Metabolism 1 Flashcards
(36 cards)
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%
