CELL MOLECULAR COMPOSITION OF CELL

• Biochemistry • Water accounts for about 70-75% of the

explores weight of the cell.
molecular • Organic compounds accounts for 25-30% of
mechanisms the cell weight.
of normal • They are nucleic acids, proteins,
cellular polysaccharides (carbohydrates) and lipids.
processes as • Inorganic compounds account for the rest of
well as the cell weight. (electrolytes or ions) ; salt,
diseases. potassium, magnesium and manganese
• All higher
living EUKARYOTIC CELL (humans)
organisms
including humans are made up of cells.
• Two major classes:
o Prokaryotes
o Eukaryotes

HISTORICAL NOTES
• Robert Hooke was the first person to use the
term “cell”. He referred to the small empty
chambers in the structure of cork as cells.
• Matthias Schleiden and Theodor Schwann
concluded that all plant and animal tissues
were composed of cells.
• Rudolf Virchow proposed the theory of
biogenesis where cells only arise from pre- • Eukaryotic cells have a membrane-bound
existing cells. nucleus and a number of other membrane-
bound subcellular (internal) organelles, each
CELL THEORY of which has a specific function.
• A cell is the basic structural and functional
unit of living organisms. PLASMA MEMBRANE
• The activity of an organism depends on the
collective activities of its cells.
• According to the principle of
complementarity, the activities of cells are
dictated by their structure (anatomy), which
determines function (physiology).

EUKARYOTIC CELL vs. PROKARYOTIC CELL

EUKARYOTES PROKARYOTES
DNA is found in the DNA is not enclosed
nucleus of the cell. within the membrane. • Structure: Phospholipid bilayer containing
Contain membrane- cholesterol and proteins and some
bound organelles carbohydrates; forms a selectively permeable
which include boundary of the cell.
Lack membrane- • Functions: Acts as a physical barrier to
mitochondria,
enclosed organelles enclose cell contents; regulates material
endoplasmic
reticulum, and Golgi movement into and out of the cell; functions in
complex cell communication with the environment and
Cell division involves Usually divide by other cells
mitosis. binary fission.

1
 NUCLEUS
• Structure: It is enclosed within a double
membrane called nuclear envelope; contains
nucleolus
• Nucleolus: It consists of RNA and proteins
which functions in ribosomal unit assembly.
• Nucleoplasm: It surrounds the chromatin
and the nucleoli.
▪ Function: It contains the DNA that serves
as the genetic material for directing protein
synthesis.
• Structure: Double-membrane-bound
organelles containing a circular strand of DNA
• Outer membrane is highly permeable to
small molecules, due to the presence of a pore-
forming protein called porin.
• Intermembrane contains many proteins that
participate in oxidative phosphorylation.
Inner membrane has multiple folds
projecting inwards, called cristae
• Function: It is responsible for the production of
energy in the form of ATP.
LYSOSOMES

CYTOPLASM

• Structure: Spherical shaped membrane bound

organelles formed from the golgi apparatus;
contain digestive enzymes
• The fluid inside lysosomes is much more acidic, at
about pH 4.8, than the normal pH of about 7.0–
7.3.
• Function: Digest microbes or materials by the
cell

ENDOPLASMIC RETICULUM
• Structure: This can be seen between the
plasma membrane and the nucleus where the
other cellular elements are embedded.
• Organelles are membrane-bound structures
which carry out specific metabolic activities
of the cell.
• Cytosol provides support for organelles and
serves as the viscous fluid medium.
• Function: It is responsible for various
cellular processes.

MITOCHONDRIA
• It is further subdivided into:
• Rough endoplasmic reticulum
• Structure: Extensive interconnected
membrane network that varies in shape;
ribosomes attached on the cytoplasmic
surfaces
• Ribosomes are involved in the protein
synthesis.

2
 • Functions: Modifies, transports, and stores
proteins produces by attached ribosomes
• Smooth endoplasmic reticulum
• Structure: Extensive interconnected
membrane network lacking ribosomes
GOLGI APPARATUS
• Structure: Series of several elongated,
flattened saclike membranous structures.
• Functions: Modifies, packages, and sorts
materials, that arrive from the endoplasmic
reticulum in transport vesicles
• Vesicles transport cellular material.
Mature vesicles are called secretory
vesicles.
PEROXISOMES
• Structure: smaller, spherical membrane
bound organelles formed from the
endoplasmic reticulum.
• Functions: Detoxify specific harmful
substances either produced by the cell or
taken into the cell
CYTOSKELETON
• Cytoskeleton
• Structure: Organized network of protein
filaments
• Function: Maintains integral structural
support and organization of cells
• Microfilaments maintain cell shape.
• Intermediate filaments give mechanical
support to structures like nucleus and
plasma membrane.
• Microtubules provides structural support.
IMPORTANT NOTES IN PROKARYOTIC CELL
• Prokaryotes (Eubacteria and Archaebacteria)
are the most abundant organisms on earth.
• A prokaryotic cell does not contain a
membrane-bound nucleus.
• Each prokaryotic cell is surrounded by a
plasma membrane.
• The cell has no subcellular organelles, only
infoldings of the plasma membrane called
mesosomes.
• The deoxyribonucleic acid (DNA) is condensed
within the cytosol to form the nucleoid.
• Some prokaryotes have tail-like flagella.
CELL MEMBRANE TRANSPORT
Passive Transport Process
• Diffusion is the movement of a substance from
an area of its higher concentration to an area
of its lower concentration.
3
 MITOSIS
• Simple diffusion is the type of diffusion of
dissolved solutes through the plasma
membrane
• Facilitated Diffusion is the type of diffusion
that requires a protein carrier.
• Osmosis is the diffusion of water point
across a selectively permeable membrane.

Active Transport Process

• This type of cell membrane transport uses
energy (ATP) provided by the cell.
• For example, cell has low intracellular
sodium; but concentration of potassium
inside the cell is very high. This is maintained
by the sodium–potassium activated
ATPase, generally called as sodium pump.
• Exocytosis refers to bulk movement of
substance out of the cell by fusion of
secretory vesicles with the plasma
membrane.
• Endocytosis refers to bulk movement of
substance into the cells by vesicles forming
at the plasma membrane.
CEL LIFE CYCLE
Interphase
• It is the longer phase of the cell cycle where
the cell is active and preparing for cell
division.
• The DNA molecule is duplicated exactly in a
process called DNA replication which
occurs toward the end of the interphase.
Cell Division
• Cells arise from the division of other cells.
• Mitosis consists of four stages-prophase,
metaphase, anaphase, and telophase. The
result is two daughter nuclei, each identical
to the mother nucleus.
• Prophase- each chromosome consists of
two chromatids joined at the centromere.
• Metaphase- chromosomes align at the
center of the cell
• Anaphase- chromatids separate at the
centromere and migrate to opposite poles.
• Telophase- two new nuclei assume their
normal structure, and cell division is
completed, producing two new daughter
cells.
ADDITIONAL NOTES:
CELL
• Fundamental units of life all living things are
composed of cells therefore, all organisms are
highly organisms including humans are
constructed are made up of cells
• All biochemical processes are carried out by
our cells
• One cell is grouped accordingly once they are
group, they can be organized and function as
multi-cellular organisms
• The cells of the multi-cellular organisms can
be specialized in form and it can be function to
carry out sub processes of the multi-cellular
microorganisms
• Cell only arises on the pre-existing cells
BINARY FISSION
• A sexual reproduction wherein we separate
one cell into to new bodies
• It will duplicate the genetic material and
divide into two parts which is knows as
cytokinesis.
PLASMA MEMBRANE
• It’s the cell boundary it defines the perimeter
of the cell
• It is a place of communication

4
Occurrence and Functions of Carbohydrates
• Carbohydrate oxidation provides energy.
• Carbohydrate storage, in the form of
glycogen, provides a short-term energy
reserve.
• Carbohydrates supply carbon atoms for the
synthesis of other biochemical substances
(proteins, lipids, and nucleic acids)
• Carbohydrates form part of the structural
framework of DNA and RNA molecules.
• Carbohydrates linked to lipids are structural
components of cell membranes.
• Carbohydrates linked to proteins function in
a variety of cell–cell and cell–molecule
recognition processes.
• A carbohydrate is a polyhydroxy aldehyde, a
polyhydroxy ketone, or a compound that
yields polyhydroxy aldehydes or polyhydroxy
ketones upon hydrolysis.
• The carbohydrate glucose is a polyhydroxy
aldehyde, and the carbohydrate fructose is a
polyhydroxy ketone.
CARBOHYDRATES
• is the most abundant class of bio organic
molecules on earth
• In a living organism on what we called the
biochemical substances.
• biochemical substances are we found in a
living organism
o Bio-inorganic molecules – do not contain
carbon in their structure example is the
water and inorganic compounds such as salt
o Bio-organic molecules – This substance
contains carbon in their structure such as
carbohydrates, lipids, proteins, nucleic acids
• Glycogen are stored in liver and muscle
• Among the bio-organic substances the
carbohydrates is a major role in different
biochemical metabolism
• DNA and RNA have different sugar unit
o Deoxyribose (DNA)
o Ribose (RNA)
• Without your sugar unit no nucleic acid can be
formed because one of the major components
of the cell structure the monomer nucleotide is
your sugar
• Carbohydrates once it’s bound or attach to a
lipid is known as glycolipid. Glycolipid is part
of the plasma membrane or specifically
structural component of your cell membrane
• Carbohydrates once it’s bound or attach to a
protein is known as glycoprotein.
Glycoprotein it serves as the marker or
recognition between different cell or the
molecules
Carbohydrate - CnH2nOn or Cn(H2O)n
• Simplest type of sugar is monosaccharide
• CHO - represent for carbohydrates because all
carbohydrates contain carbon, hydrogen and
an oxygen
• Carbon has a double bond O (C=O) –
functional group
• -OH – hydroxyl group
• Derivatives of Carbohydrates – phosphates,
sulfates, amines
• Poly (many) hydroxy (used for hydroxyl
group)
• Aldehyde – RCHO
• Ketone – RCOR’
o R- represent the side chain which are known
to be alkyl group
o O – double bonded to your central atom
which is your carbon
5
 • Aldehyde is always at the carbon number one
(function group) while for the ketone its
always found at the carbon number two
• Why is ketone always found at the carbon
number two?
o Because of the alkyl group must be bonded at
the terminal end or prior to the carbon
which contains the double bond O
• If sugar contains aldehyde structure – aldose
• If the carbohydrate contains a ketone – ketose

MONOSACCHARIDES
• 3-7 carbon atoms in the structure
• Also known as monoses or glycoses
• -ose prefix
• Triose (3)
• Tetrose (4)
• Pentose (5)
• Hexose (6)
• Heptose (7)
• Pentose and hexose usually biochemically
CLASSIFICATION OF CARBOHYDRATES significant and are more abundant than the
• Monosaccharides are classified as aldose or other type of monosaccharide
ketose on the basis of the type of carbonyl • Ribose and deoxyribose which are also
present. known as pentose sugar. The ribose and
• Disaccharides are glycosides formed from the deoxyribose is for nucleic acid
linkage of two monosaccharides. • Hexose; glucose, fructose and galactose are
• Oligosaccharides are carbohydrates that biochemically important because the complex
contain three to ten monosaccharide units. carbohydrates. Also, the three of them have 6
• Polysaccharides are polymers in which carbon atoms in their structure
monosaccharides are the monomers. • They cannot be broken down into simpler
CHO substance because monosaccharides are
CH2 OH
already known as the monomer unit of
H OH O
carbohydrates
HO H HO H • This is the simplest from
H OH H OH • It also known as simple sugar
H OH H OH • Straight chain compound
CH2 OH CH2 OH • The simplest aldose is the D- glyceraldehyde
Fructose
it is considered as triose
Glucose
• Ex: 5 C + RCOR’ = Ketopentose
Glucose and fructose are monosaccharides 7 C + RCHO = Aldoheptose
• Reaction involves for breaking down of the
carbohydrates is the hydrolysis – water
• Pure monosaccharides are water soluble

DISACCHARIDES
• Linkages that could be found between the two
or more monosaccharides unit in the complex
carbohydrates is the glycosidic
• Example of covalent bond
• SACCHARIDE – saccharum means sugar

6
 • D- glyceraldehyde – being the one being
occupited there is the handedness or the
chirality of the molecule
When we say handedness it’s the form of
isomerism
CHIRALITY: HANDEDNESS IN MOLECULES
Objects and Mirror Images
• Most monosaccharides exist in two forms: a
“left-handed” and “right-handed” form.
• Superimposable (Achiral) – mirror images
are images that coincide at all points when
the images are laid upon each other.
• Nonsuperimposable (Chiral) – mirror
images are images where not all points
coincide when the images are laid upon each
other.
CHIRALITY
• A chiral center is an atom in a molecule that
has four different groups bonded to it in a
tetrahedral orientation.
• A molecule that contains a chiral center is
said to be chiral.
• A chiral molecule is a molecule whose mirror
images are not superimposable.
CHIRAL CENTER OR CHIRAL MOLECULE
• The carbon atom must be seen attach to
four different groups in a tetrahedral
orientation
• Example:
CH3
H – C – OH
CHO
CH3
ACHIRAL
H – C – OH If you see 2 atoms
attach to carbon atom
H 7
STEREOISOMERISM: ENANTIOMERS AND
DIASTEREOMERS
• Stereoisomerism. The atoms of stereoisomers
are connected in the same way but are
arranged differently in space.
Two types: enantiomers and diastereomers.
Enantiomers
• have structures that are nonsuperimposable
mirror images of each other.
• They have chiral center
• Left and right handedness
• Greek word enantios which means opposite
• Single chiral center
Diastereomers
• have structures that are not mirror images of
each other
• Same side and opposite side; cis and trans
• It contains more than 1 chiral center
• Also inform of enantiomers
FISCHER PROJECTION FORMULAS
• A Fischer projection formula is a two-
dimensional structural notation for showing
the spatial arrangement of groups about chiral
centers in molecules.
• In a Fischer projection formula a chiral center
(Carbon) is represented as the intersection of
vertical and horizontal lines
• It is important to right the functional group
of high priority
• Aldehyde is the high priority than
ketone
• D – dextro (right)
• L – levo (left)
• We check on the last OH group
• D and L system used to designate the
handedness of glyceraldehyde enantiomers.
 • The D,L system used to designate the Galactose and Ribose
handedness of glyceraldehyde enantiomers D-Galactose CHO
can be extended to other monosaccharides 1. Milk sugar H OH
with more than one chiral center. 2. Synthesize in human HO H
• The carbon chain is numbered starting at the 3. Used to differentiate between HO H
carbonyl group end of the molecule, and the blood types H OH
highest-numbered chiral center is used to 4. Six membered cyclic form CH2 OH
determine D or L configuration. D-Galactos e
• Other name is also known as (aldohexose)
CLASSIFICATION OF MONOSACCHARIDES brain sugar
• Monosaccharides • ABO blood group system
CHO CH2OH
are often • Why is it named as brain sugar? Because it is
classified by both H OH O part of the brain and nerve tissue
their number of HO H HO H • Less sweet than your glucose
carbon atoms and H OH H OH
• They are actually seldom free
their functional monosaccharides
group. H OH H OH
• Galactosemia difficulty in breaking down or
• A six-carbon CH2OH CH2OH converting galactose to glucose
monosaccharide D-Glucose D-Fructose
with an aldehyde
(aldohexose) (ketohexose)
D-Ribose CHO
functional group is an aldohexose; a five- 1. Part of RNA H OH
carbon monosaccharide with a ketone 2. Part of ATP H OH
functional group is a ketopentose. 3. Part of DNA H OH
4. Five membered cyclic form CH2 OH
Biochemically Important Monosaccharides D-Ribose
Glucose (C6H12O6) CHO • Fructose is also having five (aldopentose)
• Dextrose or blood sugar and membered cyclic form
H OH
also known as grape sugar
• Grape sugar is the good HO H

source of your glucose H OH Carbohydrates – almost all of the

• Among all the type of H OH monosaccharides their handedness is
monosaccharides this is the biochemically significant right handedness or d
CH2OH
biochemically important it is designation
D-Glucose
the aldohexose (aldohexose) Amino acids – left handedness
• Most common
monosaccharides HAWORTH PROJECTION FORMULAS
• Source of energy and metabolic intermediate • A Haworth projection formula is a two-
• D-glucose is the most abundant in nature and the dimensional structural notation that specifies the
most important from a human nutritional three-dimensional structure of a cyclic form of a
standpoint. monosaccharide.
• Named after Walter Norman Haworth
Fructose (C6H12O6)
CH2OH CH2 OH
• D-Fructose is biochemically O
CH2 OH
O
CH2 OH

the most important O

OH
ketohexose. It is also known HO H OH

as levulose and fruit sugar. H OH

OH OH OH
OH
• Sweetest tasting of all sugar -D-Glucose
OH
 -D-Fructose
H OH
(fruit sugar)
CH2OH
• Semen contains fructose CH2OH CH2 OH CH2 OH
O O

• Dietary sugar due to D-Fructose

(ketohexose)
OH

sweetness OH
OH OH
OH
OH
• More water-soluble compare to glucose -D-Fructose -D-Ribose

• Can serve as for preservative for food and for

intravenous nutrient

8
What are we going to check to know if it is
Dextro or Levo
• We check the CH2OH position
• Upward CH2OH used the D (right)
• Downard CH2OH used the L (left)
Pyranose – six atom ring (glucose)
Furanose – five atom ring (fructose and ribose)
ALPHA AND BETA CONFIGURATION
• Alpha or Beta configuration is determined by
the position of the —OH group on C1 relative
to the CH2OH group that determines D or L
series.
• In a Beta configuration, both of these groups
point in the same direction
• In an Alpha configuration, the two groups
point in opposite directions.
REACTIONS OF MONOSACCHARIDES
Five important reactions of monosaccharides:
• Oxidation to acidic sugars
• Reduction to sugar alcohols
• Glycoside formation
• Phosphate ester formation
• Amino sugar formation
OXIDATION
• Oxidation to acidic sugars: The redox
chemistry of monosaccharides is closely
linked to the alcohol and aldehyde functional
groups present in them.
• Oxidation can yield three different types of
acidic sugars depending on the type of
oxidizing agent used:
Aldose
Weak oxidizing agent (c1): tollens and
benedicts (aldehyde) → aldonic acid (RCOOH)
carboxylic acid
• Ex: Glucose to gluconic acid
Strong Oxidizing agent (c1 and c6)
• RCHO + CH2OH → aldoric acid
• 2 RCOOH → di-carboxylic acid
• Ex: glucose → glucaric acid
Enzyme reacts with aldehyde containing sugar
(c6)
CH2OH → alduronic acid
Glucose → Glucoronic acid
SUGAR ALCOHOLS
• Reduction to sugar alcohols: The carbonyl
group in a monosaccharide (either an aldose
or a ketose) is reduced to a hydroxyl group
using hydrogen as the reducing agent.
• Either aldose or ketose
• Form of hydroxyl group
• Hydrogen as reducing agent
Glucose (RCHO) -→ Glucitol
Ex: of sugar alcohol – D – Sorbitol –
common name of Glucitol
GLYCOSIDE
• The general name for monosaccharide acetals
is glycoside.
• A glycoside is an acetal formed from a cyclic
monosaccharide by replacement of the
hemiacetal carbon -OH group with an -OR
group.
• Reaction of your sugar specifically of
monosaccharide with alcohol will form your
glycoside
Monosaccharide + ROH → glycoside
• Ex: Glucose → Glucoside
Galactose → Galactoside
BLOOD TYPES AND MONOSACCHARIDES
• Blood Types and Monosaccharides: Human
blood is classified into four types: A, B, AB, and
O:
• The biochemical basis for the various blood
types involves monosaccharides present on
plasma membranes of red blood cells.
• The monosaccharides responsible for blood
groups are D-galactose and its derivatives.
• Need cross matching it will not yield in
transfusion reaction
• AB+ → They are known to be as the universal
recipient
• They do not have Anti-A and Anti-B which the
antibodies for the AB
• Universal donor is the Blood Type O-
PHOSPAHATE ESTER FORMATION
• Phosphate ester formation: The hydroxyl
groups of a monosaccharide can react with
inorganic oxyacids to form inorganic esters.
• Phosphate esters of various monosaccharides
are stable in aqueous solution and play
important roles in the metabolism of
carbohydrates.
• Glucose – 6- phosphate dehydrogenase
• G6pd deficiency
9
AMINO SUGAR FORMATION MALTOSE (C12H22O11)
• Amino sugar formation: An amino sugar - • Maltose, often called malt sugar, is produced
one of the hydroxyl groups of a whenever the polysaccharide starch breaks
monosaccharide is replaced with an amino down, as happens in plants when seeds
group germinate and in human beings during starch
• Amino sugars and their N-acetyl derivatives digestion.
are important building blocks of • Structurally, maltose is made up of two D-
polysaccharides. glucose units, one of which must be 𝒂-D-
• Galactosamine example of amino sugar glucose.
• Amines (formula) : NH2 • Common on baby foods
• C2 – OH → NH2 • Also known as reducing sugar
Glucose → glucosamine • The water was released during the reaction to
Galactose → galactosamine form the glycosidic bond
• Humans can digest your maltose because we
have an enzyme responsible for the digestion
DISACCHARIDES or for breakdown of disaccharide
• Two • The enzyme that could breakdown for the said
monosaccharides disaccharide is maltase
can react to form • During the breakdown of the maltase acidic
disaccharide condition is needed
• The bond that
links the two LACTOSE
monosaccharides • Lactose is made up of 𝜷-D-galactose unit and
of a disaccharide a 𝜷-D-glucose unit joined by a b(1-4)
(glycoside) glycosidic linkage.
together is called • Lactose is the major sugar found in milk.
a glycosidic • Lactose intolerance: a condition in which
linkage. people lack the enzyme lactase needed to
hydrolyze lactose to galactose and glucose.
• Monosaccharides that has cyclic form will • Lactase hydrolyzes b(1-4) glycosidic linkages.
react with an alcohol to form a glycoside • Deficiency of lactase can be caused by a
• Glycosidic linkage- it forms of C – O – C genetic defect, physiological decline with age,
bond. The type of reaction that will happen or by injuries to intestinal mucosa.
is condensation. Because they elicit water • Is known the principal carbohydrate in
during the reaction mineral
• It is important to distinguish between the • In human 7-8% is lactose
structural notation used for an 𝒂 (1 : 4) • The cow’s milk is 4-5%
glycosidic linkage and that used for a 𝜷 (1 • Lactose it could be breakdown by human
: 4) glycosidic linkage. • Lactose → Lactase is the enzyme
• 𝒂 (1: 4) – both downward
• 𝜷 (1: 4) – c1 (upward) and C4 (downward) • D-Galactose
CH2OH
O OH
 (1-4)
CH2OH H
CELLOBIOSE OH O
OH
O
• Cellobiose is produced as an intermediate in OH
OH
the hydrolysis of the polysaccharide
cellulose. OH • D-Glucose
• Cellobiose contains two 𝜷 - D-glucose Lactose

monosaccharide units linked through a 𝛽

(1—4) glycosidic linkage. SUCROSE
• Cellobiose cannot be digested by humans. • Sucrose (table sugar): The most abundant of
• Cellulose - we do not have an enzyme that all disaccharides and found in plants.
could breakdown for 𝛽 (1—4) glycosidic • It is produced commercially from the juice of
linkage. CH2OH sugar cane and sugar beets
CH2OH  (1-4)
O OH • Sucrose is a nonreducing sugar.
H
O OH
O
OH
OH 10
OH
OH
Cellobiose
 • Common table sugar • All of the glycosidic linkages in starch (both
• It also called as saccharose amylose and amylopectin) are of a type.
• Best known disaccharides Amylose
• It could only exist in one form, either solid or • straight chain polymer
aqueous solution • glycosidic bond: 𝜶 𝟏 − 𝟒
• Provide a major portion of the carbohydrate • 15-20%
intake for many individual • Molecular mass: 50,000 amu
• Sucrose → sucrase is the enzyme needed to • Glucose unit: 1,000
break glucose molecules which is present in
our human body Amylopectin
• Sucrose, lactose, maltose could be break by • Branched chain polymer
human because it has enzymes. • Straight chain: 𝜶 𝟏 → 𝟔
CH2 OH • 80-85%
O • Molecular mass: 300,000
OH
CH2 OH • Glucose unit: 100,000
O
OH OH

OH OH
• Humans can hydrolyze alpha linkage but
-D-Glucose OH
not beta linkage
+ OH  (1-2) • When starch breaks down we have maltose
O
Linkage
CH2 OH CH2 OH
OH
GLYCOGEN
O O

• Glycogen, like starch, is a polysaccharide

OH OH

CH 2OH CH 2OH containing only glucose units.

OH OH • Liver cells and muscle cells are the storage
-D-Fructose Sucrose sites for glycogen in humans.
• Glycogen is an ideal storage form for glucose.
• It also known as animal starch
General Characteristics of Polysaccharides
• Is known to be branched chain polymer
the Polymer Chain
• Molecular mass: 3,000,000
• A polysaccharide is a polymer that contains
many monosaccharide units bonded to • Glucose unit: 1,000,000
each other by glycosidic linkages. • 3 times more highly branched than
amylopectin
• A homopolysaccharide is a
polysaccharide in which only one type of • Excess glucose in the body it could be stored
monosaccharide monomer is present. (ex: in the form of glycogen
glucose)
• Polysaccharides is also known as glycans
• A heteropolysaccharide is a
polysaccharide in which more than one
CELLULOSE
(usually two) type of monosaccharide
monomer is present. (ex: lactose or • Linear homopolysaccharide with 𝛽 (1 → 4)
sucrose) glycosidic bond
o Humans don’t have enzymes that hydrolyze 𝛽
(1 → 4) - so humans cannot digest cellulose --
STARCH (C 1 and 6)
animals also lack these enzymes but they can
• A storage polysaccharide is a polysaccharide
digest cellulose because they have bacteria in
that is a storage form for monosaccharides
their guts to hydrolyze cellulose
and is used as an energy source in cells.
o It serves as dietary fiber in food-- readily
• Starch is a homopolysaccharide containing
absorbs water and results in softer stools.
only glucose monosaccharide units.
• Dietary fiber: 20-35 grams needed by
• It is the energy-storage polysaccharide in
our body everyday
plants
• Molecular mass: 900,000
• Amylopectin, the other polysaccharide in
• Sugar unit: 5,000 glucose
starch, has a high degree of branching in its
polyglucose structure. • Example: cotton 95% , wood 50%
•

11
 • Intermediate product during the breakdown • Highly viscous - serve as lubricants in the fluid
of cellulose is the cellubiose of joints and part vitreous humor of the eye.
HO
• Enzyme reacts with aldehyde containing
HO O O
sugar (c6)
HO O O
OH Glucose → Glucoronic acid
OH (1-4) OH
HO O O
OH (1-4)
O O OH
OH (1-4)
O OH
OH

CHITIN
• Similar to cellulose in both function and
structure
• Linear polymer with all b (1→4) glycosidic Heparin:
linkages - it has a N-acetyl amino derivative • An anticoagulant-prevents blood clots.
of glucose • This polysaccharide contains 15-90
• Function is to give rigidity to the exoskeleton disaccharide residue
s of crabs, lobsters, shrimp, insects, and • sulfate or carboxyl group
other arthropods.
HO

HO O O
OH
HO O
O
OH HN
O O
HO
OH HN O
O O
O OH HN O N-Acetyl
HN O

O
𝜷-D-Glucoseamine

Glucoseamine GLYCOLIPIDS AND GLYCOPROTEINS

• an amino group replace the OH group of • A glycolipid is a lipid molecule that has one or
the carbon number 2 of your glucose unit more carbohydrate (or carbohydrate
on that said amino group and its acetyl derivative) units covalently bonded to it.
group • A glycoprotein is a protein molecule that has
one or more carbohydrate (or carbohydrate
ACIDIC POLYSACCHARIDES derivative) units covalently bonded to it.
• Acidic polysaccharides - polysaccharides
with a repeating disaccharide unit
containing an amino sugar and a sugar with
a negative charge due to a sulfate or a
carboxyl group.
• Structural polysaccharide present in
connective tissue associated with joints,
cartilage, synovial fluids in animals and
humans
• They are considered as
heteropolysaccharides
• Examples:
o Hyaluronic acid
o Heparin

HYALURONIC ACID AND HEPARIN

Hyaluronic acid:
• Alternating residues of N-acetyl-b-D-
glucosamine and D-glucuronic acid.

12
Blood glucose level
Fasting blood sugar (FBS) 8hrs fasting Specimen: serum
Tube:
red top (non additive)
Serum separator tube (SST)
Oral Glucose Tolerance Test (OGTT) 75 g oral glucose load Gray top – sodium chloride
Random Blood Sugar (RBS) Anytime of the day Specimen: Serum
Glycosylated Hemoglobin (HbA1C) - Glycemic control Whole blood: EDTA (purple top)
- Diabetes mellitus - Ethylene diamine tetra acetic acid
- 2-3 months
2-hr PPBS (Post-Prandial) Specimen: serum
2hrs after meal Tube:
red top (non additive)
Serum separator tube (SST)
Oral Glucose Challenge Test (OGCT) - Screening of gestational
diabetes mellitus
- 50 grams
Fructosamines - is known as glycosylated Specimen: Serum
albumin
- monitoring every 3 weeks

13
 PROTEINS
• Monomer unit: Amino acid
• Comes from the Greek word “proteios”,
• 15% of the cell has a protein
meaning primary importance
• Water has 70-75%
• Molecules were first described and named
by the Swedish chemist Jons • Carbohydrates has 2%
Jakob Berzelius in 1838. • Ex: P - casein
Fe - Hemoglobin
• Naturally occurring, unbranched polymers
• Most abundant molecules in the cells after water
• Elemental composition: Contain C, H, O, N,
most also contain S
• The average nitrogen content of proteins is 15.4%

BUILDING BLOCKS OF PROTEINS • Building blocks of proteins is the amino acid

• All protein has amino acid and all amino acid
has amino group NH2, carboxyl group COOH
and a hydrogen group in the structure
• Based on the common R groups there are 20
standard amino acid which are common in the
proteins
• In the proteins more than 700

AMINO ACID STRUCTURES

Methaionine (M) Isolucine (I) Valine (V) leucine (L) Aspartic acid (D)

Glutamic acid (E)

phenylalanine (F) tyrosine (Y) tryptophan (W) aspargine (N)

glutamine (Q)
glycine (G)
lysine (K) arginine (R) histidine (H)

threonine (T)
alanine (A)

serine (S)
cysteine proline

14
GROUPS OF AMINO ACIDS
1. Non-Polar Amino Acids ONE LETTER AMINO ACID CODES
• insoluble to water; polar solvent
• 8 Standard amino acids are non-polar
• When present in proteins, they are located in
the interior of protein where there is no
polarity
• It is also known as hydrophobic or water
fearing
• 9- Tryptophan – polar neutral (weak
interaction to water) borderline member of
non-polar amino acids)
• they are in the interior because there is no
polarity

2. Polar Amino Acids RSR’ (sulfur

a. Polar Neutral (7/20) • Aliphatic it means open chain /sulfide)
One carboxyl and one amino group, and a side • Your carbon as a central proof has capacity and
chain that is polar but neutral the ability for different groups meaning to say
b. Polar Acidic your proteins and amino acids could be
• 2 carboxyl and one amino group. 2nd carboxyl categorized based on chirality
group being part of the side chain. • All the amino acid are chiral
• Negative charge ; lost H+
• Glycine is the only amino acid considered as
• 2 (aspartic and glutamic acid)
achiral
o Is the simplest amino acid
c. Polar Basic
• One carboxyl and two amino group. 2nd • Alanine- side chain is the methyl group (CH3)
amino group is a part of the side chain • Proline is not considered as a true amino acid
• Positive charge ; accept H+ instead it is considered as imino acid. It is
• 3 (lysine, arginine, histidine) because of the cyclic chain
o Propyl group as the side chain in Proline,
Single-letter Abbreviation Full name however the side chain is bonded on both
code alpha carbon and to the nitrogen of the
A Ala Alanine amino group it gives a cyclic side chain
R Arg Arginine • Imino acid – carbon bonded to a nitrogen and a
N Asn Asparagine
carbon to carbon bonded to a carboxylic group
D Asp Aspartic acid
C Cys Cysteine
Q Gln Glutamine
E Glu Glutamic acid
G Gly Glycine
H His Histidine
I Ile Isoleucine
L Leu Leucine
K Lys Lysine
M Met Methionine
F Phe Phenylalanine
P Pro Proline • Phenylalanine- is a non-polar
S Ser Serine • Tyrosine and Tryptophan – is known as the
T Thr Threonine npolar neutral
W Trp Tryptophan • If the benzene is used as the side chain, we call
Y Tyr Tyrosine it as phenyl
V Val Valine • Tryptophan- it is actually considered as a
border line member of a non-polar
o It contains indole ring as it side chain
o Has a specific test to identify the tryptophan
15
 Aspartic acid Asp D negative
Glutamic acid Glu E negative
Arginine Arg R positive
Lysine Lys K positive
Histidine His H positive
POLAR AMINO ACIDS
(hydrophilic)

Asparagine Asn N uncharged polar

Glutamine Gln Q uncharged polar
Serine Ser S uncharged polar
Theonine Thr T uncharged polar
Tyrosine Tyr Y uncharged polar
NONPOLAR AMINO ACIDS
• It is also known as polar neutral (hydrophobic)
• Serine – contains hydroxy methyl
• Cysteine (Thiol) – is the derivative of
alcohol, instead of oxygen a sulfur is bonded AMINO ACID SIDE CHAIN
to a hydrogen Alanine Ala A nonpolar
• Asparagine and Glutamine- related to polar Glycine Gly G nonpolar
acidic amino acid Valine Val V nonpolar
• Cysteine and Methionine have a sulfur in Leucine Leu L nonpolar
their structure Isoleucine Ile I nonpolar
Proline Pro P nonpolar
Phenylalanine Phe P nonpolar
Methionine Met M nonpolar
Tyrtophan Trp W nonpolar
Cysteine Cys C nonpolar
NONPOLAR AMINO ACIDS
(hydrophobic)

ESSENTIAL AMINO ACIDS

• Aspartate and Glutamate – the reason they
are acidic because of their carboxyl in their
structure
• Aspartate – the side chain is acetic acid
• Glutamate – the side chain is propanoic acid
• 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.
• 10 out of 20 There are 10 essential amino
acids
• 9 essential amino acids for adults
• 10th amino acids are for the children growth

Proteins are made up of about 20 common amino

• Histidine – the side chain is imidazole
acids. The first column lists the essential amino
acids for human beings (those the body cannot
make – that must be provided in the diet). The
second column lists the nonessential amino acids I
special cases, some nonessential amino acids may
become conditionally essential (see the text). In a
newborn, for example, only five amino acids are
truly nonessential; the other nonessential amino
acids are conditionally essential until the metabolic
pathways are developed enough to make those
amino acids in adequate amounts.

16
 Try THis VIP MALL

Essential Amino Acids Nonessential Amino Acids

Histidine (HISS-tuh-deen) Alanine (AL-ah-neen)
Isoleucine (eye-so-LOO-seen) Arginine (ARJ-ih-neen) Arginine
Leucine (LOO-seen) Asparagine (ah-SPAR-ah-geen) Essential only for
Lysine (LYE-seen) Aspartic Acid (ah-SPAR-tic acid) children not for adults
Methionine (meh-THIGH-oh-neen) Cysteine (SIS-the-een)
Phenylalanine (fen-il-AL-ah-neen) Glutamic acid (GLU-ta-mic acid)
Threonine (THREE-oh-neen) Glutamine (GLUE-tah-meen)
Tryptophan (TRIP-toe-fan) Glycine (GLY-seen)
(TRIP-toe-fane) Proline (PRO-leen)
Valine (VAY-leen) Serine (SEER-een)
Tyrosine (TIE-roe-seen)

CHIRALITY
Acid-Base Behavior of Amino Acids
Amino acids exist as a zwitterion: a dipolar ion
having both a formal positive and formal negative
charge (overall charge neutral).

• 19 out of 20 have a chiral center

• They can exist as left or right-handed forms
pKa ~ 5 pKa ~ 9
TWO ENANTIOMERS POSSIBLE FOR MOST
AMINO ACIDS
• Zwitterion it is a German term which means
double ion because it considered as di-polar ion
there is positive and negative charges both of the
same molecule in amino and carboxyl group
• There is no net charge
• Negative charge – carboxyl
• Positive charge – amino group

Amino acids are amphoteric: they can react as

• The side chain and COOH is always at a
vertical position
• Hydrogen and NH3 they are always in a
horizontal position
• The one that we check for the handedness or
the enantiomer’s we check for the amino
group position or the NH3
• For amino acid the naturally occurring
proteins or amino acid are always in form of
L-form or left
• Amino group can also represent as NH2
• Bacteria have dextro or right-handed amino
acid
either an acid or a base. Ammonium ion acts as an
acid, the carboxylate as a base.
Isoelectric point (pI): The pH at which the amino
acid exists largely in a neutral, zwitterionic form
(influenced by the nature of the sidechain)
acidic amino acid
• Aspartate - 2.77ph
• Glutamate - 3.22ph
Basic amino acid
• Arginine – 10.76ph
• Lysine – 9.74ph (basic)
• Histidine – 7.59ph (slightly basic)

17
 PEPTIDES - the chain covalently link of the amino acid
Amino Acid + Amino Acid --> Dipeptide Amino Acid + Dipeptide --> Tripeptide

A.A. + A.A. + …..+ Tripeptide --> Polypeptide

• Oligopeptide: 10-20 amino acid residues

• The linkage the amino group and the carboxyl group of the amino acid to form your peptide bond
• Every peptide has the N-terminal end (left side) and also C-terminal end (right side)
Amino group Carboxyl group

DIPEPTIDE Alanine Phenylalanine Condensation

Water is liberated during the process because of condensation

Amino acid residues

It’s the portion of amino
acid structure that remains
after the water is release

18
POLYPEPTIDE – unbranched

Di sulfide bonds
Di sulfide bond - Responsible for the hardness of the
We can only see the
keratin (nails and hair)
di-sulfide branch in 2
Cysteine in amino acid

Protein Classification Based on Chemical

Composition
1. Simple protein- A protein in which only amino
acid residues are present:
• More than one protein subunit may be present
but all subunits contain only amino acid
2. Conjugated protein- A protein that has one or
more non-amino acid entities (prosthetic groups)
present in its structure: Organic – lipid and carbohydrate
• One or more polypeptide chains may be present Inorganic – metals
• Non-amino acid components- may be organic or
inorganic – prosthetic groups Proteins- 40 amino acid residues to be
o Lipoproteins; Glycoproteins; considered as protein
Metalloproteins

Levels of Organization
• Primary structure
o Amino acid sequence of the protein

• Secondary structure
o H bonds in the peptide chain backbone
▪ -helix and -sheets

• Tertiary structure
o Non-covalent interactions between the R groups
within the protein

• Quaternary structure
o Interaction between 2 polypeptide chains

STRUCTURE OF PROTEIN
• PRIMARY STRUCTURE
The first protein that was sequenced and determine
o Primary structure of protein refers to the order
is the insulin
in which amino acids are linked together in a
protein
Example:
o Every protein has its own unique amino acid
M-E-R-R-Y
sequence
(Methionine-glutamic acid-Arginine-Tyrosine)
▪ Frederick Sanger (1953): Sequenced and
determined the primary structure for the
first protein

19
 • SECONDARY STRUCTURE Beta-pleated sheet
- Refers to the regular geometric pattern • Example is the globular protein
along a polypeptide brought about by • Completely extended amino acid chains
hydrogen bonding • H-bonding between two different chains- inter-
- Two Arrangements and/or intramolecular
- Alpha – helix • Side chains below or above the axis
- Beta – pleated sheet

TERTIARY STRUCTURE
- Refers to the three-dimensional folding of
polypeptide to form a complex molecular shape
- Globular irregular ball shape form

Example: Chain B of Protein

Kinase C

• QUATERNARY STRUCTURE
- Refers to the organization among the various
Alpha-helix peptide chains in a multimeric protein:
• Example is fibrous proteins - Highest level of protein organization
• A single protein chain adopts a shape that - Present only in proteins that have 2 or more
resembles a coiled spring (helix): polypeptide chains (subunits)
• H-bonding between same amino acid chains- - Subunits are generally independent of each
intramolecular other- not covalently bonded
• R-group outside of the helix- not enough room for - Proteins often referred to as oligomeric
them to stay inside proteins
- Contain even number of subunits
- Some proteins are made of several polypeptide
subunits.
- (e.g. hemoglobin has four)
- 2 alpha and 2 beta chain

Protein
Kinase C

Myoglobin

20
Fibrous proteins Collagen
• Tend to have simple, regular, linear structure • Is the most abundant protein in humans
• Tend to aggregate together to form • Rich in proline -> (imino acid) 20% of collagen
macromolecular structures made up of proline
• (e.g. hair, nails)
• Involved in structure: tendons, ligaments, blood Keratin
vessels and skin • 30%
(e.g. collagen and keratin) • Hydrophobic amino residues
• Contractile proteins in movement: muscle, • Cysteine
microtubules
(cytoskeleton, mitotic spindle, cilia, flagella) • NUTRIENT: ovalbumin (in eggs), casein (in
milk), zein (in maize)
Globular proteins
• Protein molecule with peptide chain that are
• most proteins which move around (e.g. albumen,
casein in milk) folded into either sphere or globular
• Proteins with binding sites: • Enzymes – that the largest type of protein
o enzymes, haemoglobin, immunoglobulins, • BUFFER: hemoglobin
membrane receptor sites

• Hemoglobin- oxygen carier molecule in blood; • Hemoglobin – is responsible for transporting the
transports O2 from lungs to tissues oxygen
o Tetramer: 4 peptide chains (each subunit has
a heme group)
o has 2  globin subunits and 2  globin
subunits

• Myoglobin- oxygen storage molecule in muscles; • The myoglobin has a higher affinity for oxygen
binds one O2 molecule than hemoglobin
o Monomer: single peptide chain with one
heme unit

PROTEIN FUNCTIONS • Denaturation - There is a complete disorganization

• Protein structure determines protein function
or partial disorganization of your protein structure
• Denaturation or inhibition which may change
• Protein are being denature if the are subjected in
protein structure will change its function
high temperature
• Coenzymes and cofactors in general may enhance
the protein's structure

Proteins classified by function • Enzymes – are used to speed up the reaction

• CATALYTIC: enzymes • Example of immunoglobulin (antibodies): IgG,
• DEFENSE/PROTECTIVE: Immunoglobulin, IgM, igA, IgE, IgD
fibrinogen, blood clotting factors o Past or chronic – IgG
• TRANSPORT: haemoglobin, transferrin, HDL, o Recent/acute- IgM
LDL • Fibrinogen
• MESSENGER/COMMUNICATION: hormones (eg o clotting factor 1
insulin) and neurotransmitters o They are responsible of formation of the clot to
• CONTRACTILE: actin, myosin, dynein (in stop bleeding
microtubules) • Transferrin – main protein of the blood that binds
• STRUCTURAL: cell membrane proteins, keratin the iron from liver to bone marrow
(hair), collagen • HDL and LDL – lipoprotein they are the carry the
• TRANSMEMBRANE cholesterol in the blood stream (high and low
• STORAGE: myoglobin
density)
• REGULATORY: insulin
• Transmembrane - responsible for the passage of the
molecules
• Insulin is the only hormone that could lower
21 the
blood glucose level
• FLUID BALANCE: albumin and globulin • The oxygen concentration or the saturation of
• TOXINS: snake venom oxygen place a role on the buffer system of the
body which is the bicarbonate buffer system
• Oxygen saturation – to make sure that are blood
ph is normal (7.35-7.45)
• Liver function: albumin and globulin

Peptides: A Variety of Functions

• Hormones and pheromones
• Sex peptide – is responsible for the how the
– insulin (think sugar)
opposite sex of the certain specie or organism is
– oxytocin (think childbirth)
attracted to its partner
– sex-peptide (think fruit fly mating)
• Neuropeptides
– substance P (pain mediator)
• Antibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)
• Protection, e.g., toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)

Proteins are:
• Polypeptides (covalently linked -amino acids) +
possibly:
o cofactors
− functional non-amino acid component
− metal ions or organic molecules
o coenzymes
− organic cofactors • NAD – nicotinamide adenine dinucleotide
− NAD+ in lactate dehydrogenase o Always utilize in most of the biochemically
o prosthetic groups processes
− covalently attached cofactors • Prosthetic groups – metal ions
− heme in myoglobin
o other modifications
− example: have metal ions or carbohydrates
and lipids

22

CHARACTERISTICS
• Occur frequently in nature
• Solubility: marginally soluble in
water, soluble in organic solvents
• Lipids provide a major way of storing the
chemical energy and carbon atoms in our body
• Example of their function is they are possible
for thermal regulation so individuals with
more fat in their body or lipocytes must
regulate the body temperature
• As well as it can also be used for protection
from mechanical shock
• Lipids is primarily composed of mostly carbon
in hydrogen bonds
• The defining parameter for lipids is solubility
rather than the structure the reason why is
because the structure of lipids is diverse
• Lipids it plays a role of storing the chemical
energy, it’s a rich source of energy and it has an
efficient way to store in the body the excess
calories
• Lipids also it provides or it plays a variety of
biologic roles it could also provide the
structure example in cell membrane and also
to furnish biochemical energy

CLASSIFICATION • Hydrophilic (water-loving) it could be

• Open-chain compounds with polar head groups and
long nonpolar tails (fatty acids, triacylglycerols,
sphingolipids, phosphoacylglycerols, glycolipids)
• Fused-ring compounds or closed chain ring (steroids
e.g. cholesterol)
• Hydrophobic (water-heating) it is insoluble
soluble in water when its open-chain
compounds with polar head groups
Example of open-chain compounds
o Fatty acids – the simplest lipid class
o Triacylglycerols also known as
triglycerides
o Phosphoacylglycerols also known as
phospholipids
in water when it’s a long non-polar tail

CLASSIFICATION BY FUNCTION 1. Energy storage lipids

1. Energy storage lipids • Triacylglycerol (TAG) – the most abundant
2. Membrane lipids fatty acids
3. Emulsification lipids 2. Membrane lipids
4. Messenger lipids • Sphingoglycolipids
5. Protective-coating lipids
• Phospholipid
• Cholesterol
3. Emulsification lipids
• Bile acids it emulsifies the fats
4. Messenger lipids
• Steroid hormones
• Eicosanoids
5. Protective-coating lipids
• Biological waxes

23
SAPONICATION CLASSIFICATION 1. Saponification lipids
1. Saponification lipids • Energy storage
Converted into smaller molecules when • Membrane lipids
hydrolysis occurs • Protective-coating lipids
2. Non-saponification lipids
Cannot be broken into smaller units since they do 2. Non-saponification lipids
not react with water • cholesterol
• Emulsification lipids
• Messenger lipids

Complex lipids
CLASSIFICATION BY STRUCTURE • Aside from the lipid itself, they have
1. Simple lipids (fats and waxes) organic molecule that is bonded to the
2. Complex lipids lipids structure
3. Steroids o phospholipids
4. Prostaglandins, thromboxanes, leukotrienes o glycolipids
o lipoprotein

LIPID TYPES • Characterized as:

FATTY ACIDS – simplest lipid class
• Carboxyl group at the polar end and a
hydrocarbon chain at the nonpolar tail
• Amphipathic – both hydrophilic and
hydrophobic
• Saturated fatty acids – single bond
• Unsaturated fatty acids – double bond
• Monounsaturated – has single double bond
• Polyunsaturated – 2 or more double bonds
• Nearly always contain an even number of carbon
atoms and have a carbon chain that is
unbranched
o Long-chain - >12 (12-16)
o Medium-chain – 8-10
o Short-chain – 2-6 even number
Fatty acids
• It’s known to be naturally occurring
monocarboxylic acid
• One could be functional group that could be
found in the structure is carboxylic acid
(COOH) can react to water to form
hydrogen bonds
• It could be classified based on the number
of double bonds
Unsaturated fatty acids are known to be
dehydrogenated because once they undergo
hydrogenation

Dietary Fatty acids usually have the carbon

chain size is 4-24 carbon atoms they are known
to be straight-chain compounds

• For the size of the carbon chain could actually

related to the water solubility of the fatty
acids
• For its relation as the carbon chain length
increases the water solubility decreases

• Long-chain – insoluble to water

• Short-chain – slightly/marginally soluble to
water

• For the relationship of the solubility of water

of carbon-chain length it is inversely
proportional

24
 SATURATED FATTY ACIDS

Number Melting
Acid of Formula point
Carbon (°C) Saturated fatty acids
Atoms
• solid at room temperature
Lauric 12 CH3(CH2)10COOH 44
• Straight chain
• There have a carboxylic acid and hydrocarbon
Myristic 14 CH3(CH2)12COOH 58
• The relationship of melting point and carbon-
chain length is directly proportional, when
Palmitic 16 CH3(CH2)14COOH 63
carbon chain increases, melting point is also
increasing
Stearic 18 CH3(CH2)16COOH 71
• Usually found in animal source
Arachidic 20 CH3(CH2)18COOH 77

Unsaturated fatty acids

UNSATURATED FATTY ACIDS • Liquid at room temperature
• The degree of unsaturation we have to
Number Melting consider that in melting point of unsaturated
Acid of Formula point fatty acids. The relationship of the two they
Carbon (°C) are inversely proportional
Atoms • The higher degree of unsaturation then the
Palmitoleic 16 16:1 - 9 -0.5 lower melting point has
• Mostly they are from plant source
Oleic 18 18:1 – 9 16 • The healthier one is the unsaturated fatty
acids it makes easily broken down by the body
Linoleic 18 18:2 – 9,12 -5
first number- represents the number of carbon
Linolenic 18 18:3 – -11 atom
9,12,15 after the colon – number of double bonds
last number – position/location of double bonds
Arachidonic 20 20:4 – -11
5,8,11,14 • the term that we used to specify the location
of double bond is delta
• function of fatty acid is the building blocks of
Unsaturated fatty acids will be converted to triglycerides and phospholipids
saturated fatty acids o also sources of metabolic energy

Oleic- only have a single bond

cis – same side of double bond

trans – opposite or across

25

TRYGLICERIDES – (UFA)
• Animal fats and plant oils
• Triester of glycerol and long chain of
carboxylic acids called fatty acids.
PHOSPHOACYLGLYCEROLS (PHOSPHOLIPIDS)
• Two fatty acids are esterified to the glycerol
molecules → phosphatidic acid
• Component of biological membrane
One phosphoric acid can form ester bonds both to
glycerol and to some alcohol
B D-Galactose
• on relation of the fatty acids that could be
found on its structure
• other term is triacylglycerol
• there are three fatty acid are present and a 1
glycerol
• ester – linkage bond between the glycerol and
fatty acids
• role:
o can be part of the cell membrane
o storage form of the lipids
• energy storage lipid – the most abundant
type of lipid
• most of triglycerides are from plant sources
o example: corn and sunflower seeds
• In room temperature most of them or typically
In liquid state, they are in form of oils
• Neutral lipid because it has no charge or polar
hydrophilic group meaning its water
insoluble for hydrophobic
• Structurally similar to triglycerides
• 2 fatty acids and phosphate group
• Also known as phosphoglyceride
• Since its charge group it could interact with
water it has a polar and non-polar end
• ester – linkage bond
• esterification – alcohol and carboxylic acid
react to form ester (ROR)
• The most abundant type of membrane lipid
• 80% of mass of a cell membrane
• Amphipathic
• Polar or the charge portion is the hydrophilic
and the non-polar is the hydrophobic is the
non-charge is the fatty acids
26
 WAXES • Fatty acids could be found is saturated fatty
• Lipid that is a monoester of long-chain acids and 14-36 carbon atoms
carboxylic acids and long chain alcohols • alcohol – unsaturated or saturated and 16-30
• Protective coatings for both plants and animals carbon atoms
• They are saponifiable
Sphingolipids
• Do not contain glycerol but contain long-chain
amino alcohol sphingosine
• Abundant in nervous system
• Ceramides- consist of one fatty acid linked to • Sphingosine – is abundant in nervous system
the amino group of sphingosine by an amide • Amide bond – linkage bond
bond
• Amino group of sphingosine can from an amide
bond with a FA carboxyl

ceramide

Sphingomyelin
Common constituents of plasma membranes

GLYCOLIPIDS • Its sugar containing lipid

• Carbohydrate is bound to an alcohol group of a • Glycosidic linkage bond
lipid by a glycosidic linkage • Cerebroside
• Cerebroside (primary alcohol of ceramide + o the simplest glycolipid
sugar residue) o single monosaccharide unit either galactose
• Gangliosides or glucose
o glycolipids with complex sugars • Gangliosides
o Often found as markers on cell membranes o It could be branched of up to 7
and play a large role in tissue and organ monosaccharides residues
specificity o Major lipid of cell membrane of the brain
and central nervous system

27
Glycosphingolipids
Cerebroside
STERIODS – (UFA)
• A fused-ring containing 3 six membered rings
and 1 five membered ring
• Cholesterol – unsaturated steroid alcohol
o hydrophilic group – OH (single)
o Hydrophobic
o Precursor of other steroids and of Vitamin D3
however it is best known for its harmful
effects
Cholesterol
Important constituents of cell membranes
• Decreases the mobility of hydrocarbon tails of
phospholipids
• Interferes with the closely packing of FA tails in
the crystalline state thus inhibits transition to
the crystal state
• Phospholipid membranes with high conc. of
cholesterol have a fluidity intermediate between
crystal and crystal state.
• Hydroxyl group on the aqueous side while the
ring is towards the FA chains of phospholipids.
• OH group of cholesterol forms H bond with the
polar phospholipid head groups.
Cerebroside and Ganglioside
• 7% of dry mass of the brain is cerebroside
• Present in myelin sheet of nerve
•Also known as steroid nucleus
•important constituent of cell membrane
•ester – linkage bond and 1 fatty acid
•cholesterol
o found exclusively in animals
o is the most abundant steroid in the body
o has 27 carbon atoms
o alcoholic group is found in the carbon 3 of
steroid nucleus
o a waxy material could form a platelike crystal
o responsible for the fat that are being deposited
on the lining of your blood vessel which is
known as plaque it plays a role in the plaque
formation
o The condition wherein plaque condition is
atherosclerosis the one being responsible is
the cholesterol
different functions
o use for manufacture and repair of the cell
membrane
o for synthesis for bile acids and vitamin D3
what is the function of bile acid based on its
function? It is emulsification
• bile acid is synthesis in the liver
• example of bile acid is cholic acid
pre-courser of 5 major classes of steroid
hormones
• androgens
• estrogens
• glucocorticoids
• mineralocorticoids
• progestin
unsaturated of the one that we are referring to is
the steroid nucleus
how the cholesterol convert to cholic acid through
the help of hepatic enzyme but the example of is
hepatic lipase 28
Lipid Soluble Vitamins
Vitamins A • unsaturated hydrocarbon
• Β carotene it has a double and triple bond on its structure
o unsaturated hydrocarbon
o Precursor of vitamin A (retinol) opsin
• A derivative of Vit A plays a crucial role in • universal photo receptor molecules
vision when it is bound to a protein called • visual system for animal kingdom
opsin • light sensitive and it is found on the retina

Vitamin D
• Major role in regulation of calcium and
phosphorus metabolism
• Vitamin D3 (cholecalciferol) formed from
cholesterol by the action of UV from the sun
o Further processed in the body to
hydroxylated derivatives
o Presence of Vit D3 leads to increase
synthesis of a Ca2+ binding protein,
increases absorption of dietary calcium in
the intestines → inc calcium

Vitamin E
• α-tocopherol is the active form
• Antioxidant – good reducing agent • a-tocopherol is the most biologically active
• It reacts with oxidizing agents before they can form of Vitamin E
attack other biomolecules
• Reacts with free radicals

Vitamin K
• Comes from the German word “Koagulation”
because it is an important factor in the blood- • Vit K dependent –Factors II, VII, IX, X
clotting process • Vitamin K is other term for Phytonadione
• Requirement to modify prothrombin and other
proteins involved in the clotting process

EICOSANOIDS
• Messenger lipid; oxygenated C20 fatty acid
derivative
• It has 4 double bonds have the arachidonic
• Metabolic precursor is arachidonic acid
acid and poly unsaturated fatty acids
• Almost all cells produce eicosanoids
• Exception is the red blood cells
• Physiological effects of eicosanoids include
mediation of:
o Regulation of blood pressure
o Production of pain and fever
o Inflammatory response
o Induction of blood clotting
o Control of reproductive functions
o Regulation of sleep/wake cycle

29
PROTAGLANDINS
• Metabolic precursor is arachidonic acid
• Dense tubular system of platelets • It has a cyclopentane ring and it has an oxygen
• Functions: containing functional group
o Control of blood pressure • It was named after the gland human’s body it is
o Stimulation of smooth muscle contraction the prostate gland
o Induction of inflammation
o Raise body temperature
o Inhibit the secretion of gastric juices

LEUKOTRIENES
• Found in leukocytes and have 3 conjugated
double bonds
• Constriction of smooth muscle • It also has hydroxyl group on its structure
• Inflammatory properties • Inflammation and hypersensitivity (allergy)
• Maybe involved in rheumatoid arthritis

THROMBOXANE
• Derivative of arachidonic acid
• Contains cyclic ethers as part of its structure • It has cyclic ether ring and oxygen containing
• Thromboxane A2 is the most widely studied, is final group
known to induce platelet aggregation and
smooth muscle contraction • Aspirin: known to be blood thinner

30
 NUCLEIC ACIDS
• Unbranched polymer in which a monomer unit
is a nucleotide
• Nucleic Acid it was actually discovered
• Nucleotide- is a three-subunit molecule in
while Friedrich Miescher (1869) was
which a pentose sugar is bonded to both
studying the nucleus of the wbc, since the
phosphate group and nitrogen-containing
wbc or the nucleus of the cell was said to be
heterocyclic base
acidic and it was then discovered that the
ph of the nucleus its because of the nucleic • If your protein has amino acid as its
acid that was found inside it. monomer unit or its building block
• The building block of nucleic is nucleotide
TYPES OF NUCLEIC ACID • Your cell in an organism are have exact
• DNA replicas, they have information on how to
o Found within the cell nucleus and small make a new cells and those information are
amounts in mitochondria stored on the nucleic acids Specifically, we
o Storage and transfer of genetic information have DNA for genetic information
• Nucleic acid or the DNA are found in the
• DNA is passed from existing cells to new cells
nucleus and are acidic in nature
during cell division.
• DNA is replicated during the cell cycle.
Nucleotide
Specifically, during S phase of interphase.
• Pentose sugar 5 carbon atom is found on
Replicated DNA is the one passed from
the sugar unit
existing cells to new cells during cell division.
o RNA – Ribose
• Double stranded
o DNA - Deoxyribose
• Heterocyclic base and also known as
nitrogenous bases
• RNA
o Occurs in all parts of a cell.
o 90% in cytoplasm and 10% on nucleolus
o Synthesis of proteins

• 90% in cytoplasm because ribosomes contain

RNA in their structure where in there are
free ribosomes in the cytoplasm as well
as ribosomes that are attached in the rough
endoplasmic reticulum
• 10% in nucleolus because they synthesis
some of the RNA
• RNA is translated to form amino acid and
once you have a sequence of the specific
amino acid, it could produce proteins coded Contains deoxyribose
based on the amino acid sequence
• Single stranded

• One of the microorganisms are classified
based on the type of the nucleic acid that
could be found inside them
• Viruses they could be classified whether they
have DNA or RNA
• Example is the corona virus is a single
stranded RNA virus
PENTOSE SUGAR
• First sub-unit of nucleic acid and are the bases
of the name of your nucleic acid types
• The sugar unit of nucleotide is either pentose
ribose or pentose 2’-deoxyribose

31
 Beta D- deoxyribose Beta D- ribose
• The highlighted side chains make it your
ribose different from your deoxyribose
• The only difference between the two sugar
units is the side chain which is found on the
carbon 2 of both sugar units
• Based on the name of deoxyribose, you might
figure out what it is that he doesn’t have that
the ribose has and that is oxygen. Purine
• Hayworth projection is used. (Cyclic form is
used)
NITROGEN-CONTAINING HETEROCYCLIC Pyrimidine
BASE (BASES)
• Purine – a bicyclic base with fused five and
six- membered rings
• Pyrimidine – a monocyclic base with a six-
membered ring
• The reason why they are known to be bases
it’s because of the specific functional group
that is found on their structure
• Amine group (NH2) this functional group is
the reason why nitrogenous bases exhibit
basic behavior meaning they could accept
protons and hydrogen ions
• Purine has 2 types of bases while the
Pyrimidine has 3 types of bases however, not
all pyrimidine bases could occur on both DNA
and RNA there is specific base
• Adenine and Guanine, they could occur
in both DNA and RNA
• N9 – bond with sugar unit during the
nucleotide
• Cytosine the only side chain has the
NH2 on its structure
• Uracil and Thymine they have almost
similar structure except that the
Thymine has methyl on its structure
• Not all pyrimidine could occur or found
in DNA and RNA
• Uracil can only occur on RNA and also
known as unmethylated thymine
• Thymine could only be found on DNA
• Cytosine can also occur in both DNA
and RNA
• N1 - bond with sugar unit during the
nucleotide
PHOSPHATE
It will bond on sugar
to form nucleotide
32
 • Third component of the nucleotide from the
Phosphoric acid which is H3PO4 it loses two
hydrogen atoms and then giving off what we
called now the hydrogen phosphate ion
Nucleotide Formation
1. Condensation, with formation of water molecule
between sugar-base and sugar-phosphate
2. Base – C-1’ of sugar. For purine base (N-9),
pyrimidine (N-1); sugar and base (β-N)
glycosidic linkage
3. Phosphate to sugar (C-5’) phosphate-ester
linkage
• In nucleotide the reaction involve for the
formation of nucleotide is the condensation
• There are also macro molecules where in the
reaction involve to form their linkages is also
condensation
• Proteins, to form the peptide chains it utilizes
the reaction condensation to form what we
called the peptide bonds
• During the reaction water molecule is yield
and also, the carbohydrates for the glycosidic
linkage
Adenosine
Nucleoside
• Prior to the formation of your nucleotide
which a three sub-unit molecule the
nucleoside is formed first
• Sugar unit – ribose
• Nitrogenous base – adenine
In naming the nucleoside the first thing that
you need to do is to check if the sugar unit is
ribose or deoxyribose
Deoxycytidine
• Sugar unit – deoxyribose
• Nitrogenous base – cytosine
• if the sugar unit is deoxyribose, we used
prefix deoxy
• if the sugar unit is ribose there is no
prefix
• Purine -osine
Adenine – Adenosine
Guanine – Guanosine
• Pyrimidine – idine
Cytosine – Cytidine
Uracil – Uridine
Thymine - Thymidine
Nucleotide Formation
Deoxyadenosine
• Once we are done in nucleoside, we could
now form the nucleotide, to form the
nucleotide we need the sub-unit of
phosphate group, for the phosphate group
it is bonded in the nucleoside
• The nucleotide is sequencing at 5’ → 3’
meaning the leading strand or the
arrangement of nucleic acid will always
start at 5’ and it ends at 3’
• 3’ can only be seen after the formation of
the nucleotide sequence to from the nucleic
acid but, initially their always bonded at 5’
• Since the phosphate group could be bond
also to the carbon 3 of another sugar unit
we have what we called phosphodiester
bond.
• For the primary nucleic acid structure, you
had the sequence in which molecules are
link together in a nucleic acid, it depends on
the sequence bases it usually depends on
the sequence of bases present 33
 MONONUCLEOTIDES

• are nucleosides in which single monophosphate Comparison of the General Primary

group is attached to hydroxyl group of the Structures of Nucleic Acids and Proteins
pentose sugar. • Backbone: -Phosphate-Sugar- Nucleic acids
• Ex. AMP= adenine + ribose + phosphate • Backbone: -Peptide bonds – Proteins

• 2 phosphate groups = nucleoside diphosphate

• 3 phosphate groups = nucleoside triphosphate
Nucleoside + prefix for the no. of phosphate
group + phosphate

A- Represents the nucleoside name

M- represents the prefix

Example:
• Deoxyribose + guanine + 2 phosphate
Deoxyguanosine diphosphate = dGDP
DNA Structure and Function
• Ribose + uracil + 3 phosphate • Serves as genetic material for cells both
Uridine Triphosphate= UTP prokaryotes and eukaryotes
• In eukaryotes
o Located in the nucleus separated from the
cytoplasm by the nuclear membrane.
• In prokaryotes
o DNA is not separated from the rest of the
cellular contents they are known to be
nucleoids which are scattered on the
cytoplasm
• Chromatin
o Complex of eukaryotic DNA bound to
proteins
Base Ribonucleoside Ribonucleotide
Adenine Adenosine Adenosine Structure of DNA
monophosphate
Guanine Guanosine Guanosine • DNA is a very long, thread like macromolecule
monophosphate made up of a large number of
Uracil Uridine Uridine deoxyribonucleotides (N+S+P)
monophosphate • Base of DNA molecule
Cytosine Cytidine Cytidine o Carry genetic info
monophosphate o Purine (A and G)
BASE Deoxy Deoxyribonucleotide o Pyrimidine (T and C)
nucleoside • Sugar and phosphate groups
Adenine Deoxyadenosine Deoxyadenosine o Structural role
monophosphate o Deoxyribose
Guanine Deoxyguanosine Deoxyguanosine
monophosphate • N- Nitrogenous base
Cytosine Deoxycytidine Deoxycytidine • S – sugar
monophosphate • P- Phosphate group
Thymine Deoxythymidine Deoxythymidine
monophosphate NSP is the sub-unit of the nucleotide

34

• B form of DNA (B-DNA) which is a right-
• A-DNA and Z-DNA
• Under physiologic conditions, almost entirely
• Thee 3’ → 5’ strand it compliments your 5’ → 3’,
so the leading strand is the 5’ → 3’, while your
3’ → 5’ strand it is the complimentary strand.
• Complimentary strand it has bases and they are
paired on bases that they are found on 5’ and 3’
strand.
• We call them as Antiparallel strands they ran
at the opposite direction it compliments the 5’
and 3’ strand
• For the DNA molecule it is composed of two
strands which are held together by your
hydrogen bonds
• The one that binds the two strands of DNA is
hydrogen bond
• For the hydrogen bonds are found on the bases
• Complimentary bases they are pair of bases
that are held together y hydrogen bond.
• In a DNA sequence we write the sequence using
the first letter of the bases
• The broken lines it represents the number of
hydrogen bonds that are found on the
complimentary bases
• We always start at the 5’ and end at the 3’
Leading strand: 5’-A-G-T-A-C-G-3’
Complimentary strand: 3’-T-C-A-T-G-C-5’
A-T- 2 hydrogen bonds
C-G - 3 hydrogen bonds
C-A - 1 hydrogen bond
G-T – 1 hydrogen bond
Watson-Crick DNA Double-Helical Structure
• Hydrogen bonds
o held the chains
o adenine and thymine
• 2 H bonds
o Guanine and cytosine
o 3 H bonds
• In DNA structure, the content of A is equal to
that of T and the contents of G equals to that of
C. (Chargaff’s Rule)
handed helix of 10 pairs per turn, containing
grooves of alternate size known as major and
minor grooves.
B-DNA.
• The A and the B form of DNA are based on
the conformation/positioning of
deoxyribose sugar
In most cases, we have B form of DNA
• Francis Crick & James Watson these two
individuals are attributed to base
composition of patterns associated with the
DNA nucleus.
• The A and the B form of the DNA are based
on the confirmation of deoxyribose sugar
• Zigzag pattern is based on the
phosphodiester bond or linkage
• The backbone of DNA is the phosphodiester
linkage between sugar and phosphate
• group, that is why we have 5’ to 3’ – leading
strand, 3’ to 5’ – complementary strand
Chargaff’s Rule
• Was named after Erwin Chargaff
• In DNA structure, the content of A is equal to
that of T and the contents of G equals to that
of C.
• Watson and Crick deduced that A must pair
with T and G to C because of stearic and
hydrogen bonding factors.
• Thus, one member of a base pair in a DNA
must always be a purine and the other a
pyrimidine.
• Adenine and Guanine – Both purine
• Thymine and cytosine – Both pyrimidine
• Purine is always with pyrimidine
• The bases are located at the center and they
are known to be hydrogen bond
• In base composition, the ratio of bases is
always 1
• The percentage of adenine is equal to the
percentage of thymine
• Percentage of guanine is equal to percentage
of cytosine
• Example: 20 % A = 20 % T & 30 % G = 30 % C
= 100 % nucleic acid
35
 Function of DNA
• store genetic information
o source of information for the synthesis
of all protein molecule of the cell however,
it is not the one who directly produces the
proteins
o responsible in the information in
synthesizing protein but not directly
producing protein
o provides the information inherited by
daughter cells or offspring’s
o In cell cycle, DNA is being replicated in
interphase
o It only replicates one regardless of the cell
division (mitosis or meiosis), DNA
replication is only done once in a cell cycle
Comparison of DNA and RNA
Unlike double-stranded DNA, RNA is a single-
stranded molecule
• While DNA contains deoxyribose, RNA
contains ribose
• Complementary base to adenine is
not thymine, as it is in DNA, but rather uracil,
which is an unmethylated form of thymine
Flow of Biologic Information
(Central Dogma)
• DNA contains the genes that encode the
information for the synthesis of a protein
• Sequence of the bases in the DNA codes for the
sequence of the amino acids in proteins
• However, the DNA does not direct protein
synthesis.
• The genetic information in the DNA is decoded
in the form of messenger RNA, which is then
translated to Amino acid sequence of a protein
• Central Dogma is the backbone of molecular
biology without central dogma it will be hard
for us to check for the amino acids that could
be coded based on the genetic information
• DNA replication – duplicate exact copy of DNA
(genes passed from existing cell to new cell,
from parent cell to progeny or daughter cell)
• mRNA – messenger RNA translated in amino
acid
• Protein synthesis / production
• According to Francis Crick, this information
cannot be transferred from protein to either
protein or nucleic acid
• This dogma also includes the replication of DNA
• It may start from RNA to DNA, and RNA can also
be replicated
• backbone of molecular biology
Three Major Stages in Central Dogma
1. DNA Replication
• Produces two identical molecules
2. Transcription
• Genetic information in the DNA is copied
in mRNA.
• Sequence of the mRNA bases is the same
as that of the DNA
3. Translation
• Codons in the mRNA direct the sequence
of aa in the protein
Replication
DNA replication
• The doubling/duplication of DNA & occurs
during the interphase period of mitosis (S)
• Replicated only once
• If replicated from a single ori, with same rate
as bacteria, this would take over 150 hours
• DNA to be copied is fed through the proteins
of the replication factory
• The duplex DNA to be copied is first split into
single strands
• Each of the two template strands is copied and
becomes half of a new DNA double helix
(semi-conservative)
36
Function
o Region in the chromosome which is the
• Provision of progeny with the genetic
initiation point for DNA replication
information possessed by the parent
o Form a structure known as replication fork
• The daughter cells or offspring will get the
genetic information form the parent
Replication Enzymes

Proteins/Enzymes Function
Helicase Processive unwinding of
DNA

- split/unzipped the
double strand of DNA 2. Primase
into two • Binds the initiation point of the 5’-3’ parent
- first enzyme involved chain and synthesizes the RNA primer
in DNA replication • RNA primer
Topoisomerase Relieves torsional strain o Has the required 3’-OH end for the addition
that results from of a new nucleotide
helicase-induced
unwinding

- To relax the DNA

from local unwinding
Primase Initiate’s synthesis of
RNA primers

- will attached/bind in
the strands that are
split from the DNA 3. DNA Polymerase
DNA polymerase Polymerization of DNA
- polymer means
multiple
- responsible for the
elongation
Sliding clamp Anchors DNA
polymerase
Single-strand binding Prevents premature
proteins (SBB) reannealing of ssDNA
RNase H/DNA Removes RNA primers
Polymerase I (E. coli)
DNA Ligase Links short DNA pieces
together
4. DNA Polymerase I
General Steps in DNA Replication in
Prokaryotes
1. DNA Helicase
• Break the hydrogen bonds between bases of
5. DNA Ligase
the two anti-parallel strands resulting in the
unwinding of the helix
• Origin of replication
• Elongates the new DNA strand at a 5’-3’
direction using the 3’-5’ template
• 5’-3’ strand that proceeds to the direction of
the replication fork (leading strand)
• New strand using the 5’-3’ template is
synthesized in a discontinuous manner
(lagging strand)
• Okazaki fragment are the short DNA
fragments added.
o There are possible nicks that could be form
during the DNA replication
o Nicks – dent or gaps that could be found in
short DNA fragments – known as Okazaki
fragments
• Removes the primer in the lagging strand and
fill the gap with appropriate nucleotides
• If there are nicks that could be found in the
lagging strand, DNA polymerase will fill
necessary nucleotides
• Gaps between the Okazaki fragments are
sealed

37
 Replication
RNA
• Another type of nucleic acid
• Made up of unbranched chain of nucleotides
as in DNA
• D-ribose, U instead of T and single stranded.
• Instead of Thymine , Uracil is the pyrimidine
that is paired with/or complements the base
of adenine
TRANSCRIPTION
• Second step or stage of Central Dogma prior
to transcription, we have to unwind the
chromosomes which essential to allow RNA
polymerase to access the DNA
• Responsible to relax the DNA is the enzyme
topoisomerase, it removes the torsional
strain for your DNA
• Process by which the DNA directs the
synthesis of mRNA, it a two-step process
o First step is to synthesized heterogenous
nuclear RNA
o Second step is editing it to yield your
mRNA molecule
• Process of copying of a DNA template in the
form of RNA
• All RNA’s are synthesized using DNA template
• Process requires the enzyme RNA polymerase
o RNA polymerase can access the DNA it does
is it makes a complementary strand or it
complements the bases that are found on
the DNA
• For the transcription it unwinds the DNA
double-helix to expose the bases which are the
gene
• A gene it’s a segment of a DNA base sequence
responsible for the production of specific
hnRNA or mRNA molecules
• For the human genes has about 20,000 to 25,
000 thousand genes it makes up the genome
• Genome it’s the sum of all genes that are found
in an organism
• Most of the human genes they have about
1,000-3500 nucleotides units long
• RNA polymerase will catalyze the linkage of
ribonucleotides 1 by 1 to form the mRNA
DNA IS A DOUBLE STRANDED MOLECULE
Sense strand
• Codes for the sequence of the gene
• The bases or the nucleotides that are found
on the sense strand are the one which are
responsible for the sequencing of the gene
Anti-sense strand
• Opposite complimentary strand that is
used as the template for RNA synthesis
• RNA base sequence is identical with that of
the sense strand except for the presence of
U and T
• Instead of thymine which paired to
Adenine, Uracil will be used as the
complementary base for Adenine
TYPES OF RNA MOLECULES
Heterogeneous nuclear RNA (hnRNA)
• formed directly by DNA transcription
• During the post transcription processing the
hnRNA is converted into mRNA
• The process involved in converting the
hnRNA to mRNA is splicing
mRNA
• carries instructions for protein synthesis
• genetic information that came from the DNA
• the molecular mass of mRNA it depends to
on the length of proteins can produce
38
Small nuclear RNA (snRNA) hnRNA → mRNA
• facilitates the conversion of hnRNA to mRNA 3’ UAA GCA ACA – AAA GGG – UCA CGG 5’
• it contains little amount of nucleotides A B C D E
• 100-200 nucleotides
Ribosomal RNA (rRNA) mRNA (combined exons)
• Structural component of the ribosomes (sites 3’ UAA-ACA-AAA-CGG 5’
of protein synthesis)
• It is usually combined with a specific protein codon- will be translated into amino acid
the ribosomes are formed 5’ GGC-AAA-ACA-AAU 3’
• Ribosomes are known to be physical site for
protein synthesis anti-codon
• Molecular masses 3 million 3’ CCG-UUU-UGU-UUA 5’
Transfer RNA (tRNA)
• delivers amino acids to the site for protein amino acids: Gly-Lys-Thr-Asn
synthesis
• is known to be the smallest type of RNA example:
• it has 75-90 nucleotide units
5’ CGC – ATA TTA TAG GTA ACG AAA – CAT 3’
• It acts as what you called the anti-codon
A B C D E F

POST-TRANSCRIPTION PROCESSING: exons: B, D, E, F

FORMATION OF mRNA
C=G
• Involves conversion of hnRNA to mRNA A=U
• Splicing: Excision of introns and joining of T=A
exons
o Exon - a gene segment that codes for hnRNA → mRNA
genetic information 3’ GCG – UAU AAU AUC CAU UGC UUU – GUA 5’
o Intron – a DNA segments that interrupt a A B C D E F
genetic message
▪ The splicing process is driven by mRNA (combined exons)
snRNA 5’ AAU-CAU-UGC-UUU-GUA 3’
• Alternative splicing - A process by which
several different protein variants are codon- will be translated into amino acid
produced from a single gene 5’ AUG – UUU – CGU – UAC – UAA 3’
o The process involves excision of one or
more exons anti-codon
3’ UAC – AAA – GCA – AUG – AUU 5’
Splicing- we have first the leading strand coming
from the DNA amino acids: Met – Phe – Arg – Tyr – stop codon
Sequence of nucleotide – 5’ →3’
hnRNA- will act as the complementary strand
TRANSCRIPTOME
Example: • Transcriptome: All of the mRNA molecules that
Exons – A, C, E can be generated from the genetic material in a
Introns – B, D genome.
o Transcriptome is different from a genome
C=G o Responsible for the biochemical complexity
A=U created by splice variants obtained by hnRNA
T=A

5’ ATT CGT TGT – TTT CCC – AGT GCC 3’

A B C D E

39
 GENETIC CODE
• 1966, it was discovered
• Scientist are now able to predict characteristics
by studying DNA.
• Genetic code is the assignment of the 64 mRNA
codons to specific amino acids.
• Leads to genetic engineering, genetic
counseling.
• Codons – three nucleotide sequence in a mRNA
molecule that codes for a specific amino acid
• 61 codons amino acids
• 4 different bases (U,C,A,G)
• Stop codon is known to be termination codons
they are known as stop signal
• UAA, UAG, UGA are known to be stop codon
• AUG - the only start codon
• Marshall Nirenberg and Har Gobind Khorana
they were awarded for noble prize in chemistry
because they were able to know/illuminate how
the mRNA encodes for the proteins
ANTICODONS AND tRNA MOLECULES
• During protein synthesis amino acids do not
directly interact with the codons of an mRNA
molecule.
• tRNA molecules as intermediaries deliver
amino acids to mRNA.
• Two important features of the tRNA
structure
• The 3’ end of tRNA is where an amino acid is
covalently bonded to the tRNA.
• The loop opposite to the open end of tRNA is
the site for a sequence of three bases called an
anticodon.
• Anti-codon - a three-nucleotide sequence on a
tRNA molecule that is complementary to a
codon on an mRNA molecule.
TRANSLATION
• Protein synthesis
• Process by which the sequence of nucleotides
in an mRNA molecule directs the
incorporation of amino acid into protein
• The site of the protein synthesis is the
ribosome, ribosome is known as ribosomal
RNA protein complex wherein the ribosome
has 65% rRNA ; 35% protein by mass
(Ribosome- rRNA – protein complex)
FIVE STEPS OF TRANSLATION PROCESS
Activation of tRNA:
• addition of specific amino acids to the 3’-OH
group of tRNA.
• Bonded on the sugar unit
Initiation of protein synthesis:
• Begins with binding of mRNA to small
ribosomal subunit such that its first codon
(initiating codon AUG) occupies a site called
the P site (peptidyl site)
Elongation:
• Adjacent to the P site in an mRNA–ribosome
complex is A site (aminoacyl site) and the next
tRNA with the appropriate anticodon binds to
it.
Termination:
• The polypeptide continues to grow via
translocation until all necessary amino acids
are in place and bonded to each other.
Post-translational processing
• gives the protein the final form it needs to be
fully functional
TRANSCRIPTION-TRANSLATION
40
TRANSLATION

41
ENZYMES
• Catalyst that speeds up chemical reactions in
our cells by lowering the energy required for
the reaction.
• They are extremely effective, up to 1020 times
faster
• They are not consumed in the reaction
instead they just help in speeding up the
reaction itself
• Enzymes are the most effective catalyst are
known
• Most of them are globular proteins
• Enzymes are classified based on their
function (type of reaction where they are
involved) rather than their structure
• Specific – they will only react on certain
substance
• 1,500- 3,000 different enzymes
• Since enzymes are protein it could also
undergo denaturation
• Almost every reaction may cell require its
own specific enzymes (specific enzyme
reacts with specific substrate)
• Catalyst
o Substance that lowers the activation
energy of a reaction without being
changed itself
Example of enzyme:
• Hydrolysis of protein in our diet (trypsin or
pepsin)
• Carbonic anhydrase in blood
o 35M reactants in a minute
ENZYME STRUCTURE
2 General Structural Classes:
1. Simple Enzyme
An enzyme composed an only one protein
2. Conjugated Enzyme
• An enzyme that has a nonprotein part in
addition to protein part
• Apoenzyme – protein part, part of the
enzyme which lacks the cofactor
• its catalytically inactive and incomplete, it
needs a cofactor for it to react on a certain
substrate or substance (cofactor is needed
for it to be activated)
• Cofactor – non-protein part of
conjugated enzyme
• Hemp in making sure that apoenzyme will
be activated
• Cofactors will bind tightly or loosely with
the apoenzyme – cofactor convert
apoenzyme to holoenzyme apoenzymes
• Cofactors could either be small organic
molecules or coenzymes, inorganic ions
• Important for the chemically reactive
enzymes, it needs to be bonded to apoenzyme
to activate it
• Organic molecule cofactors they are known
coenzyme or co-substrate
• Inorganic ion cofactors – metal ion cofactors:
zinc, magnesium, manganese and iron and
non-metallic – chlorine
• Holoenzyme – biochemically active
conjugated enzymes. apoenzyme + cofactor
= holoenzyme
• Once cofactor is removed in apoenzyme
/holoenzyme, apoenzyme will be converted
back into inactive and incomplete
• A conjugated enzyme containing apoenzyme
and cofactor (inorganic ions or organic
molecules)
• Coenzyme – also known as co-substrate
• Organic molecule cofactors
• Derive from dietary vitamins
Nomenclature and Classification of Enzymes
• Enzyme could be named or classified based on
their function, reaction involved, substrate
where they react
• For nomenclature, they are commonly named
with their function, type of reaction catalyze
by an enzyme and identify of the substrate
• In enzyme catalyze reaction we have substrate
– reactant in an enzyme catalyze reaction
• Suffix: End in –ase
Identifies a reacting substance
• sucrase – reacts sucrose
• lipase - reacts lipid
• lactase – reacts with lactose
• maltase – reacts with maltose
Describes function of enzyme
• oxidase – catalyzes oxidation
• hydrolase – catalyzes hydrolysis
Common names of digestion enzymes still use
–in
• pepsin, trypsin
Identify of the substrate is often noted in
addition to the type of reaction
• glucose oxidase – reacts with glucose and
the type of reaction involved is oxidation
42
 • succinate dehydrogenase – it reacts with
succinate and the reaction involved is
dehydration organs –
increase: liver
Classification and Names of Enzymes damage, fatty
liver
Class Reaction Examples
catalyzed Kinases: transfer
Oxidation – Oxidases – phosphate group
reduction oxidation from ATP to
reactions
substrate. (ADP
Ex: Glucose
- Redox oxidase will be yield as
reaction product – one
Reductases – phosphate group
- It is a linked reduction of ATP is
process –
consumed)
oxidation is Dehydrogensase
always linked s – removes
Es: creatine
to reduction hydrogen
Oxidoreducta kinase (CK)/
se - Example: creatine
oxidoreducta Lactate phosphokinase –
se requires dehydrogenases cardiac marker
enzyme that (LDH) – remove
could either hydrogen in Isomers of CK:
oxidize or lactic acid
reduce the (substrate), CK-MB – in heart
substrate in cardiac marker
the reaction CK-MM – skeletal
Transfer a Transaminases/ muscle
group from aminotransferas
one molecule es: catalyze the CK-DB - brain
to another transfer of amino
group to a Hydrolysis
- catalyzes substrate
reactions
transfer of
functional SGOT (serum - addition of Proteases – react
group from glutamic
water during in peptide bond
one molecule oxaloacetic
to another transaminase) / the reaction
Lipases – react in
AST (aspartate
Transferase aminotransferas Carbohydrates, ester linkage
e) – increase of proteins and
AST indicates Hydrolase Carbohydrases –
lipids - During
problem in liver, react in
the formation
fatty liver glycosidic linkage
of bond water
SGPT (serum is elicit Phosphatases
glutamic-pyruvic (condensation) and Nucleases –
transaminase)/ water react with
ALT (alanine The phosphodiester/
aminotransferas hydrolysis phosphate ester
e) – found in reaction are linkage
liver and in other central to the
process of
digestion

43
 Decarboxylases – Models of Enzyme Action
react in carboxyl Enzyme active site
group and releases • Small part of an enzyme’s structure that is
Add or remove carbon dioxide actually involved in catalysis/reaction
groups during the reaction • It is the place where substrate (substance that
involving a (decarboxylation) acts to an enzyme) bind to an enzyme
double bond
Lyase • A three – dimensional entity formed by groups
without Deaminases –
that come from different parts of the protein
hydrolysis deamination – react
chains
with amino group
It doesn’t • It is formed due to folding and bending of
involve Dehydratases – proteins
hydrolysis or water is removed • Crevice-like appearance – narrow or small
oxidation opening
Hydratases – • Active site has different geometrical shape –
addition of water basis on what substrate could react on that
during the reaction enzyme
Rearranging • There are some enzymes that has more than
atoms in a
one active site
molecule to
• Once substrate binds to enzyme – it is called as
Isomerases enzyme-substrate complex (ES complex)
form an
Isomerase isomer Epimerases Enzyme – substrate Complex
- conformation • The intermediate reaction species that is
Racemases
of atoms in a formed when a substrate binds to the active
molecule Mutases site of an enzyme.
• This type of complex is needed for the activity
– changes the of the enzyme
position • The orientation a proximity is favorable and
making the reaction fast.
Form bonds
• Enzyme just helps in making sure that the
between
desired product will be formed during the
molecules
reaction
using ATP
energy

- ATP
hydrolysis

- used when
simultaneous Synthetases
Ligase
input of energy
is required or Carboxylases
when high Enzyme Action: Lock and Key Model
energy is • Active site in the enzyme has the fixed, rigid
needed in geometrical conformation. (predetermined
reaction
shape)
• enzyme and substrate are complementary by
- We chemical nature and geometrical shape (just
converted like Cinderella – the shoes fit perfectly to her)
ATP to ADP in • Shape of active site does not change, it will not
during adjust for others (loyal to one another, they fit
hydrolysis for each other)
• only substrate of a specific shape and chemical
nature can bind with the active site to form ES
complex
44
 • Substrate with a complementary geometry
can be accommodated.

Enzyme Specificity

Enzyme Reaction Example

specificity Type
Absolute
One type of
reaction for
one substrate

restricted to
specific
Urease – will only
substrate, it
react to urea
will only react
for only one Catalase – will only
substrate reacts to hydrogen
peroxide
Enzyme Action most
• Enzyme catalyzed reaction restrictive Catalase test – for
among staphylococcus
specificity specie

it is not
common

stick to one
• Substrate will bind and after the reaction is (loyal)
done the product will be released in the
Hexokinase –
circulation and the enzyme can be use again One type of
for another reaction reacts with sugar
reaction for (hexose – glucose
substrate with or galactose -
Enzyme Action: Induced -Fit Model
• “ipilit natin” “mag aadjust si enzyme” the same
aldohexose)
• Substrate contact with enzyme will change functional
the shape of the active site groups Glucose
• Enzyme’s active site is not rigid and static. Group determination –
- Involve
(marupok) hexokinase is
structurally
• There’s a constant change in shape similar used
• Allows for changes in the shape or geometry compounds,
of the active site of an enzyme to reacts for Carboxypeptidase
accommodate a substrate. substrate – react with
• Result of the enzyme’s flexibility; it adapts with same proteins
the incoming substrate. functional (carboxyl group
• It allows for changes group of peptide
• There is a constant change in shape chains).

45
 Factor Influencing Enzyme Activity
One type of
• Enzyme and substrate concentration
reaction for a
particular o E+ S= EA
chemical
bond
o Increase enzyme and the amount of
Lipase – react substrate is constant it will yield increase
- It is with ester
enzyme activity
irrespective o The enzymes are not consumed in the
bond
Linkage of the
reaction they just hasten the reaction
Phosphatase– o The greater the enzyme concentration, the
structural
hydrolyses greater the reaction rate
features in o At a constant substrate concentration, the
phosphate
the vicinity of enzyme activity increase for as long as you
ester bond
the bond increase the enzyme concentration as well
- most o E+ S = SATURATION CURVE
general of
o When enzyme is constant and the substrate
enzyme
is increased it will reach saturation curve
specificity
o Saturation curve – It already reached the
One type of
reaction for
maximum rate, there will be plateau, there
a particular will be no increase of enzyme reaction
stereoisomer because it already reached the maximum

An enzyme Temperature
that can • Changes the conformation of the enzyme
distinguish • Enzyme can be denatured in extremely high
between temperature - the enzyme will be destroyed
stereoisomer pH
• R groups of amino acids have proper charge;
Chirality variation of pH can affect the ions of groups on
the substrate
Amino acid
are known to Factors Affecting Enzyme Action
be chiral
compound
Stereochemical Isomerase
Ex: Enzyme:
L-amino acid
oxidase – it
will only
catalyze
reaction
involving L
amino acids
and not D
amino acids

The • Extremely high temperature will yield to

arrangement decrease enzyme activity
be disrupted • Denaturation of enzyme (proteins) in high
to from temperature
another type
of substrate

46
• Until we haven’t reached the optimum
temperature, the higher temperature result
in higher kinetic energy which causes
increase in number of reactant collision,
because of that enzyme activity increases.
• Optimum temperature – is the temperature
at which the rate of the enzyme catalyze
reaction is maximum
• In human body the optimum temperature for
human enzyme is 37 degrees Celsius (normal
body temp.)
• At the normal body temperature, the
enzymes are at their maximum activity
• When we have fever, enzyme activity
decreases which could be fatal.
• pH when changes it affects the enzyme
activity
• drastic change in pH, enzyme (protein) can
denature – the structure and integrity of the
enzyme will be destroyed; therefore, the
enzyme will no longer have a reaction or
activity.
• Optimum pH at which the enzyme has
maximum activity – 7.0 – 7.5
• Ave Blood pH: 7.35 – 7.45
• except digestive enzymes: Optimum pH
• pepsin in stomach: 2.0 and;
• trypsin in small intestine: 8.0
• At a constant enzyme concentration, the
enzyme activity increases with increase
substrate concentration, but it could reach
saturation curve
• Saturation curve – the concentration at which
maximum rate is reached and all active sites of
enzyme is already full, then enzyme activity will
not increase no matter how much substrate,
unless you add more enzymes to increase the
activity
• once substrate reaches its maximum rate, all
active site of enzymes is full
Turnover number
• Number of substrate molecules transformed
per minute by one molecule of enzyme under
optimum conditions of temperature, pH and
saturation of the substrate.
Example:
• Catalase: 5,600,000
• Lactate dehydrogenase: 60,000
• DNA Polymerase I: 900
Enzyme Inhibition
Inhibitors
• Slows or stops the normal catalytic activity of
the enzyme (by binding to enzyme)
• Change the protein structure of an enzyme
(like in induced-fit)
• May be competitive or noncompetitive
• Some effects are irreversible
Competitive Inhibition
A competitive inhibitor
• Has a structure similar to
substrate
• Occupies active site
• Competes with substrate
for the same active site
• It will have similar charge and shape, will
occupy the active site
• Has effect reversed by increasing substrate
concentration
• For as long as you add more substrate, the
active site can be recovered again and that is
the time when the active site can react to the
substrate
Noncompetitive Inhibition
A noncompetitive inhibitor
• Does not have a structure like substrate
• Binds to the enzyme but not active site
47
 • It binds in allosteric site – site other than
active site, wherein the noncompetitive
inhibitor binds
• Changes the shape of enzyme and active site
• Change in the structure of enzyme and
therefore preventing enzyme activity
• Substrate cannot fit altered active site
• No reaction occurs
• Effect is not reversed by adding substrate
• Increasing the concentration of substrate
does not completely overcome the inhibition
Example
• Heavy metal ions – lead, silver, mercury
Analogy: gender orientation

Irreversible Inhibition
A irreversible inhibitor
• Inactivates enzymes by forming a strong
covalent bond to an amino acid side-chain
group at the enzyme’s active site
• Does not reverse the inhibition process
• Enzyme is permanently deactivated
• Effect is not reversed by adding substrate
• Binds in active site and irreversible
Medical Uses of Enzymes
• Example: chemical warfare agents (nerve
gases), insecticides (organophosphate) • Used to diagnose certain diseases. (SGOT &
SGPT – marker for liver, LDH – marker for
Feedback Regulation heart, amylase, lipase – marker for pancreas)
Feedback control – process in which you either • Appearance of these enzymes in the blood
activate (positive feedback) or inhibit (negative often indicates that there is tissue damage in
feedback) the first reaction in a reaction an organ and that cellular contents are spilling
sequence out into the bloodstream. (normal value for
• Negative feedback – pathway is inhibited by enzymes in the body)
accumulation of final product • Used in the treatment of disease. (Example:
• Positive feedback – a regulatory molecule antibiotics
stimulates the activity of the enzyme, usually
between 2 pathways
o  ADP levels cause the activation of the
glycolysis pathway to make more ATP

48
GENERAL CHAACTERISTICS OF VITAMINS
• Organic compounds
• The term vitamins it was derived from the
word vita which means life
• The vitamins originally, we know them as
vitamine wherein beta/vita means life
• They thought that the substances actually
contain amine as their functional group that
is why it was known to be or called as
vitamins
• Some vitamins contain amine functional
group but not all
• Must be obtained from dietary sources
• Vitamins are actually considered as cofactor
of most of the enzymes, your enzymes
contain vitamins as part of their structure
• The vitamins must be obtained from dietary
sources because human body can’t synthesize
in enough amounts
• Essential for proper functioning of the body
• Needed in micro and milligram quantities per
day in comparison with the 50-200 grams per
day of major food categories
• Vitamins are actually differed from major
classes it can be carbohydrates, lipids and
proteins
• 1 gram of vitamin B is sufficient for 500,000
people
• Only micro and milligram quantities is
needed by the body
• Our body has what we called RDA or
Recommended Daily Allowance we have to
get that certain vitamin intake
• Example: Vitamin B12 we only need 2
micrograms per day for adults
• Enough vitamin can be obtained from
balanced diet
• Supplemental vitamins may be needed after
illness
• Whether it synthetic (manufacture in our
laboratory which are known to be taken as
supplement) or natural resources (from our
food intake) they are similar so the body
cannot differentiate whether the vitamins we
get are from synthetic or from our food
intake
• Same benefits just what we can get
regardless if natural resources or synthetic
• Many enzymes contain vitamins as part of
their structures – conjugated enzymes
o Conjugated enzymes – this are enzymes
which has protein and non-protein part
o Protein part – called as apoenzyme
o Non-protein part – we have cofactor
o Your vitamins play as cofactors for many
enzymes
• Two classes
o Water soluble and Fat soluble
o There are two classes they could be
characterized or divided based on their
solubility
o Water soluble – they can only be soluble in
water
o Fat soluble – they are not soluble in water but
rather they could be soluble to lipids
• Synthetic and natural vitamins are same
o 13 known vitamins
o They could be divided based on their solubility
o 9 of known vitamins are actually water soluble
and 4 of them fat or lipids soluble
o Lipids soluble vitamins – A, D, E, K
o Water soluble – Vitamins C, and B complex
WATER-SOLUBLE VITAMINS
Vitamin C
• The water-soluble vitamins need constant
replenishment in our body so they can be
eliminated quickly from the body and they are
excreted along with urine
• They are rapidly excreted in our body together
with the urine
• The water-soluble vitamins they are carried in
the bloodstream or circulation so we need
them in frequent and small dozes
• Water-soluble vitamins are actually
considered to be unlikely toxic, even though
we take them in unusually large dozes they are
not that toxic however, they must only be
taken frequent but small dozes only
• They function as coenzymes and most of the
important biochemical reactions in humans,
animals and microorganisms the coenzyme
used are water-soluble vitamins
• 8 of which vitamins are under the B complex
• 9th one is the vitamin C
• Vitamin C is the simplest structure out of the
13th vitamins
• Regarding to its fat or water soluble the most
simple or simplest is the Vitamin C
• Humans, monkeys, apes and guinea pigs need
dietary vitamins
• Co-substrate in the formation of structural
protein collagen
• Vitamin C have 2 forms that exist in our body
o Oxidized
o Reduced
• Vitamin C is also known as ascorbic
acid/ascorbate
49
• Vitamin C was actually the first Vitamin, it was
discovered in 1928
• Also, the first Vitamin that was characterized
the structure in 1933
• And it was also the first Vitamin that could be
synthesized in the laboratory since they were
able to figure out the structure of the vitamin
C on that same year that was also the Vitamin
C was synthesized in the laboratory which is in
1933
• Involved in metabolism of certain amino acids
• This amino acid they end up being converted
to the hormones; norepinephrine and
thyroxine
• Vitamin C is involved in the metabolism of the
certain amino acids
• It also functions as a general antioxidant in
water-soluble substances in our body and
other body fluids
• It also has anti-oxidant properties but as we
all know that Vitamin E is the anti-oxidant
vitamin
• Your Vitamin C actually helps the Vitamin E
because the active form of Vitamin E which
acts as antioxidant is regenerated by the
Vitamin C
• The Vitamin C aside from being known to be
general antioxidant and it is involved in the
amino acid metabolism it could also be used as
preservatives
• 100 mg/day saturates all body tissues – excess
vitamin is excreted
• RDA (mg/day):
o Great Britain: 30
o United States and Canada: 60
o Germany: 75
o Men: 90
o Female: 75
• When our body lacks Vitamin C it could cause
the condition of scurvy
• It was named ascorbic acid because it is known
to be anti-scurvy
• When it is deficient in Vitamin C it causes this
condition is scurvy it has hemorrhages in the
skin, delayed in wound healing, have anemia
and alimentary and urinary track is also
affected
• If it is too much Vitamin C it depends to person
to person it could cause diarrhea, nausea,
headache, heartburn and insomnia
Two forms of Vitamin C
Vitamin B
• The preferred and alternative names for the B
vitamins
• When we say Vitamins, they are essential and
required for normal human growth and it gets
by food and diet because cannot afford the
body to manufactured however, the other
types of vitamin is supposedly are part before
of B complex does not meet the said definition
of your Vitamin
• B4 is nitrogenous based (adenine) however B4
is not considered as vitamin anymore
• Thiamin (vitamin B1)
• The function is for carbohydrate metabolism
• Responsible for (decarboxylation’s)
• If there are deficiency in Vitamin B1
o infants it may cause dyspnea – difficulty in
breathing, cyanosis and diarrhea
o Adults – beriberi (fatigue and peripheral
neuritis – there is inflammation on the
peripheral nervous system)
• Riboflavin (vitamin B2)
• Function is redox reaction
• If the patient is suffering from deficiency in
riboflavin, they will suffer in angular
stomatitis it means that there is lesion,
dermatitis, photophobia
• Niacin (nicotinic acid, nicotinamide, vitamin
B3)
• Function is redox reaction
• If the individual is suffering from deficiency in
the Vitamin B3 it could suffer from the
condition Pellagra
• Pellagra – could suffer from dermatitis,
diarrhea, weight loss, mental disturbance,
mucous membrane inflammation
• Found in meat poultry fish
• Vitamin B6 (pyridoxine, pyridoxal,
pyridoxamine)
• Involve in amino acid such as transaminases,
phosphorylase and decarboxylases
• Co-substrate and coenzyme
50
• If you are suffering from deficiency in Vitamin
B6
o Infants – irritability; seizures, anemia
vomiting and weakness
o Adults – facial seborrhea (dandruff)
• Vitamin B is usually we do is we take them as
complex rather than taking 1 by 1 it is more
convenient to take them as one
o For adults is recommended is 400mg daily
• If there excess of Vitamin B its possible it will
cause increase blood sugar level, and it will
cause liver damage that’s why you take them
in the RDA only because it can cause mood
swing, even panic attacks if you take too much
of Vitamin B
• But even in the large dozes most of under the
Vitamin B complex is relatively safe
• Found in meat poultry fish
• Folate B9 (folic acid)
• Function is for the amino acid and nucleic acid
synthesis
• If you have deficiency in Folic acid you might
suffer from megaloblastic anemia
• megaloblastic anemia – very large of red blood
cells and anemia therefore, there is a
decreased number of the RBC
• Usually, this type of anemia could either be
due to deficiency in B9 or B12
• Vitamin B12 (cobalamin)
• Could suffer from megaloblastic anemia
• DNA synthesis and folate interconversion
• The reason why it can cause megaloblastic
anemia if there are deficiency in B12 is because
it also functions on folic acid interconversions
• It is being found exclusive in animals (meat,
poultry fish eggs and milk)
• Pantothenic acid (vitamin B5)
• Responsible for the acyl group transfer reaction
is a part of the coenzyme
• What if the Vitamin B5 is too low, it will caused
depression (not just on the mental health but
could also caused our immune system to be
depressed as well), muscle weakness
• Biotin (vitamin B7)
• The only common thread of the structure is
that they have heterocyclic nitrogen ring
system with the exemption of the pantothenic
acid
• B1 and B7 they have sulfur on their structure
• B12 – cobalt
• B7 – it doesn’t contain tin as what the name
implies but it does contain sulfur on its
structure
• Most of under the Vitamin B they are usually
found in dietary sources in plants, grains, beans
and vegetables
• If there are deficiency it will cause dermatitis,
anorexia, nausea in neurologic changes and
vasoconstriction
• It is a co-enzyme for carbon dioxide in
carboxylation for reaction
• Exhibit structural diversity
• Major function: B Vitamins are components of
coenzymes
FAT-SOLUBLE VITAMINS
Vitamins A, D, E, K
• Involved in plasma membrane processes
• More hydrocarbon like with fewer functional
groups
• They’re structure are known to be non-polar
which enhances their solubilities in cell
membrane
• Vitamin A
o Has role in vision – only 1/1000 f vitamin A
is in retina
o 3 forms of vitamin A are active in the body
o Derived from b-carotene
Functions of Vitamin A
• Vision: In the eye – vitamin A combines with
opsin protein to form the visual pigment
rhodopsin which further converts light
energy into nerves impulses that are sent to
the brain
• Vitamin A has a pre-formed type which is
known to be retinoids: retinal, retinol;
retinoic acid
• Common name of Vitamin A is retinol
• 0.1% of Vitamin A which could be found in
the eyes
• Regulating Cell Differentiation – process in
which immature cells change to specialized
cells with function
• During the hematopoiesis it differentiate the
cells into specialized cells
o Examples: Differentiation of bone marrow
cells white blood cells and red blood cells
• Vitamin A it binds the protein receptors
which could be responsible for the specific
type of white blood cell
• Maintenance of the healthy of epithelial
tissues via epithelial tissue differentiation:
51
 o Lack of vitamin A causes such surfaces to
become drier and harder than normal
o It plays a role on the body surfaces as well
as lining of internal cavities and tubes such
as your bladder. Vagina, lungs, mouth and
stomach
• Reproduction and Growth: In men, vitamin A
participates in sperm development. In
women, normal fetal development during
pregnancy requires vitamin A.
• Its role is to differentiate the cells your
Vitamin A also place a role in cancer
prevention the reason why is because the
retinoic acid actually used as a positive
control when studying the formation of
blood vessels, they could decrease the
formation of blood vessels
• If they have the formation of blood vessels it
could attribute the cancer formation so that’s
why the retinoic acid helps in cancer
prevention
• If the Vitamin A is too low it will cause
blindness, growth retardation, abnormal
taste response, dermatitis and recurrent
infection
Vitamin D
• Two forms active in the body: Vitamin D2 and
D3
o D2 – ergocalciferol
o D3 – cholecalciferol
• Sunshine Vitamin: Synthesized by UV light
from sun (D3 – It is produced in the skin of
the humans and animals by action of UV
light)
• The precursor molecule you have the
cholesterol the cholesterol it can be
converted into cholecalciferol of UV light
• It controls correct ratio of Ca and P for bone
mineralization (hardening)
• No matter how much calcium we have in our
body, if you don’t get enough Vitamin D,
calcium will become useless
• Vitamin D plays a role in the calcium how it
makes our bones strong
• You need to have enough Vitamin D for it to
utilize the calcium and phosphorus for bone
mineralization
• As a hormone it promotes Ca and P
absorption in intestine
• In Vitamin D there are few food natural
resources such as liver, fatty fish, salmon, egg
yolks, fish liver oils, fortified milk, butter
• Function of Vitamin D is calcification of bones
and teeths for hardening or mineralization of
bone
• If there is deficiency in Vitamin D it could
cause the condition of:
o rickets (bone deformation) – young
individuals
o Osteomalacia (soft bones) – adults
Vitamin E
• Four forms of Vitamin Es: a-, b-, g- and d-
Vitamin E
• Alpha-tocopherol is the most active biological
active form of Vitamin E
o Gamma – Vitamin E rich food
• Peanut oils, green and leafy vegetables and
whole grain products are the sources of
Vitamin E
• Primary function: Antioxidant – protects
against oxidation of other compounds
• After we use the Vitamin E as an anti-oxidant
once it reacts with the Vitamin C It will be
regenerated by the restoring the hydrogen
atom which is previously loss of Vitamin E
• Vitamin E – important location in the lungs
because lungs can expose the cells to oxygen
and air pollutants that is why it needs Vitamin
E for anti-oxidation
• If there is deficiency in Vitamin E it could
cause mild hemolytic anemia (newborn), red
cell fragility and ataxia
Vitamin K
• Two major forms; K1 and K2
o K1 – phylloquinone
o K2 – menaquinone
• K1 found in dark green, leafy vegetables
(plants)
• K2 is synthesized by bacteria that grow in
colon
• Dietary need supply: ~1/2 synthesized by
bacteria and ½ obtained from diet
• Leafy vegetables like spinach, cabbage they
are rich in Vitamin K
• Oher vegetables example is the peas,
tomatoes, animal tissue such as liver they only
have lesser amounts compare to what as we
can get Vitamin K in cabbage and spinach or
leafy green vegetables
• If there is deficiency in Vitamin K it could
cause hemorrhage
• There are clotting factors that are known to be
Vitamin K dependent: II, VII, IX, X
52
• Vitamin K is also required for synthesis for
other proteins which can be seen in plasma,
bone and kidney
• If the Vitamin K is too low it can cause easy
bruising to even massive bruising and post
traumatic bleeding
GENERAL CHARACTERISTICS OF MINERALS
• Unlikely vitamins which are organic
substances, minerals are inorganic
substances which is needed in small amounts
that must be obtained from food
• Minerals can be divided into two groups –
those needed in large quantities (major
minerals) and those only required in tiny
amounts (trace elements)
• Sodium and potassium are considered as
major cations while chlorine is known to be
major anion
MAJOR FUNCTIONS OF MINERALS
• Body building – teeth and bones like the
calcium
• Control of body processes, especially the
nervous system
• Essential part of body fluids and cells
• Form part of enzymes and other proteins
necessary for the release of energy
IRON
• Functions: Production of hemoglobin in red
blood cells to carry oxygen in the blood
• It very necessary for the production of
energy it also responsible for the synthesis of
collagen and also for the functioning of the
immune system
• If their iron deficiency usually common only
among children and pre-menopausal women
but if there is a case if the iron is too low it
could cause this type of anemia: Iron
Deficiency anemia (IDA)
• As much as possible we should not take to
much iron because what will happen is the
excess amount are stored in the body tissues,
they could affect the body immune function,
cell growth and even the heart
• If it is too much it could be toxic to the body
especially on the liver
• The iron is related to hemoglobin
• Sources: red meat, liver, eggs, bread,
green vegetables
• Deficiency: Anemia (IDA)
CALCIUM
• Functions: Teeth and bones, blood clotting,
nerve and muscle contraction, heart
regulation
• Without your Vitamin D the Calcium can’t be
utilized properly
• It is vital for the building for strong bones and
teeth usually it is very important during
childhood and teen years
• It is very important to get enough calcium to
fight the bone loss later in life
• Sources: Dairy products, fortified white bread,
green vegetables, nuts and seeds, canned
foods
• Deficiency: Stunted growth can cause rickets
and osteoporosis
PHOSPHORUS
• Same as calcium it also helps for the formation
of the bones and teeths and it also helps the
body make energy
• It’s a part of every cell membrane, each cell
needs a phosphorus for it to function
• Usually if the phosphorus is too low it will lead
to bone demoralization it means possible
softening the bones or weak bones
• Phosphorus and calcium are responsible for
bone mineralization or hardening of the bones
• Functions: Bones and teeth accompanied by
calcium, muscle contraction
• Sources: Dairy products, nuts, meat, fish, oats,
cocoa
• Deficiency: Rarely deficient but could cause
tiredness and depression
SODIUM
• A major cation, it’s a major extra cellular
cation
• It is very important component of body fluids
• Functions: Maintains water balance in the
body and controls body temperature, helps
you sweat when body temperature rises
53
 • It also helps in maintaining muscles and
nerves for it to work properly
• It works together with potassium the reason
why is because when sodium enters your
potassium will come out
• potassium is known to be your major
intracellular cation
• sodium is known to be your major
extracellular cation
• They are responsible for it to be balance or
to regulate the fluid in our body
• Sources: Cheese, smoked meats, fish, table
salt
• Deficiency: deficiency is highly unlikely
• If you are suffering in diarrhea or vomiting
it can have a deficiency in sodium it causes
dizziness, muscle crumps and dehydration
• If the sodium is too low your water follows
the sodium, if the sodium is low in the body
also the sodium level is low
• Hyponatremia – low (hypotension)
• Hypernatremia – high
• We differentiate elements and minerals:
minerals are actually ions they have charges
• PISO – potassium in; Sodium out
POTASSIUM
• potassium is known to be your major
intracellular cation
• It helps with the muscle and nervous system
function
• Functions: Muscle contraction and in
maintaining body fluid. It is necessary for
the building of muscle and for normal body
growth
• Sources: Banana, celery, meat, fruits, milk,
grains, legumes, raisins, dates, figs
• Deficiency: dry skin, acne, muscle spasms or
weakness
• It could also cause excessive vomiting,
chronic diarrhea or even kidney failure
• Potassium deficiency the common side
effect of the individual taking laxatives and
diuretic because when the water is low the
potassium also is low just like the sodium
• If the potassium increases there could be a
problem in the nervous and muscle function
• Hypokalemia – decrease in water
• Hyperkalemia – increase (problem in
nervous and muscle function it could also
affect your heart (arrythmia), numbness,
chest pain, heart attack
ZINC
• Functions: Aids the immune system. Cofactor
in enzymes. Needed for the senses of smell
and taste
• It basically supports the health of the immune
system
• Responsible for the normal synthesis of
protein and the reproductive organs specially
for the men
• Zinc could actually found on the sperm of
men
• Sources: Meat esp. lamb meat, oats, eggs, nuts
• Deficiency: Retarded growth, skin and nerve
health, hearing ability, and immune function
(infants)
• Excess: Enlarged liver
• Smoking and excessive alcohol consumption
could actually adversely affect the zinc levels
• The zinc enables the male body for it to
produce testosterone
• Levels of zinc can affect erectile disfunction
• Individuals who can’t sleep properly it is
actually an excellent sleep aid because it has
antidepressant effect
IODINE
• Functions: Thyroid gland function (controls
how quickly the body uses energy) and body
metabolism
• Sources: Milk, eggs, yogurt, seafood, iodized
salt
• Deficiency: enlargement of gland which
causes goiter
• When iodine is deficient during pregnancy
and infancy it can lead to abnormality in brain
development and in the growth of the
children
• Disease involved Goiter
MAGNESIUM
• Functions: muscle contraction, DNA synthesis,
controls blood sugar and blood pressure,
cofactor of enzymes
• Most of the time your magnesium and calcium
are the two evident cofactors of the enzymes
• It helps the muscle and nerve function as well
• Magnesium could actually steady the heart
bleeding and it could also keep the bone
strong it also helps the body create energy and
proteins we need
• Sources: Cheeses, cocoa, chocolate, nuts, beans
• Deficiency: it can cause muscle twitches,
nervousness and arrythmia and disorientation
it could also associated to hypocalcemia or
calcemia meaning there is a decrease in
calcium
54
• We have different biochemical reactions that
takes place in a living organism
• The totality or sum of those biochemical
reactions called metabolism
• For the metabolism or biochemical reactions
once the food being take goes into our body,
they will undergo different biochemical
reactions depending on what our body needs
• For the metabolism essentially our body
composed of 6,000 of solid foods and 10,000
gallons of water
• 70% of our body is made up of water
• The food that we intake once they undergo
specific biochemical reactions, they will be
used for different processes such as protein
synthesis, DNA replication, RNA
transcription and other biochemical
processes
• For the metabolism there are 2 types:
o Catabolism and Anabolism – they are
opposite to one another if one metabolism
is responsible for energy consumption or it
requires energy during the process while
the other one it releases energy during the
process
o Between the two the catabolism is the one
which releases energy during the process.
All the metabolic reaction in catabolism
will break down large molecules into
smaller molecules. Hence if you’ll break
down large molecules an energy will be
release during the process
o While the anabolism its opposite of the
catabolism, in anabolism the small
molecules they are joined or combined
together to form larger molecules. Hence
for you to form larger molecules you need
energy during the reactions
o catabolism: oxidation of glucose
o anabolism: synthesis of protein from your
monomer units (amino acids)
• For the metabolic reactions or metabolic
pathways is a series of molecular or
biochemical reactions which are organized in
sequence which means you have starting
materials and you also have an end product
• Two types of metabolic pathways:
o Linear pathways – starting point and
specific end product; series of reactions to
generate a final product
o Cyclic pathways – is a series of reaction
which generates the first reactant
• In the citric acid cycle the end product is
oxaloacetate but it also takes part on the first
step of your citric acid cycle
• The Kreb’s Cycle is one of the most important
metabolic pathways in our body because it
generates the energy that we need in our
everyday lives. Aside from that it could also
generate carbon dioxide
Overview of the Biochemical Energy Production
• Energy needed to run human body is obtained
from food
• Multi-step process that involves several
different catabolic pathways
• There are four stages in the biochemical
production process:
o Stage 1: Digestion
o Stage 2: Acetyl group formation
o Stage 3: Citric acid cycle
o Stage 4: electron transport chain (ETC) and
oxidative phosphorylation
• For biochemical energy production humans
have eukaryotic cells and eukaryotic cells has
different structure which is found on the cell
itself it has a DNA, enclosed in the nucleus,
different organelles, has a cytoplasm, etc.
• Cytoplasm – water-based material of eukaryotic
cell and the organelles are located on it
• Cytosol – is the water-based fluid of the
cytoplasm of a cell
• There are certain processes which undergo on
specific organelle or part of your cell and most
of the important processes they take place on
the mitochondria (powerhouse of the cell)
• Most of the energy of the cell found in the
mitochondria
• Most of the biochemical processes or pathway
they undergo in mitochondria usually on the
matrix of the mitochondria (inner membrane)
responsible of the ATP synthesis
• Each stage also involves numerous reactions
Stage 1: Digestion
• It is not considered as part of metabolism
because it is extracellular
• Metabolic processes this processes or this
biochemical reaction happens inside the cell
or intracellular. Hence, it will start that on the
Stage 2
• Begins in mouth (saliva contains starch
digesting enzymes), continues in the stomach
(gastric juice), completed in small intestine:
55
• Majority of the digestive enzymes such as the
trypsin and other bile salts (responsible for
breaking down of lipids)
• The end product of digestion are the monomer
units of your macromolecules
• The carbohydrates your monosaccharides are
the monomer units but basically it was
pointed out. Hence, we have glucose and other
saccharides such as galactose and fructose
o Results in small molecules that can cross
intestinal membrane into the blood
• End Products of digestion:
o Glucose and monosaccharides from
carbohydrates
o Amino acids from proteins
o Fatty acids (simplest form of lipids) and
glycerol from fats and oils
• This end products of the digestion they are
small enough to absorb it in our body for it to
pass across the intestinal membrane.
• The digestion products are absorbed int the
blood and transported to body’s cell
STAGE 2. Acetyl Group Formation
• The metabolic processes will start here
• The small molecules from Stage 1 are further
oxidized.
• End product of these oxidations is acetyl CoA
and reduced coenzyme (nicotinamide
adenine dinucleotide NADH)
• Involves numerous reactions:
o Reactions occur both in cytosol (glucose
metabolism) as well as mitochondria (fatty
acid metabolism) of the cells.
• The final product is acetyl CoA and as the
initial reactant is oxaloacetate
Stage 3: Citric Acid Cycle
• In this stage the acetyl CoA is oxidized to
produce carbon dioxide and energy
• And the energy we are pertaining here are
reduced coenzyme (NADH) and Flavin
adenine dinucleotide FADH2
• The reduced coenzymes most energy is
trapped because the NADH and FADH2 they
have equivalent ATP molecules
• Takes place in inside the mitochondria
• First intermediate of the cycle is citric acid
(citrate) – therefore designated as Citric acid
cycle
• In this stage acetyl group is oxidized to
produce CO2 and energy
• The carbon oxide we exhale comes primarily
from this stage
• Most energy is trapped in reduced coenzymes
NADH and FADH2
• Some energy produced in this stage is lost in
the form of heat
• Carbon dioxide and reduced coenzyme are
formed
Stage 4: Electron Transport Chain (ETC) and
oxidative phosphorylation (respiratory chain)
• Same as the Stage 2 and 3 it also takes place in
mitochondria however in Stage 2 it can also
take place in cytosol
• The reduced coenzymes that were produced
on your citric acid cycle they are needed to
produced ATP molecules which are primarily
the energy carriers in metabolic pathways
• NADH and FADH2 are oxidized to release H+
and electrons
• H+ are transported to the inter-membrane
space in mitochondria
• Electrons are transferred to O2 and O2 is
reduced to H2O
• The molecular oxygen it will react with the
electrons and those electrons are the
hydrogen ions to form the water
• H+ ions reenter the mitochondrial matrix and
drive ATP- synthase reaction to produce ATP
• ATP is the primary energy carrier in metabolic
pathways
• The final product on this stage is water
Citric Acid Cycle
• Citric acid cycle: A series of biochemical
reactions in which the acetyl portion of acetyl
CoA is oxidized to carbon dioxide and the
reduced coenzymes FADH2 and NADH are
produced
• It utilizes he final product of the Stage 2 as its
first reactant
• It is mainly a cycle or pathway with 8 steps
• The 8 steps they actually takes place in
mitochondria specifically on the mitochondrial
matrix the reason why is because the enzymes
that are needed or necessary for the
metabolism is found on the mitochondrial
matrix except for the enzyme used in Step 6
which takes place on the inner mitochondrial
membrane
• Also known as tricarboxylic acid cycle (TCA)
or Krebs cycle:
o Citric acid is a tricarboxylic acid – TCA cycle
56
 o Named after Hans Krebs who elucidated • Pink – enzyme
this pathway • Blue – intermediate product
• Two important types of reactions: • Red – for the other product that could be form
o Oxidation of NAD+ and FAD to produce after the reaction
NADH and FADH2 • Green – reactant
o Decarboxylation of citric acid to produce
carbon dioxide oxaloacetate to form
o The citric acid cycle also produces 2 ATP by citrate
substrate level phosphorylation from GTP • The reaction involve is
• Summary of citric acid cycle reactions: condensation
Acetyl CoA + 3NAD+ + FAD + GDP + Pi + • During the reaction the
2H2O -> 2CO2 + CoA-SH + 3NADH + 2H+ + enzyme involve is citrate
FADH2 + GTP synthase
• Once oxaloacetate and
• Out of 8 steps there are 4 steps in which the acetyl CoA react to one
type of reaction involve is oxidation; Step another through
3,4,6,8 condensation it will
• And then for the decarboxylation; step 3 and 4 formed the intermediate
• For those 4 steps which has oxidation as product citryl CoA
reaction not the same as NADH and FADH2 are • For the citryl CoA it will
formed, there is only one between those two then proceed in
that can be produced during the reactions and hydrolysis
it because during the reactants are also used • Water is involved during
during the reactions the reaction and then the
• For the citric acid cycle the product after the enzyme will still be used
reaction is oxaloacetate which is also, is citrate synthase
considered as the first reactant, together with • Once it hydrolyse it will
the acetyl CoA this are the two reactants that now then form the
are being utilized as the starting point citrate
• Primarily Step 2 to 7 considered as • The product that will be
intermediate product they are not being listed form aside from citrate is
as part of the reaction because they are still or CoA- SH + H+
being consumed during the reaction • Citryl CoA undergo
• While the oxaloacetate since it works as your hydrolysis it needs water
first reactant and it also consider as the final during the reaction
product it is not stated on the chemical
reaction Synthase – is an enzyme
wherein he can form a bond
1. Condensation • The carbon atom even without the
Acetyl CoA (C2) present on the involvement of ATP
molecule molecule
• The 2 carbon atoms 2. Isomerization • Citrate is converted in
on Acetyl CoA will be Citrate (C6) less symmetrical isomer
transfer to and that isomer is
oxaloacetate. Hence, isocitrate. Hence, the
that’s how we will reaction is known as
able to form your isomerization
citrate • There are other
• We need to combine reactions involved we
the carbon atoms of have the dehydration
acetyl CoA and the 4 and hydration it
carbon atoms of necessary for the
isomerization

57

• The enzyme involve is
aconitase
• The aconitase will react
to the citrate forming
an intermediate
product
• During the process the
citrate will be first
dehydrated
• After the citrate being
dehydrated forming the
cis-aconitate
• Cis-aconitate will still
react with the enzyme
still aconitase
• Cis-aconitate will react
to your aconitase to
form your isocitrate
• Aconitase it will
hydrate the cis-
aconitate
• When cis-aconitate is
hydrated the water
molecules will separate
and form a hydroxyl
sidechain and hydrogen
sidechain on the
isocitrate
• They change the
conformation or the
position of the
sidechain
- Citrate is considered as
tertiary alcohol they are
not readily oxidized
- We try to find a way to
for the molecule to
undergo oxidation. Hence,
we change citrate into
isocitrate
- From tertiary alcohol
after isomerization the
type of alcohol formed is
secondary alcohol
(isocitrate)
3. Oxidation and • Aside from the
carboxylation isocitrate it also has the
Isocitrate (C6) NAD as reactant
• Another reactant is
being used is the H+
• For the oxidation it
needs to be
oxidized to form
the oxalosuccinate
it is form through
the reaction of
isocitrate together
with the NAD and
H+
• Enzyme involve
isocitrate
dehydrogenase
• For the oxidation
process the
enzymes name the
follow this format
the name of the
reactant followed
by dehydrogenase
• The oxaloacitate it
will still undergo
another reaction
the reaction will be
decarboxylation
• For the
decarboxylation it
requires hydrogen
ions and then after
that carbon dioxide
will be released
from the carboxyl
group
• Once the carbon
dioxide been
removed it will now
form your
intermediate
product of this step
which is a-keto-
glutarate, CO2 and
NADH
CO2 it is from the
carboxyl group of
oxalosuccinate
4. Oxidation and • The product will be
carboxylation formed is the CO2
a-keto-glutarate NADH and H+
(C5) and formation • It also involved
of carbon dioxide redox reaction
• And the enzyme
involve is a-keto-
glutarate
dehydrogenase
complex
58
 • It also utilizes the NAD
H+ and CoA-SH as the
reactant
• The a-keto-glutarate
once it undergoes
oxidation it will
produced succinyl CoA
• The carboxyl group
from COO it will form
S-CoA
5. Phosphorylation • Thiol-ester bond
Succinyl CoA (C4) cleaving in succinyl
CoA and
phosphorylation of
GDP
• The succinyl CoA will
react to GDP, Pi
• The enzyme involve
here for the cleaving is
succinyl CoA
synthetase
• There is a removal of
the thiol-ester bond
using your succinyl
CoA synthetase
• The Pi will be bonded
or will have
phosphorylation from
GDP it will now form
the GTP, CoA-SH
• Once you are done with the Step 1 to 5, Step
6 to 8 there is a sequence of functional group
changes
• During the Step 6 succinate it has only a
single bond between the two carbon, it’s
between C2 and C3 but after the oxidation it
will become double bond those in C2 and C3
forming your fumarate
• And then for fumarate when the double bond
being hydrated, when undergoing hydration,
other bond will break it will go back to one
bond carbon to carbon, it will be break and
forming the malate
• The hydration of fumarate will form a
secondary alcohol and it is malate
• When malate is oxidized, the product of this
reaction is ketone (C2)
• The succinate is considered as alkene. It has
two carboxyl group on both ends of structure
• The hydroxyl group is considered as a
functional group for the alcohol. Hence, malate
is secondary alcohol
6. Oxidation • This is the third redox
Succinate (C4) reaction
• Enzyme: succinate
dehydrogenase
• It has a COO, CH2, CH2, COO, when
you oxidized it, the two
hydrogen atoms are
removed, and it will from
the double bonds
• For the structure its more
extensive since it has double
bonds it could either be cys
or trans types of molecule
• In this case, the fumarate its
consider as a trans double
bond, meaning at opposite
direction is the sidechain
• Out of all the steps in citric
acid cycle only the step 6
doesn’t undergo or they take
place in mitochondrial
matrix because the reaction
is involves is FAD
• The enzyme that catalyzes
• This reaction is in the inner
mitochondrial complex and
that enzyme is the succinate
dehydrogenase
• product: fumarate
• aside from fumarate the FAD
which is a reactant will be
reduced during the process
• FAD it works as an oxidizing
agent, since it has an
oxidizing agent it will also
reduced forming the FADH2
7. Fumarate • It has a trans double bonds
(C4) structure
• The reason why it is trans
double bond because the
enzyme was used during the
step 6 the only thing it can
produce is trans isomer it
cannot form cys double bond
• Enzyme: Fumerase
• Reaction: hydration
• The other reactant is H20 it
• also helps for the hydration
59
 you add water, it will react on the
double bond of the fumarate
• The fumarase is stereospecific
it could only yield the l-isomer
of malate
• Levo isomer can the fumarase
can form. Therefore, the
product that will be formed
after the reaction is L-malate
• Fumarate breaks the double
bond and the carbon will have
free valence. The first one is
hydroxyl group and the other
is hydrogen
• Malate – secondary alcohol;
and it is possible that it will
undergo oxidation
immediately unlike the citrate
8. L-Malate • Enzyme: Malate
(C4) dehydrogenase
• Oxidizing agent or reactant:
NAD it can be reduced forming
NADH and it will now yield
another hydrogen ion (H+)
Reactions of the Citric Acid Cycle
• Step 1: Formation of Citrate
• Step 2: Formation of Isocitrate
• Step 3: Oxidation of Isocitrate and
Formation of CO2: involves oxidation–
reduction as well as decarboxylation
• Step 4: Oxidation of Alpha-Ketoglutarate
and Formation of CO2
• Step 5: Thioester bond cleavage in Succinyl
CoA and Phosphorylation of GDP
• Step 6: Oxidation of Succinate
• Step 7: Hydration of Fumarate
• Step 8: Oxidation of L-Malate to Regenerate
Oxaloacetate
Regulation of the Citric Acid Cycle
• The rate at which the citric acid cycle
operates is controlled by ATP and NADH
levels
• When ATP supply is high, ATP inhibits
citrate synthase (Step 1 of citric acid cycle)
• When ATP levels are low ADP, ADP
activates citrate synthase
• Similarly, ADP and NADH control isocitrate
dehydrogenase (Step 3)
o NADH acts an inhibitor
o ADP as an activator
• Stage 1 – final product are the small molecules
or the monomer units of the macromolecules
• Stage 2 – end product is the acetyl CoA
• Stage 3 – the final products are carbon dioxide
and reduced coenzymes such as NAD, NADH,
FADH2
• Stage 4 – ETC the final product is ATP; have a
water and being formed after the process itself
• The electron transport chain (ETC) facilitates
the passage of electrons trapped in FADH2 and
NADH during citric cycle
• ETC is a series of biochemical reactions in
which intermediate carriers (protein and non-
protein) aid the transfer of electrons and
hydrogen ions from NADH and FADH2
• The ultimately receiver of electrons is
molecular oxygen
• The electron transport (respiratory chain)
gets its name from the fact electrons are
transported to oxygen absorbed via
respiration
• For this process basically the NADH and
FADH2 they are being oxidized in the process
once they were oxidized in the process it will
return to the oxidizing reagent (NAD and FAD)
• The hydrogen ions that were utilize during
oxidation will be come free hydrogen ions and
have extra electrons that could be used during
the process
• For the ETC the water is formed when the
electrons and hydrogen ions is reacted to each
other it will form your water molecule is
produced
o The overall ETC reaction: 2 H+ + 2e- + 1/2 O2
-> H2O + energy and O2 + 4e- + 4H+ -> 2H2O
o The oxygen involved in the water formation
is associated in ETC
• Energy is used to synthesize ATP in oxidative
phosphorylation
• Note that 2 hydrogen ions, 2 electrons, and
one half-oxygen molecule react to form the
product water
• This relatively straight forward reaction
actually requires eight or more steps
• The reaction releases energy (exothermic
reaction)
• The energy released is coupled with the
formation of three ATP molecules per every
molecule of NADH processed through ETC
• The enzymes and electron carriers needed for
the ETC are located along inner mitochondrial
membrane
60
 o Citric acid cycle is on the mitochondrial
matrix with the exception of the Step 6
which is on the inner mitochondrial
membrane
• They are organized into four distinct protein
complexes and two mobile carriers
• The four protein complexes tightly bound to
membrane; and two mobile carriers they are
not tightly associated in any four complexes
• Complex I: NADH-coenzyme Q reductase
• Complex II: Succinate-coenzyme Q reductase
• Complex III: Coenzyme Q - cytochrome C
reductase
• Complex IV: Cytochrome C oxidase
• Two mobile electron carriers are:
o They work or serves as shuttle of electrons
o They just carry or transport the electrons
between the complexes
o Coenzyme Q and cytochrome c
Complex I: NADH-coenzyme Q reductase
• NADH from citric acid cycle is the source of
electrons for this complex
• It is the largest complex out of the four
complexes
• It contains >40 subunits including flavin
mononucleotide (FMN) and several iron-
sulfur protein clusters (FeSP)
o Flavin mononucleotide – it basically
works also as reactant for the oxidation
reduction process
• Net result: Facilitates of single steps direct
transfer of electrons from NADH to
coenzyme Q
• Several intermediate reactions are involved
in this electron transfer but basically the
type of reaction is involved is oxidation
• NADH is will be oxidized and when it became
oxidized NADH lose the hydrogen and will
just form the NAD. Hydrogen ions (2), and
two electrons
o The 2 hydrogen ions and 2 electrons they
will react with the flavin mononucleotide
and it will reduce the said structure
forming the FMNH2
Complex II: Succinate-coenzyme Q reductase
• Smaller than complex I
• Contains only four subunits including two
iron-sulfur protein clusters (FeSP)
• Succinate is converted to fumarate by this
complex
• The only step occurring in the inner
mitochondrial membrane is step 6 which is
forming the succinate to form fumarate hence
the complex II is form in that process
• In the process it generates FADH2
• CoQ is the final recipient of the electrons from
FADH2
• The common product for the Complex I and
Complex II is the reduced CoQH2
Complex III: Coenzyme Q - cytochrome C
reductase
• Complex III contains 11 different subunits
• Several iron-sulfur proteins and cytochromes
are electron carriers in this complex
• Cytochrome is a heme iron protein in which
reversible oxidation of an iron atom occurs
o Heme – is a compound which is present in
hemoglobin and myoglobin
• Various cytochromes, e.g., cyt a, cyt b, cyt c,
differ from each other by:
o Their protein constituents
o The manner in which the heme is bonded to
the protein
o Attachments to the heme ring
• The reduced CoQH2 it will be oxidized when it
became oxidized it will lose the H+ and it will
form the CoQ, 2H+ and extra 2e-, and after
which the electrons and hydrogen ions will be
utilized by the iron-sulfur proteins
Complex IV: Cytochrome C oxidase
• Contains 13 subunits including two
cytochromes
• The electrons flow from cyt c to cyt a to cyt a3
o The difference of cyt c and cyt a is the
attachment or how heme ring bonds to
protein constituent
• In the final stage of electron transfer, the
electrons from cyt a3, and hydrogen ion (H+)
combine with oxygen (O2) to form water
• O2 + 4H+ + 4e- -> 2 H2O and ATP after the
process
• It is estimated that 95 % of the oxygen used by
cells serves as the final electron acceptor for
the ETC
• NAD, NADH, FADH2 produce during the citric
acid cycle they are utilize in the ETC
61
Digestion and Absorption of Carbohydrates
Digestion is the biochemical process by which
food molecules, through hydrolysis, are broken
down into simpler chemical units that can be
used by cells for their metabolic needs.
Glycolysis
• Conversion of glucose to pyruvate
• The process is oxidation but there is no
molecular oxygen to utilize
• Oxidation: NAD, hence aside for pyruvate
NADH-reduced coenzymes are produced
• Glycolysis is the metabolic pathway by which
glucose (a C6 molecule) is converted into
two molecules of pyruvate (a C3 molecule),
chemical energy in the form of ATP is
produced, and NADH-reduced coenzymes
are produced
• Anaerobic pathways
o metabolic pathways in which molecular
oxygen is not a participant
o Example: glycolysis – ten step process
wherein every step is known to be enzyme
catalyzed
• Aerobic pathways – pathways that require
molecular oxygen
Six-Carbon Stage of Glycolysis (Steps 1–3)
• It is known to be energy consuming meaning
it utilize energy
• Energy consuming: Step 1 and 3 because it
utilize the ATP during the reaction
• Energy utilized in the process is the ATP
• In this process it produces the phosphate
derivatives glucose and fructose meaning,
the glucose and fructose coupled by ATP
• Phosphate group to be bond to glucose and
fructose It will come from the ATP
Step 1: Phosphorylation: Formation of Glucose 6-
Phosphate. Glycolysis begins with the
phosphorylation of glucose to yield glucose 6-
phosphate.
• The enzyme will react to glucose to produce
glucose 6-phosphate
• Hexokinase its needs magnesium ion for its
activity
• For the phosphorylation the enzyme involves
in glycolysis they end with kinase
• We utilize ATP to from the glucose 6-
phosphate.
• One phosphate group from the ATP it will be
attached to the carbon number 6 of glucose
• The energy needed is derived from ATP
hydrolysis
• Also, endothermic reaction is involved in step
1
Step 2: Isomerization: Formation of Fructose 6-
Phosphate
• Glucose 6-phophate is isomerized into
fructose 6-phosphate basically the net result
of the chain is the carbon 1 is no loner part of
the ring structure
• The Glucose 6-phosphate is a six membered-
ring after it become isomerized it became 5
membered-ring
• Glucose 6-phophate it will now produce
fructose 6-phosphate through the help of the
enzyme phospoglucoisomerase which is
responsible for the isomerization of this
molecule
• The phosphate is still in carbon 6 what has
changed is that carbon 1 is no longer part of
the ring structure. Aside from that, the
functional group that could be found on the
two structure is different
• Functional group in glucose 6-phosphate is
aldehyde but in fructose 6-phosphate it is
known to be a ketose therefore, ketone is the
functional group
• Once fructose 6-phosphate was produced on
this step it could then proceed to another
phosphorylation
62

Step 3. Phosphorylation: Formation of Fructose
1,6-Bisphosphate. This step, like Step 1, is a
phosphorylation reaction and therefore requires
the expenditure of energy.
• The enzyme involve in the reaction is
phospofructokinase, for this enzyme it also
requires magnesium ion for its activity
• Fructose 6-phosphate additional phosphate
group is bonded to your phosphate
derivative of fructose it will become 2
phosphate group
• The additional phosphate group coming from
ATP will be bonded to the carbon 1 of the
fructose. Hence, it will be produced fructose
1,6-biphosphate
• The biphosphate we used it when the two
phosphate groups are bonded to different
carbon atoms it means they are not
connected to each other
• In Step 3 its product can enter glycolysis
while the other product in step 1 and 2 they
can enter another metabolic pathway but the
fructose 1,6-biphosphate it could only enter
glycolysis
Three-Carbon Stage of Glycolysis (Steps 4–10)
• It is known to be energy generating meaning
it produces ATP during the three-carbon
stage
• The three-carbon stage of glycolysis they are all
phosphorylated derivatives either glycerol or
acetone bonded to the phosphate group
• Step 4: Cleavage: Formation of Two Triose
Phosphates. In this step, the reacting C6
species is split into two C3 (triose) species.
• Because fructose 1,6-bisphosphate, the
molecule being split, is unsymmetrical, the
two trioses produced are not identical. One
product is dihydroxyacetone phosphate, and
the other is glyceraldehyde 3-phosphate.
• The six-carbon molecule are cleaved which is
the fructose 1,6-biphosphate, when it cleaves
two molecules with three carbons are formed
meaning it is being split into 2 triose species
• Fructose 1,6-biphospahte is unsymmetrical
hence, the formed product is different one is
dihydroxyacetone which is derivative of
acetone (has ketone as its functional group)
while the glyceraldehyde 3-phosphate
aldehyde is the functional group we can see on
its structure and its derivative is glycerol
• The enzyme involve for the cleaving of
fructose 1,6-biphosphate to produced two
molecules of triose is aldolase
Step 5: Isomerization: Formation of
Glyceraldehyde 3-Phosphate.
• The one in the triose form it being converted
into glyceraldehyde 3-phosphate
• From the acetone phosphate derivative, it will
from another glycerol phosphate derivative
• Dihydroxyacetone phosphate it will be
isomerize using the enzyme triosephosphate
isomerase
• The double seen in carbon 2 in the structure of
dihydroxyacetone phosphate it will be broken
down to from your aldose which is your
glyceraldehyde 3-phosphate
Step 6: Oxidation and Phosphorylation:
Formation of 1,3 Bisphosphoglycerate. Phosphate
group is added to glyceraldehyde 3-phosphate to
produce 1,3-bisphosphoglycerate.
• Step 6 to Step 10 you have 2 molecules of
three-carbon compound participate for every
step
63
• The two molecules is glyceraldehyde 3-
phopshate that will undergo oxidation and
phosphorylation
• For the oxidation it requires oxidizing agent,
the oxidizing agent is the NAD and Pi for the
reaction
• The enzyme involve for the reaction is
glyceraldehyde 3-phosphate dehydrogenase
• The NAD is also reduced forming your NADH
• The Pi it will bond to carbon 1 of
glyceraldehyde it will replace the hydrogen
that is bound to carbon 1, the hydrogen of
aldehyde it will be replaced by the phosphate
group from the Pi forming the 1,3-
bisphosphoglycerate that is why bis the
phosphate group is bounded to different
carbon atoms
• The newly added phosphate group in 1,3-
bisphosphoglycerate is a high-energy
phosphate group. A high-energy phosphate
group is produced when a phosphate group
is attached to a carbon atom that is also
participating in a carbon–carbon or carbon–
oxygen double bond.
o High-energy phosphate group – when the
phosphate group is bonded to a carbon
participating in a double bond it could be
double bond to an oxygen or carbon
• Since the two glyceraldehyde the
glyceraldehyde 3-phosphate the ones that
undergo oxidation and phosphorylation
means need two NAD and two phosphate
groups meaning two molecules of 1-3
bisphosphoglycerate, two molecules of
NADH and two molecules of hydrogen ions
are produced after the reaction
Step 8: Isomerization: Formation of 2-
Phosphoglycerate. In this isomerization step, the
phosphate group of 3-phosphoglycerate is moved
from carbon 3 to carbon 2.
• Step 7: Phosphorylation of ADP:
Formation of 3-Phosphoglycerate. The
diphosphate species just formed is
converted back to a monophosphate
species.
• Meaning two bisphosphoglycerate will
participate it means that it will be utilized 2
ADP to produce 2 ATP molecules
• In this step 2 ATP will be produced aside from
the product which is 3-phosphoglycerate, two
molecules of 3-phosphoglycerate will also be
produced
• The reaction involve is phosphorylation of
ADP
• What happens here is from diphosphate
specie which is the 1,3-bisposphylglecerate it
will become monophosphate hence, we will
have 3-phosphoglycerate because the
phosphate that comes from carbon 1 can be
utilized to form ATP hence, step 7 is known to
be energy generating because this is where
ATP production takes place
• ATP produce 2 molecules
• The enzyme involve is phosphoglycerokinase
• ATP production in this step involves
substrate-level phosphorylation.
• Substrate-level phosphorylation is the
biochemical process by which a high energy
phosphate group from an intermediate
compound (substrate) is directly transferred
to ADP to produce ATP.
• The high energy phosphate compound is 1,3-
bisposphylglecerate forming the 3-
phosphoglycerate once the phosphate group
was removed from the 1,3-
bisposphylglecerate
• The isomerization of 3-phosphoglycerate it
forms 2-phospoglycerate therefore from being
attached to carbon 3 it will go to carbon 2
• The enzyme involve for this reaction is
phospoglyceromutase it moves the phosphate
from carbon 3 to carbon 2 forming the 2-
phospoglycerate
• Once it is isomerized it will then proceed to
the step 9
• Mutase – it changes or transfers the position of
one functional group to another functional
group within a molecule
64
 • 2 ATP molecules and 2 pyruvate molecules
that being produced after the glycolysis

Step Reaction ATP Change

per Glucose
1 Glucose -> glucose 6- -1
Step 9: Dehydration: Formation of phosphate
Phosphoenolpyruvate. The result is another 3 Fructose 6-phosphate -> -1
compound containing a high-energy phosphate fructose 1,6- bisphosphate
7 2(1,3-bisphospoglycerate -> +2
group; the phosphate group is attached to a
3 phosphoglycerate)
carbon atom that is involved in a carbon–carbon
10 2 (phosphoenolpyruvate -> +2
double bond pyruvate
• The reaction is alcohol dehydration Net +2
• The enzyme involve is enolase Net overall equation: (glycolysis)
• Same as the Step 1 and Step 3 enzyme it also Glucose + 2NAD + 2ADP + 2Pi -> 2 pyruvate +
requires magnesium for its activity 2NADH + 2ATP + 2H+ + 2 H20
• Carbon 2 and 3 are dehydrated to form a
double bond Entry of Galactose and Fructose into Glycolysis
• Since dehydration the reaction involved it • Galactose and Fructose, they are not directly
means water-molecule will be released it is utilized in the bloodstream they were
one of the product in the reaction converted first in the liver. When they are
• 2 water-molecule will be produced because 2 converted then they can enter the glycolysis
molecules of 2-phosphoglycerate will be pathway
utilized • The galactose it undergoes isomerization and
• The final product is phosphoenolpyruvate phosphorylation to produce glucose 1-
• Energy rich compound produced same as the phosphorate
step 6 • For the galactose it can enter step 2 which is
the glucose 1-phosphate will be isomerized to
glucose 6-phosphate then it will proceed with
the same step of the glycolysis
• The fructose will be phosphorylated forming
the fructose 1-phosphorate it will not go
through step 1-3 it will go straight to step 4
and the it can be cleaved into 2 triose species
Step 10: Phosphorylation of ADP: Formation of
Pyruvate. Fates of Pyruvate
• Pyruvate kinase as the enzyme
• From ADP we could now produce ATP
• The phosphate will come from
phosphoenolpyruvate the phosphate group
that will bond to ADP to form the ATP
• The pyruvate kinase it requires 2 ions to
activate it, it needs a magnesium and
potassium ions for its activity
• Once your pyruvate kinase react with the
phosphoenolpyruvate it will now for the
pyruvate
• The Pyruvate is also a ketose because at
carbon 2 its double bonded to an oxygen
hence, pyruvate is derivatives of acetone
• Phosphoenolpyruvate transfers its high-
energy phosphate group to an ADP molecule
to produce ATP and pyruvate

65
 • When it is aerobic condition or oxygen-rich
condition it will proceed with oxidation to
acetyl CoA
• When it is anerobic it can be lactate or
ethanol fermentation
Oxidation to Acetyl CoA
Under aerobic (oxygen-rich) conditions,
pyruvate is oxidized to acetyl CoA.
• The pyruvate it has a carboxyl group, the
carboxyl group is the one that was removed
and it will be replaced by CoA to form your
acetyl CoA
• The removed carboxyl group will become
carbon dioxide
• Pyruvate formed in the cytosol through
glycolysis crosses the two mitochondrial
membranes and enters the mitochondrial
matrix, where the oxidation takes place.
• Utilizes CoA -SH and NAD it because of
oxidation it requires oxidizing agent
• The enzyme involve is pyruvate
dehydrogenase complex
• The acetyl CoA is being produced
• The acetyl CoA they enter TCA and most of
the pyruvate they are converted into acetyl
CoA
Lactate Fermentation
• Fermentation is a biochemical process by
which NADH is oxidized to NAD without the
need for oxygen.
• Lactate fermentation is the enzymatic
anaerobic reduction of pyruvate to lactate
o The sole purpose of this process is the
conversion of NADH to NAD. The lactate so
formed is converted back to pyruvate
when aerobic conditions are again
established in a cell.
• The enzyme id lactate dehydrogenase (LDH)
Oxidation to Acetyl CoA
• This reaction, which involves both oxidation
and decarboxylation (because Co2 is
produced)
o You removed the carboxyl group in pyruvate
then it will be produced carbon dioxide.
Oxidation hence, the enzyme is pyruvate
dehydrogenase complex because it is
oxidation
• The overall reaction process involves four
separate steps and requires NAD, CoA—SH,
FAD, and two other coenzymes (lipoic acid and
thiamine pyrophosphate, the latter derived
from the B vitamin thiamine)
• Most acetyl CoA molecules produced from
pyruvate enter the citric acid cycle
• Th citric acid cycle – it change more NAD to its
reduced form, NADH from glycolysis and from
pyruvate to acetyl CoA and also from the citric
acid cycle, all NADH can enter the electron
transport chain directly or indirectly
• Electron transport chain – the electrons from
the NADH are transferred to the oxygen it
means NADH was converted back into NAD
• The NAD needed for glycolysis is the one from
the citric acid cycle and the pyruvate acetyl
CoA conversion is regenerated when NADH
goes to ETC, the NAD that is produced can be
used again in glycolysis in oxidation to acetyl
CoA of pyruvate and citric acid cycle
• Net overall rection:
Glucose + 2ADP + 2Pi +4NAD + 2CoA-SH ->
2acetyl CoA + 2CO2 + 2ATP + 4NADH + 4H+ +
2H2O
Lactate Fermentation
• When the reaction for conversion of pyruvate
to lactate is added to the net glycolysis
reaction, an overall reaction for the conversion
of glucose to lactate is obtained:
• The red blood cells also form lactate it because
RBC has no mitochondria therefore it will
always form lactate. Lactate is coming from
the RBC as well as from the muscles
Ethanol Fermentation
• Ethanol fermentation is the enzymatic
anaerobic conversion of pyruvate to ethanol
and carbon dioxide
66
• The first step in conversion of pyruvate to
ethanol is a decarboxylation reaction to
produce acetaldehyde.
• Decarboxylation – carboxyl group will be
removed hence it will produce carbon
dioxide
• The hydrogen ion it will be replacing the
carboxyl group in pyruvate forming the
acetaldehyde and carbon dioxide
• The enzyme involve is pyruvate
decarboxylase
• Ethanol fermentation – involving yeast, when
there is yeast after undergoing ethanol
fermentation it can cause the rise of bread
and other related products because carbon
dioxide is produced, so the carbon dioxide
bubbles is the reason why there is a rise of
bread and other related products during
baking. Also, in alcoholic beverages they are
produced by the ethanol fermentation
• The second step involves acetaldehyde
reduction to produce ethanol.
• Redox is the reaction then dehydrogenase is
the enzyme
• Specifically, we have alcohol,
dehydrogenase from acetaldehyde it will
now form the ethanol
• An overall reaction for the production of
ethanol from glucose is obtained by
combining the reaction for the conversion of
pyruvate with the net reaction for glycolysis
• The ethanol and lactate fermentation the
NADH and NAD they do not appear in the
equation but they are both generated and
consume during the process
Regeneration of NAD+ from NADH+
ATP Production for the Complete Oxidation of
Glucose
• NADH produced during Step 6 of Glycolysis
cannot directly participate in the electron
transport chain (ETC) because mitochondria
are impermeable to NADH and NAD+
• Glycerol 3-phosphate-dihydroxyacetone
phosphate transport system shuttles electrons
from NADH, but not NADH itself, across the
membrane:
o Dihydroxyacetone phosphate and glycerol
phosphate freely cross the mitochondrial
membrane
o The interconversion shuttles the electrons
from NADH to FADH2
• Total of 30 ATP molecules produce of muscle
and nerve cells
o 26 ATP– ETC
o 2 ATP – oxidation of glucose to pyruvate
o 2 ATP – GTP -> ATP
• The aerobic condition of glucose is 15x more
efficient to produce ATP production as
compared to when aerobic lactate and ethanol
processes are used
• In other cells, instead of 30, 32 ATP
molecules (heart and liver cells) it can
produced
67
Glycogen Synthesis and Degradation:
Glycogenesis
• Glycogen it’s the storage form of
carbohydrates in humans and animals and it
is also known as animal starch
• Glycogen it is primarily found in muscle and
liver tissue
o When glycogen is in the muscle it is the
source of glucose when needed for
glycolysis
o When glycogen is in the liver it is the
source of glucose to maintain the normal
blood glucose level

Step 2: Formation of UDP-glucose. Glucose 1-

Glycogenesis is the metabolic pathway by which
glycogen is synthesized from glucose 6-
phosphate.
• Step 1: Formation of Glucose 1-phosphate.
The starting material for this step is not
glucose itself but rather glucose 6-phosphate
(available from the first step of glycolysis).
• The glucose 6-phosphate was the one which
was formed during the first step of glycolysis
it means we need to convert glucose into 6-
phosphate first
• It utilizes hexokinase as the enzyme for the
phosphorylation of the glucose
• When there is glucose 6-phosphate from step
1 of glycolysis, glucose 6-phosphate can
enter glycogenesis, it enters when it needs to
store glucose in the body
• If you think you have enough glucose in the
circulation and we need to store some of the
glucose in our body in form of glycogen from
conversion of glucose to glucose 6-phosphate
it could now enter glycogenesis
• The enzyme is phosphoglucomutase it needs
to isomerized glucose 6-phosphate to
glucose 1-phosphate
• The reaction involve is isomerization
• From carbon 6 where phosphate is attached
or bonded, it will go now to carbon 1 which
will form the glucose 1-phosphate
• Once it forms the glucose 1-phosphate it
could now proceed in the second step
phosphate from Step 1 must be activated before it
can be added to a growing glycogen chain. The
activator is the high energy compound UTP
(uridine triphosphate).
• In the formation of UDP-glucose you need UTP
• The Uridine Monophosphate (UMP) will be
attached there in the phosphate group of
glucose 1-phosphate
• The enzyme involve is UDP glucose
pyrophosphorylase
• For the Step 2 high-energy compound the one
used (UTP) and the UMP it will be bonded to
the phosphate of the glucose1-phosphate
hence, we remove the UMP, ATP will have 2
phosphate group as a product as well
• Product: Uridine diphosphate glucose (UDP-
glucose) and 2 phosphate groups
• It requires high-energy compound as activator
Step 3: Glucose Transfer to a Glycogen Chain. The
glucose unit of UDP-glucose is then attached to the
end of a glycogen chain.
• Glycogen synthase as the enzyme
• The UDP it will then remove in the UDP-
glucose it means we will have a free UDP
after the glucose unit from UDP glucose is
attached to your glycogen chain
• The UDP form in the product it can be
converted back to UTP
• UDP will be converted to UTP through the
help of ATP (UDP + ATP -> UTP + ADP)
• UDP + ATP -> UTP + ADP – the UTP form
here can be used again in step 2 that is the
reason why we need to convert the UDP that
was formed in step 3

68
Glycogen Synthesis and Degradation:
Glycogenolysis
Glycogenolysis
• Breakdown the glycogen, when the glycogen
break it will return to glucose 6-phosphate
• is the metabolic pathway by which glucose 6-
phosphate is produced from glycogen.
• It does not require high-energy compounds
which is your UTP hence, it’s not simply the
reverse of the glycogenesis
Step 1: Phosphorylation of a Glucose Residue.
• Phosphorylation – it needs phosphate group
to react with glycogen
• In glycogen will remove a glucose unit, the
glucose unit that comes from glycogen is
phosphorylated to form glucose 1-phosphate
• The enzyme involve is phosphorylase.
Specifically, glycogen phosphorylase
• The enzyme it catalyzes the cleavage of the
bond by phosphate
• In hydrolysis the cleavage of the bond is
through the help of water, when
phosphorylase is the enzyme used it uses to
cleave the bond by phosphate group. That is
why we could attach the phosphate group in
glucose taken from the glycogen
Step 2: Glucose 1-phosphate Isomerization
• Once we have glucose 1-phosphate it can be
converted to glucose 6-phosphate through
isomerization
• The enzyme is phosphoglucomutase
• It is the reverse of the step 1 of glycogenesis
Glycogen synthesis and degradation:
Glycogenolysis
• In muscle and brain cells an immediate need
for energy is the stimulus that initiates
glycogenolysis
• The glucose 6-phospahte that is produced
directly enters the glycolysis pathway at step
1 and its multistep conversion to pyruvate
begins
• A low level of glucose is the stimulus that
initiates glycogenolysis is liver cells. Here, the
glucose 6-phosphate produced must be
converted to free glucose it can be enter the
bloodstream, as glucose 6-phosphate cannot
cross cell membranes.
• This change is affected by the enzyme glucose
6-phosphatase that will covert glucose 6-
phosphate to glucose for it to be converted it
needs water
• an enzyme found in liver cells but not in
muscle cells or brain cells
Glycogen Synthesis and Degradation:
Gluconeogenesis
• Gluconeogenesis is opposite to the glycolysis
but not exact opposite
• Gluconeogenesis is the metabolic pathway by
which glucose is synthesized from
noncarbohydrate materials.
• The noncarbohydrate starting materials for
gluconeogenesis are lactate (muscles),
glycerol (triacyl glycerol hydrolysis) and
certain amino acids (protein hydrolysis,
muscle protein during starvation).
• About 90% of gluconeogenesis takes place in
the liver. Hence gluconeogenesis helps to
maintain normal blood-glucose levels in times
of inadequate dietary carbohydrate intake
• Step 1: the pyruvate it converted first to
oxaloacetate
• For it to be converted the enzyme requires is
pyruvate carboxylase it means we add a
carboxyl group to pyruvate, carboxylic acid
becomes carbon 4 of pyruvate
• The carboxyl group will be coming from the
carbon dioxide
69
• In pyruvate it has only 3 carbon molecules
when it is converted into oxaloacetate it will
be 4 carbon molecules, it requires ATP and
carbon dioxide for the conversion of
pyruvate into oxaloacetate
• It also needs water during the reaction and
the carbon dioxide it utilizes and bonded in
the carbon 4 (after the reaction: ADP + Pi)
• For the oxaloacetate together with the acetyl
CoA they can procced in the citric acid cycle
• If our body needs energy it will enter the
TCA, but if will need glucose in our body it
will proceed to the metabolic pathway of
gluconeogenesis
• The process after if it will proceed with
gluconeogenesis it will be converted into
phosphoenolpyruvate the enzyme involve is
phosphoenolpyruvate carbokinase it means
it requires energy
• This time the energy that we will used is GTP
• GTP its phosphate group will remove the 4th
carbon of oxaloacetate, the carboxyl group of
oxaloacetates will be removed, which means
it will produce carbon dioxide during the
step, and then there is also phosphorylation.
A phosphorylation reaction is also involved
• The phosphate group will come from the GTP
• In carbon 2 of phosphoenolpyruvate there
the phosphate group will bond
• Phosphoenolpyruvate – because there is a
phosphate group and it has a pyruvate as the
sugar and then enol because it has a carbon-
to-carbon double bond, and OH group.
However, the hydrogen of the OH group it
has been replaced by phosphate
• The enzyme involve is phosphoenolpyruvate
carboxykinase (the carboxyl will be
removed and kinase it requires high-energy
compound during the process)
• For the gluconeogenesis in step 9 instead of
phosphofructokinase the enzyme required is
fructose 1,6-bisphosphatase (no ATP
required)
• The step 9 and step 11 of gluconeogenesis
they don’t require ATP. However, in step 1
and step 3 the ATP is required for glycolysis
• In step 11 of gluconeogenesis to convert
glucose 6-phosphate into glucose the enzyme
required is glucose 6-phosphatase
• For the overall net reaction (gluconeogenesis):
2Pyruvate + 4ATP + 2GTP + 2NADH + 2H20 ->
glucose + 4ADP + 2GDP + 6Pi + 2NAD
• Gluconeogenesis it happens in the liver;
glycolysis active skeletal muscle
The Cori Cycle
Cori cycle is a cyclic biochemical process in which
glucose is converted to lactate in muscle tissue, the
lactate is reconverted to glucose in the liver, and
the glucose is returned to the muscle tissue
• Lactate forms from glucose under anerobic
condition in muscle cells, and when it is
transferred to the liver, that is the time at
which it is converted into glucose, then it can
be transferred back again into muscles
• The enzyme involve is lactate dehydrogenase
(LDH)
• Cori cycle – the substrate and as oxidizing
agent it will reduced into NADH and from
lactate it will be pyruvate, it means it has an
extra hydrogen that will be become your
hydrogen ion
• The pyruvate form it can be converted via
gluconeogenesis to form your glucose, then it
will go into the bloodstream and then will go
the muscle
The glycogenesis is a 3-step process
• The glycogenesis is the formation of the
glycogen from the glucose 6-phosphate
• The glucose 6-phosphate is from the glycolysis
The glycogenolysis is a 2-step process wherein its
lice’s the glycogen into glucose 6-phosphate
• The glucose 6-phosphate can be converted to
glucose
• The glycogenolysis produce the glucose 6-
phosphate it could proceed to glycolysis
• For the gluconeogenesis it could also produce
the glucose which usually regulates for the
blood glucose level
•
70
• For the pyruvate produced by glycolysis can
proceed with lactate fermentation, acetyl CoA
and ethanol fermentation
• Pyruvate could also enter to the
gluconeogenesis
• The reason why lactate has 2 arrows is it can
be converted back again to pyruvate if its
condition is aerobic

The Pentose Phosphate Pathway

• Pentose phosphate pathway is the
metabolic pathway by which glucose is used
to produce NADPH, ribose 5-phosphate (a
pentose phosphate), and numerous other
sugar phosphates.
• Major function of the alternative pathway
is • glucose 6-phosphate is the initial substrate
o To produce co-enzyme NADPH • it has 3 steps and therefore, it also has 3
o To produce ribose 5-phosphate (which is a enzyme that is involved
pentose derivative that is needed in the • 1st and 3rd steps are both utilizing NADP
nucleic acid) • Glucose 6-phosphate it reacts with the enzyme
• NADPH it needed to produced/synthesized glucose 6-phosphate dehydrogenase. Once it
is because it is needed for lipid synthesis reacts with its enzyme it will then form your 6-
• NADPH (Nicotinamide Adenine Dinucleotide phosphoglucono-1,5-lactone. And after it will
Phosphate) it is the reduced form react with gluconolactonase forming your 6-
• NADPH is structurally similar to NADH but phosphogluconate. It also needs NADP for the
step 3. The enzyme needed for it is 6-
the difference is NADPH has phosphate
phosphogluconate dehydrogenase. Remember
group
that since it has NADP, it is still oxidation that
• NADPH is mainly involved in the reaction to is why the enzyme has dehydrogenase it means
lipids and nucleic acids there is a redox reaction for step 1 and step 3
• NAD is mainly for the common metabolic • The first 3 steps are under oxidative stage
pathway • The product for the oxidative stage is the
ribulose 5-phosphate. This will undergo non-
Two stages within the pentose phosphate
oxidative stage
pathway:
• For the non-oxidative stage, you will convert
• Oxidative stage- involves three steps
the ribulose 5-phosphase into ribose 5-
through which glucose 6-phosphate is
phosphate or into aldose especially if it will be
converted to ribulose 5-phosphate and CO2.
used for nucleic acid synthesis.
• Nonoxidative stage- first step involves
• For the other product aside from ribose 5-
isomerization of ribulose 5-phosphate (a
phosphate we use the ribulose 5-phosphase 3-
ketose) to ribose 5-phosphate (an aldose)
epimerase it can form xylulose 5-phospjate,
and then further conversion of ribose 5-
this xylulose 5-phosphate is basically a ketose
phosphate to numerous other sugar
o Xylose – aldose
phosphates. Ultimately, glyceraldehyde 3-
o Xylulose – ketose
phosphate and fructose 6-phosphate (both
glycolysis intermediates) are formed.
o Ribose 5-phosphate is a ketose that is
needed to be converted into aldose which
is the ribose 5-phosphate
o Its goal is to produce glyceraldehyde 3-
phosphate and fructose 6-phosphate which
are both intermediates of glycolysis

71

• Transketolase: is a key enzyme in the non-
oxidative branch of the pentose phosphate
pathway that transfers a two-carbon
aldehyde unit from ketose-donor to aldose-
acceptor sugars.
• Transaldolase: is a key enzyme in the non-
oxidative branch of the pentose phosphate
pathway that transfers a three-carbon
aldehyde unit from ketose-donor to aldose-
acceptor sugars.
• The difference between the two is the number
of carbon aldehyde unit that they can transfer
• The pentose phosphate pathway, with its
many intermediates, helps meet cellular
needs in numerous ways:
1. When ATP demand is high, the pathway
continues to its end products, which enter
glycolysis.
2. When NADPH demand is high, intermediates
are recycled to glucose 6-phosphate (the start of
the pathway), and further NADPH is produced.
3. When ribose 5-phosphate demand is high, for
nucleic acid and coenzyme production, most of
the nonoxidative stage is nonfunctional, leaving
ribose 5-phosphate as a major product it means
when the product is converted to the oxidative
stage and the product is the ribulose 5-phosphate
• The pentose ribose is a component of ATP,
GTP, UTP, CoA, NAD, FAD and RNA
• For the non-oxidative stage, it contains
provision for the conversion of ribose 5-
phosphate and it could proceed to numerous
sugar phosphate
• For the overall net reaction of pentose
phosphate pathway:
3 glucose-6-phosphate + 6NADP + 3H2O -> 2
fructose-6-phosphate + 3CO2 +
glyceraldehyde-3-phosphate + 6NADPH + H+
Hormonal Control of Carbohydrate
Metabolism
• Insulin, Glucagon and Epinephrine are the
three major hormones for the regulation of
carbohydrate metabolism
• The second major method for regulating the
carbohydrate metabolism is the hormonal
control.
Insulin- is a hormone produced by the beta cells
of the pancreas.
• Insulin is a 51 amino acid protein (51 A.A)
which is considered as hormone. This
hormone is producing by the beta cells of the
pancreas and insulin promotes the uptake
and utilization of glucose by cells. Thus, its
function is to lower blood glucose levels.
• It is the only hormone in our body that could
lower the blood glucose level.
• It is also involved in lipid metabolism.
• The release of insulin is being triggered if the
blood glucose level of the body is too high.
The mechanism for the insulin action is that it
binds to the protein receptor in the outer
surface of the cell which facilitates the
entrance of glucose inside the cell.
• Your insulin also produces an increase in the
rates of glycogen synthesis
Glucagon- polypeptide hormone it has 29 amino
acid (20 A.A) produced in the pancreas by alpha
cells. It is released when blood-glucose levels are
low. Its principal function is to increase blood-
glucose concentrations by speeding up the
conversion of glycogen to glucose (glycogenolysis)
and gluconeogenesis in the liver.
• Your glucagon is only polypeptide hormone
because it is less than 40 amino acids
• For the glucagon, it is released when the
blood glucose level is low
• Blood glucose level is being increased by
speeding up the conversion of glycogen into
glucose which is your glycogenolysis and also
gluconeogenesis in liver it means the effect of
glucagon is opposite with the effect of insulin
Epinephrine- stimulation of glycogenolysis, the
release of glucose from glycogen. Its primary
target is muscle cells, where energy is needed for
quick action. It also functions in lipid metabolism.
• Epinephrine is also known as adrenaline. It is
release in the adrenal glands in response of
being excited, afraid, angry.
• Epinephrine is similar with the effect of
glucagon. They both increase the blood
glucose levels
• Epinephrine acts by binding in the receptor
outside the cell membrane
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