Studying at York
Genes to Proteins - CHE00021I
Module summary
This first half of this module covers Gene Regulation and Genetic Engineering with a strong Biological Chemistry perspective. This leads into the second half of the module which concerns Protein Architecture and Action including how proteins are assembled and/or modified to carry out their functions.
Module will run
| Occurrence | Teaching period |
|---|---|
| A | Semester 2 2024-25 |
Module aims
This module builds on core biological chemistry material taught in Year 2 of the chemistry degree. The first half of the course (for Chemists only) provides a detailed overview of molecular biology – a field which over the last 50 years has transformed biological chemistry. After a brief introduction to genes and genomes, the factors regulating gene expression in bacteria and higher organisms will be explored. The course will consider how genes are translated into proteins and how DNA is replicated with high fidelity. With this foundation the course will go on to describe how genes can be isolated and precisely manipulated – leading to the field of genetic engineering, which is underpinning our understanding of protein function. Methods for tailoring enzyme properties using random and rational approaches will be described with examples.
The second half of the module (for both Chemists and Biochemists) explores advanced aspects of protein science – including protein structure and function, determination of structure and protein engineering. Our appreciation of almost all aspects of biochemistry and molecular biology has been enhanced by the elucidation of atomic resolution structures that reveal the underlying chemical mechanisms responsible for biological function. In addition, our ability to exploit this understanding through the use of genetic approaches to engineer proteins, is leading to the generation of improved proteins for therapeutic and biotechnology applications. Students studying this module will be equipped to go on to further studies in biochemistry/molecular biology related fields of study, as well as having valuable insight into the growing biotechnology sector of industry.
Module learning outcomes
Students will be able to
- discuss transcription and translation of genetic information in detail including the way (i) transcription is regulated and (ii) genetic decisions are made.
- discuss the roles of the macromolecular machines RNA polymerase, DNA polymerase and the ribosome and how the information stored within DNA is disseminated.
- discuss and explain how knowledge of gene structure and function can be exploited through genetic engineering methods and design oligonucleotides for PCR, sequencing and mutagenesis.
- apply the engineering of proteins using various techniques – including rational amino acid mutagenesis, random mutagenesis and DNA shuffling experiments and computer aided design - rationalise and predict how modification of proteins can alter their behaviour and properties.
- use examples from a case study based on applications of genetic engineering technology to demonstrate and apply key concepts.
- discuss the basic principles of how protein structures are determined using the methods of X-ray crystallography, electron microscopy or NMR spectroscopy
- design experimental approaches using these techniques to answer questions about structure-function relationships
- integrate results from different techniques to provide a fuller understanding of the structural biology of a target system
- discuss how protein structure relates to protein mechanism and thus to biological function.
- discuss how the relationship between sequence, structure and function can be exploited to model the structure of homologous proteins
- describe the wide range of functions that can be performed by proteins, such as enzymes, signalling proteins, membrane bound transport proteins and structural proteins - rationalise the behaviour of different proteins based on their structural features.
- use case studies to develop and demonstrate their understanding of the key topics.
Module content
This module begins by exploring the factors that regulate gene expression in bacteria leading to a consideration of how knowledge of gene control allows us to understand the molecular basis of decision-making by cells. We will then discuss how knowledge of gene control and protein synthesis can be exploited for the expression of foreign (such as human) genes in genetically modified micro-organisms. The module will go on to describe the products of these genes - proteins, the most versatile of all molecules. After a discussion of the main features of protein structure, the course will cover the determination of 3D structure through diffraction, microscopy and NMR methods. After a brief discussion of the patterns that are emerging in protein structure (and how this can be exploited to predict protein structure), the course continues with detailed examples of proteins in action.
Transcription & Control of Gene Expression: 5 lectures AJW (5) 1×1h unassessed workshop (AJW)
- Key components of transcriptional regulatory circuits - repressors, activators, promoters, operators.
- Transcription termination and attenuation in gene regulation.
- Gene regulatory mechanisms in bacteriophage lambda.
Protein Synthesis and DNA Replication: 4 lectures AJW (4)
- Aminoacyl tRNA Synthetases, tRNA, and the Ribosome.
- Replication Forks, DNA polymerase, and Replication Initiation, ori sequences and DnaA.
Genetic Engineering and Protein Engineering: 7 lectures GJG (7), 1 workshop (AJW)
- Methods and tools of gene cloning and sequencing of DNA.
- Polymerase chain reaction (PCR).
- Recombinant protein production.
- Tailoring enzyme properties using random and rational approaches.
Protein Structure, Diversity, and Fold Prediction. 4 lectures (JA)
- Introduction. Essential features of protein structure. The Protein Data Bank.
- From sequence to structure, and from structure to function. Factors involved in protein folding and assembly.
- Protein evolution. Relations between proteins.
- Use of Artificial Intelligence in protein fold prediction: advantages and limitations.
Protein Crystallography 4 lectures (CH)
- Understand how X-rays interact with biological macromolecules, and the basic principles of X-ray diffraction.
- Appreciate the key experimental steps in structure determination, from growing crystals and collecting diffraction data to solving the structure.
- Using case-studies, explain how crystallography can provide mechanistic insight into the workings of a variety of macromolecular machines - from single enzymes to large multiprotein complexes.
Spectroscopic Approaches to the Study of Proteins 4 lectures MJP
- appreciate the complexity of non-globular and intrinsically disordered proteins and unique features of their structural biology
- understand how biophysical techniques such as circular dichroism, small angle scattering and NMR spectroscopy can be applied to interrogate the structure/function relationships of proteins (and other biomacromolecules) in solution
- appreciate how fundamental parameters in biomolecular NMR spectroscopy such as chemical shift, j-coupling, NOE and relaxation can be used probe the structural biology of proteins
Electron Microscopy 4 lectures (JNB)
- Understand the main principles of electron cryo-microscopy (cryo-EM) as applied to biological problems, such as how biological samples are prepared, how they are imaged within the microscope, and how the data are processed to provide interpretable information.
- Be familiar with three prominent imaging and analysis techniques: single particle analysis, helical reconstruction, and tomography.
- Understand the major benefits and difficulties of cryo-EM and how they can respectively be leveraged and mitigated against.
The Proteins component of the course contains a workshop (KDC and JA) in which Molecular Graphics will be used. It will feature Electron Density Map Fitting and the Structural Basis of Enzyme Action
Indicative assessment
| Task | % of module mark |
|---|---|
| Closed/in-person Exam (Centrally scheduled) | 80 |
| Essay/coursework | 20 |
Special assessment rules
None
Additional assessment information
Workshop and Genetic Engineering exercise. This workshop takes the form of a 1 hour session in which the students work though some examples of oligonucleotide design for DNA cloning, mutagenesis and sequencing. After the workshop, the students have up to a week to complete and hand in answers to a set of similar questions on a related system.
Indicative reassessment
| Task | % of module mark |
|---|---|
| Closed/in-person Exam (Centrally scheduled) | 80 |
| Essay/coursework | 20 |
Module feedback
Students will receive feedback on their performance in the workshop assessments. They will receive verbal feedback on their progress in the formative workshops, which support lectures.
The closed examinations held in the Summer term are marked typically within 4 weeks with mark slips (with per-question break-down) being returned to students and supervisors in week 10 of the Summer Term. Outline answers are made available via the Chemistry VLE siteswhen the students receive their marks, so that they can assess their own detailed progress/achievement. The examiners reports for each question are made available to the students via the Chemistry VLE.
Indicative reading
This is provided by the individual lecturers in the form of suggested textbooks and review articles listed on hand-out material and as citations on slides.