Download Intro metabolism

Metabolism
Metabolism refers to the cell's capacity to acquire
energy and use it to build, store, break apart, and
eliminate substances in controlled ways.
Energy and the Underlying Organization of Life
A. Defining Energy
1. Potential energy is the capacity to make things
happen, to do work.; it can also be called chemical
energy, measured in kilocalories.
2. Kinetic energy is the energy of motion; it includes
heat energy.
B. What Can Cells Do With Energy?
1. Energy from the sun or from organic substances
becomes coupled to thousands of energy-requiring
processes in cells.
2. Cells use the energy to perform chemical,
mechanical, and electrochemical work.
C. How Much Energy Is Available?
1. First law of thermodynamics states that the total
amount of energy in the universe is constant; it cannot
be created nor destroyed; it can only change form.
2. Energy cannot be produced by a cell; it can only be
borrowed from someplace else.
3. Energy can be of high quality, that is, highly
concentrated and usable; or it can be of low quality,
such as heat that is released into the universe.
D. The One-Way Flow of Energy
1. Second law of thermodynamics states that the
spontaneous direction of energy flow is from high- to
low-quality forms.
2. Each conversion produces energy (usually heat)
that is unavailable for work.
3. As systems lose energy they become more
disorganized; the measure of this disorder is called
entropy.
4. The world of life (plant and animal) maintains a
high degree of organization only because it is being
re-supplied with energy from the sun.
Energy Inputs, Outputs, and Cellular Work
A. Cells and Energy Hills
1. Endergonic (“energy in”) reactions require energy
input resulting in products with more energy than the
reactants had; for example: photosynthesis.
2. Exergonic (“energy out”) reactions release energy
such that the products have less energy than the
reactants had; for example: cellular respiration.
B. ATP Couples Energy Inputs With Outputs
1. ATP is composed of adenine, ribose, and three
phosphate groups.
a. Energy input links phosphate to ADP to
produce ATP (phosphorylation).
b. ATP can in turn donate a phosphate group
to another molecule, which then becomes
primed and energized for specific reactions.
2. ATP's role is like currency in an economy: earning
ATP during exergonic reactions and spending it
during endergonic ones.
3. ADP can be recycled to ATP very rapidly in the
ATP/ADP cycle.
C. Phosphorylation – transferring of a phosphate group from
one molecule to another (this is how ATP is made)
-2 types of phosphorylation result in ATP formation
1. substrate level phosphorylation (the phosphate is
simply removes from one chemical and placed onto
another)
2. Oxidative phosphorylation – Electron Transfers
Drive ATP Formation
***OIL – RIG or LEO - GER
redox reactions release energy, which is used to form
ATP
B. Electron transfer chains are similar to staircases where
electrons flow down the steps from the top (most energy) to
the bottom (least energy), releasing a small amount at each
step.
C. The energy is harnessed to move hydrogen ions, which in
turn establish pH and electric gradients necessary for ATP
production.
Cells Juggle Substances as Well as Energy
A. Participants in Metabolic Reactions
1. Reactants are substances that enter reactions.
2. Intermediates are the compounds formed
between the start and the end of a pathway.
3. Products are the substances present at the
conclusion of a pathway.
4. Energy carriers are mainly ATP.
5. Enzymes are proteins that catalyze (speed up)
reactions.
6. Cofactors are small molecules and metal ions
that help enzymes by carrying atoms or
electrons.
7. Transport proteins are membrane-bound
proteins that participate in adjusting
concentration gradients that will influence the
direction of metabolic reactions.
B. What Are Metabolic Pathways?
1. Metabolic pathways form series of reactions that
regulate the concentration of substances within cells
by enzyme-mediated linear and circular sequences.
2. In biosynthetic (anabolic) pathways, small
molecules are assembled into large molecules; for
example, simple sugars are assembled into complex
carbohydrates.
3. In degradative (catabolic) pathways, large
molecules such as carbohydrates, lipids, and proteins
are broken down to form products of lower energy.
Released energy can be used for cellular work.
D. No Vanishing Atoms at the End of the Run
1. The law of conservation of mass states that the
total mass of all substances entering a reaction equals
the total mass of all the products. This is why you
must always "balance" a chemical equation by having
an equal number of atoms of
each element on
both sides of the arrow.
Enzymes Help With Energy Hills
A. Enzymes are catalytic molecules that alter the rate of a
chemical reaction without being used in them.
1. there names usually reflect their function and end
in “ase”
B. Enzymes have four features:
1. Enzymes speed up reactions.
2. Enzymes can be reused.
3. Enzymes, at least some of them, can recognize both
reactants and products in order to catalyze a reaction
in both directions.
4. Enzymes are very selective about the substrates to
which they will bind and thereby bring about change
C. Enzymes increase the rate of a reaction by lowering the
activation energy (the amount of energy needed to get a
reaction going).
D. they don’t “force” reactions, they just speed up reactions
that already occur
E. enzymes are specific
1. most catalyze only a few closely related chemical
reactions; many only 1
How Do Enzymes Lower Energy Hills?
A. The Active Site
1. Enzymes increase the rate of reactions by creating
a microenvironment that is energetically more
favorable for the reaction.
2. Each enzyme molecule has an active site where the
substrate binds to the enzyme during a reaction
B. Transition at the Top of the Hill
1. Activation energy brings the reactive chemical
groups into alignment so that chemical bonds can be
broken, created, and rearranged.
2. The substrate is brought to its transition state, the
point when a reaction can occur.
3. enzyme + substrate enzyme-substrate complex
(intermediate) enzyme + product
C. How Enzymes Work
1. Binding energy helps bring about the transition
state by four mechanisms:
a. Helping substrates get together;
b. Orienting substrates in positions favoring
reaction;
c. Shutting out water;
d. Inducing changes in enzyme shape (inducedfit model).
-induce strain in the substrate
D. About Those Cofactors
-Some enzymes have 2 parts; a protein called the apoenzyme and
an additional cofactor
1. Cofactors are nonprotein groups that bind to many enzymes
and make them more reactive. Without the cofactors, the enzyme
doesn’t function properly
a. coenzymes – organic, nonpolypeptide compounds that
serve as cofactors
-they are not permanently bonded to the enzyme
-they also act as carrier molecules that transfer
electrons or part of a substrate between molecules
b. prosthetic groups – permanently bonded to the enzyme
2. Inorganic metal ions such as Fe++ also serve as cofactors when
assisting membrane cytochrome proteins in their electron
transfers in chloroplasts and mitochondria.
E. Why Are Enzymes So Big?
1. A large molecule affords structural stability.
2. The extensive folding of the polypeptide chains puts
amino acids and functional groups in locations and
orientations that favor interaction with water and
substrate.
Enzymes Don't Work in a Vacuum
A. How Is Enzyme Activity Controlled?
1. Some controls regulate the number of enzyme
molecules available by speeding up/slowing down their
synthesis.
a. remember, genes direct the synthesis of each
type of enzyme and genes can be switched on
and off; therefore controlling the amount of
enzyme present in the cell
2. we refer to the series of chemical reactions in which
the product of one reaction is the substrate of the next
as a metabolic pathway
3. inhibitors – substances that bind to an enzyme and slow
down the reaction
a. some inhibitors occur naturally, some are artificial
b. reversible vs irreversible
-reversible inhibitors can leave the enzyme and
the enzyme will return to normal function
-irreversible inhibitors never allow the enzyme
to return to normal function
c. competitive vs noncompetitive
-competitive inhibitors bond to the enzymes in their
active site so the substrate cannot; they are in
direct competition with the substrate for the active site
-noncompetitive inhibitors bond to the enzyme
somewhere other than the active site; but, their
bonding causes a conformational change in the
enzyme which changes the active site so that it no
longer accepts the substrate
4. feedback inhibition – type of enzyme regulation in which
the formation of a product inhibits an earlier reaction
5. Allosteric enzymes have (in addition to active sites)
regulatory sites where control substances can bind to alter
enzyme activity; if this control substance is the end product in
the enzyme’s metabolic pathway, feedback inhibition can
occur.
a. allosteric regulators bind to a site on the enzyme
that is not the active site
b. negative regulators – act as inhibitors; when they
are in place the enzyme is not active
c. positive regulators – act as activators; when they
are in place the enzyme can function
B. Do Temperature and pH Affect Enzymes?
1. Because enzymes operate best within defined
temperature ranges, high temperatures decrease
reaction rate by disrupting the bonds that maintain
three-dimensional shape (denaturation occurs); cold
temperatures decrease the movement of particles and
therefore the reaction. Some archaebacteria can
survive extreme temperatures.
2. Most enzymes function best at a pH near 7 (pepsin
in the stomach is an exception); higher or lower values
disrupt enzyme shape and halt function.
C. Substrate Concentration can affect reaction rate
1. adding more substrate will increase the reaction
rate to a certain point, after which the enzymes are
working at a maximum rate and all of the active sites
are filled; therefore, adding more substrate will no
increase the rate