46

Human 2.9x109 bp

(Berg JM et al, 2002)

 II. MATERI GENETIK

Mahluk hidup tersusun dari  SEL

yang dapat membelah dan menurunkan
INFORMASI GENETIK nya

Dibawa oleh DNA : rantai polimer panjang yang merupakan

rangkaian dari jutaan nukleotida

Fragmen DNA yang mengkode protein, suatu unit

keturunan  Gena

Molekul DNA yang terdiri dari beberapa gena di

paking membentuk CHROMOSOM

Total informasi genetik yang tersimpan

dalam kromosom  GENOM
 The Making of Dolly
Cloning depends on DNA
Step 1: Take the Nuclei out of a sheep egg
Step 2: Transfer nuclei from the Mother

Empty
DNA DNA

Sheep Egg Mother’s Egg

 HUMAN GENOME

 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.

 Genes instruct cells to make proteins

that determine everything from eye
and hair color to our susceptibility to
disease.
 Genome = total genetic makeup of
an organism
 DNA cont.
 Genes come in
homologous
pairs
 The location of a
gene on a
chromosome =
locus.
 Alternative forms of
genes that
influence a
characteristic =
alleles.
DNA Introduction, cont.

 A gene pair of two same

alleles (i.e., AA) =
homozygous

 A gene pair of two different

alleles (i.e., AO) =
heterozygous.
DNA Introduction, cont.

 Genotype: The particular

combination of genes present in the
cells of an individual (AA or AO)
 Phenotype: The physical trait such
as, shape, color, blood type, etc.
 DNA

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?

• Less than 2% of the genome codes for proteins.

 
• Repeated sequences that do not code for proteins ("junk DNA") make up
at least 50% of the human genome.
 
• Repetitive sequences are thought to have no direct functions, but they
shed light on chromosome structure and dynamics. Over time, these
repeats reshape the genome by rearranging it, creating entirely new
genes, and modifying and reshuffling existing genes.
 
• The human genome has a much greater portion (50%) of repeat
sequences than the mustard weed (11%), the worm (7%), and the fly
(3%).

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

Gene Testing  Pharmacogenomics  Gene Therapy

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

Renaturation driven by homologous base pairing

Will also hybridize with a radiolabeled 5’-ACGGCTA-3’ “probe”.

 DNase I

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

In RNA, G pairs with C The loops and

and A pairs with U. hairpins have few
or no base-pairs
TRANSKRIPSI
 Flow of information
replication
DNA  DNA
transcription 
RNA
translation 
protein
Eukaryotic Transcription

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

TATA box (TATAAAA)

• located approximately 25-30 bp upstream of the +1 start site
• determines the exact start site (not in all promoters)
• binds the TATA binding protein (TBP) which is a subunit of TFIID
GC box (CCGCCC)
• binds Sp1 (Specificity factor 1)
CAAT box (GGCCAATCT)
• binds CTF (CAAT box transcription factor)
Octamer (ATTTGCAT)
• binds OTF (Octamer transcription factor)
Bacteria contain a single type of RNA polymerase

*Regulation of transcription in eucaryotes vs. in bacteria

08_13_gene.activation.jpg
08_14_chromatin.struc.jpg
 1 gene with exons and introns
E I E I E I E

transcription

1 RNA representing exons and introns

(primary transcript)
TB
b. Primary transcripts

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

AGO2: member of the

Argonaute protein family

Kim and Rossi (2007)

Nat Rev Gen 8:173-184
 RNAi in the clinic

Kim and Rossi (2007) Nat Rev Gen

TRANSLASI
SINTESIS PROTEIN
SKEMA TRANSLASI
INTERAKSI 16 s rRNA vs
SD
 Initiation
 Initiation site selected not just by AUG (Why not?)
 -10 region, “Shine-Delgarno sequence”
– Purine-rich tract (3-10 n.t. sequence) matches pyrimidine-rich sequence
on 16S RNA.
– Positions ribosome for intiation at AUG, and establishes reading frame.

 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!

Position of the AUG (1st?)

AUG sequence context
5’ cap accessibility
Length of the 5’ UTR
Secondary structure up- and
downstream of the AUG
 AUG recognition

m7G ORF (A)n

AUG UAA

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)

The sequence is always shown with N-terminus on the left

 Levels of protein structure

Primary structure: sequence of amino acid
residues

Secondary structure: -helix, -sheet, -turn

Tertiary structure: variety of other bonds – final
level for some proteins

Quaternary structure: association of folded
monomers (hydrophobic)
 -Helix
 3.6 residues per turn
 Right-handed helix
 H-bonds between:
 C = O of residue n

 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

 unusual in that many victims are < 30 years old

 incubation time is 10 to 15 years

 Microarray analysis
Microarrays are mRNAs
Spotted at high density onto
glass chips. Expression of
thousands of genes over
hundreds of cell states is
measured.

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)