Metabolism-
all of organism’s chemical processes
Participants in a metabolic reaction:
Reactants,Intermediate,Products
Reactants
substances that enter a reaction
Intermediate
any substance that forms during reaction
Products
substances produced or left at the end
Catabolic pathways
processes that release energy by breaking down complex substances into simpler substances
ex catabolic pathways
o Ex- cellular respiration, in which glucose is broken down toCO2 and water, releasing energy
Anabolic pathways-
consume energy to build complex substances from simpler ones
Anabolic pathways- ex
Ex- synthesis of proteins from amino acids
Energy
capacity to do work
Kinetic energy + ex
energy of motion. ex–Water, electrons, leg muscles, light
Potential energy + ex;
stored energy. Water behind a dam
measurement chemical energy
kcal
Chemical energy-
potential energy of molecules stored in bonds
Can energy be converted? Ex?
Energy can be converted from one form to another, ex- respiration turns chemical energy into kinetic energy (then glucose is broken down). Organisms secure energy from their environment and use it to perform energy-required processes.
Types of work performed in cell:
mechanical, transport, chemical
mechanical work
movement–muscle cell contraction, beating of cilia (little hairs in respiratory tract that sweep away dirt and dust caught in mucus)
Transport
active transport/electrochemical work. pumping of substances across membranes against the direction of spontaneous movement
Chemical work
powering reactions that do not occur spontaneously
Thermodynamics-
study of energy transformations that occur in a collection of matter
First Law of Thermodynamics
energy can be transferred and transformed, but it cannot be created or destroyed. Also known as law of conservation of energy`
Second Law of Thermodynamics-
with every energy transfer, entropy, or disorder increases. Energy tends to flow from concentrated to less concentrated forms.
spontaneous-
-reaction that doesn’t require energy
example 1 of SLoT
Example- energy in cells mainly comes from breaking the bonds in organic molecules. However, in every energy transfer, some energy is lost to surroundings as heat and can’t be recaptured
Exergonic reactions
reactions that have net release of G; spontaneous
Ex exergonic reactions
Ex- respiration- breaking down glucose will release energy stored in the sugar molecules (catabolic)
Endergonic reactions-
a reaction that has a positive delta G–requires net input of energy; non spontaneous
Ex endergonic reactions
Ex- photosynthesis (opposite of respiration)- producing sugar by absorbing energy from the sun (anabolic)
Are reactions reversible?
mostly— Most reactions are reversible- can run in forward or reverse direction
equilibrium
when forward and backward reactions occur at same rate
- ATP has the same structure as an RNA nucleotide, except…
3 phosphate groups, not 1
Why is the triphosphate tail unstable (ATP)
because each phosphate has a negative charge so they repel each other–short lived energy molecule. Therefore, phosphates can break off by hydrolysis.
phosphorylation
(ATP) after phosphates break off by hydrolysis, the phosphate group then breaks off and joins another molecule, priming that molecule for a reaction
ATP +H2O –>
ADP + Pi (adenosine diphosphate, Pi=inorganic phosphate group)
∆G of ATP
-7.3 kcal/mol
When a phosphate group is removed from the ATP…
7.3kcal of energy is released. ATP can reform when ADP joins with an inorganic phosphate.
Energy coupling
using the energy from the exergonic reactions to power endergonic ones; Cells usually use ATP as a coupling agent. By breaking down ATP and releasing energy, that energy can be used to power an endergonic reaction
why enzymes are necessary
Spontaneous reactions may proceed on their own, but the rate could be very slow
enzyme
catalyst that can make a reaction happen hundreds to millions of times faster than they would on their own/Protein molecules that bind substrates
Activation energy (free energy of activation)-
minimum amount of energy that is required to get the reaction to the point that it can run on its own. - Even for exergonic reactions, the activation energy “bump” must be overcome in order for the reaction to occur. Enzymes help lower this activation energy.
enzyme characteristics
Often end in –ase; named for what they act on; Folded in such a way that they have active sites
substrates
reactants (enzymes)
active sites
pockets or crevices (made up of a few amino acids) where the substrates bind and where specific reaction occurs. Each active site will only bind to one particular substrate-enzymes are specific
How does an enzyme bonding a substrate lower the activationenergy?
In order for a reaction to occur, energy must be put in to put a substrate into a transition state- at this state, bonds can be broken or changes made. An enzyme will bind to a substrate, releasing energy. This energy will stabilize the transition state so that the reaction can occur.
o The enzyme may help lower the activationenergy by:
Allowing two substrates to find each other Orienting the substrate in a way to favor a reaction Induced fit
Induced fit
squeezing the substrate into an active site, although it may not be a perfect fit. If it is squeezed next to another molecule, it can move the substrate into the transition state
enzyme-substrate complex
- While the enzyme and substrate are temporarily bound together, the resulting structure is called an enzyme-substrate complex.
post enzyme reaction
After the reaction, the product departs from the active site Enzyme can take another substrate (enzyme remains in original form)o Cycle happens fast- single enzyme converts ~ 1,000 substrate molecules per second enzyme wears out eventually
Rate is dependent on…
concentration of substrate and enzymes–More substrate, higher rate. At some point, adding substrate won’t help because all the enzymes will be used up –> enzyme is saturated. At enzyme saturation, only way to increase rate is to add more enzyme
4 Important Enzyme Features
Enzymes can’t change non-spontaneous reactions into spontaneous reactions- they simply speed up reactions that would happen on their own anyway2- Enzymes are not permanently used up in reactions- they can be reused repeatedly3- Same type of enzyme usually catalyzes the forward and reverse directions of reversible reactions4- Enzyme is “picky” about its substrates lock and key model
Factors affecting enzyme activity
environmental, cofactors, enzyme inhibitors, allosteric reactions, Cooperativity
temp (Factors affecting enzyme activity)
Usually, reaction rate increases with increasing temperature because the substrates collide with active sites more frequently when the molecules move rapidly At some point- temp is too high and it disrupts H bonds, ionic bonds, weak interactions so the protein/enzyme denatures Each enzyme has optimum temp- humans-37c
pH
Most enzymes have optimal pH at 7
Salt concentration
Most enzymes can’t tolerate saline (salty)environments because ions intefere w ionic bonds Exceptions- algae and bacteria inhabit pools with high salt conc
cofactors
help at the active site or bring electrons or H+ ions or functional groups to the reaction, Are either metal ions or are coenzymes, Can be bound tightly to active sites permanently or diffuse throughout cytoplasm
coenzymes
organic compounds if helping at active site–metal ions
cofactors–ex of being bound tightly to active sites permanently
Ex- heme in catalase has an iron atom which speeds up thebreakdown of H2O2
cofactors–Others may diffuse throughout the cytoplasm ex
NAD+ or NADP+–both bring H+ ions and electrons
Enzyme Inhibitors-
chemicals can inhibit the action of specific enzymes
Competitive inhibitors-
resemble the normal substrate molecule and competes for active site, reducing productivity of enzymes bc active site is blocked
overcoming competitive inhibitors
can be overcome by increasing concentration of substrate
Noncompetitive inhibitors-
bind to part of enzyme away from active site, causing the enzyme to change shape and making the active site unreceptive to the substrate
Enzyme Inhibitors- ex
Examples: Pesticides (DDT and parathion) are inhibitors in nervous system Antibiotics are inhibitors of enzymes in bacteria (penicillin is inhibitor in bacteria of enzymes that build cell walls)
Allosteric Regulation
Some enzymes have allosteric site- receptor site far from the active site.
two choices for bonding at allosteric site–
either an activator or an inhibitor. Activators and inhibitors attach to enzyme by weak bonds,so activity of enzyme can change from moment to moment.
If the allosteric site can accept an activator
when the activator binds, the active conformation of the enzyme is stabilized. When the activator leaves, the active site becomes inactive
If the allosteric site can accept an inhibitor
when the allosteric site is free, the active form of the enzyme exists. When the inhibitor binds, the inactive form of the enzyme is stabilized with a nonfunctional active site
goal of cellular respiration-
-produce ATP
Cooperativity
Resembles allosteric activation- substrate molecules bind toenzyme and canstimulate other active sites to bind other substrates
Feedback Inhibition
when a metabolic pathway is switched off by its end product–end product acts as an inhibitor of the enzyme within a pathway. Prevents cell from wasting chemical resources in synthesizing more than necessary
ex Feedback Inhibition
Example- 5 steps in changing isoleucine from threonine, another amino acid. As isoleucine accumulates, it switches off its own synthesis by inhibiting the enzyme that catalyzes the first step of the pathway
quantity v quality bc of thermodynamics
Therefore- quantity of energy in the universe is constant(always the same amount of energy), but quality isn’t. Organisms, however, become more organized because we take in energy to decrease our entropy (make things more ordered)
Ex 2 SLoT
Other example- car uses chemical energy of gasoline and converts it into mechanical energy to move the car- but only 20 – 30 % is used. Other 70 – 80 % isreleased as heat
