Fundamentals of Microbiology

Lesson 21. DNA STRUCTURE

Module 6. Bacterial genetics

Lesson 21

DNA STRUCTURE

21.1 Introduction

21.1.1 Deoxyribonucleic acid (DNA)

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms with the exception of some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Within cells, DNA is organized into long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm.

The information in DNA is made up of four bases which combine to form chains. These bases include two purines (Adenine and Guanine) and two pyrimidines (Cytosine and Thymine). These are commonly referred to as A, G, C and T respectively (Fig.21.1)

Fig. 21.1 Bases in DNA

Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.

21.2 Chargaff's Rules

These state that DNA from any cell of all organisms should have a 1:1 ratio of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal tocytosine and the amount of adenine is equal to thymine. This Pattern is found in both strands of the DNA. They were discovered by Austrian chemist Erwin Chargaff.

DNA bases pair up with each other, A with T and C with G, to form units called base pairs. Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar, and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix. The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder’s rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder.

21.2.1 Structure

In 1953 Watson and Crick postulated a three dimensional model of DNA structure. It consists of two helical DNA chains wound around the same axis to form a right handed double helix. The hydrophilic backbones of alternating deoxyribose and phosphate groups are on the outside of the double helix, facing the surrounding water. The purine and pyrimidine bases of both strands are stacked inside the double helix, with their hydrophobic and nearly planar ring structures very close together and perpendicular to the long axis. The offset pairing of the two strands creates a major groove and minor groove on the surface of the duplex. Each nucleotide base of one strand is paired in the same plane with a base of the other strand. Watson and Crick found that the hydrogen-bonded base pairs, G with C and A with T, are those that fit best within the structure, providing a rationale for Chargaff’s rule. It is important to note that three hydrogen bonds can form between G and C, but only two can form between A and T. This is one reason for the finding that separation of paired DNA strands is more difficult the higher the ratio of GC to AT base pairs. Other pairings of bases tend (to varying degrees) to destabilize the double-helical structure. When Watson and Crick constructed their model, they had to decide at the outset whether the strands of DNA should be parallel or antiparallel whether their 5’-3’ phosphodiester bonds should run in the same or opposite directions. An antiparallel orientation produced the most convincing model, and later work with DNA polymerases provided experimental evidence that the strands are indeed antiparallel, a finding ultimately confirmed by x-ray analysis. (Fig.21.2)

Fig. 21.2 Structure of DNA

21.2.2 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. Ribose is the sugar in the backbone of RNA, ribonucleic acid (Fig. 21.3).

Fig. 21.3 Ribose

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. Deoxyribose, as the name might suggest, is ribose which has lost an oxygen atom – ‘de-oxy’ (Fig.21.4).

Fig. 21.4 Deoxyribose

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 (Fig. 21.5).

Fig. 21.5 Deoxyribose with carbon numbering

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’.

21.2.3 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 (Fig. 21.6).

Fig. 21.6 Deoxyribose with phosphate group

21.2.4 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).

These bases attach in place of the -OH group on the 1' carbon atom in the sugar ring (Fig. 21.7).

Fig. 21.7 Deoxyribose with phosphate group and base

What we have produced is known as a nucleotide (Fig.21.8).

Here are their structures:

Fig. 21.8 Nucleotides

The nitrogen and hydrogen atoms shown in blue on each molecule show that 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: (Fig. 21.9).

Fig. 21.9 Nucleotide containing cytosine

21.2.5 Joining the nucleotides into a DNA strand

A DNA strand is simply a string of nucleotides joined together. 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 (Fig. 21.10).

Fig. 21.10 Condensation reaction

21.2.6 Building a DNA chain concentrating on the essentials

What matters in DNA is the sequence the four bases take up in the chain (Fig. 21.11).

Fig. 21.11 Single chain structure of DNA

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 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 (Fig.21.12).

Fig. 21.12 DNA chain

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.

21.2.7 Joining the two DNA chains together

If you look at the diagram 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. 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 (Fig.21.13).

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 (Fig. 21.14).

The base pairs fit together as follows.

The A-T base pair:

Fig. 21.13 Hydrogen bonding in nitrogen bases

The G-C base pair:

Fig. 21.14 Hydrogen bonding

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

Fig. 21.15 Final structure for DNA showing the important bits

Notice that the two chains run in opposite directions and the right-hand chain is essentially uside-down. The ends of these bits of chain are labeled with 3' and 5' (Fig. 21.15). The genetic code in genes is always written in the 5' to 3' direction along a chain