Plasmids

[Architectonic]

I'll address the tools issue on another day, but the issue is that biological systems are very complex, yet biologists only have the tools to investigate the systems in somewhat simplistic and labour intensive ways. I'm not kidding when I say it is hard to imagine some of the tools that will be in use in the biological systems in 50-100 years.

Oh, just writing here to say that I like the thread. How much of these experiments would be possible to "bring home"? Is the basic equipment/supply very expensive?

Its pretty much impossible to do anything sophisticated at home these days - as governments think you're trying to make biological weapons, or drugs etc. Supplies are strictly regulated in most western countries. If you have serious ideas you wish to investigate, then the options are pretty much academic research, convince an existing company to research your idea or start up a new company.

 

[enfp can be shy]

Why do governments get to make biological weapons, and I don't? Obviously they suspect me of doing this, because they are doing it. They wouldn't suspect me of doing something really original. I wouldn't suspect them of that either, so at least that part is fair.

 

[InTheWomblikeCocoon]

if there are 2 sites that the enzymes recognizes, how many dna fragment will result if the dna is linear? circular?
circular makes copies easier, i think...but can someone tell

 

[Morgain]

if there are 2 sites that the enzymes recognizes, how many dna fragment will result if the dna is linear? circular?
circular makes copies easier, i think...but can someone tell

You mean restriction enzymes?

If you have a circular dna fragment and the enzyme cuts in two places, you will have 2 fragments. If you dna fragement is lineair and the enzyme cuts in two placies, you will have 3 fragments

you can copy a circular DNA fragment by bringing it in a bacteria, cultivating the bacteria so you have a lot of them and than purifing the plasmid out of the bacteria.
A small lineair fragment can be multiplied by PCR. You need two small pieces of DNa (primers) that match with the ends of your fragment and than you ad a polymerase enzyme witch will multiply the DNA.

answers that your question?

 

[InTheWomblikeCocoon]

You mean restriction enzymes?

If you have a circular dna fragment and the enzyme cuts in two places, you will have 2 fragments. If you dna fragement is lineair and the enzyme cuts in two placies, you will have 3 fragments

you can copy a circular DNA fragment by bringing it in a bacteria, cultivating the bacteria so you have a lot of them and than purifing the plasmid out of the bacteria.
A small lineair fragment can be multiplied by PCR. You need two small pieces of DNa (primers) that match with the ends of your fragment and than you ad a polymerase enzyme witch will multiply the DNA.

answers that your question?

ok. i said 2 for circular and 4 for linear. is the polymerase a ligase? or ligase comes before polymerase?

 

[Morgain]

ok. i said 2 for circular and 4 for linear. is the polymerase a ligase? or ligase comes before polymerase?

a ligase links together two DNA pieces. In molecular biology it is used in cloning experiments where the aim is to bring a DNA fragement into a plasmid. Both sides of the DNA fragement usualy have an overlapping end that is complemantairy to the overlapping end of the linearised plasmid. And Ligase repairs the di-ester bounds between the two fragments

Polymerase (very simplistically) makes DNA. DNA is dubble stranded, so you normally have two complementaire strands. Polymerase needs one of those strands and a primer that binds to the 5' side of the strand and than it prologes that primer till the end of the template DNA with nucleotides that are complementary to the template.

In cellular replication it is polymerase that replicates the DNA by copying both strands of the DNA and than when the job is done, ligase comes in to ficks the gaps.

but I can recommand wikipedia, it gives a very good and understandable information about DNA replication and such

 

[Architectonic]

if there are 2 sites that the enzymes recognizes, how many dna fragment will result if the dna is linear? circular?
circular makes copies easier, i think...but can someone tell

While Morgan easily guessed the answer, you still need to learn an important lesson when dealing with the scientific method. You have to be as specific as possible in recording all possible conditions, even those which you think are irrelevant to the experiment as well as other specificities relating to what you are using for experiment. For your hypothesis might be wrong and they may turn out to be relevant after all.

There are many different types of enzymes, so the idea of adding enzymes to a circular DNA strand, it doesn't necessarily follow that the enzyme will cut the DNA strand. Unless you specify the function of the enzyme first.

As such, you should also be talking about DNA polymerase or DNA ligase.

By the way, some of these concepts are much easier to understand and remember if you watch an animation that details the process (found even on Youtube etc). The molecules and interactions are usually represented simplistically, but the key concepts are always there.