This course can be read by any Part IB scientist, physical or biological, who wishes to pursue the study of biological processes at the molecular and cellular level. It builds on basic concepts discussed in the Part IA course ‘Biology of Cells’. The aims of the course are to describe how information is stored as DNA and expressed as specific proteins, how enzymes and other proteins exert their functions, how cells function as integrated and co-ordinated metabolic systems, and how the growth and differentiation of cells is controlled.

The first term is concerned with Molecular Biochemistry: genes and proteins in action. The three main themes are firstly gene cloning and manipulation, secondly the control of gene expression in prokaryotes and eukaryotes, and finally the structure of proteins, the molecular mechanisms of enzyme action and the manipulation of protein structure to modify function.

The second term builds on these basic molecular concepts to deal with Cell Biochemistry: properties and functions of membranes and organelles and the integration of metabolism. There is an initial discussion of the mechanisms by which metabolism is controlled and integrated, followed by bioenergetics (how cells obtain their energy supply on which all metabolism is based). The hormonal control of metabolism and mechanisms of signal transduction across the cell membrane is followed by consideration of signal transduction and chemotaxis in microorganisms, and a lecture covering basic aspects of immunology. The term ends with a discussion of the control of eukaryotic cell proliferation and how signalling pathways in mammalian cells are activated by growth factors.

The third term covers aspects of more unusual biology (‘How the other three quarters lives – how protists break the rules of biochemistry’) and cancer biology. This topic is concerned with a discussion of ‘cancer genes’ (oncogenes and tumour suppressor genes) and how the control of the cell cycle may be subverted in the development of tumours.

Practical work is designed to complement the lectures. It involves experiments and integrated discussion sessions, the use of computers in the analysis of DNA and protein sequences and in the simulation of metabolic control, and journal clubs where small groups are guided by a senior scientist in the interpretation of a recent scientific paper.  An experimental design discussion has been introduced, where students are set an experimental problem to work through, led by a staff member, and are then set a second problem to consider themselves, working in small groups.  This is designed to develop critical thinking about experimental objectives, methods, controls and planning.

The Structure of the BMB course

BMB is taught by means of lectures, laboratory-based exercises with linked discussions, Journal Clubs and Experimental Design sessions organised by the Biochemistry Department and also supervisions organised by your college.

The Lectures

• • Each lecturer will prepare a handout. Our general policy for the handouts is that they should reflect the structure of the lectures. Handouts may be used to make compact statements about key features of the lectures, where tricky points may get additional explanation, or may be a more detailed set of the lecture slides. The handouts may contain copies of significant items displayed during lectures: they are not a literal script of the lectures, and don’t include extended commentary or background reference information. Colour versions of the lecture handout, along with lecture slides, are available on Moodle.
  • Lecturers will also provide some questions related to the material that they have presented, which you and your supervisors may wish to discuss.

Practicals

Progress in science is achieved through observation and experiment. Biochemistry (and its close cousin, molecular biology) is an experimental science that advances from well thought out investigations in the laboratory. No serious student should neglect the opportunities which this course provides to appreciate this fact. The BMB course includes experiments for you to gain some insight into how laboratory investigations are carried out and how data are processed and interpreted. To obtain useful results an experiment should be designed to answer a definite question and the detailed planning should be sufficiently rigorous to exclude adventitious errors. The BMB course provides the opportunity to plan some experiments, and students should benefit from the practicals in three ways:

1. 1. students will learn a variety of experimental techniques, all of which are currently used in biochemical research. The practicals have been designed to complement the lectures and fit in with their sequence as far as possible. The hands-on experience should link to the mental framework provided by the lectures and provide a deeper understanding and more realistic perspective of the topics discussed.
   2. Students will learn to handle experimental data effectively and to extract the maximum information content without falling into the trap of over-interpretation.
   3. Students will be helped when it comes to the data handling questions in the Tripos examination. Question papers from the last three years are included on Moodle.

BMB practicals are scheduled every day of the week, so provide an excellent opportunity for students to work in a relatively small group (maximum 30 students each day) where the ratio of student to demonstrators is high.

Journal Clubs

These small group sessions comprise structured exercises to help introduce students to reading primary scientific literature. There are two Journal Clubs, one on a molecular topic and the other more cell biological. A published paper is given to students, along with guidance notes and questions, to analyse during the week before the interactive session directed by one of the Biochemistry staff. This provides an excellent opportunity for students to critically evaluate the paper in a small group; most students find this a challenging but worthwhile exercise, since it gives exposure to the raw material of the scientific literature.

Experimental Design

Experimental design will be discussed throughout the course, and to consolidate this aspect of teaching in biochemistry there will be a teaching session on this in Lent Term.

Biochemistry is the study of living organisms at the molecular and cellular level. As a core course for the whole of biological sciences, a training in Biochemistry leaves you with the widest choice when you come to select an area of cell/molecular biology in any subsequent research programme or career. Recruiters in industry, government, investment management, regulatory authorities, and industrial law appreciate the breadth and diversity of biological knowledge that Biochemistry provides.

Students have a choice between a one-year Part II (B.A. degree) and two years of study, in which Part II is followed by Part III (B.A. and M.Sci. degrees). Part II Biochemistry also provides an appropriate training for Part III Systems Biology. The subject Part IB Biochemistry and Molecular Biology is the normal precursor to the Part II course but is not compulsory e.g. Part IB Cell and Developmental Biology is an adequate background to Part II Biochemistry. MVST students who are considering a career in medical research after qualifying will find the Part II course an excellent foundation.

The Part II course provides an advanced Biochemistry education, with modules entitled “Structural and Chemical Biology”, “From Genome to Proteome”, “Cell Cycle, Signalling and Cancer”, “The Dynamic Cell” and either “Molecular Microbiology of Infectious Disease” or “Bioenergy – The Exploitation of Plants and Microorganisms”. Teaching of transferable laboratory and communication skills (such as graphic illustration, record keeping, data analysis, database searching, seminar presentation, and report writing) is included in the course. Notice also that we place an emphasis through our extended critical essay on communication between scientists and society. See http://www.bioc.cam.ac.uk/teaching/third-year/biochemistry/part-ii-biochemistry.

The Part II course offers research experience through an eight-week research project. Students choose from possible research areas ranging from literature-based projects to bioinformatics or bench work and write a report.  In the project each student will work closely with one of the research teams in the Department. There are also departmental-based group supervisions involving students and staff throughout the year.

Structure of the Part II Biochemistry course

General structure of the course

There are three main strands to the teaching: lectures, research work and group supervisions, including Journal Clubs. Students also attend specialist supervisions.

A.    Lectures

The course is grouped into four 24 lecture modules, one of which has a branched structure to provide internal choice (Module C). In addition, there is a series of methods and skills sessions and students are expected to attend the Departmental Research Seminar Series.

• Module A: Structural and Chemical Biology

This module will discuss how modern techniques of structural and chemical biology are being used to solve biological problems. The topics will draw on multiple aspects of macromolecular biochemistry including nucleic acid structure and interactions, signalling proteins and membrane proteins. Finally, new approaches to studying enzyme kinetics will be discussed and how the knowledge so gained can be used in drug discovery and protein design.

• Module B: From Genome to Proteome

This module will examine all steps in eukaryotic gene expression from chromatin accessibility through to translation and mRNA turnover. Particular emphasis will be paid to: Regulation of gene expression, the co-transcriptional nature of RNA processing, functional coupling between different steps in gene expression, the impact of global and “systems” level approaches to understanding gene expression.

• Module C: Stem – the Dynamic Cell

The first half of this module is a common stem of cell biology, whose theme is the dynamics of proteins and membrane- bound organelles in eukaryotic cells. The stem is followed by a choice between two branches concerned with, respectively, exploitation of plants and microorganisms for energy provision and molecular microbiology of infectious disease.

• Module C: Branch 1 – Bioenergy

The bioenergy option aims to explore how photosynthesis in plants and algae can be harnessed for renewable energy production, whether directly using photovoltaic systems, or indirectly through production of oils or other forms of biomass such as cell walls. The module also looks at the conversion of biomass to other fuels.

• Module C: Branch 2 – Molecular Microbiology of Infectious Disease

The molecular microbiology option explores prokaryotes as agents of disease and as source of antibiotics. It also examines virulence and resistance. Molecular aspects of eukaryotic protozoan pathogens are also studied.

• Module D: Cell Cycle, Signalling and Cancer

The themes of this module draw on most modern biological techniques and impinge on core cell and molecular biology topics of signaling, DNA repair and apoptosis among others.

• Experimental Methods and Skills

These feature key methods such as bioinformatics. Also included are data handling classes using past examination papers as core material to study approaches to data analysis and interpretation. Teaching of transferable laboratory and communication skills (such as graphic illustration, record keeping, data analysis, database searching and essay and report writing) are embedded in the course.

B.     Research Work

There is an eight-week project during the Lent term (commencing on the first day of Full Term) that can be laboratory-, literature-, or computer-based. These projects will be carried out under the supervision of a member of the teaching staff or senior research staff.

C.     Peer Group discussions

Peer Groups in Part II and Part III Biochemistry are arranged by the Department. Part II and Part III students are organised into mixed groups and a senior member of staff is responsible for facilitating the sessions, which take place once a week. Peer Group discussions are an essential part of the taught course.

Topics addressed include

• • Journal Clubs: It is essential to acquire the ability to source, read and evaluate original papers; reliance should not be placed on review articles alone. The Journal Clubs help to develop these skills.
  • Reviewing particular experimental techniques or selected areas of research.
  • Critical evaluation of data.
  • Science that affects Society.This can take the form of a supervision exercise structured and moderated by the staff members, where designated student discussants research the topic and lead off a debate.
  • Integrated scientific essay: some time will be devoted to rehearsing the skills needed to tackle the Part III integrated scientific essay drawing on the overall scope of the landmark papers.
  • Development of presentational skills. Students will be given the opportunity to make presentations on their project work, the problem-based learning bioinformatics exercise and on scientific papers

The aim of Part II Biological and Biomedical Sciences (BBS) is to provide a rigorous and intellectually challenging biological Part II subject, for both third year Natural Scientists and Medical and Veterinary Science students. NST Part II BBS allows students to maintain some flexibility in their study at Part II, allowing them to combine courses from more than one single subject biological Part II and a choice of non-biology subjects. It requires the submission of a dissertation.

Course structure

The course has three main components

1. 1. A ‘Major’ Subject, which will typically draw on the core teaching of a single Part II subject but may draw on modules offered by more than one department. The ‘major subject’ will involve a minimum of 96 contact hours (excluding supervisions).
   2. A ‘Minor’ Subject, which can be provided by another department, which will involve 24-30 contact hours (excluding supervisions)
   3. A dissertation of up to 6000 words

Major subject allocation:

Registration for NST Part II BBS is part of the Part II Allocations Procedure used by biological departments for selection of students for the single subject Part II. Students will submit their choice for their major subject via CamSIS, by the beginning of Easter Term.

Minor subject allocation:

Once students are registered for their BBS Major Subject at the beginning of the long vacation, they will gain access to the BBS Moodle Site that contains detailed information regarding subject timetables and compatibility between subjects.

Students must register their Minor Subject choice by 1st September.

The department in which a student is taking their Major Subject will be designated as their “home” department. BBS students will have access to the same resources and support, such as soft skills training, journal clubs, seminars and facilities, as single subject NST Part II students in that department.

BBS in Biochemistry

As a Major Subject:

• • Students are required to attend all the Biochemistry lectures Michaelmas and Lent Terms, as outlined above for Biochemistry Part II (i.e. Modules A-D).
  • The course also requires attendance at the Part II & III weekly peer group sessions.
  • Assessment of the BBS course is the same as for Part II Biochemistry – i.e. four written papers covering Modules A-D, and one ‘data handling’ paper dealing with the analysis and assessment of biochemical data and hypotheses.

• • As well as the Biochemistry Major subject, students also take a 1-paper Minor subject in NST Part II BBS, provided by another Department.

For permissible subject combinations see https://www.biology.cam.ac.uk/undergrads/nst/bbs/subject-combinations.

Two of the Biochemistry modules may be taken as minor subjects in BBS:

• • Module B (Michaelmas Term)
  • Module D (Lent Term)

Dissertation

• • According to the Regulations for NST Part II BBS, students must write a dissertation that “must not exceed 6,000 words, excluding appendices, tables, figures, footnotes and bibliography.”
  • The dissertation is not a report of laboratory work as the Biochemistry Major subject has no experimental work included. The dissertation is typically an extensive literature review on a chosen topic.
  • Students can expect to receive a maximum of 4 supervisions from their dissertation supervisor.
  • Students are expected to meet with their supervisor at least twice during the preparation of their dissertation. Supervisors are only permitted to view a single draft of the dissertation prior to submission.
  • Dissertation titles will be released no later than the first day of the full Michaelmas term.
  • Dissertations are prepared in accordance with the Guidelines for the dissertation issued by the Faculty Board, which can be found at http://www.biology.cam.ac.uk/undergrads/nst/bbs/dissertations.

The Part III Biochemistry course is followed by undergraduates who have successfully completed the Part II Biochemistry course having met the set criterion in Part IB and Part II in order to be accepted for the 4-year course. The course allows students who wish to become professionals in the molecular biosciences to pursue a two-term research project during their fourth year, together with continuing advanced teaching in lectures and discussion groups. Success in the course leads to the award of the MSci degree. 

The individual research project is conducted in the laboratory of the supervising member of staff and chosen from an extensive list. With prior approval by the Course and Projects Organisers, projects may be undertaken in other parts of the University, such as the Gurdon Research Institute, the Systems Biology Centre, Cambridge Institute for Medical Research, Institute of Metabolic Science, Department of Veterinary Medicine, MRC Human Nutrition Unit, MRC Mitochondrial Biology Unit, MRC Molecular Biology Laboratories, Hutchison/MRC Research Centre, Unilever Cambridge Centre for Molecular Informatics or the Department of Chemical Engineering and Biotechnology. The experimental work will start at the beginning of the first term and be written up as a dissertation (8,000-word limit, excluding footnotes and bibliography) by early in the third term. For many of the Part III class the project is the highlight of their degree as well as providing a real insight into the world of research. 

In two research symposia (one to the Part III class and one to their weekly Peer Group), students present 20-minute reports and answer questions on their project. Production of these presentations is an excellent training for postgraduate and business careers. The research environment is reinforced by a series of seminars on “Scientific Method and Experimental Design”. 

The training also includes Journal Clubs and advanced lectures. Weekly biochemical discussion sessions amongst other students and members of staff continue through the year. The third term is, as for Part II, otherwise free to devote to examination preparation through the departmental-based group supervisions, specialist supervisions with individual lecturers and self-guided supervision. At this stage, four-year students graduate with the BA and MSci degrees. 

There are opportunities for students who satisfactorily complete the Part III course in Biochemistry to proceed to doctoral degrees by research, in Cambridge or elsewhere; the Department is well equipped for research on a wide range of biochemical topics. 

Structure of the Part II Biochemistry course

General structure of the course

There are four main strands to the teaching: lectures, seminar series, research work and supervisions. There are no lectures or research work during the Easter Term, i.e. after the Easter Vacation: the early part of that term is available for general reading and revision.

A.    Lectures

In Michaelmas Term, Part III students choose either:

• MT1: Molecular Recognition and Interaction:

Lectures present case studies in precisely understood contexts, within broad themes of protein-protein recognition (e.g. in molecular signalling), protein-nucleic acid recognition (e.g. in the RNA degradosome and DNA repair) and protein-small molecule recognition (e.g. in molecular assembly lines and drug screening). (12-lecture module); or

• MT2: Cell Fate:

How the developmental paths of cells (from cradle to grave) are determined, regulated and manipulated. Our current biochemical understanding of stem cells, differentiation, neurodegeneration, cell death and ageing. The experimental approaches and models used to study cell fate (12-lecture module).

In Lent Term, students choose either:

• LT1: The Biochemistry and Biophysics of Neuronal and Metabolic Disorders:

This module will show how molecular and systems approaches can further understanding of diseases that perturb metabolic integration, cardiovascular function and neurotransmitter and hormonal signalling. Contexts will include circadian and cardiac rhythm disturbance, neuronal disorders, obesity, and thrombotic disease (6 x 2-hour lecture module); or

• LT2: Contemporary Cancer Studies:

This module will look at a series of recent advances in our molecular understanding of cancer, with a combination of lectures and workshop-style discussions (7-8-workshop module).

B.   Seminar Series on Scientific Method and Experimental Design

The overall aim is to develop the student’s understanding of scientific method and process – the development of hypotheses, the choice of experimental systems and the design of experimental tests of the hypotheses. These sessions use two complementary approaches: (a) investigating deployment of methodological resources and (b) discussion of landmark papers.

1. 1. The methodological sessions will cover choice and use of model organisms, genome projects, microarrays, proteomics, RNAi, interactomics and measurement of interactions, recombinant protein expression and imaging.
   2. The landmark paper discussions will provide an opportunity to understand what makes brilliant science, a sense of why current knowledge has accumulated as it has, and what limitations were imposed by the available technology. Each session, led by a member of staff, is assigned a landmark paper (or small group of papers) that represents a leap forward in biochemistry. Papers may be historic, such as the proposal of the lac operon, or more recent, such as advances in stem cell technology. Whilst the format may vary, one approach is where groups of students will research and make presentations to the class as a whole on various aspects of the paper being considered. These will include the state of knowledge before publication of the landmark paper, and the impact of the paper on biochemistry.

C. Research Work

There is a 17-week project during the Michaelmas and Lent Terms that may be laboratory-, literature-, or computer-based. The projects will be carried out under the supervision of a member of the teaching staff or senior research staff. The project weighting is 50% of the total marks in the examination. Throughout the project it is vital that students achieve a reasonable balance between project work and other aspects of the course. Whilst students are largely responsible for policing their own work programme, it is important that staff are mindful of the need for students to achieve this balance and to guard against any suggestion of undue pressure. It is important that students commence the Project write-up before the end of the Lent Term to ensure maximum revision time.

Part III students are invited to the weekly Friday seminars, where the academic staff present an overview of their research to other members of the department.

D.     Project Symposium

There is a symposium at the start of Lent term when Part III students report on the progress of their research projects.  Each student will have a total of 20 minutes (including 5 minutes for questions).  All students must attend all the talks on the two days.  Students are also called upon in group supervisions (see below) to report on their research progress.  At the start of Easter term, students will be expected to give a final presentation summarizing their research project to their general supervision group.

E.     Peer Group discussions

Peer Groups in Part II and Part III Biochemistry are arranged by the Department. Part II and Part III students are organised into mixed groups and a senior member of staff is responsible for facilitating the sessions, which take place once a week. Peer Group discussions are an essential part of the taught course.

Topics addressed include

• • Journal Clubs: It is essential to acquire the ability to source, read and evaluate original papers; reliance should not be placed on review articles alone. The Journal Clubs help to develop these skills.
  • Reviewing particular experimental techniques or selected areas of research.
  • Critical evaluation of data.
  • Science that affects Society. This can take the form of a supervision exercise structured and moderated by the staff members, where designated student discussants research the topic and lead off a debate.
  • Integrated scientific essay: some time will be devoted to rehearsing the skills needed to tackle the Part III integrated scientific essay drawing on the overall scope of the landmark papers.
  • Development of presentational skills. Students will be given the opportunity to make presentations on their project work, the problem-based learning bioinformatics exercise and on scientific papers