chapter 13 Flashcards
Life needs energy
-Recall that living organisms are
-Building complex structures that are
-The ultimate source of this energy on Earth is
-Recall that living organisms are built of complex structures
-Building complex structures that are low in entropy is only possible when energy is spent in the process
-The ultimate source of this energy on Earth is the sunlight
-Autotrophs and heterotroph
Cycling of carbon dioxide and oxygen between the autotrophic (photosynthetic) and heterotrophic domains in the biosphere.
Metabolism is the sum of all chemical reactions in the cell
-Series of related reactions form
-Some pathways are primarily
-Some pathways are primarily using
-Series of related reactions form metabolic pathways
-Some pathways are primarily energy-producing
–This is catabolism
-Some pathways are primarily using energy to build complex structures
–This is anabolism or biosynthesis
-Energy relationships between catabolic and anabolic pathways
Law of Thermodynamics
First Law-for any change, the energy of the universe remains constant; energy may change form or it may be transported, but can not be created or destroyed.
Second law- the entropy law can be stated in 3 ways:
1. systems tend from ordered to disordered
2. entropy can remain the same for reversible processes but increases from irreversible processes.
3. all processes tend towards equilibrium
everything-> equlibrium= death
third law-entropy goes to zero when ordered substances approach absolute zero=0K
Thermodynamics
Gibbs free energy G and Delta G
Enthalpy H and delta H
Entropy S and delta S
Delta G=Delta H-T Delta S
Thermodynamic quantities
-Gibbs free energy, G, expresses the amount of
-This energy allows prediction of the direction of
-Gibbs free energy, G, expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure. When a reaction proceeds to release free energy, ΔG is negative and the reaction is exergonic. The system has less free energy when ΔG is negative. The units of ΔG are joules/mole (J*mol-1)
-This energy allows prediction of the direction of chemical reactions, the equilibrium position and a theoretical amount of work that can be performed
Thermodynamic quantities
-Enthalpy,H, is the
-Entropy, S, is a
-Enthalpy,H, is the heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products. When a chemical reaction releases heat, it is exothermic, the heat content of the products is less than the reactants and ΔH is negative. The units are joules/mole (Jmol-1)
-Entropy, S, is a quantitative expression for the randomness or disorder of a system. When the products of a reaction are less complex and more disordered than the reactants, the reaction has proceeded with a gain in entropy. The units are joules/mole.Kelvin (J mol-1*K-1)
Thermodynamic quantities
-Under conditions existing in
-Remember that the ΔG of a
-Under conditions existing in biological systems (including constant temperature and pressure)
-ΔG= ΔH-T ΔS where T is the absolute temperature
-Remember that the ΔG of a spontaneously reacting system is negative- this can be because the ΔH was negative, i.e. the reaction was exergonic, or the ΔS was positive i.e. the amount of disorder in the system increased.
Laws of thermodynamics
apply to living organisms
-Living organisms cannot create energy from
-Living organisms cannot destroy energy into
-Living organism may transform energy from one
-In the process of transforming energy, living organisms must
-In order to maintain organization within themselves, living systems must be able to
-Living organisms cannot create energy from -nothing
-Living organisms cannot destroy energy into nothing
-Living organism may transform energy from one form to another (energy transductions)
-In the process of transforming energy, living organisms must increase the entropy of the universe (2nd Law)
-In order to maintain organization within themselves, living systems must be able to extract useable energy from their surroundings, and release useless energy (heat) back to their surroundings
Laws of thermodynamics
apply to living organisms
-Living organisms preserve their internal order by taking
-Heterotrophic cells acquire free energy from
-Living organisms preserve their internal order by taking nutrients or sunlight from their surroundings (taking free energy from their surroundings) and releasing back into their surroundings and equal amount of energy as heat or entropy
-Heterotrophic cells acquire free energy from nutrient molecules and photosynthetic cells acquire free energy from absorbed solar radiation. They then transform the free energy to ATP and other energy-rich compounds that can provide energy for biological work at constant temperature
Standard transformed constants- biochemical standard state
-Examples- ΔG’º and K’eq
-Standard conditions of 298K (25ºC); reactants and products are initially at 1M concentrations (if gasses, 1 atm); since reactions usually occur at pH 7, then the [H+] is 10 -7 M and the concentration of water is 55.5 M
-If Mg2+ is involved, its concentration is 1mM
Free energy, or the equilibrium constant, measure the direction of processes
ΔG’º = -RT ln K’eq
The standard free energy change is an alternate mathematical way to express the equilibrium constant
Energetics of Some Chemical Reactions
-Hydrolysis reactions tend to be
-Isomerization reactions have ___ free-energy
-Complete oxidation of reduced compounds is
–This is how chemotrophs obtain
–In biochemistry the oxidation of reduced fuels with
–Recall that being thermodynamically favorable is not the same as
-Hydrolysis reactions tend to be strongly favorable (spontaneous)
-Isomerization reactions have smaller free-energy changes
–Isomerization between enantiomers: ΔG° = 0
-Complete oxidation of reduced compounds is strongly favorable
–This is how chemotrophs obtain most of their energy
–In biochemistry the oxidation of reduced fuels with O2 is stepwise and controlled
–Recall that being thermodynamically favorable is not the same as being kinetically rapid
Contrast ΔG’º to ΔG
-ΔG’º tells the direction and how far a reaction
-The ΔG is the
-The ΔG or any reaction proceeding spontaneously toward
-ΔG is related to
-ΔG’º tells the direction and how far a reaction must go to reach equilibrium and the initial concentration of each component is 1M, the pH is 7 the temp is 25ºC and the pressure is 1 atm. This value is constant and is unchanging for a given reaction
-The ΔG is the actual free energy change and is a function of reactant and product concentrations and of the temperature that the reaction is being conducted at.
-The ΔG or any reaction proceeding spontaneously toward equilibrium is always negative and becomes zero when equilibrium is reached. At this point, no more work can be done by the system
-ΔG is related to ΔG’º by the following: ΔG= ΔG’º +RT ln (product concentration)/reactant concentrations
Energetics within the cell are not
-The actual free-energy change of a reaction in the cell depends on:
-Standard free-energy changes are
-A thermodynamically unfavorable reaction can be driven forward by
standard
-The actual free-energy change of a reaction in the cell depends on:
–The standard change in free energy
–Actual concentrations of products and reactants
–For the reaction aA + bB cC + dD:
-Standard free-energy changes are additive:
(1) A B ΔG°’1
(2) B C ΔG°’2
Sum: A C ΔG°’1 + ΔG°’2
-A thermodynamically unfavorable reaction can be driven forward by coupling it to an exergonic reaction through common intermediates
Reaction spontaneity
-The criterion for spontaneity is the value of
-Recall the equation ΔG= ΔG’º +RT ln [C][D]/[A][B]
-If RT ln [C][D]/[A][B] has a larger
-Removal of product as soon as it is
-The criterion for spontaneity is the value of ΔG not the value of ΔG’º
-Recall the equation ΔG= ΔG’º +RT ln [C][D]/[A][B]
-If RT ln [C][D]/[A][B] has a larger negative value than ΔG’º, then ΔG’º can have a positive value and the reaction will have an overall negative value. Remember that as long as the ΔG is negative, the reaction can proceed till equilibrium is reached
-Removal of product as soon as it is formed ensures that the mass action ratio is a fraction and the ln of of a fraction is a negative value therefore ΔG is negative
Does having a large negative value mean that the reaction is thermodynamically favorable?
-Yes
-Does this mean that a reaction will proceed forward?
-Not necessarily- remember burning firewood does not spontaneously happen, it requires activation energy to get the reaction going.
-An enzyme provides an alternative reaction pathway with a lower activation energy- this affects the rate of the reaction NOT the free energy change for the reaction which is independent of the reaction pathway
K’eq for coupled reactions is multiplicative
-K’eq overall is [glucose 6-phosphate] [ADP] [Pi]/ [glucose] [Pi] [ATP]= K’eq1 x K’eq2= 3.9 x10 -3 M -1 x 2.0 x10 5 M = 7.8 x10 2
-By coupling ATP hydrolysis to glucose 6-phosphate synthesis has been raised by a factor of 2.0 x10 5
-The strategy works if ATP is continuously available
Review of Organic Chemistry
-Most reactions in biochemistry are
-Nucleophiles react with
-Heterolytic bond breakage often gives rise to
-Oxidation of reduced fuels often occurs via
-Most reactions in biochemistry are thermal heterolytic processes
-Nucleophiles react with electrophiles
-Heterolytic bond breakage often gives rise to transferable groups, such as protons
-Oxidation of reduced fuels often occurs via transfer of electrons and protons to a dedicated redox cofactor
Chemical Reactivity
Most reactions fall within few categories:
Most reactions fall within few categories:
-Reactions that make or break C–C bonds;
-Internal rearrangements, Isomerizations and eliminations (without cleavage);
-Free-radical reaction;
-Group transfers (H+, CH3+, PO32–);
-Oxidations-reductions (e– transfers).
Chemistry at Carbon
-Homolytic cleavage is very
-Heterolytic cleavage is
C-ovalent bonds can be broken in two ways
-Homolytic cleavage is very rare
-Heterolytic cleavage is common, but the products are highly unstable and this dictates the chemistry that occurs
Homolytic vs. Heterolytic Cleavage
