Konsep Dasar Biologi Molekuler
Konsep Dasar Biologi Molekuler
Konsep Dasar Biologi Molekuler
Human 2.9x109 bp
Empty
DNA DNA
NUCLEAR GENOME
* 23 pairs of chromosomes 2 X (
3 X 109 b.p) 2 meters DNA /
Cell
* 2 X ( 3 X 1012 ) meters DNA in
human body 8,000 X (earth to
moon)
MITOCHONDRIAL GENOME
Each cell has 46
chromosomes (in
23 pairs)
~30,000 genes
are arranged
along the 23
types of
chromosomes
DNA Introduction, cont.
CHROMOSOME
Human Genome Project
Goals:
■ identify all the approximate 30,000 genes in human
DNA,
■ determine the sequences of the 3 billion chemical
base pairs that make up human DNA,
■ store this information in databases,
■ improve tools for data analysis,
■ transfer related technologies to the private sector, and
■ address the ethical, legal, and social issues (ELSI)
that may arise from the project.
http://doegenomes.org
http://www.sanger.ac.uk/HGP/overview.shtml U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
What does the draft human
genome sequence tell us?
http://doegenomes.org U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
Chromosomes
78 40 46
Medicine and the New Genetics
Anticipated Benefits:
• improved diagnosis of disease
• earlier detection of genetic
predispositions to disease
• rational drug design
• gene therapy and control systems for
drugs
• personalized, custom drugs
http://doegenomes.org U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
Melting and Renaturation of DNA
DNase II
Exonuclease
Palindromic* sequences (inverted repeats) in DNA or
C T
RNA can form hairpin or cruciform structures
A C
5’ TGCGATACTCATCGCA 3’ T A
A T
3’ ACGCTATGAGTAGCGT 5’
G C
inverted repeats in an antiparallel double helix C G
G C
C T T A
5’ 3’
A C
T A 3’ 5’
A T A T
G C C G
cruciform
C G hairpin G C
G C C G
T A T A
5’ 3’ A T
T G
G A
Mirror repeats cannot form these structures.
*A palindrome reads the same in either direction (“Radar,” “Madam, I’m Adam”).
Most RNA molecules consist of a single strand that
folds back on itself to form double-helical regions
single hairpin
internal
strands loop A C
A
A
AG bulge
A A C U
CA U A C A
U G C UACC U G
A CCU CGU A
G
AG
AAC GAUGG
G
U GG GCA
CC
C G G
G A
CG
U
GC
A A
G
A A
T
Nuclear
Cytoplasm
pores
DNA
Transcription
RNA
RNA
Processing
mRNA G AAAAAA G AAAAAA
Export
Nucleus
A. Functions of the major RNAs
1. messenger RNAs (mRNA) contain
genetic information to encode a protein
phe
2. transfer RNAs (tRNA) act as adapters
between the mRNA nucleotide code and
amino acids during protein synthesis
3. ribosomal RNAs (rRNA) are structural and
catalytic component of ribosomes
4. Complementary base pairing
CCCTTTGGGAAA DNA
GGGAAACCCUUU RNA
hydrogen
bonding
GGGAAACCCUUU RNA
CCCUUUGGGAAA RNA
TB
Sequence elements within a typical eukaryotic gene 1
1
based on the thymidine kinase gene
octamer
transcription
+1
promoter
element
ATTTGCAT GC CAAT GC TATA
-130 -95 -80 -50 -25
transcription
primary transcript
processing
1 mRNA
1 polypeptide TB
RNA processing
Splicing
MUTASI -THALASSEMIA
POLA SPLICING KARENA
MUTASI
POLA KEMUNGKINAN
SPLICING GENA
-TROPOMISIN
11.4 HIV Rev protein
regulates the transport of
unspliced viral mRNAs
Figure 11-38
RISC: RNA induced silencing
complex
Eucaryotes: no Shine-
Delgarno sequence:
eIF2 – cap binding
protein helps position
40S near start of mRNA
& migrate towards AUG
Ribosomes initiate translation at ribosome-binding sites
07_33_mRNA.encode.jpg
in polycistronic procaryotic mRNAs, which can encode
more than one protein
INISIASI
Elongation
A polyribosome from a
07_35_polyribosome.jpg
eucaryotic cell
Initiation of Translation in
Eukaryotes
Cap AUG----------------Stop AAAAAAAAA
5’UTR 3’UTR
Important points:
• No direct binding between mRNA and rRNA
• Small ribosome subunit binds directly to cap – requires
specific initiation factor – eIF4e
• Other initiation factors can unwind double stranded regions
in the mRNA – eIF4 group
• Small subunit scans mRNA till it finds correct AUG
• Correct AUG is embedded in preferred sequence
GccAccAUGG
G
Scanning model of translation
initiation
40S 40S
Most translation is regulated at
the initiation step
Why?
Features of mRNA that regulate
translation efficiency
All mRNAs are not created equal as
viewed by the ribosome!
A
CTACCTA GCCAUGGTACTACCTA Kozak consensus
-3 +1 +4
sequence
TARGET
TRANSPORT
Proteins
Essential for all biological events
DNA carries the information
Protein does the business
Enormous diversity
– functional
– structural
Simple building-blocks -
– L-amino acids
3.1 All amino acids have the same
general structure but the side chain (R
group) of each is different
Figure 3-1
A tripeptide (from Lodish)
N - H of residue
n+4
-Sheet (from Lodish) Note extended
shape
H-bonds
between
strands
Quaternary structure
Occurs in some proteins (multimeric proteins)
2 - dimer
3 - trimer
4 - tetramer
6 - hexamer etc
Mainly hydrophobic interactions bring fully- folded
monomers (subunits) together, non-covalently
3.3 Mechanisms that regulate
protein function
Allosteric transitions
– Release of catalytic subunits, active inactive states,
cooperative binding of ligands
Phosphorylation dephosphorylation
Proteolytic activation
Compartmentalization
3.3 Allosteric release of
catalytic subunits
Figure 3-27
Proteolytic maturation of insulin
C Peptide
PC2 G E L A L P Q L S G P G G L E V
Q G
S V
cleavage L Q
Q L
K N
R E
G S S
S
S A Chain A
F I E
V
V E Q C C T S I C S L Y Q L E N Y C N R PC3
N R
S S
Q
H
S S
K
T cleavage
L C G S H L V E A L Y L V C E R G F F Y T P
B Chain
3.4 Glycophorin: an example
transmembrane protein
Figure 3-33
"new variant" Creutzfeldt-Jacob syndrome
human disease thought to be caused by eating BSE-infected beef
bee
about 92 cases, most victims have died
Identifying coregulated
genes is not so simple.
Many physicists work
in this field-- one recent
publication:
Super-paramagnetic clustering
of data , Eytan Domany,
Physica A 263, 158 (1999)