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Introduction and Biomolecules

CHAPTER 1
INTRODUCTION & Subtopic:

BIOMOLECULES Definition of biochemical engineering

Carbohydrates
Amino acids and protein
The central Dogma of molecular biology
Buffer solution

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What is Biochemical Engineering? What do Biochemical Engineer do?

The application of engineering principles to
conceive, design, develop, operate, or use processes Typical employers come
and products based on biological and biochemical from all sectors of the
phenomena. biotechnology industries,
including those with
It is a subset of chemical engineering that mainly
deals with the design and construction of unit interests in
processes that involve biological organisms or pharmaceuticals,
molecules. food,environment, waste
treatment, and
It enhances the quality of our lives by defining ways consulting.
in which new biological discoveries can be
sensitively translated into practical realities. 3 4

What are carbohydrates?

Play key roles as structural and storage
compounds in cells.
Polyhydroxyl compounds (poly-alcohols) that

Carbohydrates 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.

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Carbohydrates - The Functions Classifying carbohydrates

Most important source of energy for living
Simple carbohydrates
organisms.
1) Monosaccharides
Linked to proteins or lipids.
Glucose, fructose, galactose
Form structural tissues in plants and in
2) Disaccharides
microorganisms (cellulose, lignin, murein).
Lactose, sucrose, maltose
Participates in biological transport, cell- cell
Complex carbohydrates
recognition, activation of growth factors, modulation
1) Oligosaccharides
of the immune system.
Raffinose, stachyose
DNA and RNA framework.
2) Polysaccharides
Starch, glycogen, cellulose

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* 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 Aldose sugars

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Ketose sugars Ketose sugars

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D and L notation 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 D notation

O
H C

H C OH

H C OH

C H 2 OH
Right = D

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Structural of representation of sugars Rules of drawing Haworth projections

Draw either a six or 5-membered ring including
oxygen as one atom.
O O
Fisher projection: straight chain representation.
Haworth projection: simple ring in perspective.
Conformational representation: chair and boat
configurations. Most aldohexoses are six-membered.
Aldotetroses, aldopentoses, ketohexoses are 5-
membered.

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Rules of drawing Haworth projections Rules of drawing Haworth projections

Next: number the ring clockwise starting next to For D-sugars the highest numbered carbon
the oxygen (furthest from the carbonyl) is drawn up. For L-
5 sugars, it is drawn down.
O O
4 1 4 1 For D-sugars, the OH group at the anomeric
position is drawn down for and up for . For L-
3 2 3 2 sugars is up and is down.

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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Haworth Structure for D-Glucose Haworth Structure for D-Galactose

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-Fructose 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 Disaccharides
Isomerism in which two isomers are mirror
images of each other (D vs L). Consist of 2 monosaccharides bonded
together.

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Disaccharides 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 Polysaccharides
3-10 monosaccharides. >10 monosaccharides.
Components of cell membranes and part of milk, Most are made up of hundreds of monosaccharides
particularly human milk. bonded together.

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Cellulose
Amino Acids &
Protein

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Types of Protein Protein play key roles in a living system

Type Examples
Structural tendons, cartilage, hair, nails
Almost all chemical reactions in a living cell are
catalyzed by protein enzymes.
Contractile muscles
Storage and transport of biochemical molecules,
Transport hemoglobin such as oxygen, ions, and so on.
Storage milk Physical cell support and shape (collagen).
Hormonal insulin, growth hormone Regulatory and information transfer (hormones).
Enzyme catalyzes reactions in cells Mechanical movement (flagella, mitosis, muscles).
Protection immune response

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Bacteria cell wall Amino acid: Basic unit of protein

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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Examples of Amino acid 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 The peptide bond ( CO - NH linkage)

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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 Basic structural units of proteins:

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.

Helix (-helix, triple helix)

Sheet (-sheet).
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Tertiary Structure 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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Quaternary Structure Protein Hydrolysis

The way in which two or more polypeptide
chains associate to form a single three-
dimensional 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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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 Denaturation

Disruption of secondary, tertiary and quaternary

protein structure by
OH heat/organics
+ Break apart H bonds and disrupt hydrophobic
CH3 O CH2 O H2 O, H attractions
+
H3N CH C N CH C OH acids/ bases
H heat Break H bonds between polar R groups and
OH ionic bonds
heavy metal ions
CH3 O CH2 O
+ + React with S-S bonds to form solids
H3 N CH COH + H3N CH C OH 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 The Central Dogma of
Cooking food to destroy E. coli.
Heat used to cauterize blood vessels
Molecular Biology
Autoclave sterilizes instruments
Milk is heated to make yogurt

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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 Nucleotide - Adenosine Mono Phosphate (AMP)

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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Base Pairing - Guanine & Cytosine

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Base Pairing - Adenine & Thymine 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 Central Dogma

Proposed by Francis Crick in 1958 to
describe the flow of information in a cell.
DNA DNA

Information stored in DNA is transferred

residue-by-residue to RNA which in turn
RNA
transfers the information residue-by-
residue to protein.
RNA
DNA
The Central Dogma was proposed by Crick
to help scientists think about molecular
Protein
biology. It has undergone numerous Protein

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revisions in the past 45 years.

Terminology of DNA

DNA

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DNA Structure Central Dogma

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

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Terminology of RNA Terminology of RNA

Base Nucleoside (RNA) Deoxynucleoside (DNA)

Adenine Adenosine Deoxyadenosine

Guanine Guanosine Deoxyguanosine

Cytosine Cytidine Deoxycytidine

Uracil Uridine (not usually found)

Thymine (not usually found) (Deoxy)thymidinea

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RNA Compairing RNA and DNA

How does RNA differ from DNA? There are three important differences
between 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, and (3) RNA contains uracil in
place of thymine.
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(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 and72
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 RNA Synthesis

How does the cell make RNA?

We first examine the simplest way of
looking at protein synthesis as expressed in
the so called Central Dogma of Biology, In transcription, segments of DNA serve as
namely that the direction of information templates to produce complementary RNA
flow in the cell is from DNA to mRNA to molecules.
proteins.

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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) - 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
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)
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
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
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
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specializes in a different aspect of this job.
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Function of RNA Messenger of RNA

Most genes contain
instructions for
The three main types of RNA are assembling amino acids
messenger RNA, ribosomal RNA, and into proteins.
transfer RNA.
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
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cell. 86

Messenger of RNA Ribosomal of RNA

Proteins are assembled

A critical feature of mRNA and how it is on ribosomes, small
translated is the fact that each three organelles composed of
nucleotides in the mRNA is called a codon two subunits.
and it is the codon that is translated.
Thus the sequence of codons corresponds to These ribosome subunits
the sequence of amino acids in the are made up of several
polypeptide. ribosomal RNA (rRNA)
molecules and as many
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as 80 different proteins. 88

Transfer of RNA Transfer of RNA

You will see that the tRNA molecules When a protein is

have a set of three nucleotide bases built, a transfer RNA
at one end that are complementary to (tRNA) molecule
a corresponding codon. The bases on transfers each amino
the tRNA are called the anti codon. acid to the ribosome
This is critical because the anti as it is specified by
codons make the connection between the coded messages in
the codons and the correct amino mRNA.
acids that go with each codon.
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Compartmentalization of processes
(thus, transport is important)
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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
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 Solution
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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. 94
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. 96
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Buffer Solutions
97
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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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. 101
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Buffer Solutions
98
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
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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