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Molecular structure

DNA (deoxyribonucleic acid) is the genetic material of the cell.

DNA contains the instructions for a cell developments and functions. Everyone, except identical twins, has different DNA. However, the basic structure is the same for most living organisms.

DNA is a large polymer (repeating subunits) formed from long chains of nucleotides. The sequence of nucleotides in DNA forms the blueprint of the cell.

If the DNA in a single human cell was stretched out, it would be over 2 metres long!

The DNA molecule actually consists of two separate strands. These strands (shown in green) wrap around each other. This structure is called a double helix.

The structure of DNA was discovered by Francis Crick and James Watson in 1953. This discovery revolutionised biology!

Nucleic acids are macromolecules (very large molecules) that are essential for storing and expressing genetic information.

A nucleic acid is a polymer, a long chain of small similar units.

There are two types of nucleic acid in a cell:

DNA (deoxyribonucleic acid) stores genetic information. In eukaryotes, DNA is found in the nucleus (hence the generic name "nucleic acid").

RNA (ribonucleic acid) uses the information encoded in the DNA and is associated with making proteins.

In eukaryotes, DNA is only found in the nucleus while RNA is found in the nucleus and the cytosol.

DNA is a double strand whereas RNA is a single strand.

There are several different types of RNA such as messenger, transfer and ribosomal RNA.

A pentose sugar is a ring-shaped sugar with five carbon atoms (from the Ancient Greek pente). They are one of the three components of nucleic acids (together with the phosphate group and a nucleic base).

The carbon atoms are numbered from 1 to 5. When the sugar is part of a nucleic acid the numbers are 1' (read "one prime") to 5'.

There are two important pentose sugars in genetics. The nucleic acids are named for the sugars:

  • Deoxyribose is the sugar in deoxyribonucleic acid (DNA).
  • Ribose is the sugar in ribonucleic acid (RNA).

Ribose and deoxyribose differ only in the functional group on the second (2') carbon atom. Ribose has an $$\ce{-OH}$$ group and deoxyribose has a simple hydrogen attached to the carbon.

A nitrogenous base is a molecule that contains nitrogen and that has the chemical properties of a base (rather than an acid). They are a component of nucleic acids such as DNA.

There are five different nitrogenous bases (abbreviated by their first letter) that occur in nucleic acids. They fall into two groups:

  • Pyrimidines: thymine (T), cytosine (C) and uracil (U) contain only a single hexagonal ring of carbon and nitrogen atoms.
  • Purines: adenine (A) and guanine (G) contain two rings of carbon and nitrogen atoms.

Thymine and uracil are similar in structure but thymine only bonds with deoxyribose and uracil only bonds with ribose. Uracil would make DNA less stable so thymine is used instead.

As a result, DNA contains thymine, adenine, guanine and cytosine. RNA contains uracil, adenine, guanine and cytosine.

Pyrimidines have one ring of carbon and nitrogen atoms while purines contain two.
Pyrimidines have one ring of carbon and nitrogen atoms while purines contain two.

A nucleotide is the smallest repeating unit in DNA (and RNA).

A single strand of DNA (or RNA) is made from a long chain of nucleotides. The precise order of the nucleotides forms a unique sequences.

Each nucleotide consists of three components:

  • Pentose sugar (deoxyribose in DNA and ribose in RNA) forms the backbone of DNA
  • Phosphate group forms bonds to two sugars
  • Nitrogenous base (A, T, C, G or U) encodes the DNA's instructions

There are four different nitrogenous bases in DNA: Adenosine (A), thymine (T), cytosine (C) and guanine (G). These four bases can be combined in different ways to make unique sequences of DNA.

DNA is more stable than RNA.

This makes DNA a better carrier of genetic information.

One reason is that deoxyribose sugar is more stable than ribose sugar as it has one less oxygen atom. This makes it less reactive.

Another reason relates to the use of thymine rather than uracil in DNA. Cytosine sometimes converts to uracil through a chemical reaction. Having thymine in DNA instead of uracil allows the right base to be converted back.

Uracil is also less specific in its bonding than thymine and can cause more errors in replication.

Some viruses store genetic information in RNA. As a result, they have very high mutation rates (rates at which the code changes because of errors in replication).

Ribose sugar found in RNA and deoxyribose sugar found in DNA.
Ribose sugar found in RNA and deoxyribose sugar found in DNA.

The nucleotides in a strand of nucleic acids are connected by phosphodiester bonds.

The phosphodiester "bond" actually consists of two bonds:

  • A bond between the 3' carbon atom (or 3' end) of one pentose and a phosphate group
  • A bond between the same phosphate group and the 5' carbon atom (or 5' end) of the next pentose

The chain of phosphodiester bonds (sugar-phosphate-sugar-phosphate-...) in a nucleic acid strand is called the sugar-phosphate backbone.

The end of a strand is named depending on the unbounded sugar.

The end with a 5' carbon exposed is called the 5' end. The end with a free 3' carbon is called the 3' end.

The phosphodiester bond consists of a phosphate group connecting two pentose sugars. The sugar-phosphate backbone is a chain of such pentose-phosphate-pentose links.
The phosphodiester bond consists of a phosphate group connecting two pentose sugars. The sugar-phosphate backbone is a chain of such pentose-phosphate-pentose links.

Complementary base pair describes the way in which nitrogenous bases from opposite DNA strands interact.

Not all bases can interact with each other. Their different shapes and sizes mean that only certain pairs are allowed. This is called the base pairing rule:

  • Adenine (A) pairs with thymine (T)
  • Cytosine (C) pairs with guanine (G)

Each base only pairs with one other base, so if you know the sequence of one strand of a DNA molecule you can work out the sequence of its complementary strand!

The complementary sequence of A-G-A-C is T-C-T-G

Complementary base pairings.
Complementary base pairings.

Two nitrogenous bases form a complementary base pair if they match in terms of size and ability to form hydrogen bonds between adjacent positions on two strands of DNA.

Each complementary pair of bases contains one pyrimidine and one purine base. This ensures that the combination of two bases connecting the two strands is always of equal length.

Adenine (purine) and thymine (pyrimidine) form two hydrogen bonds. Guanine (purine) and cytosine (pyrimidine) form three hydrogen bonds.

Only two base pairs are possible in DNA: adenine-thymine and guanine-cytosine.

A strand of RNA complementary to DNA will have uracil instead of thymine opposite adenine.

Complementary base pairings.
Complementary base pairings.

A strand of a nucleic acid (DNA or RNA) has directionality. The information contained in the sequence of nitrogenous bases can only be read in one direction.

The directionality implies that a base sequence such as GTA is not equivalent to ATG. For example, UUG codes for the amino acid leucine while GUU codes for valine.

Directionality also applies to natural language. The sentences "Tom likes Jane." and "Jane likes Tom." have quite different meanings.

The asymmetry of the phosphodiester bond ensures that the direction of the strand is always evident.

The code in DNA is organised into higher structures.

A gene is a section of DNA that codes for a protein. One DNA molecule can contain thousands of genes!

Every protein in the cell has a complementary gene that contains the instructions for making the protein.

In humans, the genetic information is separated into multiple DNA molecules. Each individual DNA molecule is called a chromosome . Human cells have 46 chromosomes, split into 23 pairs.

Bacterial cells typically have a single DNA molecule that contains all of their genetic information.