Kamis, 30 Juli 2015

Composed of Nucleic Acid and Protein Envelope Virus

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A Virus is not a cell (acellular). A virus contains a particle called virion, which can be crystallized and shows a mineral characteristics rather than life. For that matter, some scientists consider viruses as non-living. Still, other think the opposite because viruses can reproduce which is a characteristic of life. Nevertheless, viral reproduction can only be done inside a living cell. The cell in which the virus resides is called the host cell.

Because a virus is not a cell, it does not have cellular component such as the cell membrane, cytoplasm, and nucleus. A virus is composed of a nucleic acid and protein coat called a capsid.

Nucleic Acid

Nucleic Acid Are the molecules that carry the genetic information. A virus has only one type of the nucleic acids, i.e. DNA or RNA

The genetic material may be in the shape of single of double stranded chain, circular, or linier.

Protein Envelope (capsid)

The protein coat covering the genetic material is called the capsid

Composed of a large number protein subunits called capsomers. The capsid giving the virus its shape. It can be a helical structure of capsomeres, giving the virus its rod shape, or polyhedral, or a more complex shape

The T shape virus has a head and tail part and the head is usually polyhedral and the tail is composed of three structures called sheath, base plate, and tail fibers. The base plate and tail fiber are used to attach and infect cell. An example of one of these complex viruses is the T shape bacteriophage.

Body and structure of a virus. Virus is composed of nucleid acid and capsid

a. helical such as tobacco mossaic virus
b. polyhedral such as adenovirus
c.complex such as Bacteriophage
d.virus with envelope in influenza

Nucleic acid and capsid from a structure called nucleocapsid. In some viruses, the nucleocapsid. In some viruses, the nucleocapsid has a membrane called envelope. it is composed of lipids and protein and helps the virus to infect cells. An example of a virus with an envelope is the Influenzavirus. Viruses without an envelope are called naked virusses

Minggu, 26 Juli 2015

Virus Structure

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All viruses contain the following two components: 1) a nucleic acid genome and 2) a protein capsid that covers the genome. Together this is called the nucleocapsid. In addition, many animal viruses contain a 3) lipid envelope. The entire intact virus is called the virion. The structure and composition of these components can vary widely. 

A: Viral Genomes: While the genomes of all known cells are comprised of double stranded DNA, the genomes of viruses can be comprised of single or double stranded DNA or RNA. They can vary greatly in size, from approximately 5-10 kb (Papovaviridae, Parvoviridae, etc.) to greater than 100-200 kb (Herpesviridae, Poxviridae). The known structures of viral genomes are summarized below. 

All viruses contain the following two components: 1) a nucleic acid genome and 2) a protein capsid that covers the genome. Together this is called the nucleocapsid. In addition, many animal viruses contain a 3) lipid envelope. The entire intact virus is called the virion. The structure and composition of these components can vary widely. 

A: Viral Genomes: While the genomes of all known cells are comprised of double stranded DNA, the genomes of viruses can be comprised of single or double stranded DNA or RNA. They can vary greatly in size, from approximately 5-10 kb (Papovaviridae, Parvoviridae, etc.) to greater than 100-200 kb (Herpesviridae, Poxviridae). The known structures of viral genomes are summarized below. 

DNA: Double Stranded - linear or circular
          Single Stranded - linear or circular
          Other Structures - gapped circles
RNA: Double Stranded - linear
          Single Stranded - linear : These single stranded genomes can be either + sense, - sense, or ambisense The sense         strand is the one that can serve directly as mRNA and code for protein, so for these viruses, the viral RNA is infectious. The viral mRNA from - strand viruses is not infectious, since it needs to be copied into the + strand before it can be translated. In an ambisense virus, part of the genome is the sense strand, and part is the antisense.
The genome of some RNA viruses is segmented, meaning that a virus particle contains several different molecules of RNA, like different chromosomes.

B: Protein Capsid
 Viral genomes are surrounded by protein shells known as capsids. One interesting question is how capsid proteins recognize viral, but not cellular RNA or DNA. The answer is that there is often some type of "packaging" signal (sequence) on the viral genome that is recognized by the capsid proteins. A capsid is almost always made up of repeating structural subunits that are arranged in one of two symmetrical structures, a helix or an icosahedron. In the simplest case, these "subunits" consist of a single polypeptide. In many cases, however, these structural subunits (also called protomers) are made up of several polypeptides. Both helical and icosahedral structures are described in more detail below. 

1) Helical Capsids: The first and best studied example is the plant tobacco mosaic virus (TMV), which contains a SS RNA genome and a protein coat made up of a single, 17.5 kd protein. This protein is arranged in a helix around the viral RNA, with 3 nt of RNA fitting into a groove in each subunit. Helical capsids can also be more complex, and involve more than one protein subunit.
A helix can be defined by two parameters, its amplitude (diameter) and pitch, where pitch is defined as the distance covered by each turn of the helix. P = m x p, where m is the number of subunits per turn and p is the axial rise per subunit. For TMV, m = 16.3 and p= 0.14 nm, so P=2.28 nm. This structure is very stable, and can be dissociated and re-associated readily by changing ionic strength, pH, temperature, etc. The interactions that hold these molecules together are non-covalent, and involve H-bonds, salt bridges, hydrophobic interactions, and vander Waals forces.

Several families of animal virus contain helical nucleocapsids, including the Orthomyxoviridae (influenza), the Paramyxoviridae (bovine respiratory syncytial virus), and the Rhabdoviridae (rabies). All of these are enveloped viruses (see below). 

2) Icosahedral Capsids: In these structures, the subunits are arranged in the form of a hollow, quasi spherical structure, with the genome within. An icosahedron is defined as being made up of 20 equilateral triangular faces arranged around the surface of a sphere. They display 2-3-5 fold symmetry as follows:
- an axis of 2 fold rotational symmetry through the center of each edge.
- an axis of 3 fold rotational symmetry through the center of each face.
- an axis of 5 fold rotational symmetry through the center of each corner.
These corners are also called Vertices, and each icosahedron has 12.
Since proteins are not equilateral triangles, each face of an icosahedron contains more than one protein subunit. The simplest icosahedron is made by using 3 identical subunits to form each face, so the minimum # of subunits is 60 (20 x 3). Remember, that each of these subunits could be a single protein or, more likely, a complex of several polypeptides.
Many viruses have too large a genome to be packaged inside an icosahedron made up of only 60 polypeptides (or even 60 subunits), so many are more complicated. In these cases, each of the 20 triangular faces is divided into smaller triangles; and each of these smaller triangles is defined by 3 subunits. However, the total number of subunits is always a multiple of 60. The total number of subunits can be defined as 60 X N, where N is sometimes called the Triangulation Number, or T. Values for T of 1,3,4,7,9, 12 and more are permitted.

When virus nucleocapsids are observed in the electron microscope, one often sees apparent "lumps" or clusters on the surface of the particle. These are usually protein subunits clustered around an axis of symmetry, and have been called "morphological units" or capsomers

C: Viral Envelope
In some animal viruses, the nucleocapsid is surrounded by a membrane, also called an envelope. This envelope is made up of a lipid bilayer, and is comprised of host-cell lipids. It also contains virally encoded proteins, often glycoproteins which are trans-membrane proteins. These viral proteins serve many purposes, such as binding to receptors on the host cell, playing a role in membrane fusion and cell entry, etc. They can also form channels in the viral membrane.
Many enveloped viruses also contain matrix proteins, which are internal proteins that link the nucleocapsid to the envelope. They are very abundant (ie, many copies per virion), and are usually not glycosylated. Some virions also contain other, non-structural proteins that are used in the viral life cycle. Examples of this are replicases, transcription factors, etc. These non-structural proteins are present in low amounts in the virion.
Enveloped viruses are formed by budding through cellular membranes, usually the plasma membrane but sometimes an internal membrane such as the ER, golgi, or nucleus. In these cases, the assembly of viral components (genome, capsid, matrix) occurs on the inside face of the membrane, the envelope glycoproteins cluster in that region of the membrane, and the virus buds out. This ability to bud allows the virus to exit the host cell without lysing, or killing the host. In contrast, non-enveloped viruses, and some enveloped viruses, kill the host cell in order to escape.

D: Virus Classification/Nomenclature
Viruses are classified using a combination of characteristics, including the following
1) Morphology: size, shape, presence of envelope, etc.
2) Physicochemical properties: thermal stability, detergent stability, molecular mass, etc.
3) Genome: size, type of nucleic acid, strandedness, etc.
4) Proteins: number, size, sequence, etc.
5) Lipids: content, character, etc.
6) Carbohydrates: content, character, etc.
7) Genome organization and replication: strategy of replication, number and position of open reading frames, transcriptional and translational strategies, site of virion assembly and release.
8) Antigenic properties: serological relationships.
9) Biological properties: Host range, mode of transmission, pathogenicity, tissue tropisms, geographic distribution, etc.

Using these and other criteria, the International Committee on Nomenclature of Viruses (ICTV) produced the following the hierarchical system for viral classification.
1) Orders (virales): Groupings of families of viruses that share common characteristics and are distinct from other orders and families.
2) Families (-viridae): Groupings of genera of viruses that share common characteristics and are distinct from the member viruses of other families.
3) Subfamilies (-virinae): Not used in all families, but allows for more complex hierarchy of taxa.
4) Genera (-virus): Groupings of species of viruses that share common characteristics and are distinct from the member viruses of other species.
5) Species (virus); The definition accepted by ICTV is "a virus species is defined as a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche". A species can be further broken down into strains, variants, etc.

In addition to this formal taxonomy, David Baltimore proposed that viruses be classified according to the nature of their genome and the relationship between the genome and the viral mRNA. The classes that he proposed are the following:
Class I: Double Stranded DNA Genomes
Class II: Single Stranded DNA Genomes
Class III: Double Stranded RNA Genomes
Class IV: Positive Strand RNA Genomes
Class V: Negative Strand RNA Genomes
Class VI: Retroviruses

So, the classification of viruses is quite complex, and to some extent is constantly evolving. 

Sabtu, 25 Juli 2015

Research Tobacco on Plant Viruses

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Virus is the Latin word for toxin, Before The advancement of science, all mysterious disease in human kind were called viruses. Virus history began when a man A. Mayer, a German scientist, discovered one in 1883. His research was on the cause of tobacco mosaic disease. The disease hindered the growth of the tobacco plant (dwarfism) and resulted in spotted leaves. Mayer found that other healthy plant could be infected just by spraying the extract of the disease plant.

Mayer concluded that the disease was caused by a very small bacterium. This bacterium cannot be seen even with a microscope.

Mayer’s hypothesis was tested by a Russian Scientist named Dmitri Iwanowski in 1892. He filtered the tobacco leaf extract in away. Once the filtrate was spayed to healthy plants, they also got infected by the mosaic disease.

Iwanowski suspected that the mosaic disease was caused by another organism smaller than a bacterium . However, he was still in doubt. He thought that he could have made an error with the filtration. Just as Mayer did, he concluded that a bacterium was the cause of the disease.

Six years later, a Dutch scientist named Martinus W. Beijerick did an experiment the same as what Iwanoski’s method of filtration was the correct method. He postulated the presence of an agent that infected the tobacco plant, although he did not know what it was. He called the infected agent as filterable virus because it could no be observed with microscope.

We now understand that viruses cause disease in humans, animals and plants. The term filterable virus was shortened into virus. Iwanowski and Beijenerick were considered the discoverers of viruses.

Viruses have distinct characteristics that separate them from the rest of the living organism. They differ from other organism in the classification system. Virology is the study of virus. We will know more about the characteristic and the roles viruses have in human life

Rabu, 17 September 2014

Genetic Manipulation - Plasmid And Enzyme

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Plasmid  is a double DNA molecule  in a ring shape  that only exists
in bacteria.  In genetic manipulation  activity, plasmid  functions  as vector
(vehicle) used  to transfer and duplicate  foreign genes.
Plasmid, a bacteria cell part that has important roles in genetic manipulation activity


The  two kinds of enzyme  involved  in genetic manipulation  process are as follows.
  1. Restriction endonuclease  enzyme  functions  to cut DNA chain, so that it is called biology  scissors. This enzyme  has abilities  to recognize and cut specific nucleotide series  in DNA.  !
  2. Ligase enzyme  functions to adhere DNA  fragments. Look above Picture

Mechanism  in the enzyme's work.  Nucleotide  series known as restriction enzyme,  sticky end' motecule  of ecombinant  DNA

source: Essential Biology, 2006

Conventional Biotechnology And Modern Biotechnology

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Conventional Biotechnology 

conventional  biotechnology  is a biotechnology  practice  conducted  by
using simple method  and  instruments,  without genetic manipulation. It has
been done since  thousands  years ago to produce many  kinds of products,
such as beer, wine, tuak,  sake, yogurt,  bread, cheese, soysauce,  tempe,
tapai, and oncom.

a. Kecap, b. Tahu, c. tempe are the product of conventional biotechnology

Modern Biotechnology

Modern biotechnology is a biotechnology  practice  developed with
genetic manipulation  technique,  in which  transfer  of genetic material
(transfer  of gene) from one  living organism to the other occurs. Through  this
technique,  human can control the production  according  to his desire. For
examples,  the production  of pest and disease resistant  plants,  imperishable
fruits, and cattle which are able  to produce more milk.

In genetic manipulation process, organisms whose body contains
foreign  gene  are called transgenic  organisms. They can be  transgenic plant,
transgenic  animal,  and  transgenic  bacteria.

Example: Modern Biotechnology

Source: Essential Biology, 2006

Senin, 09 Juni 2014

Evidence And Anatomical Comparison

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When we look at the anatomy of some animal groups, we will find similarities on the structure of certain parts of the body. For example, if we compare the front legs of bird, bat, whale, cat, horse, and human, then there are similarities in components of the movement organs. The front movement organs of those animals are composed of long bone, radius and ulna bone, wrist bone, palm bone, and finger bone. Generally, each bone in each animal has different in size.

The similarities of the structure of the animals show the relation between them. It is assumed that the animals come from the same ancestor. shape and size differences on certain organ structure are resulted from functional adaptation process to different habitat. The same basic structure of some organs which have different function is called homologous. The example of it can be found in circulatory and urogenital system of vertebrate.

The homologous of front movement organs of some species

Fossil can discover the relation between groups of organisms

  1. a.Fossil Archaeopteryx 
  2. b.Comparison between dinosaur (left) and Archaeopteryx (right) 

 Source: Biology. The unity and diversity of life, 2004

Biogeographical Evidence

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Geographical spread coverage of living organism shows a lot of weird things that can be explained well as a result of evolution. Darwin noted that some animal found in Galapagos island looked like with the animals living in south America. The condition shows that the animals he found in Galapagos were the result of evolution from the animal that came from South America.

The weird spread patterns can be explained by the assumption That every species is inherited from the ancestors who naturally live in the continent. Moreover, the following generations spread to suitable habitat. The animal spread will stop when it come across barrier in the continent. The spread of terrestrial animal is blocked by sea so that the species will have geographical isolation. The isolated animals will mate to each other and produced individuals that are able to adapt certain environmental condition.

Source: Biology, Evolution Indicator

Kamis, 03 April 2014

Human Genetic Disorder Procedure Test

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Clinical genetic experts and other professional health experts usually use several tests and procedures to determine whether a person has a genetic disorder or has a child who risks to carry genetic disorder. The test may be conducted several times in the person's life. The following procedures are usually conducted.

The Following Procedures are Usually Conducted

  • Human Genetic Disorder Procedure Test Pre-Implantation Diagnoses, Pre-implantation diagnose is a kind of test that can be conducted in early possibility of life stage. The test is conducted along with in vitro insemination, that is, a procedure to integrate egg cell with sperm cell in a laboratory. Before an embryo resulted from in vitro insemination is attached in mother's womb, the doctor will first remove one cell from the developing embryo to analyze its DNA. DNA analysis is conducted to find out the correlation between abnormality and certain genetic disease that comes up.
  • Human Genetic Disorder Procedure Test Pre-natal Observation There are two types of prenatal tests to determine whether the fetus has abnormal gene or chromosome. The first test is conducted by examining genetic abnormality toward villous in chorion in the tenth week of pregnancy. The tissues are taken from the parts of the growing placenta. 
The second test is taken by using amniosynthesis technique, particularly towards mother above 35 years old. The test is conducted on the 14th and 20th weeks of pregnancy. In his case, the doctor will take several spoons of amnion fluid containing urine and fetus cells which can be used to find out the chromosome condition within cell. The cells inside amnion fluid can also be used to check the presence of DNA mutation and enzymes that become identification mark of genetic abnormality.

  • Human Genetic Disorder Procedure Test Prenatal Screening

Prenatal Test Technique for Genetic Disorder

  1. Chorionic villous sampling (CVS)
  2. amniosynthesis

Prenatal screening is a genetic screening conducted during pregnancy period to identify fetus towards the risk of the presence of genetic abnormality. The screening is conducted by analyzing the existence of 3 substances in pregnant mother's blood, which are fetoprotein, estriol and gonadotropin in human chorion. The substances are important to sign a certain problem happening to the fetus.

  • Human Genetic Disorder Procedure Test Observation After Birth Genetic observation to the newborn baby is needed to identify genetic disorder that can affect the baby. The newborn baby that has a sicklemia anemia disease is at risk of death. To prevent the risk, the baby will be given antibiotic immediately after being diagnosed. If the baby has PKU case, the doctor will give a special diet recipe that does not contain phenylalanine. If the baby has galactosemia case, the doctor will usually give a diet of galactose. The purpose of the diet is to prevent from such additional substance on the level that can cause mental disorder and death. 
  • Human Genetic Disorder Procedure Test Observation toward. Carrier Individual This test is usually aimed to diagnose recessive gene abnormality within autosome which is usually experienced by a person with certain ethnic background. For example, Jew descendants in East Europe territory will be observed to find out the carrier possibility toward Tay-Sach disease, cystic fibrosis and Canavan disease (a sort of nerve abnormality disease). Jew or Italian descendants will always be observed toward the case of thalassemia B, while Southeast Asian and Chinese descendants will always be observed toward thalassemia alfa case.
  • Human Genetic Disorder Procedure Test FamiIy Tree Observation Family tree can be used to trace back certain genetic characteristic pathway to three or more generations. 
 For example, a family tree which illustrates a gene inheritance related to cystic fibrosis will be very useful for the genetic advisor to determine a person within the family who risks to inherit one genetic abnormality or abnormal gen carrier. A family health history will be useful to identify the level of person health toward the risk of a genetic abnormality development. To gain the family's historical data, the health Expert will ask the health history of the family members to three or more generations. The information will be recorded as a graphic picture.

Example Human Genetic Disorder Procedure Test FamiIy Tree Observation

Hemophilia Inheritance In Russian Kingdom family. Through family tree map, genetic characteristic pathway is traced back to three or more generations.

Source: Biology, concept &connection, 2006

Chemical, Physical, Biological Mutagen

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Mutagen or known as mutation agent is any thing that can cause mutation, Based on the type, mutagen is distinguished into chemical mutagen, physical mutagen (radiation), and biological mutagen.

Chemical Mutagen

Chemical mutagen is a mutation agent which is in the form of chemical substance, It can mimic nitrogen base in normal DNA' but they cannot couple during DNA replication. Moreover, chemical mutagen has an ability to insert between nitrogen bases and disturb DNA replication' The examples of chemical mutagen can be seen in Types And Characteristics Of Mutagen .

Physical Mutagen

Physical mutagen is a mutation agent which is in the form of physical substances, such as short wave (ultraviolet and radiation ray such as alpha, beta, and gamma). Some physical mutagens can cause ionization while some others cannot.

Ionization usually occurs because the radiation source has very large energy, For example, radiation from radioactive substances (uranium, radium, cobalt), X-ray, and cosmic ray, If DNA molecules are hit by the radiation, the DNA chain will loose. In consequence, the DNA chain cannot function in protein synthesis.

Ultraviolet ray generally do not cause ionization, However, the energy from ultravlolet ray will be absorbed by purine and ppimidine so that the atom becomes more reactive (the electron undergoes exitation). Consequently, DNA double-helix becomes in disorder and inhibits replication, One of the effects caused by ultraviolet ray is skin cancer.

When we watch black and white television in an hour, we will be hit by I mrem radiation every hour, If we watch colored television, the effect becomes doubled, If we are diagnosed by X-ray, we will be hit by 150 mrem radiation, and every time we have our teeth portrayed, we get hit by 20 mrem radiation, Note that I to 2 dosage of mrem is already able to induce mutation.

Biological Mutagen

Biological mutagen is a mutation agent in the from of virus or bacteria Which can include mutation in every living organisms

When cell divides, virus will change the genetic material (DNA) Composition of the attacked cell I order to damage the cell and tissues Toxin produced by bacteria can also cause disorder or damage on genetic Material or certain cell and tissues. Hepatitis, chickenpox, measles, yellow Fever, or food poisoning (botulism) may begin from genetical material change induced either by virus or bacteria

Source: Human Biology, 2004