Genetics

IMAT
Dr. Abtin Fouladi
MD., HMBA.,
Biology teacher,
Iranian university entrance exam,
IMAT
Contents:

01 The molecule of life

The structure of DNA

02 and RNA

03 DNA replication
 01-The molecule of life
If you wanted to design a molecule that could act as the genetic material in
living things, it would have to have two key features:
• The ability to store information – the information needed is a set of
instructions for controlling the behaviour of cells
• The ability to copy itself accurately – whenever a cell divides it must
pass on exact copies of the ‘genetic molecule’ to each of its daughter
cells so no information is lost.
Until the mid 1940s, biologists assumed that such a molecule must be a
protein. Only proteins were thought to be complex enough to be able to
carry the huge number of instructions which would be necessary to make
such a complicated structure as a living organism.
But during the 1940s and 1950s, evidence came to light that proved
beyond doubt that the genetic molecule was not a protein at all, but DNA.
 02-The structure of DNA & RNA
DNA stands for deoxyribonucleic acid, and RNA stands for ribonucleic acid.
As you saw in Chapter 2, DNA and RNA are macromolecules (giant
molecules).
Together they are known as nucleic acids because they were originally
found in the nucleus. Proteins and polysaccharides are also
macromolecules. You also saw in Chapter 2 that macromolecules are
polymers, made up of many similar, smaller molecules (monomers) joined
together to form a long chain. The monomers from which DNA and RNA
molecules are made are nucleotides. DNA and RNA are therefore
polynucleotides.

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 Nucleotides
Nucleotides are made up of three smaller components.
These are:
• a nitrogen-containing base
• a pentose sugar
• a phosphate group.

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 Nitrogen-containing base
There are four different nitrogen-containing bases found in DNA and four in
RNA.
 In DNA the bases are: Adenine, Guanine, Thymine and Cytosine.
 In RNA thymine is replaced by a similar base called Uracil.
 The bases are often referred to by their first letters: A, G, T, C and U.
Two of the bases, adenine and guanine, are related to the chemical
purine and are referred to as purines. The other three bases, thymine,
cytosine and uracil, are related to the chemical pyrimidine and are
referred to as pyrimidines.
Purine has two rings in its structure; pyrimidine has one ring.

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 Pentose sugar

You saw in Chapter 2 that sugars with five carbon atoms are called

pentoses. Two pentoses are found in nucleic acids, ribose and

deoxyribose.

• A nucleic acid containing ribose is called a ribonucleic acid (RNA).

• One containing deoxyribose is called a deoxyribonucleic acid (DNA).

As the name suggests, deoxyribose is almost the same as ribose except

that it has one fewer oxygen atoms in its molecule.

 Phosphate group
The phosphate group gives nucleic acids their acid nature.
 The structure of ATP
Although ATP (adenosine triphosphate) is not part of DNA or RNA, you will look at its
structure here because it is also a nucleotide.
The structure of ATP is shown in Figure 6.3. Its three components are adenine,
ribose and phosphate. Adenine plus ribose forms a sugar–base called adenosine.
Adenosine can be combined with one, two or three phosphate groups to give, in
turn, adenosine monophosphate (AMP), adenosine diphosphate (ADP) or adenosine
triphosphate (ATP).
Do not confuse adenine with adenosine, which is part of the name of ATP
(adenosine triphosphate); adenosine is adenine with a sugar joined to it. And do not
confuse thymine with thiamine; thiamine is a vitamin.

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 Dinucleotides and polynucleotides
Two nucleotides can be joined together by a condensation reaction (the
same type of reaction used to join one amino acid to another, or one sugar
to another).
The molecule formed by joining two nucleotides is called a dinucleotide
(Figure 6.4a). The bond formed is called a phosphodiester bond. The term
diester is used because the phosphate group involved now has two ester
bonds, one to each of the sugars it is connected to. The process can be
repeated up to several million times to make a polynucleotide which has
the form of a long, unbranching strand of nucleotides as shown in Figure
6.4b. The sugars and phosphates are linked by the phosphodiester bonds
to form a backbone from which the bases stick out sideways at right angles
to the backbone.
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 The structure of DNA
By the 1950s the structure of polynucleotides as shown in Figure 6.4b was known, but this structure did not
explain how DNA could store information or copy itself.
A race was under way to solve this problem by learning more about the structure of DNA. The race was won
in 1953 when James Watson and Francis Crick, working in Cambridge, England, published a model
structure for DNA that turned out to be correct. According to James Watson, it was too pretty not to be true.
The key to Watson and Crick’s success was trying to make models of DNA using all the available evidence.
Apart from Chargaff’s data (see Question 3, Table 6.1), another vital piece of evidence came from X-ray
diffraction photographs of DNA produced by Rosalind Franklin. Franklin worked at King’s College in London
(Figure 6.5) and her photographs suggested that DNA had a helical structure.
 The structure of DNA
By playing with models, Watson and Crick eventually came up with the idea of the molecule having two
polynucleotide chains, not one. The two chains could be held together by hydrogen bonding between the
bases of the two chains. The model showed that the only way this could be done would be to twist each of
the two strands into a helical shape – a double helix – and to run the strands in opposite directions. A sketch
of this is shown in Figure 6.6.

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 Features of the DNA molecule
The 5′ (say: five-prime) and 3′ (say: three-prime) on Figure 6.8 refer to carbon atoms 5 and 3 of the sugar.
The two ends of a DNA strand are called the 5′ end and the 3′ end. At the 5′ end is phosphate and at the 3′
end is sugar.

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 Features of the DNA molecule
The DNA molecule has the following features:
• It is made of two polynucleotide chains.
• Each chain is a right-handed helix.
• The two chains coil around each other to form a double helix.
• The chains run in opposite directions – they are said to be antiparallel.
• Each chain has a sugar-phosphate backbone with bases projecting at right angles.
• The bases in one chain are attracted to the bases of the other chain by hydrogen bonding between the
bases. This holds the chains together.
• Because of the way they fit together, like jigsaw pieces, adenine (A) always pairs with thymine (T) and
guanine (G) always pairs with cytosine (C) (complementary base pairing). (This explains Chargaff’s data
– see Question 3.)
• A links with T by two hydrogen bonds; G links with C by three hydrogen bonds.
• Adenine and guanine are purines; thymine and cytosine are pyrimidines. A purine always pairs with a
pyrimidine.
• Purines are two rings wide and pyrimidines are one ring wide; the distance between the two backbones
is therefore constant and always three rings wide.
• A complete turn of the double helix takes place every 10 base pairs.
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 Features of the DNA molecule

Because A must pair with T and G with C, the sequence of bases in one strand determines the sequence of
bases in the other strand. The two strands are said to be complementary. Watson and Crick realised
immediately how this structure explained how DNA stores information and how it copies itself.
The information is the sequence of bases – represented by the four letters, A, G, T and C, in any order
along the whole molecule. Any sequence is possible within one strand, but the other strand must
be complementary. The sequence acts as a coded message.
The molecule can copy itself (replicate) accurately by ‘unzipping’ down the middle. This is relatively easy
because the two strands are only held together by weak hydrogen bonds. Each half can then make a
complementary copy of itself. Thus, two identical molecules of DNA are produced.
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DNA structure
The 3'–5' linkage:
A DNA nucleotide consists of the sugar deoxyribose to which are attached a phosphate group and a
nitrogenous base. The carbons in the sugar are numbered from 1 to 5 in a clockwise direction starting after
the oxygen at the apex (Figure 7.1).
The base is attached to carbon 1.
Carbon 2 has just a hydrogen attached instead of an OH group – this is the reason the sugar is called
deoxyribose.
Carbon 3 is where the next nucleotide attaches in one direction.
Carbon 5 has a phosphate group attached to it, which is where the next nucleotide attaches in the other
direction.
This means that each nucleotide is linked to those on either side of it through carbons 3 and 5. The linkages
are called 3'–5' linkages.
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Antiparallel strands:
Look back at Figure 2.21. This shows part of a DNA molecule, in which two polynucleotide strands, running
in opposite directions, are held together by hydrogen bonds between pairs of bases.
Notice that the deoxyribose molecules are orientated in opposite directions.
Figure 7.2 also shows this – at one end of each DNA strand there is a free 3' carbon and at the other there
is a free 5' carbon. (Ignore the fact that there is a phosphate group attached to this 5' carbon.)
One strand runs in a 5' → 3' direction whereas the other runs in a 3' → 5' direction.
The strands are described as being antiparallel.
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 The structure of RNA

Unlike DNA, an RNA molecule is a single polynucleotide strand.

Later in the chapter you will consider protein synthesis (Section 6.5). This

involves three types of RNA, namely messenger RNA (mRNA), transfer

RNA (tRNA) and ribosomal RNA (rRNA).

Transfer RNA and rRNA fold up into complex structures, but mRNA

remains as an unfolded strand.

 03- DNA replication

Watson and Crick were quick to realise how DNA could replicate – copy itself.
Scientists now know in detail how this process occurs and that it takes place during the S phase of the cell
cycle.
Replication is controlled by enzymes.
It starts by the unwinding (separation) of the two strands of DNA by the breaking of the hydrogen bonds that
normally hold the two strands together. This is the ‘unzipping’ mentioned earlier.
The enzyme DNA polymerase is then used for the copying process. A molecule of DNA polymerase
attaches to each of the single strands. It adds one new nucleotide at a time, which is held by hydrogen
bonding to the strand being copied.
 DNA replication

DNA polymerase can only copy in the 5′ to 3′ direction along each strand. This creates a problem. If you
look at Figure 6.9, you can see that the top parent strand is being copied in the same direction as the
unwinding process. The DNA polymerase simply follows the unwinding process, copying the DNA as it is
unwound. The new strand being formed is called the leading strand.
In contrast to the top parent strand, for the bottom parent strand the 5′ to 3′ direction of copying is in the
opposite direction to the unwinding. This means that the DNA polymerase has to copy an unwound piece of
DNA and then go back and copy the next piece of unwound DNA. It has to keep repeating this process. The
result is a series of short fragments of copied DNA (Figure 6.9). These are called Okazaki fragments after
the biochemist who discovered them. In this case, the new strand being formed is called the lagging strand.
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 DNA replication
Another enzyme called DNA ligase finishes the process.
Its job is to connect all the new nucleotides with covalent bonds. Before this they are only holding on to the
parent strand with hydrogen bonds between complementary bases. DNA ligase connects neighbouring
nucleotides with phosphodiester bonds to form the sugar-phosphate backbone of the new DNA molecule.
The Okazaki fragments are connected in the same way at the same time. Figure 6.10 shows you some
more details of replication, including base pairing.

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 Semi-conservative replication
The method of copying DNA described is called semi-conservative replication. This is because each time a
DNA molecule is replicated, half the original molecule is kept (conserved) in each of the new molecules.
If replication was conservative, the parent DNA molecule would remain at the end of the process and the
new DNA molecule would have two newly made strands.
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