Chapter 6 Flashcards
Metabolism
The totality of an organisms chemical reactions (emergent properties)
Metabolic pathway
A series of chemical reactions that either builds a complex (anabolic) or breaks down a complex (catabolic).
What are the types of energy
Kinetic- energy associated with the relative motion of objects
Thermal energy- kinetic energy due to the random motion of atoms and molecules.
Potential energy- energy matter possesses as a result of its location.
Chemical energy- energy available in molecules for release in a chemical reaction (potential)
Thermodynamics
Study of the energy transformations that occur in a collection of matter.
Laws of thermodynamics
- Energy can be transferred and transformed but never created or destroyed.
- Energy transfer or transformation increases the entropy of the universe.
Entropy
A measure of disorder or randomness (heat released)
Spontaneous process
A process that occurs without an overall input of energy. It is energetically favourable.
Ex: gravity pushes ball down hill
Free energy
The portion of a systems energy that can perform work when temperature and pressure are uniform throughout the system
/\G=
G(final state) -G(initial state)
If you have a -/\G what can be implied
- no input of energy needed
- spontaneous
- exergonic
- loses free energy
- final state more stable
Where is the /\G value at equilibrium
The lowest G can be for the system
A process is spontaneous and can perform work only when it’s moving ____
Towards equilibrium
Exergonic reaction
Proceeds with a new release of free energy (negative G). Occurs spontaneously.
Endergonic reactions
A non-spontaneous chemical reaction, in which free energy is absorbed from the surroundings
Reactions in isolated system eventually reach____
Equilibrium
What powers cellular work?
Energy coupling?
ATP- coupling exergonic reactions to endergonic reactions.
The use of an exergonic process to drive an endergonic one.
Describe the hydrolysis process of ATP
Bonds between the phosphate groups are broken by hydrolysis or the addition of a water molecule. The Terminal phosphate is broken by this molecule. Exergonic reaction releases energy. All phosphate groups in ATP are negatively charged so the like charge repels. This makes it very unstable.
If the /\G of a reaction is less than the amount of energy released from ATL hydrolysis what can happen?
Two reactions can be coupled to the overall they are exergonic. (Involves phosphorylation)
Phosphorylated intermediates
A molecule (often reactant) with a phosphate group covalently bound to it, making it more reactive (less stable) than the unphosphorylated molecule.
Hydrolysis leads to a change in _____ in proteins that enables its ability to _____
Shape, bind to another molecule
Regeneration of ATP
Free energy required to phosphorylate ADP comes from exergonic breakdown reactants in the cell.
Enzyme
A macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction.
Activation Energy
The amount of energy that reactants must absorb before a chemical reaction will start.
How does heat help with reaching the activation energy barrier?
What is at the top of activation energy?
Thermal energy results in more collisions and the breaking of bonds.
Transition state
Catalysis
A process by which a catalyst selectively speeds up a reaction without itself being consumed.
How does an enzyme catalyze a reaction
Lowering the EA barrier
Substrate
The reactant an enzyme acts on
Enzyme substrate complex
A temporary complex formed when an enzyme binds to its substrate molecule.
Active site
Pocket or groove on the surface of the enzyme where catalysis occurs. Typically formed by a few of the enzymes amino acids.
Induced fit
Cause by the entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate.
How many substrates can be turned to products per second per enzyme?
~1000
What holds the substrate to the active site?
Weak interactions p, such as hydrogen bonds and ionic bonds
How do enzymes lower activation energy
- Orients substrates so that reaction can occur
- Stretches/ bends substrate to break critical bonds
- Provides microenvironment suitable for reaction
- Brief covalent bonding between substrate and amino acid side chain helps with reaction.
When talking about Enzymes what does saturation mean?
How does a cell deal with saturation
As soon as the product exits an active site, another substrate enters.
Cell makes more enzymes
As temperature increases, enzyme reaction rates ______
Why?
Increase- causes more substrates to enter active sites.
To a point!! Then the enzyme is desaturated at higher temps
Cofactors
Any non protein molecule or ion that is required for the proper functioning of an enzyme. Can be permanently bound to the active site or may bind loosely and reversibly, along with the substrate during catalysis.
Types of cofactors
Inorganic -zinc, iron
Organic-vitamins
Many are trace elements
Enzyme inhibitors
Certain chemicals that selectively inhibit the action of specific enzymes. If Inhibitor attaches by covalent bond it is irreversible. Most are weak though.
Can be toxins, poisons or antibiotics or naturally produced by cell to regulate metabolic activity.
Competitive inhibitor
A substance that reduced the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics.
Non competitive inhibitor
A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzymes shape so that the active site no longer effectively catalyzes the conversion of substrate to product.
Allosteric regulation
The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
How do molecules naturally regulate enzymes
By non competitive binding. They change enzyme shape and function at active site.
Cooperativity
Kind of allosteric regulation whereby a shape change in one subunit of a protein causes by substrate binding is transmitted to all other subunits, facilitating binding of additional substrate molecules to those subunits.
Feedback inhibitor
A metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway.
Is catalysis reversible?
Yes, but they mainly move in one direction because net direction always goes towards equilibrium.
Changing confirmation of one active site of a multi subunit..
Changes confirmation of all subunits
