Konsep Dasar

Biokimia Sel dan

Molekuler
Kusumo Hariyadi
Dari
Sofia Mubarika (FK UGM)

NOBLE, D (2002) Nature Reviews Molecular Cell Biology 3, 460-463.

Unravelling complexity
Need to work in an integrative way at all levels:

Systems level
triggers of
cell signalling

organism
organ
tissue
cellular
sub-cellular
pathways
protein
gene

Systems level
controls of
gene expression

Protein machinery
reads genes

There are feed-downs as well as upward between all these levels

Physiological systems & function

Top-down
systems

tissues

Middle-out

pathways
Sydney Brenner
Nobel Prize2001
Middle-out!!

organs

organelles

Bottom-up
Molecular data & mechanisms

cells

DOGMA CENTRAL

DNA

RNA

Protein

Mathematical Biosciences Institute (Ohio State Univ), 2 October 2003

Central dogma of molecular

biology

DNA Sequence
(splited by
genes)

RNA

Amino
Acid
sequence

protein

Adapted from http://www.bioinfbook.org/

phenotype

3 Molecules of Life

All life depends on three critical molecules:

DNAs
Hold information on how cell works
RNAs
Act to transfer short pieces of information to
different parts of cell
Provide templates to synthesize into protein
Proteins
Form enzymes that send signals to other
cells and regulate gene activity
Form bodys major components (e.g. hair,
skin, etc.)

DNA
Sugar
Phosphate
Base (A,T, C or G)

DNA is composed of basic molecules called

nucleotides
Each nucleotide contains phosphate, sugar
and a nitrogen base.
There are four bases: Adenine (A), Guanine
(G), Cytosine (C), and Thymine (T)

DNA: structure
The sugar-phosphate bonds of
nucleotides form the backbone of a DNA
strand.
The four bases of DNA are arranged
along the backbone in a particular order,
which is called the DNA sequence.
Two DNA strands are held together by
weak bonds between the base pairs.
Two possible base pairs: A-T, C-G.
Two strands of DNA forms a double
helix structure.

Source of diagram: http://www.cs.utexas.edu/users/s2s/latest/dna1/src/page2.html

DNA: packaged in
chromosomes

Each chromosome is essentially a

package for a very long, continuous
DNA double strand.

Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

DNA: splitted by genes

promoter

Exon 1

Intron 1

Exon 2

Intron 2

Exon 3

gene

A gene is a region of DNA that carries the information for

constructing a protein.
2-3% of humans DAN are genes, the rest is called junk DNA.
Promoter is the upstream portion of a gene. It determines under
which conditions the associated gene will be expressed.
Most Eukaryotic genes have their coding sequences, called
exons, interrupted by non-coding sequence called introns.

DNA: replications

Before a cell can divide, it must replicate all its DNA.

From one end, the double helix is unwound, expose single
bases on each strand.
Each strand works as a template to reform a new double helix.
The new double helix is formed by strict base pairing
requirement, i.e., A-T, C-G.

RNA

RNA (ribonucleic acid) is the

intermediary between DNA and
protein.
RNA is a single strand of nucleic
acid.
Instead of having nitrogen base T
(Thymine), RNA has U (Uracil)
Unlike DNA, which is located
primarily in the nucleus, RNA can
also be found in the cytoplasm.
In nucleus, the gene code is
transcribed to a RNA. Then RNA
move out of nucleus into cytoplasm,
where the RNA code is translated to
amino acid sequence.

Source of diagram: http://en.wikipedia.org/wiki/RNA

Proteins

Protein is a folded amino acid chain.

20 different amino acids can be found in
proteins.
A proteins 3-D structure determine its
functions in the cell.
Proteins do all essential work for the cell
build cellular structures
digest nutrients
execute metabolic functions
Mediate information flow within a cell
and among cellular communities.

Another view of central

dogma

A gene is expressed in 3 steps:

1) Transcription: RNA synthesis
2) Splicing: removal of intron sequence from RNA
3) Translation: Protein synthesis

Transcription
Transcription is initiated by a complex of
transcription factors binding to the promoter site
located upstream of the gene
An enzyme, RNA polymerase II, travels along
the gradually unzipped DNA template and
polymerizes nucleotides into an RNA.
The sequence of nucleotides on DNA template
determines the sequence on RNA by following
the rule of base-pair complementarity, i.e., A
U, T- A, C G, G C.
Transcription continues until entire gene is
copied to RNA.

Animation

Source of diagram: http://ghs.gresham.k12.or.us/science/p

s/sci/ibbio/chem/nucleic

Splicing

pre mRNA
Exon 1

Intron 1

Exon 2

mature mRNA

Intron 2

Exon 3

Translation (1)
By translation, the nucleotide
sequence on mRNA
determines the amino acid
sequence by genetic code.
Genetic code: three base pairs
of RNA (called a codon)
determine one amino acid based
on a fixed table.
Translation always starts at
AUG (start codon), and ends
with any of UAA, UAG, or
UGA (stop codon)

Translation (2)

Transfer RNAs (tRNAs): small

RNA molecules. Most of the
tRNAs function as carriers of
amino acids and participate in
protein synthesis.

For example, the tRNA with the

anticodon CGG corresponds
with the codon GCC and
attaches alanine amino acid
onto the peptide chain.

Ribosome: a complex of protein

and rRNA
Animation
Source of diagram: http://www.wiley.com/legacy/college/boyer/0470003790/structure/tRNA/

Summary

Central dogma of molecular biology

Three components
DNA
RNA
Protein
Three steps
transcription
splicing
translation

More terms

Genome: an organisms genetic material

Gene: a discrete units of hereditary information located on the

chromosomes and consisting of DNA.

Genotype: The genetic makeup of an organism

Phenotype: the physical expressed traits of an organism

Nucleic acid: Biological molecules (RNA and DNA) that allow

organisms to reproduce;

Modern Technology in
Medicine
Modern technology:
Diagnostic
Early Screening
Prognostic
Follow up

Human genome:
Gene ther. in 2010
Individualized Ther.

New approaches:
Genome Analysis:
Expression gene
analysis
Micro Array
Protein analysis

Stem cell
Antisense

Biomedical Engineering

New hopes:
Cancer
Vascular/Heart dis.
Diabetes
Alzheimers
Parkinson

How much DNA do we

have?

humans have 2 x 23
chromosomes
EACH cells contains 6
billion bases DNA
that is 1 meter of DNA
a human being has
>100.000.000.000.000
cells
that is 100 billion km of
DNA

Cell cell communication

Receptors
Signal transductions
Second messengers molecules
Nuclear transcription factors
Gene activations
Protein Respons

Cellular signal transduction

Aprocessbywhichsignalsfromoutsidethecellaretransferred inside
thecellthroughcascadeofproteinsinteraction.Involvedinallcellular
activities(death,growth,differentiation,etc.)

Regulatebyproteinphosphorylation.

Protooncogenes
encode
components of
growth factor
signal
transduction
pathways
Components
shown in yellow
are known
proto-oncogenes

The VEGF family and its

receptors
VEGF-A
VEGF-B
PlGF

VEGF-A
VEGF
receptor-2

VEGF
receptor-1

P
P

P
P

VEGF-C
VEGF-D
VEGF
receptor-3

P
P

P
P

P
P

P
P

Migration, permeability, DNA synthesis, survival

Angiogenesis

Lymphangiogenesi
s
Adapted from Ferrara N. Nat Med 2003;9:66976

VEGF signal transduction

and its effects
VEGF

Permeability

VEGF
VEGF
receptor-1

VEGF
receptor-2

P
P

P
P

Cation
channel

P
P

P
P

Ca

PLC

PLC
DAG
DAG

VEGF-C
VEGF-D

2+

VEGF
receptor-3

P
P

IP3
Calcium
release

P
P

PLC
P13K

Protein kinase C

Raf-1

MAPK

Proliferation, migration
Permeability

SAPK/
JNK
Apoptosis
Survival

Protein kinase B
Proliferation
Migration

VEGF binding to VEGF receptor-2 activates a signalling cascade resulting in

cellular effects
Shibuya M. Cell Struct Funct 2001;26:2535

Agents targeting the

VEGF pathway
Antibodies inhibiting
VEGF receptors

Soluble VEGF receptors

(VEGF-TRAP)

Antibodies inhibiting VEGF

(e.g. bevacizumab)

Permeability

VEGF

Cation
channel

VEGF
receptor-2

P
P

P
P

Small-molecules
inhibiting VEGF
receptors (TKIs)
(e.g. PTK-787)

P
P

P
P
P
P

Migration, permeability, DNA synthesis, survival

Ribozymes
(Angiozyme)

Angiogenesis

Lymphangiogenesi
s

P
P

Signal Transduction from Receptor to Nucleus

Via RAS p21
Growth factor
P

Ras
Ras
P
Grb2
GTP
GTP
GDP
Sos
P120-GAP
14-3-3
Neurofibromin
1 2

14-3-3
1

14-3-3
1

2
3

Active
Raf

3
MEK
P13-K

14-3-3
1

Rac and Rho

pathway

ERK1

ERK1

3
Inactive Raf

Transcription
factors etc.
Nucleus

Morphological
change

DNA
synthesis

Regulators : proliferation,
differentiation, apoptosis,
repair

Genome :
Genes :

Cell cycle
Differentiati
o
Apoptosis
Repair
Metabolism
etc

Transcriptome

RNA
RNA

Proteome
Protein:

RNA
RNA
RNA
RNA

cyclin, CDK,CDKI
GF : GM-CSF, FGF
Bcl-2, p53,
caspase
Gadd, enzym
repair
dll

How to understood ??

GENE:
Cytogenetics
FISH
DNA analysis
Southern
blot +/PCR
specific
MLPA
Sequencing :
SSCP

Gene activ:
RNA
Northern blot
RT- PCR

Gene active :
Protein

RNA-se protection
Assay

Western Blot

Micro array

SDS-PAGE

R-ISH

ELISA
FISH