The functions of DNA and RNA in Protein Synthesis

Triplet codes and the processes of transcription and translation.

Coding DNA, non-coding DNA, mRNA and tRNA

Doc Brown's Biology Revision Notes

Suitable for GCSE/IGCSE/O level Biology/Science courses or equivalent

 This page will help you answer questions such as ...

 What is a nucleotide? What is its structure?

 What is the structure of DNA? Why is it classed as a polymer?

 How does DNA code for amino acids and hence proteins?

 What is the function of DNA? How are proteins synthesised?

 What is RNA? What is the function of RNA? What is a triplet code? How can we extract DNA from cells?

How do cells make proteins in the cytoplasm? What functions to proteins have in living organisms?

How was the structure of DNA was discovered?

What were the roles of the scientists Watson, Crick, Franklin and Wilkins?

In the 1950s, Rosalind Franklin working for Maurice Wilkins examined strands of DNA using a technique called X-ray diffraction.

The sample under investigation, e.g. a DNA crystal strands, is bombarded with X-rays and the layers of atoms behave like a diffraction grating and scatter the X-rays in particular pattern that depends on the 3D arrangement of atoms in the molecule. The path of the scattered X-rays is recorded on a photographic plate.

Rosalind Franklin died tragically young from cancer, and never received the Nobel Prize she would have undoubtedly received, BUT, in one of the last things she wrote in her laboratory notebook, she speculated that DNA had a helix structure.

Later Frances Crick and James Watson gathered together this X-ray data (Crick had access to Rosalind Franklin's 'classic' X-ray photograph of crystallised DNA, characteristic of a helical structure) with other information ...

e.g. the chemical analysis of DNA, particularly the ratios of the four bases (adenine, cytosine, guanine and thymine), the shape of the four base molecules ...

and then built a model and deduced what we recognise today as the double helix structure of DNA - brilliant insight, more Nobel Prize winners along with Maurice Wilkins.

The important thing is that the experimental observations from chemical and structural analysis fitted the evidence based model.

Rosalind Franklin, Physicist and Biologist, tragically dying young from a combination of pneumonia and advanced cancer. All the other three scientists mentioned above received the ultimate accolade of a Nobel prize. Rosalind Franklin would also have received a Nobel prize, if she had not died so tragically young..


The structure of nucleotides and DNA - deoxyribonucleic acid


DNA (deoxyribonucleic acid) is a large molecule essential for life and cell replication and is another example of a natural polymer.

Its structure was worked out in the 1950s, notably by the Nobel Prize winners Crick and Watson, though several other notable scientists made important contributions.

DNA, a natural polymer is made up of string of repeating units (the monomer) called nucleotides.

The DNA form two linked strands coiled together in the shape of a double helix (more DNA structure later).

DNA molecules hold all of an organism's genetic material, that is all the chemical instructions for individual cells and complex organisms to grow and develop.

All the instructions that are needed for an organism to grow, develop and reproduce is encoded in the DNA.

The contents of your DNA directly determines what your inherited characteristics are.

The DNA is organised into long coiled up sections called chromosomes, and within the chromosomal DNA there are shorter sections called genes.

Your total DNA, that is the full contents of your genes, is called the genome.

Chromosomes normally come in pairs.

DNA encodes genetic instructions for the development and functioning of living organisms and viruses.

e.g. every protein molecule needed by a living organism down to individual cell level is synthesised by other molecules reading the genetic DNA code and combining the right amino acids in the right order.

The DNA not only codes for all the necessary proteins, it also determines what type a cell becomes e.g. blood cell, brain cell, muscle cell, skin cell etc.

Proteins are polymers of amino acids. DNA is a polymer of nucleotides.

So amino acids and nucleotides are monomers.

Every protein has a specific structure for a particular function including enzymes, and most be encoded in DNA.


The structure of DNA

Most DNA molecules consist of two polymer chains, made from four different monomers called nucleotides, connected together in the form of a double helix.

Unlike man-made poly(ethene), from the monomer ethene etc. DNA is a naturally occurring polymer - long molecular chains of joined up monomer (single) molecules.

The nucleotide is the small basic molecular unit - the monomer from which the polymer is formed.

Nucleotides form the building blocks of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). An individual nucleotide consists of three molecular bits combined together - the same phosphate group, a variable base (adenine, cytosine, guanine or thymine), and the same pentose sugar (pentose just means having a ring of 5 atoms). The phosphate group and base are attached to the sugar (see left diagram of a single nucleotide).

The DNA (and RNA) polymer chain is formed by a large number of phosphate-sugar linkages. The base is a sort 'branch' off the main chain, but this helps it to intermolecular bond with a base of another opposite strand of DNA.

The result is full DNA molecule consists of two 'molecular' strands coiled together to form a double helix, but how is this helix held together?

The two polymer strands of DNA are cross-linked by a series of complementary base pairs joined together by weak intermolecular bonds - cross links (base-pairing bonds shown here as on the diagram):

There are four bases in DNA holding the structure together and the same two bases are always paired together - known as complementary base pairing.

Adenine (A) with thymine (T)  AT, and cytosine (C) with guanine (G) CG.

Whererepresents the weak (but crucial) intermolecular attractive bonding force between the pairs of bases. This weaker intermolecular bond is actually called a hydrogen bond, but you don't need to know any more detail at GCSE level.

These cross linking complementary base pair bonds hold the DNA strands tightly together giving it the necessary stability to perform their genetic roles.

Here complementary means 'matching pairs'. A with T and C with G are the linked complimentary base pairs.

The double helix structure is shown in the diagram above on the right, illustrating how the DNA is held together by the cross-linking hydrogen bonds between the bases to hold together the double helix together.

A short section of DNA is illustrated in more detail below.

A more detailed diagram of a very short section of a double-helix DNA molecule showing the two different base pairings holding the two molecular strands together.

It is the order of the bases in the DNA strands of a gene that decides the order of amino acids in a protein.



DNA code, bases, genes and the triplet code

As already mentioned, DNA polymer molecules contain the genetic codes that determine which proteins are synthesised.

These synthesised proteins control how all the cells in an organism function, in other words the DNA controls the production of all proteins - protein synthesis in the ribosomes, one of the sub-cellular structures in the cytoplasm of cells.

A short section of DNA that codes for a particular protein is known as a gene.

This means each gene codes for a particular set of amino acids that form a protein.

It is the order of the bases in the gene that determines the order of the amino acids in the protein.

Every gene has a different sequence of bases to code for all the proteins an organism requires.

Only 20 different amino acids are used to synthesise all the thousands of different proteins.

It is the genes of the DNA that tells the ribosomes in cells the correct order to assemble the amino acids to make a specific protein.

A ribosome, a tiny structure in the cytoplasm, is essentially a protein factory that makes everything from enzymes, keratin, muscle fibre cells, red blood cells etc. and all based on the DNA codes.

Every protein, a polymer chain of amino acids, has a unique structure based on a specific number of amino acids AND a specific sequence of amino acids.

Each protein also has a specific 3D shape, essential for it to carry out its particular function e.g. an enzyme or type of tissue.

The order of bases in a gene of the DNA determines the order of amino acids which will combine to form a specific the protein, which in turn, will perform a specific function in the living organism.

Every amino acid is coded for by a sequence of three bases in the gene, known as a triplet code (illustrated by diagram below for three 'fictitious' amino acids).

Every gene contains a different sequence of bases so it can code for a particular protein.

The order of bases on an organism's DNA is called the genetic code of the genome.

The genome is the whole of an organism's genetic material. See Introduction to the GENOME and gene expression - considering chromosomes, alleles, genotype, phenotype, variations

Adenine A, thymine T, cytosine C, guanine G

The amino acids are joined together to make the various proteins dependent on the order of the bases in the gene.

Notes on non-coding DNA: There are parts of the DNA strands that do NOT code for any proteins.

However, some of these non-coding sections switch genes on and off, in other words, they control whether or not a gene is expressed to make a protein.

Therefore some of these non-coding regions of the DNA are involved in protein synthesis.

Before transcription can occur, the RNA polymerase has to bind to a non-coding section of DNA adjacent to the specific gene (for a specific protein).

If a mutation has occurred in this section of the DNA it can affect the ability of the RNA polymerase to bind to it - it might be harder or easier (or no effect).

The quantity and accuracy of how much mRNA is transcribed depends on how well this binding takes place - and therefore affects how well the protein is produced.

Therefore the production of the protein may be affected, and, depending on its function, that specific phenotype may also be affected.

This means that genetic variants in non-coding regions of DNA can affect the phenotypes exhibited by an organism, despite the fact that these non-coding sections of DNA done code for proteins themselves.

The diagram above shows how the triplet codes on DNA work. A sequence of three bases (e.g. CCA) on a single strand of DNA codes for a particular amino acid. A sequence of three triplet codes will code for three amino acids in that particular sequence on that part of the gene.

Using letters to represent the sequence of bases on a strand of DNA is an example of a scientific model. The double helix structure of DNA is another spatial scientific model. All these models must be tried and tested in the laboratory and all observations must back up any hypothesis to become a workable scientific model.

The cell chemistry allows the reading of the genetic triplet codes (sequence of bases) on the DNA code to eventually join these three amino acids together in the precise order dictated by the DNA code. In fact for any protein you are actually dealing with sequences of dozens-hundreds of triplet codes for a particular protein.

In the next section we look at how we get from DNA triplet codes to the actual production of a protein and unfortunately its a bit more complicated than the above diagram suggests!


The formation of mRNA and the actual synthesis of proteins in cytoplasmic ribosomes

DNA is found in a cell's nucleus and cannot move from it through the nucleus membrane because of the large size of its molecules.

Therefore there must be a means of getting the genetic information from the nucleus to the tiny structures, called ribosomes in the cytoplasm, in which the proteins are synthesised.

This is achieved using a molecule called messenger ribonucleic acid (mRNA, a type of RNA) i.e. how the cell gets the code from the nucleus to the ribosomes - the mRNA is a sort of 'messenger'.

mRNA is shorter than DNA and a single strand molecule, but still another polymer of nucleotides, but small enough to exit the membrane of the nucleus.

Note that there is an important difference between DNA and RNA.

In RNA the base thymine (T) is replaced by the base uracil (U), so the base pairings in RNA are C-G (as in DNA) but A-U (not A-T).

As illustrated above, the DNA contains the gene's triple coding system for the amino acids to needed to be combined to form a specific protein - with specific molecular properties to perform a particular chemical function in an organism.



In the nucleus, using enzymes, the two strands of the DNA double helix unzip and become a template for the production of mRNA (messenger ribonucleic acid).

The enzyme RNA polymerise binds to the non-coding DNA in front of a gene sequence of bases.

The two DNA strands unzip and the RNA polymerase moves along one of the strands of the DNA (see diagram on right).

Therefore the DNA coding of a gene is used as a template to make the mRNA.

By pairing up the complementary bases (on the DNA and nucleotide), the correct sequential nucleotides in the nucleus are brought together to form a complementary strand of mRNA, a step in the process called transcription (this takes place in the nucleus, diagram on right).

The smaller mRNA molecule can now migrate out of the cell nucleus into the cytoplasm and attach themselves to a ribosome (the actual protein 'factory'!).



In the cytoplasmic ribosomes, the mRNA now itself acts as a template of triplet codes for amino acids to be joined together in the correct sequence for a specific protein.

In order for this to happen, the amino acids in the cytoplasm are drawn into the ribosome complex and assembled in order to match the complementary triplet codes.

The correct amino acids are brought to the ribosomes by a carrier molecule called transfer ribonucleic acid (tRNA).

The amino acids are then joined together, by enzymes, in the correct order to make a particular protein.

The order of the amino acids connected together in the ribosome will match the order of the base triplets (called codons) on the mRNA molecule.

The complimentary triplet base sequence on the tRNA structure is called the anticodon.

This production of the protein, dictated by the complementary triplet codes on the mRNA, is called the translation stage, and this takes place in the cytoplasm.

So, the RNA and appropriate enzymes in the ribosome, join the amino acids together to form the protein - a polypeptide - meaning a polymer formed from the amino acid monomer units.


The above diagram shows translation in more detail, including the role of another type of RNA - transfer ribonucleic acid (tRNA) which brings the amino acids together onto the mRNA.

  • Points to consider when studying the translation diagram above
  • The joining together of the amino acids on the mRNA is done using transfer ribonucleic acid (tRNA).
  • These relatively short molecules of tRNA actually bring the amino acids together to match the mRNA triplet codes.
  • In other words the triplet codes of tRNA and mRNA are also complementary.
  • Note that In RNA (mRNA or tRNA) the base thymine (T) has been replaced by the base uracil (U), so complimentary base pairing is now U-A (not A-T), but C-G retained and its still all about matching complimentary base pairs.
  • The sequence of events is as follows:
  • The attachment of the mRNA to the ribosome
    • The mRNA has exited from the nucleus and docks into a ribosome
  • The coding by triplets of bases (codons) in the mRNA for specific amino acids
    • The triplet base codes for particular amino acids and their joining up sequence can now be read from the mRNA molecules.
  • The transfer of amino acids to the ribosome by tRNA (transfer ribonucleic acid)
    • After the mRNA joins onto a ribosome, molecules of transfer RNA (tRNA) bring the amino acid that matches the code on the mRNA, the complimentary base codes of the mRNA and tRNA ensure that all proteins are synthesised with their specific protein sequence, so all proteins are completely reproducible.
  • The linking of amino acids to form polypeptides
    • The ribosome then acts as the catalytic site for linking the amino acids together to synthesise a specific protein.
    • This second process is called translation because the triplet base code sequence is read and translated into the amino acid sequence of a protein.
    • A sequence of amino acids joined together in a chain is called a polypeptide, a natural polymer or macromolecule.
    • All of these reaction are catalysed by enzymes.


SUMMARY of protein synthesis

So, to summarise, you start with DNA in the nucleus, then to complementary mRNA in the nucleus (transcription stage), mRNA moves into the cytoplasm and then the amino acids are joined together in the ribosomes via the complementary triplet codes (translation stage).

The diagram 'sketch' below also 'attempts' to summarise what is actually a very complicated process!


The diagram below puts protein synthesis in perspective of starting with the genome of a cell's nucleus.

The genome is the whole of an organism's genetic material.

You are now ready for the following sections, in order:

Introduction to the GENOME, gene expression - considering chromosomes, alleles, genotype, phenotype, variations

An introduction to genetic variation and the formation and consequence of mutations  gcse biology revision notes

Introduction to the inheritance of characteristics and genetic diagrams (including Punnett squares)

How to extract DNA from plant cells

1. You need an appropriate source e.g. split peas, strawberries, kiwi fruit, onions or bananas etc.

However, it is reported that the 'white strands' of DNA from fruit, may actually be pectin.

2. The starting plant material is well mashed.

3. The mash is scraped into a beaker containing a solution of detergent and salt.

The detergent helps break down the cell membranes to release the DNA.

The salt makes the DNA strands stick together.

4. The resulting mixture is filtered into a test tube.

You can use a normal filter funnel and filter paper, as in your chemistry lessons!

This removes the froth and the bigger insoluble bits of the plant cells.

5. Some ice-cooled alcohol is carefully added to the filtered mixture. in the test tube

6. A band of white precipitated DNA strands should form - DNA is not soluble in cold alcohol.

7. You can then extract the DNA from this band with a glass rod.


A more detailed diagram of the base sequence replication using the DNA template.

1. The DNA double helix molecules splits in two, and the two strands then act as templates.

2. Freely moving nucleotides can be matched up to form the weak bonds between the complimentary base pairs.

3. Two identical strands of DNA produced, both identical in their original sequence of bases.


The  full DNA molecule consists of two 'molecular' strands coiled together to form a double helix.

The two polymer strands of DNA are cross-linked by a series of complementary base pairs joined together by weak bonds - cross links

There are four bases in DNA holding the structure together and the same two bases are always paired together - known as complementary base pairing.

Complementary means 'matching pairs'. A with T and C with G links.

i.e. adenine (A) with thymine (T)  AT, and cytosine (C) with guanine (G) CG.

These cross linking complementary base pair bonds hold the DNA strands tightly together giving it the necessary stability to perform their genetic roles.

The different functions of proteins

As already mentioned, protein molecules adopt a very specific folded 3D shape in order to be able to carry out their specific function - so what are these functions?

These proteins may end up in muscle cells, brain cells, enzyme catalysts, haemoglobin molecules etc.

BUT, note that proteins, particularly enzymes, are involved in building up non-protein molecules e.g. fats, cell walls, glycogen etc.

Reminder: Enzymes have active sites of a specific shape that connect with substrate molecules, and this allows them to catalyse a specific chemical reaction in the biochemistry of living organisms.

(a) Enzymes are biological catalysts that control most chemical reactions in living organisms..

(b) Many tissues are built of proteins e.g. collagen a strong structural protein that strengthens connective tissue like ligaments and cartilage of muscle systems of the joints.

(c) Carrier molecules like haemoglobin (conveys oxygen to cells) are also protein molecules.

(d) Some antibodies are protein molecules.

(e) Many hormones are protein molecules e.g. insulin, the hormone released into the blood from the pancreas, controls blood sugar levels.

(Note there are many hormones which are NOT proteins e.g. some hormones involved in the menstrual cycle.)


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