DNA Is a Polynucleotide

 
DNA is composed of nucleotides strung together to make a long chain called a polynucleotide. There are four basic nucleotides in DNA. They are; deoxyadenylate (A), deoxyguanylate (G), deoxycytidylate (C), and deoxythymidylate (thymidylate) (T).


There are a few things you need to know about the nucleotides in order to properly understand the structure of double-stranded DNA.

First, a nucleotide is composed of a base (adenine, guanine, cytosine, thymine) attached to a sugar (deoxyribose) to form a nucleoside. The nucleoside has an attached phosphate group and that makes it a nucleotide. The name of the nucleoside containing the base adenine is deoxyadenosine and if the phosphate group is attached at the carbon numbered 5′ (five prime) then the formal name of the nucleotide is 2′deoxyadenosine 5′-monophosphate (dAMP).

Those little numbers are important. The phosphate group can also be attached to the 3′ carbon to make another kind of nucleotide called 2′-deoxyadenosine 3′-monophosphate.

Normally the carbon atoms of the sugar are numbered 1, 2, 3 etc. but in a nucleoside the numbering of the nitrogen and carbon atoms of the base takes precedence. Thus, the sugar carbon atoms are numbered 1′, 2′ 3′ etc as shown on the left.

If you want to follow the discussion about DNA you have to take a bit of time right now and get familiar with the numbering of the sugar carbon atoms. Note that there's no attached hydroxyl group on the 2′ carbon atom. That's why this is 2′-deoxyribose.

You can string together a bunch of nucleotides to make single-stranded DNA. Inside the cell it's the job of DNA polymerase to make polynucletides from nucleotides. The structure of a typical polynucleotide (right) shows that the individual units are attached through their phosphate groups. The phosphate group on one 5′ carbon atom is attached to the 3′ carbon atom of the nucleotide above it.

This gives rise to the characteristic sugar-phosphate backbone of DNA. This linkage is called a 3′-5&prime (three prime, five prime) phosphodiester linkage. The bases are not involved in the covalent linkages between nucleotides.

This single-stranded polynucleotide chain has a free 5′ end at the top and a free 3′ end at the bottom and that's going to be true for all single-stranded chains. We're often interested in describing the directionality of this chain because it's important in synthesis and in degradation by nucleases. For example, the chain is synthesized in the 5′→3′ (five prime to 3 prime) direction. Which means that incoming nucleotides are added to the bottom of the chain during elongation.

By convention, the directionality is determined by reading across an individual nucleotide residue. In practice this means reading across a single deoxyribose sugar. Thus, reading from the top to the bottom of the strand shown above you cross the sugar carbons in the order 5′, 4′ and 3′. The direction is 5′→3′ (five prime to three prime). If you're talking about the direction from bottom to top then you read across the sugar in the order 3′, 4′, and 5&prime and the direction is 3′→5′ (three prime to five prime).

Are You a Non-Conformist?

 

You Are 79% Non Conformist

You are a pretty serious non conformist. You live a life hardly anyone understands. And while some may call you a freak, you're happy with who you are.

Are You a Nonconformist?

[Hat Tip: Mike, of course. It's scary to note that I'm slightly more of a non-conformist than he is.]

The Oldest Organisms on Earth

 
Today's Botany Photo of the Day is Pinus longaeva, bristlecone pine. Trees of this species are generally considered to be "the longest-lived of all sexually reproducing, nonclonal species." Many of them are over 4000 years old including this one, from Wheeler Peak in Nevada.

It is located in the same area as the oldest known tree, the 4,862 year old tree formerly known as "Prometheus" before it was cut down [The Martyred One].

If the world was created in 4004 B.C. then the deluge can be reliably dated to about 2450 B.C., which means that Prometheus was living for 400 years before the flood and must have survived it. Isn't that amazing?

The Calvin Cycle

Are You an Intelligent Designer?

The Rubisco reaction results in fixation of carbon dioxide and the production of two molecules of glyceraldehyde 3-phosphate each of which contains three caron atoms [Fixing Carbon: the Rubisco Reaction]. The starting substrate is ribulose 1,5- bisphosphate, a 5-carbon sugar derivative [Monday's Molecule #34]. Here's a schematic diagram of the reaction showing the carbon skeletons with the newly incorporated carbon atom in blue.
In order for this to become a cycle you have to regenerate the original substrate—a five-carbon compound. And in order for it to be a biosynthesis pathway you have to have net synthesis of one of the products. It was the working out of this stoichiometry that got Melvin Calvin the Nobel Prize in 1961 [Nobel Laureate: Melvin Calvin]. Do you think you can figure out the strategy for regenerating the five-carbon substrate? Here are the rules.

1. You start with three cycles of the Rubisco reaction, using up three 5C molecules and producing six 3C molecules. One of the 3C molecules enters the normal metabolic pathways and the other five are used to regenerate three 5C molecules (5 x 3C = 3 x 5C).
2. You can fuse molecules to create larger ones (e.g., 3C + 3C = 6C).
3. You can cleave large molecules to create smaller ones (e.g. 6C = 3C + 3C) as long as there are no intermediates with only one carbon (1C) or two carbons (2C).
4. You can swap 2C units between molecules provided that no products are 1C or 2C (e.g, 7C + 3C = 5C + 5C is allowed).
5. You can swap 3C units between molecules provided that no products are 1C or 2C (e.g, 7C + 3C = 4C + 6C is allowed).

Here's an outline of the Calvin Cycle. Your task, should you choose to accept it, is to design the regeneration pathway beginning with five molecules of glyceraldehyde 3-phosphate (5 x 3C) and ending with three molecules of ribulose 1,5- bisphosphate (3 x 5C). You just need to account for the carbon shuffling reactions.

Monday's Molecule #35

 
This is a very common chemical found in most biochemistry labs. There's a very familiar form of this molecule and most of you will know it by the name of the salt. You need to supply the correct IUPAC name in order to win the prize.

There's an extremely obvious, but indirect, connection between this Monday's Molecule and Wednesday's Nobel Laureate(s).

The reward (free lunch) goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are no ineligible candidates for this Wednesday's reward since many recent winners haven't collected their prize. The prize is a free lunch at the Faculty Club.

Comments will be blocked for 24 hours. Comments are now open.

Casy Luskin Gets it Wrong (Again)

 
This is getting to be really annoying. What is it about the concepts of junk DNA and Darwinism that confuse the IDiots? It's not rocket science.

In today's posting on the Discovery Institute anti-science website, Casey Luskin leads off an anti-evolution posting with,

It’s beyond dispute that the false “junk”-DNA mindset was born, bred, and sustained long beyond its reasonable lifetime by the neo-Darwinian paradigm.

Let me try and make this simple for the IDiots.

1. Junk DNA is here to stay. It's a lie to claim that the concept has been abandoned by scientists. True, there are some stupid scientists who don't understand what's going on but they do not represent the consensus.


2. The concept of junk DNA is anti-Darwinian. There's no possible way that a true Darwinist could accept junk DNA. It is incredibly ignorant to claim that the idea of junk DNA was "born, bred, and sustained" by the neo-Darwinian paradigm. On the contrary, it has helped overturn that paradigm, replacing it with a more pluralistic approach to evolution.

It goes without saying that Intelligent Design Creationists think they have a better "paradigm" than real scientists. Luskin is amazed by recent discoveries that some heritable diseases are caused by mutations in regulatory sequences, which he, in his ignorance, thinks are equivalent to junk DNA.

How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?

Me, me, me (pumping his hand in the air). I know the answer ...

Poufs of Art

 
Leslie (Mrs. Sandwalk) has a friend, Carmi, who lives in a small town north of Toronto.^* She makes these wonderful things called poufs of art. Here's the description from her Etsy site [Carmi's Art].

Cushion is "pouf" in French.

These are tiny "poufs of art" that I create to celebrate my love of vintage imagery, fabric, beads, embellishments, sewing and quotes. Together, I use all these items to create one-of-a-kind keepsakes. They are handmade by me and no two will ever be alike.

I think these are perfect gifts to commemorate a special birthday, achievement or life event. No doubt, you will think of someone in particular when you read the quotes. They can be displayed on a picture stand, hung from a hook or light fixture or simply displayed in a box.

They are each approximately 2½ X 2 ½ inches wide. I will ship them in very pretty wrapping in a bubble wrap envelope.

Leslie has just ordered a bunch of them. Here's my favorite, I hope she bought it for me ...


Carmi also has a couple of blogs. Carmi's Art/Life World is about her life as an artist [see poufs to go] and My Napoleon Obsession is about Napoleon Bonaparte [Big Head's Crib].

^* Kleinburg, for those of you who know the area.

A Strange Molecule

 
Last Wednesday an image of strange base pair was published on Discovering Biology in a Digital World [Puzzle]. We were asked to figure out what was so strange about his base pair (see below). I got part of the answer but not the complete answer.



The answer has already been posted but I won't link to it just yet in order to give you a chance to figure it out. Please don't comment if you've already seen the answer.

Here's another view that promises to be a lot more helpful.

Gene Genie #11

 
The 11th edition of Gene Genie has been published at Med Journal Watch [Gene Genie #11].

Get on over there to find out where this photograph comes from.

Banned in China

 
Back on March 3, 2007 Sandwalk was not blocked on Chinese servers [Not Banned in China]. Today it is blocked. Test your own site at Great Firewall of China.

Personality Quiz

 
I wonder what the common personalities look like? Has anyone posted one of those?

Your Personality is Very Rare (INTP)

Your personality type is goofy, imaginative, relaxed, and brilliant. Only about 4% of all people have your personality, including 2% of all women and 6% of all men You are Introverted, Intuitive, Thinking, and Perceiving.

How Rare Is Your Personality?

[Hat Tip: GrrlScientist]

Friday the 13th in Port Dover

 
More than 100,000 people and 10,000 motorcycles are expected to descend on Port Dover, Ontario today [Port Dover hogs Friday 13th fame]. It happens every Friday the 13th but the crowd is much larger when the date falls in the summer months. Todays entertainment will include Steppenwolf and the Jeff Healey Band [PD13 News]. I'm told that beer is sometimes served at these events. Go figure.

Sandwalk Resists

 

Afer considerable debate, and much agonizing, I've decided not to join ScienceBorg ScienceBlogs at this time.

When I first started Sandwalk, I was anxious to be part of that group but now, seven months later, there doesn't seem to be a good reason to give up this site for one in the SEED consortium. There are very few advantages to joining ScienceBlogs. They do not come close to outweighing the one major disadvantage—you have to give up a great deal of independence in order to become part of the SEED site.

At one time it seemed as though ScienceBlogs was cornering the market on good science blogging so it was desirable to be associated with a group that had a reputation for quality blogging. That time has past. Now there are lots of good science blogs that have resisted assimilation so it's not so bad to remain on the outside.

[The image is from Borg trioM copyright Paramount Pictures and CBS Television. Its use is consistent with fair use laws in many jurisdictions throughout the world.]

Can You Recognize Propaganda When You See it?

 
Michael Yon is a (very) freelance reporter in Iraq. He has a blog where he solicits support for his mission in Iraq. The mission is to bring the "truth" to the American public. Why does he do it?

I do it because we need to see this clearly: what happens in and to Iraq is a defining moment for our nation, and the world. This enemy is smart and they are deadly, but they are also losing. Iraq can become a strong and free nation. But it will take the constant application of pressure over time to stem the flow of blood. If we back off too soon, they will rebound. If we cut our losses and run, they will follow us home. Peace can prevail here, if we can use our strength to maintain our progress.

It's sort of refreshing to see a "journalist" who lays his cards on the table. At least he doesn't pretend to be objective, like many other journalists.

But, having declared his intentions, it falls upon his readers to interpret his writings with a great deal of skepticism. That doesn't seem to have happened recently when his story about "baked Iraqi boys" attracted the attention of the right-wing warmongers in the USA and elsewhere. It spread like wildfire.

Here's what Michael Yon wrote on July 5, 2007 [Baqubah Update: 05 July 2007].

At a meeting today in Baqubah one Iraqi official I spoke with framed the al Qaeda infiltration and influence in the province. Although he spoke freely before a group of Iraqi and American commanders, including Staff Major General Abdul Kareem al Robai who commands Iraqi forces in Diyala, and LTC Fred Johnson, the deputy commander of 3-2 Stryker Brigade Combat Team, the Iraqi official asked that I withhold his identity from publication. His opinion, shared by others present, is that al Qaeda came to Baqubah and united many of the otherwise independent criminal gangs.

Speaking through an American interpreter, Lieutenant David Wallach who is a native Arabic speaker, the Iraqi official related how al Qaeda united these gangs who then became absorbed into “al Qaeda.” They recruited boys born during the years 1991, 92 and 93 who were each given weapons, including pistols, a bicycle and a phone (with phone cards paid) and a salary of $100 per month, all courtesy of al Qaeda. These boys were used for kidnapping, torturing and murdering people.

At first, he said, they would only target Shia, but over time the new al Qaeda directed attacks against Sunni, and then anyone who thought differently. The official reported that on a couple of occasions in Baqubah, al Qaeda invited to lunch families they wanted to convert to their way of thinking. In each instance, the family had a boy, he said, who was about 11 years old. As LT David Wallach interpreted the man’s words, I saw Wallach go blank and silent. He stopped interpreting for a moment. I asked Wallach, “What did he say?” Wallach said that at these luncheons, the families were sat down to eat. And then their boy was brought in with his mouth stuffed. The boy had been baked. Al Qaeda served the boy to his family.

We're used to thinking of propaganda as something that's just made up by a disinformation committee whose job it is to discredit and demonize the enemy. But that's not how effective propaganda works. The best kinds of stories are those that can be attributed to an apparently reliable but unnamed source such as an "Iraqi official." That way you can repeat it ad nauseum without invoking any of the normal skepticism that a journalist should use. This is how we learned about rape rooms [Rape Rooms: A Chronology] and weapons of mass destruction. In some cases the source is identified but later exposed a liar (e.g. the Kuwait incubator story [ The Lie]). It doesn't seem to matter if a story turns out to be untrue once it has served its purpose.

Remember that the point of propaganda is to make your enemy look as evil as possible. That's how you justify killing them and sacrificing the lives of your troops. Both sides do it. In the case of the insurgents, the propaganda consists of endless stories about the brutality of the occupying forces and this includes stories that are just as horrible as the one quoted above.

The key for rational people is to recognize that the "good guys" aren't all that "good" and the "bad" guys aren't all bad. War is hell.

[Hat Tip: Canadian Cynic]

Francis Crick Isn't Always Right

 
A few days ago I posted pictures of the telegram notifying Francis Crick that he had won the Nobel Prize [Wellcome Trust Images]. The photos were from the Wellcome Images website.

Since then, a number of bloggers have commented on a brief note that Crick wrote on the back of a letter in 1989. I deliberately skipped that image last week because I thought it was embarrassing. I still do, in spite of the fact that the famous PZ Myers has declared it a nice quote [That's a nice quote].

What's so nice about it? It looks pretty stupid to me. What is there about DNA that gives support to evolution by natural selection—or even just "evolution" for that matter? Are my fellow bloggers just mesmorized by the juxtaposition of Francis Crick's name with the words "evolution" and "natural selection"?

Remember that 1989 corresponds to Crick's dotty period in La Jolla.

[Some people will argue that the sequences of various DNA's from different species lend support to evolution. Of course that's true but it's not what Crick wrote and I doubt very much it's what he meant. He was probably thinking about the beauty of the DNA molecule and it's appearance of "design" by natural selection.]