INTRODUCTION

TO
BIOCHEMISTRY

Department of Chemistry and Physics

University of San Agustin
 I ST RY ?
I O CHE M
HAT I S B
W
 BIOCHEMISTRY

• chemistry of life processes

• Study of life at the molecular level
• Studying the chemical processes of living
organisms
 BIOCHEMISTRY
3 primary areas of biochemistry:
1. Structural and functional biochemistry
- focuses initially on discovering the chemical
structures and three-dimensional arrangements of
biomolecules (protein, carbohydrates, lipids,
nucleic acids), those chemicals that are found in
living matter

2. Informational biochemistry
- defines the language(s) for storing biological data
and for transmitting that data in cells and
organisms.
 BIOCHEMISTRY

3. Bioenergetics
- describes the flow of energy in living
organisms and how it may be transferred from
one process to another.
 M I ST RY
B I O C H E
D I D
HOW E TO B E ?
CO M
 History of Biochemistry

• The Chinese in the fourth century B.C.

believed that humans contained five
elements: water, fire, wood, metal, and earth.

• When all elements were present in proper

balance, good health resulted. An imbalance
in the elements caused illness.
 History of Biochemistry
• The early Greeks, including Plato (428–348
B.C.), attempted to explain the body in terms
of cosmological theories and stressed diet for
treatment of disease.

• The Greek term for digestion, pepsis, a word

indicating inner heat, is the origin of the word
pepsin, a digestive enzyme.
 History of Biochemistry
• The Greek physician Galen (A.D. 129–199) campaigned
for a pharmacological approach using plant and animal
products for disease treatment.

• Paracelsus (A.D. 1493–1541) asserted that man is made

out of the same material as the rest of creation.

• Chinese physicians discovered in the seventh century

A.D. that night blindness could be treated with pig and
sheep livers.
 History of Biochemistry
• Fredrich Wöhler (1800-1882) demonstrated in
1828 that urea, a compound that had only
been associated with living cells, could be
synthesized from an inorganic compound
outside of the cell.

• 1903: Neuberg defined Biochemistry as the

CHEMISTRY OF LIFE
Development of Biochemistry
Development of Biochemistry
Development of Biochemistry
 A R E T H E
W H A T E ?
S O F L I F
R I B U T E
ATT
 Origins of life on earth
• About 4 billion years ago, life arose on earth
• Simple organisms that were able to extract
energy from organic compounds or from
sunlight, which they used to make more
complex biomolecules from the simple
elements and compounds on the surface of
the earth.
 BIOCHEMISTRY
Attributes of Life – distinguishing features of
living organisms
1. High degree of Complexity and Organization
2. Possess a characteristic size and shape
3. Growth and Repair
4. Reproduction
5. Metabolism
6. Adaptation
7. Regulation
 BIOCHEMISTRY
Attributes of Life
8. Response to stimuli or sensitivity
9. Variation and Change
10. Stereospecificity
11. Systems for extracting, transforming,
and using energy from the environment
 C E S O R
U B S TA N
E T H E S G
T A R R N I N
WHA U L E S G O V E
MO L EC RY ?
H E M I S T
B I O C
 BIOCHEMISTRY
Chemicals of Life
• Water
Human cells (70%), Blood (80%), whole body
(60-70%)
• Organic Compounds
Nucleic Acids, Proteins, Carbohydrates, Fats and
Lipids
• Inorganic Compounds
Bulk elements: N, Na, Mg, P, S, Cl, K, and Ca
Trace elements: Fe, Zn, I, Ar, Br, Mo, V
Functional Groups

Biomolecules
-compounds of
carbon with a
variety of
functional groups
 BIOCHEMISTRY
• Small molecules:
– Lipid, phospholipid, glycolipid, sterol,
– Vitamin
– Hormone, neurotransmitter
– Carbohydrate, sugar
• Monomers:
– Amino acids
– Nucleotides
– Monosaccharides
• Polymers:
– Peptides, oligopeptides, polypeptides, proteins
– Nucleic acids, i.e. DNA, RNA
– Oligosaccharides, polysaccharides (including cellulose )
 S P EC I A L
AT I S S O
W H B O N ?
U T C A R
A B O
 Chemistry of carbon
• Carbon is a tetravalent atom

• Carbon can form single, double,

and triple bonds

• Carbon atoms are able to bond

together to form long chains and
rings.
• How are single bonds, double bonds and triple bonds
formed?
• Single bonds – is formed by the formation of a σ-bond
(sigma bond). A σ-bond can be formed by the
overlapping of orbitals in three ways: s-s orbitals, s-p
orbitals and p-p orbitals.
This phenomenon of overlapping of atomic orbitals is
called hybridization. In the carbon atom’s electronic
configuration in the ground state, the carbon atom only
has two unpaired electron. In order for the carbon atom
to satisfy the octet rule in bond formation, the electron
have to be in an excited state for it to have 4 unpaired
electrons to be capable of forming 4 bonds (figure 7).
• How the four bonds are formed depends on the hybridization of the
atom.
• When carbon forms four single bonds, the hybridization of the bond
is sp3 because the bond was formed from one s orbital and three p
orbitals such as in the case of methane.
• The arrangement of electron pairs in all the bonds follows a stable
tetrahedral geometry, (bond angle of 109.5°). This alone already justifies
why carbon is capable of making long chains of carbon-carbon bonds.
• The formation of a double
bond is composed of a
σ―bond and a π―bond (pi
bond).
• A π―bond is formed when
the p orbitals in the same
axis of two different atoms
overlap such as px―px or
py―py to form the π bond.
• When an atom contains a π-
bond, this atom
is sp2 hybridized since it is
composed of one s orbital
and two p orbitals to
hybridize.
• Trigonal planar, 120°
• When only one s and one p orbital will hybridize (to
form sp hybridization) leaving 2 p orbitals unhybridized and
available to overlap, this will create one σ-bond and two π-bonds.
When two carbons participate in this orientation, this will give rise
to the triple bond.
Hybridization Summary
• Bond
angle
• 109.5°

• 120°

• 180°
Water, Acids and Bases, Buffers

Prepared by:
Justin Brian Chiongson, M. Sc., RCh
Relicardo M. Coloso, Ph. D., RCh
Department of Chemistry and Physics
University of San Agustin, Iloilo City
Water is an essential nutrient vital
to existence of both animals and plants

In the body, water is found inside and

around the cells and within all blood vessels
 Functions of water that are essential to life
•Principal fluid medium in which nutrients, gases,
and enzymes are dissolved
•Extracellular water bathes the cells, serving as
medium for transport of nutrients and oxygen
to the cells and removing wastes from the cells
•Intracellular water is the physicochemical medium
that allows various metabolic processes
to take place
•Intracellular fluid volume provides form to
tissues and organs and ultimately to the body
•Regulation of body temperature
HUMAN BODY MAS

60% WATER

17 % PROTEIN

15 % FAT

3 % NITROGEN
 CHEMISTRY OF WATER

Mp = 0⁰C, Bp = 100⁰C, max density at 4 ⁰C, high

specific heat, high heat of vaporization and
fusion, high dipole moment
WATER MOLECULES FORM HYDROGEN
BONDS

Tetrahedral hydrogen bonding of water

 WATER IS A UNIVERSAL SOLVENT
Interactions:
1. H-bonding – bond between H and an
electronegative atom such as O or N
2. Ion-dipole - bond between an ion and a
molecule with an electric dipole moment such
as H2O
3. Dipole-dipole - bond between 2 molecules with
electric dipole moments such as H2O and an
amide or amine functional group
IMPLICATIONS …
A solvent is good at dissolving a substance
(solute) in solution.
•Water is polar, so it can dissolve ions
and other polar organic molecules such as
proteins and carbohydrates which are
hydrophilic (water-loving). Like dissolves like.
•Water is a poor solvent for non-polar
molecules which are hydrophobic
(water-fearing) such as fats and oils resulting
Hydrophobic aggregation.
Fat droplet in fat cells – example of
hydrophobic aggregation

Fat droplet
 Review Acids, Bases and pH
• pH = -log [H+ or H3O+]
• ACID- STRONG ACID, WEAK ACID
• Ka, pKa
• BASE- STRONG BASE, WEAK BASE
• Kb
• Kw
 Acids, Bases and pH
Importance of pH in living cells:
• In animals, for example, the maintenance of
blood pH (7.35 < pH < 7.45) is crucial for life.

Slightly acidic pH (6.95) →coma and

death.
Slightly basic pH (7.7) → convulsions and
muscle spasms.
 Acids, Bases and pH
Importance of pH in living cells:
• Dramatic shifts in pH can play a role in
controlling cellular activities such as egg
division after fertilization and enzymatic
activities

• Consequently, cells must work constantly to

maintain an acid-base balance.
 O G I C A L
D O B I O L H ?
HOW T H E I R p
A I N TA I N
ST E M S M
SY
 Buffer
• Buffer solution is a solution containing a weak acid or
base that is capable of resisting or minimizing the
change in pH upon addition of a strong acid or base.
• Buffers solutions are made up of a weak acid and its
conjugate base or a weak base and its conjugate acid.
• Used in all biochemical work to control pH.
• Blood contains the carbonic acid-bicarbonate buffer
system and physiologic fluids in cells contain the
phosphate buffer system.
 Buffer
• Buffer problems are solved using the Henderson-
Hasselbach equation.
• Henderson-Hasselbalch Equation:

pH = pKa + log [salt/acid]

pOH = pKb + log [salt/base]

Buffer

• Inflection point
pH=pKa
• Equivalence point
complete deprotonation
Change in pH upon addition of Strong
Acid/Base to the Buffer
Blood is an example of a buffered system – pH
maintained at pH 7.35-7.45

Bicarbonate buffering system of the blood

 Major Buffering Systems in the Body
• Carbonic Acid-Bicarbonate Buffer System
• Extracellular
• CO2 + H2O ⇌ H2CO3 ⇌ H+ + HCO3-
• If there are too many H3O+ ions in the blood, the H3O+ binds with
the HCO3- to form carbonic acid. This carbonic acid will be
dissociated into water and CO2, and will be released out by the
lungs
• If there are too few H3O+ ions in the blood, the carbonic acid will
react to form H3O+ and HCO3-
• During hyperventilation, CO2 is rapidly excreted in the body, causing
the equilibrium to shift to the left, therefore, pH increases
• During hypoventilation, CO2 builds up in the body causing the
equilibrium to the right, consequently decreasing the pH.
 Major Buffering Systems in the Body
• Phosphate Buffer System
• Intracellular
• H2PO4- + OH ⇌ HPO42- + H3O+
• involves dihydrogen phosphate H2PO4- (proton donor)
and hydrogen phoshphate HPO42- ( proton acceptor)
• When there is excess OH- in the cell, it is neutralized by
the dihydrogen phosphate, shifting the equilibrium to
the right
• When there is excess H3O+ in the cell, it is neutralized
by the hydrogen phosphate, shifting the equilibrium to
the left
 Major Buffering Systems in the Body
• Protein Buffer
• Nearly all proteins can act as buffer.
• Proteins are made up of amino acids.