Metabolism and Bioenergetics Flashcards
Define metabolism.
All the reactions in a living cell, pathways are all interconnected and allow for compounds to come in and out
Why is metabolism essential?
For energy production
Define intermediary metabolism.
Reactions that involve the interconversion of small molecules (less than 1000Da)
Define catabolism.
Breakdown -> generates E (convergent)
Define anabolism.
Use small components as building blocks -> uses energy (divergent)
Name the 3 laws of thermodynamics.
1) Energy cannot be created or destroyed, only transformed (E = mc^2)
2) Universe has a tendency to increase disorder
3) As T approaches absolute 0, atomic motion ceases
How many oC = K?
25oC = 298K
Define exergonic reactions.
-x kJ/mol is released
spontaneous
- delta G
Define endogenic reactions.
x kJ/mol is released
not spontaneous
+ delta G
What does delta G = 0 mean?
Reaction is at equilibrium, rate of substrate to product = rate of product to substrate
Name an example of an exergonic reaction
Oxidation of glucose
What is the oxidation of glucose reaction formula?
C6H12O6 + 6O2 -> 6 CO2 + 6 H2O
How does the oxidation of glucose work?
High energy electrons come from photosynthesis, oxygen is required to pick up low energy electrons at the end of the cycle and make H2O
Define delta G ++
Energy of activation (double dagger)
Since we can’t measure delta G and delta H directly, what do we do?
Compare under standard conditions
Define delta G^o
Standard free energy change (298 K, 1 atm, solution of 1 M)
Define delta G^o’
Biochemical free energy change (298 K, 1 atm, solution of 1 M, pH = 7.0)
Why is measuring delta G^o’ difficult?
Because monitoring delta S is difficult
Why do we need to know keq?
To know the processes in the cell, you need to understand all the interconnected reactions in a cell
What is the equation for keq?
keq = ((C)(D))/((A)(B))
What is the equation for delta G^o’?
G^o’ = -RT ln(keq)
What does a small keq mean? Large?
Small: delta G^o’ is positive and large (not spontaneous)
Large: delta G^o’ is negative and large (spontaneous)
How would you find keq experimentally?
Add 20 mol of reactant, at various times take measurements of reactant and product, at some point, there will be no more change -> equilibrium -> find keq
What is important to know about delta G^o’?
STANDARD FREE ENERGY IS AT 1 MOLAR
Name 2 ways we can drive unfavourable reactions.
1) Coupling reactions
2) Changing the position of the equilibrium
Do coupling reactions consume energy?
Yes
How do you find the overall keq when coupling reactions?
keqs are MULTIPLIED, not added
How does the delta G for ATP hydrolysis when the concentrations of ATP and ADP in the cell are taken into consideration compare to the delta G^o’ if its in a cell?
- delta G increases when you factor in the concentration of a cell compared to delta G^o’
- Delta G^o’ =-30.5kJ/mol
- Delta G = -50 to -65 kj/mol
What is the primary source of energy to get work done?
ATP
Which compounds are high energy compounds?
Compounds with a delta G^o’ of hydrolysis > -25 kJ/mol = high energy
Name 4 reasons why phosphoanhydride bonds are high energy.
1) At pH 7, ATP carries 4 negative charges (hydrolysis releases electrostatic stress)
2) Resonance delocalization of PO4^2- (following hydrolysis, ionization increases randomness)
3) ADP and HPO4^2- ionizes releasing a proton (increase delta S)
4) ATP hydrolysis increase the solvation of ADP and pi
How do the number of water molecules needed to solvate ATP compare to inorganic phosphate and ADP?
number of H2O molecules needed to solvate ATP is less than inorganic phosphate and ADP, increase delta S
What else do these physiochemical properties of phosphohydride bonds account for?
Energy released by hydrolysis of ADP to AMP or compounds such as G-6-P
How can energy be stored?
In the form of reducing electron carriers (NADH, NADPH, FADH2)
How are electrons transported?
As a hydride
Define a hydride.
A proton with two electrons (negatively charged)
Describe the 2 half cell reactions and the overall reaction.
Ared -> A ox + ne-
Box + ne- -> B red
—> A red + Box Bred + Aox
What does the equilibrium point for a red-ox reaction depend on?
On the relative affinity of Aox and Box for electrons
How can the flow of electrons be measured?
Measured by a voltmeter
Define reduction potential.
Tendency of a compound to ACQUIRE electrons, and thereby be reduced
The more positive the V, the better the oxidizing agent (gains electrons)
The more negative the V, the better the reducing agent (loses electrons)
What is delta E^o’?
Reduction potential tendency (1M, 1 atm, 25oC, at pH=7)
What is one of the half reactions in a biological system? What is E^o’
2 H+ + 2e- H2
What does a negative delta E^o’ mean? Positive?
Positive: tendency to gain electrons (the more oxidizing potential)
Negative: tendency to give up electrons (the more reducing potential)
Describe the equation involving delta G^o’ and delta E^o’. What is n? What is F?
delta G^o’ = -nF delta E^o’
n = nb of electrons transferred
F = Faraday’s constant (96.5 kJ/Vmol)
How do you calculate delta E^o’?
delta E^o’ = E^o’ (e- acceptor) - E^o’ (e- donor)
e- acceptor always has a ____ potential.
lower
What happens when you increase reducing potential?
Increase negative volts
Define reduction and oxidation.
Reduction: gain of electrons
Oxidation: loss of electrons
Name 2 things that decrease down the electron transport chain cascade.
- Electron energy decreases
- Reducing potential decreases
What is the oldest pathway?
Glycolysis
Define glycolysis.
the breakdown of glucose by enzymes, releasing energy and pyruvic acid.
Is glycolysis aerobic?
It is anaerobic
Where does glycolysis occur? Where does extra extraction occur?
- Occurs in cytosolic compartment
- Extra extraction in the mitochondria
What % of energy is captured without oxidative phophorylation?
5%
Name the 2 phases of glycolysis.
1) Preparatory phase
2) Payoff phase
Why does glycolysis need a preparatory phase?
You need to do something to make it unstable to activate glucose molecule -> break bonds
What is the overall reaction for glycolysis?
Glucose + 2 ADP + 2 NAD+ + 2 Pi -> 2 pyruvate + 2 ATP + 2 NADH + 2 H2O
How many molecules of ATP and NADH does one glucose molecule generate?
2 ATP + 2 NADH
What happens if you deplete NAD+?
Glycolysis stops
What does the preparatory phase require?
Requires 2 ATP
What is glucose catabolyzed to during the preparatory phase?
Glyceraldehyde-3-phosphate and dihydroxyacetone phosphate
Why is the final compound in the preparatory phase unstable?
2 negatively charged phosphates = repulsive forces
Describe the enzymatic steps of the preparatory phase.
1) Hexokinase
2) Phosphohexoisomerase
3) Phospho-fructosekinase-1
4) Aldolase
5) Triose phosphate isomerase
What does the payoff phase require? What does it produce?
Requires high energy intermediates
Produces ATP and NADH
What enters the payoff phase?
2 glyceraldehyde-3-phosphate molecules
What does the payoff phase generate?
Converts to 2 pyruvates which generate 4 ATP and 2 NADH/glucose units
What is the net production of the payoff phase?
2 ATP
Describe the enzymatic steps of the payoff phase.
6) Glyceraldehyde-3
7) Phospho-glycerate kinase
8) Phospho-glycerate mutase
9) Enolase
10) Pyruvate kinase
Describe substrate level phosphorylation. When does it occur?
Phospho-glycerate kinase moves phosphate from ADP to make molecules of ATP, occurs when you have high energy phosphate
Where is 90% of the energy trapped?
Trapped in the 2 molecules of pyruvate
What is a characteristic of C=C and phosphoesther?
Very high energy
Define a pathway
Product of first reaction is the substrate of the second reaction
What is glucose normally in the blood?
4-5 mM
Why does high levels of glucose relate to vision problems?
Modification of some proteins = problems with vision (lens proteins don’t turn over fast)
What is the role of glycogen?
Reservoir for fight/flight under anaerobic conditions
What inhibits hexokinase? What kind of inhibition is it?
High levels of G-6-P (competitive)
What does hexokinase do?
Uses ATP to generate G-6-P
Is adding a phosphate to glucose favourable?
Not spontaneous
Coupling with ATP -> both favourable
Is isomerization : conversion of G-6-P to F-6-P favourable?
Not spontaneous, so we change the position of the equilibrium
Is making fructose 1,6-biphosphate favourable?
Not spontaneous
Coupled with hydrolysis of ATP
Define allosteric enzyme.
Provide subtle regulations to control and meet cells metabolic processes
Explain PFK-1 versus the reaction velocity.
Low ATP: reaction rates are faster
High ATP: reaction rates are slower
What happens when ATP levels drop?
ADP increases, which will bind to enzyme
Where is citrate found? What does it do?
From TCA cycle - found in matrix of mitochondria
Will inhibit PFK-1
Name 2 allosteric compounds (inhibitors and activators of PFK-1).
1) ATP and citrate are allosteric inhibitors of PFK-1
2) ADP and AMP, F-2, 6-P are allosteric activators of PFK-1
Is aldol cleavage favourable?
No
Driving reaction by changing position of equilibrium
Is the conversion of glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate favourable?
Delta G^’o is not favourable
BUT Delta G IS (temperature in red blood cells, all that matters)
Is substrate level phosphorylation favourable?
It is favourable, delta G is negative
Compare delta G and delta G^’o for the glycolysis reaction.
Delta G^’o: -130.9 kJ/mol
Delta G: -103.8 kJ (stays flat - reaction equally favourable forward and reverse)
How are the 4 points of allosteric effects and inhibition regulation in glycolysis?
1) Hexokinase
2) Phosphofructokinase
3) Glyceraldehyde-3-phosphate dehydrogenase
4) Pyruvate kinase
Under anaerobic conditions, 2 pyruvates retain what % of energy in glucose?
90%
What kind of energy does catabolism release?
Some as ATP and reduced electron carriers (NADH)
ATP and NADH generated from catabolism are used for what?
As energy to power anabolic reactions
Describe Gibbs free energy equation? What is the unit of T?
G = H - TS
T is in Kelvin
In the oxidation of glucose, what is BEING reduced and what is being oxidized?
Oxidized: C6H12O6 -> 6 CO2 (losing electrons)
Reduced:
6O2 -> 6H2O (gaining electrons)
What does glucose in the presence of oxygen need in order to oxidize?
Needs energy of activation
Does delta G provide information on the reaction rates?
NO
In what form are chemical reactions written in?
They are all written in the REDUCING form, so you need to flip them around
Which glycolysis steps need to be coupled in order to drive unfavourable steps?
- Phosphorylation of glucose by hexokinase (driven by ATP hydrolysis)
- F-6-P to F-1,6-P (driven by ATP hydrolysis)
- Isomerization of DHAP to G-3-P by triosephosphate isomerase (coupled to other Rx which have a large negative delta G^o’)
What kind of agent would the electron acceptor be? Electron donor?
Electron acceptor: oxidizing
Electron donor: reducing
Why is oxygen a very good electron acceptor?
It has a high delta E^o’
What is Faraday constant?
96.5 kJ/Vmol
How many ATP molecules and NADH molecules are produced per glucose unit entering glycolysis? What is the NET production?
- 4 ATP and 2 NADH
- Net: 2 ATP
What are glucose levels regulated by?
Insulin and glucagon
How is glucose taken into the cell? How is it trapped in cytosol?
- Taken in by transporters
- Trapped in cytosol by phosphorylation
What enzyme is a major point for the regulation of glycolysis?
Phosphofructokinase-1
What happens to glycolysis when levels of of ATP are high?
Mechanisms inhibit glycolysis
What happens to Fructose-6-Phosphate when ATP levels are high? Low?
High ATP: low F-6-P
Low ATP: high F-6-P
Which steps in glycolysis are driven by changing the equilibrium?
- Aldol cleavage of F-1,6-P into G-3-P and DHAP (driven by rapid removal of G-3-P)
- Conversion of G-6-P to F-6-P
Which reaction in the glycolytic pathway is readily reversible?
Aldolase and triose phosphate isomerase catalyzed reactions
Which step in glycolysis has a postive delta G^o’ but a negative delta G?
Conversion of G-3-P to 1,3-biphosphoglycerate (at 37oC using steady state concentration in red blood cell)
What is the first step in recovery of energy from glycolysis? What does it produce? What is it catalyzed by?
- Conversion of G-3-P to G-1,3-P
- Produces 2 NADH/glucose
- Catalyzed by glyceraldehyde-3-phosphate dehydrogenase
How does G-3-P get converted to G-1,3-P?
1) Aldehyde group of G-3-P reacts with an active sulhydryl group (cysteine) on enzyme
2) Formation of covalent intermediate + transfer of a hydride group to NAD+ to form NADH
3) NADH is released from the enzyme and Pi attach the thiol acyl bond release G-1,3-P
What are the inhibitors for hexokinase?
ATP and G-6-P
What regulates the levels of glyceraldehyde-3-phosphate dehydrogenase?
NAD+
What inhibits pyruvate kinase? What activates it?
Inhibitors: acetyl-CoA and ATP
Activators: fructose-1,6-biphosphate and AMP
Define reducing potential.
The likelihood of reducing something else
What are the three possible fates of pyruvate after glycolysis?
1) Alcohol fermentation (anaerobic)
2) Homolactic acid fermentation (anaerobic)
3) TCA cycle (aerobic)
Define fermentation.
The process of generating NAD+ from NADH is termed fermentation
NADH + H+ -> NAD+
What does alcohol fermentation produce?
CO2 + Ethanol
What is produced in homolactic acid fermentation?
Lactic acid
What is produced in the TCA cycle?
CO2 + H2O
What is used in the TCA cycle?
NAD+ -> NADH + H+
