Introduction Biology Molecular

Pendahuluan Biologi Molekuler

Mathematical Biosciences Institute (Ohio State Univ), 2 October 2003RNAProteinDNADOGMA CENTRAL2Im betting that an intimate understanding of cell cycle regulation and apoptosis is key to understanding the process of carcinogenesis.If nothing else, the main idea emphasized here is that the coupling between the cell cycle and apoptosis how these processes are coordinated is key.This talk will focus on the links and controls of the onset of the cell cycle and apoptosis.Dogma central Biologi MolekulerAdapted from http://www.bioinfbook.org/DNA Sequence(splited by genes)RNAfenotip

proteinAsam aminoDNA

FosfatBasa (A,T, C or G)Gula DNA adalah komponen yang tersusun dari dari molekul-molekul yang disebut nukleotidMasing-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 DNAEmpat 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.htmlDNA: 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-gengenepromoterExon 1Exon 2Exon 3Intron 1Intron 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 DNAPromotor 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 RNA2) Splicing: penghilangan intron dari RNA3) Translasi: Sintesis ProteinTranskripsi 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/nucleicAnimationSplicingpre mRNAExon 1Exon 2Exon 3Intron 1Intron 2mature mRNA

Translation (1)

By translation, the nucleotide sequence on mRNAdetermines 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 biologyThree components DNARNAProteinThree steps transcriptionsplicingtranslation

Cell cell communication

Proto-oncogenes encode components of growth factor signal transduction pathwaysComponents shown in yellow are known proto-oncogenes

The VEGF family and its receptorsAdapted from Ferrara N. Nat Med 2003;9:66976Migration, permeability, DNA synthesis, survivalLymphangiogenesis P PP P P PP P P PP P VEGF-AVEGF-BPlGFVEGF receptor-1VEGF-AVEGF receptor-2VEGF-CVEGF-DVEGF receptor-3Angiogenesis19Two types of VEGF receptors have been identified. VEGF receptor-1 (Flt-1) and VEGF receptor-2 (KDR/Flk-1) bind VEGF with high affinity. Both VEGF receptor-1 and VEGF receptor-2 have seven immunoglobulin (Ig)-like domains in the extracellular domain (ECD). VEGF receptor-2 has the highest binding affinity for VEGF165.1Another member of the receptor family with seven Ig-like domains in the ECD is VEGF receptor-3 (Flt-4). Though not a receptor for VEGF, it binds VEGF-C and -D. In the embryo, VEGF receptor-3 is expressed in angioblasts and venules. Later on in development, it becomes restricted to lymphatic endothelium, suggesting that it has a role in the regulation of lymphangiogenesis.1

Ferrara N, Gerber HP, LeCouter J. The biology of VEGF and its receptors. Nat Med 2003;9:66976.

VEGF signal transduction and its effectsShibuya M. Cell Struct Funct 2001;26:2535VEGF binding to VEGF receptor-2 activates a signalling cascade resulting in cellular effectsCation channel Permeability P PP P P PP P P PP P VEGFVEGF receptor-1VEGFVEGF receptor-2VEGF-CVEGF-DVEGF receptor-3DAGDAGPLCPLCProtein kinase CRaf-1MAPKProliferation, migration PermeabilitySAPK/ JNKApoptosisSurvivalCalcium releaseCa2+ProliferationMigrationIP3PLCP13KProtein kinase B20Evidence suggests that VEGF receptor-1 and VEGF receptor-2 have differing signal transduction properties and may mediate different functions.VEGF receptor-2 undergoes strong ligand-dependent tyrosine phosphorylation in intact endothelial cells and mediates mitogenesis and chemotaxis in response to VEGF, whereas VEGF receptor-1 produces weak or undetectable responses. It has been suggested that VEGF receptor-1 is not a signalling receptor but a decoy receptor, negatively regulating the activity of VEGF on the vascular endothelium by sequestering and rendering this ligand less available to VEGF receptor-2. Conversely, later studies show that VEGF receptor-1 can interact with signal-transducing proteins and generate a mitogenic signal. More recent studies suggest that VEGF receptor-1s main role is as a ligand-binding receptor, rather than a signal-transducing receptor.1VEGF is also thought to have a role in the control of HSC survival and repopulation by means of an internal autocrine loop, i.e. the ligand interacts with its receptors within the cell.2 Mouse studies suggest, in contrast to their action on endothelial cells, that both VEGF receptor-1 and VEGF receptor-2 have roles in HSC development and survival.2 These observations could have implications for the toxicity of intracellular receptors blockers, e.g. tyrosine kinase inhibitors such as PTK787, which may interfere with the autocrine loop. Externally activating agents such as bevacizumab would not be expected to have these effects.Stimulation of signalling through VEGF receptor-2 on endothelial cells by VEGF binding results in the activation of a number of signalling pathways, including the MAPK and ras pathways. This results in cellular effects including endothelial cell proliferation, survival and migration, as well as increased vascular permeability.3

Ferrara N. Role of vascular endothelial growth factor in the regulation of angiogenesis. Kidney Int 1999;56:794814.Gerber H-P, Ferrara N. The role of VEGF in normal and neoplastic hematopoiesis. J Mol Med 2003;81:2031.Shibuya M. Structure and function of VEGF/VEGF-receptor system involved in angiogenesis. Cell Struct Funct 2001;26:2535.

Agents targeting theVEGF pathwayVEGFVEGF receptor-2Cation channel PermeabilityAntibodies inhibiting VEGF(e.g. bevacizumab)Antibodies inhibiting VEGF receptorsSoluble VEGF receptors(VEGF-TRAP)Small-molecules inhibiting VEGF receptors (TKIs)(e.g. PTK-787)Ribozymes(Angiozyme) P PP P P PP P P PP P Migration, permeability, DNA synthesis, survivalLymphangiogenesisAngiogenesis21Over expression of VEGF by tumour cells can be targeted by:antibodies against VEGFantibodies against VEGF receptorssoluble VEGF receptors that bind circulating VEGFsmall molecule inhibitors of VEGF receptorscatalytic RNA molecules (ribozymes), which cleave VEGF receptor mRNA.GDPSosGrb2PPGTPGTPRasGrowth factorP120-GAP Neurofibromin14-3-312314-3-3123Inactive Raf14-3-312314-3-3123Transcription factors etc.DNA synthesisNucleusMEKERK1ERK1?Active RafP13-KRac and Rho pathwayMorphological changeRasSignal Transduction from Receptor to Nucleus Via RAS p21Regulators : proliferation, differentiation, apoptosis, repairGenome :Genes : Cell cycleDifferentiatioApoptosisRepairMetabolismetc

ProteomeProtein: cyclin, CDK,CDKIGF : GM-CSF, FGFBcl-2, p53, caspaseGadd, enzym repairdllTranscriptome

RNARNARNARNARNARNA

A process by which signals from outside the cell are transferred inside the cell through cascade of proteins interaction. Involved in all cellular activities (death, growth, differentiation, etc.)
Regulate by protein phosphorylation.
Cellular signal transduction