The document provides an extensive syllabus for a biochemical engineering course, detailing the instructor's contact information, lecture schedule, textbooks, grading criteria, and a project assignment. It covers fundamental concepts of biochemical engineering, exploring applications, processes, regulatory constraints, and the various types of cells involved in this field. Additionally, it highlights the relationship between scientists and engineers, as well as the foundational biological knowledge necessary for understanding biochemical processes.

1. Biochemical Engineering (CHE – 362)
Instructor’s Name: Sri Sivakumar
Office: NL II 204
Email: srisiva@iitk.ac.in
Phone: 7697
(3L-0T-0P-0D;Weightage 09)
Lecture
Mondays (12.00 to 1.15 pm) - L4
Tuesdays (9.00 to 10.15 am) – L5

2. Text Book:
1. M.L. Shuler and F. Kargi, “Bioprocess Engineering”, Second Edition, Prentice
Hall, NJ
Reference Book:
1.Biochemical engineering, H. W. Blanch, D. C. Clark
2. D. G. Rao, Introduction to Biochemical Engineering, Tata McGraw-Hill.
3. J.E. Bailey and D.F. Ollis, “Biochemical Engineering Fundamentals”, McGraw-Hill,
2nd ed..
Recommended Journals
Nature, Nature Biotechnology, Science, Applied and Environmental Biotechnology,
Bioprocess Engineering, Biotechnology and Bioengineering, Biotechnology
Progress, Enzyme and Microbial Technology
Readings

3. Grading
Mid sem. examination - 25%
End sem. examination - 35%
Quizzes (2) - 15% (Surprise quizzes)
Project report - 10%
Project presentation – 5%
Attendance – 10%
Project – Presentation and submission at the end of semester

4. Project
1. Two research articles (NOT review article) must be chosen from the
same research field. Articles must possess some biochemical
engineering of biotechnology concepts.
2. The article can be from different or same group
3. Publication of the research articles must be after 2019
4. Research papers must be approved by the TAs. Hard copies of the
article will be signed by TAs
5. Deadline for the choosing the research papers – March 15th
6. Format of the report and presentation will be discussed later
7. Every group will have three members. Google form will be circulated
for forming the group.

5. A typical biological process
We study these
processes

6. 1. An Overview of Biological Basics- Cell Structure and Cell Types (1
lecture) – Slides
2. Kinetics of Enzyme Reactions (5 lectures) – Green Board
3. Metabolic Stoichiometric and Energetics (3 lectures) - Slides
4. Molecular Genetics and Control (3 lectures) - Slides
5. Biomass Production (4 lectures) - Green Board
6. Transport Phenomena in Biosystems (3 lectures) - Green Board
7. Design and Analysis of Biological Reactors (5 lectures) - Green Board
8. Downstream Product Recovery and Purification (5 lectures) - Slides
9. Fermentation (3 lectures) - Slides
10.Interaction of Mixed Microbial Populations (2 lectures) - Green Board
11.Biological Wastewater Treatment (2 lectures) - Slides
Syllabus

7. Relationship of Scientists and Engineers
Microbiologists, biochemists, biophysicists, and molecular biologists
are scientists, well-trained in empirical testing of hypotheses.
Engineers develop theories based on mathematical models, use
models to predict performance, optimize and develop processes.
Research scientists often pursue knowledge while applications may
take a secondary role.
The work of engineers is often driven by economics of an application
and problem solving.
What is biochemical engineering?

8. What is biochemical engineering?
A multidisciplinary field?

9. Example Applications
1. New Medicines and delivery modes
2. Organ growth in reactors
3. Nutritious Foods
4. Computers based on biological molecules rather an silicon (Green computers)
5. Superorganisms to degrade pollutants
6. Consumer products
7. Industrial processes
8. State of the art biosensor
What is biochemical engineering?
Involves the use of micro-organisms, animal or plant cells or their components
to generate products and services to human beings
We have been using micro-organisms for several processes for several
centuries

10. Biotechnology – use or development of methods of direct genetic manipulation for
a socially desirable goal, e.g., a chemical, a plant, gene therapy, an organism to
degrade a waste.
Bioengineering – Engineers working with biotechnology, including work on medical
and agricultural systems.
Biological Engineering – Emphasizes applications to plants and animals.
Biochemical Engineering – Extension of chemical engineering to systems using a
biological catalyst to bring about desired chemical transformations
Biomedical Engineering – getting closer to biochemical engineering, especially in
the areas of cell surface receptors and animal cell culture.
Biomolecular Engineering – defined by National Institutes of Health as “…
research at the interface of biology and chemical engineering and is
focused at the molecular level.”
What is biochemical engineering?

11. Bioprocess vs Biochemical Engg – Bioprocess Engg. is broader than biochemical
engg. and includes the work of mechanical, electrical, and industrial engineers to
apply their disciplines to processes based on living calls or subcomponents of cells.
Includes: equipment design, sensor development, control algorithms, manufacturing
strategies, etc.
What is biochemical engineering?
Related disciplines to biochemical engineering:
1. Metabolic engineering, including metabolic modeling
2. Bioprocess engineering, including process control
3. Bioseparations
4. Bioinformatics
5. Biomaterials engineering
6. Tissue engineering
7. Manufacturing engineer and reactor design

12. a. 1928, Alexander Fleming, St. Mary’s Hospital in London,
Observations – lack of bacterial growth near contaminated Staphylococcus
Aureus particle.
Killing organism was Penicillium notatum
b. Norman Heatley – biochemist, play the role of bioprocess engineer. He developed
an assay to monitor amount of penicillin made to determine the kinetics of the
fermentation. He made few batches of penicillin.
c. During WWII, Howard Florey (of Oxford) approached U.S. companies – Merck,
Pfizer, Squibb, and the USDA I Illinois. In 1940 fermentation for the production of a
pharmaceutical was an unproved approach (versus chemical synthesis which had
more confidence), and penicillin is a fragile and unstable product.
e. Northern Regional research Lab in Peoria, IL, USA, made major contributions,
including development of a medium (corn steep liquor lactose based medium) to
increase productivity about 10 fold. New strain, Penicillium chrysogenum, is superior
and was used.
Story of Penicillin

13. Bioprocess Regulatory Constraints
a. U.S. Food and Drug Administration – Three phases for drug approval,
takes 15 years from discovery-through-process approval.
i. Phase I – safety
ii. Phase II – efficacy & side effects
iii. Phase III – large scale testing (1000 to 3000 patients)
b. GMP – Good Manufacturing Practices. (also GLP – Good Laboratory
Practices, and SOP – Standard Operating Procedures).
c. FDA approval is for the product AND the process together.
FDA Approval

14. Basic Chemicals
Organic acids (Citric acid, Lactic acid)
Alcohols (1,3 Propanediol)
Amino acids (Glutamic acid, Lysine)
Biochemicals
Enzymes (Proteolytic Enzymes)
Surfactants (Lecithin, Esters)
Biopharmaceuticals
Antibiotics (Penicillin)
Antibodies
Hormones (Growth Hormones)
Vaccines (Hep B Vaccine)
Therapeutic Proteins
Engineered Bioproducts
Bio-devices
Examples of biochemicals

15. Transport Processes in Biochemical Engineering
Biochemical reactors used in
- microbial fermentations
- waste treatment systems, and
- some biomedical devices
Several phases are involved. Substrates/nutrients must be
transferred from one phase to another

16. Mass & Heat Transfer are Very Important
Gas-liquid mass transfer
Oxygen is a key nutrient for all aerobic cells.
Sparingly soluble in water and supply of oxygen from the gas phase to the liquid
phase is critical
Carbon dioxide is another gas that is important
It regulates the pH in mammalian cells
Its transport and inter-conversion between CO3
2-, HCO3
- and H2CO3 must be
considered in anaerobic waste water treatment
Liquid-liquid mass transfer is required for the recovery of bioproducts
E.g., aqueous-organic extraction and aqueous two phase systems for
enzymes and whole cell reactions
Heat transfer is important since temperature needs to be controlled for all
biological reactors

17. Basics of Biology
•Diversity of Microorganisms
•Naming and Taxonomy of Cells
•Procaryotes
•Eucaryotes
•Viruses
•Cell Structure - major classes of compounds
•Culture Media Components

18. 1. Temperature
i. Grows best below 20˚C Psychrophiles
ii. Grows best between 20 and 50˚C Mesophiles
iii. Grows best above 50˚C Thermophiles
2. pH
i. Grows best near neutral pH
ii. Grows well at pH of 1 to 2 Acidophiles
iii. Grows well at pH as high as 9
Diversity of Microorganism - Environmental Conditions
3. Moisture
i. Most cells require a minimum moisture content
ii. Some cells grow in the near absence of moisture
4. Salinity
i. Most cells require a moderate level of salinity
ii. Some cells can exist in very high salt concentrations

19. 5. Oxygen Availability
i. Require oxygen for growth Aerobic
ii. Require lack of oxygen for growth Anaerobic
iii. Aerobic or anaerobic Facultative
6. Nutrient Availability
i. Most microorganisms require organic and inorganic nutrients
to grow and survive
ii. Grow in the absence of key nutrients: e.g. can convert CO2 from air into
organic cellular molecules.
Diversity of Microorganism - Environmental Conditions
Size and Shape
i. Spherical or Elliptical - Coccus
ii. Cylindrical - Bacillus
iii. Spiral - Spirillum

20. Cell Names are in Latin E. coli
Genus Name: Escherichia
Species Name: coli
Naming the cells

21. Primary types of Cells
Prokaryotes
1. No nuclear membrane
2. No organelles
3. Simple structure
4. Single chromosome
Bacteria
Eukaryotes
1. Nuclear membrane
2. Organelles
3. Complex structure
4. >1 chromosome
Animals, Plants, Protists (Algae, Fungi)
Eubacteria
Cell chemistry
similar to eucaryotes
e.g. Most bacteria
Archaebacteria
Distinctive cell chemistry
e.g. Thermoacidophiles
Gram +ve Gram -ve
Types of Cells

22. Comparison of Procaryotes and Eucaryotes
(Kargi)

23. Eubacteria: Gram Negative Cells
Fig 2.2 (Kargi)

24. A. Cell Envelope
Outer membrane: 10 - 20 nm thick, a protein-polysaccharide lipid complex
Petidoglycan: 5-10 nm thick, 50% protein - 30% lipid - 20% carbohydrate
Periplasmic space: space between membranes
Flagellum: 10-20 nm thick hair-like structures, provides mobility
B. Cytoplasm
Nuclear material: a single chromosome of DNA with no nuclear membrane.
Ribosomes: sites of protein synthesis. Cells contain about 10,000 of them. Size is
about 10 - 20 nm. 63% RNA and 37% protein.
Storage granules: storage of key metabolites. 0.5-1 μm each.
Spores: used by cell to survive harsh conditions of high heat, dryness, and antibiotic
agents. One spore formed per cell.
Eubacteria: Gram Negative Cells

25. E.g. E. coli
Eubacteria: Gram Negative Cells

26. E.g. Bacillus Subtilus
Eubacteria: Gram Positive Cells

27. • Mycoplasma - Pneumonia
• Actinomycetes (resemble molds - have branched hyphae; are useful for
the production of antibiotics
• Thermomonospora
• Streptomyces - useful for antibiotic production and other natural and
"non-natural" products
• Cyanobacteria (formerly blue-green algae; have chlorophyll and can fix
CO2 into sugars)
Eubacteria: Neither Gram +/- Cells

28. Arcahebacteria
Archaebacteria – Looks similar to Eubacteria, but differ at the molecular level.
a. No peptidoglycan, different lipid composition of cytoplasmic membrane.
b. Methanogens, thermoacidophiles, halobacteria
c. Sources of active enzymes with novel properties.

29. Eucaryotes
Fig. 2.3 in Kargi

30. I. Cell Envelope - provides rigidity
Cell wall: Animal cells - no cell wall (fragile). Plant cells – made up of peptidoglycan,
polysaccharides and cellulose.
Plasma membrane: Animal cells do have it. Made up of proteins and phospholipid
bilayer structure. Major proteins are hydrophobic and are embedded in lipids. They
are similar to procaryotes, but major difference is the presence of sterols, which
impart rigidity.
Main functions
Regulates transport of material (selective permeable) and maintains electric potential
of the cell
Eucaryotes- Cell structure

31. II. Cytoplasm - inside the membrane and contains many salts and biomolecules
1. Nucleus: Contains chromosomes and surrounded by a membrane.
•DNA replication and RNA synthesis (transcription) occurs
•Nucleolus is a specialized region where ribosomes subunits are assembled
•Contains nuclear pores for regulation of material flow
•In procaryotes, DNA processing takes place in the cytoplasm
2. Mitochondria: 1-3 μm cylindrical bodies. The powerhouses of the cell where
respiration and oxidative phosphorylation occur.
Occur in various shapes, sizes and numbers in the cytoplasm of eucaryotes
Self replicating and contain DNA similar to procaryotes
Eucaryotes- Cell structure
3. Endoplasmic reticulum: Membrane complex extending from cell membrane,
sites of protein synthesis and modification.
Rough – contains ribosomes in the inner surface – synthesis and modification of
protein structure
Smooth – Lipid synthesis

32. Eucaryotes- Cell structure
4. Ribosomes - large complex of RNA and protein molecules
5. Lysosomes: Small membrane-bound particles that contain digestive
enzymes. Worn-out organelles, food particles, viruses and bacteria
8. Golgi bodies: small particles with multiple compartments composed of
membrane aggregates responsible for excretion of proteins and other products.
Modification of proteins by addition of sugars (glycosylation)
9. Vacuoles: membrane bound organelles of plant cells responsible for nutrient
digestion, osmotic regulation, and waste storage.
6. Peroxisomes – similar to lysosome in structure. Destroys toxic peroxides
7. Glyoxisomes – contains enzymes (isocitrate lyase and malate synthase)
for the glycosylation process
10. Chloroplasts: Large and chlorophyl-containing structures that are
responsible for photosynthesis in plants and algae. They have their own DNA
and protein synthesizing machinary.

33. Eucaryotes - Fungi
Yeasts
5-10 μm in size; spherical, cylindrical or oval in shape.
Reproduction: sexual and asexual
Most common yeast used in industry is Saccharomyces cerevisiae, which
is used for baker’s yeast production under aerobic conditions and for
alcohol production under anaerobic conditions.
Fungi – heterophs, and larger than bacteria. Two major types: Yeasts and molds

34. Molds
Filamentous fungi with a mycellial structure. Mycelium is a highly branched
system of tubes that contain mobile cytoplasm with many nuclei. Molds are
used for production of citric acid and many antibiotics.
Pore - Resistance to heat, freezing, drying conditions.
Eucaryotes - Fungi

35. Viruses
Parasites - need host cell to be functionally active, are NOT free- living
Size – 30 to 200 nm (nano- meters)
Genetic material: DNA (DNA viruses) or RNA (RNA viruses)
Capsid: a protein coat over the genetic material
Outer envelope: Some contain a lipoprotein outer envelope
Types of Viruses
i. Bacteriophage: virus that infects a bacteria
ii. Plants: tobacco mosaic virus
iii. Humans: polio virus, SARS virus
Advantages
Production of virus-like particles that are empty shells (capsid) used a vaccines
Gene therapy – replace virus genetic material with a desired gene; capsid acts
as a vehicle to protect the gene and to deliver it selectively to a cell type. In this
case, the virus is a biotechnology tool.

37. Cell Construction
Living Cells contain High-Molecular-Weight Polymeric Compounds such as
Proteins, nucleic acids, polysaccharides, lipids, storage materials (fats,
polyhydroxy-butyrate, glycogen) and inorganic salts
Elemental composition of a typical bacterial cell:
Carbon (50%),
Oxygen (20%),
Nitrogen (14%),
Hydrogen (8%),
Phosphorous (3%),
Sulfur (1%),
Small amounts of K+, Na+, Ca2+, Mg2+, Cl-,
Vitamins

38. The cellular macro-molecules are functional in their proper 3D configuration and
function in its unique environment
Biological system – levels of understanding:
i. Molecular (molecular biology, biochemistry)
ii. Cellular (cell biology, microbiology)
iii. Population (microbiology, ecology)
iv. Production (bioprocess engineering)
Cell Construction

39. Cell Construction
1. Amino acids and Proteins
2. Carbohydrates
3. Lipids, Fats and Steroids
4. Nucleic acids, RNA and DNA
5. Cell nutrients

40. Cell Construction
Amino Acids
Amino acids are the building blocks (monomers) of proteins and enzymes. Amino
acids have acidic (COOH) and basic (NH2) groups. Both groups can exchange
protons (H+) and alter the charge as a function of pH. This pH - charge behavior
allows for their separation using a column apparatus.
About 40 to 70% of cells dry weight
Biopolymers with a-Amino acid monomers; MW of 6000 to several hundred
thousands amino acids sequence determines protein’s primary structure
the secondary and tertiary structure are determined by the weak interaction
among various side groups
Two types of protein conformation: fibrous and globular proteins
The L-isomer is the most common
form. The D isomer (switch
COOH and NH2 groups) is rare.
21 amino acids

41. Cell Construction- Amino acids

42. Cell Construction- Amino acids

43. Cell Construction- Amino acids

44. Proteins are biopolymers composed of numerous amino acid units, created
through enzyme-mediated condensation reactions forming a peptide bond.
Cell Construction- Amino acids/Proteins
Proteins
Poly peptides contains ~ 50 amino
acids
Proteins can have >50 amino acid
chains

45. Cell Construction- Amino acids/Proteins
Acid groups are neutral at low pH and negatively
charged at high pH
At intermediate pH values an amino acid has
positively and negatively charged groups
(zwitterion)
Proteins may contain other components besides amino acids: Prosthetic groups
metal atoms, oligosaccharides (chains of maltose and other sugars – these proteins
are said to be glycosylated), small functional molecules (e.g. heme group –
hemoglobin).
Proteins containing prosthetic groups - Conjugated proteins

46. Cell Construction- Amino acids/Proteins
Protein conformation

47. Classification of proteins
Cell Construction- Amino acids/Proteins
1. Structural proteins: glycoprotein, collagen, keratin
2. Catalytic proteins: enzymes (largest class of proteins), most
enzymes are globular proteins
3. Transport proteins: haemoglobin, serum albumin
4. Regulatory proteins: hormones (insulin, growth hormones)
5. Protective proteins: antibodies, thrombin

48. Cell Construction- Amino acids/Proteins
Structure of proteins
Primary structure
The linear sequence of amino acids.
(1-d length)
Each protein has a unique sequence
of amino acids.
Sequence has a profound effect on
the 3-D structure and function
Example – Ribonuclease containing
124 amino acids

49. The way the molecule is extended. Hydrogen bonding between adjacent R groups
that are not widely separated. Formation of local structure within proteins,
such as α-helix or β-sheet.
Secondary structure
Cell Construction- Amino acids/Proteins
α-helix
β-sheet

50. Tertiary structure
Cell Construction- Amino acids/Proteins
Interactions of R groups far apart on the
chain (hydrogen, covalent, and disulfide
bonding, hydrophobic/hydrophillic).
3-dimensional form of the protein.
Quaternary structure
Proteins possessing more than one
polypeptide chain
Hemeglobin (oligomeric) has four
subunits that interact with each
other
Interactions occur by disulfide or
other weak bonds
Assembly of multiple polypeptide chains.
Some enzymes (catalytic proteins) have
this structure.

51. Cell Construction- Amino acids/Proteins
Antibodies (IgG, IgA, IgD, IgM, Ige)
Are proteins that bind to foreign
macromolecules (antigens) with high
specificity (immune response).
Antibodies have binding sites that are
structurally complimentary to antigens,
which induce their formation
Two binding sites are usually present and
form 3D lattice of alternating Ag and Ab
molecules
Complex precipitates as precipitin
Industrial Applications
• diagnostic kits
• protein separation
• drug delivery