DNA is an replicative unit or commanding unit

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DNA is an replicative unit or commanding unit

Postby Biosapien on May 3rd, 2015, 2:39 am 

In virus what makes the DNA to replicate and protect its DNA by forming an protein coat. How DNA has the knowledge of synthesizing the structure which can protect itself from envinomental damage
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Re: DNA is an replicative unit or commanding unit

Postby neuro on May 5th, 2015, 9:17 am 

Well, the DNA (or RNA) contains the code for the cell that will be infected to synthesize the proteins needed to assemble the coat.
This way, the infected cell will replicate both the nucleic acid and the proteins, assemble the whole thing (a new virus) and release it (or blow up when full of viruses)
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on May 10th, 2015, 10:40 am 

Hi neuro, I know the mechanism you talked above but my question is why DNA wants to replicate or synthesize something to protect itself. Does DNA has a brain like stuff to know what to do and how to do exactly
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Re: DNA is an replicative unit or commanding unit

Postby BioWizard on May 10th, 2015, 11:57 am 

Biosapien » 10 May 2015 09:40 am wrote:Hi neuro, I know the mechanism you talked above but my question is why DNA wants to replicate or synthesize something to protect itself. Does DNA has a brain like stuff to know what to do and how to do exactly


Are you familiar with biological evolution? Pieces of DNA/RNA that can get cells to replicate them get propagated, and those that can't simply vanish. Then, over time, the replicative DNA/RNA changes (due to mutation) and can slowly add other features. Some can be advantegous for the process (for example if they help ot replicate faster), and some can be disadvantagous (for example if they make it very sensitive to temperature changes. If those features (such as adding a protein capsid) assist the process of replicating itself, they help it outcompete other versions that don't have them. It's a trial and error process, and what you see now is the product of that process over huders or thousands or millions of years.
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on June 1st, 2015, 11:02 pm 

Hi Bio long time no see, what you said above is mutation and development mutant/resistance strain. My question is simple and straight forward, why DNA wants to protect itself from various dangers in case of virus or any other life form. An epitome for this is the neutralizing the effect of free radical damage caused to DNA. what makes the DNA to maintain its topology and sequence in a specific manner.
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on June 1st, 2015, 11:05 pm 

Also if you the reason for evolution of nuclear membrane please add a note on it, I know eukaryotes have nuclear membrane but still don't know the reason why the prokaryotes developed NM to become an eukaryotes.
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Re: DNA is an replicative unit or commanding unit

Postby Paralith on June 2nd, 2015, 1:43 pm 

Biosapien » Mon Jun 01, 2015 9:02 pm wrote:Hi Bio long time no see, what you said above is mutation and development mutant/resistance strain. My question is simple and straight forward, why DNA wants to protect itself from various dangers in case of virus or any other life form. An epitome for this is the neutralizing the effect of free radical damage caused to DNA. what makes the DNA to maintain its topology and sequence in a specific manner.


What Bio said above, describing evolution, is how all changes to DNA occur. It is not limited to antibiotic resistance.

DNA does not want to do anything. It does not have a mind, a will, an ability to desire. Usually when we talk about DNA or genes "wanting" to do something, it is a figure of speech, it is not meant to be taken literally.

Genomes (sets of DNA) evolved mechanisms that protect them and keep them stable because genomes that did not do this were broken down and degraded, and were unable to pass copies of themselves to the next generation, and so they ceased to exist. Genomes that were lucky enough to inherit mutations that helped them protect themselves were able to hold their form long enough to have copies of themselves made, allowing those copies to hold their form long enough to have copies of themselves made, etc etc, and because of that genomes with those qualities still exist today. They did not die out. This is evolution by natural selection.
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on August 1st, 2016, 5:42 am 

Hi Paralith,

Very long time no see, the following query is regarding the topic "DNA is an replicative unit or commanding unit" which i am posted on May 3rd, 2015. My question is what makes the DNA to protect its structural integrity from various environmental hazardous. I know DNA is not a brain but may i know what makes the DNA to protect itself from the compounds that causes the disturbance in their structural integrity. Thank you
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Re: DNA is an replicative unit or commanding unit

Postby BioWizard on August 13th, 2016, 10:57 pm 

Hi BioSapien. Where did you read that DNA protects itself from compounds that disturb its structural integrity? Can you provide a reference so that we know more precisely what you're talking about?
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on August 15th, 2016, 11:34 pm 

Hi BioWizard it's been a very long time and hope your doing great.

Regarding your above question, i never read anywhere in the text that DNA protect itself from hazardous agent rather its an hypothesis just strikes on my mind because of following reason.

1) When we compare between prokaryote vs eukaryotes we clearly know the rate of mutation is higher in prokaryotes than in eukaryotes and one of the reason for this is due to lack of nuclear membrane. Now my question is for what primary reason eukaryotes developed nuclear membrane? and i believe, to protect its structural integrity through avoiding mutation induced by various physical and chemical hazards.

2) When i read about the epigenetic facts, it also makes me wonder how DNA prevents itself from methylation and other process in order to avoid unwanted gene regulation. I mentioned unwanted because, if its wanted all the time then why the region of transcription is enclosed?

3) Does the primary function of super-coiling is just to make the DNA more compact or its also for protecting its structural integrity?
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Re: DNA is an replicative unit or commanding unit

Postby neuro on August 17th, 2016, 6:18 am 

Biosapien » August 16th, 2016, 4:34 am wrote:1) When we compare between prokaryote vs eukaryotes we clearly know the rate of mutation is higher in prokaryotes than in eukaryotes and one of the reason for this is due to lack of nuclear membrane. Now my question is for what primary reason eukaryotes developed nuclear membrane? and i believe, to protect its structural integrity through avoiding mutation induced by various physical and chemical hazards.

There is no "primary reason" for eukaryotes to develop a nuclear membrane. This is Lamarckian.
If it happens that a series of mutations and DNA combinations produce a cell that has a nuclear envelope, this may turn out so profitable that these cells will tend to be favorably selected for.
2) When i read about the epigenetic facts, it also makes me wonder how DNA prevents itself from methylation and other process in order to avoid unwanted gene regulation. I mentioned unwanted because, if its wanted all the time then why the region of transcription is enclosed?

This is not a mechanism of preventing "unwanted gene regulation". This is one of the most powerful means of regulating transcription (i.e. of gene regulation). Contrary to initial beliefs, DNA methylation appears to be reversible (as histone methylation and acetylation are)
3) Does the primary function of super-coiling is just to make the DNA more compact or its also for protecting its structural integrity?

I don't realize what would be the threats to structural integrity the DNA should protect itself from.
If DNA could not be accessed by transcription factors, and polymerases, etc., then DNA would be almost completely useless.
Transcriptional regulation possibly is the most important aspect of DNA usefulness.
Just consider that a lymphocyte of yours is almost identical to a mouse lymphocyte whereas it is terribly different from a neuron of yours, although it contains exactly the same DNA.
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on August 18th, 2016, 2:45 am 

Neuro: There is no "primary reason" for eukaryotes to develop a nuclear membrane. This is Lamarckian.

Biosapien: The genetic difference between humans and chimps is very less yet it results in completely new species you call this too is Lamarkian rather than Evolution. So i consider the presence of nuclear membrane is because of some evolutionary reason rather than just just Lamarckian. Even if its Lamarkian there should be some prime reason for transferring to next generation.


Neuro: This is not a mechanism of preventing "unwanted gene regulation". This is one of the most powerful means of regulating transcription (i.e. of gene regulation). Contrary to initial beliefs, DNA methylation appears to be reversible (as histone methylation and acetylation are)

Biosapien: In my earlier comment i was about to say unwanted methylation rather than methylation because of the following reason
1) Much of the DNA methylation study confirms that hypermethylation is the cause for onset of cancer.

Neuro: If DNA could not be accessed by transcription factors, and polymerases, etc., then DNA would be almost completely useless.

Biosapien: You should also believe that if DNA is accessed all the time then it would lead to cancer and death. My question to you is, what happens to the DNA structure after the so called transcription, i believe it rewind to its original state. Can you explain precisely why the DNA uncoil for transcription and why recoils after transcription.
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Re: DNA is an replicative unit or commanding unit

Postby neuro on August 18th, 2016, 1:37 pm 

DNA is continuously, dynamically modified by epigenetic factors, and is continually interacted with by proteins that regulate its transcription.

You seem to be interpreting the coiling of DNA as a means for it to protect itself. But there is no mechanical threat to it, and all the interactions it can undergo are finely regulated, so you should rather see uncoiling and recoiling as aspects of dynamic functional regulation.

Cancer does not result from a change in accessibility of DNA. Hypermethylation, on the other hand, is in most cases repressive of transcription. And in most cases pro-apoptotic genes (such as p53 and other proteins that would favor the death of the cell in case of DNA mutations and errors) are methylated and repressed in cancer.
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on August 19th, 2016, 12:38 am 

Hi Neuro,

Can you further comment on the following statement by comparing Norma vs Cancer cell in relation to the cell cycle. Since you mentioned DNA is continuously and dynamically modified then i don't see the difference between normal and cancer cell. I will accept your statement is true for cancer cell because it don't obey the rules of cell cycle (i.e., continuous and dynamic) which i don't see in the normal cell.
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Re: DNA is an replicative unit or commanding unit

Postby neuro on August 21st, 2016, 9:15 am 

Well, Biosapien,
I fear we have had a misunderstanding.
When I say the DNA "is continuously, dynamically modified by epigenetic factors, and is continually interacted with by proteins that regulate its transcription" I do not mean that the nucleotide sequence in DNA is modified.

In cancer (a subpopulation of) cells keeps dividing and typically has badly working "proof-reading" controls, so that mutations (here we are talking about changes in the nucleotide sequence) keep occurring. This may lead to the death of some cancerous cells because they may lose needed cellular functions, but it also leads to cells particularly active in replicating, capable of migrating elsewhere, and often resistant to chemiotherapy (much like the bacteria that develop antibiotic resistance).
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on August 25th, 2016, 12:11 am 

Hi Neuro,

I accept what you said from the last conversation, because that is what i too learned from the text"Failure in Proof Reading Mechanism" but i am not currently interested to talk about that because i am still unable to find the answers for the current thread. When i look into the history people long ago believed in theory of "Abiogeneisis" later it was disproved by Theory of Biogenesis. After discovery of the fact that "DNA is the Replicating unit" most of the scientist in the world was levitated by thinking they can bring miracle through Gene therapy. Since they don't understand what is the role of Non-Coding sequence they called it as Junk sequence. Now they introduced Epigenetics. The reason why i mentioned those is "The existence of something in some form has multiple reason" like that, the DNA supercoiling it's not to bring the only the compactness to fit into the nucleus but also for some other reason and the reason i believe is "May be the DNA don't want to replicate or transcribed in the first place". Also many of the people say DNA is a "self replicating unit" i wonder how the event is possible in the absence of DNA Polymerase, single stranded binding protein and other co-factors.

May be you can ask then what is the Purpose of the DNA existence if doesn't want to replicate or transcribe? That's an another interesting question which i have to answer with philosophy.
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Re: DNA is an replicative unit or commanding unit

Postby neuro on August 25th, 2016, 11:48 am 

Well, Biosapien,
if you ask about "the Purpose of the DNA existence if doesn't want to replicate or transcribe", then you should switch to the "personal theories" section of the philosophy forums (not even "anything philosophy", because even in that forum some rigor is required).

In general, your questions tend to be Lamarckian (google him).
Scientifically, you must consider "why" to require a BEACAUSE answer, not an "IN ORDER TO" answer.
And since the theory of Evolution + natural selection suggests that a useful feature will tend to be stabilized, then the question should not be "what is the PURPOSE", but possibly "why did it stabilize this way".

If you look for an answer to this last question, regarding DNA, I would suggest that the much wider possibility of regulating replication and transcription, which histones, chromatin dynamics and epigenetic modification bring about, constitutes a sufficiently large advantage to justify its persistence.
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Re: DNA is an replicative unit or commanding unit

Postby BioWizard on August 26th, 2016, 11:26 pm 

Biosapien,

Remember that cells have mechanisms for fixing DNA mutations. So if a cell accumulates more mutations, that might mean its DNA is more susceptible, but it can also mean its DNA repair machinery is less efficient. Generally, single cell organisms are more tolerant of mutations (because if a bacterium mutates and dies the rest of the colony goes in) than multi cellular organisms (because if say a cell turns cancerous it can kill the entire host). So eukaryotic cells tend to have more sophisticated DNA repair machinery.

It's usually better to resist the temptation of using simple chemical or physical reasoning to explain highly regulated biological events, because that almost always fails. You need to consider all the biochemical and enzymatic factors regulating the effect before you can begin to understand its kinetics.
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Re: DNA is an replicative unit or commanding unit

Postby vivian maxine on August 27th, 2016, 1:41 pm 

biospan wrote:
DNA is an replicative unit or commanding unit

Postby Biosapien on May 3rd, 2015, 1:39 am
In virus what makes the DNA to replicate and protect its DNA by forming an protein coat. How DNA has the knowledge of synthesizing the structure which can protect itself from envinomental damage


Please, someone, is this virus already inside a host living cell when it makes this protein coat? My dictionary says it cannot multiply outside a host living cell. It does not say it cannot exist outside said cell. Yet it has no cellular structure itself.
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Re: DNA is an replicative unit or commanding unit

Postby bangstrom on August 27th, 2016, 4:24 pm 

vivian maxine » August 27th, 2016, 12:41 pm wrote:
Please, someone, is this virus already inside a host living cell when it makes this protein coat? My dictionary says it cannot multiply outside a host living cell. It does not say it cannot exist outside said cell. Yet it has no cellular structure itself.


The viral DNA contains the genetic code for a protein coat. Inside the host, the cell’s own mechanisms construct the protein coat and and more viral DNA and assemble these into new virus particles. The invading viral DNA is totally passive.

Viruses can survive outside the cell after the cell ruptures and the protein coat helps protect the virus. The protein coat is also necessary for the virus to attach to and invade new host cells.
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Re: DNA is an replicative unit or commanding unit

Postby vivian maxine on August 27th, 2016, 4:47 pm 

bangstrom » August 27th, 2016, 3:24 pm wrote:
vivian maxine » August 27th, 2016, 12:41 pm wrote:
Please, someone, is this virus already inside a host living cell when it makes this protein coat? My dictionary says it cannot multiply outside a host living cell. It does not say it cannot exist outside said cell. Yet it has no cellular structure itself.


The viral DNA contains the genetic code for a protein coat. Inside the host, the cell’s own mechanisms construct the protein coat and and more viral DNA and assemble these into new virus particles. The invading viral DNA is totally passive.

Viruses can survive outside the cell after the cell ruptures and the protein coat helps protect the virus. The protein coat is also necessary for the virus to attach to and invade new host cells.


Let's see if I have this. The virus invades the host cell, bringing along its own DNA and genetic code for the coat.. (The host cell constructs) or (the virus cell constructs) the coat around the virus?

I need to sort out for certain which cell is doing what. I did not think viruses had a cellular construct. But what I read in the thread is confusing me.

Thanks for helping. I don't want to read any more until I sort out that much.
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Re: DNA is an replicative unit or commanding unit

Postby bangstrom on August 28th, 2016, 3:06 am 

vivian maxine » August 27th, 2016, 3:47 pm wrote:

Let's see if I have this. The virus invades the host cell, bringing along its own DNA and genetic code for the coat.. (The host cell constructs) or (the virus cell constructs) the coat around the virus?

I need to sort out for certain which cell is doing what. I did not think viruses had a cellular construct. But what I read in the thread is confusing me.

Thanks for helping. I don't want to read any more until I sort out that much.

Viruses don’t have a cellular construct so the host cell alone is capable of reproducing new viruses. Typically, the virus protein coat attaches to the cell wall and the viral DNA (sometimes RNA) is injected into the cell leaving the protein coat behind. The host cell has difficulty distinguishing viral DNA from its own DNA so it begins to reproduce more viruses following the instructions found on the viral DNA.

There are usually a few enzymes involved that are a part of the protein coat. Some enzymes degrade the cell wall allowing the viral DNA to enter and another acts like a spring in a spring loaded device to inject the DNA into the cell.
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Re: DNA is an replicative unit or commanding unit

Postby bangstrom on August 28th, 2016, 4:23 am 

With this mosquito virus, the DNA is divided among several virus particles so it takes more than one to cause an infection.

New Virus Breaks The Rules Of Infection

http://www.npr.org/sections/goatsandsod ... -infection?

“Most viruses have simple architecture. They have a few genes — say about a half-dozen or so — that are packaged up into a little ball, 1/500th the width of a human hair.
"You can think of it like a teeny-weeny tennis ball with spikes," Holmes says.
When the virus infects a cell, the ball latches onto the cell's surface, opens up and pops its genes into the cell.
Poof! The cell is infected. That's all it takes. One ball, sticking to one cell.”
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Re: DNA is an replicative unit or commanding unit

Postby vivian maxine on August 28th, 2016, 7:13 am 

All right. Thank you, Bangstrom. I was apparantly mis-reading the OP. Now I can start over.
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Re: DNA is an replicative unit or commanding unit

Postby Biosapien on August 28th, 2016, 11:52 pm 

I experienced my past college life by reading those earlier messages, especially about the virus.Once again i have to delve further to know these mysteries and i thank you all for sharing your thoughts and opinion which really helps me think better regarding this topic. Hope we will further discuss about this topic sooner or later.
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