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
Anabolism
Catabolism
Catabolism vs 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
ADP + Pi --> ATP
• Theoretical Yield ~ 93 ATP
• Actual (aerobic) ~ 36 ATP
ΔG°’= -686 kcal/mol
ΔG°’= +7.3 kcal/mol
39% efficient
– Marathon runner
• Actual (anaerobic) = 2 ATP
– Sprinter
2% efficient
Glycolysis
• Glucose + 2NAD + 2ADP + 2Pi --> 2pyruvate + 2ATP + 2NADH
ΔG for
actual cell
conditions
K’eq
ΔG°’
• 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
ATP --> ADP + Pi
ADP + ADP --> ATP + AMP
ATP = allosteric inhibitor
AMP = allosteric activator
AMP = allosteric inhibitor
Regulation of enzyme activity by
covalent modification
• Phosphorylation
– Serine
uncharged
charged
H2C-OH --> H2C-O-PO32protein kinases
enz
P
enz
protein phosphatases
– 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
Metabolism: cell overview