DNA, RNA and Protein Synthesis

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 (mRNA)? What is a triplet code?



The structure of nucleotides and DNA - deoxyribonucleic acid

Introduction

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 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.

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

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 code and combining the right amino acids in the right order.

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 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. Its actually called a hydrogen bond, but you don't need to know about the hydrogen bond 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.

 


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PROTEIN SYNTHESIS

DNA code, 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.

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 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 combined in the protein.

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 its 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 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 size of the DNA polymer molecules.

Therefore there must be a means of getting the genetic information from the nucleus to the ribosomes in the cytoplasm where the proteins are synthesised.

This is achieved using a molecule called messenger ribonucleic acid (mRNA, a type of RNA).

mRNA is shorter than DNA and a single strand molecule, but still another polymer of nucleotides.

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.

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

This production of the protein, dictated by the complementary triplet codes on the mRNA, is called the translation stage.

Translation

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.

 

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!


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