Biochemistry and Enzyme Technology

Teacher

Dr. Shantanu Bhattacharyya

Category

Core Courses

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Course Name : Biochemistry and Enzyme Technology

Code(Credit) : CUTM1433(3-1-0)

Course Objectives

This course provides the theory and knowledge relevant to the plant Biochemistry and enzymology principles including fundamental properties of enzymes, enzyme catalytic mechanisms and enzyme kinetics. Techniques employed in enzymes purification and characterization are also emphasized in this course. Students will also be introduced to the theory as well as applications of enzyme technology in food, medical, and household industries. Finally this course serves to provide an awareness of the current and possible future applications of enzyme technologies

Learning Outcomes

Upon successful completion of this course, the student will be able to:

Understand on the kingdoms of biomolecules, Bioenergetics principals that are the prerequisites and consequences of physiological phenomenon for further manipulations.

Develop integrative approach for visions in biological problems.

Distinguish the fundamentals of enzyme properties, nomenclatures, characteristics and mechanisms

Apply biochemical calculation for enzyme kinetics

Compare methods for production, purification, characterization and immobilization of enzymes

Discuss various application of enzymes that can benefit human life

Discover the current and future trends of applying enzyme technology for the commercialization purpose of biotechnological products.

Plot graphs based on kinetics data

Course Syllabus

Module-I Essential Biochemistry and Bioenergetics

1.1 Structure of atoms and molecules, chemical bonds.

1.2 Stabilizing Interactions (thermodynamics of folding, conformational entropy, charge charge interaction, Vander wall force, hydrophobic effect, disulfide bonds, prosthetic group, ion binding protein stability),

1.3 pH, buffer, Acid Base Equilibria, Water.

1.4 Biological Thermodynamics, Enthalpy and Entropy, Standard Free Energy Concept and Calculation, Biological Energy transducer Cellular energy currency, Energy rich compounds

 

Practice:   Demonstration of weak interaction on stability of protein

 

Module-II Biochemistry of Protein

2.1 Building Block of Proteins: Chemical Properties of Proteins, common plant Protein Sources, Protein Databases.

2.2 Amino acids (genetically coded, Rare genetically coded, modified), Dissociation constant, Isoelectric point, Assay of Amino acids, protein denaturation and renaturation; Prions

2.3 Structural Organization: Structural organization of Protein (different models), Dynamics of Protein Structure (globular, Fibrous), chaperon concept

2.4 Ramachandran Plot. Specialized Secondary Structure protein structure (TMV, Hemoglobin, Myoglobin, collagen, Carboxypeptidase, RuBisCo)

2.5 Domain and Motifs: Motifs, domains, Models, Functional relationship between domains and function of proteins, super secondary structures of proteins Classification of proteins based on the structures like Zn finger, lucine zipper proteins etc

 

Practice:

Quantitative estimation of proteins Biuret, Lowry, BCA and Bradford methods

Quantitative estimation of amino acids

 

Module-III Biochemistry of Nucleic Acid, Carbohydrates,

3.1 Nucleic Acid: Structure, Models and Stability of Nucleic Acids (DNA/RNA), Nucleotide Databases,

3.2 Primary and Secondary Structure, Alternate Secondary Structure: Hairpin, Cruciform, triple Helix, G-quadrates etc. Denaturation, Tm value, Protein DNA interaction

3.3 Carbohydrate: Structure types and Nomenclature, Structure Function relationship Carbohydrate Databases.

 

Practice:

Quantitative estimation of Carbohydrates

 

Module-IV Biochemistry of Lipid, Vitamins, and Antioxidants

4.1 Lipid: classification, structure, properties and functions of fatty acid, essential fatty acids, fats, phospholipids, sphingolipids, cerebrosides, steroids, lipoproteins, membrane protein. Plant Biofuel

4.2 Vitamins and Antioxidants: Structure and functions of vitamins, Source of phytovitamins, Natural Antioxidants

 

Practice:

Determination of Unknown Concentration of Vitamin C

 

Module-V Enzymology

5.1 Overview of enzyme: Chemical Nature, Characteristics, Classification (IUB), Nomenclature,

5.2 Enzyme conformation, Active Sites, Ribozyme, isozymes, multi enzyme complex.

5.3. Enzyme kinetics: Michelis Menten equation, Treatment of Data (Briggs-Haldane, lineweaver-burk, Eadie-hofstee, cornish-bowden, Van Slyke-Cullen behavior) Enzyme inhibitiion, Significance of Km. Kcat,Vm

5.4 Single substrate, bi substrate, multi substrate reaction, Significance and Evaluation of activation energy.

5.5 Mechanism of enzyme action: Enzyme catalytic reaction mechanism, chymotrypsin, lysozyme, Serine protease, Alcohol dehydrogenase, carboxypeptidase,

5.6 Co enzymes and its role in Enzyme action (NAD+/NADP+, FAD, lipoic acid, thiamine pyrophosphate, tetrahydrofolate, biotin, pyridoxal phosphate, B12 etc.)

5.7 Allosteric enzyme and its mechanism

5.8 Enzyme catalysis: Acid-base catalysis, covalent catalysis, metal ion catalysis, proximity, orientation effect, site directed mutagenesis of enzyme.

 

Practice:

Effects of pH, Temperature, and Substrate Concentration on enzyme activity

Detection of Active site of enzyme using computational tool

 

Module-VI Enzyme Technology

6.1 Enzyme Purification, Assay, Large Scale production of Enzyme

6.2 Enzyme Immobilization (kinetics), enzyme reactor,

6.3 Biotransformation, Nobel Enzyme,

6.4 Scope of enzyme technology in medicine, Detergents, Food and breverage industry, Leather Industry, Textile industry etc).

 

Practice:

Isolation and purification of enzyme/proteins

 

Module-VII Industrial Biochemistry

7.1 Industrial Enzymes – production & applications,

7.2 Biofuel: production of biomethane and bioethanol from agro-food wastes/Microalgae,

7.3 Nutritional profiling of agricultural products,

7.4 Biopolymer, Microbial polysaccharides. Dextrans. Polyhydroxy alkanoates. Polyhydroxybutyrate (PHB). Biodegradable plastics

 

Practice:

Bio-diesel production from Biomass and its Characterization

 

Text Book

  • Donald Voet, Judith G. Voet,Biochemistry, Wiley
  • David L. Nelson; Michael M. Cox,Lehninger Principles of Biochemistry, W.H freeman and Company
  • Satyanarayana, U. and Chakrapani, U,Biochemistry, Elsevier
  • Murray, Darryl K. Granner, Peter A. Mayes,Harper's Illustrated Biochemistry, Tata Mc Graw hill

Reference Book

  • Trevor Palmer, Philip L. Bonner - Enzymes_ Biochemistry, Biotechnology, Clinical Chemistry-Woodhead Publishing
  • Leskovacs V. Comprehensive enzyme kinetics, Kluwer
  • Lemuel Wingard, Applied Biochemistry and Bioengineering. Enzyme Technology, Elsevier Science
  • Robert_Rastall_Novel_Enzyme_Technology_for_Food, Woodhead Publishing

Session 2

Stabilizing Interactions (thermodynamics of folding, conformational entropy, charge charge interaction, Vander wall force, hydrophobic effect, disulfide bonds, prosthetic group, ion binding protein stability),

Hydrogen Bond PDF ; Stabilizing interaction PDF

https://www.youtube.com/watch?v=ErQORXtdpEg

https://www.youtube.com/watch?v=AD7CoDwns7o

https://www.youtube.com/watch?v=HGc9RFD7iSE

https://lab.concord.org/embeddable.html#interactives/samples/3-100-atoms.json

Session 3: (Practice-1: 1hr)

Demonstration of weak interaction on stability of protein

https://lab.concord.org/embeddable.html#interactives/samples/3-100-atoms.json

Session 5

Biological Thermodynamics, Enthalpy and Entropy, Standard Free Energy Concept and Calculation, Biological Energy transducer Cellular energy currency, Energy rich compounds

energy currency PDF;  Thermodynamic principle PDF

https://www.youtube.com/watch?v=P2WD9jFePwo

https://www.youtube.com/watch?v=DPjMPeU5OeM

https://www.youtube.com/watch?v=t6AwXiWyybk

https://www.youtube.com/watch?v=rrFi7GWt_GY

https://www.youtube.com/watch?v=dWe8vtztW-4

Session 7: (Practice-2: 2hr)

Session 8

Amino acids (genetically coded, Rare genetically coded, modified), Dissociation constant, Isoelectric point, Assay of Amino acids, protein denaturation and renaturation; Prions

http://courseware.cutm.ac.in/wp-content/uploads/2020/06/amino-acid-ppt-1.pdf

https://www.youtube.com/watch?v=9Qi3225yrmw

https://www.youtube.com/watch?v=NNijmxsKGbc

Session 9: (Practice 3: 2hr)

Session 10

Session 11

Ramachandran Plot, Specialized Secondary Structure protein structure (TMV, Hemoglobin, Myoglobin, collagen, Carboxypeptidase, RuBisCo)

ramachandran plot pdf

https://www.youtube.com/watch?v=aO0l1PReGo0&t=5s

https://www.youtube.com/watch?v=Q1ftYq13XKk

https://www.youtube.com/watch?v=Kewhg5spUjs

https://www.youtube.com/watch?v=jQIuTgnl2xQ

Session 12

Domain and Motifs: Motifs, domains, Models, Functional relationship between domains and function of proteins, super secondary structures of proteins Classification of proteins based on the structures like Zn finger, lucine zipper proteins etc

domain pdf

https://www.youtube.com/watch?v=2-qFLfVymnw

https://www.youtube.com/watch?v=WyU2v7HT6bw

https://www.youtube.com/watch?v=9z3ghXZztWY&t=118s

Session 14

Primary and Secondary Structure of Nucleic Acid, Alternate Secondary Structure: Hairpin, Cruciform, triple Helix, G-quadrates etc. Denaturation, Tm value, Protein DNA interaction

RNA Secondary structure;

RNA structure;

G-quadruplex PDF

https://www.youtube.com/watch?v=o_-6JXLYS-k&t=9s

Session 15

Carbohydrate: Structure types and Nomenclature, Structure Function relationship Carbohydrate Databases.

Carbohydrate PDF

https://www.youtube.com/watch?v=LeOUIXbFyqk&t=9s

https://www.youtube.com/watch?v=JxK5rZxbyQY&t=107s

Session 16: (Practice-4 :2hr)

Quantitative estimation of Carbohydrates

https://vlab.amrita.edu/?sub=3&brch=63&sim=631&cnt=1

Session 17

Lipid: classification, structure, properties and functions of fatty acid, essential fatty acids, fats, phospholipids, sphingolipids, cerebrosides, steroids, lipoproteins, membrane protein. Plant Biofuel

LIPID ppt

LIPID PDF

https://www.youtube.com/watch?v=v2ZxmdYwk1E

https://www.youtube.com/watch?v=aUIqXB1KQ0s

Session 18

Vitamins and Antioxidants: Structure and functions of vitamins, Source of phytovitamins, Natural Antioxidants

antioxidant PDF

https://www.slideshare.net/ISFCPISFCollegeofPha/antioxidants-102691615

https://www.youtube.com/watch?v=XPjq2uxZWnM

Session 19:(Practice-5 :2hr)

Determination of Unknown Concentration of Vitamin C

http://vlab.amrita.edu/?sub=2&brch=294&sim=1350&cnt=3

Session 22 (Practice 6: 2hr)

Effects of pH, Temperature, and Substrate Concentration on enzyme activity

https://www.youtube.com/watch?v=mBlMI82JRfI

Session 23

Enzyme kinetics: Michelis Menten equation, Treatment of Data (Briggs-Haldane, lineweaver-burk, Eadie-hofstee, cornish-bowden, Van Slyke-Cullen behavior) Enzyme inhibitiion, Significance of Km. Kcat,Vm

ENZYME_KINETICS PDF

https://www.youtube.com/watch?v=TTr2ADsjU10

https://www.youtube.com/watch?v=3VCZWPcaxJU

https://www.youtube.com/watch?v=8woEVmLWTbk

https://www.youtube.com/watch?v=_qSJFBoxdwQ

Session 24

Single substarte, bi substrate, multi substrate reaction, Significance and Evaluation of activation energy.

Bi substrate reaction PDF

https://www.youtube.com/watch?v=KueNVfv8fNY

https://www.youtube.com/watch?v=KpgGWEiGmzA

Session 25

Session 26

Co enzymes and its role in Enzyme action (NAD+/NADP+, FAD, lipoic acid, thiamine pyrophosphate, tetrahydrofolate, biotin, pyridoxal phosphate, B12 etc.)

https://www.slideshare.net/polly0007/co-enzymes

https://www.youtube.com/watch?v=vUG7SW7VFUY

https://www.youtube.com/watch?v=2rV8vty5UF8

Session 28

Enzyme catalysis: Acid-base catalysis, covalent catalysis, metal ion catalysis, proximity, orientation effect, site directed mutagenesis of enzyme.

https://www.slideshare.net/RangikaMunaweera/enzyme-mechanisms?qid=5edd9772-ac81-4029-84e1-818581090882&v=&b=&from_search=1

https://www.youtube.com/watch?v=4cN60VBXNlw

Session 36: (Practice-8: 2hr)

Case Studies

Case Studies

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    Our Main Teachers

    Dr. Shantanu Bhattacharyya

    Assistant Professor, Department of Botany, School of Applied Science ( Bolangir Campus)
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    Dr. Shantanu Bhattacharyya works as an Assistant Professor, Department of Botany, at the Centurion University of Technology and Management, Bolangir Campus, Odisha, India. He has received his M.Sc. (Life Science- Botany) and M.Phil (Life Sciences) from Sambalpur University, Orissa, India and B.Ed. from Singhania University, Rajasthan India. He qualified GATE-2007, CSIR-UGC NET LS -2008. He […]

    Mr. Srimay Pradhan

    Assistant Professor in Department of Botany, School of Applied Sciences, Centurion University of Technology and Management
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    Mr. Srimay Pradhan is presently working as an assistant professor (Botany) in School of applied Sciences, Centurion University of Technology and Management. Apart from this, he is also persuing his doctoral research on diversity, distribution and ethnomedicinal uses of Lichens from Centurion University of Technology and Management. He has completed his Master (Botany) from Department […]