Course syllabus

Code: BCH 4027

Title: Advanced Molecular Biology
Type of course : “UE Mixte”

Department : Biochemistry

Level : Master 1

Name of Lecturer in charge : Prof. Wilfred Mbacham DS, ScD. wfmbacham@yahoo.com

Grade : Professor

Other Lecturers: Prof. Marceline Djuidje Ngounoue, Prof. Boris Gabin Azantsa Kingue

Grade: Associate Professor

Objectives : In this course, we introduce the basic concepts in molecular biology and molecular
genetics (e.g. protein structure and function, DNA structure and replication, transcription, RNA
processing and translation, recombinant DNA technology). The tutorials and practical sessions will lay
special emphasis on experimental approaches to understanding molecular biology.

Number of Lectures : 14

Duration of lectures : 3 hours

Lectures room : R108, new pedagogic Bloc

Lectures :

Lecture 1. Genes are DNA sequences, and the "Central Dogma of Molecular Biology", simply stated,
that information flows from DNA to RNA to protein. Architectural properties of DNA, topological
properties of DNA, reassociation kinetics of melted DNA, the packaging of DNA, genetic mapping.
Cells and chromosomes.

Lecture 2. Human Genome

Lectures 3. Anopheles genome

Lecture 4. Plasmodium Genome & Viral genomes

Lectures 5-6. Transcription. The basics of making RNA, in bacteria; an introduction to regulation. How
RNA polymerase recognizes (and distinguishes) genes; promoters, σ (sigma) factors. Interaction of
transcription and DNA supercoiling. Elongation and termination.

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Lectures 7-8. Transcription in eukaryotes. An introduction to the complexity of the transcriptional
apparatus in higher organisms. A focus on Pol II, TFIID and the TBP.

Lectures 9. Post-transcriptional processing of RNA. Changes in RNA after synthesis and (usually)
before use. Splicing, including alternative splicing; capping; polyadenylation, RNA Editing, Trimming.
mRNA degradation.

Lectures 10-11. DNA replication. DNA polymerases. Issues of the replication process: getting started,
priming, unwinding the template, working accurately, hanging on, finishing and untangling. The
replication apparatus, or replisome. Damage and Repair processes; topoisomerases. DNA replication
in prokaryote and Eukaryote

Lectures 12. Translation. Formation of initiation complex, prokaryotes and eukaryotes. Genetic code:
standard and variations; recoding. The players... mRNA, tRNA, activating enzymes, ribosomes,
"factors". Nuclear translations - evidence

Lectures 13. Protein structure; role of weak bonds. Mutations, Special features of tRNA, Protein
splicing - Mechanism, Properties of inteins

Lectures 14. Gene regulation; DNA-protein interactions. Proteins interact with DNA and modulate its
structure and function. The Lac operon paradigm, plus a sampling of other regulatory systems. Types
of DNA-binding proteins; sequence recognition; DNA-bending.

Lectures 15. Final exam.

Bibliographic references:

Wilfred Mbacham 2002: Biotechnology for Innovation and Discovery, summer course manual.

R F Weaver, Molecular Biology, 2/e, 2002, WCB/McGraw-Hill. ISBN 0072345179 or Newer editions:
3/e, 2005, is ISBN 0072846119. 4/e, 2008.

D P Clark & L D Russell, Molecular Biology made simple and fun, 2/e. Cache River Press, 2000. ISBN
1889899046. This book presents the basics of molecular biology in a way that is readable and fun, yet
scientifically quite sound. It may be helpful as an introduction for some students. Others will just find
it fun. (Caution: it cannot be used to replace Weaver.) 3rd edition, 2005: ISBN 1-889899-07-0. 4th
edition, 2010: ISBN 978-1889899091.

T A Brown, Gene Cloning and DNA Analysis: An Introduction (2001); Genomes 3 (2006).

H Lodish et al, Molecular Cell Biology, 6/e. Freeman, 2008. ISBN 978-0-716-77601-7. Web site (for
4th, 5th and 6th editions): http://www.whfreeman.com/catalog/static/whf/lodishbridgepage/.
Useful material, including animations. New edition added May 8, 2012: The 7th edition is available,
2012. ISBN 978-1-4292-3413-9.

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 • B Alberts et al, Molecular Biology of the Cell. 5/e, 2007. (This edition is also listed as Lewis et
al.) ISBN 978-0815341055. The Problems Book (Study guide) by Wilson & Hunt. ISBN
9780815341109.
• G M Cooper & R E Hausman, The Cell - A Molecular Approach. 5/e, 2009. ISBN 978-0-87893-
300-6. Web site, with links keyed to the chapters: http://www.sinauer.com/cooper5e/. Some
web site features require registration.
• B Alberts et al, Essential Cell Biology: An Introduction to the Molecular Biology of the Cell.
2/e, 2003. ISBN 0-8153-3480-X (with CD-ROM). A short version of the Alberts book listed
above.
• J D Watson et al, Molecular Biology of the Gene, 6/e. Benjamin/Cummings, 2007. ISBN 978-
080539521-1. (An earlier edition of this book was the course textbook for several years.)
• J D Watson et al, Recombinant DNA: Genes and Genomes -- A Short Course. 3/e. Freeman,
2007. ISBN 978-07167-78158.
• J E Krebs et al, Lewin's Genes X. Jones & Bartlett, 2011. ISBN 9780763766320. A web site for
Genes IX remains, with supplemental materials, including
animations:http://biology.jbpub.com/book/genes/index.cfm. New edition added November
2, 2011.
• G Williams, Hyper CELL. 1997. ISBN 0-8153-289-82. CD-ROM, from publisher of Alberts et al,
but it is general. Excellent animations.
• B R Glick et al, Molecular Biotechnology -- Principles & Applications of Recombinant DNA.
4/e, 2009. ISBN 978-1555814984. (Previous editions were by Glick & Pasternak.)
• J J Pasternak, An introduction to human molecular genetics - Mechanisms of inherited
diseases. 2/e, 2005. ISBN 978-0471474265.
• A N Glazer & H Nikaido, Microbial Biotechnology -- Fundamentals of Applied Microbiology.
2/e, 2007. ISBN 9780521842105.
• F C Neidhardt et al (ed.), Escherichia coli and Salmonella -- Cellular and Molecular Biology.
2/e, 1996. ISBN 1-55581-084-5. CD-ROM version, 1999; ISBN 1-55581-164-7C. This is now
maintained as a web resource, called EcoSal: http://ecosal.org/. UC Berkeley provides
subscription access.
• R C King et al, A Dictionary of Genetics. 7/e, 2006. ISBN 0-19-530761-5, paperback.
• K Drlica, Understanding DNA and Gene Cloning - A guide for the curious. 4/e, 2003. ISBN 978-
0471434160.
• L Gonick & M Wheelis, The Cartoon Guide to Genetics. 1991. ISBN 0-06-273099-1.
• Palmer Masumbe Netongo (2009). Molecular Indices of failure to Anti-Malarial Drug in
Cameroon. Thesis presented and defended at the Department of Biochemistry, University of
Yaounde I.
• Marceline Djuidje Ngounoue (2009). Hepatitis C virus infection in people living with
HIV/AIDS: seroprevalence, immunological and biochemical analyses, and genetic variability.
Thesis presented and defended at the Department of Biochemistry, University of Yaounde I.
Sites consulted :

Materials necessary for students:

Evaluation method: Written Final Examination with multiple choice questions and conceptual
questions requiring short answers.

Lecture portion (50%):

Final Exam (January, 2024) = 50 points

Name of Lecturers in charge of Tutorials: Prof. Djuidje /Prof. Azantsa

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Grade: Associate Professors

Number of Tutorial sessions: 5

Duration of each Tutorial session: 1:30 min

Tutorial rooms/Practical Room: E206 & R106

Tutorial session 1 or TD 1: Types of nuclei acid, e.g. single stranded circular-M13 phage DNA,
PhiX174 phage DNA, single stranded linear RNA, double stranded linear-Lambda phage DNA (inside
the virus particle), double stranded circular-Lambda phage DNA (inside a host cell), pBR322, pUC 19
plasmid DNA; Primers Linkers, adaptors. Properties of good cloning vectors.

TD 2: Stability of nucleic acids (heat/nucleases/alkali/acid). Exonuclease III activity, 5’ 3’

exonuclease activity; DNase I activities, S1 nuclease activities, Bal 31 activities, mung bean nuclease
activities, application of nuclease activities in cloning.

TD 3: Manipulation of nuclei acids, digestion of DNA with restriction enzymes. Types of Restriction
enzymes, Isochizomers, guidelines for choosing restriction endonucleases. How to set up a digestion
experiment.

TD 4: Gene cloning, preparing competent cells, transformation of E. coli XL-1 Blue cells, Blue/white
color screening,

TD 5: Manipulation of nuclei acids; ligation, phosphorylation, labelling, dephosphorylation, mutation,

TD 6: Midterm Evaluation II

Bibliographic references :

Wilfred Mbacham (2002): Biotechnology for innovation and Discovery, summer course manual.

Palmer Masumbe Netongo (2009). Molecular Indices of failure to Anti-Malarial Drug in Cameroon.
Thesis presented and defended at the Department of Biochemistry, University of Yaoundé I.

Djuidje Ngounoue M, Fepa Kwesseu AG, Nwobegahay J, Moundipa Fewou P. (2018). HBV and HCV
Seroprevalence and the Predominant HCV Genotypes in a Hospital Setting in Cameroon. Virology and
Mycology (Life Sciences Journal) 7: 178. doi:10.4172/2161-0517.1000178.

Djuidje-Ngounoue M., Ndjomou J., Lindenbach B. (2021). Enabling HCV replication in cell culture: An
approach for vaccine and drug development. International Journal of Infectious Diseases 101 (S1)
(2021) 492-528. https://doi.org/10.1016/j.ijid.2020.09.1325.

Materials necessary for students : Tutorial hand-outs will be given to students before the start of the
tutorial sessions.

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Evaluation method : oral and written participation in tutorials, and 2 midterm written evaluations.
Midterm 1 = 10 points

Midterm 2 = 10 points

Name of Lecturer in charge of Practical sessions: Dr. Foupouapougnigni

Grade : Senior Lecturer

Number of laboratory Practical sessions : 6 sessions organised for groups of 20 students.

Duration of each practical session : 4 hours

Practical laboratories /rooms : E206 & R106

TP 1: Extraction and purification of Plasmodium falciparum genomic DNA from Blood by Methanol
method. Checking for purity of DNA. Extraction of plasmid DNA -miniprep. Strategies to increase
the quantity of DNA.

TP 2: Deletions mutations to identify promoters

Reverse Transcriptase -PCR in determination of Initiation of transcription
Enzymes that modify DNA features and properties
TP 3: Electrophoretic Mobility shift assay for sequences that bind factors
DNA foot printing to determine regions of DNA that bind factors
Experiments of Meselson at Stahl
TP 4: Experiments to show bi-directionality of replication
Identification of replication deficient cells - temperature sensitive mutants
TP 5: TA cloning -
a. Vectors
b. Recipe steps for PCR, digestions and ligation,
c. Competent cells
d. Transformation and analysis for transformants
TP 6: DNA & RNA Sequencing (Chain termination sequencing/Sanger sequencing vs Next
Generation Sequencing (NGS))

Pedagogic material used: LCD Projector, laptop

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List of reagents and equipment for Practical lessons;

Quantity Description
01 Lancets (100/pk)

01 Filter paper
01 Methanol (100g) from Biorad

01 1.5 ml micro-centrifuge tubes (Eppendorf) 1000/pk

01 0.2ml micro-centrifuge tubes (Eppendorf) 1000/pk

01 NaCl 100g
01 Saponin (50g)
01 EDTA (100g)
01 Na2HPO4 (100g)
01 NaH2PO4 (100g)
01 NaOH (100ml)
01 HCl (100ml)
01 10x PCR buffer 1000ml ( composition: Tris base, (NH4)2SO4, MgCl2, DTT, Triton X
100, BSA)
01 5x DNA loading buffer ( Composition Bromophenol Blue, Xylene Cyanol, ficoll,
EDTA, H2O) from New England Biolabs
01 Primers msp 2 (forward and reverse)
01 Primers dhfr-ts (forward and reverse)
04 PCR-quality water (250ml)
01 Taq Polymerase 250 ml
01 Lambda DNA (from new England Biolabs)
01 Hind III Restriction Endonuclease (from new England Biolabs)
01 Bsr I Restriction Endonuclease (from new England Biolabs)
01 Alu I Restriction Endonuclease (from new England Biolabs)
01 100bp ladder (from new England Biolabs)
01 Ethidium bromide 10g
01 Agarose 100g
10 Distilled water 5 liters
Tris base 500g
Boric acid 500g
02 Micropipette tips blue 1000/pk
02 Micropipette tips yellow 1000/pk
10 Powder free Gloves 100/pk
Instruments
Forceps
Pair of scissors
pH meter
Thermocycler
Micro centrifuge
Vortex
Autoclave
Micropipettes P1000, P200, P100, P20, P10
Electrophoresis setup (Generator, tank)
Heating block

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 Spectrophotometer

Materials necessary for students: Hand-outs for practical lessons will be made available to students
before the practical sessions.
Evaluation method: Lab session reports, and final practical exams

Lab portion (30%):

Lab 1-4 (lab reports will be scored on 25 points for each Lab session) = 100 points which will
constitute 30% of the midterm evaluations, i.e. 6/20 points.

Lab-related question on Final Exam = 30 points

Date and Signature of Lecturer in Date and signature of the Head of

charge of course Department :