Hc13 Chembiol 150513 i&II Fbs
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Transcript of Hc13 Chembiol 150513 i&II Fbs
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Have fun, enjoy, but do NOT sit back
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About me Systems microbiologist Interested on evolu>on of Life
How environmental dynamics shape Life Model organisms are mostly Lac>c acid bacteria and cyanobacteria Combine experimental and theore>cal approaches Facilitate applica>ons related to Sustainability and Health Sciences Very limited knowledge of Dutch (my apologies)
Filipe Branco dos Santos
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Ac>va>on of Prior Knowledge what you have to bring into this lecture 1st year (Structures of Life) Cell components Cell composi>on This year (Dynamic aspects of Life) Enzyme mechanisms Transport and signaling Catabolism Bioenerge>cs DNA and RNA processing Protein synthesis Here we will focus on: How all processes in a cell are intertwined and regulated Usefulness of models to understand LIFE
Joselyn Vreede
Joost Texeira de MaUos
Paul Franz
Filipe Branco dos Santos
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1st lecture Re-cap of cellular metabolism
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Metabolism (metabolikos) meaning changeable. Refers to chemical processes occurring within a living cell.
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Reac>ons in cells do not work in isola>on Together they form a network => Represented as maps!
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Reac>ons in cells do not work in isola>on Together they form a network => Represented as maps!
Complexity can be overwhelming! Models can be used to summarize and help understand Life
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What is the most important feature of a model? a. Completeness b. Accuracy c. Usefulness d. other
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Reac>ons in cells do not work in isola>on Together they form a network => Represented as maps!
Models (e.g. maps) are a representa>on of reality => INCOMPLETE! Accuracy depends on quality of informa>on used to develop model There is no point in making a model if this is not useful somehow to us (personal view)
Models are useful ONLY if they can help us, so lets simplify
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From this
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Catabolism Hydrolysis of polymers to amino acids, nucleo>des, monosaccharides and faUy acids. Further degrada>on by oxida>ve reac>on. Energy conserved in ATP and reduced co-enzymes [NAD(P)H] Why do cells need high energy molecules?
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Anabolism Large molecules (oden polymers) are synthesized. Fueled by catabolism. Is that so???
Heterotroph u>lize an organic carbon source Autotroph u>lize inorganic sources of essen>al elements How? Chemotrophs oxida>on of inorganic molecules (NH4+, H2, H2S) Phototrophs metabolic energy is generated by (sun)light
Key concept
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Reac@on classica@on Anabolic synthesis of biomass components Catabolic synthesis of high energy compounds and reduced co-enzymes Same principle can be used to classify pathways!
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How would you classify Acetate kinase?
Acetyl-P + ADP Acetate + ATP
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How would you classify Acetate kinase?
Acetyl-P + ADP Acetate + ATP
Catabolic
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How would you classify Acetate kinase?
Acetyl-P + ADP Acetate + ATP
Anabolic
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How would you classify Glucose transport in a chemoheterotroph?
Glucose (e) => Glucose (c)
a. Catabolic b. Anabolic c. Not sure
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How would you classify Glucose transport in a chemoheterotroph?
Glucose (e) => Glucose (c)
Key concept: Amphibolic reac>on
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Can you think of an amphibolic pathway?
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hUp://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TCA. Licensed under CC BY-SA 3.0 via Wikimedia Commons
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Re-cap
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Key concept: Shared metabolism across species Suggests common origin of LIFE!
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Standard Gibbs free energy
Actual Gibbs free energy
Ac7va7on of Prior Knowledge back to the basics
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Ini>al condi>ons
If G = 0, If G < 0, If G > 0,
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If mass ac>on ra>o (Q) Keq => near-equilibrium reac>ons => reversible If mass ac>on ra>o (Q) Keq => metabolically irreversible reac>ons => irreversible
Key concept:
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Why are the beakers not the same size? What happens if ?
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Key Concept: steady-state
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WC_2
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How do cells distribute resources amongst dierent func@ons?
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How is this regulated?
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How is this regulated?
Please read Rossell S et al. (2006) Unraveling the complexity of ux regula>on: a new method demonstrated for nutrient starva>on in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 103:216671.
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[email protected] Exam level ques>on, preferably mul>ple choice