Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway often physically interact to form large complexes –Limits amount of diffusion needed at each step of the pathway –The product of the preceding step is the reactant in the following step –Metabolic intermediates are the products formed along the way towards the ‘final’ product Pyruvate dehydrogenase 3 enzyme activities oxaloacetate

Metabolism Catabolic: breakdown from complex to simple –Yield raw materials for synthesis of other molecules –Convergent: diverse starting materials broken down to conserved set of intermediates (pyruvate, Acetyl-CoA) –Yield chemical energy transiently stored in NADH and ATP Anabolic: synthesis from simple to complex –Consume raw materials and chemical energy stored in NADPH and ATP –Divergent

Metabolism Catabolic: breakdown from complex to simple –Yield raw materials for synthesis of other molecules –Convergent: diverse starting materials broken down to conserved set of intermediates (pyruvate, Acetyl-CoA) –Yield chemical energy transiently stored in NADH and ATP Anabolic: synthesis from simple to complex –Consume raw materials and chemical energy stored in NADPH and ATP –Divergent

Oxidation and reduction Redox reactions: the gain (reduction) or loss (oxidation) of electrons –Reducing agents = lose e- = get oxidized –Oxidizing agents = gain e- = get reduced Fe 0 + Cu 2+ Fe 2+ + Cu 0 Reducing agent + oxidizing agent oxidized + reduced –Metals show complete transfer of e- Reducing agents reduce the charge on oxidizing agents

Oxidation and reduction Redox reactions: the gain (reduction) or loss (oxidation) of electrons –Changes in organic molecules shift the degree of e- sharing Carbon in C-H bond is reduced Carbon in C=O bond is oxidized –EN diffs result in e- spending less time around C when bonded to O CH4 + 2O2 --> CO2 + 2H2O

Capture and Use of E Alkanes are highly reduced organic compounds (E rich) –Not well tolerated by most cells Fatty acids and sugars are well tolerated C 6 H 12 O 6 + 6O 2 --> 6CO 2 + 6H 2 OΔG°’= -686 kcal/mol ADP + Pi --> ATPΔG°’= +7.3 kcal/mol Theoretical Yield ~ 93 ATP Actual (aerobic) ~ 36 ATP39% efficient –Marathon runner Actual (anaerobic)= 2 ATP2% efficient –Sprinter

Glycolysis Glucose + 2NAD + 2ADP + 2Pi --> 2pyruvate + 2ATP + 2NADH

K’eq ΔG°’ ΔG for actual cell conditions

Two modes of E extraction 1. Extraction of H+ and 2e- (:H - ) –NAD + + H: --> NADH –Extraction of :H - is done by dehydrogenase enzymes

Nicotinamide Adenine Dinucleotide (NAD) add :H - to the nicotinamide ring Most NADH destined for electron-transport chain Add phosphate to ribose 2’-OH creates NADP/NADPH rAMP

Another example of an ES complex with a covalent intermediate

Two modes of E extraction 2. Substrate level phosphorylation of ADP --> ATP –transfer of phosphate from higher energy compounds to lower energy ones ATP is not the highest energy compound

Another substrate- level phosphorylation in step 10

Glycolysis: summary Steps 1, 3 –2 ATP consumed Step 4 –6C sugar split into two 3C sugars Step 6 –Redox reaction: NAD + + :H - --> NADH Step 7, 10 –Substrate level phosphorylation Glucose + 2NAD + + 2ADP + 2Pi --> 2Pyruvate + 2ATP + 2NADH No O2 used, anaerobic

Fermentation can regenerate NAD + Under anaerobic conditions –Skeletal muscle: Pyruvate + NADH ---> Lactate + NAD + –Yeast: Pyruvate ---> Acetaldehyde + CO2 Acetaldehyde + NADH ---> Ethanol + NAD + - O2

Fermentation can regenerate NAD + Under anaerobic conditions –Skeletal muscle: Pyruvate + NADH ---> Lactate + NAD + –Yeast: Pyruvate ---> Acetaldehyde + CO2 Acetaldehyde + NADH ---> Ethanol + NAD + Under aerobic conditions –Pyruvate enters TCA cycle –NAD+ regenerated by electron transport chain (oxidative phosphorylation) + O2

Reducing power Synthesis of fats from sugar requires reduction of metabolites H-C-OH + :H - + H + ---> H-C-H + H2O NADPH is used as reducing agent for Anabolic pathways NADH + NADP + NAD + + NADPH transhydrogenase

Metabolic regulation Covalent modification of enzymes –Phosphorylation uncharged charged SerineH 2 C-OH --> H 2 C-O-PO 3 2- protein kinases protein phosphatases Threonine Tyrosine e.g., phosphorylation activates glycogen phosphorylase enz P

Metabolic regulation Allosteric modulation (Allostery) –Binding of a molecule to the enzyme activates or inhibits it –Binding occurs at an ‘allosteric site’ on the enzyme –Feedback inhibition: Final product of a pathway inhibits the first enzyme in the pathway Keeps level of product from getting higher than needed A + B --> C ; C + D --> E E is an allosteric inhibitor that binds to allosteric site blocking 1st rxn

Metabolic regulation Most cells have enzymes for both glycolysis and gluconeogenesis Allostery controls which is dominant and provides sensitivity to energy needs Step 2, phosphofructokinase –ATP = allosteric inhibitor –AMP = allosteric activator Step 2, fructose bisphosphatase –AMP = allosteric inhibitor ATP --> ADP + Pi ADP + ADP --> ATP + AMP

Metabolism: cell overview

The Metabolome The collection of all metabolites within a given cell or organism Metabolomics: the systematic study of the unique chemical fingerprints of various cellular processes –The liver metabolome versus the muscle metabolome –The cancer metabolome(s) dogs can smell breast, lung, skin cancer with 88-97% accuracy! –Other disease metabolomes