Structure of DNA and RNA

Author: Agnieszka Mizera

lntroduction

DNA (deoxyrbonucec acd) and RNA (rbonucec acd) are nucec acds functonng as nformatona macromoecues n
the ce. Deoxyrbonucec acd s a carrer of genetc nformaton n eukaryotes and prokaryotes ocated n the eukaryotc
nuceus, mtochondra and pant choropasts, as we as n the bactera ce. The rbonucec acd (RNA) s the heredtary
matera n some vruses, but n a ces t functons n other actvtes. Ony the Pessenger RNA (mRNA) carres codng
nformaton from DNA to the rbosomes servng as a tempate for proten synthess. The rbosoma RNA ( rRNA) and the
transfer RNA (tRNA) are nvoved n the transaton and other types of RNAs are nvoved n the processng and transport of
tRNAs, rRNAs and protens |1;2|.
DNA and RNA are poymers made of monomerc subunts, caed nucleotides, whch can be nked together n any order.
Thenuc eotde sthebasc,repeateduntofDNAorRNAstrandandcontansantrogenousbase-adoube-rng Surine ora
snge-rng S\riPidine,nkedto ShosShor\latedsugar. Thesugarwthanattachedbase,butwthoutaphosphategroup
s caed a nucleoside. The addton of the phosphates converts the nuceosde nto the nuceotde. In DNA moecue, the
sugar s deox\ribose and n RNA moecue - ribose. The sugars comprse the backbone of every DNA or RNA chan,
nked by covaent phosphodester bond between 5- and 3-carbons of two ad|acent sugars.
EveryDNAorRNAcha nhastwoposs b echem cadrectons:53or35,becauseofhavngtwochemca ydst nctends,
caed end and 3end. At the 5 end, there s a phosphate group attached to 5-carbon of sugar, whereas at the 3 end
there s a hydroxy group attached to 3-carbon of sugar. A natura poymerases extend a DNA or RNA poymer n the 53
drecton. They catayze the repacement the hydroxy group at the 3 end n the ast nuceotde of the second nuceotde,
after removng the two outer phosphates from t |1;3|.
DNA nuceotdes contan adenine (A), guanine (G), c\tosine (C) or th\Pine (T). A and G are purnes and C and T are the
pyrmdne bases. They are attached to 1-carbon of 2-deoxyrbose n DNA by a Ngl\cosidic bond nkng ntrogen
number 1 of the pyrmdne or number 9 of the purne wth the sugar | |. 2-deoxyrbose, as a pentose, s composed of fve
carbon atoms. It s a dervatve of sugar caed rbose, n whch the hydroxy (-OH) group attached to the 2-carbon has been
repaced by a hydrogen (-H) group |3|.
In ces, DNA moecues are comprsed of two poynuceotdes assembed together formng the rght-handed structure caed
double helix or the B-form of DNA. In doube hex, two strands of DNA run n opposte drectons. There are two types of
chemca nteracton, whch stabze ths structure and hod the two poynuceotdes together. The frst type of nteracton s
the base-parng between an adenne on one strand and a thymne on the other, or between a cytosne and a guanne. The
hydrogenbondsformedbetweenthsbases,twoandthreerespectvey,stabzethedoubehe x. Thesecondnteract ons
base-stackng, sometmes caed the p-p nteractons. It nvoves hydrophobc nteractons between ad|acent bases |3|.
The structure of RNA s very smar to the DNA structure, athough there are three man dfferences between these two
nucec acds. RNA nuceotdes have rbose as a sugar, and contan uracil base nstead of thymne n one of the nuceotde
types. RNA s usuay a one strand nucec acd but t can form RNA-RNA dupexes n a ces durng the RNA processng and
gene expresson. The four nuceotde substrates for synthess of RNA are: adenosne 5-trphosphate (ATP), cytdne
5-trphosphate (CTP), guanosne 5-trphosphate (GTP) and urdne 5-trphosphate (UTP), whch are abbrevated to A, C, G
and U, respectvey |3|.
Available Paterials:
]1| Nucleic Acids ]required|
]| DNA and RNA as large Sol\Pers ]additional|
]3| The structure of DNA ]required|
]4| DNA: Alternative ConforPations ]required|
]| BDNA and ADNA ]required|
]6| The structure of nucleotide ]additional|
]7| The structure of the ShosShodiester bond ]additional|
]8| The chePical differences between DNA and RNA ]additional|
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]9| The double helix structure of DNA ]additional|
]10| CoPSutergenerated iPages of BDNA (left), ADNA (center) and ZDNA (right) ]additional|
Available test questions:
1. uestion:
:hat s a monomerc subunt of the DNA or RNA poymer?
Possbe answers Correct?
nuceosde no
nuceotde \es
purne base no
pyrmdne base no
rbose no
References: DNA sanear,unbranchedpoymer nwhchthemonomercsubuntsarefourchemcaydstnctnuceotdes
that can be nked together n any order n chans hundreds, thousands or even mons of unts n ength |1|.

. uestion:
:hat are the man components of the DNA nuceosde?
Possbe answers Correct?
purne or pyrmdne base and 2-deoxyrbose \es
purne or pyrmdne base and phosphoryated 2-deoxyrbose no
sugars nked by covaent phosphodester bond between 5- and 3-carbons no
References: A moecue made up of |ust the sugar and base s caed a nuceosde | |. Nucleoside A purne or pyrmdne
base attached to a fve-carbon sugar |1*|.
3. uestion:
Choose the statement(s) beow that s/ are correct:
Possbe answers Correct?
There s a phosphate group attached to 5-carbon of sugar at the 5 end of DNA \es
There s a hydroxy group attached to 5-carbon of sugar at the 5 end of DNA no
There s a phosphate group attached to 3-carbon of sugar at the 3 end of DNA no
References: Note that the two ends of the poynuceotde are chemcay dstnct, one havng an unreacted trphosphate
group attached to the 5-carbon (the or 3 terPinus) and the other havng an unreacted hydroxy attached to the
3-carbon (the 3 or 32+ terPinus) |1|.
4. uestion:
:hch carbon n the 2-deoxyrbose moecue does not have the hydroxy (-OH) group?
Possbe answers Correct?
4 no
3 no
2 \es
References: The name 2-deoxyrbose' ndcates that ths partcuar sugar s a dervatve of rbose, one n whch the
hydroxy (-OH) group attached to the 2-carbon of rbose has been repaced by a hydrogen (-H) group |1|.
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. uestion:
:hat are the nteractons whch stabze the doube hex DNA?
Possbe answers Correct?
hydrogen bonds formed between opposte base pars \es
base-stackng \es
hydrophobc nteractons between ad|acent bases \es
References:
The hex s stabzed by two types of chemca nteracton:
Base-parng between the two strands nvoves the formaton of hydrogen bonds between an adenne on one strand and a
thymne on the other strand, or between a cytosne and a guanne ( Figure J.JJ8 ).
Base-stackng,sometmescaed interactions, nvoveshydrophobcnteract onsbetweenad|acentbaseparsandadds
stabty to the doube hex once the strands have been brought together by base-parng |1|.

6. uestion:
Confrm or deny: RNA nuceotdes have rbose as a sugar and contan urac base n one of the nuceotde types.
Possbe answers Correct?
correct \es
References:
The sugar n an RNA nuceotde s rbose. RNA contans urac nstead of thymne |1|.
7. uestion:
The typca DNA:
Possbe answers Correct?
s a doube hex \es
s a rght-handed structure \es
has two antparae strands \es
References: Canonca B-DNA s a doube hex made of two antparae strands that are hed together va hydrogen
bondng n the AT and GC base pars (fg. 1) |5|.
8. uestion:
Are these forms the conformatons of DNA?
Possbe answers Correct?
C-, C-, C-DNA \es
A-, B-, Z-DNA \es
B-, D-, E- and T-DNA \es
References: The modfed verson of the doube hex caed the A-form ( Figure J.J2 ). Other varatons ncude B-, C-, C-,
C-, D-, E- and T-DNAs. A these are rght-handed heces ke the B-form. A more drastc reorganzaton s aso possbe,
eadng to the eft-handed Z-DNA ( Fgure 1.12 ), a smmer verson of the doube hex wth a dameter of ony 1.84 nm |3|.
9. uestion:
Confrmordeny:TheB-formofDNAhasanent re ysmoothsurfaceanddoesnothavetwogrooves,caedthema| orgroove
and the mnor groove, whch spra aong the ength of the A-DNA hex.
Possbe answers Correct?
correct no
References: The B-form of DNA does not have an entrey smooth surface; nstead, two grooves spra aong the ength of
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thehex.Oneofthesegroovessreat veywdeanddeepandsca edthe ma|orgroove;theother snarrowand essdeep
and s caed the mnor groove |3|.
10. uestion:
Aternatve DNA structures can be mportant for
Possbe answers Correct?
nteractons wth protens nvoved n repcaton, gene expresson and recombnaton \es
formaton of nuceosomes and other supramoecuar structures nvovng DNA \es
provdng enormous potenta for autoreguaton of DNA functons \es
References: 6evera non-B-DNA structures (oftentmes caed unusua or aternatve DNA structures) can be mportant for
interactions with Sroteins involved in reSlication, gene exSression and recoPbination. They may aso pay
dfferent roes n the forPation of nucleosoPes and other suSraPolecular structures involving DNA Together wth
varatons n DNA supercong, oca aternatve structures provde enormous Sotential for autoregulation of DNA
functions |4|.

11. uestion:
:hat s the boogca reevance of the A-DNA?
Possbe answers Correct?
A-ke conformaton s adopted by the DNA n the target ste for the TATA-box bndng proten \es
(TBP)
The Eschercha co cycc AMP receptor proten (CAP) may have a 8 bp spacer whch adopt \es
A-form
A-DNA may form compexes wth enzymes that cut or sea at the (O3'-P) phosphodester nkage \es
References:
The DNA ogomer, GCGTATATAAAACGC, whch contans a target ste for the TATA-box bndng proten (TBP), adopts an
A-ke conformaton n the regon of the TATA-box and undergoes bendng reated to that seen wthn the compex wth the
TBP.
The (VFKeriFKia FROi cycc AMP receptor proten (CAP) has two symmetrcay reated nverted recognton eements
separatedbyaspacer. CAPbndngnducesDNAbend ngwthDNAreman ngntheB-formwhenthespacers6bp. Forthe
8 bp spacer, an addtona transton nto the A-form s necessary to shorten the dstance between TGTGA stes for CAP
bndng.
The B-to-A transton may occur n DNA compexes wth enzymes that cut or sea at the (O3'-P) phosphodester nkage |5|.
1. uestion:
The crucform structure conssts of:
Possbe answers Correct?
two reatvey ong dupex DNA arms \es
two reatvey short harpn arms \es
unpared oops of 3-4 bp typcay exst at the tp of the crucform arms \es
References:
The crucform conssts of two rather ong dupex DNA arms, and two comparatvey short harpn arms whch form a
four-way |uncton |5|. An unpared oop of 3-4 bp typcay exsts at the tp of the crucform arms.

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http://www.ncb.nm.nh.gov/books/bookres.fcg/eurekah/ch260f2.gf
13. uestion:
Confrmordeny:Thebasetr adsareun tb ocksofatr p e-stranded(tr p ex)DNAthatconsstoftheB-formdoub ehe xand
the thrd strand bound n the ma|or groove.
Possbe answers Correct?
correct \es
References:
Basetradsthatareun tb ocksoftrpe-stranded(trp ex)DNAthatconsstsoftheB-formdoub ehexandthethrdstrand
bound n the ma|or groove |5|.
14. uestion:
:hat are the boogca processes n whch superco-drven aternatve structures: crucforms Z-DNA, and H-DNA may pay
roes?
Possbe answers Correct?
moduaton of supercong, nuceosome excuson \es
postonng of sequence eements, moecuar swtch \es
transcrpton repcaton recombnaton \es
References:
Possbe Boogca Roes of 6uperco-Drven Aternatve 6tructures:
Moduaton of 6upercong
Nuceosome Excuson
Postonng of 6equence Eements, Moecuar 6wtch
Roes n Transcrpton
Roes n Repcaton
Roes n Recombnaton |5|.

1. uestion:
Confrm or deny: A spped-strand DNA (6-DNA) structure s formed when a secton of the repeatng dupex unwnds so that
onereg onofthedrectrepeatformsthe:atson-Crckbasepa rswthanotherregonoftherepettvesequenceformngtwo
oop-out regons n opposte strands.
Possbe answers Correct?
correct \es
References: A spped-strand DNA (6-DNA) structure forms when a secton of the repeatng dupex unwnds so that one
regon of the drect repeat forms the :atson-Crck base pars wth another regon of the repettve sequence formng two
oop-out regons n opposte strands (fg. 4A) |5|.

16. uestion:
:hch drecton s possbe n the RNA or DNA chan:
Possbe answers Correct?
ony 53 no
ony 35 no
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53 or 35 \es
References:
An mportant consequence of the poarty of the phosphodester bond s that the chemca reacton needed to extend a DNA
poymer n the 53 drecton s dfferent to that needed to make a 35 extenson |3|.
17. uestion:
Confrm or deny: -N-gycosdc bond nks ntrogen number 1 of the pyrmdne or number 9 of the purne wth the sugar.
Possbe answers Correct?
correct \es
References:
The base s attached to the 1-carbon of the sugar by a gl\cosidic bond attached to ntrogen number 1 of the
pyrmdne or number 9 of the purne |3|.
18. uestion:
RNA-RNA dupexes can be form n a ces:
Possbe answers Correct?
durng RNA processng \es
answer a and c are not correct no
durng gene expresson \es
19. uestion:
Choose the proper reaton:
Possbe answers Correct?
snge-rng - purne and doube-rng - pyrmdne no
doube-rng - pyrmdne and doube-rng - purne no
doube-rng - purne and snge-rng - pyrmdne \es
snge-rng - pyrmdne and snge-rng - purne no
References: Cytosne, thymne : snge-rng pyrmdnes, adenne or guanne: doube-rng purnes |1|.
0. uestion:
:hch end(s) of prmer s extended by the DNA poymerase?
Possbe answers Correct?
3 end \es
5 end no
3 end and 5 end no
References:An mportant consequence of the poarty of the phosphodester bond s that the chemca reacton needed to
extend a DNA poymer n the 53 drecton s dfferent to that needed to make a 35 extenson |3|.
1. uestion:

Match the ntrogen bases wth the proper group:
1 - adenne, 2 - guanne, 3 - cytosne, 4 - thymne, 5 urac
a purne bases, b pyrmdne bases
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Possbe answers Correct?
1,2-b; 3,4,5-a no
1,3-b; 2,4,5-a no
1-a,2-a,3-b,4-b,5-b \es
2,3-a; 1,4,5-b no
References:Cytosne, thymne : snge-rng pyrmdnes, adenne or guanne: doube-rng purnes |1|.
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