CHAPTER 1

INTRODUCTION &
BIOMOLECULES

Introduction and Biomolecules

Subtopic:
Definition of biochemical engineering
Carbohydrates
Amino acids and protein
The central Dogma of molecular biology
Buffer solution

What is Biochemical Engineering?

The application of engineering principles to
conceive, design, develop, operate, or use processes
and products based on biological and biochemical
phenomena.
It is a subset of chemical engineering that mainly
deals with the design and construction of unit
processes that involve biological organisms or
molecules.
It enhances the quality of our lives by defining ways
in which new biological discoveries can be
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sensitively translated into practical realities.

What do Biochemical Engineer do?

Typical employers come
from all sectors of the
biotechnology industries,
including those with
interests in
pharmaceuticals,
food,environment, waste
treatment, and
consulting.
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Carbohydrates

What are carbohydrates?

Play key roles as structural and storage
compounds in cells.
Polyhydroxy compounds (poly-alcohols) that
contain a carbonyl (C=O) group.
The formula for a carbohydrate is (CH2O)n, where
n 3.
D form is biologically more abundant than L form.
The usual chemical test for the simpler
carbohydrates is heating with Benedict's solution.

Carbohydrates - The Functions

Most important source of energy for living organisms.
Linked to proteins or lipids.
Form structural tissues in plants and in
microorganisms (cellulose, lignin, murein).
Participates in biological transport, cell- cell
recognition, activation of growth factors, modulation
of the immune system.
DNA and RNA framework.

Classifying carbohydrates
Simple carbohydrates
1) Monosaccharides
Glucose, fructose, galactose
2) Disaccharides
Lactose, sucrose, maltose
Complex carbohydrates
1) Oligosaccharides
Raffinose, stachyose
2) Polysaccharides
Starch, glycogen, cellulose

* chaining relise on 'bridging' of oxygen atoms - glycoside bonds

Classifying carbohydrates

Monosaccharides
Smallest carbohydrates, also known as simple sugars.
Monosaccharides are categorized by:
1) number of carbons (typically 3-9)
2) whether an aldehyde or ketone
Sugar containing an aldehydes is known as an aldose.
Sugar containing a ketones is known as a ketose.

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Aldose sugars

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Aldose sugars

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Ketose sugars

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Ketose sugars

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D and L notation
D, L tells which of the two chiral isomers we are
referring to.
If the OH group on the next to the bottom
carbon atom points to the right , the isomer is a
D-isomer; if it points left, the isomer is L.
The D form is usually the isomer found in nature.

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D and L notation

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D and L notation

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D notation

OH

OH

C H 2 OH

Right = D
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Structural of representation of sugars

Fisher projection: straight chain representation.

Haworth projection: simple ring in perspective.
Conformational representation: chair and boat
configurations.

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Rules of drawing Haworth projections

Draw either a six or 5-membered ring including
oxygen as one atom. O
O

Most aldohexoses are six-membered.

Aldotetroses, aldopentoses, ketohexoses are 5membered.

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Rules of drawing Haworth projections

Next number the ring clockwise starting next to
5
the oxygen
O
O

4
3

4
3

If the substituent is to the right in the Fisher

projection, it will be drawn down in the Haworth
projection (Down-Right Rule)
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Rules of drawing Haworth projections

For D-sugars the highest numbered carbon
(furthest from the carbonyl) is drawn up. For Lsugars, it is drawn down.
For D-sugars, the OH group at the anomeric
position is drawn down for and up for . For Lsugars is up and is down.

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Haworth Structure for D-Glucose

Write OH groups on the right (C2, C4) down.
Write OH groups on the left (C3) up.
The new OH on C1 has two possibilites: down
for anomer, up for anomer.

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Haworth Structure for D-Galactose

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Haworth Structure for D-Fructose

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Isomers
Isomers are molecules that have the same chemical formula but
different structures.
Stereoisomer differs in the 3-D orientation of atoms.
Diastereomers are isomers with > 1 chiral center.
Pairs of isomers that have opposite configurations at one
or more of the chiral centers but that are not mirror
images of each other
Epimers are a special type of diastereomer.
Stereoisomers with more than one chiral center which
differ in chirality at only one chiral center
A chemical reaction which causes a change in chirality at
one of many chiral center is called an epimerisation
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Enantiomers
Isomerism in which two isomers are mirror
images of each other (D vs L).

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Disaccharides
Consist of 2 monosaccharides bonded
together.

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Glycosidic Bond
This is when two monosaccharides join to form a
Disaccharide.
The reaction is similar to condensation.
The reaction involves the water been given off.

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Oligosaccharides
3-10 monosaccharides.
Components of cell membranes and part of milk,
particularly human milk.

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Polysaccharides
>10 monosaccharides.
Most are made up of hundreds of monosaccharides
bonded together.

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Cellulose

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Amino Acids &

Protein

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Types of Protein

Type
Structural
Contractile
Transport
Storage
Hormonal
Enzyme
Protection

Examples
tendons, cartilage, hair, nails
muscles
hemoglobin
milk
insulin, growth hormone
catalyzes reactions in cells
immune response

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Protein play key roles in a living system

Almost all chemical reactions in a living cell are
catalyzed by protein enzymes.
Storage and transport of biochemical molecules,
such as oxygen, ions, and so on.
Physical cell support and shape (collagen).
Regulatory and information transfer (hormones).
Mechanical movement (flagella, mitosis, muscles).

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Amino acid: Basic unit of protein

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Examples of Amino acid

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Zwitterionic form of Amino Acids

Zwitterion (dipolar ions) has both + and charge

Zwitterion is neutral overall
Under normal cellular conditions amino acids are
zwitterions:
Amino group = -NH3+
Carboxyl group = -COO-

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pH and Ionization

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The peptide bond ( CO - NH linkage)

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Bacteria cell wall

Provide strength and rigidity for the organism.
Consists of a polypeptide-polysaccharide known as
petidoglycan or murein.
Determines the Gram staining characteristic of the
bacteria.

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Primary Structure of Proteins

Primary structure of a proteins is the particular
sequence of amino acids connected by peptide bonds.

Proteins are linear polymers of amino acids

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Secondary Structure
Secondary structure of a protein is the arrangement
of polypeptide backbone of the protein in space.
The secondary structure includes two kinds of
repeating pattern known as helixes (-helix, triple
helix) and sheet (-sheet).
Hydrogen bonding between backbone atoms are
responsible for both of these secondary structures.

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Basic structural units of proteins:

Secondary structure

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Tertiary Structure
The overall three dimensional shape that results
from the folding of a protein chain.
Tertiary structure depends mainly on interactions
of amino acid R groups that are far apart along the
same backbone.
Cross links between R groups of amino acids in
chain:
disulfide
SS
+
ionic
COO
H3N
H bonds
C=O
HO
hydrophobic
CH3
H3C
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Tertiary Structure

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Quaternary Structure
The way in which two or more polypeptide
chains associate to form a single threedimensional protein unit. Non-covalent
forces are responsible for quaternary
structure essential to the function of proteins.
Example is hemoglobin that carries oxygen
in blood.
-Four polypeptide chains

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Protein Hydrolysis

Break down of peptide bonds

Requires acid or base, water and heat
Gives smaller peptides and amino acids
Similar to digestion of proteins using
enzymes
Occurs in cells to provide amino acids to
synthesize other proteins and tissues
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Hydrolysis of Dipeptide

OH
+
CH3 O
CH2 O
H2O, H
+
H3N CH C N CH C OH
heat
H

OH
CH3 O

+
H3 N CH COH

CH2 O
+
H3N CH C OH
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Denaturation
Disruption of secondary, tertiary and quaternary
protein structure by
heat/organics
Break apart H bonds and disrupt hydrophobic
attractions
acids/ bases
Break H bonds between polar R groups and
ionic bonds
heavy metal ions
React with S-S bonds to form solids
agitation
Stretches chains until bonds break
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Application of Denaturation
Hard boiling an egg
Wiping the skin with alcohol swab for
injection
Cooking food to destroy E. coli.
Heat used to cauterize blood vessels
Autoclave sterilizes instruments
Milk is heated to make yogurt

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The Central Dogma of

Molecular Biology

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What is DNA and RNA?

DNA Deoxyribonucleic acid
RNA Ribonucleic acid
DNA stores and preserves genetic
information
RNA plays a central role in protein synthesis
Both DNA and RNA are large polymers
made of their corresponding nucleotides
(condensation)
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Nucleotide
Building block of DNA and RNA
Consists of 3 major components:
1) phosphoric acid
2) pentose (5-carbon sugar)
-ribose or deoxyribose
3) base (purine or pyrimidine)

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Nucleotide - Adenosine Mono Phosphate (AMP)

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Base Pairing - Guanine & Cytosine

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Base Pairing - Adenine & Thymine

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Think About it!!!!

DNA is the genetic material of cells. The
sequence of nucleotide bases in the
strands of DNA carries some sort of code.
In order for that code to work, the cell
must be able to understand it.
What, exactly, do those bases code for?
Where is the cells decoding system?
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Central Dogma
DNA

RNA

Protein

Proposed by Francis Crick in 1958 to

describe the flow of information in a cell.
Information stored in DNA is transferred
residue-by-residue to RNA which in turn
transfers the information residue-byresidue to protein.
The Central Dogma was proposed by Crick
to help scientists think about molecular
biology. It has undergone numerous
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revisions in the past 45 years.

Central Dogma
DNA

RNA

DNA

Protein
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DNA

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Terminology of DNA

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DNA Structure
1. DNA is double stranded
2. DNA strands are
antiparallel
3. G-C pairs have 3 hydrogen
bonds
4. A-T pairs have 2 hydrogen
bonds
5. One strand is the
complement of the other
6. Major and minor grooves
present different
surfaces
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Central Dogma
DNA

RNA

RNA

Protein
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Terminology of RNA
Base Nucleoside (RNA)Deoxynucleoside (DNA)
Adenine

Adenosine

Guanine

Guanosine Deoxyguanosine

Cytosine

Cytidine

UracilUridine
Thymine

Deoxyadenosine

Deoxycytidine
(not usually found)

(not usually found)

(Deoxy)thymidinea
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Terminology of RNA

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RNA
How does RNA differ from DNA?
There are three important differences
between RNA and DNA: (1) the sugar in RNA
is ribose instead of deoxyribose, (2) RNA is
generally single-stranded and not doublestranded, and (3) RNA contains uracil in
place of thymine.
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Compairing RNA and DNA

There are three important differences
between RNA and DNA:
(1) The sugar in RNA is ribose instead of
deoxyribose.
(2) RNA is generally single-stranded and
not double-stranded.
(3) RNA contains uracil in place of thymine.
These chemical differences make it easy
for the enzymes in the cell to tell DNA and
RNA apart.
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Central Dogma
DNA

RNA

Protein

Protein
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Protein
Structure

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The central of Dogma

We first examine the simplest way of

looking at protein synthesis as expressed in
the so called Central Dogma of Biology,
namely that the direction of information
flow in the cell is from DNA to mRNA to
proteins.

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RNA Synthesis
How does the cell make RNA?
In transcription, segments of DNA serve as
templates to produce complementary RNA
molecules.

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Transcription
Most of the work of making RNA takes
place during transcription. During
transcription, segments of DNA serve as
templates to produce complementary
RNA molecules.
The base sequences of the transcribed
RNA complement the base sequences of
the template DNA.

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The role of RNA (Translation)

Genes contain coded DNA instructions that
tell cells how to build proteins.
The first step in decoding these genetic
instructions is to copy part of the base
sequence from DNA into RNA.
RNA, like DNA, is a nucleic acid that
consists of a long chain of nucleotides.
RNA then uses the base sequence copied
from DNA to direct the production of
proteins.
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The role of RNA (Translation) - cont

The roles played by DNA and RNA are
similar to the master plans and blueprints
used by builders.

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The role of RNA (Translation) - cont

A master plan has all the information
needed to construct a building. Builders
never bring a valuable master plan to the
building site, where it might be damaged
or lost. Instead, they prepare inexpensive,
disposable copies of the master plan
called blueprints.

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The role of RNA (Translation) - cont

Similarly, the cell uses DNA master plan
to prepare RNA blueprints.
The DNA molecule stays safely in the
cells nucleus, while RNA molecules go to
the protein-building sites in the
cytoplasmthe ribosomes.
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The role of RNA (Translation) - cont

You can think of an RNA molecule, as a
disposable copy of a segment of DNA, a
working copy of a single gene.
RNA has many functions, but most RNA
molecules are involved in protein
synthesis only.
RNA controls the assembly of amino acids
into proteins. Each type of RNA molecule
specializes in a different aspect of this job.

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Function of RNA
The three main types of RNA are
messenger RNA, ribosomal RNA, and
transfer RNA.

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Messenger of RNA
Most genes contain
instructions for
assembling amino acids
into proteins.
The RNA molecules that
carry copies of these
instructions are known
as messenger RNA
(mRNA): They carry
information from DNA
to other parts of the cell.
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Messenger of RNA
A critical feature of mRNA and how it is
translated is the fact that each three
nucleotides in the mRNA is called a codon
and it is the codon that is translated.
Thus the sequence of codons corresponds to
the sequence of amino acids in the
polypeptide.

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Ribosomal of RNA
Proteins are assembled
on ribosomes, small
organelles composed of
two subunits.
These ribosome subunits
are made up of several
ribosomal RNA (rRNA)
molecules and as many
as 80 different proteins.

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Transfer of RNA
You will see that the tRNA molecules
have a set of three nucleotide bases
at one end that are complementary to
a corresponding codon. The bases on
the tRNA are called the anti codon.
This is critical because the anti
codons make the connection between
the codons and the correct amino
acids that go with each codon.
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Transfer of RNA
When a protein is
built, a transfer RNA
(tRNA) molecule
transfers each amino
acid to the ribosome
as it is specified by
the coded messages in
mRNA.
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Compartmentalization of processes
(thus, transport is important)

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Buffer Solution

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Buffer Solutions
A buffer is a solution characterised by the
ability to resist changes in pH when limited
amounts of acid or base are added to it.
Buffers contain either a weak acid and its
conjugate base or a weak base and its
conjugate acid.
Thus, a buffer solution contains both an acid
species and a base species in equilibrium.
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Buffer Solutions
In a solution there is an equilibrium between a
weak acid, HA, and its conjugate base, A-.

When hydrogen ions are added to the solution

the equilibrium moves to the left, in
accordance with Le Chatelier's principle, as
there are hydrogen ions on the right-hand side
of the equilibrium expression. When hydroxide
ions are added the equilibrium moves to the
right as hydrogen ions are removed in the
reaction H+ + OH- H2O.
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Buffer Solutions
The acid dissociation constant for a weak
acid, HA, is defined as

Simple manipulation with logarithms gives

the Henderson-Hasselbalch equation, which
describes pH in terms of pKa

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Buffer Solutions
In this equation [A] is the concentration of the
conjugate base and [HA] is the concentration of the
acid. It follows that when the concentrations of
acid and conjugate base are equal, often described
as half-neutralization, pH = pKa.
Maximum buffering capacity is found when pH =
pKa, and buffer range is considered to be at pH =
pKa1.
In general a buffer solution may be made up of
more than one weak acid and its conjugate base; if
the individual buffer regions overlap a wider
buffer region is created by mixing the two
buffering agents.

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Buffer Solutions

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Buffer Solutions

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Application of Buffer
Their resistance to changes in pH makes buffer
solutions very useful for chemical manufacturing
and essential for many biochemical processes. The
ideal buffer for a particular pH has a pKa equal to
that pH, since such a solution has maximum buffer
capacity.
Buffer solutions are necessary to keep the correct
pH for enzymes in many organisms to work. Many
enzymes work only under very precise conditions; if
the pH strays too far out of the margin, the enzymes
slow or stop working and can denature, thus
permanently disabling its catalytic activity.

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Application of Buffer
A buffer of carbonic acid (H2CO3) and bicarbonate
(HCO3) is present in blood plasma, to maintain a
pH between 7.35 and 7.45.
Industrially, buffer solutions are used in
fermentation processes and in setting the correct
conditions for dyes used in colouring fabrics. They
are also used in chemical analysis and calibration
of pH meters.
Majority of biological samples that are used in
research are made in buffers specially PBS
(phosphate buffer saline) at pH 7.4.
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Summary
Biological systems are composed of carbon,
oxygen, hydrogen, and nitrogen.(Note: some
cellular molecules contain metals and sulfur
is frequently present in disulfide bonds.)
These molecules are used to build lipids,
proteins, carbohydrates, and nucleic acids,
the building blocks for cell structure and
chemical reagents for cell function.
Proteins conduct the business of the cell by
regulating cell function.
Carbohydrates serve primarily as energy
sources.
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Summary
The receptors on the surface of the cell are
primarily carbohydrates. They are highly
specific and receive molecules destined to
enter the cell.
The information structure of the cell is
found in nucleotides.

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