Department of

Department of Biochemistry
Biochemistry

Natural Sciences Tripos

Part IB Biochemistry and Molecular Biology
2018-2019
Part 1B Biochemistry
& Molecular Biology (BMB)

CONTENTS

Overview of the NST Part IB Biochemistry and

Molecular biology course 4-5

Lectures (Michaelmas, Lent and Easter Terms) 6-14

Practicals and Examinations 15

Timetables - Lectures and Practicals 16-18

3
Overview of the Natural Sciences Tripos Part IB Course
in Biochemistry and Molecular Biology
Biochemistry and molecular biology are the fundamental disciplines that underpin the study
of living organisms. Both fields are developing rapidly, providing fascinating insights into the
assembly and function of biological molecules, machines, cells and tissues. Equally important,
the theoretical background and underlying experimental strategies provide the foundation
for the current exciting developments in molecular genetics, cell biology, neurobiology,
developmental biology, medical science and biotechnology.

The Part IB Biochemistry and Molecular Biology (BMB) course offers an in-depth
understanding of biological molecules and processes that is essential for proper
comprehension of all modern biomolecular sciences. The course introduces state-of-the-art
concepts of molecular structure and function, cellular development and metabolic control,
and builds naturally on the foundations that will be familiar to you from Part IA Biology of
Cells. Between 100 and 150 students take the IB BMB course each year. IB BMB can be
combined successfully with many other subjects in both biological and physical sciences. It
complements Part IB Cell and Development Biology (CDB) particularly well, providing the
molecular insights that underpin and explain the breadth of phenomena described in that
course. Equally, it adds the biological dimension to courses more focused on Chemistry. In
recent years, Part IB students have combined BMB with CDB, Chemistry A, Chemistry B,
Pathology, Experimental Psychology, Animal Biology, Physiology, Plant Sciences,
Pharmacology, Ecology, History and Philosophy of Science, Mathematics, Advanced Physics
and Fluid Mechanics.

The Biochemistry Department is a large teaching and research institution with some 45
independent research groups and around 300 post- and pre-doctoral researchers, between
them studying physiological, pathological, cellular and molecular processes in all types of
organism: animals, plants and microbes. Laboratories in the department employ the whole
spectrum of cell and molecular biological techniques, together with state-of-the-art facilities
in biophysics, computational biology, advanced cell and whole body imaging,
electrophysiology and genetically engineered mouse models. Our research portfolio is
summarized at: http://www.bioc.cam.ac.uk/research.

The Department is especially strong in systems biology (bioinformatics; mass spectrometry

in metabolomics and proteomics), structural biology (protein NMR and x-ray
crystallography) and drug design (computational, fragment-based, and antibody engineering),
stem cell biology (developmental biology; cell signalling), cancer biology (cell cycle, DNA
damage sensing, mouse models, whole body NMR and PET imaging of tumours to monitor
therapeutic mechanism and efficacy), cardiovascular research (live cell imaging of
thrombosis, and electrophysiology of cardiac arrythmias and other channelopathies),
microbiology (bacterial virulence, quorum sensing, bacterial viruses and antibiotics),
parasitology, chemical biology and biofuel development. Arguably our greatest strengths in
research and teaching lie in the cross-fertilisation between research fields that this
rich diversity provides. 4
Practical classes are held in the basement of the Department's Hopkins Building on the
Downing Site, which faces onto Tennis Court Road about 100 metres from Downing Street.
Lectures take place in our Sanger Building, also on Tennis Court Road, closer to the
Chemistry Department on Lensfield Road. You are very welcome to visit the buildings
when choosing your Part IB subject.

See Downing Site and Old Addenbrooke's Site on University map:

http://map.cam.ac.uk/

5
 Lectures

The power of modern Biochemistry and Molecular Biology

lies in their ability to explain the mechanisms underlying co-ordinated processes in cells and
organisms by identifying the specific underlying molecular interactions.

The course considers two main questions:

What are the specific molecular structures and dynamic interactions between nucleic acids,
proteins and enzymes on which life is based?
How do these interactions mediate the organisation and regulation of cellular processes?

NST Part IB Biochemistry and Molecular Biology is organised by a small committee,

convened by Dee Scadden, who can be contacted in the Biochemistry Department
(Network tel: 33671/66012; e-mail: [email protected]) and will be pleased to provide
more information or answer any questions.

The course is designed to start a little earlier (on the first Wednesday) in the Lent and
Easter Terms and to finish a little later (on the last Friday) in the Michaelmas and Lent
Terms than is customary, so that there is a clear period at the end of the lectures in the
Easter Term for consolidation and revision before the examinations begin. Please note
this in your diaries.

Below we provide a summary of current teaching in the course. From time to time there
may be some modifications to accommodate sabbatical leave.

Since the 2016/17 academic year, the Department has been involved in a University-wide
pilot for lecture capture, so the BMB lectures have been recorded and available via Moodle.

Michaelmas Term
In this term the course examines the molecular biology of DNA and protein structure.
How is DNA packaged in cells? How does chromatin structure affect gene expression?
How is genetic engineering actually carried out? How are transcription and translation
regulated? What are the principles of protein design and how can we exploit them through
protein engineering?

(i) Gene cloning and Manipulation

These lectures introduce the techniques of gene cloning and manipulation that underpin
much of the work described in the rest of the course. Building on material covered in the
Part IA Biology of Cells lectures, we look at the use of various techniques to ask
specific experimental questions. 6
 We first look at the polymerase chain reaction and its
various applications, and then consider vectors and
hosts that are used in more conventional gene
cloning. Once a clone is obtained, we investigate
various ways that this may be used experimentally.
For instance, we look at how genes can be expressed
to make large quantities of the proteins they encode, and how those proteins may be
modified for use in specific experiments (e.g. localization, protein interactions, etc.). We
conclude by looking at various methods for reducing gene expression (e.g. RNAi, CRISPR-
Cas9), and for creating transgenic mice.

(ii) Nucleic Acid Structure, Protein-Nucleic Acid

Interactions and Transcription
These 5 lectures cover the first step in gene expression -
transcription of RNA using genomic DNA as template.
How do RNA polymerases recognise the correct locations
at which to initiate transcription, and how can this be
regulated? Six main topics will be covered:

1. DNA & RNA structure

2. Prokaryotic transcription mechanisms
3. Prokaryotic transcriptional regulation
4. Packaging of eukaryotic DNA into chromatin
5. Eukaryotic transcription – core promoter and
general transcription factors (GTFs)
6. Eukaryotic transcription – activating transcription
factors and enhancers

The overarching theme of DNA-protein interactions - both sequence-specific and non-

specific - runs through all of these topics. At appropriate points, relevant experimental
approaches and techniques will be highlighted.

(iii) Post-Transcriptional Control of Gene Expression

The production of functional proteins involves multiple processes in addition to
transcription. Although these steps are usually referred to as post-transcriptional, many
of them occur concurrently with transcription. These lectures will introduce the
processes required for the formation of a mature RNA in eukaryotic cells (capping, splicing
and 3’ end processing), translation (in both prokaryotes and eukaryotes) and RNA decay.
The basic machinery that carries out these processes, as well as the mechanisms by which
this machinery is modulated in a gene-specific manner, will be addressed.
7
(iv) Protein Structure, Function and Evolution
Proteins play most of the effector roles in living organisms. They maintain the structures
of cells, of the extracellular matrix and tissues; they catalyze most reactions in cells and
generate mechanical force in the muscles; they are involved in information transfer
through recognition of other molecules and can act as ligands, as receptors, as
messengers, and as transcription factors; they act as receptors, gates and channels in
membranes. The aim of these lectures is to understand the unique principles of protein
structure from primary structure to formation of large oligomeric complexes and
molecular machines and to introduce the methods that are used to study protein
structures from optical spectroscopies through X-ray crystallography and NMR to cryo
electron microscopy. We will also discuss how proteins have evolved and how analysis of
protein structure can help us to understand the evolutionary relationships between
different proteins and their function.

The three-dimensional structures

of haemoglobin, myoglobin and
leghaemoglobin: members of the
globin family with limited
sequence identity but highly
similar structures and a conserved
binding site for the haem co-
factor.

(v) Enzyme Catalysis and Protein Engineering

This lecture series focuses on how the
peptide and protein structures
discussed in the
preceding module can assume
functions - and on experiments that
delineate the mechanisms involved.
First we develop ideas about enzyme
catalysis, mechanism and kinetics. We
look in detail at the co-operative
(allosteric) molecular basis of
metabolic regulation. Other protein
structures that are discussed include
immunoglobulins and their binding to
specific antigens, and the principles of
protein folding and stability.

Finally we look at the ‘holy grail’ of protein engineering and mechanistic enzymology –
how to create novel, functional proteins, by rational design, semi-rational approaches, and
by directed evolution.
8
 Lent Term

The course now builds on the molecular foundations laid in the Michaelmas Term to
develop an integrated view of cellular processes. How do cells make a continuous supply of
energy available for transcription, translation, ion pumping, biosynthesis and a host of other
processes? How is metabolism regulated according to the varying needs of the cell? What
are the mechanisms by which hormones regulate intracellular processes? How is normal
eukaryotic cell growth controlled, and what goes wrong when such control is pathologically
disturbed in cancer?

(i) Energy Transduction in Bacteria,

Mitochondria and Chloroplasts

Bioenergetics is the study of how energy is acquired

and used in living systems. Recent discoveries of key
structures and mechanisms have greatly enhanced our
understanding of this process. This knowledge is being
applied to medicine, nanotechnology, and the energy
industries, informing our attempts to develop
renewable biological energy sources. The six lectures The scanning electron micrograph of a
explore how bacteria, plants and animals use light, mammalian cell shows (some) cross-
electrons, protons and ATP to transduce energy from sections through the mitochondria that
are responsible for our own energy
the sub-molecular to the cellular level. The lectures production.
use an evolutionary emphasis to make it easier to
understand the diversity of bioenergetics
systems in nature.

(ii) Control of Metabolism

The aims of these lectures are:

 To examine the different ways in which enzyme activity may be controlled.

 To consider the benefits these different modes of control offer for the regulation of
flux in metabolic pathways.

9
 This discussion takes place in a wider context, as
these various modes of control are employed
throughout biological systems. Textbook
descriptions of control in the metabolic
pathways tend to assume that the enzymes
involved are ‘soluble’ and homogeneously
distributed in the cell cytoplasm. We will see
how this is not the case: rather, a high degree of
spatial organisation is critical to the control of
these pathways.

Various experimental approaches are described

Imaging brain function through changes in cell for studying how metabolism is controlled, with
metabolism. particular emphasis on methods that may be
used to study intact systems.

These include:

 Metabolic control analysis, which allows for quantitative determination of the

importance of any enzyme for flux control in vivo.
 Two key non-invasive spectroscopic techniques - fluorescence and NMR - that
permit the study of metabolic events in intact
cells and tissues.

(iii) Transmembrane Signalling: Molecules and Mechanisms

Cells are continuously bombarded by many different types of signal; the ability of these cells
to respond appropriately to such signals is critical for cell survival, adaptation, and
specification of function, whether they are individual amoebae or components of a large,
complex organism such as a human. This lecture course explores how cells monitor the
presence of specific extra-cellular signalling molecules and how these signals then instigate
and drive complex and interwoven intracellular
responses.
The course will focus on:

 The diversity of signals carrying information to

cells; these range from single photons and small
molecules to complex proteins.
 The relatively few mechanisms, usually involving
plasma membrane receptors, by which the cell
perceives the signal.
 The means by which the cell decodes 'the Cartoon of a nerve cell which will transmit
message', a process which may be very rapid, as information from the incoming action
potential to the adjacent cell, using neuro-
neurotransmission, or much slower, as in the transmitters stored in the synaptic vesicles.
signals that regulate gene expression and control Neuronal signaling is one of the many types
of signaling that will be explored in this
growth. 10
course.
The lectures will, for example, examine the roles of the ‘second messengers’ that often
mediate part of cell signalling cascades, and will explore how these cascades allow very low
concentrations of initiating signals to generate large responses in their target cells. Special
attention is paid to G-protein coupled responses, and to the multiple roles played by
protein phosphorylation in relaying intracellular signals.

This lecture course will be complemented by two successive practical classes in which
students gain hands-on experience of the techniques used to probe the roles of proteins in
three different cell signalling pathways.

(iv) Control of Eukaryotic Cell Growth

The cell cycle is the term used to describe the succession of events that occur to produce
two cells from one. An understanding of the molecular events involved in progression
through the cell cycle is central to solving the larger problems of how the tightly controlled
expansion of cell populations during the development and growth of any organism occurs
and how the loss of regulation of the cycle results in disease - not just cancer but also the
inappropriate growth of normal cells.

The aims of the lectures are:

a) To give an understanding of the experimental approaches that can be taken to

investigate the molecular machinery of a complex biological process.
b) To explain how the molecular components that regulate cell cycle progression were
identified and how their function was determined. (3) To discuss a model of how the
ordering of transitions that ultimately lead to cell division is regulated.

(v) Oncogenes, Tumour Suppressor Genes and Cancer

The next four lectures build on the story of the cell cycle in eggs and yeasts by describing
how normal mammalian cell proliferation is controlled. The focus is on the mechanisms of
normal signalling pathways - growth factors and mitogens, their receptors and the mitogenic
signals they generate inside the cell, and the pathways that then transduce such mitogenic
signals to the various intracellular effectors that precipitate cell growth and replication. The
principal effector responses to mitogenic signalling are transcriptional activation of
proliferation-associated and cell survival genes and repression of growth suppressing genes,
activation of RNA and protein synthesis, and an abrupt shift of metabolism to biosynthesis
and aerobic glycolysis.

11
These lectures address the question of what happens in diseases, such as cancer, where
control of cell growth, proliferation, survival and migration is lost through activating
mutations in proto-oncogenes, and inactivating mutations in tumour suppressor genes. This
introduction to molecular oncogenesis sets the scene for a more comprehensive analysis of
cancer biology in one of the Part II Biochemistry courses.

Easter Term
This final group of lectures considers bacteria and protozoa as model systems and the
course now brings together the themes explored in the first two terms to examine key
questions relating to prokaryotic and protist biochemistry such as motility, chemotaxis and
the importance of protein targeting and other systems in virulence and pathogenicity.

(i) Bacterial Chemotaxis and Signal Transduction

The field of bacterial chemotaxis and motility encompasses perhaps the best-understood
prokaryotic signalling pathway. We start by using video footage of motile E. coli cells to
define the basic swimming behaviour of bacteria in the unstimulated state. We then look at
how this behaviour is altered when the cells are challenged with chemostimuli, and
demonstrate that the observed changes correlate with the sense of flagellar motor rotation.
The altered bias in flagellar motor rotation brought about by exposure to chemostimuli
causes structural changes in the architecture of the flagellar filaments, and we examine how
these subtle molecular alterations can give rise to substantial changes in the behaviour of
the whole cell.

We also look at how the molecular components of the chemotaxis and motility apparatus
of the cell were discovered, and at the techniques that have been used to piece together
the complex signal transduction pathway that is involved in integrating the multiple
chemosensory inputs received by the cell at any given time into a single output. This signal
transduction pathway involves multiple protein components, transient protein-protein
interactions, phospho-transfer events and other chemical modifications, and its
workings are now beginning to be understood at the atomic level. 12
We look at how the signalling
pathway is assembled, how it
works, and how its output
influences the rotational bias
of the flagellar motor (and
therefore, ultimately, the
swimming behaviour of the
cell). Finally, we look at what
is known about the flagellar
motor itself - the world’s
smallest multi-speed motor,
incorporating both forward
and reverse gears. The
ingenious methods that have
been developed to study this
remarkable device are
discussed, including some video footage of the motor in action. Moreover, the study of
chemotaxis and motility is not simply an esoteric branch of microbiology. With the recent
completion of many eukaryotic genome sequences (including the human genome), it has
become clear that homologues of the chemotaxis proteins are widespread in “higher”
organisms, so these findings are likely to yield valuable insights into the function of many
other organisms.

(ii) Bacterial Secretion Systems

Protein secretion mechanisms are of fundamental importance in bacteria. Prokaryotes are

highly tractable model systems for analysis of the basic principles of protein targeting and
the ability to manipulate such targeting can be exploited in some biotechnological
processes. Furthermore, the ability to actively secrete and regulate the production of
structurally diverse proteins involved in bacterial virulence is a key aspect of pathogenesis
in plant and animal diseases. The lectures summarise the main protein secretion systems in
Gram-negative bacteria, with examples taken from pathogens of animals and plants.
Evolutionary connections between secretory machines is highlighted.

The general nature of bacterial cell surfaces is discussed and the exploitation of prokaryotic
surface molecules that are parasitized as “receptors” by bacterial viruses (bacteriophages)
is highlighted.

In the lab classes associated with these lectures, students conduct experiments on protein
targeting using bacterial mutants generated via transposon insertions that can generate
protein fusions. In addition, global gene regulation and intercellular chemical signalling
(quorum sensing) in a bacterium that makes antibiotics are both addressed.

13
 (iii) Molecular Biology of Protozoa

Protozoa encompass over 60,000 species of eukaryote

including many that are highly divergent from animals,
there is more evolutionary diversity within the protozoa
than between green plants, metazoa and fungi. The best-
studied protozoans are parasites that cause diverse
chronic diseases, such long-term infections provide a
model for studying the complex molecular interactions
between pathogen and host.

Protozoa have evolved a number of novel strategies for

overcoming host resistance to infection and, in this con-
text, lectures will address the unusual strategies for regu-
lation of gene expression, especially of the Variable Sur-
face Glycoproteins (VSGs) in trypanosomes. Such studies
of parasitic protozoa have provided unique insights into
our understanding of basic molecular processes, for ex-
ample, the structure and biosynthesis of GPI anchors in
Trypanosome VSGs have divergent the context of cell surface architecture.
primary, but conserved tertiary,
structures to function in antigenic
variation and as a protective coat on
the external surface of the plasma
membrane.

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Practicals &
Examinations
Practicals

The practical classrooms are in the basement of the Hopkins Building, accessed from the
Downing Site car park, via steps at the north-east corner of the building between Genetics
and Biochemistry (see map on Page 5).

In most weeks, experimental work is scheduled for one day, which involves informal classes
of about 20 students working in pairs. Practical classes provide a unique opportunity for
you to experience at first hand the techniques and experimental strategies of modern
biochemical and molecular biological research, and give you another chance to consolidate
and expand the lecture material. Our aim is to provide interesting practicals that work and
are closely integrated with the lecture course. The senior demonstrator is often the course
lecturer as well, so the practicals are also a good opportunity for you to discuss with your
lecturers and other demonstrators (who are usually post-docs or research students
working on a relevant problem) interesting aspects of the course or any questions that may
have arisen in the lectures. In each of the Michaelmas and Lent Terms one practical class
takes the form of a “Journal Club” in which students read, analyse and discuss a particular
research paper. There is also an interactive session on Experimental Design in the Lent
Term.

Topics covered include PCR, cloning, in vitro protein synthesis, biochemical analysis of
protein-DNA interactions, protein engineering, investigation of subcellular enzyme
localisation, metabolic control analysis, signal transduction, protein targeting, bacterial gene
regulation, and hands-on computer analysis of DNA and protein sequences with
interrogation of databases. Methods you will use include purification of macromolecules,
gel electrophoresis, chromatography, use of computers in molecular biology, cell
fractionation, micro-scale handling of biological materials and spectrophotometric,
electrode, polarographic and enzymatic assays.

Examinations

The course is examined through two written papers dealing with the lecture material and
one data handling paper based on the content of the practical course. Past exam papers can
be obtained from Moodle.

15
Timetables
Last year’s timetable as an example of the course this year:

NST PART IB BIOCHEMISTRY & MOLECULAR BIOLOGY

LECTURE TIMETABLE 2017-18
Course Organiser: Dr A D J Scadden ([email protected])

MICHAELMAS TERM Genes and proteins; macromolecules in action

First Lecture of the Term is on Friday, October 6; Last Lecture on Friday, December 1
Date No. Title Lecturer

Oct 6 5 Introduction to the course (in lecture 1) Dr A D J Scadden

Oct 6, 9, 11, 13, 15 5 Gene cloning and manipulation Dr A D J Scadden

Nucleic acid structure, protein-nucleic

Oct 18, 20, 22, 25, 27 5 Prof C W J Smith
acid interactions and transcription
Post transcriptional control of gene
Oct 30, Nov 1, 3, 6, 8, 5 Dr J Mata
expression

Nov 10, 13, 15, 17, 20 5 Protein structure, function and evolution Dr M Hyvonen

Nov 22, 24, 27, 29, Dec

5 Enzyme catalysis and protein engineering Prof F Hollfelder
1

LENT TERM Energy transduction, cell signalling and cell proliferation

First Lecture on Wednesday, January 17; Last Lecture on Friday, March 16
Date No. Title Lecturer

Energy transduction in bacteria,

Jan 17, 19, 22, 24, 26, 29 6 Prof C J Howe
mitochondria and chloroplasts

Jan 31, Feb 2, 5, 7, 9, 12 6 Control of metabolism Prof K M Brindle

Feb 14, 16, 19, 21, 23, Transmembrane signalling: molecules and
6 Dr D Owen
26 mechanisms

Feb 28, Mar 2, 5, 7 4 Control of eukaryotic cell growth Prof D M Carrington

Oncogenes, tumour suppressor genes and Prof G I Evan &

Mar 9, 12, 14, 16 4
cancer Dr T D Littlewood

16
 EASTER TERM Biochemistry of Microorganisms
First Lecture on Wednesday, April 25; Last Lecture on Monday, May 14
Date No. Title Lecturer

Apr 25, 27, 30 3 Bacterial chemotaxis Dr M Welch

May 2, 4 2 Bacterial signalling and secretion systems Prof G P C Salmond

May 7, 9, 11, 14 4 Molecular biology of protozoa Prof D M Carrington

PRACTICAL TIMETABLE 2017-18

MICHAELMAS TERM 2017

Dates Practical Senior
Demonstrator
Week 1 Safety. (1) Cloning of Oct1 POU domain gene into
Dr A D J Scadden
Oct 5 -11 E. coli plasmid. Restriction mapping of plasmid.

Week 2 (2) Expression of POU domain in E. coli. Melting

Prof B Luisi
Oct 12 -18 properties of DNA.

Week 3 Prof N Gay &

(3) Purification of POU domain
Oct 19 - 25

Week 4
(4) Electrophoresis mobility shift assay Dr N M Standart
Oct 26 - Nov 1

Week 5 (5) Using online databases as tools

Dr A D J Scadden
Nov 2 - 8 Venue: Craik Marshall Building 1.30

Week 6 (6) Discussion in lab of (1, 2, 3, 4) 11.00 a.m. Dr D Owen

Nov 9 - 15 (7) Journal Club (2.00) Venue: see Moodle Staff: Dr M Welch
Week 7 (8) Protein structure by molecular graphics
Dr R W Broadhurst
Nov 16 - 22 Venue: Craik Marshall Building 1.30
(9) Reactivity and enzyme catalysis.
Week 8 Prof F Hollfelder
Venue: Teaching rooms 1 and 2
Nov 23– 29
See Moodle

17
 LENT TERM 2018
Week 1
(10) Subcellular fractionation Dr M de la Roche
Jan 18 - 23

Week 2
(11) Kinetic analysis of catalysis by chymotrypsin Dr D Nietlispach
Jan 25 - 31
Week 3
(12) Mitochondrial oxidative phosphorylation Prof G Brown
Feb 1 - 7
(13) Experimental design 11.00-1.00 Venue: see
Week 4 Moodle Staff: Prof D M Carrington
Feb 8 - 14 Prof J Griffin
(14) Metabolic Control in silico 2.00-4.30
Venue: Craik Marshall Building
Week 5 (15) Cell signalling (1): Tyrosine phosphorylation in
Dr A Git/Dr D Owen
Feb 15 - 21 platelets

Week 6 (15) Cell signalling (1): Tyrosine phosphorylation Dr A Git/Dr D Owen

Feb 22 - 28 continued and discussion
Week 7 (16) Cell signalling (2): Thromboxane production Dr M Hyvonen
Mar 1 - 7 by platelets
(16) Cell signalling (2): Thromboxane produc- Dr M Hyvonen
Week 8 tion by platelets: data analysis & discussion
Mar 8– 14 (11.00)
Staff: Dr M Welch
(17) Journal Club (2.00) Venue: see Moodle
EASTER TERM 2018

Week 1
(18) Microbial Biochemistry Prof G P C Salmond
Apr 26 - May 2

Week 2
(18) Microbial Biochemistry Prof G P C Salmond
May 3 - May 9
Notes
Part IB BMB Brochure 2018-2019

Department of Biochemistry

Tennis Court Road

Cambridge CB2 1QW

Tel: 01223 (3)33600