Metabolism 1 Flashcards
Metabolism is
A highly integrated network of chemical reactions from which___ and ____ ____ are derived.
___ and____ pathways.
Essentially the same in ___ ___ and ____
Metabolism is
A highly integrated network of chemical reactions from which energy and biological precursors are derived.
Coupled and interconnected pathways.
Essentially the same in bacteria, plants, and animals.
Catabolism is the ____ pathways to salvage ___ and ___ from ____ such as nucleotides, proteins, lipids and polysaccharides. The process ____ energy. (___gonic reaction)
Anabolism is the____ of _____ such as nucleotides, proteins, lipids and polysaccharides from ___ ____ molecules. This process ____energy. (___gonic reaction)
Catabolism is the degradation pathways to salvage components and energy from biomolecules such as nucleotides, proteins, lipids and polysaccharides. The process generates energy. (Exergonic reaction)
Anabolism is the biosynthesis of biomolecules such as nucleotides, proteins, lipids and polysaccharides from simple precursor molecules. This process requires energy. (Endergonic reaction)
Four Principles of Metabolic Pathways
Metabolic pathways are_____
Every metabolic pathway has a ___ ____
Other reactions are ___ ____
All metabolic pathways are ____
Metabolic pathways in eukaryotes occur in specific ___ ____
Four Principles of Metabolic Pathways
Metabolic pathways are irreversible.
Every metabolic pathway has a committed step.
Other reactions are near equilibrium
All metabolic pathways are regulated.
Metabolic pathways in eukaryotes occur in specific cellular locations.
Bioenergetic Concepts
Standard biological free energy change DG°’
Free energy change under a ____ set of conditions
pH = ___ for biological reactions
Directly related to _____of ___ and ____
Bioenergetic Concepts
Standard biological free energy change DG°’
Free energy change under a standard set of conditions
pH = 7.0 for biological reactions
Directly related to concentration of reactants & products
Adenosine Triphosphate—ATP
___ high energy bonds (______ bonds)
Currency of free energy for the cell
DG° = ____ kcal/mol Hydolyze ATP and you release 7.3 kcal/mol
Adenosine Triphosphate—ATP
2 high energy bonds (phosphoanhydride bonds)
Currency of free energy for the cell
DG° = -7.3 kcal/mol Hydolyze ATP and you release 7.3 kcal/mol
“High energy bonds” is a misleading term
DGo for phosphoryl transfer potential for ATP:
Difference in free energies between the reactants and products due to
- ___ ___
- Electron Cloud can move around
- In _____ (part of ATP) you have less resonance structures
- Single phosphate group (______) has more resonance structuresà more stable
- ___ ___
- Phosphate groups have high amount of – charges
- These – charges will_____ each other so molecule is ___
- Prefers to be in less negative state than a more negative state. It likes to be cleaved. In that process, E is expelled
- ____ due to ____
- Phosphate groups are highly ___ compared to ____ form
- These 3 factors contribute to the -7.3 kcal/mol
“High energy bonds” is a misleading term
DGo for phosphoryl transfer potential for ATP:
Difference in free energies between the reactants and products due to
Resonance stabilization
Electron Cloud can move around
In pyrophosphate (part of ATP) you have less resonance structures
Single phosphate group (orthophosphate) has more resonance structuresà more stable
Electrostatic repulsion
Phosphate groups have high amount of – charges
These – charges will repel each other so molecule is unstable
Prefers to be in less negative state than a more negative state. It likes to be cleaved. In that process, E is expelled
Stabilization due to solvation
Phosphate groups are highly soluble compared to pyrophosphate form
These 3 factors contribute to the -7.3 kcal/mol
Central role of ATP
Hydrolysis of ATP produces ___ ____ that is ____ to a molecule involved in an ____ process (It is activated)
Phosphorylation is the process of ATP _____ _____to a molecule
Results in a ____ ____that can complete the intended reaction
Phosphate is ____ when second substrate binds
Central role of ATP
Hydrolysis of ATP produces inorganic phosphate that is attached to a molecule involved in an endergonic process (It is activated)
Phosphorylation is the process of ATP transferring phosphate to a molecule
Results in a phosphorylated intermediate that can complete the intended reaction
Phosphate is released when second substrate binds
Energy Charge
Measure of relative amounts of ___ ___ ____ in cell
Much of metabolism controlled by energy charge
If all ATP: energy charge = __
If all AMP: energy charge = __
Most cells: energy charge = __-__
Catabolic reactions are favored when the energy charge is __, while anabolic reactions are favored when the energy charge is ___
Energy Charge
Measure of relative amounts of ATP, ADP, AMP in cell
Much of metabolism controlled by energy charge
If all ATP: energy charge = 1.0
If all AMP: energy charge = 0
Most cells: energy charge = 0.8-0.95
Catabolic reactions are favored when the energy charge is low, while anabolic reactions are favored when the energy charge is high
Summary
Metabolism is an ___ and ____ network of reactions from which energy and biological precursors are derived.
Near equilibrium reactions are freely ___, where as reactions that function far from equilibrium server as ___ points and make metabolic pathways ___
Exergonic reactions are coupled to endergonic reactions to make them more favorable.
The ___ ___ of a cell determines the fate of catabolic and anabolic reactions.
Summary
Metabolism is an integrated and interconnected network of reactions from which energy and biological precursors are derived.
Near equilibrium reactions are freely reversible, where as reactions that function far from equilibrium server as regulatory points and make metabolic pathways irreversible.
Exergonic reactions are coupled to endergonic reactions to make them more favorable.
The energy charge of a cell determines the fate of catabolic and anabolic reactions.
Pathways directly involved in ATP synthesis
_______
______
_______
Pathways directly involved in ATP synthesis
Oxidative phosphorylation
Glycolysis
Citric acid cycle
The Mitochondrion
Site of ___ ____
____ membrane
Most of chemistry takes place in ___ ___
Folded into___
Contains proteins of___
All dependent on ___ ___ ___
High [H+] in ____
Low [H+] in ___
The Mitochondrion
Site of oxidative phosphorylation
Double membrane
Most of chemistry takes place in inner membrane
Folded into cristae
Contains proteins of ETC
All dependent on proton motive force
High [H+] in intermembrane space
Low [H+] in matrix
Components of the respiratory chain
- 4 Enzyme complexes (____ in the membrane–>____ protein))
- I: ____-_ ______ (I) (____ _____ complex)
- II: ____-_ _____ (II) (____ _____)
- III: ___ ____ (III) (____ _-_complex)
- IV: ____ ______ (IV)
- Only complexes _ _ _ pump protons
- 2 ___ carriers
- _ (__________)
- ____ _
Components of the respiratory chain
4 Enzyme complexes (Fixed in the membraneàtransmembrane protein))
NADH-Q Reductase (I) (NADH dehydrogenase complex)
Succinate-Q Reductase (II) (Succinate dehydrogenase)
Cytochrome Reductase (III) (Cytochrome b-c complex)
Cytochrome Oxidase (IV)
Only complexes I, III, IV pump protons
2 Mobile carriers
Q (Ubiquinone)
Cytochrome c
Electron carriers involved in oxidative phosphorylation
_____________
______________
*Connect other metabolic pathways to oxidative phosphorylation
Electron carriers involved in oxidative phosphorylation
NAD++ 2H++2e-→ NADH+H+
FAD+ 2H++2e-→ FADH2
*Connect other metabolic pathways to oxidative phosphorylation
Sources of Reduced Coenzymes
Breakdown of ___ ___ and ___
____
Sources of Reduced Coenzymes
Breakdown of
Carbs
Fats
Proteins
CAC
Oxidative Phosphorylation
___ ___ and ___ ____ are separate processes that are ____
Two parts to oxidative phosphorylation
Tramsfer of electrons
Synthesis of ATP
à If one shuts down, so will the other. They __ __ __ coupled
Oxidative Phosphorylation
Electron transport and ATP synthesis are separate processes that are coupled.
Two parts to oxidative phosphorylation
Tramsfer of electrons
Synthesis of ATP
à If one shuts down, so will the other. They have to be coupled
Flow of electrons through the chain
NADH will transfer electrons to _______
Electrons move thru _____–>_____-> _____–>_____
Cytochrome oxidase will transfer the electrons to __ forming water.
In order for electrons to move down this way
The electric potentials should become more positive
Electrons are negatively charged and drawn twd more positive potential
If you look carefully, it drops in the middle
_________ drives that electron
The Gibbs Free Energy should become more negative
Used to __ ___ from __ to the __
Flow of electrons through the chain
NADH will transfer electrons to NADH dehydrogenase
Electrons move thru Ubiquinoneàb-c complexà cytochrome C à cytochrome oxidase
Cytochrome oxidase will transfer the electrons to O2 forming water.
In order for electrons to move down this wayThe electric potentials should become more positive
Electrons are negatively charged and drawn twd more positive potential
If you look carefully, it drops in the middle
High Gibbs free Energy drives that electron
The Gibbs Free Energy should become more negative
Used to pump protons from matrix to the intermembrane space
Electron transfer and proton flow
Pump Protons from ___ to ____
Build a proton gradient
High [H+] in _______–> ____ Gradient
High amount of __ ____ on one side compared to other–>_______
Total: _____ gradient
Electron transfer and proton flow
Pump Protons from MatrixàIntermembrane Space
Build a proton gradient
High [H+] in Intermembrane Spaceà Concentration Gradient
High amount of + charge on one side compared to otheràelectrical gradient
Total: Electrochemical gradient
Other complexes transfer electrons to ___ without ___ ___
___ ____
- ___ transfers its electrons thru here
___ __ ___ ______ (____)
Other complexes transfer electrons to CoQ without translocating protons
Succinate dehydrogenase
FAD transfers its electrons thru here
Glycerol 3-phosphate dehydrogenase (shuttle)
Specific Inhibitors Block at Specific Sites
___ ___ Blocks I
____ Blocks 3
____ Blocks 4
They used inhibitors to determine ___ of the ____
Specific Inhibitors Block at Specific Sites
Amytal rotenoneà Blocks I
Antimycin Aà Blocks 3
CN- COà Blocks 4
They used inhibitors to determine fcn of the complexes
Proton Motive Force (gradient) can drive a variety of processes
Proton Motive Force (gradient) can drive a variety of processes
ATP synthesis
Heat production
NADPH synthesis
Flagellar Rotation in Bacteria
Active Transport
Electron potential
Chemiosmotic Hypothesis
Proposed by Peter Mitchell
___ ___ ___ drives synthesis of ATP
Evidence includes artificial ___ ___ and ____ experiments
He made a ___ vesicle and incorporated bacteriorhodopsin (a protein that responds to light).
Flash light on it and it actively transports___ from the ___ into the__. Create a gradient.
He also incorporated an ___
When he added ADP and Pi he was able to create ___
Chemiosmotic Hypothesis
Proposed by Peter Mitchell
Proton motive force drives synthesis of ATP
Evidence includes artificial pH gradients and reconstitution experiments
He made a lipid vesicle and incorporated bacteriorhodopsin (a protein that responds to light).
Flash light on it and it actively transports protons from the media into the vesicle. Create a gradient.
He also incorporated an ATPase
When he added ADP and Pi he was able to create ATP.
ATP Synthase (ATPase)
___ enzyme
- __ Subunit
- Contains____ site for ATP synthesis
- Spherical ___
- 5 different subunits (a-e)
- __ Subunit
- Contains ___ ____
- Transmembrane
- 4 subunits
- ___ ____
- Regulates __ __ & __ __
- ___ between F1 & F0
- ____ ____ ____ ____ (OSCP)
Located in ___ ___ ____
Active site facing ____
____ catalyzes ATP ↔ ADP + Pi
Membrane sector forms __ ____
___ ____ regulates H+ transfer
ATP Synthase (ATPase)
Multisubunit enzyme
F1 Subunit
Contains catalytic site for ATP synthesis
Spherical headpiece
5 different subunits (a-e)
F0 Subunit
Contains proton channel
Transmembrane
4 subunits
F1 Inhibitor
Regulates proton flow & ATP synthesis
Stalk between F1 & F0
Oligomycin-sensitivity-conferring protein (OSCP)
Located in inner mitochondrial Membrane
Active site facing matrix
Head catalyzes ATP ↔ ADP + Pi
Membrane sector forms H+ pore
Connecting region regulates H+ transfer
Binding Change Mechanism for ATP Synthase
Mechanism proposed by Paul Boyer & John Walker
__ catalytic sites cycle through _ conformational states
As substrate binds, it takes 3 conformational states
___ ____ drives interconversion of forms of binding sites in enzyme allowing synthesis and release of __
Different conformation at 3 catalytic sites
___: allows ADP and Pi to enter
___: allows ADP + Pi to interact
___ produces ATP
Conformation changes due to___ ____
Requires influx of ____ protons to get one ATP
Binding Change Mechanism for ATP Synthase
Mechanism proposed by Paul Boyer & John Walker
3 catalytic sites cycle through 3 conformational states
As substrate binds, it takes 3 conformational states
Proton gradient drives interconversion of forms of binding sites in enzyme allowing synthesis and release of ATP
Different conformation at 3 catalytic sites
Open: allows ADP and Pi to enter
Loose: allows ADP + Pi to interact
Tight: produces ATP
Conformation changes due to proton influx
Requires influx of three protons to get one ATP
Yield of ATP produced during oxidative phosphorylation
NADH à O2 __ ATP
FADH2 à O2 __ ATP
For each Glucose ____ ATP
Efficiency of Ox/Phos compared to “burning” glucose = ___%
Ox/Phos more efficient by 32%
Yield of ATP produced during oxidative phosphorylation
NADH à O2 2.5 ATP
FADH2 à O2 1.5 ATP
For each Glucose 30 (32) ATP
Efficiency of Ox/Phos compared to “burning” glucose = 32% àOx/Phos more efficient by 32%
Respiratory Control
Electrons are transferred to O2 only if________________
Acceptor Control: ___must be available for oxidative phosphorylation to proceed
Availability of substrates – ___ ___and ____
Respiratory Control
Electrons are transferred to O2 only if ADP is phosphorylated to ATP
Acceptor Control: ADP must be available for oxidative phosphorylation to proceed
Availability of substrates – NADH, phosphate and O2
Remember that glycolysis takes place in the cytoplasm,
Aerobic oxidation of cytosolic NADH
NADH CANNOT___ ___ ____
We have shuttles
_______ shuttle
__directional
Mostly in ___ ___
First identified in ___ ___ ___
___ ____ shuttle
__directional
Mostly in ___ and ___
Remember that glycolysis takes place in the cytoplasm,
Aerobic oxidation of cytosolic NADH
NADH CANNOT cross mitochondrial membranes
We have shuttles
Glycerol 3-phosphate shuttle
Unidirectional
Mostly in skeletal muscle
First identified in Insect flight muscle
Malate-Aspartate shuttle
Bidirectional
Mostly in liver and heart
Glycerol 3-phosphate Shuttle (___ energy)
NADH from glycolysis will reduce __ to __
G3P can freely move thru outer membrane into intermembrane space.
IMS space has glycerol 3 phosphate dehydrogenase
It has __ that will be reduced to ___
and that will enter ETC
Glycerol 3-phosphate Shuttle (“Costs” energy)
NADH from glycolysis will reduce DHA to G3P.
G3P can freely move thru outer membrane into intermembrane space.
IMS space has glycerol 3 phosphate dehydrogenase
It has FAD that will be reduced to FADH2
and that will enter ETC
Malate-Aspartate Shuttle (_ energy cost)
Takes __ and converts it to ___
___–> ___
Malate ___ ____ equivalents into mitochondria
Malate ___ to oxaloacetate, _____ ____ to ____
Malate-Aspartate Shuttle (No energy cost)
Takes Malate and converts it to Aspartate.
Oxaloacetateà Malate
Malate carries reducing equivalents into mitochondria
Malate oxidized to oxaloacetate, NAD reduced to NADH
Transport across inner & outer mitochondrial membranes
- Inner membrane
- ____ number of molecules can cross membrane
- This is because otherwise you can’t establish____ ____
- ___ _____ gradient drives transport
- Specific____
- For the molecules that must move across like ___ and___
- ____ number of molecules can cross membrane
- Outer membrane has larger __ ____ ____(_____=____ ____ ___ ___)
Transport across inner & outer mitochondrial membranes
Inner membraneLimited number of molecules can cross membrane
This is because otherwise you can’t establish electrochemical gradient
Electrical potential gradient drives transport
Specific translocases
For the molecules that must move across like ADP and Pi
Outer membrane has larger less specific pores (VDAC=voltage-dependent anion channels)
Transport of ATP, ADP and Pi across the inner membrane
- ATP ____ to move ATP from ___ to ____
Inhibitors
______: Blocks ATP Translocase
_____: Bloccks ATP Synthase proton channel
Transport of ATP, ADP and Pi across the inner membrane
ATP translocases to move ATP from mitochondrion to cytoplasm
Inhibitors
Atractyloside: Blocks ATP Translocase
Oligomycin: Bloccks ATP Synthase proton channel
Uncouplers of Oxidative Phosphorylation
Breakdown ___ ____ from ___ ____
Make the ___ ___ more ____
Uncouplers are __ ____ molecules which can ___ the inner mitochondrial membrane
Stimulate the ___ of substrates in the ___ of ____ ____
___ the ___ ____by ___ ____ across the inner membrane
Energy release during electron transport is generated as ___
Uncouplers of Oxidative Phosphorylation
Breakdown Electron Transport from ATP synthesis
Make the inner membrane more permeable
Uncouplers are lipid soluble molecules which can cross the inner mitochondrial membrane
Stimulate the oxidation of substrates in the absence of ATP synthesis
Disrupt the proton gradient by transporting protons across the inner membrane
Energy release during electron transport is generated as heat
Uncoupling of oxidative phosphorylation generates heat
- Maintain __ ___
- Who? ___ ,____ and ____
- ___ adipose tissue which abundant in ____
- Uncoupling protein (UCP); _____
- Channel-_____ membrane to ____
- Regulated by __ __ (______)
- Babies and hibernating animals have brown fat.
- The mitochondria have protein called thermogenin which is activated when its cold thru sym NS. This allow thermogenin to be incorporated into inner membrane. It has a channel and it disrupts the proton gradient. Now you synthesize heat instead of ATP.
Uncoupling of oxidative phosphorylation generates heat
Maintain body temperature
Hibernating animals, newborns, animals adapted to cold
Brown adipose tissue which abundant in mitochondria
Uncoupling protein (UCP); thermogenin
Channel-permeabilizes membrane to protons
Regulated by fatty acids (norepinephrine)
Babies and hibernating animals have brown fat.
The mitochondria have protein called thermogenin which is activated when its cold thru sym NS. This allow thermogenin to be incorporated into inner membrane. It has a channel and it disrupts the proton gradient. Now you synthesize heat instead of ATP.
Mitochondrial Diseases
Mitochondrial DNA codes for __ ___ (~__%) of the subunits of ___ ____complexes and ATP synthase
Phenotypic effects of mutations reflect ____of tissue to ___ ___
___ ___ ___ most sensitive
Also effects on ___ ___, ____ , ___ ,___
___, ____
Wide variety of symptoms
Mitochondrial Diseases
Mitochondrial DNA codes for only some (~20%) of the subunits of respiratory chain complexes and ATP synthase
Phenotypic effects of mutations reflect reliance of tissue to oxidative phosphorylation
Central nervous system most sensitive
Also effects on skeletal muscle, heart muscle, kidney, liver
Aging, cancer
Wide variety of symptoms
Leber’s hereditary optic neuropathy (LHON)
Causes ___ ____ ____ and ___ ____
Mutations in subunits of ___ ____
Often exhibit ___ ___ ___
Leber’s hereditary optic neuropathy (LHON)
Causes loss of vision and cardiac dysrhythmia
Mutations in subunits of NADH dehydrogenase
Often exhibit swollen optic nerve
Potential Oxidative Damage
One electron ___ of O2 yields _____anion
Potentially ___ ___; ____ oxygen species
(ROS); _____ damage
Protective Mechanism
Degenerative diseases - _____ _____ ______
From mutations in protective enzymes
Electrons can move out of the chain.
Radicals can break down proteins, fats
ROS: Reactive Oxygen Species
ROS dependent aging: As you get older you build up more free radicals and that’s why most of proteins in bodies getting damaged and that increases aging
Potential Oxidative Damage
One electron reduction of O2 yields superoxide anion
Potentially destructive radical; reactive oxygen species
(ROS); oxidative damage
Protective Mechanism
Degenerative diseases - Parkinson’s, Alzheimer’s and Huntington’s
From mutations in protective enzymes
Electrons can move out of the chain.
Radicals can break down proteins, fats
ROS: Reactive Oxygen Species
ROS dependent aging: As you get older you build up more free radicals and that’s why most of proteins in bodies getting damaged and that increases aging
Summary
Oxidative phosphorylation occurs in _____
Electron transfer through respiratory chain results in___ ____
Proton gradient used to ___ ____
Oxidative phosphorylation ____ by need for ATP
Summary
Oxidative phosphorylation occurs in mitochondria
Electron transfer through respiratory chain results in proton gradient
Proton gradient used to synthesize ATP
Oxidative phosphorylation regulated by need for ATP
