DNA question.

[cameron marical]

so http://learn.genetics.utah.edu/content/begin/tour/ is a website that i looked at to learn as much as possible about genetics, and on the link it talks about in the dna section{the first one on the top left of the little black screen} how only a and t can connect, and c and g can connect. yet in the next slide it shows how they get put as dna and include what appears to be random sequencing orders, is that just a typo or am i misenterpriting?

 

thanks.

[Paralith]

The connectivity is referring to the bases on opposite strands. The binding of a's and c's on one strand to t's and g's on the other strand, respectively, keeps the double helix together. So, if one strand has a sequence like this:

 

ATTGCAAGCTACGT

 

then the sequence on the opposite strand will be:

 

TAACGTTCGATGCA

 

Make sense?

[mrburns2012]

so http://learn.genetics.utah.edu/content/begin/tour/ is a website that i looked at to learn as much as possible about genetics, and on the link it talks about in the dna section{the first one on the top left of the little black screen} how only a and t can connect, and c and g can connect. yet in the next slide it shows how they get put as dna and include what appears to be random sequencing orders, is that just a typo or am i misenterpriting?

 

thanks.

 

This picture explains it all: http://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg

 

If the picture doesn't isn't helpful, you might first want to read some basics of organic chemistry. If it doesn't even help then, you're too far ahead of yourself.

[GDG]

so http://learn.genetics.utah.edu/content/begin/tour/ is a website that i looked at to learn as much as possible about genetics, and on the link it talks about in the dna section{the first one on the top left of the little black screen} how only a and t can connect, and c and g can connect. yet in the next slide it shows how they get put as dna and include what appears to be random sequencing orders, is that just a typo or am i misenterpriting?

 

thanks.

 

The As and Ts are on complementary strands, as are the Cs and Gs. In double stranded DNA, you would have a structure like (for example) this:

 

ATGGCGATTAC

|||||||||||

TACCGCTAATG

 

One strand is the "sense" strand, and the other is the complementary strand (although both strands can encode proteins). The DNA is transcribed into mRNA (which looks just like DNA, except that you have the base "U" (uracil) instead of T, and have one more hydroxy group on the sugar part of the molecule). When the mRNA is translated to protein, the enzymes that do the transcribing (a complex called a ribosome) reads the bases three at a time: each group of three is called a "codon", and each codon codes for a specific amino acid (or for "stop").

 

ATG GCG ATT ACC

||| ||| ||| |||

TAC CGC TAA TGG

(Note: I'm only putting in the spaces to identify codons -- the ribosome does not physically separate the bases.)

[Brandon]

so http://learn.genetics.utah.edu/content/begin/tour/ is a website that i looked at to learn as much as possible about genetics, and on the link it talks about in the dna section{the first one on the top left of the little black screen} how only a and t can connect, and c and g can connect. yet in the next slide it shows how they get put as dna and include what appears to be random sequencing orders, is that just a typo or am i misenterpriting?

 

thanks.

 

The nitrogen base pairs dont change. yes the sequece of the pairing do change. for example; if you lay the double helix horizontally and look at one backbone of DNA mad up of deoxyribose and phosphate molecules, you will see the nitogen bases like this AGTCATGATTCA. the complemetary nitrogen base of each would be this .....TCAGTACTAAGT. in the first nitrogen base pair of adenine and thymine the base pair does not change like cytosine to tymine. but the sequece could change like instead of adenine to thymine the pair could be thymine to adenine. if you have any further questions just let me know. like if you need to know that diffrent codons make certain amino acids.I can explain how RNA works.

[cameron marical]

its ribosomes that synthesize that protein from the mRNA codons right?

 

i do have a question about transcription, what is it that moves the rna into the nucleolus?

 

also, how does it know where to start?

 

I read that the find a certain combination of nucleotides{i certain codon} and start form there, but then how does it "know" that that codon is what it is?

 

Also, dna is a big polymer, so just one codon is bound to pop up more than once, and i dont understand how the enzyme helicase can identify that one codon in the first place, let alone for different codons for different proteins, but again, dna is a big polymer, how does it not have certain "start here" codons for different proteins twice?

 

and how does it recognize say ATA from GCG?

 

big load, but anyone who can answer them all gets reputation points. thanks.

[GDG]

its ribosomes that synthesize that protein from the mRNA codons right?

 

Yep.

 

i do have a question about transcription, what is it that moves the rna into the nucleolus?

 

The nucleolus forms around the rRNA sites in the chromosomes

 

also, how does it know where to start?

 

Which "it" are you referring to?

 

I'm not sure if this has been demonstrated yet or not, but the nucleolus location is probably a matter of the relevant enzymes having DNA sequence recognition sites that are specific for a sequence at the relevant site(s).

 

If you're talking about where transcription starts, the polymerase enzymes in the nucleus recognize specific DNA sequences (polymerase binding sites), and start there. The gene to be transcribed is probably opened up (unwound) by helicases and promoter proteins so that the bare sequence is accessible, and the polymerase is statistically certain to bump into it eventually. Once the mRNA is transcribed, it gets further processed (spliced, 5'-capped, etc.), and exported from the nucleus to the cytoplasm by enzymes that recognize the cap structure, where it encounters ribosomes and is translated into protein.

 

I read that the find a certain combination of nucleotides{i certain codon} and start form there, but then how does it "know" that that codon is what it is?

 

By their shape and charge distribution: basically the same way that an antibody recognizes a specific antigen. The protein will have a binding site that has a very particular shape, and the target sequence will fit into the binding site in a way that is energetically favorable. Non-target sequences will not fit as well, and their affinity for the binding site will be low enough that the protein does not stay there and start transcription.

 

Also, dna is a big polymer, so just one codon is bound to pop up more than once, and i dont understand how the enzyme helicase can identify that one codon in the first place, let alone for different codons for different proteins, but again, dna is a big polymer, how does it not have certain "start here" codons for different proteins twice?

 

A recognition site is usually more than a single codon: frequently 8+ bases. Still, it is true that 8mers probably occur repeatedly in the genome.

 

A large fraction of the cell's genes are shut off in the process of differentiation (differentiation is the process by which a stem cell turns into whatever its final form is, e.g., a fibroblast). For example, a fibroblast never needs to make antibodies (B cells take care of that), so part of its differentiation from stem cells is to shut down the genes that code for antibody production -- and so on for every other function that a fibroblast does not need to perform. You end up with a much reduced number of active genes, basically the genes needed to perform "housekeeping" functions (basic metabolism, mitosis, etc.) and whatever specialized function the terminally differentiated cell needs to do (e.g., making collagen if you're a fibroblast). The genes are shut down by a combination of direct methylation on specific bases, winding up the gene on histone proteins (and methylating the histones), and probably several others, which renders those gene inaccessible.

 

Of the genes that are left available, even though relatively available they will probably not be transcribed unless a specific protein unwinds that section of the chromosome and attracts a polymerase over to begin transcription. The specific proteins recognize a number of enhancer, inhibitor, and other sequences, so they are not limited to the 8-15 base promoter recognition site.

 

and how does it recognize say ATA from GCG?

 

By its shape and charge distribution, as set forth above. ATA has a different shape from GCG, and a different distribution of + and - charges.

 

big load, but anyone who can answer them all gets reputation points. thanks.

 

No problem

[Brandon]

its ribosomes that synthesize that protein from the mRNA codons right?

 

i do have a question about transcription, what is it that moves the rna into the nucleolus?

 

also, how does it know where to start?

 

I read that the find a certain combination of nucleotides{i certain codon} and start form there, but then how does it "know" that that codon is what it is?

 

Also, dna is a big polymer, so just one codon is bound to pop up more than once, and i dont understand how the enzyme helicase can identify that one codon in the first place, let alone for different codons for different proteins, but again, dna is a big polymer, how does it not have certain "start here" codons for different proteins twice?

 

and how does it recognize say ATA from GCG?

 

big load, but anyone who can answer them all gets reputation points. thanks.

 

 

GDG is correct the RNA know how to read codons by the polymerase enzymes in the nucleus. By knowing this, the RNA can read a certain pair of nitrogen bases(codon) to start the DNA replication process. There are also certain codons that tell the RNA to stop reading the DNA. Each codon is an instruction for makeing an amino acid. Inside the ribosome takes place the linkege of amino acids to make a pacific protein.

[CharonY]

Brandon, I am sorry to say, but your post makes little sense.

RNA does not read codons. The only pairing relevant to codon generation is the antisense pairing of tRNA. And it surely does nothing with regards to DNA replication. You are mixing up transcription, translation and replication. Badly.

[GDG]

Just to forestall confusion, there is a second recognition system that is employed in the ribosomes. Proteins that bind directly to DNA or RNA work as described. In the ribosome, the process of translating mRNA codons into the correct amino acids is basically due to transfer RNA ("tRNA") molecules.

 

tRNA molecules have an "anti-codon" that hybridizes to the codon that is being read. There is a separate tRNA for each anticodon (although some of the anticodons accomodate "wobble", and can bind to several different codons): thus, you have less than the theoretical maximum number of tRNAs. The correct amino acid is attached to each tRNA before it goes to the ribosome, by an enzyme known as an aminoacyl-tRNA synthetase. This enzyme binds an amino acid, recognizes the anticodon on the tRNA, and binds the amino acid to the tRNA. You have one aminoacyl-tRNA synthetase enzyme for each different amino acid.

 

The ribosome (which is a big complex of proteins and ribonuclear RNA (rRNA) takes care of finding the appropriate spot on the mRNA to start translating, matching up the tRNAs to the codons, taking the tRNA's amino acid and attaching it to the end of the growing protein chain, ejecting the "empty" tRNA, and moving down to the next codon.

 

There's a decent animation at

.

[cameron marical]

ok, i was actually wondering that. thanks.

 

You have one aminoacyl-tRNA synthetase enzyme for each different amino acid.

 

does that mean that there are every amino acid possible "codes" from these tRNA in every cell? is there different ones for different cells depending on what proteins are synthesized? if so, how do the cells regulate what types of tRNA codes are in it?

 

thanks.

[iNow]

There's a decent animation at

.

Thanks for sharing that. I watched part 2, as well. Useful and accessible. Two of my favorite things in newly acquired knowledge.

[CharonY]

does that mean that there are every amino acid possible "codes" from these tRNA in every cell? is there different ones for different cells depending on what proteins are synthesized? if so, how do the cells regulate what types of tRNA codes are in it?

 

The genetic code is realized by those tRNAs (together with the right coupling of the respective synthetase). In a given organism all cells share the same genetic code. That is, all have the same complement of tRNAs.

[Brandon]

Brandon, I am sorry to say, but your post makes little sense.

RNA does not read codons. The only pairing relevant to codon generation is the antisense pairing of tRNA. And it surely does nothing with regards to DNA replication. You are mixing up transcription, translation and replication. Badly.

 

I answered all of his questions in one summary. 1:how RNA moves into the nucleus. 2:how RNA knows how to stop and start reading codons, but i did say RNA it is actualy MRNA that reads the codons and carriers the message to the ribosome. 3:I even said how proteins are made,so; what reads DNA again?

[GDG]

ok, i was actually wondering that. thanks.

 

does that mean that there are every amino acid possible "codes" from these tRNA in every cell? is there different ones for different cells depending on what proteins are synthesized? if so, how do the cells regulate what types of tRNA codes are in it?

 

thanks.

 

Here's how it works: there are 64 possible codons (4 bases in each of 3 positions in the codon), and 20 common amino acids (there are a few other amino acids, but they are mainly made by post-translational modifications of the "main 20"). Three of the possible 64 codons are "stop" codons, which do not encode an amino acid (usually: there are a few exceptions here too). The number of different codons for each amino acid is not distributed evenly: some amino acids have only one possible codon (e.g., Met -- ATG, AND TRP -- TGG), while others have up to six (e.g., Leu, with TTA, TTG, CTT, CTC, CTA, and CTG). Most have 2 or 4 possible codons.

 

For each amino acid, there is at least one tRNA. Some tRNA molecules can "recognize" or hybridize to more than one different codon (up to 4), but all of those codons will still encode the same amino acid. In the case of tRNAs that hybridize to more than one different codon, the codons will differ only in the 3rd position. For example, there could be only one Proline ("Pro") tRNA, which could pair with CCX (X being any of the 4 bases).

 

For each amino acid, there is one enzyme that attaches that amino acid to each of the tRNAs that pair to codons for that amino acid. Thus, you have 20 amino acids; 20 aminoacyl tRNA synthetase enzymes; between 20 and 61 tRNAs; and 64 possible codons.

 

Different species have different codon "preferences", which means that, for example, in species A you would find most Pro codons are CCA or CCC, while in species B you would find that most Pro codons are CCG or CCT. I suspect that all tRNAs are used in every cell in an organism, even though some are more abundant.

 

tRNAs are probably regulated pretty much the same way as every other protein and RNA in the cell: inducers and inhibitors, etc. IIRC, there are a few cases in which a "rare" tRNA is required, and the relative scarcity of that tRNA regulates the speed with which the corresponding protein is made.

[cameron marical]

Why is there ribosomes floating around at random?

 

Why arent all ribosomes attached to the rough endoplasmic retticulum and the golgi apparatus?

 

and how does the smooth endoplasmic retticulum find the proteins?

thanks.

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Whats the difference between virus rna and mrna?

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are all virus's retrovirus's?

 

thanks.

[Mokele]

The ribosomes in rough ER only make transmembrane proteins, those proteins which cross cell membranes. The ribosomes floating free in the cytoplasm make proteins which likewise float around inside the cell.

 

Not all viri are retroviri - most viri use DNA.

 

The difference between retroviral RNA and mRNA is what happens to them more than structure - one is made into a protein, the other is reverse-transcribed into the cell's nuclear DNA.

[CharonY]

One probably should add that there are also RNA viruses that in contrast to retroviruses do not have a DNA phase. Essentially they are a kind of mobile mRNAs.