1. dasar mekanisme genetika

8/3/2019 1. Dasar mekanisme genetika

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Dasar Mekanisme Genetika 1

1. Nama Matakuliah : GENETIKA MOLEKULAR2. Kode / SKS : BIO 4044/2-03. Prasyarat Matakuliah : Biologi Sel dan Molekular (BIO 3002)

Genetika (BIO 3041)4. Status Matakuliah : pilihan

Rencana Program dan Kegiatan PembelajaranSemester (RPKPS)


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Setelah mengikuti kuliah ini diharapkan mahasiswa dapat memahamidan mampu menjelaskan mekanisme genetika di dalam proseskehidupan organisme yang melibatkan DNA, RNA, protein, gen,

ekspresi gen, fungsi protein di dalam regulasi genetika melaluiperannya dalam metabolisme dan pembentukan struktur organisasi sel.

Selain itu mahasiswa dapat mengetahui perkembangan terkinipenelitian genetika molekular dan teknik-teknik yang digunakan dalam

penelitian tersebut..

Tujuan Pembelajaran :


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Materi Pembelajaran dan Rencana Kegiatan Pembelajaran Mingguan

Minggu ke: Tanggal Dosen

1 2006/2/8 N Pendahuluan:

2 2006/2/15 N Dasar Mekanisme Genetika: a. Sintesis DNA, RNA dan Protein;

b. DNA Repair;c. Rekombinasi Genetika; d. Virus, Plasmid dan Transposon

3 2006/2/22 N Teknologi DNA Rekombinan: a. Fragmentasi, separasi dan sekuensing

DNA; b. Hibridisasi asam nukleat

4 2006/2/27 N c. Kloning DNA; d. Rekayasa DNA

5 2006/3/1 N Nukleus: a. DNA kromosom dan packagingnya; b. Struktur global kromosom;

c. Replikasi kromosom;

6 2006/3/8 N d. Sintesis dan proses ing RNA

7 2006/3/15 N Organisasi dan Evolusi Nuklear Genom8 2006/3/22 E Fungsi Protein: a. Making machines out of proteins;

b. The birth, assem bly and death of proteins

9 2006/4/5 N/E Ujian Tengah Semester

10 2006/4/12 E Kontrol Ekspresi Gen: a. Overview kontrol gen; b. Motif DNA-binding

dalam protein regulator ekspresi gen

11 2006/4/19 E Regulasi Genetik, Struktur Kromatin dan Kontrol Ekspresi Gen

12 2006/4/26 E Mekanisme genetika molekular untuk spesialisasi tipe-tipe sel

13 2006/5/3 E Kontrol posttranskripsional

14 2006/5/10 E Perkembangan Penelitian Genetika Terkini: Kloning

15 2006/5/17 E Transfer Gen ke Mikrobia, Sel Hewan, dan Sel Tanaman;

Transgenik Hewan dan Transgenik Tanaman

16 2006/5/26 N/E Presentasi Makalah

N: Niken Satuti NH

E: Endang Semiarti

Topik


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No. Komponen Nilai Presentase

1.2.3.4.

KuisTugasUjian Tengah SemesterUjian Akhir Semester

5103550

Total 100

Evaluasi dan Komponen Penilaian

Nilai akhir dalam bentuk huruf : A, B, C, D, E ditentukan berdasarkanpada ranking populasi nilai di kelas yang sedang berlangsung


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Referensi

Wajib:

Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K.,Watson, J.D. (2002).Molecular Biology of The Cell. 4th ed. Garland Publ. Inc., New York.

Watson, J. D., Gilman, M., Witkowski, J., and Zoller, M. (1992). RecombinantDNA. 2nd ed, Freeman and Co., New York

Tambahan:

Brown, T.A. (1999). Genomes. John Wiley & Sons, Inc., USA.

Reece, R. J. (2004). Analysis of Genes and Genomes. John Wiley & Sons,Inc., USA.

Elliot, H.E. and Elliot, C.E. (2002). Biochemistry and Molecular Biology. 2nded, Oxford University Press Inc., New York.


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Dasar Mekanisme Genetika

Replikasi DNA DNA Repair Sintesis RNA dan Protein

Rekombinasi Genetik


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Molekul DNAWatson and Crick (1953)Menggunakan data X-ray crystallography, yang dibuat oleh Rosalind Franklin

dan Maurice Wilkins di King's College London, menjelaskan struktur

DNA.

Molekul DNA:1. Terdiri atas subunit-subunit yang disebut nucleotide

(adenosine, guanosine, cytidine, thymidine monophosphate)2. Tiap nucleotidetersusun atas gula, fosfat dan basa nitrogen.

3. Ada 4 basa pada DNA molekul:Adenine - A (purine)Cytosine - C (pyrimidine)Guanine - G (purine)Thymine - T (pyrimidine)

The number of purine bases equals the number of pyrimidine bases (A+G) = (C+T)

The number of adenine bases equals the number of thymine bases A = T

The number of guanine bases equals the number of cytosine bases G = C

CHARGAFF`s Ratios or CHARGAFF`s Rule



Fred Griffith (1928)

When he added dead, virulentpneumonia bacteria to a mouse,it lived; but if he added deadvirulent bacteria to live non-virulentbacteria some mice died.

He termed the material thatchanged the non-virulent bacteria tovirulent was the transformingprinciple.

Bukti bahwa DNA adalah Genetic Material



Avery, MacLeod, and McCarty (1944)

They used biochemical purification of cellular fractions to determine that DNA andnot RNA or protein was the transforming principle.

Transformation - the alteration of phenotype by the addition of foreign DNA


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Alfred Hershey dan Martha Chase (1952)

They knew that:DNA - has P but no S ; Protein - has S but not PThey assumed that the genetic material was the material that entered the cell.

In separate experiments they infected E. colicells with 35S or 32P labeled phage.By analyzing the products they determined that 32P entered the cell.


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Central Dogma

Aliran informasi genetik dari DNA ke PROTEIN

Informasi yang berada di gen (DNA) akan diekspresikan dalam Phenotype(PROTEIN)


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What is DNA?

DNA, deoxyribonucleic acid, adalah the hereditary materialpadamanusia dan hampir seluruh organisme yang lainnya.

Hampir setiap sel di tubuh manusia mempunyai DNA yang sama.

Sebagian besar terletak di nukleus (nuclear DNA) Sejumlah kecil DNA dapat juga ditemukan di mitokondria

( mitochondrial DNA atau mtDNA) dan juga di kloroplas

Pada proses pembelahan sel, terjadi duplikasi segala sesuatu yang

ada didalam sel =========== dipertahankan pada daughter cells

`the accurate, efficient and rapid duplication of the cellular genome`DNA replication


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Cell Cycle (1)The cycle of cell growth, replication of the genetic material, nuclear andcytoplasmic division.

1. Mitosis (nuclear division): corresponding to the separation of

daughter chromosomes and usuallyending with cell division. The events

in this stage of the cell cycle leadingto cell division are prophase,metaphase, anaphase and telophase.

2. Interphase: is the time during which both cell

growth and DNA replication occurin an orderly manner in preparationfor cell division.


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The eukaryotic cell cycle is divided into 4 major periods:

1. M phase (mitotic phase or mitosis) is the period when cells prepare for andthen undergo cytokinesis. During mitosis the chromosomes are paired and

then divided prior to cell division.2. G1phase corresponds to the gap in the cell cycle that occurs following

cytokinesis. During G1 cells begin synthesizing all the cellular componentsneeded in order to generate two identically complimented daughter cells. As aresult the size of cells begins to increase during G1.

3. S phase is the phase of the cell cycle during which the DNA is replicated. Thisis the DNA synthesis phase.

4. G2 phase is reached following completion of DNA replication.

The high variability of cell cycle times is due to the variability of the G1phase of the cycle.

Cell Cycle (2)The ultimate conclusion of one cell cycle is cytokinesisresulting in two identical daughter cells.


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Replikasi DNA


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DNA Replication(M.S. Meselson and F.W. Stahl,1957)


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New nucleotides can beadded to DNA only duringreplication in the 5` to 3`direction


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Replication Fork


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A gene is the basic physical and functional unit of heredity. Gene, yang merupakan DNA, berperan dalam memberi instruksi untuk membuatprotein.

Pada manusia, ukuran gen bervariasi dari beberapa ratus basa DNA s/d lebih dari2 juta basa (jumlah + 25,000 gen). Setiap individu mempunyai 2 copy dari masing-masing gen, berasal dari keduaparental.

Most genes are the same in all people, but a small number of genes (less than 1

percent of the total) are slightly different between people.

Alleles are forms of the same gene with small differences in their sequence of DNAbases. These small differences contribute to each persons unique physical

features.

What is a gene?


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What is a chromosome?

In the nucleus of each cell, the DNA molecule is packaged into thread-like structurescalled chromosomes. Each chromosome is made up of DNA tightly coiled many timesaround proteins called histones that support its structure.


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A chromosome is the visible state of geneticmaterial during a phase of the division of the cell

(prometafase/metaphase)

DNA in metaphase chromosomes must beshortened 10,000-fold by very efficient packing.

Chromosome structure

The DNA molecule is twisted onto itself, and thesupercoiled molecule is wrapped around proteinswhich maintain its shape.

The complex DNA protein is called chromatin,while the structure formed by two turns of DNAaround one histone is called a nucleosome.

These proteins arehistone proteins.


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The DNA is wrappedaround the protein, andthen, twisted togetheragain in the shape of a

spring.


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There are 5 types of histone

molecules: H1, H2A, H2B, H3,and H4.

Except for H1, they occur inexactly equal numbers.

In less condensed chromatin

fibers, it becomes apparentthat DNA between nucleosomeis bound to H1 histones.

HISTONESare proteins with ahigh proportion of positivelycharged amino acids (lysine andarginin), which enable them to

bind firmly to the negativelycharged DNA double helix.


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Sel prokaryot

Tidak ada nukleus; nuclear bodydisebut nucleoid

Pembelahan biner menghasilkan daughter cells

yang identik (tidak ada mitosis) Organisme bersifat haploid (tidak ada meiosis)

Mempunyai satu circular chromosome(beberapa dg linear

chromosome), yang tersusun dari deoxyribonucleic acid(DNA) yang

berasosiasi dg histone-like proteins

Tidak mempunyai internal membrane-bound organelles(mitokondria,retikulum endoplasma, apparatus golgi, vakuola, dan lisosom)

representative organisms: bakteri


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Struktur Kromosom Prokaryot

Lebih simpel daripada kromosomeukaryot

merupakan DNA yang berasosiasidengan protein (histone-like protein),tetapi komponen protein lebih sedikitdaripada di kromosom eukaryot

nucleoid

kromosom apabila diulur berupacircular loop yang melekat padaplasma membran


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How does a gene make a protein?

G E i


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Gene Expression

Aliran informasi genetik:

Dari DNA ke RNA (transcription) dan

dari RNA ke protein (translation)

(Essential Cell Biology, by Alberts et al., 1998,

Garland Publishing Inc.)

During the process of transcription, the information stored in a

gene's DNA is transferred to a similar molecule called RNA(ribonucleic acid) in the cell nucleus.Translation, the second step in getting from a gene to a protein,takes place in the cytoplasm. The mRNA interacts with aspecialized complex called a ribosome, which "reads" thesequence of mRNA bases.A type of RNA called transfer RNA (tRNA) assembles theprotein, one amino acid at a time. Protein assembly continuesuntil the ribosome encounters a stop codon.


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Relationships3 tipe RNA

1. messengerRNA (mRNA):membawainformasi genetikkeluar dari nucleus untuk

protein synthesis.

2. transferRNA (tRNA):membaca informasi genetik.

3. ribosomalRNA (rRNA):merupakan molecular assembly

yang berperan dalam sintesisprotein


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mRNA

Merupakan copyinformasi yang dibawa oleh gen pada DNA

`Tugas` mRNA adalah memindahkan informasi yang ada

pada DNA ke perlengkapan translasi Pada eukaryot mRNA tidak langsung terbentuk, tetapi

ditranskrip sbg hnRNA (heterogeneous nuclear RNA) di nukleus.

hnRNA mengandung intron dan exon

(intron dihilangkan pada proses RNA splicing, exon-exon yang mengandung

`informasi`akan bergabung/menyambung)

RNA editing: penyisipan nukleotida pada mRNA


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mRNA pada bakteri

Satu mRNA dapat disandikan oleh:

- satu gen (monogen/monosistron)

- lebih dari satu gen (poligen/polisistron)


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tRNA

Membaca genetic informationpada DNA. > 20 tRNA molekul tRNA dari semua organisma mampunyai strukturyang sama (tRNA pada manusia dapat berfungsi di

sel khamir (yeast cells)

4 lengan (arms) dan 3 loops Lengan acceptor, D, T pseudouridine C dan lengananticodon

LoopD, T pseudouridine C dan anticodon loop

tRNA molekul mempunyai sebuah extra loopThe acceptor stem is the site at which a

specific amino acid is attached by an

amino-acyl-tRNA synthase. The

anticodon reads the information in a

mRNA sequence by base pairing.


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rRNA

Ribosomal RNA (rRNA) merupakan komponen ribosom; the protein

synthetic factories in the cell.

Eukaryotik ribosom terdiri dari empat rRNA molekul: 18s, 5.8s, 28s,

dan 5s rRNA.

rRNA molekul sangat berlimpah. They make up at least 80% of the

RNA molecules found in a typical eukaryotic cell.


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snRNA

Small nuclear RNA (snRNA); small RNA molekul yangditemukan dalam nukleus.

Berperan penting pada sejumlah proses di dalam

nukleus (mis.: splicing(removal of the introns from hnRNA)dan telomeremaintenance).

Berasosiasi dengan protein spesifik dan membentukkompleks yang disebut small nuclear ribonucleoproteins

(SNRNP) atau snurps.


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Transkripsi

Transcription is the synthesis of RNA from a DNA template.

Transkripsi pada prokaryot dan eukaryot:

1. Initiation - melekatnya RNA polymerase pada double-strandedDNA; RNA polymerase melekat pada sekuens DNA yang disebutpromoter.(Initiation is the most important step in gene expression)

2. Elongation pemanjangan RNA

3. Termination penyelesaian sintesis RNA.


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The promoter region contains important sequences that are requiredfor RNA polymerase to bind.These sequences are similar in both prokaryotic and eukaryoticgenes, but the locations are different.

Cell Type Location Sequence

Prokaryotic -10-35

TATAATTTGACA

Eukaryotic about -25about -80

TATA (TATA box)CAAT (CAAT box)

Conserved Sequences in Promoters

Promoter


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Protein synthesisTranslasi

Transcription is the synthesis of RNA from a DNA template.

Translasi pada prokaryot dan eukaryot:

1.Initiation ribosom akan menempel pada mRNA pada daerah yangspesifik

2.Elongation - penambahan nucleotidespada 3' end dari rantaipolinukleotida; melibatkan pertmbuhan untai pendek DNA yangtransiently single-stranded.

3.Termination - dikenalinya transcription termination sequencedandilepasnya RNA polymerase.


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Protein Synthesis

In the first step in protein synthesis, thesmall 30S subunit of the ribosome binds

to the mRNA molecule: this containstriplet codon (AUG, or GUG) at whichprotein synthesis starts.


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Elongation

Binding of the bigger subunit of the

ribosome to the small one , to formthe complete 70S ribosome.


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Then the second AA-tRNAarrives in the Aminoacyl

site (acceptor site), andbinds to the complex.

The reaction between the firstamino acid and the second

one leads to the formation of apeptide bond. A molecule ofwater is released (it is acondensation reaction).


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The second tRNA has now

moved into place and the nowfree tRNA has been released.

The third AA (R)-tRNA can

then bind to the mRNA /ribosome complex, and anew peptide bond is formed.


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This step is a repeat, to show that once the process starts, it is fast,and repetitive.


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Termination

Termination of the polypeptide occurs when the ribosome reaches aStopCodon.

Chain termination leads to the release of a polypeptide, and tRNA,and the dissociation of the ribosome into 30S and 50S subunits.

Stop codons are triplets which are not recognized by any tRNA

(UAA, UAG, UGA), but by two proteins: the releasing factors (R),(R1 recognizes UAG and UAA, R2 recognizes UAA and UGA).

The polypeptide released will be processed in different parts of the cell,depending on its role, and destination.All the processing involved depends on the polypeptide sequence,therefore on the mRNA sequence (and therefore on the original DNAbase sequence).


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mRNARibosome Codon for

specific AA

Codon

Freeaminoacids

AA:tRNA

GrowingProtein Chain

freetRNA

Anti-codon

Translation: RNA to PROTEIN

1. dasar mekanisme genetika

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