CHAPTER 1:

INTRODUCTION TO BIOCHEMISTRY
Biochemistry
Biochemistry seeks to describe the structure,
organization and functions of living matter in
molecular terms.
It takes into account the studies related to the
nature of the chemical constituents of living
matter, their transformations in biological
systems and the energy changes associated
with these transformations.
Area to study
Chemical
structure & 3D
arrangement of
molecules
Language for storing
biological data & for
transmitting that
data in cells &
organisms.
The flow of energy in living
organisms and how it is
transferred from one
process to another.
Outlines
1.1 The Chemical Elements of Life
1.2 Important Biomolecules
1.3 The Cell Basic of Life
1.3.1 Prokaryotic cell
1.3.2 Eukaryotic cell
1.4 Biochemical Process
1.5 Thermodynamics of Biological Systems
1.1 Chemical Elements of Life
Living creature on earth composed mainly of a very
few elements, principally:
Carbon, Hydrogen, Oxygen, Nitrogen (C, H, O, N)
..make up 99+% of atoms in the human body
ELEMENT PERCENTAGE
Oxygen 63
Hydrogen 25.2
Carbon 9.5
Nitrogen 1.4




What property unites H, O, C and N and
renders these atoms so appropriate to the
chemistry of life?

Answer: Their ability to form covalent bonds
by electron-pair sharing.

A "second tier" of essential
elements includes sulfur and
phosphorus, which form covalent
bonds, and the ions Na
+
, K
+
, Mg
2+
,
Ca
2+
, and Cl
-
.
Sulfur is an important constituent
of proteins
Phosphorus plays essential roles
in energy metabolism and the
structure of nucleic acids.
Most of these third- and fourth-
tier elements are metals, and
some serve as aids to catalysis of
biochemical reactions.
Table: Elements found in organisms
1.2 Important Biomolecules
Living organism are composed of thousands of
different kinds of inorganic and organic molecules.
Most biomolecules can be considered to be
derived from the simplest type of organic
molecules; hydrocarbons

What is Biomolecules?
Complex lifeless organic substances
Build up living organisms
Required for growth and maintenance

Major classes of biomolecules
Monomer Polymer General functions
Amino acids Protein 20 amino acid in total
Used as building block for protein
Sugars Carbohydrate Energy source
Structural elements
Fatty acids Lipid Organic compounds that are not
very water soluble
Used as sources of cellular energy
Components of cell membranes
Nucleotides DNA
RNA
5 in total
Genetic information
Protein synthesis
Biomolecules are complex, but are
made up of simpler components
Carbon is extremely versatile in forming
covalent bonds with other atoms or
itself
Carbon accounts for more than half of the dry
weight of cells.
Covalently linked carbon atoms can form
linear chains, branched chains and cyclic
structures.
All kinds of functional groups (e.g., alcohol,
amino, carboxyl) can be attached to the
hydrocarbon backbones (thus making the
major biomolecules like proteins, nucleic acids,
carbohydrates, lipids and etc.).

Important Functional Groups in
Biomolecules
1.3 Cell Basic of Life
Cell = smallest unit of life
Cell Function
Releasing energy from food.
Making new cells for growth and repair.
Getting rid of body wastes.
Cell work together to perform basic life processes that keep organisms alive.
Tissues, Organs, & Systems
Cells that work together to perform a specific function form
a tissue.
Just as cells that work together form a tissue, tissues that
work together form an organ.
Organs that work together to perform a function form a
system. Example: circulatory system.
Plant cells also form tissues, such as the bark of a tree. And
plant cells work together, forming organs, such as roots and
leaves.

Two major cell types
Cell Type Example
Prokaryotic Bacteria
Archaea
Eukaryotic Protists
Fungi
Plants
Animals
1.3.1 Prokaryotic cell
Prokaryotes are molecules surrounded by a membrane
and cell wall. Prokaryotic cells lack characteristic
eukaryotic subcellular membrane enclosed "organelles,"
but may contain membrane systems inside a cell wall.

Prokaryotic cells possess:
-cell wall
-plasma membrane
-genetic material in the nucleoid
-cytoplasm
-ribosomes
-no membrane-bound organelles

Prokaryotic Cell Structure
1.3.2 Eukaryotic Cells
Eukaryotic cells are a type of cell more complex.
Eukaryotic organisms also have other specialized,
membrane-bounded structures, called organelles,
which are small structures within cells that perform
dedicated functions.

Eukaryotic cells
-possess a membrane-bound nucleus
-more complex than prokaryotic cells
-five to ten times larger than prokaryotes (diameter)
-compartmentalize many cellular functions within
organelles and the endomembrane system


20
21
Two Main Types of Eukaryotic Cells
Plant Cell
Animal Cell
Eukaryotic Cell Structure
Nucleus
Surrounded by nuclear envelope
Has nucleolus, and rich in RNA
RNA synthesized on a DNA template in nucleolus and
transport to cytoplasm
Near nuclear membrane has chromatin, aggregate of DNA
and proteins
Mitochondrion
Double membrane with inner membrane has many fold
called cristae
In matrix oxidation process occur to yield energy for the cell
Mitochondrial DNA located in internal matrix, also has
ribosome in matrix
Endoplasmic Reticulum (ER)
Rough ER : contain ribosome, site of protein synthesis &
modification of protein structure after synthesis
Smooth ER : involved with lipid synthesis
Chloroplast
Photosynthetic apparatus found in grana, membranous body
stacked
Also has DNA that differ from nucleus and has ribosomes
Golgi apparatus
Stacks of flattened sacs
Have a shipping side & a receiving side
Receive & modify proteins made by ER
Transport vesicles with modified proteins pinch off the ends


Lysozomes
Contain digestive enzymes
Break down food and worn out cell parts
Programmed for cell death (lyse & release enzymes to
break down & recycle cell parts)
Cytosol
Liquid interface of cells
Organelles held in places by fine strands (microtubules)
of proteins
Cell wall
External cell wall other than plasma membrane
Gives structure and shape to plant and bacterial cells
Vacuoles
Responsible for food digestion, osmotic regulation &
waste product storage
1.4 Biochemical Process
Biochemical reactions have simple organic
reaction mechanisms. Among the most common
reaction types encountered in biochemical
processes are the following:
1. Nucleophilic Substitution Reactions
2. Elimination Reaction
3. Addition Reaction
4. Isomerization Reaction
5. Oxidation Reduction Reaction

30
Biochemical Processes
Nucleophilic Substitution Reactions: Synthesis of Glucose-6-phosphate:
Glucose is phosphorylated by adding phosphates from ATP to give a
glucose 6-phosphate











Hydrolysis Reaction:
ATP + H
2
O ADP + Pi + Energy + H
+

31
Biochemical Processes
Elimination Reaction: Dehydration of 2-phosphoglycerate
This is the second reaction of glycolysis in which is a high-energy
phosphate compound, phosphoenolpyruvate is formed.
32
Biochemical Processes
Addition Reaction:
33
Biochemical Processes
Isomerization Reaction:
Biochemical isomerizations is the interconversion between aldose and
ketose sugars. The glucose-6-phosphate is changed into an isomer,
fructose-6-phosphate.

34
Biochemical Processes
Oxidation Reduction Reaction:
In cellular respiration, the energy in glucose is transferred to ATP.




In respiration, glucose is oxidized and thus releases energy. Oxygen is
reduced to form water.
1.5 Thermodynamic of Biological Systems
1.5.1 Properties of water
1.5.2 Acid, base & pH
1.5.3 Buffer

IMPORTANCE
OF WATER
About 70% of our total
body weight is water;
as much as 95% of
jellyfish
A large part of the
mass of most
organisms is simply
water.
In human tissues, the percentage of
water ranges from 20% in bones to
85% in brain cells. water content is
greater in embryonic and young
cells and decreases as aging occurs.
Water is the solvent the
medium and the participant in
most of the chemical reactions
occurring in our environment.
Physical and chemical properties of
water have permitted living things
to appear, to survive, and to evolve
on this planet.
One of the principal environmental
factors affecting organisms. Many
organisms live within the sea or in
freshwater rivers, lakes.
1.5.1 Properties of water
Water is polar molecule
Oxygen atom with its unshared electron each carry a
partial negative charge (-)
Hydrogen atoms carry partial positive charge (+)
Bond with positive and negative ends are called
dipoles
Neighboring water molecules tend to orient
themselves so that O-H bond of one water molecule
(the positive end) points toward one of the electron
pairs of the other water molecule (the negative end)
Hydrogen bond

In H
2
O hydrogen bonding forms tetrahedral
structure of molecule
1 H
2
O is hydrogen bonded to 4 others

Hydrophilic molecule in aqueous
solution
Polar character of water makes it an excellent
solvent for polar and ionic materials
Hydrophilic
Non polar substances are virtually insoluble in
water
Hydrophobic
Why do salts (e.g NaCl) dissolve in
water?
Polar solvent (water) weaken the
attractive force between oppositely
charged ion (Na+ and Cl-) & hold the
ion apart.
An ion immerse in a polar solvent such
as water attracts the oppositely
charged ends of the solvent dipoles
The ion surrounded by concentric
shells of oriented solvent molecules.
Hydrophobic molecules in aqueous
solution
Hydrophobic molecules, e.g hydrocarbons are
virtually insoluble in water
Do not form hydration shell
The regular water lattice forms icelike
clathrate structure about nonpolar molecules
Amphipathic molecules in aqueous
solution
Contain both polar and nonpolar groups
When mixed with water, amphipathic molecules form
structures called micelles
In micelles the charged species (polar head) orient
themselves so they are in contact with water
Nonpolar hydrocarbon
tails become in hydrophobic
interior
E.g. bilayer forming of
phospholipid molecules as
basic membrane structure
Ionization of water
H
2
O + H
2
O H
3
O
+
+ OH
-
H
2
O H
+
+ OH
-
K
eq
= [H
+
] [OH
-
]
[H2O]
In pure water the [H
+
] = [OH
-
] = 1.0 x 10
-7
Ion product of water, K
w
= [H
+
] [OH
-
] at 25C
is 1.0 x 10
-14
pH = -log [H+]= log 1/[H+]

pH Scale
Devised by Sorenson (1902)
[H+] can range from 1M and1 X 10
-14
M
using a log scale simplifies notation
pH = -log [H
+
]
Neutral pH = 7.0
Weak Acids and Bases Equilibria
Strong acids / bases disassociate completely
Weak acids / bases disassociate only partially
Enzyme activity sensitive to pH
weak acid/bases play important role in protein
structure/function


Acid/conjugate base pairs
HA + H
2
O A
-
+ H
3
O
+

HA A
-
+ H
+
HA = acid ( donates H
+
)(Bronstad Acid)
A
-
= Conjugate base (accepts H
+
)(Bronstad Base)


K
a
= [H
+
][A
-
]
[HA]
K
a
& pK
a
value describe tendency to
loose H
+

large K
a
= stronger acid
small K
a
= weaker acid
pK
a
= - log K
a

pKa values determined by titration
Buffers
Buffers are aqueous systems that resist changes in
pH when small amounts of a strong acid or base are
added.
A buffered system consist of a weak acid and its
conjugate base.
The most effective buffering occurs at the region of
minimum slope on a titration curve
(i.e. around the pKa).
Buffers are effective at pHs that are within +/-1 pH
unit of the pKa
Henderson-Hasselbach Equation
1) K
a
= [H
+
][A
-
]
[HA]
2) [H
+
] = K
a
[HA]
[A
-
]
3) -log[H
+
] = -log K
a
-log [HA]
[A
-
]
4) -log[H
+
] = -log K
a
+log [A
-
]
[HA]
5) pH = pK
a
+log [A
-
]
[HA]
HA = weak acid
A
-
= Conjugate base
* H-H equation describes
the relationship between
pH, pKa and buffer
concentration
Case where 10% acetate ion 90%
acetic acid



pH = pK
a
+ log
10
[0.1 ]




[0.9]

pH = 4.76 + (-0.95)
pH = 3.81



pH = pK
a
+ log
10
[0.5 ]




[0.5]

pH = 4.76 + 0
pH = 4.76 = pK
a
Case where 50% acetate ion 50% acetic acid



pH = pK
a
+ log
10
[0.9 ]




[0.1]

pH = 4.76 + 0.95
pH = 5.71
Case where 90% acetate ion 10% acetic acid