ch. 6 biochem test

activation energy

threshold energy required to produce a chemical reaction; minimum amount of energy needed for a reaction to occur

active site

cleft in the surface of enzyme where substrate binds

allosteric enzyme

enzyme whose activity is affected by the binding of effector molecules

apoenzyme

protein portion of enzyme that requires cofactor to function in catalysis; missing cofactor

carbanion

carbon w/ negative charge; carbon atom w/ greater electron density

carbocation

carbon w/ positive charge; carbon atom w/ less electron density

catalyst

substance that enhances rate of chemical reaction but is not permanently altered by reaction; speed up reaction w/o getting used up

coenzyme

small organic molecule required in catalytic mechanisms of certain enzymes

cofactor

nonprotein component of enzyme required for catalysis

competitive inhibition

reversible type of enzyme inhibition in which inhibitor molecule competes w/ substrate for occupation of active site; binds to active site; resembles substrate

enzyme

biomolecule that catalyzes biochemical reaction; catalyst in biology often a protein

enzyme induction

process in which signal molecule stimulates increased synthesis of specific enzyme

enzyme kinetics

study of rates of enzyme-catalyzed reactions; analyze rates involved w/ biological catalyst

free radical

atom or molecule that has unpaired electron; single pair of electrons

holoenzyme

complete enzyme consisting of apoenzyme plus cofactor

inhibitor

molecule that reduces enzyme’s activity

intermediate

species produced in course of reaction that exists for finite period of time; possible step in reaction mechanism

irreversible inhibition

form of enzyme inhibition in which inhibitor molecule permanently impairs enzyme, usually through binding via covalent bond

isomerase

enzyme that catalyzes conversion of one isomer to another; moves functional group within molecule

ligase

enzyme that catalyzes joining of two molecules; connects to two molecules

lyase

enzyme that catalyzes cleavage of C—O, C—C, or C—N bonds, thereby producing product that contains double bond; removes functional group to create double bond by elemination

noncompetitive inhibition

inhibition of enzyme in which inhibitor binds to both free enzyme and enzyme-substrate complex; binds somewhere else not the active site

oxidoreductase

enzyme that catalyzes oxidation-reduction reaction; catalyze movement of electrons

pH optimum

pH value at which enzyme’s activity is maximal

proenzyme

inactive precursor of enzyme; unactivated form of enzyme

reaction mechanism

step-by-step description of chemical reaction process; explains in step wise detail how transition state is reached and how reaction occurs

reversible inhibition

form of enzyme inhibition in which inhibitory effect of compound can be counteracted by increasing substrate or removing inhibitor while enzyme remains intact

substrate

reactant in chemical reaction that binds to enzyme active site and is converted to product

transferase

enzyme that catalyzes transfer of functional group from one molecule to another; movement of one functional group to another molecule

transition state

in catalysis, unstable intermediate formed by enzyme that has altered substrate so that it now shares properties of both substrate and product; high-energy and unstable movement in reaction where bonds break and form simultaneously

uncompetitive inhibition

inhibitor binds only to enzyme-substrate complex

velocity

rate of biochemical reaction; change in concentration of reactant or product per unit time

vitamin

organic molecule required by organisms in minute quantities; some vitamins are coenzymes required for function of certain cellular enzymes

zymogen

inactive form of proteolytic enzyme

compare/contrast lock & key with induced fit

1) lock(active site) & key(substrate) - understand specificity

2) induced fit - binding affects both substrate (stabilizes transition state) & alters active site

— substrate binds to active site

6 classifications of enzyme

1) oxidoreductases - catalyze redox reaction (catalyze movement of electron) → alcohol dehydrogenase catalyzes oxidation of ethanol & other alcohols

2) transferases - transfer molecular groups from donor molecule to acceptor molecule (movement of one function group to another molecule) → hexokinase

3) hydrolases - catalyze reactions in which cleavage of bonds is accomplished by addition of water (uses water to cleave) → chymotrypsin

4) lyases - catalyze reactions in which groups are removed by elimination to form double bond (removes functional group to create double bond by elimination) → pyruvate decarboxylase

5) isomerases - catalyze intramolecular rearrangements (moves functional group within molecule) → alanine racemase

6) ligases - catalyze bond formation btw two substrate molecules (connects to two molecules) → DNA ligase

3 types of enzyme inhibition

1) competitive inhibition - binds at active site; E+S ⇌ ES → E+P; E+I ⇌ EI; rotate on y-int; same Vmax, lower Km

2) noncompetitive inhibition - binds somewhere else not active site; E+S ⇌ ES → E+P; E+I ⇌ EI; ES+I ⇌ ESI; rotate on x-int; lower Vmax, same Km

3) uncompetitive inhibition - only binds ES complex; affect both Km & Vmax; E+S ⇌ ES → E+P; ES+I ⇌ ESI; lowers both Vmax and Km; same slope, parallel lines

4 ways enzyme stabilize transition state

1) proximity & orientation - active site will bring together substrate(s) and put them into proper position (energy used). reactions occur faster when substrates are correctly positioned.

2) electrostatic effects - interior acidic/basic residue can have charged (positive/negative) effect to promote carbocation/carbanion. charge distribution in relatively anhydrous active site facilitates optimum positioning of substrate molecules and influences their chemical reactivity.

3) acid-base catalysis - accept/donate H+ (most often histidine).

4) covalent catalysis - temporary covalent bond is created then destroyed (often slow step).

cofactors (2 metals & 2 vitamins)

1) metals

• group 1 & 2 (alkali & alkaline earth metals)→ Na+, K+, Ca+2, Mg+2 (structural roles)

• transition metals (group 3-12) → catalytic roles (either bound to functional groups or as components of prosthetic groups)

2) vitamins (organic molecules)

• water-soluble → B, C

• fat-soluble → A,D,E,K

how pH and heat affect enzyme (graph)

1) heat - higher temperature → higher reaction rate; rates of enzyme-catalyzed reactions increase w/ increasing temperature; optimum temperature → temperature at which enzymes operate at max efficiency

2) pH - changes in H+ concentration can affect ionization of active site groups & substrates. If pH becomes so alkaline that group loses its proton, enzyme’s activity may be depressed. Change in pH alters substrate’s capacity to bind to active site. Changes in pH can lead to denaturation, changing tertiary structure of enzyme. pH optimum → pH value at which enzyme’s activity is maximal

4 regulation of enzyme

1) genetic control - enzymes are produced when needed (enzyme induction is synthesis of enzymes in response to changing metabolic needs)

2) covalent modification - adding something covalently or removing part of enzyme

3) allosteric regulation - enzyme w/ quaternary structure

4) compartmentation - separate enzymes from substrates (cell barrier)