Week 1 Lecture 1+2 PDF

 Weeks 1 – 6: Dr. Paula Meleady  Weeks 7 – 12: Dr. Naomi Walsh Assessments  2 x MCQs (10% each) at end of each block ◦ Weeks 1-6 (Paula) – in class test – to be held in week 6 ◦ Weeks 7-12 (Naomi) – format TBC  End of semester exam (80%)  The purpose of this mod...

 Weeks 1 – 6: Dr. Paula Meleady  Weeks 7 – 12: Dr. Naomi Walsh Assessments  2 x MCQs (10% each) at end of each block ◦ Weeks 1-6 (Paula) – in class test – to be held in week 6 ◦ Weeks 7-12 (Naomi) – format TBC  End of semester exam (80%)  The purpose of this module is to help students build on their understanding of advanced concepts of cell biology, focusing on structure and function of proteins, lipids and extracellular vesicles; signaling pathways, cell cycle and cellular-cross talk with immune cells.  Students will gain insight into dysregulation of cellular processes which can lead to diseases such as cancer and diabetes.  They will also focus on tools (particularly lipidomics, proteomics, extracellular vesicles, targeted therapies) used for advancing molecular medicine, disease diagnosis and treatment. 1. Value why lipids and extracellular vesicles are considered a new platform for drug delivery, biomarker discovery and future cancer therapies. 2. Describe the functional characteristics of human pancreatic beta cells and evaluate the most promising sources of new beta cells for functional replacement in Type 1 diabetes. 3. Discuss the advancement in proteomic/mass spec methods to detect specific proteins in biological samples 4. Define the molecules, cell types and pathways that uniquely distinguish the cells in the body including those of the immune system 5. Knowledge of molecular, genomic and cellular processes of immunological and cancer diseases 6. Identify and discuss the cell dysregulations that lead to the hallmarks of cancer Week 1 Week 4  Why study lipids?  Extracellular Vesicles as ‘natural’  Overview of lipid classes drug delivery systems  ‘Synthetic’ lipid-based drug Week 2 delivery systems  Lipid transport mechanisms ◦ Liposomes  Importance of lipids in health and ◦ Solid Liquid Nanoparticles disease (e.g., cell signalling events) Weeks 5 and 6  Introduction to Proteomics & Mass Week 3 Spectrometry in cell biology  Lipidomics and Lipid Analysis applications  Lipids are small hydrophobic molecules that carry out a multitude of crucial roles. act as structural elements in biological membranes store energy function as signalling molecules in cellular response pathways  Disruption to their levels of expression — as occurs in obesity, diabetes, autoimmunity or inborn errors of lipid metabolism leads to dysfunction and disease in many organs  A major class of biological molecules that play many key roles Diversity of lipids is of the same order of magnitude as proteins cells express 10000s of different lipids and 100s of proteins to regulate their metabolism and transport. Technological developments in 21st century have helped to characterise lipids more comprehensively 1. A perception among many scientists that lipids are too difficult to work with! E.g., poorly soluble in water, needs solvents to solubilise them 2. The nature of lipids and how they function 3. A lack of techniques comparable to protein analysis to visualise lipids and manipulate their levels, both globally and locally. Much easier to analyse DNA and RNA  Lipids make up over 10% of the human body Disruptions of the sensitive lipid metabolism are highly correlated with different types of diseases thrombocytopenia metabolic syndrome diabetes obesity Hyperlipidemia Cardiovascular disease Obesity is reaching pandemic levels, causing a larger annual health burden than infectious diseases. Therefore, lipid metabolism is becoming an emerging scientific field and is a central part of pharmacological research today statins, cyclooxygenase (COX) inhibitors  A number of drugs are already being used to regulate cholesterol uptake in the body  Treatment/management of diseases ◦ E.g. cardiovascular disease, stroke prevention, etc. ◦ Statins  mode of action is primarily via inhibition of HMG-CoA (hydroxymethylglutaryl-coenzyme A) reductase, the rate-limiting enzyme in the cholesterol biosynthesis pathway ◦ Bile acid binding resins  drugs that bind to bile acids in the intestinal lumen & prevent their normal reabsorption. Bile acids are synthesized by the liver by oxidation from cholesterol  Greater understanding of role of lipids in disease mechanisms disease progression Biomarkers of disease, e.g. cancer New therapeutic targets (e.g. in cancer) New tools to do this E.g. Lipidomics  Biomarkers of disease, e.g., cancer lipid metabolism in cancer provides the necessary building blocks required to sustain tumour growth an alternative fuel source for ATP generation. Fatty acid synthase (FASN) functions as a central regulator of lipid metabolism and plays a critical role in the growth and survival of tumours with lipogenic phenotypes New therapeutic targets ceramide (tumour suppressor) fatty acid syntase Enzymes of sphingosine metabolism as potential pharmacological targets for therapeutic intervention in cancer  Detailed analysis and global characterisation, both spatial and temporal, of the structure and function of lipids (the lipidome) within a living system. To understand lipids in context with their proteins (enzymes) and building blocks (metabolites) in a true systems biology way.  Lipids – Back to Basics Lipids are fundamental building blocks of all cells and play many important and varied roles. Key components of the plasma membrane and other cellular compartments nuclear membrane, endoplasmic reticulum, Golgi apparatus, and trafficking vesicles such as endosomes and lysosomes. Lipid composition of different organelles, cell types, and ultimately tissues can vary substantially, suggesting that different lipids are required for different functions Mammalian cells express 10000s of different lipid species and use 100s of proteins to synthesize, metabolize and transport them. Lipid Classes An important feature of lipids is their hydrophobic nature Little affinity for water Readily soluble in non polar solvents, e.g chloroform, ether Some lipids are amphipathic- polar and non polar regions and important for membrane structure I. Fatty acids II. Triacylglycerols III. Phospholipids IV. Glycolipids V. Steroids  Fatty acid is a long unbranched hydrocarbon chain with a carboxyl group at one end Amphipathic Carboxyl group (often called the ‘head’) is polar Hydrocarbon tail is nonpolar Fatty acids contain a variable but usually even number of carbon atoms/chain C16 and C18 are especially common Fatty acid a straight chain of an even number of carbon atoms with hydrogen atoms along the length of the chain and at one end of the chain and a carboxyl group (―COOH) at the other end. BE314  Fatty Acids – some properties Fatty acids with even numbers of carbon atoms are efficient forms of energy storage Their synthesis involves step wise addition of 2C units to a growing chain They are highly reduced (have many H and few O), so they yield a lot of energy upon oxidation 1 g fat contains >2 times usable energy (9 kcal/g) than 1 g sugar (4 kcal/g) Fatty acids without C=C are saturated; every C atom in chain has max no. of H atoms attached toit. Unsaturated fatty acids contain 1 or >1 C=C; This introduces a bend/kink in the chain that prevents tight packing BE314  Trans FA - contain C=C that causes less of a bend in the fatty acid chain. Naturally present in small amounts in meat/ dairy products, but produced artificially during commercial production of shortening and margarine Linked to changes in blood [cholesterol] that are associated with increased risk of heart disease https://www.megalac.com/resources- advice/fats-advice/100-cis-and-trans-fatty-acids BE314  Consist of glycerol molecule with 3 fatty acids linked to it by ester bonds formed by removal of H2O {A condensation reaction} TGs are synthesised stepwise, with one fatty acid added at a time Monoacylglycerols Diacylglycerols Triacylglycerols The 3 fatty acids of a given TG need not be identical. They can vary in length, degree of unsaturation or both. BE314  In some animals, TGs also provide insulation against low temps Walruses, seals, penguins store TG under skin, depend on insulating properties for survival TGs containing SFA are usually solid/semisolid at room temp… called fats Prominent in animals In plants most of TGs are liquid at room temperature, vegetable oil (e.g. soyabean oil, corn oil) Unsaturated, hydrocarbon chains have kinks that prevent orderly packing of molecules Lower melting temperatures than animal fats Vegetable oil can be converted into solid products like margarine /shortening by Hydrogenation (saturation) of C=C  Phospholipids are important in membrane structure Due to amphipathic nature Critical to bilayer structure in membranes Classified as Phosphoglycerides or Sphingolipids Phosphoglycerides are predominant PLs in most membranes Consist of 2 fatty acids esterified to glycerol Basic component is phoshatidic acid, which has 2 fatty acids and phosphate group attached to glycerol back bone Key intermediate in synthesis of other phosphoglycerides but is itself not prominent in membranes Membrane PLs have in addition a small hydrophilic alcohol linked to a phosphate by an ester bond, (R group) Alcohol is usually serine, ethanolamine, choline, inositol. They contribute to polar nature of the PL head group BE314  Highly polar head and 2 long non-polar chains Amphipathic nature critical to role in membrane structure Fatty acids can vary in both length and position of sites of unsaturation C16 and C18 are most common Typical PL might have 1 SFA and 1 UFA Length and degree of unsaturation can profoundly affect membrane fluidity Can be regulated by some organisms  Discovered by Johann Thudicum a German-born physician and biochemist in 1840s "A Treatise on the Chemical Constitution of the Brain“ SLs named after the Sphinx of Greek mythology in reference to the unresolved riddle of their function Sphingolipids are not based on glycerol but on amine alcohol, Sphingosine Long hydrocarbon chain, with single site of unsaturation near polar end Sphingosine can form amide bond with long chain fatty acid (up to 34 carbons) to form ceramide Polar region flanked by 2 long nonpolar tails Shape approximates to phospholipid BE314  Components of SL family differ in chemical nature of the polar head group attached to OH group of ceramide (R group) SLs are predominant in outer leaflet of plasma membrane bilayer, often found in lipid rafts- localised microdomains within a membrane that facilitate communication with external environment of a cell Glycolipids are specialised membrane components Contain carbohydrate group instead of phosphate Glycosphingolipids May contain 1-6 sugar units, D-Glucose, D-Galactose, N- Acetyl-D-Galactosamine Hydrophilic..given amphipathic nature Specialised constituents of some membranes, plant cells, cells of nervous system GLs occur in outer monolayer of plasma membrane Sites of biological recognition on surface of plasma membrane  Distinct Class of lipids Derivatives of 4 ringed hydrocarbon skeleton; so structurally very distinct from all other lipids Non polar, hydrophobic Steroids differ from one another in number and position of C=C and functional groups Exclusive to eukaryotic cells Cholesterol- Polar head group (OH on C3) and non polar hydrocarbon body and tail on C17 Insoluble, found in membranes primarily Occurs in plasma membranes of animal cells and in most organelles (except inner membranes of mitochondria) Stigmasterol and sitosterol are found in plants Ergosterol is found in fungal cells 1. Male and female sex hormones Oestrogens produced by ovaries of females, e.g. β oestradiol Androgens produced by testes of males, e.g. testosterone 2. Glucocorticoids Cortisol family of glucocorticoids that promote gluconeogenesis and suppress inflammation 3. Mineralocorticoids Aldosterone is mineralocorticoid that regulates ion balance by promoting reabsorption of sodium, chloride, bicarbonate ions in kidney