Genes are small sections of DNA within the genome that code for proteins. They contain the instructions for our individual characteristics – like eye and hair colour.

A gene is a small section of DNA that contains the instructions for a specific molecule, usually (but not exclusively) a protein. The purpose of genes is to store information. Each gene contains the information required to build specific proteins needed in a human.

Genes come in different forms, called alleles. In humans, alleles of particular genes come in pairs, one on each chromosome (we have 23 pairs of chromosomes). If the alleles of a particular gene are the same, the organism is described as homozygous for that gene. If they are different the organism is described as heterozygous for that gene.

An individuals phenotype is determined by the combination of alleles they have. For example, for a gene that determines eye colour there may be several different alleles. One allele may result in blue eyes, while another might result in brown eyes. The final colour of the individual’s eyes will depend on which alleles they have and how they interact.

The characteristic associated with a certain allele can sometimes be dominant or recessive.

A genome is an organism’s complete set of genetic instructions. Each genome contains all of the information needed to build that organism and allow it to grow and develop.

A genome is an organism’s complete set of genetic instructions. The instructions in our genome are made up of DNA. This code is determined by the order of the four nucleotide bases that make up DNA, adenine, cytosine, guanine and thymine, A, C, G and T for short. DNA has a twisted structure in the shape of a double helix. Single strands of DNA are coiled up into structures called chromosomes.

Genomics is the study of genomes. Genomics looks at the DNA code packaged within the chromosomes found in the nucleus of a plant or animal’s cell.

The human genome contains 20,687 protein-coding genes. The human genome is made of 3.2 billion bases of DNA but other organisms have different genome sizes.

Genetics began in Cambridge, much of the material you will be taught has its beginnings at the university and surrounding institutes.

We will start with a Cambridge perspective, that may help you understand where some of the ideas mentioned above first arose, and where some of the key terms we use first came from.

Most talks on genetics begin with Mendel and his pea plants, experiments that took place in the mid 1800s. We are going to fast forward to the start of the 20^th Century, and pick up the story here in Cambridge at Newnham College.

Between 1900-1910 William Bateson directed a rather informal school of genetics, mostly of the women associated at Newnham College, who could not yet study for degrees. Unaware of the work Mendel had performed, Bateson has been working hard on understanding the basis for variation, even coining the phrase homeotic mutation to describe the effect of one body part being replaced with another. This term will become familiar to you if you have encountered the Hox gene family. When Gregor Mendel’s two part research paper was re-read in 1900 Bateson became the chief populariser of the ideas and termed Mendel’s observations Mendelian laws. At this point the concept of chromosomes and inheritance were still separate.

In 1906 Bateson coined the phrase genetics, and our discipline was born. Many of you will be aware of the “punnet square” which identifies the inheritance pattern for dominant and recessive characteristics. This was co-developed by Bateson and his student Reginald Punnet, they performed all of their experiments, with the Newnham college Mendelians, to confirm Mendel's work with pea plants. Chief amongst the Newnham women was Muriel Wheldale Onslow who joined William Bateson's genetics group at Cambridge in 1903.

Out of their work came the terms that we rely on today such as genetics, genotype, phenotype, gene, epistasis and many others that will be explained throughout this programme.

They performed this work at the Balfour laboratory in central Cambridge, using species that they could easily follow traits in such as snapdragon flowers, pea plants, chickens and rabbits. Most genetics text books use these original examples to illustrate the basic principles of inheritance involved.

In the fundamentals of genetics primer we are going to start by looking at the simple rules of inheritance, and how they relate to chromosomes.

It should be noted that although we refer to these as Mendel’s laws, and Mendelian genetics, these rules were described by Bateson and others to explain Mendel's observations. Mendel did not use the term gene or allele.

The laws of Mendelian genetics are:

Dominance: Some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele.

Segregation: The alleles for each gene segregate from each other so that each gamete carries only one allele for each gene

Independent assortment: Genes of different traits can segregate independently during the formation of gametes

Cells are the building blocks of life, each cell of the human body contains a copy of the human genome in the cells nucleus

All life revolves around the concept of the cell. It is the smallest unit of life, with each cell containing all of the necessary information to grow, survive and replicate itself. This principle is conserved from the smallest bacteria such as E.coli to single celled eukaryotes and large multi-cellular eukaryotes such as humans like us. Our bodies are made up of millions of cells (100,000,000,000,000), each with their own complete set of instructions for making us. This set of instructions is known as our genome and is made up of DNA. Each cell in the body, for example, a skin cell or a liver cell, contains this same set of instructions (there is always an exception - red blood cells lose the nucleus containing DNA as they develop).

Chromosomes are linear pieces of DNA. The name means coloured body.

We've just been introduced to chromosomes, but how do we know about them? In 1842 structures were discovered in cells that would later became known as chromosomes. Chromosome literally means “coloured body” in Greek.

Khroma (colour) soma (body)

The term chromosome was used to describe structures that formed during the process of cell division. How were they seen? Well remember the name means coloured body. The use of stains to visualise chromosomes was integral to identifying the location of genes in the pre-genomic era as we will soon discuss.

If we take a look at a genome browser, such as Ensembl, you will see the human chromosomes displayed as in the image to the left. The characteristic banding pattern is a result of the staining.

To view information on a chromosome in a genomic context we use a genome browser.

To look at a chromosome we can make use of a tool called a genome browser. There are many different browsers available. During the programme you will make use of Ensembl. For this primer we are going to use a simple but powerful genome browser called the Integrative Genomics Viewer (IGV). We can view many things on a genome browser, the position of genetic variation, the location of genes, exons, introns, in fact anything we can provide co-ordinates for.