LESSON 1: INTRODUCTION TO c.

It expands in freezing
BIOCHEMISTRY
d. High degree of intermolecular hydrogen
BIOCHEMISTRY – is a systematic study of chemicals bonding.
of the living system, their organization and the principles  Exhibits surface tension
involved in their participation in the living process.  High boiling point, heat of vaporization,
 Once part of organic chemistry specific heat.
It rose in 1940’s due to the following reasons:
 Many inquiries in the field of medicine that e. Exhibit capillary action.
needs to be addressed  Ability to creep upward in narrow
 Multi enzyme of the living cell has been passages.
recognized.
 Heredity recognized that has a molecular basis. BIOLOGICAL FUNCTIONS OF WATER
CELL – key element of biochemistry; basic unit of life;
building block of life. 1. It regulates body temperature.
2. Universal solvent.
REQUIREMENT FOR CELL TO BE ALIVE: 3. Good transport medium.
1. Material Requirement: 4. Good buffer.
 Macromolecules 5. Reactant - biological processes.
 Water
 Inorganic ions (Na, K, Mn etc.) INORGANIC IONS

2. Energy Requirement: Atoms with unshared electrons in the outer shell.

 network of energy transformation in a form of
chemical reactions. FUNCTIONS OF INORGANIC IONS
 Conversion of stored energy to useful energy
1. Activates enzyme.
 Possible – multi enzyme system
2. Maintenance – biological conformation of
macromolecules
3. Information system – control, regulation and
3. Fluid retention.
continuance of activities of the cell.
4. Component of buffer system.
Composed of the following:
 Multi enzyme system – chemical reactions
POTENTIAL HYDROGEN (PH)
 Hormones – self regulation
 DNA – self replication
 0-14 represents H3O+ concentration
 7 at 25C – neutral
4. Organization – components are distributed –
 Less than 7 – acidic
simultaneous activities.
 More than 7 – basic
INORGANIC PROPERTIES OF CELL
FORMULA:
WATER pH=−log ⁡¿
Note: the number of significant figures on H 3O+
PROPERTIES OF WATER corresponds to the decimal places of pH.
a. Polar
 Bent shape; most of negative charge CALCULATING PH FROM OH.
from oxygen and positive charge from
the hydrogen side. 1. Find the pOH find the formula:
pOH =−log ⁡( OH )
b. Amphoteric 2. Calculate pH with pOH using the formula:
 Can act either base or acid. pH + pOH =14
pH=14− pOH
CALCULATING pH FROM H3O+.
 b. Tetrose – four-carbon sugar like erythrose
1. Substitute the given with the formula: c. Pentose – five-carbon sugar like ribose
− pH

H 3 O+ ¿=10 ¿ d. Hexose – six-carbon sugar like glucose

e. Heptose – seven-carbon sugar like
seduheptulose
Note: Same formula and calculations with pOH.
FISCHER PROJECTIONS
BUFFERS  devised by Emil Fischer
 is a method using two-dimensional
A solution that maintains the pH by neutralizing added representation of a three-dimensional structure
acid or base. of molecules on a page.

CALCULATING THE PH OF A BUFFER HAWORTH PROJECTION FORMULA

By rearranging the Ka (constant) expression to  emphasizes the existence of a 6-membered ring
give [H3O+], we obtain the ration of acetic acid/acetate for aldohexoses and 5-membered ring for
buffer. ketohexoses

EXAMPLES OF MONOSACCHARIDES
SAMPLE PROBLEM
 Glucose – energy and structure
The Ka for acetic acid (C2H3COOH), is 1.8x10-5.
 Fructose – used to produce glycogen
What is the pH of a buffer prepared with 1.0M
 Galactose – formation of myelin
CH3COOH and 1.0 M C2H3O2?
 Ribose – RNA and DNA
 Deoxyribose – phosphate backbone; DNA

2. DISACCHARIDES
 composed of two monosaccharide linked
together
 quick source of energy

EXAMPLES OF MONOSACCHARIDES
 Sucrose – glucose + fructose
 Maltose – glucose + glucose
 Lactose – galactose + glucose
 Cellobiose – glucose + glucose arranged
differently.

LESSON 2: CARBOHYDRATES 3. POLYSACCHARIDES

CARBOHYDRATES
 most abundant of all organic compounds in
nature.
TYPES OF CARBOHYDRATES
1. MONOSACCHARIDE
 simplest form of carbohydrates and cannot be
split or hydrolyzed into smaller carbohydrates.
 KETOSE - carbonyl group on the second
carbon as ketone
 ALDOSE - carbonyl on the first carbon atom as
an aldehyde
 A monosaccharide is a single unit of sugar
which can be classified into:
a. Triose – three-carbon sugar like
glyceraldehyde
 a polymer of many monosaccharides joined
together.
 Structure, energy storage and cellular
messaging.
EXAMPLES OF POLYSACCHARIDES
 Amylopectin – plant energy storage.
 Cellulose – plant structure.
 Glycogen – used as energy storage.
 Amylose – plant energy storage.
PHYSICAL PROPERTIES OF CARBS
1. The mono and disaccharides are optically active
except sucrose.
 they have the ability to rotate plane-polarized
light
2. Solubility and Diffusion Tendencies. 5. Iodine Test for starch.
 mono and disaccharides form true solutions with  the presence of starch
water – osmosis.  reddish-purple and brown colors.
 Polysaccharides on the other hand, do not form
true solutions with water – basis in storing 6. Barfoed’s reaction
energy.  Monosaccharide + Barfoed’s reagent - Cu2O +
other products.
3. Taste.  distinguish between monosaccharide and
 mono and disaccharides are sweet in taste. disaccharides
 Polysaccharides are tasteless and are insoluble in
water. 7. Nylander solution.
 used for testing sugar in urine.
CHEMICAL PROPERTIES OF CARBS
8. Fehling’s Test.
1. Hydrolytic Property.  used to quantify sugar by weighing Cu2O
 Not for monosaccharides.
 Di and poly split – simple carbs w/ reax to 9. Ammoniacal silver nitrate.
water.  Reducing sugar + ammoniacal silver nitrate -
a. Boiling in an acidic medium. Silver + other products.
b. Enzymatic hydrolysis in chemical digestion
of food. 10. Potassium permanganate reaction.
 Gives colorless solution and brown precipitate
2. Reducing properties of monosaccharide and of Manganese oxide.
disaccharides (except sucrose).
 analysis of sugars 11. Picric acid reaction.
 disease diagnosis like diabetes mellitus  basis of the colorimetric method of determining
 protective synthesis sugars.

3. Esterification or formation of Esters STRUCTURAL POLYSACCHARIDES

 activation of sugar metabolites
1. Cellulose in plants.
4. Fermentation.  most abundant polysaccharide.
 Degradation of sugars through the actions of  liner chain of β-D-glucose units about 100-2000
enzymes units

5. Dehydration of monosaccharide 2. Inulin.

 synthesis of bigger molecules from the simple  a fructosan - composed of about 30 units of
sugar molecules. frustose.

CHEMICAL TEST FOR CARBS 3. Chitin.

 polymer of N-acetyl-glucosamine
1. Osazone formation.
 formation of yellow crystal. 4. Hyaluronic acid.
 made up of glucoronic acid and N-acetyl-
2. Molisch Reaction. glucosamine.
 general test  mucopolysaccharide in cell coats
 violet color – positive.
5. Peptidoglycan.
3. Moore’s Test.  polymer of amino acid sugars
 alkali on carbohydrates  component of bacterial cell wall
 Brown product with caramel odor
BIOCHEMICAL FUNCTIONS OF CARBS
4. Benedict’s Test for reducing sugars.
 blue color into green or yellow. 1. Source of energy
2. stored energy like cellulose and starch in plants
3. for structural material and protective covering
4. regulatory function in the form of glycolipids and
glycoproteins
PROTEINS
 Geek word “proteios”, meaning “first”.
 AMINO ACIDS - building blocks of protein.
 generally, provides structure in membranes,
build cartilage and connective tissue, transport
oxygen in blood and muscle, direct biological
reactions as enzymes, defend the body against
infection and control metabolic processes as
hormones.
 Proteins can even be a source of energy.
STRUCTURE OF AMINO ACIDS
 central carbon atom (α carbon) bonded to an
ammonium group (---NH3+),
 a carboxylate group (---COO-),
 a hydrogen atom (---H+) and
 a side chain called an R group.
CLASSIFICATION OF AMINO ACIDS
1. NON-POLAR AMINO ACID.
 contain alkyl or aromatic R groups
 hydrophobic (“water-fearing”).
 ala, val, leu, ile, met, phe, trp and pro.
2. POLAR AMINO ACIDS.
 neutral amino acids.
 contain polar R groups such as hydroxyl (--OH),
thiol (--SH) and amide (--CONH2)
 hydrophilic (“water-attracting”)
 ser, thr, tyr, sys, asn,gln, gly, lys,arg and his.
3. ACIDIC AMINO ACID
 Contains R groups that have carboxylate (--
COO-), a negatively charged R group
 asp and glu.
4. BASIC AMINO ACID
 contain R groups that have ammonium (---
NH3+),a positively charged R group
 1. Primary Structure
ESSENTIAL AMINO ACIDS
 amino acids cannot be biosynthesized.
 Lysine, Tryptophane, histidine, leucine,
isoleucine, threonine, methionine, arginine,
glycine and phenylalanine.
PHYSICAL PROPERTIES OF AMINO ACIDS
1. insoluble in non-polar solvents, soluble in water.
2. They have high melting points – decomposition.
3. they are dipolar
 zwitterion - ionized amino acid structure.
CHEMICAL PROPERTIES OF AMINO ACIDS
1. Amphoteric
 they react both as an acid and base
2. Reaction with nitrous acid.
 react with nitrous acid (HNO2) to form an
alcohol, free nitrogen and water.
3. Ninhydrin reaction
 test for the presence of amino acid and proteins
4. Deamination of amino acids.
 removal of amino group from the amino acid.
 used as metabolites in glycolysis and Kreb cycle
5. Decarboxylation.
 removal of carboxyl group of the amino acid
 resulting into amines - being precursors to many
hormones
6. Peptide bonding.
 linking of amino acids through the amino group
+ carboxyl group of another amino acid =
PEPTIDES
PEPTIDE FORMATION
 peptide bond is an amide bond that forms when
–NH3+ group of one amino acid reacts with the
–COO- group of the next amino acid
 planar in structure
 (a) dipeptide with two amino acids;
 (b)tripeptide- with three amino acids;
 (c) tetrapeptide with four amino acids;
 (d) pentapeptide with 5 amino acid in the
peptide chain and
 (e) polypeptide with 6 or more amino acids in
the peptide chain.
FOUR STRUCTURAL LEVELS OF PROTEIN
 particular sequence of amino acid held together
by a peptide bond.
2. Secondary Structure
 type of structure that forms when amino acid
form hydrogen bonds within a polypeptide or
between polypeptides
 The three most common types of secondary
structure are:
 a. Alpha helix (α-helix). CLASSIFICATION OF PROTEINS
b. Beta-pleated sheet (β-pleated).
c. Triple helix. BASED ON SOLUBILITY

3. Tertiary Structure 1. Fibrous protein.

 attractions and repulsions between the R groups  Insoluble in water and dilute salt solution
of the amino acid in the polypeptide chain  helical and in pleated sheets
 structural needs of the tissues.
4. Quaternary Structure a. Collagens in bones, teeth, skin, tendon and
 consists of two or more polypeptide chains or connective tissues
subunits b. Elastin in ligaments, walls of blood vessels
 two or more protein subunits combine to form c. Keratin in hair, wool, nails, hooves.
one protein
2. Globular protein.
CHEMICAL PROPERTIES OF PROTEIN  Soluble in water or in water that contains certain
salts
1. Hydrolysis.  folded and compact.
 can be hydrolyzed to give individual amino acid. a. Albumin in egg white and blood
b. Globulins as part of the defense mechanism
2. Denaturation. against diseases
 occurs when there is a disruption of any of the
bonds that stabilize the secondary, tertiary and BASED ON COMPOSITION
quaternary structure
 Denaturation can be: 1. Glycoproteins – with sugar units like globulins
a. Heat
b. Mixed with acid/base 2. Hemorproteins – with heme units like hemoglobin
c. Mixed with organic compounds (like ethanol
and isopropyl)
d. Mixed with heavy metal ion (Ag, Pb and 3. Lipoproteins – with lipids which carry lipids
Hg) including cholesterol.
e. Undergo mechanical agitation like whipping
4. Metalloproteins – proteins incorporated with metal
COLOR REACTION FOR PROTEINS AND AMINO ions like some enzymes
ACIDS
5. Nucleoproteins – bound to nucleic acids such as
ribosomes
1. Ninhydrin reaction
 gives blue or violet complex - presence of alpha 6. Phosphoproteins- with phosphate ester on the side
amino acids chain or group such as serine.

2. Biuret test. BASED ON NUTRITION

 lavender product is obtained - presence of 2 or
more peptide bonds
3. Xanthoproteic Test
 gives orange precipitates of NaOH
4. Sulfur Test.
 gives black precipitates of lead sulfide
5. Liebermann’s Test.
 gives violet colored product – tryptophan
6. Hopkins-Cole Test
 gives violet ring if the tryptophan is present
1. Complete or high-quality proteins
 They contain all the essential amino acids in
about the same ratio as they occur in man.
2. Incomplete or low-quality proteins
 They lack one or more essential amino acid.
3. Complementary proteins.
 These are combinations of proteins that when
taken together, provide about the same ratio of
essential amino acid in complete proteins.
BASED ON FUNCTION IN BIOLOGICAL SYSTEM
1. Enzymes 4. Lyases
 acts as biological catalyst.  remove groups from the substrate (other than by
2. Hormones hydrolysis) to form a double bond or conversely
 regulates chemical reactions like growth add groups to double bonds.
hormones  Fumarase, aldolase, glycogen synthase
3. Storage proteins
 they provide the essential amino acids for the 5. Isomerases.
body like cereals.  isomerization of the substrate
4. Neurotransmitter  alanine isomerase, epimerase
5. Transport proteins
 they carry essential nutrients for the body. 6. Ligases
6. Structural proteins  allows joining two molecules
 that provide support like collagen, elastin and  DNA ligase, carboxylase
keratin.
7. Toxins ENZYME NOMENCALTURE
 they serve to defend the organism and are  given a trivial name based on its source
extremely toxic to other forms of animals in a  named based on the rules set by the Enzyme
very little amount like venom. Commission of the International Union of
8. Protective proteins Biochemistry (IUB)
 they protect organisms from foreign substances  change the ending of the name of the substrate
like antibodies. (substance to be catalyzed) to “-ase”

ENZYMES AND VITAMINS ENZYME ACTION

Enzymes as a biological catalyst, increases the rate of a 1. The substrate interacts with the enzyme at the
reaction by changing the way a reaction takes place active site.
2. The enzyme binds the substrate holding it in
 HOLOPROTEIN is an enzyme composed of place until a second substrate molecule is
combined proteins. brought nearer.
 APOENZYME is the protein part of the 3. The colloidal nature of the enzyme provides a
holoprotein. greater surface area of adsorption of the
 COFACTOR is component of the enzyme substrate molecules, thus, increasing the
protein which is necessary in carrying out probability of effective collision of substrate
catalytic functions. molecules.

CLASSIFICATION OF ENZYMES BASED ON ACTIVE SITE

FUNCTION:  is a portion of an enzyme that binds the substrate
or reactant during the reaction
1. Oxidoreductases  site has a catalytic site and a binding site
 oxidize and reduce substances by transferring
hydrogen or electron. BINDING SITE
 Catalase, peroxidase.  is an area that holds substrate in proper place.
 shape of the binding site is complementary to
2. Transferases. the substrate and determines the specificity of
 These removes groups including hydrogen, and the enzyme.
transfer them to acceptors including water.
 Kinase, aminotransferase. THEORIES ON ENZYME ACTION

3. Hydrolases 1. Lock and Key Theory

 catalyze the splitting of covalent bond of the
substrate and that of water molecules with the
subsequent addition of hydrogen and hydroxide
ions to the fragments of the substrate molecule.
 Amylase, protease, lipase.
 states that the structure of the substance must fit
into that of the enzyme for catalysis to occur.
2. Induced-Fit Theory
  presents, that during enzyme action, the enzyme
is induced by the substrate to undergo structure
changes to be able to interact with it
FACTORS AFFECTING ENZYME ACTIVITY
2. Vitamin P or Citrin
 helps vitamin C in keeping the walls of small
blood vessels firm and in preventing small
hemorrhages.

1. Concentration of enzyme 3. B Vitamins

 The higher the concentration of enzyme, the  act as coenzymes in the different metabolic
faster is the rate of reaction. pathways.
 B1 – Thiamin
2. Concentration of substrate  B2 – Riboflavin
 reaction rate will increase with the increase in  B3 – Niacin
the concentration of substrate  B5 – Pantothenic Acid
 B6 – Pyridoxine
3. pH level  B8 - Biotin
 Enzymes are most active at their optimum Ph  B9 – Folate
 B12 – Cobalamin
4. Temperature
 Temperature increases the rate of reaction THE FAT-SOLUBLE VITAMINS
increases.
 At high temperature, enzyme denatures. 1. Vitamin A or the retinols
 provitamins in the form of beta-carotene and
ENZYME INHIBITION cryptoxanthines
 prevent blindness and xeropthalmia
INHIBITORS
 prevent the active site from binding with a 2. Vitamin D or the calciferols.
substrate.  Promotes absorption of calcium
 cause enzymes to lose catalytic activity  Prevents rickets
1. Reversible Inhibitors 3. Vitamin E or the tocopherols
 enzymatic activity that can be reversed  Antioxidants
 doesn’t form covalent bond  protect cellular membranes from damage by
a. Competitive Inhibitor reacting with free radicals
b. Non-competitive Inhibitor
4. Vitamin K or the anti-hemorrhagic vitamins
2. Irreversible Inhibitors
 synthesis of proconvertin and prothrombin
 A toxic substance causes an enzyme to which are both necessary in the conversion of
permanently lose enzymatic activity fibrinogen into fibrin
 form a covalent bond with an amino acid side  essential for formation of blood clot
group within the active site, which prevents the
substrate from entering the active site or
prevents catalytic activity

ENZYME CO-FACTORS AND VITAMINS

 Coenzymes are simple organic substances with
specific structural features that could help in
accelerating enzymatic reactions by providing
additional binding sites
 Vitamins, or metal ions called cofactors

THE WATER-SOLUBLE VITAMINS

1. Vitamin C or Ascorbic Acid

 easily destroyed by oxidation – heat or bas
 synthesis of collagen and neurotransmitter.