Bioenergetics Intro Flashcards
(124 cards)
1
Q
Different forms of energy: Physics
A
- Conversion of mass and energy
- Inter-conversion of subatomic particles
- Various energy forms: Light, electrical (including magnetic), mechanical (kinetic and potential), heat, sound, and wave
2
Q
Different forms of energy: Chemistry
A
Interactions between atoms through electrons in outer orbit of atoms at various temperature, pressure, pH, and solvent
3
Q
Different forms of energy: Biochemistry
A
- Interaction between macromolecules
- Atoms in a similar way as in chemistry, except at normal temperature, pressure, pH, and strictly in aqueous media
4
Q
What are the states of matter?
A
- Solid: Cold; Ice crystal liquid
- Liquid - Warm; Water
- Gas - Hot; Steam
- Plasma - Very hot; Nuclei and electrons separated (only protons and neutrons exist; H exists as a proton in this state)
5
Q
Most of the chemistry in living systems results from the interplay of elections in the outer orbit of which atoms?
A
C, H, O, N, P, and S
6
Q
Many of the reactions in biological systems are catalyzed by enzymes and involve the lone pair of electron on which atoms?
A
N, O, S, and P
7
Q
What are metabolic pathways?
A
Sequence of biological reactions that produce one or more specific products
8
Q
What are metabolites?
A
The reactant intermediates and products of metabolic pathways
9
Q
In many complex reactions, what particular groups of atoms are actively involved in the reactions?
A
Functional groups
10
Q
Why are cells isothermal systems?
A
They function at constant temperature and pressure and can only use free energy to do work unlike other systems that can use heat release in the system
11
Q
What is catabolism also known as?
A
Degradation
12
Q
What is catabolism and what is an example of it?
A
Nutrients and cell constituents that are broken down so as to salvage their components and/or generate energy
- E.g., Plants that acquire free energy from absorbed sunlight and synthesize nutrients that transform the free energy into ATP
13
Q
What is anabolism also known as?
A
Biosynthesis
14
Q
What is anabolism?
A
Free energy stored in energy-rich compounds like biomolecules and used by cells to synthesize various compounds and ingredients from simpler components
15
Q
ATP is generated during catabolic reactions and the free energy of ATP hydrolysis is used in synthetic reactions to do what?
A
To do mechanical work; to produce light or sound; or to conduct neuronal action potentials
16
Q
HPO42- + ADP <–> ATP + H2O
A
Energy-generating processes that produce ATP from adenosine diphosphate and a phosphate ion
17
Q
ATP + H2O <–> ADP + HPO42-
A
Energy-consuming processes driven by the ATP hydrolysis
18
Q
How are the anabolic and catabolic processes coupled together?
A
Through the mediation of the universal biological energy “currency,” ATP
19
Q
How is the free energy by the catabolic process conserved?
A
Through the synthesis of ATP from ADP and phosphate or through the reduction of the coenzyme NADP+ to NADPH
20
Q
What are the five principal characteristics of metabolic pathways?
A
1) Irreversible
2) Catabolic and anabolic pathways must differ
3 Has an exergonic first committed step
4) Regulated - usually at the first committed step
5) In eukaryotes, they occur in specific cellular components
21
Q
Explain the first principle characteristic of metabolic pathways.
A
Irreversible
- Highly exergonic reaction with a large negative free energy change goes to completion
- If such a reaction is part of a multistep pathway, it makes the entire pathway irreversible
22
Q
Explain the second principle characteristic of metabolic pathways.
A
Catabolic and anabolic pathways must differ
- If two metabolites are interconvertible, the synthetic route from the first to the second must differ from the route from the second to the first because if metabolite 1 is converted to metabolite 2 by an exergonic process, the conversion of metabolite 2 to metabolite 1 requires that free energy be supplied in order to bring this otherwise endergonic process “back up hill”
- The existence of independent interconversion routes is an independent control of the two processes
23
Q
Explain the third principle characteristic of metabolic pathways.
A
Has an exergonic first committed step
- Early in each pathway there is an irreversible exergonic reaction that “commits” the intermediate it produces to continue down the pathway
24
Q
Explain the fourth principle characteristic of metabolic pathways.
A
Regulated - usually at the first committed stop
- The first committed step functions too slowly to permit its substrates and products to equilibrate
- Most metabolic pathways are controlled by regulating the enzymes that catalyze their first committed steps
- Efficient to exert control because it prevents the unnecessary synthesis of metabolites further along the pathway when they are not required
25
Explain the fifth principle characteristic of metabolic pathways.
In eukaryotes, they occur in specific cellular components
- The compartments of the eukaryotic cell allows different metabolic pathways to operate in different locations
26
What is Earth's present atmosphere?
Oxidizing atmosphere
27
What provides the energy requirements of all organisms?
Solar energy (directly or indirectly)
28
What is solar energy?
Conversion of mass into energy which causes a very large increase in disorder
29
What does solar plasma consist of?
4 hydrogen nuclei that come together to make helium
- 4 H -> 4He because of photons of visible light by thermonuclear fusion
30
What is the energy and mass relationship?
E = mc^2
- m is mass
- c is the velocity of light (3x10^8 m/sec)^2
31
What are thermodynamics?
Relationships among the various forms of energy and how energy affects matter on the macroscopic level as opposed to the molecular level; that is, it deals with amounts of matter large enough for their average properties, such as temperature, and pressure, to be well defined
- Most frequently concerned with describing the conditions under which processes occur spontaneously (by themselves)
32
What is the first law of thermodynamics?
Energy can be neither created nor destroyed
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What is a system?
The part of the universe that is of interest, such as a reaction vessel or an organism
34
What is an open system?
One that can exchange matter and energy with its surroundings
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What is a closed system?
One that can exchange matter energy with its surroundings
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What is an isolated system?
One that can't exchange matter or energy with its surroundings
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What is the surrounding?
The rest of the universe
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What is an exothermic process (-q/-delta H)?
One in which the system releases heat
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What is an endothermic process (+q/+delta H)?
One in which the system gains heat
40
What is enthalpy?
The measure of total heat present in the thermodynamic system where pressure is constant
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What is the second law of thermodynamics?
A spontaneous chemical or physical change is always accompanied by an increase in disorder of the universe
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What is a spontaneous process?
The conversion or order to chaos
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What is entropy (+delta S)?
A quantitative expression for the randomness or disorder in the system
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What is Gibbs free energy?
The required indicator of spontaneity for constant temperature and pressure processes
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What does it mean to be exergonic (-delta G)?
Spontaneous process that can be utilized to do work
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What does it mean to be endergonic (+delta G)?
Non-spontaneous process driven by the input of free energy
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delta G =
delta H - (T)(delta S)
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What does it mean to be enthalpically favoured?
Exothermic
49
What does it mean to be entropically favoured?
Exergonic
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delta G: - delta H; + delta S
Exothermic and exergonic at all temperatures
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delta G: -delta H; - delta S
Exothermic and only exergonic at temperatures below T = delta H/delta S
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delta G: + delta H; + delta S
Endothermic and only exothermic at temperatures above T = delta H/delta S
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delta G: + delta H; - delta S
Endothermic and endergonic at all temperatures
54
Enzymatic reactions that proceed in either direction are dependent on what?
The relative concentrations of their reactants and products
55
What is standard free energy?
The free energy change of a reaction at standard conditions (298K and 1 atm) when the initial concentrations of reactants and products are at 1M each
56
For a general reaction, what is the change in the Gibbs free energy (delta G)?
delta G naught' + RTln(c^c x d^d/a^a x b^b)
57
The expression for the free energy change of a reaction consists on what two parts?
1) A constant term whose value depends only on the reaction taking place
2) A variable term that depends on the concentrations of the reactants and the products, the stoichiometry of the reaction, and the temperature
58
Why is there no net change for a reaction at equilibrium?
The free energy of the forward reaction exactly balances that of the backward reaction
59
What is the biochemical standard state (delta G naught)?
The standard free energy in dilute aqueous solution at pH7 in which the activities of water and H+ are both at equilibrium when delta G = 0
60
What is the equation for the biochemical standard state (delta G naught)?
= -RTlnK'eq
61
When the reactants in a process are in excess in their equilibrium concentrations, how with the reaction proceed?
Their net reaction will proceed in the forward direction until the excess reactants have been converted to products and equilibrium is obtained
62
When the products in a process are in excess in their equilibrium concentrations, how will the reaction proceed?
The net reaction will proceed in the reverse direction so as to convert products to reactants until the equilibrium concentration is likewise achieved
63
What is the free energy of formation?
The change in free energy accompanying the formation of 1 mol of that substance, in its standard state, from its component elements in their standard states
64
What is the phenomenon for the thermodynamic basis for the operation of metabolic pathways?
Coupled reactions
65
What occurs in a coupled reaction?
The activity of free energy changes allows an endergonic reaction to be driven by an exergonic reaction under the proper conditions
66
If delta G is greater than or equal to 0, will the reaction occur spontaneously?
No
67
Explain how would a highly exergonic reaction drive an endergonic reaction.
If delta G2 was sufficiently exergonic so that delta G1 + delta G2 were less than 0, the equilibrium concentration of the product in reaction 1 will be larger than the concentration of the same reactant in reaction 2 being converted to products, so reaction 1 will operate in the forward direction to replenish the equilibrium concentration
68
What is metabolism?
Overall process through which living systems acquire and utilize free energy they need to carry out their various functions
69
Are living organisms are equilibrium?
No. They require a continuous influx of free energy to maintain order in a universe that maximizes disorder.
70
What are the categories that almost all metabolic reactions fall into?
1) Group-transfer reactions
2) Oxidation-reduction reactions
3) Eliminations, isomerization, and rearrangements
4) Reactions that make or break carbon-carbon bonds
71
What happens during a homolytic bond cleavage?
Electron pair separates such that one electron accompanies each of the atoms when a covalent bond breaks
- Usually produces unstable radicals
- Occurs mostly in oxidation-reduction reactions
72
What happens during heterolytic bond cleavage?
Electron pair remains with one of the atoms when a covalent bond breaks
- Involves either carbanion and proton formation or carbonation and hydride ion formation
73
When does hydride ion abstraction occur?
Only if the hydride is transferred directly to an acceptor such as NAD+ or NADP+
74
What broad classes are compounds participating in reactions involving heterolytic bond cleavage and bond formation categorized into?
Electron rich and electron deficient
75
What are nucleophiles?
Electron rich compounds that are negatively charged or contain unshared electron pairs that easily form covalent bonds with electron-deficient centers
76
What are electrophiles?
Electron-deficient compounds that may be positively charged, contain an unfilled valence electron shell, or contain an electronegative atom (electron lover)
77
What are the ways in which electrons are transferred from one molecule to another?
1) Direct electron transfer
2) As a hydrogen atom
3) As a hydride ion
4) Through direct combination with oxygen
78
What is a group-transfer reaction?
The transfer of an electrophilic group from one nucleophile to another
79
What do oxidation-reduction (redox) reactions involve?
Reactions involving the loss or gain of elections
80
What is oxidation referred to in biological systems?
Dehydrogenation
81
What is the result of an elimination reaction?
The formation of a double bond between two previously single-bonded saturated centers
82
What do biochemical isomerization reactions involve?
The intramolecular shift of a hydrogen atom so as to change the location of a double bond
83
What are the experimental approaches to the study of metabolism?
- Nutrient to product
- Intermediate steps
- Isolation and characterization of specific enzymes
- Regulatory mechanism in metabolism
84
What are the endergonic processes that maintain the living state driven by?
The exergonic reactions of nutrient oxidation
85
What does ATP consist of?
An adenosine moiety to which three phosphoryl groups are sequentially linked via a phosphoester bond followed by two phosphoanhydride bonds
86
What is the delta G naught of ATP hydrolysis?
-30.5 kJ/mol
87
What is the delta G of ATP hydrolysis?
-50 kJ/mol (under physiological conditions)
88
Why is ATP exergonic?
1) Resonance stabilization of products
2) Electrostatic repulsion between negatively charged oxygen atoms in ATP
3) High solvation energy of products
4) ATP is more soluble than other phosphoanhydride compound
89
What is the strongest oxidizing agent?
Fluorine but it is present in only trace amounts in living systems so oxygen is the strongest in biological systems
90
What is oxidizing ability?
The capacity to accept electrons depending on the electronegativity of the atom
91
How can the free energy change of a redox reaction be determined?
By measuring its redox potential with a voltmeter
92
What is the standard reduction potential (E naught)?
The electrical potential generated by a redox reaction against a hydrogen electrode when the concentration of reduced and oxidized species are at 1M concentration
93
What does the reduction potential of a half-cell depend on?
It's activity of reduced and oxidized species which is approximated by their concentrations
94
What is the Nernst equation?
E = E naught + RT/nf ln(e- acceptor/e - donor) where n is the number of electrons transferred and f is Faraday's constant
95
What is the Nernst equation at 25 degrees C?
E = E naught + 0.026V/n ln(e- acceptor/e - donor)
96
How is the standard reduction potential used for the free energy calculation?
delta G = -nf deltaE
97
How is the standard reduction potential used for the standard free energy calculation?
delta G naught = -nf delta E naught
98
What are voltage measurements commonly employed to do?
Characterize the sequence of reactions comprising a metabolic electron-transport pathway
99
How is the measurement of standard reduction potential measured using a platinum electrode and half-cell?
- The half-cell undergoing oxidation passes through the liberated electrons through the wire to the half-cell undergoing reduction
- Electronegativity in the two half-cells is maintained by the transfer of ions through the electrolyte-containing salt bridge
100
What can be used to do useful work as is done in battery-operated motors, the electromotive force?
Flow of electrons
101
What is the generated EMF used for?
Various energy transduction reactions
102
What reactions can produce NADH?
1) NAD+ + 2e- + 2H+ = NADH + H+
2) CH3CH2OH + NAD+ = CH3CHO = NADH + H+
103
What is an SN1 reaction?
Reaction that occurs one step at a time
1) Take nucleophile out leaving carbonation intermediate behind
2) New nucleophile attacks the carbon and makes a new compound
- Configuration stays the same because it's being added to the same side but once the carbonation and nucleophile attach, it can reconfigure - racemic mixture
104
What is an SN2 reaction?
Reaction carried out by two steps at a time
1) Outgoing group nucleophile starts fighting with existing bond and weakening the other one on the other side
2) Attacking strong nucleophile causes an inverted configuration
- Driven by enzymes that force the existing nucleophile out
105
What are metabolic inhibirors?
Glucose --> G6P --> Iodoacetamide --> F6P --> FBP --> GAP + DHAP
106
What causes genetic defects?
- Mutation in a particular gene
- Defective protein enzyme
- Blockage of metabolic reaction
- Accumulation of an intermediate
107
1a. Life is a result of chemical interactions of various elements in the environment. Reactions in the living system occur due to?
Interaction of electrons in the outer orbit of the atom
108
1b. The most complex creation of nature, a human body, is?
A molecular assembly of mostly a few elements found in Earth's atmoshphere
109
2a. In the following nuclear reaction, H + H + H + H = He + 2e- + Light and heat, 4 protons fuse to make one He nuclei and 2 positrons. Is there an overall increase or decrease in entropy in this reaction?
Decrease in entropy. Disorder is decreased because 4 nuclei are coming together to make 1 due to loss of mass.
110
2b. In the following nuclear reaction, H + H + H + H = He + 2e- + Light and heat, 4 protons fuse to make one He nuclei and 2 positrons. If there is an increase in entropy during this reaction, in what form is it occurring?
Mass to energy
111
4. What is the original source of energy on the planet?
Nuclear energy (on solar plasma and Earth in nuclear power plants)
112
5. Plants synthesize different compounds and create beautiful order from disorder like flowers. How is disorder created?
In solar plasma - plants are growing at the cost of light energy which comes from solar energy
113
6. How is disorder created as a child grows in an ordered way under proper nourishment?
Created in the surroundings - child grows at the cost of burning fuel from nutrients breaking down
114
7. Describe the conversion of energy during exercise.
Chemical energy is being burned and creates disordered CO2 which makes ATP, and leads to kinetic energy, thermal energy, and friction with the air
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8. What is the best chemical group to do a nucleophilic attack on?
Electron rich atom
116
9. Is burning of wood a favourable (spontaneous) reaction? If so, how and why?
It is a favourable/spontaneous reaction because it involves oxygen and a hydrocarbon and oxygen is desperate to react
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11. Which component is the oxidizing agent in the following reaction: R-CHO + NAD+ + PO42- = R-COO-PO4 + NADH + H+
NAD+ because it is reduced to NADH
118
13. If the reaction product in any reaction is resonance stabilized, the reaction proceeds spontaneously in the forward direction. Give a thermodynamic explanation for this.
Entropy increases with an increase in the number of resonance structures
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14. What would the free energy change (delta G) for a reaction that is at equilibrium be?
0
120
15. A flask containing boiling water is left on the desk. Water molecules in boiling water move at a faster rate. After 1 hour water cools down to room temperature. This is a spontaneous reaction. Explain the entropy change for this reaction.
Entropy decreases as it cools down. Heat is condensed in the flask and dispersed and randomized outside, making the air molecules move faster. Overall, entropy increases but the entropy of water cooling down deceases.
121
17. What is the difference between burning cellulose (wood) in a fireplace and glucose in the body?
In both reactions, carbohydrate is converted to CO2.
- Fireplace is not controlled and burns hydrocarbons to oxygen immediately
- Body is controlled but glucose never gets burned directly by oxygen in the body - it is catabolized so the hydrogens can be harvested and transferred to oxygen
122
19. Fe3+ is involved in many redox reactions and has different standard reduction potentials ranging from very positive to very negative. Why?
Surrounded by electron-rich atoms prevents the attraction of electrons
123
20. Can you measure free energy of some reactions (happening at standard temperature and pressure) without measuring concentrations?
Yes, for redox reactions depending on the voltage created
124
21. What is the difference between catabolism and anabolism and which is favourable?
Catabolism is when nutrients are broken down and generate energy and anabolism is free energy is stored and then used by cells to synthesize compounds. Catabolism is favoured.
