Biochemistry and Molecular Biology

Lectures

Biochemistry and Molecular Biology, or BMB as most call it, is a popular subject choice with those that enjoy learning about molecular processes of the cell. Most topics in BMB can be seen as a more detailed extension of the content learnt in Part IA Biology of Cells such as gene expression, bioenergetics and the cell cycle. The course also places emphasis on fundamental experimental techniques which are used to help discover the biological processes that we learn about.

BMB is one of the two subjects that can be taken as a prerequisite to Part II Biochemistry, the other subject being Cell and Developmental Biology (CDB). Many people intending for the Biochemistry route often take both BMB and CDB together, as these two subjects have some content overlap and have great synergy. Topics like immunology and oncogenes are also covered in BMB, which overlaps with the Part IB Biology of Disease (BoD) course.

Lectures are at 10 am on Mondays, Wednesdays and Fridays, and lecturers are generally lovely and happy to answer any questions you might have. However, it is important to note that lecture notes are not provided for all the topics, and that some lecturers will only provide copies of their slides.

The lecture synopses are given below:

Michaelmas:

Gene Cloning and Manipulation: The course starts with covering the experimental tools and methods used in genetic engineering. It starts off with PCR, leading to cloning into vectors and finally the experiments to study the function of the gene, such as analysing expression levels, gene localisation, interacting proteins etc.
Control of Gene Expression: This course extends from Part IA BoC, starting off with the structure of DNA and how it can be specifically recognised despite its regular structure. This is followed by the mechanisms of transcription in eukaryotes and prokaryotes, explained much more in detail.
Control of Gene Expression: These lectures will explore how gene expression is controlled at the post-transcriptional level along with the translational processes. They complement the previous lectures on gene expression.
Protein Structure and Evolution: This course builds up nicely, starting from the sequence of amino acids and finishing with large macromolecular complexes. It examines how sequence analyses can help us to understand the structure and function of the protein, before discussing how structures are determined, by X-ray crystallography and nuclear magnetic resonance spectroscopy.
Enzyme Catalysis and Protein Engineering: Complementing the previous lecture course, these lectures examine well-defined protein structures such as catalysts and binders in detail. Ideas about enzyme catalysis, kinetics and mechanism are explored, followed by a discussion on immunoglobulins and how their binding to antigens can be understood and exploited. Lastly, the idea of directed evolution will be introduced to identify novel proteins.

Lent:

Control of Metabolism: Exploring the different ways in which enzyme activity can be controlled, this course describes the regulation and flux in metabolic pathways, as well as experimental approaches for studying the control of metabolism. These topics will be discussed largely by using examples from glucose metabolism in muscle and liver: i.e., glycolysis, gluconeogenesis, glycogen synthesis and glycogenolysis.
Bioenergetics: This course will first explore the basic concepts of thermodynamics, followed by the diversity of electron transfer systems and their similarities. Building upon IA BoC, the lectures will go through the processes of electron transfer, and the evolution of the organelles containing them.
Trans-Membrane Signalling: The aim of this course is to understand the essential properties of signalling pathways and the components that make them up, such as the receptors and second messengers.
Regulation of Cell Cycle: Yet another course than builds from IA BoC, this course introduces the molecular components that regulate cell cycle progression and show how cell division is regulated. The experimental methods used to determine these molecular processes will also be explored.
Immunology: A rather short lecture series that introduces antibodies – how they work, are produced, and their relevance to vaccination. This course overlaps with BoD.
Oncogenes, Tumour Suppressor Genes and Cancer: These lectures serve as an introduction to the multi-step process of cancer, exploring the roles of oncogenes and tumour suppressor genes with many examples, and how they contribute to cancer. Also overlaps with BoD.

Easter:

Protists: An interesting lecture series designed to broaden our understanding of eukaryotes, organisms outside the typical “model organisms” will be explored. Their biology includes some dramatic exceptions to the conventional way of doing things we’re used to from the model organisms.
Chemotaxis: The last course of BMB explores bacterial motility and chemotaxis, starting with the structures of the flagellin, and exploring how their conformation can be changed, to give rise to the tumble/run behaviour of the bacteria. There will also be discussion on how attractants and repellents work to affect the movement of the bacteria, on a molecular scale.

Supervisions

Supervisions are the best place to go through and clear your doubts about the lecture content. Many lectures are very information-dense, and going through it one more time with your supervisor will be very helpful. Supervision work is usually a mix of essay writing, short-answered questions, and practical questions to gear you to the final exam. It is worth noting that supervisors often like to spam essay questions, especially since the level of essay writing required in BMB is a step up compared to BoC. There are also no written answers to any of the questions or tripos papers, so it is paramount that you go through your work thoroughly with your supervisor as this is the only avenue of obtaining feedback. It is also always a good idea to come prepared to supervision with a list of questions or discussion points – don’t be afraid to ask questions!

Practicals

Being an experimental based subject, BMB practicals are very important and aim to give you experience to perform experiments on methods used in research. There is one BMB practical a week, scheduled from 12 – 5 pm and you will typically work in pairs. The practical itself is not graded, but the method and theory behind the practicals will be tested in a practical exam paper at the end of the year, similar to IA BoC. Most of the practicals will come with a set of pre-practical handouts and quizzes available on Moodle that aim to familiarise you with the theory and methods. Though not compulsory, completing these will aid immensely in the actual practical. Often, there are also small interactive simulations or videos on Moodle that are in no way necessary to do, but also supplement the understanding of the practical.

Most practicals are experimental and require you to sit in the lab for the better part of the afternoon. These mostly go through the experimental techniques first discussed in lectures and provide exposure to many techniques or equipment used in biochemical labs. Other than the experimental labs, a couple of BMB practicals are used as “Journal Clubs”, where you would have to read a chosen paper and try to answer the set of questions that come along with it before the actual practical slot. The demonstrator will then go through the paper and questions during the practical. This was interesting and is definitely a good way to start understanding how to read research papers and apply it to the content we study! There are also a couple of computational labs, where software like COPASI has to be downloaded.

Like IA BoC, the yellow sheet with the practical answers will be released at the end of the week, once everyone has attended the practical. However, even though the answers are provided, I would strongly recommend discussing the practical theory, results and questions with the supervisors at hand as this will help to deepen your understanding of the practical! Math is also very important in these practicals so make sure to understand the formulae you use! Lastly, even though the practical slot runs from 12 to 5 pm (with possible lunch break), more often than not, it is very possible to finish before 5 pm, so make sure to plan your time wisely!

Revision and Exams

It is important to note that BMB is an extremely content heavy subject, requiring much memorisation and a thorough understanding of the lecture content throughout the year. Spaced repetition is your best friend here, so make sure to keep revisiting and reviewing past lectures throughout the year. Past tripos papers are as always, important in revision. However, as mentioned before, there will not be any written answers, and hence you should always check with your supervisor.

There has been a change in examination format and syllabus, revised in 2021. What used to be a 3-paper exam format has been changed to 2 papers, and some of the sections have also been removed and switched around. However the questions themselves in the past papers beyond 2021 are largely the same format and are definitely an important tool in your revision. Certain parts of the syllabus have also been removed, so do not be too alarmed if you see a question with keywords you have not learnt! The BMB examinations are closed book and to be conducted online on the Inspera exam portal (for now).

Paper 1 is 3 hours long and contains a total of 15 essay questions divided into 5 sections, of which you will need to choose 1 from each section (so total 5) to write. Each section contains the essay questions pertaining to the lecture content taught from half a term, i.e. you can only answer one essay question per half a term. Hence it is important to plan your revision out and see if you would prefer to focus on a few topics rather than the entire syllabus. Throughout the year, you will be writing many essays for your supervisions. With consistent practice and revision, the goal of writing an essay in just 36 minutes can be achieved! A couple of tips I have for essay writing is that firstly, lecturers and supervisors love it when you integrate content across the lecture topics for your essays (e.g. you are writing an cell signalling essay but bring in some information about the control of metabolism). Secondly, similar to BoC, putting information outside lecture content is highly rewarded. One way to do this is to regularly read research reviews related to the lectures in your own time.

However, spotting is not an option with the short-answered questions (SAQs) in paper 2, which you also get 3 hours for. There are 10 of these questions, and can test absolutely anything from the lecture content, from an experiment you never thought was important in your notes, to an organism that was briefly mentioned in a couple of slides. Ideally, you should spend an hour in this section and hence 6 minutes to each SAQ.

This is followed by the practical sections, which are divided into 2 parts (should take an hour each). The first part consists of 3 smaller questions, mostly testing the Michaelmas practicals. The second part only contains one question, but it is much longer and extended, testing content from the lent practicals. There will be several calculation questions in these so do make sure to familiarise yourself with the formulae well. Constant practise as well as reviewing the past practical tripos questions are essential to do well.

Useful resources

Moodle! There are many hidden gems on the BMB Moodle page that aid in learning.
Lehninger’s Principles of Biochemistry (Nelson and Cox; Freeman) – your general biochemistry textbook with a wide coverage of topics!