Biomolecules

Teacher

Dr. Srikanta Sahu

Category

Core Courses

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Course Name : Biomolecules

Code(Credit) : CUTM1479 (3-2-1)

Course Objectives

• To Know the basic of Bio-Organic chemistry and its application in industry

• This course gives idea about the structure of different bases of nucleic acid,    DNA and RNA.

• Number of amino acids, there functions and the peptide bond that connect di, tri and polypeptides.

• To study about proteins, lipid and carbohydrates

Course Outcome

COs Course outcomes Mapping COs with POs (High-3, Medium-2, Low-1)
CO1 Able to gain knowledge in understanding the basics of bio-organic chemistry PO1(3)
CO3 Able to enhance the ability to understand the chemistry pharmaceutical compounds and it will help in trouble shooting of organic reaction PO4(2), PO3(1)
CO4 Able to get skill on extraction, purification and separation techniques and can be applied to organic synthesis. PO4(3)

• After completion of the course, students will able to understand regarding the essential and nonessential amino acids and can predict how their ionic charges change with pH.
• They know how enzyme activity is regulated and affected by temperature, pH and concentration in biochemical reaction.
• It also learns about DNA replication, transcription and translation including the role of RNA.
• This course will provide a real value addition for higher study especially for research where one can apply this fundamental chemistry in making new drug molecule against various diseases
• This course gives total idea about the organic chemistry and basic biology and how it will be applicable in Industry
• This course will help students for getting jobs in pharmaceutical industry
and pursue their dream in higher study

Course Syllabus

Module I (8 h)
Nucleic Acids: Introduction of Nucleic Acids, Components of nucleic acids, Nucleosides and nucleotides, Structure, synthesis and reactions of: Adenine, Guanine, Cytosine, Uracil and Thymine, Structure of polynucleotides.

Practice 1: Isolation and characterization of DNA from cauliflower

Practice 2: Isolation and characterization of DNA from onion

Assignment 1: Structure of polynucleotides

Module II (13 h)
Amino acids, peptide and proteins: Introduction to amino acid, peptide and protein, Classification of amino acid and peptides, α-Amino Acids: Synthesis, ionic properties and reactions, Zwitterions, pKa values, isoelectric point and electrophoresis, Study of peptides: determination of their primary structures-end group analysis, methods of peptide synthesis (Synthesis of peptides using N-protecting, C-protecting and C-activating groups -Solid-phase synthesis)

Practice 3: Estimation of glycine by Sorenson’s formalin method

Practice 4: Study of the titration curve of Amino acid

Practice 5: Estimation of proteins by Lowry’s method.

Assignment 2: Reactions, Zwitterions, pKa values, isoelectric point and electrophoresis

Assignment 3: α-Amino Acids: Study of peptides: determination of their primary structures-end group analysis

Module III (6 h)
Enzymes: Introduction, classification and characteristics of enzymes, Salient features of active site of enzymes, Mechanism of enzyme action, Factors affecting enzyme action, Coenzymes and Cofactors and their role in biological reactions, specificity of enzyme action (including stereospecificity), Enzyme inhibitors: Importance of enzyme inhibition phenomenon of inhibition (competitive, uncompetitive and non-competitive inhibition including allosteric inhibition).

Assignment 4: Enzyme inhibitors: Importance of enzyme inhibition phenomenon of inhibition (non-competitive inhibition including allosteric inhibition)

Module IV  (10 h)
Lipids: Introduction to oils and fats (Properties and functions), Classes of Lipids (common fatty acids present in oils and fats, Examples of diff. Lipids), Hydrogenation of fats and oils, Saponification value, acid value, iodine number, Reversion and rancidity

Practice 6: Saponification value of an oil or a fat

practice 7: Determination of Iodine number of an oil/ fat.

Module V (8 h)
Concept of Energy in Biosystems: Introduction to metabolism (catabolism, anabolism), ATP: ATP hydrolysis and free energy change, Biological redox systems: NAD+, FAD , Conversion of food to energy, Outline of catabolic pathways of carbohydrate- glycolysis, Fermentation and Krebs cycle, Catabolic pathways of fat and protein, Metabolic pathways of protein, fat and carbohydrate

Practice 8: Extraction of starch from potatoes

Assignment 5: Outline of catabolic pathways of carbohydrate-glycolysis , Fermentation and Krebs cycle

 Assignment 6: Catabolic pathways of fat and protein, Metabolic pathways of protein, fat and carbohydrate

Module VI  (9 h)
Pharmaceutical Compounds: Structure and Importance: Classification, structure and therapeutic uses of antipyretics: Paracetamol (with synthesis) , Analgesics: Ibuprofen (with synthesis), Antimalarials: Chloroquine, Antibiotics and detailed study of chloramphenicol, Medicinal values of curcumin (haldi), azadirachtin (neem), vitamin C and antacid (ranitidine)

Practice 9: Preparation of triphenylmethanol via Grignard

Practice 10: Handling Pyrophoric Materials like n-Butyl Lithium

Assignment 7: Medicinal values of curcumin (haldi), azadirachtin (neem), vitamin C and antacid (ranitidine)

Module VII (12 h)
Bio-imaging and Bio-Medical science: Introduction to basic cell biology, Optical fluorescent probe and photophysical property, Optical probe for bio-imaging application, Protein labelling, Diagnostic kit and Device fabrication

Practice 11: Live Cell Imaging using small molecular probe

Practice 12: Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

Assignment 8: Diagnostic kit development

Assignment 9: Device fabrication

Books Recommended:
Berg, J.M., Tymoczko, J. L. and Stryer, L. (2006) Biochemistry. VIth Edition. W.H. Freeman and Co.

Nelson, D. L., Cox, M. M. and Lehninger, A. L. (2009) Principles of Biochemistry. IV Edition. W.H. Freeman and Co.

Murray, R. K., Granner, D. K., Mayes, P. A. and Rodwell, V.W. (2009) Harper’s Illustrated Biochemistry. XXVIII edition. Lange Medical Books/ McGraw-Hill.

Session Plan

Session 1 

Session 2  (1h)

Session 3  (1h)

Structure, synthesis and reactions of: Adenine, Guanine, Cytosine, Uracil and Thymine

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

Reference:

https://www.youtube.com/watch?v=4GFKdLy2fOE

Session 4  (2h)

Practice 1 : Isolation and characterization of DNA from cauliflower

https://www.youtube.com/watch?v=9-oIhcH4Nl4

Session 5  (Assignment 1, 1h)

Assignment 1: Structure of polynucleotides

https://www.youtube.com/watch?v=r4wD-zS8SWc

Session 6  (2h)

Practice 2 (Module I): Isolation and characterization of DNA from onion

https://www.youtube.com/watch?v=f9hC8lpPNTg

Session 7  (1h)

Session 8 (1h)

Session 9 (1h)

Session 10 (Assignment 2, 1 h)

Session 11  (Assignment 3, 1 h)

Session 12 

Session 13 (1h)

Session 14 (2h)

Practice 3 (Module II): Estimation of glycine by Sorenson’s formalin method

https://www.youtube.com/watch?v=WLv8r_zBdVA&t=341s

Session 15 (2h)

Practice 4 (Module II): Study of the titration curve of Amino acid.

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

https://www.youtube.com/watch?v=MpvA75l5oPw

Session 16 (2h)

Practice 5 (Module II): Estimation of proteins by Lowry’s method.

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

https://www.youtube.com/watch?v=3id3MJlpFKk

Session 17 (1h)

Introduction, classification and characteristics of enzymes

https://www.youtube.com/watch?v=vhIN8e8_dgU

Session 18  (1h)

Session 19  (1h)

Session 20  (1h)

Session 21  (1h)

Session 22 (Assignment 4, 1h)

Session 23   (1h)

Session 24 (1h)

Classes of Lipids (common fatty acids present in oils and fats, Examples of diff. Lipids)

https://www.youtube.com/watch?v=kNDh1Ba0U9k

https://www.youtube.com/watch?v=3z4XNWCnY-I

Reference:

https://byjus.com/biology/lipids/

Session 25 (1h)

Session 26  (1h)

Session 27  (1h)

Session 28   (1h)

Session 29   (2h)

Practice 6 (Module IV): Saponification value of an oil or a fat

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

Session 30   (2h)

Practice 7 (Module IV): Determination of Iodine number of an oil/ fat.

https://www.youtube.com/watch?v=WQ7WQrJ1A1U

Session 31 (1h)

Concept of Energy in Biosystems: Introduction to metabolism (catabolism, anabolism)

https://www.youtube.com/watch?v=-6VyMFQ7rRo

https://www.youtube.com/watch?v=ST1UWnenOo0

Session 32 (1h)

Concept of Energy in Biosystems: Catabolism and anabolism

https://www.youtube.com/watch?v=ST1UWnenOo0

Session 33  (1h)

ATP: ATP hydrolysis and free energy change, Biological redox systems: NAD+, FAD

https://www.youtube.com/watch?v=pRf3x1wEFq4

Session 34  (1h)

Session 35  (Assignment 5, 1h )

Outline of catabolic pathways of carbohydrate- glycolysis , Fermentation and Krebs cycle
https://www.youtube.com/watch?v=rtTq7dylLJ8

https://www.youtube.com/watch?v=A1nJRoPGkRs

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

Session 36  (Assignment 6, 1h)

Session 37  (2h)

Practice 8 (Module V): Extraction of starch from potatoes

https://www.youtube.com/watch?v=PgKR6EsKl5I

Session 38  (1h)

Pharmaceutical Compounds: Structure , Importance, and Classification

https://www.youtube.com/watch?v=6EcmH3c0qwc

Session 39  (1h)

Structure and therapeutic uses of antipyretics: Paracetamol (with synthesis)

https://www.youtube.com/watch?v=6EcmH3c0qwc

Session 40  (1h)

Session 41 (1h)

Antibiotics and detailed study of chloramphenicol

https://www.youtube.com/watch?v=DUvQDkJdZ6g

Session 42  (Assignment 7, 1h)

Medicinal values of curcumin (haldi), azadirachtin (neem), vitamin C and antacid (ranitidine)

Session 43  (2h)

Practice 9 (Module VI): Preparation of triphenylmethanol via Grignard

https://www.youtube.com/watch?v=Pgv0y8iSBWk

Session 44  (2h)

Practice 10 (Module VI): Handling Pyrophoric Materials like n-Butyl Lithium

https://www.youtube.com/watch?v=iLMl10X0Naw

Session 45  (1h)

Session 46 (1h)

Session 47 (1h)

Session 48   (1h)

Session 49    (Assignment , 2h)

Session 50   (Assignment, 2h)

Session 51   (2h)

Practice 11 (Module VII): Live Cell Imaging using small molecular probe

https://www.youtube.com/watch?v=XjsOGVF4c2I

Session 52   (2h)

Practice 12 (Module VII): Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

https://www.youtube.com/watch?v=w3ifXpjuE-M

Case Studies

Case Studies

Our Main Teachers

Srikanta Sahu completed his Ph.D.  from IIT Delhi in Bio-organic chemistry under the supervision of Prof. V. Haridas. After his PhD, he moved for postdoctoral work at National University of Singapore (NUS) in the field of Bio-medical science and chemical biology under the guidance of Prof. Young Tae Chang. Later, he joined as a core […]