Nucleotides Can Adopt Many Different Conformations

 
Individual nucleotides in solution can adopt many different conformations. For example, the deoxyribose sugars can bend and twist in many different ways. Two of the most stable conformations are shown on the left. They are the conformations found in some DNA structures.

The C-2′ endo conformation (top) allows the maximum separation between the oxygen atoms at the 5′ and 3′ positions. What this means is that any polynucleotide strand with sugars in this conformation will be extended. On the other hand, strands and helices with sugars in the C-3′ endo conformation will be much more compact with tighter helices.

If you look at all of the bonds that make up the sugar-phosphate backbone of a polynucleotide strand you will see that there are a lot of possible conformations. You can have free rotations around many of these bonds. Now, as it turns out, the structure of double-stranded DNA has a well-defined conformation where many of these bond angles are fixed but if you were handed two strands of DNA you would be hard pressed to bend them into the proper conformation of real DNA.

This is one of the reasons why it was so hard to predict the structure of DNA even though the chemical structure of the polynucleotides was known.

In addition to sugar puckers and bond rotations around the backbone, there are also many conformations of the base relative to the sugar. The two extreme conformations involve rotation around the β-N- glycosidic bond shown in green in the figures below. In the anti- conformation (left) the base is rotated so that it is as far from the sugar as possible. This is the most stable conformation and it's found in most DNAs. In the syn conformation (right) the base is rotated so that it's over the sugar leading to a much more compact structure.

When the structure of double-stranded DNA was being worked out, the conformations of the nucleotides were not known. It wasn't even obvious that the more stable anti conformation of free nucleotides would necessarily be the conformation in DNA. You can see that attempts to build a model of DNA without lots of additional information were doomed to failure. Several people tried and failed, including the greatest chemist of the day Linus Pauling.

©Laurence A. Moran 2007
[Figures are from Moran/Scrimgeour et al. Biochemistry 2nd ed. (1994) ©Neil Patterson Publishers/Prentice Hall.]

The Calvin Cycle: Regeneration

 
Nobody took me up on the offer to become an intelligent designer. The goal was to figure out a way of converting the five products of the Rubisco reaction into three new substrate molecules [The Calvin Cycle]. The five products are three carbon (3C) compounds and the three new substrate molecules are five carbon (5C) compounds. Here's how it's done ...

Two 3C molecules are joined to make one six carbon (6C) compound (fructose). Then two of the carbon atoms from fructose are transferred to another 3C molecule to make the first of the five carbon products (red, ribulose). This leaves a 4C molecule that is joined to another one of the 3C molecules to produce a seven carbon (7C) sugar called sedoheptulose. Two carbon are transferred from sedoheptulose to the last 3C molecule to produce a second 5C molecule. This leaves the third and last 5C molecule.

Of course there's a lot of fiddling in the pathway to get the molecules into the right form for these reactions. Here's the complete Calvin Cycle in all its glory. Click on it to see a bigger picture.



You can simplify the pathway a great deal by writing it like this ...

This shows you that, in spite of the complexity, the overall pathway takes three molecules of carbon dioxide and converts it to one molecule of glyceraldehyde 3-phosphate. That's the purpose of the Calvin Cycle, it fixes carbon.

The pathway is expensive. It uses two types of energy currency, ATP and NADPH, but these are produced in abundance by photosynthesis. It's a fair bet that this particular reaction is the ultimate source of 99% of the carbon atoms in your food.

There's a neat trick we can do with this reaction. We can use it to estimate the cost of synthesizing acetyl CoA—the substrate for the citric acid cycle and the product of the pyruvate dehydrogenase reaction. The pathway from glyceraldehyde 3- phosphate to acetyl CoA is coupled to the synthesis of two molecules of NADH and two molecules of ATP. If we subtract these from the cost of making glyceraldehyde 3-phosphate then the total cost of synthesizing acetyl CoA from CO₂ is 7 ATP + 4 NAD(P)H. This can be expressed as 17 ATP equivalents since each NADH is equivalent to 2.5 ATP.

Since the net gain from complete oxidation of acetyl CoA by the citric acid cycle is 10 ATP equivalents, the biosynthesis pathway is more expensive than the energy gained from catabolism. In this case, the "efficiency" of acetyl CoA oxidation is only about 60% (10/17 = 59%) but this value is misleading since it is actually the biosynthesis pathway (costing 17 ATP equivalents) that is complex and inefficient.

Tautomers of Adenine, Cytosine, Guanine, and Thymine

 
The four bases of DNA can exist in at least two tautomeric forms as shown below. Adenine and cytosine (which are cyclic amidines) can exist in either
amino or imino forms, and guanine, thymine, and uracil (which are cyclic amides) can exist in either lactam (keto) or lactim (enol) forms. The tautomeric forms of each base exist in equilibrium but the amino and lactam tautomers are more stable and therefore predominate under the conditions found inside most cells. The rings remain unsaturated and planar in each tautomer.


Fifty years ago it wasn't clear whether the amino or imino forms of the purines were stable under physiological conditions. (Or the lactam lactim forms.) As we will see, this uncertainty played a significant role in events leading up to the discovery of the structure of DNA.

We now know that all of the bases in the common nucleotides can participate in hydrogen bonding. The amino groups of adenine and cytosine are hydrogen donors, and the ring nitrogen atoms (N-1 in adenine and N-3 in cytosine) are hydrogen acceptors (see below). Cytosine also has a hydrogen acceptor group at C-2. Guanine, cytosine, and thymine can form three hydrogen bonds. In guanine, the group at C-6 is a hydrogen acceptor, and N-1 and the amino group at C-2 are hydrogen donors. In thymine, the groups at C-4 and C-2 are hydrogen acceptors, and N-3 is a hydrogen donor. (Only two of these sites, C-4 and N–3, are used to form base pairs in DNA.) The hydrogen-bonding patterns of bases have important consequences for the three-dimensional structure of nucleic acids.



©Laurence A. Moran and Pearson/Prentice Hall 2007

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.