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Biology

Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Introduction to Molecular and Cellular Biology(BY1101))

(10 ECTS credits) 12 weeks Semester 1 NA CA (including Lab MCQ test) - 33.3% End of Semester Written Exam - 66.6% c.80 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

This module is an introduction to molecular and cellular biology, including biochemistry, genetics, developmental biology and microbiology. The levels of understanding in biology are covered, from ecosystems to molecules. A description of the possible origin of life, from the abiotic world to multicellular organisms will be given, and the ultrastucture of the eukaryotic cell will be covered in detail. The major properties and functions of each class of biochemicals (carbohydrates, lipids, proteins and nucleic acids) will be described. Students will then be introduced to some basic concepts in genetics, considering the experimental evidence on which they are based and gaining insights into the central place of genetics in the biological sciences. Developmental biology deals with how a complex organism is established from a single cell - the fertilized egg cell - and has relevance to our understanding of stem cells and how normal cells are regulated. Finally, Microbiology deals with prokaryotic and eukaryotic microorganisms, and viruses. Students study cell and virus structure, cell growth and viral replication, infectious diseases and host immunity.

Learning Outcomes:

On successful completion of the module, students will be able to:

  • define fundamental principles of biology and provide an account of the origin of life, from the abiotic world to multicellular organisms (including an account of endosymbiosis)
  • describe the properties and functions of the major groups of biologically important molecules, and the structure and functions of the plasma membrane and the major organelles that occur in eukaryotic cells.
  • provide an overview of developments in the field of genetics and heredity - from Mendel to genetic engineering
  • outline the major steps involved in how a complex animal is formed and relate the morphological changes that occur to the molecular and cellular changes that underlie and drive embryo development.
  • describe the structure and properties of prokaryotic and eukaryotic microorganisms and the structure and replication of viruses.
  • explain the mechanisms of action of and resistance to antibiotics, how pathogens cause infection, and host innate and induced immunity.
  • use general texts, reference books and a range of other resources to further develop knowledge of biological issues through continued independent learning
  • apply the scientific method as a fundamental mechanisms for critical analysis and problem solving
  • employ a range of laboratory techniques, demonstrating the development of practical scientific skills and the interpretation of results.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Introduction to Evolution, Biodiversity and the Environment (BY1102)

(10 ECTS credits) 12 weeks Semester 2 NA CA (including Study Week essay) - 40% End of Semester MCQ test - 60% c.60 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

This module will introduce students to the biology of individuals, species, populations and communities, and how humans affect, are effected by, and benefit from, other living organisms. We will cover evolutionary (past) and ecological (present) responses to their environment, using examples from the multicellular Animal and Plant Kingdoms. Topics covered in this module will incorporate the diversity of life, interactions between organisms and between organisms and the environment, the biological context of climate change, human impacts on the environment, and the value and conservation of biodiversity.

Learning Outcomes:

On successful completion of this course, the student will be able to:

  • Recognise the diversity of life on earth and define the evolutionary relationships of major plant and animal groups and
  • Describe the ecological relationships between individuals, populations, communities and ecosystems, and between organisms and their environment
  • Explain how humans can positively and negatively influence other living organisms and their environment
  • Demonstrate practical, numerical and analytical skills
  • Collate, synthesise, organise and present information in written reports
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Cell Structure and Function BY2201)

(5 ECTS credits) 5 weeks Semester 1 Year 1 Introductory Biology module(equivalent to BY1101) CA (including Lab tests and write-ups) - 35% End of Semester Written Exam - 65% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

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:

  • Describe the structure and function of the cell and its constituting organelles.
  • 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.
  • 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.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Vertebrate Form and Function BY2202)

(5 ECTS credits) 5 weeks Semester 1 NA CA (5 Lab tests) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

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:

  • Explain the nature of vertebrate skeletal structure, support and movement.
  • Interpret cell-cell communication in the nervous and endocrine systems.
  • Describe and contrast the functions of different muscle types.
  • Outline the evolution and development of the human renal and digestive systems.
  • Describe the fundamental structure and function of the human cardiovascular, respiratory, renal and digestive systems.
  • Interpret endocrine function and reproduction.
  • Make simple measurements of basic sensory, neurophysiological, cardiovascular and respiratory variables in human subjects.
  • Dissect the rat thorax and abdomen, and identify the major organs.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Metabolism BY2203)

(5 ECTS credits) 5 weeks Semester 1 Year 1 Introductory Biology module (equivalent to BY1101) and preferably BY2201 CA (including Lab tests and write-ups) - 30% End of Semester Written Exam - 70% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

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:

  • Demonstrate an understanding of the metabolic pathways - the energy-yielding and energy-requiring reactions in life.
  • Demonstrate an understading of the diversity of metabolic regulation, and how this is specifically achieved in different cells.
  • Describe and appreciate the modern techniques utilised in understanding the key mechanistic steps at atomic-level detail.
  • Describe how these biochemical processes are not isolated but tightly integrated, with specific control sites and key junctions.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Evolution BY2204)

(5 ECTS credits) 5 weeks Semester 1 NA CA (3 practical assignments) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

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:

  • 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.
  • Show how organisms change as the result of interacting with their dynamic environment.
  • Describe how life evolves and the processes driving its diversity. Examples will be provided through the lectures demonstrating that our knowledge of historical changes at the molecular level can aid in answering why organisms present different morphological traits.
  • Demonstrate a knowledge of evolution can help shed light on many applied aspects of biology including agriculture, medicine and conservation.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Microbiology BY2205)

(5 ECTS credits) 5 weeks Semester 2 Year 1 Introductory Biology module (equivalent to BY1101) CA (including Lab MCQ test) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

BY2205 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:

  • Describe the diversity of bacteria, viruses and eukaryotic microorganisms.
  • Discuss the interactions of microbes with humans, plants and animals during health and disease.
  • Explain the importance of the human microbiome.
  • Describe the mammalian immune system and the interactions of microbes with the immune and other physiological systems.
  • Describe the structure of Gram-positive and Gram-negative bacteria and the importance of each component of the bacterial cell envelope.
  • Describe bacterial cell division and biosynthesis of the cell wall.
  • Describe how infectious organisms such as viruses and bacteria cause disease and give examples of these.
  • Discuss the virus replication cycle and how viruses spread.
  • Describe the basic life cycles of budding and fission yeasts.
  • Explain why Saccharomyces cerevisiae is a model organism for the study of molecular biology of eukaryotic cells.
  • Explain the mating process and the molecular basis of mating type determination and switching in Saccharomyces cerevisiae.
  • Explain the molecular basis of genetic switches that control gene expression in bacteria and their viruses (bacteriophages).
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Ecosystem Biology and Global Change BY2206)

(5 ECTS credits) 5 weeks Semester 2 NA CA (4 Lab/practical assignments) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

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:

  • Demonstrate knowledge of how the global climate system operates.
  • Describe examples of the major terrestrial and aquatic ecosystems.
  • Demonstrate knowledge of how biotic and abiotic factors impact on ecosystems.
  • Describe how energy and nutrients flow through ecosystems.
  • Demonstrate knowledge of the basic concepts of ecological modeling.
  • Run ecological models using EcoBeaker software.
  • Demonstrate knowledge of the impact of environmental change on global ecosystems.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Behaviour BY2207)

(5 ECTS credits) 5 weeks Semester 2 NA CA (2 practical assignments and 4 on-line quizz es) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre (rchfordj@tcd.ie)

Description

The animal behaviour module comprises a series of lectures, four assessments carried out online after watching a video and two practicals. One of the practicals is carried out in your own time, at Dublin Zoo, and assessed online. The other is carried out as a group in a timetabled slot, and is followed by an explanatory lecture, and an online assessment. The module covers a wide range of topics, beginning with a brief history of behavioural research. You then have a series of lectures on different influences on behaviour including group dynamics, genetic, hormonal, developmental and neurobiological influences. These lectures will be given by experts in each of these fields. You are then introduced to various aspects of learning, cultural transmission, cognition and intelligence in animals. The module concludes with a lecture and then a class debate on the ethics of animal-human interactions.

Learning Outcomes:

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

  • Place the study of behaviour in context related to a historical perspective.
  • Describe the range of factors which influence animal behaviour, linking the understanding of behaviour to a number of other biological study areas.
  • Outline the basics of learning, both through classical mechanisms and through cultural transmission.
  • Discuss the concept of animal intelligence and our understanding of consciousness in non-humans.
  • Form a reasoned ethical position about human interactions with animals.
  • Build from a sound basis of understanding of basic behavioral ecological concepts.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Genetics BY2208)

(5 ECTS credits) 5 weeks Semester 2 Year 1 Introductory Biology module (equivalent to BY1101) CA (including 2 practical assessments and Lab MCQ test) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

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:

  • Describe the fundamental molecular principles of genetics.
  • Interpret the structure and function of DNA, RNA and protein.
  • Explain the way in which genes code for proteins.
  • Demonstrate the relationship between phenotype and genotype in human genetic traits.
  • Describe the basics of genetic mapping.
  • Show how gene expression is regulated.
  • Describe the genetic basis of cancer.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Infection and Immunity BY2209)

(5 ECTS credits) 5 weeks Semester 2 Year 1/2 Basic Biochemistry and Microbiology(equivalent to BY2201 and BY2205) CA (including Lab MCQ test) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

The focus of this module is 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:

  • Describe the general features of the major microbial pathogens covered and explain the mechanisms by which they cause disease and the methods used to control them
  • Describe the innate and acquired immune responses to the pathogens covered and explain how host defence can be manipulated, e.g. by vaccination
  • Discuss the molecular processes and genetic influences underpinning resolution or exacerbation of infection
  • Demonstrate experimental skills in the microbiological and immunological techniques covered.
  • Demonstrate an appreciation of the ways in which our knowledge of infection and immunity is based on the results of experimentation.
Module Code & Name ECTs credits Duration and semester Prerequisite Subjects Assessment Contact Hours Contact Details

(Agriculture, Environment and Biotechnology BY2210)

(5 ECTS credits) 5 weeks Semester 2 NA CA (including 4 Lab assessments) - 25% End of Semester Written Exam - 75% c.35 Prof. John Rochford, Biology Teaching Centre(rchfordj@tcd.ie)

Description

By 2050 the UN estimates that the world will need 70% more food, 55% more clean water and 60% more energy than it does today. These demands will have to be addressed alongside changing climate, increased pollution and depleting natural resources. Plants are central to our efforts to sustainably use biological resources and are among our most valuable resources. Their sustainable utilization is crucial for the future of humankind as plants provide the food we eat, many of the medicines we depend on and the air we breathe. They also regulate our climate. This module discusses how plants, and to a lesser extent animals, are exploited as bioresources in agriculture, environmental sciences and biotechnology. It covers domestication, sustainable agriculture, plant breeding and biotechnology, biological pest control, pollination services, non-food crops, conservation of genetic resources, bioprospecting and ethnobiology, the regulation of the global carbon cycle, climate change, water technology and pollution.

Learning Outcomes:

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

  • Demonstrate a detailed knowledge of agricultural plants, domestication and non-food crops
  • Show how biotechnology and plant breeding methods are used to produce new plants for agriculture and medicine
  • Explain how agriculture can be made more sustainable
  • Explain the major methods of biological pest control and the use of insects as pollination services
  • Demonstrate a detailed knowledge of plant genetic resource conservation
  • Explain the key concepts of bioprospecting and ethnobiology

* not suitable for a one semester visiting student as the major CA component cannot be completed, for logistic reasons, until mid way through semester 2.

** takes place during week 34. Additional charge (c.250.00) applies.