Chapter 6

Biology & Chemistry Bi105 with Godrick at Boston University

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By: Katherine Quintana
Textbook: Biology

Biology
Created: 2011-06-03
Size: 62 flashcards
Views: 18

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thermodynamics

the branch of chemistry concerned with energy changes
means "heat changes"

energy

the capacity to do work

kinetic energy

the energy of motion

potential energy

stored energy

work

much of the work that living organisms carry out involves transforming potential energy into kinetic energy

forms of energy

mechanical energy
heat
sound
electric current
light
radioactivity

heat

the most convenient way of measuring energy because all other forms of energy can be converted into heat

kilocalorie (kcal)

the unit of heat most commonly employed in biology
equal to 1000 calories (cal)

calorie (cal)

the heat required to raise the temperature of one gram of water one degree Celsius (*C)

joule

equals 0.239 cal

photosynthesis

energy absorbed from sunlight is used to combine small molecules (water and carbon dioxide) into more complex ones (sugars)
converts carbon from an inorganic to an organic form
energy from the Sun is stored as potential energy in the covalent bonds between atoms in the sugar molecules

oxidation

an atom or molecule that loses an electron is said to be oxidized
oxygen is the most common electron acceptor in biological systems

reduction

an atom or molecule that gains an electron
the reduced form of a molecule has a higher level of energy than the oxidized form

oxidation-reduction or redox reactions

oxidation and reduction always take place together, because every electron that is lost by one atom through oxidation is gained by another atom through reduction

First Law of Thermodynamics

concerns the amount of energy in the universe
energy cannot be created or destroyed
it can only change from one form to another
the total amount of energy in the universe remains constant

heat

a measure of the random motion of molecules (and therefore a measure of one form of kinetic energy
heat can be harnessed to do work only when there is a heat gradient--that is, a temperature difference between two areas

Second Law of Thermodynamics

concerns the transformation of potential energy into heat, or random molecular motion
the disorder in the universe, more formally called entropy, is continuously increasing
energy transformations proceed spontaneously to convert matter from a more ordered, less stable form to a less ordered, but more stable form
called "time's arrow"
"entropy increases"

free energy

the net effect, the amount of energy actually available to break and subsequently form other chemical bonds
the energy available to do work in any system
denoted by the symbol G

enthalpy

G is equal to the energy contained in a molecule's chemical bonds (called enthalpy and designated H) together with the energy term (TS) related to he degree of disorder in the system, where S is the symbol for entropy and T is the absolute temperature expressed in the Kelvin scale (K = *C +273):
G = H - TS

change in free energy

when a chemical reaction occurs under conditions of constant temperature, pressure, and volume, the change symbolized by the Greek capital letter delta, ^, in free energy (^G) is simply:
^G = ^H - T^S

endergonic

the ^G is positive, which means that the products of the reaction contain more free energy than the reactants
the bond energy (H) is higher, or the disorder (S) in the system is lower
such reactions do not proceed spontaneously because they require an input of energy
"inward energy"

exergonic

the ^G is negative
the products of the reaction contain less free energy than the reactants
either the bond energy is lower, or the disorder is higher, or both
such reactions tend to proceed spontaneously
these reactions release the excess free energy as heat
"outward energy"

spontaneous reaction

proceeds if the difference in disorder (T^S) is greater than the difference in bond energies between reactants and products (^H)
may proceed very slowly

equilibrium constant

for each reaction, an equilibrium exists at some point between the relative amounts of reactants and products
an exergonic reaction has an equilibrium favoring the products
an endergonic reaction has an equilibrium favoring the reactants

activation energy

the extra energy needed to destabilize existing chemical bonds and initiate a chemical reaction
reactions with larger activation energies tend to proceed more slowly because fewer molecules succeed in getting over the initial energy hurdle
not constant

rate of reactions

can be increased in two ways:

by increasing the energy of reacting molecules (by heating up the reactants)
by lowering activation energy (to use a catalyst to lower the activation energy)

catalysis

the process of influencing chemical bonds in a way that lowers the activation energy needed to initiate a reaction

catalysts

substances that accomplish catalysis
cannot violate the basic laws of thermodynamics
by reducing the activation energy, a catalyst accelerates both the forward and the reverse reactions by exactly the same amount
reduce the energy barrier that is preventing the reaction from proceeding
cannot change spontaneous exergonic reactions
can make a reaction proceed much faster
enzymes

adenosine triphosphate (ATP)

Definition

structure of ATP

a five-carbon sugar, ribose, which serves as the framework to which the other two subunits are attached
adenine, an organic molecule composed of two carbon-nitrogen rings

each of the nitrogen atoms in the ring has an unshared pair of electrons and weakly attracts hydrogen ions, making adenine chemically a weak base

a chain of three phosphates

hydrolysis of ATP

has a negative ^G
the energy it releases can be used to perform work

inorganic phosphate (Pi)

in most reactions involving ATP, only the outermost high-energy phosphate bond is hydrolyzed, cleaving off the phosphate group on the end
when this happens adenosine diphosphate (ADP) plus Pi
energy equal to 7.3 kcal/mol is released under standard conditions

adenosine monophosphate (AMP)

both of the two terminal phosphates can be hydrolyzed to release energy, leaving AMP, but the third phosphate is not attached by a high-energy bond

enzymes

the agents that carry out most of the catalysis in living organisms
most are proteins, but some are RNA molecules

substrates

the molecules that will undergo the reaction

carbonic anydrase

reactions that proceed very slowly are of little use to a cell
vertebrate red blood cells overcome this problem by employing an enzyme within their cytoplasm

active sites

most enzymes are globular proteins with one or more pockets or clefts on their surface

enzyme-substrate complex

substrates bind to the enzyme at the active sites

induced fit

proteins are not rigid
the binding of a substrate induces the enzyme to adjust its shape slightly
is the fit between enzyme and substrate

multienzyme complexes

often several enzymes catalyzing different steps of a sequence of reactions are associated with one another in noncovalently bonded assemblies
each complex has multiple copies of each of the three enzymes--60 protein subunits in all

advantages of multienzyme complexes

The rate of any enzyme reaction is limited by how often the enzyme collides with its substrate. If a series of sequential reactions occurs within a multienzyme complex, the product of one reaction can be delivered away.
Because the reacting substrate doesn't leave the complex while it goes through the series of reactions, unwanted side reactions are prevented.
All of the reactions that take place within the multienzyme complex can be controlled as a unit.

ribozymes

RNA catalysts
greatly accelerate the rate of particular biochemical reactions and show extraordinary substrate specificity

intramolecular catalysis

some ribozymes have folded structures and catalyze reactions on themselves

intermolecular catalysis

other ribozymes act on other molecules without being changed themselves

factors affecting enzyme function

temperature
pH
the binding of regulatory molecules

temperature

increasing the temperature of an uncatalyzed reaction increases its rate because the additional heat increases random molecular movement
the rate of an enzyme-catalyzed reaction also increases with temperature, but only up to a point called the optimum temperature

ionic interactions between oppositely charged amino acid residues also hold enzymes together
most enzymes have an optimum pH that usually ranges from pH 6 to 8
enzymes able to function in very acidic environments are proteins that maintain their 3-D shape even in the presence of high hydrogen ion concentrations

inhibitor

a substance that binds to an enzyme and decreases its activity

feedback inhibition

the end product of a biochemical pathway acts as an inhibitor of an early reaction in the pathway

competitive inhibitors

compete with the substrate for the same active site, occupying the active site and thus preventing substrates from binding

noncompetitive inhibitors

bind to the enzyme in a location other than the active site, changing the shape of the enzyme and making it unable to bind to the substrate

allosteric enzymes

many enzymes can exist in either in active or inactive conformation

allosteric site

most noncompetitive inhibitors bind to a specific portion of the enzyme
these sites serve as chemical on/off switches

allosteric inhibitor

a substance that binds to an allosteric site and reduces enzyme activity

allosteric activator

binds to allosteric sites to keep an enzyme in its active configuration, thereby increasing enzyme activity

cofactors

enzyme function is often assisted by additional chemical components

coenzyme

when the cofactor is a nonprotein organic molecule

metabolism

the total of all chemical reactions carried out by an organism

anabolism

chemical reactions that expend energy to build up molecules

catabolism

reactions that harvest energy by breaking down molecules

biochemical pathways

many reactions in a cell occur in sequences
the product of one reaction becomes the substrate for the next
are the organizational units of metabolism--the elements an organism controls to achieve coherent metabolic activity