Control,Genomes and environment(F215)

A gene is a length of DNA that codes for one or more polypeptides,including enzymes

The sequence of the bases on a gene is a code with instructions for the construction of proteins. It has a number of characteristics:
It is a triplet code- three bases code of an amino acid
It is a degenerate code- All amino acids bar one have more than one code
Some codes don’t code for amino acids but are ‘stop’ codons- they indicate the end of the
polypeptide chain
It is widespread but not universal- Codons generally always code for the same amino acid
in every organism, but this is not always the case.

1. Free RNA nucleotides are activated, two extra phosphoryl groups are added to make ATP, GTP,CTP and UTP.
2. The gene to be transcribed unwinds and unzips. To do this the length of DNA that makes up thegene dips into the nucleolus & the hydrogen bonds between the nucleotide bases break.
3. Activated RNA nucleotides binds, using Hydrogen Bonds, with their complementary exposed
bases on the template strand. This is catalysed by RNA polymerase
4. The two extra phosphoryl are released, releasing energy for bonding two adjacent nucleotides
The mRNA produced is complementary to the nucleotide base sequence on the template
strand of DNA and therefore is a copy of the base sequence on the coding strand of DNA
5. The mRNA is released from the DNA and passes out of the nucleus through a pore in the
nuclear envelope to a ribosome

This process is called Translation-the assembly of polypeptides(proteins) at ribosomes

1. A molecule of mRNA binds to a ribosome. Two codons are attached to the small subunit of the
ribosome and exposed to the large subunit. The first exposed mRNA codon is always AUG.
Using ATP energy and an enzyme, a tRNA molecule with the amino acid methionine and the
anticodon UAC forms hydrogen bonds with this codon
2. A seconds tRNA molecule, bearing a different amino acid, binds to the second exposed condonwith its complementary anticodon
3. A peptide bonds forms between the two adjacent amino acids. This is catalysed by an enzyme
in the small ribosomal sub unit
4. The ribosome now moves along the mRNA reading the next codon. A third tRNA brings anotheramino acid and a peptide bonds forms between it and the dipeptide. The first tRNA leaves and is able to collect and bring another of its amino acids.
5. The polypeptide chain grows until a stop codon is reached, for which there are no
corresponding tRNAs and the polypeptide chain is complete

mutations cause changes to the sequence of nucleotides in DNA molecules

• Beneficial
  The mutation changes the sequence of amino acids and therefore the phenotype, but this
  gives the organism an advantageous characteristic
  E.g. Paler skin in more temperate climates absorbs more vitamin D
• Neutral
  It is a mutation in a non-coding region of the DNA
  It is a silent mutation- although the base triplet has changed, it still codes for the same
  amino acid and so the protein is unchanged.
• Harmful
  The mutation changes the sequence of amino acids and therefore the phenotype, and the
  resulting characteristic is harmful
  E.g. paler skin in a hotter climate burns more easily

cyclic AMP activates proteins by altering their three-dimensional structure

E. coli grown in a culture medium with no lactose can be placed in a growth medium with lactose.
At first they cannot metabolise the lactose because they only have tiny amounts of the enzymes needed to catalyse the reaction. A few minutes after the lactose is added, E. coli increases the rate of synthesis of these enzymes by about 1000 times, so lactose must trigger the production of them it is the inducer.
When lactose is absent:
1. The regulator gene is expressed and the repressor protein is synthesised. It has two binding sites. One binds to lactose and one that binds to the operator region
2. In binding to the operator region, it covers part of the promoter region where RNA polymerase normally attaches
3. RNA polymerase cannot bind to the promoter region so the structural genes cannot be transcribed into mRNA
4. Without mRNA the genes cannot be translated and the enzymes cannot be synthesised
When lactose is added:
1. Lactose binds to the other site on the repressor protein, causing the molecule to change shape. This prevents the other binding site from binding to the operator region. The repressor dissociates from the operator region
2. The leaves the promoter region unblocked. RNA polymerase can now bind to it and initiate the transcription of mRNA.
3. The operator- repressor- inducer system acts as a molecular switch. It allows synthesis of the structural genes
4. As a result, the bacteria can now use the lactose permease enzyme to take up lactose from the medium into their cells. They can then convert it to glucose and galactose using the β-galactosidase enzyme. These sugars can then be used for respiration

• Homeotic genes are similar in plants, animals and fungi. These genes control the
  development of body plans and are expressed in specific patterns and in particular stages of development depending on when they are activated.
• The homeobox is a sequence of DNA that codes for a region of 60 amino acids, and theresulting protein is found in most, if not all, eukaryotes. The region binds to DNA so that they can regulate transcription. In animals the homeobox is common in genes concernedwith the control of developmental events, such as segmentation, the establishment of theanterior-posterior axis and the activation of genes coding for body parts such as limbs

Apoptosis is an integral part of plant and animal tissue development. It is a series of biochemical events that leads to an orderly and tidy cell death, in contrast to cell necrosis, which leads to the release of harmful hydrolytic enzymes. Apoptosis ensures that the rate of cells produced by mitosisis the same as the rate of cells dying, so the number of cells remains constant. Not enough apoptosis leads to cancer.
Apoptosis causes the digits (toes and fingers) to separate from each other during development:
1. Enzymes break down the cell cytoskeleton
2. The cytoplasm becomes dense with organelles tightly packed
3. The cell surface membrane changes and blebs form
4. The Chromatin condenses and the nuclear envelope breaks. DNA breaks into
fragments
5. The cell breaks down into vesicles that are taken up by phagocytosis. The cellular
debris is disposed of so that it does not damage other cells or tissue.