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BGM3063 : Biochemistry of Gene Expression

  • Offered for Year: 2019/20
  • Module Leader(s): Dr Nick Watkins
  • Lecturer: Dr Simon Whitehall, Prof. Rick Lewis, Dr Yulia Yuzenkova, Dr Elizabeth Veal, Dr Jeremy Brown, Dr Luisa Wakeling, Professor David Elliott, Dr Claudia Schneider
  • Owning School: Biomedical, Nutritional and Sports Scien
  • Teaching Location: Newcastle City Campus
Semester 1 Credit Value: 20
ECTS Credits: 10.0


Our understanding of how gene expression is regulated has improved enormously over recent years, and it is now appreciated that the amount of each gene product produced is determined by both transcription and post-transcriptional events up to RNA degradation, which may be generic or specific to some or even individual genes. This module will build on information received by students in the first and second years, developing appreciation of the biochemistry of core aspects of gene expression and its regulation at various levels, and introduce students to original literature associated with the field. The module also aims to develop core skills including data interpretation and exam essay skills.

Outline Of Syllabus

The core module lectures will cover key features of gene expression and associated biochemistry. Topics will be:

1) Nucleic acid structure, key nucleic acid-protein interactions and protein motifs that occur in multiple nucleic acid binding proteins.

2) DNA-dependent RNA polymerases. These enzymes are responsible for the first step in expression of information in our genes – generation of the pre-mRNA transcript. Structure and mechanism of DNA-dependent RNA polymerases, key features of eukaryotic RNA pol II, and particularly the C-terminal domain (CTD) of its largest subunit with which it interacts with many factors including the RNA processing machinery.

3) RNA polymerases are highly sensitive to local chromatin conformation, and both the mechanisms for modulating chromatin structure and the regulation of nucleosome dynamics during transcription will be discussed. Gene expression is also affected by methylation of DNA and mechanisms and consequences of this epigenetic modification to DNA will be discussed.

4) The production of mature mRNA via capping, splicing, polyadenylation and editing will be discussed, as will mRNA export form the nucleus. Alternative patterns of splicing, as well as the position of transcription initiation and polyadenylation, yield a huge diversity to the products of gene expression. The importance, mechanisms and regulation of alternative transcript processing will be discussed, as will the links between transcription, RNA processing and downstream events in RNA metabolism.

5) Mechanism and regulation of protein synthesis. Regulation of translation is a much more rapid response than changing transcription patterns, providing cells with a primary response to changing environment: key translational regulatory mechanisms and pathways will be discussed, as will the various pathways through which mRNAs are degraded.
6) Non-coding RNAs and ribonucleoproteins (RNPs) play key roles in the cell that extend beyond the standard gene expression pathway, and the importance of these will be discussed.

Complementing the core lectures, research lectures and seminars will form the remainder of the taught material. Both of these will be used to enhance the material in lectures, with examples of current research being discussed in the research lectures, and topics related to the course (structural biology and nucleic acids as tools in biomedicine) forming the material to be discussed in seminars. Both these exercises will require students to read papers beforehand.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion110:0010:00ICA preparation
Scheduled Learning And Teaching ActivitiesLecture261:0026:00N/A
Guided Independent StudySkills practice21:002:00Generic Skills Session
Scheduled Learning And Teaching ActivitiesWorkshops41:004:00Seminars
Scheduled Learning And Teaching ActivitiesWorkshops11:001:00Course Induction& Information on ICA
Guided Independent StudyReflective learning activity11:001:00Feedback session on timed essay
Guided Independent StudyIndependent study1156:00156:00N/A
Teaching Rationale And Relationship

Lectures introduce the material on the course, delivering the bulk of the key knowledge required, so that students can meet the learning outcomes. Skills practice sessions are generic, used to support development of core analytical and numerical skills across the curriculum. Research Seminar workshops will expand on the material presented in lectures and also provide students with the opportunity to practise their critical and analytical skills further. The first session of the course (Introductory Workshop) will include information on the in course assessments, including the Graphical Abstract and Highlights exercise. The feedback session will be a discussion of the timed essay in which the students, guided by the academic staff present, will pool knowledge to generate a model answer to the question, and review essay writing skills.

Assessment Methods

The format of resits will be determined by the Board of Examiners

Description Length Semester When Set Percentage Comment
Written Examination1202A802 essay questions from choice of 4
Other Assessment
Description Semester When Set Percentage Comment
Essay1M10Timed Essay (60 mins)
Prof skill assessmnt1M10Graphical Abstract and Highlights Exercise (2 slides)
Assessment Rationale And Relationship

The written exam paper assesses each student’s knowledge base, comprehension and ability to discuss the subject critically.

The professional skills exercise is designed to test the student’s ability to distil key knowledge from a document (a research paper) into both pictorial (graphical abstract) and written (bullet point) form.

The timed essay will provide the students with opportunity to develop their skill at essay writing under exam conditions and receive feedback before the final exam.

Reading Lists