Perkembangan Biologi

Molekuler dan
Pembelajarannya
Sutiman B. Sumitro
Laboratorium Biologi Sel dan Molekuler
Fakultas MIPA
Universitas 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 bagianbagian 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-

Reductionist
approach
October 24, 2016

www.divinecigarette.com

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-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

Sifat Reduksionistik
bidang kajian Biologi SelMolekuler
Reductionism contain so many
simplification and assumptions which
generate misinterpretation

Versu
Complexity
Science
s

The emerging complexity science in respond to

the disadvantage of reductionism in studying
complex phenomena such as living system

What is Complexity
Complexity science is a broad term for
Science?
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
Seth Bullock, 2006
property of the interactions of the components.

Physic is the origin of Complexity

Complexity theory
developed from the
Science
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 111). 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 (m)

Set of
Human
Chromoso
mes

Nano meter (nm)

size chromatin
filaments
(sepermiliar meter)

Mikrometer (m)
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

Functional
Structures of
biological
molecules are
within this
range

Quantum
Physics
Atom and Subatomic,
particles

Newtonian
Gravitation, speed
Space and time
Measurable
dimension, weigh,
and speed

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)

The phonon in twisting and stetching

modes of DNA
(Mller 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 o

*

H2O* UV

H + OH

OH

Negative Fragment

Kosower
(1968)

P
n P

diamagnetic

Paramagnetic

P
P
P

www.smartbio.org

Large electron density

P
P

Mobile Electron in associated HO cyclohexadienyl

*

ar
l
So

solar
OH

HO

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

Heme

Proses
Hidup
dan
Molekul
Komple
k

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.

Cytochrome-c

Hemoglob
in
Catalase

Cytochro
me-c

Myoglobul
in

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
Albert et al.,
2007
paramagnetic (suggesting at least one
unpaired

The whole is greater and smarter

than the sum of the parts
Complex compoundor
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

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