I.

DNA replication
When a cell divides to yeield two daughter cells, genetic material must be reproduced accurately, or
replicated, so that two daughter cells have identical DNA copies.
Replication begins at a specific point in the DNA sequence called an origin of replication. In the linear
eukaryotic DNA molecules of the chromosome, there are multiple origins.
+ In prokaryotic DNA molecules, there is one origin of replication. The DNA double helix seperates at
this site and two replication forks are formed. When replication proceeds from the replication forks, it is
called bidirectional replication. The replications of bateria are also called θ replication.
+ In eukaryotic DNA, multiple origins produce multiple replication sites, each replicating
bidirectionally. Each replicating unit of DNA, called a replicon, extends outward until it meets a
neiboring replicon. These two replicons then fuse.
Protein enzymes in the process of replication

DNA synthesis the 5’-3’ direction of the new strand, require RNA primers
DNA Polymerase III: synthesis the leading and lagging strands
DNA Polymerase I: removal of RNA primers, filling the resulting gaps with
DNA polymerase
nucleotides.

Helicase Unwinds double strand DNA at the replication fork

Synthesis of short RNA sequence; primer for DNA synthesis
Primase
Single strand binding Binds to single-strand DNA to keep strand from base pairing
proteins
In bacteria, relaxes super-coiling ahead of the DNA replication fork
DNA gyrase
Join DNA fragments and Okazaki fragments of the lagging strand during DNA
DNA ligase replication
Replication process:
1. Initiation of replication
A small area of the DNA double helix is unwound at the origin of replication.
2. Unwinding of the DNA helix
The DNA helicase continues to unwind the DNA and DNA gyrase aids in seperating the two DNA
strands. Single-strand binding proteins (SSB) attach to each strand to stabilize amd to keep them from
reannealing. The juncture forms a replication fork. DNA gyrase relaxes super-coling ahead of the DNA
replication fork.
3. Synthesis of RNA primers
RNA primer initiates replication. It is synthesized by the enzyme primase. DNA polymerase removes
the RNA primers and the appropriate nucleotides are added where gaps left by primer removal.
4. The DNA polymerase binds to each strand and move along from the RNA primer, using information
in the template DNA to mediate the formation of the new DNA strand. DNA polymerase synthesize the
new strand 5’ to 3’. And on the template DNA 5’ to 3’, the DNA synthesis is discontinuous that form
Okazaki fragments,
5. Connection of Okazaki fragments to form one continuous DNA molecules by enzyme DNA ligase.
II. Transciption
The process of transmission of genetic information stored in DNA into the intermediate – RNA.
The promoter
 1. In both eukaryote and prokaryote genes, RNA polymerase recognizes the nucleotide sequences
usually upstream, just before the start of the coding region, or gene. These sequences called
promoters, allow the RNA polymerase to be correctly on the DNA strand near the gene to be
transcribed.
2. The common bacterial promoter composed of two highly conserved boxes, at approximately -10
and -35 regions upstream of the gene.
3. A small transiently bound protein (called σ) determines which type of promoter the enzyme
will bind and thus which gene will be transcribed à providing the binding specificity of RNA
polymerase to the promoter and initiate the transcription.
4. Promoter in eukaryote is more complex than in prokaryote and differ from them in sequence and
position.
RNA polymerase
There are 3 types of RNA polymerases involved in the transcription in eukaryote
(1) RNA polymerase I transcribes ribosomal RNA genes for 5.8S, 18S and 28S.
(2) RNA polymerase II transcribes genes encoding protein.
(3) RNA RNA polymerase III transcribes tRNA, 5S rRNA, and small nuclear and cytoplasmic
RNAs.
Transcription process:
1. Binding of the RNA polymerase to promoter. The DNA helix unwinds in this region.
2. Initiation of transription. RNA polymerase begins synthesizing RNA from the template strand of the
DNA.
3. Elongation of the RNA. As the RNA polymerase moves along the DNA strand in the 3’ to 5’
direction, the DNA helix unwinds and the two strands separate. The RNA elongates by the addition og
ribonucleotides to the 3’ end of the newly synthesized RNA.
4. Termination of transription. The RNA polymerase disengages the DNA, and the new RNA molecule
is released.
Factors that take part in transcription process:
+ RNA polymerase
+ transcription factors : help initiate transcription by increasing the binding affinity of RNA polymerase
for the promoters.
+ regulatory proteins : control transcription
+ enhancers: influence the level of transcription from great distances.
RNA processing:
In eukaryotic cells, most newly synthesized RNA must be modified to become a mature mRNA
+ Addition of a 5’ cap structure
+ Addition of a 3’ poly-A tail
+ the introns are spliced out of the newly synthesized RNA so that the exons are adjacent to one another
The function of 5’ and 3’ modification :
+ facilitate transport out of the nucleus
+ protect the mRNA from degradation in the cytoplasm
+ maintain stability for translation
III. Translation
The process in which the genetic information from RNA can be translated into the amino acid chain
(polypeptide).
In prokaryote, the translation occur simultaneously with the transcription. In eukaryote, RNA was
synthesized in the nucleus and brought to the cytoplasm, here, it initiates the translation
The major components required for protein synthesis are:
(1) mRNA that encodes the linear sequence of the amino acids of polypeptides.
(2) tRNA molecules that carry amino acids to the site of protein synthesis in the appropriate order
specified by the linear sequence of amino acids encoded within the mRNA.
(3) Ribosomes, composed of rRNA and proteins, that help carry out protein synthesis.
(4) Protein factors that help carry out the different steps of protein synthesis.
Translation process:
1. Initiation
The small ribosome subunit binds to the initiator tRNA and its amino acid methionine. This ribosome
subunit-tRNA-methionine complex binds to the end of the mRNA near the 5’ cap site. The snall subunit
then moves along the mRNA until the initiator AUG is recognized. The large ribosomal subunit is then
added. Many initiation protein factors play important roles in the initiation process.
2. Elongation
Amino acids are added stepwise to the growing polypeptide chain. The amino acid attached to the first
tRNA is transferred to the amino acid on the second aminoacyl-tRNA. A peptide bond is made between
2 amino acids. The first tRNA , without its amino acid, is released from the ribisome and mRNA. The
elongation continues.
3. Transclocation
The process that ribosome complex moves by one codon on mRNA called translocation.
4. Termination
Elongation of the polypeptide chain continues until a stop codon is reached (UAA, UAG, UGA) and a
protein release factors interacts with stop codon to terminate translation. The ribosomal subunits
dissociate, the mRNA and tRNA are released and can be used again.
IV. Regulation of gene expression
1. Prokaryotic gene expression
In bacteria, a single promoter often controls several structural genes or coding region, called cistrons.
This arrangement is called an operon. An operon consits of structural genes, a promoter, a repressor
binding site (operator).
* Regualtion of lac operon
When the active repressor binds to the operator in the absence of lactose, RNA polymerase cannot bind
to the promoter and transcription is blocked. In the presence of lactose, a derivative of the sugar binds to
the repressor and inactivates it so that the repressor can no longer bind to the operator, thus allowing
RNA polymerase to bind to the promoter and transcription to proceed.
* The trp Operon
The trp operon has five structural genes and the promoter region. In the absence of tryptophan, the
repressor is inactive and cannot bind to the operator, thus allowing RNA polymerase to bind to the
promoter and transcription to proceed. When tryptophan is present it binds to and activates the reprssor,
thus allowing the activated repressor to bind to the operator and block transcription.
2. Eukaryotic gene expression
The regulation of gene expression in eukaryoties is more complex because of larger genome size,
compartmentalization in the cell, more extensive transcript processing, own gene’s promoter-regulatory
region, regualation from a distance, cell- and tissue-specific gene expression.
There are many control points:
- transcriptional control
- regulation of RNA processing and transport out the nucleus to the cytoplasm
- translational control
- posttranslational control