Metabolism: Basic Concepts
Light energy
ECOSYSTEM
CO2 + H2O
Photosynthesisin chloroplasts
Cellular respirationin mitochondria
Organicmolecules
+ O2
ATP
powers most cellular work
Heatenergy
Catabolic pathways•Break down complex molecules into simpler compounds•Release energy
Anabolic pathways•Build complicated molecules from simpler ones•Consume energy
MetabolismThe sum total of all the chemical reactions cell needs to carry out to survive, grow, and reproduce. This control is central to the chemistry of life.
Amino acids
Sugars Glycerol Fattyacids
GlycolysisGlucose
Glyceraldehyde-3- P
Pyruvate
Acetyl CoA
NH3
Citricacidcycle
Oxidativephosphorylation
FatsProteins Carbohydrates
Cells obtain energy by the oxidation of organic Molecules
Not all of a system's energy is available to do work. The amount of energy that is available to do work is described by the concept of free energy.Significance of Free Energy:•Indicates the maximum amount of a system's energy which is available to do work.•Indicates whether a reaction will occur spontaneously or not.Free Energy and MetabolismReactions can be classified based upon their free energy changes:•Exergonic reaction= A reaction that proceeds with a net release of free energy and is spontaneous.•Endergonic reaction= An energy-requiring reaction that proceeds with a net gain of free energy; a reaction that absorbs free energy from its surroundings and non spontaneous.
Organisms live at the expense of free energy
Reactants
Products
Energy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ne
rgy
(a) Exergonic reaction: energy released
Energy
Products
Amount ofenergyreleased (∆G>0)
Reactants
Progress of the reaction
Fre
e e
ne
rgy
(b) Endergonic reaction: energy required
•If a chemical process is exergonic, the reverse process must be endergonic.•In cellular metabolism, endergonic reactions are driven by coupling them to reactions with exergonic reactions.•ATP plays a critical role in this energy coupling.
ATP is the immediate source of energy that drives most cellular work, which includes:
•Mechanical work
•Transport work
•Chemical work
(c) Chemical work: ATP phosphorylates key reactants
P
Membraneprotein
Motor protein
P i
Protein moved
(a) Mechanical work: ATP phosphorylates motor proteins
ATP
(b) Transport work: ATP phosphorylates transport proteins
Solute
P P i
transportedSolute
GluGlu
NH3
NH2
P i
P i
+ +
Reactants: Glutamic acid and ammonia
Product (glutamine)made
ADP
+
P
ATP powers cellular work by coupling exergonic to endergonic reactions
•Renewable resource by adding phosphate to ADP•The free energy required for the phosphorylation of ADP comes from the exergonic reactions(catabolism) in the cells.•Shuttling of inorganic phosphate and energy is called the ATP cycle
ATP AS A METABOLIC ENERGY STORAG
NADPH is an important carrier of electrons.
•The hydrogen gradient across the membrane created by ATP synthaseis used to drive cellular work of ATP synthesis
•It couples the electron transport chain to the ATP synthesis
Chemiosmosis: The energy coupling mechanism.
Kyoto Encyclopedia of Gene and Genomes
Major pathways of glucose utilization
Glycolysis
The Citric acid cycle coupled withOxidative phosphorylation
Electronscarried
via NADH
Glycolsis
Glucose Pyruvate
ATP
Substrate-levelphosphorylation
Electrons carried via NADH and
FADH2
Citric acid cycle
Oxidativephosphorylation:
electron transport andchemiosmosis
ATPATP
Substrate-levelphosphorylation
Oxidativephosphorylation
MitochondrionCytosol
An overview of cellular respiration
The glyoxylate cycle
Glyoxylate cycle
Cori cycle
General scheme of the pentose phosphate pathway
Glycolate pathway
Photorespiration adjacent to the calvin cycle
C2 pathway
Stoichiometry of Co2 assimilation in the Calvin cycle
C3 pathway
Carbon assimilation in C4 plants
•Co₂ is fixed at the cost of 3 ATPs where as C2 takes 5 ATPs
•Useful for the plants growing under reduced Co ₂ conditions
CAM pathway
Fatty acid biosynthesis
Oxidation of fatty acidsin mitochondria and peroxisomes
Overview of amino acid catabolism
Links between the urea cycle and citric acid cycle
Aspartate-Arginino shunt
Summary of amino acidcatabolism.
Biosynthesis of Amino Acids
Nucleic acid metabolism
http://seqcore.brcf.med.umich.edu/mcb500/na/purdegr.html
Inosine Monophosphate Oratidine-5’monophosphate
•They are controlled, often by modulation of key regulatory enzymes.
•They are compartmentalized within cells. some processes are associated with regions on the inner face of the cell membrane.
•They usually involve coenzymes, molecules that are second substrates in a number of different reactions.
•The pathways that break particular molecules down are different from those used to synthesize them. This allows them to be controlled separately
Regulation of Metabolic pathways
References
•Lehninger-Principles of biochemisty (forth edition)Authors-D.Nelson, M. Cox•Biochemistry (fifth edition)Authors-J.berg, J.Tymoczko, L.Styer•Biology(seventh edition)Authors-N.Campbell J.Reece•Harper’s Illustrated Biochemistry(26th edition)Authors-R.Murray, D.Granner, V.Rodwell•Biochemistry(second edition)Authors-Garrett and Grisham•Molecular biology of the cellAuthor-Bruce Albert•Molecular cell biology(fifth edition)Authors-Lodish, Berk