metabolism collection of biochemical rxns within a cell metabolic pathways –sequence of rxns...

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

oxaloacetate

Catabolism vs Anabolism• Catabolic: breakdown from complex to simple

– Yield raw materials (amino acids, etc) and chemical energy (NADH, ATP) – Convergent: diverse starting materials broken down to conserved set of

intermediates (pyruvate, Acetyl-CoA)

• Anabolic: synthesis from simple to complex– Consume raw materials and chemical energy stored in NADPH and ATP– Divergent: small set of molecules assembled into a diversity of products

Catabolism vs Anabolism

Catabolism

Anabolism

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

Fe0 + Cu2+ <---> Fe2+ + Cu0

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

C6H12O6 + 6O2 --> 6CO2 + 6H2O ΔG°’= -686 kcal/molADP + Pi --> ATP ΔG°’= +7.3 kcal/mol

• Theoretical Yield ~ 93 ATP• Actual (aerobic) ~ 36 ATP 39% efficient

– Marathon runner• Actual (anaerobic) = 2 ATP 2% efficient

– Sprinter

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

K’eq ΔG°’

ΔG foractual cell

conditions

• Kinase: an enzyme that can transfer phosphate from ATP to another molecule

• Phosphatase: hydrolyzes phosphate from a molecule

• Isomerase: an enzyme that can catalyze structural rearrangements

• Steps 1-3: 2 ATP used

• Aldolase: an enzyme that cleaves an aldol (which is a beta-hydroxy ketone)

Two modes of E extraction• 1. Extraction of H+ and 2e- (:H-)

– NAD+ + H: --> NADH– Extraction of :H- is done by dehydrogenase enzymes

• Dehydrogenase: oxidizes substrates by transferring hydride (H-) ions to an electron acceptor (e.g. NAD+).

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

• Regenerate enzyme in last step using inorganic phosphate (Pi)

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

• Reverse reaction looks like a classic kinase

• Mutase: shifts the position of a functional group

• aka as a hydratase

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

Reducing power: NADH vs NADPH• Synthesis of fats from sugar requires reduction of metabolites

H-C-OH + :H- + H+ ---> H-C-H + H2O

• NADH is generated from Catabolic pathways

NADH + NADP+ <---> NAD+ + NADPH transhydrogenase

• NADPH is used as reducing agent for Anabolic pathways

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

Regulation of enzyme activity• 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 + D --> E

• E is an allosteric inhibitor that binds to allosteric site blocking 1st rxn

Allosteric regulation of metabolism• Most cells have enzymes for both

glycolysis and gluconeogenesis

• Allostery controls which pathway is active versus inhibited to provide sensitivity to energy needs

Allosteric regulation of metabolism

AMP = allosteric inhibitorATP = allosteric inhibitorAMP = allosteric activator

ATP --> ADP + Pi

ADP + ADP --> ATP + AMP

Regulation of enzyme activity by covalent modification

• Phosphorylation uncharged charged

– Serine H2C-OH --> H2C-O-PO32-

– Threonine also subject to phosphorylation– Tyrosine also subject to phosphorylation– These subtle changes to the chemical information guiding

protein folding can yield conformational changes in protein structure that increase or decrease enzyme activity

enz enzP

protein phosphatases

protein kinases

Metabolism: cell overview