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Biochemical

Engineering

Dr. Syed Nadir Hussain


Contents

• Introduction-Biochemical Engineering
• Fundamentals of Microbiology
• Basics of Biochemistry
GENERALIZED VIEW OF BIOPROCESS

RAW MATERIALS

UPSTREAM
PROCESSES

Media Formulation
Inoculum Equipment
and
Preparation Sterilization
Sterilization

BIOREACTOR -
FERMENTER

Transport
Reaction Kinetics Phenomena Instrumentation
and Bioactivity and Fluid and Control
Properties

DOWNSTREAM
PROCESSES

Waste Recovery,
Recovery and
Separation Reuse and
Purification
Treatment

THE BOTTOM LINE

HEALTH AND
REGULATION ECONOMICS
SAFETY
Bioprocessing is an essential part of many food, chemical and
pharmaceutical industries. Bioprocess operations make use of
microbial, animal and plant cells and components of cells such as
enzymes to manufacture new products and destroy harmful
wastes.

Use of microorganisms to transform biological materials for


production of fermented foods has its origins in ancient times.
Since then, bioprocesses have been developed for an enormous
range of commercial products, from relatively cheap materials
such as industrial alcohol and organic solvents, to expensive
specialty chemicals such as antibiotics, therapeutic proteins and
vaccines.
Industrially-useful enzymes and living cells such as bakers'and
brewers'yeast are also commercialproducts of bioprocessing.
Table 1.1 gives examples of bioprocesses employing whole cells. Typical
organisms used and the approximate market size for the products are also listed.
The table is by no means complete; not included are processes for wastewater
treatment, bioremediation, microbial mineral recovery and manufacture of
traditional foods and beverages such as yoghurt, bread, vinegar, soy sauce, beer and
wine. Industrial processes employing enzymes are also not listed in Table 1.1; these
include brewing, baking, confectionery manufacture, fruit-juice clarification and
antibiotic transformation. Large quantities of enzymes are used commercially to
convert starch into fermentable sugars which serve as starting materials for other
bioprocesses.
Our ability to exploit the capabilities of cells and enzymes has been
closely related to advancements in microbiology, biochemistry and
cell physiology. Knowledge in these areas is expanding rapidly; tools
of modern biotechnology such as recombinant DNA, tissue culture
offer new opportunities to develop novel products or improve
bioprocessing methods. Visions of sophisticated medicines, cultured
human tissues and organs, biochips for new-age computers,
environmentally-compatible pesticides and powerful pollution-
degrading microbes indicate a revolution in the role of biology in
industry.
A Typical New Product From Recombinant DNA
The interdisciplinary nature of bioprocessing is evident if we look
at the stages of development required for a complete industrial
process. As an example, consider manufacture of a new
recombinant-DNA-derived product such as insulin, growth
hormone or interferon. As shown in Figure 1.1, several steps are
required to convert the idea of the product into commercial reality;
these stages involve different types of scientific expertise.
The first stages of bioprocess development are concerned with
genetic manipulation of the host organism; in this case, a gene
from animal DNA is cloned into Escherichia coil. Genetic
engineering is done in laboratories on a small scale by scientists
trained in molecular biology and biochemistry. Tools of the trade
include Petri dishes, micropipettes, microcentrifuges, nano-or
microgram quantities of restriction enzymes, and electrophoresis
gels for DNA and protein fractionation.
In terms of bioprocess development, parameter of major
importance is stability of the constructed strains. After
cloning the growth and production characteristics of the
cells must be measured as a function of culture
environment. Practical skills in microbiology and kinetic
analysis are required; small-scale culture is mostly carried
out using shake flasks of 250-ml to 1-1itre capacity.
Medium composition, pH, temperature and other
environmental conditions allowing optimal growth and
productivity are determined. Calculated parameters such as
cell growth rate, specific productivity and product yield
are used to describe performance of the organism.
Genetic Engineering
Microbiology
• Study of microscopic organisms
• Important branch of science
• As a basic biological science
– Deals with nature of life processes and principles
behind, genetics
• As an applied biological science
– Study of useful as well as pathogenic
microorganisms
Industrial Microbiology
• Study of the exploitation of the biochemical
potential of microbes for the production of
various products
• Antibiotics, vaccines, steroids, solvents,
vitamins etc.
• Developments of new products using genetic
engineering
Microsopy
• Microorganisms are measured in smaller units
such as microns, nanometers, millimicrons
and Angstrom
• Various microscopes
• Difference between ordinary and electron
microscope
Range of microscopic measurements
Why microbiology is important?
• In biochemical engineering
– To understand and analyze the process of
biotechnology
– Design and operate different units in rational a way
– Therefore, a basic knowledge of cell growth and
function is required
– A living microorganism may be conceptualized as a
chemical reactor (take nutrients from environment,
grows, reproduces and releases products)
– Products formed and released during cellular activities
could be commercially important
Why microbiology is important?
• Rates of nutrient utilization, growth and release
of products depends upon:
• Type of the cells involved
• Temperature
• Composition of media etc.
• Quantitative understanding of biological systems
(correlation of friction factor and Reynolds No.)
• Understanding above interactions requires a
foundation built on microbiology and
biochemistry
Industrial Microbiology
• Study of the exploitation of the biochemical
potential of microbes for the production of
various products
• Antibiotics, vaccines, steroids, solvents,
vitamins etc.
• Developments of new products using genetic
engineering
Building block of organisms
• All living organisms are composed of cells
• What is true for Escherichia coli is true for
elephants (J. Monod)
• Cells are b/w 1 and 50 micrometer in diameter
• Basic components of living cell
– Cytoplasm
– Cell membrane
– Nucleus
– Ribosome
– Mitoch
Cell Nucleus (DNA Structure)
Cell componets
DNA
• DNA determines
– Heredity
– Cell reproduction
– Protein synthesis
– When DNA is damaged by foreign substances,
various toxic effects, including:
• Mutations
• Cancer
• Birth effects
• Defective immune system
Cell Membrane
• Acts as a barrier from external environment
• It closes the cell and regulates the passage of
ions, nutrients, metabolic products and fat
soluble substances into and out of it
• It is composed of phospholipid bilayer about 8
nm thick
• Highly selective membrane enabling the cell to
concentrate specific metabolites and excrete
waste
• A number of complex transformation takes place
across the membrane
A bacterial membrane
Cell Membrane
• Passive Transport
• Active Transport
Cytoplasm
• Colloidal in nature
• Thick semi-transparent and has higher water
contents
• It contains:
– Hydrophilic components (protein particles,
carbohydrates and salts)
– Hydrophobic components (lipids or fats)
Main function of cytoplasm is absorption and
excretion
Eucaryotic cells
• These cells are 1000-10,000 times larger than
procaryotes
• All cells of higher organisms belong to this
family
• Eucaryotic cells exist in a variety of forms
(Figure)
• Internal structure of eucaryotes is more
complex than procaryotes
• Cell membrane, cell wall
Prokaryotes and Eukaryotes
• Prokaryotic cell
– Genetic material is not enclosed within the membrane
– Cell walls contain complex polysaccharide
peptidoglycan
– Simple method of reproduction
– Size is usually 0.5 to 3 micrometer in diameter
• Eukaryotic cell
– Eukaryote means true nucleus
– Genetic material enclosed in a specialized membrane
– They are larger and more complex than prokaryotes
– Size range from 2 to 200 micrometer
Applications of Prokaryotes
• Metabolically the most diverse of all living systems
• Responsible for most degradation processes
• Can be grown aerobically and anaerobically
• Form a wide range of organic products (this property has both positive
and negative impact on society)
• Positive
– represent a massive resource of biocatalysis for the biotransformation
of organic materials and the degradation of herbicides, insecticides
and other man-made chemicals
• Negative
– Represent the principal agents causing the deterioration of
biomaterial e.g food and wood and are major hazards to public health
(food poisoning and other diseases)
Classification of organisms
• Classified according to their structure and
function
• Divided into three kingdoms
– Plants
– Animals
– Protists (Neither plants nor animals)
• Most are unicellular but some have many cells
• Cells have a membrane around the nucleus
(eukaryotes)
Classification of organisms
• Classifications show differences in several
characteristics including:

– Energy and nutritional requirements

– Rates of growth and product release

– Method of reproduction

– Morphology
Classification of organisms
Morphology
Naming the microorganisms
• They are named in Latin using binary
nomenclature
– First name represents the group or genus
– Second name represents the species
– Escherichia coli C600
– National collection of industrial and marine bacteria
(NCIMB)
– American type culture collection (ATCC)
– Strain (A strain is a subset of a bacterial
species differing from other bacteria of the same
species by some minor but identifiable difference)
Aspergillus awamori
Escherichia coli (E. coli)
• Escherichia coli (E. coli) chosen as a test microorganism.
• E. coli is currently the most specific indicator for faecal contamination of a
water source and therefore it is considered as a model organism in
laboratory research.
• The cells are about 2 μm long and 0.5 μm in diameter, with a cell volume
of 0.6 – 0.7 μm3 (Kubitschek, 1990).
• Optimal growth of E. coli occurs at 37ºC. Under a microscope,
• E. coli is a rod-shaped prokaryotic cell which has a long, rapidly rotating
flagellum (tail) used for movement.
• A strain of E. coli is a sub-group within the species that has unique
characteristics that distinguish it from other E. coli strains.
• These differences are often detectable on the molecular level and may
result in changes to the physiology or life cycle of the bacterium.
• For example, a strain may gain pathogenic capacity or the ability to resist
antimicrobial agents.
• Different strains of E. coli are often host-specific, making it possible to
Different Bacteria
• Pseudomonas aeruginosa
• Pseudomonas aeruginosa (P. aeruginosa) is a gram-
negative rod shaped free living bacterium that is
ubiquitous in the environment
• Staphylococcus aureus
• Staphylococcus aureus (S. aureus) is a gram positive
bacterium usually arranged in grape like irregular
clusters. Although it occurs widely in the environment
it is found mainly on skin and the mucous membranes
of animals. S. aureus can be released into
environments including swimming pools, spa pools and
other recreational waters by human contact.
• Legionella pneumophila
• Legionella pneumophila (L. pneumophila) is a
gram negative rod shaped bacterium.
Yeasts
• Rhodosporidium turoloides

• Rhodosporidium turoloides (R. turoloides) Y4 is oil


producing or oleaginous yeast (Wu et al. 2011).
Since these species contain intracellular valuable
compounds such as lipids, therefore the
disruption of this yeast would be interesting in
order to release the lipids contained in vacoules
within the yeast cell. Once the lipids are released
biodiesel could be produced via a conventional
transesterification process.