Exam 2 Vocabulary

chemical reaction

any process in which one or more substances (the reactants) are converted to one or more different substances (the products); involved the making and breaking of chemical bonds; occurs when atoms have sufficient energy to combine or change their bonding partners

reactants

the substances undergoing the chemical change

products

the new molecules formed

chemical bond

an attractive force that links two atoms together in a molecule

law of conservation of matter

matter is conserved in a chemical reaction; reactions cannot create or destroy matter but can only rearrange it

metabolism

the sum total of an organism’s chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resources of the organism

metabolic pathway

a set of enzymatically controlled steps that begins with a specific molecule and results in the completion of a product or process in an organism

substrate

the name for reactants in a chemical reaction

energy

the capacity to do work; the capacity to bring about movement against an opposing force; the capacity for change

potential energy

energy stored in chemical bonds, as a concentration gradients, or as an electric charge imbalance

kinetic energy

the energy of motion; the type of energy that does work, that makes things change

chemical energy

stored in bonds

electrical energy

separation of charges

heat energy

transfer due to a temperature difference

light energy

electromagnetic radiation stored as photons

mechanical enegy

energy of motion

energy changes in living systems

chemical changes in which energy is stored in, or released from, chemical bonds

anabolism

condensation reactions; link smaller molecules to form larger, more complex molecules; require an input of energy; energy is captured in the chemical bonds that are formed; this captured energy is stored in bonds as potential energy

catabolism

hydrolysis reactions; break down larger, more complex molecules into smaller ones; release the energy in the chemical bonds; released energy may be recaptured in new chemical bonds or used as kinetic energy

coupled reactions

linkage between anabolic and catabolic reactions

law of thermodynamics

energy changes; apply to all matter and energy transformations in the universe

1st law of thermodynamics

energy is neither created nor destroyed, it is only transformed; when energy is converted from one form to another, the total energy before and after the conversion is the same

2nd law of thermodynamics

when energy is converted from one form to another, some of that energy becomes unavailable to do work

conversion

from the ordered, concentrated energy of chemical bonds to the disordered, dispersed energy of heat

entropy (S)

a measure of the amount of disorder (randomness) in a system; less energy = more disorder (and vice versa)

spontaneous process

a process that can occur without input of energy

enthalpy (H)

total energy = usable energy + unusable energy

free energy (G)

usable energy that can do work; cells require it in chemical reactions

unusable energy (S)

unusable energy lost to disorder (heat)

ΔG

the overall change in free energy (ΔG = G_products - G_reactants)

- ΔG

free energy is released, reactants > products

+ ΔG

input of free energy is required for the reaction to occur; reactants < products

exergonic

“energy outward”; reactions release free energy (-ΔG); these reactions are spontaneous; complex molecules → free energy + small molecules

endergonic

“energy inward”; reactions consume free energy (+ΔG); these reactions are non-spontaneous; free energy + small molecules → complex molecules

ATP

adenosine triphosphate; contains the sugar ribose, the nitrogenous base adenine, and a chain of three phosphate groups; universal energy currency for cells and all forms of life

P_i

inorganic phosphate; this is a phosphate ion free in solution

energy coupling

uses energy released from one reaction to power another reaction

energy barriers

between reactants and products; control the rate of chemical reactions

transition state

the state reactants must reach (a reactive mode where its bonds are destabilized)

activation energy (E_a)

the energy needed to destabilize existing chemical bonds in a reactant and initiate a chemical reaction; initial investment of energy for starting a reaction

catalyst

substance that speeds up chemical reactions without being consumed or permanently altered; reduces the energy barrier that is preventing the chemical reaction from proceeding; increases the rate of chemical reactions

catalysis

the process of influencing chemical bonds in a way that lowers the activation energy needed to initiate a chemical reaction; increases the rate of chemical reactions

enzymes

most biological catalysts are proteins; act as molecular framework in which chemical catalysis takes place; catalyse a reaction by lowering activation energy enabling the reactant molecules to absorb enough energy to reach the transition state; facilitate nearly every chemical process that takes place in living things

oxidoreductases

transfer electrons between molecules (energy metabolism)

transferases

transfer functional groups between molecules

hydrolases

add water to covalent bonds to break down molecules

lyases

catalyse nonhydrolytic bond breakage and aid in new bonds forming

isomerase

move functional groups within a molecule (forms an isomer)

ligases

joins two molecules together

active site

where substrate molecules bind; the region where catalysis occurs

enzyme-substrate complex (ES)

held together by different types of bonds and electrical attractions (E + S → ES → E + P)

cofactors

nonproteins helpers to aid in enzyme’s to function normally; may be inorganic or organic; often provide chemical groups or functionalities that enzymes along cannot; are usually part of the active site of the enzyme

coenzymes

organic cofactors; example would be vitamins

inducted fit

enzyme changes shape when it binds the substrate; this alters the shape of the active site

initiation

enzymes orient substrates precisely as they bind within the active site

transition state facilitation

the act of binding induces the formation of the transition state

termination

reaction products have less affinity for the active site; binding ends; enzyme returns to original conformation; products are released

inhibitors

molecules that bind to the enzyme and slow reaction rates

irreversible inhibition

inhibitor covalently bonds to side chain in the active site and permanently inactivates the enzyme

reversible inhibition

inhibitors bonds noncovalently to the active site and prevent substrate from binding

competitive inhibitors

compete with the natural substrate for binding sites; degree of inhibition depends on concentrations of substrate and inhibitor

uncompetitive inhibitor

bind to the enzyme-substrate complex, preventing release of products

noncompetitive inhibitor

bind to the enzyme at a different site (not the active site)

denaturation

the process in which a protein loses its native structure due to the disruption of weak chemical bonds and interactions, thereby becoming biologically inactive; occurs under extreme environmental conditions of temperature, pH, or salt concentration

saturation limit

once all substrate molecules are bound to available enzyme molecules, further increasing enzyme concentration will not increase the reaction rate

temperature

a measure of the kinetic energy of the molecules in a system

pH

“potential of hydrogen”; a measure of the relative amount of free hydrogen ions (H+) and free hydroxyl ions (OH-) in a substance

glucose

the most common fuel used by cells; cells get energy from a series of metabolic pathways

oxidation-reduction (redox) reactions

a chemical reaction involving the complete or partial transfer of one or more electrons from one reactant to another; drive the formation of ATP

oxidation

loss of electrons; gain O, lose H; component have been oxidized; the more oxidized, the less potential energy; the reducing agent donate electrons and becomes oxidized; a reducing agent is oxidized as it reduces another compound

reduction

gain of electrons; lose O, gain H; component has been reduced; the more reduced, the more potential energy; the oxidizing agent accepts electrons and becomes reduced; an oxidized agent is reduced as it oxidizes another compound

electron carriers

molecules that transport electrons during cellular processes like respiration and photosynthesis, facilitating energy transfer and production

NAD

nicotinamide adenine dinucleotide; a key electron carrier in redox reactions

NAD+

empty of electrons; ionic (+ charge; protons > electrons); in redox reaction, picks up one H atom (e- and p+) and a solo e- from a second H atom; isolated e- takes it from + charge to neutral (NAD+ → NAD); the whole H atom takes it from NAD → NADH; NAD+ has become NADH by oxidizing a substance (accepting electrons from it)

NADH

loaded with electrons; proceeds down the energy hill to donate e- to molecules that have a greater potential to accept e- than it does; after dropping off the e-, it can return to being the empty NAD+ and ready for another pickup; this is how NADH transfers energy from one molecule to another

glycolysis

takes place in the cytoplasm and involve ten enzyme-catalyzed steps; steps 1-5 are energy-investing reactions (require 2 ATP); steps 6-10 are energy-harvesting reactions (yield 4 ATP and 2 NADH)

oxidation-reduction (glycolysis)

energy released by glucose oxidation is trapped via the reduction of NAD+ to NADH

substrate-level phosphorylation

the production of ATP from ADP by a direct transfer of a high energy phosphate group from a phosphorylated intermediate metabolic compound in an exergonic catabolic pathway

glycolysis step 1

energy investment; glucose moves back and forth across the cell membrane; inside the cell, glucose is phosphorylated by hexokinase which transfers a phosphate group from 1 molecule of ATP to the glucose molecule; it is now glucose-6-phosphate; G6P is trapped inside the cell because of the charge of the phosphate that traps G6P in the cell since the cell membrane is impermeable to ions

phosphorylation

a phosphate group from one molecule of ATP is transferred; makes glucose more chemically reactive

hexokinase

the enzyme that catalyses transfers a phosphate group from 1 molecule of ATP to the glucose molecule; it is now glucose-6-phosphate

glucose-6-phosphate

created when a phosphate group is added to glucose

glycolysis step 2

energy investment; phosphoglucoisomerase rearranges G6P to convert it to its isomer, fructose-6-phosphate; this allows a second site for a phosphate group to be added

phosphoglucoisomerase

the enzyme that catalyses the rearrangement of glucose-6-phosphate to fructose-6-phosphate; G6P isomer

fructose-6-phosphate

created when glucose-6-phosphate is rearranged by phosphoglucoisomerase

glycolysis step 3

energy investment; this step is the commitment to glycolysis; phosphofructokinase transfers a phosphate group from ATP to the sugar molecule, 1 molecule of ATP is invested; fructose-1,6-bisphosphate has a phosphate group on its opposite ends so it can be split in half

phosphofructokinase

the enzyme that catalyses that transfer of a phosphate group from ATP to the sugar, F6P, to form fructose-1,6-bisphosphate

fructose-1,6-bisphosphate

the molecule that is formed when a phosphate group, from ATP, is transferred to fructose-6-phosphate

glycolysis step 4

energy investment; aldolase cleave fructose-1,6-bisphosphate into two different 3-carbon sugars (glyceraldehyde-3-phosphate and dihydroxyacetone phosphate) which are both isomers of each other

aldolase

is a lyase; the enzyme that catalyses the action of cleaving fructose-1,6-bisphosphate into two different 3-carbon sugars

glyceraldehyde-3-phosphate

created when fructose-1,6-bisphosphate is split into two sugars; is a 3-carbon sugar molecule; dihydroxyacetone phosphate is the other 3-carbon sugar created and is an isomer of G3P

glycolysis step 5

energy investment; energy requirements of the body will determine which isomer is needed; isomerase catalyses the conversion between the two 3-carbon sugars; glycolysis uses two molecules of glyceraldehyde-3-phosphate; glucose (6 carbons) → G3P (3 carbons) + G3P (3 carbons)

isomerase

the enzyme that catalyses the conversion of dihydroxyacetone phosphate to glyceraldehyde-3-phosphate; two molecules of G3P are use in glycolysis

glyceraldehyde-3-phosphate (G3P) x2

dihydroxyacetone phosphate is converted to G3P to have two molecules of G3P

allosteric regulation

the binding of a regulatory molecule to an enzyme that affects its shape and the functioning of its active site; this can result in either inhibition or stimulation of an enzyme’s activity

glycolysis step 6

energy payoff; there are two molecules of G3P; G3P dehydrogenase catalyses the two reactions of 1) G3P being oxidized by the transfer of electrons and H+ to NAD+ forming NADH and 2) a phosphate group is attached to the oxidized substrate (which creates 1,3-bisphosphoglycerate) making a product of very high potential energy

G3P dehydrogenase

the enzyme that catalyses that reaction of G3P 1) being oxidized by the transfer of electrons and H+ to NAD+ forming NADH and 2) a phosphate group is attached to the oxidized substrate (making 1,3-bisphosphoglycerate)

1,3-bisphosphoglycerate

what is created when G3P is catalysed by the enzyme G3P dehydrogenase (a phosphate group is attached to the oxidized substrate)

glycolysis step 7

energy payoff; phosphoglycerokinase removes a phosphate group from 1,3-bisphosphoglycerate to form 3-phosphoglyerate; the phosphate group removed is transferred to ADP to make ATP via substrate-level phosphorylation; because there are 2 molecules of 1,3-bisphosphoglyerate, 2 molecules of ATP are produced in this step

phosphoglycerokinase

the enzyme that catalyses the removal of a phosphate group from 1,3-bisphosphoglyerate to form 3-phosphoglycerate (occurs to both molecules of 1,3-bisphosphoglycerate)