Download TITLE OF MODULE: From Gene to Function MODULE NUMBER

TITLE OF MODULE: From Gene to Function
MODULE NUMBER: Bio00007I
ORGANISER: Dr. James Moir
SUBJECT COMMITTEE: MBB
VERSION: January 2011
TERM TAUGHT: Autumn, Spring and Summer
PREREQUISITES: First year degree programme in Biology or Biochemistry
SUMMARY:
This module will examine the molecular processes involved in enabling expression of genetic
information in both prokaryotic and eukaryotic cell types. The module will examine the mechanisms by
which genetic information is transformed into functional information, and how the processes involved
are regulated. This includes the mechanism and regulation of transcription and translation, and
subsequent events such as post-translational modification and trafficking that enable the regulation of
the activity of the fully functional gene product at the level of cellular function.
AIMS:
The module aims to:
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Explain how gene expression is achieved and controlled in prokaryotic and eukaryotic cells.
Put this information into the context of the function of prokaryotic cells & communities and
complex multicellular eukaryotes.
LEARNING OUTCOMES:
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How core methods are used for analysing gene function
The make-up of microbial genomes, how these are derived from genetic material that has been
both vertically and horizontally transmitted
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The features of bacteriophages (bacterial viruses) that infect prokaryotic cells and can become
incorporate into genomes
The basic mechanisms of regulation of microbial gene expression at the transcriptional and
post-transcriptional level
How environmental signals are sensed, and the mechanisms used to respond to these signals
The molecular basis of cell growth and division in Prokaryotes
How prokaryotes use a variety of metabolic processes to support life in unusual environments
A basic understanding of metagenomics
An understanding of how eukaryotic gene expression is regulated at many different levels
The importance of chromatin structure and chromatin modifications in control of transcription
How transcription initiation is controlled by cis- and trans-acting factors
The role that RNA processing plays in modulating gene expression
The role of non-coding RNAs in controlling gene expression
The generation of protein diversity through alternative splicing and RNA editing
How mRNAs are exported from the nucleus and localized in the cytoplasm
How proteins are generated by translation and subsequently modified for biological activity,
either within the cell or as a secreted product
The importance of mRNA and protein stability in gene expression and how these
macromolecules are degraded
ASSESSMENT:
A formative assessment will take place in week 1 of Spring term, based on the Autumn term material.
The summative assessment will be by a 3 hr closed written examination in week 6 of summer term,
which will include an essay question, methods questions and short answer conceptual / factual recall
questions. The module mark will consist of marks from the examination (90 %) and assessment based
on practical sessions (10 %).
LECTURES:
Autumn term. Prokaryotes.
Lectures 1 & 2. Organisation of microbial genomes. What are the genetic requirements for construction
of a bacterial cell? How microbial genomes are made up of horizontally and vertically transmitted genes.
A walk-through of a microbial genome. Including a digression to introduce bacteriophages –their
lifestyles and how they contribute to the make-up of microbial genomes. Organisation of genes on the
chromosome and packaging in the cell. (GHT)
Lecture 3. Transcription. RNA polymerase and regulatory sequences (promoters, operators,
terminators). Description of RNA polymerase enzyme, processes of transcription, alternative sigma
factors. (DB)
Lectures 4 & 5. Regulation of transcription. Notion of the operon. Specific examples, such as lac operon.
Repressors and activators. (DB)
Lecture 6 & 7. Regulation at post-transcriptional level. The trp operon and mechanism of attenuation.
Other modes of regulation post-transcriptionally including small RNAs and riboswitches. (MVDW)
Lecture 8. Sensing and responding to environmental signals. Two-component sensor regulator systems:
integrating the response of the cell to environmental signals. Other modes of environmental sensing –
e.g.catabolite repression and diauxie. (MVDW)
Lecture 9. How the prokaryotic cell is made. Assembly of the cell structure, targeting biomolecules to
the cell envelope. Post-translational modification of proteins. (JM)
Lecture 10. Molecular basis of microbial growth and division. Bacterial cell division. (DB)
Lectures 11 & 12. Bacterial growth and nutrition. How genetic factors alter gene expression during the
transition from lag to exponential to stationary phase. Methods for culturing bacteria and how these can
be used to investigate gene function and analyse microbial physiology. (GHT)
Lectures 13 & 14. Regulation and assembly of bacterial metabolic systems. Using a globally important
variable (oxygen availability) as an example the diversity of regulatory strategies and resultant microbial
functions will be explored from the level of DNA up to the level of cellular output. (JM)
Lecture 15. Responding to nutrient availability and stress. Global regulation in the context of processes
important for biogeochemical nutrient cycling and bacterial pathogenesis, such as biological nitrogen
fixation and iron metabolism. (JM)
Lecture 16. Physiology of microbes in real environments. Microbial populations. Metagenomics. (JM)
Spring term. Eukaryotes.
Lecture 17. DNA to RNA to Protein. Genome structure in eukaryotes. How is genetic information
transformed into functional information in eukaryotic cells and how does this compare with
prokaryotes. An introductory overview of the multiple control points of eukaryotic gene expression.
(DFS)
Lecture 18-19. Chromatin structure. How is naked DNA packaged into chromosomes? The role of
histones in this process and the effect of histone modifications on chromatin structure and template
accessibility. Higher order nuclear structure, topological effects of packaging and the role of
topisomerases. An introduction to chromatin assembly and the importance of chromatin re-modeling
enzymes. (DC)
Lecture 20. Transcription Initiation 1. Exploring the structure, composition and role of RNA polymerases
in transcription of eukaryotic genes with emphasis on RNA polymerase II (RNAPII). How does RNAPII
initiate transcription and what are basal transcription factors? Introduction to some basic techniques
used in studying transcription and transcription factors using some classic examples. (SSC)
Lecture 21. Transcription Initiation 2. What is the difference between basal and regulated transcription?
How are promoters modular? How is initiation of transcription from some RNAPII promoters regulated?
Further explanation of some basic techniques used in studying regulation of transcription and
transcription factors using some classic examples. (SSC)
Lecture 22. Transcription Initiation 3, Elongation and Termination. More on transcription initiation. Brief
summary of how RNAP processes and elongates nascent RNA and how it terminates transcription to
result in the correct message. What are some of the factors involved? (SSC)
Lecture 23. Nuclear Processing Events. The mechanism of co-transcriptional RNA modifications: capping,
polyadenylation and splicing. Splice site choice. (ALJ)
Lecture 24. Alternative splicing and RNA editing. Processes that can increase the protein coding capacity
of eukaryotic cells. Mechanism of alternative splicing using specific examples. Mechanism of RNA editing
with specific examples. (ALJ)
Lecture 25. Nuclear export, cytoplasmic localisation and RNA decay. How is mRNA exported from the
nucleus. Mechanism and significance of specific mRNA localisation in the cytoplasm. Pathways of mRNA
decay with an emphasis on quality control mechanisms. (ALJ)
Lecture 26. Non-coding regulatory RNAs. How RNAs can regulate gene expression by directing mRNA
cleavage, inhibition of translation or chromatin modifications. (ALJ)
Lecture 27.Translation –initiation. How is the cellular machinery specialized for translation initiation in
eukaryotes? The ribosome scanning model. Protein-RNA and protein-protein interactions; translation
factors and their function. (DFS)
Lecture 28.Translation –regulation. What are the cis- and trans-acting factors that regulate eukaryotic
translation? A range of examples in specific cell types and during early development will be discussed.
(DFS)
Lecture 29. Post-translational modifications. How are proteins modified after synthesis and how are
these processes regulated? Phosphorylation, glycosylation, lipidation – mechanisms and functional
consequences. (DFS)
Lecture 30.Protein secretion. An over-view of the different routes that proteins take to exit cells.
Regulated, constitutive and non-classical secretory pathways: what protein features are required and
what are the subcellular export pathways? (DFS)
Lecture 31.Protein degradation. An over-view of intra-cellular protein degradation mechanisms; how
and why the cell may need to degrade proteins and how this process is regulated, targeted and
executed. Specific examples of regulated proteolysis in the mammalian cell cycle, focusing on well
known proteins like cyclins. (DC)
Lecture 32.The big picture: genes to proteins. How does our understanding of the complexities of gene
expression allow us to determine the global expression patterns of biologically important proteins. The
importance of transcriptomics and proteomics, specific examples and practical applications. (DFS)
PRACTICALS
Autumn term
Experimental investigation of regulation of sugar utilization by E. coli (JM)
Practical 1 Session 1: Introduction, experimental design and set up. (3 hours)
Practical 1 Session 2: Bacterial growth under various conditions. Monitoring of growth and expression
and activity. (6 hours)
Practical 1 Session 3: Data analysis and summary of findings. (3 hours)
Students write a short practical write-up summarising their findings and conclusions, and answer some
problems related to microbial genetics.
Spring term
Practical 2: Nuclear Extraction from HeLa Cells (SSC/DC/DFS) (3 hours)
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Extraction of histones and analysis by protein gel electrophoresis
Use of micrococcal nuclease to reveal nucleosome spacing
Morning session in Biolab 1 (fume hoods)
Practical 3: Analysis of DNA topology (SSC/DC/DFS) (3 hours)
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Extraction and digestion of DNA
Analysis of conformational changes by gel electrophoresis
Afternoon session in Biolab 1 (fume hoods)
Students will be required to write a short report (1000 word maximum) on the
experiments in Practicals 1 and 2, including primary data and data analysis.
The first three sessions in the Autumn term are different "sessions" of the same practical. This practical
is the same as the one that ran in module 402 last term. Session 2 should be on the day after session 1,
session 3 should no more than a week after session 2. The practical should not start until after lecture 8.
WORKSHOPS
Spring term
1. Data analysis and feedback session on Practicals 2 and 3 (SSC/DC/DFS)
2. CHIP assays – identification of transcription factor binding sites (SSC)
3. Analysis of gene expression data, development of hypotheses and experimental
design (ALJ)
Summer term
2 x 3 hour workshop sessions as refreshers to help support student learning with an emphasis on
synoptic thinking about the whole module, and on preparation for the assessment, which will include an
essay.
SUGGESTED TIMETABLING SCHEDULE
Autumn
Week 2 L1 L2
Week 3 L3 L4
Week 4 L5 L6
Week 5 L7 L8
Week 6 P1Session 1 P1Session 2 L9
Week 7 L10 P1Session 3
Week 8 L11 L12
Week 9 L13 L14
Week 10 L15 L16
Spring
Week 2 L17 L18
Week 3 L19 L20
Week 4 L21 P2 P3 tbc
Week 5 L22 W1
Week 6 L23 L24 W2
Week 7 L25 L26
Week 8 L27 L28
Week 9 L29 L30 W3
Week 10 L31 L32
Summer
Week 1
Week 2 W1SuppLearn
Week 3
Week 4 W2SuppLearn
CONTACT HOURS
32 x 1hr lectures
18 hr practicals
3 x 3hr workshops
3 x 2 hr supported learning workshops
Workshops to take place in Biolabs
65 hr contact + 131 hr private study + 4 hr assessment = 200 hr
STAFF:
JM: James Moir.
GHT: Gavin Thomas.
DB: Daniella Barilla
MVDW: Marjan van der Woude.
DFS: Deborah Smith
SSC: Setareh Chong
DC: Dawn Coverley
LJ: Louise Jones
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