1. Bioprocess Engineering
Course Outline
Basics of Cell Biology and Biochemistry
Enzymes
Enzyme kinetics
Immobilized enzymes
Fermentation and Cell Culture
Cell Growth ; Batch Growth Kinetics
Product formation kinetics; Nutrient limitation
Ideal Chemostat; Modeling approaches.
Design and Analysis of Bioreactors
Suspension bioreactors
Immobilized cell bioreactors
Scale-Up and Optimization of Bioreactors
Oxygen Mass Transfer; Mixing; Sterilization
Instrumentation and Control

2. Bioprocess Engineering
Course Outcomes
Upon completion of this course, students shall be able to:
1. Describe the growth of microorganisms.
2. Analyze enzyme systems.
3. Determine the reaction stoichiometry for bioreactors and understand the operation of bioreactors.
4. Recognize principles of bioreactor analysis and design.
5. Develop sufficient skills to read current literature in the bioprocess engineering field.
6. Understand where the field is heading and identify future opportunities.

3. Bioprocess Engineering
Required Textbook
M. L. Shuler and F. Kargi, Bioprocess Engineering: Basic Concepts, 2e, Prentice-Hall (2002).
Course Grading
Homework %
Quizzes %
Class contributions %
Mid-term exams %
Final Exam %

4. Bioprocess Engineering
Typical Bioprocess
– Raw materials preparation
– Inoculums preparation
– Sterilization
– Production in bioreactors
– Recovery
– Separation
– Packaging

5. Bioprocess Engineering
Typical stirred tank bioreactor

6. Bioprocess Engineering

7. Bioprocess Engineering

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9. Bioprocess Engineering
Airlift bioreactor

10. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Eukaryotic and Prokaryotic cells
Living cells are divided into two types - prokaryotic and eukaryotic. This division is based on internal complexity.
Eukaryotic: The cells of protozoa, higher plants and animals are highly structured. These cells tend to be larger than the cells of bacteria, and have developed specialized packaging and transport mechanisms that may be necessary to support their larger size.

11. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Eukaryotic and Prokaryotic cells
Prokaryotic: These cells are simple in structure, with no recognizable organelles. They have an outer cell wall that gives them shape. Just under the rigid cell wall is the more fluid cell membrane. The cytoplasm enclosed within the cell membrane does not exhibit much structure when viewed by electron microscopy.
Prokaryotic cells are
found in bacteria,
including both
Archaebacteria and
Eubacteria, and
including the
blue-green algae.

12. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Eukaryotic and Prokaryotic cells
Prokaryotic cells are found in bacteria, including both Archaebacteria and Eubacteria, and including the blue-green algae.

13. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Eukaryotic and Prokaryotic cells
Prokaryotes share several characteristics:
 Prokaryotes DO NOT have a membrane-bound nucleus.
 Prokaryotes DO have a cell membrane, but DO NOT have
membrane bound organelles.
 Prokaryotes HAVE ribosomes that are different from
those of Eukaryotes.
 Almost all Prokaryotes are smaller than the smallest
Eukaryotes.
 Most Prokaryotes are single – celled organisms (Unicellular).

14. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Eukaryotic and Prokaryotic cells

15. Bioproces Engineering
STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL v v
Cell Wall
protects the cell and gives shape, made up of polysaccharides

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STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL
Cell Membrane
regulates movement of materials into and out of the cell;  contains enzymes important to cellular respiration v v

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STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL v v
Chromosome
carries genetic information inherited from past generations

18. Bioprocess Engineering
STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL v v
Plasmid
contains some
genes obtain
through genetic recombination

19. Bioprocess Engineering
STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL v v
Flagellum
moves the cell

20. Bioprocess Engineering
STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL
Pilus (Pili)
assist the cell in attaching to other surfaces,
which is important for genetic recombination v v

21. Bioreactors Engineering
STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL
Cytoplasm
contains DNA, ribosomes, and organic compounds required to carry out life processes v v

22. Bioprocess Engineering
STRUCTURAL CHARACTERISTICS OF A BACTERIAL CELL
Outer Membrane
protects the cell against some antibiotics
Capsule, and slime layer
protects the cell and assist in attaching the cell to other surfaces
Endospore
protects the cell against
harsh environmental
conditions, such as
heat or drought

23. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Bacteria (cell) growth
Bacteria are all around us. Given good growing conditions, a bacterium grows slightly in size or length, a new cell wall grows through the center forming two daughter cells, each with the same genetic material as the parent cell. If the environment is optimum, the two daughter cells may divide into four in 20 minutes.
Scientists who study bacteria try to create the optimum environment in the lab:
culture medium with the necessary energy source, nutrients, pH, and temperature, in which bacteria grow predictably.

24. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
Bacteria (cell) growth
a new cell wall grows through the center forming two daughter cells

25. Bioproces Engineering
Basics of Cell Biology and Biochemistry
Bacteria (cell) growth
LAG PHASE: Growth is slow at first, while the cells acclimate to the food and nutrients in their new habitat.
LOG PHASE: Once the metabolic machinery is running, they start multiplying exponentially, doubling in number every few minutes.
STATIONARY PHASE: As more and
more cells are competing for food and
nutrients, booming growth stops and the
number of bacteria stabilizes.
DEATH PHASE: Toxic waste products
build up, food is depleted and the cells
begin to die.

26. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
Bacteria (cell) growth
Traditionally, bacteria have been grouped based on their Structure, Physiology, Molecular Composition, and Reaction to specific types of stains, (Gram Stain), rather than on their evolutionary relationships.
Bacteria can be one of THREE Different SHAPES:

27. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
GRAM STAINING
Most species of Eubacteria can be grouped into
GRAM-POSITIVE BACTERIA and GRAM-NEGATIVE BACTERIA
based on their response to a laboratory technique called
GRAM STAINING.
Hans Christian Gram, a Danish Microbiologist, developed
the Gram-stain technique in 1884.

28. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
GRAM STAINING
The technique involves STAINING Bacteria with a PURPLE
DYE (Crystal Violet), and IODINE, and RINSED with ALCOHOL.
 Then Restained with A PINK DYE (Safarinin).

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GRAM STAINING
Depending on Structure of their cell walls, the bacteria absorb either the purple dye or the pink dye.
Gram-Positive Bacteria will retain the PURPLE DYE and appear Purple.
Gram-Negative Bacteria will appear PINK from the PINK DYE.

30. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
GRAM-POSITIVE BACTERIA
Have a thicker layer of PEPTIDOGLYCAN
in their cell walls, made of a protein
sugar complex that takes on the purple
color during gram staining.

31. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
GRAM-POSITIVE BACTERIA
Gram-positive bacteria include;
Organisms that produce BENEFICAL Substances
Example: Bacteria used to make yogurt, pickles and buttermilk.
Bacteria used to make ANTIBIOTICS, including Tetracycline
and Streptomycin These bacteria are called ACTINOMYCETES.
Organisms that cause important human DISEASE, including
Scarlet fever, Toxic shock syndrome, and Pneumonia.

32. Bioprocess Engineering
Basics of Cell Biology and Biochemistry
GRAM-POSITIVE BACTERIA
Many of these bacteria produce TOXINS, which are poisons
to our bodies. Toxins can be deadly; a single gram of the toxin
produced by Clostridium botulinum  (Botulism) could kill more
than one million people.
Antibiotics kill other Gram-positive bacteria by preventing
them from making proteins.  They affect only the GROWTH of bacteria without harming the body cells of humans.

33. Bioreactors Engineering
ANTIBIOTICS 
Antibiotics are drugs that fight bacteria by interfering with their cellular functions.
PENICILLIN interferes with Cell Wall Synthesis.
TETRACYCLINE interferes with Protein Synthesis.
Many Antibiotics are derived from chemicals that bacteria or fungi produce.
SULFA DRUGS are Antibiotics that are Synthesized in Laboratories. (Man Made)

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Basics of Cell Biology and Biochemistry
GRAM-NEGATIVE BACTERIA
Have an extra layer of lipids on the outside of the cell wall
and appear pink after gram staining.
The extra lipid layer stops the
PURPLE Stain from entering the
CELL WALL.  They do absorb the
PINK Stain, so they are easily
distinguished with a microscope.

36. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
GRAM-NEGATIVE BACTERIA
The extra lipid layer also stops many ANTIBIOTICS from
entering the bacteria. Treatment for these requires a different ANTIBIOTIC than those used for infections caused by Gram-positive bacteria.
These bacteria photosynthesis differ from plants, they do not release oxygen as a by-product, but produce SULFUR as a by-product.
Bacteria that produce sulfur are also called SULFUR PRODUCING BACTERIA.

37. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
NUTRITION AND GROWTH
TWO major differences between groups of BACTERIA are their SOURCE OF ENERGY AND WHETHER OR NOT THEY USE OXYGEN FOR CELLULAR RESPIRATION.
Most BACTERIA are HETEROTROPHS; they get their energy by consuming Organic Matter as a source of Nutrition.
Heterotrophic bacteria that feed on dead or decaying material are called SAPROPHYTES.
Some are AUTOTROPHS, they obtain their energy by making their own Food from SUNLIGHT OR MINERALS.

38. Bioreactors Engineering

39. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
NUTRITION AND GROWTH
PHOTOAUTOTROPHS ARE BACTERIA THAT USE SUNLIGHT AS AN ENERGY SOURCE.
CHEMOAUTOTROPHS OBTAIN THEIR FOOD FROM OXIDIZING INORGANIC COMPOUNDS INSTEAD OF SUNLIGHT.

41. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
NUTRITION AND GROWTH
The Second important Metabolic difference between BACTERIA groups has to do with CELLULAR RESPIRATION.
ORGANISM THAT USE OXYGEN DURING CELLULAR RESPIRATION ARE CALLED AEROBES.
THOSE THAT DO NOT USE OXYGEN ARE CALLED ANAEROBES, TYPICALLY THEY GET ENERGY FOR THEIR CELLULAR RESPIRATION THROUGH FERMENTATION.

42. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
NUTRITION AND GROWTH
THE PRESENCE OR ABSENCE OF OXYGEN IN THE ENVIRONMENT IS A LIFE DETERMINING CONDITION FOR SOME BACTERIA:
A. BACTERIA CALLED OBLIGATE AEROBES CANNOT LIVE WITHOUT OXYGEN.
B. BACTERIA CALLED OBLIGATE ANAEROBES CANNOT LIVE IN THE PRESENCE OF OXYGEN.
C. BACTERIA CALLED FACULTATIVE ANAEROBES CAN USE OXYGEN WHEN IT IS AVAILABLE, BUT THEY DO NOT DEPEND UPON IT.

43. Bioreactors Engineering
Basics of Cell Biology and Biochemistry
NUTRITION AND GROWTH
Bacteria have varying Temperature Requirements for Growth.  Some bacteria grow best in Cold Temperatures of 0-20 degrees C .  Others grow best in Temperatures between degrees C.
Thermophilic (Heat Loving) bacteria grow best in Temperatures between degrees C.
Most bacteria Grow BEST at a pH of 6.5 to 7.5 (7.0 is neutral).