Dna dan rna unit struktural dalam sel
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DNA dan RNA UNIT STRUKTURAL DALAM SEL. Agustina Setiawati , M.Sc., Apt. Albert, 1994, Molecular Biology of the Cell, Mc Graw Hill. REFERENSI. Nucleus. Kromosom dalam sel. Chromosome. Kromosom tanpa histon. Each cell has 46 chromosomes (in 23 pairs)

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DNA dan RNA UNIT STRUKTURAL DALAM SEL

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DNA dan RNAUNIT STRUKTURAL DALAM SEL

AgustinaSetiawati, M.Sc., Apt


  • Albert, 1994, Molecular Biology of the Cell, Mc Graw Hill

REFERENSI


Nucleus

Kromosomdalamsel

Chromosome


Kromosom

tanpa histon


  • Each cell has 46 chromosomes (in 23 pairs)

  • ~30,000 genes are arranged along the 23 types of chromosomes


  • Genes come in homologous pairs

  • The location of a gene on a chromosome = locus.

  • Alternative forms of genes that influence a characteristic = alleles.


  • A gene pair of two same alleles (i.e., AA) = homozygous

  • A gene pair of two different alleles (i.e., AO) = heterozygous.

DNA Introduction, cont.


  • Genotype: The particular combination of genes present in the cells of an individual (AA or AO)

  • Phenotype: The physical trait such as, shape, color, blood type, etc.

DNA Introduction, cont.


Human 4 x 109

 22 autosom yang berbeda

2 sex kromosom

Masing2 single linier DNA

E. Coli 4.7 x 106 1 Chromosom

40 – 50 loop superkoil


  • Merupakan material intiygmengandungkodegenetik

  • Kodegenetiktsbtersimpandlmkromosom

  • Bdskdayaserapnyathdplarpewarnadibedakanmjd 2 : heterokromatin (menyerapwrn dg kuat) & eukromatin (kurangkuatmenyerapwrn)

  • Heterokromatinmerupbtkrapat (condensed) drkromatin, shgterlihatsptnodaygrapat. Bnykterlihatsaatselistirahat, sptlimfositatauselmemoriygmenanti antigen asing. Heterokromatininaktifdlmtranskripsi

  • Eukromatinbbtkhalus, bnyktdptdlmkeadaanaktif (selaktifmelakukantranskripsi).

Kromatin


  • Berdasarkan lokasinya kromatin dibedakan mjd 3 daerah :

    • Kromatin perinukleolar, berada di sekeliling nukleolus

    • Kromatin internukleolar, berada dlm nukleolus

    • Kromatin periferal, berikatan dg selaput sel.

      Kromatin nukleolar & periferal merup heterokromatin

Kromatin


  • Ditinjau dr peranannya sbg materi genetik, heterokromatin dibagi mjd 2 : heterokromatin fakultatif & heterokromatin konstitutif.

  • Heterokromatin konstitutif selamanya tdk aktif & tetap dlm keadaan mampat selama daur hdp sel

  • Heterokromatin fakultatif tdk selamanya berada dlm keadaan mampat. Pd saat ttt secara ajeg kromatin ini terurai & saat terurai mrk dpt disalin

  • Dr analisis kimia ternyata kromatin tdr dr DNA, RNA & protein. Protein yg tdpt di kromatin tdr dr 2 jenis : histon & non-histon

Kromatin


  • Histon merupakan protein bersifat sangat basa, yg disebabkan oleh adanya asam amino lisin & arginin dlm jml cukup bnyk.

  • Protein non-histon tdpt lbh dr bbrts jns, bervariasi sesuai dg jenis selnya, mis. Aktin, tubulin, RNA polimerase, asetil transferase dll

  • 146 pasang basa DNA, 1 oktamer histon. 8 buah histon mbtk oktamer yg tdr dr 4 psg masing2 : H2A, H2B, H3 & H4

  • Set 8 histon tsb dsbt nuklosome, 10 nm fibril nukleoprotein. Nukleosome dipisahkan oleh daerah antara 4 nm filamen DNA

PROTEIN HISTON


DNA

CHROMOSOME


Kromosom

  • Sblm pembelahan sel (stlh sintesis DNA), kromatin mengalami pembelahan kondensasi mbtk individu kromosom metafase, yg nampak sbg sepasang kromatid (tampak spt 2 pasang lengan)


  • Jmlh kromosom di dlm sel berbeda2 sesuai jns organismenya

  • Btk & ukuran kromosom selama mitosis berubah2 , sebag bsr memp 2 lengan & tdpt lekukan dsbt kinetokor / sentromer

  • Sentromer ini merup tempat melekatnya kromosom pd mikrotubul dr gelendong mitosis & sekaligus sbg pusat pergerakan kromosom pd stadium anafase.

  • Kromosom tanpa sentromer dsbt kromosom asentrik & umumnya gagal memisahkan diri selama pembelahan sel.

  • Kromosom saat interfase seakan2 hilang, yg tampak dlm nukleus hanya anyaman filamen halus, dsbt kromatin

Kromosom


TTAGGG

Gene 1

Gene 2

DNA

Telomeres

Telomeres

Chromosome


8,000

3,000

1,500

0

35

65

Age (years)

Telomere length in base pairs

(human white blood cells)

Telomere Length Declines


A HISTORY OF DNA

SEE p. 292-293

  • Discovery of the DNA double helix

    A. Frederick Griffith – Discovers that a factor in diseased bacteria can transform harmless bacteria into deadly bacteria (1928)

    B.Rosalind Franklin- X-ray photo of DNA.

    (1952)

    C.Watson and Crick- described the DNA molecule from Franklin’s X-ray.

    (1953)


“Rungs of ladder”

Nitrogenous

Base (A,T,G or C)

“Legs of ladder”

Phosphate &

Sugar Backbone

DNA Double Helix


UNIT FUNGSIONAL DNA/RNA


Perbedaanstrukturgulaantara RNA dan DNA


Basa DNA/RNA


IKATAN RANTAI DNA


IKATAN FOSFODIESTER


G

C

N

N

C

5’

O

CH

5’ end

HC

C

PO-CH2

NH2

C

N

N

O

1’

4’

C

C

CH

N

NH2

pGCUA

3’

2’

OH

OH

OH

C

CH

O

O

O

O

N

O P O CH2

O P O CH2

O P O CH2

O

O

O

O

O

O

O

CH

U

HN

C

N

C

CH

C

HN

O

N

CH

H2N-C

C

  • ribose sugars

  • Phosphodiester linkages

  • Directional chain (5’ to 3’)

  • 4 Bases

  • purines: adenine & guanine

  • pyrimidines: cytosine & uracil

N

N

A

3’

OH

3’ end

O-H

RNA is a polymer of ribonucleotides


DNA/RNA BERSIFAT ANTIPARALEL


DNA

Double Helix

Guladeoksiribosa

Adenine pairs with Thymine (A-T)

Tetapadadinukleus

RNA

Rantaitunggal

Gularibosa

Uracil replaces Thymine!

Ditransportkesitoplasma

DNA vs. RNA


G

C

N

N

C

5’

O

CH

5’ end

HC

C

OPO-CH2

NH2

C

N

N

O

1’

4’

C

C

CH

N

NH2

pGCTA

3’

2’

C

CH

O

O

O

O

N

CH3

O P O CH2

O P O CH2

O P O CH2

C

HN

O

O

O

O

O

O

O

C

CH

T

O

N

C

N

C

HN

CH

H2N-C

C

  • 2’-deoxyribose sugars

  • Phosphodiester linkages

  • Directional chain (5’ to 3’)

  • 4 Bases

  • purines: adenine & guanine

  • pyrimidines: cytosine & thymine

N

N

A

3’

3’ end

OH

DNA is a polymer of2’-deoxyribonucleotides


.

.

.

.

.

.

.

.

.

.

.

.

OH

OH

O

OH

OH

O

O

O

N

N

N

O

O P O-CH2

O P O-CH2

O P O-CH2

O

O

OH

O

O

O

O

O

O

P

N

O

HOCH2

O

N

O P O CH2

O P OH

O

O

O

O

+

H

O

O

...

...

O P O

O P O

O

O

H2O

mixture of 2’- and 3’- monophosphate derivatives

RNA

shortened RNA

RNA is easily hydrolyzed under alkaline conditions

The reaction proceeds through a 2’,3’-cyclic monophosphate intermediate. Enzymatic hydrolysis of RNA by RNase proceeds through a similar intermediate. Because DNA lacks the 2’-OH group, it is stable under alkaline conditions.


O

C

H2O

uracil

cytosine

NH2

CH

HN

C

C

CH

CH

N

O

N

C

CH

O

N

Cytosine deaminates non-enzymatically to form uracil. If this happens in DNA, it constitutes a mutation. A proof-reading system recognize the error, and replaces the U by C.

Why does DNA contain T rather than U?

Deamination of cytosine is of little consequence in RNA, which is not the permanent repository of genetic information.


N

HO-CH2

O

+

+

+

+

M

M

M

M

O

N

O P OCH2

O

O

O

O

O

N

O P OCH2

O

N

O

O P OCH2

O

O-PO32

5’

A phosphodiester group has a pKa of about 1, and so will always be ionized and negatively charged under physiological conditions (pH ~7).

Nucleic acids require counterions such as Mg2+, polyamines, histones or other proteins to balance this charge.

The phosphate groups of DNA and RNA are negatively charged

3’


OH

HO-CH2

O

5’

H-C=O

N

HO-CH2

H-C-OH

O

H-C-OH

OH

H-C-OH

OH

OH

OH

OH

O

H-C-OH

N

CH2OH

O P O CH2

b-furanose (ring) form

O

O

ribose in its aldehyde form

5’

O

N

4’

O P O CH2

O

O

endo

O

1’

3’

N

O P O CH2

C-2’ exo

O

N

O

3’

The ring can adopt various puckered conformations in which C-2’ and C-3’ are in either exo or endo positions relative to the base and C-5’.

OH

O-PO32

The sugars are always in the b-furanose (cyclic) form


NH2

C

N

C

N

N

C

N

C

CH

HC

HC

C

CH

NH2

C

N

N

N

N

C

CH

N

NH2

HOCH2

HOCH2

HOCH2

HOCH2

C

CH

O

N

anti-Adenosine

syn-Adenosine

O

O

O

O

The bases can adopt either syn or anti conformations, but anti conformations are preferred.

OH

OH

OH

OH

OH

OH

OH

OH

NH2

C

HC

N

HC

C

O

N

anti-Cytosine

syn-Cytosine

The nucleotide base can rotate with respect to the sugar


3 TIPE DNA


BENTUK DNA


~20 Å

Base pairs fill the center of the helix; the phosphates ( ) are on the outside.

The B-form DNA helix has a diameter of about 20 Å

A base pair is more exposed to the solvent on one side (the “major groove”, at the top in these views) than the other (the “minor groove”, bottom).


5’

3’

minor

major groove

major groove

minor groove

3.4 Å per bp

34 Å (10 bp) per turn

B-form DNA consists of a right-handed double helix with antiparallel strands

3’

5’

These dimensions are for DNA fibers. In solution, there are ~10.5 base-pairs per turn.


Melting and Renaturation of DNA

Renaturation driven by homologous base pairing


Untai ganda DNA A260 = 1.00

Untai tunggal DNA A260 = 1.37

Basa bebas A260 = 1.60


The temperature at which this “denaturation” or “melting” occurs depends on the pH and salt concentration, and increases with the GC content of the DNA. (The curves drawn here are schematic.)

If the temperature is lowered, the strands recombine. The rate of reassociation is inversely proportional to the complexity of the DNA.

The two strands of the double helix separate reversibly at high temperatures


dA

nucleotides

dG

ssDNA

dU

dsDNA

dC

Double-stranded and single-stranded DNA differ in their optical absorption at 260 nm

The conjugated p-electron systems of the purine & pyrimidine bases absorb strongly in the UV. (That’s why UV light is mutagenic and carcinogenic.)

The absorbance of double-stranded DNA (dsDNA) at 260 nm is less than that of either single-stranded DNA (ssDNA) or the free bases. This is called “hypochromism.”


TERIMA KASIH


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