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DNA dan RNA UNIT STRUKTURAL DALAM SEL Agustina Setiawati, M.Sc., Apt

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) - PowerPoint PPT Presentation

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Page 1: DNA dan RNA UNIT STRUKTURAL DALAM SEL

DNA dan RNAUNIT STRUKTURAL DALAM

SEL

Agustina Setiawati, M.Sc., Apt

Page 2: DNA dan RNA UNIT STRUKTURAL DALAM SEL

REFERENSI

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

Page 3: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Kromosom dalam selNucleus

Chromosome

Page 4: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Kromosom tanpa histon

Page 5: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Each cell has 46 chromosomes (in 23 pairs)

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

Page 6: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Genes come in homologous pairs

The location of a gene on a chromosome = locus.

Alternative forms of genes that influence a characteristic = alleles.

Page 7: DNA dan RNA UNIT STRUKTURAL DALAM SEL

DNA Introduction, cont.

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

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

Page 8: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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.

Page 9: DNA dan RNA UNIT STRUKTURAL DALAM SEL

E. Coli 4.7 x 106 1 Chromosom40 – 50 loop superkoil

Human 4 x 109

22 autosom yang berbeda 2 sex kromosom

Masing2 single linier DNA

Page 10: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Kromatin Merupakan material inti yg mengandung kode genetik

Kode genetik tsb tersimpan dlm kromosom

Bdsk daya serapnya thdp lar pewarna dibedakan mjd 2 : heterokromatin (menyerap wrn dg kuat) & eukromatin (kurang kuat menyerap wrn)

Heterokromatin merup btk rapat (condensed) dr kromatin, shg terlihat spt noda yg rapat. Bnyk terlihat saat sel istirahat, spt limfosit atau sel memori yg menanti antigen asing. Heterokromatin inaktif dlm transkripsi

Eukromatin bbtk halus, bnyk tdpt dlm keadaan aktif (sel aktif melakukan transkripsi).

Page 11: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 12: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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

Page 13: DNA dan RNA UNIT STRUKTURAL DALAM SEL

KromatinDitinjau 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

Page 14: DNA dan RNA UNIT STRUKTURAL DALAM SEL

PROTEIN HISTON 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

Page 15: DNA dan RNA UNIT STRUKTURAL DALAM SEL
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Page 21: DNA dan RNA UNIT STRUKTURAL DALAM SEL

DNA

CHROMOSOME

Page 22: DNA dan RNA UNIT STRUKTURAL DALAM SEL

KromosomSblm pembelahan sel (stlh sintesis DNA), kromatin

mengalami pembelahan kondensasi mbtk individu kromosom metafase, yg nampak sbg sepasang kromatid (tampak spt 2 pasang lengan)

Page 23: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 24: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 25: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Kromosom 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

Page 26: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 27: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Chromosome DNA

Gene 1

Gene 2

Telomeres

Telomeres

TTAGGG

Page 28: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Telomere Length Declines

0 35 65

1,500

3,000

8,000

Age (years)

Telomere length in base pairs(human white blood cells)

Page 29: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 30: DNA dan RNA UNIT STRUKTURAL DALAM SEL

A HISTORY OF DNA

Discovery of the DNA double helixA. 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)

SEE p. 292-293

Page 31: DNA dan RNA UNIT STRUKTURAL DALAM SEL

DNA Double Helix

NitrogenousBase (A,T,G or C)

“Rungs of ladder”

“Legs of ladder”

Phosphate &Sugar Backbone

Page 32: DNA dan RNA UNIT STRUKTURAL DALAM SEL

UNIT FUNGSIONAL DNA/RNA

Page 33: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Perbedaan struktur gula antara RNA dan DNA

Page 34: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Basa

DN

A/RN

A

Page 35: DNA dan RNA UNIT STRUKTURAL DALAM SEL

IKATAN RANTAI DNA

Page 36: DNA dan RNA UNIT STRUKTURAL DALAM SEL

IKATAN FOSFODIESTER

Page 37: DNA dan RNA UNIT STRUKTURAL DALAM SEL

RNA is a polymer of ribonucleotides

ribose sugars Phosphodiester linkages Directional chain (5’ to 3’) 4 Bases

purines: adenine & guanine

pyrimidines: cytosine & uracil

pGCUAC

G

U

A

5’ end

3’ end

1’

2’3’

4’

5’

3’

OH

PO-CH2

O

H2N-CC

CHN

N

NCH

CO

N

O

O

O P O CH2

O

O

C

N

N

CHC

CH

NH2

OH

O

O

O P O CH2

O

N

CHCO

HN

CHCO

OH

NH2

C

CN

N

N

CH

C

NHC

O

O

O P O CH2

O

O-HOH

Page 38: DNA dan RNA UNIT STRUKTURAL DALAM SEL

DNA/RNA BERSIFAT ANTIPARALEL

Page 39: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 40: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 41: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 42: DNA dan RNA UNIT STRUKTURAL DALAM SEL

DNA vs. RNADNA Double HelixGula deoksiribosaAdenine pairs with

Thymine (A-T)Tetap ada di nukleus

RNARantai tunggalGula ribosaUracil replaces

Thymine!Ditransport ke

sitoplasma

Page 43: DNA dan RNA UNIT STRUKTURAL DALAM SEL

2’-deoxyribose sugars Phosphodiester linkages Directional chain (5’ to 3’) 4 Bases

purines: adenine & guanine

pyrimidines: cytosine & thymine

DNA is a polymer of2’-deoxyribonucleotides

pGCTA

5’ end

3’ end

C

G

T

A

OPO-CH2

O

H2N-CC

CHN

N

NCH

CO

N

O

O

O P O CH2

O

O

C

N

N

CHC

CH

NH2

NH2

C

CN

N

N

CH

C

NHC

O

O

O P O CH2

O

OH

O

O

O P O CH2

O

N

CCO

HN

CHCO

CH3

1’

2’3’

4’

5’

3’

Page 44: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 45: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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 P O-CH2

O

OO

N

OHO

O P O CH2

OO

N

OHO

O P OO

...

OH

ON

OHO

O P OO

...

HOCH2

O

..

..

O P O-CH2

O

O

N

OOP

OO

H+

..

..

O P O-CH2

O

OO

N

OHO

O P OHO

mixture of 2’- and 3’- monophosphate derivatives

H2O

shortened RNA

RNA

Page 46: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Why does DNA contain T rather than U?

N

CHCO

HN

CHCO

CNH2

N

N

CHCO

CH

cytosine uracil

H2O

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.

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

Page 47: DNA dan RNA UNIT STRUKTURAL DALAM SEL

The phosphate groups of DNA and RNA are negatively charged

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.

5’

3’

HO-CH2

ON

O

O P O CH2

OO

N

O

O P O CH2

OO

N

O

O P O CH2

OO

O-PO32

N

+M

+M

+M

+M

Page 48: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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

5’

3’

HO-CH2

ON

OH

O P O CH2 ON

O

O

OHO

O P O CH2

OO

N

OHO

O P O CH2

OO

O-PO32

N

OH

N

3’ 1’

5’

4’

endo

C-2’ exo

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’.

CH2OHH-C-OH

H-C-OH

H-C-OHH-C-OHH-C=O

ribose in its aldehyde form

b-furanose (ring) form

HO-CH2OH

OHOH

O

Page 49: DNA dan RNA UNIT STRUKTURAL DALAM SEL

The nucleotide base can rotate with respect to the sugar

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

syn-Adenosine

NH2

C

C N

N

NHC

C

NCH

OHOCH2

OH OH

NH2

C

CN

N

N

CH

C

NHC

OHOCH2

OH OH

anti-Adenosine

O

C

N

N

CHC

CH

NH2

OHOCH2

OH OH

syn-Cytosine anti-Cytosine

OHOCH2

OH OH

ON

N

CHC

NH2

HCC

Page 50: DNA dan RNA UNIT STRUKTURAL DALAM SEL
Page 51: DNA dan RNA UNIT STRUKTURAL DALAM SEL

3 TIPE DNA

Page 52: DNA dan RNA UNIT STRUKTURAL DALAM SEL
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Page 57: DNA dan RNA UNIT STRUKTURAL DALAM SEL

BENTUK DNA

Page 58: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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

~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).

Page 59: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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

34 Å (10 bp) per turn

major groove

minor groovemajor groove

minor

3.4 Å per bp

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

5’ 3’

5’3’

Page 60: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Melting and Renaturation of DNA

Renaturation driven by homologous base pairing

Page 61: DNA dan RNA UNIT STRUKTURAL DALAM SEL

Untai ganda DNA A260 = 1.00Untai tunggal DNA A260 = 1.37Basa bebas A260 = 1.60

Page 62: DNA dan RNA UNIT STRUKTURAL DALAM SEL

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

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.)

100

80

60

40

20

0

% D

enat

ured

110100908070Temperature / o

C

40 50 70% GC60If the temperature is lowered, the strands recombine. The rate of reassociation is inversely proportional to the complexity of the DNA.

Page 63: DNA dan RNA UNIT STRUKTURAL DALAM SEL

dsDNAssDNAnucleotides

dA

dC

dGdU

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.”

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

Page 64: DNA dan RNA UNIT STRUKTURAL DALAM SEL

TERIMA KASIH