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Muh. Nasrum Massi

Chromosome replicates through DNA

DNA replication is a process of copying
DNA double strand.
Since DNA are antiparalell and
complementary, each strand can serve as
a template for the new opposite strand.
Because a new synthesized DNA double
strand consists of an old strand and a new
antiparalel double strand, DNA synthesis is
termed semiconservative replication.

Semiconservative Replication

DNA replication is made up of three phases:

1. Initiation, involves recognition of the
position(s) on a DNA molecule where
replication begins.
2. Elongation, concerns the events
occuring at the replication fork, where the
parent nucleotide are copied.
3. Termination, occurs when the parent
molecule has been completely replicated.

A. Initiation
Initiation of replication is not a random
process and always begins at the same
position(s) on a DNA molecule, these
points being called the origins of
A circular bacterial genome has a single
origin of replication, whilest eukaryotic
chromosomes have multiple origins.

An initiatior protein binds to the origin of

replication sequence and slightly unwind
the double helix using ATP energy.
In most cases, DNA replication is
bidirectional: Two replication forks are
fromed at an origin, and replication
proceeds simultanously in both direction.
For circular bacterial DNA this process is
called theta replication, whilest in linear
eukaryotic DNA this process is called Y

Theta replication

Y Replication

A.1. Unwinding the DNA

For DNA replication to proceed, the DNA
must unwind to expose the single strands
to the enzymes responsible for copying
The proteins responsible for unwinding
the DNA are called helicase. These are
enzymes that use the energy of ATP to
unwind DNA in advance of the replication

Gyrase is an enzyme that serves as a swivel

that prevents overwinding of the DNA ahead of
the replication fork.
Once strand separation begun, molecules of
single strand binding protein (SSB), quickly
attach to the exposed single strands at the
replication fork, in such a way that they do not
cover the nitrogenous bases.
The SSB molecules hold the separated strands
in a semiextended position that makes the
separated DNA strands more accessible to the
DNA replication machinery.

DNA Replication

B. Elongation
Enzymes capable of adding successive
nucleotides to a growing DNA strand are called
DNA polymerase.
DNA polymerase requires a template, all use
deoxyribonucleoside triphosphate as their
Each successive nucleotide is linked to the
growing chain by a phosphodiester bond
between the phosphate group on its 5 carbon and
the hydroxyl group on the 3 carbon of the previous

Chain elongation therefore always occurs at

the 3 end of a DNA strand, and the strand
grow in 53 direction.
Since DNA polymerase is only able to
synthesize DNA in the 53 direction, one
strand of the double helix can be coupled in
continous manner (leading strand), but
replication in the other strand (lagging
strand) has to be carried out in a
discontinous fashion, as a series of short
segments (okazaki fragments) that must be
ligated together to produce intact daughter

DNA polymerase can not initiate DNA

synthesis because it is template dependent.
This means that primers are needed, one to
initiate complemetary strand synthesis on the
leading polynucleotide, and on for every
segment of discontinous DNA synthesized on
lagging strand.
The primers are a short piece (3-10 bp) RNA
Initiation of primers are done by non
transcriptional RNA polymerase called
primase. In prokaryotes primase binds with
unwinding proteins forming a primosome, but
is a part of DNA polymerase in eukaryotes.

B.1. Prokaryotic DNA

In prokaryotes, DNA polymerase involved in
replication are DNA polymerase I, II, and III.
DNA polymerase I consists of one subunit,
functions in DNA synthesis and DNA repair.
DNA polymerase II consists of one
subunit, functions in DNA repair.
DNA polymerase III consists of at least 10
subunits, and is the main replicating

B.2. Eukaryotic DNA

In eukaryotes, DNA polymerase involved in
DNA synthesis are DNA polymerase , ,
, , dan
DNA polymerase , consists of 4
subunits, functions in priming during
replication, contains a primase.
DNA polymerase , consists of one
subunit and functions in DNA repair.

DNA polymerase , consists of 2 subunits

and functions in mitochondrial DNA
DNA polymerase , consists of 2 to three
subunits, functions as main replicating
DNA polymerase , consists of at least
one subunit, function in DNA replication,
but precise function is still unknown.

C. Termination
Termination occurs when DNA replication
forks meet one another or run to the end
of a linear DNA molecule.
Also, termination may occur when a
replication fork is deliberately stopped by
a special protein, called a replication
terminator protein, that binds to specific
sites on a DNA molecule

When the polymerase reaches the end of a linear

DNA molecule, there is a potential problem due
to the antiparallel structure of DNA.
Because an RNA primer must be regularly laid
down on the lagging strand, the last section of
the lagging-strand DNA cannot be replicated
because there is no DNA template for the primer
to be synthesized on.
To solve this problem, the ends of most
chromosomes consist of noncoding DNA that
contains repeat sequences.

The end of a linear chromosome is called the

Cells can endure the shortening of the
chromosome at the telomere to a degree, since
it's necessary for chromosome stability.
Many cells use an enzyme called telomerase
that adds the repeat units to the end of the
chromosome so the ends do not become too
short after multiple rounds of DNA replication.
Many simple, single-celled organisms overcome
the whole problem by having circular

Organization and
Muh. Nasrum Massi

A. Chromosom
Beside genes containing codes for
protein synthesis (exons), DNA also
contain non-coding proteins like introns,
promoters, and enhancers.

A.1. Exons
An exon is any region of DNA within a
gene that is transcribed to the final
messenger RNA (mRNA) molecule,
rather than being spliced out from the
transcribed RNA molecule. Exons of
many eukaryotic genes interleave with
segments of non-coding DNA (introns).

A.2. Introns
Introns are sections of DNA that will be
spliced out after transcription, but before
the RNA is used. Introns are common in
eukaryotic RNAs of all types, but are
found in prokaryotic tRNA and rRNA
genes only.
The number and length of introns varies
widely among species and among genes
within the same species.

A.3. Promoter
a promoter is a DNA sequence that
enables a gene to be transcribed. The
promoter is recognized by RNA
polymerase, which then initiates
transcription. In RNA synthesis,
promoters are a means to demarcate
which genes should be used for
messenger RNA creation - and, by
extension, control which proteins the cell

A.4. Enhancer
an enhancer is a short region of DNA
that can be bound with proteins (namely,
the trans-acting factors, much like a set
of transcription factors) to enhance
transcription levels of genes (hence the
name) in a gene-cluster. An enhancer
does not need to be particularly close to
the genes it acts on, and need not be
located on the same chromosome

An enhancer does not need to bind close to

the transcription initiation site to affect its
transcription, as some have been found to
bind several hundred thousand base pairs
upstream or downstream of the start site.
Enhancers do not act on the promoter
region itself, but bind to activator proteins.
These activator proteins interact with the
mediator. The mediator is the protein that
communicates with the polymerase II and
the general transcription factors.
Enhancers can also be found within introns.

B. Chromosome
Genomes are dynamic entities that
evolve over time due to the cumulative
effects of small scale sequence
alterations caused by mutation, and
larger scale rearrangements arising from

B.1. Mutation
A mutation is a change in the nucleotide
sequence of a short region of a genome.
Many mutations are point mutations that
replace one nucleotide with another.
Other mutation involve insertion or deletion of
one or a few nucleotides.
Mutations result either from errors in DNA
replication or from the damaging effects of
mutagens such as chemicals and radiation that
react with DNA and change the structures of
individual nucleotides.

A mutagen is a chemical or physical agent

that cause mutation.
Chemical mutagens are base analogs,
deaminating agents, alkylating agents, and
intercalating agents.
Physical mutagens are UV radiation,
ionizing radiation, and heat.
The effects of mutation to the genome are
silent mutation, missense mutation, and
non sense mutation.

Silent mutation is the mutation where the

new codon specifies the same amino acid
as the unmutated codon.
Missense mutation, where mutation
altering the codon so that it specifies a
different amino acids.
Non sense mutation results in a shortened
protein because translation of the mRNA
stops at a new termination codon rather
then proceeding to the correct termination
codon which is further downstream.

All cells possess DNA repair enzymes

that attempt to minimize the number of
mutations that occur.
Most cells possess five different categories
of DNA repair system: direct repair system,
base excision repair, nucleotide excision
repair, mismatch repair, and recombination
Direct repair system, act directly on
damaged nucleotides, converting each one
back to its original structure.

Base excision repair, involves removal of

a damaged nucleotide base, excision of a
short peace of the polynucleotide around
the AP site thus created, and resynthesis
with a DNA polymerase.
Nucleotide excision repair, is similar to
base excision repair but is not preceeded
by removal of a damaged base and can
act on more substantially damaged areas
of DNA.

Mismatch repair, corrects errors of

replication, again by excising a stretch of
single-stranded DNA containing the
offending nucleotide and then repairing the
resulting gap.
Recombination repair, is used to mend
doublestrand breaks.

B.2. Recombination
Recombination results in a restructuring
of part of a genome, for example by
exchange of segments of homologous
chromosomes during meiosis or by
transposition of a mobile element from
one position to another within a
chromosome or between chromosomes.