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Entropy
a measure of disorder or randomness
In biology, equilibrium=
Death
What are enzymes always?
Proteins
What do enzymes do?
Catalyze chemical reactions by lowering activation energy
Are enzymes parts of the reaction? In other words, do they change with the chemical reaction?
No, they do not change
Metabolism
the totality of an organism's chemical reactions
What is metabolism? (Hint: something to do with a chemical property)
An emergent property of life that arises from orderly interactions between molecules.
Metabolic Pathway
how a specific molecule travels through a cell’s metabolism
What happens to a molecule in a metabolic pathway?
A specific molecule is altered in a series of defined steps, resulting in a product
How is each step made successful in a metabolic pathway?
Each step is catalyzed by a specific enzyme
Catabolic pathways
a metabolic pathway that releases energy by breaking down complex molecules into simpler ones
What is an example of a way the cell releases energy?
Breaking down ATP to ADP
Anabolic Pathway
metabolic pathways that consume energy to build complicated molecules from simpler ones
What are anabolic pathways sometimes called?
A biosynthetic pathway
What is an example of an anabolic pathway?
Synthesis of a protein
Bioenergetics
study of how energy flows through living organisms
Energy
the capacity to cause change, the ability to arrange a collection of matter
What does the work of life depend on?
The ability of cells to transform energy from one form to another
Kinetic energy
the relative motion of objects
Thermal energy
kinetic energy associated with the random movement of atoms or molecules
Heat
transfer of thermal energy from one object to another
Potential energy
an object’s not moving energy
Chemical energy
used to refer to the potential energy available for release in a chemical reaction
Thermodynamics
the study of the energy transformations that occur in a collection of matter
System
matter under study
Surroundings
everything outside the system
Isolated System
unable to exchange either energy or matter with its surroundings
What is an isolated system also known as?
A closed system
Open System
energy and matter can be transferred between the system and its surroundings
Are organisms open or closed systems?
Open systems
First Law of Thermodynamics
energy can be transferred and transformed but cannot be created or destroyed
What is the First Law of Thermodynamics also known as?
The Law of Conservation of Energy
Second Law of Thermodynamics
every energy transfer or transformation increases the entropy of the universe
When does an organism have a high entropy?
When an organism has more randomly arranged collection of matter in it
Spontaneous Process
when a process occurs without energy required
Are all spontaneous reactions instantaneous?
No, some are much slower like rust
Nonspontanously
a process that cannot occur on its own
What is another way to state the Second Law of Thermodynamics?
For a process to occur spontaneously, it must increase the entropy of the universe
How are cell structures created? (Hint: don’t over think, has to do with Entropy)
cells create ordered structures from less organized starting material
Can the entropy of a particular system decrease?
Yes as long as the total entropy of the universe increases
Define the Universe in terms of Entropy
system and its surroundings
Equilibrium
the forward and reverse reactions occur at the same rate and there is no further net change in the relative concentrations of products and reactants
When is a process spontaneous and can perform work?
Only when it is moving toward equilibrium
Exergonic Reaction
proceeds with a net release of free energy
What does the greater decrease in free energy mean?
The greater amount of work can be done, change in G is negative
Spontaneous change
free energy of the system decreases, system becomes more stable, released free energy can be harnessed to do work
What does the breaking of bonds do?
Not release energy but requires energy and releases energy when it makes new bonds
Endergonic Reaction
absorbs free energy from its surroundings, essentially stores free energy, change in G is positive
What do reactions in an isolated system eventually do?
Reach equilibrium
Is metabolism as a whole ever at equilibrium?
No
What prevents metabolism from ever being at equilibrium?
The constant flow of materials in and out
Are organisms open or closed systems?
Open systems
Chemical work
the pushing of endergonic reactions that would not occur spontaneously
Transport work
the pumping of substances across membranes against the direction of the concentration gradient
Mechanical work
the beating of cilia, contraction of muscle cells and the movement of chromosomes during cellular respiration
Energy Coupling
use of an exergonic process to drive an endergonic one
What is responsible for mediating most energy coupling in cells and most cases acts as the immediate source of energy that powers cellular work?
ATP
ATP (adenosine triphosphate)
contains the sugar ribose with the nitrogenous base adenine and a chain of three phosphate groups
What splits ATP to ADP?
Hydrolysis
Phosphorylated Intermediate
the recipient with the phosphate group covalently bonded to ti
What is the key to coupling exergonic and endergonic reactions?
The formation of phosphorylated intermediate which is more reactive than the original unphosphorylated molecule
What functions of cells are nearly always powered by the hydrolysis of ATP?
Transport and mechanical work
Enzyme
a macromolecule that acts as a catalyst
Catalyst
a chemical agent that speeds up a reaction without being consumed by the reaction
What does charming one molecule into another general involve?
Controlling the starting molecule into a highly unstable state before the reaction can proceed
What happens when the new bonds of the product molecules form?
Energy is released as heat and the molecules return to stable shapes with lower energy that the contracted state
Activation Energy
the energy required to contrast the reactant molecules so the bonds can break
How is activation energy often 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
Transition State
when the molecules have absorbed enough energy for the bonds to break
What state are the reactants in?
The transition state
What does activation energy provide?
A barrier that determines the rate of the reaction
In most cases, what is true about the activation energy?
It is so high and the transition state is reached so rarely that the reaction will hardly proceed at all
How does heat speed a reaction?
By allowing the reactants to attain the transition state more often
Why does heating not work for life?
High temperatures denatures proteins and kills cells and would speed up all reactions, not just those that are needed
What does an enzyme catalyze?
A specific reaction by lower the EA barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures
Can an enzyme make a reaction endergonic to exergonic?
No
Can an enzyme change the change in G for a reaction?
No
Substrate
the reactant an enzyme acts on
Enzyme-Substrate Complex
created when an enzyme binds to a substrate
What do most enzyme names end in?
-ase
What does the specificity of an enzyme result from?
Its shape, consequence of its amino acid sequence
Active site
the restricted region of the enzyme molecule that actually binds to a substrate
What usually forms the active site of an enzyme?
A few of the enzymes amino acids
Is the active site a rigid receptacle?
No, it changes shape slightly due to interactions between the substrate’s chemical groups on the side chains of the amino acids that form the active site
Induced Fit
brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical creation
Are most metabolic reactions reversible?
Yes
What is the activation energy proportional to?
The difficulty of breaking the bonds
Optimal Conditions
conditions that the enzyme works better under, favor the most active shape for the enzyme molecule
Denaturation
a process where a protein loses its native shape overtime due to the disruption of weak chemical bonds and interactions thereby becoming inactive
Cofactors
non protein helpers for catalytic activity that many enzymes require
Where are cofactors found on an enzyme-substrate complex?
Tightly bound to the enzyme as permanent residents or bound loosely and reversibly along the substrate
Coenzyme
when a cofactor is an organic molecule
What can most vitamins act as?
Coenzymes or the raw materials to make a coenzyme
How do cofactors and coenzymes function?
In various ways bit in all cases they perform a crucial chemical function in catalysis
How does an inhibitor usually attach itself to the enzyme?
By covalent bonds
Are inhibitors reversible?
Usually irreversible
Competitive Inhibitors
some reversible inhibitor who resembles the normal substrate molecules and competes for admission into the active site
How can competitive inhibitors be overcome?
By increasing the concentration of substrate so that the active sites become available
Noncompetitive inhibitors
do not directly compete with substrate to bind to the enzyme at the active site but instead impede enzymatic reactions by binding to another part of the enzyme
Note
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