Pendahuluan Biologi Molekuler

1. Pendahuluan Biologi Molekuler

2. DNA DOGMA CENTRAL RNA Protein Mathematical Biosciences Institute (Ohio State Univ), 2 October 2003

3. Dogma central Biologi Molekuler Asam amino fenotip DNA Sequence (splited by genes) protein RNA Adapted from http://www.bioinfbook.org/

4. DNA Gula Fosfat Basa (A,T, C or G) • 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)

5. 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

6. 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.

7. DNA: di-splid oleh gen-gen Exon 3 Intron 2 Exon 2 promoter Exon 1 Intron 1 gene • 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.

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

9. Another view of central dogma Gen diekspresikan pada 3 step: 1) Transkripsi: Sintesis RNA 2) Splicing: penghilangan intron dari RNA 3) Translasi: Sintesis Protein

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

11. Splicing pre mRNA Exon 3 Intron 2 Exon 2 Exon 1 Intron 1 mature mRNA

12. 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)

13. 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/

14. Summary • Central dogma of molecular biology • Three components • DNA • RNA • Protein • Three steps • transcription • splicing • translation

16. Cell – cell communication

18. Proto-oncogenes encode components of growth factor signal transduction pathways Components shown in yellow are known proto-oncogenes

19. The VEGF family and its receptors VEGF-AVEGF-BPlGF VEGF-A VEGF-CVEGF-D VEGF receptor-2 VEGF receptor-1 VEGF receptor-3 – P P– – P P– – P P– P– – P P– – P P– – P Migration, permeability, DNA synthesis, survival Angiogenesis Lymphangiogenesis Adapted from Ferrara N. Nat Med 2003;9:669–76

20. VEGF signal transduction and its effects VEGF  Permeability VEGF-C VEGF VEGF-D VEGF receptor-1 VEGF receptor-2 Cation channel VEGF receptor-3 – P P– – P P– – P P– P– – P P– Ca2+ – P PLC P– – P IP3 PLC Calcium release DAG PLC DAG P13K Protein kinase C MAPK SAPK/ JNK Raf-1 Protein kinase B Proliferation Migration Proliferation, migration  Permeability Apoptosis Survival VEGF binding to VEGF receptor-2 activates a signalling cascade resulting in cellular effects Shibuya M. Cell Struct Funct 2001;26:25–35

21. Agents targeting theVEGF pathway Antibodies inhibiting VEGF receptors Soluble VEGF receptors (VEGF-TRAP) Antibodies inhibiting VEGF(e.g. bevacizumab)  Permeability VEGF Cation channel VEGF receptor-2 Small-molecules inhibiting VEGF receptors (TKIs)(e.g. PTK-787) – P P– – P – P P– P– – P P– P– P– – P – P Migration, permeability, DNA synthesis, survival Ribozymes (Angiozyme) Angiogenesis Lymphangiogenesis

22. Growth factor Ras Ras P P 14-3-3 14-3-3 Grb2 GTP GDP GTP Sos 1 2 Active Raf P120-GAP Neurofibromin 14-3-3 3 1 1 2 2 1 2 3 3 3 MEK P13-K ERK1 ERK1 ? 14-3-3 Rac and Rho pathway Transcription factors etc. DNA synthesis Inactive Raf Nucleus Morphological change Signal Transduction from Receptor to Nucleus Via RAS p21

23. Genome : Genes : Cell cycle Differentiatio Apoptosis Repair Metabolism etc Proteome Protein: cyclin, CDK,CDKI GF : GM-CSF, FGF Bcl-2, p53, caspase Gadd, enzym repair dll Regulators : proliferation, differentiation, apoptosis, repair Transcriptome RNA RNA RNA RNA RNA RNA