THE UNIVERSITY OF THE WEST INDIES, ST. AUGUSTINE
FACULTY OF SCIENCE & TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
Course Code: BIOC2262
Course Title: Gene Expression
No. of credits: 3
Level: Undergraduate -Year II
Semester: II
Prerequisite(s): BIOL1362 Biochemistry I or BIOL1061 Cell Biology and Genetics and, either
CHEM1066 Introduction to Chemistry I and CHEM1067 Introduction to Chemistry II or
CHEM1060 Introductory Chemistry.
Anti-requisites: BIOL2362 Further Metabolism & Gene Expression
Enrolment capacity: 90 students (maximum)
COURSE DESCRIPTION:
Chemistry of nucleic acids, gene expression events and regulation, DNA surveillance and repair
mechanisms; nucleotide biosynthesis, gene expression and developmental biology. The course
will be delivered using a number of pedagogical tools and will be myeLearning supported.
Course materials will include class handouts e.g. illustrations and diagrams and the course will
be fully myeLearning-supported. The course is a theoretical course.
COURSE RATIONALE:
This course provides a foundation for current advanced concepts in Biochemistry specifically
with respect the chemistry of nucleic acids, gene expression events and regulation, DNA
surveillance and repair mechanisms; nucleotide biosynthesis, gene expression and developmental
biology.
INSTRUCTOR INFORMATION:
Name of instructor(s): Sephra N. Rampersad
Office address and phone: Rm 319, 2nd Floor-Old Wing, Natural Sciences Bldg
Email address: sephra.rampersad@sta.uwi.edu
Preferred method of contact: E-mail
Communication policy: Students should use their UWI e-mail account for communication and/or
leave a note or message with the Biochemistry secretary.
LETTER TO THE STUDENT:
Welcome to Gene Expression. This course aims to complete the degree offering for a major in
Biochemistry and presents critical elements of current concepts Biochemistry specifically with
gene expression in eukaryotes. The jargon will be new and a glossary of terms for each topic in
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the course would be a key learning tool. Practice in writing out answers including tutorial
assignments is also important to understanding the course material. Course materials will include
class handouts e.g. illustrations and diagrams and the course will be fully myeLearningsupported. This course will enable students to have a foundation in these core aspects
Biochemistry for teaching at secondary level, conducting research in medicine, molecular
biology and/or related disciplines. It is important to engage with the materials provided online, in
face-to-face lectures and tutorials in order to successfully complete this course. Engagement
with all facets of this course will enable you to develop skills of critical thinking (clarity,
accuracy, relevance, logic, breadth, depth, precision, significance, completeness and fairness).
You are encouraged to ask questions during class time and during tutorial sessions, offer new
ideas or ways of studying a topic, offer new approaches to problem solve to support a studentcentered learning experience. It is critical that you read the syllabus carefully and pay attention to
important assessment dates. The University’s policy and plagiarism and attendance requirements
will be enforced. It is important to us that you succeed in this course. Please come to us with any
academic or other challenges you may face that could affect your attendance and performance.
COURSE CONTENT:
TOPIC 1: Biochemistry of Nucleic Acids (4 lectures)
 Structure and components of DNA and RNA - comparative treatment
 Ultrastructure and conformations of DNA and RNA – comparative treatment
 DNA replication in eukaryotes
 Central dogma of molecular biology
TOPIC 2: Genome Expression (19 lectures)
 DNA packaging and chromosome structure
 Genome organization and complexity, concept of a gene, genome, transcriptome and
proteome
 Steps at which genome expression can be regulated: Accessing the genome
 Assembly of the transcription initiation complex
 Synthesis of RNA –The transcription process
 Processing of RNA
 RNA export
 RNA degradation
 Assembly of the translation initiation complex
 Protein synthesis – The translation process
 Post-translational protein modification
 Protein degradation
 Spatiotemporal expression
 Differential cell development and gene expression
 Gene expression and aging/mental disorders
TOPIC 3: DNA damage surveillance and repair (5 lectures)
 SS break repair mechanisms
 DS break repair mechanisms
 Differential pathogenesis and gene expression
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TOPIC 4: Nucleotide Biosynthesis (3 lectures)
 de novo synthesis, the pyrimidine ring is assembled from bicarbonate, aspartate, and
glutamine
 purine bases can be synthesized de novo or recycled by salvage pathways
 deoxyribonucleotides can be synthesized by the reduction of ribonucleotides through a
radical mechanism
 the key steps in nucleotide biosynthesis are regulated by feedback inhibition, disruptions
in nucleotide metabolism can cause pathological conditions
LEARNING OUTCOMES:
At the end of this course, students should be able to:TOPIC 1 – Biochemistry of Nucleic Acids
Biochemistry of Nucleic Acids
1. State the general constituents of nucleosides and nucleotides and what type of bonds are
involved in each of these structures.
2. Identify which bases are commonly found in DNA? Which in RNA.
3. State which components form the backbone of DNA and RNA molecules.
4. Explain all of Chargaff’s Conclusions.
5. Describe the type of non-covalent interaction is critical for specific base-pairing between
nucleotides of complementary DNA strands.
6. State the functions of three named nucleotide analogs.
7. Write out the DNA and RNA base sequence of the complementary strand.
8. Describe the various bonds, linkages and forces which make up and stabilize the DNA
double helix.
Conformations of DNA and RNA
1. Describe the 3-D structure of the DNA double helix.
2. Compare the 3 conformations of DNA.
3. Explain the types of RNA conformations.
4. Evaluate the importance of the minor and major grooves in DNA B form in terms of
DNA-binding proteins.
DNA Replication in Eukaryotes
1. State the 3 main rules of DNA replication.
2. List the enzymes involved in DNA replication and give their respective functions.
3. Outline the process of replication.
4. Explain the 7 main features of eukaryotic replication.
5. State 3 mechanisms used by cells as cell cycle check-points in DNA replication.
6. Explain how DNA replication and transcription are mechanistically similar.
7. Describe at what point does an origin of replication become licensed to undergo
replication.
8. Explain why the ORC the first to bind at the origin of replication.
9. Explain the function of CDKs and DDKs in DNA replication.
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10. Describe the assemblies of the Pre-RC and the RIC as they occur in different phases of
the cell cycle.
11. Assess the relationship between replication and the cell cycle.
TOPIC 2 – Gene expression
Outline of Genome Expression
1. Compare the following terms: (i) gene (ii) genome (iii) transcriptome (iv) proteome
2. Explain briefly how cell development and differentiation affects genome expression.
3. Identify at which points in the events of genome expression regulation occurs.
Genome Expression Event 1 – Accessing the genome
1. Discuss the 6 levels of DNA packaging into chromosomes.
2. Compare the following terms: (i) heterochromatin (ii) euchromatin (iii) histone (iv)
nucleosome
3. Explain how chromatin can be chemically and physically modified to activate and silence
genome expression.
4. Discuss the role of histone acetyltransferases and how they affect genome expression.
Genome expression event 2 – Assembly of Transcription Initiation Complex
1. Describe the RNA content of the cell.
2. State the basic components of a typical protein-coding gene.
3. State 3 examples of class II eukaryotic promoters.
4. Identify the consensus sequences of these promoters.
5. List the proteins in order of their appearance in the step-wise assembly of the Transcription
Initiation Complex.
6. Assess the function of the transcription initiation complex.
Genome expression event 3 – RNA synthesis
1. Outline the main steps involved in transcription elongation and termination.
2. Explain CTD Phosphorylation.
3. Explain how transcription terminated in eukaryotes.
5. Evaluate the functions of regulatory elements in transcription.
6. Explain the role of mutations in controlling gene expression.
7. Assess how chromatin structure affects transcription.
Genome expression event 4- RNA Processing
1. Describe the structure of a transcription activator factor.
2. Assess the role of RNA splicing in producing different mRNAs from the same DNA which
code for different proteins.
3. Explain alternative splicing and discuss the adaptive value of this phenomenon.
4. Explain the functions of the cap structure placed at the 5' end of the RNA.
5. Describe the end modification of mRNA.
6. Explain the recognition mechanism of mRNA capping enzyme.
7. Describe the processes which eukaryotic mRNA molecules undergo after transcription has
been completed and before translation starts.
8. Explain why polycistronic eukaryotic mRNAs cannot work.
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9. Explain the basic structure/organization of a typical eukaryotic promoter.
10. Discuss how this structure facilitates the precise regulation of transcription of specific genes
by transcription factors in different tissues or in the same tissue under different conditions.
Genome expression event 5-Mature mRNA Export
1. Explain the need for mRNA export.
2. Describe the events that occur after RNA processing and before translation.
Genome expression event 6-RNA degradation
1. Explain the need for mRNA be degradation.
2. Assess the effect RNA degradation has on the transcriptome.
Genome expression event 7-Assembly of the translation initiation complex
1. Describe briefly, the assembly of translation initiation factors.
2. Account for where this assembly occurs and why.
Genome expression event 8-Protein synthesis
1. Evaluate the role of rRNA and tRNA as adaptor molecules in protein synthesis.
2. Describe the eukaryotic ribosome.
3. Explain the process of scanning and how is it carried out.
4. Define the genetic code.
5. Explain the 6 features of the genetic code
6. Compare the following terms giving examples where appropriate: (i) codon vs. anticodon (ii)
start codon vs. stop codon (iii) ‘charged’ tRNA vs. ‘uncharged’ tRNA.
7. Outline the 3 stages in elongation in translation.
8. Outline termination of translation.
9. Describe what is meant by amino acid activation and why is this necessary for translation.
10. Explain what you understand by proof-reading by aminoacyl synthetase enzyme.
11. Examine the functions of the P and A sites of a eukaryotic ribosome.
12. Assess how tRNAs bind correctly to the ribosome so that the mRNA code is correctly
translated into amino acid sequence.
13. Identify the consensus sequences that are involved in protein synthesis.
Genome expression event 9-Post-translational modification of proteins
1. State 5 protein modifications.
2. Examine why protein modifications must occur.
Genome expression event 10-Protein degradation
1. Explain protein turnover in cells.
2. Describe how turn-over affects the proteome.
DNA damage, surveillance and repair
1. Explain what DNA surveillance is and its function in maintaining genome integrity.
2. Identify 2 causes of DNA damage.
3. Describe the effects of DNA lesions.
4. Explain the fate of a cell carrying DNA damage.
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5. Discuss the sources of DNA damage.
6. Identify which aspect of DNA structure is affected by lesions.
7. Describe 4 processes that result in DNA damage.
8. Explain the effects of DNA damage on DNA replication and transcription.
9. Compare stability of mtDNA with nDNA.
10. Evaluate SSB mechanisms of repair in terms of principles of repair, mechanisms of repair,
and whether specific tissues require a specific type of repair mechanism and identify what type
of damage is repaired in each case.
11. Discuss the effects of DNA damage on nucleosome assembly.
12. Assess the pathological effects of DNA damage and poor repair on aging, cancer and
evolution .
TOPIC 3 – Nucleotide Biosynthesis
1. Describe de novo synthesis, the pyrimidine ring is assembled from bicarbonate, aspartate, and
glutamine
2. Explain how purine bases can be synthesized de novo or recycled by salvage pathways
3. Explain how deoxyribonucleotides can be synthesized by the reduction of ribonucleotides
through a radical mechanism
4. Describe the key steps in nucleotide biosynthesis are regulated by feedback inhibition
5. Explain how disruptions in nucleotide metabolism can cause pathological conditions
COURSE ASSESSMENT:
Assessment will be based on a student’s final mark from the coursework components below.
Item
2 In-course tests
Mark Weighting
each worth 10%
1 group assignment
10%
4 quizzes
each worth 5%
Final exam
50%
Description
2 tests (50 mins duration)
based on multiple choice,
true/false, short answer
questions; exams will cover 4
weeks worth of teaching
1500 word investigative
report and oral presentation
based on current research in
gene expression
4 tests (30 mins duration)
based on multiple choice,
true/false, short answer
questions; will cover 2 weeks
worth of teaching
2-hour written exam to
answer 3 out of 5 essay
questions; may include a
compulsory section or
question
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EVALUATION:
 Student opinion on the course with respect to delivery and assessment will be obtained
through informal and regular discussions with students. Discussions with demonstrators,
teaching assistants and instructor for the course will also be used to identify and address
student issues.
 Class Representatives are required to sit on the Departmental Student-Staff Liaison
Committee meetings held twice during the semester and at each meeting, to submit a
completed reporting form. Class reps are to be guided by the Department’s Standard
Operating Procedures.
 The UWI Course Evaluation questionnaire administered anonymously and confidentially
at the end of the semester will also be used to assist in identifying student issues.
 All feedback will be considered on an on-going basis; actions will be taken immediately
(preferred and as applicable) or incorporated the following year.
TEACHING STRATEGIES:
Contact hours (36 credit hours):
Lectures: 33 h
Tutorials: 3 h
Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of
available information, update current issues and events, and prioritise content relevant to course
assessment. For this second year course, the delivery strategy will be chalk-and-talk with
continuous class interaction and engagement. Posting lecture notes prior to class times will not
be practiced as this has resulted in a drop in attendance.
Tutorials: Tutorials will cover course topics in a problem-solving format to engage collaborative
and active learning techniques.
myeLearning: myeLearning will be used extensively during this course for official
communication among students and staff (email, discussions), official posting of important
notices (coursework assessment notices, instructions, glossaries, and in-course marks/results),
official posting of syllabus, lecture notes, tutorials, posting of important web-related resource
materials and links.
RESOURCES:
Most resources will be posted to myeLearning and will include:
 Lecture notes and outlines - include learning objectives, summaries, recommended
readings
 Resources - links to papers, articles and websites with interactive resources and you tube
videos and animations to support delivery
 Tutorials – tutorial questions
Note: Answers to tutorials will not be posted as a strategy to encourage students to attend all
tutorial sessions.
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READINGS:
Books
1. Genes 2000 On-Line. Lewin, B. 1999.
2. Genes VII. Lewin, B. 1999 Oxford University Press; ISBN: 0198792778
3. Genomes. 2002 On-Line. Brown, T.A. Oxford, United Kingdom: Wiley-Liss; ISBN 0471-25046-5.
4. Instant Notes Biochemistry. 2005. Hames, D. and Hooper, N.. ISBN: 0415367786
5. Lehninger Principles of Biochemistry. 2001. Nelson, D.L. and M.M. Cox. 3rd Ed.
6. Molecular Biology of the Cell. 2002 On-Line. Alberts B., Johnson, A., Lewis, J., Raff,
M., Roberts, K., Walter, P. and print ISBN 0-8153-3218-1 (hardbound) -- ISBN 0-81534072-9 (pbk.).
7. The cell – a molecular approach On-Line. Cooper, G. 2nd Ed. Sinauer Publishers.
8. Stryer’s Biochemistry
Journal Articles
1. H. Nishitani, Z. Lygerou. 2002. Control of DNA replication licensing in a cell cycle.
Genes to Cells 7:523–534.
2. S. Pollok, J. Stoepel, C. Bauerschmidt, E. Kremmer, and H.P. Nasheuer. 2003.
Regulation of eukaryotic DNA replication at the initiation step. Biochemical Society
Transactions 31: 266-269.
3. R. D.Wood and M.K.K.Shivji. 1997. Which DNA polymerases are used for DNA-repair
in eukaryotes? Carcinogenesis 18 :.605–610.
4. O. Fleck and O. Nielsen. 2004. DNA repair. The Company of Biologists 117: 515-517
COURSE CALENDAR:
WEEK LECTURES
LECTURER
Introduction & Course
Overview
wk1
wk 2
Chemistry Nucleotides
Rampersad
DNA/RNA structure
Rampersad
Nucleotide analogues
Rampersad
*
*
Nucleotide biosyn
Rampersad
Nucleotide biosyn
Rampersad
Nucleotide biosyn
Rampersad
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WEEK LECTURES
wk 3
wk 4
wk 5
wk 6
wk 7
wk 8
LECTURER
*
*
Lect/Tutorial
Rampersad
DNA replication
Rampersad
DNA replication/Quiz#1
Rampersad
*
*
Lect/Tutorial
Rampersad
Incourse Exam 1
Rampersad
Gene expression
Rampersad
*
*
Gene expression
Rampersad
Gene expression
Rampersad
Gene expression
Rampersad
*
*
Gene expression
Rampersad
Gene expression
Rampersad
Gene expression/Quiz#2
Rampersad
*
*
Gene expression
Rampersad
Gene expression
Rampersad
Lect/Tutorial
Rampersad
*
*
Gene expression
Rampersad
Gene expression
Rampersad
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WEEK LECTURES
wk 9
wk 10
LECTURER
Gene expression
Rampersad
*
*
Gene expression
Rampersad
Gene expression
Rampersad
Incourse Exam 2
Rampersad
*
*
Gene expression
Rampersad
Gene expression
Rampersad
Gene expression/Quiz #3 Rampersad
wk 11
wk 12
wk 13
*
*
Lect/Tutorial
Rampersad
DNA repair
Rampersad
DNA repair
Rampersad
*
*
DNA repair
Rampersad
DNA repair
Rampersad
DNA repair
Rampersad
DNA repair/Quiz#4
Rampersad
Submission of group
assignment
Rampersad
Tutorial –review of
topics
Rampersad
Tutorial –review of
topics
Rampersad
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HOW TO STUDY FOR THIS COURSE:
 Attendance is mandatory for lectures and tutorials.
 Continuous reading and studying of lecture material are strongly encouraged to maintain
learning momentum.
 Students are strongly advised to become familiar with navigating myelearning and look
out for new postings and messages. Students are asked to utilize correct e-mail etiquette
in any and all correspondence to staff.
 Students are encouraged to interact regularly with staff on their projects, even outside of
the assigned tutorial times to ensure prompt, satisfactory solution of any problems and to
monitor progress.
ADDITIONAL INFORMATION:
Students must pay attention to the following important information concerning assessment,
attendance and plagiarism: The Life Sciences Undergraduate Handbook available from
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 The General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 As a general principle, medicals or other excuses may only excuse a student’s absence
from the original exam. Students must sit the makeup exam at the assigned date and time.
 All course work submissions must be attached to a signed Coursework Accountability
Statement in order to be assessed. Refer to ‘University Regulations on Plagiarism’
available from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
 While it is known that students form FaceBook groups for a particular course,
myeLearning remains the official communication platform for the course.
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