Molecular Genetics

Molecular Genetics
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Genetics is the study of heredity (from the Latin genesis = birth). The big question to be answered is: why do organisms look almost, but not exactly, like their parents? There are three branches of modern genetics:

•  Molecular Genetics (or Molecular Biology), which is the study of heredity at the molecular level, and so is mainly concerned with the molecule DNA. It also includes genetic engineering and cloning, and is very trendy. This module is mostly about molecular genetics.

•  Classical or Mendelian Genetics, which is the study of heredity at the whole organisms level by looking at how characteristics are inherited. This method was pioneered by Gregor Mendel (1822-1884). It is less fashionable today than molecular genetics, but still has a lot to tell us. This is covered in Module 5.

• Population Genetics, which is the study of genetic differences within and between species, including how species evolve by natural selection. Some of this is also covered in Module 5.

Structure and Function of Nucleic Acids [back to top]

DNA and its close relative RNA are perhaps the most important molecules in biology. They contain the instructions that make every single living organism on the planet, and yet it is only in the past 50 years that we have begun to understand them. DNA stands for deoxyribonucleic acid and RNA for ribonucleic acid, and they are called nucleic acids because they are weak acids, first found in the nuclei of cells. They are polymers, composed of monomers called nucleotides.

Nucleotides   [back to top]

 Nucleotides have three parts to them:                             

• a phosphoric acid

• a deoxyribose (5-carbon or pentose sugar). By convention the carbon atoms are numbered as shown to distinguish them from the carbon atoms in the base. If carbon 2 has a hydroxyl group (OH) attached then the sugar is ribose, found in RNA.

• a nitrogenous base. There are five different organic bases, but they all contain the elements carbon, hydrogen, oxygen and nitrogen.  They fall into groups, purines (two rings of carbon and nitrogen atoms) and pyrimidines (a single ring of carbon and nitrogen atoms). The base thymine is found in DNA only and the base uracil is found in RNA only, so there are only four different bases present at a time in one nucleic acid molecule.

Nucleotide Polymerisation   [back to top]

Nucleotides can join together by a condensation reaction (results in the removal of water) between the phosphate group of one nucleotide and the hydroxyl group on carbon 3 of the sugar of the other nucleotide.  The bonds linking the nucleotides together are strong, covalent phosphodiester bonds. 

The bases do not take part in the polymerisation, so there is a sugar-phosphate backbone with the bases extending off it. This means that the nucleotides can join together in any order along the chain. Many nucleotides form a polynucleotide.

Each polynucleotide chain has two distinct ends

• a 3’ (‘three prime’) end à carbon 3 of the deoxyribose is closest to the end
• and a 5’ (‘five prime’) end à carbon 5 of the deoxyribose is closest to the end

Structure of DNA   [back to top]

The three-dimensional structure of DNA was discovered in the 1950's by Watson and Crick. The main features of the structure are:

• DNA is double-stranded, so there are two polynucleotide stands alongside each other. The strands are antiparallel, i.e. they run in opposite directions (5'à 3’ and 3’à5’)

• The two strands are wound round each other to form a double helix.

• The two strands are joined together by hydrogen bonds between the bases. The bases therefore form base pairs, which are like rungs of a ladder.

• The base pairs are specific. A only binds to T (and T with A), and C only binds to G (and G with C). These are called complementary base pairs. This means that whatever the sequence of bases along one strand, the sequence of bases on the other strand must be complementary to it. (Incidentally, complementary, which means matching, is different from complimentary, which means being nice.)

Function of DNA   [back to top]

DNA is the genetic material, and genes are made of DNA. DNA therefore has two essential functions: replication and expression.

·         Replication means that the DNA, with all its genes, must be copied every time a cell divides.

·       Expression means that the genes on DNA must control characteristics. A gene was traditionally defined as a factor that controls a particular characteristic (such as flower colour), but a much more precise definition is that a gene is a section of DNA that codes for a particular protein. Characteristics are controlled by genes through the proteins they code for, like this:

Expression can be split into two parts: transcription (making RNA) and translation (making proteins).   These two functions are summarised in this diagram (called the central dogma of genetics).

No one knows exactly how many genes we humans have to control all our characteristics, the latest estimates are 60-80,000. The sum total of all the genes in an organism is called the genome.

The table shows the estimated number of genes in different organisms:

^*kbp = kilo base pairs, i.e. thousands of nucleotide monomers.

 Amazingly, genes only seem to comprise about 2% of the DNA in a cell. The majority of the DNA does not form genes and doesn’t seem to do anything. The purpose of this junk DNA remains a mystery!

RNA    [back to top]

RNA is a nucleic acid like DNA, but with 4 differences:

• RNA has the sugar ribose instead of deoxyribose

• RNA has the base uracil instead of thymine

• RNA is usually single stranded

• RNA is usually shorter than DNA

Messenger RNA (mRNA)

mRNA carries the "message" that codes for a particular protein from the nucleus (where the DNA master copy is) to the cytoplasm (where proteins are synthesised). It is single stranded and just long enough to contain one gene only. It has a short lifetime and is degraded soon after it is used.

Ribosomal RNA (rRNA)

rRNA, together with proteins, form ribosomes, which are the site of mRNA translation and protein synthesis. Ribosomes have two subunits, small and large, and are assembled in the nucleolus of the nucleus and exported into the cytoplasm.

Transfer RNA (tRNA)

tRNA is an “adapter” that matches amino acids to their codon. tRNA is only about 80 nucleotides long, and it folds up by complementary base pairing to form a looped clover-leaf structure. At one end of the molecule there is always the base sequence ACC, where the amino acid binds. On the middle loop there is a triplet nucleotide sequence called the anticodon. There are 64 different tRNA molecules, each with a different anticodon sequence complementary to the 64 different codons. The amino acids are attached to their tRNA molecule by specific enzymes. These are highly specific, so that each amino acid is attached to a tRNA adapter with the appropriate anticodon.

Replication - DNA Synthesis   [back to top]

DNA is copied, or replicated, before every cell division, so that one identical copy can go to each daughter cell. The method of DNA replication is obvious from its structure: the double helix unzips and two new strands are built up by complementary base-pairing onto the two old strands.

1. Replication starts at a specific sequence on the DNA molecule called the replication origin.

2. An enzyme unwinds and unzips DNA, breaking the hydrogen bonds that join the base pairs, and forming two separate strands.

3.  The new DNA is built up from the four nucleotides (A, C, G and T) that are abundant in the nucleoplasm.

4.  These nucleotides attach themselves to the bases on the old strands by complementary base pairing. Where there is a T base, only an A nucleotide will bind, and so on.

5.  The enzyme DNA polymerase joins the new nucleotides to each other by strong covalent bonds, forming the sugar-phosphate backbone.

6.  A winding enzyme winds the new strands up to form double helices.

7.  The two new molecules are identical to the old molecule.

DNA replication can take a few hours, and in fact this limits the speed of cell division. One reason bacteria can reproduce so fast is that they have a relatively small amount of DNA.

The Meselson-Stahl Experiment    [back to top]

This replication mechanism is sometimes called semi-conservative replication, because each new DNA molecule contains one new strand and one old strand. This need not be the case, and alternative theories suggested that a "photocopy" of the original DNA could be made, leaving the original DNA conserved (conservative replication). The evidence for the semi-conservative method came from an elegant experiment performed in 1958 by Meselson and Stahl. They used the bacterium E. coli together with the technique of density gradient centrifugation, which separates molecules on the basis of their density.

The Genetic Code   [back to top]

The sequence of bases on DNA codes for the sequence of amino acids in proteins. But there are 20 different amino acids and only 4 different bases, so the bases are read in groups of 3. This gives 4³ or 64 combinations, more than enough to code for 20 amino acids. A group of three bases coding for an amino acid is called a codon, and the meaning of each of the 64 codons is called the genetic code.

There are several interesting points from this triplet code:

• It is a linear code i.e. the code is only read in one direction (5’à3’) along the mRNA molecule

• The code is degenerate i.e. there is often more than one codon for an amino acid i.e. there are more base combinations than there are amino acids.  This means that several base sequences may code for the same amino acid. E.g. CCA, CCC, CCG and CCT all code for the same amino acid: proline.  The first two bases of the code are more important than the third base in specifying a particular amino acid

• The code is non-overlapping, i.e. each triplet in DNA specifies one amino acid.  Each base is part of only one triplet, and is therefore involved in specifying only one amino acid.  

• At the start and end of a sequence there are punctuation codes i.e. there is a ‘start’ signal given by AUG (codes for methionine) and there are three ‘stop’ signals (UUA, UAG and UGA).  The three stop signals do not code for an amino acid.

• It is a universal code i.e. the same base sequence always codes for the same amino acid, regardless of the species

DNA and Protein Synthesis  [back to top]

Transcription - RNA Synthesis

DNA never leaves the nucleus, but proteins are synthesised in the cytoplasm, so a copy of each gene is made to carry the “message” from the nucleus to the cytoplasm. This copy is mRNA, and the process of copying is called transcription.

• The start of each gene on DNA is marked by a special sequence of bases.

• The RNA molecule is built up from the four ribose nucleotides (A, C, G and U) in the nucleoplasm. The nucleotides attach themselves to the bases on the DNA by complementary base pairing, just as in DNA replication. However, only one strand of RNA is made. The DNA stand that is copied is called the template or sense strand because it contains the sequence of bases that codes for a protein. The other strand is just a complementary copy, and is called the non-template or antisense strand.

• The new nucleotides are joined to each other by strong covalent bonds by the enzyme RNA polymerase.

• Only about 8 base pairs remain attached at a time, since the mRNA molecule peels off from the DNA as it is made. A winding enzyme rewinds the DNA.

• The initial mRNA, or primary transcript, contains many regions that are not needed as part of the protein code. These are called introns (for interruption sequences), while the parts that are needed are called exons (for expressed sequences). All eukaryotic genes have introns, and they are usually longer than the exons.

• The introns are cut out and the exons are spliced together by enzymes

• The result is a shorter mature RNA containing only exons. The introns are broken down.

• The mRNA diffuses out of the nucleus through a nuclear pore into the cytoplasm.

Translation - Protein Synthesis [back to top]

 A single piece of mRNA can be translated by many ribosomes simultaneously, so many protein molecules can be made from one mRNA molecule. A group of ribosomes all attached to one piece of mRNA is called a polysome.

 Post-Translational Modification   [back to top]

In eukaryotes, proteins often need to be altered before they become fully functional. Modifications are carried out by other enzymes and include: chain cutting, adding methyl or phosphate groups to amino acids, or adding sugars (to make glycoproteins) or lipids (to make lipoporteins).  

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Last updated 20/06/2004