What is DNA? The story so far...

[vosh]

So, dna is a molecule, a long chain molecule, also known as a macromolecule, because it's large, and also known as a polymer. Polymers are made of many molecules called monomers that are linked together to make the long chain molecule.

 

The monomers of the dna polymer (macromolecule, long chain molecule) are molecules called nucleotides. I don't know why they're called that except that nucleo- refers to be found in the nucleus. These "nucleotides" are made out of groups of atoms, one being a phosphate group, meaning that it's made out of the phosphate polyatomic ion and something else, but I don't know what, a pentose sugar, and I don't know what a pentose sugar is, and a base. I think it's called a base because it is "basic" in solution, meaning that in an aqueous soln. it has a pH higher than 7.

 

Monomer type molecules are configured such that the part of them that bonds to each other to form a chain ends up forming a backbone, with another part of the monomer hanging off the backbone, sometimes referred to as a pendant, although that term doesn't turn up much in discussions about genetics. This is like a ladder that has runs but only one frame instead of two. So, if you saw a ladder in half vertically down the middle, you'd have two representations of a polymer. The half length rungs would represent the so called bases of the dna polymer. These bases join up with the bases on another half ladder dna polymer. Now twist them around to make a double helix and one big dna molecule.

 

In the dna chain molecule, there are 4 different kinds of nucleotides, the so called letters that spell out the information dna contains.

 

What I can't figure out is what a codon is.

 

TFYT.

[iNow]

What I can't figure out is what a codon is.

Maybe this will help:

 

 

D5vH4Q_tAkY

 

 

llNwYz9qcB8

 

 

 

Hat Tip: GDG

[Mr Skeptic]

What I can't figure out is what a codon is.

 

A codon is 3 nucleotides coding for a specific amino acid.

[vosh]

A codon is 3 nucleotides coding for a specific amino acid.

 

I haven't quite worked out what an amino acid is, yet. I mean, there are molecules that make the protein polymers (also called polypeptides?) and then there are the molecules that make the dna... are they both "amino acids"?

 

note: I don't need to know the deep down chemistry - I know that it's called amino acid because it has a part that is called an amine and it has an H atom that makes it an acid... and that's enough for now, regarding the chemistry. Unless, of course, someone has an accessible explanation for the chemistry.

 

And, does this mean that an amino acid is that which is made of 3 molecules?

 

Thanks for your patience. I'm trying to form a picture here.

[Mr Skeptic]

A nucleotide is one of the monomers of DNA or RNA (there are 5 total, but only 4 get used in either RNA or DNA), and an amino acid is the monomer of a protein (there are about 20).

[vosh]

A nucleotide is one of the monomers of DNA or RNA (there are 5 total, but only 4 get used in either RNA or DNA), and an amino acid is the monomer of a protein (there are about 20).

 

Wow. That's good to have straightened out. Much obliged. 5 total, huh. Never knew that. Oh... is that the uracil!?

 

So, nucleotides are floating around in the nucleus, and when enzymes (complicated story there, too, I know) unzip a part of the double helix (dhelix), those nucleotides line up to make an RNA polymer. And amino acids are floating about in the cytoplasm available to be strung together.

 

You know what drives me nuts? Ok, I tell ya. The pendant part of the dna polymer is always called a base. Apparently, this is not meant to mean that it has a low pH. I can't find any explanation for why it's called a base.

 

It's odd; I can't recall having seen any reference to amino acids being composed of just three molecules. Hmmmm.

 

 

TFYT

Edited May 7, 2009 by vosh

[CharonY]

Actually there are more than five. In tRNA you have got additional modified nucleotides. But that is not really important for basic understanding.

[GDG]

Wow. That's good to have straightened out. Much obliged. 5 total, huh. Never knew that. Oh... is that the uracil!?

 

So, nucleotides are floating around in the nucleus, and when enzymes (complicated story there, too, I know) unzip a part of the double helix (dhelix), those nucleotides line up to make an RNA polymer. And amino acids are floating about in the cytoplasm available to be strung together.

 

You know what drives me nuts? Ok, I tell ya. The pendant part of the dna polymer is always called a base. Apparently, this is not meant to mean that it has a low pH. I can't find any explanation for why it's called a base.

 

It's odd; I can't recall having seen any reference to amino acids being composed of just three molecules. Hmmmm.

 

TFYT

 

They're called "bases" because chemically they are basic (i.e., not acidic). Each has nitrogen atoms in the molecule that are capable of accepting H+ ions from water at neutral pH - that makes them bases by definition.

[vosh]

They're called "bases" because chemically they are basic (i.e., not acidic). Each has nitrogen atoms in the molecule that are capable of accepting H+ ions from water at neutral pH - that makes them bases by definition.

 

Hmmm. Yes. I'm reading that, now... trying to find how these bases make up an acid...

 

Much obliged.

[GDG]

For that you have to look at the backbone: all those phosphates. Phosphoric acid is pretty strong - much stronger than the bases are basic...

[vosh]

A codon is 3 nucleotides coding for a specific amino acid.

 

I found an article at howstuffworks that explained that amino acids are put together by 3 nucleotides. I didn't quite get that it's always three, that three pieces of something get aligned together to make an amino acid. Not sure if I know what those somethings are or not...

[Mr Skeptic]

A codon is always 3 nucleotides. Since each letter of DNA can be four choices, two letters would give you 4*4=16 which isn't enough for the 20 amino acids they would need to code for. Hence, we have 3 nucleotides per codon, and several codons code for the same protein.

 

The codon is in no way related to the amino acid itself. It just codes for it. The amino acid is attached to a tRNA molecule that has an anticodon that matches to the codon. DNA gets copied into mRNA, the mRNA goes to the ribosome, and tRNAs bring amino acids matching the codons in the mRNA. The ribosome chains the amino acids together into proteins, and removes the tRNAs that brought them.

[CharonY]

I found an article at howstuffworks that explained that amino acids are put together by 3 nucleotides. I didn't quite get that it's always three, that three pieces of something get aligned together to make an amino acid. Not sure if I know what those somethings are or not...

 

It sounds to me that you would profit from a more thorough explanation of the basics. More thorough than one can gather by reading most internet pages. Personally, I would recommend grabbing a good textbook. These give more information in a broader context than those one-click-web-answers.

[vosh]

It sounds to me that you would profit from a more thorough explanation of the basics. More thorough than one can gather by reading most internet pages. Personally, I would recommend grabbing a good textbook. These give more information in a broader context than those one-click-web-answers.

 

Read any good text books?

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Merged post follows:

Consecutive posts merged

Proteins are put together by enzymes following the template laid out by mRNA and DNA... but DNA wasn't put together by anything; it was already there. I guess that means that the answer to the question, where did the DNA come from, is that it evolved billions of years ago.

[GDG]

I found an article at howstuffworks that explained that amino acids are put together by 3 nucleotides. I didn't quite get that it's always three, that three pieces of something get aligned together to make an amino acid. Not sure if I know what those somethings are or not...

 

Here are the basics:

• Your chromosomes are made up of DNA (there are some proteins involved, but we'll save that for another time). Each chromosome is one, long, double-stranded DNA molecule.
  
• Each chromosome is divided up into regions called "genes". The genes come in many different sizes. Each gene encodes a protein (there are some more details here that I'm leaving out for purposes of clarity).
  
• In between the genes are other regions that are responsible for regulating transcription and expression of the genes: proteins bind to these regions to turn the genes on or off.
  
• When a gene is expressed, what happens is that a complex of proteins unwinds that part of the chromosome, makes an RNA copy of the DNA sequence, and zips the chromosome back up. The RNA copy is called "messenger" RNA (mRNA).
  
• The mRNA is processed a bit (introns removed, sequence spliced in some cases, and a cap put on one end), and exported from the cell nucleus into the cytoplasm.
  
• A complex of proteins and "ribosomal" RNA (rRNA) latches onto the "start" end of the mRNA. The complex is called a "ribosome".
  
• Also present in the cytoplasm are "transfer" RNA molecules (tRNA). Each tRNA has 3 specific bases that form an "anticodon" that can hybridize to a codon (sometimes capable of hybridizing to several related codons), and has an amino acid attached at one end. There is a different tRNA for each amino acid.
  
• The ribosome reads the mRNA 3 bases (i.e., one codon) at a time. It finds a tRNA with an anticodon that matches the current codon in the mRNA, and takes the amino acid that is attached. Then it shifts to the next codon, ejects the first tRNA, and finds a tRNA that matches the new current codon. It then takes the amino acid from that tRNA, and attaches it to the first amino acid.
  
• This step repeats until you get to the stop codon. Each time the ribosome shifts down the mRNA by another 3 bases (i.e., 1 codon), it finds a tRNA that matches that codon, takes its amino acid off, and attaches the amino acid to the growing chain of amino acids.
  
• Each possible amino acid is specified by a particular 3 base code. For example, methionine is encoded by ATG. Some amino acids have more than one possible codon. For example, glycine can be encoded by GGU, GGC, GGA, or GGG.
  
• At the end of the mRNA, the ribosome encounters a "stop" codon. The tRNA that recognizes this codon (actually, there are 3 different stop codons) does not have an amino acid (and so is called "release factor" instead). So, when the ribosome reaches the stop codon, it stops translating the mRNA, releases the amino acid chain (now a full protein or polypeptide), and falls off the mRNA.
  
• The mRNA can be translated multiple times, until it is degraded by other enzymes in the cytoplasm, and the bases are recycled.
  
• The proteins can be further processed too, e.g., by having carbohydrates or other molecules added, parts snipped out by proteases, etc.
  

 

Does that clear things up for you?

[vosh]

Here are the basics:

• Your chromosomes are made up of DNA (there are some proteins involved, but we'll save that for another time). Each chromosome is one, long, double-stranded DNA molecule.
  
• Each chromosome is divided up into regions called "genes". The genes come in many different sizes. Each gene encodes a protein (there are some more details here that I'm leaving out for purposes of clarity).
  
• In between the genes are other regions that are responsible for regulating transcription and expression of the genes: proteins bind to these regions to turn the genes on or off.
  
• When a gene is expressed, what happens is that a complex of proteins unwinds that part of the chromosome, makes an RNA copy of the DNA sequence, and zips the chromosome back up. The RNA copy is called "messenger" RNA (mRNA).
  
• The mRNA is processed a bit (introns removed, sequence spliced in some cases, and a cap put on one end), and exported from the cell nucleus into the cytoplasm.
  
• A complex of proteins and "ribosomal" RNA (rRNA) latches onto the "start" end of the mRNA. The complex is called a "ribosome".
  
• Also present in the cytoplasm are "transfer" RNA molecules (tRNA). Each tRNA has 3 specific bases that form an "anticodon" that can hybridize to a codon (sometimes capable of hybridizing to several related codons), and has an amino acid attached at one end. There is a different tRNA for each amino acid.
  
• The ribosome reads the mRNA 3 bases (i.e., one codon) at a time. It finds a tRNA with an anticodon that matches the current codon in the mRNA, and takes the amino acid that is attached. Then it shifts to the next codon, ejects the first tRNA, and finds a tRNA that matches the new current codon. It then takes the amino acid from that tRNA, and attaches it to the first amino acid.
  
• This step repeats until you get to the stop codon. Each time the ribosome shifts down the mRNA by another 3 bases (i.e., 1 codon), it finds a tRNA that matches that codon, takes its amino acid off, and attaches the amino acid to the growing chain of amino acids.
  
• Each possible amino acid is specified by a particular 3 base code. For example, methionine is encoded by ATG. Some amino acids have more than one possible codon. For example, glycine can be encoded by GGU, GGC, GGA, or GGG.
  
• At the end of the mRNA, the ribosome encounters a "stop" codon. The tRNA that recognizes this codon (actually, there are 3 different stop codons) does not have an amino acid (and so is called "release factor" instead). So, when the ribosome reaches the stop codon, it stops translating the mRNA, releases the amino acid chain (now a full protein or polypeptide), and falls off the mRNA.
  
• The mRNA can be translated multiple times, until it is degraded by other enzymes in the cytoplasm, and the bases are recycled.
  
• The proteins can be further processed too, e.g., by having carbohydrates or other molecules added, parts snipped out by proteases, etc.
  

 

Does that clear things up for you?

 

Yes. Some of that I got from the exchange above, some from other sources, websites, textbooks... I can't express my gratitude enough here for your efforts. However, and this is in no way a rebuke of your effort here, I feel I should mention that I have not had anything but success with the question and answer session in this thread. Indeed, it has taken me exactly where I wanted to be with my questions. I wanted to make that clear in case there was an impression that it all left me none the less lost and unclear about everything in spite of my queries. I'm afraid that following one question with another might have given the impression that I wasn't having any luck, so I thought I would point out that this isn't the case. I can hardly believe what I've managed to put together about this subject just by asking. I believe this is the result of asking my own questions, and I believe this has taken me to an over all understanding much faster than having someone decide for me what questions and answers I should be studying. Hope that made sense. If not, well, communication is an ongoing thing, isn't it. Anyway, thanks again.

[GDG]

Yes. Some of that I got from the exchange above, some from other sources, websites, textbooks... I can't express my gratitude enough here for your efforts. However, and this is in no way a rebuke of your effort here, I feel I should mention that I have not had anything but success with the question and answer session in this thread. Indeed, it has taken me exactly where I wanted to be with my questions. I wanted to make that clear in case there was an impression that it all left me none the less lost and unclear about everything in spite of my queries. I'm afraid that following one question with another might have given the impression that I wasn't having any luck, so I thought I would point out that this isn't the case. I can hardly believe what I've managed to put together about this subject just by asking. I believe this is the result of asking my own questions, and I believe this has taken me to an over all understanding much faster than having someone decide for me what questions and answers I should be studying. Hope that made sense. If not, well, communication is an ongoing thing, isn't it. Anyway, thanks again.

 

No problem: just trying to set things out systematically, so that one can follow the whole process with a consistent use of terms.

 

The communication here is probably the best feature of this website, and one that makes it much more useful than wikipedia. Wikipedia is great for browsing, or if you already know something about your question and are just looking for details. If you are just getting started, this is a great place to come first.

[Mr Skeptic]

The communication here is probably the best feature of this website, and one that makes it much more useful than wikipedia. Wikipedia is great for browsing, or if you already know something about your question and are just looking for details. If you are just getting started, this is a great place to come first.

 

Isn't that rather backwards? It's slightly rude to ask about something that can be found extremely easily. Wiki is usually the top search result, and gives a very good general explanation. But if you are looking for a specific detail, that is not so easily found, then asking on a forum is a good idea.

[GDG]

Isn't that rather backwards? It's slightly rude to ask about something that can be found extremely easily. Wiki is usually the top search result, and gives a very good general explanation. But if you are looking for a specific detail, that is not so easily found, then asking on a forum is a good idea.

 

It's the dictionary paradox: how do you find the spelling of a word if you don't know how to spell it? For example, if you were talking to somebody (orally), and they told you about an ox-like animal with a name something like "new", how would you look it up? Looking under "new" or "knew" or "nu" would not be fruitful; "gnu" would probably be the last thing you'd expect.

 

With many scientific concepts, it is easy to find the answers once you know enough about the field to know the terms. Not so easy when you start out. Some of the questions I've seen here are d@mn near impossible to parse: I can't imagine that google is much help to those questioners...

 

As we wander seriously OT...

[vosh]

Isn't that rather backwards? It's slightly rude to ask about something that can be found extremely easily. Wiki is usually the top search result, and gives a very good general explanation. But if you are looking for a specific detail, that is not so easily found, then asking on a forum is a good idea.

 

And you can't possibly know how another person should learn something, what's in their head, etc. etc. That's the beauty of a student led session. The student knows better than anyone what they need.

Edited May 14, 2009 by vosh