On successful completion of this module, students should be able to demonstrate knowledge of: - how to use a microscope to study cells; - the basic structure, function and mechanism of cellular compartmentalization and macromolecules contained within; - why and how cells communicate; - an understanding of basic cellular respiration, fermentation and photosynthesis; - mitosis and meosis; -Mendelian genetics; - The chromosomes' role in inheritance; - DNA, its structure, function and replication; - DNA transcription and translation; - Genetics and inheritance and its role in evolution; - Genome structure and genome diversity in life; - Basic molecular biological techniques - PCR, Electrophoresis, Genome sequencing, fingerprinting. The student should be able to work safely in a Biology laboratory, carry out a range of routine laboratory procedures and gain experience in using scientific equipment. The student should also be able to record observations, collate and analyse data, and write scientific reports.

Lecture 1: General introduction to cell biology. Topics covered include (1) what is cell biology, (2) how do we study cells, (3) what types of cells exists, (4) where do we get cells from to study them, (5) what is inside a cell.
Lecture 2: General introduction to cellular organelles. Topics covered include (1) the organelles of eukaryotic cells, (2) the nucleus, (3) ribosomes and protein synthesis, (4) the endomembrane system, (5) mitochondria, chloroplasts and energy, (5) the cytoskeleton.
Lecture 3: Membrane structure and function. Topics covered include (1) plasma membrane structure, (2) membrane fluidity, (3) proteins found in plasma membrane and their functions, (4) transport across the plasma membrane, (5) case study of cystic fibrosis as a disease resulting from alterations in plasma membrane transport, (6) case study of HIV entry into cells via interactions with plasma membrane proteins, (7) bulk transport across the plasma membrane: endocytosis, exocytosis, phagocytosis, pinocytosis, receptor-mediated endocytosis.
Lecture 4: The nucleus and nucleolus. Topics covered include (1) nucleus as a control centre for storage and maintenance of genetic information, (2) nucleus shape and structure, (3) nuclear pores, (4) maintenance of nucleus shape by the nuclear lamina, (5) variations in nucleus shape and examples of disease conditions like Hutchinson-Gilford progeria syndrome, (6) DNA as the genetic material inside the nucleus, (7) DNA packaging in the nucleus, the nucleosome and role of histone proteins in DNA packaging, (8) the role of the nucleolus in rRNA synthesis, rRNA processing and assembly of ribosomal subunits, (9) functions of ribosomes.
Lecture 5: Mitochondria. Topics covered include (1) mitochondria as the powerhouse of the cell, (2) mitochondria as autonomous organelles, (3) mitochondrial DNA and maternal inheritance, (4) mitochondria and cellular respiration, glycolysis, Kreb’s cycle, oxidative phosphorylation, electron transport chain.
Lecture 6: Plastids. Topics covered include (1) different types of plastids, (2) chloroplasts, (3) role of chloroplasts in photosynthesis, (4) organisation of the light harvesting complexes, photosystem I and photosystem II, (5) light reactions and dark reactions in photosynthesis, linear electron flow Lectures 7 and 8: The endomembrane system. Topics covered include (1) the smooth and rough endoplasmic reticulum (ER) and their functions, (2) translocation of proteins across the ER, (3) vesicular transport, (4) the Golgi apparatus, (5) Golgi transport, (6) functions of the Golgi in assembly of proteoglycans, secretion, (7) lysosomes and function of lysosomes for digestion of macromolecules, (8) lysosomes in phagocytosis and autophagy, (9) case study of lysosomal storage disease, e.g., I-Cell disease, (9) vacuoles in plant and fungal cells, (10) peroxisomes and their
functions, (11) case study of peroxisomal disorders, e.g. X-linked adrenoleukodystrophy (ALD).
Lecture 9: The cytoskeleton. Topics covered include (1) the different types of cytoskeleton, (2) functions of the cytoskeleton (3) accessory proteins, molecular motors, cytoskeleton in muscle contraction, (4) cytoskeleton function in the mitotic spindle, centrosomes and centrioles, function of cytoskeleton in cilia and flagella.
Lectures 10 and 11. Cell cycle. Topics covered include (1) cellular division, (2) different phases of the cell cycle, (3) mitosis, (4) cytokinesis in animal and plant cells, (5) regulation of the cell cycle and the cell cycle control system, (6) roles of cyclins and cyclin-dependent protein kinases, cell cycle can cancer
Lecture 12: Meiosis and sexual reproduction. Topics covered include (1) heredity, variation and genetics, (2) comparison of asexual and sexual reproduction, (3) types of life cycles in multicellular organisms, (4) stages of meiosis, (5) synapsis and crossing over, (6) origins of genetic variation among offsprings, (7) independent assortment of chromosomes.
Lectures 13 and 14: Mendelian genetics. Topics covered include (1) law of segregation, (2) law of independent assortment, (3) degrees of dominance, (4) relationship between dominance and phenotype, (5) case study: Tay-Sachs disease, (5) multiple alleles, (6) pleiotropy, (7) epistasis, (8) polygenic inheritance, (9) ‘nature’ vs. ‘nurture’, (10) multifactorial characters, (11) pedigree analysis,
Lecture 15 and 16: Chromosomal basis of inheritance. Topics covered include (1) chromosomal behaviour and Mendelian inheritance, (2) Drosophila as a experimental model for genetic studies, (3) sex-linked genes and inheritance, (4) chromosomal basis of sex, (5) SRY gene and sex determination, (6) inheritance of X- and Y-link genes, examples of X-linked disorders (7) X-inactivation in female mammals, (8) linked genes and how linkage affects inheritance, (9) genetic recombination and linkage, (10) recombination of linked genes, (11) linkage maps, (12) alterations of chromosome number or structure and genetic disorders, e.g. Down syndrome and trisomy 21, (13) aneuploidy, polyploidy (14) genomic imprinting, (15) inheritance of organelle genes
Lectures 17 and 18: Discovery of DNA and DNA replication. Topics include (1) genetic role of DNA, (2) viral DNA and cellular reprogramming, (3) structural model of DNA, (4) DNA double helix, (5) DNA replication and repair
Lectures 19 and 20: Transcription and translation. Topics covered include (1) the genetic code, (2) transcriptional unit, (3) stages of transcription, (4) RNA polymerase, (5) alterations of mRNA ends, (6) split genes and RNA splicing, (7) functional and evolutionary importance of introns, (8) translation, (9) molecular components of translation, (10) structure and function of transfer RNA, (11) ribosomes in protein synthesis, (12) ribosome association and initiation of translation.

There are 5 laboratory practicals associated with this module The duration of each practical is 3 hours. Practicals are run in small laboratories with a maximum of 32 students. Groups of 10-16 students are allocated a Demonstrator/Teaching Assistant who will be responsible for guiding the students in the practicals. There will be 2-3 Demonstrators/Teaching Assistants in each laboratory. The Module Coordinator who is also an academic member of staff will have oversight of the practicals being run simultaneously in 5-6 laboratories.
Practical 1: Cytochemistry. Overall aim: To learn to distinguish the distribution of macromolecules in organisms. Specific aims: (1) revise the use of a light microscope, (2) basic chemistry of stains, (3) use of stains to add specific colour contrasts to specimens, (4) specific distribution of macromolecules in cells and tissues, (5) how to measure sizes of structures imaged in a light
microscope. Skills: (1) application of stains to specimens, (2) making sections and preparing slides, (3) estimate the size of cells, (4) making representative drawings and notes to record observations. Comprehension: (1) understanding of the relationship between tissue slices (sections) prepared for microscopy and the whole organ from which they were cut, (2) realisation that macromolecules are localised to very specific structures down to the finest level of detail that one can see with a light
microscope, (3) understanding of the scale of microscopic structures.
Practical 2: Cell ultrastructure. Aims: (1) to learn about the types of information that can be obtained from electron micrographs of tissues and cells, (2) appreciating the 3-D shape that is represented by the 2-D images, (3) recording the size and number of structures from electron micrographs. Skills: (1) observing and distinguishing the structures in electron micrographs, (2)
identification of subcellular organelles, (3) converting micrograph measurements to real cell sizes in metric units, (4) estimating the volume of the cell components from micrographs. Comprehension: (1) understanding the size of macromolecular cellular components, (2) appreciating the relative numbers of sub-cellular components, (3) development of a 3-D understanding of a cellular unit.
Practical 3: The cell cycle. Aims: (1) to become familiar with identifying different stages of the cell cycle, and of mitosis, (2) to estimate the relative duration of the different stages of mitosis, and the relative length of mitosis to the rest of the cell cycle. Skills: (1) staining whole tissues to identify the location of a specific macromolecule, DNA, (2) identification of stages of mitosis and cell cycle in plant tissues, (3) using sampling to arrive at an estimate of the total population available. Comprehension: (1) an understanding of the relative frequency of cell division in a growing tissue, (2) an appreciation of the variation of cell cycle states existing at any one time between cells of the same tissue, (3) an appreciation of the relative duration of the cell cycle and mitotic events in the life of a cell.
Practical 4: Genetics I. Aims: (1) to extract DNA from wheat germ, (2) to examine DNA on an agarose gel, (3) to demonstrate the monohybrid and dihybrid cross. Skills: (1) Recording observations by counting and determining ratios of features, (2) DNA extraction and visualisation, (3) agarose gel electrophoresis. Comprehension: (1) using observation of offspring to infer the genetics of the parents and determine the expected phenotype (2) using observation of structures (phenotype), the genetic makeup may be determined by simple calculation if the principles of inheritance are understood.
Practical 5: Genetics II. Aims: (1) to transcribe and translate DNA, (2) to identify introns and exons
and reconstruct an animal, (3) to learn about genome sequencing and reconstruction. Skills: (1) understand the genetic code, (2) assess phenotypic variance from DNA, (3) understand genome assembly and next generation sequencing. Comprehension: (1) using the genetic code to understand what an organism should look like, (2) how genomes are assembled and annotated.

Leaving Certificate Biology

• Feedback individually to students, on an activity or draft prior to summative assessment
• Online automated feedback

For online Mastering Biology assignments, feedback will be provided automatically by the online Mastering Biology system. For laboratory reports, written feedback will be provided for each lab report. This will comprise annotated feedback throughout the lab report as well as a summary feedback at the end of the report.