AP Bio Unit 2

Chemical reactions

reactants to products, always reversible, either spontaneous, exergonic/favorable, or nonspontaneous, endergonic/unfavorable

Spontaneity

determined by enthalpy (- good + bad) and entropy (+ good - bad), does not have to be fast, spontaneous reactions occur under current conditions without an input of energy

Free energy

the energy in a system that can do work when temperature and pressure are constant, free energy of products must be less than of reactants to be spontaneous (final - initial), meaning the system loses energy to the universe, increasing entropy, high free energy = unstable, needs to be released through stable bonds

Free energy at equilibrium

free energy is at its lowest possible value for a system when its at equilibrium, so reaching equilibrium is favorable and pushing that system away from equilibrium requires an input of free energy and is therefore unfavorable

Gibbs Free Energy

describes whether a reaction is favorable/exergonic/spontaneous (negative) or unfavorable/endergonic/nonspontaneous (positive) under current conditions

Collision Theory

reactions only occur if reactants collide with sufficient energy/speed as well as proper orientation

Activation Energy

the free energy input required for a reaction to reach its transition state, where reactant bonds are unstable/weak and easily broken by water, input is usually provided by thermal energy, can be so high that even spontaneous reactions never occur under standard conditions

Transition state

point of a reaction where the reactants' bonds absorbed enough energy to become unstable and easily broken by water

Methods of speeding up reactions

increasing temperature, surface area, pressure, or reactant concentration, the first three do not work for biological systems without causing death

Catalysts

Enzymes (protein catalyst, -ase) and ribozymes (RNA catalyst) facilitate reactions by temporarily binding to substrate(s) at active site, straining/weakening their bonds and assisting in proper orientation, lowering the Ea and rate of reaction

Enzyme shape variation

enzymes "dance" around in different shapes due to "breathing" hydrogen bonds, each shape has slight differences in free energy, but the shape best fit for the substrate(s) does not have to have the lowest free energy or be most favorable

Reaction Cycle

Substrate(s) enters active site of enzyme, active site of enzyme wraps around substrate(s) due to interactions between the molecules, creating an induced fit, E-S complex facilitates reaction by properly positioning substrate(s), product released and enzyme is free to catalyze next substrate(s), pH of active site may be helpful by donating/accepting H+, and amino acids of active site may temporarily bind to substrate(s)

Saturated enzymes

enzymes with all of its active sites engaged due to high enough reactant concentration, at this point reaction rate is solely determined by the enzyme's catalyzation rate, and the only way to increase it is increasing enzyme concentration

Temperature in regards to enzyme activity

an increase in temperature (kinetic energy of molecules) can speed up reaction rate by providing energy to reach transition state more easily, but past a certain point enzymes begin to denature, and each enzyme has its own optimal temperature and pH

Metabolism

the sum of an organism’s chemical reactions, managing the material and energy of the cell, each pathway catalyzed by a specific enzyme

Bioenergetics

the study of how energy flows through living organisms

Thermodynamics

the study of energy (capacity to cause change) transfer and transformation that occur in or between a system, its surroundings, and the universe (both together)

Kinetic energy

energy associated with motion of objects, can be applied to other objects on contact

Thermal energy

kinetic energy associated with random movement of atoms, transfer of thermal energy is heat

Potential energy

energy an object has due to location or structure, even if at rest

Chemical energy

energy available for release in reactions (stored in bonds), complex molecules are high in chemical energy as they have many energy storing bonds

First law of thermodynamics

energy can be transferred and transformed, but never created or destroyed

Second law of thermodynamics

every transfer or transformation of energy within a spontaneous/exergonic reaction increases the entropy of the universe, some released as thermal energy (heat), which speeds up other atoms

Catabolic/breakdown reactions

Substrate(s) bound to enzyme/ribozyme in active site, bond to be broken is stretched and stressed until easily broken by water, releasing net energy when more stable bonds are formed after, allowing for anabolic reactions to occur

Anabolic/synthetic reactions

monomers/substrates combined into larger, complex molecules, unfavorable as it decreases entropy of the universe, so requires the input of energy provided by catabolic reactions

Cofactors

non protein enzyme helpers that bind either permanently/covalently to the enzyme or reversibly with weak interactions (hydrogen bonds, ionic attractions, van der waals forces), cofactors can also reversibly bind to the substrate, can be inorganic (such as metal atoms) or organic (coenzymes) such as vitamins (which can be broken down into raw materials)

Inhibition

inhibitors prevent enzyme activity and can bond either covalently (permanently, such as toxins) to enzymes or reversibly through weaker interactions

Competitive inhibition

inhibitors shaped like substrate compete with it for active site, resulting in less substrate being catalyzed, can be overcome by increasing substrate concentration

Noncompetitive inhibition

inhibitors bind to the enzyme outside of the active site, distorting its shape through interactions between the molecules and thus preventing enzyme activity

ATP

sugar ribose (-OH on 2' carbon) bound to nitrogenous base adenine and a chain of three negatively charged phosphate groups, breaks down into ADP and Pi (inorganic phosphate) through hydrolysis, which is favorable due to increased entropy (more molecules) and ATP's bonds being unstable due to the phosphate groups repelling each other

ATP energy coupling

ATP hydrolysis has a negative free energy change (-31 kJ/mol or -7.3 kcal/mol), so it is exergonic and can be coupled with endergonic reactions to make the overall reaction more favorable

Phosphorylation

Inorganic phosphate from ATP can bind to a substrate, making a phosphorylated intermediate, during energy coupling, making the reaction even more favorable since Pi (negatively charged) distorts the bonds of the substrate, making them easier to break

Phosphorylation in action

Pi repeatedly binds to transport proteins, changing its shape in a way so that it flips directions and allows molecules to cross the membrane, Pi also repeatedly binds to motor protein, changing its shape in a way that makes it "step" forward

ATP regeneration

Since ATP hydrolysis is exergonic, ATP regeneration (or ADP phosphorylation) is endergonic, and requires the input of energy from catabolic pathways to occur

ATP’s effect on enthalpy

ATP itself is unstable due to the chain of three negatively charged phosphate groups, and inorganic phosphate binds to other molecules, making their bonds unstable, these unstable bonds require less energy to break, and more energy is released when forming stable bonds after

ATP’s effect on entropy

ATP hydrolysis breaks it down into ADP and Pi, 2 molecules instead of 1, increasing entropy which makes it favorable

Equilibrium in regards to metabolism

all metabolic reactions are reversible, but biological systems are open systems (materials and energy constantly flowing in and out of living cells), so equilibrium is never reached unless cells are dead

Cell work

chemical work by driving endergonic reactions, transport work pumping substances across cell membrane against spontaneous movement, mechanical work physically moving an organism

Metabolic regulation

reversible noncompetitve inhibitors usually regulate when an enzyme is being encoded/active in metabolic pathways

Allosteric regulation

form of metabolic regulation in which a multisubunit enzyme (quaternary structure), each with its own active site, is regulated by either an activator or an inhibitor, which binds to the regulatory/allosteric site (where the subunits join) and either stabilizes the functional enzyme shape or an inactive shape

ATP and ADP in allosteric regulation

ATP acts as an inhibitor for some catabolic enzymes, while ADP acts as an activator for those same enzymes, since ATP synthesis requires energy from catabolic pathways, if ATP concentration is too high, more catabolic enzymes are inhibited by ATP and less ATP is regenerated, but if ATP concentration is too low, more catabolic enzymes are activated by ADP and more ATP is regenerating, regulating ATP levels and preventing waste (also an example of feedback regulation)

Cooperativity

form of allosteric regulation (even though it involves active site) in which substrate(s) binding to one of the subunits active sites increases activity of all other subunit active sites

Feedback inhibition

form of metabolic regulation in which the product of a metabolic pathway acts as an inhibitor for an enzyme early on in the pathway, regulating its own production and preventing waste

Multienzyme complex

multiple enzymes arranged together (quaternary structure) so that the product of one is easily passed over as the substrate of another, facilitating a sequence of reactions