* 8 Flashcards
metabolism
The totality of an organism’s chemical reactions.
metabolic pathway
begins w/ a specific molecule, which is then altered in a series of defined steps, resulting in a certain product. each step of the pathway is catalyzed by a specific enzyme.
catabolic pathways
degradative metabolic pathways that release energy by BREAKING DOWN complex molecules to simpler compounds.
anabolic pathways
consume energy to BUILD complicated molecules from simpler ones.
bioenergetics
(1) The overall flow and transformation of energy in an organism. (2) The study of how energy flows through organisms.
thermodynamics
The study of energy transformations that occur in a collection of matter.
spontaneous process
- process that can occur w/o an input of energy
- energetically favorable
- must increase the entropy of the universe
free energy
The portion of a biological system’s energy that can perform work when temperature and pressure are uniform throughout the system.
a cell does a few main kinds of work:
- chemical: the pushing of endergonic rxns that wouldn’t occur spontaneously
- transport: pumping substances against the direction of spontaneous mvmnt
- mechanical
energy coupling
In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction. Mostly mediated by ATP.
ATP phosphate bonds
- the phosphate bonds of ATP aren’t unusually strong bonds
- rather, the reactants (ATP and water) have high energy relative to the energy of the products (ADP + phosphate group)
- the release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, NOT from the phosphate bonds themselves.
- ATP is useful b/c the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver.
why does ATP hydrolysis release so much energy?
- all 3 phosphate groups are negatively charged
- these like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule
transition state
- changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the rxn can proceed
- the transition state is when the reactants have absorbed enough energy (activation energy) from surroundings to reach unstable state; now, bonds can break
enzyme
- catalyzes rxn by lowering activation energy barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temps
- specific b/c of their shape
substrate
- the reactant an enzyme acts on.
- enzyme + substrate(s) = enzyme-substrate complex
- when the two are joined, the catalytic action of the enzyme converts the substrate to the product(s) of the rxn
active site
- only this restricted region of the enzyme molecule actually binds to the substrate
- typically a pocket/groove on the surface of the enzyme where catalysis occurs
- usually, the active site is formed by only a few of the enzyme’s amino acids; the rest of the protein provides a framework that determines the active site’s configuration
induced fit
- as substrate enters active site, enzyme changes shape slightly due to interactions btwn the substrate’s chemical groups and the chemical groups on the side chains of the amino acids that form the active site
- this shape change makes the active site fir even more snugly around the substrate
- brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical rxn
catalysis in the enzyme’s active site
- in most rxns, the substrate is held in the active site by weak interactions (H, ionic bonds)
- R groups of a few of the amino acids that make up the active site catalyze the conversion of substrate to product; product departs
saturated enzyme
when the concentration of substrate is so high that all enzyme molecules have their active sites engaged
ways that enzymes lower activation energy and speed up rxn
- in rxns involving 2 or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a rxn to occur btwn them
- as the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the rxn
- provides microenvironment
- direct participation of the active site in the chem rxn; may involve brief covalent bonding btwn the substrate and the side chain of an amino acid of the enzyme
enzymes and temp
- up to a point, the rate of the rxn increases w/ increasing temp, partly b/c substrates collide w/ active sites more frequently when the molecules move rapidly
- above this temp, the speed of the rxn drops sharply b/c the thermal agitation disrupts weak interactions
- most human enzymes have optimal temps of about 35 to 40 deg C (close to human body temp)
coenzyme
An ORGANIC molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.
cofactors
- nonprotein helpers required by many enzymes for catalytic activity
- may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along w/ the substrate
- some are inorganic, such as Zn, Fe, Cu in ionic form
competitive inhibition
- reduce enzyme productivity by blocking substrates from entering active sites; these inhibitors’ shape resembles that of the normal substrate molecule
- they compete for admission into the active site
- can be overcome by increasing the concentration of substrate
reversible vs irreversible enzyme inhibition
- inhibitor attached to enzyme by covalent bonds: irreversible
- weak interactions: reversible
noncompetitive inhibitors
- don’t bind to active site
- bind to another part of the enzyme; this binding causes the enzyme molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of substrate to product
ATP as a regulator
- ATP is an inhibitor for catabolic enzymes; ADP is activator
- this is logical b/c catabolism breaks down complex molecules, RELEASING ENERGY (ATP)
- if ADP production < ATP use, ADP accumulates and activates the enzymes that speed up catabolism, producing more ATP
- if there’s more ATP than needed, then catabolism slows down as ATP molecules accumulate and bind to the same enzymes, inhibiting them
allosteric regulation
- when a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. (may result in inhibition or activation)
- most allosterically regulated enzymes are constructed from 2 or more subunits, each composed of a polypeptide chain w/ its own active site
- the entire complex oscillates btwn 2 diff shapes (one active, one not)
cooperativity
- a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits (this is why cooperativity is considered ALLOSTERIC), thereby increasing catalytic activity at the other active sites
- so named b/c one substrate molecule primes an enzyme to act on additional substrate molecules more readily
hemoglobin and cooperativity
- hemoglobin: 4 subunits, each of which has an O-binding site
- the binding of an O2 to one binding site increases the affinity for O of the remaining binding sites; thus, where O is at high levels, hemoglobin’s affinity for O increases as more binding sites are filled
- in O-deprived tissues, the release of each O molecule decreases the O affinity of the other binding sites, resulting in the release of oxygen where it’s most needed
why are allosteric regulatory molecules hard to characterize?
b/c they tend to bind the enzyme at low affinity and are therefore hard to isolate
why have pharmaceutical companies recently begun to turn their attention to allosteric regulators?
these molecules are attractive drug candidates for enzyme regulation b/c they exhibit higher specificity for particular enzymes than do inhibitors that bind to the active site. (an active site may be similar to the active site in another, related enzyme, whereas allosteric regulatory sites appear to be quite distinct btwn enzymes)
feedback inhibition
when a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway.
