNA and
RNA genetic materials and energy production. This is
because protein contains a long chain of amino acids.
- Protein metabolism is the process of breaking down
foods that are used by the body to gain energy.
- During protein metabolism, some of the protein will - After transamination, the original amino acid
be converted into glucose through the contains only C, O, and H atoms.
gluconeogenesis process. - After accepting the amino group, glutamate is
degraded through oxidative deamination to
regenerate a-ketoglutarate and to make NH4+.
- The NH4+ then enters the urea cycle, where it is
converted into urea, (NH2)2 C=O, in the liver and
excreted by the kidneys in urine.
- Oxidative deamination of glutamate:

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FATE OF TTHE
HE CARBON SKELETON
There are three common fates of the carbon skeleton
of amino acids:
- Conversion to pyruvate
- Conversion to acetyl CoA
- Conversion to an intermediate in the citric acid
cycle.

- Glucogenic amino acids are catabolized to

pyruvate or an intermediate of the citric acid cycle.
- These products can be used for gluconeogenesis,
which is synthesizing glucose.
- Ketogenic amino acids are converted to acetyl CoA
or a related thioester acetoacetyl CoA.
- These products can be used to synthesize ketone
bodies and can yield energy in that path.

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