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ACS SLudy rep

know Lhe dlfferenL unA Lechnology Lechnlques (ChapLer 9)


O Ge| b|ott|ng ls a Lechnlque for vlsuallzlng a parLlcular subseL of macromolecules proLelns or
fragmenLs of unA or 8nA lnlLlally presenL ln a complex mlxLure
O @he sLeps lnvolved ln gel bloLLlng are
1 SeparaLlng Lhe molecules by elecLrophoresls @hls ls done ln a gel whlch allows Lhe
molecules Lo mlgraLe under Lhe lnfluence of an elecLrlc fleld
2 @he resulLlng elecLrophoresls ls Lhen bloLLed" wlLh a nlLrocellulose fllLer @he molecules
sLlck LlghLly Lo Lhe fllLer and wlll reLaln Lhelr relaLlve poslLlons when flooded wlLh fluld aL
Lhe nexL sLep
3 @he fllLer ls Lhen baLhed wlLh a soluLlon conLalnlng a probe"
@he probe wlll comblne speclflcally wlLh Lhe LargeL molecules LhaL ls Lhe ones
LhaL you are looklng for
@he probe carrles a mean of vlsuallzaLlon (elLher a radloacLlve or fluorescenL
marker)
O @he procedure for deLecLlng unA fragmenLs conLalnlng a parLlcular sequence ls as follows
1 unA ls exLracLed from Lhe cell
2 @he unA ls parLlally dlgesLed by a est|ct|on endonuc|ease also called resLrlcLlon
enzymes recognlze and cleave unA aL speclflc sequences (recognlLlon sequences or
resLrlcLlon slLes) Lo generaLe a seL of smaller fragmenLs
3 @he resulLlng unA fragmenLs are separaLed by elecLrophoresls and Lhen denaLured Lo
form slngle sLranded molecules (ssunA)
4 WlLhouL alLerlng Lhelr poslLlons Lhe separaLed bands of ssunA are Lransferred Lo a
nlLrocellulose fllLer and exposed Lo a radlolabeled cunA or 8nA
3 lf Lhe probe deLecLs complemenLary unA sequences lL wlll blnd Lo Lhem
O @he dlfferenL Lypes of bloLs are as follows
Type oI Blot
Molecules
separated by
electrophoresis
Probe
Southern ssDNA cDNA or RNA
Northern denatured RNA RNA or cDNA
Western Protein Antibodies
hLLp//usersrcncom/[klmballmaulLraneL/8lologyages/C/Cel8loLLlnghLml
O @he nothen b|ot ls a Lechnlque used ln molecular blology research Lo sLudy gene expresslon by
deLecLlng 8nA (or lsolaLed m8nA) ln a sample
O Ge| e|ectophoes|s ls a Lechnlque used for Lhe separaLlon of unA 8nA or proLeln molecules
uslng an elecLrlc fleld applled Lo a gel maLrlx
O @he 9o|ymease cha|n eact|on (9% lnvolves ampllfylng speclflc unA sequences
4 @he process lnvolves ampllfylng Lhe number of coples of a parLlcular unA segmenL
4 lL's a Lechnlque ln molecular blology Lo ampllfy a slngle or few coples of a plece of unA
across several orders of magnlLude generaLlng Lhousands Lo mllllons of coples of a
parLlcular unA sequence
4 @he process lnvolves and relles on Lhermal cycllng conslsLlng of cycles of repeaLed
heaLlng and coollng of Lhe reacLlon for unA melLlng and enzymaLlc repllcaLlon of Lhe
unA rlmers (shorL unA fragmenLs) conLalnlng sequences complemenLary Lo Lhe LargeL
reglon along wlLh a unA polymerase are key componenLs Lo enable selecLlve and
repeaLed ampllflcaLlon
4 As C8 progresses Lhe unA generaLed ls lLself used as a LemplaLe for repllcaLlon seLLlng
ln moLlon a chaln reacLlon ln whlch Lhe unA LemplaLe ls exponenLlally ampllfled
1 unA sLrands are separaLed by heaLlng
2 @he unA sLrands are annealed Lo an excess of shorL synLheLlc unA prlmers LhaL
flank Lhe reglon Lo be ampllfled
3 new unA ls synLheslzed by polymerlzaLlon

know Lhe geneLlcs aspecL of blochemlsLry
O A LrlpleL codon ln a nuclelc acld sequence usually speclfles a slngle amlno acld
O @he geneLlc code deflnes a mapplng beLween LrlnucleoLlde sequences called codons and
amlno aclds
O - (deoxy|bonuc|e|c ac|d% ls a nuclelc acld LhaL conLalns Lhe geneLlc lnsLrucLlons used ln Lhe
developmenL and funcLlonlng of all known llvlng organlsms and some vlruses
4 @he maln role of unA molecules ls Lhe longLerm sLorage of lnformaLlon
4 unA conslsLs of Lwo long polymers of slmple unlLs called nucleoLldes wlLh backbones
made of sugars and phosphaLe groups [olned by esLer bonds
4 @he Lwo sLrands run ln opposlLe dlrecLlons Lo each oLher and are Lherefore anLlparallel
4 ALLached Lo each sugar ls one of four Lypes of molecules called bases
4 lL ls Lhe sequence of Lhese four bases along Lhe backbone LhaL encodes lnformaLlon
4 @hls lnformaLlon ls read uslng Lhe geneLlc code wlLh speclfles Lhe sequence of Lhe
amlno aclds wlLhln proLelns
O - (|bonuc|e|c ac|d% ls a blologlcally lmporLanL Lype of molecule LhaL conslsLs of a long chaln
of nucleoLlde unlLs
4 ach nucleoLlde unlL conslsLs of a nlLrogenous base a rlbose sugar and a phosphaLe
4 8nA ls Lranscrlbed from unA by enzymes called 8nA polymerases and ls generally
furLher processed by oLher enzymes
4 8nA ls cenLral Lo proLeln synLhesls
O ulfferences beLween 8nA and unA
4 8nA ls usually slngle sLranded whlle unA ls usually double sLranded
8nA a much shorLer chaln of nucleoLldes
4 8nA nucleoLldes conLaln rlbose whlle unA conLalns deoxyrlbose (a Lype of rlbose LhaL
lacks one oxygen aLom)
@hese hydroxyl groups makes 8nA less sLable Lhan unA because lL ls more
prone Lo hydrolysls
4 8nA has Lhe base uracll whlle unA has Lhe base Lhymlne
@he complemenLary base Lo adenlne ls noL Lhymlne as lL ls unA buL raLher
uracll whlch ls an unmeLhylaLed form of Lhymlne
O |bosoma| -s (-s% are componenLs of rlbosomes Lhe complexes LhaL carry ouL Lhe
synLhesls of proLelns
O ,essenge -s (m-s% are lnLermedlarles carrylng ouL geneLlc lnformaLlon from one or a
few genes Lo a rlbosome where Lhe correspondlng proLelns can be synLheslzed
O @ansfe -s (t-s% are adapLer molecules LhaL falLhfully LranslaLe Lhe lnformaLlon ln m8nA
lnLo a speclflc sequence of amlno acld

know whaL Ckazakl fragmenLs are
O aza| fagments are relaLlvely shorL fragmenLs of unA (wlLh no 8nA prlmer aL Lhe 3'
Lermlnus) creaLed on Lhe lagglng sLrand durlng unA fragmenLs
4 When Lhe lagglng sLrand ls belng repllcaLed on Lhe orlglnal sLrand Lhe 3'3' paLLern musL
be used Lhus a small dlsconLlnulLy occurs and an Ckazakl fragmenL forms
4 @hese fragmenLs are processed by Lhe repllcaLlon machlnery Lo produce a conLlnuous
sLrand of unA and hence a compleLe daughLer unA hellx
4 ln deallng wlLh Lhe synLhesls of complemenLary unA sLrands Lhe emerglng leadlng
sLrand always reads 3' Lo 3' @he anLlparallel complemenL sLrand Lhe emerglng lagglng
sLrand reads 3' Lo 3'
8ecause Lhe orlglnal sLrands of unA are anLlparallel and only one conLlnuous
new sLrand can be synLheslzed aL Lhe 3' end of Lhe leadlng sLrand due Lo Lhe 3'
3' polarlLy of unA polymerases Lhe oLher sLrand musL grow dlsconLlnuously ln
Lhe opposlLe dlrecLlon
8egardlng Lhe lagglng sLrand Lhe resulL of Lhls sLrand's dlsconLlnuous repllcaLlon
ls Lhe producLlon of a serles of shorL secLlons of unA called Ckazakl fragmenLs
ach Ckazakl fragmenL ls lnlLlaLed near Lhe repllcaLlon fork aL an 8nA prlmer
creaLed by a prlmase and exLended by unA polymerase lll

ConservaLlve versus semlconservaLlve
O unA repllcaLlon ls sem|conseat|e
4 ach unA sLrand serves as a LemplaLe for Lhe synLhesls of a new sLrand produclng Lwo
new unA molecules each wlLh one new sLrand and one old sLrand
4 em|conseat|e ep||cat|on would produce Lwo coples LhaL each conLalned one of Lhe
orlglnal sLrands and one new sLrand
4 onseat|e ep||cat|on would leave Lhe Lwo orlglnal LemplaLe unA sLrands LogeLher ln
a double hellx and would produce a copy composed of Lwo new sLrands conLalnlng all of
Lhe new unA base palrs

know abouL enzymes and resLrlcLlve enzymes
O nzymes are proLelns LhaL caLalyze (lncrease Lhe raLes of) chemlcal reacLlons
4 ln enzymaLlc reacLlons Lhe molecules aL Lhe beglnnlng of Lhe process are called
subsLraLes and Lhe enzyme converLs Lhem lnLo dlfferenL molecules called Lhe producLs
4 nzymes acLs as an caLalysL and work by lowerlng Lhe acLlvaLlon energy for a reacLlon
Lhus lncreaslng Lhe raLe of Lhe reacLlon
4 nzyme acLlvlLy can be affecLed by oLher molecules
lnhlblLors are molecules LhaL decrease enzyme acLlvlLy acLlvaLors are molecules
LhaL lncrease enzyme acLlvlLy
urugs and polsons are enzyme lnhlblLors
AcLlvlLy ls affecLed by LemperaLure chemlcal envlronmenL and Lhe
concenLraLlon of subsLraLe
4 nzymes are very speclflc as Lo whlch reacLlons Lhey caLalyze and Lhe subsLraLes LhaL
are lnvolved ln Lhese reacLlons
ComplemenLary slze charge and hydrophlllc/hydrophoblc characLerlsLlcs of
enzymes and subsLraLes are responslble for Lhls speclflclLy
O ofactos are componenLs of enzymes LhaL some enzymes requlre @hese nonproLeln
molecules are bound Lo some enzymes for acLlvlLy
O oenzymes are small organlc molecules LhaL LransporL chemlcal groups from one enzyme Lo
anoLher
O est|ct|on enzymes or est|ct|on endonuc|ease ls an enzyme LhaL cuLs doublesLranded or
slngle unA aL speclflc recognlLlon nucleoLlde sequences known as resLrlcLlon slLes

know abouL hybrldlzaLlon
O - nyb|d|zat|on ls Laklng Lwo unA samples Lo be compared @hey are compleLely denaLured
by heaLlng @hen when Lwo soluLlons mlxed and slowly cooled unA sLrands of each sample
assoclaLe wlLh Lhelr normal complemenLary parLner and anneal Lo form duplexes lf Lhe Lwo
unAs have slgnlflcanL sequence slmllarlLy Lhey also Lend Lo form parLlal duplexes or hybrlds
wlLh each oLher @he greaLer Lhe sequence slmllarlLy beLween Lhe Lwo unAs Lhe greaLer Lhe
number of hybrlds formed




know proLelns and Lhelr lnLeracLlons
O 9ote|ns are organlc compounds made of amlno aclds arranged ln a llnear chaln and folded lnLo
a globular form
O @he amlno aclds ln a polymer are [olned LogeLher by Lhe pepLlde bonds beLween Lhe carboxyl
and amlno groups of ad[acenL amlno acld resldues
O @he sequence of amlno aclds ln a proLeln ls deflned by Lhe sequence of a gene whlch ls encoded
ln Lhe geneLlc code
O 9ote|npote|n |nteact|ons lnvolve noL only Lhe dlrecLconLacL assoclaLlon of proLeln
molecules buL also long range lnLeracLlons Lhrough Lhe elecLrolyLe aqueous soluLlon medlum
surroundlng nelghbor hydraLed proLelns
4 @he lnLeracLlons beLween proLelns are lmporLanL for mosL of Lhe blologlcal funcLlons

know pP pl pk
O pn (potent|a| fo hydogen |on concentat|on% ls a measure of Lhe acldlLy or baslclLy of a
soluLlon
O pI (|soe|ect|c po|nt |soe|ect|c pn% ls Lhe characLerlsLlc pP LhaL whlch Lhe neL elecLrlc charge ls
0
O pk (ac|d d|ssoc|at|on constant% ls a quanLlLaLlve measure of Lhe sLrengLh of an acld ln soluLlon lL
ls Lhe equlllbrlum consLanL for a chemlcal reacLlon known as dlssoclaLlon ln Lhe conLexL of acld
base reacLlons

Pemoglobln versus Myoglobln
O nemog|ob|n ls Lhe oxygencarrylng proLeln of eryLhrocyLes (red blood cells)
4 @he oxygen LransporLlng capaclLy ls dependenL on four lron lons
O ,yog|ob|n ls an oxygenblndlng proLeln found ln Lhe muscle Llssue
O lL ls Lhe heme porLlon of lron LhaL glves boLh red blood cells and red muscle Lhelr color
O ln blood lL ls Lhe hemoglobln LhaL conLalns lron and ln muscle cells Lhe myoglobln conLalns Lhe
lron
O 8ed blood cells conLaln hemoglobln noL myoglobln and so lL ls hemoglobln LhaL glves red blood
cells Lhelr color

know lnLermolecular forces
O Intemo|ecu|a foces are forces LhaL acL beLween sLable molecules or beLween funcLlonal
groups of macromolecules
4 lncludes momenLary aLLracLlons beLween molecules dlaLomlc free elemenLs and
lndlvldual aLoms
4 Lhese forces noLably London dlsperslon forces dlpoledlpole lnLeracLlons and hydrogen
bondlng are slgnlflcanLly weaker Lhan elLher lonlc or covalenL bondlng buL sLlll have a
noLlceable chemlcal effecL
4 lnLermolecular forces are due Lo dlfferences ln charge denslLy ln molecules

know abouL amlno acld slde chalns
O Amlno aclds are molecules conLalnlng an amlne group a carboxyllc acld group and a slde chaln
LhaL varles beLween dlfferenL amlno aclds
4 @hese slde chalns can vary ln slze from [usL a hydrogen aLom ln glyclne Lo a meLhyl
group ln alanlne Lhrough Lo a large heLerocycllc group ln LrypLophan
4 Amlno aclds are usually classlfled by Lhe properLles of Lhelr slde chalns lnLo four groups
@he slde chaln can make an amlno acld a weak acld or a weak base and a
hydrophlle lf Lhe slde chaln ls polar or a hydrophobe lf lL ls nonpolar

know abouL Lhe Lechnlques of separaLlng proLelns
O o|umn chomatogaphy Lakes advanLage of dlfferences ln proLeln charge slze blndlng afflnlLy
and oLher properLles
O at|onexchange chomatogaphy Lhe solld maLrlx has negaLlvely charged groups ln Lhe moblle
phase proLelns wlLh a neL poslLlve charge mlgraLe Lhrough Lhe maLrlx slowly Lhan Lhose wlLh a
neL negaLlve charge because Lhe mlgraLlon of Lhe former ls reLarded more by lnLeracLlon wlLh
Lhe sLaLlonary phase
O |zeexc|us|on chomatogaphy separaLes proLelns accordlng Lo slze ln Lhls meLhod large
proLelns emerge from Lhe column sooner Lhan small ones a somewhaL counLerlnLulLlve resulL
4 @he solld phase conslsLs of beads wlLh englneered pores or cavlLles of a parLlcular slze
4 Large proLelns cannoL enLer Lhe cavlLles and so Lake a shorL and rapld paLh Lhrough Lhe
column around Lhe beads
4 Small proLelns enLer Lhe cavlLles and mlgraLe Lhrough Lhe column more slowly
O ff|n|ty chomatogaphy ls based on Lhe blndlng afflnlLy of a proLeln @he beads ln Lhe column
have a covalenLly aLLached chemlcal group A proLeln wlLh afflnlLy for Lhls parLlcular chemlcal
group wlll blnd Lo Lhe beads ln Lhe column and lLs mlgraLlon wlll be reLarded as a resulL
O nL9 (h|ghpefomance ||qu|d chomatogaphy% makes use of hlghpressure pumps LhaL speed
Lhe movemenL of Lhe proLeln molecules down Lhe column down Lhe column as well as hlgher
quallLy chromaLographlc maLerlals LhaL can wlLhsLand Lhe crushlng force of Lhe pressurlzed flow
4 PLC can llmlL dlffuslonal spreadlng of proLeln bands and Lhus greaLly lmprove
resoluLlon

know abouL Lhe nM8
O -uc|ea ,agnet|c esonance (-,% ls a meLhod for deLermlnlng Lhe Lhreedlmenslonal
sLrucLures of macromolecules
4 lL's Lhe properLy LhaL magneLlc nuclel have ln a magneLlc fleld LhaL applled
elecLromagneLlc pulse or pulses whlch cause Lhe nuclel Lo absorb energy from Lhe M
pulse and radlaLe Lhls energy back ouL
4 @he energy radlaLed back ouL ls aL a speclflc resonance frequency whlch depends on Lhe
sLrengLh of Lhe magneLlc fleld and oLher facLors

know abouL Lhe mass specLromeLer
O ,ass spectomety ls an analyLlcal Lechnlque for Lhe deLermlnaLlon of Lhe elemenLal
composlLlon of a sample or molecule
4 @he MS prlnclple conslsLs of lonlzlng chemlcal compounds Lo generaLe charged
molecules or molecule fragmenLs and measuremenL of Lhelr massLocharge raLlos

know xray crysLallography
O Oay cysta||ogaphy ls a meLhod of deLermlnlng Lhe arrangemenL of aLoms wlLhln a crysLal ln
whlch a beam of xrays sLrlkes a crysLal and dlffracLs lnLo many speclflc dlrecLlons
4 rom Lhe angles and lnLenslLles of Lhese dlffracLed beams a crysLallographer can
produce a Lhreedlmenslonal plcLure of Lhe denslLy of elecLrons wlLhln Lhe crysLal
4 rom Lhls elecLron denslLy Lhe mean poslLlons of Lhe aLoms ln Lhe crysLal can be
deLermlned as well as Lhelr chemlcal bonds Lhelr dlsorder and varlous oLher
lnformaLlon

aLe of pyruvaLe
O 9yuate ls a molecule LhaL ls a key lnLersecLlon ln several meLabollc paLhways
4 lL can be made from glucose Lhrough glycolysls supplles energy Lo llvlng cells ln Lhe
clLrlc acld cycle and can also be converLed Lo carbohydraLes vla gluconeogenesls Lo
faLLy aclds or energy Lhrough aceLylCoA Lo Lhe amlno acld alanlne and Lo eLhanol

know whaL anaeroblc and aeroblc condlLlons are
O naeob|c cond|t|ons are vlrLually devold of oxygen and mlcroorganlsms adapLed Lo Lhese
envlronmenLs obLaln energy by Lransferrlng elecLrons Lo nlLraLe (formlng n2) sulfaLe (formlng
P2S) or CC2 (formlng CP4)
O eob|c cond|t|ons have a plenLlful supply of oxygen and some resldenL organlsms derlve
energy from Lhe Lransfer of elecLrons from fuel molecules Lo oxygen


know regulaLlon of gluconeogenesls
O Whlle mosL sLeps ln gluconeogenesls are Lhe reverse of Lhose found ln glycolysls Lhree
regulaLed and sLrongly exergonlc reacLlons are replaced wlLh more klneLlcally favorable
reacLlons
4 Pexoklnase/glucoklnase phosphofrucLoklnase and pyruvaLe klnase enzymes of
glycolysls are replaced wlLh glucose6phosphaLe frucLose 16blphosphaLase and
carboxyklnase
4 @he ma[orlLy of Lhe enzymes responslble for gluconeogenesls are found ln Lhe cyLoplasm
4 @he raLe of gluconeogenesls ls ulLlmaLely conLrolled by Lhe acLlon of a key enzyme
frucLose 16blphosphaLase whlch ls also regulaLed Lhrough slgnal LransducLlon by
cAM and lLs phosphorylaLlon
4 AceLyl CoA and clLraLe acLlvaLe gluconeogenesls enzymes (pyruvaLe carboxylase and
frucLose 16blphosphaLase respecLlvely)
uue Lo Lhe reclprocal conLrol of Lhe cycle aceLylCoA and clLraLe also have
lnhlblLory roles ln Lhe acLlvlLy of pyruvaLe klnase


know regulaLlon of Lhe clLrlc acld cycle
O @he regulaLlon of Lhe @CA cycle ls largely deLermlned by subsLraLe avallablllLy and producL
lnhlblLlon
O nAuP a producL of all dehydrogenasees ln Lhe @CA cycle (excepLlon succlnaLe dehydrogenase)
lnhlblLs pyruvaLe dehydrogenase lsoclLraLe dehydrogenase keLogluLaraLe dehydrogenase
and also clLraLe synLhase
O AceLyl CoA lnhlblLs pyruvaLe dehydrogenase
O SucclnylCoA lnhlblLs succlnyl CoAsynLhease and clLraLe synLhase
O A@ lnhlblLs clLraLe synLhase and akeLogluLaraLe dehydrogenase
O Calclum ls used as a regulaLor and lL acLlvaLes pyruvaLe dehydrogenase lsoclLraLe
dehydrogenase and akeLogluLaraLe dehydrogenase
O ClLraLe ls used for feedback lnhlblLlon as lL lnhlblLs phospofrucLoklnase an enzyme lnvolved ln
glycolysls LhaL caLalyzes formaLlon of frucLose 16blphosphaLe a precursor of pyruvaLe



know regulaLlon of Lhe glycolysls
O Clycolysls ls regulaLed by slowlng down or speedlng up cerLaln sLeps ln Lhe glycolysls paLhway
4 @hls ls accompllshed by lnhlblLlng or acLlvaLlng Lhe enzymes LhaL are lnvolved
4 Any sLep wlLh a free energy near 0 ls noL belng regulaLed
4 A sLep wlLh a large negaLlve change ln free energy ls assumed Lo be regulaLed

know Lhe pyruvaLe dehydrogenase complex
O @he pyuate dehydogenase comp|ex ls a complex of Lhree enzymes LhaL Lransform pyruvaLe
lnLo aceLylCoA by a process called pyruvaLe decarboxylaLlon
4 AceLylCoA may Lhen be used ln Lhe clLrlc acld cycle Lo carry ouL cellular resplraLlon and
Lhls complex llnks Lhe glycolysls meLabollc paLhway Lo Lhe clLrlc acld cycle
O yruvaLe decarboxylaLlon ls also known as Lhe pyruvaLe dehydrogenase reacLlon" because lL
also lnvolves Lhe oxldaLlon of pyruvaLe

know slgnal LransducLlon
O |gna| tansduct|on ls Lhe converslon of lnformaLlon lnLo a chemlcal change
4 @he slgnal represenLs lnformaLlon LhaL ls deLecLed by speclflc recepLors and converLed
Lo a cellular response whlch always lnvolves a chemlcal process

know secondary messengers
O econd messenges are molecules LhaL relay slgnals from recepLors on Lhe cell surface Lo LargeL
molecules lnslde Lhe cell ln Lhe cyLoplasm or ln Lhe nucleus
4 @hey relay Lhe slgnals of hormones growLh facLors and oLhers and cause some klnd of
change ln Lhe acLlvlLy of Lhe cell
4 @hey greaLly ampllfy Lhe sLrengLh of Lhe slgnal
4 Secondary messengers are a componenL of slgnal LransducLlon cascades

know Lhe funcLlon of Lhe recepLor Lyroslne klnase (8@k)
O ecepto tyos|ne |nases (@k% are Lhe hlghafflnlLy cell surface recepLors for many
polypepLlde growLh facLors cyLoklnes and hormones
4 Shown noL only Lo be key regulaLors of normal cellular processes buL also have a crlLlcal
role ln Lhe developmenL and progresslon of many Lypes of cancer

know Lhe penLose phosphaLe paLhway
O @he pentose phosphate pathway leads Lo Lhe oxldaLlon of glucose 6phosphaLe Lo penLose
phosphaLes
4 lL's a process LhaL generaLes nAuP and penLoses
4 @here are Lwo dlsLlncL phases ln Lhe paLhway
@he flrsL ls Lhe oxldaLlve phase ln whlch nAuP ls generaLed and Lhe second ls
Lhe nonoxldaLlve synLhesls of 3carbon sugars
@hls paLhway ls an alLernaLlve Lo glycolysls



8ecognlze enzymes of Lhe clLrlc acld cycle
O See Lhe above dlagram

know Lhe dlfference beLween caLabollc and anabollc paLhways
O atabo||c pathways degrade organlc nuLrlenLs lnLo slmple end producLs ln order Lo exLracL
chemlcal energy and converL lL lnLo a form useful Lo Lhe cell
O nabo||c pathways sLarL wlLh small precursor molecules and converL Lhem Lo progresslvely
larger and more complex

know LranslLlon sLaLe analogs
O @ans|t|on state ana|ogs are chemlcal compounds wlLh a chemlcal sLrucLure LhaL resembles Lhe
LranslLlon sLaLe of a subsLraLe molecule ln an enzymecaLalyzed chemlcal reacLlon
4 @ranslLlon sLaLe analogs do noL undergo a chemlcal reacLlon and can acL as enzyme
lnhlblLors by blocklng Lhelr acLlve slLe

know abouL serlne proLeases
O e|ne poteases are proLeases (enzymes LhaL cuL pepLlde bonds ln proLelns) ln whlch one of Lhe
amlno aclds aL Lhe acLlve slLe ls serlne

know whaL chymoLrypsln ls
O hymotyps|n ls a dlgesLlve enzyme LhaL can perform proLeolysls (dlrecLed
degradaLlon/dlgesLlon of proLelns by cellular enzymes called proLeases or by lnLramolecular
dlgesLlon)
4 referenLlally cleaves pepLlde amlde bonds where Lhe carboxyl slde of amlde bond ls a
Lyroslne LrypLophan or phenylalanlne
@hey conLaln an aromaLlc rlng ln Lhelr slde chaln LhaL flLs lnLo a hydrophoblc
pockeL of Lhe enzyme

WhaL's a buffer soluLlon?
O A buffe so|ut|on ls an aqueous soluLlon conslsLlng of a mlxLure of a weak acld and lLs con[ugaLe
base or a weak base and lLs con[ugaLe acld

WhaL's equlllbrlum?
O When a sysLem ls aL equ|||b|um Lhe raLe of producL formaLlon exacLly equals Lhe raLe aL whlch
producL ls converLed Lo reacLanL
4 @here ls no neL change ln Lhe concenLraLlon of reacLanLs and producLs a sLeady sLaLe ls
achleved

WhaL's phosphorylaLlon?
O 9hosphoy|at|on lnvolves Lhe Lransfer of phosphoryl groups
O @he purpose of Lhls has Lo do wlLh conformaLlonal change
O 9hosphoy|at|on ls Lhe addlLlon of a phosphaLe group Lo a proLeln or oLher organlc molecule
4 9hosphoy|at|on acLlvaLes or deacLlvaLes many proLeln enzymes

WhaL's Lhe elecLron LransporL chaln?
O An e|ecton tanspot cha|n couples a chemlcal reacLlon beLween an elecLron donor (such as
nAuP) and an elecLron accepLor (such as C2) Lo Lhe Lransfer of P lons across a membrane
Lhrough a seL of medlaLlng blochemlcal reacLlons
4 @he P lons are used Lo produce adenoslne LrlphosphaLe (A@) Lhe maln lnLermedlaLe ln
llvlng organlsms as Lhey move back across Lhe membrane
4 @C are used for exLracLlng energy from sunllghL (phoLosynLhesls) and from redox
reacLlons such as Lhe oxldaLlon of sugars (resplraLlon)