ap bio - energy and metabolism

metabolism

the collective total of a system’s chemical reactions.

metabolic pathway

where a specific molecule is altered in a series of defined steps, resulting in a product. each step is catalyzed by an enzyme.

catabolic pathways

break down molecules and therefore, release energy.

anabolic pathways

build larger, more complex molecules: requires absorption of energy.

bioenergenetics

the study of how energy flows through living organisms.

energy

the capacity to cause change.

kinetic energy

energy associated with active movement.

thermal energy

kinetic energy associated with the movement of atoms or molecules, causing heat. this movement is random.

radiant/light energy

energy associated with photons and light waves.

potential energy

energy that matter possesses due to it’s location or structure. examples: standing on top of a cliff has more potential energy than standing in a flat field.

chemical energy

term used by scientists to describe the potential energy stored in chemical bonds within a structure. by breaking those bonds, the energy is released.

thermodynamics

the study of energy transformation through a collection of matter.

first law of thermodynamics

energy cannot be created nor destroyed.

second law of thermodynamics

entropy (disorder) of the universe can only increase. even if a specific reaction decreases entropy locally, small amounts of heat and other forms of energy are released, and those things cannot be harnessed for further use. thus, the entropy of the entire universe increases.

entropy

disorder. a large, organized molecule has lower entropy than a group of random small molecules.

open system

all living organisms are open systems. this means that we interact with both our environment and ourselves. we get energy from food in our environment, then used that energy to perform metabolic processes inside of our body, then release by-products back out into the environment.

spontaneous / feasible reaction

if a given process, by itself, leads to an increase in entropy, that process can proceed without requiring an outside input of energy- it is spontaneous. remember that a spontaneous reaction DOES NOT mean it occurs quickly; rusting is a spontaneous reaction, but it occurs over time. This happens because matter tends to move towards states with lower free energy.

free energy

the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system. change in free energy is denoted as 𝞓G

calculating free energy

𝞓G=𝞓H-((T)𝞓S, where 𝞓G is change in free energy, 𝞓H is change in enthalpy, T is temperature, and 𝞓S is change in entropy

𝞓H

change in enthalpy or heat between reactants and products. If it is positive, it absorbed heat (endothermic). If it is negative, it released heat energy (exothermic).

𝞓S

change in entropy or disorder. positive 𝞓S means disorder has increased, and this usually favors spontaneity.

T

temperature- is always denoted in kelvin!

exergonic reaction

net release of energy. negative 𝞓G. catabolic.

endergonic reaction

net intake/absorption of energy. positive 𝞓G. anabolic.

can a cell be at equilibrium?

NO. if something is at equilibrium then there is no free energy to be used to start a reaction. no reactions would occur so life would not be supported.

energy coupling

using energy from an exergonic reaction to support an endergonic reaction.

ATP

adenosine triphosphate. one of the most important molecules in cellular metabolism. ATP can be turned into ADP + P by breaking up the triphosphate group. this releases a large amount of energy.

phosphorylated intermediate

a reactant with one phosphate group (the one separated from ATP in ATP hydrolysis) covalently bonded to it. this causes the reactant to be more reactive (less stable)

ATP cycle

ATP can be regenerated by adding a phosphate group to ADP. energy to do so comes from catabolic reactions ( breakdown of molecules )

enzyme

a macromolecule (protein) that acts as a catalyst inside of a cell.

catalyst

something that lowers the activation energy of a reaction

activation energy

energy required for a reaction to start and move foward. abbreviated E_A

substrate

what is bonding to an enzyme in order to work on and lower activation energy / speed up reaction time.

enzyme-substrate complex

the completed “puzzle” that is the enzyme and it’s substrates all together.

active site

where on the enzymes that substrates bond to

induced fit

the idea that instead of an enzyme and it’s substrate(s) being like a lock and key, the enzyme actually bonds to the substrate(s) first and then changes it’s shape to comfortably fit around the substrate(s).

affect of temp on enzymatic activity

activity will slowly increase as temperature increases closer to that specific enzyme’s optimal conditions. then once that optimal condition is met, but temp continues to increase then activity will decrease drastically.

affects of pH on enzymatic activity

activity will increase equally, getting closer to optimal conditions, from both sides of those optimal conditions.

cofactors

nonprotein helpers that aid in enzymatic processes. are connected directly to an enzyme, whether it’s permanently or loosely bound depends on each cofactor. cofactors are usually inorganic (zinc, magnesium, etc) and if it is organic then it’s considered a coenzyme ( next vocab word )

coenzyme

not actually an enzyme, rather an organic molecule that works alongside an enzyme. important examples are vitamins.

enzyme inhibitors

block/inhibit the function of an enzyme,

competitive inhibitors

reduce the productivity of an enzyme by bonding directly to it’s active site, blocking substrate(s) from bonding to it. is reversible by adding more substrate to the system.

noncompetitive inhibitors

do not directly compete with substrate for the active site, rather they attach to somewhere else on the enzyme. This causes the enzyme to change shape and become unable to perform it’s intended activity.

enzyme mutation

a change in an enzyme’s DNA, causing different configurations of amino acids, can have an effect on an enzyme’s function and/or efficiency

allosteric regulation

term used to describe any case in which a protein's function at one site is affected by the binding of a regulatory molecule at another site. a regulatory molecule could stimulate or inhibit activity.

cooperativity

amplifies the response of enzymes to substrates. one substrate binds to enzyme and primes it to act more readily on the second substrate.

feedback inhibition

a metabolic pathway is halted by the inhibitory binding of it’s end product to an enzyme that acts early in the pathway.