Pendahuluan Biologi Molekuler

Mathematical Biosciences Institute (Ohio State Univ), 2 October 2003

RNA

Protein

DNADOGMA CENTRAL

Dogma central Biologi Molekuler

Adapted from http://www.bioinfbook.org/

DNA Sequence(splited by

genes)

RNA fenotipproteinAsam amino

DNA

Fosfat

Basa (A,T, C or G)

Gula

• DNA adalah komponen yang tersusun dari dari molekul-molekul yang disebut nukleotid

• Masing-masing nukleotid mengandung fosfat, gula dan basa nitrogen.

• Ada empat basa: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)

DNA: structure• Ikatan gula-fosfat pada nukleotid

merupakan backbone dari ikatan pada DNA

• Empat basa dari DNA dibentuk sepanjang “backbone” disebut dengan DNA sequence.

• Dua DNA saling berikatan di antara pasangan basa

• Dua ikatan basa yang mungkin yaitu: • A-T, C-G. • Dua untai DNA mempunyai formasi

struktur double helixTwo.

Source of diagram: http://www.cs.utexas.edu/users/s2s/latest/dna1/src/page2.html

DNA: tersusun dalam kromosom

Each chromosome is essentially a package for a very long, continuous DNA double strand.

Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

DNA: di-splid oleh gen-gengene

promoter Exon 1 Exon 2 Exon 3Intron 1 Intron 2

• Gen merupakan bagian dari DNA yang membawa informasi untuk membentuk protein.

• 2-3% dari DNA manusia adalah gen, gen yang tidak aktif (rest) disebut junk DNA

• Promotor terlelak di bagian awal dari komponen gen. Promotor aktif saat gen akan bekerja.

• Pada banyak gen euryotic, gen adalahsekuen DNA yang mempunyai kode, yang juga disebut sebagai exon. Bagian yang tidak membawa kode genetik disebut sebagai intron.

RNA

Source of diagram: http://en.wikipedia.org/wiki/RNA

• RNA (ribonucleic acid) adalah intermediet antara DNA dan protein.

• RNA merupakan single strand dari asam nukleat.

• Basa nitrogen T (Thymine) pada RNA terganti oleh U (Uracil)

• Tidak seperti DNA, yang terlokasi di inti, RNA juga dapat ditemukan di sitoplasma.

• Pada inti, kode gen ditranskripsikan pada RNA. Selanjutnya RNA akan keluar dari inti ke nukleus dalam sitoplasma, dimana RNA ditranslasi menjadi asam amino.

Another view of central dogma

Gen diekspresikan pada 3 step:

1) Transkripsi: Sintesis RNA

2) Splicing: penghilangan intron dari RNA

3) Translasi: Sintesis Protein

Transkripsi• Transkripsi diinisiasi oleh kompleks dari

faktor=faktor transkripsi yang berikatan dengan promotor.

• An enzyme, RNA polymerase II, travels along the gradually unzipped DNA template and polymerizes nucleotides into an RNA.

• The sequence of nucleotides on DNA template determines the sequence on RNA by following the rule of base-pair complementarity, i.e., A – U, T- A, C – G, G – C.

• Transcription continues until entire gene is

copied to RNA.

Source of diagram: http://ghs.gresham.k12.or.us/science/ps/sci/ibbio/chem/nucleicAnimation

Splicing

pre mRNAExon 1 Exon 2 Exon 3Intron 1 Intron 2

mature mRNA

Translation (1)• By translation, the nucleotide

sequence on mRNA

determines the amino acid sequence by genetic code.• Genetic code: three base pairs of

RNA (called a codon) determine one amino acid based on a fixed table.

• Translation always starts at AUG (start codon), and ends with any of UAA, UAG, or UGA (stop codon)

Translation (2) Transfer RNAs (tRNAs): small RNA

molecules. Most of the tRNAs function as carriers of amino acids and participate in protein synthesis.

For example, the tRNA with the anticodon CGG corresponds with the codon GCC and attaches alanine amino acid onto the peptide chain.

Ribosome: a complex of protein and rRNA

Animation

Source of diagram: http://www.wiley.com/legacy/college/boyer/0470003790/structure/tRNA/

SummaryCentral dogma of molecular biology

Three components DNARNAProtein

Three steps transcriptionsplicingtranslation

Cell – cell communication

A process by which signals from outside the cell are transferredinside the cell through cascade of proteins interaction. Involved in all cellular activities (death, growth, differentiation, etc.)

Regulate by protein phosphorylation.

Cellular signal transduction

Proto-oncogenes

encode components

of growth factor signal transduction

pathways

Components shown in yellow are known proto-oncogenes

The VEGF family and its receptors

Adapted from Ferrara N. Nat Med 2003;9:669–76

Migration, permeability, DNA synthesis, survival

Lymphangiogenesis

– P– PP–

P–

– P– P

P– P–

– P– P

P– P–

VEGF-AVEGF-B

PlGF

VEGF receptor-1

VEGF-A

VEGF receptor-2

VEGF-CVEGF-D

VEGF receptor-3

Angiogenesis

VEGF signal transduction and its effects

Shibuya M. Cell Struct Funct 2001;26:25–35

VEGF binding to VEGF receptor-2 activates a signalling cascade resulting in cellular effects

Cation channel

Permeability

– P– PP–

P–

– P– P

P– P–

– P– P

P– P–

VEGFVEGF receptor-1

VEGF

VEGF receptor-2

VEGF-CVEGF-D

VEGF receptor-3

DAGDAG

PLCPLC

Protein kinase C Raf-1 MAPK

Proliferation, migration Permeability

SAPK/ JNK

ApoptosisSurvival

Calcium release

Ca2+

ProliferationMigration

IP3

PLC

P13K

Protein kinase B

Agents targeting theVEGF pathway

VEGFVEGF

receptor-2

Cation channel

PermeabilityAntibodies inhibiting VEGF

(e.g. bevacizumab)

Antibodies inhibiting VEGF receptors Soluble VEGF receptors

(VEGF-TRAP)

Small-molecules inhibiting VEGF receptors (TKIs)(e.g. PTK-787)

Ribozymes(Angiozyme)

– P– PP–

P–

– P– P

P– P–

– P– P

P– P–

Migration, permeability, DNA synthesis, survival

Lymphangiogenesis

Angiogenesis

GDPSos

Grb2

P PGTP

GTP

Ras

Growth factor

P120-GAP Neurofibro

min14-3-3

1 23

14-3-31 2

3Inactive Raf

14-3-31 2

3

14-3-31 2

3

Transcription factors

etc.

DNA synthesis

Nucleus

MEK

ERK1 ERK1 ?

Active Raf

P13-K

Rac and Rho

pathway

Morphological change

Ras

Signal Transduction from Receptor to Nucleus Via RAS p21

Regulators : proliferation, differentiation, apoptosis, repair

Genome :Genes :

Cell cycleDifferentiati

oApoptosisRepairMetabolis

metc

ProteomeProtein:

cyclin, CDK,CDKI

GF : GM-CSF, FGF

Bcl-2, p53, caspase

Gadd, enzym repair

dll

Transcriptome

RNA

RNA

RNA

RNA

RNA

RNA