Metabolism Fundamentals Andy Howard Biochemistry Lectures Fall 2010

Metabolism Fundamentals Andy Howard Biochemistry Lectures, Fall 2010 13 October 2010 Biochemistry: Metabolism 1 10/13/2010

Metabolic principles learned here. . . n n … will be useful throughout the remainder of the course We’ll need concepts of energy flux, feedback, feed-forward, posttranslational modification, thermodynamics, kinetics, reduction potential, . . . 10/13/2010 Biochemistry: Metabolism 2

What we’ll discuss n n Definitions Pathways Anabolism n Catabolism n Control n Flux n Feedback PTM n n Energy Oxygen n Phosphorylation Other PTMs Evolution 10/13/2010 Biochemistry: Metabolism 3

Metabolism n n n Almost ready to start the specifics (chapter 11) Define it! Metabolism is the network of chemical reactions that occur in biological systems, including the ways in which they are controlled. So it covers most of what we do here! 10/13/2010 Biochemistry: Metabolism 4

Intermediary Metabolism n n Metabolism involving small molecules Describing it this way is a matter of perspective: Do the small molecules exist to give the proteins something to do, or do the proteins exist to get the metabolites interconverted? 10/13/2010 Biochemistry: Metabolism Chart courtesy Wormbook. org 5

Metabolic pathways n n We can understand metabolic pathways in terms of macromolecular behavior as well as small-molecule behavior. Cofactors and vitamins are components of those pathways 10/13/2010 Biochemistry: Metabolism 6

Pathway n n n A sequence of reactions such that the product of one is the substrate for the next Similar to an organic synthesis scheme (but with better yields!) May be: n n n Unbranched Branched Circular 10/13/2010 Biochemistry: Metabolism 7

Metabolic pathways n n n Anabolism: buildup of complex molecules from simple ones, generally with the insertion of energy in the form of ATP hydrolysis Catabolism: breakdown of complex molecules into simpler ones, usually with release of energy in the form of ATP production or reduction of NAD to NADH Amphibolism: Overlap of anabolism with catabolism within one pathway 10/13/2010 Biochemistry: Metabolism 8

Why multistep pathways? n n Limited reaction specificity of enzymes Control of energy input and output: n n Break big inputs into ATP-sized inputs Break energy output into pieces that can be readily used elsewhere 10/13/2010 Biochemistry: Metabolism 9

Anabolic Pathways n n Buildup of complex molecules Specific pathways: n n n Gluconeogenesis (ch. 12) TCA cycle and glyoxalate pathway (12 -13) Calvin cycle (chapter 15) Starch and glycogen synthesis (12) Nucleotide and amino acid synthesis (chapters 17, 18) Fatty acid and lipid synthesis (chapter 16) 10/13/2010 Biochemistry: Metabolism 10

Anabolic pathways n Horton 10. 5; this from Citizendium. org 10/13/2010 Biochemistry: Metabolism 11

Anabolic divergence n n A few simple precursor molecules get combined and modified to form many end products Building blocks generated from various metabolites, e. g. : n n n -amino acids derived by (trans)amination of -ketoacids Fatty acids built up two carbons at a time from acetyl Co. A Carbohydrates built up from pyruvate 10/13/2010 Biochemistry: Metabolism 12

Catabolic pathways n Energy-yielding oxidations Breakdown of storage molecules (chapter 12) n Breakdown of N-containing molecules (chapter 17) n Glucose to TCA cycle (chapters 11, 13) n TCA cycle (chapter 13) n Electron transport and oxidative phosphorylation (chapter 14) n 10/13/2010 Biochemistry: Metabolism 13

Catabolic pathways n Horton 10. 6; this from citizendium. org 10/13/2010 Biochemistry: Metabolism 14

Catabolism: convergence n n Stage 1: break nutrients into building blocks Stage 2: break building blocks into a very small number of end products 10/13/2010 Biochemistry: Metabolism 15

Note that some pathways are both anabolic and catabolic! n n These pathways are amphibolic Specific metabolites are both intermediaries in these pathways and they’re useful in other contexts If a metabolite is depleted out of a pathway, we generally need a replenishment reaction to rebalance things Replenishment reactions are called anapleurotic 10/13/2010 Biochemistry: Metabolism 16

Are build-up and breakdown identical? n n No Energetics say we can’t do that n n n Some enzymes (catalyzing nearly isoergic reactions) are shared Others differ in ATP or other energy requirements Control elements can be different too 10/13/2010 Biochemistry: Metabolism 17

Common metabolic themes n n n Maintenance of internal concentrations of ions, metabolites, enzymes Extraction of energy from external sources Pathways specified genetically Organisms & cells interact with their environment Constant degradation & synthesis of metabolites and macromolecules to produce steady state 10/13/2010 Biochemistry: Metabolism 18

Metabolism and energy 10/13/2010 Biochemistry: Metabolism 19

Energy & carbon n Autotrophs n n n Photoautotrophs: get energy from light and C from CO 2 Methanopyrus, a chemiautotroph Chemiautotrophs (bacterial only) (Wikipedia) get energy from food and C from CO 2 Heterotrophs n n Photoheterotrophs (bacterial only): energy from light, require organic carbon Chemoheterotrophs: energy from food, require organic carbon 10/13/2010 Biochemistry: Metabolism Theocapsa, A photoheterotroph Kenyon microwiki 20

Energy flow n Energy flows from the sun via photosynthesis and then flows through biological systems through the ingestion of food, generation of heat, and othermodynamic processes 10/13/2010 Biochemistry: Metabolism 21

The role of oxygen n Oxygen is necessary to survival in most organisms—namely, aerobic organisms—where it functions as the final electron acceptor for the electron transport chain. It is, however, toxic because it’s reactive in ways that are often deleterious. Many mechanisms exist for detoxifying the undesirable side-products of oxygen metabolism, particularly in aerobic organisms, where the organism can’t simply escape O 2. 10/13/2010 Biochemistry: Metabolism 22

Regulation n Organisms respond to change n n Fastest: small ions move in msec Metabolites: 0. 1 -5 sec Enzymes: minutes to days Flow of metabolites is flux: n n steady state is like a leaky Cartoon courtesy bucket commonwealthsolar. com Addition of new material replaces the material that leaks out the bottom 10/13/2010 Biochemistry: Metabolism 23

Feedback and Feed-forward n Mechanisms by which the concentration of a metabolite that is involved in one reaction influences the rate of some other reaction in the same pathway 10/13/2010 Biochemistry: Metabolism 24

Feedback realities Control usually exerted at first committed step (i. e. , the first reaction that is unique to the pathway) n Otherwise, it occurs on irreversible steps n Controlling element is usually the last element in the path n 10/13/2010 Biochemistry: Metabolism 25

Feed-forward Early metabolite activates a reaction farther down the pathway n Has the potential for instabilities, just as in electrical feed-forward n Usually modulated by feedback n 10/13/2010 Biochemistry: Metabolism 26

Activation and inactivation by post-translational modification n n Most common: covalent phosphorylation of protein usually S, T, Y, sometimes H, D, E Kinases add phosphate Protein-OH + ATP Protein-O-P + ADP … ATP is source of energy and Pi Phosphatases hydrolyze phosphoester: Protein-O-P +H 2 O Protein-OH + Pi … no external energy source required 10/13/2010 Biochemistry: Metabolism 27

Phosphorylation’s effects n n n Phosphorylation of an enzyme can either activate it or deactivate it Usually catabolic enzymes are activated by phosphorylation and anabolic enzymes are inactivated Example: glycogen phosphorylase is activated by phosphorylation; it’s a catabolic enzyme Cartoon courtesy Molecular Bioinformatics Center, Tawian 10/13/2010 Biochemistry: Metabolism 28

Glycogen phosphorylase n n n Reaction: extracts 1 glucose unit from non-reducing end of glycogen & phosphorylates it: (glycogen)n + Pi (glycogen)n-1 + glucose-1 -P Activated by phosphorylation via phosphorylase kinase Deactivated by dephosphorylation by phosphorylase phosphatase 10/13/2010 Biochemistry: Metabolism 29

Amplification n n Activation of a single molecule of a protein kinase can enable the activation (or inactivation) of many molecules per sec of target proteins Thus a single activation event at the kinase level can trigger many events at the target level 10/13/2010 Biochemistry: Metabolism 30

Other PTMs n Are there other reversible PTMs that regulate enzyme activity? Yes: n n Adenylation of Y (gln synthetase) ADP-ribosylation of R (cholera toxin A 1) Uridylylation of Y (protein-DNA crosslinks) Oxidation of cysteine pairs to cystine (ubiquitous in oxidizing environments) 10/13/2010 Biochemistry: Metabolism 31

Metabolism and evolution n Metabolic pathways have evolved over hundreds of millions of years to work efficiently and with appropriate controls 10/13/2010 Biochemistry: Metabolism 32

Evolution of Pathways: How have new pathways evolved? n n n Add a step to an existing pathway Evolve a branch on an existing pathway Backward evolution Duplication of existing pathway to create related reactions Reversing an entire pathway 10/13/2010 Biochemistry: Metabolism 33