Perkembangan Biologi Molekuler dan Pembelajarannya

Sutiman B. SumitroLaboratorium Biologi Sel dan Molekuler

Fakultas MIPAUniversitas Brawijaya

sutiman@ub.ac.id

• 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

Biologi Klasik: Berbasis Morfologi

Ekologi:Berbasis populasi

Biologi ModernBerbasis Seluler dan Molekuler

Holism

ReduksionistikMolecular and Cellular Biology, Genetic engineering, Modern Medical sciences, etc.

Ada kecenderungan parsialisme yang harus disikapi dengan kehati-hatian

Disiplin Ilmu diklasifikasikan berdasarkan cara pendekatan berfikir

May 4, 2023 www.divinecigarette.com

Reductionist approach

The linear causal pathway implied in the central dogma of molecular biology.

F Mazzocchi . WIREs Syst Biol Med 2012. DOI: 10.1002/wsbm.1181, Copyright © 2012 Wiley Periodicals, Inc.

The epigenetic control pathway of gene expression as circular (including bidirectional causal influences) and dynamic (open to environment).

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-Two-Hybrid, 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

Complexity ScienceThe emerging complexity science in respond to the disadvantage of reductionism in studying complex

phenomena such as living system

Versus

Seth Bullock, 2006

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.

What is Complexity Science?

Seth Bullock, 2006

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.

Physic is the origin of Complexity Science

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?

Nucleosome

Kompleksitas Sistem Makro Molekul di Dalam Sel(Dicirikan oleh fenomena “self assembly” dan “kecerdasan”)

Nano meter (nm) size chromatin filaments(sepermiliar meter)

Mikrometer (µm)Size Cromosomes

(sepersejuta meter)

Set of Human Chromosomes

Mikrometer (µm)

All creatures

can be describe as

atomic,an angle to view living

system Where is the ideas of performing life

is located?

1 nm 100 nm

Newtonian

Gravitation, speed

Space and time

Measurable dimension, weigh,

and speed

Modern Physics

Quantum Physics

Atom and Subatomic, particles

Time and space less

Nano Science

Functional Structures of

biological molecules are

within this range

• 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)

Electricity and Magnetism in Biological Molecules

The phonon in twisting and stetching modes of DNA

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).

(Müller et al., 2002)

2121212121

ParamagneticUnpaired electron

2p

DiamagneticPaired electron

2p

7.8

Magnetic in moving electron

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.

Biradical and magnetism

Negative Fragment

H2O* H• + •OHUV

*

P• P • P P P P diamagnetic Paramagnetic

n P• P• P P P P

P P Large electron density

Aromaticc Phenantren Structures Rich of Electron Moving on Its Surface

Kosower (1968)

OH

www.smartbio.org

Phenanthrene

1,2-Benzanthracene

Phenanthrene*

1,2-Benzanthracene*

Chrysene Chrysene*

solar

solar

˙OH

Mobile Electron in associated HO• cyclohexadienyl

Solar

Biradical

Biradical

Biradical

*

*

*⁺˙OH

⁺˙OH

HO OHH H

HO

OH

HO

OH

Atomic level and subatomic

a particle a wave

Energy packets “quanta” Varied waves

At atomic level ,matter has dual aspect ,it appears particles and 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

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

Heme

Proses Hidup dan Molekul Komplek

Cytochrome-c

MyoglobulinCytochrome-c

Catalase

Hemoglobin

Iron's oxidation state in oxyhemoglobinAssigning 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).

Heme of red blood hemoglobin

Albert et al., 2007

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

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.

The whole is greater and smarter than the sum of the parts

Complex compound or Coordination compound (in atomic language)

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.

Ringkasan Pembicaraan

•Water Diamagnitism

•Levitating frog