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Examination

MOLECULAR GENETICS

Joni Hendri

NIM.12/336568/PMU/07330

BIOTECHNOLOGY STUDY PROGRAMME

POST-GRADUATE SCHOOL

UNIVERSITY OF GADJAH MADA

YOGYAKARTA

2013

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Several modes of genetic materials replication in viruses

Viruses are a particle that contains the genetic material in the form of DNA or

RNA that is enveloped by protein called capsid. Besides DNA viruses and RNA

viruses, there is a simpler particle of virus called prion. Prions or viroids are small

RNA molecules consisting of 359 nucleotide bases and not enveloped by the protein.

Prions are known as infective agent that causes several diseases in both humans and

animals.

Viruses may contain double-stranded DNA, double-stranded RNA, single-

stranded DNA or single-stranded RNA. In addition, there is the viral genom in the

form of linear and circular nucleic acid moleculs. The mechanism for double-stranded

DNA, single-stranded DNA, double-stranded RNA and single-stranded RNA viral

replication will differ.

Replication of DNA viruses

Some viruses had a genetic material DNA in the form of double-stranded or

single-stranded which is different in mechanism of replication. Mechanism of double-

stranded DNA viral replication is a semiconservative models consisting of several

stages: (1). Denaturation of DNA strands, (2). Initiation of DNA synthesis, (3).

Elongation of DNA strand, (4). Ligation of DNA fragments and (5). Termination of

DNA synthesis. However, if that virus is a single-stranded DNA, replication will

going through three phases: (1). Duplex replicative form, (2). Rolling-circle

replication and (3). Synthesis of strands (+) which is generating a single strand of

molecules. Furthermore, the replication mechanism will vary between linear and

circular DNA, for example, in replication of circular DNA molecule, the replication

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fork will moving into two directions (Bidirectional replication) to form the ɵ (theta)

structure.

Generally, DNA viruses replicate their genetic material by one of three modes:

1. Bidirectional replication from a circular substrate. This process may proceed via a

“theta-form” intermediate (eg, papillomaviruses), or in some cases via a “rolling

circle” mechanism that results in the generation of concatemeric (head-to-tail) viral

genomes.

2. Replication from a linear substrate. In this case, synthesis of new DNA strands is

not simultaneous. Rather, it occurs sequentially (ie, first one strand is made in its

entirety & then the next strand is made). Examples include adenoviruses.

3. Replication via an RNA intermediate. Hepadnaviruses (hepatitis B virus) are

unique since they contain a partially dsDNA genome that must be converted into

an RNA form by the virion enzyme reverse transcriptase during the virus life cycle

.

Replication of RNA virus

RNA viruses have a variety of modes of replication, for example, retroviruses

replication is done by converting single-stranded RNA into double-stranded DNA in

advance using reverse transcriptase enzyme. On the contrary, RNA replication in

TMV (tobacco mosaic virus) is replicated directly from RNA to RNA. Although

commonly RNA replication refers to several important points of replication which are

shown as follows:

1. The viral RNA genome can act as its own message (positive strand viruses) or the

complementary strand can be the mRNA (negative strand viruses).

2. All RNA viruses except retroviruses encode an RNA-dependent RNA polymerase.

In the negative strand RNA viruses this polymerase is part of the virion, and it

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must enter the cytosol along with the viral genome. This is necessary in order for

the virus to generate mRNAs from its genome.

3. All RNA viruses replicate in the cytoplasm except orthomyxoviruses (influenza A

& B), borna disease virus, hepatitis delta virus and retrovirses. Additional feature

of orthomyxoviruses: these viruses have segmented genomes.

4. Retroviruses are unique. These viruses have a positive sense RNA genome which

must be converted into a dsDNA form by the virion enzyme reverse transcriptase.

This double-stranded DNA is then integrated into the host cell chromosome by the

viral integrase enzyme. Upon integration into the host chromosome, the viral DNA

can then be transcribed by cellular RNA polymerase II, to produce new genomic

RNA molecules.

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Interrealtionship betwen DNA replication and genetic expression with the

phenomenon of cell geowth

In the biological sense, cells are the smallest unit of organization which is the

foundation of life. All functions of life are organized and took place inside the cell.

Cell growth and development cannot be separated from the cycle of life which is

experienced by the cell in order to survive. This cycle regulate cell growth by

regulating fission time and cell growth by regulating gene expression or gene

translation amount respectively.

Surrounded by a phospholipid bilayer, cells contain proteins as functional

polymers and have DNA as genetic information that dictates cell structures and

functions. As the smallest units of organisms, all cells divide and multiply to create

progeny cells. Although multicellular organisms produce offspring as a function on

the level of individual organisms, this function is supported by the multiplication of

component cells, and cell multiplication is a basic function of the process by which a

fertilized egg develops into an individual organism. Cell multiplication is the most

basic and common of cell functions, and has survived a long process of evolution.

Cells multiply by binary fission. Before cell division, all cellular components

must be doubled. However, cellular components consist of a great number of

molecules, and the concept of “doubling” here is applied loosely; components are not

necessarily equally divided and distributed precisely into two cells (i.e., daughter

cells). DNA, which consists of genetic information, is quite different. Prokaryotes

have only one DNA molecule per cell. Although eukaryotes have a structure slightly

more complex than that of prokaryotes, they also have only one molecule of the same

DNA type per cell. Since DNA molecules contain all the genetic information of the

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organism to which they belong, a DNA molecule identical to that of the parent cell

must be replicated during cell multiplication, and the two resulting identical copies of

the DNA must be equally distributed to the two daughter cells. This phenomenon,

which involves individual molecules, presents a rigorous condition not found in other

cellular molecules

Genetic material replication is a process that initiated the cell growth;

however, growth is simultaneous reactions involving many processes related to each

other. Replication of genetic material is followed by forming of progeny that carry

genetic material duplicate from replication results.

The replication of DNA involves the production of high-molecular DNA by

polymerizing deoxyribonucleotides, which are units of DNA.Generally, this process is

expressed as follows: Double strands of DNA always run in opposite directions. This

is the case for completed DNA as well as for DNA during the process of replication.

When DNA synthesis is considered based on the Watson-Crick model, one of the

daughter strands must be synthesized in the 3’→5’ direction. However, DNA

polymerase always synthesizes in the 5’→3’ direction. Let’ look at this in more detail.

During the synthesis of the daughter strands following the uncoiling of the parent

strand, three double strands of DNA appear in a structure called the replication fork.

Looking closely at this fork structure, at the point where DNA synthesis occurs (i.e.,

the replication point), one of the daughter strands (i.e., the leading strand) is

synthesized in the same direction as that in which the replication fork runs. The other

daughter strand (i.e., the lagging strand) is synthesized in the direction opposite to that

of the replication fork, because DNA is synthesized in the 5’→3’ direction. Along the

lagging strand, short DNA fragments of approximately 100 nucleotides are

continually synthesized, and are subsequently linked with each other. These short

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strands are called Okazaki fragments after Reiji Okazaki, the molecular biologist who

discovered them. This type of replication is called discontinuous replication. In the

Contrary, synthesis of DNA strand wich has an opposite direction to the direction of

the opening fork geometry replication is done step by step (discontinue synthesis

type). Generally, it can be said that the mechanism of DNA replication takes place in

semi-discontinue type, because of differences in the mechanism synthesis of both

DNA strand synthesis.

Mechanisms of DNA replication requires a variety of proteins and enzymes.

Proteins and enzymes are produced by genetic expression mechanisme. Specifically,

genetic information refers to the nucleotide (base) sequence of DNA strands; mRNA

is synthesized using DNA as a template, by which the genetic information of the DNA

is transcribed as the sequence of the mRNA. The base sequence of mRNA is defined

as a series of genetic codes, and such codes in mRNA are used to synthesize proteins

on cytoplasmic granules called ribosomes. One piece of mRNA code corresponds to

one amino acid, and these amino acids are linked together following the order of the

codes, thus synthesizing proteins.

Therefore, it can be said that the replication process will not occurs without the

process of genetic expression. In other words, there is an interrelationship between

DNA replication and genetic expression with the phenomenon of cell growth

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References :

1. Yuwono, T. (2005). Biologi Molekuler. Penerbit Erlangga. Jakarta

2. Cann, A.J. (2005). Principles of Molecular Virology Fourth Edition. Elsevier

Academic Press. USA.

3. Wagner, E.K and Hawlett, M.J. (2004). Basic virology . Second edition.Balckwall

Publishing. USA