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Basic text/notes on DNA structure (for non-biologists)


I am a mathematics grad student researching knot theory, and I've recently discovered that there is a connection between knot theory and DNA structure (if I understand correctly, when DNA strands repackage, they do it in a way similar to what is known as Skein relations in knot theory, therefore tools from knot theory can be applied to DNA research).

The problem is that I have almost no background in biology, therefore it is difficult for me to understand how exactly DNA repackages and what happens on the molecular level.

Could anyone suggest some basic (and preferably not too long) text which gives an introduction to the structure of DNA? I have some basic background in organic chemistry, and I am not really looking to understand the topic thoroughly, just to visualize what's going on so I could see the analogy to the mathematical theory.

Thanks in advance!


this is a special topic, I'm assuming you have looked over the basic Watson and Crick stuff.

Maybe closer to your interests DNA does tangle and needs constant maintenance of the amount of winding to keep it properly ordered.

I would look at topoisomerases and DNA origami to start with.

Topoisomerases are a class of enzymes that help DNA pack up and wind up into the compact forms of the chromosome when its wound into solenoids in chromatin and unwind into the looser forms when it is loose.

DNA origami is a field of study which uses DNA as a self assembling template for making three dimensional structures.

Maybe this helps? let me know if we can narrow the specifics of your interests.


We could help you more if you explained how DNA is similar to Skein relations or, conversely, explain what Skein relations are so we can understand how they're similar to DNA.

As always, the best and most accessible resource will be a university text book. I would recommend Alberts, as I recall, it explains this topic quite well.

If you're after something a bit more visual, I found some nice ones (click on an image to be taken to its source):


Fundamentals of Biology

An illustration showing the double helix structure of DNA (Image courtesy of the National Human Genome Research Institute).

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The Central Dogma: DNA Encodes RNA RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma (Figure 9.14), which states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

Figure 9.14 The central dogma states that DNA encodes RNA, which in turn encodes protein.

The copying of DNA to mRNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every complementary nucleotide read in the DNA strand. The translation to protein is more complex because groups of three mRNA nucleotides correspond to one amino acid of the protein sequence. However, as we shall see in the next module, the translation to protein is still systematic, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.


Basic text/notes on DNA structure (for non-biologists) - Biology

This page, looking at the structure of DNA, is the first in a sequence of pages leading on to how DNA replicates (makes copies of) itself, and then to how information stored in DNA is used to make protein molecules. This material is aimed at 16 - 18 year old chemistry students. If you are interested in this from a biological or biochemical point of view, you may find these pages a useful introduction before you get more information somewhere else.

Note: If you are doing biology or biochemistry and are interested in more detail you can download a very useful pdf file about DNA from the Biochemical Society.

Chemistry students at UK A level (or its various equivalents) should not waste time on this. The booklet is written for A level biology students, and goes into far more detail than you will need for chemistry purposes.

A quick look at the whole structure of DNA

These days, most people know about DNA as a complex molecule which carries the genetic code. Most will also have heard of the famous double helix.

I'm going to start with a diagram of the whole structure, and then take it apart to see how it all fits together. The diagram shows a tiny bit of a DNA double helix.

Note: This diagram comes from the US National Library of Medicine. You can see it in its original context by following this link if you are interested.

Normally I prefer to draw my own diagrams, but my drawing software isn't sophisticated enough to produce convincing twisted "ribbons".

Exploring a DNA chain

The sugars in the backbone

The backbone of DNA is based on a repeated pattern of a sugar group and a phosphate group. The full name of DNA, deoxyribonucleic acid, gives you the name of the sugar present - deoxyribose.

Deoxyribose is a modified form of another sugar called ribose. I'm going to give you the structure of that first, because you will need it later anyway. Ribose is the sugar in the backbone of RNA, ribonucleic acid.

This diagram misses out the carbon atoms in the ring for clarity. Each of the four corners where there isn't an atom shown has a carbon atom.

The heavier lines are coming out of the screen or paper towards you. In other words, you are looking at the molecule from a bit above the plane of the ring.

So that's ribose. Deoxyribose, as the name might suggest, is ribose which has lost an oxygen atom - "de-oxy".

The only other thing you need to know about deoxyribose (or ribose, for that matter) is how the carbon atoms in the ring are numbered.

The carbon atom to the right of the oxygen as we have drawn the ring is given the number 1, and then you work around to the carbon on the CH2OH side group which is number 5.

You will notice that each of the numbers has a small dash by it - 3' or 5', for example. If you just had ribose or deoxyribose on its own, that wouldn't be necessary, but in DNA and RNA these sugars are attached to other ring compounds. The carbons in the sugars are given the little dashes so that they can be distinguished from any numbers given to atoms in the other rings.

You read 3' or 5' as "3-prime" or "5-prime".

Attaching a phosphate group

The other repeating part of the DNA backbone is a phosphate group. A phosphate group is attached to the sugar molecule in place of the -OH group on the 5' carbon.

Note: You may find other versions of this with varying degrees of ionisation. You may find a hydrogen attached instead of having a negative charge on one of the oxygens, or the hydrogen removed from the top -OH group to leave a negative ion there as well.

I don't want to get bogged down in this. The version I am using is fine for chemistry purposes, and will make it easy to see how the DNA backbone is put together. We are soon going to simplify all this down anyway!

Attaching a base and making a nucleotide

The final piece that we need to add to this structure before we can build a DNA strand is one of four complicated organic bases. In DNA, these bases are cytosine (C), thymine (T), adenine (A) and guanine (G).

Note: These are called "bases" because that is exactly what they are in chemical terms. They have lone pairs on nitrogens and so can act as electron pair donors (or accept hydrogen ions, if you prefer the simpler definition). This isn't particularly relevant to their function in DNA, but they are always referred to as bases anyway.

These bases attach in place of the -OH group on the 1' carbon atom in the sugar ring.

What we have produced is known as a nucleotide.

We now need a quick look at the four bases. If you need these in a chemistry exam at this level, the structures will almost certainly be given to you.

Here are their structures:

The nitrogen and hydrogen atoms shown in blue on each molecule show where these molecules join on to the deoxyribose. In each case, the hydrogen is lost together with the -OH group on the 1' carbon atom of the sugar. This is a condensation reaction - two molecules joining together with the loss of a small one (not necessarily water).

For example, here is what the nucleotide containing cytosine would look like:

Note: I've flipped the cytosine horizontally (compared with the structure of cytosine I've given previously) so that it fits better into the diagram. You must be prepared to rotate or flip these structures if necessary.

Joining the nucleotides into a DNA strand

A DNA strand is simply a string of nucleotides joined together. I can show how this happens perfectly well by going back to a simpler diagram and not worrying about the structure of the bases.

The phosphate group on one nucleotide links to the 3' carbon atom on the sugar of another one. In the process, a molecule of water is lost - another condensation reaction.

. . . and you can continue to add more nucleotides in the same way to build up the DNA chain.

Now we can simplify all this down to the bare essentials!

Note: You will notice that I have drawn the P-O bonds attaching to the two sugar molecules opposite each other in the diagram above. You will also find diagrams where they are drawn at right angles to each other. Which is right?

Both are right and, equally, both are misleading! The shape of the bonds around the phosphorus atom is tetrahedral, and all of the bonds are at approximately 109° to each other. Whichever way you choose to draw this in 2-dimensions on paper, it still represents the same molecule in reality.

To take a simpler example, if you draw a structural formula for CH2Cl2 using simple bond notation, you could equally well draw the chlorine atoms at right angles to each other or opposite each other. The molecule would still be exactly the same. This is one of the things you had to learn when you first started drawing structures for organic molecules. If you still aren't sure about this, look again at the page about drawing organic molecules.

Building a DNA chain concentrating on the essentials

What matters in DNA is the sequence the four bases take up in the chain. We aren't particularly interested in the backbone, so we can simplify that down. For the moment, we can simplify the precise structures of the bases as well.

We can build the chain based on this fairly obvious simplification:

There is only one possible point of confusion here - and that relates to how the phosphate group, P, is attached to the sugar ring. Notice that it is joined via two lines with an angle between them.

By convention, if you draw lines like this, there is a carbon atom where these two lines join. That is the carbon atom in the CH2 group if you refer back to a previous diagram. If you had tried to attach the phosphate to the ring by a single straight line, that CH2 group would have got lost!

Joining up lots of these gives you a part of a DNA chain. The diagram below is a bit from the middle of a chain. Notice that the individual bases have been identified by the first letters of the base names. (A = adenine, etc). Notice also that there are two different sizes of base. Adenine and guanine are bigger because they both have two rings. Cytosine and thymine only have one ring each.

If the top of this segment was the end of the chain, then the phosphate group would have an -OH group attached to the spare bond rather than another sugar ring.

Similarly, if the bottom of this segment of chain was the end, then the spare bond at the bottom would also be to an -OH group on the deoxyribose ring.

Joining the two DNA chains together

The importance of "base pairs"

Have another look at the diagram we started from:

If you look at this carefully, you will see that an adenine on one chain is always paired with a thymine on the second chain. And a guanine on one chain is always paired with a cytosine on the other one.

So how exactly does this work?

The first thing to notice is that a smaller base is always paired with a bigger one. The effect of this is to keep the two chains at a fixed distance from each other all the way along.

But, more than this, the pairing has to be exactly . . .

adenine (A) pairs with thymine (T)

guanine (G) pairs with cytosine (C).

That is because these particular pairs fit exactly to form very effective hydrogen bonds with each other. It is these hydrogen bonds which hold the two chains together.

The base pairs fit together as follows.

If you try any other combination of base pairs, they won't fit!

Note: If the structures confuse you at first sight, it is because the molecules have had to be turned around from the way they have been drawn above in order to make them fit. Be sure that you understand how to do that. As long as you were given the structures of the bases, you could be asked to show how they hydrogen bond - and that would include showing the lone pairs and polarity of the important atoms.

If hydrogen bonding worries you, follow this link for detailed explanations. Use the BACK button on your browser to return here later.

A final structure for DNA showing the important bits

Note: You might have noticed that I have shorten the chains by one base pair compared with the previous diagram. There isn't any sophisticated reason for this. The diagram just got a little bit too big for my normal page width, and it was a lot easier to just chop a bit off the bottom than rework all my previous diagrams to make them slightly smaller! This diagram only represents a tiny bit of a DNA molecule anyway.

Notice that the two chains run in opposite directions, and the right-hand chain is essentially upside-down. You will also notice that I have labelled the ends of these bits of chain with 3' and 5'.

If you followed the left-hand chain to its very end at the top, you would have a phosphate group attached to the 5' carbon in the deoxyribose ring. If you followed it all the way to the other end, you would have an -OH group attached to the 3' carbon.

In the second chain, the top end has a 3' carbon, and the bottom end a 5'.

This 5' and 3' notation becomes important when we start talking about the genetic code and genes. The genetic code in genes is always written in the 5' to 3' direction along a chain.

It is also important when we take a very simplified look at how DNA makes copies of itself on the next page . . .

Questions to test your understanding

If this is the first set of questions you have done, please read the introductory page before you start. You will need to use the BACK BUTTON on your browser to come back here afterwards.


9.1 The Structure of DNA

In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure of DNA. Other scientists, such as Linus Pauling and Maurice Wilkins, were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. X-ray crystallography is a method for investigating molecular structure by observing the patterns formed by X-rays shot through a crystal of the substance. The patterns give important information about the structure of the molecule of interest. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray crystallography to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule using Franklin's data (Figure 9.2). Watson and Crick also had key pieces of information available from other researchers such as Chargaff’s rules. Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types were always present in equal amounts and the remaining two types were also always present in equal amounts. This meant they were always paired in some way. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine for their work in determining the structure of DNA.

Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group , and a nitrogenous base (Figure 9.3). There are four types of nitrogenous bases in DNA. Adenine (A) and guanine (G) are double-ringed purines, and cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines. The nucleotide is named according to the nitrogenous base it contains.

The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, and so on, forming a long polymer of nucleotide monomers. The sugar–phosphate groups line up in a “backbone” for each single strand of DNA, and the nucleotide bases stick out from this backbone. The carbon atoms of the five-carbon sugar are numbered clockwise from the oxygen as 1', 2', 3', 4', and 5' (1' is read as “one prime”). The phosphate group is attached to the 5' carbon of one nucleotide and the 3' carbon of the next nucleotide. In its natural state, each DNA molecule is actually composed of two single strands held together along their length with hydrogen bonds between the bases.

Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix . Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C. In other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. This is the basis for Chargaff’s rule because of their complementarity, there is as much adenine as thymine in a DNA molecule and as much guanine as cytosine. Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds. The two strands are anti-parallel in nature that is, one strand will have the 3' carbon of the sugar in the “upward” position, whereas the other strand will have the 5' carbon in the upward position. The diameter of the DNA double helix is uniform throughout because a purine (two rings) always pairs with a pyrimidine (one ring) and their combined lengths are always equal. (Figure 9.4).

The Structure of RNA

There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. In the case of RNA, the five-carbon sugar is ribose, not deoxyribose. Ribose has a hydroxyl group at the 2' carbon, unlike deoxyribose, which has only a hydrogen atom (Figure 9.5).

RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine. However, they do not contain thymine, which is instead replaced by uracil, symbolized by a “U.” RNA exists as a single-stranded molecule rather than a double-stranded helix. Molecular biologists have named several kinds of RNA on the basis of their function. These include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)—molecules that are involved in the production of proteins from the DNA code.

How DNA Is Arranged in the Cell

DNA is a working molecule it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules, such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure (the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features (Figure 9.6). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, Escherichia coli, is 4.6 million base pairs, which would extend a distance of about 1.6 mm if stretched out. So how does this fit inside a small bacterial cell? The DNA is twisted beyond the double helix in what is known as supercoiling. Some proteins are known to be involved in the supercoiling other proteins and enzymes help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure 9.7). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The DNA is wrapped tightly around the histone core. This nucleosome is linked to the next one by a short strand of DNA that is free of histones. This is also known as the “beads on a string” structure the nucleosomes are the “beads” and the short lengths of DNA between them are the “string.” The nucleosomes, with their DNA coiled around them, stack compactly onto each other to form a 30-nm–wide fiber. This fiber is further coiled into a thicker and more compact structure. At the metaphase stage of mitosis, when the chromosomes are lined up in the center of the cell, the chromosomes are at their most compacted. They are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, the phase of the cell cycle between mitoses at which the chromosomes are decondensed, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. There is a tightly packaged region that stains darkly, and a less dense region. The darkly staining regions usually contain genes that are not active, and are found in the regions of the centromere and telomeres. The lightly staining regions usually contain genes that are active, with DNA packaged around nucleosomes but not further compacted.


Chapter 05 - The Structure and Function of Macromolecules

  • Carbohydrates include sugars and their polymers.
  • The simplest carbohydrates are monosaccharides, or simple sugars.
  • Disaccharides, or double sugars, consist of two monosaccharides joined by a condensation reaction.
  • Polysaccharides are polymers of many monosaccharides.

Sugars, the smallest carbohydrates, serve as fuel and a source of carbon.

  • Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O.
    • For example, glucose has the formula C6H12O6.
    • Depending on the location of the carbonyl group, the sugar is an aldose or a ketose.
    • Most names for sugars end in -ose.
    • Glucose, an aldose, and fructose, a ketose, are structural isomers.
    • Glucose and other six-carbon sugars are hexoses.
    • Five-carbon backbones are pentoses three-carbon sugars are trioses.
    • For example, glucose and galactose, both six-carbon aldoses, differ in the spatial arrangement of their parts around asymmetrical carbons.
    • Maltose, malt sugar, is formed by joining two glucose molecules.
    • Sucrose, table sugar, is formed by joining glucose and fructose. Sucrose is the major transport form of sugars in plants.
    • Lactose, milk sugar, is formed by joining glucose and galactose.

    Polysaccharides, the polymers of sugars, have storage and structural roles.

    • Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages.
    • Some polysaccharides serve for storage and are hydrolyzed as sugars are needed.
    • Other polysaccharides serve as building materials for the cell or the whole organism.
    • Starch is a storage polysaccharide composed entirely of glucose monomers.
      • Most of these monomers are joined by 1–4 linkages (number 1 carbon to number 4 carbon) between the glucose molecules.
      • The simplest form of starch, amylose, is unbranched and forms a helix.
      • Branched forms such as amylopectin are more complex.
      • Animals that feed on plants, especially parts rich in starch, have digestive enzymes that can hydrolyze starch to glucose.
      • Glycogen is highly branched like amylopectin.
      • Humans and other vertebrates store a day’s supply of glycogen in the liver and muscles.
      • Plants produce almost one hundred billion tons of cellulose per year. It is the most abundant organic compound on Earth.
      • The difference is based on the fact that there are actually two slightly different ring structures for glucose.
      • These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the plane of the ring.
      • While polymers built with alpha glucose form helical structures, polymers built with beta glucose form straight structures.
      • The straight structures built with beta glucose allow H atoms on one strand to form hydrogen bonds with OH groups on other strands.
      • In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils, which form strong building materials for plants (and for humans, as lumber).
      • Cellulose in human food passes through the digestive tract and is eliminated in feces as “insoluble fiber.”
      • As it travels through the digestive tract, cellulose abrades the intestinal walls and stimulates the secretion of mucus, aiding in the passage of food.
      • Some fungi can also digest cellulose.
      • Chitin is similar to cellulose, except that it contains a nitrogen-containing appendage on each glucose monomer.
      • Pure chitin is leathery but can be hardened by the addition of calcium carbonate.

      Concept 5.3 Lipids are a diverse group of hydrophobic molecules

      • Unlike other macromolecules, lipids do not form polymers.
      • The unifying feature of lipids is that they all have little or no affinity for water.
      • This is because they consist mostly of hydrocarbons, which form nonpolar covalent bonds.
      • Lipids are highly diverse in form and function.

      Fats store large amounts of energy.

      • Although fats are not strictly polymers, they are large molecules assembled from smaller molecules by dehydration reactions.
      • A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids.
        • Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon.
        • A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long.
        • The many nonpolar C—H bonds in the long hydrocarbon skeleton make fats hydrophobic.
        • Fats separate from water because the water molecules hydrogen bond to one another and exclude the fats.
        • If the fatty acid has no carbon-carbon double bonds, then the molecule is a saturated fatty acid, saturated with hydrogens at every possible position.
        • If the fatty acid has one or more carbon-carbon double bonds formed by the removal of hydrogen atoms from the carbon skeleton, then the molecule is an unsaturated fatty acid.
        • Most animal fats are saturated.
        • Saturated fats are solid at room temperature.
        • Plant and fish fats are liquid at room temperature and are known as oils.
        • The kinks caused by the double bonds prevent the molecules from packing tightly enough to solidify at room temperature.
        • The phrase “hydrogenated vegetable oils” on food labels means that unsaturated fats have been synthetically converted to saturated fats by the addition of hydrogen.
          • Peanut butter and margarine are hydrogenated to prevent lipids from separating out as oil.
          • A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch.
          • Because plants are immobile, they can function with bulky energy storage in the form of starch. Plants use oils when dispersal and compact storage is important, as in seeds.
          • Animals must carry their energy stores with them and benefit from having a more compact fuel reservoir of fat.
          • Humans and other mammals store fats as long-term energy reserves in adipose cells that swell and shrink as fat is deposited or withdrawn from storage.
          • This subcutaneous layer is especially thick in whales, seals, and most other marine mammals.

          Phospholipids are major components of cell membranes.

          • Phospholipids have two fatty acids attached to glycerol and a phosphate group at the third position.
            • The phosphate group carries a negative charge.
            • Additional smaller groups may be attached to the phosphate group to form a variety of phospholipids.
            • The fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head.
            • This type of structure is called a micelle.
            • Again, the hydrophilic heads are on the outside of the bilayer, in contact with the aqueous solution, and the hydrophobic tails point toward the interior of the bilayer.
              • The phospholipid bilayer forms a barrier between the cell and the external environment.

              Steroids include cholesterol and certain hormones.

              • Steroids are lipids with a carbon skeleton consisting of four fused rings.
              • Different steroids are created by varying functional groups attached to the rings.
              • Cholesterol, an important steroid, is a component in animal cell membranes.
              • Cholesterol is also the precursor from which all other steroids are synthesized.
                • Many of these other steroids are hormones, including the vertebrate sex hormones.

                Concept 5.4 Proteins have many structures, resulting in a wide range of functions

                • Proteins account for more than 50% of the dry mass of most cells. They are instrumental in almost everything that an organism does.
                  • Protein functions include structural support, storage, transport, cellular signaling, movement, and defense against foreign substances.
                  • Most important, protein enzymes function as catalysts in cells, regulating metabolism by selectively accelerating chemical reactions without being consumed.
                  • Each type of protein has a complex three-dimensional shape or conformation.

                  Amino acids are the monomers from which proteins are constructed.

                  • Amino acids are organic molecules with both carboxyl and amino groups.
                  • At the center of an amino acid is an asymmetric carbon atom called the alpha carbon.
                  • Four components are attached to the alpha carbon: a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain).
                    • Different R groups characterize the 20 different amino acids.
                    • One group of amino acids has hydrophobic R groups.
                    • Another group of amino acids has polar R groups that are hydrophilic.
                    • A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.
                      • Some acidic R groups are negative in charge due to the presence of a carboxyl group.
                      • Basic R groups have amino groups that are positive in charge.
                      • Note that all amino acids have carboxyl and amino groups. The terms acidic and basic in this context refer only to these groups in the R groups.
                      • The resulting covalent bond is called a peptide bond.
                      • At one end is an amino acid with a free amino group (the N-terminus) and at the other is an amino acid with a free carboxyl group (the C-terminus).

                      The amino acid sequence of a polypeptide can be determined.

                      • Frederick Sanger and his colleagues at Cambridge University determined the amino acid sequence of insulin in the 1950s.
                        • Sanger used protein-digesting enzymes and other catalysts to hydrolyze the insulin at specific places.
                        • The fragments were then separated by a technique called chromatography.
                        • Hydrolysis by another agent broke the polypeptide at different sites, yielding a second group of fragments.
                        • Sanger used chemical methods to determine the sequence of amino acids in the small fragments.
                        • He then searched for overlapping regions among the pieces obtained by hydrolyzing with the different agents.
                        • After years of effort, Sanger was able to reconstruct the complete primary structure of insulin.
                        • Most of the steps in sequencing a polypeptide have since been automated.

                        Protein conformation determines protein function.

                        • A functional protein consists of one or more polypeptides that have been twisted, folded, and coiled into a unique shape.
                        • It is the order of amino acids that determines what the three-dimensional conformation of the protein will be.
                        • A protein’s specific conformation determines its function.
                        • When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume the functional conformation for that protein.
                        • The folding is reinforced by a variety of bonds between parts of the chain, which in turn depend on the sequence of amino acids.
                          • Many proteins are globular, while others are fibrous in shape.
                          • For example, an antibody binds to a particular foreign substance.
                          • An enzyme recognizes and binds to a specific substrate, facilitating a chemical reaction.
                          • Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain.
                            • Morphine, heroin, and other opiate drugs mimic endorphins because they are similar in shape and can bind to the brain’s endorphin receptors.
                            • Lysozyme, an enzyme that attacks bacteria, consists of 129 amino acids.
                            • The precise primary structure of a protein is determined by inherited genetic information.
                            • The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder.
                            • The abnormal hemoglobins crystallize, deforming the red blood cells into a sickle shape and clogging capillaries.
                            • The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond.
                            • Each hydrogen bond is weak, but the sum of many hydrogen bonds stabilizes the structure of part of the protein.
                            • The presence of so many hydrogen bonds makes each silk fiber stronger than a steel strand of the same weight.
                            • These interactions include hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups.
                            • While these three interactions are relatively weak, strong covalent bonds called disulfide bridges that form between the sulfhydryl groups (SH) of two cysteine monomers act to rivet parts of the protein together.
                            • Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope.
                              • This provides structural strength for collagen’s role in connective tissue.
                              • It consists of four polypeptide subunits: two alpha and two beta chains.
                              • Both types of subunits consist primarily of alpha-helical secondary structure.
                              • The folding occurs as the protein is being synthesized within the cell.
                              • Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein.
                              • These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s shape.
                              • This explains why extremely high fevers can be fatal. Proteins in the blood become denatured by the high body temperatures.
                              • Nevertheless, it is still difficult to predict the conformation of a protein from its primary structure alone.
                              • Chaperonins do not specify the final structure of a polypeptide but rather work to segregate and protect the polypeptide while it folds spontaneously.
                              • This method does not require protein crystallization.

                              Concept 5.5 Nucleic acids store and transmit hereditary information

                              • The amino acid sequence of a polypeptide is programmed by a unit of inheritance known as a gene.
                              • A gene consists of DNA, a polymer known as a nucleic acid.

                              There are two types of nucleic acids: RNA and DNA.

                              • There are two types of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).
                                • These are the molecules that allow living organisms to reproduce their complex components from generation to generation.
                                • Each DNA molecule is very long, consisting of hundreds to thousands of genes.
                                • Before a cell reproduces itself by dividing, its DNA is copied. The copies are then passed to the next generation of cells.
                                • Proteins are responsible for implementing the instructions contained in DNA.

                                A nucleic acid strand is a polymer of nucleotides.

                                • Nucleic acids are polymers made of nucleotide monomers.
                                • Each nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and a phosphate group.
                                • The nitrogen bases are rings of carbon and nitrogen that come in two types: purines and pyrimidines.
                                  • Pyrimidines have a single six-membered ring.
                                    • There are three different pyrimidines: cytosine (C), thymine (T), and uracil (U).
                                    • The two purines are adenine (A) and guanine (G).
                                    • The only difference between the sugars is the lack of an oxygen atom on carbon two in deoxyribose.
                                    • Because the atoms in both the nitrogenous base and the sugar are numbered, the sugar atoms have a prime after the number to distinguish them.
                                    • Thus, the second carbon in the sugar ring is the 2’ (2 prime) carbon and the carbon that sticks up from the ring is the 5’ carbon.
                                    • The combination of a pentose and a nitrogenous base is a nucleoside.
                                    • This creates a repeating backbone of sugar-phosphate units, with appendages consisting of the nitrogenous bases.
                                    • One end has a phosphate attached to a 5’ carbon this is the 5’ end.
                                    • The other end has a hydroxyl group on a 3’ carbon this is the 3’ end.
                                    • Because genes are normally hundreds to thousands of nucleotides long, the number of possible base combinations is virtually limitless.

                                    Inheritance is based on replication of the DNA double helix.

                                    • An RNA molecule is a single polynucleotide chain.
                                    • DNA molecules have two polynucleotide strands that spiral around an imaginary axis to form a double helix.
                                      • The double helix was first proposed as the structure of DNA in 1953 by James Watson and Francis Crick.
                                      • The two backbones run in opposite 5’ -> 3’ directions from each other, an arrangement referred to as antiparallel.
                                      • Adenine (A) always pairs with thymine (T) and guanine (G) with cytosine (C).
                                      • The two strands are complementary.
                                      • This results in two identical copies of the original double-stranded DNA molecule, which are then distributed to the daughter cells.

                                      We can use DNA and proteins as tape measures of evolution.

                                      • Genes (DNA) and their products (proteins) document the hereditary background of an organism.
                                      • Because DNA molecules are passed from parents to offspring, siblings have greater similarity in their DNA and protein than do unrelated individuals of the same species.
                                      • This argument can be extended to develop a “molecular genealogy” to relationships between species.
                                      • Two species that appear to be closely related based on fossil and molecular evidence should also be more similar in DNA and protein sequences than are more distantly related species.
                                        • In fact, that is so.
                                          • For example, if we compare the sequence of 146 amino acids in a hemoglobin polypeptide, we find that humans and gorillas differ in just 1 amino acid.
                                            • Humans and gibbons differ in 2 amino acids.
                                            • Humans and rhesus monkeys differ in 8 amino acids.
                                            • Humans and mice differ in 27 amino acids.
                                            • Humans and frogs differ in 67 amino acids.

                                            Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 5-1


                                            Basic text/notes on DNA structure (for non-biologists) - Biology

                                            reprinted with permission from Nature magazine

                                            A Structure for Deoxyribose Nucleic Acid
                                            J. D. Watson and F. H. C. Crick (1)

                                            April 25, 1953 (2), Nature (3) , 171, 737-738

                                            We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.

                                            A structure for nucleic acid has already been proposed by Pauling (4) and Corey 1 . They kindly made their manuscript available to us in advance of publication. Their model consists of three intertwined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory for two reasons:

                                            (1) We believe that the material which gives the X-ray diagrams is the salt, not the free acid. Without the acidic hydrogen atoms it is not clear what forces would hold the structure together, especially as the negatively charged phosphates near the axis will repel each other.

                                            (2) Some of the van der Waals distances appear to be too small.

                                            Another three-chain structure has also been suggested by Fraser (in the press). In his model the phosphates are on the outside and the bases on the inside, linked together by hydrogen bonds. This structure as described is rather ill-defined, and for this reason we shall not comment on it.

                                            We wish to put forward a radically different structure for the salt of deoxyribose nucleic acid (5) . This structure has two helical chains each coiled round the same axis (see diagram). We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining beta-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their bases) are related by a dyad perpendicular to the fibre axis. Both chains follow right-handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite directions (6) . Each chain loosely resembles Furberg's 2 model No. 1 (7) that is, the bases are on the inside of the helix and the phosphates on the outside. The configuration of the sugar and the atoms near it is close to Furberg's "standard configuration," the sugar being roughly perpendicular to the attached base. There is a residue on each every 3.4 A. in the z-direction. We have assumed an angle of 36° between adjacent residues in the same chain, so that the structure repeats after 10 residues on each chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10 A. As the phosphates are on the outside, cations have easy access to them.

                                            Figure 1
                                            This figure is purely diagrammatic (8) . The two ribbons symbolize the two phophate-sugar chains, and the horizonal rods the pairs of bases holding the chains together. The vertical line marks the fibre axis.

                                            The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more compact.

                                            The novel feature of the structure is the manner in which the two chains are held together by the purine and pyrimidine bases. The planes of the bases are perpendicular to the fibre axis. They are joined together in pairs, a single base from one chain being hydroden-bonded to a single base from the other chain, so that the two lie side by side with identical z-coordinates. One of the pair must be a purine and the other a pyrimidine for bonding to occur. The hydrogen bonds are made as follows: purine position 1 to pyrimidine position 1 purine position 6 to pyrimidine position 6.

                                            If it is assumed that the bases only occur in the structure in the most plausible tautomeric forms (that is, with the keto rather than the enol configurations) it is found that only specific pairs of bases can bond together. These pairs are: adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine) (9) .

                                            In other words, if an adenine forms one member of a pair, on either chain, then on these assumptions the other member must be thymine similarly for guanine and cytosine. The sequence of bases on a single chain does not appear to be restricted in any way. However, if only specific pairs of bases can be formed, it follows that if the sequence of bases on one chain is given, then the sequence on the other chain is automatically determined.

                                            It has been found experimentally 3,4 that the ratio of the amounts of adenine to thymine, and the ratio of guanine to cytosine, are always very close to unity for deoxyribose nucleic acid.

                                            It is probably impossible to build this structure with a ribose sugar in place of the deoxyribose, as the extra oxygen atom would make too close a van der Waals contact.

                                            The previously published X-ray data 5,6 on deoxyribose nucleic acid are insufficient for a rigorous test of our structure. So far as we can tell, it is roughly compatible with the experimental data, but it must be regarded as unproved until it has been checked against more exact results. Some of these are given in the following communications (10) . We were not aware of the details of the results presented there when we devised our structure (11) , which rests mainly though not entirely on published experimental data and stereochemical arguments.

                                            It has not escaped our notice (12) that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.

                                            Full details of the structure, including the conditions assumed in building it, together with a set of coordinates for the atoms, will be published elsewhere (13) .

                                            We are much indebted to Dr. Jerry Donohue for constant advice and criticism, especially on interatomic distances. We have also been stimulated by a knowledge of the general nature of the unpublished experimental results and ideas of Dr. M. H. F. Wilkins, Dr. R. E. Franklin and their co-workers at King’s College, London. One of us (J. D. W.) has been aided by a fellowship from the National Foundation for Infantile Paralysis.


                                            1 Pauling, L., and Corey, R. B., Nature, 171, 346 (1953) Proc. U.S. Nat. Acad. Sci., 39, 84 (1953).
                                            2 Furberg, S., Acta Chem. Scand., 6, 634 (1952).
                                            3 Chargaff, E., for references see Zamenhof, S., Brawerman, G., and Chargaff, E., Biochim. et Biophys. Acta, 9, 402 (1952).
                                            4 Wyatt, G. R., J. Gen. Physiol., 36, 201 (1952).
                                            5 Astbury, W. T., Symp. Soc. Exp. Biol. 1, Nucleic Acid, 66 (Camb. Univ. Press, 1947).
                                            6 Wilkins, M. H. F., and Randall, J. T., Biochim. et Biophys. Acta, 10, 192 (1953).

                                            Annotations
                                            (1)
                                            It’s no surprise that James D. Watson and Francis H. C. Crick spoke of finding the structure of DNA within minutes of their first meeting at the Cavendish Laboratory in Cambridge, England, in 1951. Watson, a 23-year-old geneticist, and Crick, a 35-year-old former physicist studying protein structure for his doctorate in biophysics, both saw DNA’s architecture as the biggest question in biology. Knowing the structure of this molecule would be the key to understanding how genetic information is copied. In turn, this would lead to finding cures for human diseases.

                                            Aware of these profound implications, Watson and Crick were obsessed with the problem—and, perhaps more than any other scientists, they were determined to find the answer first. Their competitive spirit drove them to work quickly, and it undoubtedly helped them succeed in their quest.

                                            Watson and Crick’s rapport led them to speedy insights as well. They incessantly discussed the problem, bouncing ideas off one another. This was especially helpful because each one was inspired by different evidence. When the visually sensitive Watson, for example, saw a cross-shaped pattern of spots in an X-ray photograph of DNA, he knew DNA had to be a double helix. From data on the symmetry of DNA crystals, Crick, an expert in crystal structure, saw that DNA’s two chains run in opposite directions.

                                            Since the groundbreaking double helix discovery in 1953, Watson has used the same fast, competitive approach to propel a revolution in molecular biology. As a professor at Harvard in the 1950s and 1960s, and as past director and current president of Cold Spring Harbor Laboratory, he tirelessly built intellectual arenas—groups of scientists and laboratories—to apply the knowledge gained from the double helix discovery to protein synthesis, the genetic code, and other fields of biological research. By relentlessly pushing these fields forward, he also advanced the view among biologists that solving major health problems requires research at the most fundamental level of life.

                                            (2) On this date, Nature published the paper you are reading.

                                            According to science historian Victor McElheny of the Massachusetts Institute of Technology, this date was a turning point in a longstanding struggle between two camps of biology, vitalism and reductionism. While vitalists studied whole organisms and viewed genetics as too complex to understand fully, reductionists saw deciphering fundamental life processes as entirely possible—and critical to curing human diseases. The discovery of DNA’s double-helix structure was a major blow to the vitalist approach and gave momentum to the reductionist field of molecular biology.

                                            Historians wonder how the timing of the DNA race affected its outcome. Science, after years of being diverted to the war effort, was able to focus more on problems such as those affecting human health. Yet, in the United States, it was threatened by a curb on the free exchange of ideas. Some think that American researcher Linus Pauling would have beaten Watson and Crick to the punch if Pauling’s ability to travel had not been hampered in 1952 by the overzealous House Un-American Activities Committee.

                                            (3) Nature (founded in 1869)——and hundreds of other scientific journals—help push science forward by providing a venue for researchers to publish and debate findings. Today, journals also validate the quality of this research through a rigorous evaluation called peer review. Generally at least two scientists, selected by the journal’s editors, judge the quality and originality of each paper, recommending whether or not it should be published.

                                            Science publishing was a different game when Watson and Crick submitted this paper to Nature. With no formal review process at most journals, editors usually reached their own decisions on submissions, seeking advice informally only when they were unfamiliar with a subject.

                                            (4) The effort to discover the structure of DNA was a race among several players. They were world-renowned chemist Linus Pauling at the California Institute of Technology, and X-ray crystallographers Maurice Wilkins and Rosalind Franklin at King’s College London, in addition to Watson and Crick at the Cavendish Laboratory, Cambridge University.

                                            The competitive juices were flowing well before the DNA sprint was in full gear. In 1951, Pauling narrowly beat scientists at the Cavendish Lab, a top center for probing protein structure, to the discovery that certain proteins are helical. The defeat stung. When Pauling sent a paper to be published in early 1953 that proposed a three-stranded DNA structure, the head of the Cavendish gave Watson and Crick permission to work full-time on DNA’s structure. Cavendish was not about to lose twice to Pauling.

                                            Pauling's proposed structure of DNA was a three-stranded helix with the bases facing out. While the model was wrong, Watson and Crick were sure Pauling would soon learn his error, and they estimated that he was six weeks away from the right answer. Electrified by the urgency—and by the prospect of beating a science superstar—Watson and Crick discovered the double helix after a four-week frenzy of model building.

                                            Pauling was foiled in his attempts to see X-ray photos of DNA from King's College—crucial evidence that inspired Watson's vision of the double helix—and had to settle for inferior older photographs. In 1952, Wilkins and the head of the King's laboratory had denied Pauling's request to view their photos. Pauling was planning to attend a science meeting in London, where he most likely would have renewed his request in person, but the United States House Un-American Activities Committee halted Pauling’s trip, citing his antiwar activism. It was fitting, then, that Pauling, who won the Nobel Prize in Chemistry in 1954, also won the Nobel Peace Prize in 1962, the same year Watson and Crick won their Nobel Prize for discovering the double helix.

                                            (5) Here, the young scientists Watson and Crick call their model “radically different” to strongly set it apart from the model proposed by science powerhouse Linus Pauling. This claim was justified. While Pauling’s model was a triple helix with the bases sticking out, the Watson-Crick model was a double helix with the bases pointing in and forming pairs of adenine (A) with thymine (T), and cytosine (C) with guanine (G).

                                            (6) This central description of the double helix model still stands today—a monumental feat considering that the vast majority of research findings are either rejected or changed over time.

                                            According to science historian Victor McElheny of the Massachusetts Institute of Technology, the staying power of the double helix theory puts it in a class with Newton’s laws of motion. Just as Newtonian physics has survived centuries of scientific scrutiny to become the foundation for today’s space programs, the double helix model has provided the bedrock for several research fields since 1953, including the biochemistry of DNA replication, the cracking of the genetic code, genetic engineering, and the sequencing of the human genome.

                                            (7) Norwegian scientist Sven Furberg’s DNA model—which correctly put the bases on the inside of a helix—was one of many ideas about DNA that helped Watson and Crick to infer the molecule’s structure. To some extent, they were synthesizers of these ideas. Doing little laboratory work, they gathered clues and advice from other experts to find the answer. Watson and Crick’s extraordinary scientific preparation, passion, and collaboration made them uniquely capable of this synthesis.

                                            (8) A visual representation of Watson and Crick’s model was crucial to show how the components of DNA fit together in a double helix. In 1953, Crick’s wife, Odile, drew the diagram used to represent DNA in this paper. Scientists use many different kinds of visual representations of DNA.

                                            (9) The last hurdle for Watson and Crick was to figure out how DNA’s four bases paired without distorting the helix. To visualize the answer, Watson built cardboard cutouts of the bases. Early one morning, as Watson moved the cutouts around on a tabletop, he found that only one combination of base molecules made a DNA structure without bulges or strains. As Crick put it in his book What Mad Pursuit, Watson solved the puzzle “not by logic but serendipity.” Watson and Crick picked up this model-building approach from eminent chemist Linus Pauling, who had successfully used it to discover that some proteins have a helical structure.

                                            (10) Alongside the Watson-Crick paper in the April 25, 1953, issue of Nature were separately published papers by scientists Maurice Wilkins and Rosalind Franklin of King’s College, who worked independently of each other. The Wilkins and Franklin papers described the X-ray crystallography evidence that helped Watson and Crick devise their structure. The authors of the three papers, their lab chiefs, and the editors of Nature agreed that all three would be published in the same issue.

                                            The “following communications” that our authors are referring to are the papers by Franklin and Wilkins, published on the journal pages immediately after Watson and Crick’s paper. They (and other papers) can be downloaded as PDF files (Adobe Acrobat required) from Nature’s 50 Years of DNA website (http://www.nature.com/nature/dna50/archive.html).

                                            Here are the direct links:

                                            Molecular Configuration in Sodium Thymonucleate
                                            Franklin, R., and Gosling, R. G.
                                            Nature 171, 740-741 (1953)
                                            URL: http://www.nature.com/nature/dna50/franklingosling.pdf

                                            Molecular Structure of Deoxypentose Nucleic Acids
                                            Wilkins, M. H. F., Stokes, A. R., & Wilson, H. R.
                                            Nature 171, 738-740 (1953)
                                            URL: http://www.nature.com/nature/dna50/wilkins.pdf

                                            (11) This sentence marks what many consider to be an inexcusable failure to give proper credit to Rosalind Franklin, a King’s College scientist. Watson and Crick are saying here that they “were not aware of” Franklin’s unpublished data, yet Watson later admits in his book The Double Helix that these data were critical in solving the problem. Watson and Crick knew these data would be published in the same April 25 issue of Nature, but they did not formally acknowledge her in their paper.

                                            What exactly were these data, and how did Watson and Crick gain access to them? While they were busy building their models, Franklin was at work on the DNA puzzle using X-ray crystallography, which involved taking X-ray photographs of DNA samples to infer their structure. By late February 1953, her analysis of these photos brought her close to the correct DNA model.

                                            But Franklin was frustrated with an inhospitable environment at King’s, one that pitted her against her colleagues. And in an institution that barred women from the dining room and other social venues, she was denied access to the informal discourse that is essential to any scientist’s work. Seeing no chance for a tolerable professional life at King’s, Franklin decided to take another job. As she was preparing to leave, she turned her X-ray photographs over to her colleague Maurice Wilkins (a longtime friend of Crick).

                                            Then, in perhaps the most pivotal moment in the search for DNA’s structure, Wilkins showed Watson one of Franklin’s photographs without Franklin’s permission. As Watson recalled, “The instant I saw the picture my mouth fell open and my pulse began to race.” To Watson, the cross-shaped pattern of spots in the photo meant that DNA had to be a double helix.

                                            Was it unethical for Wilkins to reveal the photographs? Should Watson and Crick have recognized Franklin for her contribution to this paper? Why didn’t they? Would Watson and Crick have been able to make their discovery without Franklin’s data? For decades, scientists and historians have wrestled over these issues.

                                            To read more about Rosalind Franklin and her history with Wilkins, Watson, and Crick, see the following:

                                            “Light on a Dark Lady” by Anne Piper, a lifelong friend of Franklin’s
                                            URL: http://www.physics.ucla.edu/

                                            A review of Brenda Maddox’s recent book, Rosalind Franklin: The Dark Lady of DNA in The Guardian (UK)
                                            URL: http://books.guardian.co.uk/whitbread2002/story/0,12605,842764,00.html

                                            (12) This phrase and the sentence it begins may be one of the biggest understatements in biology. Watson and Crick realized at the time that their work had important scientific implications beyond a “pretty structure.” In this statement, the authors are saying that the base pairing in DNA (adenine links to thymine and guanine to cytosine) provides the mechanism by which genetic information carried in the double helix can be precisely copied. Knowledge of this copying mechanism started a scientific revolution that would lead to, among other advances in molecular biology, the ability to manipulate DNA for genetic engineering and medical research, and to decode the human genome, along with those of the mouse, yeast, fruit fly, and other research organisms.

                                            (13) This paper is short because it was intended only to announce Watson and Crick’s discovery, and because they were in a competitive situation. In January 1954, they published the “full details” of their work in a longer paper (in Proceedings of the Royal Society). This “expound later” approach was usual in science in the 1950s as it continues to be. In fact, Rosalind Franklin did the same thing, supplementing her short April 25 paper with two longer articles.

                                            Today, scientists publish their results in a variety of formats. They also present their work at conferences. Watson reported his and Crick’s results at the prestigious annual symposium at Cold Spring Harbor Laboratory in June 1953. As part of our recognition of the fiftieth anniversary of the double helix discovery, we will join scientists at Cold Spring Harbor as they present their papers at the “Biology of DNA” conference.


                                            How DNA Works

                                            ­DNA is o­ne of the nucleic acids, information-containing molecules in the cell (ribonucleic acid, or RNA, is the other nucleic acid). DNA is found in the nucleus of every human cell. (See the sidebar at the bottom of the page for more about RNA and different types of cells). The information in DNA:

                                            • guides the cell (along with RNA) in making new proteins that determine all of our biological traits
                                            • gets passed (copied) from one generation to the next

                                            The key to all of these functions is found in the molecular structure of DNA, as described by Watson and Crick.

                                            Although it may look complicated, the DNA in a cell is really just a pattern made up of four different parts called nucleotides. Imagine a set of blocks that has only four shapes, or an alphabet that has only four letters. DNA is a long string of these blocks or letters. Each nucleotide consists of a sugar (deoxyribose) bound on one side to a phosphate group and bound on the other side to a nitrogenous base.

                                            There are two classes of nitrogen bases called purines (double-ringed structures) and pyrimidines (single-ringed structures). The four bases in DNA's alphabet are:

                                            • adenine (A) - a purine
                                            • cytosine(C) - a pyrimidine
                                            • guanine (G) - a purine
                                            • thymine (T) - a pyrimidine

                                            Watson and Crick discovered that DNA had two sides, or strands, and that these strands were twisted together like a twisted ladder -- the double helix. The sides of the ladder comprise the sugar-phosphate portions of adjacent nucleotides bonded together. The phosphate of one nucleotide is covalently bound (a bond in which one or more pairs of electrons are shared by two atoms) to the sugar of the next nucleotide. The hydrogen bonds between phosphates cause the DNA strand to twist. The nitrogenous bases point inward on the ladder and form pairs with bases on the other side, like rungs. Each base pair is formed from two complementary nucleotides (purine with pyrimidine) bound together by hydrogen bonds. The base pairs in DNA are adenine with thymine and cytosine with guanine.

                                            In the next section we'll find out how long DNA strands fit inside a tiny cell.

                                            A hydrogen bond is a weak chemical bond that occurs between hydrogen atoms and more electronegative atoms, like oxygen, nitrogen and fluorine. The participating atoms can be located on the same molecule (adjacent nucleotides) or on different molecules (adjacent nucleotides on different DNA strands). Hydrogen bonds do not involve the exchange or sharing of electrons like covalent and ionic bonds. The weak attraction is like that between the opposite poles of a magnet. Hydrogen bonds occur over short distances and can be easily formed and broken. They can also stabilize a molecule.


                                            Energy Source

                                            ATP is the main carrier of energy that is used for all cellular activities. When ATP is hydrolyzed and converted to adenosine diphosphate (ADP), energy is released. The removal of one phosphate group releases 7.3 kilocalories per mole, or 30.6 kilojoules per mole, under standard conditions. This energy powers all reactions that take place inside the cell. ADP can also be converted back into ATP so that the energy is available for other cellular reactions.

                                            ATP is produced through several different methods. Photophosphorylation is a method specific to plants and cyanobacteria. It is the creation of ATP from ADP using energy from sunlight, and occurs during photosynthesis. ATP is also formed from the process of cellular respiration in the mitochondria of a cell. This can be through aerobic respiration, which requires oxygen, or anaerobic respiration, which does not. Aerobic respiration produces ATP (along with carbon dioxide and water) from glucose and oxygen. Anaerobic respiration uses chemicals other than oxygen, and this process is primarily used by archaea and bacteria that live in anaerobic environments. Fermentation is another way of producing ATP that does not require oxygen it is different from anaerobic respiration because it does not use an electron transport chain. Yeast and bacteria are examples of organisms that use fermentation to generate ATP.

                                            Signal Transduction

                                            ATP is a signaling molecule used for cell communication. Kinases, which are enzymes that phosphorylate molecules, use ATP as a source of phosphate groups. Kinases are important for signal transduction, which is how a physical or chemical signal is transmitted from receptors on the outside of the cell to the inside of the cell. Once the signal is inside the cell, the cell can respond appropriately. Cells may be given signals to grow, metabolize, differentiate into specific types, or even die.

                                            DNA Synthesis

                                            Other molecules are related to ATP and have similar names, such as adenosine diphosphate (ADP), adenosine monophosphate (AMP), and cyclic AMP (cAMP). In order to avoid confusion, it is important to know some differences between these molecules.

                                            Adenosine diphosphate (ADP), which is sometimes also known as adenosine pyrophosphate (APP), especially in chemistry, has already been mentioned in this article. It differs from ATP because it has two phosphate groups. ATP becomes ADP with the loss of a phosphate group, and this reaction releases energy. ADP itself is formed from AMP. Cycling between ADP and ATP during cellular respiration gives cells the energy needed to carry out cellular activities.

                                            Adenosine monophosphate (AMP), also called 5’-adenylic acid, has only one phosphate group. This molecule is found in RNA and contains adenine, which is part of the genetic code. It can be produced along with ATP from two ADP molecules, or by hydrolysis of ATP. It is also formed when RNA is broken down. It can be converted into uric acid, which is a component of urine, and excreted via the bladder.

                                            Cyclic adenosine monophosphate (cAMP) is derived from ATP and is another messenger used for signal transduction and activating certain protein kinases. It can be broken down into AMP. cAMP pathways may play a role in certain cancers such as carcinoma. In bacteria, it has a role in metabolism. When a bacterial cell is not producing enough energy (from insufficient glucose, for example), high cAMP levels occur, and this turns on genes that use energy sources other than glucose.


                                            DNA vs RNA – Similarities and Differences

                                            Three differences between DNA and RNA are that DNA uses the base thymine while RNA uses uracil, DNA uses the sugar deoxyribose while RNA uses ribose, and usually DNA is double-stranded and RNA is single-stranded. (image: Sponk, Creative Commons 3.0)

                                            DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are the two types of nucleic acids found in cells. Nucleic acids, in turn, are the biological molecules that code for genetic information and proteins. Here is a comparison of the similarities and differences between DNA and RNA.

                                            Similarities Between DNA and RNA

                                            As nucleic acids, DNA and RNA share some similarities:

                                            • Both DNA and RNA store genetic information.
                                            • DNA and RNA are both large biological polymers.
                                            • Both DNA and RNA consists of sugar, nitrogenous bases, and a phosphate backbone.
                                            • On both molecules, guanine and cytosine pair with each other (are complementary).
                                            • Complementary base pairs are connected by hydrogen bonding. Two hydrogen bonds form between adenine and either thymine or uracil, while three hydrogen bonds form between cytosine and guanine.

                                            Differences Between DNA and RNA

                                            DNA and RNA are different from each other in several ways.

                                            • DNA uses the sugar deoxyribose, while RNA uses the sugar ribose. The difference between deoxyribose and ribose is that deoxyribose has a hydrogen (-H) attached to the second (2′) carbon of the sugar ring, while ribose has a hydroxyl group (-OH) attached to this carbon.
                                            • Usually, DNA is a double-stranded molecule that forms a double helix, while RNA is a single stranded molecule. Rarely, DNA takes other forms, such as triple-strand DNA and quadraplex DNA. Similarly, double-stranded RNA (dsRNA) occurs in some viruses.
                                            • DNA uses the bases adenine, thymine, guanine, and cytosine. RNA uses the bases adenine, uracil, guanine, and cytosine. Uracil differs from thymine in that it lacks a methyl group.
                                            • DNA and RNA serve different functions. DNA stores and transfers genetic information, while RNA acts as a messenger between DNA and ribosomes to make amino acids and proteins. Viruses use either DNA or RNA as genetic material, but they require the hosts cellular machinery to replicate. Sometimes RNA acts as a catalyst for biochemical reactions.
                                            • RNA is less stable than DNA and is more vulnerable to mutation and attack than DNA. DNA is protected by proteins and has several repair mechanisms.

                                            Types of DNA and RNA

                                            There are different types of DNA and RNA. DNA occurs in five forms: A-DNA, B-DNA, C-DNA, D-DNA, and Z-DNA. The B form occurs in most organisms and is a right-handed helix with a major and minor groove. The main types of RNA are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Many additional types of RNA also exist. A cell typically contains one type of DNA and several forms of RNA.


                                            Watch the video: DNA animations by for Science-Art exhibition (January 2022).