CURRICULUM VITAE

NAMA : PARAMASARI DIRGAHAYU., dr., PhD Lahir : Purwokerto, 21 April 1966

PENDIDIKAN S1 : FK UNS Surakarta (1992) S2-S3 : Tottori University Japan (1999-2003) Post Doctoral : Tottori University Japan (2003-2004) Field of Interest : Immuno-Parasitology Molecular Biology and Biotechnology PEKERJAAN:

Kepala Instalasi Parasitologi Klinik dan Mikologi RSDM Kepala Pusat Bioteknologi dan Biodiversitas LPPM UNS Wa Ka Lab Parasitologi-Mikologi FK UNS Koordinator International Office UNS Sekretaris Lab Biomedik Terpadu FK UNS Assesor BAN PT DIKTI

(2007) (2005) (2007) (2009) (2006) (2007)

Pendahuluan
Kompetensi yang harus dicapai:
Memahami peran ilmu Biologi molekuler di bidang kedokteran dan kesehatan. Mengerti dasar/ jargon ilmiah di bidang biologi molekuler Memahami prinsip-prinsip dasar biologi molekuler dan Bioteknologi dibidang kedokteran sehingga mampu menyusun experimental design/memahami journal penelitian internasional berbasis molekuler.

SYLABUS MATA KULIAH BIOLOGI MOLEKULER

Kuliah 1 2 3 4 Topik Filosofi Biologi Molekuler dan Perannya di Bidang Kesehatan-1 Filosofi Biologi Molekuler dan Perannya di Bidang Kesehatan-1 Struktur dan fungsi Sel, virus, DNA, RNA dan Protein Virologi Molekular dan aplikasi di bidang kedokteran Sel structure and Gene Expression Pengampu (Prof . DR. dr. Ambar Moedigdo., SpPA(K) (Prof . DR. dr. Ambar Moedigdo., SpPA(K) (Afiono Agung S, dr., PhD) Afiono Agung P.,dr.,PhD

5 6

Paramasari Dirgahayu

7 8 9

Tehnik Biologi Molekuler dan Aplikasinya di Paramasari Dirgahayu, Paramasari Dirgahayu, dr., bidang kedokteran-1 PhD Diagnostik dan Terapi Molekuler Paramasari Dirgahayu, dr., Jurnal reading-1 PhD + (Afiono Agung S, dr., PhD) Jurnal reading-2 (Paramasari Dirgahayu, dr., PhD + (Afiono Agung S, dr., PhD)

Fungsi Ilmu Bioteknologi

1. Diagnosa penyakit 2. Prevensi penyakit herediter 3. Terapi molekuler (stem cell terapi, DNA terapi, dll) 4. Riset/Klarifikasi host-Agent relation 5. Pembuatan vaksin 6. Forensik molekular 7. Epidemiologi molekuler 8. dll

TEKNIK BIOLOGI MOLEKULER (BIOTEKNOLOGI)

Digunakan dalam identifikasi ekspresi genetik/protein secara kuantitatif/kualitatif Terpenting: Preparasi sample : dari Invivo/In Vitro experiment berupa DNA/RNA/Protein?

Tentukan metode identifikasi sample 1. Isolasi DNA 2. PCR 3. Western Blot 4. Northern Blot 5. Southern blot 6. Immunohistokimia 7. ELISA 8. Sequencing 9. Cloning

Overview
BODY
ORGANS

CELLS
KROMOSOMS
NUKLEUS
PHENOTYPE GENOTYPE

DNA
GENE

What Is a Cell?
Basic Unit of Life metabolism replication
Cell Structure composition (molecules) organization

cells acquire nutrients and convert them to energy and self (growth) all cells come from pre-existing cells (reproduction)
Laboratorium BIOMEDIK TERPADU Fakultas Kedokteran UNS

Eukaryote vs Prokaryote
Plasma Membrane Lysosome Nucleus

Eukaryotic cells have membrane-bound compartments with specialized functions.

ER Golgi Mitochondria

DNA
Deoxyribonucleic Acid

Double helix
Carries genetic information Located in the nucleus The monomer is a nucleotide
A phosphate A ribose sugar

A nitrogenous base

What are the bases in DNA

A adenine

T thymine
C cytosine G guanine Base pair rules

Where is DNA located in the Cell?

HUMAN CHROMOSOMES (KARYOTYPE)

CELLS

THE chromosmes visualized as they originally spilled from the lysed cells

THE chromosmes artifially line up in their numerical order

Human Karyotype

22 pairs of autosomes
size bands

sex chromosomes
females: X/X males: X/Y

diploid (2n)

Chromosomes
genomic DNA is very long humans, 6 x 109 bp ~1.8 meters total length total length reduced via associates with proteins individual DNA molecules packaged into chromosomes each chromosome represents one linear DNA molecule

Where are the genes located?

Genes are located on

the chromosomes. Every species has a different number of chromosomes. There are two types of chromosomes: autosomes and sex chromosomes

Gene structure
Promoter region Shine-Dalgarno box (AGGAGG) Pribnow box (TATAAT) Prokaryote -35 site (TTGACA) Terminator 5 3

ORF
Initiation codon Promoter region TATA box CAAT box (in mammals) GC box (GGGCGGG) Exon 1 5 Intron 1 Initiation codon Intron 2 Intron 3 Stop codon

Eukaryote
Exon 2 Exon 3 Exon 4

Polyadenylation signal AATAA 3 Terminator

Stop codon

N GENOME

App. 3200 KM (2000 MILES)

Genes
locus = physical location on a chromosome gene = unit of information (~protein)

}
5'ATGAAATTTTTAATACATCAATTAAACAATGATTATATAAAAAATGATATA AGATATAAATCAAATGAAGAGAAATATATGAGTAAAGTAGACTTCCTAGAAACA ATGAAAAAAGATATATCAGAACTGTACGAAGAATATGGAACGAATAATGAATCG AACACTTCGTATAACATAACGATGGATTTTGTAAACAATTTTGATAGCAGAGAT GGGTCATATATAACTGATATAAGCAGAGAAGAGTTGATGTTAAAACAACATAAT ATAATGAGATTGCAAGATGAACAACTTGAATTTCTTGAAGGAACAACACAAAAT TTAAAAAGTATTAGCTATAATATAAATAACGAAATACAAGTACATAATGAAATA TTAGATGATATAGATAGAGATATGGATGAAACAAGTGATTTATTGGATAGAAAT AGAAACATTTTTACCAGAATTACTAACAGTACGAGTAATTATTATTTGTACATG TTAATTTGTTTATTAACAGTTACACTTTTCTTTTTGATCATAATACTTTAG-3'

ekuens

Cells Structure - animation

DNA AND GENE EXPRESSION

Gene expression is the activation of a gene that results in a protein.

GENE EXPRESSION

Summary

Transcription 1 (making a mRNA copy of DNA)

The part of the DNA molecule (the gene) that the cell wants the information from to make a protein unwinds to expose the bases. Free mRNA nucleotides in the nucleus base pair with one strand of the unwound DNA molecule.

Transcription 2

The mRNA copy is made with the help of RNA polymerase. This enzyme joins up the mRNA nucleotides to make a mRNA strand.
This mRNA strand is a complementary copy of the DNA (gene) The mRNA molecule leaves the nucleus via a nuclear pore into the cytoplasm

tRNA pick up their specific amino acids from the cytoplasm

Transcription- animation

Translation
RNA
Single stranded Does not contain thymine but

has uracil instead.

tRNA carries 3 base pair code

for specific amino acid. Amino acids compose polypeptid chains. One or more polypeptide chains compose a protein proteins provide the blueprints for our characteristics and functions.

In Prokaryotes there are three (3) regulatory elements that control gene expression.
1. 2.

3.

Structural genes genes that code for a specific polypeptide (protein). Promoter DNA segment that recognizes RNA polymerase. Operator element that serves as a binding site for an inhibitor protein that blocks transcription.

Eukaryote

Translation - animation

A ribosome

Translation - outline

Translation. mRNA used to make polypeptide chain (protein)

1.

First the mRNA attaches itself to a ribosome (to the small subunit). Six bases of the mRNA are exposed. A complementary tRNA molecule with its attached amino acid (methionine) base pairs via its anticodon UAC with the AUG on the mRNA in the first position P. Another tRNA base pairs with the other three mRNA bases in the ribosome at position A. The enzyme peptidyl transferase forms a peptide bond between the two amino acids. The first tRNA (without its amino acid) leaves the ribosome.

Translation 2

The ribosome moves along the mRNA to the next codon (three bases). The second tRNA molecule moves into position P. Another tRNA molecule pairs with the mRNA in position A bringing its amino acid. A growing polypeptide is formed in this way until a stop codon is reached.

End of Translation

A stop codon on the mRNA is reached and this signals the ribosome to leave the mRNA. A newly synthesised protein is now complete!

Translation continued
4 A second tRNA molecule binds to the

ribosome
5 The amino acid from the first tRNA is

connected to the amino acid of the second tRNA with the assistance of the ribosome
6 This process continues until the stop

codon on the mRNA is reached

7 At the stop codon, a chemical

reaction frees the polypeptide chain

Protein synthesis - animation

HOW TO EXAMINE EXPRESSIONS OF THE GENES