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Senior Freshman

BY2201: Cell Structure and Function

(5 credits)
Module coordinator: Dr Emma Creagh (ecreagh@tcd.ie)

Module organisation and description:
The module runs for five weeks in the first half of the first semester (Michaelmas Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

BY2201 will provide the student with a comprehensive account of the essential principles of Cell Biology and Biochemistry. The structure, function and biochemistry of the eukaryotic cell and its sub-cellular organelles will be detailed, including mechanisms such as DNA and protein synthesis and the Cell Cycle. Cytoskeletal function (how filaments coordinate cell division, mobility and intracellular movement) will also be explained. Students will attain a good understanding of the Structure and Function of Proteins, which are the most variable macromolecules in living systems and serve crucial functions in essentially all biological processes. This will provide the background to explore topics such as Enzyme Kinetics, Signal Transduction (how cells receive, process and respond to information from the environment) and Neurochemistry (Nervous tissue metabolism and the mechanism of action of neurotransmitters). The lecture course will be delivered in parallel with a laboratory-based series of experiments in Biochemistry.

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Describe the structure and function of the cell and its constituting organelles.
  2. Demonstrate an understanding of the structures of peptides and proteins, the techniques used in purifying and characterising proteins, proteins involved in oxygen transport, and enzyme mechanisms.
  3. Demonstrate an understanding of how biological signals are sent, amplified, and received in the cellular context (signal transduction), and as an example, how this is achieved in cells of the neurosystem.

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BY2202: Vertebrate Form and Function

(5 credits)
Module coordinator:  Dr Aine Kelly (aikelly@tcd.ie)

Module organisation and description:
The module runs for five weeks in the second half of the first semester (Michaelmas Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

BY2202 covers the anatomy and physiology of humans and other vertebrates, with emphasis on the importance of anatomical structure to the function of physiological systems. The systems covered in detail include the nervous, musculoskeletal, cardiovascular, respiratory, renal, digestive, endocrine and reproductive systems. The practical component of the module includes two laboratory classes in vertebrate anatomy and three laboratory classes in which fundamental neurophysiological, cardiovascular and respiratory parameters are measured in human subjects.

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Explain the nature of vertebrate skeletal structure, support and movement.
  2. Interpret cell-cell communication in the nervous and endocrine systems.
  3. Describe and contrast the functions of different muscle types.
  4. Outline the evolution and development of the human renal and digestive systems.
  5. Describe the fundamental structure and function of the human cardiovascular, respiratory, renal and digestive systems.
  6. Interpret endocrine function and reproduction.
  7. Make simple measurements of basic sensory, neurophysiological, cardiovascular and respiratory variables in human subjects.
  8. Dissect the rat thorax and abdomen, and identify the major organs.

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BY2203: Metabolism

(5 credits)
Module coordinator:  Dr Emma Creagh (ecreagh@tcd.ie)

Module organisation and description:
The module runs for five weeks in the second half of the first semester (Michaelmas Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

The principles of metabolism and its control will be explored in BY2203 using the glycolytic pathway as the principal example. It will be seen that the rate of flux through the different enzyme reactions is determined by differences in gene regulation, kinetics, and hormonally driven phosphorylation/dephosphorylation. The way this pathway is differentially regulated in different cell types and organs will show how metabolic diversity is achieved. Storage of glucose and breakdown, and how cells and organisms generate free energy follows. In addition, the atomic-level structural aspects of the 'nanomachines' involved in key pathways will be discussed. After being introduced to the metabolism of the other two macro-nutrients (namely fats and proteins), a final integration of carbohydrate (glucose) metabolism will show how all of the pathways are highly interconnected. The lecture course will be delivered in parallel with a laboratory course.

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Demonstrate an understanding of the metabolic pathways - the energy-yielding and energy-requiring reactions in life.
  2. Demonstrate an understading of the diversity of metabolic regulation, and how this is specifically achieved in different cells.
  3. Describe and appreciate the modern techniques utilised in understanding the key mechanistic steps at atomic-level detail.
  4. Describe how these biochemical processes are not isolated but tightly integrated, with specific control sites and key junctions.

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BY2204: Evolution

(5 credits)
Module coordinator:  Dr Trevor Hodkinson (hodkinst@tcd.ie)

Module organisation and description:
The module runs for five weeks in the first half of the first semester (Michaelmas Term) of the academic year and comprises of four lectures per week (approx. 20 hours total contact time) together with 3-4 assignments, requiring a further 15+ hours.

BY2204 is designed to teach evolution and the main concepts explaining Natural Diversification. In the first part, general evolutionary concepts are covered, including an historical perspective that spans pre-Darwinian and post-Darwinian thinking and goes from
the macro-evolutionary concepts (origins of life, speciation, Natural
Selection, Kin Selection and altruism and population genetics) to the
micro-evolutionary details (molecular evolution, phylogenetics, human evolution
and evolution and development). The second part, covers evolutionary
patterns and processes in plants, including plant-animal/ plant-fungi
coevolutionary dynamics and how constraints are artificially intensified during domestication of plants and animals. Practicals, some of a computational nature, will support both parts of the module.

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Appreciate one of the most revolutionizing fields in science. Evolution has been the subject of intense studies since ancient times and the fuel of heated controversies between creationists and evolutionary scientists.
  2. Understand how organisms change as the result of intercating with their dynamic environment.
  3. Better understand of how life evolves earth and the processes driving its diversity. Examples will be provided throught the lectures demonstrating that our knowledge of historical changes at the molecular level can aid answering why organisms present different morpholical traits.
  4. Understand how a knowledge of evolution can help shed light on many biomedically important questions.

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BY2205: Microbiology

(5 credits)
Module coordinator:  Dr Joan Geoghegan (geoghejo@tcd.ie)

Module organisation and description:
The module runs for five weeks in the first half of the second semester (Hilary Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

BY2204 provides a comprehensive introduction to the microbial sciences through lectures and practical classes provided by experts in the field. Students will learn about the biology of the major groups of microbes, including bacteria, viruses, yeast and protozoa. The course explains how microorganisms grow and develop, how they interact with the environment and with one another. This module will equip the students with a sound foundation in microbial physiology, cell biology and molecular biology.

Learning outcomes:
On successful completion of this module, students will be able to:


Module details: (Local Access only)

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BY2206: Ecosystem Biology and Global Change

(5 credits)
Module coordinator:  Prof. Fraser Mitchell (farser.mitchell@tcd.ie)

Module organisation and description:
The module runs for five weeks in the second half of the second semester (Hilary Term) of the academic year and comprises of four lectures and one three-hour practical session or field trip per week (approx. 40 hours total contact time).

BY2206 focuses on exploring how organisms interact with their environment across the range of global biomes (both terrestrial and aquatic). The adaptation of organisms to their environment is a persistent theme throughout. Ecological modelling is used to investigate ecosystem functioning and maintenance in relation to environmental change. The lectures are supported by four diverse practical classes, one is held in the Biology Laboratory, one in the TCD Botanic Gardens, one in a computer lab and the final one on a field trip to the North Bull Island. These practicals serve to illustrate the wide range of ecological concepts covered in the lectures

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Demonstrate knowledge of how the global climate system operates.
  2. Describe examples of the major terrestrial and aquatic ecosystems.
  3. Demonstrate knowledge of how biotic and abiotic factors impact on ecosystems.
  4. Describe how energy and nutrients flow through ecosystems.
  5. Demonstrate knowledge of the basic concepts of ecological modeling.
  6. Run ecological models using EcoBeaker software.
  7. Demonstrate knowledge of the impact of environmental change on global ecosystems.

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BY2207: Behaviour

(5 credits)
Module coordinator:  Dr Nicola Marples (nmarples@tcd.ie)

Module organisation and description:
The module runs for five weeks in the first half of the second semester (Hilary Term) of the academic year and comprises of four lectures per week (approx. 20 hours total contact time) together with 2-3 assignments, requiring a further 15+ hours.

BY2207 comprises a series of lectures, four assessments carried out online after watching a video, and two practicals. The practicals are carried out, in your own time, at Dublin Zoo, and are also assessed online. The module covers a wide range of topics, beginning with a brief history of behavioural research. You are then introduced to various aspects of learning, cultural transmission, cognition and intelligence in animals. The module also includes a series of lectures on different influences on behaviour including genetic, hormonal, developmental and neurobiological influences. These lectures will be given by experts in each of these fields.

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Place the study of behaviour in context related to a historical perspective.
  2. Understand the range of factors which influence animal behaviour, linking the understanding of behaviour to a number of other biological study areas.
  3. Outline the basics of learning, both through classical mechanisms and through cultural transmission.
  4. Discuss the concept of animal intelligence and our understanding of consciousness in non-humans.
  5. Form a reasoned ethical position about human interactions with animals.
  6. Build from a sound basis of understanding of basic behavioural ecological concepts.

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BY2208: Genetics

(5 credits)
Module coordinator:  Dr Kevin Mitchell (kevin.mitchell@tcd.ie)

Module organisation and description:
The module runs for five weeks in the first half of the second semester (Hilary Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

BY2208 will provide an introduction to analytical, molecular and cellular genetics. Topics will include: DNA and RNA synthesis and the genetic code; principles of gene expression and the mechanisms that control it - with illustrations of importance in development and behaviour; human genetic analysis - deciphering the genetics of disease - and insights from the human genome project; variation in genetics among human populations; the genetic basis of cancer. A parallel practical course will introduce techniques in molecular genetics and bioinformatics.

Learning outcomes:
On successful completion of this module, students will be able to:

  1. Describe the fundamental molecular principles of genetics.
  2. Understand the structure and function of DNA, RNA and protein.
  3. Explain the way in which genes code for proteins.
  4. Understand the relationship between phenotype and genotype in human genetic traits.
  5. Describe the basics of genetic mapping.
  6. Understand how gene expression is regulated.
  7. Understand the genetic basis of cancer.

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BY2209: Infection and Immunity

(5 credits)
Module coordinator:  Prof. Cliona O'Farrelly (ofarrecl@tcd.ie)

Module organisation and description:
The module runs for five weeks in the second half of the second semester (Hilary Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

The focus of BY2209 will be on pathogens and their interaction with host organisms, particularly humans. Students will learn about major pathogenic bacteria, viruses, protozoa and fungi, the mechanisms by which they cause disease, and approaches to controlling them. Innate and acquired immune responses to these pathogens will be presented. Molecular processes and genetic influences underpinning resolution or exacerbation of infection will be explored. Mechanisms for manipulation of host defence will also be covered.

Learning outcomes:
On successful completion of this module, students will be able to:


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BY2210: Agriculture, Environment and Biotechnology

(5 credits)
Module coordinator:  Dr Mike Williams (michael.williams@tcd.ie)

Module organisation and description:
The module runs for five weeks in the second half of the second semester (Hilary Term) of the academic year and comprises of four lectures and one three-hour practical session per week (approx. 40 hours total contact time).

BY2210 covers the topic of how biodiversity is used as a resource, just like other non-biological resources such as water, oil and coal. It also highlights the potential of new technologies to exploit biodiversity for economic gain and for bio-resources to help regulate the global climate and carbon cycle. It provides a detailed understanding of the key concepts of bio-prospecting and ethnobiology, of animal bio-resources (for food, biological pest control and pollination services), of agricultural plants, domestication and non-food crops, how bio-resources are central to the regulation of the global carbon cycle and climate change, and how biotechnology and plant breeding methods are used to improve the use of bio-resources.

Learning outcomes:
On successful completion of this module, students will be able to demonstrate:

  1. An awareness of the major types of biodiversity and bio-resource.
  2. An understanding of the key concepts of bio-prospecting and ethnobiology.
  3. A detailed understanding of animal bio-resources (for food, biological pest control and pollination services).
  4. A detailed knowledge of agricultural plants, domestication and non-food crops.
  5. A detailed understanding of how bio-resources are central to the regulation of the global carbon cycle and climate change.
  6. A detailed knowledge of how biotechnology and plant breeding methods are used to improve the use of bio-resource.
  7. Improved laboratory skills via practical classes including pollination services of insects, carbohydrate resources of plants (sucrose, starch and assay plant enzymes) and studies of domestication syndromes in plants.

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Last updated 29 September 2015 by btcweb@tcd.ie.