Ch 8 Flashcards
metabolism
the totality of an organisms chemical reactions
metabole
greek for change
metabolism is a(n) ______ property
emergent
a metabolic pathway begins with-
a specific molecule
mechanisms that regulate___ balance metabolic supply and demand
enzymes
metabolism manages
the material and energy resources of a cell
degradative metabolic pathways which release energy by breaking down complex molecules to simpler compounds
Catabolic pathways (also called break down pathways)
A major pathway of catabolism
cellular respiration
catabolism in cellular respiration
the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water
Pathways can have _____ starting molecule and/or product
more than one
energy that was stored in organic molecules…
becomes available to do the work of the cell
anabolic pathways (also called biosynthetic pathways)
metabolic pathways consume energy to build complicated molecules from simpler ones
examples of anabolism
synthesis of amino acids and proteins from amino acids
bioenergetics
the study of how energy flows through living organisms
energy
the capacity to cause change
kinetic energy
energy associated with the relative motion of objects
heat or thermal energy
kinetic energy associated with the random movement of atoms or molecules
a type of energy that can be harnessed to perform work
ex.photosynthesis
light
potential energy
energy that matter possesses because of its location or structure ; energy that is not kinetic
potential energy examples
water behind a dam, molecules due to their structure
chemical energy
potential energy available for release in a chemical reaction
complex molecules, such as glucose
are high in chemical energy
when kinetic energy is converted into potential energy a small amount of energy
is lost as heat due to friction
thermodynamics
the study of energy transformations that occur in a collection of matter
surroundings in thermodynamics
everything outside the system (the rest of the universe)
system in thermodynamics
the matter under study
isolated system
is unable to exchange either energy or matter with its surroundings
open system
energy and matter can be transferred between the system and its surroundings
organisms are ____ systems (in thermodynamics)
open
first law of thermodynamics (principle of conservation of energy)
energy can be transferred and transformed, but it cannot be created or destroyed
entropy
a measure of disorder, or randomness
second law of thermodynamics
every energy transfer or transformation increases the entropy of the universe
spontaneous (energetically favorable) process
a process that can occur without an input of energy; must increase entropy of the universe
nonspontaneous process
energy must be added
energy flows into most ecosystems as light
and leaves as heat
the entropy of a particular system, such as an organism, may decrease as long as
the total entropy of the universe (system and surroundings) increases
Gibbs free energy of a system (G), free energy
portion of a system’s energy that can perform work when pressure and temperature are uniform throughout a system (a cell for example)
(change in free energy calculation)
Delta G = Delta H - T Delta S
Delta (change in free energy calculation)
a triangle (letter in greek alphabet)
Delta H (change in free energy calculation)
change in system’s enthalpy
enthalpy
equivalent to total energy in biological systems
delta S (change in free energy calculation)
change in system entropy
T (change in free energy calculation)
absolute temperature in Kelvin
Kelvin
K=C+ 273
only processes with a negative delta G
are spontaneous
for delta G to be negative
either delta H must be negative and/or T delta S must be positive
difference between free energy of initial state and free energy of final state
delta G= G(final state)-G(initial state)
unstable systems have
higher G
stable systems have
lower G
equilibrium
state of maximum stability
most chemical reactions are reversible and proceed to a point where
forward and backward reactions occur at the same rate
at equilibrium
G is at its lowest possible value
any change away from equilibrium
has a positive effect on G and will not be spontaneous
systems___ move spontaneously move away from equilibrium
never
a system at equilibrium cannot
do work
a process is spontaneous and can perform work only when
it is moving towards equilibrium
exergonic reaction
energy outward, net release of energy, loses free energy, delta G is negative, spontaneous
endergonic reaction
energy inward, absorbs free energy from surroundings, G increases, delta G is positive, nonspontaneous, and delta G’s magnitude=energy required to drive reaction
cellular respiration formula
C6H1206+602=6CO2+6H20
the breaking of bonds
requires energy
in an isolated system reactions will
reach equilibrium and cannot do work
if metabolism were isolated
it would reach equilibrium
cells don’t reach equilibrium because
of the constant flow of materials
key to prevent equilibrium
reaction product does not accumulate
The cell does 3 kinds of work
chemical-pushing of endergonic reactions that would not occur spontaneously, ex. polymer synthesis, transport-pumping substances across membranes against spontaneous movement direction, and mechanical-cilia beating, muscle contraction, chromosome movement in cell reproduction
energy coupling
using exergonic processes to drive endergonic ones
main mediator of energy coupling and acts as immediate source of energy in most cases, that powers cellular work
ATP
ATP
adenosine triphosphate
ATP contains
the sugar ribose, nitrogenous base adenine and a chain of three phosphate groups bonded to it
ATP phosphate bonds can be broken by
hydrolysis
in the cell most hydroxyl groups of phosphates are
ionized (-O-)
ATP hydrolysis
ATP+H2O= AN INORGANIC PHOSPHATE,ADP, and releases energy
energy in the hydrolysis of ATP comes from
lowering of free energy
all 3 phosphate groups in ATP are ___ charged
negatively
with what can a cell use ATP energy for things other than heat (such as driving reactions normally endergonic)
enzymes
if delta G of an endergonic reaction is less than the amount of energy released by hydrolysis ,than
the two reactions can be coupled so that , overall, the coupled reaction are exergonic, usually uses a phosphorylated intermediate
phosphorylated intermediate
the recipient of a transfer of a phosphate group from ATP: phosphate group is covalently bonded to it.
how is ATP regenerated
the addition of phosphate to ADP
the free energy required to phosphorylate ADP comes from
exergonic catabolism (breakdown reaction)
ATP cycle
the shuttling of inorganic phosphate and energy
the regeneration of ATP is inherently
endergonic
ATP cycle is incredibly
fast
to form ATP what is required other than a phosphate and ADP
free energy from catabolic pathways; cellular respiration and plants use light
enzyme
a macromolecule which acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction
spontaneous reactions like glucose in sterile water can be
imperceptibly slow
activation energy (free energy of activation))
initial investment energy-energy required to contort the reactant molecules so that bonds can break
were does activation energy often come from
thermal energy in the surroundings
unstable condition when molecules have absorbed enough energy for bonds to break
transition state
there must be enough energy in an exergonic reaction
to reach the transition state
many molecules in the human body are prone to decomposing spontaneously, why don’t they
few molecules can make it over the activation hump at cell temperature
an enzyme catalyzes by
lowering the activation energy barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures
an enzyme CANNOT change
the delta G for a reaction: cannot make an endergonic reaction exergonic
enzymes can only hasten reactions which
would occur anyway
dynamic metabolism
the routing of chemicals smoothly through the cell’s metabolic pathways due to enzymes
because enzymes are specific for the reactions they catalyze
they determine which chemical processes will be going on in the cell at any particular time
substrate
the reactant an enzyme acts on
enzyme-substrate complex
an enzyme bound to its substrate (or substrates when there are two or more reactants)
enzyme-substrate process
enzyme+ substrate(s)=enzyme-substrate complex=enzyme+ product(s) via catalytic action of the enzyme
most enzyme names end in
-ase
an enzyme can recognize its
specific substrate, even among closely related compounds
the specificity of an enzyme results from its
shape, which is a consequence of its amino acid sequence
active site
the restricted region of the enzyme molecule that actually binds to the substrate, typically a pocket or groove on the surface of the enzyme where catalysis occurs , usually only formed by a few of the enzymes amino acids. with the rest of the protein providing a framework that determines the configuration of the active site
an enzyme is not
a stiff structure locked into a given shape
enzymes “dance” between
subtly different shapes in a dynamic equilibrium with slight differences in free energy for each pose
the shape that best fits the substrate isn’t necessarily
the one with the lowest energy, but during the short time the enzyme takes on this shape, its active site can bind to the substrate
the active site is
not a rigid receptacle of the substrate
induced fit
the active site changes shape slightly to fit substrate due to interaction between the chemical groups. This brings them into positions which that enhance their ability to catalyze the chemical reaction
in most enzymatic reactions the substrate is held in place by
hydrogen and ionic bonds
what part of the active site catalyzes
the R groups of a few amino acids
enzymes are (speed)
fast
since most metabolic reaction are reversible
enzymes can catalyze either forward or the reverse reaction depending on negative delta G, which depends on reactant-product concentrations, with a net effect towards equilibrium
enzymes use a variety of mechanisms to lower activation energy. name them
1, in reactions containing two or more reactants, a template is provided for them to come together in proper orientation
- enymes may stretch substrate toward transition state, stressing and bending critical chemical bonds
- active sight can provide environment more conductive to a particular reaction
- direct participation of the active sight in the reaction, sometimes even involves covalent bonding of amino acids in enzyme to substrate
saturated enzyme
enough substrate so that all active sites are engaged
factors controlling rate of substrate to product conversion (excluding enzyme activity factors)
- amount of substrate in solution (pre-saturation)
- amount of enzyme (post saturation)
what controls enzyme activity factors
- general environmental factors such as pH and temperature
- chemicals that influence the enzyme
optimal conditions
when the enzymes work at their best
to a point, rate of enzymatic reaction increases
with increasing temperature, however above a certain temperature this rate drops
optimal temperature
temperatures where enzymes each work at their best
optimal pH
best pHs for each enzymes
cofactors
non-protein helpers for catalytic activity, organic or non-organic, tightly bound or bound loosely
coenzyme
organic cofactor
inhibitor is usually irreversible if
covalently bonded
competitive inhibitors
bind to enzymes reversibly with weak interactions and resemble the normal substrate; thus they compete for admission into activation site
how do you counter competitive inhibitors
add more substrate
noncompetitive inhibitors
impede enzymatic reaction by binding to another part of the enzyme and thus lowers the efficacy of the activation site
selective inhibition
inhibitors which regulate enzyme reactions naturally
mutation
a permanent change in a gene, which can result in a protein with one or more changed amino acids
if all of a cell’s metabolic pathways were operating simultaneously
chemical chaos would ensue
how does a cell regulate where and when its various enzyme are active (and thus its metabolic pathways)
by switching genes off and on that control specific enzymes or by regulating enzyme activity once made
allosteric regulation
any case where a protein’s function at one site is affected by binding a regulatory molecule to a separate site which may result in either inhibition or stimulation
most enzymes known to be allosterically regulated are constructed from
two are more subunits, each composed of a polypeptide chain with its own active site
the complex an allosterically regulated oscillate between
two different shapes, one catalytically active and the other inactive
where is a regulatory or allosteric site often located
where subunits join
what happens when an inhibitor and activator respectively bind to a regulatory sight
activator-stabilizes the shape that has functional active sites
inhibitor-stabilizes the inactive form of the enzyme
explain ATP regulation
ATP-binds to several catabolic enzymes allosterically, lowering their affinity for substrate and thus inhibiting their activity
ADP-functions as an activator for same enzymes
cooperativity
a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits
feedback inhibition
a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway
