Bchm2000_L8

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Biochemistry 2000Lecture 8 Slide 1

Chapter 5:Chapter 5:Nucleic Acids,Nucleic Acids, etc.etc.

Voet & Voet: Sectios 1 & !Voet & Voet: Sectios 1 & !"a#es 82$8% & 88$!"a#es 82$8% & 88$!

Ay itroductory Biochemistry te't(oo) *ill ha+eAy itroductory Biochemistry te't(oo) *ill ha+ea itroductory chapter o ucleic acidsa itroductory chapter o ucleic acids

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Nucleotides ad eri+ati+esNucleotides ad eri+ati+es

Nucleotidesad their deri+ati+es participate iearly all (iochemical processes

-1. /oomeric uitso ucleic acids

-2. er#y rich3 $ Nucleoside triphosphates -ie4A". are products o most eer#y$releasi#path*ays AN are cosumed i eer#y$re6uiri#processes

-!. 7e#ulatorso meta(olic path*ays ad meta(olicprocesses

-%. Coactors$ re6uired compoet o eymatic

reactios -e#4 NA

9

, A, Coeyme A.-5. Catalyticacti+ity -ie.ri(oymes.

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Biochemistry 2000Lecture 8 Slide !

Nucleic AcidsNucleic Acids

Nucleotidesare ucleoside phosphates

Nucleosidescosist o a itro#eous (ase co+aletly

attached +ia a #lycosidic (od3 to the C1; o a i+e car(o

su#ar -petose.

All ucleotides cotai a ucleoside Not all ucleosides are ucleotides

glycosidicbond

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Biochemistry 2000Lecture 8 Slide %

Nitro#eous BaseNitro#eous Base

Nitro#eous (ases are plaar, aromatic molecules that are-typically. deri+ati+es o purie or pyrimidie

"aret compouds or commo ucleic acid (ases -ucleo(ases.

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$$7i(ose$$7i(ose

7i(oses-or aldopetoses. are i+e car(o su#ars *ith a aldehydeuctioal #roup -liear orm oly< re+isit duri# eer#etics.

Nucleic acids are composed e'clusi+ely o the $ stereoisomer o ri(ose -or

deo'yri(ose.

7NA -ri(oucleic acid. cotais $$ri(ose ad NA -deo'yri(oucleic acid.

cotais $2;$deo'y$$ri(ose

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Biochemistry 2000Lecture 8 Slide =

"hosphate"hosphate

"hosphate is co+aletly attached to the $ri(ose +iaphosphate ester (ods

"hosphates are typically attached to the C5; -5;$ucleotide.

> polymers, the phosphate is attached to (oth the C5; ad C!;

Nucleic acids are acidic, polyaios due to the phosphate #roupso ucleotides

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Biochemistry 2000Lecture 8 Slide ?

Nucleic AcidNucleic Acid"olymer"olymer

Nucleic acid polymers ha+e a 5; ad !; ed

Co+etio: Nucleic Acids are *ritte rom 5; to !;

Nucleic acids are sythesied rom 5;$ucleosidetriphosphates i a 5; to !; directio

Commoly amed usi# a oe letter code

e#4 NA tetraucleotide -ri#ht.

-a. d@ddAdC assumes 5;$phosphate ad !;,5;phosphate li) (et*ee ucleotides

-(. pd@pdpdApdC all phosphates e'plicitly idicated

*ith ;p;

@AC represet ri(oucleotidesd@ddAdC represet deo'yri(oucleotides

Note: he it is uderstood that NA is (ei# cosidered, the ;deo'y; prei' -ie4@AC. is ote omitted D

"roper Name

5;$deo'y#uayl$!;,5;$deo'ythymidyl$!;,5;$deo'yadeyl$!;,5;$deo'ycytidie

-sed or small E ucommo ucleic acidpolymers *here the e'plicit locatio ophosphates is essetial.

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Nucleic Acid "olymerNucleic Acid "olymer

Schematic or [email protected] or d-AppCp@p.

etraucleotide deo'yadeyl$!;,5;$deo'ythymidyl$!;,5;$deo'ycytidyl$!;,5;$deo'y#uayl$!;$phosphate

Schematic represetatio oNA structure

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Biochemistry 2000Lecture 8 Slide

SummarySummary

F reers to :

G*he ami# (ase

ri(ose*he ami#ucleoside

ri(ose ad phospate*he ami#ucleotide

racil occurs i 7NAad hymie iNA

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/odiied Bases/odiied Bases

Similar to the case *ith amio acids, ucleic acid (asesalso occur as modiied orms o the stadard (ases

ie+ita(ly modiied (ases ha+e uctioal cose6ueces

/odiied (ases occur i NAad more commoly i 7NA

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Base automersBase automers

ach (ase has a tautomer

ad @ tautomers are sho*

automeric orms o (ase display alteredhydro#e (odi# patters

/echaism that ca lead to spotaeousmutatio duri# trascriptio adreplicatio -simple or#aisms.

C ad A tautomers are (et*ee amie ad

imie orms -ot sho*.

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Chapter 5 & 2:Chapter 5 & 2:eo'yri(oucleiceo'yri(oucleic

AcidAcid..

Voet & Voet:Voet & Voet:Chapter 5 $ Sectios 1 & !Chapter 5 $ Sectios 1 & !

pa#es 82$8% & 88$!pa#es 82$8% & 88$! Chapter 2 pa#es 11%5$115! & 1158$115 Chapter 2 pa#es 11%5$115! & 1158$115

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Biochemistry 2000Lecture 8 Slide 1!

NA -atso$Cric).NA -atso$Cric). ou(le heli'

educed rom F$ray diractiopatter -74 ra)li & /4 il)is.

Double stranded

B-DNA

Franklin's X-ray diffraction pattern

from crystalline DNA

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eaturatio o NAeaturatio o NA

A(o+e a characteristic criticaltemperature, NA dou(le heli'structure is lost -deatures. adthe t*o strads dissociate

etecta(le (y ultra+iolet spectroscopicmeasuremets

si#iicat icrease i V$a(sorptio asdsNA deatures to ssNA

"rocess is re+ersi(le i heat is remo+ed

slo*ly

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Biochemistry 2000Lecture 8 Slide 1=

eaturatio iseaturatio is

Cooperati+eCooperati+eeaturatio o oe re#io o NA

duple' desta(ilies the remaider othe duple'

hispheomeo is )o* as acooperati+e process ad is characteried(y a si#moidal cur+e

mis the melti# temperature o NA

ad +aries liearly *ith the @9C

cotet o the NA

Note: or +ery short NA species-oli#oucleotides. sie has si#iicat eecto

m

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Biochemistry 2000Lecture 8 Slide 1?

Sie o NASie o NA

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dsNA StructuresdsNA Structures

A NA

#roo+es are more e6uali sie

lar#er diameter

B NA

proouced maIor#roo+e

arro* diameter

J NA shallo* #roo+es

arro*est diameterThe red line lies within major groove

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dsNA Bac)(oedsNA Bac)(oe

NA (ac)(oe has = rotata(le(ods or torsio a#les

5 are reely rotata(le ad 1 is a

pseudorotata(le (od -ri(ose. /ore theoretical coormers tha

the polypeptide (ac)(oe

Gi#hly costraied (y dou(le heli'

results i ar e*er coormers

tha e+e the smallest protei

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7i(ose Coormatios7i(ose Coormatios

7i(ose adopts C2;$edoor C!;$edoi ormal dsNA structures

edo K atom out o plae o same side as C5;

7i(ose coormatio aects phosphate separatio

A$NA -lar#e diameter. adopts a C!;$edo ri(ose coormatio -let.*ith phosphate #roups ear to oe aother

B$NA -arro* diameter. adopts a C2;$edo ri(ose coormatio -ri#ht.*ith phosphate #roups relati+ely arther apart

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Base coormatiosBase coormatios

Coormatio o plaar (ase is depedet upo ;#lycosidic (od;torsio a#le

ati coormatio-a+ored. places (ul)y #roups a*ay rom ri(ose

G o+er ri(ose ri#

sy coormatio-disa+ored. places (ul)y #roups o+er the ri(ose

= mem(er ri# -purie. or -pyrimidie. o+er ri(ose ri#

G

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dsNA: Structural "arameterdsNA: Structural "arameter

dsNA is typically i the B$orm uder physiolo#ical coditios

Note: Lear material i red (o'es4

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Biochemistry 2000Lecture 8 Slide 2!

ther Base "airsther Base "airs

here are may o atso$Cric) (ase pairi#iteractios (et*eeucleotides

occur i uusual dsNA structures icludi# ;mismatches;

7are i dsNA (ut commo i ss7NA

ote i+ol+e N? o a purie -e#4 Goo#stee Base "air middle

structure.

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Biochemistry 2000Lecture 8 Slide 2%

Supercoili# i dsNASupercoili# i dsNA

Geli' pitchca +ary i the presece o proteis or i closed$circulardsNA

replicatio, trascriptio, chromati ormatio ad #ee re#ulatio allre6uire local cha#es to the heli' pitch

supercoili#is deied (y the *rithead t*ist

*rithe H um(er o heli' coils a(out sel t*ist H le#th -(p. E pitch -(pEtur.

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