MD1A2-30 Atoms and Molecules
MD1A2-12/MD1A3-12 - Integrated Science Atoms and Molecules
The module aims to equip students with the conceptual, theoretical and computational skills required for the analysis and engineering of atomic and molecular systems, with an emphasis on biomolecules. Students will learn to solve scientific problems and perform lab practicals in this area by integrating concepts and approaches from different scientific disciplines, including biology, physics, chemistry and computing, with the underlying mathematics serving as a common language.
This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.
Block 3 Chemistry of life
Block 3 is about the molecules of life. We'll look at the physics that holds them together, at the chemistry by which they react in watery solution and at their structures, motions and reactivities. In the lab, we will engineer artificial cytoplasm in different versions, and quantify how good a job each of these viscous solutions does in supporting life-like reactions of different types.
- Hierarchical structure of biological molecules
- Role of water in biology
- Rules governing the motions of atoms and molecules in solution
- Reaction kinetics
- Operating the eduWOSM microscope
- Running experiments in lifelike solutions
- Obtaining the progress curves of reactions
- Analysing data and writing an accurate and compelling paper
Block 4 Self-organisation
Block 4 is about self-organisation. We will discuss a very important phenomenon for all living matter: how to generate large scale and defined structures out of a bunch of individual proteins. This includes the polymerisation of proteins into larger units as well as the self-organisation of such units into larger structures. As an example, we will study actin and myosin, two key components of the cell cytoskeleton, in the classroom as well as in the lab.
- Principles of self-organisation and biological examples
- Newton mechanics of biological polymers
- Molecular motors
- Active mechanics and self-organisation in the cell cortex
- Basics of handling and fluorescent labelling of proteins.
- How to generate actin – myosin networks in vitro.
- Imaging and quantification of actin filament dynamics.
B5 Cell division
How does one cell become two?
We will explore how cell division works and how it diverges across the tree of life and compare the mitotic and meiotic versions. Because this is a mechanical process we will be looking at the forces and physical processes involved. We will also look at how human life begins and the diseases associated with chromosome mis-segregation.
Lec1 | Cell division and checkpoints
Lec2 | Spindle mechanics
Lec3 | Evolutionary divergence
Lec4 | Meiosis
Lec5 | Molecular genetics
Lec6 | Sexual reproduction
Lec7 | Write-up
Lec8 | Write-up
Lab1 | Experimental design and preparation
Lab2 | Immunofluorescence
Lab3 | Microscopy (WOSM)
Lab4 | Image analysis & live cell imaging
Lab5 | Data analysis & live cell imaging
Lab6 | Simulations
Lab7 | Write up
Lab8 | Write up
By the end of the module, students should be able to:
- Demonstrate the ability to apply creative analytical thinking in order to frame incisive, tractable scientific questions, especially about the structures, functions and mechanisms of the atoms and molecules of living systems
- Demonstrate a grasp of physical law as it applies to the structures, reactivities and behaviours of atoms and molecules, especially biomolecules
- Use mathematical approaches to solve problems relating to biomolecular structures, functions, and reactivities.
- Explain the organisation of biomolecules.
- Describe the mechanisms by which biomolecules self-organise in cells
- Demonstrate the hands-on practical skills required to perform experimental tests of tractable scientific questions, especially about the structures, functions and reactions of the molecular building blocks of living systems.
- Demonstrate the ability to accurately record experimental procedures and results in appropriate detail.
- Use computational data analysis techniques and statistical approaches to analyse data
- Access and use the scientific literature effectively
- Interpret and explain experimental data relating to the chemistry of life and the self-organisation of biological molecules.
- Demonstrate the writing skills required to report experimental results in the format of a scientific paper, including the ability to write an abstract, to write a short critical review of the relevant literature, present results in an appropriate format and detail with appropriate statistics, discuss the results and frame a clear conclusion.
- Describe and discuss quantitatively the mechanisms by which chromosomes encode and transmit genetic information
- Describe and discuss quantitatively how cells replicate, recombine and segregate their genes
- Operate safely within a laboratory environment.
Indicative reading list
Molecular cell biology Molecular Biology of the Cell, 2014. Bruce Alberts et al ISBN: 9780815344322
Cell Biology by the Numbers Milo and Phillips, Garland Science (2015), ISBN-10 : 0815345372
Physical Biology of the Cell, Phillips et al, Garland Science (2013), ISBN-10 : 9780815344506
Students will learn to solve scientific problems about atoms and molecules by integrating concepts and approaches from different scientific disciplines, including biology, physics, chemistry and computing, with the underlying mathematics serving as a common language.
Subject specific skills
The ability to apply creative analytical thinking in order to frame incisive, tractable scientific questions, especially about the structures, functions and mechanisms of the atoms and molecules of living systems
A grasp of physical law as it applies to the structures, reactivities and behaviours of atoms and molecules, especially biomolecules
Mathematical skills to solve problems relating to biomolecular structures, functions and reactivities
The ability to explain the organisation of biomolecules
The ability to describe the mechanisms by which biomolecules self-organise in cells
The ability to perform experimental tests of tractable scientific questions, especially about the structures, functions and reactions of the molecular building blocks of living systems, using light microscopy
The hands-on practical skills required to perform experiments
The ability to interpret and explain experimental data relating to the chemistry of life and the self-organisation of biological molecules.
Usage of mathematical and computational approaches to solve problems
A grasp of safety rules and an ability to work safely in the laboratory environment
The skills to accurately record experimental procedures and results, in appropriate detail
The skills to use computational and statistical approaches to analyse data
The skills to access and use the scientific literature effectively
The writing skills required to report experimental results in the format of a scientific paper
|Lectures||18 sessions of 1 hour (6%)|
|Tutorials||18 sessions of 1 hour (6%)||6 sessions of 2 hours|
|Supervised practical classes||18 sessions of 3 hours (18%)|
|Private study||98 hours (33%)|
|Assessment||112 hours (37%)|
Private study description
Self-directed study and writing lab reports
No further costs have been identified for this module.
You do not need to pass all assessment components to pass the module.
Assessment group D2
|2 x laboratory reports||50%||40 hours|
|Assessment of laboratory skills||20%||54 hours|
Assessing the proficiency in laboratory techniques, observing good laboratory practice,
|Written Examinations||30%||18 hours|
Feedback on assessment
Laboratory reports - submission annotated and returned, general comments/'what was good'/'what could be improved' alongside marking rubric.
Assessment of laboratory skills - at the end of each two-week laboratory session, block leads will provide comments on proficiency, Good Laboratory Practice (GLP) and engagement/group contribution that arise. Due to the volume of feedback, stock phrases will be provided to the block leads, which may be amended or expanded at the lead's discretion. Further verbal feedback will be given to students on request.
In terms of practicalities, following GLP, executing the laboratory protocol, attaining proficiency in techniques taught and engaging/contributing to group activities (where required) will be based at 62 on the 20-point University scale. Exceptional attainment/contributions will grade higher, whereas disengagement, not observing GLP, and an unwillingness to acquire lab proficiency will score lower. Marks will not take into account whether a student achieved a desired experimental result or not. The block lead will work with the laboratory technician in observing and recording these across the cohort. Feedback will be provided biweekly at the end of each block.
This module is Core for:
- Year 1 of UMDA-CF10 Undergraduate Integrated Natural Sciences (MSci)