Just EXACTLY what is DNA?

[timejim]

I would like to know what DNA really is. How is it formed or at what stage in cellular development does it come about. Is it contained within a Gene or is it separate? Is it the determini9ng factor as to a Humans' physical and mental traits? Thanks for helping if possible.

 

[Monique]

DNA is like a book which is made up out of four letters: Adenine, Guanine, Cytosine, and Thymine (A C G T) that appear in a certain sequence.

One chromosome is like a sentence, much of it doesn't make any sense to us: the letters seem to be in a random order. But sometimes the letter DO make sense, that is a gene, like a word.

We have 22 pairs of chromosomes called autosomes, they are equal between males and females and 2 sex chromosomes (X and Y), so in total there are 46 chromosomes.

So that is basically what DNA is. In more detail about the letters A,C,G,T you could say the following: DNA is a polymer made up of nucleotides. Each nucleotide has a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to that sugar, and a phosphate group. It is the nitrogenous base that is different between the different nucleotides (the four letters).

This molecule folds into a structure where two complementary strings hybridize with each other, in which the sugar with the negative phosphate groups facing outwards, the bases are facing inward and are paired with each other. A pairs with T from the opposite strand and C pairs with G from the opposite strand. This structure is stable.

DNA is always present in the cell nucleus in the form of the 46 chromosomes. During duplication of the cell, the DNA has to duplicate too. This is when the two strands of the chromosome separate and new bases are filled in at the free sites, generating two chromosomes.

Yes, our genes dictate our body plan, but there is a lot of interaction during development with the environment, also later in life. The environment determines which genes are turned on or of.

I hope this explains a little?

 

[Monique]

Here a nice image which depicts the two strands of the chromosome (sugar phosphate backbone) and the base pairing of the ACGT between the strands. You can see it twists like a ladder.

How thick is the book? 3 billion letters in the human.

 

[nautica]

DNA is the "information of life" it is made of pyrimidines and purines as the nucleotides with sugar phosphate backbone (or rung) The structure is a double helix, which was discovered in 1953 by Rosalin Franklin and the Nobel given to Watson, Crick and Wilkins.

The arrangement of the nucleotides A-T and C-G are what codes for proteins. A section of the DNA is transcribed to RNA and then translated to proteins or polypeptides.

Genes are merely sections of the DNA, which are what gives the organism its phenotype or physical trait. In meiosis (sexual reproduction) the offspring will receive 1/2 the info from the mother and 1/2 from the father. Each parent will bring different versions of a gene, which is called an allele. These alleles are indepently assortate to create the phenotype, which I mentioned.

It is known how DNA, does what it does, but is unknown as to how the first DNA came together, although, there are several theories on the subject.

That is the brief synopsis.
nautica

 

[nautica]

It looks as if Monique beat me to it, again.

nautica

 

[timejim]

Originally posted by Monique
DNA is like a book which is made up out of four letters: Adenine, Guanine, Cytosine, and Thymine (A C G T) that appear in a certain sequence.

One chromosome is like a sentence, much of it doesn't make any sense to us: the letters seem to be in a random order. But sometimes the letter DO make sense, that is a gene, like a word.

We have 22 pairs of chromosomes called autosomes, they are equal between males and females and 2 sex chromosomes (X and Y), so in total there are 46 chromosomes.

So that is basically what DNA is. In more detail about the letters A,C,G,T you could say the following: DNA is a polymer made up of nucleotides. Each nucleotide has a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to that sugar, and a phosphate group. It is the nitrogenous base that is different between the different nucleotides (the four letters).

This molecule folds into a structure where two complementary strings hybridize with each other, in which the sugar with the negative phosphate groups facing outwards, the bases are facing inward and are paired with each other. A pairs with T from the opposite strand and C pairs with G from the opposite strand. This structure is stable.

DNA is always present in the cell nucleus in the form of the 46 chromosomes. During duplication of the cell, the DNA has to duplicate too. This is when the two strands of the chromosome separate and new bases are filled in at the free sites, generating two chromosomes.

Yes, our genes dictate our body plan, but there is a lot of interaction during development with the environment, also later in life. The environment determines which genes are turned on or of.

I hope this explains a little?

It helps but sparks another question. How does interaction with the environment "cause" the changes that would occur with DNA? What tells the DNA to change?? thanks..Timejim

 

[timejim]

Originally posted by nautica
It looks as if Monique beat me to it, again.

nautica

Don't worry about it, keep the info coming! Timejim

 

[lnx990]

ok, to answer the original question more accurately (and detailed just for the fun of it ). DNA carries with it all of the information for life. The way it does this is by means of proteins. For the sake of simplicity i will only talk about how eucariotic sells controle heredity. The reason for this is simply we do not know enough about the human genes and controling them to really talk about it.
Anyway, Like monique said, the language is written in A T and C G. I paired these in groups for a reason. As you may know, DNA is a double helix and when unwound has a series of base pairs going down 1 side, and a complementary strand on the other side thus a segemen of DNA might look like this:

AATCGATTCGATCCCTA
TTAGCTAAGCTAGGGAT

As you can see, the A's always line up with T's, and C with G. The reason for this involves the shape of the base pair molecuels, and the hydrogen bonds.
Essentially, DNA is arranged into chromosomes (or plasmids in the case of some Bacteria)These collections of DNA (usually millions/billions of of base pairs long. In these collections of DNA there are segments called genes. These geneg could code for anything from a single protein (building block of life), or an enzimatic pathway (enzymes accelerate chemical reactions). In Bacteria certain genes are arranged into something called an operon. Simply, an operon contains a group of genes (coding for protein) required to do a certain task, plus an operator. In bacteria there are 2 types of operons, Inducable and repressable. The operons have a regulatory gene that codes for an inhibitor that binds to the DNA right in front of the rest of the genes in the operon. This regulator protein will prevent transcription of the gened by blocking RNA transcriptase (more on that later). This is where the 2 types of operons comes into play. The inducable operons have a regulator that is always bound to the DNA, Unless a certain substance is present. An example of this would be the operon in bacteria responsible for breaking down lactose (sugar in milk). What happens is the gene is only active if there is reason for it to be, in this case the presence of suger. The other type, the repressable, are exactly opposite. They usually produce the cellular equivalent of raw materials, and basically afre shut off if there is a surplus af some chemical. This set up is very efficient, well in bacteria at least.
To make things a bit more complicated, these repressors can be repressed by a gene elsware, as well as enhancers that greatly speed up the rate of transcription. Not only that, the enzyme (if its coding for one) can be regulated by several factors. Enzymes can be stopped by competative inhibition (something similar competes for the enzyme) or non competative inhibition (Lead poisoning). Also some enzymes have active and inactive forms that are controlled by another protien created else where, and even on another chromosome.

Now that I've given a glimpse as to the complexity os signaling that goes on in a cell, let's look at how DNA "becomes" a protein. A protein is made from 20 amind acids and has 4 structeral components. These are:
Primary structure: actual amino acid sequence
Secondary structure: certain combinations of amino acids produce helixes and pleated sheats
Tertiary structure: takes into account everything in the chain creating a weird 3d shape
Quatrinary structure: Multiple polypeptide chains all interacting to for the final protein.
As you can probably tell this is extremely complicated. Stanford actually has a distributed computing project devoted to the studies of protein folding (how they actually get there shape), it requires many processors and ultimately we have only reached the tip of the iceburg.
Anyway, DNA codes for amino acids by means of codons. all a codon is is a set of 3 neucleotides now if you do your math right you will figuer out that that leaces you with 64 combinations of base pairs. and your right, however, some amino acids have multiple codons, plus codons that start and stop transcription. Let's break it down.

TAC AGA TGA TAA AAT TTT CTT ACA ACC ACT
the above would code for:
Methionine (starts transcription and is often cut out of the final protein)
Serine
Threonine
Isoleucine
Leucine
Lysine
Glutamatic acid
Cysteine
Arginine
Stop

Thats just a sequence i made up but it demonstrates the how the system works.
Now, in humans, we also have sections called interons and exons. Exons are "good" DNA that codes for a protien of some sort. Introns contain no information and are often in the middle af a gene and must be cut out by a special enzyme before it is translated into a protein. Why our DNA has this, well, know one really know for sure.
Also, i keep making refrence to transcription. Transcription is the process that takes a strand of DNA and copies it into something called mRNA or messengerRiboNeucleicAcid. This mRNA is then carried into the cytoplasm of the cell where it comes into contact with ribosomes (for the sake of simplicity all I am going to say is that they read the codons and add the appropriate amino acid to the growing chain.) And essentially that is how proteins are made.

Now here's a bit of a curve ball. Our DNA has sections of DNA that repeat for no apparent reason. In fact ther is a species of crab where 50% of its DNA is ATATATATATATATATATATATATAT...



Also, i agree with monique as to environment affecting our gene. An example would be the black tail tip, aersm and nose of a siamese cat. As those genes are controlled by temperature. Another thing to note is that Identical twins have the exact same DNA but if you get to know them you will find that they are diffrent. Again, its the enviroment. There have also been interesting studies into identical twins who where separated at birth. 1 case study was 2 guys that met up wher they where in their 40's (i think). WHen comparing their history they had similar interests, had similar school grades, where married twice (in both cases there wifes had the same names ans similar traits), and had kids, all of witch had the same names. So the freaky aspect is how much does our DNA really code for?



...anyway, i hope this really helpes

 

[Monique]

Originally posted by timejim
It helps but sparks another question. How does interaction with the environment "cause" the changes that would occur with DNA? What tells the DNA to change?? thanks..Timejim

Very good Inx990! :)

I'll just repeat what he just said: so DNA is made up of ACGTs that are stringed together, some parts make sense and are coding other parts don't make sense. The sense parts on the chromosome that are read by the cell are called genes. A gene is also made up of infortmative (exons) and uninformative (introns) segments, at first a whole gene is read after which the introns are taken out and only the exons are left that code for a protein.

This whole process is very much regulated, elements have to bind to the DNA for this reading to occur and also for the translation into protein to occur. All this regulation occurs in the promotor, which is upstream of a gene. Under certain environmental conditions there will be certain molecules present that bind to the promotor, and thus allow reading to take place.

So the process would be:
- DNA chromosome with genes
- molecules bind to promotor of a gene
- machinery that allows for reading of a gene bind to the molecules on the promotor
- gene is read, which means that a small copy is made of the region on that chromosome
- now you have a copy of the gene, which is called RNA
- introns are taken out, called splicing
- the string of exons now bind to a special machinery that are going to translate the nucleotide code into an aminoacid code, which is the protein.
- this protein can signal back to the DNA that its concentration is high and that the gene should be turned off.

 

[timejim]

Originally posted by Monique
Very good Inx990! :)

I'll just repeat what he just said: so DNA is made up of ACGTs that are stringed together, some parts make sense and are coding other parts don't make sense. The sense parts on the chromosome that are read by the cell are called genes. A gene is also made up of infortmative (exons) and uninformative (introns) segments, at first a whole gene is read after which the introns are taken out and only the exons are left that code for a protein.

This whole process is very much regulated, elements have to bind to the DNA for this reading to occur and also for the translation into protein to occur. All this regulation occurs in the promotor, which is upstream of a gene. Under certain environmental conditions there will be certain molecules present that bind to the promotor, and thus allow reading to take place.

So the process would be:
- DNA chromosome with genes
- molecules bind to promotor of a gene
- machinery that allows for reading of a gene bind to the molecules on the promotor
- gene is read, which means that a small copy is made of the region on that chromosome
- now you have a copy of the gene, which is called RNA
- introns are taken out, called splicing
- the string of exons now bind to a special machinery that are going to translate the nucleotide code into an aminoacid code, which is the protein.
- this protein can signal back to the DNA that its concentration is high and that the gene should be turned off.

It is a very complex evidently, however, I am missing something. With all the processes going on, is there a "single" process that regulates what all is taking place, telling everything what to do and when? I mean, the descriptions of what is occurring I get, but what I don't see is what is the single guiding "force" or "intelligence" to all of this?

 

[Monique]

The guiding force are transcription factors which bind to the promotor either turn genes on or off. The range of transcription factors is very broad and not much is known about them, since they are in the cell at very low concentrations.

Basically a transcription factor is anything that binds to the DNA and influences the rate of transcription (the reading of the sequence).

Actually I myself am searching for transcription factors: I have a gene which is only over expressed in a certain cell type, I want to find out why only in that cell type and how I can turn the gene off.

 

[lnx990]

essentially there is no 1 gene that controles the entire cell. However in multi cellular organisms you can have cells that that send signals to other cells and those get a little bit more closer to what you are talking about. In humans it is called the endocrin system. The key piece to the endocrin system is the patuitary gland (witch is ultimately controlled by the brain). The patuitary can produce a wide variety of harmones that will controle a variety of cellular functions. An example would be the brain detecting imminent danger, the patuitary sends a hormone signal to the adrenal glands (located above the kidneys). The adrenal glands will then release adrenalin. Adrenalin will instruct the body to break down glycogen (similar to starch) in the liver and muscle cells. It will direct the blood vescles to dialate but at the same time restrict all non essential functions such as digestion (butterflys in the stomach). It will alter a brain chemical and accelerate breathing. basically, it makes your body ready to fight for its life or run like your trying to outrun a subway or something. That entire process is controlled by 1 chemical that requires only 1 gene to operate. Now certain cells have certain genes turned on and certain genes turned off. this is determined in embryology. Over simplified, when a baby is developing (usually in the 1st 2 weeks), you have embryonic stem cells (they haven't decided what to become yet) as they replicate they will get a chemical signal to become adult stem cells. There are 4 types of those. They will create (nerv cells, structeral cells, muscles, and organs) What these cells will become is determined be a complex signaling process consisting of many chemical gradients. (i can't remember the exact names for all of this stuff) So, if you have a structeral stem cell dividing and there is a concentration of "chemical X" of 10 parts per million. As long as the signal remains 10ppm it will remain a stem cell. However, if it drops of to let's say 5ppm that cell could become a bone cell. Or, if it increases to 15ppm it could become some other cell type.

...all that to say that there really isent any ont thing that controles the cell (atleast on an inteligent level that we know of).

Actually I myself am searching for transcription factors: I have a gene which is only over expressed in a certain cell type, I want to find out why only in that cell type and how I can turn the gene off.

hmm, wot condition do you have?

 

[Monique]

Originally posted by lnx990
...all that to say that there really isn't anyone thing that controles the cell (atleast on an inteligent level that we know of).

No, it is a combination of things. But under controlled conditions when we expose a cell to a certain molecule, we can predict and measure exactly what will happen, thus: there CAN be one thing that controls the cell. You already mentioned the role of adrenaline.

 

[muadib2k]

It is a very complex evidently, however, I am missing something. With all the processes going on, is there a "single" process that regulates what all is taking place, telling everything what to do and when? I mean, the descriptions of what is occurring I get, but what I don't see is what is the single guiding "force" or "intelligence" to all of this?

If you are really interested in looking at a “prime” example of “regulating process” that controls the expression of DNA, try doing a web search on the lac-operon. It is a prokaryotic “control system” that regulates the expressions of genes that are needed to create proteins that are used to transport and cleave glucose.

The lac-operon is a very good example of a cell switching on/off the transcription of the genes based on its environment (as to not waste energy expressing the genes when it is not necessary). If you find this useful and/or interesting you could further search for the various positive and negative feedback systems that are used to regulate other genes.

 

[iansmith]

This is good explanation of regulation and expression of protein. The only problem the page are sideways.
http://nitro.biosci.arizona.edu/courses/EEB320-2003/lectures/Lac-grey.pdf

 

[Nereid]

DNA complexity?

What about DNA in mitochondria? chloroplasts? other thingies in the cell?? Do they have DNA too? (Monique seems to have mentioned only the nucleus).

What are the differences between prokaryotes and eukaryotes (in terms of DNA? (lnx990 implied there are significant differences)

I remember reading that RNA can also make proteins; is RNA also part of the 'book of life'?

IIRC, there've also been some recent discoveries on the importance of the 'junk' stretches of DNA, including some possible roles in the transcription process?

 

[Another God]

Originally posted by Nereid
What about DNA in mitochondria? chloroplasts? other thingies in the cell?? Do they have DNA too? (Monique seems to have mentioned only the nucleus).

Yes, there is DNA in the Mitochondria, the Chloroplast, and at the base of FLagella (EG of a flagella = The tail on a sperm cell. That tail is a flagella and is quite common in the cellular world).

The DNA in these things is much less than the DNA in the nucleus, and they generally only express a few genes which are required for those organelles. In essence, the DNA in the Nucleus is the 'store manager', controlling the cell, while the DNA in those few organelles are the department managers, controlling aspects of that section of the cell.

What are the differences between prokaryotes and eukaryotes (in terms of DNA? (lnx990 implied there are significant differences)

The most striking difference is that Eukaryotes (PLants, animals, fungus and some single celled organisms) have their DNA in the Nucleus organelle. Prokaryotes (bacteria) have their DNA just loose in the cytoplasm (it has no compartments like the nucleus).

There are other differences in terms of how DNA is read and stuff, but these get pretty technical, to do with what sequences constitute a start sequences, and whether bits of DNA are cut out of the translated sequence etc... I'm sure we'd be happy to explain this more, but it can be complicated and there is no need to get into it really.

I remember reading that RNA can also make proteins; is RNA also part of the 'book of life'?

Ummmm...Imagine the book of life is in spanish, and RNA is the cells attempt to translate small sections of the book into English. The molecules which turn the genetic code into Proteins can only understand english (RNA).

What happens, is the DNA stores all of the information, while the cell will trancribe the little sections that it needs into RNA, so that those little bits can be translated in proteins. The RNA is a temporary holder of information, but is not part of the book itself.

IIRC, there've also been some recent discoveries on the importance of the 'junk' stretches of DNA, including some possible roles in the transcription process?

awww..yeah.. i guess. There has been a lot of debate over 'junk' DNA ever since it was found and theorized to be 'junk'. I think the debate is a waste of time. I think it will become more than obvious that some of it will do stuff, and some of it won't. But whatever.

 

[None]

Just to add to AG's explanation of RNA:
RNA can also have enzymatic activity, by forming three dimensional conformations and complexing with protein subunits. Ribosomes have this characteristic.

None

 

[lnx990]

heres some of the diffrences between the 2

Prokaryotes Eukaryotes
Genome Size:
10E4-10E7 10E8-10E11
Repeated Sequences:
Few Many
Noncoding DNA within Coding Sequence:
Rare Common
Transcriptionand translation Seprate in the cells:
No Yes
DNA segregated within a neucleus:
No Yes
DNA bound to proteins:
Some Extensive
Promoter:
Yes Yes
Enhancer / Silencer:
Rare Common
Capping and Tailing of mRNA:
No Yes
RNA splicing required:
Rare Common
number of Chromosomes in genome:
1 many

It is also of my understanding that in Eukaryots the information is not stored in a linear fasion. Like, the regulator genes could be stored on another chromosome. Also, there is a need for repeated genes. Examples would be the gene that codes for ribosomes.


anyway, those are just some of the diffrences...