Genes and Chromosomes

Chapter 24

Lehninger. Principles of Biochemistry.

by Nelson and Cox, 5th Edition; W.H. Freeman and Company
Colinearity of the coding nucleotide sequences of DNA and mRNA
and the amino acid sequence of a polypeptide chain.

codon
DNA molecules are much longer than the cellular or viral packages that contain them
DNA from a lysed E.coli cell
 Eukaryotic Chromosomes

Sister chromatids
Chromosomes
Prokaryotic Eukaryotic
• Circular • Linear
• Fairly long
• Very small
• Several chromosomes per
• 1 chromosome per cell.
cell • Histone proteins---”spools”.
• Some enzymes and Same in all eukaryotes
proteins are • Housed in a nucleus.
associated with the • Nucleosome—2 loops of
DNA. DNA wrapped around 8
histone proteins.
• Not housed in a
• Unity theme.
nucleus.
Supercoiling of DNA

Supercoiling induced by separating the strands

of a helical structure
Relaxed and supercoiled plasmid DNAs
 DNA compaction requires a special form of supercoiling

The supercoils are right-handed in a negatively supercoiled DNA molecule, and they
tend to be extended and narrow rather than compacted, often with multiple branches.

Plectonemic supercoiling
DNA compaction requires a special form of supercoiling

Solenoidal supercoiling
provides a much greater
degree of compaction
(tight left-handed turns)

Same DNA molecule, drawn in scale

Chromatin assembly
 Histone cores do not bind randomly to DNA;
rather, they tend to position themselves at certain locations

In some cases seems to

depend on a local abundance
of A=T base pairs in the DNA
helix where it is in contact with
the histone
 The structure of chromosomes

The chromosomal material, chromatin, consists of DNA and proteins.

Nucleosomes are the

fundamental organizational unit
of chromatin

Beginning with nucleosomes,

eukaryotic chromosomal DNA
is packed in a sucession of
higher-order structures that
ultimately yield the compact
chromosome
beads-in-a-string

Nucleosomes
 DNA wrapped around the nucleosome core

Eight histone proteins

Two of each: H2A, H2B, H3, and H4

Top view Side view

Histone complex

Nucleosome with 146 bp of bound DNA

The DNA binds in a left-handed solenoidal supercoil that

circumnavigates the histone complex 1.8 times
The 30 nm fiber, a higher-order organization of nucleosomes.
 Compaction of DNA in a eukaryotic chromosome.
Loops of chromosomal DNA
attached to a nuclear scaffold.

Next level of organization

(after 30 nm fiber)

DNA compaction in eukaryotes

is likely to involve coils upon coils
upon coils….
 Structure of SMC proteins.
(Structural Maintenance of Chromosomes)

also bound to additional

regulatory proteins (not shown)
Model for the roles of cohesins and condensins during the eukaryotic cell cycle.
 Bacterial DNA is also highly organized.

Looped domains of the E. coli chromosome.

E. coli nucleoids.
 What is the structure of a gene?
Gene encodes functional RNA molecule, mostly mRNA
(also tRNA, rRNA, etc.)
regulatory
region DNA encoding functional RNA

RNA primary transcript

Gene is functional part of chromosome which is
transcribed into RNA at the correct time and place in
development or cell cycle
Gene includes its adjacent regulatory region(s)

24
A Prokaryotic Gene

25
 A Eukaryotic Gene

How are eukaryotic genes different from

prokaryotic genes?

26
 Eukaryote: Introns and Exons

Intron: noncoding region of gene, excised by

processing from primary transcript
– zero to many per eukaryote gene
– variable length, may be bulk of gene
– unknown function
Exon: coding region of gene (sequence is included in
mature transcript)
transcript E1 I1 E2 I2 E3 I3 E4
nuclear processing steps

mature transcript E1 E2 E3 E4

27
Asam Nukleat: material bersifat asam yang ditemui pada
setiap sel hidup (inti sel/nuklei)
Merupakan biopolimer dengan monomer: Nukleotida
Nukleotida terdiri atas gula, basa dan fosfat
Ada dua macam asam nukleat:
- DNA (deoxyribose nucleic acid)
- RNA (ribose nucleic acid)
HOCH2 O OH HOCH2 O OH

DNA RNA
GULA
OH OH OH (no O)

ribose deoxyribose
 Senyawa amina aromatik heterosiklik
DNA: Adenine, Guanine, Cytosine, Thymine
RNA: Adenine, Guanine, Cytosine, Uracil
O O N H2
4
3 CH3
N 5 HN HN N
2 6
N O N O N O N
1
H H H
Pyrimidine Uracil (U) Thymine (T) Cytosine (C)

N H2 O
6 7
1 5 N N N N
N HN
8
2
N 4 N9 N N H 2N N N
3 H H
H
Purine Adenine (A) Guanine (G)
 uracil O

HN
1
-D-riboside O N
Nukleosida
a -N-glycosidic
5' bond
HOCH2 O
1'
4' H H
H
3' 2' H anomeric
HO OH carbon
Uridine
 Nukleosida pada DNA

Basa Gula Nukleosida

Adenine (A) Deoxyribose Deoksi-Adenosine
Guanine (G) Deoxyribose Deoksi-Guanosine
Cytosine (C) Deoxyribose Deoksi-Cytidine
Thymine (T) Deoxyribose Deoksi-Thymidine
 Nucleosides in RNA
Base Sugar Nucleoside
Adenine (A) ribose Adenosine
Guanine (G) ribose Guanosine
Cytosine (C) ribose Cytidine
Uracil (U) ribose Uridine
 Nukleotida
NH2
N N
O
5'
-
O P O CH2 N N
O
O- H H
H H
OH OH
Adenosine 5'-monophosphate
(AMP)
 Struktur Asam Nukleat
Polimer yang terdiri atas
banyak molekul nukleotida.
Dihubungkan dengan ikatan
gula-fosfat (fosfodiester).
 Struktur Primer DNA - 1°
DeoxyriboNucleic Acids (DNA)
– Molekul DNA terbentuk oleh ikatan antara atom C nomor 3
dengan atom C nomor 5 pada molekul deoksiribosa dengan
perantaraan gugus fosfat.
Struktur Primer: urutan basa sepanjang backbone (rantai induk)
pentosaphospho-diester pada molekul DNA atau RNA.
– Penulisan urutan basa dimulai dari kiri, yaitu ujung 5’ menuju
ujung 3’ O
phosphorylated CH3
5' end HN

O 5' O N
-
O-P- O-C H2 O
-
O
H H O
H H
N
NH
O H

O= P O CH2 N N N H2
O
O-
H H
H 3' H
free 3' end
OH H
STRUKTUR SEKUNDER DNA - 2o

Struktur DNA yang sangat kecil dan rumit dapat digambarkan dengan
model struktur DNA yang diusulkan oleh James Dewey Watson
dan Francis Harry Compton Crick
Model struktur DNA tersebut dikenal dengan nama model tangga berpilin
(double helix). Berikut ini model struktur DNA Watson-Crick
(double-Helix Structure).

Francis Harry James Dewey

Compton Crick Watson
United Kingdom USA
Institute of Molecular Biology Harvard University
Cambridge, United Kingdom Cambridge, MA, USA
b. 1916 b. 1928
DNA Double Helix
DNA Double Helix
DNA terdiri atas dua untai nukleotida
Ikatan hidrogen (antar basa)
menghubungkan dua untai dalam
struktur double-helix (heliks ganda)
Struktur heliks mirip dengan tangga
spiral
Pasangan basa
A–T
G-C
Kedua basa saling komplemen dalam
kedua untai
DNA Model
 Pasangan basa
• Dua ikatan H untuk A-T
• Tiga ikatan H untuk G-C
Penyebab Bentuk DNA Double Helix

Interaksi ikatan hidrogen antara masing-masing

basa nitrogen menyebabkan bentuk dari dua
rantai DNA menjadi sedemikian rupa, bentuk ini
disebut double helix. Interaksi spesifik ini terjadi
antara basa A dengan T, dan C dengan G.
Lebar dari ‘anak tangga’ adalah sama, karena
pasangan basa selalu terdiri dari satu primidin
dan satu purin.
Gula deoksiribosa memegang basa nitrogen pada atom karbon
nomor 1, sedangkan atom C nomor 5 berikatan dengan gugus
fosfat
Karena DNA merupakan rantai ganda dan atom-atom karbon
mempunyai aturan di atas untuk mengikat basa nitrogen dan
gugus fosfat maka satu rantai DNA terlihat berdiri tegak
sedangkan rantai pasangannya justru terbalik.
Maka pada notasi penulisan kode genetik DNA, ditulis 5’-kode
genetik-3’, sedangkan untuk rantai pasangannya justru ditulis 3’-
kode genetik-5’. Pengaturan ini disebut konfigurasi antiparalel.
DNA
Functions
1. Storage of genetic information
2. Self-duplication & inheritance.
3. Expression of the genetic message.
DNA’s major function is to code for proteins.
Information is encoded in the order of the nitrogenous
bases.
 Struktur tersier DNA – 3°
DNA siklis: DNA untai ganda dimana ujung
5’ dan 3’ tergabung dalam ikatan
phosphodiester

(a). konformasi DNA sirkular

(b). konformasi DNA linear
Bentuk-bentuk DNA
RNA (Ribose Nucleic Acid)
RNA merupakan rantai tunggal
polinukleotida
polinukleotida RNA tersusun dari banyak
ribonukleotida
ribonukleotida tersusun atas gula ribosa,
basa nitrogen, dan asam fosfat
Basa nitrogen RNA :
1. Basa purin: adenin (A) dan guanin (G)
2. basa pirimidin: sitosin (C) dan urasil (U)
 6 N N N
N O O O
1
Struktur
H basa
H RNA H
imidine Uracil (U) Thymine (T) Cytosine (C)
BASA PURIN
N H2 O
6 7
5 N N N N
HN
8
N 4 N9 N N H 2N N N
3 H H
H
Purine Adenine (A) Guanine (G)

BASA PIRIMIDIN
O O
O N H2
O
4
CH 3 CH 3
HN 5 HN
HN HNN
6
N N
N N
N
N
O O
O OO
1
H HH HH
midine
ra cil (U) Ura cil (U)(T)
Thymine Thymine (T)
Cytosine (C)
Perbedaan RNA dan DNA

O O NH2
4
3 CH3
N 5 HN HN N
2 6
N O N O N O N
1
H H H
Pyrimidine Uracil (U) Thymine (T) Cytosine (C)

NH
RNA mirip dengan DNA tetapi berbeda dalam hal:
– Gula pentosa pada RNA merupakan -D-ribose tidak seperti
DNA yang menggunakan -2-deoxy-D-ribose
– Basa pyrimidine pada RNA adalah uracil dan cytosine bukan
thymine dan cytosine
– RNA merupakan untai tunggal (single stranded) bukan double
stranded
– Letak : nukleus, sitoplasma, kloroplas, mitokondria
RNA Genetik
Berfungsi sama dengan DNA (molekul genetik yang secara
keseluruhan membawa sifat hereditas/bertanggung-
jawab pada penurunan sifat dari induk ke anakan)
contoh pada virus

RNA nongenetik
RNA yang tidak berperan sebagai pembawa sifat/sifat
hereditas, berdasarkan letak dan fungsinya :
1. mRNA
2. tRNA
3. rRNA
 RNA nongenetik
Molecular Weight Number of Percentage
Type Range (g/mol) Nucleotides of Cell RNA
mRNA 25,000 - 1,000,000 75 - 3,000 2
tRNA 23,000 - 30,000 73 - 94 16
rRNA 35,000 - 1,100,000 120 - 2904 82

• Ribosomal RNA (rRNA): RNA yang ditemukan pada ribosom, tempat sintesis
protein
• Merupakan RNA terbanyak dan merupakan penyusun ribosom
• Berupa pita tunggal, tidak bercabang, dan fleksibel
• Berperan penting dalam sintesa protein
• Transfer RNA (tRNA): RNA yang membawa asam
amino tertentu ke tempat sintesis protein di ribosom
• Merupkan RNA terpendek yang bertindak sebagai :
- penerjemah kodon dari mRNA
- pengikat asam-asam amino yang akan disusun
menjadi protein dan mengangkutnya ke ribosom

O
t RNA - O- P- O- CH 2 Base
O
O- H H
H H
amino acid, bound
as an este r to its O OH
specific tRNA C= O
C
H N H3 +
R
 tRNA ( transfer RNA)
is a small RNA that has a very specific secondary and tertiary structure such that it
can bind an amino acid at one end, and mRNA at the other end. It acts as an adaptor
to carry the amino acid elements of a protein to the appropriate place as coded for by
the mRNA. T

Three-
dimensional
Tertiary
Secondary structure of tRNA structure
Messenger RNA (mRNA): RNA yang membawa kode
genetik dari DNA ke ribosom untuk sintesis protein
– Berbentuk pita tunggal dan merupakan RNA
terbesar atau terpanjang yang bertindak sebagai:
- Pembawa kode-kode genetik dari DNA ke
ribosom
- Cetakan/templat dalam sintesis protein
– Disintesis berdasarkan informasi yang dikode DNA
– Untai komplemen mRNA disintesis sepanjang satu
untai DNA, mulai dari ujung hidroksil 3’-nya
– Proses sintesis mRNA dari DNA disebut transkripsi
Colinearity of the coding nucleotide sequences of DNA and mRNA
and the amino acid sequence of a polypeptide chain.

codon
 DNA Replication is Accurate
(In E. coli: 1 error/109 -1010 dNTPs added)

How?
1) Base-pairing specificity at the active site
- correct geometry in the active site occurs only
with correctly paired bases BUT the wrong base
still gets inserted 1/ 104 -105 dNTPs added
2) Proofreading activity by 3’-5’ exonuclease
- removes mispaired dNTPs from 3’ end of DNA
- increases the accuracy of replication 102 -103
fold
3) Mismatch repair system
- corrects mismatches AFTER DNA replication
 Basic rules of replication

A. Semi-conservative
B. Starts at the ‘origin’
C. Synthesis always in the 5-3’ direction
D. Can be uni or bidirectional
E. Semi-discontinuous
F. RNA primers required
DNA REPLICATION
Meselson and Stahl (1958)

AS Biology. Gnetic control of protein

structure and function
AS Biology. Gnetic control of protein
structure and function
Core proteins at the replication fork
Topoisomerases - Prevents torsion by DNA breaks
Helicases - separates 2 strands
Primase - RNA primer synthesis
Single strand - prevent reannealing
binding proteins of single strands
DNA polymerase - synthesis of new strand
Tethering protein - stabilises polymerase
DNA ligase - seals nick via phosphodiester
linkage
The mechanism of DNA replication
Arthur Kornberg, a Nobel prize winner and other
biochemists deduced steps of replication
– Initiation
• Proteins bind to DNA and open up double helix
• Prepare DNA for complementary base pairing
– Elongation
• Proteins connect the correct sequences of
nucleotides into a continuous new strand of DNA
– Termination
• Proteins release the replication complex
 Core proteins at the replication fork

Nature (2003) vol 421,pp431-435 Figure in ‘Big’ Alberts too

In what direction does DNA replication occur?
C) Synthesis is ALWAYS in the 5’-3’ direction
What happens if a base
mismatch occurs? Where does energy for addition
of nucleotide come from?
DNA replication is semi-discontinuous

Continuous synthesis

Discontinuous synthesis
Introns in two eukaryotic genes
The DNA Revolution
• 1940s-1960s
• Griffith & Avery—DNA transformed
pneumococcus bacteria.
• Encouraged the study of prokaryotic
chromosomes.
• Hershey and Chase—Bacteriophage experiment.
DNA from viruses is injected to host bacteria
cells.
Griffith and Avery
Hershey & Chase
Hershey & Chase
Hershey & Chase
The Search for the Structure of the DNA Molecule
• 1951—Rosalind Franklin—X-ray crystallography
• Chargaff—Chargaff’s rules. Ratio of nitrogenous
bases in DNA. Complimentary bases.
• Watson & Crick--1953
Franklin
Chargaff
 Watson & Crick Model of DNA

• Nucleotides • Purines—Adenine &

• Sugar—Deoxyribose Guanine
• Phosphate Group • Pyrimidines—
• Nitrogenous Bases Cytosine & Thymine
• Adenine & Thymine are • 5’ End—Phosphate
complementary. side
• Cytosine and Guanine • 3’ End—Other side
are complimentary.
Most cellular DNA is underwound DNA underwinding is defined
by topological linking number

84 bp
 Watson & Crick Model

• DNA is composed of 2 • The complimentary

chains of nucleotides that nitrogenous bases form
form a double helix shape.
hydrogen bonds
• The two strands are
between the strands.
antiparallel.
• The backbone of the • A is complimentary to
DNA molecule is T and G is
composed of alternating complimentary to C.
phosphate groups and
sugars.
 RNA

• 3 types—mRNA, tRNA, rRNA

• Ribose
• Uracil replaces Thymine
• Single stranded helix
 Transcription
• RNA polymerase
• Messenger RNA
• mRNA
• Unzipping of DNA helix.
• Sense strand or template strand
• Codons
• Genetic code
 Translation
Ribosomes Initiation
rRNA Chain Elongation
Large and small subunits
Peptide bonds
Codons
Initiator or start codon
Chain termination
Methionine (AUG) Polysome
Stop codons
tRNA
 Types of sequences in the human genome

Short interspersed elements

100 to 300 bp
Long interspersed elements
6 to 8 kbp
(encode enzymes for transposition) 1.5 to 11 kbp

Simple sequence
repeats

Large segmental
duplications
 Important structural elements of a yeast chromosome

centromere
Supercoiling of DNA

Supercoiling induced by separating the strands

of a helical structure
Relaxed and supercoiled plasmid DNAs
Most cellular DNA is underwound DNA underwinding is defined
by topological linking number

84 bp
 Linking number applied to Negative and positive
closed-circular DNA molecules supercoils

underwinding overwinding

topoisomers

Superhelical density
2,100 bp s = DLk/Lk0 = -2/200 = -0.01
1% of the helical turns present in the
DNA (in its B form) has been removed
 Regulasi pada lac operon

Sekuen pada lac operon

lac operon
Regulatory gene Promoter Operator Structural Gene

DNA lacI lacZ lacY lacA

Terekspresi lebih Tempat -galaktosidase permease transasetilase

dahulu menempelnya
menghasilkan RNA Polimerase
protein regulator
(represor) Tempat
menempelnya
protein represor

Klik di sini untuk melihat ekspresi lac operon

 Regulasi pada lac operon
a. Tidak ada laktosa, represor aktif, operon off

DNA lacI lacZ lacY lacA

RNA
polimerase
mRNA

-galaktosidase, permease dan

transasetilase tidak terbentuk

Protein
represor

Klik di sini untuk melihat ekspresi lac operon selanjutnya

Copyright:dP2010
 Regulasi pada lac operon
b. Ada laktosa, represor tidak aktif, operon on

DNA lacI lacZ lacY lacA

RNA
polimerase
mRNA

-galaktosidase permease transasetilase

Protein Protein laktosa

represor
Represor tidak aktif

Klik di sini untuk kembali ke slide pertama

Copyright:dP2010
Fig. 16.6