Transcript ch3b FA11 - Cal State LA

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
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
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 substratelevel 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
• Serine
H2C-OH --> H2C-O-PO32protein kinases
P
enz
enz
protein phosphatases
• Threonine
• Tyrosine
• e.g., phosphorylation activates glycogen phosphorylase
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