Metabolism Flashcards
What is a metabolic pathway?
a series of chemical reactions occurring within a cell.
What is metabolism?
The totality of an organism’s chemical reactions. Metabolism as a whole manages the material and energy resources of the cell.
How does a metabolic pathway work?
begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product.
How are enzymes apart of metabolic pathways?
Each step of the pathways is catalyzed by a specific enzyme.
EX. page 153 figure
Mechanisms that regulate enzymes …
balance metabolic supply and demand
Catabolic pathway
Some metabolic pathways release energy by breaking down complex molecules to simpler compounds. AKA breakdown pathways.
What is a major pathway of catabolism?
Cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water.
Energy that was stored in the organic molecules…
becomes available to do the work on the cell, such as ciliary beating of membrane transport.
Pathways can have more than one…
starting molecule and/or product.
Catabolism
breaking down complicated molecules into simple ones with the release of chemical energy.
Anabolism
building complicated molecules from simpler ones requires energy
AKA biosynthetic pathways.
downhill and uphill avenues
Catabolic and anabolic pathways are the downhill and uphill avenues of the metabolic landscape. energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways
enzymes
proteins that catalyze (speed up) chemicals reactions NOT consumed in the reaction
catalyst
chemical agent that selectively increases the rate of a reaction without being consumed by the reaction
enzyme
a catalytic protein. cells use proteins (enzymes to lower activation energies. Thousands of different enzymes are known, each catalyzing one or a few specific chemical reactions.
catalysts and enzymes
ex. hydrolysis of sucrose by the enzyme sucrase
bioenergetics
the study of how energy flows through living organisms
cells and thermodynamics
- cells create ordered structures from less ordered materials
- cells unavoidably convert organized forms of energy to heat
thermodynamics
the study of the energy transformations that occur in a collection of matter
thermodynamics and metabolism
energy of
the laws of thermodynamics
1- NRG cannot be created nor destroyed, but transformed or transferred.(during ea. NRG conversion, some nrg dissipate into the environment as heat.
2-disorder (entropy) in the universe is continuously increasing (entropy is always < b/c, as more nrg is used, more nrg is converted to heat
biological complexity and thermodynamics
the evolution complex organisms does not violate the principle of entropy
-entropy (disorder) may > in an organism, but the universe’s total entropy <
Free energy, G
- energy that can do work when temperature and pressure are uniform, as in a living cell
- Measure of a system’s free energy, its tendency to change to a more stable state.
Who defined free energy?
Willard Gibbs in 1878.
He was a professor at yale
DeltaG=deltaH-TdeltaS
The change in free energy, delta G, can be calculated for a chemical reaction by applying this equation.
delta H stands for the change in the system’s enthalpy
delta S is the change int the system’s entropy
T is the solute temperature in Kelvin
Once we know the value of delta G for a process…
we can use it to predict whether the process will be spontaneous (that is, whether it is energetically favourable and will occur without an input of energy)
process of negative delta G..
- are spontaneous
- for a negative G either H must be negative or TS is positive
- spontaneous processes decrease the system’s free energy and processes that have a positive or zero G are never spontaneous
This information is immensely interesting to biologists because…
it gives us the power to predict which kinds of change can happen without an input of energy. such spontaneous changes can be harnessed to perform work. this principle is very important in the study of metabolism, where a major goal is to determine which reactions can supply energy for cellular work
Delta G can only be negative when the process involves a loss of free energy during the change from initial state to final state…
because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously.
DeltaG= G final state-G initial state
Equilibrium
A process is spontaneous and can perform work only when it is moving toward equilibrium.
most chemical rxns are reversible and proceed to a point at which the forward and backward rxns occur at the same rate.
there is no further net change (products and reactants)
exergonic reaction (Downhill)
proceeds with a net release of free energy.
because the chemical mixture loses free energy(G>), G is negative for an exergonic reaction.
Exergonic reactions are those that occur spontaneously
The magnitude of DeltaG for an exergonic reaction represents…
the maximum amount of work the reaction can perform.
The greater the decrease in free energy,
the greater the amount of work that can be done.
endergonic reaction (uphill)
absorbs free energy from its surroundings.
Because this kind of reaction essentially stores free energy in molecules (G <), G is positive. Such reactions are non spontaneous, and the magnitude of G is the quantity of energy required to drive the reaction.
If one reaction is downhill (releasing energy in one direction),
the other must be uphill (using energy)
equilibrium and metabolism
reaction in an isolated system eventually reach equilibrium and can then do NO work
metabolism as a whole..
can never reach equilibrium
this is one of the defining features of life.
a living cell is not in equilibrium..
the constant flow of materials in and out of the cell keep the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life.
A cell does three main types of work, which are powered by the hydrolysis of ATP
Chemical
Transport
Mechanical
Energy coupling
the use of an exergonic process to drive an endergonic one
most NRG coupling in is mediated by ATP
Chemical work
the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers
Transport work
the pumping of substances across membranes against the direction of spontaneous movement
Mechanical work
such as the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction.
Energy is released from ATP when..
the terminal phosphate bond is broken by hydrolysis
ATP and work in cells
ATP is responsible for mediating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work
reactions in a closed system
eventually reach equilibrium and then do not work
a catabolic pathway in a cell releases…
free energy in a series of reactions
what can serve as analogies?
closed and open hydroelectric systems
living organisms have the ability to couple exergonic and endergonic reactions:
NRG released by exergonic reactions is captured and used to make ATP from ADP and Pi
ATP can be broken back down to ADP and Pi, releasing energy to power the cell’s endergonic reactions
ATP
- Is the cells energy shuttle
- provides energy for cellular functions
Releasing the third phosphate from ATP to make ADP…
generates energy (exergonic)
linking the phosphates together requires NRG:
so making ATP from ADP and a thrid phosphate requires NRG (endergonic)
Catabolic pathways drive the…
regeneration of ATP from ADP and phosphate
ATP drives endergonic reactions by phosphorylation,
transferring a phosphate group to some other molecule, such as a reactant
The recipient molecule is now phosphorylated
ATP is an excellent energy donor
because electrostatic repulsion, the covalent bonds between phosphates are unstable
regeneration of ATP from ADP and Pi
catabolic reactions in the cell->energy to phosphorylate ADP
Pool of ATP turns over at a very fast rate (10 million/sec in a muscle cell)
Enzymes speed up reactions
DO NOT affect the change in free energy; they speed reactions that would occur eventually (exergonic)
Free energy of activation, or activation energy (EA)
the initial energy needed to start a chemical reaction
often supplied in the form of heat from the surroundings
activation energy
- is the initial amount of energy need to start a chemical reaction
- needed to bring the reactants close together and weaken existing bonds to initiate a chemical reaction
- often supplied in the form of heat from the surroundings in a system
What reactants require an input of energy to get started?
both endergonic and exergonic ( this energy is called activation energy)
What lowers the EA barrier of reactions?
Enzymes
what is activation energy?
the amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the downhill part of the reaction can begin
What is activation energy normally supplied by?
supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings.
what does the absorption of thermal energy do?
accelerates the reactant molecules, so they collide more often and more forcefully. It also agitates the atoms within the molecules, making the breakage of bonds more likely.
what happens when the molecules have absorbed enough energy for the bonds to break?
the reactants are in an unstable condition known as the transition state
How do enzymes increase the speed of reactions?
an enzyme catalyzes a reaction by lowering the EA barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.
What can’t an enzyme do?
enzymes cannot change the delta G for a reactions; it cannot make an endergonic reaction exergonic.
What can enzymes only do?
they can only fasten reactions that would eventually occur anyway,but this function makes it possible for the cell to have a dynamic metabolism, routing chemicals smoothly through the cell’s metabolic pathways.
Because enzymes are very 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
formed when the enzyme binds to its substrate of substrates when there is more than one reactant
what happens when the enzyme and substate are joined?
the catalytic action of the enzyme converts the substate to the product (or products) of the reaction.
Enzyme changes shape such that its active site…
enfolds the substrates.
brings chemicals groups of the active site into positions that enhance their ability to catalyze the reactions.
factors that affect enzyme activity.
general environment factors-temperature and pH
chemicals that specifically influence the enzyme
Can enzymes work in forward and reverse directions?
some can
there are different forms of some enzymes,
that assist different reactions.
- cytosolic version of enzyme
- mitochondrial version of enzyme
