CHEM 130A: chemical and physical foundations

What are the main elements essential for life?

carbon, oxygen, nitrogen, phosphorous, hydrogen, and sulfur

What are the main ions essential for life?

Na+ and K+ for osmolarity and associating & Ca+, Mn+, Fe+, Zn+2, and Cl-

Why are functional groups in biomolecules important?

carbon is the backbone, heteroatoms (not C or H) create chemical reactivity and determine molecular shape, and different functional groups enable interactions and catalysis (aka are the ultimate toolkit)

What do the functions of molecules depend on?

depend on their 3D structure

What are stereoisomers?

molecules with same chemical formula and chemical bonds, but different configurations so different properties

Describe factors of geometric isomers.

single v. double bonds (double bonds → no freedom of rotation) & cis v. trans (same side v. different sides)

What are enantiomers, diasteromers, and chiral centers?

enantiomers are non-superimposable mirror images

diasteromers are not mirror images

chiral centers is a carbon attached to four different substituents

Why are interactions between biomolecules stereospecific?

small molecules fit into stereospecific pockets

What are energetics?

systems with defined boundaries

Are living organisms open or closed systems?

open systems because we exchange energy and matter with surroundings

How is energy of a system represented?

enthalpy (H): heat stored in chemical bonds

△H: amount of heat a systemic absorbs/generates

△H < 0: exothermic and favorable

△H > 0: endothermic and unfavorable

How is order of a system represented?

entropy (S): order of a system

△S > 0: more disordered and favorable

△S < 0: less disordered and unfavorable

How is Gibbs Free Energy represented?

△G = △H - T△S

G = H - TS

△G < 0: spontaneous reaction via temperature (T)

How is forward and reverse of a reaction represented?

K₁ = forward reaction

K_-1 = reverse reaction

Describe the free energy diagram

G is the y-axis, reaction coordinate is the x-axis, and △G represents the change of energy to push the reaction

How do you know if a reaction is spontaneous or non-spontaneous through the Gibbs Free Energy equation?

△G < 0 through -△H and +△S → spontaneous (heat) → exergonic (all energies)

△G > 0 through +△H and -△S → non-spontaneous → endergonic

What is the equilibrium constant? Describe what it means and its equation.

K_eq: the numerical ratio of the concentrations of reaction products to reactants when a reversible chemical reaction reaches dynamic equilibrium at a specific temperature

Q (mass quotient) = [P]/[R] = [C][D]/[A][B]

at equilibrium, Q = K_eq → constant value

K_eq > 1 → products favored

K_eq < 1 → reactants favored

What are the conditions of standard free energy change?

△G° → T = 298 K, P = 1 atm, concentration of 1 M

What is the equation for standard transformed free energy change?

△G° = -RT(ln of K_eq)

Describe coupling of reactions (Hess’ Law).

reaction coupling involves running an endergonic and an exergonic reaction at the same time → overall met process becomes exergonic and allows thermodynamically unfavorable process to proceed

ex: if the falling weight (exergonic reaction) is connected to the object on the ramp (endergonic reaction), the energy released from the falling weight drives the object up the incline (thermodynamically unfavorable process actually proceeds)

biochem ex: hydrolysis of ATP is the most common exergonic reaction used by biological systems to power otherwise unfavirable cellcular processes