This document provides information about the Metabolic Engineering course taught by Dr. Lovely at Noida Institute of Engineering and Technology. It includes details about the course syllabus, units covered, evaluation scheme, course objectives and outcomes. The key topics covered are metabolic flux analysis, experimental determination of metabolic fluxes, computational modelling of biological networks, and industrial applications of metabolic engineering including pathway engineering strategies for production of commercially important metabolites and proteins.

1. Noida Institute of Engineering and Technology, Greater
Noida
Name of Faculty:
Dr. Lovely
Department of Biotechnology
Subject Name: Metabolic Engineering
Subject Code: ABT0602
Course Details: B. Tech Biotechnology
3rd Year/ Semester –VI
Unit-V

2. Introduction of Faculty
Dr. Lovely (B.Tech, M.Tech - Ph.D)
Assistant Professor
(Department of Biotechnology, NIET Greater Noida)
Qualification:
Ph.D (Biochemical Engineering) Indian Institute of Technology, Delhi
M.Tech (Industrial Biotechnology) National Institute of Technology Karnataka, Surathkal
B.Tech (Biotechnology) (CRSCE, Murthal)
Specialization: Industrial Biotechnology and Biochemical Engineering
Experience:
Teaching Experience : 2.5 year (NIT Jalandhar, NIET)
Industrial Experience: 2.5 year (Microbiologist at Smriti Products Pvt. Ltd.)
Email id: lovely@niet.co.in
rajput.lovely811@gmail.com

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Evaluation Scheme
Lovely ABT0602 Unit-IV
Departmental Elective- III
Bioreactor Analysis and Design (ABT0611) Probabability and statistics using R in Biotechnology
Departmental Elective-IV
Biofuels and Alcohol Technology Machine learning

4. Unit-I (Introduction to Metabolic Engineering and its importance)
• Introduction to Enzymes and metabolism,
• Stoichiometry of cellular reactions,
• dynamic mass balance,
• Yield coefficients and linear rate equations,
• Black box model,
• Heat balance,
• Different models for cellular reactions
• Induction-Jacob Monod Model and its regulation,
• Differential regulation by isoenzymes,
• Concerted or cumulative feedback regulation.
• Regulation in branched pathways,
• Permeability, and transport of metabolites.
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Subject Syllabus
Lovely ABT0602 Unit-V

5. Unit-II(Metabolic flux analysis)
• Introduction to Metabolic flux analysis (MFA),
• Isotopic steady state methods (13C MFA) and Isotopic nonsteady state methods,
• Dynamic metabolic flux analysis,
• Building stoichiometric matrix;
• Steady state and pseudo steady state assumptions;
• Using different optimizing functions to solve linear programming problem;
• understanding flux cone and constraints;
• Introducing additional constraints from thermodynamics.
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Subject Syllabus
Lovely ABT0602 Unit-V

6. Unit-III (Experimental determination of metabolic fluxes)
• Technical developments in labels distribution analysis;
• Nuclear Magnetic Resonance spectroscopy (NMR) and
• Gas chromatography along with mass spectroscopy (GC-MS) based methods for flux
determination,
• C13 labelling.
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Subject Syllabus
Lovely ABT0602 Unit-V

7. Unit-IV (Computational modelling of biological networks)
• Introduction to MATLAB,
• Creating MATLAB variables,
• Using MATLAB as a calculator,
• Main features of MATLAB and capabilities of MATLAB,
• Synthetic circuit design,
• MOMA (Minimization of Metabolic adjustment),
• iFBA (Integrated Flux Balance Analysis),
• dFBA;
• Enhancement of product yield and productivity.
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Subject Syllabus
Lovely ABT0602 Unit-V

8. UNIT-V (Industrial Applications)
• Pathway engineering strategies for overproduction of some commercially important
primary and secondary metabolites or industrially relevant enzymes and recombinant
proteins,
• bioconversion- applications and factors affecting bioconversion,
• mixed or sequential bioconversions,
• regulation of enzyme production,
• Strain selection and improvement,
• the modification of existing or the introduction of entirely new metabolic pathways.
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Subject Syllabus
Lovely ABT0602 Unit-V

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Branch wise Applications
Lovely ABT0602 Unit-V

10. 1. Identify the appropriate host and/or metabolic pathways to produce a desired
product or remediate a toxin.
2. Construct genome-scale metabolic flux models using available tools and
software and perform simulations.
3. Design 13C-labeling strategies and perform metabolic flux analysis to determine
metabolic pathway utilization.
4. Compare potential metabolic engineering strategies using quantitative metabolic
modelling.
5. Devise effective strategies to implement genetic manipulations and Pathway
engineering strategies for industrial applications.
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Course Objectives
Lovely ABT0602 Unit-V

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Course Outcomes
Lovely ABT0602 Unit-V
Course outcome: After completion of this course students will be able to
CO 1 Identify the appropriate host and/or metabolic pathways to
produce a
desired product or remediate a toxin.
K1, K2
CO 2 Construct genome-scale metabolic flux models using available
tools and
software and perform simulations
K1, K2, K3,
K4
CO 3 Design 13C-labeling strategies and perform metabolic flux
analysis to
determine metabolic pathway utilization
K1, K3, K4
CO 4 Compare potential metabolic engineering strategies using
quantitative
metabolic modelling
K1, K3, K5
CO 5 Devise effective strategies to implement genetic manipulations
and
Pathway engineering strategies for industrial applications.
K2, K3, K5,
K6

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Programs Outcomes (POs)
1. Engineering knowledge
2. Problem analysis
3. Design/development of solutions
4. Conduct investigations of complex problems
5. Modern tool usage
6. The engineer and society
7. Environment and sustainability
8. Ethics
9. Individual and team work
10. Communication
11. Project management and finance
12. Life-long learning
Lovely ABT0602 Unit-V

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COs and POs Mapping
CO/
PO
PO1 PO2 PO3 PO4 PO5 PO6 PO7 PO8 PO9 PO10 PO11 PO12
CO5 3 3 3 3 3 3 2 3 3 2 1 3
Lovely ABT0602 Unit-V

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Program Specific Outcomes (PSOs)
PSO 1: To apply knowledge of basic sciences and biotechnological techniques.
PSO 2: To design, optimize, analyze and scale up bioprocess to develop useful
products with societal consideration.
PSO 3: To generate, analyze and interpret biological data using Insilico and other
relevant approaches.
Lovely ABT0602 Unit-V

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COs and PSOs Mapping
CO/PSO PSO1 PSO2 PSO3
CO5 3 3 3
Lovely ABT0602 Unit-V

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Program Educational Objectives (PEOs)
PEO 1: Student will acquire knowledge skills in the frontier areas of biotechnology
and will be able to solve societal problem individually and in the team.
PEO 2: Students will be able to think creatively and ethically about the use of
biotechnology to address local and global problems
PEO 3: Students will be able to implement the engineering principles to biological
systems for development of industrial applications, as well as entrepreneurship skills
to start biotech industries.
Lovely ABT0602 Unit-V

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Result analysis
Not Applicable
Lovely ABT0602 Unit-V

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End Semester Question Paper Templates
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Prerequisites/Recap
• Basic knowledge of Chemistry, Biochemistry, Microbiology and Molecular
Biology
Lovely ABT0602 Unit-V

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Introduction about the subject with video
Lovely ABT0602 Unit-V
https://www.youtube.com/watch?v=yIiruvpg3Pw&t=5s
https://www.youtube.com/watch?v=wtXBgDqYGBE

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Topic Objective/ Topic Outcome
In this unit students learned about
• Enzymes and their metabolism
• Stochiometry, mass balance, yield coefficients and rate equations
• Heat balance and Black box model
• Different models for regulation of cellular reactions
• Regulation of branched pathways
• Permeability and transport of metabolites
Lovely ABT0602 Unit-V

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Unit Content (CO5)
UNIT-V (Industrial Applications)
Pathway engineering strategies for overproduction of some commercially
important primary and secondary metabolites or industrially relevant enzymes
and recombinant proteins,
bioconversion- applications and factors affecting bioconversion,
mixed or sequential bioconversions,
regulation of enzyme production,
Strain selection and improvement,
the modification of existing or the introduction of entirely new metabolic
pathways.
Lovely ABT0602 Unit-V

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Unit-V Pathway engineering strategies (CO5)
Lovely ABT0602 Unit-V
Classical metabolic engineering changes cell metabolism by changing its
pathway enzyme(s) or regulatory protein(s) using recombinant DNA
technology, thus improving the productivity and yield of an industrial
fermentation product or producing novel biochemical compounds.
Secondary metabolites have complex chemical composition and are produced in
response to various forms of stress to perform different physiological tasks in
plants. They are used in pharmaceutical industries, cosmetics, dietary
supplements, fragrances, flavors, dyes, etc.

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Unit-V Pathway engineering strategies (CO5)
Lovely ABT0602 Unit-V
The most important secondary metabolites have been the anti-infective drugs and,
among these, the β-lactams are the most important class. Other important classes
include the aminoglycosides, tetracyclines, macrolides, lipopeptides, polyenes,
and the echinocandins.
Overproduction of microbial metabolites is related to developmental phases of
microorganisms. Inducers, effectors, inhibitors and various signal molecules play a
role in different types of overproduction.

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Unit-V Pathway engineering strategies (CO5)
Lovely ABT0602 Unit-V
Key Points. Primary metabolites are considered essential to microorganisms for
proper growth. Secondary metabolites do not play a role in growth,
development, and reproduction, and are formed during the end or near the
stationary phase of growth.
Secondary metabolites also called specialised metabolites, toxins, secondary
products, or natural products, are organic compounds produced by any
lifeform, e.g. bacteria, fungi, animals, or plants, which are not directly involved
in the normal growth, development, or reproduction of the organism. Instead,
they generally mediate ecological interactions, which may produce a selective
advantage for the organism by increasing its survivability or fecundity. Specific
secondary metabolites are often restricted to a narrow set of species within a
phylogenetic group. Secondary metabolites often play an important role in
plant defense against herbivory and other interspecies defenses. Humans use
secondary metabolites as medicines, flavourings, pigments, and recreational
drugs.

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Unit-V Pathway engineering strategies (CO5)
Lovely ABT0602 Unit-V
The term secondary metabolite was first coined by Albrecht Kossel, a 1910
Nobel Prize laureate for medicine and physiology in 1910. 30 years later a
Polish botanist Friedrich Czapek described secondary metabolites as end
products of nitrogen metabolism.
Secondary metabolites commonly mediate antagonistic interactions, such as
competition and predation, as well as mutualistic ones such as pollination and
resource mutualisms. Usually, secondary metabolites are confined to a specific
lineage or even species, though there is considerable evidence that horizontal
transfer across species or genera of entire pathways plays an important role in
bacterial (and, likely, fungal) evolution. Research also shows that secondary
metabolism can affect different species in varying ways. In the same forest,
four separate species of arboreal marsupial folivores reacted differently to a
secondary metabolite in eucalypts.

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Unit-V Pathway engineering strategies (CO5)
Lovely ABT0602 Unit-V
This shows that differing types of secondary metabolites can be the split between
two herbivore ecological niches. Additionally, certain species evolve to resist
secondary metabolites and even use them for their own benefit. For example,
monarch butterflies have evolved to be able to eat milkweed (Asclepias) despite the
presence of toxic cardiac glycosides. The butterflies are not only resistant to the
toxins, but are actually able to benefit by actively sequestering them, which can lead
to the deterrence of predators.

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V
Plants are capable of producing and synthesizing diverse groups of
organic compounds and are divided into two major groups: primary and
secondary metabolites. Secondary metabolites are metabolic
intermediates or products which are not essential to growth and life of the
producing plants but rather required for interaction of plants with their
environment and produced in response to stress. Their antibiotic,
antifungal and antiviral properties protect the plant from pathogens.
Some secondary metabolites such as phenylpropanoids protect plants
from UV damage. The biological effects of plant secondary metabolites
on humans have been known since ancient times. The herb Artemisia
annua which contains Artemisinin, has been widely used in Chinese
traditional medicine more than two thousand years ago.[citation needed]
Plant secondary metabolites are classified by their chemical structure and
can be divided into four major classes: terpenes, phenylpropanoids (i.e.
phenolics), polyketides, and alkaloids.

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Unit-V Plant secondary metabolites in medicine (CO5)
Lovely ABT0602 Unit-V
Many drugs used in modern medicine are derived from plant secondary
metabolites. Extraction of taxol from barks of Pacific Yew.
The two most commonly known terpenoids are artemisinin and paclitaxel.
Artemisinin was widely used in Traditional Chinese medicine and later
rediscovered as a powerful antimalarial by a Chinese scientist Tu Youyou.
She was later awarded the Nobel Prize for the discovery in 2015. Currently,
the malaria parasite, Plasmodium falciparum, has become resistant to
artemisinin alone and the World Health Organization recommends its use
with other antimalarial drugs for a successful therapy. Paclitaxel the active
compound found in Taxol is a chemotherapy drug used to treat many forms
of cancers including ovarian cancer, breast cancer, lung cancer, Kaposi
sarcoma, cervical cancer, and pancreatic cancer. Taxol was first isolated in
1973 from barks of a coniferous tree, the Pacific Yew.

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V
Morphine and codeine both belong to the class of alkaloids and are derived
from opium poppies. Morphine was discovered in 1804 by a German
pharmacist Friedrich Sertürnert. It was the first active alkaloid extracted from
the opium poppy. It is mostly known for its strong analgesic effects, however,
morphine is also used to treat shortness of breath and treatment of addiction to
stronger opiates such as heroin. Despite its positive effects on humans,
morphine has very strong adverse effects, such as addiction, hormone
imbalance or constipation. Due to its highly addictive nature morphine is a
strictly controlled substance around the world, used only in very severe cases
with some countries underusing it compared to the global average due to the
social stigma around it.

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V
Opium field in Afghanistan, the largest grower of opium. Codeine, also
an alkaloid derived from the opium poppy, is considered the most
widely used drug in the world according to World Health Organization.
It was first isolated in 1832 by a French chemist Pierre Jean Robiquet,
also known for the discovery of caffeine and a widely used red dye
alizarin. Primarily codeine is used to treat mild pain and relief
coughing although in some cases it is used to treat diarrhea and some
forms of irritable bowel syndrome. Codeine has the strength of 0.1-
0.15 compared to morphine ingested orally, hence it is much safer to
use. Although codeine can be extracted from the opium poppy, the
process is not feasible economically due to the low abundance of pure
codeine in the plant. A chemical process of methylation of the much
more abundant morphine is the main method of production.

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V
Atropine is an alkaloid first found in Atropa belladonna, a member of the nightshade
family. While atropine was first isolated in the 19th century, its medical use dates
back to at least the fourth century B.C. where it was used for wounds, gout, and
sleeplessness. Currently atropine is administered intravenously to treat bradycardia
and as an antidote to organophosphate poisoning. Overdosing of atropine may lead to
atropine poisoning which results in side effects such as blurred vision, nausea, lack of
sweating, dry mouth and tachycardia.

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V
Resveratrol is a phenolic compound of the flavonoid class. It is highly
abundant in grapes, blueberries, raspberries and peanuts. It is commonly
taken as a dietary supplement for extending life and reducing the risk of
cancer and heart disease, however there is no strong evidence supporting
its efficacy. Nevertheless, flavonoids are in general thought to have
beneficial effects for humans.[citation needed] Certain studies shown that
flavonoids have direct antibiotic activity. A number of in vitro and limited
in vivo studies shown that flavonoids such as quercetin have synergistic
activity with antibiotics and are able to suppress bacterial loads.

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V

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Unit-V Plant secondary metabolites (CO5)
Lovely ABT0602 Unit-V
Digoxin is a cardiac glycoside first derived by William Withering in 1785 from the
foxglove (Digitalis) plant. It is typically used to treat heart conditions such as atrial
fibrillation, atrial flutter or heart failure. Digoxin can, however, have side effects
such as nausea, bradycardia, diarrhea or even life-threatening arrhythmia.

37. 1. Which out of the following statements is true about the regulation of metabolic
pathway?
a) Most of the metabolic pathways are regulated
b) Most of the metabolic pathways are not regulated
c) Regulation of metabolic pathways always involves changing the amount of
enzymes
d) Metabolic regulation always depends on control by hormones
2. The rate of breakdown of metabolites is termed as ___________
a) Metabolic state
b) Metabolism
c) Steady state
d) Homeostasis
3. Diminished delivery of oxygen to tissues is termed as ___________
a) Hypoxia
b) Ischemia
c) Homeostasis
d) Metabolism
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Daily Quiz (CO5)
Lovely ABT0611 Unit-I

38. 1. How the most of the metabolic pathways are regulated?
2. How metabolic state of the substrates can be determined?
3. Which pathway is responsible for complete oxidation of sugars?
4. How peptides are formed?
5. How B-pleated sheets are formed?
6. How alpha helix are formed?
7. What is the average molecular weight of amino acids?
8. Discuss the biochemical pathway of TCA cycle.
9. Discuss the importance of gluconeogenesis cycle
10. What do you understand by TCA cycle
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Weekly assignments (CO5)
Lovely ABT0611 Unit-I

39. 1. Which out of the following statements is true about the regulation of metabolic
pathway?
a) Most of the metabolic pathways are regulated
b) Most of the metabolic pathways are not regulated
c) Regulation of metabolic pathways always involves changing the amount of
enzymes
d) Metabolic regulation always depends on control by hormones
2. The rate of breakdown of metabolites is termed as ___________
a) Metabolic state
b) Metabolism
c) Steady state
d) Homeostasis
3. Diminished delivery of oxygen to tissues is termed as ___________
a) Hypoxia
b) Ischemia
c) Homeostasis
d) Metabolism
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MCQs (CO5)
Lovely ABT0611 Unit-I

40. 4. Diminished flow of blood to tissues is termed as ___________
a) Hypoxia
b) Ischemia
c) Homeostasis
5. Which of the following statements is true about the control of muscle glycogen phosphorylase?
a) It is activated by phosphorylation by an active phosphorylase kinase
b) It is allosterically activated by ATP
c) It is allosterically activated by cAMP
6. Which of the following is not a factor determining the activity of an enzyme?
a) Association with regulatory protein
b) Sequestration
c) Allosteric regulation
d) Nucleotides
7. Which of the following statements is true?
a) High insulin/glucagon ratio activates lipolysis in muscle
b) High insulin/glucagon ratio inhibits lipolysis in liver
c) High insulin/glucagon ratio activates lipolysis in adipocytes
d) Low insulin/glucagon ratio activates lipolysis in adipocytes
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MCQs (CO5)
Lovely ABT0611 Unit-I

41. 8. Which of the following type of metabolites is used for generating glucose under severe
starvation conditions?
a) Amino acids
b) Fats
c) Glycogen
d) Starch
9. Which of the following statements is true about brain metabolism in starvation?
a) The brain can use glucogenic amino acids for energy
b) The brain can only use glucose as fuel
c) Up to a quarter of energy requirement of the brain can come from fatty acids
d) Up to a half of energy requirement of the brain can come from ketone bodies
10. Which one of the following statements about control of enzyme activity by
phosphorylation is correct?
a) Phosphorylation of an enzyme results in a conformational change
b) Phosphorylation of an enzyme occurs only at specific tyrosine residues
c) Phosphorylation of an enzyme is carried out by phosphoprotein phosphatases
d) Enzyme control by phosphorylation is irreversible
41
MCQs (CO5)
Lovely ABT0611 Unit-I

42. 1. _____ metabolizes to form sugars and alcohols
2. _____ are used used for generating glucose under severe starvation conditions
3. ______ is used for determining the yield coefficient
4. _______ is used for controlling pH, DO and other important parameters for
bioprocess function
5. ______ is introduced into the bioreactor for temperature control of the cultivation.
6. ______ is used for shear sensitive cells wherein aspect ration is kept very high.
7. ______ is used for maintainance of constant temperature in the bioreactor
8. ______ are introduced into the bioreactor to prevent vortexing.
9. ______ is used for the oxygen supply in the bioreactor.
10. ______ are used for the mixing of bioreactor contents
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Glossary questions (CO5)
Lovely ABT0611 Unit-I

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Old Question Papers
NA as the subject is newly introduced
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Expected Questions for Exam
Lovely ABT0611 Unit-I
1. How the most of the metabolic pathways are regulated?
2. How metabolic state of the substrates can be determined?
3. Which pathway is responsible for complete oxidation of sugars?
4. How peptides are formed?
5. How B-pleated sheets are formed?
6. How alpha helix are formed?
7. What is the average molecular weight of amino acids?
8. Discuss the biochemical pathway of TCA cycle.
9. Discuss the importance of gluconeogenesis cycle
10. What do you understand by TCA cycle

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Recap of Unit (CO5)
Lovely ABT0611 Unit-I

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References
• Levenspiel O, “Chemical Reaction Engineering”, 3rd Ed , John Wiley & Sons,
Singapore (1999).
• Shuler M L, Kargi F, “Bioprocess Engineering- Basic Concepts” , 2nd ed, Prentice Hall
of India Ltd. ( 2002).
• Aiba S, Humphrey A E and Millis N F ,“Biochemical Engineering” , Academic Press
(1973)
• Bioreaction Engineering, Bioprocess Monitoring (Bioreaction Engineering) by Karl
Schügerl
• Introduction to Biochemical Engineering, D. G. Rao Tata McGraw-Hill Education,
2005
Lovely ABT0602 Unit-V

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Noida Institute of Engineering & Technology
Lovely ABT0602 Unit-V