CHEM206 Week 1 2024.pdf

CHEM206 SEMESTER 2 WEEK 1 Unit Information NLIC: Chris Austin [email protected] 532.12.23 UNIT RATIONALE This unit is designed to provide students with a broad theoretical and prac...

CHEM206 SEMESTER 2 WEEK 1 Unit Information NLIC: Chris Austin [email protected] 532.12.23 UNIT RATIONALE This unit is designed to provide students with a broad theoretical and practical understanding of the metabolic biochemistry that underpins courses in general science, biomedical and plant biology. It will build on basic concepts developed in Biochemistry and will focus on the study of important molecular control and modulation of cell processes. Key topics will include enzyme production and control, the metabolic process and how it is affected by different physiological states (e.g., dieting and exercise). Students will develop their technical and communication skills using instrumentation in practical settings and through the analysis of scientific findings and preparation of written reports. LEARNING OUTCOMES On successful completion of this unit, students should be able to: 1. Describe the cellular metabolism of some key biomolecules (GA4, GA5); 2. Compare the major metabolic pathways that are involved in the production of chemical energy from nutrients in living cells (GA4, GA5) 3. Explain the controls that cells have on the correct functioning of metabolic processes (GA4, GA5) 4. Explain the effect that disease, poor nutrition and exercise can have on metabolic processes (GA4, GA5) 5. Demonstrate skills of manipulation of laboratory apparatus, careful and systematic observation, precise recording and communication of experimental data. (GA4, GA5, GA7, GA8). What to bring… Class What to bring Lecture - Lecture slides (optional, recommended), will be made available before lecture - Pen and notepad to take notes Tutorial - Tutorial questions - Pen and notepad - Lecture slides and notes - Textbook (optional) Practical - Class allocations - Safety certificate– show me before attending https://leo.acu.edu.au/course/view.php?id=26190 - LAB COAT AND SAFETY GLASSES MASK– no PPE, no lab - Enclosed shoes with a proper sole - Practical Manual - Pen and book to record observations - Please arrive on time – 15 mins – non-attendance ASSESSMENT A range of assessment procedures will be used to meet the unit learning outcomes and develop graduate attributes consistent with University assessment requirements. In order to pass this unit: you are required to attend and attempt all assessments achieve an aggregate mark of at least 50 % The assessment tasks for this unit are designed for you to demonstrate your achievement of each learning outcome. ASSESSMENT Assessment methods Weighting Date Practical times in weeks 3, 5, 7, Midsemester Quizzes (S) 30 % 10 Week 12 Practical Class Practical Assessment 30% Held during the University Written Examination 40 % Examination Period. For learning attributes assessed – please see LEO or Unit Outline Practical Report Marking Rubric (Available in ‘Assessments’ Tab on LEO) Required Text (all Ebooks available via ACU library) Moran L. A., Horton R. A., Scrimgeour G., Perry M and Rawn D. (2013) ‘Principles of Biochemistry: Pearson New International Edition, 5/E, Pearson, Prentice Hall Texts Recommended Texts Bettelheim, F A., Brown, W.H. Campbell, M. K., Farrell, S., and Torres, O.J., (2015) Introduction to General, Organic and Biochemistry (11th ed) Thomson Brook/Cole Publishers Campbell, M. K; Farrell, S. O. and McDougal O. M. (2017). Biochemistry, 9th Edition. Cengage Learning. Moran L. A., Horton R. A., Scrimgeour G., Perry M and Rawn D. (2013) ‘Principles of Biochemistry: Pearson New International Edition, 5/E, Pearson, Prentice Hall Appling D. R., Anthony-Cahill S. J. and Mathews C. K. (2016) ‘Biochemistry: Concepts and Connections’ Prentice Hall. Boyer R. F. (2001) ‘Modern Experimental Biochemistry’ 3/E, Prentice Hall Baynes J. W. and Dominiczak M. H. (2014) ‘Medical Biochemistry’ 4th Edition, Elsevier Publishers, US Voet D., Voet J. G and Pratt C. W. (2013) ‘Fundamentals of Biochemistry: Life at the Molecular Level’ 4th Edition. John Wiley & Sons My personal preference Alberts, Bruce, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Molecular Biology of the Cell. New York: Garland Science, 2002. Nelson, David L. (David Lee), 1942-. Lehninger Principles of Biochemistry. New York :W.H. Freeman, Advanced Metabolic Biochemistry Lecture outline Part 1: Introduction to Metabolic Biochemistry What is Metabolism? Metabolic concepts and pathways Pathways regulated by enzymes Important coenzymes Part 2: Thermodynamics and Mechanisms of reactions Part 3: Clinical Biochemistry – Laboratory practice Part 4: Clinical tests and disease markers Metabolism of the cell Relationships between pathways Regulation Different cells function differently What happens in different conditions  Introduction to Metabolism Metabolism is a network of reactions These reactions are group as ‘pathways’ Anabolic Catabolic Amphibolic Many share common metabolites Cell type E. coli S. serevisiae Drosophila Humans No. protein 900 5900 14,100 22,000 encoding genes % metabolic 21% 20% ~17% 23% genes in genome 11 | Directorate | Office | Faculty | School Introduction to Metabolism Five metabolic concepts to remember 1. Cells/organisms maintain specific concentrations of metabolites and enzymes; membranes are important compartments. 2. Organisms extract energy from external sources to drive reactions. 3. Metabolic pathways in each cell/organism are specified by its active genes. 4. Cells/organisms interact with and respond to their environment. 5. Molecules in these cells/organisms aren’t static. Constantly synthesised/degraded (turnover). 12 | Directorate | Office | Faculty | School  Metabolic Pathways Metabolic pathways Have discrete state and end points, but often connected to/part of other pathway(s). They: Can be linear, cyclic or spiral. Contain different number of reactions Product reaction = substrate for next reaction n ‘Metabolism’ has distinct steps enzyme specificity control energy input/output (flour fireball) Currency of Metabolism = ATP, NADH etc Highly regulated Æ key allosteric enzymes ~2900 ~2900 kJ mol-1 kJ mol-1 ATP NADH 13 | Directorate | Office | Faculty | School Regulation of Metabolic Pathways Basic concepts you need to understand In this eg all reactions are reversible [B], [C], [D] & [E], little change = steady state flux = rate of flow; can change, steady state does not (aka the amount of fluid in the glasses) Æ Æ [A] & [P] can change and affects the flux Most cases at least 1 (or more) reactions are controlled = enzymes regulated Feedback inhibition E1 (allosteric) not allowed to reach equilibrium = irreversible reaction (& flux) Feed-forward activation E4 activated by ĹĹ [B] = Ĺflux 14 | Directorate | Office | Faculty | School  Revision – regulatory enzymes Regulatory enzymes in metabolism Involves pathways Î groups of enzyme reactions in a sequence Most enzymes follow kinetic patterns One or two have greater effect on the rate of the overall sequence Rate of regulatory enzymes, can be Ĺ/Ļ by: Making more/less enzyme Covalent modification 9 Proteolytic cleavage (e.g zymogens) 9 +/- PO43- 9 Binds to regulatory protein Allosteric enzymes bind to effectors metabolites or cofactors can be activators or inhibitors 15 | Directorate | Office | Faculty ltllty ty | School ty Sch S Sc chool o l oo Revision – Enzymes Important features of enzymes [co-substrate] important for reactions (eg ATP & nucleotide molecules) Æactive site with substrate Cofactors – inorganic ions (metalloenzymes have cofactors!) Different from metal activated enzymes (eg DNA polymerase) If a cofactor or coenzyme is tightly (or covalently) bound Æ prosthetic group (eg Heme in hemoglobin) 16 | Directorate | Office | Faculty | School  Common coenzymes Most coenzymes come from our diet 17 | Directorate | Office | Faculty | School Important coenzymes Adenosine Triphosphate (ATP) 18 NAD+ + 2H+ + 2e- -> NADH + H+ Nicotinamide adenine dinucleotide (NAD+) is a biological oxidizing agent. NAD+ (oxidised form) NADH (reduced form) 19 Derived from niacin NAD+/NADH The structures shown here are the nicotinamide portions of NAD+ and NADH. NADH is an electron and hydrogen ion transporting molecule. Soluble coenzymes. 20  FAD/FADH2 Flavin adenine dinucleotide (FAD) is also a biological oxidizing agent. (vitamin B2) 21 FAD + 2H+ + 2e- -> FADH2 Only the flavin moiety is shown in the structures below. Most are tightly bound coenzymes – prosthetic group Acetyl Coenzyme A Acetyl CoA is an acetyl group carrier. – The acetyl group of acetyl CoA is bound as a high- energy thioester. End of Part 1  Lecture outline Part 1: Introduction to Metabolic Biochemistry Part 2: Thermodynamics and Mechanisms of reactions Cellular compartments and metabolism Gibbs free energy of cellular reactions ATP hydrolysis and its role in metabolism Part 3: Clinical Biochemistry – Laboratory practice Part 4: Clinical tests and disease markers Major pathways in Cells Cellular compartments and metabolism How does a cell regulate so many different pathways? Grouped: synthesis vs breakdown Use energy vs produce energy Common metabolites help regulate the direction. Location is important! (Figure 10.10) ATP 26 | Directorate | Office | Faculty | School Importance of Actual Gibbs Free Energy Change Gibbs free energy of cellular reactions Revision (CHEM106): Standard Gibbs free energy (οGιԢ) for a given reaction under standard conditions (1 atm, 25°C @ pH = 7.0); [reactants] & [products] < 1 M. Calculated by: οG°ᇱ ‫ = ݊ݔݎ‬οfG°ᇱ ‫ ݏݐܿݑ݀݋ݎ݌‬െ οfG°ᇱ ‫ݏݐ݊ܽݐܿܽ݁ݎ‬ οGιԢ = positive, reaction is not spontaneous, needs an input of energy οGιԢ = negative, reaction is spontaneous, releases energy Actual Gibbs free energy (ο۵) of cellular reactions are different from organic chemistry. Determined by [reactants] & [products] in the cell. Metabolic reactions are classified as either reversible (near equilibrium) or irreversible (one-way). 27 | Directorate | Office | Faculty | School Preview to next week’s pathway Examples reactions in metabolism Sneak peak at next week’s topic Æ Glycolysis pathways as an example 10 reactions, first two shown below: Reactants (substrates) products, on the arrow enzymes and… ATP needed for enzyme to function = coenzyme, [co-substrate] Cofactors – inorganic ions (metalloenzymes have cofactors!) Free energy of reaction: ο‫ܩ‬Ԣι +ve vs -ve values Hydrolysis of ATP is important 28 | Directorate | Office | Faculty | School ATP hydrolysis in metabolism Free energy of ATP hydrolysis Hydrolysis reactions have –ve free energy: ௞௃ ATP + H2O Æ ADP + Pi, ȟ‫ ܩ‬ᇱ ° = െ32 (1) ௠௢௟ ௞௃ ATP + H2O Æ AMP + PPi, ȟ‫ ܩ‬ᇱ ° = െ45 (2) ௠௢௟ Other equivalents to ATP: GTP, CTP and UTP. Large amount of energy released is due to: 1. Electrostatic repulsion – reduced after hydrolysis 2. Increased solubility of products 3. Delocalised electrons in the products results in a more stable molecule 4. Intracellular [ATP], [ADP] and [AMP] important to keep the system far away from equilibrium (actual free energy change is -48 kJ/mol) 29 | Directorate | Office | Faculty | School Metabolic roles of ATP Hydrolysis of ATP is coupled to reactions Coupled reactions drive reactions forward. Two separate reactions: (1) ATP + H2O ՞ADP + Pi (οGιԢ = -30.5 kJ/mol) (2) Glucose + Pi ՞ Glucose-6-phosphate + H2O (οGιԢ = 13.8 kJ/mol) Sum of οGιԢ (1 +2) = + 30  Mechanisms of reactions Readings: Ch 6 and & 7.1 Learning objectives ‰ List and describe the common types of biochemical reactions in an organic chemistry context: Group Transfer Reactions The Formation/Removal of Carbon-Carbon Double Bonds Isomerization Reactions Ligation Reactions – joining two substrates Hydrolysis Reactions - group transfer with H2O being acceptor Oxidation-Reduction Reactions ‰ Perform reaction mechanisms (i.e. electron pushing) on simplified representations of the common biochemical reactions ‰ Recognise and describe the common biochemical reactions in metabolic processes from reactants and products  Categories of reactions ORGANIC REACTION MECHANISMS Almost all of the reactions that occur in metabolic pathways are enzymatically catalyzed organic reactions – classified into 4 categories: 1. Group-transfer reactions; Transfer of electrophilic group between nucleophiles 2. Red-ox; 3. Eliminations, isomerizations, and rearrangements 4. Make/break C=C. Introduction – Basic principles Basic principles review 2. Many biochem. reactions involve nucleophiles and electrophiles Usually see them combine together C-atoms can play both roles, depends on functional groups that surround it Two types of ionic molecules: 1. electron rich – nucleophilic (-ve or unshared e- pair) 2. electron poor – electrophilic nucleophile ‘attacks’ electrophile curved arrow – movement of electron pair Intermediate between substrate and product 34 | Introduction Mechanisms of reactions - concepts Enzymatic mechanism Î breaking and forming of bonds Traced by Æ movement of electrons (follow the arrows) Similar to organic chemistry reaction mechanisms 1. Role of enzymes in a reaction 2. Enzymes use one or more of the following strategies: a) Catalysis by Proximity b) Covalent Catalysis c) Acid-Base Catalysis d) Metal Ion Catalysis 35 | Directorate | Office | Faculty | School Revision – mechanisms of catalysis Mechanisms of catalysis Enzymes use one or more of the following strategies: 1. Catalysis by Proximity 2. Covalent Catalysis – transient covalent bond formed between enzyme and substrate. 3. Acid-Base Catalysis – most common. Transfer of H+, formation of unstable charged intermediate 4. Metal Ion Catalysis – ionic interactions between M and substrate. Help with orientation, stabilize charge or mediate redox reactions. 36 | Directorate | Office | Faculty | School Mechanisms of catalysis - proximity 1 – Catalysis by Proximity E active site is pre-organized to form near-attack complexes Å aa Orientation v important: Van der Waals contact (D