D:\garima\pic\images.jpgBIOLOGI MOLEKULAR Tim Pengajar Biologi Molekular PSF FKUB 2012 Kode / SKS : DEF 4120 / 2 SKS Dosen Pengampu : 1.Dra. Diana Lyrawati, Apt. MS. PhD 2.Valentina Yurina, M.Si. 3.Ferri Widodo, S.Si. Apt. Semester : 3 (tiga) Status MK : Wajib Deskripsi singkat : Dalam MK ini akan dibahas mengenai mekanisme genetik secara molekuler termasuk sistem kontrol gen. Selain itu akan dibahas pula struktur sel, serta proses-proses yang terjadi di dalam sel (siklus sel, cell signaling, & transport molekul) serta interaksi sel dg lingkungannya. Sbg tambahan diberikan juga pemahaman konsep penyakit genetik termasuk kanker & aplikasi bioteknologi dl bidang Farmasi. Tujuan Pembelajaran Setelah mempelajari mata kuliah ini mahasiswa diharapkan: .Dpt memahami mekanisme genetik secara molekuler dl sel, termasuk mekanisme kontrolnya. .Dpt memahami proses-proses yg terjadi dl sel meliputi siklus sel, transport molekul, & cell signaling. .Dpt memahami konsep mutasi genetik & pengaruhnya, termasuk dl penyakit kanker. .Diajarkan mengenai penyakit genetik pd manusia serta penerapan Biologi Molekular dl bid Farmasi. Tanggal Pokok bahasan Sub pokok bahasan Strategi Dosen 1 Pendahuluan -Tujuan perkuliahan -Aturan perkuliahan dan sistem penilaian -Konsep dasar biologi molekular -Tatap muka yang diisi dengan ceramah dan diskusi -Tugas untuk mahasiswa, dikerjakan secara perorangan atau perkelompok, dapat berupa tugas tertulis atau lisan (presentasi) -Fasilitas: LCD viewer, whiteboard, laptop Ferri Widodo S.Si. Apt. 2 Mekanisme genetika molekular -Struktur asam nukleat -Gen, kromosom dan genom -Organisasi struktur kromosom manusia -Replikasi dan ekspresi gen Sda. Ferri Widodo S.Si. Apt. 3 Mekanisme kontrol gen -Kontrol ekspresi gen dalam proses transkripsi -Kontrol gen post-transkripsi Sda. Valentina Yurina, M.Si 4 Biomembran dan struktur sel -Komponen penyusun biomembran: lipid dan protein -Organel sel -Komponen dan struktur sitoskeleton Sda. Dra. Diana Lyrawati, Apt.MS.PhD 5 Sel dan lingkungannya -Matriks ekstraseluler -Integrin sebagai reseptor pada matriks ekstraseluler -Adhesi antar sel -Sel junction Sda. Dra. Diana Lyrawati, Apt.MS.PhD 6 Transport ion dan molekul kecil melalui membran sel -Prinsip transport melalui membran sel -Protein carier dan transport aktif -Ion channel dan potensial elektrik pada membran Sda. Dra. Diana Lyrawati, Apt.MS.PhD 7 Transport protein, mekanisme sekresi dan endositosis Prinsip protein targeting Mekanisme endositosis Mekanisme eksositosis Sda. Dra. Diana Lyrawati, Apt.MS.PhD 8 UTS Ujian tertulis 9 Cell signaling -Prinsip cell signaling -Signaling melalui reseptor terkait G-protein -Signaling melalui reseptor terkait enzim -Target cell adaptation Sda. Ferri Widodo S.Si. Apt. 10 Siklus sel dan apoptosis -overview siklus sel -M phase -Mitosis -Kematian sel dan regulasinya Valentina Yurina, M.Si 11 Mutasi gen -Prinsip mutasi -Klasifikasi jenis mutasi yang dapat terjadi -Implikasi positif dan negatif terjadinya mutasi dalam bidang farmasi Sda. Valentina Yurina, M.Si 12 Sel kanker -Sel tumor dan onset kanker -Mekanisme genetik pada kanker -Karsinogenik dan mekanisme DNA repairing pada sel kanker Dra. Diana Lyrawati, Apt.MS.PhD 13 Penyakit genetik pada manusia -Penyebab terjadinya penyakit genetik -Klasifikasi penyakit genetik -Beberapa penyakit genetik yang umum dijumpai di masyarakat dan terapinya Sda. Ferri Widodo S.Si. Apt. 14 Penerapan biologi molekular dalam bidang farmasi -Prinsip Teknologi DNA rekombinan -Prinsipdasar PCR dan aplikasinya -Rekayasa genetik pada bidang farmasi Sda. Valentina Yurina, M.Si 15 Presentasi dan diskusi kelompok Tim Dosen 16 UAS Ujian tertulis Penilaian Penilaian mahasiswa didasarkan nilai ujian, tugas, & partisipasi dg persentase sbb: UTS, bobot 35% UAS, bobot 35% Tugas, bobot 20% Aktivitas perkuliahan, bobot 10% PUSTAKA 1.Lodish, H. 2000. Molecular Cell Biology. New York: W H Freeman 2.Bruce Albert. Molecular Biology of the Cell. 3.Robinson , TR. 2005. Genetic for dummies. Canada: Wiley Publishing Inc. Peraturan Perkuliahan 1.Pakaian sopan & mengenakan sepatu. 2.Tdk diperbolehkan mengenakan celana jeans/denim. 3.Maksimum ketidakhadiran 3 kali pertemuan, > 3 kali perkuliahan mahasiswa dianggap mengundurkan diri dari MK Biologi Molekular & wajib mengulang mata kuliah yg sama. 4.Maksimum keterlambatan kehadiran dl kuliah 15 menit, > 15 mnt mahasiswa tdk boleh mengikuti perkuliahan & dianggap tdk hadir. 5.Apabila mahasiswa tdk hadir, wajib memberikan pernyataan izin tertulis. 6.Mahasiswa wajib mempersiapkan diri mengikuti perkuliahan yg akan diuji dg tanya jawab yg harus dijawab oleh mahasiswa di setiap perkuliahan. 7.Mahasiswa wajib membawa buku/sumber referensi lain yg diperlukan dl mengerjakan tugas-tugasnya. Basic Concepts of Molecular Biology Contents: 1. Life 2. Proteins 3. Nucleic Acids 4. Molecular Genetics (mechanisms). 5. How the Genome is studied 6. Sequence Databases 1. Life Living organism: due to complex array of chemical reactions, exchanges constantly matter and energy with its surroundings, no deadlock. The main actors in the chemistry of life (biochemistry) are molecules called proteins ("we are our proteins") and nucleic acids. Molecular biology research: basically devoted to the understanding of the structure and functions of proteins and nucleic acids. Basic differences between eukaryotes and prokaryotes Attribute Eukaryotes Prokaryotes Organisms Plants, animals and fungi bacteria and cyanobacteria Cell wall No (animals); Yes (plants) yes Chromosome segregation Mitotic spindle Cell membrane meiosis + _ Ribosome size 80 s 70 s Cell organelle Nuclear membrane + Absent Endoplasmic reticulum + - Golgi apparatus + - Mitochondria + - Chloroplast + - Molecular biology: definition Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. D:\garima\pic\hexagon.jpgComponents involve in molecular biology DNA RNA Protein D:\garima\pic\dhelix.jpgD:\garima\pic\rna.jpgD:\garima\pic\proteinStructure.jpghttp://andersonlab.qb3.berkeley.edu/Tutorials/Basic_Molecular_Biology_files/image002.jpgBasic players in molecular biology: DNA, RNA, and proteins. What they do is this : Cell Types Prokaryotes: bactcellEukaryote: ANIMALCELLCell Types A.Prokaryotes: bacteria, have no nucleus or membrane-bound organelles. Earths oldest fossils. prokaryote diagrambacteria salmonellaBacteria anthraxCell Types 2. Eukaryotes: contains membrane bound nucleus and organelles. Two types: plant and animal Cell Diagramplant cellPurple meshallcell Organelle PROKARYOTES PROKARYOTES + - Endomembrane Nuclear membrane + Mitochondria - - + + + Golgi Apparatus Endoplasmic Reticulum THE DIFFERENCES BETWEEN PROKARYOTES AND EUKARYOTES fuchia- - Eukaryotic Cell Types : Animal vs. Plant Anatomy of the Animal CellAnatomy of the Plant CellCell Types : Animal vs. Plant 1.Plant cells have chloroplasts 2.Plant cells have a cell wall 3.Plant cells have a large central vacuole 4.Animal cells have more lysosomes 2. Protein Most substances in our bodies are proteins: -structural proteins act as tissue building blocks -enzymes: act as catalyst of chemical reactions A protein is a chain of amino acids. It has a central carbon to which is attached : - a H -an amino group NH2 - a carboxy group COOH -a side chain particular to each amino acid %img036 img038D:\garima\pic\protein.jpgD:\garima\pic\polypeptide.gifD:\garima\pic\proteinStructure.jpgProtein Proteins (also known as polypeptides) are made of amino acids arranged in a linear chain and folded into a globular form. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. genetic code specifies 20 standard amino acids. %img039Structures: The primary structure is the sequence of the residues. The secondary structure takes in account local interactions between atoms of the backbone (a_helix, -sheet, loops). The tertiary structure expresses the folding in 3D. Quaternary structure: group of different proteins packed together. %img040Protein structure protein structureGene expression regulation gene expression controlNucleic Acids Living organisms contains two kinds of nucleic acids: - ribonucleic acid (RNA) - deoxyribonucleic acid (DNA) DNA - double chain with two strands. - backbone is formed by a sugar molecule (2'-deoxyribose) attached to a phosphate residue. - orientation: carbon atoms are labeled 1' to 5'. The basic bond of the backbone is : 3' carbon -phosphate residue- 5' carbon. By convention, a strand begins at the 5' end and finishes at the 5' end. Struktur Asam nukleat .Asam nukleat adalah suatu senyawa yang merupaka asam inti yang terdiri dari DNA dan RNA .Merupakan rantai POLINUKLEOTIDA yaitu : Makromolekul yang tersusun oleh molekul yang lebih sederhana yang disebut Nukleotida .Nukleotida merupakan molekul yang tersusun atas .satu gula, .satu basa, dan .satu fosfat. .Nukleosida adalah kombinasi suatu gula pentosa yang dihubungkan dengan basa purin atau pirimidin melalui ikatan C - N Nukleotida .Protein yang bergabung dengan asam nukleat . .Nukleotida dalam sitoplasma dan dalam inti adalah sama tetapi jenis asam nukleatnya berbeda. .Nukleotida tersusun atas : 1 Basa DNA 1 Gula Komponen yang essential 1 Fosfat RNA .Gula . Ribosa & Deoksiribosa .Basa . Adenin, Guanin, Timin, Sitosin .Polinukleotida adalah. Ikatan antara 2 nukleotida dari 2 gugus fosfat yang terikat pada 2 pentosa . ikatan Fosfodiester .Tiap struktur DNA / RNA merupakan suatu polinukleotida yang ujung-ujungnya C3 & C5 %img037- To each 1' carbon is attached a base: adenine A, guanine G,(they are purines), cytosine C, thymine T (they are pyrimidines). - A nucleotide is a set sugar + phosphate + base - An oligonucleotide is a DNA molecule having a few (ten of) nucleotides. %img041 %img042- DNA molecules are double strands which are tied together in a helix structure (James Watson and Francis Crick, 1953). - A (resp. C) is the complement of T(resp. G). Unit of length: bp (base pair) - The two strands are antiparallel. one can be deuced from the other by reverse complementation Example: s = AGACGT, s' = TGCAGA (reverse) s = AGACGT (reverse complement) img043RNA Differences with DNA - Sugar is ribose instead of 2'deoxyribose. - Instead of T, one finds U (uracil) which binds also with adenine. - RNA does not form a double helix. It may have a far more varied three dimensional structure. - They are different kinds of RNA which perform different functions. Genes and the genetic code - Chromosome: long DNA molecule which contains coding parts which contains genes which code for proteins. - Each amino acid is specified by a codon, a triplet of nucleotide. The correspondence between each triplet (using RNA) and each amino acid is given by the genetic code : - There are 64 possible triplets, but only 20 amino acids. - Several codons can code for one amino acid (ie. AAG and AAA for lysine) - Three codons STOP are used to signal the end of a gene. Future of molecular biology Personalised medicine Target-specific drugs (e.g. adipose tissue) Gene therapy Comparative genomics ReferencesMolecular biology informationBiology, Campbell and Reece (6thEd.), Very readable general biology textbookwww.ebi.ac.uk/2can, good introduction to bioinformatics and molecular biologyhttp://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html-online biology book http://biology-pages.info, good glossary/information sitehttp://www.genomicglossaries.com/http://www.gene.ucl.ac.uk/nomenclature/guidelines.html, defines the nomenclature for human genesDatabaseswww.ebi.uniprot.org, excellent protein sequence databasewww.ncbi.nih.gov, numerous protein/genome databaseswww.ensembl.org, information on genes/proteins/exons of completed genomeshttp://www.ebi.ac.uk/embl/, European gene sequence databankMichael Y. Galperin, The Molecular Biology Database Collection: 2005 update, NARwww.bioinfo.no/links, list of useful biological linksGene/Protein naming conventionsBioinformatics. 2005 Jan 15;21(2):248-56. Epub 2004 Aug 27. Gene name ambiguity of eukaryotic nomenclatures.Chen L, Liu H, Friedman C. D:\garima\pic\dna1.bmpThank you