Biochemistry Basics Flashcards
what are the two relevant forms of energy in chemistry?
kinetic energy (movement of molecules) and potential energy (energy stored in chemical bonds)
First Law of Thermodynamics/Law of Conservation of Energy
The energy of the universe is constant; if the energy of a system decreases, the energy of the system must increase and vice versa
Second Law of Thermodynamics
Entropy (disorder) of the universe tends to increase; spontaneous reactions tend to increase the disorder of the universe
entropy
S, disorder
enthalpy
H, bond energy, delta H=delta E+(P*delta V)
spontaneous
delta G is negative, reaction is favourable, occur without a net addition of energy and have energy to spare
non-spontaneous
delta G is positive, reaction is unfavourable, requires energy input
exergonic
energy exits the system, describes reactions with negative change in free energy
endergonic
reaction requires energy input, describes reactions with positive change in free energy
how are endergonic reactions completed in the body?
by reaction coupling to exergonic reactions
exothermic
reactions with a negative change in enthalpy, releases heat into the surroundings
endothermic
reactions with a positive change in enthalpy, requires input of heat from the surroundings
in which direction of free energy does a system always move?
towards lowest free energy
what does the value of delta free energy depend on?
the concentration of reactants and products
delta G naught=
standard free energy with all reactants and products at 1M concentration
delta G naught prime=
1M concentration of all solutes except H+ and a pH of 7, standardized for human physiological conditions
what is the formula for delta G naught prime?
= -RTlnKeq’
what is the formula for delta G (real life)?
=delta G naught prime + RTlnQ
equilibrium
the point where the rate of reaction in the forward direction equals the rate of reaction in the reverse direction
if a system in equilibrium is disturbed (ex. by adding excess reactant or product), will the value of K change?
no, but the value of Q will change
what are the two factors that determine whether a reaction will occur spontaneously (negative free energy change) in the cell?
1) the intrinsic properties of the reactants and products (K)
2) the concentration of reactants and products (RTlnQ)
do all spontaneous reactions occur rapidly?
no, spontaneous means a reaction is energetically favourable (thermodynamics) but says nothing about rate of reaction (kinetics)
does free energy change depend on the reaction pathway?
no, it is only a measurement of the difference in free energy between reactants and products
chemical kinetics
the study of reaction rates
why are some spontaneous (thermodynamically favourable) reactions slow to proceed or do not proceed at all?
because of a large activation energy barrier
transition state (TS)
unstable state that all reactions proceed through, takes large amounts of energy to produce
activation energy Ea
the energy required to produce the transition state
what is the barrier that prevents many reactions from proceeding (even thermodynamically favourable ones)?
activation energy
what determines the kinetics of a reaction?
activation energy
catalyst
lowers the activation energy of a reaction without changing the free energy change by stabilizing the transition state, it is regenerated with each reaction cycle
enzymes
biological catalysts that lower Ea without changing delta G
what kind of role do catalysts (enzymes) have?
a kinetic role, NOT a thermodynamic one
photosynthesis
the process by which plants store energy from the sun in the bond energy of carbohydrates
photoautotrophs
generate energy from light to make their own food ex. plants
chemoheterotrophs
use energy of food/chemicals produced by other living things ex. humans
oxidation
loss of electrons
reduction
gain of electrons
what determines whether a molecule is oxidized or reduced?
it depends on the other atoms that they are bound to
what is indicative of oxidation reactions?
gain of oxygen atoms, loss of hydrogen atoms, loss of electrons
what is indicative of reduction reactions?
loss of oxygen atoms, gain of hydrogen atoms, gain of electrons
redox pair
describes the pair resulting from oxidation/reduction; when one atom gets reduced, another one must be oxidized
catabolism
the process of breaking down molecules
anabolism
the process of building up molecules
what is the term to describe the process of extracting energy from glucose to produce CO2 and H2O?
oxidative catabolism
are anabolic processes generally reductive or oxidative?
reductive
Bronsted-Lowry acid
proton donors
Bronsted-Lowry base
proton acceptors
Lewis acid
electron-pair acceptors
Lewis base
electron-pair base
what is the relationship between acid-ionization constant Ka and acidity?
the larger the Ka, the stronger the acid; the smaller the Ka, the weaker the acid
what is the relationship between base-ionization constant Kb and basicity?
the larger the Kb, the stronger the base; the smaller the Kb, the weaker the base
polyprotic
molecules with more than one proton to donate
amphoteric
substances that can act as either an acid or a base
evertime a polyprotic acid donates a proton, what is the effect on acidity of the resulting species?
the resulting species will be a weaker acid than its predecessor
low pH means:
higher [H+] and the solution is acidic
high pH means:
lower [H+] and the solution is basic
what is the relationship between pKa and acidity?
lower pKa = stronger acid
what is the relationship between pKb and basicity
lower pKb=stronger base
buffer
a solution that resists changing pH when a small amount of acid or base is added
what does a buffer consist of?
presence of a weak acid and its conjugate base (or weak base and its conjugate acid) in roughly equal concentrations
what is the most important buffer system in our blood plasma?
the bicarbonate buffer system: H2CO3—>H+ + HCO3-
