2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$!

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Examination Specifications (2002)1

Building Blocks of Life Course (41)
I. Physical-Chemical Principles (3) %! Basic &rinci&les '2( B! %&&lied &rinci&les '1( II. Biological Compounds ( ) %! )*gars and car+ohydrates '1( B! %mino %cids and &roteins '2 ( ! "i&ids '1( $! N*cleic %cids and meta+olism '1( ,! Interdisci&linary clinical-cross correlation '.( III. !e"a#olism (13) %! Bioenergetics '1( B! ,n/ymology '1( ! ata+olism '2( $! %na+olism '2( ,! Reg*lation '2( 0! Interdisci&linary clinical-cross correlation '5(

--- of $% --Biochemis"ry in o"her +1 Courses (13)

&. Connec"i,e -issues (') 'in Basic Tissues( %! )oft tiss*e '2( B! 2ard 3iss*e-calcification '3( ! Interdisci&linary and clinical-cross correlation '3( &I. !em#ranes (4) 'most in Cell Organelles ( %! )tr*ct*re '1( B! 0*nction '1( ! Interdisci&linary clinical-cross correlation '2( &II. )er,ous .ys"em ( ) 'most in Organ Systems( %! General &ro&erties '2( B! entral nervo*s system '1( ! %*tonomic nervo*s system '1( $! )omatic nervo*s system 'with refle4es( '2( ,! )&ecial senses '1( 0! Interdisci&linary and clinical-cross correlation '2( &III. !uscle (*) '( %! )5eletal '2( meta+olism and myoglo+in B! )mooth '1( ! ardiac '1( $! Interdisci&linary and clinical-cross correlation '3( I(. Circula"ion ( ) 'in Basic Tissues-clotting-gas trans&ort %! 0l*id content and dynamics '2( B! oag*lation '1( ! ardiodynamics and electro&hysiology '2( ! Reg*lation '1( $! Interdisci&linary and clinical-cross correlation '3( (. /espira"ion (*) 'in Basic Tissues( %! 6echanical as&ects '1( B! Gas e4change and trans&ort '1( ! Reg*lation '1( $! Interdisci&linary and clinical-cross correlation '3( (I. /enal (*) 'see Organ Systems( %! 0*nctional anatomy '1( B! Blood flow and filtration '1( ! Rea+sor&tion and secretion '1( meta+olites $! Interdisci&linary and clinical-cross correlation '2( (II. 0cid-Base Balance (1) 'in Organ Systems( (III. +iges"ion (%) 'in Organ Systems( %! Ne*rom*sc*lar '1( B! )ecretions '1( en/ymes ! %+sor&tion '1( $! Reg*lation '1( ,! Interdisci&linary and clinical-cross correlation '1( (&. 1ndocrines (') 'in Organ Systems( %! Pit*itary-hy&othalam*s '1( B! Re&rod*ction '1( ! )ignaling systems '2( ins*lin-gl*cagon 7 c%6P $! Pancreas-&arathyroid '1( ,! %drenal-thyroid '1( 0! Interdisci&linary and clinical-cross correlation '2(

---$% --I&. !olecular Biology (') %! $N%-RN% and &rotein synthesis '. ( B! Genetic engineering '2( ! Interdisci&linary clinical-cross correlation '2( (I&. )u"ri"ion (') %! N*trients-minerals '3( 1! Re1*irements '1( 2! 0*nctions '2( B! Interdisci&linary and clinical-cross correlation '2(

---1* of $% ---

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$!

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In"egra"ed Biochemis"ry Review and Study 2ues"ions

3o assist yo* in reviewing Biochemistry for the Part I National Boards# re,ie3 4ues"ions were &re&ared and are accom&anied +y s*ggested st*dy or tho*ght 1*estions in red te4t! %dditionally# written answers - as endnotes 8 are &rovided to foster easier review rather than new learning! 3o see the answer# move the mo*se c*rsor over the endnote n*m+er 'e4&onent( and the endnote &o&s *&! Gree5 letters# s*&er-s*+scri&ts formatting are lost in the &o&*& note# so cons*lt the act*al endnote as needed! 9%dditional information is within +rac5ets in grey tone# which is also lost in the &o&*& note!:! 3he 3;PI headings 'centered( and their )<B3;PI headings 'left margin( are also in gray scale . -opics in Building Blocks of Life course are in #lue "e5"! ;ther to&ics ta*ght in the &revio*s traditional +iochemistry co*rse are in other $1 co*rses# these o"her "opics are in green "e5"! 6any s*+to&ics can not +e incl*ded in a short 50 1*estion format# so the related st*dy 1*estions attem&t to e4&and the s*+to&ics in the 1*estions! Not all answers '=( are reviewed or disc*ssed in the endnote material! P2>)I %"8 2,6I %" PRIN IP",) '3( B%)I PRIN IP",) 1. 6hich of "he follo3ing func"ional groups #eha,es as a 3eak acid7 i.e.7 dissocia"e a pro"on in a4ueous solu"ion7 a" physiological p89 0. /:C8$:/; B. /C8$:<8 C. /:)83= > +. /:C<<8 1. Ph:<8 Related st*dy 1*estions! 91: ?hat is &hysiological &2@2 ?hat is a wea5 acid com&ared to a strong acid@3 92: Identify each f*nctional gro*& a+ove# which can dissociate at &hysiological &2A and why.@ 93: ?hy is the &Ba of C ;;2 and CN22 on the 8car+on of amino acids a+o*t 182 &2 *nit higher and lower# res&ectively5@ $. 6hich of "he follo3ing pairs of compounds is INCORRECTLY ma"ched 3i"h i"s respec"i,e "ype of s"ereoisomerism9 0. +- and L?glyceraldehyde @ a#solu"e configura"ion B. ? and -glucose @ anomer pair C. glucose and mannose @ epimers +. cis- and trans?fumara"e @ geome"ric isomers > 1. ri#ose and glucose @ dias"ereomers Related st*dy 1*estions! 91: 2ow many config*rations can an asymmetric tetrahedral car+on and a chiral car+on have D@ 2ow many different config*rations do all of the asymmetric car+ons ' =( contri+*te in a s*gar@ E 2ow many = in aldosesFA ri+ose# gl*cose# and mannoseA in 5etosesGH ri+*lose# 4yl*lose# fr*ctose@ 92: Regarding car+ons 1C 5 or 1C D# which chiral car+ons in those s*gars define &airs of anomers '/(10# e&imers11 'e!g!# gl*cose and mannose( # $-"8s*gar families12 'e!g!# $-"8gl*cose(! 93: 2ow many of the asymmetric car+on atoms of these s*gars rotate &olari/ed light# i!e!# are o&tically active@ 13 If a $8s*gar always give a 'I( o&tical rotation does the corres&onding mirror image "8s*gar always give a 'C( rotation@1. Is there any consistent relationshi& +etween the asymmetrical tetrahedral car+ons and the direction 'I or C( of o&tical light rotation &ro&erties@15 9.: ?hat are meso stereoisomers vers*s diastereoisomer@ 1D ite an e4am&le1E! %PP"I,$ PRIN IP",) 3. 6hich "hermodynamic parame"er deals 3i"h randomness and disorder9 0. en"halpy > B. en"ropy C. free energy +. ac"i,a"ion energy 1. po"en"ial energy Related st*dy 1*estions! 91: ?hat is the meaning of each the terms listed1F@ 92: ?hat is the significance of random disorder vers*s s&ecified order in +iological systems 1G@

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$!

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93: Is entro&y increased or decreased +y s*ch &rocesses as glycogenesis# fatty acid synthesis# &rotein synthesis# $N% and RN% synthesis20 com&ared to others 'e!g!H glycogenolysis# 8o4idation# &roteolysis# and hydrolysis of $N% and RN%(21@ BI;";GI %" ;6P;<N$) 'G( )<G%R) %N$ %RB;2>$R%3,) 4. -he C1 of ri#ose and glucose has all of "he follo3ing proper"ies EXCEPT ONE. 6hich is "he EXCEPTION9 0. 0nomeric car#on forms / racemic mi5"ure. B. 0cyl aldehyde groups reac" 3i"h primary and secondary alcohols7 amines7 and mercap"ans. > C. +AL isomers define "he specific op"ical ro"a"ion. +. In solu"ion7 mu"aro"a"ion of ei"her pure in"ramolecular hemiace"al yields an e4uili#rium mi5"ure of / anomers. 1. Borms ace"al ri#osides and glucosides7 respec"i,ely7 "ha" canC" mu"aro"a"e. Related st*dy 1*estions 91: 2ow do &lanar aldehydes and 5etones gro*&s give rise to an asymmetric tetrahedral car+on racemic &air 22@ 92: om&are the total n*m+er of asymmetric centers in the o&en8chain and cyclic8forms of aldoses ri+ose# deo4yri+ose# gl*cose# mannose# galactose have 'and 5etose fr*ctose( 23! 93: 6*tarotation may or may not invert 1 config*ration of cyclic8aldoses# +*t when 1 is in an '18.( acetal lin5age no inversion is &ossi+le# for e4am&le# for the 1 of the glucosyl moiety of maltose 'glucosyl'18.(8gl*cose(# or for the glucosyl moiety of cello+iose 'glucosyl'18.(8gl*cose( or for the ri#osyl moiety of adenosine 'Nri+osyl adenine(A e4&lain!2. 9.: $oes this acetal ty&e of chemistry have significance for RN% and $N% sta+ility and f*nction@ 25 %6IN; % I$) %N$ PR;3,IN) %. 0ll of "he follo3ing are charac"eris"ic of amino acids EXCEPT. 0. -he -car#on (C$) is a chiral cen"er (e5cep" for glycine). > B. 0ll migra"e "o "he ca"hode in an elec"ric field a" physiological p8. C. -hey ha,e side chains 3i"h differen" physical and chemical proper"ies. +. !os" can form dipolar ions (D3i""erions) a" physiological p8. 1. <nly a reper"oire of $E amino acids are incorpora"ed in"o pro"eins. 91: 2ow do $8 and "8amino acids relate to the $8 and "8glyceraldehyde reference com&o*nds@2D 92: ?hat f*nctional gro*&s are &resent in the side8chains of free amino acids that acco*nt for their ioni/ation to /witterion forms at &hysiological &2@2E 93: 2ow do some amino acids ac1*ire a net 'I1( or 'C( charge in a1*eo*s sol*tion@2F 9.: ?hat changes in net charge occ*r in free amino acids if the &2 is adJ*sted from &2 2 to &2 12 that effects their net charge and therefore their electro&horetic mo+ility at different &2s@2G 95: ?hich amino acids are always incor&orated into &roteins com&ared to others in the +ody that arise either as &athway meta+olites 'e!g!# ornithine in the *rea cycle( or as a res*lt of &osttranslational modification of in a &rotein 'e!g!# hydro4y&roline from &roline hydro4ylation in collagen chains@ 30 *. 6hich amino acid is INCORRECTLY ma"ched "o i"s side-chain9 0. lysine @ amino?alipha"ic hydrocar#on chain B. isoleucine @ #ranched alipha"ic hydrocar#on chain > C. "yrosine @ aroma"ic imidaDole +. glu"amic acid @ ?car#o5yla"e ?alipha"ic hydrocar#on chain 1. me"hionine @ -me"hylmercap"o?alipha"ic hydrocar#on chain Related st*dy 1*estions 91: 2ow is the tertiary '3K( and 1*aternary '.K( str*ct*re of &roteins affected +y the &ro&erties of the amino acid side8chains '&olar# a&olar# acidic# +asic# ne*tral# ali&hatic# aromatic# and reactivity(@ 31 92: ?hich amino acids are *s*ally in the hydro&ho+ic interior and which are on the hydro&hilic e4terior in contact with water when the &rimary se1*ence folds to yield the f*nctional 3$8str*ct*re@ 32 93: ?hich amino acids are most often modified with s*gars and li&ids &osttranslationally that are then involved in non8+onded vers*s covalent cross8lin5s in com&le4 str*ct*res@ 33 "IPI$) F. .elec" "he INCORRECT s"a"emen" a#ou" lipids.

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$! 0. B. C. +. 1. Lipids are small nonpolar molecules e5"rac"ed #y organic sol,en"s. !os" of our fa" is s"ored as "riglyceride drople"s in adipose "issue cells. Phospholipids are "he maGor class of lipids in mem#ranes. 0B<-#lood group an"igens are glycosphingolipids (glycolipids). !os" fa""y acids are presen" as free acids in cells.

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>

Related st*dy 1*estions 91: ?hat are the maJor classes of li&ids and their constit*ent com&o*nds fo*nd in the +ody@ 3. 92: ?hat are some of the 5ey &ro&erties of li&ids that ma5e them s*ita+le for energy storage# as thermal and electrical ins*lators# and a&&ro&riate for mem+rane &artitions@35 93: ?hat core com&onent disting*ishes &hos&holi&ids from s&hingoli&ids 3DA what car+ohydrate com&onents of glycos&hingoli&ids constit*te the %B; +lood gro*& antigens on red +lood cells@ 3E N< ",I % I$) %N$ 6,3%B;"I)6 '. 6hich one of "he follo3ing compounds DOES NOT supply a"oms for "he syn"hesis of "he purine ring sys"em9 0. glycine B. aspar"a"e C. )1E-formyl--8B0 +. C<$ > 1. .-adenosyl me"hionine (.0!) Related st*dy 1*estions 91: ?hat are the s*+strates and se1*ence of incor&oration of atoms or fragments into the &*rine ring system d*ring de novo synthesis of I6P@3F 92: 2ow is I6P converted to %6P or G6P@3G ?hy are some &*rine and &yrimidine reaction ste&s co*&led to %3P hydrolysis@ .0 93: hoices to , are com&o*nds involved in 18car+on fragment meta+olism for the synthesis of which n*cleotides@ .1 IN3,R$I) IP"IN%R> "INI %"- R;)) ;RR,"%3I;N) . 0ll of "he follo3ing EXCEPT one correc"ly comple"es "he s"a"emen" #elo3. 6hich is "he EXCEPTION9 <5ida"ion of glu"a"hione (H.8) "o disulfide H..H in red #lood cells pro"ec"s pro"eins from o5ida"i,e damage #y@ 0. <$I?. B. reac"i,e o5ygen species. > C. )0+P=. +. me"hylglyo5al. Related st*dy 1*estions 91: ?hat is gl*tathione 'G)2(# which of its f*nctional gro*&s has an antio4idant role against vario*s reactive o4ygen s&ecies 'R;)(# and which two cells8ty&es have G)2 levels that reach D8F m6@.2 92: 3he glyo4alase &athway in all cells &rotects &roteins against o4idative ins*lt from what small gl*cose fragments originating from glycolysis@.3 93: ?hat is the chemical relationshi& of o4ygen# o4ygen s*&ero4ide# hemoglo+in# methemoglo+in# and 2ein/ +odies@ .. 1E. Hou" disease and Lesch-)yhan syndrome are due "o deficiency of one or "3o enDymes in purine me"a#olism and can #e "rea"ed 3i"h allopurinol. 6hich s"a"emen" a#ou" allopurinol #iochemis"ry is INCORRECT9 0. 0llopurinol decreases "he ra"e of o5ida"ion of purines "o ura"e. > B. 0llopurinol increases ura"e solu#ili"y. C. 0llopurinol inhi#i"s 5an"hine o5idase. +. 0llopurinol ac"s as a suicide inhi#i"or. 1. 0llopurinol increases "he oppor"uni"y for purine sal,age. Related st*dy 1*estions 91: ?hat two salvage en/ymes and their reactions are deficient in &*rine meta+olism that leads to hy&er*ricemia and e4cessive acc*m*lation of &oorly sol*+le *rate in the Joints of cooler e4tremities and 5idney stones in middle8aged men@ .5 92: ?hat moly+den*m8re1*iring en/yme is inhi+ited +y allo&*rinol@ ?hy is allo&*rinol an e4am&le of a s*icide inhi+itor@ .D 93: %cco*nt for the effect of allo&*rinol in reg*lating &*rine +iosynthesis and alleviating sym&toms@ .E 11. 6hich of "he follo3ing represen"s "he chemical su#s"ance "ha" is an addi"ional reser,e of energy for muscle con"rac"ion9 0. Hlycogen B. Lac"ic acid

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$! > C. 0ce"yl Co0 +. Crea"ine phospha"e 1. 0denosine "riphospha"e

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Related st*dy 1*estions 91: ?hat is the &rimary so*rce of energy for m*scle contraction@ .F 92: ?hat com&o*nd is the secondary +ac5*& energy reserve the m*scle cell *sed to regenerate %3P# which is ra&idly de&leted d*ring short +*rsts of contraction there+y giving time for activation of glycogenolysis to s*&&ly gl*cose thereafter@ .G 93: ?hy is creatine &hos&hate a high energy molec*le li5e %3P@50 9.: ?hat dead8end cata+olite of creatine &hos&hate is e4creted from the m*scle cell into &lasma and then into *rine that +etrays +*rsts of vigoro*s m*scle contraction@51 1$. 0 se,ere pyru,a"e car#o5ylase (PCase) deficiency 3ould likely produce -C0 cycle dysfunc"ion and ,ery lo3 0-P le,els in cells #ecause@ 0. pyru,a"e concen"ra"ion is "oo lo3. B. lac"ic acid concen"ra"ion is "oo lo3. C. of insufficien" fa""y acid syn"hesis for mem#rane forma"ion. +. of respira"ory acidosis from ongoing rapid #rea"hing. > 1. of insufficien" o5aloace"ic acid (<00) "o condense 3i"h ace"yl Co0 "o form ci"ra"e. Related st*dy 1*estions 91: ?hat are ana&lerotic reactions and why is &yr*vate car+o4ylase so critical for normal 3 % cycle activity@ 52 92: ?hy do high &yr*vate and lactate levels occ*r in P ase deficiencyA why wo*ld that lead to lactic acidosis@ 53 93: ?hy does li&ogenesis increase significantly '*& to several fold d*ring this deficiency(A 5. and what &athway maintains the s*&&ly of N%$P2 re1*ired@55 6,3%B;"I)6 '13( BI;,N,RG,3I ) 13. 8e5okinase JJ1JJ "he free energy from 0-P hydrolysis "o phosphoryla"e glucose "here#y dri,ing an unfa,ora#le endergonic reac"ion 3i"h an spon"aneous JJ$JJ reac"ion. 0. 1 K uncouples $ K endergonic B. 1 K uncouples $ K e5ergonic C. 1 K couples $ K endergonic = +. 1 L couples $ L e5ergonic 2el&f*l hints 91: ?hat is the significance of free energy change 'G( com&ared to free energy 'G(A what is enthal&y change# in +iological systems and why is G more *sef*l as a meas*re of meta+olic achievement@ 5D 92: If GKM L C E!3 5cal-mol for %3P hydrolysis 'R4 I(H %3P I 22; CN %$P I PiA and if GKM L I 3!3 5cal-mol for the &hos&horylation of gl*cose *sing a &hos&hate 'R4 II(H gl*cose I P CN G8D8PA then acco*nt for the ? 3 5cal-mol ne" GKM that res*lts from the co*&led reaction 'R4 III( of he4o5inaseH gl*cose I %3P CN G8D8P I %$P@5E 93: Reactions that are spontaneous are generally exergonic! In the individ*al and co*&led reactions in the review 1*estion 92:# which reaction is e4ergonic# which is endergonic@5F ;verall# is cata+olism e4ergonic or endergonicA is ana+olism e4ergonic or endergonic@5G ,NO>6;";G> 14. 6hich "erm of "he !ichaelis-!en"en e4ua"ion7

v=

Vma4 [ S ] Km + [S]

>

can #e de"ermined from "he x-in"ercep" of a Line3ea,er-Burke plo"9 0. v B. &ma5 C. Lm +. M.N

Related st*dy 1*estions 91: ?hat is a do*+le reci&rocal &lot# and why is it advantageo*s in determining B m and Pma4@D0 92: ?hat is the meaning of Bm and Pma4 for an en/yme reaction@D1

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93: ?hy is the initial velocity 'v o( im&ortant for determining v of an en/yme reactionA what are /ero and first order 5inetics# relative the Bm@D2 %3%B;"I)6 1%. 0ll "he follo3ing reac"ions occur during glycolysis EXCEPT ONE. 6hich is reac"ion is "he EXCEPTION9 0. fruc"ose-*P = 0-P (phospho ructo!inase"#) fruc"ose-17*-BP > B. fruc"ose-$7*-BP (a$do$ase) $ glyceraldehyde-3P C. glyceraldehyde-3P = )0+= (%&P dehydro'enase) 173-#isphosphoglycera"e = )0+8 +. 173-#isphosphoglycera"e = 0+P (phospho'$ycerate !inase( P)) 3-phosphoglycera"e = 0-P 1. pyru,a"e = )0+8 ($actate dehydro'enase) lac"a"e = )0+= Related st*dy 1*estions and &ers&ectives on glycolysis 91: ?hat is the &*r&ose of glycolysisD3A why is reaction Q%R the commi""ed s"ep@D. ?hat is the maJor &rod*ct of aero#ic vers*s anaero#ic glycolysis@D5 92: 3he red +lood cell 'RB #( li5e all cells# contains only trace 1*antities of coen/ymes 'hence Scatalytic 1*antitiesT(! 3he RB wo*ld convert the tiny s*&&ly of N%$I to N%$2 very 1*ic5ly and then glycolysis wo*ld sto&U ?hich listed en/yme reaction Q@R &revents this meta+olic colla&se@ DD 93: Reactions and $ constit*te a catalytic &rocess 5nown as su#s"ra"e le,el o5ida"i,e phosphoryla"ion# which is one of two s*+strate level means of %3P regeneration 'from %$P( essential for s*staining all %3P8de&endent RB meta+olic reactions from colla&se! Ironically com&lete reliance on and $ &rod*ces a lower net %3P yield com&ared to all other cells! ?hat cell*lar organelle is *ni1*ely missing in the RB that other cells have and rely *&on e4tensively for most %3P regeneration and there+y +y&ass cytosolic lactate dehydrogenase to regenerate their N%$I@DE 9.: ?hich highly e4ergonic en/yme reaction 'not listed# which in contrast to $ doesnRt need an o4idative reaction li5e (# &rovides the second su#s"ra"e le,el &hos&horylation of %$P in the RB 'all other glycolytic cells too(@ DF 95: In other cells# which have mitochondria and can f*nnel N%$2 into +oth cytosolic lactate dehydrogenase or the mitochondrial respiratory chain 'in &ro&ortion to dynamic hy&o4ic o4ygen levels(# the net %3P regeneration ratio goes *& or down +etween the e4tremes of 2 and F %3P &er gl*cose o4idi/ed! ?hat is the name given to glycolysis at either e4treme@DG 9D: ?ith the a+ove in mind# can yo* a&&reciate why the glycolytic thro*gh&*t m*st end in lactate not &yr*vate@ 2ence# the maJor so*rce of &lasma lactate is *nderstood@ E0 ?hat other maJor tiss*e can &rod*ce and secrete massive 1*antities of lactate into the &lasma *sing glycolysis@ E1 1*. 6hich of "he follo3ing glycoly"ic li,er enDymes is NOT produc"-inhi#i"ed and is a#sen" in muscle cells9 0. 8e5okinase B. 1nolase C. 0ldolase > +. Hlucokinase 1. Hlucose-*-phospha"ase Related st*dy 1*estions 91: %fter a meal# gl*cose *&ta5e in liver cells is facilitated and ra&id com&ared to m*scle cells +eca*se liver has an additional gl*cose 5inase that is not &rod*ct8inhi+ited and has a higher Bm for gl*cose! ?hy are these distinctions im&ortant for a&&reciating s&ecial liver cell f*nctions com&ared to m*scle cell f*nction@E2 92: %n a+r*&t and s*stained increase in diet gl*cose ind*ces gene e4&ression of one of these liver 5inases# which en/yme is ind*ci+le and why is that advantageo*s for liver f*nctions@E3 %N%B;"I)6 1F. .elec" "he s"a"emen" a#ou" glycogen #iochemis"ry "ha" is INCORRECT. 0. Hlycogen is composed of highly #ranched chains of glucose residues. B. HlycogenCs ou"3ard #ranching pro,ides reac"i,e ends for e5"remely rapid incorpora"ion and release of glucose. C. Hlucose residues are linked #y ace"al (1 4) #onds. +. 0ppro5ima"ely 1 in ' glucose residues are linked #y an ace"al (1 *) #ond. > 1. Hlycogen is hydrophilic and "herefore is less dense "han "riacylglycerides. Related st*dy 1*estions 91: ?hat s&ecial as&ects of acetal lin5age &ro&erties and associated en/ymes are advantageo*s with res&ect to storage of gl*cose in starch and glycogen or for *se of gl*cose for str*ct*ral strength characteristic of cell*lose@ E.

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92: ,4&lain how the highly +ranched &olymer str*ct*re of glycogen &rovides a maJor advantage com&ared to the str*ct*re of the linear starch &olymer in facilitating different in rates of synthesis and +rea5down 'i!e!# storage and release( for +oth &olymers@E5 93: Is this consistent with m*scle *sing glycogen rather than starch# which is *sed in &lants@ ED 1'. Onlike -o5ida"ion of fa""y acids7 fa""y acid syn"hesis re4uires only@ 0. )0+= > B. )0+P8 C. B0+ +. B0+8$ Related st*dy 1*estions 91: In the fatty acid synthesis &athway# which two reactions *se N%$P2A in contrast# which of the listed redo4 coen/ymes are *sed in the 8o4idation cata+olic &athway@ EE 92: ?hich meta+olic &athway's( or reaction's( s*&&ly N%$P2 for 0% synthesisA which vitamin# if deficient# therefore interferes with 0% synthesis# which second vitamin# if deficient with the first interferes with +oth 0% &athways@ EF 93: ?hich inherited en/yme deficiency was first revealed when an antimalarial '&rima1*ine( was &rescri+ed that lead to ins*fficient N%$P2 &rod*ction in the he4ose mono&hos&hate sh*nt in RB s that develo&ed into hemolytic anemia@ EG R,G<"%3I;N 1 . /egula"ion of glycoly"ic enDyme ac"i,i"y includes pos""ranscrip"ional phosphoryla"ionAdephosphoryla"ion of@ > 0. pyru,a"e kinase B. glycogen syn"hase C. phosphorylase kinase +. phosphorylase a 1. phosphofruc"okinase-1 Related st*dy 1*estions 91: % variety of reg*latory mechanisms control the fl*4 of molec*les thro*gh the glycolytic &athway! 3hese incl*de s*+strate availa+ility# inhi+ition# allosterism# and &osttranslational modification! ?hich en/ymes are reg*lated +y these mechanisms@ F0 92: ?hich small glycolytic molec*les# incl*ding those from other &athways# are involved in the reg*latory mechanisms of glycolysis@F1 93: ?hich &ancreatic hormone's( stim*lates or inhi+its glycolytic activity@ F2 By what mechanisms@F3 $E. 6hich key su#s"ra"e of fa""y acid syn"hesis also con"rols "he inhi#i"ion of -o5ida"ion and "here#y pre,en"s a fu"ile cycle9 0. ace"yl Co0 > B. malonyl Co0 C. ci"ra"e +. pyru,a"e 1. propionyl Co0 Related st*dy 1*estions 91: ?hat is a f*tile cycleA why wo*ld meta+olic f*tile cycles +e life threatening@ F. 92: ?hat is the activated s*+strate for cytosolic fatty acid synthesisA which molec*le inhi+its the en/yme8driven entry of acyl o% fatty acids into the mitochondria for 8o4idation@F5 2ow do those &ro&erties &revent a f*tile cycle in fatty acid meta+olism@FD 93: ,4cess dietary gl*cose is easily converted to fat and stored! ;ddly eno*gh# acetyl o% arises from &yr*vate via cyto&lasmic glycolysis of the e4cess gl*cose! ?hy does acetyl o% +ecome tra&&ed inside the mitochondrion after mitochondrial &yr*vate dehydrogenase acts on &yr*vate@ FE 9.: 2ow does acetyl o% esca&e the mitochondrionFFA how does acetyl o% 'and ;%%( arise from cytosolic citrateFGA how is acetyl o% activated with ;2 to form malonyl o%!G0 95: 2ow does &ro&ionyl o% arise from 8o4idation of odd8n*m+ered fatty acids@G1 IN3,R$I) IP"IN%R> "INI %"- R;)) ;RR,"%3I;N $1. )ucleoside deri,a"i,es are effec"i,e an"i#io"ics compared "o "heir free #ases #ecause af"er phosphoryla"ion "o nucleoside "riphospha"es7 "he appropria"e cellular polymerases "hen incorpora"e "hem in"o 0. "he primary se4uence of full leng"h his"one nucleopro"eins in #ac"eria in"erfering 3i"h "ransfec"ion.

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B. polysaccharides "ha" unfold +)0 supercoils in"erfering 3i"h chromosome replica"ion. C. "he %;"erminal cap of hn/)0 pre-m/)0 in"erfering 3i"h pos""ranscrip"ional processing. +. /)0 or +)0 "ranscrip"s ei"her for su#se4uen" inhi#i"ory effec"s or "ermina"ion of fur"her polymeriDa"ion.

Related st*dy 1*estions 91: ?hat is a/ido thymidine# dideo4yadenosine# and &*romycinA what str*ct*ral feat*res ma5e each of these n*cleosides effective anti+iotics d*e to their mode of action@G2 92: ?hich cell*lar en/ymes interconvert n*cleosides and n*cleotides# e4change s*gars of n*cleosides# salvage &*rine and &yrimidine +ases directly to n*cleotides there+y allowing n*cleotides and their dr*g analogs meta+olic effectiveness@ G3 93: ite at least one e4am&le of a n*cleoside with a modified s*gar that terminates $N% synthesis there+y inhi+iting &rod*ctive infection +y the %I$) vir*s@G. $$. 0n immigran" migran" farm 3orker presen"s her %-year old male child "o "he emergency room complaining P0ll his "ee"h are ro""ing7 he cries all "he "ime and seems "o #e in pain.Q 15amina"ion re,eals "ha" "he #oy is una#le "o unders"and and ans3er simple 4ues"ions and has an unusual gai"7 si""ing pos"ure7 and ,ery ligh" pigmen"a"ion. -he family his"ory indica"es male men"al re"arda"ion and epilepsy7 #u" o"her3ise normal den"al his"ories. Orine analysis indica"es e5cessi,e phenylpyru,a"e7 phenyllac"a"e and a mousey smell. Bur"her "es"s confirm phenylalanine hydro5ylase deficiency. -he mos" likely diagnosis is@ 0. 0l#inism. B. 0lkap"onuria. C. !aple syrup urine disease (!.O+). > +. Phenylke"onuria. Related st*dy 1*estions 91: ?hat sim&le test detects &henyl5eton*ria 'PB<( shortly after child+irth +eca*se it is mandated +y law in most states# +*t often is not &erformed in foreign co*ntries@ ?hich as&ect of meta+olism is affected@ G5 92: ?hat adJ*stment is made to the dietary form*la to &revent mental retardation from develo&ing in the infant@ GD 93: ,4&lain why a &atient with PB< is on the horns of a dilemma in trying to +alance a &ossi+le essential amino acid deficiency against ne*roto4icity of &henylalanine@GE 9.: ?hy is ram&ant caries and very light &igmentation +oth irrelevant for the diagnosis of this case@ GF 95: ?hy can a tyrosine s*&&lement com&ensate for occasional *nintended &henylalanine dietary e4cess@ GG $3. Raundice in a pa"ien" 3i"h a his"ory of alcoholic cirrhosis is mos" likely due "o a me"a#olic dysfunc"ion in@ 0. #iliru#in syn"hesis #y "he li,er. > B. #iliru#in ca"a#olism #y "he li,er. C. cy"ochrome syn"hesis #y "he pancreas. +. cy"ochrome ca"a#olism #y "he pancreas. Related st*dy 1*estions 91: ?hat is the &athway of heme synthesis and cata+olism@100 92: ?here do each of these synthetic and cata+olic reactions occ*r@ 101 93: ?hat are Ja*ndice and he&atomegaly@ 102 $4. 0ll of "he follo3ing correc"ly comple"e "he sen"ence a#ou" sickle-cell anemia EXCEPT ONE. 6hich is "he EXCEPTION9 PSic!$e ce$$ ane*ia was the irst co*p$ex disease discovered to +e due to S 0. a single nucleo"ide mu"a"ion in "he gene coding for -hemoglo#in 0.Q > B. a nonsense codon mu"a"ion in "he gene coding for -hemoglo#in 0.Q C. an al"ered hemoglo#in conforma"ion "ha" promo"es insolu#le fi#ril forma"ion.Q +. dis"or"ed cell shape and cell infle5i#ili"y "ha" leads "o #locked capillaries and localiDed micro hypo5ia. Q 1. a ,arie"y of clinical signs and symp"oms. Q Related st*dy 1*estions 91: ?hat is the nat*re of the m*tation in sic5le cell anemia@ 103 92: ?hat ca*ses the change in sha&e and fle4i+ility d*ring hy&o4ia@ 10. 93: ?hy does sic5le cell anemia show a variety of clinical signs and sym&toms@ 105 $%. 0ll of "he follo3ing are "rue s"a"emen"s concerning Dymogen ac"i,a"ion cascades EXCEPT ONE. 6hich is "he EXCEPTION9 Tymogens@ 0. are of"en "riggered in emergency si"ua"ions 3hen rapid response is essen"ial. B. pro,ide ,ery rapid amplifica"ion of ac"i,e enDyme ca"alysis. C. a,oid life-"hrea"ening circums"ances #y accelera"ing enDymological responses.

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+. pro,ide a mechanism for rapid serial feedfor3ard ca"aly"ic ac"i,a"ions 3i"hin a response pa"h3ay. 1. pro,ide cri"ical cC!P hydrolysis ac"i,a"ions for rapid signal "ransduc"ion mechanisms.

Related st*dy 1*estions 91: ?hat is a /ymogen@10D 92: ?hy do we need /ymogen cascades@10E 93: ?hich +ody systems re1*ire /ymogen cascades@ 10F 6;", <"%R BI;";G> 'F( $N%-RN% %N$ PR;3,IN )>N32,)I) $*. 0ll of "he lis"ed pro"eins EXCEPT ONE con"ains an )-"erminal signal pep"ide "ha" is #ound #y "he .ignal /ecogni"ion Par"icle (./P) and is su#se4uen"ly clea,ed as a pos""ransla"ional modifica"ion. 6hich nascen" pro"ein lacks "he signal pep"ide and is no" e5por"ed #y "he cell9 0. Collagen B. Bi#rinogen > C. -u#ulin +. Immunoglo#in 1. Bi#ronec"in Related st*dy 1*estions 91: ?hat is *ni1*e a+o*t the amino acid se1*ence of the signal &e&tide and where in the &oly&e&tide chain is it located@ 10G 92: 2ow does the signal &e&tide differentiate ri+osomes synthesi/ing collagen# fi+rinogen# &lasma fi+ronectin# and imm*noglo+in &oly&e&tide chains for e4cretion from other ri+osomes synthesi/ing &roteins that will remain inside a fi+ro+last# liver# or imm*ne cell@110 $efine intracell*lar vers*s an e4tracell*lar &rotein# and endogeno*s vers*s e4ogeno*s &roteins from those listed@111 93: ?hat is the cyto&lasmic )RP com&le4 that sorts &roteins for secretion or retention +ased *&on the signal &e&tide@ 112 9.: ?hy do ri+osomes doc5 to the endo&lasmic retic*l*mA what is the fate of the signal &e&tideA what is the fate of the remaining C ;;2 end of the newly synthesi/ed &oly&e&tideA what organelle's( may &erform additional &osttranslational modifications@113 $F. -he -0-0 #o5 is impor"an" for ini"ia"ion of 3hich process9 0. m/)0 capping B. +)0 replica"ion and > C. /)0 "ranscrip"ion +. /)0 "ransla"ion 1. 8n/)0 splicing Related st*dy 1*estions 91: ?hat is a n*cleic acid consens*s se1*ence# where are they located and what ty&e of &roteins interact with them@ 11. 92: ?hat is the role of the 3%3% +o4 in a &romoter# do all genes have this se1*ence# if not# cite an e4am&le@ 115 93: ?hat consens*s se1*ences are involved in mRN% synthesis# &rocessing# and translation@ 11D 9.: ?hat role does ca&&ing and &olyadenylation &lay in e*5aryotic mRN% mat*ration and translation@ 11E $'. 6hich s"a"emen" is INCORRECT a#ou" "he "ypical purine-rich7 0HH0HH consensus se4uence in #ac"eria and #ac"eriophages9 0. I" is appro5ima"ely 1E nucleo"ides ups"ream from "he ini"ia"or 0OH codon. > B. I" is usually capped 3i"h mFHpppH. C. I" ensures appropria"e polycis"ronic "ransla"ion. +. I" #inds near "he 3C "erminus of 1*. ri#osomal /)0. 1. I" is called "he .hine-+algarno in m/)0. Related st*dy 1*estions 91: om&are str*ct*res of &ro5aryotic mRN% and e*5aryotic mRN% that are involved in the initiation &hase of &rotein synthesis@11F 92: 2ow does the )hine8$algarno se1*ence align the ri+osome with the %<G start codon@ 11G In &olycistronic &ro5aryotic mRN%# how does the )hine8$algarno ens*re all cistrons of +acterial mRN% are translated@ 120 93: ?hy wo*ld coordinated m*lti8&rotein e4&ression fail in &olycistronic mRN% witho*t the &*rine8rich )hine8$algarno se1*ence@121 $ . -he mFHppp) cap is a pos""ranscrip"ional modifica"ion of eukaryo"ic@

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Related st*dy 1*estions 91: ?hat as&ect of the entral $ogma '?atson and ric5# 1G53( does the 1*estion address@ 122 92: ?hat is a &osttranscri&tional modificationA which modifications occ*r d*ring and which after transcri&tion is com&lete@ 123 93: ?hich str*ct*ral modification re1*ires# G3P and )8adenosyl methionine ')%6(A which need only )%6@12. 9.: ?hich initiation factor +inds recogni/es the I1 charge in the 5R8mEG&&&N ca& of e*5aryotic mRN% that facilitates translation@125 95: ?hich three meta+olic coen/ymes have a str*ct*ral feat*re similar to the mRN% ca&@ 12D 3E. 0 sample of +)0 from a pa"ien"Cs amnio"ic fluid cells is prepared for +)0 fingerprin"ing #y "rea"men" 3i"h an enDyme "ha" 3ill hydrolyDe specific phosphodies"er #onds of #o"h s"rands 3i"hin "he se4uence7 %C?H00--C ?. 6hich "ype of enDyme is used9 0. "opoisomerase > B. res"ric"ion endonuclease C. ligase +. e5onuclease 1. polymerase Related st*dy 1*estions 91: ?hat s*+strates do restriction en/ymes# to&oisomerases# ligases# e4o8 and endon*cleases# and &olymerases act on@ 12E 92: ?hat role does each listed en/yme &erform in a +acterial cell# in a h*man cellA12F how does the cell disting*ish its $N% from foreign $N% in order to a+ort the +iological threat of the foreign $N%@ 12G 93: ?hat is a $N% finger&rintA what a&&lications does it have in medicine@ 130 G,N,3I ,NGIN,,RING 31. By 1 F%7 "he cloning of ds+)0 fragmen"s #ecame possi#le af"er 3hich pair of enDymes 3ere disco,ered9 > 0. +)0 res"ric"ion enDyme and +)0 ligase B. +)0 res"ric"ion enDyme and polynucleo"ide phosphorylase C. +)0 endonuclease I and +)0 ligase +. +)0 polymerase I (Lorn#erg) and +)0 ligase 1. -opoisomerase I and +)0 ligase Related st*dy 1*estions 91: ?hat is the s*+strate s&ecificity of hydrolytic $N% restriction en/ymesA why m*st a cell methylate its $N% if it e4&resses a restriction en/yme@131 ?hat are +l*nt ends com&ared to cohesive or Sstic5yT ends &rod*ced +y restriction en/ymes@ 132 92: ?hat does $N% ligation accom&lishA why are $N%8ligases N%$8 or %3P8de&endent@ ?hy do $N% ligases yield sta+le recom+inant $N% molec*les s*ita+le for molec*lar cloning 93: ?hat as&ect of the &olymerase reaction do $N% ligases mimic# +*t also lac5 that &revents them from +eing a $N% &olymerase@133 9.: ?hat is similar-dissimilar a+o*t $N% to&oisomerases and ligases@ 13. 95: om&are RN% &olymerase to &olyn*cleotide &hos&horylase 'PNP( discovered in 1G55# in the +acteri*m ! vinelandii@135 3$. 6hy are plasmids used for molecular cloning of +)0 designed 3i"h "3o an"i#io"ic resis"ance genes9 0. +ou#le resis"ance ensures replica"ion and resis"ance of hos" cell "o "he recom#inan". B. +ou#le resis"ance #oos"s plasmid copy num#er and replica"ion efficiency in "he hos" cell. > C. +ou#le ,erifica"ion "ha" recom#ina"ion occurred and "ha" "he hos" cell 3as successfully "ransfec"ed. +. +ou#le ,erifica"ion "ha" recom#inan" plasmid can kill "ransfec"ed cells7 lea,ing uninfec"ed cells for cloning. Related st*dy 1*estions 91: ?hat is a &lasmid# transfection# &lasmid co&y n*m+er# an anti+iotic resistance gene@ 13D ?hat is the connection +etween am&icillin# tetracycline# and &lasmids@13E 92: $N% inserted into a gene for dr*g resistance a+olishes the dr*g resistance for the cell! $oes the loss of dr*g resistance verify that the $N% insertion was s*ccessf*l@13F 93: ?hat is the rationale for &*tting two anti+iotic resistance genes into a &lasmid s*ch that one gene contains a restriction site@ 13G IN3,R$I) IP"IN%R> "INI %"- R;)) ;RR,"%3I;N

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33. 0 ne3ly arri,ed shor"7 %E-year-old female ,isi"ing from a remo"e region of Cen"ral 0merica 3eighs $%E l#s and presen"s "o an oral surgery clinic. .he is referred "o "he hospi"alCs dia#e"es clinic. In spi"e of daily insulin (porcine) inGec"ions for 4 mon"hs7 her glycosyla"ed 8#01c is 14U (normal *U)7 and she has a high "i"er of an"i#odies "o insulin. -he clinic physician 3ill mos" likely conclude "ha"@ 0. she mus" #e pu" on a lo3 car#ohydra"e die" immedia"ely. B. her car#ohydra"e me"a#olism 3as no" con"rolled for "he las" 3-mon"hs. C. her immune response "o porcine insulin has made her hyperglycemic. +. she mus" #e pu" on cloned human insulin "o #ypass "he immuni"y "o "he porcine insulin. > 1. all of "he a#o,e. Related st*dy 1*estions 91: ?hy is glycosylation of 2+%1c of G812V indicative of hy&erglycemia and &oor management of dietary gl*cose@ 1.0 92: ,4&lain why dia+etes is referred to as Sstarvation in the &resence of &lenty!T 1.1 93: ,4&lain how ty&e 1 and 2 dia+etes mellit*s are similar and dissimilar@ 1.2 9.: ?hy is *se of animal ins*lin for treatment of dia+etic &atients &ro+lematical whereas h*man ins*lin is not@ 1.3 95: ?hy is molec*larly cloned h*man ins*lin &referred for treatment of dia+etes@ 1.. 34. 6hich of "he follo3ing an"i#io"ics 3ould mos" likely #e adminis"ered "o "rea" an oral cancer #y specifically inhi#i"ing "he comple5 enDyme reac"ion@ dO!P d-!P9 0. 0c"inomycin + > B. !e"ho"re5a"e C. Puromycin +. -e"racycline 1. -rime"hoprim Related st*dy 1*estions 91: ?hat meta+olic en/yme or &rocess does each of the listed anti+iotics inhi+it@ 1.5 92: ?hat is methotre4ateA what other dr*gs resem+le methotre4ate and are folate antagonists@ ?hy m*st the &atient +e inJected with tetrahydrofolate within 15 min*tes after administration@ 1.D 93: ?hat +iochemical &rocess'es( do %ctinomycin $# &*romycin# tetracycline# and trimetho&rim inhi+it@ 1.E 9.: ?hich +odily cells wo*ld +e most affected +y methotre4ate# in addition to the cancer cells@ 1.F 95: ?hich of the listed anti+iotics are effective in &ro5aryotes# which are effective in e*5aryotes@ 1.G N<3RI3II;N N<3RI,N3)-6IN,R%") 3%. 6hich of "he follo3ing B-comple5 ,i"amins should NOT #e adminis"ered "o correc" "he respec"i,e deficiency disease9 0. B1 "hiamine @ #eri#eri > B. B$ ri#ofla,in @ megalo#las"ic anemia B. B3 niacin @ pellagra C. B* pyrido5ine @ neurologic disease +. B1$ co#alamin @ pernicious anemia Related st*dy 1*estions 91: ;f the listed vitamins# which is a coen/yme# which is inactive *ntil com+ined with other molec*le's(@ 150 92: ?hich vitamin's( is involved in o4idation8red*ction reactionsA in 18car+on transfers# in 28car+on transfers@ 151 93: ?hich are water sol*+le vitamins# which are fat sol*+le vitamins@ 152 9.: ?hat is at least one maJor characteristic of each deficiency disease@ 153 3*. +ie"ary deficiency of ,i"amin B* significan"ly affec"s "he me"a#olism of@ > 0. amino acids #y decreasing "ransamina"ion reac"ions. B. nucleic acids #y increasing syn"hesis. C. fa""y acids #y decreasing "heir ac"i,a"ion. +. car#ohydra"es #y increasing glucosamine syn"hesis. Related st*dy 1*estions 91: ;f the three formsH &yrido4ine# &yrido4al# and &yrido4amine# which is the maJor form of BD in the diet# which is the active form of the vitamin# and which form of BD or corres&onding &hos&hates are water or li&id sol*+le@15. 92: ?hich form is *s*ally involved in a )chiff +ase intermediate that can yield an amination-deamination# decar+o4ylation# or dehydration reaction@155

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93: ?hat en/yme reaction# *sing BD as cofactor# is the first ste& in the synthesis# cata+olism# and interconversion of amino acids@15D 3F. 6hich of "he follo3ing me"a#olic processesAcompounds 3ould #e nega"i,ely affec"ed in copper and iron deficiency anemia9 > 0. o5ida"i,e phosphoryla"ion7 o5ygen "ranspor"7 and myoglo#in B. glycolysis7 glycogenesis7 and respira"ory cy"ochromesAnonheme Be. C. lipogenesis7 ke"ogenesis7 and "ransferrin +. o5ida"i,e phosphoryla"ion7 "ricar#o5ylic acid cycle7 and ceruloplasmin Related st*dy 1*estions 91: ?hat trace metal n*trients are essential for res&iratory trans&ort chain en/ymes# ade1*ate hematocrit for o4ygen trans&ort# and myoglo+in retention of o4ygen in m*scle@15E 92: %ltho*gh a m*scle &rotein for iron storage# the traces of ser*m ferritin level is GGV s&ecific for which anemia@ 15F 93: ?hich &lasma co&&er8carrying &rotein scavenges s*&ero4ide and other o4ygen free radicals that damage &lasma &roteins 'incl*ding hemoglo+in( and is defective in ?ilsonRs disease@ 15G 9.: ?hat effect does co&&er deficiency anemia have on iron trans&ort# on methemoglo+in level and on the synthesis of two im&ortant connective tiss*e &roteinsA what 5inds of anemia are associated with co&&er and iron deficiencies@ 1D0 R,W<IR,6,N3) 3'. Inade4ua"e die"ary in"ake of essen"ial amino acids can lead "o me"a#olic dis"ur#ances such as@ > 0. nega"i,e ni"rogen #alance B. posi"i,e ni"rogen #alance C. e5cessi,e pro"ein syn"hesis +. increased #lood ,olume 1. increased lipogenesis and glycogenesis Related st*dy 1*estions 91: ?hy are eight of the 20 amino acids incor&orated into &roteins essential or indis&ensa+le to the +odyA identify them@ 1D1 92: ?hat is nitrogen +alanceA why does &rotein meta+olism acco*nt for most +iochemically *sa+le nitrogen in the +ody@ 1D2 93: ?hat is the +est so*rce of &rotein for h*mans# i!e!# has o&timal amino acid ratios# com&lete digesti+ility# a+sor&tion# and *tili/ation@1D3 9.: If dietary methionine s*ddenly dro&s to 50V of the minimal recommended daily allowance 'R$%(# why does &rotein synthesis in all tiss*es decrease +y a&&ro4imately the same &ercentage *ntil methionine inta5e increases to the R$%@ 1D. 95: $*ring essential amino acid deficiency# why does the +ody +egin to lose essential nitrogen from its amino acids and &roteins@1D5 0<N 3I;N) 3 . -3o key enDymes7 d-!P syn"hase and deo5yri#onucleoside diphospha"e reduc"ase7 are in,ol,ed in syn"hesis of deo5yri#onucleo"ides from "heir corresponding ri#onucleo"ides. 6hich coenDyme lis"ed #elo3 is nei"her "he reac"an" nor produc" form of "he coenDymes in,ol,ed in "hose reac"ions9 0. )%71E-me"hylene "e"rahydrofola"e B. dihydrofola"e C. )0+P8 > +. )0+8$ Related st*dy 1*estions 91: In h*mans# all $N% n*cleotides are synthesi/ed from their RN% co*nter&arts via two 5ey en/yme reactions# one red*ces ri+ose to deo4yri+ose# the other methylates *racil to thymine# o*tline +oth reactions! 1DD 92: 0or the conversion of d<6P to d36P# o*tline the two essential ancillary reactions that 5ee& it going! 1DE 93: Both ancillary reactions *tili/e coen/ymes that are vitamin8de&endent! ?hich vitamins are they@ 1DF 9.: onversion of ri+ose to deo4yri+ose involves a hydride transfer! ?hat is a hydrideA which vitamin com&onent of the coen/yme involved transfers the hydride to 2 of ri+ose@1DG 95: d36P synthesis involves a 18car+on fragment transfer *sing folate! ?hat are the two other carriers of 18car+on fragments fo*nd in meta+olism# +oth of which &artici&ate in n*cleic acid syntheses@ 1E0 4E. 6hich of "he follo3ing is INCORRECT a#ou" Dinc9 0. Tinc is in,ol,ed in car#ohydra"e and energy me"a#olism. B Tinc is in,ol,ed in syn"hesis of me"allo"hioneine7 3hich #inds Tn for i"s a#sorp"ion in "he gu". > C. Tinc is a di,alen" hea,y me"al "ha" is as "o5ic as lead.

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$! +. Tinc7 in increased oral doses7 in"erferes 3i"h copper a#sorp"ion and deficiency. 1. Tinc deficiency affec"s gro3"h7 impairs of "as"e and smell7 and delays 3ound healing.

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Related st*dy 1*estions 91: ?hich car+ohydrate meta+olism en/ymes re1*ire /inc# i!e!# their holoen/yme is an active /inc metalloen/yme# +*t their nonmetalloen/yme a&oen/yme is inactive@1E1 92: ?hat is metallothioneine &rotein# where is it synthesi/ed# and what is its role in trace metal a+sor&tion@ 1E2 93: ?hat is the connection of ?ilsonRs disease to co&&er and /inc meta+olism and li5ely effect on en/ymes re1*iring them@ 1E3 IN3,R$I) IP"IN%R> %N$ "INI %"- R;)) ;RR,"%3I;N 41. 6hich ,i"amin is INCORRECTLY paired 3i"h "he conse4uence(s) of i"s deficiency9 0. ,i"amin + @ ricke"s B. ,i"amin C @ scur,y C. niacin @ derma"i"is7 diarrhea and demen"ia > +. "hiamine @ polycy"hemia 1. fola"e @ anemia Related st*dy 1*estions 91: ;f the vitamins listed# which tiss*e's( is *s*ally affectedA what signs and sym&toms are o+served +y clinicians d*ring e4amination of &atients with the listed deficiency diseasesA what deficiency disease corrects the "NCO##ECT answer &air@1E. 92: ?hich of the vitamins listed are water sol*+leA which are li&id sol*+le@ 1E5 93: ?hat foods are *s*ally recommended to restore health# if that is &ossi+le@ 1ED 4$. 0 den"is" recommends pos"ponemen" of oral surgery upon learning "he pa"ien" has leukemia and is scheduled for fola"e an"agonis" (me"ho"re5a"e) "rea"men" in "3o days. -he pos"ponemen" recogniDes "he complica"ions of an"ifola"e #iochemis"ry and i"s effec"s on pos" opera"i,e "issue healing. 6hich is INCORRECT a#ou" fola"e an"agonis"s9 -heyS 0. indirec"ly #lock "he syn"hesis of d-!P from dO!P #y "hymidyla"e syn"hase. B. inhi#i" dihydrofola"e reduc"ase. C. mimic "he isoallo5aDine ring of "e"rahydrofola"e. > +. #lock hydride "ransfer #y nucleoside diphospha"e reduc"ase. 1. "rea" #lood leukemia disorders. Related st*dy 1*estions 91: ?hy does methotre4ate indirectly inhi+it the thymidylate synthase and also indirectly inhi+it all other tetrahydrofolate8 de&endent meta+olism@1EE 92: ?hat gl*cose &athway s*&&lies N%$P2 re1*ired to regenerate dihydrofolate '02 2( to tetrahydrofolate '02.(@1EF 93: % &art of $N% synthesis is serine8de&endent! ?hat &art of serineRs str*ct*re s*&&lies the 18car+on fragment s*+se1*ently added to N5 in the isoallo4a/ine ring of folate@1EG 9.: N5#N108methylene tetrahydrofolate is converted to what folate form +y thymidylate synthase that has no other meta+olic *tility# i!e!# is a dead8end meta+olite@1F0

Biochemistry in other D1 Courses (13)

;NN, 3IP, 3I))<,) );03 3I))<, 43. Iden"ify "he INCORRECT s"a"emen" a#ou" collagen@ PCollagen is an impor"an" componen" of e5"racellular ma"ri5 (1!C) in connec"i,e "issues #ecause "he S Q 0. repea"ed Hly-(-V "ripep"ide in all "hree su#uni" chains permi"s "he re4uired "er"iary and 4ua"ernary s"ruc"ure for collagenCs s"ruc"ural role.Q B. "er"iary s"ruc"ure of each of "he "riple s"rands coils in"o a lef"-handed7 -helical conforma"ion.Q C. "riple-s"randed7 cross-linked7 righ"-handed super helical 4ua"ernary s"ruc"ure forms s"rong7 s"a#le7 rigid7 rod-like molecules "ha" aggrega"e in"o fi#rils.Q +. hydro5yproline on "he surface can #e linked "o ,arious car#ohydra"es. P > 1. "riple s"randed su#uni"s are also s"a#iliDed #y a clus"er of cys"ine cross links.Q Related st*dy 1*estions '''' 1ndno"es edi"ing s"ops here '''' 91: ?hat is e4tracell*lar matri4A why is it needed in connective tiss*e@ 1F1 92: ?hat are the chemical feat*res of collagenRs re&eated tri&e&tide Gly8X8> that are res&onsi+le for collagenRs *ni1*e 2Y# 3Y# .Y str*ct*res and role in connective tiss*e@1F2

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$! 93: ?hat intermolec*lar arrangement acco*nts for the +anded a&&earance of fi+rillar collagen@ 1F3 2%R$ 3I))<, 44. 8yaluronic acid7 heparin7 and chondroi"in-7 derma"an-7 heparin-7 and kera"in-sulfa"es are found in@ 0. an"icoagulan"s > B. pro"eoglycans C. hormones +. fi#ronec"ins 1. simple lipopro"eins

Page 1. of 35

Related st*dy 1*estions 91: ?hat are sim&le8 and derived8s*garsA which are fo*nd in com&le4 car+ohydrates@ ?hich s*gar is in RN% vers*s $N%@ 1F. 92: ?hat are the different chemical forms of glycoconJ*gatesA which are classified as glycoli&ids@ 1F5 93: ?hich f*nctional gro*&s are added to gl*cose# galactose# mannose# gl*c*ronic acid# etc!# that give rise to the car+ohydrates and their molec*lar categories listed in the 1*estion!1FD 4%. 6hich proper"y a#ou" enamel is INCORRECT in comparison "o o"her mineraliDed "issues 3i"hin "he #ody9 0. 1namel is "he hardes". B. 1namel con"ains mos"ly hydro5yapa"i"e. > C. 1namel con"ains amelogenin pro"eins. +. 1namel con"ains he5agonal rod crys"als "ha" are larger and more firmly packed. Related st*dy 1*estions 91: ?hat are the seven systems that all crystalline minerals are categori/ed intoA calci*m &hos&hate 'em&irical form*laH a10'P;.(D';2(2( a mem+er of which system@ ?hat is its common mineral name@1FE 92: Is this mineral harder than calci*m &hos&hate mineral fo*nd in +one@ ?hat scale is *sed to determine-classify mineral hardness@1FF 93: ?hat are amelogenins and where are they fo*nd in hard tiss*e@ ?hat feat*res ma5e them s*ited for their role in minerali/ation@1FG 9.: ?hich calci*m &hos&hate e4changes a fl*oride ion for a hydro4yl ion# and what &ro&erty is enhanced +y fl*oride@ 1G0 6,6BR%N,) )3R< 3<R, 4*. 6hich of "he follo3ing compounds are #onded "o phospha"e in diacyl phosphoglycerol "o comple"e "he reper"oire of phospholipids found in #ody mem#ranes9 0. <nly choline B. Be"aine and sphingosine C. Choline7 #e"aine7 and sphingosine +. Choline7 serine7 and sphingosine > 1. Choline7 serine7 e"hanolamine7 inosi"ol Related st*dy 1*estions 91: ?hat are diacyl&hos&hoglycerol# &hos&hatidyl choline# &hos&hotidyl serine# &hos&hatidyl ethanolamine# and &hos&hatidyl inositol@1G1 92: ?hich amino acid is converted to ethanolamine# choline# and +etaineA which s*lf*r8containing amino acid is salvaged in which +etaine is involved@1G2 93: ?hat f*nction's( do &hos&hatidyl li&ids serve in the mem+ranes or the cytosol@ 1G3 N,RP;<) )>)3,6 G,N,R%" PR;P,R3I,) 4F. -he enDyme ,NI-,E "o ner,e "issue is@ > 0. glu"ama"e decar#o5ylase B. orni"hine decar#o5ylase C. "ryp"ophan decar#o5ylase +. glycine decar#o5ylase 1. aspar"a"e decar#o5ylase Related st*dy 1*estions 91: ?hich amino acid meta+olism en/yme listed is tiss*e8s&ecific for nerve tiss*e@ 1G. 92: ?hat is the amino acid &rod*ct of each listed en/yme and what vitamin-coen/yme is involved@ 1G5 93: G%B% is an a++reviation for what amine derived from gl*tamate@ 1GD

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$! 9.: ?here is G%B% synthesi/ed and stored and what is G%B% *sed for@1GE 6<) ", )B,",3%" 4'. 6hich comparison #e"3een hemoglo#in and myoglo#in of skele"al muscle is INCORRECT9 0. !yoglo#in is more o5ygen sa"ura"ed a" lo3er P<$ le,els "han hemoglo#in. B. Bo"h are inside cells. C. Bo"h con"ain Be$= com#ined 3i"h porphyrin. > +. 1ach molecule is composed of differen" su#uni" pro"eins. 1. 8emoglo#in "ranspor"s o5ygen 3hile myoglo#in s"ores o5ygen.

Page 15 of 35

Related st*dy 1*estions 91: ?hat are myoglo+in and hemoglo+in# what tiss*es contain them# what are their f*nctions@ 1GF 92: ?hat is the &or&hyrin familyA where are they synthesi/ed@ 1GG 93: ?hat divalent metal cation does &or&hyrin +ind in h*mans and what common name is given to the metallo&or&hyrin@ 200 9.: ?hat is the significance of the myoglo+in ;2 sat*ration c*rve +eing hy&er+olic +*t hemoglo+inRs is sigmoidal@ 201 IR <"%3I;N ;%G<"%3I;N 4 . -he coenDyme for car#o5yla"ion of glu"amyl residues re4uired for syn"hesis of Ca$= chela"ion clus"ers near "he )"erminus of Dymogens II7 I(7 (7 and I( con"ains 3hich ,i"amin9 0. pan"o"henic acid B. B1 > C. L +. lipoic acid 1. #io"in Related st*dy 1*estions 91: ?hat chemical &ro&erties does the 8car+o4ygl*tamyl side8chain have that ena+les it to act as a divalent metal cation chelation gro*&@202 92: ?hat f*nction res*lts from the cl*ster of 8gl*tamates near the N8termin*s of s&ecific coag*lation /ymogens@ ?hy those fo*r factors and not some of the others@203 93: ?hen tra*ma disr*&ts endothelial cells lining +lood vessels there+y e4&osing &hos&holi&ids# factors# II# IX# X# and XI concentrate on the &hos&holi&ids e4&osed at the tra*ma siteA what en/ymological &rinci&les and effects on reaction rates are demonstrated@20. 9.: ?hat role's( does 8car+o4ygl*tamyl resid*es in +one osteocalcin s*ggest for a role's( of vitamin B in osteo&orosis@ 205 95: an yo* thin5 of an e4am&le of car+o4ylations that are on the , , , and car+ons of other meta+olites@ ?hich of these might act as chelators@20D R,)PIR%3I;N G%) ,X 2%NG, %N$ 3R%N)P;R3 %E. 0ll of "he follo3ing are "rue for o5ygen carriage #iochemis"ry EXCEPT one. 6hich is "he EXCEPTION 9 0. Binding of $73?#isphosphoglycera"e "o hemoglo#in lo3ers <$ affini"y for hemoglo#in in capillaries. B. 0ssocia"ion of 8= "o hemoglo#in decreases i"s affini"y for o5ygen. C. C<$ is a nega"i,e allos"eric effec"or "ha" promo"es <$ dissocia"ion from 8#<$ 3hen i" forms car#aminohemoglo#in. > +. +eo5yhemoglo#in (reduced) has a lo3er pLa "han o5yhemoglo#in. Related st*dy 1*estions 91: ?hat &athway in the red +lood cell does 2#38BPG arise fromA how does the nearly molar e1*ivalent ratio of 2#38BPGH deo4yhemoglo+in chains affect ;2 +inding@20E 92: ?hich has a greater affinity for 2IH deo4y2+ or 2+;2@20F 93: ,4&lain BohrRs o+servation that increasing the ;2 in +lood released o4ygen from it! ?hat other molec*le is involved@20G 93: ?here on the 8glo+in chain of 2+ does ;2 react to form car+amino 2+A how m*ch ;2 is trans&orted as ;2# as 2 ;3C# as car+amino 2+ in RB # in &lasma@210 ,;0Hgcl

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$!

Page 1D of 35

National Board art ! Examination Specifications (2002)

Building Blocks of Life Course (41)
I. Physical-Chemical Principles (3) %! Basic &rinci&les '2( B! %&&lied &rinci&les '1( II. Biological Compounds ( ) %! )*gars and car+ohydrates '1( B! %mino %cids and &roteins '2 ( ! "i&ids '1( $! N*cleic %cids and meta+olism '1( ,! Interdisci&linary clinical-cross correlation '.( III. !e"a#olism (13) %! Bioenergetics '1( B! ,n/ymology '1( ! ata+olism '2( $! %na+olism '2( ,! Reg*lation '2( 0! Interdisci&linary clinical-cross correlation '5(

--- of $% --Biochemis"ry in o"her +1 Courses (13)

&. Connec"i,e -issues (') 'in Basic Tissues( %! )oft tiss*e '2( B! 2ard 3iss*e-calcification '3( ! Interdisci&linary and clinical-cross correlation '3( &I. !em#ranes (4) 'most in Cell Organelles ( %! )tr*ct*re '1( B! 0*nction '1( ! Interdisci&linary clinical-cross correlation '2( &II. )er,ous .ys"em ( ) 'most in Organ Systems( %! General &ro&erties '2( B! entral nervo*s system '1( ! %*tonomic nervo*s system '1( $! )omatic nervo*s system 'with refle4es( '2( ,! )&ecial senses '1( 0! Interdisci&linary and clinical-cross correlation '2( &III. !uscle (*) '( %! )5eletal '2( meta+olism and myoglo+in B! )mooth '1( ! ardiac '1( $! Interdisci&linary and clinical-cross correlation '3( I(. Circula"ion ( ) 'in Basic Tissues-clotting-gas trans&ort %! 0l*id content and dynamics '2(

---$% --I&. !olecular Biology (') %! $N%-RN% and &rotein synthesis '. ( B! Genetic engineering '2( ! Interdisci&linary clinical-cross correlation '2( (I&. )u"ri"ion (') %! N*trients-minerals '3( 1! Re1*irements '1( 2! 0*nctions '2( B! Interdisci&linary and clinical-cross correlation '2(

---1* of $% ---

2003 Biochemistry Review for the National Boards Part I 2003 Gene ! "avers# Ph!$! B! oag*lation '1( ! ardiodynamics and electro&hysiology '2( ! Reg*lation '1( $! Interdisci&linary and clinical-cross correlation '3( (. /espira"ion (*) 'in Basic Tissues( %! 6echanical as&ects '1( B! Gas e4change and trans&ort '1( ! Reg*lation '1( $! Interdisci&linary and clinical-cross correlation '3( (I. /enal (*) 'see Organ Systems( %! 0*nctional anatomy '1( B! Blood flow and filtration '1( ! Rea+sor&tion and secretion '1( meta+olites $! Interdisci&linary and clinical-cross correlation '2( (II. 0cid-Base Balance (1) 'in Organ Systems(

Page 1E of 35 (III. +iges"ion (%) 'in Organ Systems( %! Ne*rom*sc*lar '1( B! )ecretions '1( en/ymes ! %+sor&tion '1( $! Reg*lation '1( ,! Interdisci&linary and clinical-cross correlation '1( (&. 1ndocrines (') 'in Organ Systems( %! Pit*itary-hy&othalam*s '1( B! Re&rod*ction '1( ! )ignaling systems '2( ins*lin-gl*cagon 7 c%6P $! Pancreas-&arathyroid '1( ,! %drenal-thyroid '1( 0! Interdisci&linary and clinical-cross correlation '2(

1)+ )<-1. ? 0ns3ers "o /ela"ed ."udy 2ues"ions

3he Biochemistry8Physiology Part I National Boards ,4amination covers 15 to&ic areas with F0 s*+to&ics in 100 1*estions listed +elow divided into the 3o&ics covered +y B*ilding Bloc5s of "ife and other $1 +asic science co*rses! Plasma &2 E!.5# altho*gh stomach '3!5(# d*oden*m 'F!0(# etc may differ! 3he strength of an acid is determined +y 'a( the strength of its conJ*gate +ase# '+( the +asic strength of the solvent# and 'c( the dielectric constant of the o&&ositely charged &articles dissolved in them# which necessarily favors dissociation! In a1*eo*s sol*tion# strong acids com&letely ioni/e 'e!g!# 2 l# +eca*se 2;2# water is a wea5 acid(# whereas wea5 acids 'acetic acid in water( ioni/e to the e4tent of the density of negative charge on the conJ*gate +ase ' 23 ;;C(! Iodoacetic acid is stronger than acetic acid +eca*se iodine on 2 ind*ctively wea5ens the acid +ond and decreases the car+o4ylate anion negative charge density# hence# &rotons dissociate more easily and are less attracted to the wea5er iodocar+o4ylate anion 'I 23 ;;C(! com&ared to the acetate ion! 3his &henomenon is called the neigh#oring group effec"! )*+stit*tion of an amino gro*& on 2 'instead of Iodine( yields glycine# the CN23I there+y ind*ctively ma5es the C ;;2 a stronger acid than the C ;;2 of acetic acid so the &Ba of former is lower than acetic acidRs! ;f those listed# only $! C ;;2# car+o4ylic acid gro*& is dissociated at &2 E!5! %! 22 methylene hydrogens# B! C;2 alcohol gro*&# ! CN23I ammoni*m# ,! &henol all are not dissociated at &2 E!5 to any significant degree# which is what the 1*estion as5ed! 2owever# strong electron withdrawing# neigh+oring gro*&s 'e!g!# in malonyl o%( may lower the &Ba s*fficiently close to &2 E!5# for the C 22C middle methylene to +e significantly ioni/ed C;; C 22C ;8 o% yielding a car+anion C;; C 2'C(C ;8 o%! In the ioni/ed /witterion 'C-I(of an amino acid# the &rotonated CN23I ammoni*m gro*& strongly attracts electron density from the ioni/ed C ;;C anion ma5ing it a wea5er conJ*gate +ase 'less electron dense(# hence the &roton dissociates more readily then an isolated car+o4ylate anion 'e!g!# as in acetate(! onversely# the electron density availa+le on the C ;; C can +e donated to the electron deficient '&ositively charged( amino gro*& there+y lessening its electron deficiency! 3he m*t*al neigh+oring gro*& effects shift the &Ba of each gro*& +y a+o*t 182 &2 *nit! 3wo# analogo*s to a &air of left and right hands! <sing 0ischer re&resentation# when several asymmetric car+on ' =( atoms are in a chain molec*le# and the end gro*&s are not identical and not asymmetric# the remaining n*m+er of stereoisomers &ossi+le is e1*al to 2'e4& n(# or 2n# where n is the n*m+er of asymmetric car+on atoms! ?hen linear s*gars cycli/e# an additional = is formed '+eca*se the 1 aldehyde reacts with the internal alcohol 'to form an intramolec*lar cyclic or internal hemiacetal# which is a new asymmetric center(! 9NoteH a hemiacetal can condense with a second mole of alcohol to form an acetal# e!g!# $8gl*cose I methanol methylC and C$Cgl*coside# same n*m+er of isomers are &ossi+le!: 0or linear aldopen"osesH 2'3( L FA for aldohe5osesH 2'.( L 1D! 0or ring8closed '2aworth &roJection( &entosesH 2'.( L 1D# for he4osesH 2'5( L 32! 0or linear ke"ohe5osesH 2'3( L F! 9 2 5etone the internal 5eto gro*& and two non identical end gro*&s leave only 3 =! 0or closed8ring he4oseH 2'.( L 1D! 9 2 5etone adds an alcohol to form an intramolec*lar cyclic or internal hemi$etal# which is asymmetric 'can form D8 and 58mem+ered rings(! 9NoteH a hemi5etal condenses with an alcohol to form a 5etal# e!g!# $8 fr*ctose I methanol CN methylC and C$Cfr*ctoside# same n*m+er of isomers &ossi+le!: 1 is the anomeric car+on of aldose s*gars! 2emiacetal formation creates a new = center# th*s two anomers are formedH and $8aldose s*gars# e!g!# linear $8gl*cose cycli/es CNcyclic $8gl*cose 'I112K( and cyclic $8gl*cose 'I1GK(# an anomeric &air with a 1H2 ratio of : forms 'I52!5K( 9Note# racemic &airs have a 1H1 ratio# they have no net o&tical rotation!: %n e&imer is a &air of s*gars that differ at only one asymmetric car+on# e!g!# $8gl*cose and $8mannose have o&&osite config*rations at 2 and gl*cose and galactose differ only at .! In 0ischer &roJection# the +ottom most = center of all s*gars relates to 2 of glyceraldehyde and defines the s*gar as $ or "! 93he sole 2= of glyceraldehyde 'sim&lest aldose s*gar# also named glyceric aldehyde( e4its in two stereo isomer formsH 2C;2 'on right side( defines $8form# 'left( 2;C 2 defines the "8form! %ll the $8aldose s*gars '.8# 58# D8# E8 car+ons( are considered derivatives of $8glyceraldehyde +y adding one 22;2 at a timeA all "8s*gars are mirror image molec*les and are derived from "8glyceraldehyde!: ,ach = center is asymmetric and rotates &olari/ed light left or right de&ending *&on which one of the con fig*rational isomers is +eing meas*red# if +oth are &resent# racemate &air '1H1 ratio(# no net rotation occ*rs '*nless another str*ct*ral infl*ence shifts the ratio higher or lower(! Reference glyceraldehydeH $8glyceraldehyde rotates &olari/ed light rightward 'de4tro# 9:$ L I13!5K( and "8 glyceraldehyde rotates &olari/ed light leftward 'levo# 9:$ L C13!5K(! 6ore com&le4 s*gars# aldo&entoses and aldohe4oses may give different rotations de&ending *&on the s*mmation of all the = ' C or I ( rotations! 9 NoteH de4tro and levo are also notated as# d and l# res&ectively# e!g!# l8lactic acid or d8lactic acid! No# the S$T and S"T &refi4es have no relationshi& to the direction of o&tical rotation! $ and " sim&ly designate s&atial relationshi& of the gro*&s on the &en*ltimate = of the com&o*nd in reference to the $ and " forms of glyceraldehyde!

2 3

D E

10

11

12

13

1.

15

1D

1E

In a meso stereoisomer# two halves of the molec*le are mirror images! )*ch a diastereomer is *ni1*ely o&tically inactiveA the mirror halves constit*te a racemic mi4t*re# th*s the o&tical rotation of one halve is reversed 'cancelled( +y the second half! 3he sim&lest e4am&le of a meso vers*s diastereoisomers com&arison is tartaric acid '2#38dihydro4y81#.8s*ccinic acid(# which has two middle =s! In 0ischer &roJection# the to& and +ottom car+on are identical ' ;;2(! 3he config*ration of the C;2 gro*& on 2 and 3 areH left8right 'I(# right8left 'II(# and left8left 'same as right8right(# res&ectively! 0orm I is levo8 or l8 or $8tartaricA form II is de4tro8 d8 or "8tartaric# and form III is meso tartaric or m8tartaric! "iving systems o&erate at constant tem&erat*re 'isothermally( and constant &ress*re 'iso+arically( and cannot convert heat energy directly into wor5 as an engine does! 1n"halpy '8( is the heat energy cons*med or released in a system at constant &ress*re! 1n"ropy '.( is the energy that is *navaila+le to do wor5 and is lost to disorderliness of a system# entro&y increases as tem&erat*re increases! Bree energy 'H( is the energy of a system that is availa+le to do wor5# at constant tem&erat*re and &ress*re# so it is *sef*l in st*dying the +ioenergetics of living systems! 0c"i,a"ion energy '1ac"( is that amo*nt of energy molec*les most &ossess +efore they are ca&a+le of reacting! Po"en"ial 1nergy is the energy of a molec*le d*e to its &osition! ;nly the change ' ( in 87 .# 1ac" is meas*ra+le and has &ractical significance! 9Potential energy is converted to Line"ic energy while the molec*le is moving from its original &osition to another! %s a +all rises in the earthRs gravitational field# 5inetic energy is converted to &otential energy C ma4imal at the instant the +all is s*s&ended C+efore descendingA while descending# the &otential energy is converted to 5inetic energy 'motion:! 3he more random disorder 'the higher the entro&y# .( in a system# the less energy is availa+le to do wor5! "ive systems e4&end energy to organi/e molec*les into highly organi/ed f*nctional str*ct*res and systems 'mem+ranes# filaments# organelles# $N% se1*ences of s&ecific order# etc!(! Reversi+le reactions rarely reach e1*ili+ri*m in vivo so entro&y is 5e&t lower than at death# where*&on all e1*ili+ri*m reactions tend towards e1*ili+ri*m# and entro&y is ma4imi/ed! 3he energy *sed to create orderly $N% se1*ences is released as $N% is hydroly/ed to disordered n*cleotides moving with Brownian motion in sol*tion! 3he &ro+a+ility of the n*cleosides randomly reorgani/ing +ac5 into the original ordered se1*ence is highly im&ro+a+le# the energy lost to entro&y &revents it! )&ontaneo*s regeneration of life from thermodynamic death is virt*ally im&ro+a+le# altho*gh# theoretically it is not entirely im&ossi+le! %ssem+ly of monomer *nits into &olymeric se1*ences increases orderliness and decreases entro&y# hence glycogenesis# 0% synthesis# and the synthesis of &roteins# $N% and RN% have lower entro&y than their corres&onding monomers! %ssem+ly of monomers decreases entro&y# disassem+ly of &olymers increases entro&y! 3herefore# degradation of glycogen# fatty acids# &roteins# $N% and RN% to gl*cose# acetyl o%# amino acids# deo4yri+on*cleotides and ri+on*cleotides# res&ectively# decreases orderliness and increases disorderliness# so entro&y increases d*ring the &rocesses of glycogenolysis# 8o4idation# &roteolysis# and hydrolysis# res&ectively! N*cleo&hilic attac5 +y an alcoholic ;@ 'or# amino N@ # merca&to )@ ( from a%ove or %elow a planar& trigonal# electron deficient C of an aldehyde 'RCC2L;# or 5etone RRZC L;( forms a tetrahedral &rod*ct! 0o*r different chemical gro*&s are +onded to the anomeric C in the hemiacetal so it an asymmetric ' =(! If attac5 from +elow or a+ove is e1*ally &ro+a+le 'no str*ct*ral restraints( then a &*re 1H1 ratio of enantiomeric isomer &rod*cts forms! In aldoses s*ch as gl*cose# the 5C W2 attac5s intramolec*larly yielding a sta+le D8mem+ered ring '2aworth diagram( held +y a hemiacetal lin5age! C1 is +onded to 'our different chemical gro*&s# is asymmetric ' =(! Ignoring the reaction mechanism# the aldehydic L; +ecomes 1C;2 in the hemiacetal gro*&! %ttac5 from a+ove yields the 8anomeric config*ration '8;2( *nder the ring# in 2aworth &roJection(A attac5 from a+ove yields the 8;2 anomeric config*ration! Refer to st*dy answer to W*estion 291:! In forming the intramolec*lar ring# the aldoses are e4&ected to gain an additional asymmetric car+on 'o&tically active( in the res*lting hemiacetals and hemi5etals! 3h*s# aldose $8gl*cose '. =( ring closes CN $gl*cose '5 =( I $gl*cose '5 =(A and 5etose $8fr*ctose '3 =( CN $fr*ctose '. =( I $fr*ctose '. =(! $8ri+ose '3 =( CN /8$8ri+ose! 3he &rocess of m*tarotation o&ens and closes the ring of s*gars again and again! If freshly dissolved &*re 'or (# is o+served thro*gh a &olarimeter# initial degrees of &olari/ed light rotation slowly changes *ntil an *nchanging reading is achieved# i!e!# an e1*ili+ri*m mi4t*re of / anomers is &resent! 92owever# in 8gl*cose# the ;2 gro*&s are crowded together 'a4ial# flag&ole interactions( a+ove and +elow the ringA in the 8anomer# these +*l5y gro*&s &oint o*tward in the &lane of the ring 'e1*atorial( so steric crowding is minimal# the 8gl*cose is more sta+le 'lower free energy(! 0or gl*cose# a &*re 1H1# /, racemate mi4t*re is not formed# instead a 1H2 '/( ratio is esta+lished at e1*ili+ri*m!: losed8ring hemiacetals and hemi5etals react with hydro4yl ions in sol*tion# at &hysiological &2# there+y reverting +ac5 to the aldehydic 'C 2;( or 5etone ' L;( ring8o&en formA th*s# ;2C ions cataly/e the m*tarotation rate *&wards of a+o*t .0#0008foldU In contrast# ace"als and ke"als are very sta+le to ;2C ions '+eca*se the anomeric car+on is lin5ed to an C;R gro*& not an C;2(! 2ence# disaccharides and &olymers with 8acetal-5etal lin5ages are very sta+le 'donRt hydroly/e readily and are e4cellent for storage of gl*cose f*el 'glycogen# starch(! )imilarly# acetal lin5ages 'cell*lose in wood(

1F

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21

22

23

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25

are sta+le and strong &olymeric molec*les! 9NoteH in a &olymer 'starch# glycogen# or cell*lose(# the end gl*cose resid*e has a free hemiacetal or 5etal gro*& and can m*tarotate# while all the other gl*cose resid*es in the &olymer will not!: ommon ta+le s*gar# sucrose is an acetal-5etal com+inationH gl*cose8 1C 28fr*ctoseA +oth anomeric car+ons are in the one Joining lin5age# this disaccharide doesnRt m*tarotateU >es# the n*cleoside com&onents contain N$Cri+ose in an N-acetal lin5age to adenine# cytosine# g*anine# or *racil in RN%# and N$Cdeo4yri+osides of adenine# cytosine# g*anine# or thymine in $N%! $irect str*ct*ral corres&ondence of "8amino acids to "8glyceraldehyde! )ome +acteria and anti+iotics *se $8amino acids! )ee Big $.3 in Baynes and $ominic/a5# (edical Biochemistry# for a list of str*ct*res# then Big. $.% for those that are acidic or +asic according to the side8chain f*nctional gro*&! ?hich amino acids have acidic car+o4yl C ;;2A +asic amine CN22A imida/ole 'histidine HN8ring(# g*anidino 'arg(! %lso see Big $.F for conJ*gate acid-+ase forms and &Ba val*es!( %mino acids are am&hoteric molec*les# they have at least one +asic and acidic gro*&! <&on dissolving glycine in water# for e4am&le# the 8N22 amino gro*& '&Ba G!F( +ecomes &rotonated to CN23I ammoni*mA the ;;2 '&Ba 2!.( ioni/es to C ;;C A +oth ionic gro*&s define a /witterion 'do*+le ion( with net charge '0( at &2E!5! 9 : 0or the %s& and Gl*# the side8chain C ;;2 '&Ba 3!G( ioni/es yielding a net 'C1( charge at &2 E!5! 0or lys# his# an arg# these +ecome &rotonated yielding a net 'I1( charge at &2 E!5! %t &2 2 all amino acid car+o4yl gro*&s are ;;2# all +asic gro*&s are &rotonated! $e&ending on the &Ba of each gro*&# as hydro4yl ions are added# the &2 changes from 2 to 12# each acid and +ase gro*& is titrated in order of their increasing &Ba val*e! %t &2 12# all acids gro*&s are ;;C and all &rotonated +ases are now in free8+ase form 'e!g!# C N22(! %t &2 2# most amino acids move to the anode# each will not move when the &2 e1*als their isoelectric &oint# as &2 +ecomes increasingly +asic# the amino acids will +egin to move to the cathode# res&ectively! )ee Big. $.* in Baynes for the titration c*rve descri+ing the &rogression of cation to /witterion to anion of alanine# as an e4am&le of a sim&le amino acid! )ome amino acids have a third acid or +asic gro*& on their side chain! 3heir titration c*rves are slightly more com&le4# +*t managea+le(! 9,lectro&horetic migration of the 20 amino acids is &28de&endent on either side of their &I isoelectric &ointH 'a( sim&le amino acidsH asn 5!.1# gln 5!D5# ser 5!DF# met 5!E5# gly 5!GE# val 5!GE# le* 5!GF# &he 5!GF# ala D!02# ile D!02 '2 =(# thr D!53A '+( acidic amino acidsH as& 2!GE# gl* 3!22A 'c( +asic amino acidsH lys# G!E.# arg 10!EDA 'd( other ioni/a+le side chain gro*&sH cys 5!0F# tyr 5!D5# tr& 5!FF# &ro D!10# his E!5F! %gain# lower acidity moves them to the ') anode# higher to the 'I( cathode! 3he &I is the average of the 2 or 3 &Ba val*es! 3he 'a( gro*& give di&olar /witterions +etween &2 3 and F and +arely migrate e4ce&t at their isoelectric &oint '/ero net charge# no movement(! %t &hysiological &2# the net charge of free amino acids and when in a &oly&e&tide is given for referenceH %t &2 E!5# free amino acids# net charge '0(H asn# gln# ser# met# gly# val# le*# &he# ala# ile# thr# his# cys# tyr# tr&# &ro two '1(H as&# gl* two 'I1(H lys and arg! %t &2 E!5# within a &oly&e&tide# /ero charge '0(H asn# gln# ser# met# gly# val# le*# &he# ala# ile# thr cys# tyr# tr&# &ro '1(H as&# gl*# his 'I1(H lys# arg! : 3he 20 amino acids given in footnote 2F are always incor&orated into &roteins d*ring synthesis of their &rimary str*ct*re! )&ecific amino acids '13( *ndergo &osttranslational modification in certain &roteins 'see 0ig 2!3( so the n*m+er and variety of s*ch modifications is com&le4! 6ethylations 'lys# arg(# &hos&horylations 'ser# thr# tyr(# car+o4ylations 'gl*(# dis*lfide o4idations 'cys( amidations 'as&# asn# gl*# gln(# and hydro4ylations '&ro &he# tyr( are some commonly enco*ntered &ost translational modifications! )ome &athways create-cons*me other amino acids# e!g!# ornithine# citr*lline# argininos*ccinate '*rea cycle(# homocysteine 'from )8adenosyl methionine(# 8alanine '&yrimidine cata+olism(# G%B% 'from gl*(# and many others! % very com&le4 s*+Ject! )ee Big $.1$ in Baynes for fo*r maJor sets of side8chain interactions! 3he 3$8folding of &roteins with more than a+o*t 200 amino acids consists of several smaller folded *nits designated as domains s*ch as al&ha8heli4# &leated8sheets# random coil# and others! 3hese and other 3$ tertiary '3K( str*ct*res of a &rotein are sta+ili/ed +y side8 chain f*nctional gro*&sH covalent s*lfhydryl +onds 'cys8)[)8cys(# hydrogen +onds ';C2 IIIN(# salt +ridges 'C ;;C III2=N22C( and hydro&ho+ic interactions 'e!g!# &he8&he# le*cine /i&&ers# /inc fingers# etc!(! ')ee Baynes h 2 *nder -er"iary ."ruc"ure# 2ua"ernary s"ruc"ure headings(! )olvent effects# infl*enced +y salts# and other s*+stances can +e im&ortant! )ome or all of these &ro&erties can +e involved in 1*aternary str*ct*re# e!g!# tetrameric hemoglo+in ' 22( 3he non&olar hydro&ho+ic amino acids 'gly# ala# le*# ile# val! &he# met# etc!( associate in hydro&ho+ic &oc5ets inside the &rotein# water is e4cl*ded into the s*rro*nding sol*tion! 3he &olar hydro&hilic and acid +ase side8chain amino acids 'are *s*ally on the s*rface in contact with water# also anions and cations of a wide variety! )ome domains are folded to e4&ose

2D 2E

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a hydro&ho+ic s*rface 'e!g!# mem+rane &roteins# le*cine /i&&ers(! Glyco8 and li&o&roteins can have s*gars and li&ids +onded to the side8chains of ser# thr# try# hy&# lys# etc!(! In Baynes# see 0ig 1F!2A $4!1# 2# 3# .A $*!.# D# 12! lassificationH 'a( Ba""y acids are long chain hydrocar+ons with a terminal car+o4ylate 'not fo*nd free +*t always in ester lin5age with tri&le alcohol glycerol +eca*se free fatty acids are soa&s and wo*ld dissolve cell mem+ranes and organelles( or are a in thioester lin5age with o%# QactivatedR fatty acid# '+ ) "riglycerols 'f*el energy( are most a+*ndant# 9also wa4esH fatty acid esters of alcohols other than glycerol:# 'c( phospholipids 'mem+rane str*ct*resA derivatives of glycerol &hos&hate# diesters most a+*ndant# second# derivatives of s&hingosine &hos&hate# which contain an esterified fatty acid '0%( and a nitrogeno*s +ase 'choline# ethanolamine( which may also +e esterified with a &hos&hate! 'd( )onphosphoryla"ed lipids '1! cere+rosides# glycoli&idsH derivatives of s&hingosine having a 0% and he4ose s*+stit*ent! 2! )*lfoli&idsH derivatives of s&hingosine# 0% and s*lfated he4ose s*+stit*ent! 3! GangliosidesH derivatives of s&hingosine# 0%# he4osamine# he4ose and sialic acid! .! Proteoli&idsH com&le4es of li&id and &rotein! 5! )teroidsH derivatives of cyclo&entano&erhydro&henanthrene! 3riacylglycerol or triacylglycerides or triglycerides are idea as )uelH +eca*se the fatty acids are essentially &olymeri/ed hydrocar+on# ' 22( molec*les# that meta+olic o4idation converts to ;2 and a+o*t G 5cal-gram of 0%# the highest caloric value com&ared with car+ohydrates and &roteins '+oth a+o*t . 5cal-gram(! Solu%ilityH e4tracta+le +y ether# chloroform or alcohol! 0% less than D are sol*+le in water 'e!g!# acetic C +*tyric acids(! *ensityH as low as 0!E g-ml ma5es them lighter than water! (elting pointsH 1 to G are +elow +ody tem&erat*re# 10 s and more are li5ely solidsA cis L +onds lower m& eno*gh to +e li1*id oils at +ody tem&erat*re C thatRs im&ortant for mem+rane fl*idity! "nsulatorH effective thermal and electrical! +adding,supportingH the 5idneys are s*rro*nded +y li&id fat! Phos&holi&ids form +ilayer sheets in water# and if sha5en will form s&herical +ilayers filled with solvent 'water( called micelles# which are a &rimitive model of a cell or cell organelles that serve to se&arate '&artition( molec*les and str*ct*res with different com&ositions and f*nctions! 0*rther considerations of li&ids and mem+ranes are ta5en *& in Cell Organelles Course +y Prof! Roy# refer to yo*r notes! Phospholipids 'or &hos&hatides( are a heterogeneo*s gro*& of com&o*nds fo*nd in virt*ally every living cell and may +e the chief cell*lar li&id com&onent! In general# nat*ral &hos&holi&ids have the "8config*ration# so &hos&hatidic acids contain "CC &hos&hatidic acid with two 0% esterified to the and 8car+on of glycerol! 3he &hos&hate may +e esterified to choline 'lecithins(# ethanolamines 'ce&halins(# +oth are the most a+*ndant '&hos&hatidyl8inositol# 8serine# 8glycerol# also occ*r(! In contrast# s&hingoli&ids have a *ni1*e core molec*le# s&hingosine# $8erythro81#38dihydro4y828amino8.8 trans8octadecen '1F car+on chain length(! 2ydrolysis of s&hingomyelins yields s&hingosine# &hos&hate# a fatty acid# and a nitrogeno*s +ase 'mostly choline# altho*gh ethanolamine is fo*nd too(! 3he relationshi& +etween the 2# %# and B +lood8gro*& s*+stances 'see Big $%.1% in Baynes( relates to the terminal oligosaccharide lin5ed via other s*gars to &roteins and li&ids on the red cell mem+rane! 3he 28s*+stance has &rotein and s&hingoli&id attached! Individ*als with "ype 0 +lood designation have Gal8N8%c81#3 attached to the galactose of 28 s*+stance to form the %8ty&e glycoli&id! -ype B have Gal81#3 to the galactose of 28s*+stance to form the B8ty&e glycoli&id! -ype 0B have +oth Gal and Gal8N8%c attached to the galactose of 28s*+stance! -ype < have neither s*gars added to the galactose of 28s*+stance! In each +lood ty&eH %# %B# and B# a s&ecific trans'erase gene is e4&ressed that adds the s&ecific s*gar's(A neither gene is e4&ressed in ty&e ; individ*als# who lac5 +oth en/ymes! )ee 0ig 2F!3 in Baynes! %toms incor&orated onto &*rine ring of I6P derive from H NG8gl*tamine# .#5 NE8glycine# F8N108 formyl 320%# N38gl*tamine# D8 ;2# as&artate# 28N108formyl 320% yields hy&o4anthine ring of inosine85P 'I6P(! )ee 0ig 2F!. in Baynes! 0!P \C adenylos*ccinate \C I!P CN X6P CN H!P! %s& is *sed to ma5e %6PA N%$I# then gln are *sed to ma5e G6P! )&ecificallyH R4s 11! I6P I as& I H-P% CN adenylos*ccinate 'similar to argininos*ccinate in *rea cycle( 12! adenylos*ccinate CN %6P I f*marate 11! I6P I N%$I CN X6P I N%$2 12! X6P I gln I 0-P% CN amide 'rearranges( to imide of g*anine in G6P! 0ive s&ecific ste&s involve co*&ling to %3P hydrolysis for synthesis of an amide in each case! %mides re1*ire high energy in&*t *s*ally o+tained from co*&led to 0-P hydrolysis! 3he following 12 ste&s review &*rine de novo synthesis! 3he fo*r for hy&o4anthine and %3P or G3P co*&led reactions for %6P and G6P are #old! 0ive total for %6P and G6P! 1! PRPP I Gln ?X 5P8ri+osyl818amine I gl* I PPi $! %P-ri#osyl-1-amine = gly = 0-P1 ?X glycinamide r" = 0+P = Pi 9noteH 5P8ri+osyl L ri+on*cleotide L rt: 3! glycinamide rt I N108f802. CN formyl8glycinamide rt I 02. 4. formyl-glycinamide r" = gln = 0-P$ ?X f-gly-amidine r" = glu = 0+P = Pi 9amidine is a 2N amide# LN s*+stit*tes for L;:

3.

35

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3E

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%! f-gly-amidine r" = 0-P3 (ring closure) ?X %-)8$-imidaDole r" =0+P = Pi 9closed8ring amide that rearranges to imida/ole: D! PR858N228Im rt I ;2 CN 58N228.8car+o4yate8Im rt F! %-)8$-4-car#o5yla"e-Im r" = asp = 0-P4 ?X %-)8$-Im-4-)-succinocar#o5amide n" = 0+P = Pi F! 58N228Im8.8N8s*ccinocar+o4amide nt CN 58N228Im8.8car+o4amide nt I f*marate G! 58N228Im8.8car+o4amide nt I N108f802. CN 58f8N228Im8.8car+o4amide rt I 02. 10! 58f8N228Im8.8car+o4amide rt I 22; CN hy&o4anthine rt L inosinate L I!P 11! I!P = asp = H-P% ?X adenylosuccina"e 'similar to argininos*ccinate in *rea cycle( 12! adenylos*ccinate CN %6P I f*marate 11! I6P I N%$I CN X6P I N%$2 12! (!P = gln = 0-P% ?X amide 'rearranges( to imide in g*anine of G6P!
.1

N108formyl8320% s*&&lies F and 1 in hy&o4anthine in I6P synthesisA mRN% CN mEG&&&N8mRN%# other RN%s and &roteins!

;2 s*&&lies

of I6PA )%6 for G&&&N8

.2

.3

..

Gl*tathione 'G)2( is "88gl*8cys8gly 9note the side chain C ;;2 of gl* is +onded to cys:! 3he cys8)2 is the active antio4idant f*nctional gro*&# it s*&&lies electrons there+y &reventing other molec*les '&roteins( from +eing o4idi/ed 'loss of electrons +ro*ght a+o*t +y interaction with reactive o4ygen s&ecies! By donating electrons G)2 +ecomes o4idi/ed instead and it forms dimer G))G! 3here are two tiss*es that m*st deal with high levels of o4idative ins*lt that are highly differentiated# the red cell and the eye lens# +oth have G)2 levels +etween D8F m6! Red cells are constantly e4&osed to high levels of o4ygen! In contrast the &;2 in lens is so low 'o4ygen diff*sion from vasc*lari/ed retina( that it canRt +e acc*rately meas*red! "ens o4idation is d*e to &hotoo4idation +y *ltraviolet radiation! )ince vis*al clarity m*st +e maintained# and all lens &roteins are &resent thro*gho*t life 'no t*rnover(# antio4idant &rotection +y G)2 is a+sol*tely essential to &revent cataracts 'o&acity# d*e to light scattering +y o4idi/ed &roteins and other &hysicochemical effects(! In Baynes# last to&ic# S% small fraction of triose &hos&hates &rod*ced d*ring meta+olism s&ontaneo*sly degrades to methylglyo4alT 238 ;8 2;# adJacent# highly reactive aldehyde85etone gro*&s Smethylglyo4al '6G( reacts with amino# g*anidino 'arg(# imida/ole 'his( and s*lfhydryl 'cys( gro*&s in &roteins# leading to en/yme inactivation and &rotein crosslin5ing! 6ethylglyo4al is also formed d*ring meta+olism of acetone ' 2 38 ;8 23( and glycine! 3he glyo5alase pa"h3ay 'Big 11.1%( is a 38R4n &athway to deto4ify methylglyo4al to $8lactate! 6G and H.2 form a hemithioacetal '&yr*vate8.H( that glyoxalase " rearranges to $8lactate8.H that glyoxalase "" hydroly/es to $8lactate and releases G)2 to +e *sed again# i!e!# 6G I H.2 CN 6G8.H 'glyoxalase "( CN Pyr8.H 'I 22;# glyoxalase ""(CN $8lactate I H.2 ;4ygen is the indis&ensa+le final reci&ient of meta+olic electrons! ?hen red*ced +y cytochrome a3 to water all latent energy in the larger &ers&ective that is derived *ltimately from &hotosynthesis has +een converted to free energy to drive the +ody# any energy difference is lost to other thermodynamic energies# s*ch as heat and randomness# relate to the efficiency of the +ioenergetics of life &rocesses! %ny dimin*tion of o4ygen s*&&ly entering the mitochondria &ro&ortionately diminishes the entire o4idative meta+olic a&&arat*s# which ra&idly manifests as hy&o4ia in all vasc*lari/ed tiss*e cells# es&ecially the +rain! 6olec*lar o4ygen is relatively inert# +*t is a strong o4idi/ing agent! Iron heme and mem+rane li&ids are easily o4idi/ed! %ll o4idases and o4ygenases 'metalloen/ymes( *se molec*lar ;2 and &rod*ce &artially red*ced reac"i,e <$ species 'R;)( s*ch as o5ygen supero5ide radical anion '<$I? (# its &rotonated form 'hydro&ero4y radical 2;;] # &Ba ^ .!5(# and hydrogen &ero4ide '22;2( that are more reactive then ;2 and are &rec*rsors to strongly o4idi/ing s&ecies s*ch as hydro4yl radical ';2] ( and metal8o4o com&le4es 'Baynes Big 11.1E(! 0*nctional hemoglo+in '2+( contains ferro*s iron '0e2I( which +inds ;2! 2+ can s&ontaneo*sly &rod*ce ;2]C in a side reaction associated with ;2 +inding that converts hemoglo#in '0e2I# red( to me"hemoglo#in '0e3I# reddish +rown(! !e"8# may &reci&itate in the RB # forming incl*sions 5nown as 8einD #odies# and may also release heme# which reacts with ;2]C and 22;2 to &rod*ce ;2] and reactive iron8o4o s&ecies! 9R;) s&ecies form li&id &ero4ides that decom&ose to reactive car+onyl s&ecies that react with &roteins# damaging the integrity of the cell mem+rane and the activity of trans&orter &roteins# colla&sing ion gradients and leading to cell death!: Both se&arate salvage R4ns *ses PRPP to s*&&ly ri+ose85PH 1nDH adenine-phosphori%osyltrans'eraseH ade CN %6PA 1nDH hyp-gua +#taseH hy& or g*a CN I6P or G6P! Both en/ymes convert free +ase to n*cleotide in one ste&! 3he most &revalent deficiency '2GPR3ase( res*lts in e4cessive o4idative loss of hy& and g*a to *ric acid that &resents as hy&er*ricemia! 3he conse1*ences come from the s&aring sol*+ility and needle8shar& sodi*m *ricate crystals! 3hese most easily a&&ear in the cooler Joints of the hands and feet leading to ac*te go*t8li5e e&isodes +eginning in middle age in men! If +rain levels of 2GPR3ase +elow 1V# *ncontrolla+le &sychiatric# self8m*tilation occ*rs# with life8s&an limited at +est to teenage years if *ntreated chiefly d*e to renal fail*re!

.5

.D

.E

-anthine oxidase 'X;# a moly+den*m '6oDI8iron8containing flavo&rotein( o4idi/es hy&o4anthine CN 4anthine CN *ric acid *sing molec*lar o4ygen 'which is red*ced to 22;2 # then decom&osed to water and ;2 +y catalase.! ;nce X; acts on allo&*rinol as a s*+strate# its o4idation &rod*ct# allo4anthine 'o4i&*rinol(# +inds strongly to X;# inhi+its the en/yme# hence the designation as a suicide inhi#i"or! 0llopurinol is an analog of hy&o4anthine in which F and NG are switched 8 the two ring NRs ne4t to each other! 9%llo&*rinol &revents 6o.I reo4idi/ation +ac5 to 6oDI 'active en/yme(! ?ith X; inhi+ited +y allo&*rinol# PPRP levels are higher in go*t 'may a&&roach normal levels( salvage o&erates more normally so free ade# hy&# and g*a +ases go +ac5 into %6P# I6P# and G6P n*cleotides for contin*ed *sage rather than o4idative loss to *rate! ?itho*t allo&*rinol# &*rine +ase levels decrease and insol*+le *ric acid increases 'hy&er*ricemia(! %dditionally# the high PRPP levels stim*late more de novo &*rine n*cleotide synthesis that leads to f*rther *ric acid increases 'in "esch8Nyhan syndrome of *& to 50 mg *rate-5g +ody weight-day( a+ove the normal o*t&*t of 10 mg *rate-5g +ody weight-day! %3P hydrolysis! reatine &hos&hate 'creatine8P(! 3his secondary# high8energy reserve 'GYZ P L C 12!0 5cal-mol com&are to 'GYZ%3P L C E!3( converts %$P to %3P I creatinine! 3he &hos&hate of creatine8P is in a very high8energy +ond 'GYZ P L C 12!0 5cal-mol(! 3he 1*anidino gro*& of creatine 'from arg( ma5es an N8anhydride 'similar to ;8acid anhydrides# e!g!# acetyl anhydride# car+amoyl8P(# all of which have a high 'GYZ( of hydrolysis! ?hen the creatine8P cycli/es# the attac5ing ;; 'from the other end of the molec*le( forms an cyclic amide and the sta+le leaving gro*&# Pi# leave s*fficient free energy to &hos&horylate %$P! reatinine is the cyclic N8anhydride &rod*ct of creatine8P# it has no other meta+olic *se and is e4creted from the &lasma into the *rine! 0naplerosis reactions convert meta+olites to 3 % cycle intermediates to re&lace those diverted o*t into other synthetic &athways 'e!g!# s*ccinyl o% into heme synthesis(! 3he most immediate reaction s*&&lies ;%% 'from &yr*vate via pyruvate car%oxylate(# which together with &yr*vate starts the cycle and ends +y regenerating ;%%! 3he ne4t ana&lerotic en/yme 'glu transaminase( converts gl*tamate CN 85etogl*tarateA then malic en/yme converts cyto&lasmic &yr*vate CN malate which enters the mitochondrion! 3h*s# ana&lerosis ens*res that ;%% is availa+le for contin*ed 3 % f*nction and also ens*res that gluconeogenesis can occ*r *sing the car+on s5eletons of gl*cogenic amino acids 'when gl*cose s*&&lies are diminished(! ?itho*t +Case to convert &yr*vate to ;%%# &yr*vate is converted to lactate# +oth acc*m*late! Increased cell*lar lactic acid leaves and enters the &lasma acidifying it# i!e!# ca*sing lactic acidosis 'one ty&e of meta+olic acidosis(! ?itho*t P ase# high &yr*vate leads to increased acetyl o% via pyruvate dehydrogenase# which then f*nnels into fatty acid synthesis! Gl*coneogenesis is inhi+ited# so the increases &yr*vate goes to acetyl o% increasing li&ogenesis significantly! 3he &entose sh*nt s*&&lies the N%$P2! 9Note# if gl*coneogenesis is inhi+ited# then gl*cose is availa+le to enter the &entose sh*nt yielding 2 N%$P2 &er gl*cose and the car+ons reenter glycolysis to give even more &yr*vate# hence# acetyl o% for contin*ed li&ogenesis!: 3he free energy content of a s*+strate 'or its &rod*ct( cannot +e meas*red directly# only the difference or change 'G( of free energy content +etween s*+strate and &rod*ct can +e meas*red! ,nthal&y change '2( in heat gained or lost among the molec*les of a reaction system# at constant &ress*re# decreases or increases the tem&erat*re of the reaction system s*rro*ndings 'water# cytosol# mitosol# n*cleosol# etc(! 3he +iochemical a&&arat*s of the cell cannot convert heat per se into wor5# as a mechanical engine can! 3hermal homeostasis mechanisms dis&ose of the heat thro*gh res&iratory# circ*latory# and &ers&iration mechanisms +*t most *sef*l meta+olic wor5 wo*ld not occ*r otherwise 'a hi+ernating +ear(! %merican chemist# ?illard Gi++s develo&ed the thermodynamics of free energy which relates the heat gained or lost in a reaction at constant &ress*re 'iso+aric( +*t reconciled it with the condition of constant tem&erat*re '3 L is constant# isothermal(# which are the conditions of +iochemical reactions in animals with thermal homeostasis reg*lation! 2ence# G L 2 8 3) too5 into acco*nt the *n*sa+le difference in '2( heat as related to changes in system randomness ')( at a &artic*lar tem&erat*re! ?hat was left was G# energy free for *sef*l &hysico8chemical wor5 or achievement! %dd alge+raically R4 II I R4 I L 'C E!3( I 'I 3!3( L C 3!0 5cal-mol# the net energy difference is e4ergonic for gl*cose &hos&horylation +y he4o5inase 'or gl*co5inase(! ,4ergonicH R4 IA endergonicH R4 II! ata+olism is e4ergonicA ana+olism is endergonicA overall meta+olism 'cata+olism I ana+olism( is e4ergonic! % do*+le reci&rocal &lot gra&hs 1-x vers*s 1-y! 3he "ineweaver8B*r5 &lot gra&hs 1-9): vers*s 1-P# res&ectively# and is advantageo*s# for the *s*al hy&er+olic c*rve of the ty&ical 6ichaelis86enten &lot is there+y lineari/ed! 3he y8interce&t gives 1-Pma4# the x8a4is gives C1-Bm! )im&le calc*lation gives Bm and Pma4!

.F .G

50

51

52

53

5.

55

5D

5E

5F 5G

D0

D1

D2

3he Bm is the s*+strate concentration '9):( at which the reaction rate is half the ma4imal velocity 'P ma4-2(! %s 9): increases# reaction rate 'P( increases and a&&roaches the ma4imal velocity &ossi+le# Pma4# asym&totically 'for the amo*nt of en/yme &resent# if the amo*nt of en/yme do*+les the rate do*+les(! Bm is also a meas*re of the affinity of the s*+strate for the en/yme! 3he initial velocity 'v o( gives the most acc*rate e4&erimental meas*re of rate at the initial 9):# which is 5nown most acc*rately! Intermediate v val*es are more diffic*lt to determine +eca*se of e4&erimental *ncertainties! In reference to the 6ichaelis86enton hy&er+olic c*rve# the section of the rate c*rve where 9)_ is +elow the Bm is first order +eca*se the rate is &ro&ortional to 9):! 3he &art of the rate c*rve corres&onding to more than 58 or 108times 9): a+ove the Bm is demonstrating /ero order 5inetics +eca*se the en/yme is wor5ing as fast as &ossi+le# inde&endent of 9):# +eca*se ) is so a+*ndant that any f*rther addition of ) does not increase the reaction rate significantly! Glycolysis is the central meta+olic &athway for o4idi/ing gl*cose to smaller car+on fragments that have diverse ana+olic and cata+olic fates!

D3

%naero+ic glycolysis also yields 2 net %3P# while aero+ic glycolysis also yields F net %3P! are &rod*ced# 2 %3P are cons*med ! It serves as a &re&aratory &athway for either com&leting the o4idation '3 %( or storing the car+ons in fatty acids '0% synthesis( as a de&ot f*el# or other *ses 'cholesterol# etc(! ?hen o&erating anaero+ically it recovers only a+o*t 5V of the energy availa+le from gl*cose that can +e e4tracted# when o&erating aero+ically# red*ced N%$2# &rod*ced +y glycolysis# is o4idi/ed with o4ygen involvement 'aero+ically( in a mitochondria to e4tract nearly .0V of the energy in gl*cose! D. Phos&horylation of 0DP to 01DBP +y +)K-1 commits irreversi+ly the D8car+on s5eleton to o4idative glycolysis! 3he &hos&ho8s*gars in reactions &receding fr*ctose8DP can flow into other &athways# so their car+on s5eleton is not committed to glycolysis! ;nce 0DP is acted *&on +y +)K-0# the only fate of 01DBP is cleavage +y aldolase and f*rther glycolytic o4idations of each 38car+on fragment to &yr*vate 'or lactate(! D5 Pyr*vate is the maJor &rod*ct of aero#ic glycolysis# lactate is the maJor &rod*ct of anaero#ic glycolysis! %3P is also a maJor &rod*ct of +oth glycolytic &rocess# anaero+ic glycolysis yields a net of 2 %3P whereas aero+ic glycolysis yields a net of F %3P 'd*e to mitochondrial &artici&ation(! 9Both glycolytically &rod*ced N%$2s have their electrons sh*ttled into the mitochondrion to yield an additional D net %3P:! and the &yr*vate car+on s5eleton is f*rther o4idi/ed in the mitochondrion to 3 ;2 and an additional 15 %3P are &rod*ced from red*ced coen/ymes
DD

1actate dehydrogenase '1*( &revents meta+olic colla&se +y recycling the catalytic amo*nt of N%$2 to N%$ I so glycolysis contin*es regenerating %3P from %$P! 3his is made &ossi+le +y red*cing &yr*vate '5etone( to lactic 'alcohol(! DE 6itochondria! DF +yruvate $inase &hos&horylates %$P to %3P *sing the high CG of P,P hydrolysis of the enol that yields &yr*vate! DG %naero+ic glycolysis 'yields net of 2 %3P &er gl*cose( vers*s aero+ic glycolysis 'yields net of F %3P &er gl*cose(! E0 3he red +lood cell can only &rod*ce glycolytic lactateU It lac5s mitochondriaU 2ence# the RB is a contin*o*s# maJor so*rce of &lasma lactate! %s the sim&lest of cells# the net 2 %3P yield is s*fficient to meet RB meta+olic energy needs +eca*se cellRs role is trans&orting and delivering o4ygen is ma4imi/ed +y having no need for o4ygen! E1 3he m*scle cells constit*te the maJor tiss*e mass of the +ody! ?hen wor5ing anaero+ically &rod*ce massive amo*nts of lactate which enters the &lasma d*ring stren*o*s e4ercise!
E2

E3

0ree gl*cose and gl*cose released from &olymeric car+ohydrates 'starches( in foods are a+sor+ed +y the intestines and trans&orted via the &ortal vein into the liver! Gl*cose *tili/ation re1*ires &hos&horylation! 2exo$inase has low Bm for gl*cose and is GDP &rod*ct inhi+ited# which is ade1*ate for m*scle cell glycogenesis and glycolysis needs# +*t inade1*ate for liver gl*cose meta+olism needs# which m*st s*&&ly its own needs as well as s*&&ly the +rain and all other tiss*es! <nli5e m*scle cells# liver cells also have hexo$inase iso/yme "V 'glucokinase(# which has +etter 5ineticsH high Bm and no GDP &rod*ct inhi+ition so GDP flows easily and ra&idly into liver glycogenesis and glycolysis! %t rest after a meal# a E0 5g man will store 200 g of gl*cose as liver glycogen and 150 g gl*cose as m*scle glycogen# +*t overnight only F0 g of gl*cose in liver glycogen will remain! 3he other 120 g of glycogen gl*cose was released +y the liver to s*&&ly the +rain and other tiss*es with gl*cose overnight! $*ring wa5ing ho*r activities# additional amo*nts of gl*cose is o4idi/ed +y the liver for varied meta+olic needs! Gene e4&ression of the liver gluco$inase gene is ind*ced +y higher than *s*al dietary gl*cose loads if s*stained over several days there+y ena+ling the liver to ada&t to e4traordinarily elevated dietary gl*cose and higher than *s*al hyperglycemia! 3he other en/ymes listed in the 1*estion are &art of glycolysis!

E.

E5

3he acetal f*nctional gro*& 'C +earing two ;R gro*&s( defines ;8glycosides 'e!g!# glycogen and cell*lose(! It contains two sta+le e"her-like #onds 'C?;? a and C?;? +( on the anomeric = so glycosides are sta+le# it will not hydroly/ed on its own! ;ne ;R is in the s*gar ring# the second ;R is a lin5ed s*gar resid*e 're&laces 2 in the hemiacetal of free gl*cose(! 3here are two &ossi+le stereochemical isomers ' and at the =( for the ;8s*garH either a+ove or +elow the ring# res&ectively. Glycoside synthesis and hydrolysis en/ymes are stereos&ecific for 8 or 8glycoside anomer lin5age# i!e!# 1,4 'starch# amylase( and 1#D 'glycogen# de%ranching en/yme# then amylase( or 1#. 'cell*lose# cellulase(! $ietary starch 'f*el( digestion +egins in the mo*th with salivary amylase# later in the g*t with pancreatic amylase! ?e lac5 cellulase# so the +eta8cell*lose &olymer fi+ers are eliminated in feces! ell*lose +eta8str*ct*re &rovides considera+le hydrogen +onding among its &olar gro*&s there+y conferring strength to the fi+ers for load +earing in &lants and trees! 9$*ring &olymeri/ation# the 1 of the incoming gl*cose lin5s to .;2 of the terminal 'nonred*cing( gl*cose of the e4isting &olymer 'or to D;2# d*ring +ranch creation(A s*+se1*ent additions occ*r at +oth .;2 ends!: ,ach +ranch introd*ced do*+les the s*+strate concentration of nonred*cing ends to which new resid*es can +e added! ?hen E811 resid*es are added from the last +ranch# the o*ter fo*r resid*es are moved to D of the 5th resid*e to create a +ranch! ;nce +ranched# the original molec*le has 2# then .# F# 1D# 32# D.# 12F# 25D# 512# 102. termini after ten8+ranch events! If the glycogen molec*le already had 1#000 linear chains# and each elongated and added 102. +ranches# the concentration of s*+strate termini is over 1 million! '103 4 103 L 10D(! In shar& contrast# in starch# only one nonred*cing . ;2 end &er &olymer is availa+le for addition or removal of resid*es! 3h*s# glycogen +ranching can accelerate gl*cose storage or de+ranching decelerates gl*cose release for mo+ili/ation from glycogen! )*ch e4&onential nonlinear growth hel&s +ring &ost&randial hy&erglycemia *nder control faster 'glycemia(# and &rovides for 1*ic5 mo+ili/ation of gl*cose from glycogen d*ring a heavy demand event 'ra&id e4ercise(! >es! In &lants# gl*cose is released from stored starch d*ring seedling growth 'ho*rs8days( +efore &hotosynthesis is availa+le to synthesi/e gl*cose! Plant growth has no need for a 1*ic5 'seconds8min*tes( high demand addition-release &olymer str*ct*re! 3he +iochemical +arrier that se&arates storage 'starch# glycogen( from str*ct*ral 'cell*lose( &olymers is via a8 and +8gl*cosides and their stereo s&ecific en/ymes! Note# after a meal# liver and s5eletal m*scle can store gl*cose into glycogen e4&onentiallyA conversely when s*dden# high demand for gl*cose occ*rs# at the onset of vigoro*s e4cise# enormo*s 1*antities of gl*cose can +e released from the considera+le amo*nt of glycogen macromolec*lar glo+*les in these cells! 9% short delay occ*rs d*ring which stored %3P and creatine8P 5ee& *& with m*scle demand for %3P *ntil glycogenolysis# o4idative glycolysis# and mitochondrial res&iratory o4idation ta5e over %3P regeneration!: ;f the five R4ns within the 0% synthesis cycle# the 2nd and .th *se N%$P2! 3he 2nd R4 red*ces the 85eto CN 8;2# the .th red*ced the 2L 2 to 228 22! In the 8o4idation &athway# choice then %! 91st R4# 0%$ 'to 0%$22 introd*ces L # then 3rd R4# N%$I 'to N%$2 converts +8 22;2 to L;(:! 3he he4ose mono&hos&hate &athway '&entose sh*nt( &rod*ces N%$P2 in the 1st and 3rd dehydrogenase reactions! $eficiency of niacin# B3 or nicotinic acid 9fo*nd in meats# n*ts# leg*mes: leads to &ellagra! $eficiency interferes with a&&ro&riate N%$'P(-N%$'P(2 levels for 0% synthesis# cholesterol# and com&le4 li&ids need for cell mem+ranes and nerve ins*lation! o8deficiency of ri+oflavin# B2 9same food so*rce# &ellagra: wo*ld interfere with 0%$-0%$2 levels for vario*s dehydrogenases and with 8o4idation '1st and 3rd reactions *se 0%$ and N%$I# res&ectively(! 2ence# niacin deficiency interferes with li&id ana+olism and cata+olism! 3lucose-4-phosphate dehydrogenase '34+*2( deficiency leads to hemolytic anemia 'see linical ase Presentation +riefing sheet(! Prima1*ine 'and related antimalarials( *ndergoes redo4 reactions in the cell that &rod*ce large 1*antities of s*&ero4ide and 22;2! Superoxide dismutase converts s*&ero4ide into 22;2# which is inactivated +y glutathione peroxidase that *ses N%$P2 as coen/yme! If an individ*al has a genetic defect in 34+ dehydrogenase '*s*ally have an *nsta+le en/yme with a shorter half8life in the RB or an en/yme *n*s*ally sensitive to inhi+ition +y N%$P2! 2ence# ins*fficient N%$P2 is &rod*ced +y 34+*2 res*lting in im&aired recycling of G))G to G)2! Prima1*ine ind*ced o4idative stress leads to lysis of RB s 'hemolysis( and hemolytic anemia! Patients may develo& Ja*ndice from released heme +eing cata+oli/ed into yellow +ilir*+in# and if severe eno*gh# 2+ a&&ears in the *rine# hemat*ria 'dar58colored *rine(! RB s lac5 $N% gene e4&ression# so &roteins-en/ymes# incl*ding 34+*2& damaged +y o4idative damage &rogressive acc*m*late leading to &remat*re cell death when %3P &rod*ction and cell*lar ion gradients canRt +e maintained! )*+strate availa+ility in vivo is *s*ally +elow the Bm so that all the glycolytic reactions e4hi+it first order 5inetics com&ared to /ero order# which is *s*ally never achieved e4ce&t in vitro! %llosterism +y three en/ymesH hexo$inase,gluco$inase iso/yme& +)K-0& and pyruvate $inase reg*late glycolysis! Posttranslational covalent modification via &rotein 5inase % &hos&horylates 'P( +)K-0 CN P0B81P 'inact!(A similarly +K CN PB P 'inact!( in liver!

ED

EE

EF

EG

F0

96ore de&th! In m*scle and most tiss*es# hexo$inase 'Bm gl*cose 0!1 m6 is m*ch lower than +lood gl*cose `5 m6( limits gl*cose entry into glycolysis! In contrast# liver &arenchymal cells contain gluco$inase 'Bm `10 m6# an iso/yme of hexo$inase# 'hexo$inase "V(# its gene is ind*ci+le +y high dietary gl*cose to increase gluco$inase levels to meet demand! 2ence# +oth liver en/ymes ena+le it to S+*fferT +lood gl*cose levels when elevated gl*cose after a meal! 6*scle hexo$inase is &rod*ct inhi+ited 'GDP(# which may hel& divert some gl*cose into re&lenishing or maintaining glycogen while gl*cose is also cons*med glycolytically 'if m*scles are wor5ing lightly or moderately d*ring and after a high gl*cose meal:! F1 %llosteric reg*lation of liver gluco$inase is +y 'C0DP# I01P# also +inding of inhi+itory &rotein( of +)K-0 'C%3P# I%6P# Ccitrate(# and of pyruvate $inase 'I01DBP# C%3P(! F2 Glycolysis activity is stim*lated +y &ancreatic ins*lin! ItRs antagonist# &ancreatic gl*cagon# inhi+its glycolysis! Both are small &rotein hormones! F3 Both hormones! Ins*lin and gl*cagon +ind to s&ecific cell rece&tors which trigger de&hos&horylation-&hos&horylation# res&ectively of pyruvate $inase! Before +rea5fast# glycolysis is relatively inactive 'PB&( +eca*se gl*cagon has +een 5ee&ing the liver gl*coneogenic! % significant &ortion of the liver glycogen has +een de&leted d*ring the &ost a+sor&tive state overnight! 6*scle glycolysis is +asal in the resting +ody and m*scle &roteolysis has s*&&lied the liver with a&&ro&riate amino acids for gl*coneogenesis 5ee&ing vario*s active tiss*es 'e!g!# +rain# heart and dia&hragm m*scles com&ared to other less active cells( s*&&lied with gl*cose to s*stain +asal meta+olic energy needs! %fter a gl*cose8rich meal '100 gm or more gl*cose( digestion and a+sor&tion floods the liver and +ody with a hy&erglycemia s&i5e! %s soon as the &ancreas 8cells detect the rise in +lood s*gar# stored ins*lin is released! Ins*lin stim*lates rece&tors which leads to glycogenesis to re&lenish glycogen# glycolysis is activated 'PB & de&hos&horylated to active +K( and stim*lated +y 2#DBP0# fatty acid synthesis is stim*lated( and the 3 % ra&idly re&lenishes +odily %3P levels after the cessation of the +odyRs resting &eriod! %fter the a+sor+ed gl*cose is de&leted# the ins*lin levels dro& after the second &hase of ins*lin release# and as glycemia declines into early hy&oglycemia# &ancreas a8cells release gl*cagon to t*rn on glycogenolysis# slow glycolysis '+K to PB& inact(# inhi+it fatty acid synthesis! %s glycogen de&ots decline# gl*coneogenesis +ecomes activated again as is a&&ro&riate to maintain glycemia *ntil the ne4t meal! 9noteH any given cell may have large m*lti&le sets of glycolytic &athway en/ymes# at any given time! $*ring which# a greater or lesser &ro&ortion of them may +e at different activity levels# i!e!# s*+strate# allosteric# modification!:
F.

F5

FD

FE

FF

FG

G0

G1

% f*tile cycle consists of s*+strate % converted to &rod*ct B +y one &athway# which is converted +ac5 to s*+strate % +y a different &athway# no net wor5 accom&lished# again and again! If %3P hydrolysis is involved# than the net effect of the f*tile cycle is the cons*m&tion of %3P! 3he meta+olism of B doesnRt occ*r and %3P is cons*med# not re&laced! ;nce %3P is de&leted# the cell# tiss*e# organ# or animal dies! 3o &revent f*tile cycles# one or +oth of the &athways is reg*lated and &*t into different cell com&artments# e!g!# fat synthesis and o4idation! 6alonyl o% 'synthesi/ed in the cyto&lasm( is the activated form of acetyl o% incor&oration into fatty acids! 6alonyl o% also inhi+its the carnitine acyl transferase ' %3( in the mitochondrial mem+rane# there+y &reventing fatty acids from entering the mitochondria Inhi+ition of %3 +y the s*+strate of fatty acid synthesis &revents reo4idation of newly synthesi/ed fatty acids +ac5 to acetyl o%A that &revents a f*tile cycle! Indirectly# malonyl o% inhi+its +8o4idation +y c*tting off the s*&&ly of its s*+strateH acyl o% fatty acids! 6alonyl o% therefore controls +oth as&ects of fatty acid meta+olism! %cetal o% in the mitochondria has no mem+rane trans&orter for it to leave the mitochondria! 3h*s# the flow of e4cess gl*cose car+ons into fatty acids in the cyto&lasm m*st enter as &yr*vate +*t canRt leave the mitochondrion as acetyl o%! 0atty acid synthesis in the cyto&lasm is +loc5ed +eca*se its s*+strate# acetyl o% is tra&&ed in the mitochondrion! %cetyl o% condenses with o4aloacetate ';%%( via the first ste& of the 3 % cycle forms citrate! itrate easily leaves the mitochondrion via the 3 % anti&orter in e4change for a molec*le of malate that enters into the mitochondrion! 6itochondrial citrate in the cyto&lasm is cleaved to acetyl o% and ;%% +y cytoplasmic citrate lyase which *ses %3P and o% as co8s*+strates! Brea5ing a 8 +ond re1*ires the considera+le energy %3P hydrolysis &rovides# and eno*gh also for the synthesis of the thioester of acetyl o%H citrate I o% I %3P 88N ;%% I acetyl o% I %$P I Pi cetyl Co car%oxylase is a +iotin8de&endent en/yme with distinct en/yme f*nctions and a carrier &rotein f*nctionH %iotin car%oxylase# a transcar+o4ylase# and a +iotin[car+o4yl8carrier &rotein! 3he %iotin car%oxylase adds ;L L; to the 2 of acetyl o%! 3hat occ*rs in two stagesH 1C car+o4ylation of +iotin to +iotin8N8 ;;C '%3P CN %$P I Pi(# 2C followed +y transfer of the car+onyl gro*& to acetyl o% CN malonyl o% with release of the free en/yme[+iotin com&le4! Beta o4idation of an odd8car+on fatty acid near its final stage yields &ro&ionyl o% as the last fragmentH 238 228 228 228 ;8 o% CN 238 228 <8 228 ;8 o% 'cleavage( CN 238 228 <8 o% '&ro&ionyl o%( I 238 ;8 o% 'acetyl o%(! %ll three n*cleoside dr*gs terminate chain elongation once incor&orated into the chain +eca*se their str*ct*re lac5s the gro*& re1*ired for the ne4t addition! 'a( %/ido thymidine '%O3(85R8tri&hos&hate contains the reactive CNLNILNC on the

G2

G3

G.

3R car+on 'i!e!# 3RCN3 car+on that re&laces the C;2( of the deo4yri+ose com&onent! '+( $ideo4yadenosine8 5Rtri&hos&hate contains 3R82 instead of C;2 on the 3R car+on of the deo4yri+ose com&onent! 'c( P*romycin resem+les an the 3R resid*e of a charged tyrosinyl8tRN% 9the 3R termin*s adenosine of a charged tRN% containing tyrosine 'i!e!# dimethylaminoadenine88N83Ramino8';8methyltyrosinyl( ri+ose: and mimics the acce&tor role of the ne4t amino charged tRN% into the %8site! ;nce the peptidyltrans'erse reaction transfers the nascent &oly&e&tide to the &*romycin# elongation ceases 'the remainder of the tRN% str*ct*re is missing# the &oly&e&tide8&*romycin molec*le is not +o*nd to the ri+osome(! %3P8de&endent $inases &hos&horylate n*cleosides to N6P# N$P# and N3P n*cleotides# phosphatases remove the &hos&hates! Nucleoside transglycosylases e4change one +ase for another! Salvage en/ymes directly convert free +ases to the n*cleoside8mono&hos&hate n*cleotide in one ste& *sing PRPP as &hos&hori+osyl donor! %O3 deo4yn*cleoside is &hos&horylated to 5Rd%/33P and mimics 5Rd33P! "ac5ing phenylalanine hydroxylase# &henylalanine cannot +e hydro4ylated to tyrosine in &atients with PB<# hence the corres&onding deaminated 5eto acid# &henyl&yr*vate# and its red*ced analog# &henyllactate# are elevated in the *rine of *ntreated &atients! If PB< is *ndetected in new+orns# severe mental retardation develo&s! % dro& of +lood is ta5en from the heel of all new+orns in the <) 're1*ired +y law( for re1*ired ro*tine &henylalanine analysis! 3he mental retardation of PB< is &reventa+le# if detected soon after +irth! Poorly ed*cated immigrants from remote areas of the world may +e ignorant of this in+orn error of meta+olism# they# their develo&ing *n+orn children# and infants are sensitive to the to4ic effects of high concentrations of &henylalanine and related &henyl5etones! % diet restricted in &henylalanine +*t s*&&lemented with tyrosine &revents the mental retardation and ne*ro&athology from develo&ing! 3oo little &henylalanine '&he( in the diet can ca*se negative nitrogen +alance accom&anied +y lower &rotein synthesis in +ody tiss*es# with wide ranging conse1*ences! 3oo m*ch dietary &he is associated with ne*roto4icity effects! )*&&lementary tyrosine can lessen itRs the ris5 of deficiency '&he is an essential amino acid +y definition for PB<(# +y +y&assing the missing en/yme ste& that ma5es tyrosine non essential in the normal &o&*lation!! %ltho*gh mil5 caries co*ld acco*nt for the rotting teeth# and the very light &igmentation might s*ggest al+inism d*e to a defect or lac5 of tryrosinase and the two ste& &rocess involving the hydro4ylation of tyrosine to dihyro4y&henylalanine '$;P%( and s*+se1*ent o4idation to a 1*inone# which leads to the formation of melanin in melanocytes! Neither sit*ation is germane# +*t the mental retardation is! 3he *n*s*al gait# sitting &ost*re# and family history of e&ile&sy are telling! Interestingly# very light &igmentation may accom&any PB<! ;ccasional *nintended &henylalanine dietary e4cess can +e treated with tyrosine s*&&lementation to decrease the increased &heHtyr ratio to the more normal range# there+y ma5ing &he relatively less &rono*nced!

G5

GD

GE

GF

GG

100

2eme synthesis +egins and ends in the mitochondrion 'Baynes 0ig! 2E!.(! 2eme is &art of cytochromes of the electron trans&ort system ',3)(! )ynthesis +egins with glycine and s*ccinyl o% '3 % intermediate( yielding 58%"% via 1 synthase 'heme is allosteric inhi+itor(! 3wo 58%"% molec*les e4it to the cyto&lasm where they condense into a &yrrole '58mem+ered N8ring com&o*nd(! 0o*r &yrroles assem+le into a &or&hyrin in the cyto&lasm! )ide8chain modifications lead to *ro&or&hyrinogen III# then to co&or&hyrinogen III# which reenters the mitochondrion! %dditional side8chain modification yields &roto&or&hyrinogen IX# then &roto&or&hyrin IX! )errochelatase adds 0e2I to yield heme! Genetic defects in the &athway are associated with vario*s Porphyrias de&ending *&on which synthetic en/yme ste& is deficient! 101 3he synthesis +egins and ends in the mitochondrion# with &rec*rsor &or&hyrins formed in the cyto&lasm that enter the mitochondrion for final reaction ste&s! 2eme is cata+oli/ed to +ilir*+in 'yellow( in the liver! %+o*t E5V is derived from hemoglo+in of senescent red +lood cells which are &hagocyti/ed +y '1( monon*clear cells of the s&leen# '2( +one marrow# and '3( liver# which yields a daily load of 2508350 mg +ilir*+in! 102 aa*ndice is a yellow color im&arted to the s5in and eye whites d*e to e4cess +ilir*+in 'more than 50 mol-" or 3 mg-d" in the &lasma( often d*e to enlarged liver 'he&atomegaly(# which can have vario*s etiologies# e!g!# chemical 'alcohol( and viral 'he&atitis vir*s(# and others! In 8glo+in# Gl*D 'normal hemoglo+in % '2+%( CN PalD in 2+) involves an 0 CN - s*+stit*tion in the $N% 'G0G CN G-G(! 10. <nder conditions of low o4ygen tension 'low &;2( or hy&o4ia# the single amino acid nonconservative m*tation 'i!e!# amino acid change has different &hysical and chemical &ro&erties than the original( change 'acidic for a non&olar# hydro&ho+ic side8chain( ca*ses the 2+) molec*le to change sha&e that leads to 2+) &olymeri/ation into rod8sha&ed str*ct*res that deform and alter the rheological &ro&erties of red +lood cells 'Baynes 0ig 31!3(! 105 Intermittent e&isodes of hemolysis and es&ecially vaso8occl*sive crises lead to severe &ain in +ones# chest# and a+domen! %lso li5ely is an increased s*sce&ti+ility to infections and m*lti&le organ damage!
103

10D

)ome en/ymes are synthesi/ed inactive# in a &rec*rsor form '&roen/yme or /ymogen(! ?hen needed# /ymogens are activated# *s*ally +y &roteolysis so the &rotein conformation changes to the active en/yme ! 10E If an en/yme can cataly/e the a&&earance of a second active en/yme +y 10#0008fold# and it can cataly/e the a&&earance of another active en/yme +y 10#0008fold# the rate of the reaction of the last en/yme increases +y ten million8foldU 0or certain &rocesses# e4tremely short d*ration activation is essential if the res&onse is to co*nter a s*dden time8de&endent# life threatening event s*ch as loss of +lood +y tra*ma! )erial /ymogen activations are referred to as /ymogen cascades! 10F Blood coag*lation has two serial /ymogen cascades that have different /ymogens +*t activate the same final /ymogen# &rothrom+in! 3he intrinsic &athway circ*lates all the /ymogens in the +loodA the a second extrinsic pathway 'o*tside of the +lood( is triggered when cells mem+ranes are r*&t*red at the site of &hysical tra*ma! In a different /ymogen cascade# signal transd*ction ra&idly triggers cascade8li5e intracell*lar events after rece&tor +inding of s&ecific ligand# e!g!# ins*lin# gl*cagon# e&ine&hrine# cortisol and other hormones!
10G

3he signal &e&tide is com&osed of &redominantly hydro&ho+ic amino acids 'ala# val# le*# ile# &he# met( and is located at the N8termin*s of certain &roteins! 110 ;nly &roteins e4creted +y the cell contain the signal &e&tide! 111 Proteins inside the cell are intracell*lar# those o*tside the cell are e4tracell*lar! Proteins synthesi/ed +y the cell that remain in the cell are endogeno*s &roteins! ,4ogeno*s &roteins made o*tside the cell they enter! 112 3he )ignal Recognition Particle ')RP( com&le4 +inds the signal &e&tide emerging from the ri+osome that is actively translating the mRN% coding for an e4tracell*lar &rotein 'e!g!# collagen# fi+rinogen# &lasma fi+ronectin# imm*noglo+ins# etc( there+y the nascent &oly&e&tide is identified and sorted from the other mRN%s coding for endogeno*s &roteins 'e!g!# meta+olic &athway en/ymes# t*+*lin# etc(! 113 3he )RP8mRN%8ri+osome com&le4 +inds to the )RP doc5ing com&le4 on the endo&lasmic retic*l*m mem+rane! 3he signal &e&tide is fed thro*gh the ,R into the l*men where the signal peptidase removes the signal &e&tide 'later digested to amino acids(! Removal of the signal &e&tide is a &osttranslational modification! 3he ri+osome com&letes translating the mRN% coding region and the &oly&e&tide chain ends *& within the l*men where it is *ndergoes additional &osttranslational modification in the Golgi a&&arat*s! 9$escri+ed in the ell ;rganelles co*rse!:
11.

% n*cleic acid consens*s se1*ence is com&osed of nearly the same se1*ence +ases fo*nd in different $N%s! ,!g!#
3%3%% +o4 in &romoters# homeo+o4 in homeotic genes# etc!

115

3he &romoter *&stream 3%3% +o4 se1*ence is +o*nd +y a &rotein factor that assists the RN% &olymerase align at the 1I n*cleotide of the gene transcri&tion region d*ring the initiation stage of RN% synthesis! Not all genes have a 3%3% se1*ence# the lac o&eron lac5s a 3%3% +o4# for e4am&le! 11D 0or mRN% synthesis# 3%3% 'Pri+now +o4 at C10 +& in &ro5aryotes +o*nd +y sigma factor# 2ogness +o4 at C35 in e*5aryotes +o*nd +y the 3BP(# %%3 +o4 'a+o*t CF0 +&# +o*nd +y N081- 30 &rotein(# G +o4 '+o*nd +y )P81 &rotein(! ,nhancers and res&onse elements are often within 1 5+& of I1 start8nt! 0or &rocessing# consens*s s&lice sites 88%G-G<8intron8%G-GN88# %%<%%% signals &oly % tail addition! 0or translation in pro$aryotes# &*rine8rich )hine8 $algarno %GG%GG< se1*ence is a+o*t 10 +& *&stream from first 5R%<G and aligns with 3R< < %5R in 1D) rRN%A in eu$aryotes# 5Rca&# mEG&&&N[# is +o*nd +y eI082! 11E a&&ing &rotects the 5RmRN% termin*s from e4on*cleases! 3he mEG&&&N[ ca& has 'I( charge recogni/ed +y eI082# *nca&&ed '&&&N8mRN%( or G&&&N8ca&&ed mRN% have only a+o*t 1V translation efficiency of mEG&&&N8ca&&ed8 mRN%! 3he 3R &oly % tail is added to only a few &ercent of 2nRN% &rimary transcri&ts synthesi/ed! 3he &oly % li5ely assists in trans&ort of mat*re mRN% from n*cle*s into cyto&lasm for translation into &rotein!
11F

Pro5aryotic mRN% has 5R&&&N8terminated mRN% with )hine8$algarno ')8$( consens*s se1*ence near first 5R%<G! ,*5aryotic mRN% has 5RmEG&&&N ca& 'with I charge# +o*nd +y eI082( translation +egins at first 5R%<G! 11G 3he distance +etween the )8$ se1*ence *&stream from the %<G start codon ens*res the correct alignment of the &ro5aryotic ri+osomal s*+*nit P8site at the first 5R%<G d*e to com&lementarity the 1D) rRN% in the smaller s*+*nit! 120 0or a second or additional cistron in a &olycistronic mRN%# each cistron has a )8$ se1*ence *&stream of the initiation %<G of that cistronRs coding region! 2ence# each internal cistron can +e translated correctly +eginning at the corres&onding N8terminal f8met amino acid se1*ence! 121 3he 30) ri+osomal s*+*nit wo*ld not +e a+le to locate the correct 5R%<G at the +eginning of the coding region for the affected internal cistron &roteins and they wo*ld li5ely not +e synthesi/ed! oordinated synthesis of the m*ltigene o&eron &roteins wo*ld fail! ?o*ld this li5ely +e fo*nd in via+le cells@ 9Not li$ely:!
122 123

3he transcri&tion of $N% into RN% in e*5aryotes# ca&&ing does not occ*r in &ro5aryotic RN% transcri&tion! % modification of the &olyn*cleotide after its synthesis is com&leted +y the $N%8de&endent RN% &olymerase! 3he e4ce&tion is the 5Rca&&ing and ca& methylation's(! 3hese occ*r on the nascent RN% transcri&t shortly after transcri&tion has +eg*n 'i!e!# long +efore transcri&tion is com&lete(! Posttranscri&tional modifications incl*de any removal of se1*ences

from mRN%# tRN%# and rRN% &rimary transcri&ts 'these are longer than their mat*re and f*nctional molec*les(# methylations# s&licing# &olyadenylation# and other changes to the s*gar or +ase of s&ecific n*cleotides in the RN%! 12. a&&ing transfers pH 'G6P( of &&pH 'G3P( to the 5Rpp)8termin*s of the &re8mRN% '2nRN%# in the n*cle*s( yielding the 5Rca&&ed mRN% 'Hppp)8termin*s(! )*+se1*ently it is methylated *sing )%6 to yield ca&H mFG&&&N8! %dditional +ase or ri+ose methylations can occ*r# mFG&&&Nm-7 mFG&&&mNm8 de&ending *&on which geneRs mRN% is +eing synthesi/ed!
125

,*5aryotic initiation factor eI082! 9;ocyte maternal mRN% have G&&&N8terminated mRN%s and these are not translated *ntil fertili/ation after with the ca&s are methylated and are then translated for the first em+ryonic develo&mental se1*ences to +egin!: 12D oen/yme N%$H nicotinamide'5R(&&%# N%$PH nicotinamide '5R(&&%&A 0%$H flavin8ri+itol'5R(&&% resem+le mRN% ca&sH mEG'5R(&&&N 'where N L %#G G5V(!
12E

%ll act on n*cleic acids! ds$N% is acted on +y restriction en/ymes 'site8s&ecific cleavage(# to&oisomerase '*nwind# and wind a8heli4# winding is %3P8de&endent(# ligase 're&airs single8strand nic5s( ss$N% e4o8 and endon*clease 'hydroly/e nt at end or within the strand# res&ectively( and &olymerases 'most are tem&late8directed assem+ly of linear $N% or RN%(! RN% viral8encoded en/ymes act on dsRN% and ssRN% de&endent *&on the +iological entity *nder consideration! Reverse transcri&tase co&ies RN% into com&lementary ss$N% then co&ies the ss$N% into ds$N% 'e!g!# lysogenic t*mor vir*ses(!

12F

Restriction en/ymes restrict 'i!e!# &revent( e4ogeno*s genetic n*cleic acid '*s*ally $N%( from e4&ressing its +iological &otential in &ro5aryotic cells! % 5ind of en/yme8+ased anti8$N% defense system! 12G 3he cellRs $N% is methylated at the s&ecific se1*ences recogni/ed and cleaved +y the restriction en/yme's( in the cell! Incoming e4ogeno*s $N% that lac5s site methylation &rotection is restricted +y the cell*lar en/yme there+y fragmenting the $N% ma5ing it *nvia+le 'es&ecially if the cleavage's( occ*r in foreign genes! 130 If a &iece of $N% has one or more restriction sites and is treated with one or the other corres&onding restriction en/ymes# the lengths of the $N% &rod*ced will +e *ni1*e for each restriction en/yme digest and e1*ivalent to a 'length( finger&rint! 0or medical detection of &athologic m*tations# the sic5le cell anemia m*tation 'Gl* D G%G PalD G-G( can +e screened in a &atientRs $N% +eca*se the m*tation a+olishes a recognition site for (st "" ' 3N'%CN-(GG(! 3he 3N%GG in 2+% gene 'corres&onding to Gl*D( is cleaved +*t the 3N-GG in the 2+) gene 'PalD( is not cleaved! 3h*s# &atients with sic5le cell anemia will show only one +and '1!.5+(# while carriers will have 2 +ands 'one 1!. 5+ and another 1!2 5+# and *naffected individ*als will have a single 1!2 5+ +and 'see Baynes 0ig 33!1E!(
131

$N% restriction en/ymes cleave at s&ecific tetramer or he4amer +& se1*ences that are &alindromic 'same se1*ence on +oth anti&arallel strands(! 6ethylation 'once or twice( &rotects the site from cleavage! 3h*s the cell methylates these se1*ences &reventing destr*ctive hydrolysis and fragmentation of its own $N%! 132 )ome restriction en/ymes c*t straight thro*gh +oth strands at a s&ecific +& yielding fragments with +l*nt8'fl*sh(8ends 'e!g!# 2ae III# ,coRP# Bal I(A others restriction en/ymes stagger the c*t of each strand to yield stic5y ends 'self8adhesive or annealing ends# e!g!# ,coRI# 6s& I( 9see Baynes 0ig 33!F:! 133 3he $N% ligase wor5s +y a two8ste& mechanism! 'a( It activates the &hos&hate at the nic5# &N[+y adding %6P# i!e!# %&8pN888intermediate 'i!e!# mimic5ing the incoming dN3P# &&pN in the &olymerase reaction(! '+( 3he );23R at the nic5 dis&laces the %6P forming the C):p-N8 &hos&hodiester +ond# the same o*tcome as the $N% &olymerase reaction! 3he ligase is not tem&late directed# it doesnRt re&lace any n*cleotides# it acce&ts whatever 5R&N88 is o&&osite the );23R# and merely re&airs a +ro5en ;[P +ond! 13. $N% to&oisomerases# li5e $N% ligases can ma5e a ;[P +onds to com&lete the &hos&hodiester lin5age of the +ac5+one! 2owever# to&oisomerases first +ro5e that +ond# wind '%3P8de&endent( or *nwind the $N% one t*rn 'to&o I(# or two t*rns 'to&o II(# +efore re&airing the same ;[P +rea5s! 135 Polyn*cleotide &hos&horylase 'PNP( reversi+ly &olymeri/es 5Rri+on*cleoside di8&hos&hates 'i!e!# n*cleoside &yro&hos&hates( to &olyn*cleotides according toH n N$P 88N 'N&(n I n Pi! $N%8directed RN% &olymerase reversi+ly &olymeri/es 5Rri+on*cleoside tri8&hos&hates to &olyn*cleotides according toH n N3P I $N%tem&late88N '&&&N'N&(n-0 I n Pi! 3he PNP differs from $N% tem&late8directed RN% &olymerases +eca*se it lengthens an RN% &rimer to generate a random se1*ence whose com&osition 'ratio of +ases( is de&endent *&on the s*+strate ratio of %$P# $P# G$P# and <$P in the reaction mi4t*re! RN% &olymerase generates a n*cleotide se1*ence com&lementary to the tem&late# it needs no &rimer! 13D % &lasmid is a self8re&licating e4trachromosomal $N% fo*nd in some +acteria! 3he n*m+er of co&ies the &lasmid re&rod*ces of itself in the +acteri*m carrying it is the co&y n*m+er# it is de&endent *&on the &lasmid e4amined and may range from none to almost two do/en! )ome &lasmids carry genes coding for en/ymes that inactivate &artic*lar anti+iotics 'am&icillin# tetracycline# are e4am&les( th*s &roviding the +acterial cell with &rotection against the anti+iotic!

13E

3hese am&icillin 'li5e &enicillin( and tetracycline resistance genes were e4&erimentally incor&orated into the &BR322 &lasmid in the la+oratory for *se in monitoring the ste&s involved in the molec*lar cloning of a &iece of $N%! ?ithin the am&icillin resistance gene is a +st " restriction site# and within the tetracycline resistance gene is a Sal " siteA +etween these genes is an Eco #" site! Insertion at the Eco #" site has no effect on +oth dr*g resistances! Insertion of $N% into the Pst I site inactivates the am&icillin gene 'insertional inactivation(! ells containing this recom+inant '&assenger $N% in the &lasmid vehicle( are 5illed +y am&icillin +*t are still resistant to tetracycline# for e4am&le! 13F In &ractice# the &lasmid &re&aration is a mi4t*re of original &lasmid molec*les with dr*g resistance and new recom+inant &lasmid molec*les with inactivated resistance genes containing the inserted $N%! %t a m*lti&licity of infection '6;I( s*ch that each cells receives# on average# only one &lasmid! ells receiving no &lasmid or the recom+inant die# while cells receiving the original &lasmid s*rvive e4&os*re of the dr*g! 13G 3wo &ro+lems occ*rH was the insertion s*ccessf*l# and did the &lasmid get into the test cells@ Insertion of a $N% into the ,coRI site +etween the am&icillin and tetracycline genes of &BR322 may not +e s*ccessf*l# +*t how does one 5now! By *sing inser"ional inac"i,a"ion at the Pst I site in the am&icillin gene# the $N% is inserted# the cells with the inactive am&icillin gene die when given am&icillin! 3h*s# the recom+ination is verified for the &assenger $N% insert! 3he tetracycline gene is still active! 3etracycline resistance verifies that the &lasmid was s*ccessf*lly introd*ced into the host +acteri*m 'transfection( +eca*se the cells s*rvive treatment +y tetracycline! Bnowing the transfected cells contain the a&&ro&riate recom+inant# the molec*lar cloning can &roceed! 3h*s# one co*ld &rod*ce large 1*antities of ins*lin $N% +y growing a large vol*me of transfected cells!
1.0

3he o&en8ring form of gl*cose e4&oses the highly reactive 18aldehyde that can react with e4&osed amino gro*&s! Blood distri+*tes gl*cose contin*o*sly thro*gho*t the +ody! 3he rate of &rotein glycosylation +y gl*cose is concentration8 de&endent! 3he mole fraction of the N8terminals of the 8chains of hemoglo+in % in red cells derivati/ed +y gl*cose is *sed as a meas*re of +lood gl*cose level d*ring &revio*s wee5s! 3he 1208day life s&an of the RB &rovides a +ac5ward assessment of acc*m*lated glycosylation that reveals 1*antitatively the &atientRs management of 'a( dietary gl*cose load and '+( how the +ody has managed gl*cose meta+olism! Normal meta+olic control of glycemia gives *& to DV glycosylation '2+%1c(! Increasing dietary gl*cose inta5e &rolongs increases the net d*ration and severity of hy&erglycemia s&i5es and the 2+%1c val*es are &rogressively a+ove DV! 0or dia+etics# this &rovides an o+Jective meas*re of the &atientRs history inde&endent of &ersonal memory of diet and medication &ractices for at least 3 months! 1.1 Im&aired ins*lin secretion and-or effectiveness 'ins*lin resistance d*e to &rolonged high dietary gl*cose inta5e( correlates with fa*lty gl*cose homeostasis and *tili/ation of fatty acids as f*el +y +ody tiss*e cells that is also associated with polyphagia 'e4cess a&&etite( accom&anied +y decreasing +ody weight! 3he +ody &erceives starvation# &oly&hagia ina&&ro&riately ingests more n*trients even tho*gh s*fficient dietary n*trients are availa+le within the +ody! 1.2 -ype 1 and 2 $6 differ in early v! later age onsetA a+r*&t vs! grad*alA normal v! o+ese weightA 2"% associated as &ositive v! negativeA little or no +lood ins*lin v! some8normal8highA islet cell anti+odies &resent at onset v! a+sentA islet anti+odies &resent at diagnosis v! noA ins*lin synthesis is a+sent imm*ne destr*ction of +8cells v! com+ination of im&aired +8cell f*nction and ins*linA &revalence is 0!28 0!3V v! 28.VA &oly*ria# &olydi&sia# &oly&hagia# weight loss# 5etoacidosis v! &oly*ria# &r*ritis 'itching(# &eri&heral ne*ro&athology# 5etoacidosis after maJor stressA 1.3 %nimal &rotein is recogni/ed as non8self +y the imm*ne system# which &rod*ces anti+odies that co*nter the effectiveness of e4ogeno*s animal ins*lin treatment! ,4ogeno*s h*man ins*lin is non antigenic! 1.. 3he molec*larly cloned ins*lin can +e o+tained in highly &*re form and is not antigenic!
1.5

%ctinomycin $ at different doses differentially inhi+its *N and #N polymerase! 6ethotre4ate inhi+its 'olate reductase! 3etracycline and &*romycin inhi+it elongation and initiation of &rotein synthesis# res&ectively! 3rimetho&rim inhi+its +acterial met8tRN%imet trans'ormylase! 1.D 6ethotre4ate is a folate analog that inhi+its 'olate reductase# which is &art of the three en/ymes concerned with d36P synthesis from d<6P! 3he folate inhi+itors effectively sto& d36P synthesis! 6ore meta+olically active cancer cells are 5illed than normal +ody tiss*e cells! %fter a cali+rated &eriod of treatment# f*rther inhi+ition is sto&&ed +y inJecting folate to o*t com&ete the dr*g# i!e!# significantly increase the folateHmethotre4ate ratio in cells! 3he most active cells of the +ody are more severely affected then less meta+olically active cells acco*nting for the side affects of chemothera&y! 1.E )ee footnote 1.5! 1.F GI tract e&ithelia have a fast t*rnover rate and active hair follicle cells are &artic*larly affected leading to GI malaise and hair loss# res&ectively! 1.G In &ro5aryotesH tetracycline and trimetho&rimA in e*5aryotesH methotre4ateA in +oth cellsH actinomycin $ and &*romycin!

'''' 1ndno"es edi"ing s"opped here ''''

150

o+alamine is +oth vitamin and active coen/yme! 3he others re1*ire an additional com&onent for activityH thiamine and &yrido4ine have a &yro&hos&hate and a &hos&hate added# res&ectively# as coen/ymeA ri+oflavin is com+ined with %6P and niacin is com+ined with ri+osyl8%$P +efore active as coen/ymes!

151

;4idation-red*ctionsH 0%$ and N%$ dehydrogenasesA 18car+on transfersH folate 'not listed# e!g!# N108formyl8022(# 28 car+on transfersH coen/yme % 'not listed# e!g!# acetyl o% is *sed for N8terminal acetylation# e!g!# eye lens 8crystallin &rotein(! 152 %ll listed vitamins are water sol*+le# also vitamin # folate# &antothenate# +iotin! 0at8sol*+le vitamins are %# $# ,# and B! 153 -hiamine 'B1(H maJor signs and sym&toms is &eri&heral ne*ro&athy# loss of a&&etite# consti&ation and na*sea occ*r early# then de&ression and conf*sion! Im&aired nerve cell f*nction leads to +eri+eri characteri/ed &rimarily +y advanced ne*ro8m*sc*lar sym&toms! /i#ofla,inH inflammation of the corners of the mo*th 'ang*lar stomatitis(# tong*e 'inflammation of glossitis( and scaly dermatitis! )iacinH dermatitis# diarrhea and dementia in severe deficiency in &ellagra 'rarely seen in the modern world(! Pyrido5ineH &eri&heral ne*ro&athy# conv*lsions# coma in later severe form# early onset shows irrita+ility# nervo*sness and de&ression in mild form! Co#alaminH megalo+lastic anemia also involves folate 'methylmalonic acid*ria and homocystin*ria( and &ernicio*s anemia 'd*e to lac5 of intrinsic factor &rotein 'I0( in the stomach and hence a+sor&tion of B12 is &revented(!
15.

Pyrido4ine is the maJor form in the diet# and &yrido4al &hos&hate 'via pyridoxal $inase( is the active form of the vitamin! %ll non&hos&horylated and &hos&horylated forms are water sol*+le! 155 Pyrido4al8P forms a )chiff +ase intermediate with the 8N22 of amino acids! ;ne of three +onds can then +rea5 yielding 'a( amination-deamination# '+( loss of car+o4yl gro*&# or 'c( dehydration 'serine( of the amino acid! 15D %mination converts their 85eto forms to amino acids 'e!g!# &yr*vate to ala# ;%% to as&# a8BG to gl*( for amino acid synthesis via aminases,transaminases! $eamination to the 85eto forms is the first ste& in cata+olism! ,ither is *sed to interconvert 85eto and 8amino acid forms!
15E

Iron in RB hemoglo+in# m*scle myoglo+in# cytochromes and iron8s*lf*r com&le4es in mitochondria are im&ortant for o4ygen trans&ort and energy meta+olism! o&&er in several o4ygenases# these incl*de cytochrome c o4idase# and several c*&roen/ymes involved in heme synthesis# s*&ero4ide dism*tase# and cer*lo&lasmin synthesis and f*nction! 15F Iron anemia! 15G er*lo&lasmin in &lasma scavenges s*&ero4ide and other o4ygen free radicals! er*lo&lasmin is defective in ?ilsonRs disease! 9 er*lo&lasmin &rod*ces a s5y +l*e color in sol*tion similar to cer*lean +l*e &igment! Recall sol*tions of co&&er ions are +l*e s*ch as co&&er s*lfate!: 1D0 0erro*s iron is stored +y ferritin &rotein in most +ody cells# ferric iron is trans&orted +y transferrin &rotein! er*lo&lasmin is the maJor trans&ort &rotein of co&&er to the +ody and is also essential for the reg*lation of the o4idation8 red*ction reactions# trans&ort# and *tili/ation of iron 'see Baynes 0ig 3!D(! 3hat is# ferritin80e2I I cer*lo&lasmin8 *2I \CN transferritin80e3I I cer*lo&lasmin8 *I! 0erritin scavenges free iron 'generally to4ic# es&ecially in the central nervo*s system(! ;4ygen or o4idi/ed thiol gro*&s red*ce *I to *2I in cer*lo&lasmin! 2ence# if co&&er is deficient# iron meta+olism is effected! 0*nctional hemoglo+in and myoglo+in contain 0e2I! ;ccasionally it is o4idi/ed to 0e3I when +o*nd ;2 is red*ced to s*&ero4ide nonen/ymatically to yield ferrihemoglo+in or methemoglo+in 'r*st +rown color(# which +inds o4ygen &oorly! (ethemoglo%in reductase restores the 2+'0e2I(! 9in &atients with met2% reductase deficiency 'methhemoglo+inemia( have a dar5 cyanotic a&&earanceA vitamin treatment red*ces the iron +ac5 to ferro*s 0e2I!!: o&&er deficiency also is associated with degeneration of vasc*lar tiss*e with +leeding d*e to defects in elastin and collagen &rod*ction! )ince co&&er deficiency infl*ences iron meta+olism# small co&&er deficiency manifests as microcytic 'small erythrocytes( microchromic '&ale erythrocytes( anemia that is resistant to iron thera&y!
1D1

%ll 20 amino acids are need to synthesi/e a+o*t 200 g total &rotein &er day in the healthy E0 5g h*man! 3he +ody can synthesi/e 12 amino acids +y meta+olic &athways# +*t eight amino acids cannot# those eight areH &henylalanine# valine# threonine# try&to&han# isole*cine# methionine# histidine# arginine# le*cine# lysine 'memory acronymH Pvt! 3im 2all(! 3heir car+on s5eletons cannot +e synthesi/ed +y the +ody th*s the diet +ecomes essential in s*&&lying them in an ade1*ate amo*nt +ased *&on their com&osite average mole fraction of daily &rotein synthesis! 1D2 Nitrogen +alance occ*rs when the dietary inta5e of *tili/a+le nitrogen e1*als the nitrogen e4creted 'sweat# *rine# feces(! Body com&osition of nitrogen is mostly acco*nted for +y &rotein mass 'a+o*t 1DV N(# the N in n*cleic acids and some other meta+olites is ignored! 1D3 0or infants# h*man mil5 is the +est so*rce +eca*se the ratio or mole fractions of the amino acids matches the amino acids com&rising the total +ody &roteins of the infant! 6oreover# h*man mil5 &rotein is com&letely digesti+le and a+sor+a+le for f*ll *tili/ation! Bovine mil5 is ideal for calves for the same reason and is the ne4t +est so*rce for h*mans# hence its wide commercial availa+ility! ,ggs are the ne4t +est so*rce of &rotein# the high cholesterol content notwithstanding! 9Beside the lactose intolerance# a &ortion of the &o&*lation has allergic res&onses to cows mil5!:! 1D. %s an essential amino acid# the +ody canRt synthesi/e it to maintain its re&resentation in the daily re1*irement for &rotein synthesis needs! %ll &roteins initiate with methionine# so a 50V decrease in availa+ility co*ld decrease &rotein synthesis +y the same amo*nt! %dditionally# all other &roteins will +e affected in &ro&ortion to the n*m+er of internal methionines!

;nce started# &oly&e&tide elongation halts at internal methionine codons in &ro&ortion to the decreased methionine concentration# in this case 50V# th*s# the overall rate of elongation is decreased +y at least 50V# &erha&s more in selected cases! 1D5 ?hile essential amino acid deficiency is ongoing# the t*rnover of &roteins will release some of the deficient amino acid's( +ac5 into the amino acid &ool 'cell*lar# tiss*e# organ# whole +ody( and that hel&s de novo &rotein synthesis# +*t the nonessential amino acids canRt +e incor&orated +eca*se overall &rotein synthesis is a+o*t 50V 'met e4am&le(! 3he nonessential amino acids are &rocessed cata+olically thro*gh o4idation which +egins with deamination! 3he deaminated N is incor&orated into *rea to &revent ammonia to4icity! 3he net res*lt is the loss of +ody N now e4ceeds diet inta5e# hence# negative nitrogen +alance ens*es and contin*es *ntil the deficiency of essential amino acids ceases!
1DD

)ee Baynes 0ig 2F!E! 'a( Ri+ose red*ction# all N$P I thioredo4in8')2(2 'N%$P2( via ri%onucleotide reductase 88N dN$P I thioredo4in8)2 'N%$PI(! '+( <racil to thymine# d<6P I N5N108methylene802. via thymidylate synthase 88N d36P I dihydrofolate '022(! 1DE d<6P to d36P 'see fn 1DE(! ancillary R4 1H 022 I N%$P2 via )25 reductase 88N 02. I N%$PI! R4 2H 02. I serine via serine hydroxymethyl trans'erase 88N N5N108methylene802. I glycine I 22;! 1DF 3he ri%onucleotide reductase *ses N%$P2 which has niacin 'B3# nicotinic acid(! 3he dihydro'olate reductase 02. *ses folate 9also m*lti&le &e&tide com&osed of gl*tamate:! 1DG % hydride is a &roton with two electrons or 2@C# the hydride e1*ivalent is donated +y the two cysteine C)2 gro*&s that form a +ridged thioredo4inC)8)8intra&e&tide! 3hese are red*ced in t*rn +y N%$P2! Nicotinic acid is the vitamin and its amidation yields the active nicotinamide *nit of N%$P2! 9noteH $*ring deo4yri+ose formation# the two C)2 gro*&s in thioredo4in 'Ctr&8Cys8gly8&ro8Cys8( donate a hydride e1*ivalent '2C( and are o4idi/ed to cross lin5ed cystine dis*lfide! Red*ction +ac5 to a &air of cysteines 'Ctr&8Cys8gly8&ro8Cys8( is via flavo&rotein thioredoxin reductase! N%$P2 'from &entose sh*nt( as electron so*rce red*ces the C)8)8 +ac5 to active thioredo4inC')2( 2 ! In the second reaction 'red*ction of 022 to 02.(# N%$P2 donates the hydride I 2I 'i!e!# 22( hydrogenation e1*ivalent!: 1E0 In addition to tetrahydrofolate transferring car+on atoms 'in the forms of formaldehyde# formyl# hydro4ymethyl# methyl# or forminimo(# )8adenosyl methionine ')%6( for methylations# and ;28+iotin for car+o4ylations!
1E1 1E2

-here are o,er 3EE kno3n Dinc-con"aining enDymes ! %ldolase# alcohol dehydrogenase! 6etallothioneines are small &roteins containing a+o*t D2 amino acids with a+o*t 30 mole V as cysteine! 3hese &rovide &oc5ets of )8donor atoms that can +ind heavy metals# es&ecially *2I and On2I! admi*m ind*ces the cell*lar resistance to heavy metal cytoto4icity +y stim*lating thionein synthesis# which is mediated in most s&ecies +y the +inding of metal ions either to a cysteine8rich &oly&e&tide in the metallothioneine family or to short cysteine8containing gamma8gl*tamyl &e&tides! 3he thioneines are im&ortant in heavy metal deto4ification and e4cretion! 1E3 0or metalloen/ymes# deficiency of the metal cofactor inhi+its en/yme activity +eca*se the chemistry of the catalysis involves the metal ion! In ?ilsonRs disease# the liverRs ca&acity to synthesi/e cer*lo&lasmin is im&aired leading to chronic acc*m*lation of co&&er in +ody tiss*es associated with hemolysis and damage to +oth liver 'cirrhosis( and +rain cells! 3he activities of co&&er# /inc# iron# and other metalloen/ymes will +e affected +y the e4cessive co&&er acc*m*lation# which can interfere with a+sor&tion and *tili/ation of other metal ions!
1E.

Pit $H +ones# c*rved legs! Pit H s*+c*taneo*s and other hemorrhages# m*scle wea5ness# soft# swollen +leeding g*ms# osteo&orosis# and &oor wo*nd healing and anemia! NiacinH dermatitis# diarrhea# and dementia! 3hiamineH +eri8+eri# early loss of a&&etite# consti&ation# and na*sea# later de&ression# &eri&heral ne*ro&athy and insta+ility and im&aired nerve f*nction with advanced ne*rom*sc*lar sym&toms! 0olateH megalo+lastic anemia d*e to fail*re to synthesi/e n*cleic acids 'folate8de&endent# 18car+on meta+olism(! Polycythemia 'erythrocytosis( is an increase in the hematocrit 1E5 ?ater sol*+leH vit # niacin 'B3(# thiamine 'B1(# and folate are water sol*+le 9also flavin 'B2(# &antothenic acid 'B5(# &yrido4ine 'BD(# +iotin# co+alamin 'B12(:! "i&id or fat sol*+leH Pit $ 9also vit %# ,# B:! 1ED Pit $ 'ric5ets(H fish oils and egg yol5s! Pit 'sc*rvy(H citr*s fr*its! Niacin 'the 3 $s(H meats# n*ts# leg*mes! 3hiamine '+eri8+eri(H seeds# n*ts# wheat germs# leg*mes# lean meat! 0olate 'anemia(H yeast# liver# leafy vegeta+les!
1EE

%fter d36P synthesis# dihydro'olate reductase converts 022 to 02. 'tetrahydrofolate(! *2) reductase is inhi+ited +y folate antagonists s*ch as methotre4ate 'also related dr*g amino&terin(! If 02. cannot +e regenerated# the 18car+on802. derivatives &ool +ecomes *sed *&# 18car+on meta+olism ceases# the cell dies! 3h*s# methotre4ate +loc5s 02 .# regeneration# the ne4t ancillary reaction cannot regenerate N5N108methylene802. from serine and contin*ed d<6P to d36P synthesis ceases! 1EF Pentose sh*nt! 0irst reaction via glucose-4+-dehydrogenase and 3rd dehydrogenase 'an o4idative decar+o4ylation( regenerate N%$PI to N%$P2# which s*&&lies the 22 e1*ivalents to )25 reductase to regenerate 022 to 02.! 1EG 3he 3rd car+on 'the hydro4ymethyl side chain C 22;2( of serine# is transferred to 02. onto N5N10! 1F0 3he d<6P to d36P reaction &rod*ces 022 'dihydrofolate(# 022 has no f*rther meta+olic *se!

'''' 1ndno"es edi"ing s"opped here ''''

1F1

, 6 is a com&le4 networ5 of secreted macromolec*les located in the e4tracell*lar s&ace! 3he ,6 of s5in and +one &rovides the str*ct*ral framewor5 of the +ody! In all tiss*es the ,6 has a central role in reg*lating +asic cell*lar &rocesses# incl*ding &roliferation# differentiation# migration and cell8cell interactions! 3he ,6 macromolec*lar networ5 is com&osed of collagens# elastin# glyco&roteins and &roteoglycans# secreted +y connective tiss*e cells s*ch as fi+ro+lasts and e&ithelial cells! 1F2 3he total +ody mass is a+o*t 25V collagen and collagens are the &rimary str*ct*ral com&onents of the ,6 in connective tiss*es! ollagenRs three &oly&e&tide chains 91G different collagen ty&es# com&osed of 3. related# +*t distinct &oly&e&tide chains: of D00 to 3000 resid*es are wo*nd a+o*t each other in an e4tended 8heli4 conformation fo*nd in glo+*lar &roteins! Glycine has the smallest side8chain '2(# therefore the Gly8X8> tri&e&tide allows the tri&le helical stands to fit closer together! 3he X and > 'most often &ro and hydro4y8&ro( confer rigidity to the molec*le +eca*se of their +*l5 and limited rotation a+o*t the 8amino gro*&! Intra8 and interchain helices are sta+ili/ed +y hydrogen +onds mostly +etween N2 and L; gro*&s! 3he side chains of the X and > gro*&s &oint o*twards from the heli4 where they can form lateral interactions with other tri&le helices or &roteins '.Y( stated in the correct answers of the test 1*estion! 1F3 3he long cylindrical8sha&ed collagen molec*les align in &arallel 1*arter8staggered arrays 'li5e +ric5s in a wall( s*ch that the ends overla& and a&&ear as +ands across the fi+ers 'resem+le fi+rin fi+er staggered8arrays( when viewed in the electron microsco&e!
1F.

Gl*cose# mannose# galactose# ri+ose are sim&le s*gars! Gl*cosamine# mannosamine# galactosamine# fo*nd in com&le4 car+ohydrates# and deo4yri+ose are derived s*gars! Ri+ose is in RN%# deo4yri+ose is in $N%! 1F5 GlycoconJ*gates are formed *s*ally with gl*c*ronic acid to deto4ify molec*les that have a car+o4yl or hydro4yl gro*&! ,n/ymes conJ*gate either thro*gh an ester or an ether ty&e of lin5age! Gl*c*ronic acid conJ*gates with +ilir*+in! 9%nother conJ*gateH glycine I +en/oic acid gives hi&&*ric acid# a com&o*nd *sed to meas*re liver f*nction! Gl*c*ronic acid 2;; 8' 2;2(.8 2; is formed from gl*cose +y o4idation of the 1K alcohol of the last car+on# i!e!# D8;2!: Glycoli&ids are classified into fo*r gro*&sH cere+rosides# s*lfatides# glo+osides# and gangliosides! In all these classes# the &olar head8gro*& C com&rising the s*gars C is attached to ceramide +y a glycosidic +ond at the terminal ;2 of s&hingosine! 1FD Proteoglycans are gel forming com&onents of the , 6! 3hose listed are glycosaminoglycans 'G%Gs( com&osed of re&eated disaccharidesH hyal*ronic acid 'GlcN%c and Glc<%( and is the longest of the G%Gs '250825#000 resid*es(A he&arin 'Id<% and GlcN%c(A chondroitin s*lfates 'Glc<% and GalN%c(# dermatan s*lfates 'Id<% and GalN%c(# he&arin s*lfates 'Id<% and GlcN%c(# and 5eratin s*lfates 'Gal and GlcN%c( have s*lfate on some of their amino gro*&s!
1FE

3here are seven crystal systemsH c*+ic# tetragonal# orthorhom+ic or rhom+ic# monocline# triclinic# he4agonal# rhom+ohedral or trigonal! alci*m &hos&hate is in the he4agonal system 'fo*r a4esH three e1*al co&lanar a4es at D0K# and one at right angles to them( and is 5nown as hydro4ya&atite fo*nd in +one and enamel! 1FF ,namel hydro4ya&atite is the most calcified and hardest mineral in the +ody! In decreasing hardness is enamel N dentine ` cemented N +one! 6ineralogists *s the 6ohs )cale of 2ardnessH from softest is 1! talc 2! gy&s*m# 3! calcite# .! fl*orite# 5 a&atite# D! felds&ar# E! 1*art/# F! to&a/# G! cor*nd*m or sa&&hire# to hardest 10! diamond! 1FG %melogenins are highly conserved E825 Bd &roteins *ni1*e to enamelA they com&ose a+o*t G0V of develo&ing enamel , 6 concerned with enamel minerali/ation and are high in &roline and gl*tamate! ,4creted +y the amelo+lasts# the amelogenins are +i&olar# nonglycosylated &roteins with some &hos&hoserine resid*esA the genes are on +oth h*man X and > genes! $N% se1*ences for h*man X and > genes# +ovine X and > genes# o&oss*m and mo*se genes are 5nown! %melogenins self8assem+le into nanos&heres '10820 m diameter( of a+o*t 100 monomer *nits# with the 8terminals on the s*rface! Initially they +ind to the &rotoenamel on the a8 and +8faces allowing crystal growth only on the c8face s*rfaceA as crystalli/ation &roceeds# d*ring mat*ration# the amelogenins are lost allowing growth on the a8 and +8faces! 1G0 ,4change of 0C for ;2C yields fl*oroa&atite# which is harder than hydro4ya&atite!
1G1

$iacyl&hos&hoglycerol '$%G( is glycerol esterified to two fatty acidsA esterification of the end ;2 of $%G with &hos&hate yields a &hos&holi&id! %dditional esterification the &hos&hate +y choline# serine# ethanolamine# or inositol yields the corres&onding &hos&hatidyl choline# etc! %ll these are fo*nd in cell*lar mem+ranes! 1G2 ,thanolamine is decar+o4ylated serine! holine is derived from ethanolamine +y three N8methylations ')%6( to yield a 1*aternary nitrogen with a &ositive charge! Betaines are amino acids with f*lly methylated amino gro*&s! 3h*s# the sim&lest +etaine 'of glycine( is derived from choline +y two o4idi/ation ste&sH C;2 to C 2; aldehyde then to C ;;2 yielding glycine +etaine or +etaineH ' 23(3NIC 22C ;;2! 6ethionine is salvaged from +etaine I homocysteine +y a transmethylase which also yields dimethylglycine 'two additional demethylations yield sarcosine then glycine(! 1G3 Phos&hatidyl li&ids com&rise the maJor am&hi&athic molec*les of the str*ct*ral &ortion of cell*lar mem+ranes!

1G. 1G5

3he glutamate decar%oxylase &rod*ces G%B%! Ornithine decar%oxylase yields &*trescine# tryptophan decar%oxylase yields try&tamine# glycine decar%oxylase yields ta*rine# and aspartate decar%oxylase yields 8alanine 'constit*ent of &antothenate( 9%lso im&ortant are lysine to cadaverineA tyrosine to tyramineA histidine to histamine!:! 3he vitamin is BD '&yrido4ine( is active as &yrido4ine &hos&hate in the decar%oxylases that *se &yrido4ine &hos&hate! 1GD G%B% is the a++reviation for 8amino8+*tyric acid derived from gl*tamine! 1GE G%B% is the maJor inhi+itory ne*rotransmitter in +rain tiss*e!
1GF

6yoglo+in is a 1D!G 5d single &oly&e&tide containing heme in m*scleA hemoglo+in is a D3 5d tetramer of heme8 containing glo+in &oly&e&tides '%2B2( in red cells! Both +ind o4ygen! 6yoglo+in o4ygen +inding c*rve is a stee& hy&er+olic c*rve that indicates a high o4ygen +inding affinity even at 10820 mm82g &;2 that ens*res mitochondria are s*&&lied evenly and well! ;4ygenation and deo4ygenation of 2+ ta5es &lace in stagesH 2+ . \LN 2+.;2 \LN2+.;. \LN 2+.;D \LN 2+.;F 2emoglo+inRs sigmoid c*rve indicates a &ositive coo&erative +inding among the fo*r s*+*nits that increases toward sat*ration s*ch that each o4ygen +o*nd increases the +inding affinity of the *nocc*&ied hemes for o4ygen! 93he 2ill coefficient 'e4& n( of the 2ill e1*ation 'y-100 L B4n-'1 I B4n( is 2!5 'at & ;2 of .0mm# &lasma &2 E!..( indicating each 2+ tetramer averages a+o*t 2!5 molec*les of +o*nd o4ygen and changes in &;2 acco*nt for s*fficient o4ygen e4change to accommodate res&iratory needs! 0or myoglo+in n L 1# for the hy&er+olic c*rve# no coo&erative +inding consistent with mass action!: 1GG Por&hyrins contain fo*r &yrroles# each with differing side chains 'see Baynes# 0ig 2E!.(! 3wo 58%"% 'from the mitochon8drion( condense in the cytosol to yield PBG '&or&ho+ilinogen(# then . PBG condense to form *ro&or&hyrinogen III# to co8&or&hyrinogen III# and +ac5 into the mitochondrion as &roto&or&hyrinogen IX# then to &roto&or&hyrin IX and finally to heme! 200 %ddition of ferro*s iron via 'errochelatase to &roto&or&hyrin IX yields metallo&or&hyrin called heme# in the final ste& of heme synthesis within the mitochondria! 201 3he stee& hy&er+olic o4ygen +inding c*rve of myoglo+in indicates high affinity even at low &;2 '10mm# F0V sat!( needed to store a ma4im*m amo*nt of o4ygen inside m*scle cells for release to mitochondria! 2emoglo+inRs sigmoidal +inding c*rve is ideal for facile o4ygen e4change re1*ired for trans&ort '+inding# dissociation( of o4ygen +etween l*ngs and &eri&heral tiss*es!
202

3he g8car+o4ylate gro*& &rovides a s&atial geometry for the negative charge of +oth gro*&s to +ind a2I cation in a coordinate com&le4! 203 3he f*nction of N8terminal cl*ster of chelated calci*m ions 'a+o*t 10812( of the coag*lation /ymogen hel&s it to +ind to e4&osed negative charges of &hos&holi&ids mem+ranes r*&t*red in endothelial cells that line +lood vessels! 20. 3he e4tremely dil*te factors in circ*lation are concentrated together in close &ro4imity +y their electrostatic +inding to the e4&osed &hos&holi&ids! oncentration and &ro4imity of s*+strate /ymogen and activating &rotease greatly facilitates the individ*al rates and therefore the /ymogen cascade series activation rates even more! 205 ;steoclastin has similar vitamin B8de&endent 8car+o4ygl*tamate calci*m chelating cl*sters s*ggesting a role for vitamin B deficiency in osteo&orosis! 20D ;4alate '2;; 8 ;;2(! %l&haH malonate '2;; 8 228 ;;2(A BetaH s*ccinate# citrate! GammaH a8BG! $eltaH @
20E

GlycolysisA %isphosphoglycerate mutase converts 1#38BPG to 2#38BPG in near molar e1*ivalence to hemoglo+in s*+*nits! 3he 2#3BPG facilitates the o4ygenation of 2+ in the l*ngs and dissociation of o4ygen in the tiss*e ca&illaries! 2#38BPG is degraded to 38PG via %isphosphoglycerate phosphatase# which is the ne4t s*+strate in glycolysis after 1#38 BPG! 20F $eo4y22+ has a lower affinity than 2+8;2 there+y assisting o4ygen gas diff*sion into tiss*e cells after o4ygen dissociation! 20G ar+on dio4ide reacts with water via car%onic anhydrase to yield car+onic acid# which dissociates into 2I and +icar+onate! 3he res*lting increase in acidic &rotons is ta5en *& +y 2+8;2 # which has a higher &Ba yielding 22+8;2# which has lower affinity for o4ygen there+y yielding deo4y22+# which circ*lates +ac5 to the l*ngs! 3he other molec*le is 2#38BPG# a negative allosteric effector of o4ygen affinity for 2+! P*tting the two negative allosteric effectors together# 2I and 2#38BPG# facilitates +oth o4ygen dissociation from hemoglo+in in the ca&illaries and diff*sion of o4ygen into cells! 210 3he car+on dio4ide reacts with each N8terminal of the 8chains to form a car+amino CN28 ;;C gro*&! ar+amino82+ acco*nts for a+o*t 13815V and car+amino8&lasma &roteins is a+o*t .V or a+o*t 1E81GV of the ;2 carriage is car+amino8&rotein! $issolved ;2 is a+o*t 3!5VA 2 ;3C is a+o*t F0V 'RB I &lasma(! %ll together ;2 trans&ort from &eri&heral tiss*es is acco*nted for!

,;0Hgcl