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Question 1

metabolism

Answer 1

The totality of an organism’s chemical reactions.

Question 2

metabolic pathway

Answer 2

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.

Question 3

catabolic pathways

Answer 3

degradative metabolic pathways that release energy by BREAKING DOWN complex molecules to simpler compounds.

Question 4

anabolic pathways

Answer 4

consume energy to BUILD complicated molecules from simpler ones.

Question 5

bioenergetics

Answer 5

(1) The overall flow and transformation of energy in an organism. (2) The study of how energy flows through organisms.

Question 6

thermodynamics

Answer 6

The study of energy transformations that occur in a collection of matter.

Question 7

spontaneous process

Answer 7

• process that can occur w/o an input of energy
• energetically favorable
• must increase the entropy of the universe

Question 8

free energy

Answer 8

The portion of a biological system’s energy that can perform work when temperature and pressure are uniform throughout the system.

Question 9

a cell does a few main kinds of work:

Answer 9

• chemical: the pushing of endergonic rxns that wouldn’t occur spontaneously
• transport: pumping substances against the direction of spontaneous mvmnt
• mechanical

Question 10

energy coupling

Answer 10

In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction. Mostly mediated by ATP.

Question 11

ATP phosphate bonds

Answer 11

• 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.

Question 12

why does ATP hydrolysis release so much energy?

Answer 12

• 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

Question 13

transition state

Answer 13

• 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

Question 14

enzyme

Answer 14

• 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

Question 15

substrate

Answer 15

• 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

Question 16

active site

Answer 16

• 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

Question 17

induced fit

Answer 17

• 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

Question 18

catalysis in the enzyme’s active site

Answer 18

• 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

Question 19

saturated enzyme

Answer 19

when the concentration of substrate is so high that all enzyme molecules have their active sites engaged

Question 20

ways that enzymes lower activation energy and speed up rxn

Answer 20

• 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

Question 21

enzymes and temp

Answer 21

• 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)

Question 22

coenzyme

Answer 22

An ORGANIC molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.

Question 23

cofactors

Answer 23

• 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

Question 24

competitive inhibition

Answer 24

• 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

Question 25

reversible vs irreversible enzyme inhibition

Answer 25

• inhibitor attached to enzyme by covalent bonds: irreversible
• weak interactions: reversible

Question 26

noncompetitive inhibitors

Answer 26

• 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

Question 27

ATP as a regulator

Answer 27

• 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

Question 28

allosteric regulation

Answer 28

• 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)

Question 29

cooperativity

Answer 29

• 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

Question 30

hemoglobin and cooperativity

Answer 30

• 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

Question 31

why are allosteric regulatory molecules hard to characterize?

Answer 31

b/c they tend to bind the enzyme at low affinity and are therefore hard to isolate

Question 32

why have pharmaceutical companies recently begun to turn their attention to allosteric regulators?

Answer 32

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)

Question 33

feedback inhibition

Answer 33

when a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway.