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Chapter 7 – DNA and Protein Synthesis
CHAPTER 7 – DNA and PROTEIN SYNTHESIS
7.1 Nucleic Acids
Structure of nucleotides
Individual nucleotides comprise three parts:
1. Phosphoric acid (phosphate H3PO4). This has the same structure in all
nucleotides.
2. Pentose sugar. Two types occur, ribose (C5H10O5) and deoxyribose
(C5H10O4).
3. Organic base. There are five different bases which are divided into two
groups, described on the next page.
a. Pyrimidines – these are single rings each with six sides. Examples
found in nucleic acids are: cytosine, thymine and uracil.
b. Purines – these are double rings comprising a six-sided and a fivesided ring. Two examples are found in nucleic acids: adenine and
guanine.
The three components are combined by condensation reactions to give a
nucleotide, the structure of which is shown in Fig 7.1.1. By a similar condensation
reaction between the sugar and phosphate groups of two nucleotides, a dinucleotide
is formed. Continued condensation reactions lead to the formation of a
polynucleotide (Fig 7.2.2).
Fig 7.1.1 structure of a typical nucleotide
The main function of nucleotides is the formation of the nucleic acids RNA and DNA
which play vital roles in protein synthesis and heredity. In addition they form part of
other metabolically important molecules. Table 7.1 gives some examples
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Fig 7.2.2 structure of section of
polynucleotide e.g. RNA
7.2 Ribonucleic acid (RNA)
RNA is found on the ribosomes and in the nucleus and nucleolus. RNA is a
single-stranded polymer of nucleotides where the pentose sugar is always ribose and
the organic bases are adenine, guanine, cytosine and uracil. There are three types of
RNA found in cells, all of which are involved in protein synthesis.
Ribosomal RNA (rRNA) is a large, complex molecule made up of both double and
single helices. Although it is manufactured by the DNA of the nucleus, it is found in
the cytoplasm where it makes up more than half the mass of the ribosomes. It
comprises more than the mass of the total RNA of a cell and its base sequence is
similar in all organisms.
Transfer RNA (tRNA) is a small molecule (about 80 nucleotides) comprising a
single -strand. Again it is manufactured by nuclear DNA. It makes up 10-15% of the
cell’s RNA and all types are fundamentally similar. It forms a clover-leaf shape (Fig
7.4.4), with one end of the chain ending in a cytosine-cytosine-adenine sequence. It
is at this point that an amino acid attaches itself. There are atleast 20 types of tRNA,
each carrying a different amino acid. At an intermediate point along the chain is an
important sequence of three bases, called the anticodon. These line up alongside
the appropriate codon on the mRNA during protein synthesis.
Messenger RNA (mRNA) is a long single-stranded molecule, of up to thousands of
nucleotides, which is formed into a helix. Manufactured in the nucleus, it is a mirror
copy of part of one strand of the DNA helix. There is hence an immense variety of
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types. It enters the cytoplasm where it associates with the ribosomes and acts as a
template for protein synthesis. It makes up less than 5% of the total cellular RNA. It
is easily and quickly broken down, sometimes existing for only a matter of minutes.
Fig 7.4.4 structure of transfer RNA
7.3 DNA and protein synthesis
Every living organism contains DNA. The sequence of nucleotides on the
nucleotides on the DNA molecules is a code which provides instructions for the
sequences of amino acids which are used to build protein molecules.
7.4 DNA AS THE GENETIC MATERIAL
A molecule which is to act as the genetic material in a living organism must
have certain properties. Firstly, it must be able to replicate, being copied perfectly so
it can pass unchanged into the new cells that are produced when no old cell divides.
Secondly, it must be able to store information which provides the instructions used
by the cell to determine the characteristics of the cell and the organism of which it is
a part. DNA does this by giving instructions for the making of proteins.
7.5 Deoxyribonucleic acid (DNA)
DNA is a double-stranded polymer of nucleotides where the pentose sugar is always
deoxyribose and the organic bases are adenine, guanine, cytosine and thymine, but
never uracil. Each of these polynucleotide chains is extremely long and may contain
many million nucleotide units.
The available facts about DNA included:
1. It is a very long, thin molecule made up of nucleotides.
2. it contains four organic bases: adenine, guanine, cytosine and thymine
3. The amount of guanine is usually equal to that of cytosine.
4. the amount of adenine is usually equal to that of thymine
5. It is probably in the form of a helix whose shape is maintained by hydrogen
bonding.
Using the accumulated evidence, James Watson and Francis Crick in 1953
suggested a molecular structure which proved to be one of the greatest
milestones in biology. They postulated a double helix of two nucleotide strands,
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each strands being linked to the other by pairs of organic bases which are
themselves joined by hydrogen bonds. The pairing are always cytosine with
guanine and adenine with thymine. This was not only consistent with the known
ratio of the bases in the molecule, but also allowed for an identical separation of
the strands throughout the molecule, a fact shown to be the case from X-ray
diffraction patterns. As the purines, adenine and guanine are double ringed
structures (Fig 7.3.3) they form much longer links if paired together than the
two single ringed pyrimidines, cytosine and thymine. Only by pairing one purine
with one pyrimidine can a consistent separation of three rings’ width be achieved.
In effect, the structure is like a ladder where the deoxyribose and phosphate
units form the uprights and the organic base pairings form the rungs. However,
this is no ordinary ladder; instead it is twisted into a helix so that each upright
winds around the other. The two chains that form the uprights run in opposite
directions i.e. are antiparallel. The structure of DNA is shown in Fig 7.5.5,
7.6.6. The structure allowed for its replication. The separation of the two strands
would result in each half attracting its complementary nucleotide to itself. The
subsequent joining of these nucleotides would form two identical DNA double
helices. This fitted the observation that DNA content doubles prior to cell division.
Each double helix could then enter one of the daughter cells and so restore the
normal quantity of DNA.
Fig 7.5.5 Basic structure of DNA
7.6 Difference between RNA & DNA
RNA
DNA
Single polynucleotide chain
Double polynucleotide chain
Smaller molecular mass (20 000-2 000 000) Larger molecular mass (100 000-150 000 000)
May have a single or double helix
Pentose sugar is ribose
Always a double helix
Pentose sugar is deoxyribose
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Organic bases present are adenine, guanine,
cytosine and uracil
Ratio of adenine and uracil to cytosine and
guanine varies
Manufactured in the nucleus but found
throughout the cell
Amount varies from cell to cell (and within a
cell according to metabolic activity)
Chemically less stable
May be temporary-existing for short periods
only
Three basic forms: messenger, transfer and
ribosomal RNA.
Organic bases present are adenine, guanine,
cytosine and thymine
Ratio of adenine and thymine to cytosine and
guanine is one
Found almost entirely in the nucleus
Amount is constant for all cells of a species
(except gametes and spores)
Chemically very stable
Permanent
Only one basic form, but with an almost infinite
variety within that form
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Fig 7.3.3 structure of
molecules
in
a
nucleotide
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7.7 DNA replication
With only a very few exception, every living cell contains DNA. (Red blood
cells are one such exception.) In prokaryotic cells there may be just one DNA
molecule. In eukaryotic cells there are usually several. For example, humans have
46 DNA molecules in their cells (when they are not dividing), because each of our 46
chromosomes contains one DNA molecule.
The DNA molecules carry coded instructions for the kinds of proteins which
will be made by the cell. A human begins life as a single cell that contains 23 DNA
molecules from its father and 23 from its mother. Each of these DNA molecules is
essential to the proper development of that single cell into a complete adult
organism. Therefore, before the cell divides by mitosis, each DNA molecule is copied
so that one copy can be distributed to each of the two daughter cells. At the start of
mitosis each chromosome contains two identical copies of its DNA molecule. Each
copy is called a chromatid.
DNA replication takes place during interphase in the nucleus of the cell.
Fig.7.1 shows how it is done. It requires a supply of free nucleotides (that is
nucleotides which exist singly, in solution, not joined into long chains as they are in
DNA) to which extra phosphate groups are added to activate them. The DNA
molecule unwinds and the two strands are separated by the breakage of the
hydrogen bonds between the bases. Nucleotides with the appropriate complementary
bases then slot into place opposite the exposed bases on each strand that is A with T
and C with G. Hydrogen bonds between the complementary bases hold them in
place. The sugar of one nucleotide is then joined to the phosphate of the next
nucleotide to form a new polynucleotide chain. These processes are dependent on a
number of enzymes, including DNA polymerase.
The result is that two new DNA molecules are formed from one old one. Each
new molecule contains one old polynucleotide strand and one new one, so this
method of replication is known as semi-conservative replication because half of the
old molecule is conserved.
Very few errors are made during DNA replication, because DNA polymerase
effectively ‘proof-reads’ the new molecules it is making. This enzyme will only link a
new nucleotide into the growing chain if the previous one is paired correctly. If it is
not, then the enzyme removes the wrong nucleotide and replaces it with the correct
one before it continues along the chain.
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Fig 7.1 Semi-conservative replication of DNA
PROTEIN SYNTHESIS
7.8 How DNA codes for protein synthesis
The function of DNA is to provide instructions for protein synthesis. One DNA
molecule contains enough instructions for making many proteins. A length of DNA
which contains the instructions for making a single proteins or polypeptide is called a
gene.
DNA contains a code which dictates the sequence in which amino acids are to
be linked together to make a protein. The sequence of bases in a gene is a code for
the sequence of amino acids in a protein.
The code in a DNA molecule is carried in the sequence of the four bases,
adenine (A), thymine (T), guanine (G) and cytosine (C), in one of its two strands,
the ‘reference’ strand, This base sequence is always ‘read’ in the same direction.
A group of three bases, called a triplet, codes for one amino acid (Fig.7.2).
As there are four bases, there are 64 possible different triplets. There are however,
only 20 different amino acids which need to be coded for. This means that, if only
one triplet coded for one amino acid, there would be 44 left-over triplets which coded
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for nothing. This does not happen. Most amino acids have two or more similar
triplets which code for them. There are still some ‘spare’ triplets and these are used
as ‘punctuation marks’, indicating starting and stopping points for beginning and
ending an amino acid chain. Table 7.2 shows the triplets of bases on the reference
strand of DNA molecule which code for each of the 20 amino acids used to make
proteins in cells.
Fig 7.2 How DNA codes for the sequence of amino acids in a protein. A very
small part of one gene is shown
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Table 7.2 the genetic code
7.9 An outline of protein synthesis
Protein molecules are made by linking together amino acids. This is done on
the ribosomes in the cytoplasm of a cell. The sequence of amino acids, the primary
structure, determines the overall shape and function of the protein (Fig.7.6).
DNA, in the chromosomes in the nucleus of the cell, contains the code laying
down the sequence in which the amino acids are joined together. In a eukaryotic the
DNA molecules remain inside the nucleus. The code is carried from the nucleus to
the ribosomes by a messenger molecule, messenger RNA (mRNA).
When a particular kind of protein is required, the length of DNA which carries
the instructions for making that protein-the gene-unwinds and unzips (Fig.7.6). This
exposes the bases on the two strands. Free mRNA nucleotides slot into place
opposite the exposed bases on the DNA reference strand, following the rules of
complementary base pairing. The sugars and phosphates of the mRNA nucleotides
are then linked together to form a long mRNA molecule. The sequence of bases on
the mRNA molecule is a complementary copy of the sequence formation of the mRNA
molecule is called transcription. Enzymes, including RNA polymerase, are required for
this process.
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Fig 7.6 protein synthesis
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Fig 7.9 (con)
The mRNA molecule then leaves the nucleus through a nuclear pore, and attaches to
a ribosome. The ribosome holds the mRNA so that six bases are exposed at one
time. A group of three bases on the mRNA is called a codon, so two codons are
exposed on the ribosome.
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Another type of RNA, called transfer RNA (tRNA) brings amino acids to the
ribosome. It is the tRNA which translates the code of base sequence into an amino
acid sequence. There are different tRNA molecules for each of the 20 amino acids,
and each of these tRNAs has a different sequence of three bases, called an
anticodon, at one end. At the other en, there is a site where a particular amino acid
can be joined. The amino acid is loaded on to the tRNA by an enzyme. There are as
many different kinds of these enzymes as there are different tRNA containing one
particular anticodon with one particular amino acid. The specificity of these enzymes
means that a tRNA molecule with a particular anticodon will always be loaded with a
particular, ‘matching’, amino acid.
For example, a tRNA with the anticodon AGG will be loaded with the amino
acid serine. If the codon UCC is exposed on the ribosome, then the rRNA will bond
with it. Next to it, another tRNA will then slot into place against its complementary
codon. As these two tRNAs bond with the two exposed mRNA condons, their two
amino acids are brought close together. A peptide bond is then formed between the
amino acids.
Once this is done, the ribosome moves along to the next mRNA codon. The
tRNA which was bonded to the first mRNA codon moves away, leaving its amino acid
behind. Another tRNA molecule moves in and bonds with the newly exposed mRNA
codon. Once again, a peptide bond forms between the amino acids. The process
continues until the ribosome reaches a codon signifying ‘stop’.
The formation of the protein molecule by following the base sequence on the
mRNA molecule is called translation. More detail about the process of transcription
and translation is given in Fig.7.6
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