MODULE 1: INTRODUCTION TO BIOCHEMISTRY

LECTURE | AY 2022-2023 1ST SEMESTER

WHAT IS BIOCHEMISTRY?  “security guard”, helps regulate what goes in and out of
 “Chemistry of Life” the cell
 Study of chemical substances and processes that occur  Protects cellular components from damage and leakage
in plants, animals, and microorganisms and the changes  Pores - allow/permit/screen movement of substances in
they undergo during development and life. and out of the cell
 Focuses on processes happening at a molecular level.
 Concerned with the chemical and physicochemical CYTOPLASM
substances and processes both at a cellular and  “Cytosol”, “Cell’s inner space”
molecular level.  Large fluid filled space that provides a medium for the
 Studies about substances known as carbohydrates, organelles to remain suspended
lipids, nucleic acids, and proteins, or generally known  Site for most enzymatic reactions and metabolic
as biomolecules. activities.
 Contains dissolved nutrients, aids in breakdowns of
WHAT IS A CELL? waste products.
 Basic unit of life that is vital to our daily activities.  Moves the material around the cell
 Membrane-bound unit that contains the fundamental
molecules of life and of which living things are GOLGI APPARATUS
composed.  “Post Office of the Cell”
 RECEPTORS - group of specialized cells  Stack collection of flat vesicles
 Acts as storage of the substances produced by the
FUNCTIONS OF A CELL endoplasmic reticulum.
1. Uptake and Processing  Involved in packaging and transportation of materials
2. Excretion of wastes within the cell.
3. Response to environment stimuli
4. Contains the life code that coordinates the synthesis of ENDOPLASMIC RETICULUM
proteins & transfer genetic information.  “Transport network of the molecules”
5. Reproduction  Membranous structure that contains a network of
vesicles and tubules which enable substances to move
CELL TYPES through and isolate from the rest of the cell until
EUKARYOTIC CELLS conduction of manufacturing processes are completed.
 Contains a clearly defined nucleus and membrane  Primary role in the metabolism of carbohydrates
bound organelles.  Synthesis of lipids, steroid, and proteins
 Examples: Animal, plant, fungi, and protist  ROUGH ER
 Nucleus: Present (membrane bound)  contains proteins and enzymes
 Cell size: Large (10-100 micrometers)  synthesize new proteins, contains ribosomes
 SMOOTH ER
PROKARYOTIC CELLS  Plays a role in carbohydrates and drug metabolism
 Unicellular organism that does not contain a membrane  Synthesize different types of lipids
bound nucleus or organelles.
 Example: Bacteria and Archaea LYSOSOMES
 Nucleus: Absent (nucleoid region)  Vesicles generated from golgi apparatus
 Cell size: Small (less than a micrometer to 5  Contains hydrolytic enzymes that aid in the digetsion of
micrometers) nutrients within the cell and break down excess or any
cellular debris.
PARTS OF THE CELL & THEIR FUNCTIONS  PEROXISOME - garbage disposal system of the cell
CELL WALL  Aids in self-destruction process known as APOPTOSIS
 Provides mechanical support to the cell (cell death)
 Surrounds the cell membrane
 Aids in the maintenance of pressure within the cell NUCLEUS
 Outermost layer, rigid and stiff structure, protects cell  Considered as the master control of the cell (houses
from mechanical shocks and injuries. DNA)
 Three parts: Cellulose, Hemicellulose, Pectin  Location of genes and collections of DNA

CELL MEMBRANE NUCLEOLUS

 “Plasma Membrane”  Located within nucleus
 Double-layered membrane composed of proteins and  This is an accumulation of RNA and proteins within the
lipids nucleus
 Separates the interior of the cell from the outside  Site where ribosomal RNA is transcribed from DNA and
environment. assembled

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PEROXISOMES BIOMOLECULES
 Similar to lysosomes  Consist mostly of carbon, hydrogen, oxygen, and
 Contains enzymes that neutralize substances that may nitrogen
be toxic to the cell  Naturally occur in living organism
 Plays and important role in lipid production  Essential for various body functions and manufacture
within the body.
MITOCHONDRIA  Any organic molecule present in a living cell which
 Has the ability to yield energy by breaking down includes the different macromolecules.
nutrients.
 Produces ATP which is utilized as a source of energy LIPIDS
 Has an outer and inner membrane  Monomer: Fatty Acids
 OUTER MEMBRANE - surrounds the mitochondria  Made up of glycerol attached to 1-3 fatty acid chain
 INNER MEMBRANE  Considered as the body’s primary long term energy
 Provides physical sites utilized for production storage molecules
of energy  Also used for hormones, structural elements of cell
 Contains infoldings that form shelves where membranes and vitamins.
enzymes attach and oxidize nutrients  They serve as cushion and insulator of our organs
 Generally water-insoluble
MICROFILAMENTS  Oils, waxes, phospholipids, steroids
 Solid rods made of protein known as actin
 Aid in the generation of forces utilized in cellular CARBOHYDRATES
contraction and basic cell movements  Monomer: monosaccharide
 Contribute to cells movement on surface.  Most abundant class of bioorganic molecules
 They serve as energy sources and considered as
MICROTUBULES essential constituents of all living things
 Involved in nucleic and cell division, organiztaion of  Final products of various metabolic process
intracellular structure & intracellular transport, as well  Sugars, Starches
as ciliary and flagellar motility
 Formed through polymerization of tubulin proteins. NUCLEIC ACIDS
 Monomer: Nucleotide
ANIMAL CELL  Main information-carrying molecules of the cell and can
 Absence of cell wall, the cell wall membrane is the determine the inherited characteristics of every living
outermost covering of these cells. thing.
 The shape is not definite as the cell may undergo  Stores, transmits and utilizes genetic information
changes that can alter the cell shape.
 Do not contain plastids. PROTEINS
 Will either have small vacuole or none at all.  Monomer: Amino acids
 Presence of centrosomes.  Primary building materials of the body
 Can store excess glucose as glycogen.  Naturally, unbranched polymer
 Contains the elements CHON and most also contain
PLANT CELL sulfur.
 Has an outer rigid cell wall made up of cellulose
 Has a distinct and definite shape due to rigid cell wall
 Contain plastids
 Has a large, central vacuole
 Centrosomes are only present in the cells of some lower
plants
 Store excess glucose as starch.

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 MODULE 2: LIPIDS AND RELATED SYSTEMS
LECTURE | AY 2022-2023 1ST SEMESTER

WHAT ARE LIPIDS? 5. VITAMINS

 Heterogenous group of organic compounds that are  Lipid-soluble vitamins play a major role in the
insoluble in water & soluble in nonpolar organic regulation of several critical biological processes.
solvents.(benzene, toluene, acetone, chloroform, ether).
 An important long-term source of energy. 6. VITAMIN ABSORPTION
 Naturally occur in most plants, animals, microorganisms  Dietary fat serves as a carrier of lipid soluble
and utilized as components of the cell membrane, vitamins.
energy storage molecules, insulation and hormones.
 o Glycerol + Fatty Acid. 7. PROTECTION
 Serve as shock absorber, or protective layer, for
CHARACTERISTICS OF LIPIDS the vital organs.
 Sparingly insoluble or insoluble in water but solublein
organic solvents. 8. INSULATION
 Make up the membranes of the cell.  Fat stored beneath the skin serves to insulates the
 Energy - rich molecules mostly made up of body from extremes of cold temperature.
hydrocarbons.
 Fatty Acids, glycerol,sphingosine and sterol are its FATTY ACIDS
primary building blocks.  Vital component of lipids
 Monomer or the basic unit of Lipids
 Consist of CHO, arranged as a linear carbon chain
skeleton of variable length, generally with an even
number of atoms, with a carboxyl at one end.
 Termed as "fatty acid" due to its isolation from naturally
occurring fats.

FUNCTIONS OF LIPIDS

1. ENERGY SOURCE
 When lipids are oxidized each gram of fat releases
9 kcal of energy, or more than twice the energy
released by oxidation of a gram of carbohydrate.

2. ENERGY STORAGE TYPES OF FATTY ACIDS

 Most energy stored in the body is in the form of
lipids. Fat cells known asadipocytes are a 1. SATURATED FATTY ACIDS
particularly rich source of energy for the body. 2. UNSATURATED FATTY ACIDS
i. Monounsaturated FAs
3. CELL MEMBRANE STRUCTURAL COMPONENTS ii. Polyunsaturated FAs
 Phosphoglycerides, sphingolipidsand steroids
compose the basic structure of all cell membranes.
These membranes control the movement of
molecules in and out of the cells. They also allow
cell-to-cell communications.
 Water-repellant/hydrophobic

4. HORMONES
 Steroid hormones are considered as critical
chemical messengers. They allow tissues of the
body to communicate with each other.
 Prostaglandins & Thromboxane – secondary
messengers that mediate your hormonal response.

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POLYUNSATURATED FATTY ACIDS

 Higher melting point = dugay matunaw  Fatty Acids with a carbon chain in which there is a
 Lower chain length = higher melting point presence of two or more carbon-carbon double bond.
 Dasig matunaw ang may double bonds since indi sila  Up to 6 double bonds are found in biochemically
intact unlike single bonds. important PUFAs.

UNSATURATED FATTY ACIDS

PROPERTY
 Chemical Composition:
 Chemical Structure: Hydrocarbon chain with aterminal
carboxyl group
 Carbon-carbon bonds within the hydrocarbon chain:
ONLY C-C double bonds
SATURATED FATTY ACIDS  Hydrocarbon chains are characteristic of what group of
hydrocarbons: Alkenes
PROPERTY
 " Shape" of hydrocarbon chain: bend carbon chain at
 Chemical Composition:
Chemical Structure: Hydrocarbon chain with aterminal site of C-C double bond.

carboxyl group  Physical state at room temperature: LIQUIDS
 Melting point for two FAs of the same hydrocarbon
 Carbon-carbon bonds within the hydrocarbon chain:
ONLY one C-C single bonds. chain length: Lower
 Hydrocarbon chains are characteristic of what group of  Relationship between melting point and chain length:
Longer chain length = Higher melting point.
hydrocarbons: Alkanes.
 " Shape" of hydrocarbon chain: linear, fully-extended.
Physical state at room temperature: SOLID How do you determine the number of carbon atoms and

 Melting point for two FAs of the same hydrocarbon carbon carbon double bonds in an unsaturated fatty acid?
chain length: Higher
Relationship between melting point and chain length: a. Two numbers separated by a colon.

Longer chain length = Higher melting point.
b. The number before the colon (left) indicates the carbon
chain while the number after the colon (right) indicates
Fatty Acids with a carbon chain in which all carbon-carbon
bonds are single bonds. the number of double bonds present, as well as the
degree of the unsaturation of the fatty acid

EXAMPLE:
Stearic Acid - 18:0

- This notation denotes a FA with 18 carbon atoms and no

double bonds.

MONOUNSATURATED FATTY ACIDS

 Fatty Acids with a carbon chain in which there is a
presence of one carbon-carbon double bond.

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 BIOCHEM LEC | MODULE 2: LIPIDS AND RELATED SYSTEMS

EXAMPLE
18:3 FATTY ACID SELECTED FATTY ACIDS OF BIOLOGICAL IMPORTANCE
This notation denotes a FA with 18 carbon atoms and three
double bonds. SATURATED FATTY ACIDS

Some families of unsaturated FAs are determined by the

double-bond position relative to the methyl end of a FA chain.
PHYSICAL PROPERTIES OF FATTY ACIDS UNSATURATED FATTY ACIDS

CLASSIFICATION OF LIPIDS
ILLUSTRATION OF THE STRUCTURAL DIVERSITY ASSOCIATED
WITH LIPID MOLECULES

WATER SOLUBILITY
 When carbon chain length increases, solubility
decreases
 Long Chain FA are essentially insoluble in water as the
hydrocarbon completely dominates solubility
considerations.
 Short chain FA are slightly soluble in water due to the
polarity of the carboxyl group present.

MELTING POINT
 Carbon chain length and the number of double bonds
present / degree of unsaturation determines a fatty
acid's melting point.
 For saturated FA, when carbon length increases, melting
point increases.
 For unsaturated FAs, melting point decreases as degree
of unsaturation increases. 2 METHODS OF SUBCLASSIFYING LIPIDS INTO FAMILIES
 The double bonds in unsaturated FAs produce
bendswhich prevent unsaturated FAs from packing 1. CLASSIFICATION BASED ON CHEMICAL FUNCTION
together tightly.
 The greater the number of double bonds, the less 1.1 Energy-storage lipids (Triacyglycerols)
efficient the packing which leads to fewer
intermolecular compared to saturated FAs. 1.2 Membrane Lipids (Phospholipids, Sphingoglycolipids,
Cholesterol)

1.3 Emulsification Lipids (Bile Acids)

1.4 Messenger Lipids (Steroids & Eicosanoids)

1.5 Protective-coating Lipids (Biological Waxes)

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2. CLASSIFICATION BASED ON SAPONIFICATION MIXED TRIACYLGLYCEROL

REACTION  Triester formed from the esterification of glycerol with
more than kind of fatty acid molecule.
2.1 Saponifiable Lipids  Most biochemically important TAGs are mixed TAGs.
- TAGs, Phospholipids, Sphingoglycolipids & Biological Waxes
FATS
2.2 Nonsaponifiable Lipids  Semi-solids at room temperature.
- Cholesterol, Steroid Hormones, Bile Acids & Eicosanoids  Fat is usually solid at room temperature, however, the
warmer body temperature of living animals keeps it
semi-solid.
 Generally obtained from animal sources; hence the
term “Animal fat”.
 Saturated fatty acids predominate the composition of
fats, although there are some unsaturated fatty acids
present.
 High melting point –Packed closely together because of
the “linearity”of their fatty acid chain.

OILS
 Liquids at room temperature.
 Generally obtained from plant sources.
 Contain TAGs with larger amounts of Mono and
BASED ON CHEMICAL FUNCTION polyunsaturated FAs compared to fats.
 Due to the presence of mono and polyunsaturated FAs,
1.1 ENERGY - STORAGE LIPIDS: TRIACYLGLYCEROLS (TAGS) oils tend to havelower melting point as they are not
packed as tightly because of certain “bends”in their
 Lipid formed by the esterification of three FA to a fatty acid chains.
glycerol molecule.
 Mostly concentrated primarily in special cells known as 1.2 MEMBRANE LIPIDS: PHOSPHOLIPIDS,
adipocytes.
SPHINGOGLYCOLIPIDS, CHOLESTEROL
 Efficient at storing energy compared to glycogen
because large quantities can be packed into a very small
volume. PHOSPHOLIPIDS
 MOST ABUNDANT type of lipid present in the body.  Are the most abundant type of membrane lipid.
 Contains one or more fatty acids, a phosphate group, a
platform molecule to which the FAs and the phosphate
group are attached, and an alcohol that is attached to
the phosphate group.
 The platform molecule may either be a glycerol or
a sphingosine.

 Structure of the simple TAGs produced from

esterification reaction between glycerol and three
molecules of stearic acid.
 Three molecules of water are by-products of this
reaction

GLYCEROPHOSPHOLIPIDS
 Functions almost exclusively as components of cell
membranes & are not stored.
 A polar class of lipids
 Alcohols attached to the phosphate group in a
glycerophospholipid:
SIMPLE TRIACYLGLYCEROL 1. Choline (Phosphatidylcholines)
 a simple triacylglycerol formed from the esterification of
glycerol with three identical fatty acid molecules.

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2. Ethanolamine CHOLESTEROL
(Phosphatidylethanolamines)  No fatty residues present
3. Serine (Phosphatidylserine)  Neither glycerol nor sphingosine is present
 A C27 steroid molecule that is a component of cell
Phosphatidylcholines membranes and a precursor for other steroid-based
lipids.
 Also known as “Lecithins”
 Most abundant steroid in the human body
 Waxy solids that form colloidal suspensions in  Serves as a precursor for several other important
water steroid molecules
 Prevalent in cell membrane
 Dietary sources: Egg yolks & soybeans  LIPOPROTEINS
 Cholesterol combination
Phosphatidylethanolamines & Phosphatidylserine  Serves as the carrier system of cholesterol
 Also known as “Cephalins” 2 TYPES
 - Found in the heart & liver tissue & in high a) LDLs (Low Density Lipoprotein) - carry cholesterol
concentrations in the brain. from the liver to various tissues. BAD CHOLESTEROL.
 Important in blood clotting b) HDLs (High Density Lipoprotein) - carry excess
cholesterol from tissues back to liver. GOOD
CHOLESTEROL.

THE CELL MEMBRANE

 The cell membrane is also known as the plasma
membrane because it is responsible for separating the
cytoplasm of a cell from its surroundings.
 A lipid-based structure that also controls the movement
into and out of the cell.
 Up to 80% of the mass of a cell membrane is lipid
material consistingn primarily of the three types of
SPHINGOPHOSPHOLIPIDS membrane lipids: phospholipids, glycolipids, &
 Lipids that contain one fatty acid and one phosphate cholesterol.
group attached to a sphingosine molecule and an
alcohol attached to a phosphate group.
LIPID-BILAYER
 A two-layer thick structure of phospholipids &
 SPHINGOMYELINS
glycolipids in which the nonpolar tails of the lipids are in
 sphingophospholipids in which the alcohol
the middle of the structure and the polar heads are on
esterified to the phosphate group is choline
the outside surfaces of the structure.
 found in all cell membranes and are important
structural components of the myelin sheaths.

SPHINGOGLYCOLIPIDS
 Lipid that contains both a fatty acid and one phosphate
group component attached to a sphingosine molecule.
 Presence of amide and glycosidic linkages
 Can undergo saponifictaion reactions.

 Types of Sphingoglycolipids
 Most lipid molecules in the bilayer will contain at least
 CEREBROSIDES one unsaturated FAs
 Simplest sphingoglycolipids  The presence of unsaturated fatty acids prevents
 Contains a single monosaccharide the tight packing of fatty acid chains which will
 Occur primarily in the brain impart a flexible or fluid character to the cell
 Also present in the myelin sheath of the membrane.
nerves This characteristic is necessary as it will enable

various types of biochemical molecules must pass
 GANGLIOSIDES into and out of the cell.
 contains a branched chain up to 7  Cholesterol molecules are also components of cell
monosaccharide residues membranes and they provide rigidity to the membrane.
 Occurs both in the gray matter of the brain, as  The compact shape of cholesterol enables it to fit
well as the myelin sheath. between the FA chains of the bilayer and restrict
 More complex the movement of FA chains.

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1.4 MESSENGER LIPIDS: STEROID HORMONES AND

EICOSANOIDS

HORMONE
 A biochemical substance that serves as a means of
communication between various tissues.
 Produced by a ductless gland.

 Proteins are also components of lipid bilayers. They are STEROID HORMONE
responsible for the movement of nutrients &  A hormone that is a cholesterol derivative.
electrolytes across the membrane. Aside from this, they
also act as receptor that bind hormones & 2 MAJOR CLASSES OF STEROID HORMONES
neurotransmitters (NT). 1. SEX HORMONES
 Control reproduction and secondary sex
2 GENERAL TYPES OF MEMBRANE PROTEINS characteristics.
a. INTEGRAL MEMBRANE PROTEIN - penetrate the cell 2. ADRENOCORTICOID HORMONES
membrane  regulate numerous biochemical processes in the
b. PERIPHERAL MEMBRANE PROTEIN - nonpenetrating body.
membrane protein located on the surface of the cell
membrane. SEX HORMONES
ESTROGEN
Synthesized in the ovaries & adrenal cortex
TRANSPORT ACROSS CELL MEMBRANES 
 Female sex hormones
 Responsible for the development of female
PASSIVE TRANSPORT
secondary sex characteristics at the onset of
 Transport process in which a substance moves across a
puberty & for regulation of menstrual cycle.
cell membrane by diffusion from a region of higher
 Stimulate the development of the mammary glands
concentration to a region of lower concentration.
during pregnancy.
 No energy is required.
 Induce estrus (heat) in animals.
 Molecules that can cross the membrane in this manner:
Oxygen, Nitrogen, Water, Urea, Ethanol
ANDROGEN
 Synthesized in the testes and adrenal cortex.
FACILITATED TRANSPORT
 Male sex hormones
 Transport process in which a substance moves across a
 Responsible for the development of male secondary
cell membrane, with the aid of membrane proteins.
sex characteristics.
 Movement is from the higher concentration to a lower
 Promote muscle growth.
concentration
 NO energy is required
PROGESTINS
 Molecules that can cross in this manner: Sodium ion,
 Synthesized in the ovaries & placenta
potassium, hydronium
 Responsible for preparing the lining of uterus for
implantation of fertilized ovum.
1.3 EMUSIFICATION LIPIDS: BILE ACIDS
 Can suppress ovulation.
EMULSIFIERS
 a substance that can disperse and stabilize water
insoluble substances as colloidal particles in an aqueous
solution.

BILE ACIDS
 A derivative of cholesterol that function as a lipid-
emulsifying in an aqueous environment of the digestive
tract
 Carries an amino acid attached to the side-chain
carboxyl group with the aid of an amine linkage.

BILE
 A fluid that contains emulsifying secreted by the liver,
stored in the gallbladder, and released into the small
intestine during digestion

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ADRECORTINOID HORMONES  Increase the secretion of a protective mucus layer

MINERALOCORTICOIDS into the stomach
 Control the balance of Na+ and K+ ions in cell and  Relaxation & contraction of the smooth muscle
body fluids  Directing water & electrolyte balance
 Major Mineralocorticoid: Aldosterone  Intensifying pain
 Enhancing various inflammatory responses
GLUCOCORTICODS
 Control glucose metabolism THROMBOXANES
 Counteract inflammation  A C20-fatty acid derivative that contains a cyclic ether &
 Major Glucocorticod: Cortisol oxygen- containing functional groups.
 Cortisol  Produced by blood platelets and promote platelet
 Synthesized in the largest amount by adrenal aggregation.
glands
 Exert powerful anti-inflammatory effects in LEUKOTRIENES
the body  A C20-fatty acid derivative that contains three
conjugated double bonds & hydroxy groups
 Found in leukocytes
 Various inflammatory & hypersensitivity responses are
associated with its elevated levels

EICOSANOIDS
 An oxygenated carbon dioxide fatty acid derivative 1.5 PROTECTIVE COATING LIPIDS: BIOLOGICAL WAXES
 Metabolic precursor for most eicosanoids: Arachidonic
Acid BIOLOGICAL WAX
 Hormone-like molecules because they are not  A monoester of a long-chain fatty acid & a long-chain
transported in the bloodstream to their site of action. alcohol
Their effects are exerted in the tissues where they are  Saturated fatty acids are present
synthesized  Alcohols found in biological waxes may either be
 Has a very short “life,” as they are broken down into saturated or unsaturated (may contain 16-30 carbon
inactive residues within seconds of synthesis atoms)
 Weak polar head & two long nonpolar tails
PHYSIOLOGICAL EFFECTS OF EICOSANOIDS  Water insoluble/water repellent properties
Mediation of:  Due to the complete dominance of the nonpolar
1. Inflammatory response, a normal response to tissue structure of the long hydrocarbon chains present
damage over the weakly polar nature of the ester
2. Production of pain & fever functional group that links two carbon chains
3. Regulation of blood pressure together
4. Induction of blood clotting
5. Control reproductive functions  Functions of a Biological Wax
6. Regulation of sleep/wake cycle 1. Humans and animals secrete biological waxes to
protect hair & skin and keep it lubricated.
3 PRINCIPAL TYPES OF EICOSANOIDS 2. For animal fur: Impart repellency to the fur
3. For aquatic birds: Rely on waxes secreted from
1. PROSTAGLANDINS preen glands in order to keep their feathers water
 A C20-fatty acid derivative that contains a cyclopentane repelient
ring & oxygen-containing functional groups 4. For plants: the leaves are coated with a thin layer of
 Usually involved in: biological waxes in order to prevent excessive
 Raising body temperature evaporation and for protection against parasite
 Inhibit secretion of gastric juices attack.

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5. Waxes are used for different pharmaceutical,

cosmetics and polishing industries.
EXAMPLE:
Carnauba wax - involved in high-gloss finishes
Lanolin - obtained from sheep and used as base for skin &
creams intended to enhance water retention.

PHYSIOLOGICAL SIGNIFICANCE & ITS CLINICAL

CORRELATION
GOOD FAT vs BAD FAT

1. Saturated fat are considered as “Bad Fat”

 Can increase heart disease risk
2. Monounsaturated Fats are considered as “Good Fat”
 Can decrease both heart disease risk & breast cancer
risk
 Help reduce the stickiness of blood platelets thereby
preventing the formation of blood clots.
3. Polyunsaturated Fats are considered as “good or bad fat”
 Can reduce heart disease but promote certain types
of cancers.

Additional Information:
 Avocado, canola oil and olives are example of
dietary fats with high “good” monounsaturated FA
 Tree nuts and peanuts are also good sources of
MUFAs.

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c
LECTURE | AY 2022-2023 1 SEMESTER
ST

WHAT ARE PROTEINS? NONPOLAR AMINO ACIDS

 Are naturally occurring, unbranched polymer in which
the monomer units are Amino Acids.
 Considered as the most abundant molecules in the cells
after water.

CHARACTERISTICS OF PROTEINS
 ELEMENTAL COMPOSITION:
1. Carbon
2. Nitrogen
3. Hydrogen
4. Oxygen
5. Sulfur
 Needed for the synthesis of enzymes, certain hormones The one in blue is the constant part of the structure, the one
& some blood components. in red color is the R-group or the side chain.
 Aids in the maintenance of repair of existing tissues.
 Contain one amino group, one carboxyl group, and a
AMINO ACIDS nonpolar side chain.
 Generally found in the interior of proteins.
Changes in the side chain
helps distinguish/classify POLAR NEUTRAL AMINO ACIDS
amino acids

ALPHA AMINO ACIDS

 An amino acid in which the amino group and the
carboxyl group are attached to the alpha carbon atom.
 The nature of the side-chain distinguishes alpha amino
acids from each other, both physically and chemically

Nature of the side

chain distinguishes  An amino acid that contains one amino group, one
alpha amino acids carboxyl group, and a side chain that is polar but neutral.
from each other  The side chain of a polar neutral amino acid is neither
both physically and acidic nor basic.
chemically.
POLAR ACIDIC AMINO ACIDS

 An amino acid that contains one amino group and two

carboxyl groups, the second carboxyl group being part
of the side chain.
 The side chain of a polar acidic amino acid bears a
negative charge.

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POLAR BASIC AMINO ACIDS AMINO GROUPS

 In neutral solution, amino groups have a tendency to
accept protons, producing a positively charged species.

ZWITTERION
 A molecule that
has a positive
charge on one
atom and a
negative charge on
another atom, but
which has no net
 An amino acid that contains two amino groups and one charge.
carboxyl group, the second amino group being part of
the side chain.  In acidic solution, the zwitterion accepts a proton to
 The side chain of a polar basic amino acid bears a form a positively charged ion.
positive charge.  In a basic solution, the NH3 of the zwitterion loses a
proton, and a negatively charged species is formed.
ESSENTIAL AMINO ACIDS
ISOELECTRIC POINT
 The pH at which an amino acid exists primarily.
 At the isoelectric point, almost all amino acid molecules
in a solution are present in their zwitterion form.

PEPTIDES

 A standard amino acid needed for protein synthesis that  Chain of covalently linked amino acids.
must be obtained from dietary sources because the  Unbranched chain of Amino Acids
human body cannot synthesize it in adequate amounts
from other substances.  Are further classified by the number of Amino Acids
 Note: Arginine is required for growth in children but is present in the chain.
not an essential amino acid for adults. o Dipeptide: contains 2 AAs
o Tripeptide: 3 AAs joined together in a chain.
CHIRALITY OF AMINO ACIDS o Oligopeptide: contain 10-20 AA residues
 Four different groups attached to the a-carbon atom in o Polypeptide: longer chain compared to
all of the standard amino acids except glycine, where Oligopeptide
the R group is a hydrogen atom.
 Glycine - the simplest of the standard amino acids, is PEPTIDE BOND
achiral.  A covalent bond between the carboxyl group of one
 All of the other standard amino acids are chiral. amino acid and the amino group of another amino acid.
 Links amino acids together.
ACID-BASE PROPERTIES OF AMINO ACIDS
N-TERMINAL & C-TERMINAL

A) N-Terminal - end with the free amino group

B) C-Terminal - end with the free carboxyl group

 Both an acidic group (-COOH) and a basic group (-NH2)  The sequence of amino acids is written from the
are present on the same carbon in an a-amino acid.  N-Terminal end to C-Terminal end.
o N-terminal is always on the left and C-terminal is
CARBOXYL GROUPS on the right
 In neutral solution, carboxyl groups have a tendency to  Amino residues:
lose protons, producing a negatively charged species. o portion of an amino acid structure that remains,
after the release of H2O, when an amino acid

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 BIOCHEM LEC | MODULE 3: PROTEINS

participates in peptide bond formation as it  Protein is a peptide in which at least 40 amino acid
becomes part of a peptide chain. residues are present.
 The term polypeptides are used interchangeably
PEPTIDE NOMENCLATURE with the word Protein.
IUPAC RULES
Rule 1: The The C-terminal amino acid residue (located at the PROTEINS CAN BE CLASSIFIED AS:
far right of the structure) keeps its full amino acid name. o Monomeric - contains 1 peptide chain
o Multimeric - contains more than 1 peptide chain
Rule 2: All of the other amino acid residues have names that
end in -yl. The -yl suffix replaces the -ine or -ic acid ending of PROTEIN SUBUNIT:
the amino acid name, except for tryptophan (tryptophyl),  Peptide chains present in multimeric proteins.
cysteine (cysteinyl), glutamine (glutaminyl), and asparagine
(asparaginyl). On the basis of Chemical Composition, proteins are
classified as:
Rule 3: The amino acid naming sequence begins at the N-
terminal amino acid residue.  SIMPLE PROTEIN: only AA residues are present
 CONJUGATED PROTEIN: has one or more non-AA
BIOCHEMICALLY IMPORTANT SMALL PEPTIDES entities present in the structure in addition to one or
PEPTIDE HORMONES more peptide chains.
o Prosthetic Group: non-amino acid group
 OXYTOCIN present in a conjugated protein.
o Regulated uterine contractions & lactation
o Plays a role in stimulating the flow of milk in a PROTEIN STRUCTURE
nursing mother. FOUR LEVELS OF PROTEIN STRUCTURE

 VASOPRESSIN
o Regulates the excretion of water by the kidneys.
o Can also affect blood pressure
o Also known as Antidiuretic Hormone (ADH)

PEPTIDE NEUROTRANSMITTERS

 ENKEPHALINS
o Are pentapeptide neurotransmitters produced by
the brain and bind at receptor sites within the
brain.
o Help reduce pain
o Best known enkephalins: PRIMARY STRUCTURE
1. Met enkephalin: Tyr-Gly-Gly-Phe-Met
2. Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu

PEPTIDE ANTIOXIDANTS

 GLUTATHIONE (Glu-Cys-Gly)
o a tripeptide is present in high levels in most cells
o Regulator of oxidation and reduction reactions
o Glutathione is an antioxidant and protects cellular
contents from oxidizing agents.
 Order in which the amino acid is linked together in
GENERAL STRUCTURAL CHARACTERISTICS OF PROTEINS a protein
 Order of attachment of amino acids to each other
through peptide bonds.

SECONDARY STRUCTURE

KPORTILLANO 13
 BIOCHEM LEC | MODULE 3: PROTEINS

 Arrangement in space adopted by the backbone 2. ELECTROSTATIC INTERACTIONS

portion of a protein.  also known as salt bridges
2 Most Common Types:  Always involved in the interaction between
o Alpha Helix an acidic and basic side chain
o Beta Pleated Sheets
3. HYDROGEN BONDS
Alpha Helix  Can occur between amino acids with polar
o Protein secondary structure R groups
in which a single protein chain  Relatively weak and easily disrupted by
adapts a shape that resembles changes in the pH and temperature.
a coiled spring (helix), with the
coil configuration maintained 4. HYDROPHOBIC INTERACTIONS
by hydrogen bonds.  Occurs when there are two non-polar side
o The hydrogen bond present chains close to each other
is intramolecular.  Common in phenyl & alkyl side chains

Beta Pleated Sheets

o A protein secondary structure in which two fully
extended protein chain segments in the same or
different molecules are together by hydrogen bonds.
o The hydrogen bonds can either be Intermolecular
or Intramolecular.

QUARTENARY STRUCTURE

 Organization among the

various peptide chains in,
amultimeric protein.

TERTIARY STRUCTURE

CLASSIFICATION OF PROTEINS ACCORDING TO STRUCTURE

Globular Proteins
 Proteins whose molecules have peptide chains that
are folded into spherical or globular shapes
 Compact spherical molecules that are usually
watersoluble
 Can undergo denaturation
o The overall three-dimensional shape of a protein
 Function as enzymes and intracellular signaling
that results from the interactions between amino
molecules
acid side chains that are widely separated from each
 Example: Hemoglobin, Myoglobin
other within a peptide chain.
o Interaction between amino acid side chains.
INSULIN regulatory hormone for glucose
metabolism
FOUR STABILIZING INTERACTIONS
MYOGLOBIN involved in oxygen storage in
muscles
1. COVALENT DISULFIDE BONDS
TRANSFERRIN Involved in iron transport in blood
 the strongest of the tertiary- structure
interactions, result from the groups of two IMMUNOGLOBULINS Involved in immune system
cysteine residues reacting with each other responses
to form a covalent disulfide bond.
 Disulfide bond formation may involve two
cysteine units in the same peptide chain or
two cysteine units in different chains.

KPORTILLANO 14
 BIOCHEM LEC | MODULE 3: PROTEINS

Fibrous Proteins Myosins

 Protein whose molecules have an elongated shape  Found in muscle tissue
with one dimension much longer than the others.
 Have simple, regular and linear structures
 Such proteins have the tendency to aggregate
together to form macromolecular
structures(biomolecules)
 Provide support and external protection

Examples:

Collagen
 Most abundant in the human body
 Major structural material in tendons, ligaments, Silk Fibroin
blood vessels and skin  Also known as Beta-keratin
 Organic component of bones and teeth  Consist of small amino acid residues
 Vitamin C is needed for the synthesis of collagen

Keratin
 Found in hair, wool, skin, horns, & fingernails
 Provide protective coating for organs
 Mainly made up of hydrophobic amino acid
 Residues rendering them insoluble in water

Fibrin are produced from fibrinogen, however, they classify

as fibrous proteins (insoluble).

CLASSIFICATION OF PROTEINS ACCORDING TO FUNCTION

Elastin 1) CATALYTIC PROTEINS:
 Found in blood vessels and ligaments.  Proteins are known for their role as catalysts
 Examples: Enzymes
2) DEFENSE PROTEINS:
 Proteins are known for their role as catalyst
central to the functioning of the body's
immune systems
 Examples: Immunoglobulins/ Antibodies
3) STORAGE PROTEINS
 Bind & store small molecules for future use
Fibrin  Examples: Ferritin, Myoglobin
 Found in blood clots 4) NUTRIENT PROTEINS
 Particularly important in the early stages of life,
from embryo to infant
 Examples: Casein & Ovalbumin
5) FLUID-BALANCE PROPERTIES
 Help maintain fluid-balance between blood &
surrounding tissue
 Examples: Albumin & Globulin

KPORTILLANO 15
 BIOCHEM LEC | MODULE 3: PROTEINS

CLASSIFICATION OF PROTEINS ACCORDING TO DISEASE ASSOCIATED WITH PROTEINS

COMPOSITION KWASHIORKOR
 Is a disease that arise due to an inadequate diet
andlack of protein
 Actually the result of a lack of protein in the diet.
 It is an acute form of childhood protein – energy
malnutrition characterized by the following signs
and symptoms:
o Edema,
o Irritability
o Anorexia,
o Ulcerating dermatoses,
PHYSICAL SIGNIFICANCE & DENATURATION OF PROTEINS o Enlarged liver with fatty infiltrates.

DENATURATION MARASMUS
 Involves the disruption and possible destruction of  Is a form of severe protein-energy malnutrition
both the secondary and tertiary structures of a characterized by energy deficiency.
protein.  Caused by severe deficiency of nearly all nutrients
 Most common effect of denaturation is the especially protein and carbohydrates
precipitation or coagulation of a protein.  Signs & Symptoms:
o Extensive tissue and muscle wasting
o Variable edema
o Dry skin
o Loose skin folds over buttocks and armpit
o Drastic loss of adipose tissues
o Patients are often irritable and voraciously
hungry

 The effect could be either be reversible or EHLER’S DANLOS SYNDROME

irreversible.  EDS can result from a deficiency of collagen -
 The protein or molecule affected by this process processing enzymes or from mutations in the amino
may partially or completely lose its biological activity. acid sequences of collagen types I, III, or V
 Renaturation – process where you convert  Most clinically important mutations are found in
denatured protein to its secondary or tertiary the gene for type III collagen.
structure.  Type I – strongest form of collagen
 Type III – flexible
DENATURING AGENTS
OSTEOGENESIS IMPERFECTA
 Also known as Brittle bone syndrome.
 Is also a heterogenous group of inherited disorders
distinguished by bones that easily bent and
fractured
 Common features:
o Retarded wound healing and a rotated and
twisted spine leading a hump-back
appearance.

MUTATIONS IN THE TYPE I COLLAGEN

 Type I is also known as Osteogenesis imperfecta
tarda
 Type II is also known as Osteogenesis imperfecta
congenita (most severe form)

SCURVY
 A disease resulting from a deficiency of Vitamin C,
which is required for the synthesis of collagen in
humans.
 Common symptoms:
o → Lethargy and malaise
o → Formation of spots on the skin
o → Spongy gums
o → Bleeding mucous membranes

KPORTILLANO 16
 MODULE 4: ENZYMES
LECTURE | AY 2022-2023 1ST SEMESTER

PROSTHETIC GROUP
WHAT ARE ENZYMES?  Are tightly incorporated into protein structure by
 a compound, usually a protein, that acts as a catalyst for covalent noncovalent forces
a biochemical reaction.  Examples include derivatives of B vitamins such as
 Most enzymes are globular proteins pyridoxal phosphate, flavin mononucleotide(FMN),
 Enzymes undergo all the reactions of proteins including flavin adenine dinucleotide (FAD), thiamin
denaturation pyrophosphate, biotin and METAL IONS of Co, Cu, Mg,
 Enzymes cause cellular reactions to occur millions of Mn, and Zn.
times faster than corresponding uncatalyzed reactions.

Enzyme is dramatically affected by:

 Temperature
 Alterations in pH
 Other protein denaturants

ENZYME STRUCTURE
TWO GENERAL STRUCTURAL CLASSES:

SIMPLE ENZYME
 Composed only of protein (amino acid chains)
CONJUGATED ENZYME
 Has a nonprotein part in addition to a protein part
 Apoenzyme
 Protein part of the conjugated enzyme
 The inactive form of apoenzyme is known as
Proenzyme/Zymogen = (inactive)
 Cofactor
 Also known as coenzymes
 Nonprotein part of a conjugated enzyme

HOLOENZYME
 biochemically active conjugated enzyme produced
from an apoenzyme & a cofactor
 Apoenzyme + Cofactor = Holoenzyme
 Holoenzyme
 COENZYME: small organic molecule that
serves as nonprotein in a conjugated enzyme

CO FACTOR
 Common coenzymes are vitamins & metal ions
 Metal ion activators are inorganic & may be bonded
through coordinate covalent bonds
 Typical inorganic ion cofactor
1. Zn
2. Mg
3. Mn
4. Na
5. Fe
6. Cu
7. K

KPORTILLANO 17
 Module 4: ENYMES CO FACTOR
 Common coenzymes are vitamins & metal ions
 Metal ion activators are inorganic & may be bonded
through coordinate covalent bonds
 Typical inorganic ion cofactor
1. Zn
2. Mg
3. Mn
4. Na
5. Fe
6. Cu
7. K

What are enzymes?

 a compound, usually a protein, that acts as a
catalyst for a biochemical reaction.
 ´Most enzymes are globular proteins
 ´Enzymes undergo all the reactions of proteins
including denaturation
 Enzymes cause cellular reactions to occur millions
of times faster than corresponding uncatalyzed
reactions. PROSTHETIC GROUP
Enzymes activity is dramatically affected by:  Are tightly incorporated into protein structure by
covalent noncovalent forces
o temperature  Examples include derivatives of B vitamins such as
o alterations in PH pyridoxal phosphate, flavin mononucleotide
o other protein denaturants (FMN), flavin adenine dinucleotide (FAD), thiamin
pyrophosphate, biotin and METAL IONS of Co, Cu,
ENZYME STRUCTURE
Mg, Mn, and Zn.
TWO GENERAL STRUCTURAL CLASSES:
 Simple Enzyme: Six Major Classes of Enzymes Based on the Types of
o composed only of protein (amino acid chains) Reactions they Catalyze
 Conjugated Enzyme: OXIDOREDUCTASE
o has a nonprotein part in addition to a protein
 is an enzyme that catalyzes an oxidation-reduction
part
reaction
 requires a coenzyme that is oxidized or reduced as
o Apoenzyme
the substrate is reduced or oxidized.
 Protein part of the conjugated enzyme
 Example: Lactate Dehydrogenase (cellular
 the inactive form of apoenzyme is known as
respiration)
Proenzyme/ Zymogen = (inactive)
o Cofactor TRANSFERASE
 also known as coenzymes  an enzyme that catalyzes the transfer of a
 nonprotein part of a conjugated enzyme functional group from one molecule to another.
 A transaminase catalyzes the transfer of an amino
TWO GENERAL STRUCTURAL CLASSES: group from one molecule to another. Kinases which
 HOLOENZYME: biochemically active conjugated play a major role in metabolic energy-production
enzyme produced from an apoenzyme & a reactions, catalyze the transfer of a phosphate
cofactor group from adenosine triphosphate (ATP) to give
o Apoenzyme + Cofactor = Holoenzyme adenosine diphosphate (ADP) and a
o Holoenzyme phosphorylated product
COENZYME: small organic molecule that serves
as nonprotein in a conjugated enzyme HYDROLASE
 an enzyme that catalyzes a hydrolysis reaction in
which the addition of a water molecule to a bond
causes the bond to break.

BUENO M.
 Carbohydrases effect the breaking of glycosidic ENZYME SUBSTRATE COMPLEX (ES COMPLEX)
bonds in oligo- and polysaccharides, proteases  intermediate reaction species that is formed when a
effect the breaking of peptide linkages in proteins, substrate binds to the active site of an enzyme
and lipase effect the breaking of ester linkages in
triacylglycerols. LOCK- AND - KEY MODEL
 the active site in the enzyme has a fixes, rigid
LYASE geometrical conformation. Only substrates with a
 an enzyme that catalyzes the addition of a group to complementary geometry can be accommodated at
a double bond or the removal of a group to form a such a site, much as a lock accepts only certain keys.
double bond in a manner that does not involve
hydrolysis or oxidation.
 A dehydratase effects the removal of the
components of water from a double bond and a
hydratase effects the addition of the components
of water to a double bond.

ISOMERASE
 an enzyme that catalyzes the isomerization
(rearrangement of atoms) of a substrate in a
reaction, converting it into a molecule isomeric with
itself.

LIGASE INDUCED - FIT MODEL

 an enzyme that catalyzes the bonding together of  allows for small changes in the shape or geometry
two molecules into one with the participation of of the active site of an enzyme to accomodate a
ATP. #binding substrate. A good analogy is the changes that occur
in the shape of a glove when a hand is inserted into
Class Type of Example it.
Reaction
 The induced fit is a result of the ezyme’s flexibility;
Oxidoreductase Oxidation- Lactase-
it adapts to accept the incoming substrate.
reduction dehydrogenase
Transferase Group transfer Nucleoside
monophosphate
kinase (NMP
kinase)
Hydrolase Hydrolysis Chymotrypsin
reaction
(transfer of
functional
groups to
water) ENZYME SPECIFICITY
Lyase Additional or Fumarase
 Extent to which an enzyme's activity is restricted to
removal of
groups to form a specific substrate, a specific group of substrate, a
double bonds specific type of chemical bond or a specific type of
Isomerases Isomerization Triose phosphate reaction.
(intramolecular isomerase  The degree of enzyme specificity is determined by
group) the active site.
Ligases Ligation of two Aminoacyl-tRNA
substances at synthetase ABSOLUTE SPECIFICITY
the expense of  enzyme will catalyze only one reaction. The most
ATP hydrolysis
restrictive of all specificities is not common.
 Catalase is an enzyme with absolute specificity. It
MODELS OF ENZYME ACTION
catalyzes the -conversion of hydrogen peroxide
ACTIVE SITE (H2O2) to O2 and H2O. Hydrogen peroxide is the
 relatively small part of an enzyme’s structure that is only substrate it will accept.
actually involved in catalysis.

BUENO M.
GROUP SPECIFICITY must leave the site before the cycle can be repeated.
 the enzyme will act only on molecules that have a When each enzyme molecule is working at full
specific functional group, such as hydroxyl, amino, capacity, the incoming substrate molecules must
or phosphate groups. “wait their turn” for an empty active site.
 Carboxypeptidase is group-specific; it cleaves  Turnover Number the number of substrate
amino acids, one at a time, from the carboxyl end molecules transformed per minute by one molecule
of a peptide chain. of enzyme under optimum conditions of
LINKAGE SPECIFICITY temperature, pH and saturation.
 enzyme will act on a particular type of chemical ENZYME CONCENTRATION
bond, irrespective of the rest of the molecular  If the amount of substrate present is kept constant
structure. and the enzyme concentration is increases, the
 Phosphatases hydrolyze phosphate-ester bonds in reaction rate increases because more substrate
all types of phosphate esters. Linkage specificity is molecules can be accommodated in a given amount
the most general of the common specificities. of time. (better if enzyme reaction is higher than
STEREOCHEMICAL SPECIFICITY substrates) = readily process the substrate
 enzyme will act on a particular stereoisomer.
Chirality is inherent in an enzyme active site ENZYME INHIBITION
because amino acids are chiral compounds. ENZYME INHIBITOR
 An L-amino acid oxidase will catalyze the oxidation slows or stops the normal catalytic function of an
of the L-form of an amino acid but not the D-form enzyme by binding to it
of the same amino acid.
COMPETITIVE INHIBITOR
 a molecule that sufficiently resembles an enzyme
FACTORS THAT AFFECT ENZYME ACTIVITY
substrate in shape and change distribution that it
ENZYME ACTIVITY
can compete with the substrate for occupancy of
 a measure of the rate which an enzyme converts
the enzyme’s active site. (if mang agaw – d gyapon
substrate to products in a biochemical reaction.
mag work)
 Four factors: temperature, pH, substrate
concentration and enzyme concentration.

TEMPERATURE
 When the temperature increases beyond a certain
point, the increased energy begins to cause
disruptions in the tertiary structure of the enzyme;
denaturation is occurring.
NON-COMPETITIVE INHIBITOR
 Change in tertiary structure at the active site
 a molecule that decreases enzyme activity by
impedes catalytic reaction, and the enzyme activity
binding to a site on an enzyme. (allosteric site,
quickly decreases as the temperature climbs past
where non-competitive inhibitor binds)
this point
 Optimum temperature is the temperature at which
an enzyme exhibits maximum activity. (37°C)
PH
 Small changes in pH (less than one unit) can result
in enzyme denaturation and subsequent catalytic
activity
 Most enzymes exhibit maximum activity over a very IRREVERSIBLE INHIBITOR
narrow ph range. (4-6)  a molecule that inactivates enzymes by forming a
 Optimum pH the pH at which an enzyme exhibits strong covalent bond to an amino acid side-chain
maximum activity. (7.5) group at the enzyme’s active site.
SUBSTRATE CONCENTRATION
 As substrate concentration increases, the point is
eventually reached where enzyme capabilities are
used to their maximum extent.
 Each substrate must occupy an enzyme active site
for a unit amount of time, and the products

BUENO M.
 ENZYMES IN CLINICAL USE Water soluble Vitamins Fat-soluble vitamins
DRUGS THAT INHIBIT ENZYME ACTIVITY
Vitamin C Vitamin A
 STATINS- HMG Coenzyme A reductase inhibitors (3- Thiamin Vitamin D
hydroxy-3-methylgutaryl) ; lower serum lipid Riboflavin Vitamin E
concentration. (atorvastatin) Naicin Vitamin K
 EMTRICABINE and TENOFOR DISOPROXIL Pantothenic acid
FUMARATE inhibitors of viral reverse transcriptase; Vitamin B6
block replication of HIV Biotin
Folate
 ACE INHIBITORS (Captopril, Lisinopril, Enalapril) –
Vitamin B12
antihypertensive agents
 Lactam Antiobitics (Penicillin and Amoxicilin) – Vitamin is an organic compound; essential in small
inhibitors of alanyl alanine (component of bacterial amounts for the proper functioning of the human body,
cell wall) carboxypeptidase-transpeptidase, thus that must be obtained from dietary sources because the
blocking cell wall synthesis body cannot synthesize it
 Sulfa drugs – mimic PABA (antagonist)
VITAMIN B
The preferred and alternative names for the B vitamins
SELECTED BLOOD ENZYME ASSAYS USED IN  Thiamin (vitamin B1)
DIAGNOSTIC MEDICINE  Riboflavin (vitamin B2)
 Niacin (nicotinic acid, nicotinamide, vitamin B3)
 Lactase Dehydrogenase (LDH): Heart disease, liver
 Vitamin B6 (pyridoxine, pyridoxal, pyridoxamine)
disease
 Folate (folic acid)
 Creatinine Phosphokinase (CPK): Heart disease
 Vitamin B12 (cobalamin)
(increase blood)
 Pantothenic acid (vitamin B5)
 Aspartate Transaminase (AST): Heart disease, Liver
 Biotin (Vit.B7)
disease, Muscle Damage
 Exhibit structural diversity
 Alanine Transaminase (ASL): Heart disease, liver
Major function: B Vitamins are components of
disease, muscle damage
coenzymes
 Gamma-glutamyl Transpeptidase (GGTP): Heart
disease, liver disease B vitamin Coenzymes Groups
transferred
 Alkaline Phosphate (ALP): Bone disease, liver
Thiamin Thiamin Aldehydes
disease pyrophosphate (TPP)
Riboflavin Flavin Hydrogen atoms
GENERAL CHARACTERISTICS OF VITAMINS mononucleotide
(FMN)
Water soluble Fat-Soluble Favlin adenine
Vitamins (Vitamin Vitamins dinulcleotide (FAD)
B and C) Niacin Nicotinamide Hydrogen atoms
(Vitamins A,D,E,
adenine
and K) Dinucleotide (NAD+)
Absorption Directly into the First enter into the Nicotinamide
blood lymph system adenine
Transport Travel without Many require Dinucleotide
carriers protein carriers phosphate (NADP+)
Storage Circulate in the Found in cells Pantothenic Coenzyme A (CoA) Acyl groups
water filled parts of associated with fat acid
the body
Vitamin B6 Pyridoxal-5- Amino Groups
Excretion Kidneys remove Tend to remain in
phosphate (PLP)
excess in urine fat-storage sites
Pyridoxine-5’-
Toxicity Not likely to reach Likely to reach phosphate (PNP)
toxic levels when toxic levels when Pyridozamine-5-
consumed from consumed from phsophate (PMP)
supplements supplements
Biotin Biotin Carbon dioxide
Dosage Needed in frequent Needed in periodic
doses doses
(carboxyl group)
frequency Folate Tetrahydrofolate One-carbon groups
Relationship Function as Do not function as (THF) other than CO2
to coenzymes coenzymes
Vitamin B12 Methylcobalamin Methyl groups,
coenzymes hydrogen atoms

BUENO M.
VITAMIN C (1g max)
 also known as Abscorbic Acid VITAMIN K
 co-substrate in the formation of structural protein  Two major forms; K1 and K2
collagen  K1 found in dark green, leafy vegetables
 General function: serves as antioxidant  K2 is synthesized by bacteria that forw in colon
 Often added to food as a preseratice  Dietary need supply: 1/2 synthesized by bacteria
 Involved in the metabolism of several AAs that end and 1/2 obtained from diet
up being converted to the hormones  Active in the formation of proteins involved in
norepinephrine & thyroxine regulating blood clotting.
 Cannot be taken with warfarin.
VITAMIN A
 Four Major Functions:
o Vision
o Regulating Cell Differentiation
o Maintenance of the Health of Epithelial Tissues
o Reproduction & Growth
 Vision: In the eye- vitamin A combines with opsin
protein, to form the visual pigment rhodopsin,
which further converts light energy into nerve
impulses that are sent to the brain.
 ´Regulating Cell Differentiation - process in which
immature cells change to specialized cells with
function.
 Maintenance of healthy epithelial tissues via
epithelial tissue differentiation.
- Lack of vitamin A causes such surfaces to
become drier and harder than normal.
 Reproduction and Growth: In men, vitamin A
participates in sperm development
 In women, normal fetal development during
pregnancy requires vitamin A.

VITAMIN D
Two forms active in the body: Vitamin D2 & D3
 The two most important members of the vitamin D
family of molecules are vitamin D3 cholecalciferol
and vitamin D2 ergocalciferol. Vitamin D3 is
produced in the skin of humans and animals by the
action of sunlight (ultraviolet light) on its precursor
molecule, the cholesterol derivative 7-
dehydrocholesterol (a normal metabolite of
cholesterol found in the skin)

VITAMIN E
 Alpha-tocopherol is the most active biological
active form of Vitamin E
 Peanut oils, green leafy vegetables and whole grain
products are the sources of vitamin E
 Primary function: Antioxidant – protects against
oxidation of other compounds

BUENO M.
Module 5: CARBOHYDRATES  Most common monosaccharides have 3 to 9 carbon
 Carbohydrates are considered as the MOST atoms
ABUNDANT class of bioorganic molecules.  ALDOSES: monosaccharides containing an aldehyde
 Constitute about 75% by mass of dry plant materials group
 A polyhydroxy aldehyde, a polyhydroxy ketone or a  KETOSES: monosaccarides containing a ketone
compound that yields polyhydroxy aldehydes and group
poluhydroxy ketones.

DISACCHARIDES
Carbohydrates that contain two monosaccharides
joined by a glycosidic bond.
FUNCTIONS
1) Provides energy
2) Storehouse of chemical energy
3) Supply carbon atoms for the synthesis of other
biochemical substances
4) Components of supportive structures in plants,
crustacean shells, & connective tissues in animals
5) Essential component of nucleic acids; form part of
the structural framework of DNA & RNA molecules

In the formation of a disaccharide, one of the

monosaccharide reactants functions as a hemiacetal,
and the other functions as an alcohol.

CLASSIFICATION OF CARBOHYDRATES
MONOSACCHARIDES
Carbohydrates are sugar polymers
Carbohydrates = Carbon + Water
General Formula

Disaccharide Formation

 Contains a single polyhydroxy aldehyde or

polyhydroxy ketone unit.
 Cannot be broken down into simpler units by
hydrolysis reactions.
 Pure monosaccharides: watersoluble, white &
crystalline solids

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 GLYCOSIDIC LINKAGE: bond in a disaccharide  Simplest monosaccharide
resulting from the reaction between the hemiacetal  These are trioses are important intermediates in the
carbon atom - OH group of one monosaccharide process of glycolysis
and an -OH group on the other monosaccharide.  D- glyceraldehyde is a chiral molecule while
 Bond is always a carbonoxygen-carbon bond dihydroxyacetone is not

2. D-Glucose

 Most abundant in nature

 Most important in a human
nutritional standpoint
 Utilized as a primary source of
OLIGOSACCHARIDES energy
 Contain 2-10 monosaccharide units covalently  Ripe grapes are a good source of
bonded to each other glucose; hence, it is also known as
 Disaccharides are considered as the most common grape sugar
type of oligosaccharide  Other names: Dextrose / Blood
 Often associated with lipids sugar
 Once hydrolyzed, it produces monosaccharides  Normal concentration in human
blood: 70 - 100mg/dL

INSULIN & GLUCAGON

 Play an important role in keeping blood glucose
concentration within the normal range
 Abnormal functioning of the hormonal control
process for blood glucose levels leads to Diabetes

D-Glucose L-Glucose
Tastes sweet, nutritious Tasteless and cannot be
POLYSACCHARIDES
& a vital component of used by the human body
 A polymeric carbohydrate that contain a large the human diet
number of monosaccharide units, joined to the next
by one or more glycosidic bonds

3. D – Galactose
Aka BRAIN SUGAR
 Synthesized from glucose in the mammary glands
MONOSACCHARIDES:
for use in lactose
Biochemically Important Monosaccharides
 Present as a chemical marker that distinguishes
1. D- Glyceraldehyde & Dihydroxyaceton
types of blood
 D - glucose & D - galactose are Epimers

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4. D-Fructose  FORMATION OF MALTOSE
Description & Characteristics:
 Most important ketohexose
 aka Levulose & fruit sugar
 Sweetest-tasting of all sugars
 Present in many fruits and honey
 Sometimes used as a dietary sugar 2. Cellobiose

 From the 3rd to the 6th carbon, the structure of

fructose is identical to that of D – glucose

 Produced as an intermediate in a hydrolysis

reaction
 Contains two D-glucose monosaccharides
 Cannot be digested by humans or fermented by
5. D-Ribose yeast
 D - ribose is classified as a pentose sugar
 A known component of RNAs & energy-rich 3. Lactose
compounds such as ATPs

D - RIBOSE VS. DEOXYRIBOSE  Major sugar found in Milk; aka Milk sugar
 Important ingredient in commercially produced
infant formulas that are designed to stimulate
mother' s milk
 Additional Information: Souring of milk is due to
the conversion of lactose to lactic acid by
bacteria in mi l k

4. Sucrose
DISACCHARIDES:
1. Maltose

 Also known as common table sugar

 Known as the MOST ABUNDANT out of all
 also known as Malt Sugar disaccharides
 Monosaccharide units: Glucose  Produced commercially from the juices of
 Produced whenever the polysaccharide starch sugarcane & sugar beets
breaks down  This is a non-reducing sugar
 Classified as a reducing sugar
 Undergoes hydrolysis

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Sucrose: Additional Information POLYSACCHARIDES:
 Sugarcane contains up to 20% by mass sucrose Biochemically Important Polysaccharides
 Sugar beets contain up to 17% by mass sucrose
 Easily digested substance due to the enzyme Storage Polysaccharides
sucrase 1. STARCH
 Sucrose hydrolysis produces an equimolar mixture
of glucose + fructose known as Invert Sugar

OLIGOSACCHARIDES:

Homopolysaccharide containing glucose

monosaccharide units

Polyglucose polysaccharides isolated from most

starches:
 These are carbohydrates that contain three to ten  Amylose
monosaccharide units that are bonded together by  Amylopectin
glycosidic linkages
 Raffinose & Stachyose are naturally occurring Amylose :
oligosaccharides found in onions, cabbage, broccoli, i. straight-chain glucose polymer
brussel sprouts, whole wheat, and all types of beans ii. accounts for 15-20% of the starch

1. Raffinose Amylopectin:
Monosaccharide units: galactose, glucose, and iii. branched glucose polymer
fructose iv. accounts for 80-85% of the starch

2. GLYCOGEN

2. Stachyose
Monosaccharide units: galactose, glucose, fructose,  Polysaccharide containing only glucose units
and an additional galactose  Form of stored glucose in humans & animals
 Known as animal starch
 Storage sites: Liver cells & muscle cells
 Ideal storage form for glucose
 When there is excess glucose in the blood, it is
converted to glycogen
 If glucose level in the blood drops, some stored
glycogen is hydrolyzed back to glucose

GLYCOGENESIS
 Process wherein formation of glycogen occurs
 Takes place when blood glucose levels are
POLYSACCHARIDES sufficiently high. This is to allow excess glucose
Important parameters that distinguish various to be stored in the liver and muscle cells
polysaccharides
Glycosidic linkages Degree of branching of GLYCOGENOLYSIS
between monomer units the polymer chain  Occurs primarily in the liver

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  Stimulated by glucagon & epinephrine CLASSIFYING MONOSACCHARIDES AS D OR L
 Glycogen is broken down into glucose to ENANTIOMERS
provide immediate energy & to aid in the
maintenance of blood glucose levels during
fasting

Structural Polysaccharides
CELLULOSE

D, L nomenclature:
 Gives the configuration only at the highest
numbered chiral center.
 The highest numbered chiral center in a
monosaccharide is always the chiral center that is
farthest from the monosaccharide’s carbonyl group

 Most abundant naturally occurring polysaccharide

 Structural component of cell walls
 Fibrous, water-insoluble substance
 Unbranched glucose polymer
 Not considered as a source of nutrition for human CYCLIC FORMS OF MONOSACCHARIDES
but still a vital component of a balanced diet as it
serves as a dietary fiber
 Desirable intake of dietary fiber : 25g - 35g
 Readily absorbs water, leading to softer stools and
frequent bowel action
 Many weight - loss products on the market are
composed of bulk-inducing fibers such as
methylcellulose

CHITIN

THINGS TO REMEMBER TO MAKE THIS EASIER:

1) “Down Right” – All groups found on the right side of

 Similar to cellulose in both function & structure the Fischer Projection is placed “Below” the ring
 Gives rigidity to the exoskeletonsof crabs, lobsters,
2) “Up Left” – All groups found on the left side of the
shrimps, insects, & other arthropods
Fischer Projection is placed “Above” the ring
 Occurs in the cell walls of fungi

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THINGS TO REMEMBER TO MAKE THIS EASIER:

1) A COUNTERCLOCKWISE direction is observed when

placingthe carbon atoms and the different groups.

HAWORTH PROJECTIONS
a two-dimensional structural notation that specifies the
three-dimensional structure of a cyclic form of a
monosaccharide

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