Transcript Prof. Sutiman Bambang Sumitro, SU., D.Sc

Perkembangan Biologi Molekuler
dan Pembelajarannya
Sutiman B. Sumitro
Laboratorium Biologi Sel dan Molekuler
Fakultas MIPA
Universitas Brawijaya
[email protected]
• Pengetahuan Ilmiah dilakukan dengan berpikir runtut bersifat
analitik dan sintetik.
• Kebenaran Ilmiah adalah keselarasan pikiran dengan hasil
pengamatan obyek yang bersifat inderawi (mata, telinga, rabaan,
penciuman)
• Obyek komplek dalam biologi dipelajari dengan cara mengurai
dari obyek besar dan komplek ke bagian-bagian yang lebih kecil.
Dilakukan upaya penyederhanaan dan fokus untuk dapat dibahas
dan dipahami, mencari bukti, bersifat linier dan logis
Disiplin Ilmu diklasifikasikan berdasarkan cara
pendekatan berfikir
Biologi Klasik:
Berbasis Morfologi
Ekologi:
Berbasis populasi
Biologi Modern
Berbasis Seluler dan Molekuler
Holism
Reduksionistik
Molecular and Cellular Biology, Genetic
engineering, Modern Medical sciences, etc.
Ada kecenderungan parsialisme yang harus
disikapi dengan kehati-hatian
Reductionist
approach
15 April 2015
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The linear causal pathway implied in the central
dogma of molecular biology.
The epigenetic control pathway of gene
expression as circular (including bidirectional
causal influences) and dynamic (open to
environment).
F Mazzocchi . WIREs Syst Biol Med 2012.
DOI: 10.1002/wsbm.1181, Copyright © 2012 Wiley Periodicals, Inc.
Integrative Bioinformatics
diperlukan karena fakta berikut:
• Perkembangan cepat data bidang biologi molekuler akibat dari
penggunaan teknologi genomik: Microarray, NGS, NMR, mass
spectrometry, protein chips, gel electrophoresis data, Yeast-TwoHybrid, QTL mapping, gene silencing, and knockout. Bantuan
teknik2 tersebut telah menghasilkan ribuan data, bahkan tidak
jarang banyak sekali data meskipun berasal hanya dari satu
kegiatan eksperimen
• Data Biologis tersebar di berbagai data base dan ratusan jurnal
ilmiah
• Semua ini perlu didayamanfaatkan baik melalui model, integrasi
informasi untuk menghasilkan informasi yang lebih benar sesuai
dengan kenyataan berupa siostem biologi yang komplek .
Sifat Reduksionistik bidang kajian
Biologi Sel-Molekuler
Reductionism contain so many simplification and
assumptions which generate misinterpretation
Versus
Complexity Science
The emerging complexity science in respond to the
disadvantage of reductionism in studying complex
phenomena such as living system
What is Complexity Science?
Complexity science is a broad term for understanding
a range of complex phenomena.
If we break down a ‘complicated’ system into its basic
components and analyze how the components behave, we can
recreate the behavior of the whole system by running all the
components together.
There are a wide variety of ‘complex’ scientific and engineering
problems though defying this type of analysis.
The behavior of a complex system is an emergent property of
the interactions of the components.
Seth Bullock, 2006
Physic is the origin of Complexity Science
Complexity theory developed from the physical
sciences in the mid-20th century.
It is argued that the world is made up of interwoven
orderly, disorderly, and complex parts.
Rigid rules and laws help to explain orderly
phenomena, but are limited in predicting the behavior
of complex phenomena.
Complexity science recognizes the strengths of the
orderly Newtonian framework while tackling the
unpredictability of complex and disorderly phenomena.
Seth Bullock, 2006
The contribution of reductionist and holistic (antireductionist) methodologies to the mechanistic explanation of
increasing complex biological phenomena. The kind (linear or nonlinear) of process is illustrated in the lower x-axis.
The kind of system the processes are part of (aggregative, component, or integrative) is indicated in the middle
x-axis. The degree of biocomplexity of biological phenomena is ranked in the upper x-axis (number 1–11). The left
and right y-axis portray the contribution (in percentages) of reductionist and holistic methodologies, respectively, to a
research program aiming to mechanistically explain a biological phenomenon exhibiting a given degree of
complexity. (Reprinted with permission from Ref 26. Copyright © 2002 Taylor and Francis Ltd.,
http://www.tandfonline.com)
F Mazzocchi . WIREs Syst Biol Med 2012.
DOI: 10.1002/wsbm.1181, Copyright © 2012 Wiley Periodicals, Inc.
Apa yang harus dilakukan?
Kompleksitas Sistem Makro Molekul di Dalam Sel
(Dicirikan oleh fenomena “self assembly” dan “kecerdasan”)
Nucleosome
Mikrometer (µm)
Set of Human
Chromosomes
Nano meter (nm) size
chromatin filaments
(sepermiliar meter)
Mikrometer (µm)
Size Cromosomes
(sepersejuta meter)
All creatures
can be
describe as
atomic,
an angle to
view living
system
Where is the ideas
of performing life
is located?
Nano
Science
Modern
Physics
Newtonian
Functional
Structures of
biological
molecules are
within this range
Quantum
Physics
Gravitation, speed
Space and time
Measurable
dimension, weigh,
and speed
Atom and Subatomic,
particles
Time and space less
1 nm
100 nm
Electricity and Magnetism
in Biological Molecules
• Energy generation to build complex structure of organic chemical
compounds is based on their physical and chemical characters
•Electrical properties of Biological molecules can conduct electricity
and influence development of molecular electronic (Porath, et al., 2004)
•DNA and other biological macromoleculs behave as an isolator,
semiconductor, conductor or superconductor depending on the
surounding molecules or the medium
(Braun et al., 1998; Pablo et al., 2000; Zang et al., 2002; Storm et al., 2001; Porath et al., 2005; rakitin et al., 2001; Cohen et al., 2005)
•These Biological molecules perform electronic transport and have
magnetic phenomena (Zong et al., Eds, 2003)
The phonon in twisting and stetching
modes of DNA
(Müller et al., 2002)
Phonon is collective exitation in a periodic,
elastic arrangement of atoms or molecules in
condensed matters, represents exited state in
quantum mechanical quantization of modes
of vibrations of elastic structures of
interacting particles (Igor Tamm, 1932).
Magnetic in moving electron
Paramagnetic
Unpaired electron
2p
21
Diamagnetic
Paired electron
2p
21
21
7.8
Biradical and magnetism
Edward Kosower (1967) proposed an idea of
biradical in an aromatic organic compounds. Each of
which having unpaired electrons. The magnetic
force of this compound
used for
making
agregation.
Aromaticc Phenantren Structures Rich of Electron Moving on Its Surface
*
H2O* UV H• + •OH
OH
Negative Fragment
Kosower
(1968)
P•
P•
P
P
diamagnetic
n P•
P•
P
P
Paramagnetic
P
P
www.smartbio.org
P
Large electron density
P
P
P
Mobile Electron in associated HO• cyclohexadienyl
*
solar
⁺˙OH
HO
H
H
OH
Biradical
Phenanthrene
Phenanthrene*
OH
*
solar
⁺˙OH
Biradical
HO
1,2-Benzanthracene
1,2-Benzanthracene*
OH
*
Biradical
˙OH
HO
Chrysene
Chrysene*
Atomic level and subatomic
 At atomic level ,matter has dual aspect ,it appears particles and waves
a particle
Energy packets “quanta”
a wave
Varied waves
 The packets quanta in “cage” volume varied 2n, depends on the distance of each quanta
density
 Light is emitted and absorbed in the form of “quanta” or photons, when travel through space
they appear as vibrating electric and magnetic fields, which show all character behavior of
waves. Electrons, considered to be particles, when a beam of these particles, is sent to slit it is
diffracted just like a beam of light, ---- in other words electrons, too, behave like waves
Proses
Hidup dan
Molekul
Komplek
Heme
A complex as a substance composed of two or more
components capable of an independent existence.
A coordination complex is one in which a central
atom or ion is joined to one or more ligands through
what is called a coordinate covalent bond in which
both of the bonding elecrons are supplied by the
ligand.
In such a complex the central atom acts as an
electron-pair acceptor
Cytochrome-c
Hemoglobin
Catalase
Cytochrome-c
Myoglobulin
A compound formed by union of a metal ion (usually
a transition metal ) with a non metallic ion or
molecule called ligand or complex agent
Heme of red blood hemoglobin
Iron's oxidation state in oxyhemoglobin
Assigning oxygenated hemoglobin's oxidation state is difficult
because oxyhemoglobin (Hb-O2), by experimental measurement, is
diamagnetic (no net unpaired electrons), yet the low-energy
electron configurations in both oxygen and iron are paramagnetic
(suggesting at least one unpaired electron in the complex).
Albert et al., 2007
The whole is greater and smarter than the sum
of the parts
Complex compound or Coordination compound
(in atomic language)
Complex ion:
Anions which has a molecular structure consisting of a
central atom bonded to other atoms by coordinate
covalent bonding
The notion of a complex system is distinguished from
that of complicated system, which is more than the
sum of its parts.
Ringkasan Pembicaraan
Biologi Sel dan Biologi Molekuler telah mencapai akumulasi pengetahuan dari
hasil riset yang sangat banyak
Mendorong setiap kegiatan penelitian dilakukan dengan tingkat spesialisasi
yang menjadi sangat spesifik
Hasil kajian-kajiannya tersebar dalam ratusan publikasi di jurnal-jurnal ilmiah
setiap minggunya, menyulitkan seseorang untuk melngikutinya secara
manual
Bahan ajar terus berkembang sehingga memerlukan updating terus menerus
dengan intensitas tinggi sehingga cenderung makin lama-makin terasa
menyulitkan
Perlu bantuan bantuan sistem kerja in silico berupa mekanisme akses ke basis
penyimpanan data ilmiah melalui sistem jejaring kerja sistem informasi dan
sistem piranti lunak untuk memudahkan seseorang membangun hipotesis
dengan pengetahuan terkini.
•Water Diamagnitism
•Levitating frog