bio chapter 6

metabolism

all of an organism’s metabolic pathways; anabolic and catabolic

catabolic pathways

release energy; break down complex molecules into simpler ones

ex of catabolic pathways

cellular respiration breaking glucose down into CO2 and H2O providing cell with energy

anabolic pathways

consume energy; build complex molecules from simpler ones

ex of anabolic pathways

photosynthesis making glucose molecules from CO2 and H2O; polymerization reactions

energy

capacity to do work

kinetic energy

energy of motion; energy in the process of doing work

kinetic energy ex

a ball at the top of a hill or water behind a dam (due to gravity); chemical energy stored in molecules because of arrangement of nuclei and electrons

ex of transformed energy

in photosynthesis, the kinetic energy of sunlight is transformed into potential energy; when burning gasoline, the potential energy of chemical bonds is transformed into kinetic energy which pushes engine pistons

free energy

amount of energy in a system that is available to do work; designated G

Delta G

change in free energy; change in free energy from the initial state to the final state of a reaction

free energy

indicates whether a reaction will occur spontaneously or not

spontaneous reaction

a reaction that will occur without additional energy; free energy decreases (negative delta G)

spontaneous reaction

as a reaction approached equlibrium, delta G decreases

non-spontaneous reaction

when a reaction is pushed away from equilibrium, delta G increases

no net change in system

when a system reaches equilibrium, delta G = 0

exergonic reaction

proceeds with a net loss of delta G (negative); products have less free energy than reactants; spontaneous reaction

endergonic reaction

proceeds with a net gain of delta G (positive); requires input of energy; products have more free energy than reactants; non-spontaneous reaction

if a chemical process is exergonic, the reverse process must be endergonic

ex:

cellular respiration is an exergonic process

2870 kJ (686 kcal) of energy are released from each mole of glucose in
respiration (∆G = -2870 kJ/mol or ∆G = -686 kcal/mol)
photosynthesis is an endergonic process
2870 kJ (686 kcal) of energy must be added to produce a mole of glucose in
photosynthesis (∆G = + 2870 kJ/mol or ∆G = +686 kcal/mol)

metabolic disequilibrium

necessary for life; if metabolic reactions reach equilibrium, cell dies (delta G = 0, no work can be done); metabolic reactions are “pulled forward” bc their products become reactants for the next reaction in the metabolic pathway

ATP

adenosine triphosphate; immediate source of energy that drives most cellular work; mechanical, transport, and chemical work

mechanical work

cilia beating, muscle contraction, etc.

transport work

pumping substances across membranes

chemical work

endergonic reactions like polymerization

ATP

nucleotide with unstable phosphate bonds; phosphate bonds are hydrolyzed to yield energy for endergonic reactions

components of ATP

adenine (nitrogenous base); ribose (5 carbon sugar); 3 phosphate groups

phosphate bonds

unstable; can be broken (exergonic reaction); when terminal phosphate bond is hydrolyzed, a phosphate group is removed

ADP

exergonic reaction; ATP + water = ADP

exergonic reaction

products more stable than reactants

ATP function

exergonic hydrolysis of ATP is couple with endergonic reactions; a phosphate group is transferred to another molecule; phosphorylated molecule becomes more reactive

regeneration of ATP

endergonic reaction ADP + P = ATP; occurs rapidly (10^7 molecules are used and regenerated in each cell every second; energy required comes from the exergonic process of cellular respiration

catalyst

chemical agent that speeds up a reaction without being permanently changed in the process; can be used over and over

enzymes

biological catalysts made of protein; speed up reactions by lowering energy barriers

activation energy

amount of free energy reactant molecules must absorb to start a reaction (EA); needed to break chemical bonds

exergonic reaction

reactants must absorb enough energy to reach transition state (top of hill); usually involves absorption of thermal energy from surroundings; reaction occurs and energy is released as new bonds form (downhill); delta G for overall reaction is the difference between the free energy products and reactants; free energy of products is less than reactants in an exergonic reactants

breakdown of biological macromolecules

exergonic; cannot absorb enough energy to reach transition state; need enzymes

enzymes

lower EA; transition state can be reached at cellular temperatures; very selective for the reaction will catalyze

substrate

substance an enzyme acts on (made more reactive); catalyzed to product after it binds to active site of enzyme; enzyme +substrate = enzyme-substrate complex = product + enzyme

enzyme

specific for a certain substrate; 3D shape determines specificity

active site

region of enzyme which binds to substrate; formed by a few amino acids; fits compatibly with substrate

catalytic cycle of enzymes

substrate binds to active site and held there by weak interactions; induced fit of active site around substrate, side chains in active site catalyze conversion of substrate to product; product leaves site and enzyme emerges unchanged

ways enzyme lower activation energy to speed up reactions

active site may hold reactions in proper position to react; induced fit may distort substrates chemical bonds making them easier to break; site may provide a microenvironment conducive to particular reaction types; amino acid side chains in active site may participate directly in reaction

substrate concentration

higher substrate concentration = faster reaction (to a point); enzyme can become saturated with substrate if concentration gets high enough; when saturated, reaction rate depends on how fast site can convert substrate to product; when enzyme is saturated, reaction increases with more enzyme

effects of temperature

optimal temp. allows greatest number of molecular collisions without denaturing enzymes; ( temperature =  kinetic energy =  collisions =  reaction rate) beyond optimal temperature, reaction rate slows as enzyme denatures ( thermal energy disrupts weak bonds in enzymes)

effects of pH

optimal range for most enzymes = 6-8; some operate best at more extremes of pH (stomach enzyme = 2)

cofactors

small, nonprotein molecules needed for proper enzyme function; may bind to active site or substrate

inorganic cofactors

zinc, iron, copper, etc

organic cofactors (coenzymes)

vitamins

effects of enzyme inhibitors

some chemicals may inhibit enzyme activity; irreversible and reversible inhibition

irreversible inhibition

inhibitor attaches by covalent bonds

reversible inhibition

inhibitor attaches by weak bonds

competitive inhibitors

resemble substrate; compete with substrate for active site (block site from substrate); overcome by increasing substrate concentration (if reversible)

noncompetitive inhbitors

bind to another part of enzyme molecule causing it to change shape (active site cant bind substrate); may act as toxins (DDT, antibiotics); increasing substrate WILL NOT overcome this

control of metabolism

allosteric regulation; feedback inhibition; cooperativity

allosteric regulation

controls metabolism

allosteric enzymes

2 shapes; active and inactive conformation

allosteric site

receptor site on some part of enzyme molecule (other than active site); activator binds here stabilizing active conformation of enzyme; noncompetitive inhibitor binds here stabilizing inactive conformation

feedback inhibition

metabolic pathway regulated by its own end product; end product inhibits an enzyme somewhere in the pathway

cooperativity

substrate molecules may enhance enzyme activity; substrate binds to active site of 1 enzyme subunit causing a shape change that enhances substrate binding at active site of other subunits