metabolism collection of biochemical rxns within a cell metabolic pathways –sequence of rxns...
TRANSCRIPT
![Page 1: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/1.jpg)
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
![Page 2: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/2.jpg)
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
![Page 3: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/3.jpg)
Catabolism vs Anabolism
Catabolism
Anabolism
![Page 4: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/4.jpg)
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
![Page 5: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/5.jpg)
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
![Page 6: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/6.jpg)
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
![Page 7: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/7.jpg)
Glycolysis• Glucose + 2NAD + 2ADP + 2Pi --> 2pyruvate + 2ATP + 2NADH
![Page 8: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/8.jpg)
K’eq ΔG°’
ΔG foractual cell
conditions
![Page 9: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/9.jpg)
• 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
![Page 10: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/10.jpg)
• Aldolase: an enzyme that cleaves an aldol (which is a beta-hydroxy ketone)
![Page 11: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/11.jpg)
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+).
![Page 12: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/12.jpg)
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
![Page 13: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/13.jpg)
• Another example of an ES complex with a covalent intermediate
• Regenerate enzyme in last step using inorganic phosphate (Pi)
![Page 14: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/14.jpg)
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
![Page 15: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/15.jpg)
• Mutase: shifts the position of a functional group
• aka as a hydratase
![Page 16: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/16.jpg)
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
![Page 17: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/17.jpg)
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
![Page 18: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/18.jpg)
Fermentation can regenerate NAD+
• Under anaerobic conditions– Skeletal muscle: Pyruvate + NADH ---> Lactate + NAD+
– Yeast: Pyruvate ---> Acetaldehyde + CO2
Acetaldehyde + NADH ---> Ethanol + NAD+
- O2
![Page 19: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/19.jpg)
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
![Page 20: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/20.jpg)
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
![Page 21: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/21.jpg)
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
![Page 22: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/22.jpg)
Allosteric regulation of metabolism
AMP = allosteric inhibitorATP = allosteric inhibitorAMP = allosteric activator
ATP --> ADP + Pi
ADP + ADP --> ATP + AMP
![Page 23: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/23.jpg)
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
![Page 24: Metabolism Collection of biochemical rxns within a cell Metabolic pathways –Sequence of rxns –Each step catalyzed by a different enzyme Enzymes of a pathway](https://reader038.vdocuments.net/reader038/viewer/2022103021/56649c7d5503460f9493180d/html5/thumbnails/24.jpg)
Metabolism: cell overview