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Junior Sophister Lectures

Courses

BI 3001 Proteins and Enzymes (Tipton, Khan)
BI 3002 Membrane and Cell Biology (Nolan, Voorheis)
BI 3003 Bioenergetics and Transport (Porter)
BI 3004 Gene Structure and Expression (Robinson, Bowie, Zisterer)
BI 3005 Core Concepts in Immunology (Gardiner, Bowie, O'Farrelly, O'Neill)
BI 3006 Signal transduction (Mantle)
BI 3007 Protein Structure and Enzyme Dynamics (Nolan, Tipton, Khan, Fayne, Creagh)
BI 3008 Immunology and Disease (Gardiner, Mills, Lysaght, Lavelle, Higgins, Fletcher)
BI 3009 Photosynthesis (McKillen)
BI 3010 Functional Group Chemistry (Robinson, Fayne, Voorheis)
BI 3014 Clinical Aspects of Inflammation and Infection (Jackson)
BI 3016 Development (Murphy)
BI 3017 Stem Cells (Kelly)
BI 3018 Drug Kinetics and Metabolism (Kelly, Knox)
BI 3019 Cancer (Foley)
BI 3020 Cell Imaging (Nolan)
BI 3021 Proteins of the Immune System (Mok)
BI 3023 Modulation of Immunity by Microbes (McLoughlin, Mills)
BI 3040 Data Handling (Molloy)

BI 3001 Proteins and Enzymes

Prof Keith Tipton

• What's on the web for Junior Sophisters 2010

• SMILES are fun
• Isomers and chirality in SMILES

• Enzyme Lectures Summary 2010
• Enzyme web sites 2010/11
• Principles of enzyme assay and kinetic studies
• Michaelis-Menten Equation
• Enzyme Inhibitors as Drugs
• The Effects of pH on enzyme activity
• Enzyme Nomenclature

Dr Amir Khan

• Enzymes
• Lectures 1 and 2
• Lectures 3 and 4
• Lectures 5 and 6
• Lectures 7 and 8
• Lectures 9 and 10
• References
• Pymol files

• 1
• 2
• 3
• 4

BI 3002 Membrane and Cell Biology

Dr Derek Nolan

• Membrane Potentials in Cells
• Glycosylphosphatidylinositol (GPI) anchored proteins



• Overview of oxidative phosphorylation practical

Dr Paul Voorheis

• Summary and Reading List
• Background Handout on Water Transport through Membranes

   

BI 3003 Bioenergetics and Transport

Dr Richard Porter

• Introduction 2011/12
• Electron Transport Chain Components
• Electron Transport Chain Complexes 1 to 3
• Complex 4
• ATP synthase
• Chemiosmosis
• Delta p
• Efficiency of Oxidative Phosphorylation
• Diseases & Syndromes associated with mutations in mitochondrial DNA
• Membrane transporters

BI 3004 Gene Structure and Expression

Dr Glynis Robinson

• Techniques 1
• Techniques 2
• Techniques 3
• Sample Problems for BI3004
• Reading List

Prof Andrew Bowie

• DNA structure I
• DNA structure II
• DNA structure III
• Eukaryotic Transcription I
• Eukaryotic Transcription II
• Eukaryotic Transcription III
• Eukaryotic Transcription IV
• Eukaryotic Transcription V
• Eukaryotic Transcription VI

• DNA Replication 1
• DNA Replication 2
• DNA Replication 3
• mRNA
• Translation

BI 3005 Core Concepts in Immunology

BI3005 Core Concepts in Immunology
Lecture Schedule
Reading list

Dr Clair Gardiner

• 1. Natural Killer cells and killing mechanisms
• 2. DC, MHC and antigen presentation
• 3. TCR
• 4. Effector Lymphocytes
• 5. B + T cells

• T cell development and activation

• Why Study Immunology?
• Cells & Organs of the Immune System
• Immunoregulation
• Antibodies
• Antibody Generation

• Innate Immunity and Inflammation

BI 3006 Signal transduction

Dr Tim Mantle

• Calcium Entry
• Cyclase Review 1
• Cyclase Review 2
• Cyclase Review 3
• Kit stem cell factor
• LPA signalling
• Nuclear phospholipase C
• PIKE/apoptosis
• Rack1
• Signalling with phosphoinositides
• Growth hormone signalling
• IRS-1 review

BI 3007 Protein Structure and Enzyme Dynamics

Dr Derek Nolan

• Regulation of enzyme activity

Prof Keith Tipton

• Kinetic Equations
• Progress Curves
• Enzyme kinetics
• Enzyme Kinetics and Inhibition
• Kinetic properties of allosteric and cooperative enzymes (part 1)
• Kinetic properties of allosteric and cooperative enzymes (part 2)
• Cooperativity (simpler)
• Enzyme Inhibitors - notes
• Bi-Substrate Kinetics
• Transient kinetics

Dr Amir Khan

• Enzyme structure and function lecture
• pymol file 1
• pymol file 2

• Proteomics 1
• Proteomics 2
• Movie Clip
• File 1
• File 2

Dr Emma Creagh

• Identification of Essential Amino Acid Residues I
• Identification of Essential Amino Acid Residues II


References

• Sirt5 paper
• Supplemental Sirt5 paper
• Rogers & Gibon 2009
• Sirtuin review

BI 3008 Immunology and Disease

Dr Clair Gardiner

• MHC genetics
• Autoimmunity
• Genetic Immunodeficiency
• Transplantation
• Bone Marrow Transplantation
• Effector Lymphocytes

• Bacterial Immunity
• Viral Immunity
• Vaccines

• Tumour Immunology

Dr Ed Lavelle

• Mucosal Immunity 1
• Mucosal Immunity 2
• Allergy lectures 1 and 2

• Parasites

• Autoimmunity

BI 3009 Photosynthesis

Dr Mike McKillen

• Photosynthesis
• Cyt b₆f Complex
• Bacterial Light Harvesting
• Photosynthetic Bacteria Photosystems
• ATP synthase
• Light Reactions of Photosynthesis
• Photosystem I
• Photosystem II
• Historical Aspects

BI 3010 Functional Group Chemistry

Dr Glynis Robinson

• General Principles
• Sigma Bond
• Biological Molecules and their Polymers

BI 3010 Supporting Material

• BI 3010 Reading List
• Nucleophiles (handout)
• Functional Groups (handout)
• Nomenclature (handout)
• Curley Arrows
• BI 3010 notes
• Sample Exam Question for BI3010

• Introduction to Chemical Mechanisms
• Chemical Kinetics
• Nucleophilic and Electrophilic Reactions
• Radicals and Cytochrome P450

• Lecture 1
• Lecture 2
• Lecture 3
• Lecture 4

BI 3014 Clinical Aspects of Inflammation and Infection

Dr John Jackson

• Immune response to infection 1
• Immune response to infection 2
• Inflammation

BI 3016 Development

Dr Paula Murphy

• lecture 1
• lecture 2
• lecture 3
• lecture 4

BI 3017 Stem Cells

Dr Vincent Kelly

Stem cells

• Lectures

Stem cells - recommended reading

• A Transcriptional Logic for Nuclear Reprogramming
• Adult mice cloned from migrating primordial germ cells
• Adult stem cells-assessing the case for pluripotency
• Birth of parthenogenetic mice that can develop to adulthood
• Concise Review-Epigenetic Mechanisms Contribute to Pluripotency
• Dedifferentiation of cells-new approaches
• Epigenetic Decisions in Mammalian Germ Cells
• Epigenetics in embryonic stem cells
• Generation of germline-competent pluripotent Stem Cells
• Hematopiesis & stem cells-plasticity versus development
• Induction of pluripotent stem cells from mouse fibroblasts
• Mechanisms that mediate stem cell self-renewal and differentiation
• Monoclonal mice generated by nuclear transfer from mature B & T cells
• Programming the genome in embryonic and somatic stem cells
• Recycling the abnormal
• The stem cell niches in bone
• The stem cell niche-theme and variations
• Treatment of Sickle Cell Anemia Mouse Model
• Turing back the developmental clock
• Xist and the order of silencing

BI 3018 Drug Kinetics and Metabolism

Dr Andrew Knox

• Computational Drug Design
• Peptide Therapeutics & getting across the BBB

Dr Vincent Kelly

• Drug Metabolism
• Target Identification & Validation
• Drug Kinetics
• Drug Receptors


References

• Biochemical mechanisms of drug_action
• Can the pharmaceutical industry reduce attrition rates
• Cytochromes P450-a success story
• Drug_discovery: selecting the optimal approach
• Drug-target residence time & lead optimization
• Estimating_ KI values for tight binding inhibitors from dose response plots
• Kinetic values for mechanism-based enzyme inhibition
• Modulating G-protein coupled receptors
• Nrf2–Keap1 defines a physiologically important stress response mechanism
• Pharmacogenomics - Translating Functional Genomics into Rational Therapeutics
• Polymorphic human P450 enzymes
• Predicting in vivo drug interactions
• PXR, CAR and Drug Metabolism
• Receptor Theory
• Searching the unknown with gene-trapping
• Target deconvolution strategies
• The biological magic behind the bullets
• The _elusive _nature of intrinsic efficacy
• The evasive nature of drug efficacy
• Transporters and drug therapy
• Versatility of GPCR recognition by drugs

BI 3019 Cancer

Dr Ruth Foley

• 1. Overview of Cancer
• 2. Hallmarks of Cancer
• 3. Cancer Biomarkers
• 4. Translational Cancer Medicine

BI 3020 Cell Imaging

Dr Derek Nolan

• Electron Microscopy
• Light Microscopy
• Fluorescence Microscopy
• Sample MCQ

BI 3021 Proteins of the Immune System

Dr Ken Hun Mok

• 5 Lectures

BI 3023 Modulation of Immunity by Microbes

Dr Rachel McLoughlin

• Lecture 1
• Lecture 2: Immune response to Bacteria
• Lecture 3: Immune Evasion
• Lectures 4 & 5: Beneficial interactions of bacteria with the host

Prof Kingston Mills

• Lectures 1 & 4

BI 3040 Data Handling

Dr Anne Molloy

• Data Handling lectures