L2_ Bioenergetics and Coenzyme Flashcards
(151 cards)
1
Q
a highly coordinated cellular activity in which many multi-enzymes systems (metabolic pathways) cooperate.
A
Metabolism
2
Q
Functions of metabolism
A
obtain chemical energy
convert nutrient molecules into the cell’s own characteristics molecules
polymerize monomeric precursors into biomolecules
synthesize and degrade biomolecules which may be required for some specialized cellular functions
3
Q
Two metabolic pathways
A
Catabolism
Anabolis
4
Q
metabolic reactions involving breaking down of biochemical fuels to extract energy (energy-yielding processes)
A
Catabolism
5
Q
energy-yielding processes in metabolism
A
Catabolism
6
Q
metabolic reactions involving build up of biomolecules necessary to sustain life
A
anabolism
7
Q
energy-requiring processes in metabolism
A
anabolism
8
Q
is catabolism an exergonic reaction or endergonic?
A
exergonic
9
Q
is anabolism an exergonic reaction or endergonic?
A
endergonic
10
Q
Between ATP and ADP, which of these two molecules is utilized as reactant and which is the expected product after an endergonic reaction?
A
R- ATP
P- ADP
11
Q
Between NADP+ and NADPH, which of these two molecules is utilized as reactant and which is the expected product after an anabolic reaction pathways?
A
R-NADPH
P-NADP+
12
Q
Between NADP+ and NADPH, which of these two molecules is utilized as reactant and which is the expected product after an exergonic reaction?
A
R-NADP+
P-NADPH
13
Q
Between ATP and ADP, which of these two molecules is utilized as reactant and which is the expected product after an catabolic reaction pathways?
A
R-ADP
P-ATP
14
Q
Examples of biomolecules that can undergo catabolism?
A
Stored nutrients
ingested foods
solar photons
15
Q
Examples of simple catabolic products which also act as anabolic precursors
A
CO2
NH3
H2O
16
Q
example of functions fueled by metabolism
A
Osmotic work
Mechanical work
Complex biomolecules
other cellular w
17
Q
In simplest terms, what does metabolism entails?
A
utilization and production of energy
18
Q
What fundamental laws are involved in the concept of bioenergetics?
A
Fundamental laws of thermodynamics:
1st Law (enthalpy - ΔH): Energy can neither be created nor destroyed; it can only be transformed from one form to another
2nd Law (entropy - ΔS): a process is spontaneous if such process will cause an increase in the entropy of the universe
19
Q
What fundamental laws of thermodynamics are involved in the concept of bioenergetics?
A
1st Law (enthalpy - ΔH): Energy can neither be created nor destroyed; it can only be transformed form one form to another
2nd Law (entropy - ΔS): a process is spontaneous if such process will cause an increase in entropy of the universe
20
Q
metabolism in the context of thermodynamics
A
Bioenergetics
21
Q
a branch of biochemistry which provide the rules upon which metabolism functions
A
Bioenergetics
22
Q
field in biochemistry concerned with the transformation and usage of energy by living cells, and determining the direction and extent to which biochemical reactions occur
A
Bioenergetics
23
Q
extent of biochemical reactions are dependent to what?
A
degree to which thermodynamic factors (enthalpy and entropy) changes
24
Q
Thermodynamic Factors
A
enthalpy (ΔH)
Entropy (ΔS)
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measure of the changes in heat content of the reactants and products (1st Law of Thermodynamics)
Enthalpy (ΔH)
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a measure of the change in randomness or disorder of reactants and products (2nd Law of Thermodynamics)
Entropy (ΔS)
27
What does the 1st Law of Thermodynamics says?
Energy can neither be created nor destroyed; it can only be transformed from one form to another
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What law of thermodynamics is involved in photosynthesis?
1st Law: Law of Conservation of energy (Light energy to chemical energy)
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What law of thermodynamics is involved in muscular activity?
1st Law: Law of Conservation of energy (Chemical energy to Mechanical energy)
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Law of Conservation of energy
1st Law of Thermodynamics
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What forms of energy are involved in photosynthesis?
Light energy
Chemical energy
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What forms of energy are involved in muscular activity?
Chemical energy
mechanical energy
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In most cases, what form of energy is involved in the reactions under the 1st Law of thermodynamics?
heat
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Enthalpy (ΔH) can be:
Exothermic
Endothermic
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heat is released during the course of the reaction; negative (-) ΔH value
Exothermic
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heat is absorbed during the course of the reaction; positive (+) ΔH value
Endothermic
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What does positive (+) ΔH value means?
the reaction is endothermic (heat is absorbed during reaction)
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What does negative (-) ΔH means
reaction is exothermic (heat is released during reaction)
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What does the 2nd Law of Thermodynamics says?
A process is spontaneous if such process will cause an increase in the entropy of the universe
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What does it mean if the ΔS is positive (+)?
entropy increases (process is spontaneous)
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What does it mean if the ΔS value is negative (-)?
entropy decrease (non-spontaneous process)
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What does it mean if the ΔS value is zero (0)?
system is at equilibrium
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Can ΔH and ΔS values by itself be sufficient to tell whether a chemical reaction is spontaneous in the direction it is written?
No, neither of the quantities is sufficient enough to tell so
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mathematical combination of ΔH and ΔS gives rise to what thermodynamic quantity?
Free energy (G)
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What two thermodynamic quantities are involved in free energy (G)
Enthalpy (ΔH)
Entropy (ΔS
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Two types of bioenergetic reactions concerning Gibbs' Free energy (ΔG) or the spontaneity of reactions
Exergonic
Endergon
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Cellular respiration is what type of bioenergetics reactions in terms of Gibbs' Free Energy (ΔG)?
Exergonic reaction
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Photosynthesis is what type of bioenergetics reactions in terms of Gibbs' Free Energy (ΔG)?
Endergonic reaction
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concept developed by Josiah Willard Gibbs by combining the 1st and 2nd Laws of thermodynamics
Gibbs' Free Energy (ΔG)
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Who developed the concept of Gibbs' Free Energy?
Josiah Willard Gibbs
51
Define Gibbs' Free energy
the energy available to do work
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Formula for Gibbs' Free Energy (ΔG)
ΔG = ΔH - TΔS
Where:
ΔG = change in Gibbs' Free Energy
ΔH = change in enthalpy
ΔS = change in entropy
T = absolute temperature (in Kelvin, K) [25°C or 298.15 K]
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a variable criterion of the spontaneity of reactions
Gibbs' Free Energy (ΔG)
54
If you are asked to determine if a certain reaction can proceed in a normal condition, which among reaction changes are you going to consider?
ΔH (change in enthalpy)
ΔS (change in entropy)
ΔG (Gibbs' Free Energy)
All choices are to be considered (ΔH & ΔS are used to determine ΔG
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Given the ΔS of reaction A = 35 and ΔS of reaction B = -13, which reaction do you think will proceed spontaneously?
Reaction A (+ ΔS increase entropy, process is spontaneous)
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A bioenergetic reaction characterized by the loss of free energy?
Exergonic reaction
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A bioenergetic reaction characterized by a gain of free energy?
Endergonic reaction
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What reaction would you expect if the ΔG value is negative (-)?
Exergonic reaction (loss of free energy); the reaction is spontaneous
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What reaction would you expect if the ΔG value is positive (+)?
Endergonic reaction (gain of free energy); reaction is non-spontaneous
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What would you expect in the reaction if the ΔG value is zero (0)?
reaction is in equilibrium
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How would you determine if a certain reaction is exergonic or endergonic?
Based on their Gibbs' Free Energy oΔG values; if (+), reaction is endergonic (non-spontaneous); if (-), reaction is exergonic (spontaneous)
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Standard Free Energy Change is designated by what symbols?
ΔG° (ΔG°' if pH=7)
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If the reaction is neutral, how would you write the standard free energy change symbol?
ΔG°'
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At what experimental condition is standard free energy change obtained?
25°C and 1 at
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Standard free energy change (ΔG°) is related to what expression?
Equilibrium constant expression (Keq)
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Using the given equation aA + bB <-> cC + dD, how would you write the equilibrium constant expression (Keq)?
Keq = the concentrations of the products/the concentrations of the reactants
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What is the formula for the actual free energy change in relation to the equilibrium constant (Keq)?
ΔG = ΔG°' + RT ln Keq
where:
ΔG = the actual free energy change
ΔG°' = standard free energy change
R = 1.98 cal/mol-K or 8.314J/mol-K
T = 25°C or 298.15 K
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What is the absolu value of temperature in standard free energy change?
25°C or 298.15 K
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What are the constant values of the universal gas constant (R) in standard free energy change?
R = 1.98 cal/mol-K or 8.314 J/mol-K
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What value of universal gas constant (R) are you going to use if the units of concentrations of your values in standard free energy change is Joules (J)?
R = 8.314J/mol-K
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What value of universal gas constant (R) are you going to use if the units of concentrations of your values in standard free energy change is Calories (cal)?
R = 1.98 cal/mol-K
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In an experiment, what does it means if the value of ΔG if equal to the value of ΔG°'?
the concentrations of reactants and products are at their standard levels [reactants] = [products]
The reaction quotient (Q) is = 0 or = 1 (1M solutes, 1 atm, pH 7.0)
The reaction will proceed without any driving force from the concentration differences
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What does it means if the reaction is at equilibrium (ΔG=0)?
there is no net change in the concentration of the reactants and products as the reverse and forward reactions occur at the same rate
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If the reaction is at equilibrium (ΔG=0), how would you determine the value of the standard Gibbs' free energy?
ΔG°' =−RT ln Keq
75
Consider the thermodynamically unfavorable process:
glucose + Pi <-> glucose-6-phosphate
Calculate ΔG°' if at equilibrium (pH 7.0 and 25°C), the concentrations of each component are as follows:
glucose = 5.00mM
Pi = 5.00mM
G-6-P = 0.0955mM
ΔG°' = 13, 800.84 J/mol
76
Consider the thermodynamically unfavorable process:
glucose + Pi <-> glucose-6-phosphate
Calculate ΔG if at equilibrium (pH 7.0 and 25°C), the concentrations of all components are equal to 1.00mM and the calculated value of ΔG°' = 13, 800.84 J/mol
ΔG = 13, 800.84 J/mol
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Difference of oxidation and reduction in inorganic and organic chemistry
Inorganic chemistry:
Oxidation = lost of electron(s)
Reduction = gain of electron(s)
Organic chemistry:
Oxidation = gain of O atom(s) and lost of H atom (s)
Reduction = lost of O atom(s) and gain of H atom(s)
78
In the conversion of G6P to 6-Phosphoglucono-δ-lactone coupled with the conversion of NADP+ to NADPH:
What reaction is present between (a) G6P and 6-phosphoglucono-δ-lactone, and (b) between NADP+ and NADPH?
Which among the 4 molecules are in reduced forms and oxidized forms?
Which among the 4 molecules are reducing agents and oxidizing agents?
a - oxidation b- reduction
Reduced: G6P & NADPH | Oxidized: 6-Phosphoglucono-δ-lactone & NADP+
Reducing agent: G6P | Oxidizing agent: NADPH
79
In the conversion of ethanol to acetaldehyde coupled with the conversion of NAD+ to NADH:
What reaction is present between (a) ethanol and acetaldehyde, and (b) between NAD+ and NADH?
Which among the 4 molecules are in reduced forms and oxidized forms?
Which among the 4 molecules are reducing agents and oxidizing agents?
a - oxidation b- reduction
Reduced: ethanol & NADH | Oxidized: acetaldehyde & NAD+
Reducing agent: ethanol | Oxidizing agent: NADH
80
Give the four common co-enzymes in redox reactio
NAD+
NADP+
NADH
NADPH
81
Among the 4 common co-enzymes:
NAD+
NADP+
NADH
NADPH
Which are in reduced forms and which are in oxidized forms?
Reduced:
NADH
NADPH
Oxidized:
NAD+
NADP+
82
Give the four common co-factors in redox reactions
FAD
FMN
FADH2
FMNH2
83
Among the four common co-factors in redox reactions, which among them are in reduced forms and which are oxidized forms?
Reduced:
FAD
FMN
Oxidized:
FADH2
FMNH2
84
Why FAD is considered an strong oxidizing agent?
can take 2 electrons (H) = FADH2
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Why FAD and FMN can't be written as FADH and FMNH?
because their reduced forms accept 2H
86
Between Fe2+ and Fe3+, which molecule can be reduced and which molecule can be oxidized?
Reduced - Fe2+
Oxidized - Fe3+
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it is the tendency of a substance to gain electrons and cause the oxidation of another substance.
Standard Reduction potential (E°)
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a measure of electron-transfer potential
Standard reduction potential (E°)
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If the pH is neutral, how would you write the standard reduction potential?
E°'
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What does it mean if the E°' value is more positive?
more tendency to gain electrons and be reduced
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What does it mean if the E°' value is more negative?
more tendency to loss electrons and be oxidized
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Between the two given half-reactions, which do you think is the OHR and the RHR?
OHR (E°'=-0.32V)
RHR (E°'= -0.22V)
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Formula for the overall/net reduction potential (ΔE°')
ΔE°' = E°' (red'n) + E°' (oxd'n)
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How would you determine the overall net potential of a certain reaction?
Determine the reduction half reactions involved using the standard reduction potential table
Determine the reduction half reaction
Determine the oxidation half reaction
Get the sum of the two half reactions to calculate the overall potential
95
Calculate the ΔE°' associated as a pair of electron passes from NADH to O2.
ΔE°' = +1.14V
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Formula to calculate the ΔG°' of a redox reaction
ΔG°' = -nFΔE°'
where:
ΔG°' = change in Gibbs' free energy
n= no. of electrons transferred
ΔE°' = overall cell potential
F = Faraday's constant (96.485 kJ/mol-V or 23.06 kcal/mol-V)
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What is the value of Faraday's constant?
F = 96.485kJ/mol-V or 23.06kcal/mol-V
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Calculate how much free energy would be available as a pair of electrons passes from NADH to O2
-219.9858kJ/mol
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Formula for equilibrium constant (Keq) of a redox reaction derived from ΔG°'
Keq = e^(-ΔG°'/RT)
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Calculate Keq when a pair of electron passes from NADH to O2
Keq = 3.48x10^38
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Function in such a way that metabolism becomes more economically manageable and comprehensive
Co-Enzymes (as activated carriers)
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functions of activated carriers (co-enzymes)
fuel oxidation
reduction biosynthesis
transfer of small fragments
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Meaning of NAD+?
Nicotinamide Adenine Dinucleotide
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What does NADP+ stands for?
Nicotinamide Adenine Dinucleotide Phosphate
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an active form of niacin (Vitamin B3)
NAD+/NADH & NADP+/NADPH
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both can accept a proton and two electrons (equivalent to a hydride ion, :H-) when a substrate molecule is oxidized
NAD+ & NADP+
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major electron acceptor in oxidation of fuel molecules
NAD+
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con-enzyme used almost exclusively in reductive biosynthesis
NADPH
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What does FAD stands for?
Flavin Adenine Dinucleotide
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What does FMN stands for?
Flavin Mononucleoti
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FAD and FMN are active forms of what vitamin?
riboflavin (Vitamin B2)
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NAD+ and NADP+ are active forms of what vitamin?
Niacin (Vitamin B3)
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Why are vitamin B2, Vitamin B3, Vitamin V5 important in redox reactions?
their active forms constitute the redox co-factors (B2 riboflavin - FAD & FMN, B3 niacin - NAD+ and NADP+, B5 pantothenate - Coenzyme A)
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both accept a hydride ion (H+ + 2e-) plus another proton
FAD and FMN
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also known as Coenzyme Q or CoQ, which is a mobile electron carrier in the electron transport chain
Ubiquinone
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heme-containing proteins that serve as electron carriers in respiratory and photosynthetic ETC
Cytochrome
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Cytochromes are electron carriers in the occurrence of what ETC?
respiratory and photosynthetic ETC
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components of Cytochromes which are important in redox reactions
Fe2+ or Fe3+
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Why cytochromes are important co-factor in redox reactions?
because they contain either Fe2+ (can be reduced, accept electron) or Fe3+ (can be oxidized, donate electron)
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an activated carrier of two-carbon fragments
Coenzyme A (CoA)
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cofactor in acetylation
Coenzyme A (CoA)
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Coenzyme A (CoA) is derived from what vitamin?
Pantothenate (Vitamin B5)
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Important con-enzymes in biological oxidation?
NAD+/NADH
NADP+/NADPH
FAD/FADH2
FMN/FMNH2
Ubiquinone (CoQ)
Cytochromes
Coenzyme A (CoA
iron-Sulfur proteins
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The energy currency of the cell
ATP (Adenosine Triphosphate)
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a molecule that powers most cellular work
ATP (Adenosine Triphosphate)
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How does ATP powers most cellular work?
hydrolytic cleavage of the high energy phosphate bonds is coupled with an energy-requiring (non-spontaneous) reaction
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Is the hydrolysis of ATP to ADP and Pi spontaneous or non-spontaneous?
Spontaneous (ΔG°' = -7.3kcal/mol or -30.5kJ/mol)
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Are the reactions coupled with ATP hydrolysis spontaneous or non-spontaneous?
Non-spontaneous (ΔG°' = + value), coupled with ATP hydrolysis to make reaction spontaneous (overall ΔG°' = - value)
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Why are non-spontaneous reactions coupled coupled with ATP hydrolysis to ADP and Pi?
To make the reaction spontaneous
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How is the ATP hydrolysed?
A water molecule attacks the electrostatically unstable triphosphate between the terminal (gamma) phosphate and the 2nd (beta) phosphate, causing the phosphoanhydride bond to break releasing energy and stabilizing Pi
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Why ATP is electrostatically less stable than ADP and Pi?
because of the repulsive nature of the triphosphate (-)
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Between the two products of ATP hydrolysis, which is more electrostatically more stable?
the Pi (resonance stabilization) OH attached
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How does hydrolysis of ATP results in the relief of charge repulsion?
it reduces the electrostatic repulsion between phosphates in the triphosphate releasing energy upon breakdown
134
Discuss the ATP cycle
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What is the ΔG°' value of ATP hydrolysis?
-30.5kJ/mol or -7.3kcal/mol
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What is the ΔG°' values of ATP synthesis?
+30.5kJ/mol or +7.3kcal/mol
137
Is ATP synthesis an exergonic or endergonic reaction?
Endergonic reaction (energy-consuming)
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Is ATP hydrolysis an exergonic reaction or endergonic?
exergonic (energy-releasing)
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Which reaction if more spontaneous, ATP synthesis or ATPG hydrolysis?
ATP hydrolysis
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How is ATP synthesized?
ADP and Pi is catabolized through and exergonic reaction
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Why are ATPs utilized in the coupling reactions of thermodynamically unfavorable biochemical reactions?
because they are thermodynamically favorable (more negative), rendering the overall ΔG°' = (-) and spontaneous
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What is the purpose of coupling of reactions between thermodynamically favorable and unfavorable biochemical reactions?
to attain a negative (-) ΔG°' thereby rendering the overall reaction spontaneous
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How would you determine the overall ΔG°' of a chemically coupled series of reactions?
get the sum of the ΔG°' of the individual steps or reactions
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In simplest terms, how do cells make ATP?
by phosphorylation (Pi) of ADP
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Two types of metabolism in relation to the phosphorylation of ATP
Autotrophic metabolism
Heterotrophic metabolism
146
How are ATP synthesized via autotrophic metabolism?
photosynthesis through photophosphorylation
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How are ATP synthesized via heterotrophic metabolism?
cellular respiration (aerobic and anaerobic)
substrate level phosphorylation
oxidative phosphorylation
148
Two mechanisms of ATP synthesis or phosphorylation via cellular respiration
substrate level phosphorylation
oxidative phosphorylation
149
Examples of other high-energy phosphate compounds and their hydrolysis products
Phosphoenolpyruvate (PEP)-> pyruvate (ΔG°' = -62kJ/mol)
1,3-Bis-phosphoglycerate -> 3-phosphoglycerate (ΔG°' = -49kJ/mol)
Creatine Phosphate (CP) -> creatine (ΔG°' = -43kJ/mol)
Pyrophosphate (PPi) -> 2 phosphate (ΔG°' = -33kJ/mol)
ATP -> ADP + AMP
150
Which of the following high-energy phosphate compounds can replace ATP in the synthesis of glutamine from glutamate and NH3 of which the ΔG°' = +14.2kJ/mol?
(a) phosphoenol pyruvate (ΔG°' of hydrolysis = -62 kJ/mol)
(b) glycerol-3-phosphate (ΔG°' of hydrolysis = -2.2kJ/mol)
(a) phosphoenol pyruvate (ΔG°' of hydrolysis = -62 kJ/mol)
151
Considering the ΔG°' of hydrolysis of glycerol-3-phosphate which is equal to negative (-) 2.2kJ/mol, is this molecule a high-energy compound or not?
not
