DNA - Like, HOW???

Factual Questions
1

Question for Doper biologists;

I understand that DNA is comprised of chromosomes, made of of genes, in a pretty double helix format that looks great on a scientist’s computer screen in the movies. I know it’s all sequenced and that a lot of it is junk but a lot of it decides everything about our bodies, and I know it’s all the latest scientific rage.

My question is; howe does the information on the DNA get “read” by the organic goop that makes up our bodies to direct how we grow? In other words, by what mechanical process does a cell in my body gather the information from DNA in order to know what the hell it’s supposed to do? I realize DNA exists in most of my cells, but the disk has to be read by some kind of drive, right? What’s up? How does my body read DNA?

2

Actually, DNA is not comprised of chromosomes, but the other way around. I’m not a biologist, but I’ll tell you what I know, which is good enough for me.

It is a coding system, with DNA consisting of 4 different nucleotides (or bases): guanine (G), adenine (A), cytosine © and thymine (T). A fifth, uracil (U), takes the place of thymine in RNA. It consists of the double helix of two strands, each strand is composed of alternating pentose sugar and phosphate groups, with the above named nucleotides attached to each pentose group. The bases on each srand are hydrogen-bonded and are always paired in the same way: A with T and G with C. During replication, the strands separate, with each providing a template for the new complementary strand, thus producing two identical copies of the original helix.

The coding system is a tricodon, I think that’s the name. Anyway, 3 nucleotides code for a specific amino acid. Protein is made of amino acids. Thus ACG may code for lysine. (I don’t know for which one it actually codes for.) The complete series of amino acids comprising a certain protein is coded by the corresponding series of bases, and that is called the “gene” for that protein. Chromosomes are coiled in the nucleus and, in man, there are 46 of them (23 pairs) and different genes appear on different ones.

The “junk” codons you referred to are probably not junk, altho at one time they thought so. However, they have found out that these extraneous codons are signalling something for the DNA to do, such as: stop, end of the series of amino acids for this protein. Other so-called junk nucleotides probably have some other purposes, and I’m sure we don’t know all the answers yet.

But the actual reading of the nucleotides for the protein does not occur in the nucleus where the DNA, genes, and chromosomes are located, but in the cytoplasm, where the ribosomes are. The ribosome is fhe factory which assembles the amino acids into the proteins. A DNA by the method above described forms a messenger RNA (mRNA), which differs from the DNA in having uracil isntead of thymine, and as the name states, a ribose sugar insteaad of a deoxyribose sugar.

The mRNA migrates into the cytoplasm where, by some mechanism I do not know, forms transfer RNA (tRNA). tRNA is a carrier. It transports the appropriate nucleotide to the ribosome where they are assembled in the right order to form the corresponding amino acid. The ribosome has a third RNA, ribosom RNA (rRNA), which helps with the assemblage, by some method I don’t know.

I am hazy about what happens, as you notice, in the cytoplasm. Perhaps a biologist out there will help both of us in that regard.

3

by the above post, I’m not sure if what I have to say will answer your question, but that sure won’t stop me!!

A chemist by study (with lots of course work in bio-chem), my view is that it may help you to understand that big molecules do lots of work in our bodies. They do this, actually, based on their shape (think active transport), and chemical stuff like polarities, resonance structures and stuff that allows/causes them to be part of chemical reactions.

The DNA, RNA and mRNA all act as ways (through chemical reactions driven by the shape of the DNA, RNA, mRNA and amino acids) to build these big molecules - proteins!

Simple I know, but I’d hate to be labeled “verbose” :slight_smile:

Se non e vero, e ben trovato
Spritle

4

Can I have a go at confusing him?
Trying to answer this in layman’s terms is always great fun. I’m about to make a lot of generalisations, but the gist of it is accurate.
To understand how this works you have to understand that DNA is made of a chain of molecules, each one capable of existing separately, but all linked. There are four types of links available for use in these DNA chains, each a different size and shape. I’ve always found it easiest to imagine them as a square, round, triangular and circular links in an actual chain, it’s a good analogy. The sequence of the different shapes in these incredibly long chains is how the information is encoded.
It’s also necessary to know that proteins are also chains, but they are made up of completely different types of links, called amino acids. There are hundreds of different types of amino acids, all different sizes and shapes. My favourite analogy for amino acids is that they are like pieces of metal. Some are straight, some are right angles, some 45 degrees, some corkscrews and some have springs in the middle that allow them to flex. All these pieces of metal have holes drilled in each end that allow them all to be bolted together in any combination you like. Obviously exactly what you get if you join a lot of them together in a chain is going to depend on what shapes to use and where. If you build a six-foot chain out of straight amino acids it will obviously be straight. If you put one right angle piece in the middle it will be right angled, and if you put the right angled peace near one end it will be L-shaped. The possible combinations are nearly limitless. Amino acids float free in the ‘goop’ of our cells.
Proteins are very complicated machines. There are different shaped proteins that can measure, cut, carry, glue, nail and do everything a good carpenter can do.

Basically the way information is ‘read’ is as follows
There exists in the ‘goop’ of our cells a molecule, I’ll call it a Translator, that functions like the read/write head on a drive. Imagine it like this. It’s shape is like a pole with a vice on one end and hundreds of spanners folded on the other like keys on a ring. All these spanners are different sizes and shapes and only one of these ‘spanners’ can be separated on the key ring at any time. Exactly which one is unfolded is dependant on a very complex wiring mechanism that detects which parts of the vice are in contact with something solid and which aren’t. The vice itself is exactly the right size to clamp three of the links in our imaginary chain at a time. If you can handle the illustrations up to here the rest is fairly simple.
The vice clamps onto one end of the DNA chain, and because of the pressure pattern caused by the different shaped links a specific spanner folds out the end. This ‘spanner’ is exactly the right size to grip one specific amino acid as it floats past, which it does. The whole translator then moves up to the next three links. The different pressure on the vice now causes a different spanner to spring out. This is a different spanner and grips a different amino acid. It then proceeds to bolt it to the last one allowing the original spanner to retract. The vice then moves onto the next three DNA links and this causes yet another spanner to pop out, grab an amino acid and bolt it onto the other two allowing the last spanner to retract. This continues until the protein chain is complete. It’s then let loose to cause havoc by building body parts.
The concept’s not that hard but the details are terrible. In reality the DNA isn’t read at all. It’s treated like a read only master and only copies of it are worked with. These copies are carried outside the nucleus where the DNA is usually found into the general ‘goop’ of the cell. The ‘Translator’ is actually two (three according to some) different molecules. The DNA copy is only a partial copy of the whole, only one specific gene, and this is the reason why each gene codes for one trait.
Hope that cleared things up RickJay. I wasn’t sure how simple you wanted it. And I certainly hope I haven’t confused you too much. Have fun.

5

Barbitu8 has most of the process correct. The mRNA does not form tRNAs; rather, the tRNAs are always floating around the cytoplasm, attached to the amino acids that make up the proteins. When the ribosomes start processing the mRNA, tRNAs find their way to the ribosome and begin linking up the amino acids. (The tRNAs have nucleotides that match with the codons on the mRNA.)

There are no “junk” codons (not tricodons). 61 of the possible 64 codons are used to encode amino acids–which means there’s quite a bit of redundancy. Some aa’s have six codons coding for them; very few have only one (methionine and tryptophan, I believe). The other three codons are “stop” codons. The “start” codon happens to also code for the aa methionine. Thus, before post-translation processing, all proteins will start with methionine.

There is, however, basically “junk” DNA. Most genes have junk scattered throughout them–called “introns”–between the coding regions, or “exons.” Between genes, there are even more bits that don’t code for proteins. Some of these–“pseudogenes”–used to code for proteins; some sequences are there specifically to help with transcription initiation (or to hinder it) when the right proteins are around; other sequences are just, well, there. These include:

Microsatellite repeats (pieces of DNA that run, frex, CACACACACACACA…) which are apparently useless to the body but are useful to geneticists mapping the heredity of genes from a family (although similar repeat sequences inside genes are known to cause diseases when they get extended through processing errors);

LINE elements and other sequences, of which we have quite a number in our genome; they tend to just hang out, but they can be copied to different places and that can destroy genes;

And, of course, all aorts of stuff that we just aren’t sure about yet. :slight_smile:

Let’s see–a few more things.

DNA exists in all cells except for red blood cells.

The double helix isn’t just for looks; it’s actually a protetive mechanism that prevents the genes from being mutated severely by UV light, X-rays, etc. It’s also rather compact. The double helices are wound around proteins called histones, which then form helices within helices themselves to form what you see as chromosomes during cell division. However, most of the time, chromosomes are strung out as “chromatin” and can’t really be seen except with an electron microscope.

The longest chromosome in your body, when strung out end to end and not folded in any way, would be about a meter long–and 10 nanometers wide.

OK… I’ve thrown a bunch of seemingly random information your way in no particular order. I’ll se if I can’t come up with some relatively easy references for you later. :slight_smile:

LL ← biochemist/molecular biologist

6

Tha above is from http://www.howstuffworks.com

As you note, I was inaccurate in some respects out there in the cytoplasm. the tRNA does not bring nucleotides, but amino acids into the ribosome, which is the organelle that selects the codons for the amino acids. After all, the tRNA is composed of nucleotides. And the nucleotides attact the right amino acid. Then the tRNA carries that amino acid into the ribosome, which sorts them out into the corresponding codon to form a protein.

Smeghead, or any one elsle, help us out if I’m wrong in some respects.

[note: copyrighted text replaced by a link to the page from whence it came. Please to not repost articles like that. After all, we’d be pretty mad if they posted Cecil’s column without permission! -manhattan]

[Edited by manhattan on 12-08-2000 at 05:36 PM]

7

Two notes:

  1. Barbitu8, the mods are going to come along and delete that because it’s copyrighted.

  2. You’re not wrong, they are. Not all proteins are enzymes! This is actually rather important. There are many many many proteins out there that do not catalyze reactions, but have other functions: serving as ion channel in membranes (the proteins on which I work); serving as cytoskeletal elements, or other structures such as collagen/elastin in ligaments; serving as regulatory proteins; etc., etc.

Just had to make a note.

This Page gives an even more detailed explanation.

LL

8

Everyone’s posts have been extremely helpful. I wasn’t aware of the existence of mRNA and tRNA or the way they provide interaction between the DNA and the ribosomes. That gives me the basic jist I was wondering about. Thanks!

9

I am a molecular/human geneticist in training.

I will post some stuff in a bit but my boss is kind of picky about us messing around on the internet during the day. “Research” he calls it…

Basically a short post now.

We have 50-100,000 genes in the genome. These are separated by large distances of DNA. We can identify genes by basically universal sequences that define their start and stop. Only a short portion of the gene (the open reading frame) encodes the actual protein. The rest of the gene is responsible for regulating its activity – when, where, what form, and at what levels it is produced. These regions include enhancers, promoters, splice sites, etc.

Other proteins bind to these sites and regulate activity. This starts with oogenesis (making of the egg) and continues into oocyte development. At fertilization, things change. Gene expression changes with it. It is a large, long cascade.

10

I’m curious now about DNA and what it “says”
Considered as information, what is the entropy level of DNA?
I would assume that at some point all the junk becomes burdensome to an organism. Does it ever get weeded out (selected against)? Or will the genome steadily grow in size?

Is inactived but functional DNA considered part of the junk? I seem to remember some research years back in reactivating sequences that resulted in teeth on chicken embryos.
Even more recently, research (which is probably where Bear got the idea for Darwin’s Radio from) that supressed sequences could become active when the animals being tested (fruit flies?) were under stress.

11

Kyberneticist - Actually, you bring up what is known (for reasons I won’t go into) as the C-value paradox, which is that the size of the genome seems to have no relationship to the overall complexity of the organism. There are amphibians with many times more DNA than we have. Obviously, there would be some advantage to keeping the junk trimmed out - replicating all that stuff costs energy, after all - but it doesn’t seem to matter a whole lot. OTOH, one role that’s speculated for the junk is kind of like a crumple zone in a car. If you have the good stuff hiding the middle of a bunch of crap, then when random mutations happen, they’re more likely to hit the crap than the good stuff. You’ll see people report values of ~90%+ of the DNA as junk, with very little actually coding. However, that number is steadily decreasing, as we figure out what more and more of what we thought was junk actually does.

Inactive DNA isn’t junk. There is small set of housekeeping genes that are active in every cell, but other genes are expressed only in a small number of cells and/or for a short length of time.

12

Most of the “junk” DNA is repetitive elements. Much of it is retroviral in origin (in humans, Alu sequences, in mice, LINEs, etc.) Much of it is filled by simple dinucleotide repeats. It is thought to be mostly structural – interaction with the (undiscovered) nucleoskeleton, chromatin condensation, etc.

Sure there are genes there. Sure there are interesting things happening in introns and 3’ and 5’ UTRs. Sure there are neat things happening at centromeres and telomeres. But, overall, it is phenomenally uninteresting.

Another interesting thing – I had a professor who maintained the “energy efficiency” was never selected for in evolution. This makes sense – when something becomes more adapted to get a higher fitness, it can better utilize its environment so it can breed more. There are a lot of energy wasting steps in the body – proteins get made without being used, microtubules constantly cycle, your eyes use more energy when your eyelids are closed than when they are open. DNA replication seems to be just another energy wasting but not fitness reducing step. Even if we replicate 3,000 megabases for perhaps less than 100 megabases of total coding region.

13

Rickjay, i just posted this in the RNA thread…

DNA from the Beginning

There are three major sections to the page, but the one which you might be most interested in would be the Molecules of Genetics section.

14

I wouldn’t be so quick to write off the junk in DNA. Isn’t there evidence that not having enough repetition plays a role in how cells age?

15

That I know something about. The teleomeres are not junk DNA, they are extra bits on the end of DNA to indicate when to stop copying. Unfortunately, after repeated copies, this stop sequence grows shorter and shorter. Since senescence is a useful part of the cell lifecycle (cells need to die off as they may become malignant and damaged with age) this is not necessarily a bad thing.
Teleomerase apparently can reverse this process.
Found a link when doing a quick search for teleomerase.
http://www.drcranton.com/hrt/endocrinology_of_aging.htm
At any rate, not the same thing as junk dna.