Introduction

Introduction to Microbiology

Biochemical Engineering is an extremely broad

field.
Products range enormously in value.
Pharmaceuticals
Sewage treatment

An understanding of Biochemical Engineering is

useful in many traditional Chemical Engineering
Fields

CHNG 3804
Biochemical Engineering

Mining: Acid Mine Drainage & Bio-Leaching.

Fouling of Heat Exchangers, Bacterial growth in
Cooling Water.

Fariba Dehghani

Biochemical Engineering

Biochemical engineering is not:

Multidisciplinary subject
Concerned with developing biological processes on an
industrial scale.
Chemistry

Biochemistry

Pharmacy

Genetic engineering
The Human Genome Project
Genetically modified crops
Gene therapy
Stem cell research

Microbiology

Biotechnology
Food Technology

Genetics

Engineering

Mathematics

What do we do?

Biochemical Engineering Process

insect
fungal
bacterial
viral

proteins

separation

plant

PRODUCTS
(bio)reactor

CELLS
mammalian

genetic modification

Bio-catalyst
Selection and
Manipulation

acids

Raw materials

Bio-reactor

Product
Separation and
Purification

Product
formulation

alcohol
clean water, soil
clean air

Process Control

biogas

Bio-catalyst Selection and Manipulation

The following are critical for selection of biocatalyst
It should be a pure culture,
Be genetically stable,
Be easily propagated,
Exhibit rapid growth characteristics,
Have good rate of product formation,
Be free of toxic byproducts
Be amenable to genetic manipulation.

Applications of Biochemical Engineering

Antibodies, antigens, porcine and human growth hormones interferon,

tissue plasminogen activator, diagnostic and other therapeutic
compounds
Therapeutic peptides, cytolytic toxins, nasal decongestant

Specialty chemicals

Foods and beverages

Environmental Engineering

Commodity chemicals

Bioelectronics

Amino acids, vitamins, biopolymers, enzymes, lipids

Sweeteners, alcoholic beverages, single cell protein
Bioremediation of soil, industrial effluents, and waste water treatment
Acetic acid, acetone, butanol, ethanol, etc.
Biosensors, biochips

Classical microbiological processes

Micro-organisms transformed foods:
Alcoholic beverages (beer, wine, spirits
yeast)
Bread (yeast)
Dairy products (yoghurt, cheese lactic acid
bacteria)
Vinegar (acetic acid bacteria)
Soybeans (yeast, lactic acid bacteria)

Industrial microbiology

Antibiotics
Penicillin (fungi)

Pharmaceuticals

Ethanol (yeast)
Glycerol (yeast)
Acetone (bacteria)
Butanol (bacteria)
Isopropanol (bacteria)
Butanediol (bacteria)
Lactic acid (bacteria)
Citric acid (fungi)

New microbiological processes

Carotenoids and steroids (fungi)

Amino acids, nucleotides (bacteria)
Enzymes (amylase, proteinases, pectinases)
Recombinant proteins (hormones, antigens,
antibodies)

Process design
Biochemical process design requires knowledge
of the capacity of cell cultures (biomass) to make
products
Products may be secreted externally or stored in
inclusion bodies in the cell
Profitability ($) can be determined by:
How much product is recovered per gram of
biomass?
How much substrate is consumed per gram of
biomass?
How much product is recovered per gram of
substrate consumed?

Microbiology
To study Biochemical Engineering requires
some knowledge of Microbiology.
Humans have used microorganisms for a very
long time.
Bread and cheese using yeasts
Beer Brewing may have begun 7,000 BC.
Microorganisms complete critical segments of
carbon, nitrogen and oxygen cycles.
Microorganisms are also responsible for many
human, animal and plant diseases.

What are Bacteria

Significance of Bacteria

Unicellular entities
Neither plant nor animal
Diverse lifestyles
Highly adaptable, metabolic and
biosynthetic machine
Different cell structure to other macro cells
making up higher animals and plants

Global scale: carbon, nitrogen, phosphorous and

sulfur cycling
Spoilage of foods
Pathogenic to plants and animals
Production of high value compounds, amino
acid, alcohol, antibiotics, food supplements
Used in composting

Modern Microbiology

Classification of Microorganisms

Schleiden and Schwann 1838

All living systems are composed of cells and
their products.
In the late 1800s Pasteur identifies
microorganisms as critical active agents
for fermentation and develops the germ
theory of disease.

PROTIST
KINGDOM

PROCARYOTES

Bacteria

EUCARYOTES

Blue Green Algae

Molds

Fungi

Algae

Protozoa

Yeast

Procaryote

Do not contain a membrane enclosed nucleus.

Relatively small and simple cells.
Typically 0.5 3 m.
Can grow very fast.
Usually exist alone.
May be spherical, rods or spirals.
Cell is surrounded by a rigid wall.
Large Surface area to volume ratio.

Microstructure of Bacteria

Salmonella

Pseudomonas

S. aureus

Dillow et al., Nature, 1998

E.coli

Bacteria
Gram Negative and gram positive
Spore forming bacteria
Important Industrial Examples
Lactic Acid Bacteria: Production of Yoghurt.
Rhizobium: Biological Nitrogen Fixation.
Genetically Engineered Escherichia coli: used
widely for the production of Proteins.

The cell structure

Gram positive and Gram Negative bacteria

Gram positive: thick peptidoglycan layer
Gram Negative: Thin peptidoglycan layer
Peptidoglycan composed of two sugar derivatives: Nacetylglucosamine (NAG) and N-acetylmuramic acid
(NAM)
A small peptide containing D- and L-Alanine, Dglutamic acid and either L-Lysine or m-diaminopimelic
acid

Microbiology text book

Gram positive and Gram Negative bacteria

Spore
Wall

Peptidoglycan
Plasma
membrane

Cortex
Outer
membrane
Peptidoglycan
Plasma
membrane
Microbiology text book

Microbiology text book

Blue Green Algae

(Cyano Bacteria)
Not used to great commercial benefit.
Important in Aquatic Systems and
Nitrogen Cycle.

Microstructure of the Cells

Typical animal cell

Endospores are resistant to temperature, desiccation, chemical agents, and enzyme.

Autoclaving required to use high temperature to inactivate spores.

Eucaryote
1000 to 10,000 times larger than Procaryotes.
All cells of higher organisms belong to this
family.
Greater degree of spatial organization and
differentiation.
Slower growing than Procaryotes.
Slower rates of mass transfer due to smaller
surface area to volume ratio.
Some are shear sensitive particularly animal
cells.

Saccharomyces cerevisiae

Nucleus
Typical plant cell

DNA
Ribosome
Plasma membrane
Cell wall
Prokaryotic cell

http://www.mycolog.com/chapter6.htm

Campdell, 1999

Yeasts

Molds

One of the important subgroup of Fungi

Single Small Cells 5 30 m.
Saccharomyces Cerevisae grown
aerobically for use a bakers yeast.
A number of varieties are grown
anaerobically to convert sugar to ethanol.
Saccharomyces strains used anaerobically
for beer and wine production.

Higher form of fungi.

Growing structure called mycelium.
Grow in branched structures.
Mold and yeast do not contain
chlorophyll
This has rheological, mass transfer
and growth implications.
Examples:

Algae and Protozoa

Animal and Plant Cells

Algae are of research interest for conversion of

CO2 into fuel.
Algae is used as food supplement such as
seaweed.
Protozoa can not exploit sunlight energy, and
are significant in biological waste treatment.

Large and Slow growing.

Shear Sensitive.
Animal cells are widely used for vaccine
production.
Animal cells can be used to produce proteins.
Human cells can be grown for therapeutic use.

Viruses

Phages

A non-cellular biological entity that can

reproduce only within a host cell.
Viruses consist of nucleic acid (DNA or RNA)
covered by protein; some animal viruses are
also surrounded by membrane.
Inside the infected cell, the virus uses the
synthetic capability of the host to produce
progeny virus.

Bacteriophage or phage are small viruses which

infect bacteria.
Specific to the bacterial strain.
Can be a problem in large scale pure culture
bacteria plants.
Have made essential contributions to molecular
genetics.
Used to maintain stable DNA segments.
Used in Russia and Eastern Europe to treat
infections.

Penicilium that is used for production of

antibiotics
Aspergillus niger that produces oxalic
acid (HO2CCO2H) and citric acid

Cheese ripening

Further Reading
The Birth of Penicillin, and the disarming of
microbes written by Ronald Hare, and
published in 1970 is a very readable
eyewitness account of both the discovery
and large scale production of penicillin.

Fermenter Technology

Recombinant DNA

The term Recombinant DNA refers to the combination of DNA from two
different sources.

Recombination of DNA allows the variation and diversity of living

organisms.

Temperature Control,
pH electrodes used for offline
measurement/control.
Fed-batch cultures introduced to
overcome dissolved oxygen
limitations.

The joining of the males sperm cell with the females egg cell is a natural
recombination process. The DNA of the male joins and mixes with the
females DNA resulting in an offspring cell with a combination of both
parents. This is evident in the offsprings physical appearance, which
exhibits features that are similar to both parents.

Mechanically aerated vessels, aseptic

operation,
Continuous sterilisation of feeds

Steam sterilisable pH and dissolved

oxygen electrodes.
Feedback control

1960-1970

Higher pressures to minimize DO

limitations

Computer monitoring and control;

Mathematical modelling for control of
yeast fermentations

Natural recombination is now mimicked by biotechnologists allowing the

reconstruction of DNA molecules in test tubes. In this process, the
construction of a new DNA molecule takes place from two different
sources. The techniques and procedures associated with this are known
as recombinant DNA technology and are the specialty of the geneticist
(refers to gene cloning).

1970-mid
1990s

Fluidized bed and air lift systems.

Polarographic DO probes
Model based optimal control

Era

Equipment Used

Control Employed

Pre-1900

Wooden or copper vats

barrels, shallow trays, trickle filters and
clay pots

Thermometer
Hydrometer
Heat Exchangers

1900-1945

Steel vessels introduced for acetonebutanol (first aseptic fermentation)

Sparging of air for yeast
Mechanical stirrers in small vessels

1945-1960

Development of Recombinant DNA

Gene Cloning

In 1973 Cohen, Chang, Helling and Boyer

demonstrated that a recombinant DNA molecule
can be maintained and replicated in E.coli
Boyer founded the first genetic engineering
company Genetech soon after.
Recombinant DNA technology allows cell to be
altered to make them more productive and to
use cells to make foreign proteins.

Prescot LM, Harley JP and Klein DA, 1996, Microbiology, The McGraw-Hill Companies, Inc. USA

Recombinant DNA Technology in

Biotechnology
The overall efficiency of the biotechnology process is improved with the aid of the
new recombinant techniques. The benefits of recombinant DNA technology to the
biotechnology process lie in the bio-catalyst selection stage and include

Custom design of products with desirable characteristics,

Increase of a yield of a particular product,
Improve the efficiency of the production with respect to energy utilisation,
Transfer of a particular activity to a more desirable host
Minimize the purification steps required.
Feasibility to introduce mammalian genes into bacteria for large scale
production that is advantageous for pharmaceutical industry for production
of insulin and vaccines.

Recombinant DNA Technology

Many human genes have been cloned in E. coli or in yeast.
Cultured cells (E. coli, yeast, mammalian cells) transformed
with human genes are being used to manufacture:
insulin for diabetics
factor VIII for males suffering from haemophilia A
factor IX for haemophilia B
human growth hormone (GH)
erythropoietin (EPO) for treating anaemia
three types of interferons
several interleukins
granulocyte-macrophage colony-stimulating factor (GM-CSF) for
stimulating the bone marrow after a bone marrow transplant
tissue plasminogen activator (TPA) for dissolving blood clots
adenosine deaminase (ADA) for treating some forms of severe combined
immunodeficiency (SCID)
angiostatin and endostatin for trials as anti-cancer drugs
parathyroid hormone

Summary

Text Book Reference

This Lecture

Any Microbiological text book

Bailey and Ollis (1986) Chapter 1
Campbell M. K., Biochemistry. Saunders
College publishing Harcourt Brace College
Publisher,1999

Introductory Microbiology
Penicillin and the Birth of Biochemical
Engineering

Next Lecture
Introductory Biochemistry

http://learn.genetics.utah.edu/units/ba
sics/
http://en.wikipedia.org/wiki/Dna