UCC Book of Modules, 2012/2013: Biochemistry

Credit Weighting: 10

Teaching Period(s): Teaching Periods 1 or 2.

No. of Students: Max 50.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 36 x 1hr(s) Lectures; 4 x 4hr(s) Practicals; 12 x 2hr(s) Other (Case Studies).

Module Co-ordinator: Dr John V (Eoin) Fleming, Department of Biochemistry.

Lecturer(s): Dr Maryanne Donovan, Department of Biochemistry; Prof Dmitri Papkovsky, Department of Biochemistry; Dr John V (Eoin) Fleming, Department of Biochemistry.

Module Objective: To lay the foundation for understanding of the chemistry of biomolecules and metabolic pathways of importance and relevance to dentistry both in the spheres of clinical practice and research

Module Content: Molecular logic of life. Introduction to biomolecules. Biochemical processes. Water. Non-covalent bonding. Ph, acids, bases and buffers. Amino acids. Protein structure. Enzyme catalysis. Enzyme kinetics. Lipids: structure and function. Carbohydrates: structure and function. Nucleotides and nucleic acids: structure and function. Overview and strategy of metabolism. Glycolysis. Minor pathways of carbohydrate metabolism. Gluconeogenesis. Glycogen metabolism. Regulation of carbohydrate metabolism. Pentose phosphate pathway. Citric acid cycle. Electron transport chain. Oxidative phosphorylation. Fatty acid metabolism. Ketone bodies. Nitrogen metabolism. Integration metabolism. Relevant case studies.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the structure, chemistry and functional roles of biomolecules, including nucleic acids, lipids, carbohydrates and proteins.
· Understand the chemical properties of water and how this influences biomolecular and cellular function.
· Perform calculations relating to the pH and buffering capacity of biological systems.
· Compare the catalytic mechanisms of different classes of enzymes and be capable of performing simple calculations relating to their activity and inhibition.
· Outline how energy is harvested and used to drive cellular reactions.
· Appreciate the principles and integration of cellular metabolism, with in depth knowledge of metabolic pathways associated with glycolysis, glycogenolysis, gluconeogenesis, the citric acid cycle, oxidative phosphorylation and the synthesis and degradation of fatty acids, amino acids and nucleotides.
· Outline the process of odontogenesis, highlighting the role of eukaryotic organelles and specific cell signalling events and molecules.
· Compare the development and biochemical properties of enamel and dentin in normal and diseased states and describe the specific molecular defects of dental disorders affecting enamel and dentin.

Assessment: Total Marks 200: End of Year Written Examination 120 marks; Continuous Assessment 80 marks (MCQ 60 marks, laboratory 20 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 50%.

End of Year Written Examination Profile: 1 x 3 hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 3 hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing continuous assessment, marks awarded for laboratory practical work are carried forward, failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 10

Teaching Period(s): Teaching Period 2.

No. of Students: Max 60.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 36 x 1hr(s) Lectures; 6 x 1hr(s) Tutorials; 9 x 3hr(s) Practicals; Directed Study (30hrs Directed Study).

Module Co-ordinator: Dr John V (Eoin) Fleming, Department of Biochemistry.

Lecturer(s): Prof Dmitri Papkovsky, Department of Biochemistry; Dr John V (Eoin) Fleming, Department of Biochemistry.

Module Objective: To introduce students to the chemistry of biomolecules and metabolic pathways.

Module Content: Molecular logic of life. Introduction to biomolecules. Biochemical processes. Water. Noncovalent bonding. PH, acid, bases and buffers. Amino acids. Protein structure. Enzyme catalysis. Enzyme kinetics. Lipids: Structure and function. Carbohydrates: structure and function. Nucleotides and nucleic acids: structure and function. Overview and strategy of metabolism. Glycolysis. Minor pathways of carbohydrate metabolism. Gluconeogensis. Glycogen metabolism. Regulation of carbohydrate metabolism. Pentose phosphate pathway. Citric acide cycle. Electron transport chaion. Oxidative phosphorylation. Fatty acid metabolism. Ketone bodies. Nitrogen metabolism. Integration metabolism.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the structure, chemistry and functional roles of biomolecules, including nucleic acids, lipids, carbohydrates and proteins.
· Discuss the chemical properties of water and how this influences biomolecular and cellular function.
· Perform calculations relating to the pH and buffering capacity of biological systems.
· Compare the catalytic mechanisms of different classes of enzymes and be capable of performing simple calculations relating to their activity and inhibition.
· Outline how energy is harvested and used to drive cellular reactions.
· Demonstrate an in depth knowledge of the principles and integration of cellular metabolism, including metabolic pathways associated with glycolysis, glycogenolysis, gluconeogenesis, the citric acid cycle, oxidative phosphorylation and the synthesis and degradation of fatty acids, amino acids and nucleotides.

Assessment: Total Marks 200: End of Year Written Examination 120 marks; Continuous Assessment 80 marks (MCQ examinations 60 marks; Laboratory practical work 20 marks). Oral, if required.

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 50%.

End of Year Written Examination Profile: 1 x 3 hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 3 hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing continuous assessment, marks awarded for laboratory practical work are carried forward, failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 300.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals.

Module Co-ordinator: Prof Thomas Cotter, Department of Biochemistry.

Lecturer(s): Prof Thomas Cotter, Department of Biochemistry.

Module Objective: To introduce students to the chemistry of biomolecules.

Module Content: Steroisomers-The concept of stereoisomers and how such molecules can have different properties despite having the same chemical formula. Examples of pharmaceutical products are used to illustrate concept.
Water and pH-The role of water as a biological constituent of life. The concept of pH and its importance to biological systems. Hydrogen bonding.
Amino acids-An outline of the structure and function of amino acids with a focus on their chemical properties and how they can link together to form proteins.
Protein structure & function -Understanding primary, secondary, tertiary and quaternary protein structure with detailed examples of how such structures are dependent on amino acids sequence.
Enzymes and enzyme kinetics-Introduction to the concept of enzymes and their function including the role of the active site of the enzyme. Introduction to enzyme kinetics. The concept of enzyme inhibition and inhibitors.
Carbohydates and polysaccharides-Monosaccharides structure and function. Formation of simple polysaccharides
Lipids-Structure and function of simple lipids. Role of lipids in biology.
Introduction to Biomolecules. Water ionisation, interaction with biomolecules, pH. Amino acids: structure, function, classification and reactivity. Introduction to proteins. Protein structure: primary, secondary, tertiary and quaternary structures. Lipids: structure and function. Carbohydrates: structure and function.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the basic principles of stereoisomers and their importance in determining the chemical and physical properties of compounds.
· Outline the role of water and pH and describe how hydrogen bonds are formed.
· Discuss the structure and function of amino acids and in particular how they can combine to form proteins.
· Describe the characteristics of the different levels of protein structure and how such characteristics relate to the amino acid sequence.
· Describe what an enzyme is and the basis of its function. The student should also be able to understand basic enzyme kinetics and enzyme inhibition patterns of drugs.
· Discuss the structure of simple monosaccharides and the importance of chiral carbons.
· Describe the formation of simple polysaccharides.
· Describe simple and more complex lipids and some of their roles in biology.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing continuous assessment, marks awarded for laboratory practical work are carried forward; Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 300.

Pre-requisite(s): BC2001 or BL1002, BL1004, CM1003

Co-requisite(s): None if BC2001 has been taken, otherwise CM2101, CM2003, CM2007

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals ((including problem based and self directed learning)).

Module Co-ordinator: Dr Cora O'Neill, Department of Biochemistry.

Lecturer(s): Dr Cora O'Neill, Department of Biochemistry.

Module Objective: To provide students with an introduction to metabolic pathways.

Module Content: General introduction to types of metabolic pathways and common strategies used in energy metabolism, bioenergetics. Overview of carbohydrate and lipid metabolism. Glycolysis, gluconeogenesis, glycogen metabolism and the regulation of these pathways, discussing hormonal, covalent and allosteric control of enzymes. The citric acid cycle and its central role in metabolism. Oxidative phosphorylation, electron transfer and ATP synthesis. Lipid metabolism. The mobilisation of fats. Fatty acid catabolism. Ketone body formation. Fatty acid biosynthesis. Regulation of fatty acid and lipid metabolism. Integration and overall control of metabolism.

Learning Outcomes: On successful completion of this module, students should be able to:
· Outline how energy is harvested and used to drive cellular reactions
· Describe and illustrate the metabolic pathways of; glycolysis, glycogenolysis, gluconeogenesis, the citric acid cycle, oxidative phosphorylation, the synthesis and degradation of fatty acids and the synthesis of ketone bodies
· Describe the interrelationships between the various metabolic pathways and outline their overall regulation
· Proficiently perform laboratory experiments and record, analyse and evaluate data obtained.

Assessment: Total Marks 100: End of Year Written Examination 60 marks (Written and MCQ); Continuous Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 50.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 20 x 1hr(s) Lectures; 4 x 4hr(s) Practicals; 4 x 1hr(s) Tutorials; 2 x 3hr(s) Other (Dental Case Studies).

Module Co-ordinator: Dr Sinead Kerins, Department of Biochemistry.

Lecturer(s): Dr Sinead Kerins, Department of Biochemistry.

Module Objective: To provide an introduction to Molecular Biology outlining the molecular basis for disease, of importance and relevance to dentistry both in the spheres of clinical practice and research.

Module Content: Structure of Nucleic Acids, DNA, RNA. Prokaryotic and eukaryotic gene structure. DNA replication, DNA repair. Transcription in prokaryotes and eukaryotes and relevant drugs. Gene expression in prokaryotes and eukaryotes. The genetic code. Protein synthesis in prokaryotes and eukaryotes and relevant drugs. Recombinant DNA technology: restriction endonucleases, vectors, ligation, transformation, Polymerase Chain Reaction and applications. Recombinant products in medicine. DNA repair and detection of mutations in DNA. HIV life cycle and relevant drugs. Relevant case studies.

Learning Outcomes: On successful completion of this module, students should be able to:
· Compare and contrast the structure of the nucleic acids, DNA and RNA and prokaryotic and eukaryotic genes.
· Describe the molecular mechanisms of replication, transcription, translation and the molecular targeting of drugs.
· Describe the different types of post-transcriptional and post-translational modifications.
· Outline how the expression of genes can be regulated and how this information can be used to regulate over-expression of recombinant proteins.
· Describe the different genetic engineering techniques and their applications.
· Describe the causes and nature of DNA mutations, the pathways used to repair DNA damage, and the consequences of failing to repair DNA damage.
· Explain the life cycle of the human immunodeficiency virus (HIV) and evaluate how control of gene expression has led to advances in the treatment of AIDS.
· Demonstrate competence in performing Molecular Biology and basic Microbiology techniques and understanding their basis and application.
· Design, implement and evaluate scientific investigations and assess, interpret and understand data and its meaning.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (MCQ 30 marks; Laboratory Work 10 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 50%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing continuous assessment, marks awarded for laboratory practical work are carried forward; Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 60.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 20 x 1hr(s) Lectures; 4 x 1hr(s) Tutorials; 8 x 3hr(s) Practicals; Directed Study (Directed study 10hrs).

Module Co-ordinator: Dr Sinead Kerins, Department of Biochemistry.

Lecturer(s): Dr Sinead Kerins, Department of Biochemistry.

Module Objective: To provide an introduction to Molecular Biology outlining the molecular basis for disease, and molecular targeting of drugs.

Module Content: Structure of Nucleic Acids, DNA, RNA. Prokaryotic and eukaryotic gene structure. DNA replication, DNA repair. Transcription in prokaryotes and eukaryotes and relevant drugs. Gene expression in prokaryotes and eukaryotes. The genetic code. Protein synthesis in prokaryotes and eukaryotes and relevant drugs. Recombinant DNA technology: restriction endonucleases, vectors, ligation, transformation, Polymerase Chain Reaction and applications. Recombinant products in medicine. DNA repair and detection of mutations in DNA. HIV life cycle and relevant drugs.

Learning Outcomes: On successful completion of this module, students should be able to:
· Compare and contrast the structure of the nucleic acids, DNA and RNA and prokaryotic and eukaryotic genes.
· Describe the molecular mechanisms of replication, transcription, translation and the molecular targeting of drugs.
· Describe the different types of post-transcriptional and post-translational modifications.
· Outline how the expression of genes can be regulated and how this information can be used to regulate over-expression of recombinant proteins.
· Describe the different genetic engineering techniques and their applications.
· Describe the causes and nature of DNA mutations, the pathways used to repair DNA damage, and the consequences of failing to repair DNA damage.
· Explain the life cycle of the human immunodeficiency virus (HIV) and evaluate how control of gene expression has led to advances in the treatment of AIDS.
· Demonstrate competence in performing Molecular Biology and basic Microbiology techniques and understanding their basis and application.
· Design, implement and evaluate scientific investigations and assess, interpret and understand data and its meaning.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks ( MCQ 30 marks; Laboratory Work 10 marks). Oral, if required.

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 50%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing continuous assessment, marks awarded for laboratory practical work are carried forward; Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 150.

Pre-requisite(s): BC2001

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals.

Module Co-ordinator: Prof David Sheehan, Department of Biochemistry.

Lecturer(s): Prof David Sheehan, Department of Biochemistry.

Module Objective: Structural studies of proteins and nucleic acids.

Module Content: Amino acids, peptides and proteins-Chemistry, structure and clasification of amino acids, The peptide bond, Peptide structure and bioactive peptides, The protein structural hierarchy with examples. Isolation of informational biomacromolecules- Precipitation of proteins, Chromatography of proteins including mode (ion exchange, size exclusion and affinity) and resolution (HPLC and FPLC), Protein purification tables, Alkali-phenol lysis for preparation of plasmid DNA, Isolation of mRNA by oligo dT-cellulose. Sequencing of informational biomacromolecules-Direct sequencing by Edman degradation, Sequencing of proteins by mass spectrometry, Sanger sequencing of DNA, Sequence databases. Solid Phase methods- Merrifield peptide synthesis, Synthesis of oligonulceotides. Electrophoresis-Native electrophoresis, SDS PAGE, Isoelectric focusing, 2D SDS PAGE, Blotting methods, Electroelution. Enzymes Purification of organelles, membranes and membrane proteins from cells-Basis of catalysis, Michaelis-Menten equation, Kinetic parameters, Enzyme inhibition. Allosterism and metabolic control

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the key structural features of the main informational biomacromolecules
· Outline how proteins and DNA plasmids are routinely purified
· Discuss the physical and chemical basis of chromatography
· Describe how important sequence is to function
· Appreciate the origin and use of sequence data
· Describe the basis and application of electrophoresis methods in Biochemistry.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; Data Handling test 10 marks; MCQ 20 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ and Data Handling examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 150.

Pre-requisite(s): BC2001; BC2002

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 2 x 2hr(s) Tutorials.

Module Co-ordinator: Dr Kenneth Nally, Department of Biochemistry.

Lecturer(s): Dr Kenneth Nally, Department of Biochemistry.

Module Objective: To study the metabolism of Nitrogen-containing compounds and the metabolism of complex lipids.

Module Content: Logic of metabolism and strategies for metabolic control. Overview of Nitrogen metabolism, metabolic fates of amino groups. Role of glutamate. Elimination of ammonia. Pathways of amino acid synthesis and degradation. Metabolism of biogenic amines. Review of structure of principal nucleotides and their functions. Metabolism of purines and pyrimidines: Synthesis and catabolism. Salvage pathways. Integration of hormonal regulation of mammalian metabolism. Biosynthesis of membrane lipids and related substances. Cholesterol biosynthesis and metabolism. Metabolism of lipoproteins, bile acids and steroid hormone biosynthesis.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe and illustrate the metabolic pathways of purine, pyrimidine and amino acid metabolism
· Describe and illustrate the enzymology of nitrogen fixation
· Describe and illustrate the Biochemistry of the polypeptide and steroid hormones
· Illustrate the structure of principal nucleotides and their functions
· Discuss chemotherapeutic agents that target enzymes in the nucleotide biosynthetic pathways
· Describe the biosynthesis of principal membrane lipids
· Outline cholesterol, lipoprotein and bile acid metabolism
· Describe the interrelationship and regulation of the various metabolic pathways.

Assessment: Total Marks 100: End of Year Written Examination 70 marks; Continuous Assessment 30 marks (MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated.

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 100.

Pre-requisite(s): BC2001; BC2002

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 2 x 4hr(s) Practicals; 1 x 2hr(s) Tutorials.

Module Co-ordinator: Dr Paul Young, Department of Biochemistry.

Lecturer(s): Dr Paul Young, Department of Biochemistry.

Module Objective: To overview basic aspects of cell biology and the biochemistry of biological membranes.

Module Content: Introduction to cell biology
The structure of eukaryotic cells
The structure and functions of organelles
Importance of biomembranes from an evolutionary perspective
Organisation of membranes in eukaryotic cells
Membranes and membrane proteins
Structure, lipid composition and properties of biological membranes
Classification: Integral, lipid anchored, peripheral membrane proteins
Structural features of integral membrane proteins
Transport of ions and small molecules across membranes
Membrane permeability, electrical and chemical gradients across membranes
Membrane Transport Proteins: ATP powered pumps, Ion channels, Transporters
The cellular cytoskeleton
Microfilaments, Microtubules and intermediate filaments
Structure and Properties of different cytoskeletal elements
The cytoskeleton in specialised cell types
Cellular Logistics: Targeting proteins to membranes and organelles
Targeting proteins to the endoplasmic reticulum
Transport of proteins across the nuclear envelope
Targeting of proteins to other organelles
Vesicular Trafficking
The secretory pathway and endocytic pathways
Protein quality control:
Protein ubiquitintion and degradation
Purification of organelles, membranes and membrane proteins from cells
Subcellular fractionation of cells by differential centrifugation
Purification of membrane proteins

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the organization and functions of membranes and organelles in eukaryotic cells
· Distinguish between different classes of membrane-associated proteins.
· Outline the general structural features of integral membrane proteins.
· Review the major classes of proteins involved in transport of small molecules across membranes.
· Discuss the role of the different cytoskeletal elements in a variety of cell types.
· Apply bioinformatics tools to identify targeting motifs in a protein.
· Compare the mechanisms by which newly synthesized proteins are targeted to the major organelles in eukaryotic cells.
· Illustrate how proteins are trafficked within the secretory and endocytic pathways.
· Explain and apply the principles of subcellular fractionation.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 150.

Pre-requisite(s): BC2001; BC2002

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals.

Module Co-ordinator: Prof Mary McCaffrey, Department of Biochemistry.

Lecturer(s): Prof Mary McCaffrey, Department of Biochemistry.

Module Objective: To overview cell signalling pathways.

Module Content: Hormone/Neurotransmitter classification. Steroids and tyroxine. Polypeptides: growth hormones, insulin, glucagon. Amino acid-derived, classical neurotransmitters. Eicosanoids. Cell/Cell signalling. Diversity of receptor types. Classification and biochemistry of cell surface receptors. Hierarchical nature of hormonal control. Signalling in response to steroids/thyroxine, intracellular receptor/ transcriptional regulation. Signalling via G-proteins and tyrosine kinases. Second Messengers: cAMP, IP3/DAG: synthesis, generation in cell. Protein Kinase C. Heterotrimeric G-protein role in signal transduction/sensory perception in various cell types. Signalling via ligand gated ion channels. Small GTPases. Signal transduction and oncogenesis.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the major mechanisms of cell/cell signaling in humans, including the hierarchical nature of the neuroendocrine system.
· Describe the mechanism of action of the major functional groups of signaling molecules, including polypeptides (growth hormones, insulin, glucagon), steroids, thyroxine, retinoic acid, amino acid derived signaling molecules, classical neurotransmitters & eicosanoids.
· Outline the major receptor types, their localization and function in response to the signaling molecules indicated in the point above.
· Discuss the molecular events which occur within the cell in response to the major groups of signaling molecules and the overall physiological outcomes.
· Discuss signal transduction events occurring in sensory perception, such as in vision, smell & taste.
· Describe the structure and function of GAP junctions.
· Outline the relationship between growth signal transduction and cancer.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 50.

Pre-requisite(s): BC2001; BC2002

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 2 x 3hr(s) Practicals; 20 x 1hr(s) Directed Study.

Module Co-ordinator: Prof Thomas Cotter, Department of Biochemistry.

Lecturer(s): Prof Thomas Cotter, Department of Biochemistry.

Module Objective: To overview the biochemistry of the immune system.

Module Content: Historical development of immunology, Innate and acquired immunity. Cells and organs of the immune system. Antibody structure & function MHC, Antibody based assays and methods, Antigen processing and presentation, Antigen receptors and signaling, Generation of antibody diversity. Immunologic tolerance. Transplantation immunology. Autoimmunity.

Learning Outcomes: On successful completion of this module, students should be able to:
· Illustrate the development of the field of immunology as a science.
· Describe development and function of the innate and adaptive immune systems.
· Describe the tissues and cells of the immune system and how they are integrated.
· Describe the structure and function of antibodies and how they interact with antigens.
· Outline the uses of antibodies in diagnostic and analytical assays.
· Explain the role and function of the MHC and how antigens are processed and presented by cells of the immune system.
· Explain how a diverse range of antibody molecules can be produced.
· Describe the basis of immunological tolerance, the role of the immune system in organ transplantation and autoimmune diseases.
· Demonstrate competence in performing and understanding antibody based staining and assay techniques.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks, MCQ examination 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.Practical Work and Passed MCQ examination are carried forward to the Autumn).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Min 10, Max 150.

Pre-requisite(s): ML2001 or FM1001

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 2 x 3hr(s) Practicals; 12hr(s) Directed Study.

Module Co-ordinator: Prof Thomas McCarthy, Department of Biochemistry.

Lecturer(s): Prof Thomas McCarthy, Department of Biochemistry.

Module Objective: To develop the student's knowledge and understanding of gene expression, gene regulation, recombination and recombinant DNA technology.

Module Content: DNA structure and function; DNA supercoiling; chromatin and higher order structure and organisation in eukaryotic DNA; RNA transcription in prokaryotes and eukaryotes; eukaryotic gene regulation with respect to chromatin; gene promoters; prokaryotic and eukaryotic gene regulatory mechanisms at transcriptional and translational level; RNA splicing and alternative splicing; molecular mechanisms of recombination; DNA amplification and DNA analysis technology; recombinant DNA technology and its applications including protein over expression.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the structure and function of DNA, DNA supercoiling and the molecular mechanisms of its enzymatic regulation.
· Describe chromatin and higher order structure and organisation in eukaryotic DNA and demonstrate an understanding of chromatin in gene expression and regulation.
· Outline the main principles of gene regulation in prokaryotes and eukaryotes.
· Describe using examples a range of prokaryotic and eukaryotic gene regulatory mechanisms.
· Describe the molecular mechanisms of RNA splicing and demonstrate an understanding of alternative splicing.
· Describe the molecular mechanisms of recombination and demonstrate an understanding of the role of recombination in prokaryotes and eukaryotes.
· Describe the process of DNA amplification and DNA analysis technology relevant to gene regulation analysis.
· Describe recombinant DNA technology and its applications including protein over expression.
· Demonstrate competence in performing Molecular Biology techniques and understanding their basis and application.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks ((Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Attendance and satisfactory completion of classes.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 150.

Pre-requisite(s): BC3004

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 2 x 3hr(s) Practicals.

Module Co-ordinator: Dr Thomas F Moore, Department of Biochemistry.

Lecturer(s): Dr Thomas F Moore, Department of Biochemistry.

Module Objective: To achieve an overview of the principles of medical genetics and human molecular genetics.

Module Content: Meiosis, homologous recombination, resolution of Holiday structures, illegitimate recombination. Genetic disease patterns, autosomal dominant, recessive, X linked, penetrance, polygenic, genetic imprinting. Population genetics, polymorphism/genetic variation, Hardy-Weinberg equilibrium, factors affecting allele frequencies. Quantitative traits, twin studies,heritability. Cytogenetics analysis, chromosome abnormalities and related studies. Molecular markers, RFLPs, VNTRs and micro-satellites, DNA fingerprinting. Basis of genetic mapping and positional cloning. Genetic association studies. Cancer genetics. Production of mouse mutants. Human gene therapy.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the key molecular and cellular processes that occur during meiosis, and explain how Holliday junctions determine the types of recombinant DNA molecules that are produced.
· Distinguish between different classes of autosomal and sex-linked inheritance patterns, and list the different types of mutations that contribute to human disease.
· Review the history and development of the different types of molecular markers used in genetic analysis.
· Define and discuss key concepts such as quantitative traits, heritability, twin studies, genetic mapping.
· Outline the factors affecting allele frequencies in populations.
· Discuss the underlying theory and practical pursuit of genetic association studies.
· Outline the molecular basis of selected human genetic diseases including cancer.
· Outline general approaches to the use of model organisms in the study of human disease.
· Discuss the current status of the various options for pursuing human gene therapy.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 100.

Pre-requisite(s): BC2001; BC2002

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals ((including problem based and self directed learning)).

Module Co-ordinator: Dr Cora O'Neill, Department of Biochemistry.

Lecturer(s): Dr Cora O'Neill, Department of Biochemistry.

Module Objective: To overview the biochemistry of neurotransmission in the central nervous system.

Module Content: Structure and function of neurons and glia. Basic anatomy of the central nervous system (CNS). Information transfer in the CNS. The molecular basis of the action potential, neurotransmission and synaptic function. The molecular basis of neurotransmitter release, examination of the key proteins involved in this process and current research. Neurotransmitter classification and description of the major neurotransmitters, their localisation, function., receptors and transporters. Neurotransmitter transporters: structure and function. Neurotransmitter receptors : structure and function. Detailed consideration of neurotransmission by acetylcholine, serotonin, glutamate and GABA. Key defects in neurotransmitter signalling that lead to brain malfunction for example in stroke, Parkinson's disease, depression, and psychiatric disorders. Throughout the course emphasis is based on the key techniques in molecular neuroscience that are used to understand the molecular basis of neurotransmission and brain function

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe and illustrate the structure and function of the key brain cell types and the major neuroanatomical regions of the central nervous system.
· Explain how information is transferred by neurons and the molecular basis of the action potential, neurotransmission and synaptic function.
· Describe the molecular basis of neurotransmitter release and the function of the key proteins involved in this process.
· Outline and illustrate the structure and function and mechanisms action of neurotransmitter transporters and neurotransmitter receptors.
· Review the major neurotransmitter types, their receptors,transporters, function and localisation in the brain.
· Explain in detail neurotransmission by acetylcholine, serotonin, glutamate and GABA.
· Outline key defects in neurotransmitter signalling that lead to brain malfunction.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; MCQ 30 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 100.

Pre-requisite(s): BC3001

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals; 5 x 1hr(s) Tutorials.

Module Co-ordinator: Prof Dmitri Papkovsky, Department of Biochemistry.

Lecturer(s): Prof Dmitri Papkovsky, Department of Biochemistry.

Module Objective: To introduce the principal biophysical techniques used in Biochemistry.

Module Content: Intrinsic properties of biomolecules. Interaction of light with biomaterials. Principles of the main spectroscopic techniques: UV/VIS, fluorescence and phosphorescence. Instrumentation, measurement modes and formats, practical uses of spectroscopic techniques for the identification and studies of biological objects and processes. Bioseparations. Basics and principle types of biochromatography, HPLC. Electrophoretic techniques. Detection systems used in bioseparations. Visualisation and imaging techniques, flow cytometry. Binding, hybridisation and cell based assays. Probes and labelling techniques: intrinsic and extrinsic chromo- and fluorophores, fluorescent proteins, radioisotopes, their analytical uses. Principles and biological use of NMR, ESR and mass-spectrometry techniques.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the fundamentals of core biochemical methods and techniques covered by the course: spectroscopy, bioseparations, probes, biomolecule characterisation.
· Outline the merits and limitations of each of the aforementioned techniques in studying biological objects and biomolecules.
· Demonstrate competence in performing techniques and using corresponding instrumentation.
· Compare and contrast techniques.
· Extract biologically relevant information from raw experimental data or instrumental readout, and interpret such experimental data.
· Perform basic biochemical calculations and data processing related to these techniques.
· Conduct simple biochemical experiments, including preparation of solutions and biochemical reagents, micropipetting, handling of protein and nucleic acid samples.
· Perform rational design of a biochemical experiment, document and present experimental data.
· Demonstrate use of Internet resources, textbooks to find up to date information on related topics.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (Lab work 10 marks; Data Handling test 10 marks; MCQ 20 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ and Data Handling examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 100.

Pre-requisite(s): BC2001; ML2001

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 18 x 1hr(s) Practicals ((including problem based and self directed learning)).

Module Co-ordinator: Dr Pavel Baranov, Department of Biochemistry.

Lecturer(s): Dr Pavel Baranov, Department of Biochemistry.

Module Objective: Introduction to Bioinformatics.

Module Content: Information. Bit. Information flow during gene expression. Nucleotide and protein sequences. Genetic Code and translation. Organization of bacterial, eukaryotic and viral genes. Databases and Data hubs. Genbank and RefSeq. Boolean expressions. Comparative sequence analysis. Pairwise sequence alignment. Dynamic programming. Progressive multipe alignment. Weight matrices. Heuristics methods (FASTA, BLAST). Machine learning techniques (PSI-BLAST). Molecular Evolution. Phylogenetic Analysis. Trees. Phenetics and Cladistics.

Learning Outcomes: On successful completion of this module, students should be able to:
· Quantitate information stored in biological sequences.
· Explain how biological molecules can store, replicate and transform information.
· Describe structure of eukaryotic and prokaryotic protein coding genes.
· Use NCBI resources, such ad Entrez and PubMed; read and interpret GenBank format.
· Perform simple comparative sequence analysis, such as frequency and compositional ananlysis.
· Demonstrate understanding of Dynamic Programing algorithms.
· Differentiate between optimal and heuristic solutions.
· Perform sequence similarity searches using BLAST.
· Build phylogenetic tress; Discriminate Phenetics and Cladistics.

Assessment: Total Marks 100: End of Year Written Examination 60 marks ((MCQ Paper)); Continuous Assessment 40 marks (Practical project write-up).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s) (MCQ paper).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated.

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Min 10, Max 150.

Pre-requisite(s): ML2001 or FM1001

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 3hr(s) Workshops; 12 x 1hr(s) Directed Study.

Module Co-ordinator: Prof Thomas McCarthy, Department of Biochemistry.

Lecturer(s): Prof Thomas McCarthy, Department of Biochemistry; Dr Pavel Baranov, Department of Biochemistry.

Module Objective: To develop the student's knowledge and understanding of the fundamental background, principles and applications of forensic genetics and molecular biology.

Module Content: The history and science of human identification; DNA, RNA and protein; the molecular basis of hereditary; the human genome: the molecular basis of human and genome diversity; the genome and forensic genetics; DNA fingerprinting (minisatellites, microsatellites, STRs) and profiling; paternity testing; basic principles in population genetics; forensic anthropology: mitochondrial and Y chromosome analysis in forensic science; forensic and genealogical investigations; DNA databases; ethical issues: DNA extraction and DNA amplification technology; case studies in forensic DNA, genetics and molecular biology.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the main principles of forensic genetics and relevant molecular biology.
· Outline DNA amplification and DNA analysis technology relevant to forensic applications.
· Outline the molecular basis of hereditary.
· Describe the basis of human and genome diversity and relatedness.
· Describe the main types of DNA variation found in genomes.
· Describe how DNA variations behave in human populations and an understanding of the factors influencing such behaviour.
· Describe DNA fingerprinting and DNA profiling and its application in forensic science.
· Outline the applications of mitochondrial and Y chromosome analysis in forensic science.

Assessment: Total Marks 100: End of Year Written Examination 70 marks; Continuous Assessment 30 marks (MCQ).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated.

Credit Weighting: 5

Teaching Period(s): Teaching Periods 1 and 2.

No. of Students: Min 20, Max 40.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 6 x 1hr(s) Tutorials; 1 x 12hr(s) Other (Literature Survey); 6 x 1hr(s) Other (Self directed learning).

Module Co-ordinator: Dr Paul Young, Department of Biochemistry.

Lecturer(s): Dr Paul Young, Department of Biochemistry.

Module Objective: To develop the student's ability to source relevant information and perform an up to date review of appropriate original literature on a biochemical topic. To develop the student's understanding of the scientific method, experimental design and the scientific publication process.

Module Content: Literature review on any topic in Biochemistry. The scientific method, Principles of experimental design. Scientific communication and publication. Scientific writing. Searching and retrieving information from the scientific literature.

Learning Outcomes: On successful completion of this module, students should be able to:
· Perform an up to date review of appropriate original literature on a biochemical topic.
· Source, review, critically assess and evaluate original scientific literature relevant to a biochemical topic.
· Design, plan and write a literature review on a biochemical topic.
· Demonstrate written, oral and presentation skills for scientific communication.
· Review the principles and application of the scientific method.
· Outline the principles of good experimental design.

Assessment: Total Marks 100: Continuous Assessment 100 marks (1 x 3,000 word essay (60 marks), MCQ (20 marks) and Oral examination (20 marks)).

Compulsory Elements: Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: No End of Year Written Examination.

Requirements for Supplemental Examination: Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated (as prescribed by the Department).

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 60.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 3hr(s) Practicals; 6 x 1hr(s) Tutorials; 20 x 1hr(s) Directed Study.

Module Co-ordinator: Dr John V (Eoin) Fleming, Department of Biochemistry.

Lecturer(s): Dr John V (Eoin) Fleming, Department of Biochemistry.

Module Objective: To overview the biochemistry of the immune system

Module Content: Innate and acquired immunity. Cells and organs of the immune system. Antibodies and antigens. Major histocompatibility complex. Antigen processing and presentation to T lymphocytes. Antigen receptors and accessory molecules of T lymphocytes. Maturation and activation of lymphocytes. Generation of antibody diversity. Immunologic tolerance. Cytokines. Effector mechanisms of immune responses. Immunity to microbes. Transplantation immunology. Hypersensitivity and Autoimmunity.

Learning Outcomes: On successful completion of this module, students should be able to:
· Demonstrate broad knowledge of the cell and tissues types that constitute the mammalian immune system.
· Demonstrate a deep knowledge of the structural and functional features of antigens and antibodies, and understand the chemical and physical basis for their specific interactions.
· Describe the events associated with the development and maturation of B- and T-lymphocytes including a thorough knowledge of the genetic and biochemical basis for antigen receptor diversity.
· Discuss the components and effector mechanisms of both humoral and cell mediated immunity, and how they are activated in response to microbes of clinical relevance and potential vaccination strategies.
· Explain the important role played by complement proteins and cytokines in integrating the innate and adaptive immune systems.
· Describe the importance of immunological tolerance and its relevance to organ transplant.
· Compare and contrast the different types of hypersensitivity and autoimmune diseases.
· Describe the molecular and cellular basis of clinically important congenital and acquired immunodeficiencies.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (MCQ examination 30 marks; Laboratory practical work 10 marks).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 50%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s) (Oral, if required).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing continuous assessment, marks awarded for laboratory practical work are carried forward, failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 100.

Pre-requisite(s): BC3004; BC3007

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures.

Module Co-ordinator: Prof Rosemary O'Connor, Department of Biochemistry.

Lecturer(s): Prof Rosemary O'Connor, Department of Biochemistry.

Module Objective: To study the biology/biochemistry of processes that are essential for life and that are often disrupted in disease. These include cell proliferation, cell survival, cell movement and differentiation.

Module Content: Overview of cell interactions in multi cellular organisms such as humans, and how simple cell and animal models are used to study mammalian cell biology. Exploration of the essential cellular functions that are evolutionarily conserved. Biochemistry of the cell cycle, cell survival and apoptosis, cell motility, and cell differentiation. Role of key signalling pathways and cellular organelles (mitochondria, ribosomes, cytoskeleton) in these events. Significance of disruption of essential cellular processes for diseases such as cancer, neurodegeneration, cardiovascular disease, diabetes, and autoimmunity.

Learning Outcomes: On successful completion of this module, students should be able to:
· Appreciate the essential characteristics of diverse cell types that function together in a multi-cellular animal.
· Appreciate how the core mechanisms in cells that essential for life are evolutionarily conserved.
· Describe how simple models can be applied to understand the complexities of cell function in mammals.
· Outline the key signalling pathways that control essential cellular functions.
· Appreciate the role of cellular organelles in controlling cell signalling and function.
· Develop a knowledge of how defects in key cellular functions can cause major diseases.
· Critically evaluate the potential of detailed molecular knowledge of key cellular events in our understanding of development, and in the diagnosis and therapy of disease.

Assessment: Total Marks 100: End of Year Written Examination 100 marks. (Oral if required).

Compulsory Elements: End of Year Written Examination. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013.

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 100.

Pre-requisite(s): BC3001

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 1 x 3hr(s) Tutorials (Computer Tutorial).

Module Co-ordinator: Prof David Sheehan, Department of Biochemistry.

Lecturer(s): Prof David Sheehan, Department of Biochemistry.

Module Objective: To describe advanced aspects of protein (especially enzyme) structure and function relevant to modern Biochemistry.

Module Content: The protein structural hierarchy. Protein crystallography. Solving structures by X-ray diffraction. Multi-dimensional NMR for protein structure determination and its comparison with crystallography. The protein structural database. A tutorial on structural databases and their uses followed by a computer based assignment. The protein folding problem In vitro and In vivo. Meaning and determination of kinetic parameters of enzymes. Some methods for probing kinetic mechanism. Site-directed mutagenesis and protein engineering. In vivo and In vitro environment of enzymes. Proteomics.

Learning Outcomes: On successful completion of this module, students should be able to:
· Outline the protein structural hierarchy and its origins in covalent and non-covalent bonds.
· Discuss the principal methods for determination of three dimensional structures of biomacromolecules.
· Access and navigate the protein databank.
· Download PDB files and view them with protein graphics programs.
· Determine and understand the meaning of the kinetic parameters of enzymes.
· Appreciate the limitations and advantages of particular methods to elucidate enzyme function.
· Discuss current methods for expression and purification of recombinant proteins.
· Critically compare the context of enzymes within the cell with the in vitro circumstances in which enzymes are usually studied.
· Appreciate the importance of substrate chanelling in metabolic control.

Assessment: Total Marks 100: End of Year Written Examination 70 marks; Continuous Assessment 30 marks (Computer based assignment). (Oral if required).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Where work is submitted up to and including 7 days late, 10% of the total marks available shall be deducted from the mark achieved. Where work is submitted up to and including 14 days late, 20% of the total marks available shall be deducted from the mark achieved. Work submitted 15 days late or more shall be assigned a mark of zero.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated.

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 100.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures.

Module Co-ordinator: Prof Rosemary O'Connor, Department of Biochemistry.

Lecturer(s): Prof James Heffron, Department of Biochemistry; Staff, Department of Biochemistry.

Module Objective: To introduce students to the basic concepts of the biochemistry and toxicology of environmental pollutants.

Module Content: Sources of xenobiotics and toxicants. Introduction to basic concepts in toxicology. Assessment of toxicity. Metabolism of xenobiotics. Phases of detoxification, Cytochrome P-450 system, conjugation and excretion reactions, biological oxidations, metabolism of benzo(a)pyrene and ethanol. Introduction to carcinogenesis, teratogenesis, immunotoxicity. Chemical carcinogenesis. Initiators and promoters, genotoxicity, IARC and USEPA classification of carcinogens. Synthesis and toxicity of dioxins and related chlorinated and aromatic hydrocarbons. Toxicity of metals, including transition metals, detoxification by metallothioneins. Toxicity of pesticides and chemical warfare agents; their structure and mechanisms of toxicity. Air pollutants, levels and mechanisms of toxicity. Chemical risk assessment applied to human exposure situations.

Learning Outcomes: On successful completion of this module, students should be able to:
· Have an understanding of the broad area of Environmental & Biochemical Toxicology & why it is of importance.
· Understand the importance of dose-response relationships in toxicology.
· Understand the range of disposition-relevant factors that can affect organismal responses to toxicants and xenobiotics.
· Understand the range of metabolism-relevant factors that can affect organismal responses to toxicants and xenobiotics.
· Understand the roles, benefits and limitations of toxicological risk assessment and risk management practices.
· Have an understanding of range of case-examples of environmental and biochemical toxicology in practice.

Assessment: Total Marks 100: End of Year Written Examination 100 marks. (Oral if required).

Compulsory Elements: End of Year Written Examination. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013.

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 100.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures.

Module Co-ordinator: Prof Thomas Cotter, Department of Biochemistry.

Lecturer(s): Prof Thomas Cotter, Department of Biochemistry.

Module Objective: To describe the role of the molecules in cells of the immune system in health and disease.

Module Content: Historical development of immunology, Innate and acquired immunity. Cells and organs of the immune system. Antibody structure & function MHC, Antibody based assays and methods, Antigen processing and presentation, Antigen receptors and signaling, Generation of antibody diversity. Immunologic tolerance. Transplantation immunology. Autoimmunity.

Learning Outcomes: On successful completion of this module, students should be able to:
· Illustrate the development of the field of immunology as a science.

· Describe development and function of the innate and adaptive immune systems.

· Describe the tissues and cells of the immune system and how they are integrated.

· Describe the structure and function of antibodies and how they interact with antigens.

· Outline the uses of antibodies in diagnostic and analytical assays.

· Explain the role and function of the MHC and how antigens are processed and presented by cells of the immune system.

· Explain how a diverse range of antibody molecules can be produced.

· Describe the basis of immunological tolerance, the role of the immune system in organ transplantation and autoimmune diseases.

Assessment: Total Marks 100: End of Year Written Examination 100 marks. (Oral if required).

Compulsory Elements: End of Year Written Examination. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013.

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 100.

Pre-requisite(s): BC3004

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures.

Module Co-ordinator: Prof Mary McCaffrey, Department of Biochemistry.

Lecturer(s): Prof Mary McCaffrey, Department of Biochemistry.

Module Objective: To describe the molecular basis of cancer.

Module Content: Definitions/Concepts re: Cancer. Viruses and Cancer. Oncogene transduction. Compare v-oncs with c-oncs. Functional division of oncoproteins (overview). Oncoproteins. Non-receptor tyrosine kinases. G-protein (oncs). Serine/Threonine kinases. SH2 and SH3 domains common features and specificity. Nuclear Oncoproteins. Anti-oncoproteins/Tumour suppressor proteins. Detailed consideration of Low MW GTPases: Rho Proteins, Ras proteins, Rab Proteins.

Learning Outcomes: On successful completion of this module, students should be able to:
· Provide an overview of the terms, definitions and concepts in cancer biology.
· Discuss the fundamental cellular characteristics which cancer cells acquire during carcinogenesis.
· Provide an historical perspective of research into cancer to the current day.
· Discuss the importance of viruses (DNA & RNA) both in naturally occurring human cancers and as research tools which led to the discovery of oncogenes.
· Outline how several different study approaches, ranging from karyotypic analysis to tissue culture assays, indicated that changes at the gene level are crucial for cancer development.
· Discuss the changes that typically occur in the conversion of a cellular-oncogene (c-onc) to a viral oncogene (v-onc).
· Provide a logical classification of oncoproteins, based on the major functional events in a growth factor signal transduction pathway, and indicating examples of how the proteins encoded by v-oncs aberrantly function in a selected pathway.
· Discuss tumour suppressor protein function, outlining how a number of tumour suppressor proteins are targets for tumorigenic DNA viruses.

Assessment: Total Marks 100: End of Year Written Examination 100 marks. (Oral if required).

Compulsory Elements: End of Year Written Examination. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013.

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 100.

Pre-requisite(s): ML2001 and BC3001 and BC3006

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 6 x 4hr(s) Workshops; 6 x 2hr(s) Tutorials.

Module Co-ordinator: Dr John V (Eoin) Fleming, Department of Biochemistry.

Lecturer(s): Dr John V (Eoin) Fleming, Department of Biochemistry; Prof Thomas McCarthy, Department of Biochemistry.

Module Objective: To provide a working knowledge of the concepts, applications and tools employed in routine biochemical and ultrastructural analysis.

Module Content: Advanced recombinant DNA technologies. Scientific logic in the design, structuring and reporting of experimental studies. Sampling and analysis of experimental data with emphasis on routinely employed cell biology, molecular biology, toxicology, protein chemistry and biochemical laboratory techniques. The molecular basis of human genomics and forensic genetics. Profiling and DNA fingerprinting (minisatellites, microsatellites, STRs). Forensic and genealogical investigations.

Learning Outcomes: On successful completion of this module, students should be able to:
· Demonstrate competence in planning, executing and recording of experiments.
· Demonstrate a clear ability to analyse data generated in routinely employed cell biology, molecular biology, toxicology, protein chemistry and biochemical experiments.
· Demonstrate knowledge and understanding of the main principles of forensic genetics and relevant molecular biology.
· Demonstrate an in depth understanding of DNA fingerprinting and DNA profiling.

Assessment: Total Marks 100: End of Year Written Examination 70 marks; Continuous Assessment 30 marks (Written Data Handling examination 15 marks and MCQ examination 15 marks). (Oral if required).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated.

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Min 15, Max 100.

Pre-requisite(s): BC3008

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures.

Module Co-ordinator: Dr Cora O'Neill, Department of Biochemistry.

Lecturer(s): Dr Cora O'Neill, Department of Biochemistry.

Module Objective: To describe the Molecular Basis of Neurodegeneration/Disorders of the Nervous System.

Module Content: The history and current understanding of the molecular pathogenesis of Alzheimer's disease. Focus on the structure, function and role of the key pathogenic proteins in Alzheimers disease: the amyloid precursor protein, tau, presenilin complex and Apolipoprotein E. Development of transgenic animal models of Alzheimer's disease. The amyloid hypothesis and other theories towards understanding the molecular pathogenesis of Alzheimer's disease. The history and current understanding of the molecular pathogenesis of Parkinson's disease. Focus on the structure and function of the key pathogenic proteins in Parkinson's disease: alpha synuclein and the PARK genes. Development of models and treatment strategies for Parkinson's disease. Current hypothesis of neurodegeneration in Parkinson's disease, with focus on mitochondrial dysfunction, oxidative stress and the ubiquitin proteasomal system. The history and current understanding of the molecular pathogenesis of Huntington's disease. Mechanisms of neurodegeneration brought about by mutant huntington, models and treatment. Methods used to understand molecular basis of neurodegeneration.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the clinical symptoms, risk factors including genetic predisposition, and neuropathology of Alzheimer's disease.
· Explain the structure and function of APP and tau proteins and existing knowledge of the function of APP and tau normally and in Alzheimer's disease and related neurodegenerative disorders.
· Describe the role and function of APP and amyloid beta (Abeta) and other proteolytic fragments of APP in the pathogenesis of Alzheimer's disease, and the mechanisms of action of the alpha, beta and gamma secretase enzymes, and their role in Alzheimer's disease.
· Describe the current models including transgenic models and current hypotheses used to explain the neurodegenerative process of Alzheimer's disease and progress in developing treatments for Alzheimer's disease.
· Describe the clinical symptoms, risk factors including genetic predisposition and neuropathology of Parkinson's disease, also elaborating on animal models and current treatments for the disease.
· Explain the current theories (including the role of mitochondria, oxidative stress and the ubiquitin proteasomal system) which have been put forward to explain neurodegeneration in Parkinson's disease.
· Outline the genes that cause inherited forms of Parkinson's disease, and current knowledge of the structure and function of their encoded proteins in normal brain and in Parkinson's disease.
· Describe the clinical symptoms, neuropathology and current understanding of mutant huntington protein and the molecular mechanisms that cause Huntington's disease.
· Demonstrate competence in explaining key techniques and approaches that are used to understand the molecular basis of neurodegeneration.

Assessment: Total Marks 100: End of Year Written Examination 100 marks. (Oral if required).

Compulsory Elements: End of Year Written Examination. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013.

Credit Weighting: 15

Teaching Period(s): Teaching Periods 1 and 2.

No. of Students: Max 50.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: Directed Study (Library Research); Other (8 weeks Laboratory Work).

Module Co-ordinator: Prof Dmitri Papkovsky, Department of Biochemistry.

Lecturer(s): Prof Dmitri Papkovsky, Department of Biochemistry.

Module Objective: To carry out an independent research project on a biochemical topic.

Module Content: The project requires students to research an area of interest in Biochemistry, plan and execute a programme of investigative work, write a concise scientific report and present the work in the form of a seminar to the class.

Learning Outcomes: On successful completion of this module, students should be able to:
· Demonstrate understanding of the basis and application of laboratory methods and techniques in Biochemistry and demonstrating competence in performing these in Biochemistry.
· Design, plan, execute, interpret the data from, and report on an independent research project.
· Source, review, critically assess and evaluate scientific literature relevant to an independent research project.
· Demonstrate the appropriate writing and oral communication skills for presentation of an independent research project.

Assessment: Total Marks 300: Continuous Assessment 300 marks (Laboratory Work; Submission of Research Project and Presentation of Seminar to class). (Oral if required).

Compulsory Elements: Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: No End of Year Written Examination.

Requirements for Supplemental Examination: No Supplemental Examination.

Credit Weighting: 5

Teaching Period(s): Teaching Periods 1 or 2. (as advised by the Module Co-Ordinator).

No. of Students: Max 15.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: Other (6 weeks of Laboratory Work plus Library Research).

Module Co-ordinator: Dr Sinead Kerins, Department of Biochemistry.

Lecturer(s): Dr Sinead Kerins, Department of Biochemistry.

Module Objective: To train students in Biochemistry research and problem-solving skills, library searching and presentation skills.

Module Content: The project requires students to research an area of interest in Biochemistry, plan and execute a programme of investigative research, write a concise scientific report and make an oral presentation of the work.

Learning Outcomes: On successful completion of this module, students should be able to:
· Demonstrate competence in performing Molecular Biology and basic Microbiology techniques and understanding their basis and application
· Develop, plan, conduct and report on an independent research project
· Design, implement and evaluate scientific investigations and assess, interpret and understand data and its meaning
· Critically analyse and evaluate the relevant scientific literature
· Demonstrate the appropriate written and oral communication skills.

Assessment: Total Marks 100: Continuous Assessment 100 marks (Laboratory Work; Submission of Research Project and Presentation of Research to class). (Oral if required).

Compulsory Elements: Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: No End of Year Written Examination.

Requirements for Supplemental Examination: No Supplemental Examination.

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Min 15, Max 50.

Pre-requisite(s): BC2001; BC2002

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 2 x 2hr(s) Tutorials.

Module Co-ordinator: Dr Kenneth Nally, Department of Biochemistry.

Lecturer(s): Dr Kenneth Nally, Department of Biochemistry.

Module Objective: To study the metabolism of Nitrogen-containing compounds and the metabolism of complex lipids.

Module Content: Logic of metabolism and strategies for metabolic control. Overview of Nitrogen metabolism, metabolic fates of amino groups. Role of glutamate. Elimination of ammonia. Pathways of amino acid synthesis and degradation. Metabolism of biogenic amines. Review of structure of principal nucleotides and their functions. Metabolism of purines and pyrimidines: Synthesis and catabolism. Salvage pathways. Integration of hormonal regulation of mammalian metabolism. Biosynthesis of membrane lipids and related substances. Cholesterol biosynthesis and metabolism. Metabolism of lipoproteins, bile acids and steroid hormone biosynthesis.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe and illustrate the metabolic pathways of purine, pyrimidine and amino acid metabolism
· Describe and illustrate the enzymology of nitrogen fixation
· Describe and illustrate the Biochemistry of the polypeptide and steroid hormones
· Illustrate the structure of principal nucleotides and their functions
· Discuss chemotherapeutic agents that target enzymes in the nucleotide biosynthetic pathways
· Describe the biosynthesis of principal membrane lipids
· Outline cholesterol, lipoprotein and bile acid metabolism
· Describe the interrelationships between the various metabolic pathways and understand their overall regulation.

Assessment: Total Marks 100: End of Year Written Examination 100 marks.

Compulsory Elements: End of Year Written Examination.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s) (Oral if required).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013.

Credit Weighting: 5

Teaching Period(s): Teaching Periods 1 and 2.

No. of Students: Min 15, Max 45.

Pre-requisite(s): BC3001, BC3006, BC3005

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures.

Module Co-ordinator: Dr Paul Young, Department of Biochemistry.

Lecturer(s): Dr Paul Young, Department of Biochemistry; Dr John V (Eoin) Fleming, Department of Biochemistry.

Module Objective: To describe the principles and advanced methods underlying the production, purification and applications of biotechnology-related products of relevance to research, industry, medicine and agriculture.

Module Content: Genetic basis of disease. Genomic, transcriptomic and proteomic approaches in research and disease detection. Mutagenesis and protein engineering. Disease treatment strategies. Isolation, culture and regeneration of embryonic and adult stem cells. Ex-vivo and in vivo gene therapy in regulating expression of cellular proteins . Tissue/organ generation, biomedical engineering. Cell culture and associated research/ industrial considerations. Generation of hybridomas and the production of monoclonal and humanized monoclonal antibodies. Protein production and downstream processing. Purification - tags/ chromatographic approaches. Principles and applications of plant biotechnology. Purification of products of biotech relevance from plants. Principles and applications of microbial biotechnology.

Learning Outcomes: On successful completion of this module, students should be able to:
· Have an in depth knowledge of the genetic basis of disease and be capable of evaluating the different biotech-related strategies that might be used in treatment
· Have an in depth knowledge of the cellular and molecular basis of gene therapy approaches and be capable of critically comparing different delivery strategies
· Know the factors that can impact on the production of recombinant proteins for clinical, research, industrial and agricultural applications. This should include a critical evaluation of cell culture and host species considerations (animal, yeast, plant, bacterial)
· Be capable of assessing the contribution of different downstream processes to the production of biotech products
· Be familiar with applications of plant and microbial biotechnology.

Assessment: Total Marks 100: End of Year Written Examination 100 marks.

Compulsory Elements: End of Year Written Examination. Oral if required.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated (as prescribed by department).

Credit Weighting: 10

Teaching Period(s): Teaching Periods 1 and 2.

No. of Students: Min 0, Max 0.

Pre-requisite(s): -

Co-requisite(s): -

Teaching Methods: 16 x 3hr(s) Lectures.

Module Co-ordinator: Prof James Heffron, Department of Biochemistry.

Lecturer(s): Staff, Department of Biochemistry.

Module Objective: To provide an understanding of the biochemical actions and interactions of toxicants in the human body. The effects of major classes of toxicants, the principles of chemical hazards and risk assessment, and appropriate controls and prevention strategies for toxic chemicals.

Module Content: The nature and properties of toxicants and hazardous chemicals 1 and 2; Routes of exposure and entry; Types of toxic response; Basic metabolism of compounds; Xenobiochemistry; Heavy metal pesticides; Carcinogens; Solvents; Assessment of toxicity; Bodily reactions; Chemical hazard assessment, control and prevention; Toxicity information.

Learning Outcomes: On successful completion of this module, students should be able to:
· Identify the range of properties of chemicals found in the workplace;
· Define routes of exposure and entry into the human body;
· Describe the nature and properties of chemicals;
· Describe the link between exposure to chemicals and the effects, response, health effects, symptoms etc. in man caused by such chemicals;
· Describe the biochemical actions and interactions of toxicants in the human body;
· Interpret the terminology (originating from toxicology) used in chemical safety information and risk assessment;
· Implement the principle of chemical hazard and risk assessment;
· Advise on Legislation and Codes of Practice, Standards
· Outline factors influencing toxicity.

Assessment: Total Marks 200: Continuous Assessment 200 marks (1 x 3hr End of Unit Examination 100 marks; Work-based Project 100 marks).

Compulsory Elements: Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: No End of Year Written Examination.

Requirements for Supplemental Examination: Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated (If a student fails to reach a satisfactory level in the Work-based project or End of Unit Examination, or both, he/she may, at the discretion of the Board of Examiners, submit alternative assessment).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Min 5, Max 40.

Pre-requisite(s):

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 4 x 3hr(s) Directed Study (Self-directed learning).

Module Co-ordinator: Prof Rosemary O'Connor, Department of Biochemistry.

Lecturer(s): Prof Rosemary O'Connor, Department of Biochemistry; Prof Dmitri Papkovsky, Department of Biochemistry.

Module Objective: To provide an overview of the cell at the molecular and cellular level and to provide an understanding of current key topics and technologies in the molecular and cellular biology area.

Module Content: Detailed overview of molecular and cellular biology including biomolecules, metabolism, protein function, DNA and chromosomes, gene regulation, membrane structure and function, organelles, cell communication, cell survival and cell death, cell division, genomics, proteomics, DNA technology. More than half of the module will focus on analysis and critical review of research papers in the molecular and cell biology fields.

Learning Outcomes: On successful completion of this module, students should be able to:
· Discuss prokaryotic and eukaryotic gene structure, genome organization and genomics.
· Provide a detailed overview of eukaryotic gene control, RNA polymerase and regulation of transcription control.
· Outline the composition, organization and functionality of biological membranes.
· Discuss key concepts in the synthesis and targeting of proteins with emphasis on the translocation and sorting of secretory proteins.
· Provide a detailed overview of protein post-translational modifications and post-translational dependent cellular processes.
· Discuss modern cloning strategies and their application in the production of recombinant proteins, membrane proteins and glycoproteins.
· Compare current advances in in vitro and in vivo recombinant protein production systems.
· Outline current methodologies for the production of therapeutic monoclonal antibodies.
· Discuss the application of modern technologies including cloning technologies for proteil expression, DNA microarray technologies and antibody array platforms.

Assessment: Total Marks 100: End of Year Written Examination 80 marks; Continuous Assessment 20 marks (Essays).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): None.

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s) to be taken in Spring 2013.

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. Marks in passed element(s) of Continuous Assessment are carried forward, Failed element(s) of Continuous Assessment must be repeated.

Credit Weighting: 5

Teaching Period(s): Teaching Period 2.

No. of Students: Max 60.

Pre-requisite(s): None

Co-requisite(s): BC2001

Teaching Methods: 20 x 1hr(s) Lectures; 4 x 1hr(s) Tutorials; 8 x 3hr(s) Practicals; Directed Study (Directed Study 10hrs).

Module Co-ordinator: Dr Sinead Kerins, Department of Biochemistry.

Lecturer(s): Dr Sinead Kerins, Department of Biochemistry.

Module Objective: To provide an introduction to Molecular Biology outlining the molecular basis for disease, and molecular targeting of drugs.

Module Content: Structure of Nucleic Acids, DNA, RNA. Prokaryotic and eukaryotic gene structure. DNA replication, DNA repair. Transcription in prokaryotes and eukaryotes and relevant drugs. Gene expression in prokaryotes and eukaryotes. The genetic code. Protein synthesis in prokaryotes and eukaryotes and relevant drugs. Recombinant DNA technology: restriction endonucleases, vectors, ligation, transformation, Polymerase Chain Reaction and applications. Recombinant products in medicine. DNA repair and detection of mutations in DNA. HIV life cycle and relevant drugs.

Learning Outcomes: On successful completion of this module, students should be able to:
· Compare and contrast the structure of the nucleic acids, DNA and RNA and prokaryotic and eukaryotic genes.
· Describe the molecular mechanisms of replication, transcription, translation and the molecular targeting of drugs.
· Describe the different types of post-transcriptional and post-translational modifications.
· Outline how the expression of genes can be regulated and how this information can be used to regulate over-expression of recombinant proteins.
· Describe the different genetic engineering techniques and their applications.
· Describe the causes and nature of DNA mutations, the pathways used to repair DNA damage, and the consequences of failing to repair DNA damage.
· Explain the life cycle of the human immunodeficiency virus (HIV) and evaluate how control of gene expression has led to advances in the treatment of AIDS.
· Demonstrate competence in performing Molecular Biology and basic Microbiology techniques and understanding their basis and application.
· Design, implement and evaluate scientific investigations and assess, interpret and understand data and its meaning.

Assessment: Total Marks 100: End of Year Written Examination 60 marks; Continuous Assessment 40 marks (MCQ 30 marks; Laboratory 10 marks) Oral, if required).

Compulsory Elements: End of Year Written Examination; Continuous Assessment. Oral, if required.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).

Credit Weighting: 5

Teaching Period(s): Teaching Period 1.

No. of Students: Max 20.

Pre-requisite(s): None

Co-requisite(s): None

Teaching Methods: 18 x 1hr(s) Lectures; 3 x 4hr(s) Practicals; Other (Literature assignment).

Module Co-ordinator: Prof Thomas Cotter, Department of Biochemistry.

Lecturer(s): Staff, Department of Biochemistry.

Module Objective: To introduce students to the chemistry of biomolecules

Module Content: Steroisomers - The concept of steroisomers and how such molecules can have different properties despite having the same chemical formula. Examples of pharmaceutical products are used to illustrate concept.
Water and pH - The role of water as a biological constituent of life. The concept of pH and its importance to biological systems. Hydrogen bonding.
Amino acids - An outline of the structure and function of amino acids with a focus on their chemical properties and how they can link together to form proteins.
Protein structure & function - Understanding primary, secondary, tertiary and quaternary protein structure with detailed examples of how such structures are dependent on amino acids sequence.
Enzymes and enzyme kinetics - Introduction to the concept of enzymes and their function including the role of the active site of the enzyme. Introduction to enzyme kinetics. The concept of enzyme inhibition and inhibitors.
Carbohydrates and polysaccharides - Monosaccharides structure and function. Formation of simple polysaccharides.

The students will perform a self-directed literature/library assignment. This literature/library assignment is designed to teach students how key discoveries were made, the people behind such discoveries and the scientific landscape at the time the ground breaking research was carried out. The literature project will involve independent research from available and/or provided literature in the Boole Library, the department or other literature sources. Students will be encouraged to present their own ideas and interpretations of the literature reviewed and to draw conclusions.

Learning Outcomes: On successful completion of this module, students should be able to:
· Describe the basic principles of stereoisomers and their importance in determining the chemical and physical properties of compounds.
· Outline the role of water and pH and describe how hydrogen bonds are formed.
· Discuss the structure and function of amino acids and in particular how they can combine to form proteins.
· Describe the characteristics of the different levels of protein structure and how such characteristics relate to the amino acid sequence.
· Describe what an enzyme is and the basis of its function. The student should also be able to understand basic enzyme kinetics and enzyme inhibition patterns of drugs.
· Discuss the structure of simple monosaccharides and the importance of chiral carbons
· Describe the formation of simple polysaccharides
· Describe simple and more complex lipids and some of their roles in biology
· Interpret, synthesise, and critically assess the current scientific literature on the topic of this module in a literature review format. Students will learn how key discoveries are made in science and the thinking at the time that enabled these discoveries to be made.

Assessment: Total Marks 100: End of Year Written Examination 50 marks; Continuous Assessment 50 marks ((Lab work 10 marks; MCQ 20 marks; literature assignment 20 marks)).

Compulsory Elements: End of Year Written Examination; Continuous Assessment.

Penalties (for late submission of Course/Project Work etc.): Work which is submitted late shall be assigned a mark of zero (or a Fail Judgement in the case of Pass/Fail modules).

Pass Standard and any Special Requirements for Passing Module: 40%.

End of Year Written Examination Profile: 1 x 1½ hr(s) paper(s).

Requirements for Supplemental Examination: 1 x 1½ hr(s) paper(s) to be taken in Autumn 2013. The mark for Continuous Assessment is carried forward (For students failing the continuous assessment, marks awarded for laboratory practical work and literature assignment are carried forward. Failed Continuous Assessment MCQ examination(s) must be retaken.).


		Book of Modules 2012/2013
		Biochemistry

Book of Modules 2012/2013

Biochemistry