Biochemical Engineering – CUBI 2550

Teacher

Dr. Polaki Suman

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Course Details

Course Code Course Title Credits Credit Type
CUBI2550 BIOCHEMICAL ENGINEERING 4 (2+1+1)

Course Objectives

By the end of the course, students will be able to:

  • Understand and explain fundamental bioenergetics and metabolic pathways, including their biochemical significance.
  • Develop competency in the principles and applications of various analytical chemistry techniques used in biochemical analysis.
  • Perform biochemical experiments involving the preparation of buffers, qualitative and quantitative analysis of biomolecules.
  • Apply chromatographic and electrophoretic techniques for the separation and analysis of biomolecules.
  • Demonstrate aseptic techniques and solution preparations used in biochemical laboratories.

Course Outcomes (COs)

CO Code Course Outcome Statement Bloom’s Level
CO1 Describe and interpret major metabolic pathways and their role in energy production. Understanding
CO2 Explain the principles and functioning of microscopy, spectroscopy, and chromatography. Understanding
CO3 Analyze biochemical substances using various laboratory techniques. Analyzing
CO4 Apply techniques like gel electrophoresis, chromatography, and buffer preparation. Applying
CO5 Demonstrate laboratory skills in preparing, estimating, and analyzing biomolecules. Applying

CO–PO Mapping

CO / PO PO1 PO2 PO3 PO4 PO5 PO6 PO7 PO8 PO9 PO10 PO11 PO12
CO1 3 2 2 1 2 2 2 2 2
CO2 3 3 3 2 3 2 2 2 2
CO3 3 3 3 3 3 2 2 2 2
CO4 3 3 3 2 3 2 2 2 2
CO5 3 3 3 3 3 2 2 2 2

3 – Strong Contribution    |    2 – Moderate Contribution    |    1 – Low Contribution    |    – – No Significant Contribution

📘 Theory Syllabus

🔷 Module 1: Bioenergetics and Metabolic Pathways

Topic Details
Overview of Metabolism Basic concepts and metabolic design
Bioenergetics Energy currency of the cell, ATP generation, redox reactions
Metabolic Pathways • Glycolysis
• Citric Acid Cycle (TCA Cycle)
• Oxidative Phosphorylation
• Pentose Phosphate Pathway
• Gluconeogenesis
• Glycogen and Disaccharide Metabolism
• Amino Acid Degradation and Urea Cycle

🔷 Module 2: Analytical and Biophysical Techniques

Topic Details
Water Chemistry & Buffers Properties of water, pH and buffer systems
Microscopy Principles & instrumentation of:
• Phase Contrast Microscopy
• Ultraviolet & Interference Microscopy
• Fluorescence Microscopy
• Electron Microscopy – Scanning & Transmission
• Confocal Microscopy
Spectroscopy Beer–Lambert’s Law, Principles & applications of:
• UV Spectroscopy
• Visible Spectroscopy
• IR Spectroscopy
Chromatography Basic principles and applications of:
• Thin Layer Chromatography (TLC)
• Column Chromatography
• High Performance Liquid Chromatography (HPLC)
• Gas Chromatography (GC)
Electrophoresis • Agarose Gel Electrophoresis for Nucleic Acids
• Protein Electrophoresis: PAGE, SDS-PAGE
• Isoelectric Focusing

🧪 Practical Syllabus

🔷 Module 3: Biochemical Laboratory Techniques (Practicals)

Practical Component Details / Activities
Preparation of Solutions & Buffers Preparation of molar, normal, and percentage solutions; buffer systems and their applications
Preparation of Defined pH Solutions Use of pH meter and pH adjustment techniques
Qualitative Reagent Tests • Carbohydrates
• Amino Acids
Protein Estimation Lowry’s Method for quantitative protein estimation
Pigment Separation Paper Chromatography for separation of plant pigments
Gel Electrophoresis • Agarose gel electrophoresis for nucleic acids
• Polyacrylamide gel electrophoresis (PAGE/SDS-PAGE) for proteins
Sterilization Techniques Autoclaving, dry heat sterilization, filtration methods



📘 Theory Session Plan – Biochemical Engineering (40 Sessions)

Session No. Module Topic Sub-Topics / Activities Learning Outcome
1 Module 1 Introduction to Metabolism Metabolic design and pathways LO1
2 Module 1 Bioenergetics ATP, redox reactions LO1
3 Module 1 Glycolysis I Steps, enzymes LO1
4 Module 1 Glycolysis II Energetics & regulation LO1
5 Module 1 TCA Cycle I Entry reactions LO1
6 Module 1 TCA Cycle II Energetics profile LO1
7 Module 1 Oxidative Phosphorylation ETC & ATP synthase LO1
8 Module 1 Pentose Phosphate Pathway Oxidative & non-oxidative phases LO1
9 Module 1 Gluconeogenesis Bypass reactions LO1
10 Module 1 Glycogen Metabolism Synthesis & breakdown LO1
11 Module 1 Disaccharide Metabolism Sucrose, lactose pathways LO1
12 Module 1 Amino Acid Catabolism Deamination, transamination LO1
13 Module 1 Urea Cycle Cycle, disorders LO1
14 Module 1 Metabolic Integration Cross-talk between pathways LO1
15 Module 2 Water Chemistry pH, ionization, properties LO2
16 Module 2 Buffer Systems Henderson–Hasselbalch LO2
17 Module 2 Microscopy I Phase contrast, UV, fluorescence LO2
18 Module 2 Microscopy II SEM, TEM, confocal LO2
19 Module 2 Spectroscopy Basics Beer-Lambert law LO2
20 Module 2 UV/Vis/IR Spectroscopy Principles & applications LO2
21 Module 2 Chromatography Basics TLC, Column LO3
22 Module 2 HPLC Principle, operation LO3
23 Module 2 Gas Chromatography Instrumentation LO3
24 Module 2 Electrophoresis I Agarose for DNA/RNA LO3
25 Module 2 Electrophoresis II PAGE, SDS-PAGE, IEF LO3
26 Module 2 Spectral Data Interpretation Case analyses LO3
27 Module 2 Chromatography Case Studies Plant pigments, proteins LO3
28 Module 3 Integration of Techniques Choosing correct analytical tool LO4
29 Module 3 Metabolic Engineering Concepts Flux balance, applications LO4
30 Module 3 Protein Engineering Basics Functional modifications LO4
31 Module 3 Case Studies Industrial enzymes LO4
32 Module 3 Metabolic Disorders Clinical relevance LO4
33 Module 3 Experimental Design Controls, variables LO4
34 Module 3 Data Interpretation Spectral & gel data LO4
35 Module 3 Instrumentation Troubleshooting Common faults LO4
36 Module 3 Comparing Analytical Tools Chromatography vs electrophoresis LO4
37 Module 3 Industrial Applications Fermentation & bioprocessing LO4
38 Module 3 Revision – Module 1 Quick review LO1–4
39 Module 3 Revision – Module 2 Discussion LO1–4
40 Module 3 Comprehensive Review Exam preparation LO1–4



🧪 Practical Session Plan – Biochemical Engineering (30 Sessions)

Practical No. Title / Experiment Activities / Tasks Expected Outcome
P1 Introduction to Laboratory Safety PPE, safety rules, emergency procedures Understand biochemical lab safety
P2 Glassware Handling & Calibration Pipettes, burettes, volumetric flasks Accurate measurement skills
P3 Preparation of Solutions Normality, molarity, stock & working solutions Prepare chemical solutions accurately
P4 Buffer Preparation Prepare buffer using Henderson–Hasselbalch Master buffer formulations
P5 pH Meter Handling Calibration & pH measurement Operate pH meter accurately
P6 Qualitative Tests for Carbohydrates Benedict’s, Barfoed’s, iodine tests Identify carbohydrate types
P7 Qualitative Tests for Amino Acids Ninhydrin, xanthoproteic test Detect amino acids in samples
P8 Protein Estimation – Lowry Method Standard curve, sample estimation Quantify proteins
P9 Protein Estimation – Bradford Method Assay setup, absorbance reading Understand dye-binding assay
P10 Spectrophotometer Operation Wavelength setting, blanking, absorbance Use UV–Vis spectrophotometer
P11 Beer–Lambert Law Experiment Absorbance vs concentration Interpret spectroscopic data
P12 Paper Chromatography Separation of plant pigments Analyze chromatogram
P13 Thin-Layer Chromatography (TLC) Rf calculation Perform TLC separation
P14 Column Chromatography Packing, loading, elution Separate biomolecules
P15 Agarose Gel Electrophoresis Gel casting, loading, staining Separate DNA/RNA
P16 PAGE – Protein Separation Gel preparation, SDS denaturation Resolve proteins
P17 Isoelectric Focusing Protein separation by pI Understand pI-based separation
P18 Microscopy – Bright Field Focusing, slide preparation Operate microscope
P19 Microscopy – Fluorescence Staining & visualization Analyze fluorescent samples
P20 Enzyme Kinetics Michaelis-Menten plotting Determine enzyme parameters
P21 Substrate Specificity Experiment Different enzyme substrates Identify substrate preference
P22 Temperature Effect on Enzymes Reaction rate vs temperature Understand temperature dependence
P23 pH Effect on Enzymes Determine optimum pH Interpret pH profiles
P24 Sterilization Techniques Autoclave, filtration, dry heat Perform aseptic procedures
P25 Microbial Culture Handling Media prep, inoculation Maintain microbial cultures
P26 Extraction of Plant Pigments Solvent extraction Isolate pigments
P27 DNA Isolation (Demo) Plant DNA extraction Understand extraction principles
P28 Protein Extraction Tissue homogenization Extract proteins
P29 Interpretation of Electrophoresis Results Band analysis and documentation Interpret gel images
P30 Final Revision & Viva Complete practical viva & review Demonstrate overall competency



📚 Reference Text Books

S.No. Title Authors / Publisher
1 Lehninger Principles of Biochemistry David L. Nelson, Michael M. Cox – W.H. Freeman
2 Biochemistry Jeremy M. Berg, John L. Tymoczko, Lubert Stryer – W.H. Freeman
3 Principles and Techniques of Biochemistry and Molecular Biology Keith Wilson & John Walker – Cambridge University Press
4 Biophysical Chemistry: Principles and Techniques Upadhyay, Upadhyay, Nath – Himalaya Publishing House

🌐 Online Resource – Biochemical Engineering Q&A


➤ Open Biochemical Engineering Q&A on IndiaBix

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