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Gene

A short piece of DNA which is responsible for the inheritance of a particular characteristic. It codes for the production of a specific protein

DNA

Deoxyribonucleic acid. This is the molecule which contains the genetic code. It coils up tightly inside chromosomes. DNA is a double helix made from two strands which are joined together by pairs of bases.

Rough endoplasmic reticulum

A network of membranes within a cell which has ribosomes attached to it. They are important in the synthesis and transportation of proteins.

Transcription factors

Transcription factors are proteins which bind to the nuclear DNA, regulating the transcription of the genetic material and sometimes changing the mRNA which is formed as a result.

Transfer RNA

RNA molecule found in the cytoplasm of the cell which transports specific amino acids to the surface of the ribosomes

Second messengers

Chemicals made in response to first messengers (eg steroid hormones) that cannot pass through the cell membrane.

Non-coding RNA

About 98% of the transcribed RNA thought to regulate transcription of the DNA directly, or by histone modification, or to modify the products of transcription.

Histone modification

The addition or removal of different groups from histones makes the heterochromatin structure more or less open, affecting whether the DNA can be transcribed or not.

Genetic code

Sequence of bases in a DNA molecule which codes for the sequence of amino acids in a protein. Each group of three bases, codes for an amino acid.

RNA polymerase

Enzyme involved in the transcription of DNA and the production of mRNA. The enzyme is involved in the breakdown of the hydrogen bonds between the two strands of DNA in the formation of mRNA, and the build up of the mRNA strand from 5-3 end.

DNA methylation

The addition of a methyl (CH3) group to a cytosine positioned next to a guanine in the DNA chain with a phosphate bond between them, (a CpG site) by DNA transferase.

DNA demethylation

The removal of a methyl (CH3) group from a cytosine positioned next to a guanine in the DNA chain with a phosphate bond between them, (a CpG site).

Digestive system

The organ system in the body which breaks down large insoluble food molecules into small soluble molecules which can be used by the body

Cyclic AMP

Cyclic adenosine monophosphate. The most common second messenger molecule in cells, derived from adenosine triphosphate (ATP)

Epigenetics

Epigenetics is the study of external factors which affect gene expression and differentiation, often by switching particular genes on or off, so changing the proteins made by a DNA sequence.

Spliceosomes

Enzymes that remove introns from pre mRNA and change the arrangement of exons to give different proteins from the same bit of DNA.

Polypeptide

A long chain of hundreds or even thousands of amino acids joined by peptide bonds.

Pepsin

A protein-digesting enzyme found in the mammalian stomach.

Introns

Non-coding regions of DNA or RNA

Fibrin

A protein produced during the clotting of the blood which traps platelets and red blood cells to form the clot

Exons

Coding regions of DNA or RNA.

Codon

A group of three bases within the DNA molecule which code for a specific amino acid or for the beginning or ending of a transcription sequence.

Protein synthesis

Protein synthesis is the process by which the information in the DNA code is translated into proteins. Some of these proteins form part of the cell structure. Others are enzymes that then control the production of all the other materials that make up the cell or the entire organism.

Protein synthesis is a continuous process but we break it down into stages to help us understand what is taking place and where it happens in the cell.

  • DNA is transcribed into messenger RNA (mRNA) The way the DNA is transcribed may be affected in a number of different ways
  • Modified mRNA leaves the nucleus through the nuclear pores and moves to the surface of a ribosome (often on the surface of the rough endoplasmic reticulum)
  • mRNA binds to the surface of a ribosome
  • Molecules of transfer RNA (tRNA) carry individual amino acids to the surface of the ribosome and line up against a complementary codon on the mRNA.
  • Ribosomal enzymes link the amino acids together, forming peptide bonds
  • tRNA breaks away and returns to the cytoplasm to pick up another amino acid
  • The ribosome moves along the molecule of mRNA until the end is reached. The completed polypeptide detaches. It may move into the Golgi apparatus or into the cytoplasm.
  • The mRNA may be read repeatedly before being released from the surface of the ribosome.

Protein synthesis

Animation showing protein synthesis from transcription in nucleus to packaging and exocytosis from the Golgi apparatus

For many years scientists thought each gene coded for a single protein. Now we know that a variety of different factors act on the DNA itself or on the mRNA that is formed in the nucleus. As a result, a single gene may code for many different proteins depending on both the internal and external environment of the cell.

Factors affecting gene expression

1 Transcription factors

The transcription of the DNA itself may be affected by transcription factors in a number of different ways

  • Transcription factors may stimulate the start of the transcription of a particular region of DNA
  • Transcription factors may make the structure of the chromatin more or less open to RNA polymerase, stimulating or preventing the transcription of a particular region of DNA
  • One transcription factor can affect a number of genes in different ways, switching some genes on and some genes off.
2 Spliceosomes

The initial mRNA is a transcription of all of the DNA including introns or non-coding regions of DNA. It needs to be modified before it is transported to the ribosomes for translation. The introns are removed by enzymes called spliceosomes. Sometimes spliceosomes join some of the exons, or coding regions, in different sequences so the same region of DNA can result in several different types of mRNA.

Epigenetics is a relatively new way of looking at the effect of the environment on the genome. It describes how different chemicals associated with the DNA or RNA can affect the way the genetic code is read. This external control of the genome may be brought about by

  1. DNA methylation – silencing of a gene or gene sequence. DNA methylation can also affect the histone arrangement, an alternative mechanism for affecting DNA transcription (see below). DNA demethylation has the opposite effect and activates a silenced gene.
  2. Histone modification – the addition or removal of different groups from histones makes the heterochromatin structure more or less open. This affects whether the DNA can be transcribed or not. The histones can be modified in a number of ways including levels of histone acetylation – the addition of an acetyl (ethanoyl) group - and histone methylation
  3. Non-coding RNA – only about 2% of the transcribed RNA actually codes for proteins. It appears that much of the non-coding RNA (ncRNA) regulates transcription of the DNA directly or by histone modification, or modifies the products of transcription.

Some proteins are produced in an inactive form. Post-translational changes as a result of second messengers such as cyclic AMP (cAMP) in the cell, or specific enzymes in the body, will modify and activate the proteins, changing the molecule produced. Examples are the production of fibrin from fibrinogen in the clotting cascade and the production of pepsin from pepsinogen in the digestive system.

Activity:

Investigate epigenetics and produce a poster explaining one example of this fast-growing area of research to your peers.