Chapter 8 (Notes) Flashcards
Metabolism
is the totality of an organism’s chemical reactions
Metabolism is an emergent property of life that arises from interactions between
molecules within the cells.
It is both the breaking down and building up of things.
A metabolic pathway
begins with a specific molecule and ends with a product.
Each step is catalyzed by a specific enzyme.
Catabolic pathways
release energy by breaking down complex molecules into simpler compounds.
Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a
pathway of catabolism.
Anabolic pathways
consume energy to build complex molecules from simpler ones
The synthesis of protein from amino acids is an example of
anabolism
Bioenergetics is the study of
how organisms manage their energy resources.
Catabolic Pathways
- breaking down (molecules)
- release energy
- spontaneous (just happens)
- exergonic
- Delta G=negative (the triangle G)
-on a graph:
it starts with high energy (reactants), then it ends up with low energy (products).
Anabolic Pathways
- building up
- needs/requires energy
- non-spontaneous
- endergonic
- Delta G=positive (the triangle G)
-on a graph:
it starts with low energy (reactants), then it ends up with high energy (products).
Energy is the
capacity to cause change.
Energy exists in various forms, some of which can perform work.
Kinetic energy is energy associated with
motion
Heat (thermal energy) is
kinetic energy associated with random movement of atoms or molecules
Potential energy is energy that
matter possesses because of its location or structure
Chemical energy is
potential energy available for release in a chemical reaction.
Energy can be converted from
one form to another.
Some energy is ALWAYS lost as heat when conversion occurs.
Thermodynamics is
the study of energy transformations (and how it moves around).
An isolated system, such as that approximated by liquid in a thermos, is
isolated from its surroundings.
the liquid is completely closed off
In an open system, energy and matter can be
transferred between the system and its surroundings.
Organisms are
open systems.
They are constantly bringing in energy from the outside and releasing energy from the inside
According to the First Law of Thermodynamics,
the energy of the universe is constant.
Energy can be transferred and transformed, but it cannot be created or destroyed.
((Energy is constant in the Universe))
The first law is also called the principle of conservation of energy.
During every energy transfer or transformation, some energy is
unusable, and is often lost as heat.
According to the Second Law of Thermodynamics,
every energy transfer or transformation increases the entropy (disorder) of the universe.
Entropy will always increase in energy transfer.
Living cells unavoidably convert organized forms
of energy to heat.
Spontaneous processes occur
without energy input; they can happen quickly or slowly.
For a process to occur without energy input, it must
increase the entropy of the universe.
Cells create ordered structures from
less ordered materials.
Organisms also replace ordered forms of matter and energy with
less ordered forms.
Energy flows into an ecosystem in the form of
light and exits in the form of heat.
The evolution of more complex organisms dow not violate the
second law of thermodynamics.
Entropy (disorder) may decrease in an organism, but
the universe’s total entropy increases.
Biologists want to know which reactions occur spontaneously and which require input of energy.
To do so, they need to determine energy changes that occur in chemical reactions.
A living system’s free energy is
energy that can do work when temperature and pressure are uniform, as in a living cell.
The change in free energy (delta G) during a process is related to the change in
enthalpy, or change in total energy (delta H), change in entropy (delta S), and temperature in Kelvin (T).
(Delta G)=(Delta H) - T (Delta S)
Only processes with a negative delta G are
spontaneous.
Spontaneous processess can be harnessed to
perform work.
Free energy is a measure of a
system’s instability, its tendency to change to a more stable state.
During a spontaneous change,
free energy decreases and the stability of a system increases.
Equilibrium is a state of
maximum stability.
A process is spontaneous and can perform work only when
it is moving toward equilibrium.
The concept of free energy can be applied to the
chemistry of life’s processes.
An exergonic reaction
proceeds with a net release of free energy and is spontaneous.
delta G is negative.
This is also catabolic.
It starts with high energy (reactants), then ends up with low energy (products).
((what it looks like on a graph))
An endergonic reaction
absorbs free energy from its surroundings and is nonspontaneous.
delta G is positive.
This is also anabolic.
It starts with low energy (reactants), then ends up with high energy (products).
((what it looks like on a graph))
Reactions in a closed system eventually reach
equilibrium and then do no work.
Cells are not in equilibrium; they are
open systems experiencing a constant flow of materials.
A defining feature of life is that
metabolism is never at equilibrium.
A catabolic pathway in a cell
releases free energy in a series of reactions.
Closed and open hydroelectric systems can serve as
analogis.
A cell does three main kinds of work
- Chemical
- Transport
- Mechanical
To do work, cells manage energy resources by
energy coupling, the use of an exergonic process to drive an endergonic one.
Energy coupling is the
use of an exergonic process to drive an endergonic one.
Most energy coupling is mediated by
ATP.
ATP (adenosine triphosphate) is
the cell’s energy shuttle.
(ATP=energy currency of a cell?)
((ATP=how we transport energy in a cell))
ATP is composed of
ribose (a sugar)
adenine (a nitrogenous base)
and
three phosphate groups
The bonds between the phosphate groups of ATP’s tail can be
broken by hydrolysis.
Energy is released from ATP when the
terminal phosphate bond is broken.
This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.
-3 negative phosphate groups act like a coiled spring.
The three types of cellular work (mechanical, transport, and chemical) are powered by
the hydrolysis of ATP.
how we do energy coupling.
In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used
to drive an endergonic reaction.
(energy coupling)
Overall, the coupled reactions are exergonic.
ATP drives endergonic reactions by
phosphorylation, transferring a phosphate group to some other molecule, such as a reactant.
This recipient molecule is now called a phosphorylated intermediate.
Phosphorylated Intermediate is
a molecule (often a reactant) with a phosphate group covalently bound to it, making it more reactive (less stable) than the unphosphorylated molecule.
ATP is a renewable resource that is
regenerated by addition of a phosphate group to adenosine diphosphate (ADP).
The energy to phosphorylate ADP comes from
catabolic reactions in the cell.
The ATP cycle is a
revolving door through which energy passes during its transfer from catabolic to anabolic pathways.
Just because a reaction is spontaneous, it doesn’t meant that the
rate of the reaction is fast.
A catalyst is a
chemical agent that speeds up a reaction without being consumed by the reaction.
((don’t/doesn’t change reactions???))
An enzyme is a
catalytic protein.
Hydrolysis of sucrose by the enzyme sucrase is an example of an
enzyme-catalyzed reaction.
Every chemical reaction between molecules involves
bond breaking and bond forming.
The initial energy needed to start a chemical reaction is called
the free energy of activation, or activation energy (Ea).
Even if it is spontaneous, it still requires some energy to get it going
Activation energy is often supplied in the form of
thermal energy that the reactant molecules absorb from their surroundings.
Enzymes catalyze reactions by
lowering the Ea (activation energy) barrier.
(this doesn’t change anything, just lowers it)
Enzymes do not affect the change in free energy (delta G); instead,
they hasten (speed up) reactions that would occur eventually.
((delta D is unaffected by enzyme. It will always be the same))
Enzymes function by
lowering the activation energy.
Kind of steps of how an enzyme works
Substrate Enzyme Enzyme-Substrate Complex Active Site Induced Fit Cofactor
The reactant that an enzyme acts on is called the enzyme’s
substrate.
The enzyme binds to its substrate, forming an
enzyme-substrate complex.
The active site is the
region on the enzyme where the substrate binds.
Induced fit of a substrate brings
chemical groups of the active site into positions that enhance their ability to catalyze the reactions. ((changes shape))
Enzyme specificity
every enzyme is very specific for certain substrates.
In an enzymatic reaction, the
substrate binds to the active site of the enzyme.
The active site can lower an Ea (activation energy) barrier by
(((not really important???)))
- orienting substrates correctly
- straining substrate bonds
- providing a favorable microenvironment
- covalently bonding to the substrate
An enzyme’s activity can be affected by
- general environmental factors, such as temperature and pH
- chemicals that specifically influence the enzyme
Each enzyme has an optimal temperature in which
it can function.
Each enzyme has an optimal pH in which
it can function.
Optimal contions favor the most active
shape for the enzyme molecule.
Cofactors are
non-protein enzyme helpers
Cofactors may be inorganic (such as metal in ionic form) or organic.
An organic cofactor is called a
coenzyme.
Coenzymes include vitamins.
If an inhibitor binds with covalent bonds
inhibition is usually irreversible.
This means an enzyme is then stopped for forever
Some inhibitors use
weak interactions, in which case the inhibition is reversible.
(These only stop it for a little instead of for forever)
Competitive inhibitors bind to
the active site of an enzyme, competing with the substrate.
Competitive inhibitors bind to the active spot on an enzyme keeping the substrate from binding
Noncompetitive inhibitors bind to
another part of an enzyme, causing the enzyme to change shape and making the active site less effective.
(Noncompetitive inhibitors bind away from the active site and changes the shape so that the substrate cannot bind to it)
Examples of inhibitors include
toxins, poisons, pesticides, and antibiotics.
Enzymes are proteins encoded by
genes.
Changes (mutations) in genes lead to
changes in amino acid composition of an enzyme.
Altered amino acids in enzymes may alter their
substrate specificity.
Under new environmental conditions a novel form of an
enzyme might be favored.
Chemical chaos would result if a cell’s
metabolic pathways were not tightly regulated.
A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes.
Allosteric regulation may
either inhibit or stimulate an enzyme’s activity.
Allosteric regulation is the general broad name/term for a way to turn on or off an enzyme??
Allosteric regulation occurs when a
regulatory molecule binds to a protein at one site and affects the protein’s function at another site. (like noncompetitive inhibition)
It is a way to turn enzymes off.
(We use activators or inhibitors to do this?)
Noncompetitive inhibition is a type of
allosteric regulation.
??
Most allosterically regulated enzymes are made from
polypeptide subunits.
Each enzyme has
active and inactive forms.
The binding of an activator stabilizes the
active form of the enzyme. (turns on?)
The binding of an inhibitor stabilizes the
inactive form of the enzyme. (turns off?)
Cooperativity is a
form of allosteric regulation that can amplify enzyme activity.
One substrate molecule primes an enzyme to act on additional substrate molecules more readily.
((One molecule binding on unit and makes it easier to have faster binding on other units?))
Cooperativity is allosteric because
binding by a substrate to one active site affects catalysis in a different active site.
Allosteric regulators are attractive drug candidates for enzyme regulation because
of their specificity.
Inhibition of proteolytic enzymes called caspases may help
management of inappropriate inflammatory responses.
In feedback inhibition, the
end product of a metabolic pathway shuts down the pathway ((of an enzyme??)).
(another way to regulate enzyme)
Feedback inhibition prevents a cell from
wasting chemical resources by synthesizing more product than is needed.
Feedback inhibition is a
method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.
Structures within the cell help bring order to
metabolic pathways.
Some enzymes act as
structural components of membranes.
In eukaryotic cells, some enzymes reside in
specific organelles; for example, enzymes for cellular respiration are located in the mitochondria.
