The nucleus of each of your cells contains multiple long strands of DNA with all the instructions to make your entire body. If you stretched out the DNA found in one of your cells it would be 2 to 3 meters long. To fit all of this DNA inside a tiny cell nucleus the DNA is wrapped tightly around proteins. The enzyme in meat tenderizer is a protease, which is an enzyme that cuts proteins into small pieces. As this enzyme cuts up the proteins the DNA will unwind and separate from the proteins. The protease in meat tenderizer actually comes from plants, but animals also make protease
Detergent
Add a small amount of detergent to a test tube (about 0.25 mL). Put a glove on the hand you will use to hold your test tube not the hand you will use to pour. Now carefully pour the drink containing your cheek cells into the test tube with detergent until the tube is half full.
To get the DNA out of your cheek cells you need to break open both the cell membranes and the nuclear membranes. Cell membranes and nuclear membranes consist primarily of lipids Dish washing detergent like all soaps, breaks up lipids. This is why you use detergents to remove fats from dirty dishes. Adding the detergent to you cheek cell solution will break open the cell membranes and nuclear membranes and release your DNA into the solution
To get the DNA out of your cheek cells you need to break open both the cell membranes and the nuclear membranes. Cell membranes and nuclear membranes consist primarily of lipids Dish washing detergent like all soaps, breaks up lipids. This is why you use detergents to remove fats from dirty dishes. Adding the detergent to you cheek cell solution will break open the cell membranes and nuclear membranes and release your DNA into the solution
Sample of Cells
Obtain a cup with sports drink. You will need to get thousands of your cheek cells in the sports drink in order to extract enough DNA to see. Therefore you should swish the sports drink around in your mouth vigorously for at least one minute. Then spit the drink back into the cup
DNA Extracting from Cells
Cells from the lining of your mouth come loose easily so you will be able to collect cells containing your DNA by swishing a liquid around in your mouth. The cells from the lining of your mouth also come off whenever you chew food.
How do you think your body replaces the cells that come off the lining of your mouth when you eat To extract DNA from your cells you will need to separate the DNA from the other types of biological molecules in your cells.
What are the other main types of large biological molecules in cells You will be using the same basic steps that biologists use when they extract. You will follow these 3 easy steps to extract the DNA
Detergent
eNzymes
Alcohol
How do you think your body replaces the cells that come off the lining of your mouth when you eat To extract DNA from your cells you will need to separate the DNA from the other types of biological molecules in your cells.
What are the other main types of large biological molecules in cells You will be using the same basic steps that biologists use when they extract. You will follow these 3 easy steps to extract the DNA
Detergent
eNzymes
Alcohol
Viruses
Viruses are important to biologists for several reasons. They are the simplest form of life. Indeed they are so simple that they exist on the borderline between the living and the inanimate non biological world. Viruses also reveal much about more complex biological entities including cells because viral replication is governed by the same principles that govern the lives of cells. Finally viruses are responsible for many human diseases including influenza and AIDS
Some evolutionary biologists argue that all organisms on the planet are simply complex devices whose sole purpose is to make more copies of their own genomes. Viruses take this notion to the extreme. They are mostly DNA that happens to be wrapped in a coating
The capsid affords protection for the viral genes and allows viral genes to gain entrance to appropriate host cells. Viruses exist at the border of the living and non living because they are unable to replicate on their own. They are obligate parasites in the sense that they can only replicate after they have invaded and parasitized a host cell. Because viral genomes could be isolated from the genomes of the infected cells viruses were a good source of pure DNA. This explains why viruses were studied so intensively before the advent of gene cloning. For example the SV40 virus a double stranded DNA virus carries approximately five genes in its genome and the viral DNA molecules were readily separated from the DNA of the monkey cells infected by this virus
The origins of viruses are even more obscure than the origins of cellular forms of life. Since viruses are obligate cellular parasites we can only assume that they evolved later than cells either as degenerate cells or as renegade cellular genes that learned to manipulate the replication machinery of the cells in which they arose.Viral genomes evolve more rapidly than the genomes of cellular organisms. This rapid genetic change has obscured or erased any relationships that may have existed between various types of viruses and might have been used to illuminate their ancient roots
The viruses that parasitize bacterial cells and those that parasitize animal operate on identical principles even though the details of their genes and the organization of their genomes give no hint of relatedness. We will focus on animal viruses the mechanisms by which they replicate and the consequences of their replicative strategies on their disease causing abilities
Some evolutionary biologists argue that all organisms on the planet are simply complex devices whose sole purpose is to make more copies of their own genomes. Viruses take this notion to the extreme. They are mostly DNA that happens to be wrapped in a coating
The capsid affords protection for the viral genes and allows viral genes to gain entrance to appropriate host cells. Viruses exist at the border of the living and non living because they are unable to replicate on their own. They are obligate parasites in the sense that they can only replicate after they have invaded and parasitized a host cell. Because viral genomes could be isolated from the genomes of the infected cells viruses were a good source of pure DNA. This explains why viruses were studied so intensively before the advent of gene cloning. For example the SV40 virus a double stranded DNA virus carries approximately five genes in its genome and the viral DNA molecules were readily separated from the DNA of the monkey cells infected by this virus
The origins of viruses are even more obscure than the origins of cellular forms of life. Since viruses are obligate cellular parasites we can only assume that they evolved later than cells either as degenerate cells or as renegade cellular genes that learned to manipulate the replication machinery of the cells in which they arose.Viral genomes evolve more rapidly than the genomes of cellular organisms. This rapid genetic change has obscured or erased any relationships that may have existed between various types of viruses and might have been used to illuminate their ancient roots
The viruses that parasitize bacterial cells and those that parasitize animal operate on identical principles even though the details of their genes and the organization of their genomes give no hint of relatedness. We will focus on animal viruses the mechanisms by which they replicate and the consequences of their replicative strategies on their disease causing abilities
Strategies for Virion Formation
Like bacteriophages some animal viruses use DNA while others use RNA molecules to carry their genetic information. Virus particles often termed virions are assembled through two strategies. The simplest strategy involves wrapping the viral genome in a protein coat or capsid. Without exception the capsid proteins are encoded by the viral genome
A more complex strategy for constructing a virion is used by the majority of animal cell viruses. As above their genomic DNA or RNA is wrapped in a protein coat. This protein coat:nucleic acid complex is then wrapped in a second outer coat a lipid membrane. The lipid membrane is usually acquired as the viral nucleocapsid exits the host cell
As it is being pushed though the host plasma membrane a patch of this membrane becomes wrapped around the nucleocapsid. Hence the membraneous outer layer of the virion is of host cell origin
A wide variety of animal cell viruses use this membrane scavenging strategy for forming their virions. Among these are the influenza virus, encephalitis virus, smallpox virus, rabies virus, herpes virus and the human immunodeficiency virus. In each case the membrane surrounding nucleocapsid is studded with an array of virus encoded proteins. Usually the N termini of these proteins protrude outward into the fluid outside of the viral particle the C- termini often contact the nucleocapsid inside the membrane. Since lipid bilayers are easily dissolved by detergents these lipid containing virions are readily inactivated by soaps and detergents while the purely proteinaceous virions are quite resistant to soaps
This explains why most gastrointestinal viruses have virions that are purely protein. Their virions can resist the strong detergents present in the liver bile that is constantly introduced into the small intestine to aid with digestion. Lipid containing virions are inactivated by the bile and cannot infect cells further down in the intestine
All virus capsids whether purely protein or protein lipid composites share two traits they must protect the nucleic acid inside from substances that might destroy the viral genome, and they must facilitate the adsorption of the virion to the surface of the host cell. The invasion of a cell by a virus particle always depends upon a specific and tight binding of the virus particle to some surface component of the host cells plasma membrane. Viruses have evolved the means to recognize and bind tightly to cell proteins. Invariably these tethering sites on the host cell are normal cell proteins. Each type of virus takes advantage of different proteins to gain entry to a specific type of host cell. In the case of purely proteinaceous capsids the capsid proteins have affinity for one or another of the host cells surface molecules in the case of lipid containing virions the viral proteins extending from the membrane can attach to a host cell surface protein
This adsorption must be followed by penetration where the virus succeeds in crossing the plasma membrane and entering the cytoplasm of the host cell. Since the host cell is constantly internalizing its own membrane proteins and recycling them back to the surface many viruses hitch a ride on these host cell proteins to gain entrance into the cell. Other viruses including HIV have developed the means to fuse themselves to the host cell thereby allowing the nucleocapsid direct access to the host cell interior. Once inside some viruses complete their entire replication cycle inside the cytoplasm yet others may move into the nucleus to replicate
A more complex strategy for constructing a virion is used by the majority of animal cell viruses. As above their genomic DNA or RNA is wrapped in a protein coat. This protein coat:nucleic acid complex is then wrapped in a second outer coat a lipid membrane. The lipid membrane is usually acquired as the viral nucleocapsid exits the host cell
As it is being pushed though the host plasma membrane a patch of this membrane becomes wrapped around the nucleocapsid. Hence the membraneous outer layer of the virion is of host cell origin
A wide variety of animal cell viruses use this membrane scavenging strategy for forming their virions. Among these are the influenza virus, encephalitis virus, smallpox virus, rabies virus, herpes virus and the human immunodeficiency virus. In each case the membrane surrounding nucleocapsid is studded with an array of virus encoded proteins. Usually the N termini of these proteins protrude outward into the fluid outside of the viral particle the C- termini often contact the nucleocapsid inside the membrane. Since lipid bilayers are easily dissolved by detergents these lipid containing virions are readily inactivated by soaps and detergents while the purely proteinaceous virions are quite resistant to soaps
This explains why most gastrointestinal viruses have virions that are purely protein. Their virions can resist the strong detergents present in the liver bile that is constantly introduced into the small intestine to aid with digestion. Lipid containing virions are inactivated by the bile and cannot infect cells further down in the intestine
All virus capsids whether purely protein or protein lipid composites share two traits they must protect the nucleic acid inside from substances that might destroy the viral genome, and they must facilitate the adsorption of the virion to the surface of the host cell. The invasion of a cell by a virus particle always depends upon a specific and tight binding of the virus particle to some surface component of the host cells plasma membrane. Viruses have evolved the means to recognize and bind tightly to cell proteins. Invariably these tethering sites on the host cell are normal cell proteins. Each type of virus takes advantage of different proteins to gain entry to a specific type of host cell. In the case of purely proteinaceous capsids the capsid proteins have affinity for one or another of the host cells surface molecules in the case of lipid containing virions the viral proteins extending from the membrane can attach to a host cell surface protein
This adsorption must be followed by penetration where the virus succeeds in crossing the plasma membrane and entering the cytoplasm of the host cell. Since the host cell is constantly internalizing its own membrane proteins and recycling them back to the surface many viruses hitch a ride on these host cell proteins to gain entrance into the cell. Other viruses including HIV have developed the means to fuse themselves to the host cell thereby allowing the nucleocapsid direct access to the host cell interior. Once inside some viruses complete their entire replication cycle inside the cytoplasm yet others may move into the nucleus to replicate
Viral Replication Strategies
The life cycle of most viruses is designed to maximize the production of progeny virus particles. In the case of many animal viruses the time elapsed from infection to the generation of the first progeny ranges form several hours to a day. Often the burden of producing a large number of virus particles causes the infected cell to die. This lysis of the host cell is called the viral lytic cycle and is an immediate and inevitable consequences of viral reproduction
Other viruses, in contrast will refrain from killing the host cell. They can establish a long term infection of the cell in which the cell releases a steady stream of viral particles over an extended period of time. If this continuous production of virus particles does not compromise the health of the host cell it can live on indefinitely devoting some of its resources to making virions
In general the details of a viral replication cycle are dictated by the type of nucleic acid carried into the host cell by the infecting virion. Most DNA viruses enter the nucleus where they parasitize the host cells DNA replication apparatus. There are exceptions notably the smallpox DNA virus encodes its own DNA replication machinery and thus remains in the cytoplasm. Most RNA viruses replicate in the cytoplasm because the enzymes used to replicate viral RNA are virally encoded. More detail is given below
Other viruses, in contrast will refrain from killing the host cell. They can establish a long term infection of the cell in which the cell releases a steady stream of viral particles over an extended period of time. If this continuous production of virus particles does not compromise the health of the host cell it can live on indefinitely devoting some of its resources to making virions
In general the details of a viral replication cycle are dictated by the type of nucleic acid carried into the host cell by the infecting virion. Most DNA viruses enter the nucleus where they parasitize the host cells DNA replication apparatus. There are exceptions notably the smallpox DNA virus encodes its own DNA replication machinery and thus remains in the cytoplasm. Most RNA viruses replicate in the cytoplasm because the enzymes used to replicate viral RNA are virally encoded. More detail is given below
Double stranded DNA viruses
Conceptually the simplest viruses to understand are those with genomes of double stranded DNA. Once the nucleocapsid of this type of virus enters the cell it proceeds to the nucleus where it mimics the genome of the host cell. Usually the viral genome is replicated using the host cell DNA polymerase and the viral genome is transcribed by the host cell RNA polymerase. The resulting transcripts carrying information encoding viral proteins is then transported to the cytoplasm and seen as a template by the host cell ribosomes. Some of these newly synthesized viral proteins are used as the protein capsid around newly replicated viral DNA molecules. These new virions are released from the cell where they target other host cells and trigger new rounds of infection
The dsDNA viruses that exploit the host cell machinery to complete their life cycles can carry small genomes encoding mostly viral structural proteins like those for the capsid. However the dependence of these viruses on the host cell replication machinery creates a potentially awkward situation the enzymes of DNA replication are generally not expressed in quiescent cells. Most of the cells infected will be in G and therefore inhospitable hosts. Some dsDNA viruses like the herpes virus family or the Epstein Barr virus have large genomes that contain greater than sixty genes.
These viruses encode their own DNA polymerase and thus ensure their ability replicate in quiescent cells. Other viruses circumvent this problem by producing a protein that induces the resting host cell to enter the active cell cycle. This ensures that the host cell replication enzymes are available for exploitation and reproduction of the virus. This means of producing many virions usually results in host cell death
Note however, what may happen if the infected cell is not killed by the virus. The presence of the virus and the viral growth-promoting protein can drive the host cell into unceasing growth and cell division. This converts the host cell growth from a normal pattern to a pattern typical of cancer cells. The gene that encodes the growth-promoting protein can function as an oncogene that acts to transform the infected cell into a cancer cell
More than 90% of human cervical carcinomas are associated with infection by human papilloma virus a dsDNA virus that infects the lining of the cervix. In order for HPV to create a tumor the viral genome must perpetuate itself so when the original infected cell divides into many cells each new cell contains the virus and the viral growth promoting protein
The Epstein Barr dsDNA virus that results in mononucleosis in this country. For reasons that are unclear the Epstein Barr virus triggers Burkitts lymphoma in central Africa and a tumor of the nasal cavity in Southeast Asia. These tumors are inadvertent by products of the need to replicate viral DNA. The outgrowth of tumors happens on occasion when virus infected cells are not eliminated by the completion of the viral lytic cycle
The dsDNA viruses that exploit the host cell machinery to complete their life cycles can carry small genomes encoding mostly viral structural proteins like those for the capsid. However the dependence of these viruses on the host cell replication machinery creates a potentially awkward situation the enzymes of DNA replication are generally not expressed in quiescent cells. Most of the cells infected will be in G and therefore inhospitable hosts. Some dsDNA viruses like the herpes virus family or the Epstein Barr virus have large genomes that contain greater than sixty genes.
These viruses encode their own DNA polymerase and thus ensure their ability replicate in quiescent cells. Other viruses circumvent this problem by producing a protein that induces the resting host cell to enter the active cell cycle. This ensures that the host cell replication enzymes are available for exploitation and reproduction of the virus. This means of producing many virions usually results in host cell death
Note however, what may happen if the infected cell is not killed by the virus. The presence of the virus and the viral growth-promoting protein can drive the host cell into unceasing growth and cell division. This converts the host cell growth from a normal pattern to a pattern typical of cancer cells. The gene that encodes the growth-promoting protein can function as an oncogene that acts to transform the infected cell into a cancer cell
More than 90% of human cervical carcinomas are associated with infection by human papilloma virus a dsDNA virus that infects the lining of the cervix. In order for HPV to create a tumor the viral genome must perpetuate itself so when the original infected cell divides into many cells each new cell contains the virus and the viral growth promoting protein
The Epstein Barr dsDNA virus that results in mononucleosis in this country. For reasons that are unclear the Epstein Barr virus triggers Burkitts lymphoma in central Africa and a tumor of the nasal cavity in Southeast Asia. These tumors are inadvertent by products of the need to replicate viral DNA. The outgrowth of tumors happens on occasion when virus infected cells are not eliminated by the completion of the viral lytic cycle
Single stranded DNA viruses
Some small viruses carry their genome as single stranded DNA molecules. These viruses have a simple genome: one gene for a viral nucleocapsid protein and another gene for a DNA replication enzyme. The virus with a ssDNA genome also faces a serious replication problem in the host cell. When introduced into cells these genomes can not be used to make viral proteins because the only template for transcription is double stranded DNA. For this reason the first step after infection is the conversion of the viral ssDNA into dsDNA using host cell DNA polymerase. You may recall that DNA polymerase requires a primer for replication
In some of these viruses the 3 end of the viral DNA folds back and forms dsDNA by base pairing with an internal sequence. In this way the primer is built into the genome and the 3 end can be extended to create dsDNA that serves as a template for transcription. The resulting transcripts are translated to make the viral proteins the replicated viral DNA is converted back into a ssDNA genome, and the virion is packaged for export. Canine and feline parvo viruses are members of the ssDNA virus family
In some of these viruses the 3 end of the viral DNA folds back and forms dsDNA by base pairing with an internal sequence. In this way the primer is built into the genome and the 3 end can be extended to create dsDNA that serves as a template for transcription. The resulting transcripts are translated to make the viral proteins the replicated viral DNA is converted back into a ssDNA genome, and the virion is packaged for export. Canine and feline parvo viruses are members of the ssDNA virus family
(+) Single stranded RNA viruses
(+) Single stranded RNA viruses are members of a large family of viruses also called picornaviruses because they have small RNA genomes. The single stranded RNA genome of the picornaviruses is formally and functionally identical to an mRNA molecules and as such is termed "+". This viral RNA molecule can be directly translated by the host cell ribosomes to make viral proteins. Importantly, the host cell does not have a mechanism to replicate RNA
Thus this genome must encode a viral enzyme that can replicate the ssRNA genome as well as the proteins needed for the capsid. In principle the viral enzyme could convert ssRNA into dsRNA but that is not what is seen. As the viral polymerase moves along the (+) stranded RNA template it elongates a (-) stranded RNA molecule that remains single-stranded. No hydrogen bonds are formed between the complementary RNA strands
The resulting (-) ssRNA molecules are then used as templates by the viral enzyme for polymerizing new (+) ssRNA molecules destined to serve as the genome in a progeny virion, or as mRNA for viral proteins. Members of this class of virus include many of the common cold viruses as well as poliovirus. Cold viruses replicate in the epithelial lining of the respiratory tract. Poliovirus replicates in the intestinal lining but on rare occasions escapes from the gut and infects the nerve cells in the spinal column resulting in paralysis
After entering the cell the ssRNA genome of the poliovirus is released from the nucleocapsid and is immediately translated. The genome of poliovirus is carried as a single (+) ssRNA molecule. However you know of at least two viral proteins required for propagation of this virus
Indeed poliovirus requires about six proteins yet it has a single RNA molecule. Does this pose a problem Translation of the (+) strand of RNA from the poliovirus results in a large polyprotein that is then cut into the separate required viral proteins. Interestingly, the protease needed to cut the polyprotein is part of the polyprotein. This creates a chicken and egg problem for you to ponder
Thus this genome must encode a viral enzyme that can replicate the ssRNA genome as well as the proteins needed for the capsid. In principle the viral enzyme could convert ssRNA into dsRNA but that is not what is seen. As the viral polymerase moves along the (+) stranded RNA template it elongates a (-) stranded RNA molecule that remains single-stranded. No hydrogen bonds are formed between the complementary RNA strands
The resulting (-) ssRNA molecules are then used as templates by the viral enzyme for polymerizing new (+) ssRNA molecules destined to serve as the genome in a progeny virion, or as mRNA for viral proteins. Members of this class of virus include many of the common cold viruses as well as poliovirus. Cold viruses replicate in the epithelial lining of the respiratory tract. Poliovirus replicates in the intestinal lining but on rare occasions escapes from the gut and infects the nerve cells in the spinal column resulting in paralysis
After entering the cell the ssRNA genome of the poliovirus is released from the nucleocapsid and is immediately translated. The genome of poliovirus is carried as a single (+) ssRNA molecule. However you know of at least two viral proteins required for propagation of this virus
Indeed poliovirus requires about six proteins yet it has a single RNA molecule. Does this pose a problem Translation of the (+) strand of RNA from the poliovirus results in a large polyprotein that is then cut into the separate required viral proteins. Interestingly, the protease needed to cut the polyprotein is part of the polyprotein. This creates a chicken and egg problem for you to ponder
(-) Single stranded RNA viruses
By far largest family of viruses is the (-) ssRNA family of viruses. Their viral RNA genome can not be directly translated instead the (-) strand is complementary to the viral mRNAs that need to be produced and translated into viral proteins. For reasons that are unclear nature has created hundreds of different (-) ssRNA viruses ranging from the measles and influenza viruses to the rabies and Ebola viruses. They are all without exception lipid containing viruses. Their highly peculiar replicative strategies would suggest a common ancestry but this is difficult to prove given the great differences that these modern day viruses now display. We will illustrate this type of virus through the vesicular stomatitis virus
VSV is a close relative of the rabies virus. It infects horses, cattle and pigs and produces lesions on the hooves and mouths of infected animals. It can be passed to humans where it reslts in fever and lesions in the mouth. After entering a host cell the VSV (-) strand of RNA faces a logistical problem even greater than that faced by the polio virus. As with the poliovirus there is no host enzyme that uses RNA as a template for nucleic acid synthesis. In addition, this (-) stranded RNA is not recognized as a template by the host ribosomes and thus this enzyme can not be directly produced
How does the virus break out of this circular trap It does so by packaging a viral RNA dependent RNA polymerase along with the (-) ssRNA genome within the nucleocapsid. Therefore once inside the cell, the viral polymerase begins to work on the (-) ssRNA making two kinds of (+) stranded viral RNA. Some of this (+) stranded RNA is made as short viral mRNAs that are then transcribed into viral proteins some of it is made as full length RNA that is then replicated to make the (-) ssRNA genome that is needed for the progeny virions. Some of the (-) ssRNA viruses have segmented genomes. For example Ebola virus is thought to have three distinct (-) ssRNAs in it genome each encoding a separate protein. Members of the influenza family of viruses have eight different (-) ssRNAs. The life cycle of these viruses is as described above but each viral RNA is replicated separately and packaging must be regulated to ensure that each virion receives one of each distinct RNA
VSV is a close relative of the rabies virus. It infects horses, cattle and pigs and produces lesions on the hooves and mouths of infected animals. It can be passed to humans where it reslts in fever and lesions in the mouth. After entering a host cell the VSV (-) strand of RNA faces a logistical problem even greater than that faced by the polio virus. As with the poliovirus there is no host enzyme that uses RNA as a template for nucleic acid synthesis. In addition, this (-) stranded RNA is not recognized as a template by the host ribosomes and thus this enzyme can not be directly produced
How does the virus break out of this circular trap It does so by packaging a viral RNA dependent RNA polymerase along with the (-) ssRNA genome within the nucleocapsid. Therefore once inside the cell, the viral polymerase begins to work on the (-) ssRNA making two kinds of (+) stranded viral RNA. Some of this (+) stranded RNA is made as short viral mRNAs that are then transcribed into viral proteins some of it is made as full length RNA that is then replicated to make the (-) ssRNA genome that is needed for the progeny virions. Some of the (-) ssRNA viruses have segmented genomes. For example Ebola virus is thought to have three distinct (-) ssRNAs in it genome each encoding a separate protein. Members of the influenza family of viruses have eight different (-) ssRNAs. The life cycle of these viruses is as described above but each viral RNA is replicated separately and packaging must be regulated to ensure that each virion receives one of each distinct RNA
Double stranded RNA viruses
A small group of viruses carries its genetic information around in the form of double stranded RNA (dsRNA) molecules. These are members of the reovirus class of viruses. Their genomes have ten distinct dsRNAs and virions of this class lack lipid membranes. As discussed above the virions carry an RNA polymerase that transcribes the dsRNA into (+) ssRNA. These transcripts can serve as mRNA that is then translated into the necessary viral proteins or they can act as a template for (-) strand synthesis and be converted back into a dsRNA genome for packaging
(+) ssRNA retroviruses
These viruses are lipid containing viruses whose genomes can act as mRNA. The most notorious of these is HIV the viruses resulting in AIDS. Aside from HIV retroviruses are rather uncommon in humans, but prevalent in other mammals and birds. The genomes of retroviruses are similar in structure and size to picornaviruses like polio virus and one might suppose that the replicative strategy of a retrovirus resembles that of poliovirus. This is not the case. The life cycle of a retrovirus is unique and unusual
After entering the cell the (+) strand of RNA is not associated with ribosomes, even though it has all the attributes of mRNA. Instead, the virion RNA is used as a template to make a DNA copy of the viral genome. This copying of RNA into DNA is foreign for the host cell and must be carried out by a viral enzyme that is packaged in virion
The viral enzyme called reverse transcriptase carries out this process. The terms "reverse" and "retro" imply a mechanism that is the opposite of that normally operating in all cells. The usual flow of information in a cell is from DNA to RNA not from RNA to DNA. The initial product of reverse transcription is an RNA DNA hybrid double helix.
The RNA portion of this hybrid is degraded and reverse transcriptase copies the remaining DNA strand into dsDNA. These processes take place in the cytoplasm. Once the viral dsDNA is synthesized it is transported into the nucleus where it is inserted and covalently linked to the host chromosomal DNA. The viral DNA that is integrated into the host genome is called a provirus and it is indistinguishable from the host cell genes. In effect the retrovirus has created a version of the viral genome that has all the attributes of a cellular gene found in the host. The integrated provirus can now be transcribed by the host cell into (+) RNA that is transported to the cytoplasm and used either as mRNA in viral protein synthesis or as the genome for new progeny viruses
After entering the cell the (+) strand of RNA is not associated with ribosomes, even though it has all the attributes of mRNA. Instead, the virion RNA is used as a template to make a DNA copy of the viral genome. This copying of RNA into DNA is foreign for the host cell and must be carried out by a viral enzyme that is packaged in virion
The viral enzyme called reverse transcriptase carries out this process. The terms "reverse" and "retro" imply a mechanism that is the opposite of that normally operating in all cells. The usual flow of information in a cell is from DNA to RNA not from RNA to DNA. The initial product of reverse transcription is an RNA DNA hybrid double helix.
The RNA portion of this hybrid is degraded and reverse transcriptase copies the remaining DNA strand into dsDNA. These processes take place in the cytoplasm. Once the viral dsDNA is synthesized it is transported into the nucleus where it is inserted and covalently linked to the host chromosomal DNA. The viral DNA that is integrated into the host genome is called a provirus and it is indistinguishable from the host cell genes. In effect the retrovirus has created a version of the viral genome that has all the attributes of a cellular gene found in the host. The integrated provirus can now be transcribed by the host cell into (+) RNA that is transported to the cytoplasm and used either as mRNA in viral protein synthesis or as the genome for new progeny viruses
Effect of Replication Strategies on Viral Ecology
We can define viral ecology as the way that viruses co exist with their host species. Each type of virus has a different relationship with its host and these relationships are strongly influenced by the molecular biology of each type of virus
Ecology of Poliovirus as Compared to Influenza virus
The (+) ssRNA genome of poliovirus, a single long RNA molecule, is unable to recombine with (+) ssRNA genomes from other related picornaviruses by the process of crossing over. Crossing over requires a set of highly specialized enzymes that are not available to the viruses. This means that there are only a very small number of closely related poliovirus strains and immunity against one of these strains confers immunity against the others. Influenza virus presents a dramatically contrasting example. The influenza virus genome is composed of different RNAs, each carrying different genes
When two different types of flu virus simultaneously infect a single host cell the two viral genomes may recombine by simply exchanging RNAs. A progeny virion released from this cell can have RNAs from each different infecting virus and thus a new unique strain has been created. This has devastating consequences on human health
The natural reservoir for many flu viruses is the shore bird population around the world, which includes migratory ducks and geese. At least a dozen distinct strains of flu virus live continually in these birds. In rural China and other parts of the world, ducks and pigs are kept in close proximity with one another and with humans. The ducks become infected with a flu virus originating in the wild shore birds. They can then pass the virus to a pig, which is also readily infected by human flu viruses. In the infected cells of the pig, the two viral genomes can mix and RNAs from both viruses can be packaged into one virion. In this way, a new recombinant flu virus, one quite different from pre existing strains may emerge and infect humans
The exposed humans would have not experienced this strain before and thus there is no immunity to it. The flu virus now spreads throughout the population creating a worldwide epidemic. These pandemics create serious respiratory infections but usually prove lethal to only a few mostly the weak and elderly
This is not always the case, however. The flu pandemic of 1918 killed 20 million people in Europe in a matter of months and perhaps 100 million throughout the world. Many of those affected were previously young and healthy. Why some strains of flu virus are benign while others are lethal is not understood though it clearly depends upon which viral RNAs are present in the recombinant flu virus. Modern antibiotics, which are highly effective against bacterial infections offer no protection against viral infections
When two different types of flu virus simultaneously infect a single host cell the two viral genomes may recombine by simply exchanging RNAs. A progeny virion released from this cell can have RNAs from each different infecting virus and thus a new unique strain has been created. This has devastating consequences on human health
The natural reservoir for many flu viruses is the shore bird population around the world, which includes migratory ducks and geese. At least a dozen distinct strains of flu virus live continually in these birds. In rural China and other parts of the world, ducks and pigs are kept in close proximity with one another and with humans. The ducks become infected with a flu virus originating in the wild shore birds. They can then pass the virus to a pig, which is also readily infected by human flu viruses. In the infected cells of the pig, the two viral genomes can mix and RNAs from both viruses can be packaged into one virion. In this way, a new recombinant flu virus, one quite different from pre existing strains may emerge and infect humans
The exposed humans would have not experienced this strain before and thus there is no immunity to it. The flu virus now spreads throughout the population creating a worldwide epidemic. These pandemics create serious respiratory infections but usually prove lethal to only a few mostly the weak and elderly
This is not always the case, however. The flu pandemic of 1918 killed 20 million people in Europe in a matter of months and perhaps 100 million throughout the world. Many of those affected were previously young and healthy. Why some strains of flu virus are benign while others are lethal is not understood though it clearly depends upon which viral RNAs are present in the recombinant flu virus. Modern antibiotics, which are highly effective against bacterial infections offer no protection against viral infections
Ecology of retroviruses
Retroviruses have their own peculiar ecology. Their genomes can become integrated into the host cell chromosome. Once integrated the viral genome may be transcribed or it may stay dormant and untranscribed. If dormant the retrovirus can exist undetected for a long time
This has serious implications for HIV infections. The HIV provirus can integrate into the chromosome of a host white blood cell and remain undetected for years. Only when that lymphocyte is stimulated by some physiological signal will transcription of the provirus be activated. Suddenly then virus particles can burst from the cell and infect other nearby cells. This dormant state termed viral latency, means that it is difficult, indeed virtually impossible to eradicate an HIV infection from the body. There can be many cells that harbor silent proviruses each is indistinguishable from a normal uninfected cell
This has serious implications for HIV infections. The HIV provirus can integrate into the chromosome of a host white blood cell and remain undetected for years. Only when that lymphocyte is stimulated by some physiological signal will transcription of the provirus be activated. Suddenly then virus particles can burst from the cell and infect other nearby cells. This dormant state termed viral latency, means that it is difficult, indeed virtually impossible to eradicate an HIV infection from the body. There can be many cells that harbor silent proviruses each is indistinguishable from a normal uninfected cell
Viruses
Viruses are important to biologists for several reasons. They are the simplest form of life. Indeed they are so simple that they exist on the borderline between the living and the inanimate non biological world. Viruses also reveal much about more complex biological entities including cells because viral replication is governed by the same principles that govern the lives of cells. Finally viruses are responsible for many human diseases including influenza and AIDS
Some evolutionary biologists argue that all organisms on the planet are simply complex devices whose sole purpose is to make more copies of their own genomes. Viruses take this notion to the extreme. They are mostly DNA that happen to be wrapped in a coating. The capsid affords protection for the viral genes and allows viral genes to gain entrance to appropriate host cells. Viruses exist at the border of the living and non-living because they are unable to replicate on their own. They are obligate parasites in the sense that they can only replicate after they have invaded and parasitized a host cell
Because viral genomes could be isolated from the genomes of the infected cells, viruses were a good source of pure DNA. This explains why viruses were studied so intensively before the advent of gene cloning. For example, the SV40 virus, a double stranded DNA virus carries approximately five genes in its genome and the viral DNA molecules were readily separated from the DNA of the monkey cells infected by this virus
The origins of viruses are even more obscure than the origins of cellular forms of life. Since viruses are obligate cellular parasites we can only assume that they evolved later than cells either as degenerate cells or as renegade cellular genes that learned to manipulate the replication machinery of the cells in which they arose. Viral genomes evolve more rapidly than the genomes of cellular organisms. This rapid genetic change has obscured or erased any relationships that may have existed between various types of viruses and might have been used to illuminate their ancient roots
The viruses that parasitize bacterial cells ( bacteriophages ) and those that parasitize animal cells ( animal viruses ) operate on identical principles, even though the details of their genes and the organization of their genomes give no hint of relatedness. We will focus on animal viruses the mechanisms by which they replicate, and the consequences of their replicative strategies on their disease-causing abilities
Some evolutionary biologists argue that all organisms on the planet are simply complex devices whose sole purpose is to make more copies of their own genomes. Viruses take this notion to the extreme. They are mostly DNA that happen to be wrapped in a coating. The capsid affords protection for the viral genes and allows viral genes to gain entrance to appropriate host cells. Viruses exist at the border of the living and non-living because they are unable to replicate on their own. They are obligate parasites in the sense that they can only replicate after they have invaded and parasitized a host cell
Because viral genomes could be isolated from the genomes of the infected cells, viruses were a good source of pure DNA. This explains why viruses were studied so intensively before the advent of gene cloning. For example, the SV40 virus, a double stranded DNA virus carries approximately five genes in its genome and the viral DNA molecules were readily separated from the DNA of the monkey cells infected by this virus
The origins of viruses are even more obscure than the origins of cellular forms of life. Since viruses are obligate cellular parasites we can only assume that they evolved later than cells either as degenerate cells or as renegade cellular genes that learned to manipulate the replication machinery of the cells in which they arose. Viral genomes evolve more rapidly than the genomes of cellular organisms. This rapid genetic change has obscured or erased any relationships that may have existed between various types of viruses and might have been used to illuminate their ancient roots
The viruses that parasitize bacterial cells ( bacteriophages ) and those that parasitize animal cells ( animal viruses ) operate on identical principles, even though the details of their genes and the organization of their genomes give no hint of relatedness. We will focus on animal viruses the mechanisms by which they replicate, and the consequences of their replicative strategies on their disease-causing abilities
Ecology of poliovirus as compared to influenza virus
(+) ssRNA genome of poliovirus a single long RNA molecule, is unable to recombine with (+) ssRNA genomes from other related picornaviruses by the process of crossing over. Crossing-over requires a set of highly specialized enzymes that are not available to the viruses
This means that there are only a very small number of closely related poliovirus strains and immunity against one of these strains confers immunity against the others. Influenza virus presents a dramatically contrasting example. The influenza virus genome is composed of different RNAs each carrying different genes. When two different types of flu virus simultaneously infect a single host cell, the two viral genomes may recombine by simply exchanging RNAs. A progeny virion released from this cell can have RNAs from each different infecting virus and thus a new, unique strain has been created. This has devastating consequences on human health
The natural reservoir for many flu viruses is the shore bird population around the world, which includes migratory ducks and geese. At least a dozen distinct strains of flu virus live continually in these birds. In rural China and other parts of the world, ducks and pigs are kept in close proximity with one another and with humans. The ducks become infected with a flu virus originating in the wild shore birds. They can then pass the virus to a pig which is also readily infected by human flu viruses. In the infected cells of the pig, the two viral genomes can mix and RNAs from both viruses can be packaged into one virion. In this way, a new recombinant flu virus one quite different from pre existing strains may emerge and infect humans
The exposed humans would have not experienced this strain before and thus there is no immunity to it. The flu virus now spreads throughout the population creating a worldwide epidemic (sometimes called a pandemic) These pandemics create serious respiratory infections but usually prove lethal to only a few mostly the weak and elderly
This is not always the case, however. The flu pandemic of 1918 killed 20 million people in Europe in a matter of months and perhaps 100 million throughout the world. Many of those affected were previously young and healthy. Why some strains of flu virus are benign while others are lethal is not understood though it clearly depends upon which viral RNAs are present in the recombinant flu virus. Modern antibiotics, which are highly effective against bacterial infections, offer no protection against viral infections
This means that there are only a very small number of closely related poliovirus strains and immunity against one of these strains confers immunity against the others. Influenza virus presents a dramatically contrasting example. The influenza virus genome is composed of different RNAs each carrying different genes. When two different types of flu virus simultaneously infect a single host cell, the two viral genomes may recombine by simply exchanging RNAs. A progeny virion released from this cell can have RNAs from each different infecting virus and thus a new, unique strain has been created. This has devastating consequences on human health
The natural reservoir for many flu viruses is the shore bird population around the world, which includes migratory ducks and geese. At least a dozen distinct strains of flu virus live continually in these birds. In rural China and other parts of the world, ducks and pigs are kept in close proximity with one another and with humans. The ducks become infected with a flu virus originating in the wild shore birds. They can then pass the virus to a pig which is also readily infected by human flu viruses. In the infected cells of the pig, the two viral genomes can mix and RNAs from both viruses can be packaged into one virion. In this way, a new recombinant flu virus one quite different from pre existing strains may emerge and infect humans
The exposed humans would have not experienced this strain before and thus there is no immunity to it. The flu virus now spreads throughout the population creating a worldwide epidemic (sometimes called a pandemic) These pandemics create serious respiratory infections but usually prove lethal to only a few mostly the weak and elderly
This is not always the case, however. The flu pandemic of 1918 killed 20 million people in Europe in a matter of months and perhaps 100 million throughout the world. Many of those affected were previously young and healthy. Why some strains of flu virus are benign while others are lethal is not understood though it clearly depends upon which viral RNAs are present in the recombinant flu virus. Modern antibiotics, which are highly effective against bacterial infections, offer no protection against viral infections
Strategies for Virion Formation
Like bacteriophages, some animal viruses use DNA while others use RNA molecules to carry their genetic information. Virus particles often termed virions are assembled through two strategies. The simplest strategy involves wrapping the viral genome in a protein coat or capsid. Without exception the capsid proteins are encoded by the viral genome
A more complex strategy for constructing a virion is used by the majority of animal cell viruses. As above, their genomic DNA or RNA is wrapped in a protein coat. This protein coat, nucleic acid complex (sometimes called a nucleocapsid ), is then wrapped in a second outer coat a lipid membrane. The lipid membrane is usually acquired as the viral nucleocapsid exits the host cell. As it is being pushed though the host plasma membrane a patch of this membrane becomes wrapped around the nucleocapsid. Hence the membraneous outer layer of the virion is of host cell origin.
A wide variety of animal cell viruses use this membrane-scavenging strategy for forming their virions. Among these are the influenza virus, encephalitis virus smallpox virus, rabies virus, herpes virus and the human immunodeficiency virus (HIV) In each case, the membrane surrounding nucleocapsid is studded with an array of virus-encoded proteins. Usually the N- termini of these proteins protrude outward into the fluid outside of the viral particle; the C- termini often contact the nucleocapsid inside the membrane. Since lipid bilayers are easily dissolved by detergents these lipid-containing virions are readily inactivated by soaps and detergents while the purely proteinaceous virions are quite resistant to soaps
This explains why most gastrointestinal viruses (including poliovirus) have virions that are purely protein. Their virions can resist the strong detergents present in the liver bile that is constantly introduced into the small intestine to aid with digestion. Lipid containing virions are inactivated by the bile and cannot infect cells further down in the intestine
All virus capsids whether purely protein or protein:lipid composites share two traits: they must protect the nucleic acid inside from substances that might destroy the viral genome and they must facilitate the adsorption (attachment) of the virion to the surface of the host cell. The invasion of a cell by a virus particle always depends upon a specific and tight binding of the virus particle to some surface component of the host cell's plasma membrane.
Viruses have evolved the means to recognize and bind tightly to cell proteins. Invariably these tethering sites on the host cell are normal cell proteins. Each type of virus takes advantage of different proteins to gain entry to a specific type of host cell. In the case of purely proteinaceous capsids the capsid proteins have affinity for one or another of the host cell's surface molecules; in the case of lipid-containing virions the viral proteins extending from the membrane can attach to a host cell surface protein
This adsorption must be followed by penetration where the virus succeeds in crossing the plasma membrane and entering the cytoplasm of the host cell. Since the host cell is constantly internalizing its own membrane proteins and recycling them back to the surface many viruses hitch a ride on these host cell proteins to gain entrance into the cell. Other viruses, including HIV have developed the means to fuse themselves to the host cell thereby allowing the nucleocapsid direct access to the host cell interior. Once inside some viruses complete their entire replication cycle inside the cytoplasm yet others may move into the nucleus to replicate
A more complex strategy for constructing a virion is used by the majority of animal cell viruses. As above, their genomic DNA or RNA is wrapped in a protein coat. This protein coat, nucleic acid complex (sometimes called a nucleocapsid ), is then wrapped in a second outer coat a lipid membrane. The lipid membrane is usually acquired as the viral nucleocapsid exits the host cell. As it is being pushed though the host plasma membrane a patch of this membrane becomes wrapped around the nucleocapsid. Hence the membraneous outer layer of the virion is of host cell origin.
A wide variety of animal cell viruses use this membrane-scavenging strategy for forming their virions. Among these are the influenza virus, encephalitis virus smallpox virus, rabies virus, herpes virus and the human immunodeficiency virus (HIV) In each case, the membrane surrounding nucleocapsid is studded with an array of virus-encoded proteins. Usually the N- termini of these proteins protrude outward into the fluid outside of the viral particle; the C- termini often contact the nucleocapsid inside the membrane. Since lipid bilayers are easily dissolved by detergents these lipid-containing virions are readily inactivated by soaps and detergents while the purely proteinaceous virions are quite resistant to soaps
This explains why most gastrointestinal viruses (including poliovirus) have virions that are purely protein. Their virions can resist the strong detergents present in the liver bile that is constantly introduced into the small intestine to aid with digestion. Lipid containing virions are inactivated by the bile and cannot infect cells further down in the intestine
All virus capsids whether purely protein or protein:lipid composites share two traits: they must protect the nucleic acid inside from substances that might destroy the viral genome and they must facilitate the adsorption (attachment) of the virion to the surface of the host cell. The invasion of a cell by a virus particle always depends upon a specific and tight binding of the virus particle to some surface component of the host cell's plasma membrane.
Viruses have evolved the means to recognize and bind tightly to cell proteins. Invariably these tethering sites on the host cell are normal cell proteins. Each type of virus takes advantage of different proteins to gain entry to a specific type of host cell. In the case of purely proteinaceous capsids the capsid proteins have affinity for one or another of the host cell's surface molecules; in the case of lipid-containing virions the viral proteins extending from the membrane can attach to a host cell surface protein
This adsorption must be followed by penetration where the virus succeeds in crossing the plasma membrane and entering the cytoplasm of the host cell. Since the host cell is constantly internalizing its own membrane proteins and recycling them back to the surface many viruses hitch a ride on these host cell proteins to gain entrance into the cell. Other viruses, including HIV have developed the means to fuse themselves to the host cell thereby allowing the nucleocapsid direct access to the host cell interior. Once inside some viruses complete their entire replication cycle inside the cytoplasm yet others may move into the nucleus to replicate
(+) ssRNA retroviruses
These viruses are lipid containing viruses whose genomes can act as mRNA. The most notorious of these is HIV the viruses resulting in AIDS. Aside from HIV retroviruses are rather uncommon in humans, but prevalent in other mammals and birds. The genomes of retroviruses are similar in structure and size to picornaviruses like polio virus and one might suppose that the replicative strategy of a retrovirus resembles that of poliovirus. This is not the case. The life cycle of a retrovirus is unique and unusual
After entering the cell, the (+) strand of RNA is not associated with ribosomes, even though it has all the attributes of mRNA. Instead the virion RNA is used as a template to make a DNA copy of the viral genome. This copying of RNA into DNA is foreign for the host cell and must be carried out by a viral enzyme that is packaged in virion. The viral enzyme called reverse transcriptase carries out this process. The terms "reverse" and "retro" imply a mechanism that is the opposite of that normally operating in all cells.
The usual flow of information in a cell is from DNA to RNA, not from RNA to DNA. The initial product of reverse transcription is an RNA:DNA hybrid double helix. The RNA portion of this hybrid is degraded and reverse transcriptase copies the remaining DNA strand into dsDNA
These processes take place in the cytoplasm. Once the viral dsDNA is synthesized, it is transported into the nucleus where it is inserted and covalently linked to the host chromosomal DNA. The viral DNA that is integrated into the host genome is called a provirus, and it is indistinguishable from the host cell genes. In effect the retrovirus has created a version of the viral genome that has all the attributes of a cellular gene found in the host
The integrated provirus can now be transcribed by the host cell into (+) RNA that is transported to the cytoplasm and used either as mRNA in viral protein synthesis or as the genome for new progeny viruses
After entering the cell, the (+) strand of RNA is not associated with ribosomes, even though it has all the attributes of mRNA. Instead the virion RNA is used as a template to make a DNA copy of the viral genome. This copying of RNA into DNA is foreign for the host cell and must be carried out by a viral enzyme that is packaged in virion. The viral enzyme called reverse transcriptase carries out this process. The terms "reverse" and "retro" imply a mechanism that is the opposite of that normally operating in all cells.
The usual flow of information in a cell is from DNA to RNA, not from RNA to DNA. The initial product of reverse transcription is an RNA:DNA hybrid double helix. The RNA portion of this hybrid is degraded and reverse transcriptase copies the remaining DNA strand into dsDNA
These processes take place in the cytoplasm. Once the viral dsDNA is synthesized, it is transported into the nucleus where it is inserted and covalently linked to the host chromosomal DNA. The viral DNA that is integrated into the host genome is called a provirus, and it is indistinguishable from the host cell genes. In effect the retrovirus has created a version of the viral genome that has all the attributes of a cellular gene found in the host
The integrated provirus can now be transcribed by the host cell into (+) RNA that is transported to the cytoplasm and used either as mRNA in viral protein synthesis or as the genome for new progeny viruses
Ecology of retroviruses
Retroviruses have their own peculiar ecology. Their genomes can become integrated into the host cell chromosome. Once integrated, the viral genome (provirus) may be transcribed, or it may stay dormant and untranscribed. If dormant, the retrovirus can exist undetected for a long time
This has serious implications for HIV infections. The HIV provirus can integrate into the chromosome of a host white blood cell and remain undetected for years. Only when that lymphocyte is stimulated by some physiological signal will transcription of the provirus be activated. Suddenly then, virus particles can burst from the cell and infect other nearby cells. This dormant state, termed viral latency, means that it is difficult, indeed virtually impossible, to eradicate an HIV infection from the body. There can be many cells that harbor silent proviruses, each is indistinguishable from a normal uninfected cell
This has serious implications for HIV infections. The HIV provirus can integrate into the chromosome of a host white blood cell and remain undetected for years. Only when that lymphocyte is stimulated by some physiological signal will transcription of the provirus be activated. Suddenly then, virus particles can burst from the cell and infect other nearby cells. This dormant state, termed viral latency, means that it is difficult, indeed virtually impossible, to eradicate an HIV infection from the body. There can be many cells that harbor silent proviruses, each is indistinguishable from a normal uninfected cell
Viral Replication Strategies
The life cycle of most viruses is designed to maximize the production of progeny virus particles. In the case of many animal viruses the time elapsed from infection to the generation of the first progeny ranges form several hours to a day. Often, the burden of producing a large number of virus particles causes the infected cell to die. This lysis (literally "dissolving") of the host cell is called the viral lytic cycle and is an immediate and inevitable consequences of viral reproduction
Other viruses in contrast will refrain from killing the host cell. They can establish a long-term infection of the cell, in which the cell releases a steady stream of viral particles over an extended period of time. If this continuous production of virus particles does not compromise the health of the host cell it can live on indefinitely devoting some of its resources to making virions
In general, the details of a viral replication cycle are dictated by the type of nucleic acid carried into the host cell by the infecting virion. Most DNA viruses enter the nucleus where they parasitize the host cell's DNA replication apparatus. There are exceptions, notably the smallpox DNA virus encodes its own DNA replication machinery, and thus remains in the cytoplasm. Most RNA viruses replicate in the cytoplasm because the enzymes used to replicate viral RNA are virally encoded. More detail is given below
Other viruses in contrast will refrain from killing the host cell. They can establish a long-term infection of the cell, in which the cell releases a steady stream of viral particles over an extended period of time. If this continuous production of virus particles does not compromise the health of the host cell it can live on indefinitely devoting some of its resources to making virions
In general, the details of a viral replication cycle are dictated by the type of nucleic acid carried into the host cell by the infecting virion. Most DNA viruses enter the nucleus where they parasitize the host cell's DNA replication apparatus. There are exceptions, notably the smallpox DNA virus encodes its own DNA replication machinery, and thus remains in the cytoplasm. Most RNA viruses replicate in the cytoplasm because the enzymes used to replicate viral RNA are virally encoded. More detail is given below
Effect of Replication Strategies on Viral Ecology
We can define viral ecology as the way that viruses co-exist with their host species. Each type of virus has a different relationship with its host and these relationships are strongly influenced by the molecular biology of each type of virus
(-) Single Stranded RNA viruses
By far largest family of viruses is the (-) ssRNA family of viruses. Their viral RNA genome can not be directly translated instead the (-) strand is complementary to the viral mRNAs that need to be produced and translated into viral proteins. For reasons that are unclear nature has created hundreds of different (-) ssRNA viruses ranging from the measles and influenza viruses to the rabies and Ebola viruses. They are all, without exception, lipid-containing viruses
Their highlypeculiar replicative strategies would suggest a common ancestry, but this is difficult to prove given the great differences that these modern day viruses now display. We will illustrate this type of virus through the vesicular stomatitis virus (VSV). VSV is a close relative of the rabies virus. It infects horses, cattle and pigs and produces lesions on the hooves and mouths of infected animals. It can be passed to humans where it reslts in fever and lesions in the mouth. After entering a host cell, the VSV (-) strand of RNA faces a ogistical problem even greater than that faced by the polio virus. As with the poliovirus, there is no host enzyme that uses RNA as a template for nucleic acid synthesis. In addition, this (-) tranded RNA is not recognized as a template by the host ribosomes and thus this enzyme can not be directly produced
How does the virus break out of this circular trap? It does so by packaging a viral RNA- dependent RNA polymerase along with the (-) ssRNA genome within the nucleocapsid. Therefore, once inside the cell, the viral polymerase begins to work on the (-) ssRNA making two kinds of (+) stranded viral RNA. Some of this (+) stranded RNA is made as short viral mRNAs that are then transcribed into viral proteins, some of it is made as full length RNA that is then replicated to make the (-) ssRNA genome that is needed for the progeny virions
Some of the (-) ssRNA viruses have segmented genomes. For example, Ebola virus is thought to have three distinct (-) ssRNAs in it genome, each encoding a separate protein. Members of the influenza family of viruses have eight different (-) ssRNAs. The life cycle of these viruses is as described above, but each viral RNA is replicated separately, and packaging must be regulated to ensure that each virion receives one of each distinct RNA
Their highlypeculiar replicative strategies would suggest a common ancestry, but this is difficult to prove given the great differences that these modern day viruses now display. We will illustrate this type of virus through the vesicular stomatitis virus (VSV). VSV is a close relative of the rabies virus. It infects horses, cattle and pigs and produces lesions on the hooves and mouths of infected animals. It can be passed to humans where it reslts in fever and lesions in the mouth. After entering a host cell, the VSV (-) strand of RNA faces a ogistical problem even greater than that faced by the polio virus. As with the poliovirus, there is no host enzyme that uses RNA as a template for nucleic acid synthesis. In addition, this (-) tranded RNA is not recognized as a template by the host ribosomes and thus this enzyme can not be directly produced
How does the virus break out of this circular trap? It does so by packaging a viral RNA- dependent RNA polymerase along with the (-) ssRNA genome within the nucleocapsid. Therefore, once inside the cell, the viral polymerase begins to work on the (-) ssRNA making two kinds of (+) stranded viral RNA. Some of this (+) stranded RNA is made as short viral mRNAs that are then transcribed into viral proteins, some of it is made as full length RNA that is then replicated to make the (-) ssRNA genome that is needed for the progeny virions
Some of the (-) ssRNA viruses have segmented genomes. For example, Ebola virus is thought to have three distinct (-) ssRNAs in it genome, each encoding a separate protein. Members of the influenza family of viruses have eight different (-) ssRNAs. The life cycle of these viruses is as described above, but each viral RNA is replicated separately, and packaging must be regulated to ensure that each virion receives one of each distinct RNA
(+) Single Stranded RNA viruses
(+) Single stranded RNA (ssRNA) viruses are members of a large family of viruses also called picornaviruses because they have small (pico) RNA genomes. The single stranded RNA genome of the picornaviruses is formally and functionally identical to an mRNA molecules and as such is termed "+". This viral RNA molecule can be directly translated by the host cell ribosomes to make viral proteins. Importantly, the host cell does not have a mechanism to replicate RNA
Thus, this genome must encode a viral enzyme that can replicate the ssRNA genome as well as the proteins needed for the capsid. In principle, the viral enzyme could convert ssRNA into dsRNA, but that is not what is seen. As the viral polymerase moves along the (+) stranded RNA template, it elongates a (-) stranded RNA molecule that remains single-stranded. No hydrogen bonds are formed between the complementary RNA strands. The resulting (-) ssRNA molecules are then used as templates by the viral enzyme for polymerizing new (+) ssRNA molecules destined to serve as the genome in a progeny virion, or as mRNA for viral proteins
Members of this class of virus include many of the common cold viruses as well as poliovirus. Cold viruses replicate in the epithelial lining of the respiratory tract. Poliovirus replicates in the intestinal lining, but on rare occasions, escapes from the gut and infects the nerve cells in the spinal column resulting in paralysis
After entering the cell, the ssRNA genome of the poliovirus is released from the nucleocapsid and is immediately translated. The genome of poliovirus is carried as a single (+) ssRNA molecule. However you know of at least two viral proteins required for propagation of this virus. Indeed, poliovirus requires about six proteins, yet it has a single RNA molecule. Does this pose a problem? Translation of the (+) strand of RNA from the poliovirus results in a large polyprotein that is then cut into the separate required viral proteins. Interestingly, the protease needed to cut the polyprotein is part of the polyprotein. This creates a chicken-and-egg problem for you to ponder
Thus, this genome must encode a viral enzyme that can replicate the ssRNA genome as well as the proteins needed for the capsid. In principle, the viral enzyme could convert ssRNA into dsRNA, but that is not what is seen. As the viral polymerase moves along the (+) stranded RNA template, it elongates a (-) stranded RNA molecule that remains single-stranded. No hydrogen bonds are formed between the complementary RNA strands. The resulting (-) ssRNA molecules are then used as templates by the viral enzyme for polymerizing new (+) ssRNA molecules destined to serve as the genome in a progeny virion, or as mRNA for viral proteins
Members of this class of virus include many of the common cold viruses as well as poliovirus. Cold viruses replicate in the epithelial lining of the respiratory tract. Poliovirus replicates in the intestinal lining, but on rare occasions, escapes from the gut and infects the nerve cells in the spinal column resulting in paralysis
After entering the cell, the ssRNA genome of the poliovirus is released from the nucleocapsid and is immediately translated. The genome of poliovirus is carried as a single (+) ssRNA molecule. However you know of at least two viral proteins required for propagation of this virus. Indeed, poliovirus requires about six proteins, yet it has a single RNA molecule. Does this pose a problem? Translation of the (+) strand of RNA from the poliovirus results in a large polyprotein that is then cut into the separate required viral proteins. Interestingly, the protease needed to cut the polyprotein is part of the polyprotein. This creates a chicken-and-egg problem for you to ponder
Single Stranded DNA viruses
Some small viruses carry their genome as single-stranded DNA (ssDNA) molecules. These viruses have a simple genome, one gene for a viral nucleocapsid protein and another gene for a DNA replication enzyme. The virus with a ssDNA genome also faces a serious replication problem in the host cell. When introduced into cells these genomes can not be used to make viral proteins because the only template for transcription is double stranded DNA
For this reason the first step after infection is the conversion of the viral ssDNA into dsDNA using host cell DNA polymerase. You may recall that DNA polymerase requires a primer for replication. In some of these viruses the 3 end of the viral DNA folds back and forms dsDNA by base pairing with an internal sequence. In this way, the primer is built into the genome and the 3 end can be extended to create dsDNA that serves as a template for transcription. The resulting transcripts are translated to make the viral proteins the replicated viral DNA is converted back into a ssDNA genome, and the virion is packaged for export. Canine and feline parvo viruses are members of the ssDNA virus family
For this reason the first step after infection is the conversion of the viral ssDNA into dsDNA using host cell DNA polymerase. You may recall that DNA polymerase requires a primer for replication. In some of these viruses the 3 end of the viral DNA folds back and forms dsDNA by base pairing with an internal sequence. In this way, the primer is built into the genome and the 3 end can be extended to create dsDNA that serves as a template for transcription. The resulting transcripts are translated to make the viral proteins the replicated viral DNA is converted back into a ssDNA genome, and the virion is packaged for export. Canine and feline parvo viruses are members of the ssDNA virus family
Double Stranded RNA viruses
A small group of viruses carries its genetic information around in the form of double stranded RNA (dsRNA) molecules. These are members of the reovirus class of viruses. Their genomes have ten distinct dsRNAs and virions of this class lack lipid membranes. As discussed above, the virions carry an RNA polymerase that transcribes the dsRNA into (+) ssRNA. These transcripts can serve as mRNA that is then translated into the necessary viral proteins or they can act as a template for (-) strand synthesis and be converted back into a dsRNA genome for packaging
Deoxyribonucleic Acid Information
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms with the exception of some viruses. The main role of DNA molecules is the long term storage of information. DNA is often compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed to construct other components of cells such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information
DNA is made of four types of nucleotides, containing different nucleobases: the pyrimidines cytosine and thymine, and the purines guanine and adenine. The nucleotides are attached to each other in a chain by bonds between their sugar and phosphate groups, forming a sugar-phosphate backbone. Two of these chains are held together by hydrogen bonding between complementary bases; the chains coil around each other, forming the DNA double helix
Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription
Within cells, DNA is organized into long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed
DNA is made of four types of nucleotides, containing different nucleobases: the pyrimidines cytosine and thymine, and the purines guanine and adenine. The nucleotides are attached to each other in a chain by bonds between their sugar and phosphate groups, forming a sugar-phosphate backbone. Two of these chains are held together by hydrogen bonding between complementary bases; the chains coil around each other, forming the DNA double helix
Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription
Within cells, DNA is organized into long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed
Study of Proteomics and Bioinformatics
The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics. Key experimental techniques in proteomics include 2D electrophoresis, which allows the separation of a large number of proteins, mass spectrometry, which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), protein microarrays, which allow the detection of the relative levels of a large number of proteins present in a cell, and two-hybrid screening, which allows the systematic exploration of protein–protein interactions. The total complement of biologically possible such interactions is known as the interactome. A systematic attempt to determine the structures of proteins representing every possible fold is known as structural genomics
The large amount of genomic and proteomic data available for a variety of organisms, including the human genome, allows researchers to efficiently identify homologous proteins in distantly related organisms by sequence alignment. Sequence profiling tools can perform more specific sequence manipulations such as restriction enzyme maps, open reading frame analyses for nucleotide sequences, and secondary structure prediction. From this data phylogenetic trees can be constructed and evolutionary hypotheses developed using special software like ClustalW regarding the ancestry of modern organisms and the genes they express. The field of bioinformatics seeks to assemble, annotate, and analyze genomic and proteomic data, applying computational techniques to biological problems such as gene finding and cladistics
The large amount of genomic and proteomic data available for a variety of organisms, including the human genome, allows researchers to efficiently identify homologous proteins in distantly related organisms by sequence alignment. Sequence profiling tools can perform more specific sequence manipulations such as restriction enzyme maps, open reading frame analyses for nucleotide sequences, and secondary structure prediction. From this data phylogenetic trees can be constructed and evolutionary hypotheses developed using special software like ClustalW regarding the ancestry of modern organisms and the genes they express. The field of bioinformatics seeks to assemble, annotate, and analyze genomic and proteomic data, applying computational techniques to biological problems such as gene finding and cladistics
Supercoiling of DNA
DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its relaxed state a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication
Double Strand Breaks of DNA
Double-strand breaks, in which both strands in the double helix are severed are particularly hazardous to the cell because they can lead to genome rearrangements. Three mechanisms exist to repair DSBs non homologous end joining (NHEJ) microhomology-mediated end joining (MMEJ) and homologous recombination
In NHEJ, DNA Ligase IV, a specialized DNA ligase that forms a complex with the cofactor XRCC4 directly joins the two ends.To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined. If these overhangs are compatible, repair is usually accurate
NHEJ can also introduce mutations during repair. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms translocations. NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are backup NHEJ pathways in higher eukaryotes.Besides its role as a genome caretaker, NHEJ is required for joining hairpin-capped double-strand breaks induced during V(D)J recombination, the process that generates diversity in B-cell and T-cell receptors in the vertebrate immune system
In NHEJ, DNA Ligase IV, a specialized DNA ligase that forms a complex with the cofactor XRCC4 directly joins the two ends.To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined. If these overhangs are compatible, repair is usually accurate
NHEJ can also introduce mutations during repair. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms translocations. NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are backup NHEJ pathways in higher eukaryotes.Besides its role as a genome caretaker, NHEJ is required for joining hairpin-capped double-strand breaks induced during V(D)J recombination, the process that generates diversity in B-cell and T-cell receptors in the vertebrate immune system
Genetic Engineering
Methods have been developed to purify DNA from organisms, such as phenol-chloroform extraction and manipulate it in the laboratory such as restriction digests and the polymerase chain reaction. Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology. Recombinant DNA is a man made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector.The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research, or be grown in agriculture
Grooves
Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other the grooves are unequally sized. One groove, the major groove, is 22 A wide and the other, the minor groove, is 12 A wide.The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.This situation varies in unusual conformations of DNA within the cell , but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.
Nuclear versus mitochondrial DNA damage
In human cells, and eukaryotic cells in general, DNA is found in two cellular locations inside the nucleus and inside the mitochondria. Nuclear DNA (nDNA) exists as chromatin during non replicative stages of the cell cycle and is condensed into aggregate structures known as chromosomes during cell division. In either state the DNA is highly compacted and wound up around bead-like proteins called histones. Whenever a cell needs to express the genetic information encoded in its nDNA the required chromosomal region is unravelled, genes located therein are expressed, and then the region is condensed back to its resting conformation. Mitochondrial DNA (mtDNA) is located inside mitochondria organelles, exists in multiple copies, and is also tightly associated with a number of proteins to form a complex known as the nucleoid. Inside mitochondria, reactive oxygen species (ROS), or free radicals, byproducts of the constant production of adenosine triphosphate (ATP) via oxidative phosphorylation, create a highly oxidative environment that is known to damage mtDNA. A critical enzyme in counteracting the toxicity of these species is superoxide dismutase, which is present in both the mitochondria and cytoplasm of eukaryotic cells
Basic information about Nucleic Acid
nucleic acid is a macro molecule composed of chains of nonnumeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Nucleic acids are universal in living things, as they are found in all cells and viruses. Nucleic acids were first discovered by Friedrich Miescher in 1871.Artificial nucleic acids include peptide nucleic acid, Morpholino and locked nucleic acid as well as glycol nucleic acid and threose nucleic acid. Each of these is distinguished from naturally-occurring DNA or RNA by changes to the backbone of the molecule
Types of nucleic acids: - 1.Ribonucleic acid
2. Deoxyribonucleic acid
Nucleic acid components: - 1 .Nucleo bases
2. Nucleosides
3 .Nucleotides and deoxy nucleotides
Types of nucleic acids: - 1.Ribonucleic acid
2. Deoxyribonucleic acid
Nucleic acid components: - 1 .Nucleo bases
2. Nucleosides
3 .Nucleotides and deoxy nucleotides
DNA Structure and Replication
This Bio Coach module is designed to help you understand DNA structure and replication. As you solve problems, you will be reviewing the chemical structure of DNA and the process of DNA replication. Animations and interactive activities will enrich your review experience in a dynamic way. This module is designed to be a supplement to, but not a replacement for, your textbook and classroom notes. You can test your understanding of DNA structure and replication by using the Self-Quiz at the end of the module
Nucleic Acid Components
1.
Nucleobases are heterocyclic aromatic organic compounds containing nitrogen atoms. Nucleobases are the parts of RNA and DNA involved in base pairing. Cytosine, guanine, adenine, thymine are found predominantly in DNA, while in RNA uracil replaces thymine. These are abbreviated as C, G, A, T, U, respectively. Nucleobases are complementary, and when forming base pairs, must always join accordingly: cytosine-guanine, adenine-thymine (adenine-uracil when RNA). The strength of the interaction between cytosine and guanine is stronger than between adenine and thymine because the former pair has three hydrogen bonds joining them while the latter pair has only two. Thus, the higher the GC content of double-stranded DNA, the more stable the molecule and the higher the melting temperature. Two main nucleobase classes exist, named for the molecule which forms their skeleton. These are the double-ringed purines and single-ringed pyrimidines. Adenine and guanine are purines (abbreviated as R), while cytosine, thymine, and uracil are all pyrimidines (abbreviated as Y).Hypoxanthine and xanthine are mutant forms of adenine and guanine, respectively, created through mutagen presence, through determination (replacement of the amine-group with a hydroxyl-group). These are abbreviated HX and X
2.
Nucleosides are glycosylamines made by attaching a nucleobase (often referred to simply as bases) to a ribose or deoxyribose (sugar) ring. In short, a nucleoside is a base linked to sugar. The names derive from the nucleobase names. The nucleosides commonly occurring in DNA and RNA include cytidine, uridine, adenosine, guanosine and thymidine. When a phosphate is added to a nucleoside (phosphorylated by a specific kinase enzyme), a nucleotide is produced. Nucleoside analogues, such as acyclovir, are sometimes used as antiviral agents
3.
A nucleotide consists of a nucleoside and one phosphate group. Nucleotides are the monomers of RNA and DNA, as well as forming the structural units of several important cofactors - CoA, flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. In the cell nucleotides play important roles in metabolism, and signaling
Nucleotides are named after the nucleoside on which they are based, in conjunction with the number of phosphates they contain,
for example:-
Nucleobases are heterocyclic aromatic organic compounds containing nitrogen atoms. Nucleobases are the parts of RNA and DNA involved in base pairing. Cytosine, guanine, adenine, thymine are found predominantly in DNA, while in RNA uracil replaces thymine. These are abbreviated as C, G, A, T, U, respectively. Nucleobases are complementary, and when forming base pairs, must always join accordingly: cytosine-guanine, adenine-thymine (adenine-uracil when RNA). The strength of the interaction between cytosine and guanine is stronger than between adenine and thymine because the former pair has three hydrogen bonds joining them while the latter pair has only two. Thus, the higher the GC content of double-stranded DNA, the more stable the molecule and the higher the melting temperature. Two main nucleobase classes exist, named for the molecule which forms their skeleton. These are the double-ringed purines and single-ringed pyrimidines. Adenine and guanine are purines (abbreviated as R), while cytosine, thymine, and uracil are all pyrimidines (abbreviated as Y).Hypoxanthine and xanthine are mutant forms of adenine and guanine, respectively, created through mutagen presence, through determination (replacement of the amine-group with a hydroxyl-group). These are abbreviated HX and X
2.
Nucleosides are glycosylamines made by attaching a nucleobase (often referred to simply as bases) to a ribose or deoxyribose (sugar) ring. In short, a nucleoside is a base linked to sugar. The names derive from the nucleobase names. The nucleosides commonly occurring in DNA and RNA include cytidine, uridine, adenosine, guanosine and thymidine. When a phosphate is added to a nucleoside (phosphorylated by a specific kinase enzyme), a nucleotide is produced. Nucleoside analogues, such as acyclovir, are sometimes used as antiviral agents
3.
A nucleotide consists of a nucleoside and one phosphate group. Nucleotides are the monomers of RNA and DNA, as well as forming the structural units of several important cofactors - CoA, flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. In the cell nucleotides play important roles in metabolism, and signaling
Nucleotides are named after the nucleoside on which they are based, in conjunction with the number of phosphates they contain,
for example:-
- Adenine bonded to ribose forms the nucleoside adenosine.
- Adenosine bonded to a phosphate forms adenosine monophosphate.
- As phosphates are added, adenosine diphosphate and adenosine triphosphate are formed
DNA Damage
DNA damage, due to environmental factors and normal metabolic processes inside the cell occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs) unprepared lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation.
The vast majority of DNA damage affects the primary structure of the double helix that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, super coiled and wound around "packaging" proteins called histones (in eukaryotes) and both superstructures are vulnerable to the effects of DNA damage
The vast majority of DNA damage affects the primary structure of the double helix that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, super coiled and wound around "packaging" proteins called histones (in eukaryotes) and both superstructures are vulnerable to the effects of DNA damage
RNA - Ribonucleic acid
Ribonucleic acid is a nucleic acid polymer consisting of nucleotide monomers, which plays several important roles in the processes of transcribing genetic information from deoxyribonucleic acid (DNA) into proteins. RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosome's, forms vital portions of ribosome's, and serves as an essential carrier molecule for amino acids to be used in protein synthesis. The three types of RNA include tRNA (transfer), mRNA (messenger) and rRNA (ribosomal).
Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA. RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and Ribosomal RNA, which come together to form a molecular machine that can read messenger RNA's and translate the information they carry into proteins. There are many RNA's with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.
DNA usually occurs in linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. Chromosomes set in a cell makes up its genome ,the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information carried by DNA is held in the sequence of pieces of DNA called genes transmission of genetic information is achieved via complementary base pairing. The DNA sequence is copied into complementary RNA nucleotides .RNA copy is used to make matching protein sequence in a process called translation it depends on the interaction of RNA nucleotides. DNA replication is copying of genetic material. genomic DNA is located in cell nucleus of eukaryotes, mitochondria and chloroplasts. In prokaryotes ,the DNA is held within irregular shaped body in cytoplasm called nucleotide .The genetic information n genome is held with in genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity it influences a particular characteristic in an organism .In many species only a small fraction of the total sequence of genome encodes protein. Human genome consists of 1.5% protein-coding exons, with over 50% of human DNA consisting of non coding repetitive sequences. The reasons for the presence of so much non coding DNA in eukaryotic genomes and differences in genome size among the spices represent a long standing puzzle known as C-value among the species represent. T7RNA polymerase producing mRNA from a DNA template. Other non coding DNA sequences play structural roles in chromosomes. there are two types of genes they are Telomeres and controversy they platy important role stability and functioning of chromosomes
Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA. RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and Ribosomal RNA, which come together to form a molecular machine that can read messenger RNA's and translate the information they carry into proteins. There are many RNA's with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.
DNA usually occurs in linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. Chromosomes set in a cell makes up its genome ,the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information carried by DNA is held in the sequence of pieces of DNA called genes transmission of genetic information is achieved via complementary base pairing. The DNA sequence is copied into complementary RNA nucleotides .RNA copy is used to make matching protein sequence in a process called translation it depends on the interaction of RNA nucleotides. DNA replication is copying of genetic material. genomic DNA is located in cell nucleus of eukaryotes, mitochondria and chloroplasts. In prokaryotes ,the DNA is held within irregular shaped body in cytoplasm called nucleotide .The genetic information n genome is held with in genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity it influences a particular characteristic in an organism .In many species only a small fraction of the total sequence of genome encodes protein. Human genome consists of 1.5% protein-coding exons, with over 50% of human DNA consisting of non coding repetitive sequences. The reasons for the presence of so much non coding DNA in eukaryotic genomes and differences in genome size among the spices represent a long standing puzzle known as C-value among the species represent. T7RNA polymerase producing mRNA from a DNA template. Other non coding DNA sequences play structural roles in chromosomes. there are two types of genes they are Telomeres and controversy they platy important role stability and functioning of chromosomes
FORENSIC DNA TESTING
There have been two main types of forensic DNA testing. They are often called RFLP and PCR based testing, although these terms are not very descriptive. Generally, RFLP testing requires larger amounts of DNA and the DNA must be underrated. Crime-scene evidence that is old or that is present in small amounts is often unsuitable for RFLP testing. Warm moist conditions may accelerate DNA degradation rendering it unsuitable for RFLP in a relatively short period of time
PCR-based testing often requires less DNA than RFLP testing and the DNA may be partially degraded, more so than is the case with RFLP. However, PCR still has sample size and degradation limitations that sometimes may be under appreciated. PCR-based tests are also extremely sensitive to contaminating DNA at the crime scene and within the test laboratory. During PCR, contaminants may be amplified up to a billion times their original concentration. Contamination can influence PCR results, particularly in the absence of proper handling techniques and proper controls for contamination.PCR are less direct and somewhat more prone to error than RFLP. However, PCR has tended to replace RFLP in forensic testing primarily because PCR based tests are faster and more sensitive
PCR-based testing often requires less DNA than RFLP testing and the DNA may be partially degraded, more so than is the case with RFLP. However, PCR still has sample size and degradation limitations that sometimes may be under appreciated. PCR-based tests are also extremely sensitive to contaminating DNA at the crime scene and within the test laboratory. During PCR, contaminants may be amplified up to a billion times their original concentration. Contamination can influence PCR results, particularly in the absence of proper handling techniques and proper controls for contamination.PCR are less direct and somewhat more prone to error than RFLP. However, PCR has tended to replace RFLP in forensic testing primarily because PCR based tests are faster and more sensitive
DNA Damage and Mutation
It is important to distinguish between DNA damage and mutation, the two major types of error in DNA. DNA damages and mutation are fundamentally different. Damages are physical abnormalities in the DNA, such as single and double strand breaks, 8-hydroxydeoxyguanosine residues and polycyclic aromatic hydrocarbon adducts. DNA damages can be recognized by enzymes, and thus they can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. If a cell retains DNA damage, transcription of a gene can be prevented and thus translation into a protein will also be blocked. Replication may also be blocked and/or the cell may die
In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation
Given these properties of DNA damage and mutation, it can be seen that DNA damages are a special problem in non-dividing or slowly dividing cells, where unprepared damages will tend to accumulate over time. On the other hand, in rapidly dividing cells, unprepared DNA damages that do not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell’s survival. Thus, in a population of cells comprising a tissue with replicating cells, mutant cells will tend to be lost. However infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. Thus DNA damages in frequently dividing cells, because they give rise to mutations, are a prominent cause of cancer. In contrast, DNA damages in infrequently dividing cells are likely a prominent cause of aging
In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation
Given these properties of DNA damage and mutation, it can be seen that DNA damages are a special problem in non-dividing or slowly dividing cells, where unprepared damages will tend to accumulate over time. On the other hand, in rapidly dividing cells, unprepared DNA damages that do not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell’s survival. Thus, in a population of cells comprising a tissue with replicating cells, mutant cells will tend to be lost. However infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. Thus DNA damages in frequently dividing cells, because they give rise to mutations, are a prominent cause of cancer. In contrast, DNA damages in infrequently dividing cells are likely a prominent cause of aging
RNA and its Structure
Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1 through 5. A base is attached to the 1' position, generally adenine (A) cytosine (C) guanine (G) or uracil (U). Adenine and guanine are purines cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5 position of the next. The phosphate groups have a negative charge each at physiological pH making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil. However other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair
Chemical structure of RNA :-
An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2 position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA. This results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2-hydroxyl group is that in conformation ally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone
Chemical structure of RNA :-
An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2 position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA. This results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2-hydroxyl group is that in conformation ally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone
Secondary structure of a telomerase RNA
RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but there are numerous modified bases and sugars in mature RNA's. Pseudouridine (Ψ) in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond and ribothymidine (T) are found in various places (most notably in the TΨC loop of tRNA). Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine (I). Inosine plays a key role in the wobble hypothesis of the genetic code. There are nearly 100 other naturally occurring modified nucleosides, of which pseudouridine and nucleosides with 2'-O-methylribose are the most common. The specific roles of many of these modifications in RNA are not fully understood. However it is notable that in ribosomal RNA many of the post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface implying that they are important for normal function
The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges and internal loops. Since RNA is charged, metal ions such as Mg2+ are needed to stabilize many secondary and tertiary structures
The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges and internal loops. Since RNA is charged, metal ions such as Mg2+ are needed to stabilize many secondary and tertiary structures
DNA repair Mechanisms
Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome (but cells remain superficially functional when so-called "non-essential" genes are missing or damaged). Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as a template to recover the original information. Without access to a template, cells use an error-prone recovery mechanism known as translation synthesis as a last resort
Damage to DNA alters the spatial configuration of the helix and such alterations can be detected by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place. The types of molecules involved and the mechanism of repair that is mobilized depend on the type of damage that has occurred and the phase of the cell cycle that the cell is in
Damage to DNA alters the spatial configuration of the helix and such alterations can be detected by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place. The types of molecules involved and the mechanism of repair that is mobilized depend on the type of damage that has occurred and the phase of the cell cycle that the cell is in
DNA and RNA
There are actually 2 main types of nucleic substances within cell nuclei that process information. DNA is the basic form within chromosomes that is hard-coded into every cell. RNA is a more temporary form that is used to process subsequences of DNA messages. RNA is an intermediate form used to execute the portions of DNA that a cell is using. For example, in the synthesis of proteins, DNA is copied to RNA, which is then used to create proteins: DNA->RNA->Proteins. The structure of DNA and RNA are very similar. They are both ordered sequences of 4 types of substances: ACGT for DNA and ACGU for RNA. Thus RNA uses the same three ACG substances, but uses U (uracil) instead of T (thymine). The molecules uracil and thymine are only slightly different chemically. In DNA, there is pairing between AT and CG, and in RNA, the pairings are AU and CG, but since RNA is not double-stranded, this pairing is much rarer. Hence, RNA has the 4 substances:-
- A: Adenosine
- C: Cytosine
- G: Guanine
- U: Uracil
Typically, DNA is created from RNA, and this is done by faithfully copying the sequence of base pairs, with the only change converting T to U. Hence, an RNA copy of a DNA sequence encodes the identical information, though it uses a slightly different set of 4 substances. The differences between DNA and RNA are also many. The underlying sugar molecule that traps the 4 bases is different: deoxyribose in DNA, ribose in RNA. DNA is two strands wrapped in a double-helix, but RNA is a single strand.
RNA Data Sequences in DNA
Proteins are not the only substances that are synthesized directly from data within the DNA. Some forms of RNA are specialized, and also have their formula encoded directly in digital DNA formulae. Not all types of RNA are temporary intermediate forms with their form depending on whatever DNA they are copying. There are certain forms of RNA that have a particular form that is the same across all individuals. Some of these special-purpose RNA forms are
- tRNA: transfer RNA
- rRNA: ribosome RNA
There are exactly 20 forms of tRNA, one each to transfer a particular amino acid. tRNA molecules contain about 75-80 bases. tRNA recognizes one of the 64 triplets, and matches it to one of the 20 amino acids. Since there are 20 tRNA types, and not 64, each tRNA molecule has to recognize more than one triplet ordering as a match. The DNA code contains multiple repetitions of the codes for tRNA and rRNA. About 280 copies are spread over 5 chromosomes. Presumably, this allows each cell to make multiple copies of tRNA and rRNA molecules at once from its single copy of the DNA
Bioinformatics and computational evolution in biology
Bioinformatics was applied in the creation and maintenance of a database to store biological information at the beginning of the "genomic revolution", such as nucleotide and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could both access existing data as well as submit new or revised data.In order to study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology
Important sub-disciplines within bioinformatics and computational biology include
1. the development and implementation of tools that enable efficient access to, and use and management of, various types of information
2. the development of new algorithms and statistics with which to assess relationships among members of large data sets, such as methods to locate a gene within a sequence, predict protein structure and/or function, and cluster protein sequences into families of related sequences
Important sub-disciplines within bioinformatics and computational biology include
1. the development and implementation of tools that enable efficient access to, and use and management of, various types of information
2. the development of new algorithms and statistics with which to assess relationships among members of large data sets, such as methods to locate a gene within a sequence, predict protein structure and/or function, and cluster protein sequences into families of related sequences
Computational evolutionary biology
Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to:
1. trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone
2. more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, horizontal gene transfer, and the prediction of factors important in bacterial speciation
3. build complex computational models of populations to predict the outcome of the system over time
4. track and share information on an increasingly large number of species and organisms
1. trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone
2. more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, horizontal gene transfer, and the prediction of factors important in bacterial speciation
3. build complex computational models of populations to predict the outcome of the system over time
4. track and share information on an increasingly large number of species and organisms
Genes Computational evolutionary biology
The area of research within computer science that uses genetic algorithms is sometimes confused with computational evolutionary biology but the two areas are not necessarily related
Analysis of gene expression
The expression of many genes can be determined by measuring mRNA levels with multiple techniques including microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing massively parallel signature sequencing (MPSS) or various applications of multiplexed in-situ hybridization. All of these techniques are extremely noise prone and or subject to bias in the biological measurement and a major research area in computational biology involves developing statistical tools to separate signal from noise in high-throughput gene expression studies. Such studies are often used to determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial cells to data from non-cancerous cells to determine the transcripts that are up-regulated and down-regulated in a particular population of cancer cells
Analysis of regulation
Regulation is the complex orchestration of events starting with an extracellular signal such as a hormone and leading to an increase or decrease in the activity of one or more proteins. Bioinformatics techniques have been applied to explore various steps in this process. For example, promoter analysis involves the identification and study of sequence motifs in the DNA surrounding the coding region of a gene. These motifs influence the extent to which that region is transcribed into mRNA. Expression data can be used to infer gene regulation: one might compare microarray data from a wide variety of states of an organism to form hypotheses about the genes involved in each state. In a single-cell organism, one might compare stages of the cell cycle, along with various stress conditions (heat shock, starvation, etc.). One can then apply clustering algorithms to that expression data to determine which genes are co-expressed. For example, the upstream regions (promoters) of co-expressed genes can be searched for over-represented regulatory elements
Analysis of protein expression
Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the proteins present in a biological sample. Bioinformatics is very much involved in making sense of protein microarray and HT MS data the former approach faces similar problems as with microarrays targeted at mRNA, the latter involves the problem of matching large amounts of mass data against predicted masses from protein sequence databases, and the complicated statistical analysis of samples where multiple, but incomplete peptides from each protein are detected
Genetic recombination methods
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method of DNA repair in both bacteria and eukaryotes. In eukaryotes, recombination also occurs in meiosis, where it facilitates chromosomal crossover. The crossover process leads to offspring's having different combinations of genes from those of their parents, and can occasionally produce new chimeric alleles. In organisms with an adaptive immune system, a type of genetic recombination called V(D)J recombination helps immune cells rapidly diversify and adapt to recognize new pathogens. The shuffling of genes brought about by genetic recombination is thought to have many advantages, as it is a major engine of genetic variation and also allows asexually reproducing organisms to avoid Muller's ratchet, in which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner
In genetic engineering, recombination can also refer to artificial and deliberate recombination of disparate pieces of DNA, often from different organisms, creating what is called recombinant DNA. A prime example of such a use of genetic recombination is gene targeting, which can be used to add, delete or otherwise change an organism's genes. This technique is important to biomedical researchers as it allows them to study the effects of specific genes. Techniques based on genetic recombination are also applied in protein engineering to develop new proteins of biological interest.Genetic recombination is catalyzed by many different enzymes, called recombinases. RecA, the chief recombinase found in Escherichia coli, is responsible for the repair of DNA double strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs. The RAD51 protein is required for mitotic and meiotic recombination, whereas the DMC1 protein is specific to meiotic recombination
In genetic engineering, recombination can also refer to artificial and deliberate recombination of disparate pieces of DNA, often from different organisms, creating what is called recombinant DNA. A prime example of such a use of genetic recombination is gene targeting, which can be used to add, delete or otherwise change an organism's genes. This technique is important to biomedical researchers as it allows them to study the effects of specific genes. Techniques based on genetic recombination are also applied in protein engineering to develop new proteins of biological interest.Genetic recombination is catalyzed by many different enzymes, called recombinases. RecA, the chief recombinase found in Escherichia coli, is responsible for the repair of DNA double strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs. The RAD51 protein is required for mitotic and meiotic recombination, whereas the DMC1 protein is specific to meiotic recombination
Gene conversion and recombination
Gene conversion is an event in DNA genetic recombination, which occurs at high frequencies during meiotic division but which also occurs in somatic cells. It is a process by which DNA sequence information is transferred from one DNA helix (which remains unchanged) to another DNA helix, whose sequence is altered. It is one of the ways a gene may be mutated. Gene conversion may lead to non-Mendelian inheritance and has often been recorded in fungal crosses. This conversion of one allele to the other is due to base mismatch repair during recombination: if one of the four strands during meiosis pairs up with one of the four strands of a different chromosome, as can occur if there is sequence homology, mismatch repair can alter the sequence of one of the chromosomes, so that it is identical to the other
Gene conversion can result from the repair of damaged DNA as described by the Double Strand Break Repair Model. Here a break in both strands of DNA is repaired from an intact homologous region of DNA. Resection (degradation) of the DNA strands near the break site leads to stretches of single stranded DNA that can invade the homologous DNA strand. The intact DNA can then function as a template to copy the lost DNA. During this repair process a structure called a double Holliday structure is formed. Depending on how this structure is resolved either cross-over or gene conversion products result.Gene conversion acts to homogenize the DNA sequences composing the gene pool of a species. Every gene conversion event takes as its substrate two DNA sequences that are homologous but not identical, because of sequence mismatches, and yields two identical DNA sequences. Gene conversion forms the cohesive force that links DNA sequences within different organisms of a species. Over time, gene conversion events yield a homogenous set of DNA sequences, both for allelic forms of a gene and for multi gene families. Interspersed repeats act to block gene conversion events thus catalyzing evolution of new genes and species
Gene conversion can result from the repair of damaged DNA as described by the Double Strand Break Repair Model. Here a break in both strands of DNA is repaired from an intact homologous region of DNA. Resection (degradation) of the DNA strands near the break site leads to stretches of single stranded DNA that can invade the homologous DNA strand. The intact DNA can then function as a template to copy the lost DNA. During this repair process a structure called a double Holliday structure is formed. Depending on how this structure is resolved either cross-over or gene conversion products result.Gene conversion acts to homogenize the DNA sequences composing the gene pool of a species. Every gene conversion event takes as its substrate two DNA sequences that are homologous but not identical, because of sequence mismatches, and yields two identical DNA sequences. Gene conversion forms the cohesive force that links DNA sequences within different organisms of a species. Over time, gene conversion events yield a homogenous set of DNA sequences, both for allelic forms of a gene and for multi gene families. Interspersed repeats act to block gene conversion events thus catalyzing evolution of new genes and species
Information about Genetic engineering
Genetic engineering, also called genetic modification, is the human manipulation of an organism genetic material in a way that does not occur under natural conditions. It involves the use of recombinant DNA techniques, but does not include traditional animal and plant breeding or mutagenesis. Any organism that is generated using these techniques is considered to be a genetically modified organism. The first organisms genetically engineered were bacteria in 1973 and then mice in 1974. Insulin producing bacteria were commercialized in 1982 and genetically modified food has been sold since 1994
Producing genetically modified organisms is a multi-step process. It first involves the isolating and copying the genetic material of interest. A construct is built containing all the genetic elements for correct expression. This construct is then inserted into the host organism, either by using a vector or directly through injection, in a process called transformation. Successfully transformed organisms are then grown and the presence of the new genetic material is tested for
Genetic engineering techniques have been applied to various industries, with some success. Medicines such as insulin and human growth hormone are now produced in bacteria, experimental mice such as the oncomouse and the knockout mouse are being used for research purposes and insect resistant and/or herbicide tolerant crops have been commercialized. Plants that contain drugs and vaccines, animals with beneficial proteins in their milk and stress tolerant crops are currently being developed
Producing genetically modified organisms is a multi-step process. It first involves the isolating and copying the genetic material of interest. A construct is built containing all the genetic elements for correct expression. This construct is then inserted into the host organism, either by using a vector or directly through injection, in a process called transformation. Successfully transformed organisms are then grown and the presence of the new genetic material is tested for
Genetic engineering techniques have been applied to various industries, with some success. Medicines such as insulin and human growth hormone are now produced in bacteria, experimental mice such as the oncomouse and the knockout mouse are being used for research purposes and insect resistant and/or herbicide tolerant crops have been commercialized. Plants that contain drugs and vaccines, animals with beneficial proteins in their milk and stress tolerant crops are currently being developed
Protein and its importance
Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and in certain archaea pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational
modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.Of the most distinguishing features of polypeptides is their ability to fold into a globual state, or "structure". The extent to which proteins fold into a defined structure varies widely. Data supports that some protein structures fold into a highly rigid structure with small fluctuations and are therefore considered to be single structure. Other proteins have been shown to undergo large rearrangements from one conformation to another. This conformational change is often associated with a signaling event. Thus, the structure of a protein serves a a medium through which to regulate either the function of a protein or activity of an enzyme. Not all proteins requiring a folding process in order to function as some function in an unfolded state.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.Proteins were first described by the Dutch chemist Gerhardus Johannes Mulder and named by the Swedish chemist Jöns Jakob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh. The central role of proteins as enzymes in living organisms was however not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein. The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved were hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958.The three-dimensional structures of both proteins were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, nuclear magnetic resonance and mass spectrometry
modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.Of the most distinguishing features of polypeptides is their ability to fold into a globual state, or "structure". The extent to which proteins fold into a defined structure varies widely. Data supports that some protein structures fold into a highly rigid structure with small fluctuations and are therefore considered to be single structure. Other proteins have been shown to undergo large rearrangements from one conformation to another. This conformational change is often associated with a signaling event. Thus, the structure of a protein serves a a medium through which to regulate either the function of a protein or activity of an enzyme. Not all proteins requiring a folding process in order to function as some function in an unfolded state.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.Proteins were first described by the Dutch chemist Gerhardus Johannes Mulder and named by the Swedish chemist Jöns Jakob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh. The central role of proteins as enzymes in living organisms was however not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein. The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved were hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958.The three-dimensional structures of both proteins were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, nuclear magnetic resonance and mass spectrometry
Protein biosynthesis and its methods
Protein synthesis is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA, which is then used as input to translation
The cistron DNA is transcribed into a variety of RNA intermediates. The last version is used as a template in synthesis of a polypeptide chain. Proteins can often be synthesized directly from genes by translating mRNA. When a protein needs to be available on short notice or in large quantities, a protein precursor is produced. A proprotein is an inactive protein containing one or more inhibitory peptides that can be activated when the inhibitory sequence is removed by proteolysis during posttranslational modification. A preprotein is a form that contains a signal sequence (an N-terminal signal peptide) that specifies its insertion into or through membranes; i.e., targets them for secretion.The signal peptide is cleaved off in the endoplasmic reticulum. Preproproteins have both sequences (inhibitory and signal) still present.For synthesis of protein, a succession of tRNA molecules charged with appropriate amino acids have to be brought together with an mRNA molecule and matched up by base-pairing through their anti-codons with each of its successive codons. The amino acids then have to be linked together to extend the growing protein chain, and the tRNA, relieved of their burdens, have to be released. This whole complex of processes is carried out by a giant multimolecular machine, the ribosome, formed of two main chains of RNA, called ribosomal RNA (rRNA), and more than 50 different proteins. This molecular juggernaut latches onto the end of an mRNA molecule and then trundles along it, capturing loaded tRNA molecules and stitching together the amino acids they carry to form a new protein chain.Protein biosynthesis, although very similar, is different for prokaryotes and eukaryotes
The cistron DNA is transcribed into a variety of RNA intermediates. The last version is used as a template in synthesis of a polypeptide chain. Proteins can often be synthesized directly from genes by translating mRNA. When a protein needs to be available on short notice or in large quantities, a protein precursor is produced. A proprotein is an inactive protein containing one or more inhibitory peptides that can be activated when the inhibitory sequence is removed by proteolysis during posttranslational modification. A preprotein is a form that contains a signal sequence (an N-terminal signal peptide) that specifies its insertion into or through membranes; i.e., targets them for secretion.The signal peptide is cleaved off in the endoplasmic reticulum. Preproproteins have both sequences (inhibitory and signal) still present.For synthesis of protein, a succession of tRNA molecules charged with appropriate amino acids have to be brought together with an mRNA molecule and matched up by base-pairing through their anti-codons with each of its successive codons. The amino acids then have to be linked together to extend the growing protein chain, and the tRNA, relieved of their burdens, have to be released. This whole complex of processes is carried out by a giant multimolecular machine, the ribosome, formed of two main chains of RNA, called ribosomal RNA (rRNA), and more than 50 different proteins. This molecular juggernaut latches onto the end of an mRNA molecule and then trundles along it, capturing loaded tRNA molecules and stitching together the amino acids they carry to form a new protein chain.Protein biosynthesis, although very similar, is different for prokaryotes and eukaryotes
Explanation of Genetic code
The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences, called codons, and amino acids. With some exceptions, a triplet codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code
Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, and chromosomal structural areas that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code
Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, and chromosomal structural areas that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code
Study of Proteomics and bioinformatics
The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics. Key experimental techniques in proteomics include 2D electrophoresis, which allows the separation of a large number of proteins, mass spectrometry, which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), protein microarrays, which allow the detection of the relative levels of a large number of proteins present in a cell, and two-hybrid screening, which allows the systematic exploration of protein–protein interactions. The total complement of biologically possible such interactions is known as the interactome. A systematic attempt to determine the structures of proteins representing every possible fold is known as structural genomics.
The large amount of genomic and proteomic data available for a variety of organisms, including the human genome, allows researchers to efficiently identify homologous proteins in distantly related organisms by sequence alignment. Sequence profiling tools can perform more specific sequence manipulations such as restriction enzyme maps, open reading frame analyses for nucleotide sequences, and secondary structure prediction. From this data phylogenetic trees can be constructed and evolutionary hypotheses developed using special software like ClustalW regarding the ancestry of modern organisms and the genes they express. The field of bioinformatics seeks to assemble, annotate, and analyze genomic and proteomic data, applying computational techniques to biological problems such as gene finding and cladistics
The large amount of genomic and proteomic data available for a variety of organisms, including the human genome, allows researchers to efficiently identify homologous proteins in distantly related organisms by sequence alignment. Sequence profiling tools can perform more specific sequence manipulations such as restriction enzyme maps, open reading frame analyses for nucleotide sequences, and secondary structure prediction. From this data phylogenetic trees can be constructed and evolutionary hypotheses developed using special software like ClustalW regarding the ancestry of modern organisms and the genes they express. The field of bioinformatics seeks to assemble, annotate, and analyze genomic and proteomic data, applying computational techniques to biological problems such as gene finding and cladistics
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