BANGALORE

UNIVERSITY

Ph.D. in Biochemistry
Course work Syllabus
(With effect from 2012 2013)

Department of Biochemistry
Central College Campus
Bangalore 560 001

Scheme of Examination
Sl.
No
.

Title of the Paper

Contac
t Hours
per
week

Maximum Marks
Continuous Course end
Assessmen Examinatio
t
n

01

Paper-I: Research
Methodology

03

25

02

Paper-II: Advanced
Biochemistry

03

03

Paper-III: Field of
Specialization
(Main area of the
thesis)

03

Total:
04

Viva Voce

Total

Examination
Hours

75

100

03

25

75

100

03

25

75

100

03

300
50

Minimum for pass in each written paper shall be 40% in the course end examination
and 50% in aggregate including the continuous assessment marks. There shall be no minimum for
viva-voce. Every candidate shall compulsorily attend the viva-voce examination. The result shall be
declared on the basis of courses/papers.

3
Paper-I: Research Methodology
42 Hours
Introduction ; Frontier areas of research in Biochemistry, types of research, applied and basic
research, selection of research projects, goals and objectives of research. Design of a research
project. Sources and methods of collection of Literature. Funding agencies, General strategies for
preparation of research proposals. Research Projects Implementation, Operation, annual and
completion Reports. Data representation in technical reports. Presentation of research data Oral
and poster presentation in scientific conferences and workshops. Preparation of manuscripts for
publication in national and international journals. Yardsticks employed in evaluation of
manuscripts for publications. Outline of the format of Ph.D. theses.
20 hrs
Computational methods for biological data analysis: Probability; Conventions and theories of
probability, Decision making with suitable software. Significance; theory and use of different tests
of significance. Distribution; Binomial, normal and t; distribution problems using computers.
Analysis of variance; use of ANOVA. Relations; Types of relationships, Graphical line fitting to
linear data, Correlation, regression; linear-weighted and non-weighted, nonlinear-weighted, and
non-weighted and their applications. Nonlinear line fitting.
10 hrs
Biological databases: Contents, structure, annotation, file formats, annotated databases, genome
and organism specific databases.
4 hrs
Retrieval and analysis of biological data: Entrez and DBGET/Link DB, SRS. Searching
sequence databases by similarities criteria (sequence search, amino acid substitution matrices),
FASTA and BLAST searches. Sequence alignments; multiple sequence alignments, gene and
protein families, protein families and pattern data bases, protein domain families.
8 hrs
References
1. Basic Mathematics for Biochemists; Cornish Bowden, (1998),
Oxford University Press.
2. Bioinformatics: Methods and Protocols; Stephen Misner and Stephen A. Krawtz, (2001)
Humana Press.
3. Choosing and Using Statistics; a Biologist Guide, Clavin Dythan, (1999),
Blackwell Scientific.
4. Data analysis for Bimolecular Science, Jhon Maber, (1999), Longman.
5. Developing Bioinformatics Computer Skills; Cynthia Gibas et al., (2001)
Shroff Publishers.
6. Introduction to Computational Biology, Michael S. Waterman (1995)
Champman -Hall.

7. Introduction to Bioinformatics; T K Attwood & D J Parry-Smith, (2002),

Pearson Education.

Paper II : Cognate paper : Advanced Biochemistry

42 Hours
Genetic material and its replication: Semi-conservative discontinuous synthesis of DNA,
trombone model of replication, maintenance of ends of linear DNAs, post replication repairs;
4 hrs
Transcription: Prokaryotic and eukaryotic transcription and regulation. Post transcriptional
modification in eukaryotes.
3 hrs
Translation : Deciphering of the genetic code, suppresser genes and suppresser mutations.
Mitochondrial genetic code. Translation in prokaryotes, mechanism and regulation. In-vitro/cell free
translation systems, post translational modification of proteins.
4 hrs
Regulation of genes in prokaryotes and eukaryotes: Operon model, lac and trp operons. Catabolite
repression. Patterns of gene expression in Lambda phage. Eukaryotic Chromatin domains, Chromatin
modification and gene expression. Chromatin remodeling complexes, Genome silencing, Imprinting
and X-inactivation.
Regulation of eukaryotic gene expression: Modularity of Transcription factors. DNA binding and
activation domains; Two hybrid assay, Signal integration and combinatorial control. Repression of
GALI in yeast. Transcription regulation, STAT and Ras pathways. Regulation of genes by RNAs;
RNA interference (RNAi).
6 hrs
Recombinant DNA Technology: Basic principles of Gene cloning, Cloning vectors and hosts.
Introduction of Recombinant DNA, Selection of recombinants. Expression vectors, expression
libraries, Positional cloning. Genomic and cDNA libraries and screening, PCR variants, and
application.
6 hrs
Human Genetics: Structure of chromatin; nucleosomes and higher orders of organization.
Chromosome mapping based on recombination frequency data. Overview of human genome project,
techniques for mapping of human genes.
4 hrs
Bacterial and Viral genetics: Mechanism of recombination, transposable genetic elements,
transformation and conjugation in bacteria. Linkage maps of bacteriophages, mechanism of
transduction.
4 hrs
The Immune system: Recongnition of self and non self, Antigenecity; humoral and cell mediated
immunity. T- and B- lymphocytes Differentiation, characteristics, surface receptors. Antigen
processing and presentation. T cell and B cell interaction, cytokines.
5 hrs
Molecular Immunology: Theories of antibody formation, genetics of antibody diversity, germ line
and somatic mutation theories, Immunoglobulin, MHC and TCR gene organization and their
recombination, class switch of Ig genes.
3 hrs
Clinical Immunology: Immune disorders; hyper sensitivity, autoimmune and immunodeficiency
diseases. Tissue transplantation; auto- iso-, and xenografts,

transplantation rejection and control, tumor immunology.

3 hrs

References
1.
2.
3.
4.
5.
6.

Biochemistry; Edn. Voet , D. and Voet, J.G. [Eds.] (2004) 3 Ed. John Wiley and sons.
Genes VIII; Benzamin Lewin, (2004) Pearson-Printice Hall .
Molecular Biology of the Cell; Bruce Alberts et al., (2002), Garland Publications
Molecular Biology; David Freifelder,J. (1997) Narosa publishers.
Principles of Biochemistry; Smith et al., [Ed.] (1986) McGraw-Hill.
Molecular Cloning; A Laboratory Manual; Sambrook and Russel [Eds.] (2001),
Cold spring Harbor.
7. Human Molecular Genetics; Peter Sudbery , (2002) Printice Hall.
8. Human Molecular Genetics 2; Stracham Tom & Read Andrew P.,
Bios Scientific Publishers (1999).
9. Molecular Biology of Gene; Watson, J.D. et al., 5th Edn. Pearson Education; (2004).
10. Basic and Clinical Immunology; Stites et al., [Ed.] (1982) Lange.
11. Roitts Essential Immunology; Ivan, M. Roitt & Peter J Delves (2001) Blackwell Science
12. Immunology; Jan Klein [Ed.] (1990), Blackwell Science.
13. NMS for Immunology; Hyde and Patnide [Eds.] (1990) John Wiley.
14. Microbiology; Prescott, Harley and Klein, (2003) McGraw-Hill.
15. Kuby-Immunology; Goldsby et al., (2000), WH Freeman &Co.

Paper III: Special Paper

(Based on the area of research topic. The syllabus has to be prepared by
concerned guide and submitted.)
Guidelines for awarding Continuous Assessment Marks:
The marks is awarded by the course teacher based on:
a) Assignments

: Max.Marks: 5

b) Review of Literature

: Max.Marks: 5

c) Seminar

: Max.Marks: 5

d) Tests

: Max.Marks: 10
QUESTION PAPER PATTERN
(For all the three papers)

Time: 3 Hrs.

Max. Marks: 75

Instruction: Answer any five of the following. All questions carry equal marks.
Guidelines: Total of eight questions to be set carrying 15 marks each.
There could be a maximum of three sub divisions in each question.