Principles of Biochemistry - Thermodynamics, Functional Groups, and pH

This set of vocabulary flashcards covers fundamental principles of biochemistry including thermodynamics, equilibrium, kinetic constants, organic functional groups, and acid-base chemistry as presented in Chapter 1.

Biochemistry

The use of chemical concepts to understand biological systems.

Organic chemistry

The study of carbon-containing molecules.

Inorganic chemistry

The study of compounds comprised of elements other than carbon.

Analytical Chemistry

The identification, quantitation, and precise analysis of compounds.

Physical chemistry

The study of the interactions of matter with energy.

Thermodynamics

The study of energy.

Enthalpy ($H$)

A thermodynamic property used to approximate the energy of a biochemical system.

Entropy ($S$)

A measure of randomness and disorder; the second law of thermodynamics states that the entropy of the universe is always increasing.

Gibbs free energy ($G$)

The amount of energy available to do work at a constant temperature and pressure, expressed as the change \text{\Delta} G = \text{\Delta} H - T \text{\Delta} S.

Standard State

A reference state used for calculations where Temperature is $25^{\circ} \text{C}$ ($298\, \text{K}$), Pressure is $1\, \text{atm}$, and Concentration is $1\, mol\, dm^{-3}$.

Biochemical standard state (\text{\Delta} G^{\circ \prime})

A reference state in biochemistry where the prime symbol indicates a standard $\text{pH} = 7.0$.

Equilibrium

The state when the rates of the forward and reverse reactions are equal and net product formation or reactant consumption is zero.

Equilibrium constant ($K_{eq}$)

The ratio of the concentration of products to reactants at equilibrium, expressed as $K_{eq} = \frac{[C]^c [D]^d}{[A]^a [B]^b}$.

Le Chatelier's Principle

The principle stating that if equilibrium is disturbed, the reaction will proceed back toward equilibrium.

Rate Constant ($k$)

The link between product formation and reactant consumption that factors in temperature and effective collisions.

Enzyme

A biomolecular catalyst that lowers the activation energy of the transition state (\text{\Delta} G^{\ddagger}), allowing the system to reach equilibrium more quickly.

Functional groups

Fragments of molecules that are often involved in chemical reactions.

Thioester

A sulfur analog functional group that has a large negative free energy of hydrolysis.

Phosphanhydrides

Functional groups commonly found in nucleoside triphosphates like $\text{ATP}$ that possess a large negative free energy of hydrolysis.

Dalton ($Da$)

A unit for molecular weight equivalent to $\text{g}\, mol^{-1}$ and $\text{amu}$.

Hydrogen bond

A weak bond ($10 - 40\, \text{kJ}\, mol^{-1}$) typically involving an interatomic distance of $< 3.0\, \text{\AA}$ ($0.3\, \text{nm}$).

Acid ionization constant ($K_a$)

A constant used to describe the strength of an acid, defined as $K_a = \frac{[H^+][A^-]}{[HA]}$.

$$p K_a$$

The negative logarithm of the acid ionization constant ($- \ln(K_a)$), where a smaller value indicates a stronger acid.

pH

A logarithmic measurement of hydrogen ion concentration defined as $\text{pH} = - \ln[H^+]$.

Buffer

A combination of a weak acid and its conjugate base that resists changes to $\text{pH}$, most effective within $\pm 1$ log unit of its $p K_a$.

Henderson-Hasselbalch equation

The equation used to describe buffers: $\text{pH} = p K_a + \ln\left(\frac{[A^-]}{[HA]}\right)$.