FT/GN/68/00/23.01.

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SRI VENKATESWARA COLLEGE OF ENGINEERING(AUTONOMOUS)

COURSE DELIVERY PLAN - THEORY Page 1 of 6

LP: BT16501
Department of Biotechnology
Rev. No: 00
B.E/B.Tech/M.E/M.Tech : Biotechnology Regulation: 2016 Date:
PG Specialisation : Not Applicable 11.05.2018
Sub. Code / Sub. Name : BT16501 / Protein Structure Function and Proteomics
Unit :1
Unit Syllabus: Bonds, Energies, Building Blocks of Proteins 9

Covalent, Ionic, Hydrogen, Coordinate, hydrophobic and Vander walls interactions in protein
structure. Interaction with electromagnetic radiation (radio, micro, infrared, visible,
ultraviolet, X-ray) and elucidation of protein structure. Amino acids (the students should be
sithorough with three and single letter codes) and their molecular properties (size, solubility,
charge, pKa), Chemical reactivity in relation to post-translational modification (involving
amino, carboxyl, hydroxyl, thiol, imidazole groups).

Objective: To understand the properties of aminoacids and identify the protein

structure
Session Teaching
Topics to be covered Ref
No * Aids
1. Covalent, Ionic, Hydrogen, Coordinate interactions in TB2 (139-166)
protein structure ATB1 (47-56) LCD
2. Hydrophobic interactions in protein structure ATB2 (24-25) LCD
3. Vander walls interactions in protein structure ATB3 (49-53) LCD
4. Radiowaves in elucidation of protein structure. ATB4 (509-514) LCD
5. Infrared waves in elucidation of protein structure. ATB4 (522-527) LCD
6. Ultraviolet and visible waves in elucidation of protein
ATB4 (482-493) LCD
structure.
7. Amino acids three and single letter codes TB1 (6-7) LCD
8.
Amino acids size, solubility, charge and pKa properties ATB-2(74-81) LCD
9. Chemical reactivity involving amino groups relation to
TB2(86-88) LCD
post-translational modification
10. Chemical reactivity involving thiol groups relation to post-
TB2 (98-99) LCD
translational modification
11. Chemical reactivity involving hydroxyl and carboxyl
TB2 (88,96) LCD
groups relation to post-translational modification
12. Chemical reactivity involving imidazole groups relation to
T2(96-97) LCD
post-translational modification
Content beyond syllabus covered (if any): Raman Spectroscopy

* Session duration: 50 minutes

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COURSE DELIVERY PLAN - THEORY Page 2 of 6

Sub. Code / Sub. Name : BT16501/ Protein Structure Function and Proteomics
Unit :2

Unit Syllabus : PROTEIN ARCHITECTURE 9

Primary structure: peptide mapping, peptide sequencing - automated Edman method & Mass-
spec. High-throughput protein sequencing setup Secondary structure: Alpha, beta and loop
structures and methods to determine Super-secondary structure: Alpha-turnalpha, beta-turn-
beta (hairpin), beta-sheets, alpha-beta-alpha, topology diagrams, up and down & TIM barrel
structures nucleotide binding folds..
Objective: To study about the arrangement and arrangement of protein biomolecules.
Session Teaching
Topics to be covered Ref
No * Aids
Primary structure: Peptide mapping and peptide
13. TB2 (31-34) LCD
sequencing
Primary structure: - automated Edman method,
14. TB2 (35-42) LCD
Mass- spectrometry
Primary structure: High-throughput protein
15. TB2 (28-30) LCD
sequencing setup

16. Secondary structure : Alpha structures TB1 (13-18) LCD

17. Secondary structure : Beta structures TB1 (19-20) LCD

Loop structures and methods to determine

18. TB1 (21-22) LCD
Secondary structure
Super-secondary structure: Alpha-turn alpha, beta-
19. TB1 (24-25) LCD
turn- beta (hairpin)
Super-secondary structure: Beta-sheets, alpha-beta-
20. TB1 (26-29,57) LCD
alpha
21. Nucleotide binding folds TB1 (47-60) LCD

22. TIM barrel structures TB1 (47-54) LCD

23. Up and down Beta barrel TB1 (67-70) LCD

24. Motifs of Protein Structure TB1 (13-32) LCD

Content beyond syllabus covered (if any): Nil

* Session duration: 50 mins

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SRI VENKATESWARA COLLEGE OF ENGINEERING(AUTONOMOUS)

COURSE DELIVERY PLAN - THEORY Page 3 of 6

Sub. Code / Sub. Name : BT16501/ Protein Structure Function and Proteomics
Unit :3

Unit Syllabus : TERTIARY STRUCTURE 9

Prediction of substrate binding sites, Tertiary structure: Domains, folding, denaturation and
renaturation, overview of methods to determine 3D structures. Quaternary structure: Modular
nature, formation of complexes, protein-protein interactions and methods to study it.

Objective: To gain knowledge about tertiary structure of proteins.

Session Teaching
Topics to be covered Ref
No * Aids
ATB5 (441-452)
25. Prediction of substrate binding sites LCD
ATB8 (137-139)
TB 1 (27-29,31-32, 35-
26. Tertiary structure- Domains LCD
46, 49)

27. Tertiary structure- folding TB 1 (96 - 100) LCD

28. Denaturation and renaturation of protein kinetics TB 1 (89-95) LCD

29. Overview of methods to determine 3D structures TB1 (373-391) LCD

30. Quaternary structure-Modular nature ATB6 (40-42) LCD

31. Quaternary structure- formation of complexes ATB6 (43-46) LCD

Protein-Protein interactions - Suppressor mutations, ATB5 (453-456)

32. LCD
Synthetic effects, , Dominant negatives ATB8 (134-136)

33. Protein-Protein interactions - Yeast two-hybrid system. ATB5 (458-466) LCD

Protein-Protein interactions - Fluorescence resonance

34. ATB4 (493-507) LCD
energy transfer
Protein-Protein interactions - Surface plasmon resonance
35. ATB4 (527-529) LCD
spectroscopy
Protein-Protein interactions - Informatics tools and
36. ATB5 (467-471) LCD
resources for protein interaction data
Content beyond syllabus covered (if any): Nil

* Session duration: 50 mins

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SRI VENKATESWARA COLLEGE OF ENGINEERING(AUTONOMOUS)

COURSE DELIVERY PLAN - THEORY Page 4 of 6

Sub. Code / Sub. Name : BT16501/ Protein Structure Function and Proteomics
Unit :4

Unit Syllabus : STRUCTURE-FUNCTION RELATIONSHIP 9

DNA-binding proteins: prokaryotic transcription factors, Helix-turn-Helix motif in DNA

binding, Trp repressor, Eukaryotic transcription factors, Zn fingers, helix-turn helix motifs in
homeodomain, Leucine zippers, Membrane proteins: General characteristics, Trans-
membrane segments, prediction, bacteriorhodopsin and Photosynthetic reaction center,
Immunoglobulins: IgG Light chain and heavy chain architecture, abzymes and Enzymes:
Serine proteases, understanding catalytic design by engineering trypsin, chymotrypsin and
elastase, substrate-assisted catalysis other commercial applications
Objective: To realize the structure-function relationships in proteins.
Session Teaching
Topics to be covered Ref
No * Aids
Prokaryotic transcription factors, Helix-turn-Helix
37. TB1 (129-135) LCD
motif in DNA binding,
38. DNA-binding proteins: Trp repressor TB1 (142-145) LCD

DNA-binding proteins: Eukaryotic transcription

39. TB1 (151-161) LCD
factors
DNA-binding proteins: Zn fingers, Helix-turn helix
40. TB1 (175-161) LCD
motifs in homeodomain
41. DNA-binding proteins- Leucine zippers TB1 (199-200) LCD

Membrane proteins: General characteristics, Trans- TB1 (223 -225)

42. LCD
membrane segments, Prediction TB1 (244 -246)

43. Membrane proteins: Bacteriorhodopsin TB1 (225-229) LCD

44. Photosynthetic reaction center TB1 (234-239) LCD

Immunoglobulins: IgG Light chain and heavy chain

45. TB1 (299-320) LCD
architecture
46. Abzymes and Enzymes catalysis mechanism TB1 (205-208) LCD
Abzymes and Enzymes: Serine proteases,
47. understanding catalytic design by engineering TB1 (209-214) LCD
trypsin, chymotrypsin and elastase

Substrate-assisted catalysis other commercial

48. TB1 (215-219) LCD
applications

Content beyond syllabus covered (if any): Commercial applications Ig G

* Session duration: 50 mins

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COURSE DELIVERY PLAN - THEORY Page 5 of 6

Sub. Code / Sub. Name : BT16501/ Protein Structure Function and Proteomics
Unit :5

Unit Syllabus: PROTEOMICS 9

Introduction to the concept of proteome, components of proteomics, proteomic analysis,

importance of proteomics in biological functions, cross linking methods, affinity methods,
yeast hybrid systems and protein arrays.

Objective: To practice the latest application of protein science in their research.

Session Teaching
Topics to be covered Ref
No * Aids

49. Introduction to Proteome & Components of Proteomics ATB8 (1-20) LCD

50. Proteomic analysis ATB7 (1-3) LCD

51. Protein Protein Interaction – Cross Linking Methods ATB8 (140-145) LCD

Protein Protein Interaction – Affinity Chromatography

52. ATB8 (37-46) LCD
Methods
53. Protein Protein Interaction – Yeast two-hybrid system. ATB7 (47-57) LCD

54. Protein Protein Interaction – Phage Display ATB7 (61-67) LCD

55. Protein Protein Interaction – Mass Spectrometry ATB7 (72-74) LCD

56. Protein Protein Interaction – Computational Methods ATB7 (75-79) LCD

57. Protein interaction maps ATB8 (158-163) LCD

58. Protein Arrays ATB7 (81-89) LCD

59. Protein Chips ATB7 (90-95) LCD

60. Protein microarrays ATB7 (96-101) LCD

Content beyond syllabus covered (if any): Nil

* Session duration: 50 mins

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SRI VENKATESWARA COLLEGE OF ENGINEERING(AUTONOMOUS)

COURSE DELIVERY PLAN - THEORY Page 6 of 6

Sub. Code / Sub. Name : BT16501/ Protein Structure Function and Proteomics

TEXTBOOK:
1. Branden C. and Tooze J., “Introduction to Protein Structures” 2nd Edition, Garland
Publishing Inc, 1999.
2. Creighton T.E. “Proteins” 2nd Edition. W.H. Freeman, 1993.
3. Pennington, S.R and Dunn, M.J. “Proteomics : Protein Sequence to Function”. Viva Books,
2002

REFERENCE:
1. Liebler “Introduction to Proteomics” Humana Press, 2002.

ADDITIONAL TEXTBOOK:
1. Lehninger, A. L, Nelson, D.L and Cox, M. M. “Lehninger Principles of Biochemistry”, W.
H. Freeman, 2005.
2. Voet, D.J, Voet, J.G and Pratt, C.W. “Biochemistry”, 3rd Edition, John Wiley & Sons, Inc,
2008.
3. Bernhard Rupp “Biomolecular Crystallography: Principles, Practice, and Application to
Structural Biology”, Garland Science, Taylor & Francis Group, LLC, 2010.
4. Wilson, K and Walker, J. “Principles and Techniques of Biochemistry and Molecular
Biology”, 7th Edition, Cambridge University Press, 2010.
5. Primrose, S.B. and Twyman, R.M. “Principles of Gene Manipulation and Genomics” 7th
Edition, Blackwell Publishing, 2006.
6. Petsko, G. A. and Ringe, D “Protein Structure and Function” New Science Press Ltd, 2004.
7. Palzkill. T “Proteomics” Kluwer Academic Publishers, 2002.
8. Twyman, R.M. “Principles of Proteomics” 1st Edition, Taylor & Francis Group, LLC,
2004.

Prepared by Approved by
Signature
Name Mr. S. Naga Vignesh Prof. E.Nakkeeran
Assistant Professor Professor & Head
Designation Department of Biotechnology Department of Biotechnology
Date 11.05.2018 11.05.2018
Remarks *: This lesson plan is followed from previous year lesson plan and the same can
be followed in future.

Remarks *: This lesson plan is followed from previous year lesson plan and the same can
be followed in future.
* If the same lesson plan is followed in the subsequent semester/year it should be mentioned
and signed by the Faculty and the HOD